Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer.

PubMed

Schulz, Roland; Lindner, Benjamin; Petridis, Loukas; Smith, Jeremy C

2009-10-13

A strategy is described for a fast all-atom molecular dynamics simulation of multimillion-atom biological systems on massively parallel supercomputers. The strategy is developed using benchmark systems of particular interest to bioenergy research, comprising models of cellulose and lignocellulosic biomass in an aqueous solution. The approach involves using the reaction field (RF) method for the computation of long-range electrostatic interactions, which permits efficient scaling on many thousands of cores. Although the range of applicability of the RF method for biomolecular systems remains to be demonstrated, for the benchmark systems the use of the RF produces molecular dipole moments, Kirkwood G factors, other structural properties, and mean-square fluctuations in excellent agreement with those obtained with the commonly used Particle Mesh Ewald method. With RF, three million- and five million-atom biological systems scale well up to ∼30k cores, producing ∼30 ns/day. Atomistic simulations of very large systems for time scales approaching the microsecond would, therefore, appear now to be within reach.

Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

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

Zheng, Wenjun, E-mail: wjzheng@buffalo.edu; Glenn, Paul

2015-01-21

The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, whichmore » is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.« less

Functional rotation induced by alternating protonation states in the multidrug transporter AcrB: all-atom molecular dynamics simulations.

PubMed

Yamane, Tsutomu; Murakami, Satoshi; Ikeguchi, Mitsunori

2013-10-29

The multidrug transporter AcrB actively exports a wide variety of noxious compounds using proton-motive force as an energy source in Gram-negative bacteria. AcrB adopts an asymmetric structure comprising three protomers with different conformations that are sequentially converted during drug export; these cyclic conformational changes during drug export are referred to as functional rotation. To investigate functional rotation driven by proton-motive force, all-atom molecular dynamics simulations were performed. Using different protonation states for the titratable residues in the middle of the transmembrane domain, our simulations revealed the correlation between the specific protonation states and the side-chain configurations. Changing the protonation state for Asp408 induced a spontaneous structural transition, which suggests that the proton translocation stoichiometry may be one proton per functional rotation cycle. Furthermore, our simulations demonstrate that alternating the protonation states in the transmembrane domain induces functional rotation in the porter domain, which is primarily responsible for drug transport.

Coarse-grained protein-protein stiffnesses and dynamics from all-atom simulations

NASA Astrophysics Data System (ADS)

Hicks, Stephen D.; Henley, C. L.

2010-03-01

Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid units linked by generalized (rotational and stretching) harmonic springs. We present an ab initio method to obtain the elastic parameters and overdamped dynamics for these springs from all-atom molecular-dynamics simulations of one pair of units at a time. The computed relaxation times of this pair give a consistency check for the simulation, and we can also find the corrective force needed to null systematic drifts. As a first application we predict the stiffness of an HIV capsid layer and the relaxation time for its breathing mode.

All-atom molecular dynamics of virus capsids as drug targets

DOE PAGES

Perilla, Juan R.; Hadden, Jodi A.; Goh, Boon Chong; ...

2016-04-29

Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways.more » When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Finally, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.« less

All-atom molecular dynamics of virus capsids as drug targets

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

Perilla, Juan R.; Hadden, Jodi A.; Goh, Boon Chong

Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways.more » When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Finally, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.« less

Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer

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

Schulz, Roland; Lindner, Benjamin; Petridis, Loukas

2009-01-01

A strategy is described for a fast all-atom molecular dynamics simulation of multimillion-atom biological systems on massively parallel supercomputers. The strategy is developed using benchmark systems of particular interest to bioenergy research, comprising models of cellulose and lignocellulosic biomass in an aqueous solution. The approach involves using the reaction field (RF) method for the computation of long-range electrostatic interactions, which permits efficient scaling on many thousands of cores. Although the range of applicability of the RF method for biomolecular systems remains to be demonstrated, for the benchmark systems the use of the RF produces molecular dipole moments, Kirkwood G factors,more » other structural properties, and mean-square fluctuations in excellent agreement with those obtained with the commonly used Particle Mesh Ewald method. With RF, three million- and five million atom biological systems scale well up to 30k cores, producing 30 ns/day. Atomistic simulations of very large systems for time scales approaching the microsecond would, therefore, appear now to be within reach.« less

A Free-Energy Approach for All-Atom Protein Simulation

PubMed Central

Verma, Abhinav; Wenzel, Wolfgang

2009-01-01

All-atom free-energy methods offer a promising alternative to kinetic molecular mechanics simulations of protein folding and association. Here we report an accurate, transferable all-atom biophysical force field (PFF02) that stabilizes the native conformation of a wide range of proteins as the global optimum of the free-energy landscape. For 32 proteins of the ROSETTA decoy set and six proteins that we have previously folded with PFF01, we find near-native conformations with an average backbone RMSD of 2.14 Å to the native conformation and an average Z-score of −3.46 to the corresponding decoy set. We used nonequilibrium sampling techniques starting from completely extended conformations to exhaustively sample the energy surface of three nonhomologous hairpin-peptides, a three-stranded β-sheet, the all-helical 40 amino-acid HIV accessory protein, and a zinc-finger ββα motif, and find near-native conformations for the minimal energy for each protein. Using a massively parallel evolutionary algorithm, we also obtain a near-native low-energy conformation for the 54 amino-acid engrailed homeodomain. Our force field thus stabilized near-native conformations for a total of 20 proteins of all structure classes with an average RMSD of only 3.06 Å to their respective experimental conformations. PMID:19413955

A free-energy approach for all-atom protein simulation.

PubMed

Verma, Abhinav; Wenzel, Wolfgang

2009-05-06

All-atom free-energy methods offer a promising alternative to kinetic molecular mechanics simulations of protein folding and association. Here we report an accurate, transferable all-atom biophysical force field (PFF02) that stabilizes the native conformation of a wide range of proteins as the global optimum of the free-energy landscape. For 32 proteins of the ROSETTA decoy set and six proteins that we have previously folded with PFF01, we find near-native conformations with an average backbone RMSD of 2.14 A to the native conformation and an average Z-score of -3.46 to the corresponding decoy set. We used nonequilibrium sampling techniques starting from completely extended conformations to exhaustively sample the energy surface of three nonhomologous hairpin-peptides, a three-stranded beta-sheet, the all-helical 40 amino-acid HIV accessory protein, and a zinc-finger beta beta alpha motif, and find near-native conformations for the minimal energy for each protein. Using a massively parallel evolutionary algorithm, we also obtain a near-native low-energy conformation for the 54 amino-acid engrailed homeodomain. Our force field thus stabilized near-native conformations for a total of 20 proteins of all structure classes with an average RMSD of only 3.06 A to their respective experimental conformations.

The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

DOE PAGES

Cortini, Ruggero; Cheng, Xiaolin; Smith, Jeremy C.

2017-01-16

Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning's theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order ofmore » $$1{{k}_{\\text{B}}}T$$ . Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.« less

The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

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

Cortini, Ruggero; Cheng, Xiaolin; Smith, Jeremy C.

Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning's theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order ofmore » $$1{{k}_{\\text{B}}}T$$ . Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.« less

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

Ab initio molecular simulations with numeric atom-centered orbitals

NASA Astrophysics Data System (ADS)

Blum, Volker; Gehrke, Ralf; Hanke, Felix; Havu, Paula; Havu, Ville; Ren, Xinguo; Reuter, Karsten; Scheffler, Matthias

2009-11-01

We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.

All-Atom Multiscale Molecular Dynamics Theory and Simulation of Self-Assembly, Energy Transfer and Structural Transition in Nanosystems

NASA Astrophysics Data System (ADS)

Espinosa Duran, John Michael

The study of nanosystems and their emergent properties requires the development of multiscale computational models, theories and methods that preserve atomic and femtosecond resolution, to reveal details that cannot be resolved experimentally today. Considering this, three long time scale phenomena were studied using molecular dynamics and multiscale methods: self-assembly of organic molecules on graphite, energy transfer in nanosystems, and structural transition in vault nanoparticles. Molecular dynamics simulations of the self-assembly of alkoxybenzonitriles with different tail lengths on graphite were performed to learn about intermolecular interactions and phases exhibited by self-organized materials. This is important for the design of ordered self-assembled organic photovoltaic materials with greater efficiency than the disordered blends. Simulations revealed surface dynamical behaviors that cannot be resolved experimentally today due to the lack of spatiotemporal resolution. Atom-resolved structures predicted by simulations agreed with scanning tunneling microscopy images and unit cell measurements. Then, a multiscale theory based on the energy density as a field variable is developed to study energy transfer in nanoscale systems. For applications like photothermal microscopy or cancer phototherapy is required to understand how the energy is transferred to/from nanosystems. This multiscale theory could be applied in this context and here is tested for cubic nanoparticles immersed in water for energy being transferred to/from the nanoparticle. The theory predicts the energy transfer dynamics and reveals phenomena that cannot be described by current phenomenological theories. Finally, temperature-triggered structural transitions were revealed for vault nanoparticles using molecular dynamics and multiscale simulations. Vault is a football-shaped supramolecular assembly very distinct from the commonly observed icosahedral viruses. It has very promising

Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

PubMed

Shen, Lin; Yang, Weitao

2016-04-12

We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics.

PubMed

Higo, Junichi; Umezawa, Koji

2014-01-01

We introduce computational studies on intrinsically disordered proteins (IDPs). Especially, we present our multicanonical molecular dynamics (McMD) simulations of two IDP-partner systems: NRSF-mSin3 and pKID-KIX. McMD is one of enhanced conformational sampling methods useful for conformational sampling of biomolecular systems. IDP adopts a specific tertiary structure upon binding to its partner molecule, although it is unstructured in the unbound state (i.e. the free state). This IDP-specific property is called "coupled folding and binding". The McMD simulation treats the biomolecules with an all-atom model immersed in an explicit solvent. In the initial configuration of simulation, IDP and its partner molecules are set to be distant from each other, and the IDP conformation is disordered. The computationally obtained free-energy landscape for coupled folding and binding has shown that native- and non-native-complex clusters distribute complicatedly in the conformational space. The all-atom simulation suggests that both of induced-folding and population-selection are coupled complicatedly in the coupled folding and binding. Further analyses have exemplified that the conformational fluctuations (dynamical flexibility) in the bound and unbound states are essentially important to characterize IDP functioning.

Correlating structural dynamics and catalytic activity of AgAu nanoparticles with ultrafast spectroscopy and all-atom molecular dynamics simulations.

PubMed

Ferbonink, G F; Rodrigues, T S; Dos Santos, D P; Camargo, P H C; Albuquerque, R Q; Nome, R A

2018-05-29

In this study, we investigated hollow AgAu nanoparticles with the goal of improving our understanding of the composition-dependent catalytic activity of these nanoparticles. AgAu nanoparticles were synthesized via the galvanic replacement method with controlled size and nanoparticle compositions. We studied extinction spectra with UV-Vis spectroscopy and simulations based on Mie theory and the boundary element method, and ultrafast spectroscopy measurements to characterize decay constants and the overall energy transfer dynamics as a function of AgAu composition. Electron-phonon coupling times for each composition were obtained from pump-power dependent pump-probe transients. These spectroscopic studies showed how nanoscale surface segregation, hollow interiors and porosity affect the surface plasmon resonance wavelength and fundamental electron-phonon coupling times. Analysis of the spectroscopic data was used to correlate electron-phonon coupling times to AgAu composition, and thus to surface segregation and catalytic activity. We have performed all-atom molecular dynamics simulations of model hollow AgAu core-shell nanoparticles to characterize nanoparticle stability and equilibrium structures, besides providing atomic level views of nanoparticle surface segregation. Overall, the basic atomistic and electron-lattice dynamics of core-shell AgAu nanoparticles characterized here thus aid the mechanistic understanding and performance optimization of AgAu nanoparticle catalysts.

Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension

PubMed Central

Sonne, Jacob; Jensen, Morten Ø.; Hansen, Flemming Y.; Hemmingsen, Lars; Peters, Günther H.

2007-01-01

Molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (NPT) ensemble give highly ordered, gel-like bilayers with an area per lipid of ∼48 Å2. To obtain fluid (Lα) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 ± 0.1 Å2. Compared to the 48 Å2, the new value of 60.4 Å2 is in fair agreement with the experimental value of 64 Å2. In addition, the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field. PMID:17400696

Implementation of Shifted Periodic Boundary Conditions in the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) Software

DTIC Science & Technology

2015-08-01

Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) Software by N Scott Weingarten and James P Larentzos Approved for...Massively Parallel Simulator ( LAMMPS ) Software by N Scott Weingarten Weapons and Materials Research Directorate, ARL James P Larentzos Engility...Shifted Periodic Boundary Conditions in the Large-Scale Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) Software 5a. CONTRACT NUMBER 5b

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.

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.

Interaction of human synovial phospholipase A2 with mixed lipid bilayers: a coarse-grain and all-atom molecular dynamics simulation study.

PubMed

Qin, Shan-Shan; Yu, Yang-Xin; Li, Qi-Kai; Yu, Zhi-Wu

2013-02-26

Human secreted phospholipase A2s have been shown to promote inflammation in mammals by catalyzing the first step of the arachidonic acid pathway by breaking down phospholipids, producing fatty acids, including arachidonic acid. They bind to the membrane water interface to access their phospholipid substrates from the membrane. Their binding modes on membrane surfaces are regulated by diverse factors, including membrane charge, fluidity, and heterogeneity. The influence of these factors on the binding modes of the enzymes is not well understood. Here we have studied several human synovial phospholipase A2 (hs-PLA2)/mixed bilayer systems through a combined coarse-grain and all-atom molecular dynamics simulation. It was found that hydrophobic residues Leu2, Val3, Ala18, Leu19, Phe23, Gly30, and Phe63 that form the edge of the entrance of the hydrophobic binding pocket in hs-PLA2 tend to penetrate into the hydrophobic area of lipid bilayers, and more than half of the total amino acid residues make contact with the lipid headgroups. Each enzyme molecule forms 19-38 hydrogen bonds with the bilayer to which it binds, most of which are with the phosphate groups. Analysis of the root-mean-square deviation (rmsd) shows that residues Val30-Thr40, Tyr66-Gln80, and Lys107-Arg118 have relatively large rmsds during all-atom molecular dynamics simulations, in accordance with the observation of an enlarged entrance region of the hydrophobic binding pocket. The amino acid sequences forming the entrance of the binding pocket prefer to interact with lipid molecules that are more fluid or negatively charged, and the opening of the binding pocket would be larger when the lipid components are more fluid.

Molecular dynamics simulation investigations of atomic-scale wear

NASA Astrophysics Data System (ADS)

Shao, Yuchong; Falk, Michael

2013-03-01

Frictional running-in and material transfer in wear take place at the micro- and nano-scale but the fundamental physics remain poorly understood. Here we intend to investigate wear and running-in phenomena in silicon based materials, which are widely utilized in micro/nano electromechanical systems(MEMS/NEMS). We use an atomic force microscopy (AFM) model composed of a crystalline silicon tip and substrate coated with native oxide layers. Molecular dynamics simulation has been performed over a range of temperatures, external loads and slip rates. Results show that adhesive wear takes place across the interface in an atom-by-atom fashion which remodels the tip leading to a final steady state. We quantify the rate of material transfer as a function of the coverage of non-bridging oxygen (NBO) atoms, which has a pronounced change of the system's tribological and wear behaviors. A constitutive rate and state model is proposed to predict the evolution of frictional strength and wear. This work is supported by the National Science Foundation under Award No. 0926111.

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.

PubMed

Wallace, Jason A; Shen, Jana K

2012-11-14

Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pK(a) values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future.

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH

PubMed Central

Wallace, Jason A.; Shen, Jana K.

2012-01-01

Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pKa values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future. PMID:23163362

Molecular Dynamics Simulations on Gas-Phase Proteins with Mobile Protons: Inclusion of All-Atom Charge Solvation.

PubMed

Konermann, Lars

2017-08-31

Molecular dynamics (MD) simulations have become a key tool for examining the properties of electrosprayed protein ions. Traditional force fields employ static charges on titratable sites, whereas in reality, protons are highly mobile in gas-phase proteins. Earlier studies tackled this problem by adjusting charge patterns during MD runs. Within those algorithms, proton redistribution was subject to energy minimization, taking into account electrostatic and proton affinity contributions. However, those earlier approaches described (de)protonated moieties as point charges, neglecting charge solvation, which is highly prevalent in the gas phase. Here, we describe a mobile proton algorithm that considers the electrostatic contributions from all atoms, such that charge solvation is explicitly included. MD runs were broken down into 50 ps fixed-charge segments. After each segment, the electrostatics was reanalyzed and protons were redistributed. Challenges associated with computational cost were overcome by devising a streamlined method for electrostatic calculations. Avidin (a 504-residue protein complex) maintained a nativelike fold over 200 ns. Proton transfer and side chain rearrangements produced extensive salt bridge networks at the protein surface. The mobile proton technique introduced here should pave the way toward future studies on protein folding, unfolding, collapse, and subunit dissociation in the gas phase.

Effect of water on structure and dynamics of [BMIM][PF6] ionic liquid: An all-atom molecular dynamics simulation investigation.

PubMed

Sharma, Anirban; Ghorai, Pradip Kr

2016-03-21

Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure IL but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.

All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water.

PubMed

Huang, Yandong; Chen, Wei; Wallace, Jason A; Shen, Jana

2016-11-08

Development of a pH stat to properly control solution pH in biomolecular simulations has been a long-standing goal in the community. Toward this goal recent years have witnessed the emergence of the so-called constant pH molecular dynamics methods. However, the accuracy and generality of these methods have been hampered by the use of implicit-solvent models or truncation-based electrostatic schemes. Here we report the implementation of the particle mesh Ewald (PME) scheme into the all-atom continuous constant pH molecular dynamics (CpHMD) method, enabling CpHMD to be performed with a standard MD engine at a fractional added computational cost. We demonstrate the performance using pH replica-exchange CpHMD simulations with titratable water for a stringent test set of proteins, HP36, BBL, HEWL, and SNase. With the sampling time of 10 ns per replica, most pK a 's are converged, yielding the average absolute and root-mean-square deviations of 0.61 and 0.77, respectively, from experiment. Linear regression of the calculated vs experimental pK a shifts gives a correlation coefficient of 0.79, a slope of 1, and an intercept near 0. Analysis reveals inadequate sampling of structure relaxation accompanying a protonation-state switch as a major source of the remaining errors, which are reduced as simulation prolongs. These data suggest PME-based CpHMD can be used as a general tool for pH-controlled simulations of macromolecular systems in various environments, enabling atomic insights into pH-dependent phenomena involving not only soluble proteins but also transmembrane proteins, nucleic acids, surfactants, and polysaccharides.

Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics.

PubMed

Chen, Wei; Shen, Jana K

2014-10-15

Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here, we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: (1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? (2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force-shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK(a) values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via cotitrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle mesh Ewald, considering the known artifacts due to charge-compensating background plasma. Copyright © 2014 Wiley Periodicals, Inc.

Multibillion-atom Molecular Dynamics Simulations of Plasticity, Spall, and Ejecta

NASA Astrophysics Data System (ADS)

Germann, Timothy C.

2007-06-01

Modern supercomputing platforms, such as the IBM BlueGene/L at Lawrence Livermore National Laboratory and the Roadrunner hybrid supercomputer being built at Los Alamos National Laboratory, are enabling large-scale classical molecular dynamics simulations of phenomena that were unthinkable just a few years ago. Using either the embedded atom method (EAM) description of simple (close-packed) metals, or modified EAM (MEAM) models of more complex solids and alloys with mixed covalent and metallic character, simulations containing billions to trillions of atoms are now practical, reaching volumes in excess of a cubic micron. In order to obtain any new physical insights, however, it is equally important that the analysis of such systems be tractable. This is in fact possible, in large part due to our highly efficient parallel visualization code, which enables the rendering of atomic spheres, Eulerian cells, and other geometric objects in a matter of minutes, even for tens of thousands of processors and billions of atoms. After briefly describing the BlueGene/L and Roadrunner architectures, and the code optimization strategies that were employed, results obtained thus far on BlueGene/L will be reviewed, including: (1) shock compression and release of a defective EAM Cu sample, illustrating the plastic deformation accompanying void collapse as well as the subsequent void growth and linkup upon release; (2) solid-solid martensitic phase transition in shock-compressed MEAM Ga; and (3) Rayleigh-Taylor fluid instability modeled using large-scale direct simulation Monte Carlo (DSMC) simulations. I will also describe our initial experiences utilizing Cell Broadband Engine processors (developed for the Sony PlayStation 3), and planned simulation studies of ejecta and spall failure in polycrystalline metals that will be carried out when the full Petaflop Opteron/Cell Roadrunner supercomputer is assembled in mid-2008.

Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.

PubMed

Frembgen-Kesner, Tamara; Andrews, Casey T; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A; Jain, Aakash; Olayiwola, Oluwatoni J; Weishaar, Mitch R; Elcock, Adrian H

2015-05-12

Recently, we reported the parametrization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral, and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral, and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downward in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multidomain proteins connected by flexible linkers.

Parameterization of backbone flexibility in a coarse-grained force field for proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-residue peptides

PubMed Central

Frembgen-Kesner, Tamara; Andrews, Casey T.; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A.; Jain, Aakash; Olayiwola, Oluwatoni; Weishaar, Mitch R.; Elcock, Adrian H.

2015-01-01

Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429

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

PubMed

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

2016-06-01

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

All-atom Simulation of Amyloid Aggregates

NASA Astrophysics Data System (ADS)

Berhanu, Workalemahu M.; Alred, Erik J.; Bernhardt, Nathan A.; Hansmann, Ulrich H. E.

Molecular simulations are now commonly used to complement experiments in the investigation of amyloid formation and their role in human diseases. While various simulations based on enhanced sampling techniques are used in amyloid formation simulations, this article will focus on those using standard atomistic simulations to evaluate the stability of fibril models. Such studies explore the limitations that arise from the choice of force field or polymorphism; and explore the stability of in vivo and in vitro forms of Aβ fibril aggregates, and the role of heterologous seeding as a link between different amyloid diseases.

Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics †

PubMed Central

Chen, Wei; Shen, Jana K.

2014-01-01

Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: 1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? 2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK a values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via co-titrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle-mesh Ewald, considering the known artifacts due to charge-compensating background plasma. PMID:25142416

Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): time-resolved fluorescence measurements and all-atom molecular dynamics simulations.

PubMed

Das, Anuradha; Das, Suman; Biswas, Ranjit

2015-01-21

Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Das, Anuradha; Das, Suman; Biswas, Ranjit

2015-01-01

Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ˜120-145 K above the measured glass transition temperatures (˜207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (˜70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

Structure and function of photosystem I–[FeFe] hydrogenase protein fusions: An all-atom molecular dynamics study

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

Harris, Bradley J.; Cheng, Xiaolin; Frymier, Paul

2015-12-15

All-atom molecular dynamics (MD) simulation was used to study the solution dynamics and protein protein interactions of protein fusions of photosystem I (PSI) from Thermosynechococcus elongatus and an [FeFe]-hydrogenase (FeFe H 2ase) from Clostridium pasteurianum, a unique complex capable of photocatalytic hydrogen production. This study involved fusions of these two proteins via dithiol linkers of different length including decanedithiol, octanedithiol, and hexanedithiol, for which experimental data had previously been obtained. Evaluation of root-mean-squared deviations (RMSDs) relative to the respective crystal structures of PSI and the FeFe H 2ase shows that these fusion complexes approach stable equilibrium conformations during the MDmore » simulations. Investigating protein mobility via root-mean-squared fluctuations (RMSFs) reveals that tethering via the shortest hexanedithiol linker results in increased atomic fluctuations of both PSI and the hydrogenase in these fusion complexes. Furthermore, evaluation of the inter- and intraprotein electron transfer distances in these fusion complexes indicates that the structural changes in the FeFe H 2ase arising from ligation to PSI via the shortest hexanedithiol linker may hinder electron transport in the hydrogenase, thus providing a molecular level explanation for the observation that the medium-length octanedithiol linker gives the highest hydrogen production rate.« less

Effect of water on structure and dynamics of [BMIM][PF{sub 6}] ionic liquid: An all-atom molecular dynamics simulation investigation

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

Sharma, Anirban; Ghorai, Pradip Kr., E-mail: pradip@iiserkol.ac.in

2016-03-21

Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF{sub 6}]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure ILmore » but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.« less

Heterogeneity in homogeneous nucleation from billion-atom molecular dynamics simulation of solidification of pure metal.

PubMed

Shibuta, Yasushi; Sakane, Shinji; Miyoshi, Eisuke; Okita, Shin; Takaki, Tomohiro; Ohno, Munekazu

2017-04-05

Can completely homogeneous nucleation occur? Large scale molecular dynamics simulations performed on a graphics-processing-unit rich supercomputer can shed light on this long-standing issue. Here, a billion-atom molecular dynamics simulation of homogeneous nucleation from an undercooled iron melt reveals that some satellite-like small grains surrounding previously formed large grains exist in the middle of the nucleation process, which are not distributed uniformly. At the same time, grains with a twin boundary are formed by heterogeneous nucleation from the surface of the previously formed grains. The local heterogeneity in the distribution of grains is caused by the local accumulation of the icosahedral structure in the undercooled melt near the previously formed grains. This insight is mainly attributable to the multi-graphics processing unit parallel computation combined with the rapid progress in high-performance computational environments.Nucleation is a fundamental physical process, however it is a long-standing issue whether completely homogeneous nucleation can occur. Here the authors reveal, via a billion-atom molecular dynamics simulation, that local heterogeneity exists during homogeneous nucleation in an undercooled iron melt.

Rayleigh-Plesset equation of the bubble stable cavitation in water: A nonequilibrium all-atom molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Man, Viet Hoang; Li, Mai Suan; Derreumaux, Philippe; Nguyen, Phuong H.

2018-03-01

The Rayleigh-Plesset (RP) equation was derived from the first principles to describe the bubble cavitation in liquids in terms of macroscopic hydrodynamics. A number of nonequilibrium molecular dynamics studies have been carried out to validate this equation in describing the bubble inertial cavitation, but their results are contradictory and the applicability of the RP equation still remains to be examined, especially for the stable cavitation. In this work, we carry out nonequilibrium all-atom simulation to validate the applicability of the RP equation in the description of the stable cavitation of nano-sized bubbles in water. We show that although microscopic effects are not explicitly included, this equation still describes the dynamics of subnano-bubbles quite well as long as the contributions of various terms including inertial, surface tension, and viscosity are correctly taken into account. These terms are directly and inversely proportional to the amplitude and period of the cavitation, respectively. Thus, their contributions to the RP equation depend on these two parameters. This may explain the discrepancy between the current results obtained using different parameters. Finally, the accuracy of the RP equation in the current mathematical modeling studies of the ultrasound-induced blood-brain-barrier experiments is discussed in some detail.

Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

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

Das, Anuradha; Das, Suman; Biswas, Ranjit, E-mail: ranjit@bose.res.in

2015-01-21

Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH{sub 3}CONH{sub 2}) and urea (NH{sub 2}CONH{sub 2}) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH{sub 3}CONH{sub 2} + (1 − f)NH{sub 2}CONH{sub 2}] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probemore » solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α{sub 2}) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.« less

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.

SLAC All Access: Atomic, Molecular and Optical Science Instrument

ScienceCinema

Bozek, John

2018-02-13

John Bozek, a staff scientist at SLAC's Linac Coherent Light Source (LCLS) X-ray laser who manages the LCLS Soft X-ray Department, takes us behind the scenes at the Atomic, Molecular and Optical Science (AMO) instrument, the first of six experimental stations now operating at LCLS. Samples used in AMO experiments include atoms, molecules, clusters, and nanoscale objects such as protein crystals or viruses. Science performed at AMO includes fundamental studies of light-matter interactions in the extreme X-ray intensity of the LCLS pules, time-resolved studies of increasingly charged states of atoms and molecules, X-ray diffraction imaging of nanocrystals, and single-shot imaging of a variety of objects.

Benchmarking all-atom simulations using hydrogen exchange

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

Skinner, John J.; Yu, Wookyung; Gichana, Elizabeth K.

We are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520] using long-time molecular dynamics (MD) simulations. Our results indicate that modern force fields can reproduce the energy surface near the native structure. In this paper, to test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability andmore » H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Finally and moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations.« less

Benchmarking all-atom simulations using hydrogen exchange

DOE PAGES

Skinner, John J.; Yu, Wookyung; Gichana, Elizabeth K.; ...

2014-10-27

We are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520] using long-time molecular dynamics (MD) simulations. Our results indicate that modern force fields can reproduce the energy surface near the native structure. In this paper, to test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability andmore » H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Finally and moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations.« less

Simulation and understanding of atomic and molecular quantum crystals

NASA Astrophysics Data System (ADS)

Cazorla, Claudio; Boronat, Jordi

2017-07-01

Quantum crystals abound in the whole range of solid-state species. Below a certain threshold temperature the physical behavior of rare gases (He 4 and Ne), molecular solids (H2 and CH4 ), and some ionic (LiH), covalent (graphite), and metallic (Li) crystals can be explained only in terms of quantum nuclear effects (QNE). A detailed comprehension of the nature of quantum solids is critical for achieving progress in a number of fundamental and applied scientific fields such as planetary sciences, hydrogen storage, nuclear energy, quantum computing, and nanoelectronics. This review describes the current physical understanding of quantum crystals formed by atoms and small molecules, as well as the wide palette of simulation techniques that are used to investigate them. Relevant aspects in these materials such as phase transformations, structural properties, elasticity, crystalline defects, and the effects of reduced dimensionality are discussed thoroughly. An introduction to quantum Monte Carlo techniques, which in the present context are the simulation methods of choice, and other quantum simulation approaches (e.g., path-integral molecular dynamics and quantum thermal baths) is provided. The overarching objective of this article is twofold: first, to clarify in which crystals and physical situations the disregard of QNE may incur in important bias and erroneous interpretations. And second, to promote the study and appreciation of QNE, a topic that traditionally has been treated in the context of condensed matter physics, within the broad and interdisciplinary areas of materials science.

Descriptions and Implementations of DL_F Notation: A Natural Chemical Expression System of Atom Types for Molecular Simulations.

PubMed

Yong, Chin W

2016-08-22

DL_F Notation is an easy-to-understand, standardized atom typesetting expression for molecular simulations for a range of organic force field (FF) schemes such as OPLSAA, PCFF, and CVFF. It is implemented within DL_FIELD, a software program that facilitates the setting up of molecular FF models for DL_POLY molecular dynamics simulation software. By making use of the Notation, a single core conversion module (the DL_F conversion Engine) implemented within DL_FIELD can be used to analyze a molecular structure and determine the types of atoms for a given FF scheme. Users only need to provide the molecular input structure in a simple xyz format and DL_FIELD can produce the necessary force field file for DL_POLY automatically. In commensurate with the development concept of DL_FIELD, which placed emphasis on robustness and user friendliness, the Engine provides a single-step solution to setup complex FF models. This allows users to switch from one of the above-mentioned FF seamlessly to another while at the same time provides a consistent atom typing that is expressed in a natural chemical sense.

Homogeneous nucleation and microstructure evolution in million-atom molecular dynamics simulation

PubMed Central

Shibuta, Yasushi; Oguchi, Kanae; Takaki, Tomohiro; Ohno, Munekazu

2015-01-01

Homogeneous nucleation from an undercooled iron melt is investigated by the statistical sampling of million-atom molecular dynamics (MD) simulations performed on a graphics processing unit (GPU). Fifty independent instances of isothermal MD calculations with one million atoms in a quasi-two-dimensional cell over a nanosecond reveal that the nucleation rate and the incubation time of nucleation as functions of temperature have characteristic shapes with a nose at the critical temperature. This indicates that thermally activated homogeneous nucleation occurs spontaneously in MD simulations without any inducing factor, whereas most previous studies have employed factors such as pressure, surface effect, and continuous cooling to induce nucleation. Moreover, further calculations over ten nanoseconds capture the microstructure evolution on the order of tens of nanometers from the atomistic viewpoint and the grain growth exponent is directly estimated. Our novel approach based on the concept of “melting pots in a supercomputer” is opening a new phase in computational metallurgy with the aid of rapid advances in computational environments. PMID:26311304

Developing model asphalt systems using molecular simulation : final model.

DOT National Transportation Integrated Search

2009-09-01

Computer based molecular simulations have been used towards developing simple mixture compositions whose : physical properties resemble those of real asphalts. First, Monte Carlo simulations with the OPLS all-atom force : field were used to predict t...

Hamiltonian adaptive resolution molecular dynamics simulation of infrared dielectric functions of liquids

NASA Astrophysics Data System (ADS)

Wang, C. C.; Tan, J. Y.; Liu, L. H.

2018-05-01

Hamiltonian adaptive resolution scheme (H-AdResS), which allows to simulate materials by treating different domains of the system at different levels of resolution, is a recently proposed atomistic/coarse-grained multiscale model. In this work, a scheme to calculate the dielectric functions of liquids on account of H-AdResS is presented. In the proposed H-AdResS dielectric-function calculation scheme (DielectFunctCalS), the corrected molecular dipole moments are calculated by multiplying molecular dipole moment by the weighting fraction of the molecular mapping point. As the widths of all-atom and hybrid regions show different degrees of influence on the dielectric functions, a prefactor is multiplied to eliminate the effects of all-atom and hybrid region widths. Since one goal of using the H-AdResS method is to reduce computational costs, widths of the all-atom region and the hybrid region can be reduced considering that the coarse-grained simulation is much more timesaving compared to atomistic simulation. Liquid water and ethanol are taken as test cases to validate the DielectFunctCalS. The H-AdResS DielectFunctCalS results are in good agreement with all-atom molecular dynamics simulations. The accuracy of the H-AdResS results, together with all-atom molecular dynamics results, depends heavily on the choice of the force field and force field parameters. The H-AdResS DielectFunctCalS allows us to calculate the dielectric functions of macromolecule systems with high efficiency and makes the dielectric function calculations of large biomolecular systems possible.

All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

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

Andoh, Y.; Yoshii, N.; Yamada, A.

2014-10-28

Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10{sup 6} all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000)more » can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.« less

All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

NASA Astrophysics Data System (ADS)

Andoh, Y.; Yoshii, N.; Yamada, A.; Fujimoto, K.; Kojima, H.; Mizutani, K.; Nakagawa, A.; Nomoto, A.; Okazaki, S.

2014-10-01

Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 106 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

Construction, MD simulation, and hydrodynamic validation of an all-atom model of a monoclonal IgG antibody.

PubMed

Brandt, J Paul; Patapoff, Thomas W; Aragon, Sergio R

2010-08-04

At 150 kDa, antibodies of the IgG class are too large for their structure to be determined with current NMR methodologies. Because of hinge-region flexibility, it is difficult to obtain atomic-level structural information from the crystal, and questions regarding antibody structure and dynamics in solution remain unaddressed. Here we describe the construction of a model of a human IgG1 monoclonal antibody (trastuzumab) from the crystal structures of fragments. We use a combination of molecular-dynamics (MD) simulation, continuum hydrodynamics modeling, and experimental diffusion measurements to explore antibody behavior in aqueous solution. Hydrodynamic modeling provides a link between the atomic-level details of MD simulation and the size- and shape-dependent data provided by hydrodynamic measurements. Eight independent 40 ns MD trajectories were obtained with the AMBER program suite. The ensemble average of the computed transport properties over all of the MD trajectories agrees remarkably well with the value of the translational diffusion coefficient obtained with dynamic light scattering at 20 degrees C and 27 degrees C, and the intrinsic viscosity measured at 20 degrees C. Therefore, our MD results likely represent a realistic sampling of the conformational space that an antibody explores in aqueous solution. 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Thermal conductance at atomically clean and disordered silicon/aluminum interfaces: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Ih Choi, Woon; Kim, Kwiseon; Narumanchi, Sreekant

2012-09-01

Thermal resistance between layers impedes effective heat dissipation in electronics packaging applications. Thermal conductance for clean and disordered interfaces between silicon (Si) and aluminum (Al) was computed using realistic Si/Al interfaces and classical molecular dynamics with the modified embedded atom method potential. These realistic interfaces, which include atomically clean as well as disordered interfaces, were obtained using density functional theory. At 300 K, the magnitude of interfacial conductance due to phonon-phonon scattering obtained from the classical molecular dynamics simulations was approximately five times higher than the conductance obtained using analytical elastic diffuse mismatch models. Interfacial disorder reduced the thermal conductance due to increased phonon scattering with respect to the atomically clean interface. Also, the interfacial conductance, due to electron-phonon scattering at the interface, was greater than the conductance due to phonon-phonon scattering. This indicates that phonon-phonon scattering is the bottleneck for interfacial transport at the semiconductor/metal interfaces. The molecular dynamics modeling predictions for interfacial thermal conductance for a 5-nm disordered interface between Si/Al were in-line with recent experimental data in the literature.

Quantification of evaporation induced error in atom probe tomography using molecular dynamics simulation.

PubMed

Chen, Shu Jian; Yao, Xupei; Zheng, Changxi; Duan, Wen Hui

2017-11-01

Non-equilibrium molecular dynamics was used to simulate the dynamics of atoms at the atom probe surface and five objective functions were used to quantify errors. The results suggested that before ionization, thermal vibration and collision caused the atoms to displace up to 1Å and 25Å respectively. The average atom displacements were found to vary between 0.2 and 0.5Å. About 9 to 17% of the atoms were affected by collision. Due to the effects of collision and ion-ion repulsion, the back-calculated positions were on average 0.3-0.5Å different from the pre-ionized positions of the atoms when the number of ions generated per pulse was minimal. This difference could increase up to 8-10Å when 1.5ion/nm 2 were evaporated per pulse. On the basis of the results, surface ion density was considered an important factor that needed to be controlled to minimize error in the evaporation process. Copyright © 2017. Published by Elsevier B.V.

From Aβ Filament to Fibril: Molecular Mechanism of Surface-Activated Secondary Nucleation from All-Atom MD Simulations.

PubMed

Schwierz, Nadine; Frost, Christina V; Geissler, Phillip L; Zacharias, Martin

2017-02-02

Secondary nucleation pathways in which existing amyloid fibrils catalyze the formation of new aggregates and neurotoxic oligomers are of immediate importance for the onset and progression of Alzheimer's disease. Here, we apply extensive all-atom molecular dynamics simulations in explicit water to study surface-activated secondary nucleation pathways at the extended lateral β-sheet surface of a preformed Aβ 9-40 filament. Calculation of free-energy profiles allows us to determine binding free energies and conformational intermediates for nucleation complexes consisting of 1-4 Aβ peptides. In addition, we combine the free-energy profiles with position-dependent diffusion profiles to extract complementary kinetic information and macroscopic growth rates. Single monomers bind to the β-sheet surface in a disordered, hydrophobically collapsed conformation, whereas dimers and larger oligomers can retain a cross-β conformation resembling a more ordered fibril structure. The association processes during secondary nucleation follow a dock/lock mechanism consisting of a fast initial encounter phase (docking) and a slow structural rearrangement phase (locking). The major driving forces for surface-activated secondary nucleation are the release of a large number of hydration water molecules and the formation of hydrophobic interface contacts, the latter being in contrast to the elongation process at filament tips, which is dominated by the formation of stable and highly specific interface hydrogen bonds. The calculated binding free energies and the association rates for the attachment of Aβ monomers and oligomers to the extended lateral β-sheet surface of the filament seed are higher compared to those for elongation at the filament tips, indicating that secondary nucleation pathways can become important once a critical concentration of filaments has formed.

Computing the binding affinity of Zn2+ in human carbonic anhydrase II on the basis of all-atom molecular dynamics simulations.

NASA Astrophysics Data System (ADS)

Wambo, Thierry; Rodriguez, Roberto

Human carbonic anhydrase II (hCAII) is a metalloenzyme with a Zinc cation at its binding site. The presence of the Zinc turns the protein into an efficient enzyme which catalyzes the reversible hydration of carbon dioxide into bicarbonate anion. Available X-ray structures of the apo-hCAII and holo-hCAII show no significant differences in the overall structure of these proteins. What difference, if any, is there between the structures of the hydrated apo-hCAII and holo? How can we use computer simulation to efficiently compute the binding affinity of Zinc to hCAII? We will present a scheme developed to compute the binding affinity of Zinc cation to hCAII on the basis of all-atom molecular dynamics simulation where Zinc is represented as a point charge and the CHARMM36 force field is used for running the dynamics of the system. Our computed binding affinity of the cation to hCAII is in good agreement with experiment, within the margin of error, while a look at the dynamics of the binding site suggests that in the absence of the Zinc, there is a re-organization of the nearby histidine residues which adopt a new distinct configuration. The authors are thankful for the NIH support through Grants GM084834 and GM060655. They also acknowledge the Texas Advanced Computing Center at the University of Texas at Austin for the supercomputing time. They thank Dr Liao Chen for his comments.

All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits

PubMed Central

Perilla, Juan R; Schlicksup, Christopher John; Venkatakrishnan, Balasubramanian; Zlotnick, Adam; Schulten, Klaus

2018-01-01

The hepatitis B virus capsid represents a promising therapeutic target. Experiments suggest the capsid must be flexible to function; however, capsid structure and dynamics have not been thoroughly characterized in the absence of icosahedral symmetry constraints. Here, all-atom molecular dynamics simulations are leveraged to investigate the capsid without symmetry bias, enabling study of capsid flexibility and its implications for biological function and cryo-EM resolution limits. Simulation results confirm flexibility and reveal a propensity for asymmetric distortion. The capsid’s influence on ionic species suggests a mechanism for modulating the display of cellular signals and implicates the capsid’s triangular pores as the location of signal exposure. A theoretical image reconstruction performed using simulated conformations indicates how capsid flexibility may limit the resolution of cryo-EM. Overall, the present work provides functional insight beyond what is accessible to experimental methods and raises important considerations regarding asymmetry in structural studies of icosahedral virus capsids. PMID:29708495

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.

Simulation of field-induced molecular dissociation in atom-probe tomography: Identification of a neutral emission channel

NASA Astrophysics Data System (ADS)

Zanuttini, David; Blum, Ivan; Rigutti, Lorenzo; Vurpillot, François; Douady, Julie; Jacquet, Emmanuelle; Anglade, Pierre-Matthieu; Gervais, Benoit

2017-06-01

We investigate the dynamics of dicationic metal-oxide molecules under large electric-field conditions, on the basis of ab initio calculations coupled to molecular dynamics. Applied to the case of ZnO2 + in the field of atom probe tomography (APT), our simulation reveals the dissociation into three distinct exit channels. The proportions of these channels depend critically on the field strength and on the initial molecular orientation with respect to the field. For typical field strength used in APT experiments, an efficient dissociation channel leads to emission of neutral oxygen atoms, which escape detection. The calculated composition biases and their dependence on the field strength show remarkable consistency with recent APT experiments on ZnO crystals. Our work shows that bond breaking in strong static fields may lead to significant neutral atom production, and therefore to severe elemental composition biases in measurements.

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.

Effects of Concentration on Like-Charge Pairing of Guanidinium Ions and on the Structure of Water: An All-Atom Molecular Dynamics Simulation Study.

PubMed

Bandyopadhyay, Dibyendu; Bhanja, K; Mohan, Sadhana; Ghosh, Swapan K; Choudhury, Niharendu

2015-08-27

Like-charge ion-pair formation in an aqueous solution of guanidinium chloride (GdmCl) has two important facets. On one hand, it describes the role of the arginine (ARG) side chain in aggregation and dimer formation in proteins, and on the other hand, it lends support for the direct mechanism of protein denaturation by GdmCl. We employ all-atom molecular dynamics simulations to investigate the effect of GdmCl concentration on the like-charge ion-pair formation of guanidinium ions (Gdm(+)). From analyses of the radial distribution function (RDF) between the carbon atoms of two guanidinium moieties, the existence of both contact pairs and solvent-separated pairs has been observed. Although the peak height corresponding to the contact-pair state decreases, the number of Gdm(+) ions in the contact-pair state actually increases with increasing GdmCl concentration. We have also investigated the effect of the concentration of Gdm(+) on the structure of water. The effect of GdmCl concentration on the radial and tetrahedral structures of water is found to be negligibly small; however, GdmCl concentration has a considerable effect on the hydrogen-bonding structure of water. It is demonstrated that the presence of chloride ions, not Gdm(+), in the first solvation shell of water causes the distortion in the hydrogen-bonding network of water. In order to establish that Gdm(+) not only stacks against another Gdm(+) but also directly attacks the ARG residue of a protein or peptide, simulation of an ARG-rich peptide in 6 M aqueous solution of GdmCl has been performed. The analyses of RDFs and orientation distributions reveal that the Gdm(+) moiety of the GdmCl attacks the same moiety in the ARG side chain with a parallel stacking orientation.

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.

The Molecular Structure of a Phosphatidylserine Bilayer Determined by Scattering and Molecular Dynamics Simulations

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

Pan, Jianjun; Cheng, Xiaolin; Monticelli, Luca

2014-01-01

Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 A2 at 25 C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of themore » simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na+ ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.« less

Digging into Lipid Membrane Permeation for Cardiac Ion Channel Blocker d-Sotalol with All-Atom Simulations

PubMed Central

DeMarco, Kevin R.; Bekker, Slava; Clancy, Colleen E.; Noskov, Sergei Y.; Vorobyov, Igor

2018-01-01

Interactions of drug molecules with lipid membranes play crucial role in their accessibility of cellular targets and can be an important predictor of their therapeutic and safety profiles. Very little is known about spatial localization of various drugs in the lipid bilayers, their active form (ionization state) or translocation rates and therefore potency to bind to different sites in membrane proteins. All-atom molecular simulations may help to map drug partitioning kinetics and thermodynamics, thus providing in-depth assessment of drug lipophilicity. As a proof of principle, we evaluated extensively lipid membrane partitioning of d-sotalol, well-known blocker of a cardiac potassium channel Kv11.1 encoded by the hERG gene, with reported substantial proclivity for arrhythmogenesis. We developed the positively charged (cationic) and neutral d-sotalol models, compatible with the biomolecular CHARMM force field, and subjected them to all-atom molecular dynamics (MD) simulations of drug partitioning through hydrated lipid membranes, aiming to elucidate thermodynamics and kinetics of their translocation and thus putative propensities for hydrophobic and aqueous hERG access. We found that only a neutral form of d-sotalol accumulates in the membrane interior and can move across the bilayer within millisecond time scale, and can be relevant to a lipophilic channel access. The computed water-membrane partitioning coefficient for this form is in good agreement with experiment. There is a large energetic barrier for a cationic form of the drug, dominant in water, to cross the membrane, resulting in slow membrane translocation kinetics. However, this form of the drug can be important for an aqueous access pathway through the intracellular gate of hERG. This route will likely occur after a neutral form of a drug crosses the membrane and subsequently re-protonates. Our study serves to demonstrate a first step toward a framework for multi-scale in silico safety pharmacology, and

Absorption and folding of melittin onto lipid bilayer membranes via unbiased atomic detail microsecond molecular dynamics simulation.

PubMed

Chen, Charles H; Wiedman, Gregory; Khan, Ayesha; Ulmschneider, Martin B

2014-09-01

Unbiased molecular simulation is a powerful tool to study the atomic details driving functional structural changes or folding pathways of highly fluid systems, which present great challenges experimentally. Here we apply unbiased long-timescale molecular dynamics simulation to study the ab initio folding and partitioning of melittin, a template amphiphilic membrane active peptide. The simulations reveal that the peptide binds strongly to the lipid bilayer in an unstructured configuration. Interfacial folding results in a localized bilayer deformation. Akin to purely hydrophobic transmembrane segments the surface bound native helical conformer is highly resistant against thermal denaturation. Circular dichroism spectroscopy experiments confirm the strong binding and thermostability of the peptide. The study highlights the utility of molecular dynamics simulations for studying transient mechanisms in fluid lipid bilayer systems. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova. Copyright © 2014. Published by Elsevier B.V.

SpectraPlot.com: Integrated spectroscopic modeling of atomic and molecular gases

NASA Astrophysics Data System (ADS)

Goldenstein, Christopher S.; Miller, Victor A.; Mitchell Spearrin, R.; Strand, Christopher L.

2017-10-01

SpectraPlot is a web-based application for simulating spectra of atomic and molecular gases. At the time this manuscript was written, SpectraPlot consisted of four primary tools for calculating: (1) atomic and molecular absorption spectra, (2) atomic and molecular emission spectra, (3) transition linestrengths, and (4) blackbody emission spectra. These tools currently employ the NIST ASD, HITRAN2012, and HITEMP2010 databases to perform line-by-line simulations of spectra. SpectraPlot employs a modular, integrated architecture, enabling multiple simulations across multiple databases and/or thermodynamic conditions to be visualized in an interactive plot window. The primary objective of this paper is to describe the architecture and spectroscopic models employed by SpectraPlot in order to provide its users with the knowledge required to understand the capabilities and limitations of simulations performed using SpectraPlot. Further, this manuscript discusses the accuracy of several underlying approximations used to decrease computational time, in particular, the use of far-wing cutoff criteria.

Hydration of Li+ -ion in atom-bond electronegativity equalization method-7P water: a molecular dynamics simulation study.

PubMed

Li, Xin; Yang, Zhong-Zhi

2005-02-22

We have carried out molecular dynamics simulations of a Li(+) ion in water over a wide range of temperature (from 248 to 368 K). The simulations make use of the atom-bond electronegativity equalization method-7P water model, a seven-site flexible model with fluctuating charges, which has accurately reproduced many bulk water properties. The recently constructed Li(+)-water interaction potential through fitting to the experimental and ab initio gas-phase binding energies and to the measured structures for Li(+)-water clusters is adopted in the simulations. ABEEM was proposed and developed in terms of partitioning the electron density into atom and bond regions and using the electronegativity equalization method (EEM) and the density functional theory (DFT). Based on a combination of the atom-bond electronegativity equalization method and molecular mechanics (ABEEM/MM), a new set of water-water and Li(+)-water potentials, successfully applied to ionic clusters Li(+)(H(2)O)(n)(n=1-6,8), are further investigated in an aqueous solution of Li(+) in the present paper. Two points must be emphasized in the simulations: first, the model allows for the charges on the interacting sites fluctuating as a function of time; second, the ABEEM-7P model has applied the parameter k(lp,H)(R(lp,H)) to explicitly describe the short-range interaction of hydrogen bond in the hydrogen bond interaction region, and has a new description for the hydrogen bond. The static, dynamic, and thermodynamic properties have been studied in detail. In addition, at different temperatures, the structural properties such as radial distribution functions, and the dynamical properties such as diffusion coefficients and residence times of the water molecules in the first hydration shell of Li(+), are also simulated well. These simulation results show that the ABEEM/MM-based water-water and Li(+)-water potentials appear to be robust giving the overall characteristic hydration properties in excellent agreement

A hierarchical coarse-grained (all-atom to all residue) approach to peptides (P1, P2) binding with a graphene sheet

NASA Astrophysics Data System (ADS)

Pandey, Ras; Kuang, Zhifeng; Farmer, Barry; Kim, Sang; Naik, Rajesh

2012-02-01

Recently, Kim et al. [1] have found that peptides P1: HSSYWYAFNNKT and P2: EPLQLKM bind selectively to graphene surfaces and edges respectively which are critical in modulating both the mechanical as well as electronic transport properties of graphene. Such distinctions in binding sites (edge versus surface) observed in electron micrographs were verified by computer simulation by an all-atomic model that captures the pi-pi bonding. We propose a hierarchical approach that involves input from the all-atom Molecular Dynamics (MD) study (with atomistic detail) into a coarse-grained Monte Carlo simulation to extend this study further to a larger scale. The binding energy of a free amino acid with the graphene sheet from all-atom simulation is used in the interaction parameter for the coarse-grained approach. Peptide chain executes its stochastic motion with the Metropolis algorithm. We investigate a number of local and global physical quantities and find that peptide P1 is likely to bind more strongly to graphene sheet than P2 and that it is anchored by three residues ^4Y^5W^6Y. [1] S.N. Kim et al J. Am. Chem. Soc. 133, 14480 (2011).

A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants

PubMed Central

Ewen, James P.; Gattinoni, Chiara; Thakkar, Foram M.; Morgan, Neal; Spikes, Hugh A.; Dini, Daniele

2016-01-01

For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n-hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n-hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n-hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently

A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants.

PubMed

Ewen, James P; Gattinoni, Chiara; Thakkar, Foram M; Morgan, Neal; Spikes, Hugh A; Dini, Daniele

2016-08-02

For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n -hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n -hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n -hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently

Molecular events during the early stages of aggregation of GNNQQNY: An all atom MD simulation study of randomly dispersed peptides.

PubMed

Srivastava, Alka; Balaji, Petety V

2015-12-01

This study probes the early events during lag phase of aggregation of GNNQQNY using all atom MD simulations in explicit solvent. Simulations were performed by varying system size, temperature and starting configuration. Peptides dispersed randomly in the simulation box come together early on in the simulation and form aggregates. These aggregates are dynamic implying the absence of stabilizing interactions. This facilitates the exploration of alternate arrangements. The constituent peptides sample a variety of conformations, frequently re-orient and re-arrange with respect to each other and dissociate from/re-associate with the aggregate. The size and lifetime of aggregates vary depending upon the number of inter-peptide backbone H-bonds. Most of the aggregates formed are amorphous but crystalline aggregates of smaller size (mainly 2-mers) do appear and sustain for varying durations of time. The peptides in crystalline 2-mers are mostly anti-parallel. The largest crystalline aggregate that appears is a 4-mer in a single sheet and a 4-, 5-, or 6-mer in double layered arrangement. Crystalline aggregates grow either by the sequential addition of peptides, or by the head-on or lateral collision-adhesion of 2-mers. The formation of various smaller aggregates suggests the polymorphic nature of oligomers and heterogeneity in the lag phase. Copyright © 2015 Elsevier Inc. All rights reserved.

Local-feature analysis for automated coarse-graining of bulk-polymer molecular dynamics simulations.

PubMed

Xue, Y; Ludovice, P J; Grover, M A

2012-12-01

A method for automated coarse-graining of bulk polymers is presented, using the data-mining tool of local feature analysis. Most existing methods for polymer coarse-graining define superatoms based on their covalent bonding topology along the polymer backbone, but here superatoms are defined based only on their correlated motions, as observed in molecular dynamics simulations. Correlated atomic motions are identified in the simulation data using local feature analysis, between atoms in the same or in different polymer chains. Groups of highly correlated atoms constitute the superatoms in the coarse-graining scheme, and the positions of their seed coordinates are then projected forward in time. Based on only the seed positions, local feature analysis enables the full reconstruction of all atomic positions. This reconstruction suggests an iterative scheme to reduce the computation of the simulations to initialize another short molecular dynamic simulation, identify new superatoms, and again project forward in time.

Atomic and Molecular Physics

NASA Technical Reports Server (NTRS)

Bhatia, Anand K.

2005-01-01

A symposium on atomic and molecular physics was held on November 18, 2005 at Goddard Space Flight Center. There were a number of talks through the day on various topics such as threshold law of ionization, scattering of electrons from atoms and molecules, muonic physics, positron physics, Rydberg states etc. The conference was attended by a number of physicists from all over the world.

All-Atom MD Simulation of DNA Condensation Using Ab Initio Derived Force Field Parameters of Cobalt(III)-Hexammine.

PubMed

Sun, Tiedong; Mirzoev, Alexander; Korolev, Nikolay; Lyubartsev, Alexander P; Nordenskiöld, Lars

2017-08-24

It is well established that the presence of the trivalent cobalt(III)-hexammine cation (CoHex 3+ ) at submillimolar concentrations leads to bundling (condensation) of double-stranded DNA molecules, which is caused by DNA-DNA attraction induced by the multivalent counterions. However, the detailed mechanism of this process is still not fully understood. Furthermore, in all-atom molecular dynamics (MD) simulations, spontaneous aggregation of several DNA oligonucleotides in the presence of CoHex 3+ has previously not been demonstrated. In order to obtain a rigorous description of CoHex 3+ -nucleic acid interactions and CoHex 3+ -induced DNA condensation to be used in MD simulations, we have derived optimized force field parameters of the CoHex 3+ ion. They were obtained from Car-Parrinello molecular dynamics simulation of a single CoHex 3+ ion in the presence of 125 water molecules. The new set of force field parameters reproduces the experimentally known transition of DNA from B- to A-form, and qualitatively describes changes of DNA and RNA persistence lengths. We then carried out a 2 μs long atomistic simulation of four DNA oligomers each consisting of 36 base pairs in the presence of CoHex 3+ . We demonstrate that, in this system, DNA molecules display attractive interactions and aggregate into bundle-like structures. This behavior depends critically on the details of the CoHex 3+ interaction with DNA. A control simulation with a similar setup but in the presence of Mg 2+ does not induce DNA-DNA attraction, which is also in agreement with experiment.

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)

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

Molecular dynamics simulations of substitutional diffusion

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

Zhou, Xiaowang; Jones, Reese E.; Gruber, Jacob

2016-12-18

In atomistic simulations, diffusion energy barriers are usually calculated for each atomic jump path using a nudged elastic band method. Practical materials often involve thousands of distinct atomic jump paths that are not known a priori. Hence, it is often preferred to determine an overall diffusion energy barrier and an overall pre-exponential factor from the Arrhenius equation constructed through molecular dynamics simulations of mean square displacement of the diffusion species at different temperatures. This approach has been well established for interstitial diffusion, but not for substitutional diffusion at the same confidence. Using In 0.1 Ga 0.9 N as an example,more » we have identified conditions where molecular dynamics simulations can be used to calculate highly converged Arrhenius plots for substitutional alloys. As a result, this may enable many complex diffusion problems to be easily and reliably studied in the future using molecular dynamics, provided that moderate computing resources are available.« less

MOLSIM: A modular molecular simulation software

PubMed Central

Jurij, Reščič

2015-01-01

The modular software MOLSIM for all‐atom molecular and coarse‐grained simulations is presented with focus on the underlying concepts used. The software possesses four unique features: (1) it is an integrated software for molecular dynamic, Monte Carlo, and Brownian dynamics simulations; (2) simulated objects are constructed in a hierarchical fashion representing atoms, rigid molecules and colloids, flexible chains, hierarchical polymers, and cross‐linked networks; (3) long‐range interactions involving charges, dipoles and/or anisotropic dipole polarizabilities are handled either with the standard Ewald sum, the smooth particle mesh Ewald sum, or the reaction‐field technique; (4) statistical uncertainties are provided for all calculated observables. In addition, MOLSIM supports various statistical ensembles, and several types of simulation cells and boundary conditions are available. Intermolecular interactions comprise tabulated pairwise potentials for speed and uniformity and many‐body interactions involve anisotropic polarizabilities. Intramolecular interactions include bond, angle, and crosslink potentials. A very large set of analyses of static and dynamic properties is provided. The capability of MOLSIM can be extended by user‐providing routines controlling, for example, start conditions, intermolecular potentials, and analyses. An extensive set of case studies in the field of soft matter is presented covering colloids, polymers, and crosslinked networks. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:25994597

Method for construction of a biased potential for hyperdynamic simulation of atomic systems

NASA Astrophysics Data System (ADS)

Duda, E. V.; Kornich, G. V.

2017-10-01

An approach to constructing a biased potential for hyperdynamic simulation of atomic systems is considered. Using this approach, the diffusion of an atom adsorbed on the surface of a two-dimensional crystal and a vacancy in the bulk of the crystal are simulated. The influence of the variation in the potential barriers due to thermal vibrations of atoms on the results of calculations is discussed. It is shown that the bias of the potential in the hyperdynamic simulation makes it possible to obtain statistical samples of transitions of atomic systems between states, similar to those given by classical molecular dynamics. However, hyperdynamics significantly accelerates computations in comparison with molecular dynamics in the case of temperature-activated transitions and the associated processes in atomic systems.

Atomic concentration effect on thermal properties during solidification of Pt-Rh alloy: A molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Yildiz, A. K.; Celik, F. A.

2017-04-01

The solidification process of Platinum-Rhodium alloy from liquid phase to solid state is investigated at the nano-scale by using Molecular Dynamics Simulation (MDS) for different atomic concentration ratios of Pt. The critical nucleus radius, the bond order parameter, interfacial free energies and total energy based on nucleation theory of the alloy are examined with respect to the temperature changes. The heat of fusion from high temperatures to low temperatures during solidification of the alloy system is determined from molecular dynamics simulation. The structural development is determined from the radial distribution function. It is observed from the results that the melting point of the alloy system decreases with increasing concentration of Pt and that variation of Pt ratio in the alloy shows a remarkable effect on solidification to understand the cooling process of thermal effects.

Atomic and molecular supernovae

NASA Technical Reports Server (NTRS)

Liu, Weihong

1997-01-01

Atomic and molecular physics of supernovae is discussed with an emphasis on the importance of detailed treatments of the critical atomic and molecular processes with the best available atomic and molecular data. The observations of molecules in SN 1987A are interpreted through a combination of spectral and chemical modelings, leading to strong constraints on the mixing and nucleosynthesis of the supernova. The non-equilibrium chemistry is used to argue that carbon dust can form in the oxygen-rich clumps where the efficient molecular cooling makes the nucleation of dust grains possible. For Type Ia supernovae, the analyses of their nebular spectra lead to strong constraints on the supernova explosion models.

A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation

PubMed Central

Qin, Feng

2015-01-01

The transient receptor potential (TRP) channels act as key sensors of various chemical and physical stimuli in eukaryotic cells. Despite years of study, the molecular mechanisms of TRP channel activation remain unclear. To elucidate the structural, dynamic, and energetic basis of gating in TRPV1 (a founding member of the TRPV subfamily), we performed coarse-grained modeling and all-atom molecular dynamics (MD) simulation based on the recently solved high resolution structures of the open and closed form of TRPV1. Our coarse-grained normal mode analysis captures two key modes of collective motions involved in the TRPV1 gating transition, featuring a quaternary twist motion of the transmembrane domains (TMDs) relative to the intracellular domains (ICDs). Our transition pathway modeling predicts a sequence of structural movements that propagate from the ICDs to the TMDs via key interface domains (including the membrane proximal domain and the C-terminal domain), leading to sequential opening of the selectivity filter followed by the lower gate in the channel pore (confirmed by modeling conformational changes induced by the activation of ICDs). The above findings of coarse-grained modeling are robust to perturbation by lipids. Finally, our MD simulation of the ICD identifies key residues that contribute differently to the nonpolar energy of the open and closed state, and these residues are predicted to control the temperature sensitivity of TRPV1 gating. These computational predictions offer new insights to the mechanism for heat activation of TRPV1 gating, and will guide our future electrophysiology and mutagenesis studies. PMID:25918362

All-Atom Simulations Reveal How Single-Point Mutations Promote Serpin Misfolding

NASA Astrophysics Data System (ADS)

Wang, Fang; Orioli, Simone; Ianeselli, Alan; Spagnolli, Giovanni; a Beccara, Silvio; Gershenson, Anne; Faccioli, Pietro; Wintrode, Patrick L.

2018-05-01

Protein misfolding is implicated in many diseases, including the serpinopathies. For the canonical inhibitory serpin {\\alpha}1-antitrypsin (A1AT), mutations can result in protein deficiencies leading to lung disease, and misfolded mutants can accumulate in hepatocytes leading to liver disease. Using all-atom simulations based on the recently developed Bias Functional algorithm we elucidate how wild-type A1AT folds and how the disease-associated S (Glu264Val) and Z (Glu342Lys) mutations lead to misfolding. The deleterious Z mutation disrupts folding at an early stage, while the relatively benign S mutant shows late stage minor misfolding. A number of suppressor mutations ameliorate the effects of the Z mutation and simulations on these mutants help to elucidate the relative roles of steric clashes and electrostatic interactions in Z misfolding. These results demonstrate a striking correlation between atomistic events and disease severity and shine light on the mechanisms driving chains away from their correct folding routes.

Atomic and molecular physics in the gas phase

NASA Astrophysics Data System (ADS)

Toburen, L. H.

1990-09-01

The spatial and temporal distributions of energy deposition by high-linear-energy-transfer radiation play an important role in the subsequent chemical and biological processes leading to radiation damage. Because the spatial structures of energy deposition events are of the same dimensions as molecular structures in the mammalian cell, direct measurements of energy deposition distributions appropriate to radiation biology are infeasible. This has led to the development of models of energy transport based on a knowledge of atomic and molecular interactions process that enable one to simulate energy transfer on an atomic scale. Such models require a detailed understanding of the interactions of ions and electrons with biologically relevant material. During the past 20 years there has been a great deal of progress in our understanding of these interactions; much of it coming from studies in the gas phase. These studies provide information on the systematics of interaction cross sections leading to a knowledge of the regions of energy deposition where molecular and phase effects are important and that guide developments in appropriate theory. In this report studies of the doubly differential cross sections, crucial to the development of stochastic energy deposition calculations and track structure simulation, will be reviewed. Areas of understanding are discussed and directions for future work addressed. Particular attention is given to experimental and theoretical findings that have changed the traditional view of secondary electron production for charged particle interactions with atomic and molecular targets.

Decrypting the structural, dynamic, and energetic basis of a monomeric kinesin interacting with a tubulin dimer in three ATPase states by all-atom molecular dynamics simulation.

PubMed

Chakraborty, Srirupa; Zheng, Wenjun

2015-01-27

We have employed molecular dynamics (MD) simulation to investigate, with atomic details, the structural dynamics and energetics of three major ATPase states (ADP, APO, and ATP state) of a human kinesin-1 monomer in complex with a tubulin dimer. Starting from a recently solved crystal structure of ATP-like kinesin-tubulin complex by the Knossow lab, we have used flexible fitting of cryo-electron-microscopy maps to construct new structural models of the kinesin-tubulin complex in APO and ATP state, and then conducted extensive MD simulations (total 400 ns for each state), followed by flexibility analysis, principal component analysis, hydrogen bond analysis, and binding free energy analysis. Our modeling and simulation have revealed key nucleotide-dependent changes in the structure and flexibility of the nucleotide-binding pocket (featuring a highly flexible and open switch I in APO state) and the tubulin-binding site, and allosterically coupled motions driving the APO to ATP transition. In addition, our binding free energy analysis has identified a set of key residues involved in kinesin-tubulin binding. On the basis of our simulation, we have attempted to address several outstanding issues in kinesin study, including the possible roles of β-sheet twist and neck linker docking in regulating nucleotide release and binding, the structural mechanism of ADP release, and possible extension and shortening of α4 helix during the ATPase cycle. This study has provided a comprehensive structural and dynamic picture of kinesin's major ATPase states, and offered promising targets for future mutational and functional studies to investigate the molecular mechanism of kinesin motors.

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures.

PubMed

Zhang, S; Nordlund, K; Djurabekova, F; Zhang, Y; Velisa, G; Wang, T S

2016-10-01

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop here a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures

DOE PAGES

Zhang, S.; Univ. of Helsinki; Nordlund, Kai; ...

2016-10-25

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop in this paper a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms,more » Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Finally, comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.« less

Simulation of Rutherford backscattering spectrometry from arbitrary atom structures

NASA Astrophysics Data System (ADS)

Zhang, S.; Nordlund, K.; Djurabekova, F.; Zhang, Y.; Velisa, G.; Wang, T. S.

2016-10-01

Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop here a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.

On the application of accelerated molecular dynamics to liquid water simulations.

PubMed

de Oliveira, César Augusto F; Hamelberg, Donald; McCammon, J Andrew

2006-11-16

Our group recently proposed a robust bias potential function that can be used in an efficient all-atom accelerated molecular dynamics (MD) approach to simulate the transition of high energy barriers without any advance knowledge of the potential-energy landscape. The main idea is to modify the potential-energy surface by adding a bias, or boost, potential in regions close to the local minima, such that all transitions rates are increased. By applying the accelerated MD simulation method to liquid water, we observed that this new simulation technique accelerates the molecular motion without losing its microscopic structure and equilibrium properties. Our results showed that the application of a small boost energy on the potential-energy surface significantly reduces the statistical inefficiency of the simulation while keeping all the other calculated properties unchanged. On the other hand, although aggressive acceleration of the dynamics simulation increases the self-diffusion coefficient of water molecules greatly and dramatically reduces the correlation time of the simulation, configurations representative of the true structure of liquid water are poorly sampled. Our results also showed the strength and robustness of this simulation technique, which confirm this approach as a very useful and promising tool to extend the time scale of the all-atom simulations of biological system with explicit solvent models. However, we should keep in mind that there is a compromise between the strength of the boost applied in the simulation and the reproduction of the ensemble average properties.

Fluctuating hydrodynamics for multiscale modeling and simulation: energy and heat transfer in molecular fluids.

PubMed

Shang, Barry Z; Voulgarakis, Nikolaos K; Chu, Jhih-Wei

2012-07-28

This work illustrates that fluctuating hydrodynamics (FHD) simulations can be used to capture the thermodynamic and hydrodynamic responses of molecular fluids at the nanoscale, including those associated with energy and heat transfer. Using all-atom molecular dynamics (MD) trajectories as the reference data, the atomistic coordinates of each snapshot are mapped onto mass, momentum, and energy density fields on Eulerian grids to generate a corresponding field trajectory. The molecular length-scale associated with finite molecule size is explicitly imposed during this coarse-graining by requiring that the variances of density fields scale inversely with the grid volume. From the fluctuations of field variables, the response functions and transport coefficients encoded in the all-atom MD trajectory are computed. By using the extracted fluid properties in FHD simulations, we show that the fluctuations and relaxation of hydrodynamic fields quantitatively match with those observed in the reference all-atom MD trajectory, hence establishing compatibility between the atomistic and field representations. We also show that inclusion of energy transfer in the FHD equations can more accurately capture the thermodynamic and hydrodynamic responses of molecular fluids. The results indicate that the proposed MD-to-FHD mapping with explicit consideration of finite molecule size provides a robust framework for coarse-graining the solution phase of complex molecular systems.

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.

Analysis of Adhesive Characteristics of Asphalt Based on Atomic Force Microscopy and Molecular Dynamics Simulation.

PubMed

Xu, Meng; Yi, Junyan; Feng, Decheng; Huang, Yudong; Wang, Dongsheng

2016-05-18

Asphalt binder is a very important building material in infrastructure construction; it is commonly mixed with mineral aggregate and used to produce asphalt concrete. Owing to the large differences in physical and chemical properties between asphalt and aggregate, adhesive bonds play an important role in determining the performance of asphalt concrete. Although many types of adhesive bonding mechanisms have been proposed to explain the interaction forces between asphalt binder and mineral aggregate, few have been confirmed and characterized. In comparison with chemical interactions, physical adsorption has been considered to play a more important role in adhesive bonding between asphalt and mineral aggregate. In this study, the silicon tip of an atomic force microscope was used to represent silicate minerals in aggregate, and a nanoscale analysis of the characteristics of adhesive bonding between asphalt binder and the silicon tip was conducted via an atomic force microscopy (AFM) test and molecular dynamics (MD) simulations. The results of the measurements and simulations could help in better understanding of the bonding and debonding procedures in asphalt-aggregate mixtures during hot mixing and under traffic loading. MD simulations on a single molecule of a component of asphalt and monocrystalline silicon demonstrate that molecules with a higher atomic density and planar structure, such as three types of asphaltene molecules, can provide greater adhesive strength. However, regarding the real components of asphalt binder, both the MD simulations and AFM test indicate that the colloidal structural behavior of asphalt also has a large influence on the adhesion behavior between asphalt and silicon. A schematic model of the interaction between asphalt and silicon is presented, which can explain the effect of aging on the adhesion behavior of asphalt.

Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations.

PubMed

Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

2015-06-15

In this study, we examine the temperature dependence of free energetics of nanotube association using graphical processing unit-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion, and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intratube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

PubMed Central

Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji

2015-01-01

GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310–323. doi: 10.1002/wcms.1220 PMID:26753008

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.

PubMed

Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji

2015-07-01

GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310-323. doi: 10.1002/wcms.1220.

Temperature-Dependent Conformational Properties of Human Neuronal Calcium Sensor-1 Protein Revealed by All-Atom Simulations.

PubMed

Zhu, Yuzhen; Ma, Buyong; Qi, Ruxi; Nussinov, Ruth; Zhang, Qingwen

2016-04-14

Neuronal calcium sensor-1 (NCS-1) protein has orthologues from Saccharomyces cerevisiae to human with highly conserved amino acid sequences. NCS-1 is an important factor controlling the animal's response to temperature change. This leads us to investigate the temperature effects on the conformational dynamics of human NCS-1 at 310 and 316 K by all-atom molecular dynamics (MD) simulations and dynamic community network analysis. Four independent 500 ns MD simulations show that secondary structure content at 316 K is similar to that at 310 K, whereas the global protein structure is expanded. Loop 3 (L3) adopts an extended state occuping the hydrophobic crevice, and the number of suboptimal communication paths between residue D176 and V190 is reduced at 316 K. The dynamic community network analysis suggests that the interdomain correlation is weakened, and the intradomain coupling is strengthened at 316 K. The elevated temperature reduces the number of the salt bridges, especially in C-domain. This study suggests that the elevated temperature affects the conformational dynamics of human NCS-1 protein. Comparison of the structural dynamics of R102Q mutant and Δ176-190 truncated NCS-1 suggests that the structural and dynamical response of NCS-1 protein to elevated temperature may be one of its intrinsic functional properties.

Synthesis, Characterization, and Multimillion-Atom Simulation of Halogen-Based Energetic Materials for Agent Defeat

DTIC Science & Technology

2013-04-01

DTRA-TR-13-23 Synthesis, Characterization, and Multimillion -Atom Simulation of Halogen-Based Energetic Materials for Agent Defeat Approved for...reagents for the destruction of biologically active materials and a simulation of their reactions on a multimillion atom scale with quantum...explosives for destruction of chemical & biological agents. Multimillion -atom molecular dynamics simulations with quantum mechanical accuracy were

Atomic scale friction of molecular adsorbates during diffusion.

PubMed

Lechner, B A J; de Wijn, A S; Hedgeland, H; Jardine, A P; Hinch, B J; Allison, W; Ellis, J

2013-05-21

Experimental observations suggest that molecular adsorbates exhibit a larger friction coefficient than atomic species of comparable mass, yet the origin of this increased friction is not well understood. We present a study of the microscopic origins of friction experienced by molecular adsorbates during surface diffusion. Helium spin-echo measurements of a range of five-membered aromatic molecules, cyclopentadienyl, pyrrole, and thiophene, on a copper(111) surface are compared with molecular dynamics simulations of the respective systems. The adsorbates have different chemical interactions with the surface and differ in bonding geometry, yet the measurements show that the friction is greater than 2 ps(-1) for all these molecules. We demonstrate that the internal and external degrees of freedom of these adsorbate species are a key factor in the underlying microscopic processes and identify the rotation modes as the ones contributing most to the total measured friction coefficient.

Molecular dynamics simulations of aqueous solutions of ethanolamines.

PubMed

López-Rendón, Roberto; Mora, Marco A; Alejandre, José; Tuckerman, Mark E

2006-08-03

We report on molecular dynamics simulations performed at constant temperature and pressure to study ethanolamines as pure components and in aqueous solutions. A new geometric integration algorithm that preserves the correct phase space volume is employed to study molecules having up to three ethanol chains. The most stable geometry, rotational barriers, and atomic charges were obtained by ab initio calculations in the gas phase. The calculated dipole moments agree well with available experimental data. The most stable conformation, due to intramolecular hydrogen bonding interactions, has a ringlike structure in one of the ethanol chains, leading to high molecular stability. All molecular dynamics simulations were performed in the liquid phase. The interaction parameters are the same for the atoms in the ethanol chains, reducing the number of variables in the potential model. Intermolecular hydrogen bonding is also analyzed, and it is shown that water associates at low water mole fractions. The force field reproduced (within 1%) the experimental liquid densities at different temperatures of pure components and aqueous solutions at 313 K. The excess and partial molar volumes are analyzed as a function of ethanolamine concentration.

Car and Parrinello meet Green and Kubo: simulating atomic heat transport from equilibrium ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Baroni, Stefano

Modern simulation methods based on electronic-structure theory have long been deemed unfit to compute heat transport coefficients within the Green-Kubo formalism. This is so because the quantum-mechanical energy density from which the heat flux is derived is inherently ill defined, thus allegedly hampering the use of the Green-Kubo formula. While this objection would actually apply to classical systems as well, I will demonstrate that the thermal conductivity is indeed independent of the specific microscopic expression for the energy density and current from which it is derived. This fact results from a kind of gauge invariance stemming from energy conservation and extensivity, which I will illustrate numerically for a classical Lennard-Jones fluid. I will then introduce an expression for the adiabatic energy flux, derived within density-functional theory, that allows simulating atomic heat transport using equilibrium ab initio molecular dynamics. The resulting methodology is demonstrated by comparing results from ab-initio and classical molecular-dynamics simulations of a model liquid-Argon system, for which accurate inter-atomic potentials are derived by the force-matching method, and applied to compute the thermal conductivity of heavy water at ambient conditions. The problem of evaluating transport coefficients along with their accuracy from relatively short trajectories is finally addressed and discussed with a few representative examples. Partially funded by the European Union through the MaX Centre of Excellence (Grant No. 676598).

Hyperfine excitation of CH in collisions with atomic and molecular hydrogen

NASA Astrophysics Data System (ADS)

Dagdigian, Paul J.

2018-04-01

We investigate here the excitation of methylidene (CH) induced by collisions with atomic and molecular hydrogen (H and H2). The hyperfine-resolved rate coefficients were obtained from close coupling nuclear-spin-free scattering calculations. The calculations are based upon recent, high-accuracy calculations of the CH(X2Π)-H(2S) and CH(X2Π)-H2 potential energy surfaces. Cross-sections and rate coefficients for collisions with atomic H, para-H2, and ortho-H2 were computed for all transitions between the 32 hyperfine levels for CH(X2Π) involving the n ≤ 4 rotational levels for temperatures between 10 and 300 K. These rate coefficients should significantly aid in the interpretation of astronomical observations of CH spectra. As a first application, the excitation of CH is simulated for conditions in typical molecular clouds.

A molecular fragment cheminformatics roadmap for mesoscopic simulation.

PubMed

Truszkowski, Andreas; Daniel, Mirco; Kuhn, Hubert; Neumann, Stefan; Steinbeck, Christoph; Zielesny, Achim; Epple, Matthias

2014-12-01

Mesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the atom types of molecular mechanics but molecular fragments, molecules or even larger molecular entities. For its simulation setup and output a mesoscopic simulation kernel software uses abstract matrix (array) representations for bead topology and connectivity. Therefore a pure kernel-based mesoscopic simulation task is a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequent cheminformatics approach tackles these problems and provides solutions for a considerably enhanced accessibility. This study aims at outlining a complete cheminformatics roadmap that frames a mesoscopic Molecular Fragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application. The molecular fragment cheminformatics roadmap consists of four consecutive building blocks: An adequate fragment structure representation (1), defined operations on these fragment structures (2), the description of compartments with defined compositions and structural alignments (3), and the graphical setup and analysis of a whole simulation box (4). The basis of the cheminformatics approach (i.e. building block 1) is a SMILES-like line notation (denoted f SMILES) with connected molecular fragments to represent a molecular structure. The f SMILES notation and the following concepts and methods for building blocks 2-4 are outlined with examples and practical usage scenarios. It is shown that the requirements of the roadmap may be partly covered by already existing open-source cheminformatics software. Mesoscopic simulation techniques like MFD may be considerably alleviated and broadened for practical use with a consequent cheminformatics layer that successfully tackles its setup subtleties and

All-atom molecular dynamics simulations of spin labelled double and single-strand DNA for EPR studies.

PubMed

Prior, C; Danilāne, L; Oganesyan, V S

2018-05-16

We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of electron paramagnetic resonance (EPR) spectra of spin labelled DNA. Models for two structurally different DNA spin probes with either the rigid or flexible position of the nitroxide group in the base pair, employed in experimental studies previously, have been developed. By the application of the combined MD-EPR simulation methodology we aimed at the following. Firstly, to provide a test bed against a sensitive spectroscopic technique for the recently developed improved version of the parmbsc1 force field for MD modelling of DNA. The predicted EPR spectra show good agreement with the experimental ones available from the literature, thus confirming the accuracy of the currently employed DNA force fields. Secondly, to provide a quantitative interpretation of the motional contributions into the dynamics of spin probes in both duplex and single-strand DNA fragments and to analyse their perturbing effects on the local DNA structure. Finally, a combination of MD and EPR allowed us to test the validity of the application of the Model-Free (M-F) approach coupled with the partial averaging of magnetic tensors to the simulation of EPR spectra of DNA systems by comparing the resultant EPR spectra with those simulated directly from MD trajectories. The advantage of the M-F based EPR simulation approach over the direct propagation techniques is that it requires motional and order parameters that can be calculated from shorter MD trajectories. The reported MD-EPR methodology is transferable to the prediction and interpretation of EPR spectra of higher order DNA structures with novel types of spin labels.

Complex molecular assemblies at hand via interactive simulations.

PubMed

Delalande, Olivier; Férey, Nicolas; Grasseau, Gilles; Baaden, Marc

2009-11-30

Studying complex molecular assemblies interactively is becoming an increasingly appealing approach to molecular modeling. Here we focus on interactive molecular dynamics (IMD) as a textbook example for interactive simulation methods. Such simulations can be useful in exploring and generating hypotheses about the structural and mechanical aspects of biomolecular interactions. For the first time, we carry out low-resolution coarse-grain IMD simulations. Such simplified modeling methods currently appear to be more suitable for interactive experiments and represent a well-balanced compromise between an important gain in computational speed versus a moderate loss in modeling accuracy compared to higher resolution all-atom simulations. This is particularly useful for initial exploration and hypothesis development for rare molecular interaction events. We evaluate which applications are currently feasible using molecular assemblies from 1900 to over 300,000 particles. Three biochemical systems are discussed: the guanylate kinase (GK) enzyme, the outer membrane protease T and the soluble N-ethylmaleimide-sensitive factor attachment protein receptors complex involved in membrane fusion. We induce large conformational changes, carry out interactive docking experiments, probe lipid-protein interactions and are able to sense the mechanical properties of a molecular model. Furthermore, such interactive simulations facilitate exploration of modeling parameters for method improvement. For the purpose of these simulations, we have developed a freely available software library called MDDriver. It uses the IMD protocol from NAMD and facilitates the implementation and application of interactive simulations. With MDDriver it becomes very easy to render any particle-based molecular simulation engine interactive. Here we use its implementation in the Gromacs software as an example. Copyright 2009 Wiley Periodicals, Inc.

Principal Component Analysis of Lipid Molecule Conformational Changes in Molecular Dynamics Simulations.

PubMed

Buslaev, Pavel; Gordeliy, Valentin; Grudinin, Sergei; Gushchin, Ivan

2016-03-08

Molecular dynamics simulations of lipid bilayers are ubiquitous nowadays. Usually, either global properties of the bilayer or some particular characteristics of each lipid molecule are evaluated in such simulations, but the structural properties of the molecules as a whole are rarely studied. Here, we show how a comprehensive quantitative description of conformational space and dynamics of a single lipid molecule can be achieved via the principal component analysis (PCA). We illustrate the approach by analyzing and comparing simulations of DOPC bilayers obtained using eight different force fields: all-atom generalized AMBER, CHARMM27, CHARMM36, Lipid14, and Slipids and united-atom Berger, GROMOS43A1-S3, and GROMOS54A7. Similarly to proteins, most of the structural variance of a lipid molecule can be described by only a few principal components. These major components are similar in different simulations, although there are notable distinctions between the older and newer force fields and between the all-atom and united-atom force fields. The DOPC molecules in the simulations generally equilibrate on the time scales of tens to hundreds of nanoseconds. The equilibration is the slowest in the GAFF simulation and the fastest in the Slipids simulation. Somewhat unexpectedly, the equilibration in the united-atom force fields is generally slower than in the all-atom force fields. Overall, there is a clear separation between the more variable previous generation force fields and significantly more similar new generation force fields (CHARMM36, Lipid14, Slipids). We expect that the presented approaches will be useful for quantitative analysis of conformations and dynamics of individual lipid molecules in other simulations of lipid bilayers.

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.

Solar-simulator-pumped atomic iodine laser kinetics

NASA Technical Reports Server (NTRS)

Wilson, H. W.; Raju, S.; Shiu, Y. J.

1983-01-01

The literature contains broad ranges of disagreement in kinetic data for the atomic iodine laser. A kinetic model of a solar-simulator-pumped iodine laser is used to select those kinetic data consistent with recent laser experiments at the Langley Research Center. Analysis of the solar-simulator-pumped laser experiments resulted in the following estimates of rate coefficients: for alkyl radical (n-C3F7) and atomic iodine (I) recombination, 4.3 x 10 to the 11th power (1.9) + or - cu cm/s; for n-C3F7I stabilized atomic iodine recombination (I + I) 3.7 x 10 to the -32nd power (2.3) + or -1 cm to the 6th power/s; and for molecular iodine (I2) quenching, 3.1 x 10 to the -11th power (1.6) + or - 1 cu cm/s. These rates are consistent with the recent measurements.

All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins.

PubMed

Arnautova, Yelena A; Abagyan, Ruben; Totrov, Maxim

2015-05-12

We present an extension of the all-atom internal-coordinate force field, ICMFF, that allows for simulation of heterogeneous systems including hexopyranose saccharides and glycan chains in addition to proteins. A library of standard glycan geometries containing α- and β-anomers of the most common hexapyranoses, i.e., d-galactose, d-glucose, d-mannose, d-xylose, l-fucose, N -acetylglucosamine, N -acetylgalactosamine, sialic, and glucuronic acids, is created based on the analysis of the saccharide structures reported in the Cambridge Structural Database. The new force field parameters include molecular electrostatic potential-derived partial atomic charges and the torsional parameters derived from quantum mechanical data for a collection of minimal molecular fragments and related molecules. The ϕ/ψ torsional parameters for different types of glycosidic linkages are developed using model compounds containing the key atoms in the full carbohydrates, i.e., glycosidic-linked tetrahydropyran-cyclohexane dimers. Target data for parameter optimization include two-dimensional energy surfaces corresponding to the ϕ/ψ glycosidic dihedral angles in the disaccharide analogues, as determined by quantum mechanical MP2/6-31G** single-point energies on HF/6-31G** optimized structures. To achieve better agreement with the observed geometries of glycosidic linkages, the bond angles at the O-linkage atoms are added to the internal variable set and the corresponding bond bending energy term is parametrized using quantum mechanical data. The resulting force field is validated on glycan chains of 1-12 residues from a set of high-resolution X-ray glycoprotein structures based on heavy atom root-mean-square deviations of the lowest-energy glycan conformations generated by the biased probability Monte Carlo (BPMC) molecular mechanics simulations from the native structures. The appropriate BPMC distributions for monosaccharide-monosaccharide and protein-glycan linkages are derived from

All-Atom Molecular Dynamics-Based Analysis of Membrane-Stabilizing Copolymer Interactions with Lipid Bilayers Probed under Constant Surface Tensions.

PubMed

Houang, Evelyne M; Bates, Frank S; Sham, Yuk Y; Metzger, Joseph M

2017-11-30

An all-atom phospholipid bilayer and triblock copolymer model was developed for molecular dynamics (MD) studies. These were performed to investigate the mechanism of interaction between membrane-stabilizing triblock copolymer P188 and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) lipid bilayers under applied lateral surface tension (γ) to model membrane mechanical stress. Results showed that P188 insertion is driven by the hydrophobic poly(propylene oxide) (PPO) core and dependent on bilayer area per lipid. Moreover, insertion of P188 increased the bilayer's resistance to mechanical rupture, as observed by a significant increase in the absolute lateral pressure required to disrupt the bilayer. To further investigate the specific chemical features of P188 underlying membrane stabilizer function, a series of MD simulations with triblock copolymers of the same class as P188 but of varying chemical composition and sizes were performed. Results showed that triblock copolymer insertion into the lipid bilayer is dependent on overall copolymer hydrophobicity, with higher copolymer hydrophobicity requiring a reduced bilayer area per lipid ratio for insertion. Further analysis revealed that the effect of copolymer insertion on membrane mechanical integrity was also dependent on hydrophobicity. Here, P188 insertion significantly increased the absolute apparent lateral pressure required to rupture the POPC bilayer, thereby protecting the membrane against mechanical stress. In marked contrast, highly hydrophobic copolymers decreased the lateral pressure necessary for membrane rupture and thus rendering the membrane significantly more susceptible to mechanical stress. These new in silico findings align with recent experimental findings using synthetic lipid bilayers and in muscle cells in vitro and mouse models in vivo. Collectively, these data underscore the importance of PEO-PPO-PEO copolymer chemical composition in copolymer-based muscle membrane stabilization

Molecular dynamics simulations of hydrogen diffusion in aluminum

DOE PAGES

Zhou, X. W.; El Gabaly, F.; Stavila, V.; ...

2016-03-23

In this study, hydrogen diffusion impacts the performance of solid-state hydrogen storage materials and contributes to the embrittlement of structural materials under hydrogen-containing environments. In atomistic simulations, the diffusion energy barriers are usually calculated using molecular statics simulations where a nudged elastic band method is used to constrain a path connecting the two end points of an atomic jump. This approach requires prior knowledge of the “end points”. For alloy and defective systems, the number of possible atomic jumps with respect to local atomic configurations is tremendous. Even when these jumps can be exhaustively studied, it is still unclear howmore » they can be combined to give an overall diffusion behavior seen in experiments. Here we describe the use of molecular dynamics simulations to determine the overall diffusion energy barrier from the Arrhenius equation. This method does not require information about atomic jumps, and it has additional advantages, such as the ability to incorporate finite temperature effects and to determine the pre-exponential factor. As a test case for a generic method, we focus on hydrogen diffusion in bulk aluminum. We find that the challenge of this method is the statistical variation of the results. However, highly converged energy barriers can be achieved by an appropriate set of temperatures, output time intervals (for tracking hydrogen positions), and a long total simulation time. Our results help elucidate the inconsistencies of the experimental diffusion data published in the literature. The robust approach developed here may also open up future molecular dynamics simulations to rapidly study diffusion properties of complex material systems in multidimensional spaces involving composition and defects.« less

MATCH: An Atom- Typing Toolset for Molecular Mechanics Force Fields

PubMed Central

Yesselman, Joseph D.; Price, Daniel J.; Knight, Jennifer L.; Brooks, Charles L.

2011-01-01

We introduce a toolset of program libraries collectively titled MATCH (Multipurpose Atom-Typer for CHARMM) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion from multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges and force field parameters is achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In the present work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM CGENFF force field (Vanommeslaeghe, et al., JCC., 2010, 31, 671–690), one million molecules from the PubChem database of small molecules are typed, parameterized and minimized. PMID:22042689

Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model.

PubMed

Chen, Yunjie; Roux, Benoît

2015-08-11

Molecular dynamics (MD) trajectories based on a classical equation of motion provide a straightforward, albeit somewhat inefficient approach, to explore and sample the configurational space of a complex molecular system. While a broad range of techniques can be used to accelerate and enhance the sampling efficiency of classical simulations, only algorithms that are consistent with the Boltzmann equilibrium distribution yield a proper statistical mechanical computational framework. Here, a multiscale hybrid algorithm relying simultaneously on all-atom fine-grained (FG) and coarse-grained (CG) representations of a system is designed to improve sampling efficiency by combining the strength of nonequilibrium molecular dynamics (neMD) and Metropolis Monte Carlo (MC). This CG-guided hybrid neMD-MC algorithm comprises six steps: (1) a FG configuration of an atomic system is dynamically propagated for some period of time using equilibrium MD; (2) the resulting FG configuration is mapped onto a simplified CG model; (3) the CG model is propagated for a brief time interval to yield a new CG configuration; (4) the resulting CG configuration is used as a target to guide the evolution of the FG system; (5) the FG configuration (from step 1) is driven via a nonequilibrium MD (neMD) simulation toward the CG target; (6) the resulting FG configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-ends momentum reversal prescription is used for the neMD trajectories of the FG system to guarantee that the CG-guided hybrid neMD-MC algorithm obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The enhanced sampling achieved with the method is illustrated with a model system with hindered diffusion and explicit-solvent peptide simulations. Illustrative tests indicate that the method can yield a speedup of about 80 times for the model system and up

Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics—Monte Carlo Simulations Guided by a Coarse-Grained Model

PubMed Central

2015-01-01

Molecular dynamics (MD) trajectories based on a classical equation of motion provide a straightforward, albeit somewhat inefficient approach, to explore and sample the configurational space of a complex molecular system. While a broad range of techniques can be used to accelerate and enhance the sampling efficiency of classical simulations, only algorithms that are consistent with the Boltzmann equilibrium distribution yield a proper statistical mechanical computational framework. Here, a multiscale hybrid algorithm relying simultaneously on all-atom fine-grained (FG) and coarse-grained (CG) representations of a system is designed to improve sampling efficiency by combining the strength of nonequilibrium molecular dynamics (neMD) and Metropolis Monte Carlo (MC). This CG-guided hybrid neMD-MC algorithm comprises six steps: (1) a FG configuration of an atomic system is dynamically propagated for some period of time using equilibrium MD; (2) the resulting FG configuration is mapped onto a simplified CG model; (3) the CG model is propagated for a brief time interval to yield a new CG configuration; (4) the resulting CG configuration is used as a target to guide the evolution of the FG system; (5) the FG configuration (from step 1) is driven via a nonequilibrium MD (neMD) simulation toward the CG target; (6) the resulting FG configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-ends momentum reversal prescription is used for the neMD trajectories of the FG system to guarantee that the CG-guided hybrid neMD-MC algorithm obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The enhanced sampling achieved with the method is illustrated with a model system with hindered diffusion and explicit-solvent peptide simulations. Illustrative tests indicate that the method can yield a speedup of about 80 times for the model system and up

Examining the origins of the hydration force between lipid bilayers using all-atom simulations.

PubMed

Gentilcore, Anastasia N; Michaud-Agrawal, Naveen; Crozier, Paul S; Stevens, Mark J; Woolf, Thomas B

2010-05-01

Using 237 all-atom double bilayer simulations, we examined the thermodynamic and structural changes that occur as a phosphatidylcholine lipid bilayer stack is dehydrated. The simulated system represents a micropatch of lipid multilayer systems that are studied experimentally using surface force apparatus, atomic force microscopy and osmotic pressure studies. In these experiments, the hydration level of the system is varied, changing the separation between the bilayers, in order to understand the forces that the bilayers feel as they are brought together. These studies have found a curious, strongly repulsive force when the bilayers are very close to each other, which has been termed the "hydration force," though the origins of this force are not clearly understood. We computationally reproduce this repulsive, relatively free energy change as bilayers come together and make qualitative conclusions as to the enthalpic and entropic origins of the free energy change. This analysis is supported by data showing structural changes in the waters, lipids and salts that have also been seen in experimental work. Increases in solvent ordering as the bilayers are dehydrated are found to be essential in causing the repulsion as the bilayers come together.

Dielectric relaxation of ethylene carbonate and propylene carbonate from molecular dynamics simulations

DOE PAGES

Chaudhari, Mangesh I.; You, Xinli; Pratt, Lawrence R.; ...

2015-11-24

Ethylene carbonate (EC) and propylene carbonate (PC) are widely used solvents in lithium (Li)-ion batteries and supercapacitors. Ion dissolution and diffusion in those media are correlated with solvent dielectric responses. Here, we use all-atom molecular dynamics simulations of the pure solvents to calculate dielectric constants and relaxation times, and molecular mobilities. The computed results are compared with limited available experiments to assist more exhaustive studies of these important characteristics. As a result, the observed agreement is encouraging and provides guidance for further validation of force-field simulation models for EC and PC solvents.

A model for including thermal conduction in molecular dynamics simulations

NASA Technical Reports Server (NTRS)

Wu, Yue; Friauf, Robert J.

1989-01-01

A technique is introduced for including thermal conduction in molecular dynamics simulations for solids. A model is developed to allow energy flow between the computational cell and the bulk of the solid when periodic boundary conditions cannot be used. Thermal conduction is achieved by scaling the velocities of atoms in a transitional boundary layer. The scaling factor is obtained from the thermal diffusivity, and the results show good agreement with the solution for a continuous medium at long times. The effects of different temperature and size of the system, and of variations in strength parameter, atomic mass, and thermal diffusivity were investigated. In all cases, no significant change in simulation results has been found.

How PEGylation enhances the stability and potency of insulin: a molecular dynamics simulation.

PubMed

Yang, Cheng; Lu, Diannan; Liu, Zheng

2011-04-05

While the effectiveness of PEGylation in enhancing the stability and potency of protein pharmaceuticals has been validated for years, the underlying mechanism remains poorly understood, particularly at the molecular level. A molecular dynamics simulation was developed using an annealing procedure that allowed an all-atom level examination of the interaction between PEG polymers of different chain lengths and a conjugated protein represented by insulin. It was shown that PEG became entangled around the protein surface through hydrophobic interaction and concurrently formed hydrogen bonds with the surrounding water molecules. In addition to enhancing its structural stability, as indicated by the root-mean-square difference (rmsd) and secondary structure analyses, conjugation increased the size of the protein drug while decreasing the solvent accessible surface area of the protein. All these thus led to prolonged circulation life despite kidney filtration, proteolysis, and immunogenic side effects, as experimentally demonstrated elsewhere. Moreover, the simulation results indicated that an optimal chain length exists that would maximize drug potency underpinned by the parameters mentioned above. The simulation provided molecular insight into the interaction between PEG and the conjugated protein at the all-atom level and offered a tool that would allow for the design of PEGylated protein pharmaceuticals for given applications.

Comparison of forcefields for molecular dynamics simulations of hydrocarbon phase diagrams

NASA Astrophysics Data System (ADS)

Pisarev, V. V.; Zakharov, S. A.

2018-01-01

Molecular dynamics calculations of vapor-liquid equilibrium of methane-n-butane mixture are performed. Three force-field models are tested: the TraPPE-UA united-atom forcefield, LOPLS-AA all-atom forcefield and a fully flexible version of the TraPPE-EH all-atom forcefield. All those forcefields reproduce well the composition of liquid phase in the mixture as a function of pressure at the 300 K isotherm, while significant discrepancies from experimental data are observed in the saturated vapor compositions with OPLS-AA and TraPPE-UA forcefields. The best agreement with the experimental phase diagram is found with TraPPE-EH forcefield which accurately reproduces compositions of both liquid and vapor phase. This forcefield can be recommended for simulation of two-phase hydrocarbon systems.

United polarizable multipole water model for molecular mechanics simulation

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

Qi, Rui; Wang, Qiantao; Ren, Pengyu, E-mail: pren@mail.utexas.edu

2015-07-07

We report the development of a united AMOEBA (uAMOEBA) polarizable water model, which is computationally 3–5 times more efficient than the three-site AMOEBA03 model in molecular dynamics simulations while providing comparable accuracy for gas-phase and liquid properties. In this coarse-grained polarizable water model, both electrostatic (permanent and induced) and van der Waals representations have been reduced to a single site located at the oxygen atom. The permanent charge distribution is described via the molecular dipole and quadrupole moments and the many-body polarization via an isotropic molecular polarizability, all located at the oxygen center. Similarly, a single van der Waals interactionmore » site is used for each water molecule. Hydrogen atoms are retained only for the purpose of defining local frames for the molecular multipole moments and intramolecular vibrational modes. The parameters have been derived based on a combination of ab initio quantum mechanical and experimental data set containing gas-phase cluster structures and energies, and liquid thermodynamic properties. For validation, additional properties including dimer interaction energy, liquid structures, self-diffusion coefficient, and shear viscosity have been evaluated. The results demonstrate good transferability from the gas to the liquid phase over a wide range of temperatures, and from nonpolar to polar environments, due to the presence of molecular polarizability. The water coordination, hydrogen-bonding structure, and dynamic properties given by uAMOEBA are similar to those derived from the all-atom AMOEBA03 model and experiments. Thus, the current model is an accurate and efficient alternative for modeling water.« less

Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel

PubMed Central

Li, Xianfeng; Murthy, N. Sanjeeva; Becker, Matthew L.; Latour, Robert A.

2016-01-01

A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications. PMID:27013229

Investigations into the mechanism of material removal and surface modification at atomic scale on stainless steel using molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Ranjan, Prabhat; Balasubramaniam, R.; Jain, V. K.

2018-06-01

A molecular dynamics simulation (MDS) has been carried out to investigate the material removal phenomenon of chemo-mechanical magnetorheological finishing (CMMRF) process. To understand the role of chemical assisted mechanical abrasion in CMMRF process, material removal phenomenon is subdivided into three different stages. In the first stage, new atomic bonds viz. Fe-O-Si is created on the surface of the workpiece (stainless steel). The second stage deals with the rupture of parent bonds like Fe-Fe on the workpiece. In the final stage, removal of material from the surface in the form of dislodged debris (cluster of atoms) takes place. Effects of process parameters like abrasive particles, depth of penetration and initial surface condition on finishing force, potential energy (towards secondary phenomenon such as chemical instability of the finished surface) and material removal at atomic scale have been investigated. It was observed that the type of abrasive particle is one of the important parameters to produce atomically smooth surface. Experiments were also conducted as per the MDS to generate defect-free and sub-nanometre-level finished surface (Ra value better than 0.2 nm). The experimental results reasonably agree well with the simulation results.

Uncovering molecular processes in crystal nucleation and growth by using molecular simulation.

PubMed

Anwar, Jamshed; Zahn, Dirk

2011-02-25

Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The equilibrium properties and folding kinetics of an all-atom Go model of the Trp-cage.

PubMed

Linhananta, Apichart; Boer, Jesse; MacKay, Ian

2005-03-15

The ultrafast-folding 20-residue Trp-cage protein is quickly becoming a new benchmark for molecular dynamics studies. Already several all-atom simulations have probed its equilibrium and kinetic properties. In this work an all-atom Go model is used to accurately represent the side-chain packing and native atomic contacts of the Trp-cage. The model reproduces the hallmark thermodynamics cooperativity of small proteins. Folding simulations observe that in the fast-folding dominant pathway, partial alpha-helical structure forms before hydrophobic core collapse. In the slow-folding secondary pathway, partial core collapse occurs before helical structure. The slow-folding rate of the secondary pathway is attributed to the loss of side-chain rotational freedom, due to the early core collapse, which impedes the helix formation. A major finding is the observation of a low-temperature kinetic intermediate stabilized by a salt bridge between residues Asp-9 and Arg-16. Similar observations [R. Zhou, Proc. Natl. Acad. Sci. U.S.A. 100, 13280 (2003)] were reported in a recent study using an all-atom model of the Trp-cage in explicit water, in which the salt-bridge stabilized intermediate was hypothesized to be the origin of the ultrafast-folding mechanism. A theoretical mutation that eliminates the Asp-9-Arg-16 salt bridge, but leaves the residues intact, is performed. Folding simulations of the mutant Trp-cage observe a two-state free-energy landscape with no kinetic intermediate and a significant decrease in the folding rate, in support of the hypothesis.

The atomic simulation environment-a Python library for working with atoms.

PubMed

Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D; Jennings, Paul C; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W

2017-07-12

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

The atomic simulation environment—a Python library for working with atoms

NASA Astrophysics Data System (ADS)

Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E.; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N.; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D.; Jennings, Paul C.; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R.; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S.; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W.

2017-07-01

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple ‘for-loop’ construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

An atomic and molecular fluid model for efficient edge-plasma transport simulations at high densities

NASA Astrophysics Data System (ADS)

Rognlien, Thomas; Rensink, Marvin

2016-10-01

Transport simulations for the edge plasma of tokamaks and other magnetic fusion devices requires the coupling of plasma and recycling or injected neutral gas. There are various neutral models used for this purpose, e.g., atomic fluid model, a Monte Carlo particle models, transition/escape probability methods, and semi-analytic models. While the Monte Carlo method is generally viewed as the most accurate, it is time consuming, which becomes even more demanding for device simulations of high densities and size typical of fusion power plants because the neutral collisional mean-free path becomes very small. Here we examine the behavior of an extended fluid neutral model for hydrogen that includes both atoms and molecules, which easily includes nonlinear neutral-neutral collision effects. In addition to the strong charge-exchange between hydrogen atoms and ions, elastic scattering is included among all species. Comparisons are made with the DEGAS 2 Monte Carlo code. Work performed for U.S. DoE by LLNL under Contract DE-AC52-07NA27344.

Microsecond Molecular Dynamics Simulations of Lipid Mixing

PubMed Central

2015-01-01

Molecular dynamics (MD) simulations of membranes are often hindered by the slow lateral diffusion of lipids and the limited time scale of MD. In order to study the dynamics of mixing and characterize the lateral distribution of lipids in converged mixtures, we report microsecond-long all-atom MD simulations performed on the special-purpose machine Anton. Two types of mixed bilayers, POPE:POPG (3:1) and POPC:cholesterol (2:1), as well as a pure POPC bilayer, were each simulated for up to 2 μs. These simulations show that POPE:POPG and POPC:cholesterol are each fully miscible at the simulated conditions, with the final states of the mixed bilayers similar to a random mixture. By simulating three POPE:POPG bilayers at different NaCl concentrations (0, 0.15, and 1 M), we also examined the effect of salt concentration on lipid mixing. While an increase in NaCl concentration is shown to affect the area per lipid, tail order, and lipid lateral diffusion, the final states of mixing remain unaltered, which is explained by the largely uniform increase in Na+ ions around POPE and POPG. Direct measurement of water permeation reveals that the POPE:POPG bilayer with 1 M NaCl has reduced water permeability compared with those at zero or low salt concentration. Our calculations provide a benchmark to estimate the convergence time scale of all-atom MD simulations of lipid mixing. Additionally, equilibrated structures of POPE:POPG and POPC:cholesterol, which are frequently used to mimic bacterial and mammalian membranes, respectively, can be used as starting points of simulations involving these membranes. PMID:25237736

Reinventing atomic magnetic simulations with spin-orbit coupling

DOE PAGES

Perera, Meewanage Dilina N.; Eisenbach, Markus; Nicholson, Don M.; ...

2016-02-10

We propose a powerful extension to the combined molecular and spin dynamics method that fully captures the coupling between the atomic and spin subsystems via spin-orbit interactions. Moreover, the foundation of this method lies in the inclusion of the local magnetic anisotropies that arise as a consequence of the lattice symmetry breaking due to phonons or crystallographic defects. By using canonical simulations of bcc iron with the system coupled to a phonon heat bath, we show that our extension enables the previously unachievable angular momentum exchange between the atomic and spin degrees of freedom.

Atomic and Molecular Data and their Applications★

NASA Astrophysics Data System (ADS)

Drake, Gordon W. F.; Yoon, Jung-Sik; Kato, Daiji; Karwasz, Grzegorz

2018-03-01

This topical issue on Atomic and molecular data and their applications was motivated by the 10th International Conference on Atomic and Molecular Data (ICAMDATA 2016), which was held from September 26 to 29, 2016 in Gunsan, Republic of Korea. The topics of this issue reflect those of the conference program. The scientific papers in the topical issue cover the fields of atomic and molecular structure, radiative transitions, scattering processes, data base development, and the applications of atomic and molecular data to plasma modeling. Contribution to the Topical Issue "Atomic and Molecular Data and their Applications", edited by Gordon W.F. Drake, Jung-Sik Yoon, Daiji Kato, and Grzegorz Karwasz.

Trapping hydrogen atoms from a neon-gas matrix: a theoretical simulation.

PubMed

Bovino, S; Zhang, P; Kharchenko, V; Dalgarno, A

2009-08-07

Hydrogen is of critical importance in atomic and molecular physics and the development of a simple and efficient technique for trapping cold and ultracold hydrogen atoms would be a significant advance. In this study we simulate a recently proposed trap-loading mechanism for trapping hydrogen atoms released from a neon matrix. Accurate ab initio quantum calculations are reported of the neon-hydrogen interaction potential and the energy- and angular-dependent elastic scattering cross sections that control the energy transfer of initially cold atoms are obtained. They are then used to construct the Boltzmann kinetic equation, describing the energy relaxation process. Numerical solutions of the Boltzmann equation predict the time evolution of the hydrogen energy distribution function. Based on the simulations we discuss the prospects of the technique.

Continuous all-optical deceleration of molecular beams and demonstration with Rb atoms

NASA Astrophysics Data System (ADS)

Long, Xueping; Jayich, Andrew; Campbell, Wesley

2017-04-01

Ultracold samples of molecules are desirable for a variety of applications, such as many-body physics, precision measurement and quantum information science. However, the pursuit of ultracold molecules has achieved limited success: spontaneous emission into many different dark states makes it hard to optically decelerate molecules to trappable speed. We propose to address this problem with a general optical deceleration technique that exploits a pump-dump pulse pair from a mode-locked laser. A molecular beam is first excited by a counter-propagating ``pump'' pulse. The molecular beam is then driven back to the initial ground state by a co-propagating ``dump'' pulse via stimulated emission. The delay between the pump and dump pulse is set to be shorter than the excited state lifetimes in order to limit decays to dark states. We report progress benchmarking this stimulated force by accelerating a cold sample of neutral Rb atoms.

Multiscale Molecular Simulation of Solution Processing of SMDPPEH: PCBM Small-Molecule Organic Solar Cells.

PubMed

Lee, Cheng-Kuang; Pao, Chun-Wei

2016-08-17

Solution-processed small-molecule organic solar cells are a promising renewable energy source because of their low production cost, mechanical flexibility, and light weight relative to their pure inorganic counterparts. In this work, we developed a coarse-grained (CG) Gay-Berne ellipsoid molecular simulation model based on atomistic trajectories from all-atom molecular dynamics simulations of smaller system sizes to systematically study the nanomorphology of the SMDPPEH/PCBM/solvent ternary blend during solution processing, including the blade-coating process by applying external shear to the solution. With the significantly reduced overall system degrees of freedom and computational acceleration from GPU, we were able to go well beyond the limitation of conventional all-atom molecular simulations with a system size on the order of hundreds of nanometers with mesoscale molecular detail. Our simulations indicate that, similar to polymer solar cells, the optimal blending ratio in small-molecule organic solar cells must provide the highest specific interfacial area for efficient exciton dissociation, while retaining balanced hole/electron transport pathway percolation. We also reveal that blade-coating processes have a significant impact on nanomorphology. For given donor/acceptor blending ratios, applying an external shear force can effectively promote donor/acceptor phase segregation and stacking in the SMDPPEH domains. The present study demonstrated the capability of an ellipsoid-based coarse-grained model for studying the nanomorphology evolution of small-molecule organic solar cells during solution processing/blade-coating and provided links between fabrication protocols and device nanomorphologies.

Understanding Molecular Ion-Neutral Atom Collisions for the Production of Ultracold Molecular Ions

DTIC Science & Technology

2016-06-06

Understanding Molecular Ion-Neutral Atom Collisions for the Production of Utracold Molecular Ions In the last five years, the study of ultracold...U.S. Army Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 molecular ion, quantum chemistry, atom ion interaction...Molecular Ion-Neutral Atom Collisions for the Production of Utracold Molecular Ions Report Title In the last five years, the study of ultracold molecular

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.

Structural Dynamics of Carbon Dots in Water and N, N-Dimethylformamide Probed by All-Atom Molecular Dynamics Simulations.

PubMed

Paloncýová, Markéta; Langer, Michal; Otyepka, Michal

2018-04-10

Carbon dots (CDs), one of the youngest members of the carbon nanostructure family, are now widely experimentally studied for their tunable fluorescence properties, bleaching resistance, and biocompatibility. Their interaction with biomolecular systems has also been explored experimentally. However, many atomistic details still remain unresolved. Molecular dynamics (MD) simulations enabling atomistic and femtosecond resolutions simultaneously are a well-established tool of computational chemistry which can provide useful insights into investigated systems. Here we present a full procedure for performing MD simulations of CDs. We developed a builder for generating CDs of a desired size and with various oxygen-containing surface functional groups. Further, we analyzed the behavior of various CDs differing in size, surface functional groups, and degrees of functionalization by MD simulations. These simulations showed that surface functionalized CDs are stable in a water environment through the formation of an extensive hydrogen bonding network. We also analyzed the internal dynamics of individual layers of CDs and evaluated the role of surface functional groups on CD stability. We observed that carboxyl groups interconnected the neighboring layers and decreased the rate of internal rotations. Further, we monitored changes in the CD shape caused by an excess of charged carboxyl groups or carbonyl groups. In addition to simulations in water, we analyzed the behavior of CDs in the organic solvent DMF, which decreased the stability of pure CDs but increased the level of interlayer hydrogen bonding. We believe that the developed protocol, builder, and parameters will facilitate future studies addressing various aspects of structural features of CDs and nanocomposites containing CDs.

Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations

PubMed Central

Yu, Hang; Schulten, Klaus

2013-01-01

Interplay between cellular membranes and their peripheral proteins drives many processes in eukaryotic cells. Proteins of the Bin/Amphiphysin/Rvs (BAR) domain family, in particular, play a role in cellular morphogenesis, for example curving planar membranes into tubular membranes. However, it is still unclear how F-BAR domain proteins act on membranes. Electron microscopy revealed that, in vitro, F-BAR proteins form regular lattices on cylindrically deformed membrane surfaces. Using all-atom and coarse-grained (CG) molecular dynamics simulations, we show that such lattices, indeed, induce tubes of observed radii. A 250 ns all-atom simulation reveals that F-BAR domain curves membranes via the so-called scaffolding mechanism. Plasticity of the F-BAR domain permits conformational change in response to membrane interaction, via partial unwinding of the domains 3-helix bundle structure. A CG simulation covering more than 350 µs provides a dynamic picture of membrane tubulation by lattices of F-BAR domains. A series of CG simulations identified the optimal lattice type for membrane sculpting, which matches closely the lattices seen through cryo-electron microscopy. PMID:23382665

An investigation of molecular dynamics simulation and molecular docking: interaction of citrus flavonoids and bovine β-lactoglobulin in focus.

PubMed

Sahihi, M; Ghayeb, Y

2014-08-01

Citrus flavonoids are natural compounds with important health benefits. The study of their interaction with a transport protein, such as bovine β-lactoglobulin (BLG), at the atomic level could be a valuable factor to control their transport to biological sites. In the present study, molecular docking and molecular dynamics simulation methods were used to investigate the interaction of hesperetin, naringenin, nobiletin and tangeretin as citrus flavonoids and BLG as transport protein. The molecular docking results revealed that these flavonoids bind in the internal cavity of BLG and the BLG affinity for binding the flavonoids follows naringenin>hesperetin>tangeretin>nobiletin. The docking results also indicated that the BLG-flavonoid complexes are stabilized through hydrophobic interactions, hydrogen bond interactions and π-π stacking interactions. The analysis of molecular dynamics (MD) simulation trajectories showed that the root mean square deviation (RMSD) of various systems reaches equilibrium and fluctuates around the mean value at various times. Time evolution of the radius of gyration, total solvent accessible surface of the protein and the second structure of protein showed as well that BLG and BLG-flavonoid complexes were stable around 2500ps, and there was not any conformational change as for BLG-flavonoid complexes. Further, the profiles of atomic fluctuations indicated the rigidity of the ligand binding site during the simulation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Protein folding simulations: from coarse-grained model to all-atom model.

PubMed

Zhang, Jian; Li, Wenfei; Wang, Jun; Qin, Meng; Wu, Lei; Yan, Zhiqiang; Xu, Weixin; Zuo, Guanghong; Wang, Wei

2009-06-01

Protein folding is an important and challenging problem in molecular biology. During the last two decades, molecular dynamics (MD) simulation has proved to be a paramount tool and was widely used to study protein structures, folding kinetics and thermodynamics, and structure-stability-function relationship. It was also used to help engineering and designing new proteins, and to answer even more general questions such as the minimal number of amino acid or the evolution principle of protein families. Nowadays, the MD simulation is still undergoing rapid developments. The first trend is to toward developing new coarse-grained models and studying larger and more complex molecular systems such as protein-protein complex and their assembling process, amyloid related aggregations, and structure and motion of chaperons, motors, channels and virus capsides; the second trend is toward building high resolution models and explore more detailed and accurate pictures of protein folding and the associated processes, such as the coordination bond or disulfide bond involved folding, the polarization, charge transfer and protonate/deprotonate process involved in metal coupled folding, and the ion permeation and its coupling with the kinetics of channels. On these new territories, MD simulations have given many promising results and will continue to offer exciting views. Here, we review several new subjects investigated by using MD simulations as well as the corresponding developments of appropriate protein models. These include but are not limited to the attempt to go beyond the topology based Gō-like model and characterize the energetic factors in protein structures and dynamics, the study of the thermodynamics and kinetics of disulfide bond involved protein folding, the modeling of the interactions between chaperonin and the encapsulated protein and the protein folding under this circumstance, the effort to clarify the important yet still elusive folding mechanism of protein BBL

Molecular Dynamics Simulations of Chemical Reactions for Use in Education

ERIC Educational Resources Information Center

Qian Xie; Tinker, Robert

2006-01-01

One of the simulation engines of an open-source program called the Molecular Workbench, which can simulate thermodynamics of chemical reactions, is described. This type of real-time, interactive simulation and visualization of chemical reactions at the atomic scale could help students understand the connections between chemical reaction equations…

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.

PubMed

Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji

2016-07-01

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 edited by J.C. Gumbart and Sergei Noskov. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Molecular dynamic simulations on TKX-50/RDX cocrystal.

PubMed

Xiong, Shuling; Chen, Shusen; Jin, Shaohua

2017-06-01

Dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50) is a newly synthesized energetic material with excellent comprehensive properties. Cyclotrimethylenetrinitramine (RDX) is currently one of the most widely used energetic materials in the world. TKX-50 and RDX supercell models and TKX-50/RDX cocrystal model were constructed based on their crystal cell parameters and the formation mechanism of cocrystal, respectively, then they were simulated by molecular dynamics (MD) simulations. The maximum trigger bond (NNO 2 ) length(L max ), binding energy (E bind ), radial distribution function (RDF), cohesive energy density(CED) and mechanical properties were simulated at different temperatures based on the simulated equilibrium structures of the models. The simulated results indicate that hydrogen bond and van der Waals force interactions exist in the cocrystal system and the hydrogen bonds are mainly derived from the hydrogen atom of TKX-50 with the oxygen or nitrogen atom of RDX. Moreover, TKX-50/RDX cocrystal structure significantly reduces the sensitivity and improves the thermodynamic stability of RDX, and it also shows better mechanical properties than pure TKX-50 and RDX, indicating that it will vastly expand the application scope of the single compound explosives. Copyright © 2017 Elsevier Inc. All rights reserved.

Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection.

PubMed

Toofanny, Rudesh D; Simms, Andrew M; Beck, David A C; Daggett, Valerie

2011-08-10

Molecular dynamics (MD) simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time. Taken in context with experimental data, atomic interactions from simulation provide insight into the mechanics of protein folding, dynamics, and function. The calculation of atomic interactions or contacts from an MD trajectory is computationally demanding and the work required grows exponentially with the size of the simulation system. We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts. The approach is applied to the Dynameomics project data. Spatial indexing, also known as spatial hashing, is a method that divides the simulation space into regular sized bins and attributes an index to each bin. Since, the calculation of contacts is widely employed in the simulation field, we also use this as the basis for testing compression of data tables. We investigate the effects of compression of the trajectory coordinate tables with different options of data and index compression within MS SQL SERVER 2008. Our implementation of spatial indexing speeds up the calculation of contacts over a 1 nanosecond (ns) simulation window by between 14% and 90% (i.e., 1.2 and 10.3 times faster). For a 'full' simulation trajectory (51 ns) spatial indexing reduces the calculation run-time between 31 and 81% (between 1.4 and 5.3 times faster). Compression resulted in reduced table sizes but resulted in no significant difference in the total execution time for neighbour discovery. The greatest compression (~36%) was achieved using page level compression on both the data and indexes. The spatial indexing scheme significantly decreases the time taken to calculate atomic contacts and could be applied to other multidimensional neighbor discovery problems. The speed up enables on-the-fly calculation

Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection

PubMed Central

2011-01-01

Background Molecular dynamics (MD) simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time. Taken in context with experimental data, atomic interactions from simulation provide insight into the mechanics of protein folding, dynamics, and function. The calculation of atomic interactions or contacts from an MD trajectory is computationally demanding and the work required grows exponentially with the size of the simulation system. We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts. The approach is applied to the Dynameomics project data. Spatial indexing, also known as spatial hashing, is a method that divides the simulation space into regular sized bins and attributes an index to each bin. Since, the calculation of contacts is widely employed in the simulation field, we also use this as the basis for testing compression of data tables. We investigate the effects of compression of the trajectory coordinate tables with different options of data and index compression within MS SQL SERVER 2008. Results Our implementation of spatial indexing speeds up the calculation of contacts over a 1 nanosecond (ns) simulation window by between 14% and 90% (i.e., 1.2 and 10.3 times faster). For a 'full' simulation trajectory (51 ns) spatial indexing reduces the calculation run-time between 31 and 81% (between 1.4 and 5.3 times faster). Compression resulted in reduced table sizes but resulted in no significant difference in the total execution time for neighbour discovery. The greatest compression (~36%) was achieved using page level compression on both the data and indexes. Conclusions The spatial indexing scheme significantly decreases the time taken to calculate atomic contacts and could be applied to other multidimensional neighbor discovery problems. The speed up

Molecular dynamics simulations of polarizable DNA in crystal environment

NASA Astrophysics Data System (ADS)

Babin, Volodymyr; Baucom, Jason; Darden, Thomas A.; Sagui, Celeste

We have investigated the role of the electrostatic description and cell environment in molecular dynamics (MD) simulations of DNA. Multiple unrestrained MD simulations of the DNA duplex d(CCAACGTTGG)2 have been carried out using two different force fields: a traditional description based on atomic point charges and a polarizable force field. For the time scales probed, and given the ?right? distribution of divalent ions, the latter performs better than the nonpolarizable force field. In particular, by imposing the experimental unit cell environment, an initial configuration with ideal B-DNA duplexes in the unit cell acquires sequence-dependent features that very closely resemble the crystallographic ones. Simultaneously, the all-atom root-mean-square coordinates deviation (RMSD) with respect to the crystallographic structure is seen to decay. At later times, the polarizable force field is able to maintain this lower RMSD, while the nonpolarizable force field starts to drift away.

A hybrid algorithm for parallel molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Mangiardi, Chris M.; Meyer, R.

2017-10-01

This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with Sandy Bridge and Haswell processors as well as systems with Xeon Phi many-core processors.

Laser manipulation of atomic and molecular flows

NASA Astrophysics Data System (ADS)

Lilly, Taylor C.

The continuing advance of laser technology enables a range of broadly applicable, laser-based flow manipulation techniques. The characteristics of these laser-based flow manipulations suggest that they may augment, or be superior to, such traditional electro-mechanical methods as ionic flow control, shock tubes, and small scale wind tunnels. In this study, methodology was developed for investigating laser flow manipulation techniques, and testing their feasibility for a number of aerospace, basic physics, and micro technology applications. Theories for laser-atom and laser-molecule interactions have been under development since the advent of laser technology. The theories have yet to be adequately integrated into kinetic flow solvers. Realizing this integration would greatly enhance the scaling of laser-species interactions beyond the realm of ultra-cold atomic physics. This goal was realized in the present study. A representative numerical investigation, of laser-based neutral atomic and molecular flow manipulations, was conducted using near-resonant and non-resonant laser fields. To simulate the laser interactions over a range of laser and flow conditions, the following tools were employed: a custom collisionless gas particle trajectory code and a specifically modified version of the Direct Simulation Monte Carlo statistical kinetic solver known as SMILE. In addition to the numerical investigations, a validating experiment was conducted. The experimental results showed good agreement with the numerical simulations when experimental parameters, such as finite laser line width, were taken into account. Several areas of interest were addressed: laser induced neutral flow steering, collimation, direct flow acceleration, and neutral gas heating. Near-resonant continuous wave laser, and non-resonant pulsed laser, interactions with cesium and nitrogen were simulated. These simulations showed trends and some limitations associated with these interactions, used for flow

Two-step relaxation mode analysis with multiple evolution times applied to all-atom molecular dynamics protein simulation.

PubMed

Karasawa, N; Mitsutake, A; Takano, H

2017-12-01

Proteins implement their functionalities when folded into specific three-dimensional structures, and their functions are related to the protein structures and dynamics. Previously, we applied a relaxation mode analysis (RMA) method to protein systems; this method approximately estimates the slow relaxation modes and times via simulation and enables investigation of the dynamic properties underlying the protein structural fluctuations. Recently, two-step RMA with multiple evolution times has been proposed and applied to a slightly complex homopolymer system, i.e., a single [n]polycatenane. This method can be applied to more complex heteropolymer systems, i.e., protein systems, to estimate the relaxation modes and times more accurately. In two-step RMA, we first perform RMA and obtain rough estimates of the relaxation modes and times. Then, we apply RMA with multiple evolution times to a small number of the slowest relaxation modes obtained in the previous calculation. Herein, we apply this method to the results of principal component analysis (PCA). First, PCA is applied to a 2-μs molecular dynamics simulation of hen egg-white lysozyme in aqueous solution. Then, the two-step RMA method with multiple evolution times is applied to the obtained principal components. The slow relaxation modes and corresponding relaxation times for the principal components are much improved by the second RMA.

Two-step relaxation mode analysis with multiple evolution times applied to all-atom molecular dynamics protein simulation

NASA Astrophysics Data System (ADS)

Karasawa, N.; Mitsutake, A.; Takano, H.

2017-12-01

Proteins implement their functionalities when folded into specific three-dimensional structures, and their functions are related to the protein structures and dynamics. Previously, we applied a relaxation mode analysis (RMA) method to protein systems; this method approximately estimates the slow relaxation modes and times via simulation and enables investigation of the dynamic properties underlying the protein structural fluctuations. Recently, two-step RMA with multiple evolution times has been proposed and applied to a slightly complex homopolymer system, i.e., a single [n ] polycatenane. This method can be applied to more complex heteropolymer systems, i.e., protein systems, to estimate the relaxation modes and times more accurately. In two-step RMA, we first perform RMA and obtain rough estimates of the relaxation modes and times. Then, we apply RMA with multiple evolution times to a small number of the slowest relaxation modes obtained in the previous calculation. Herein, we apply this method to the results of principal component analysis (PCA). First, PCA is applied to a 2-μ s molecular dynamics simulation of hen egg-white lysozyme in aqueous solution. Then, the two-step RMA method with multiple evolution times is applied to the obtained principal components. The slow relaxation modes and corresponding relaxation times for the principal components are much improved by the second RMA.

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.

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

PubMed Central

Chen, Alan A.; García, Angel E.

2013-01-01

We report the de novo folding of three hyperstable RNA tetraloops to 1–3 Å rmsd from their experimentally determined structures using molecular dynamics simulations initialized in the unfolded state. RNA tetraloops with loop sequences UUCG, GCAA, or CUUG are hyperstable because of the formation of noncanonical loop-stabilizing interactions, and they are all faithfully reproduced to angstrom-level accuracy in replica exchange molecular dynamics simulations, including explicit solvent and ion molecules. This accuracy is accomplished using unique RNA parameters, in which biases that favor rigid, highly stacked conformations are corrected to accurately capture the inherent flexibility of ssRNA loops, accurate base stacking energetics, and purine syn-anti interconversions. In a departure from traditional quantum chemistrycentric approaches to force field optimization, our parameters are calibrated directly from thermodynamic and kinetic measurements of intra- and internucleotide structural transitions. The ability to recapitulate the signature noncanonical interactions of the three most abundant hyperstable stem loop motifs represents a significant milestone to the accurate prediction of RNA tertiary structure using unbiased all-atom molecular dynamics simulations. PMID:24043821

The calculation of the viscosity from the autocorrelation function using molecular and atomic stress tensors

NASA Astrophysics Data System (ADS)

Cui, S. T.

The stress-stress correlation function and the viscosity of a united-atom model of liquid decane are studied by equilibrium molecular dynamics simulation using two different formalisms for the stress tensor: the atomic and the molecular formalisms. The atomic and molecular correlation functions show dramatic difference in short-time behaviour. The integrals of the two correlation functions, however, become identical after a short transient period whichis significantly shorter than the rotational relaxation time of the molecule. Both reach the same plateau value in a time period corresponding to this relaxation time. These results provide a convenient guide for the choice of the upper integral time limit in calculating the viscosity by the Green-Kubo formula.

Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling

PubMed Central

Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

2014-01-01

Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES) simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape. PMID:25340714

Multipole Algorithms for Molecular Dynamics Simulation on High Performance Computers.

NASA Astrophysics Data System (ADS)

Elliott, William Dewey

1995-01-01

A fundamental problem in modeling large molecular systems with molecular dynamics (MD) simulations is the underlying N-body problem of computing the interactions between all pairs of N atoms. The simplest algorithm to compute pair-wise atomic interactions scales in runtime {cal O}(N^2), making it impractical for interesting biomolecular systems, which can contain millions of atoms. Recently, several algorithms have become available that solve the N-body problem by computing the effects of all pair-wise interactions while scaling in runtime less than {cal O}(N^2). One algorithm, which scales {cal O}(N) for a uniform distribution of particles, is called the Greengard-Rokhlin Fast Multipole Algorithm (FMA). This work describes an FMA-like algorithm called the Molecular Dynamics Multipole Algorithm (MDMA). The algorithm contains several features that are new to N-body algorithms. MDMA uses new, efficient series expansion equations to compute general 1/r^{n } potentials to arbitrary accuracy. In particular, the 1/r Coulomb potential and the 1/r^6 portion of the Lennard-Jones potential are implemented. The new equations are based on multivariate Taylor series expansions. In addition, MDMA uses a cell-to-cell interaction region of cells that is closely tied to worst case error bounds. The worst case error bounds for MDMA are derived in this work also. These bounds apply to other multipole algorithms as well. Several implementation enhancements are described which apply to MDMA as well as other N-body algorithms such as FMA and tree codes. The mathematics of the cell -to-cell interactions are converted to the Fourier domain for reduced operation count and faster computation. A relative indexing scheme was devised to locate cells in the interaction region which allows efficient pre-computation of redundant information and prestorage of much of the cell-to-cell interaction. Also, MDMA was integrated into the MD program SIgMA to demonstrate the performance of the program over

Monolayer atomic crystal molecular superlattices.

PubMed

Wang, Chen; He, Qiyuan; Halim, Udayabagya; Liu, Yuanyue; Zhu, Enbo; Lin, Zhaoyang; Xiao, Hai; Duan, Xidong; Feng, Ziying; Cheng, Rui; Weiss, Nathan O; Ye, Guojun; Huang, Yun-Chiao; Wu, Hao; Cheng, Hung-Chieh; Shakir, Imran; Liao, Lei; Chen, Xianhui; Goddard, William A; Huang, Yu; Duan, Xiangfeng

2018-03-07

Artificial superlattices, based on van der Waals heterostructures of two-dimensional atomic crystals such as graphene or molybdenum disulfide, offer technological opportunities beyond the reach of existing materials. Typical strategies for creating such artificial superlattices rely on arduous layer-by-layer exfoliation and restacking, with limited yield and reproducibility. The bottom-up approach of using chemical-vapour deposition produces high-quality heterostructures but becomes increasingly difficult for high-order superlattices. The intercalation of selected two-dimensional atomic crystals with alkali metal ions offers an alternative way to superlattice structures, but these usually have poor stability and seriously altered electronic properties. Here we report an electrochemical molecular intercalation approach to a new class of stable superlattices in which monolayer atomic crystals alternate with molecular layers. Using black phosphorus as a model system, we show that intercalation with cetyl-trimethylammonium bromide produces monolayer phosphorene molecular superlattices in which the interlayer distance is more than double that in black phosphorus, effectively isolating the phosphorene monolayers. Electrical transport studies of transistors fabricated from the monolayer phosphorene molecular superlattice show an on/off current ratio exceeding 10 7 , along with excellent mobility and superior stability. We further show that several different two-dimensional atomic crystals, such as molybdenum disulfide and tungsten diselenide, can be intercalated with quaternary ammonium molecules of varying sizes and symmetries to produce a broad class of superlattices with tailored molecular structures, interlayer distances, phase compositions, electronic and optical properties. These studies define a versatile material platform for fundamental studies and potential technological applications.

Monolayer atomic crystal molecular superlattices

NASA Astrophysics Data System (ADS)

Wang, Chen; He, Qiyuan; Halim, Udayabagya; Liu, Yuanyue; Zhu, Enbo; Lin, Zhaoyang; Xiao, Hai; Duan, Xidong; Feng, Ziying; Cheng, Rui; Weiss, Nathan O.; Ye, Guojun; Huang, Yun-Chiao; Wu, Hao; Cheng, Hung-Chieh; Shakir, Imran; Liao, Lei; Chen, Xianhui; Goddard, William A., III; Huang, Yu; Duan, Xiangfeng

2018-03-01

Artificial superlattices, based on van der Waals heterostructures of two-dimensional atomic crystals such as graphene or molybdenum disulfide, offer technological opportunities beyond the reach of existing materials. Typical strategies for creating such artificial superlattices rely on arduous layer-by-layer exfoliation and restacking, with limited yield and reproducibility. The bottom-up approach of using chemical-vapour deposition produces high-quality heterostructures but becomes increasingly difficult for high-order superlattices. The intercalation of selected two-dimensional atomic crystals with alkali metal ions offers an alternative way to superlattice structures, but these usually have poor stability and seriously altered electronic properties. Here we report an electrochemical molecular intercalation approach to a new class of stable superlattices in which monolayer atomic crystals alternate with molecular layers. Using black phosphorus as a model system, we show that intercalation with cetyl-trimethylammonium bromide produces monolayer phosphorene molecular superlattices in which the interlayer distance is more than double that in black phosphorus, effectively isolating the phosphorene monolayers. Electrical transport studies of transistors fabricated from the monolayer phosphorene molecular superlattice show an on/off current ratio exceeding 107, along with excellent mobility and superior stability. We further show that several different two-dimensional atomic crystals, such as molybdenum disulfide and tungsten diselenide, can be intercalated with quaternary ammonium molecules of varying sizes and symmetries to produce a broad class of superlattices with tailored molecular structures, interlayer distances, phase compositions, electronic and optical properties. These studies define a versatile material platform for fundamental studies and potential technological applications.

Molecular dynamics simulation of siderite-hematite-quartz flotation with sodium oleate

NASA Astrophysics Data System (ADS)

Li, Lixia; Hao, Haiqing; Yuan, Zhitao; Liu, Jiongtian

2017-10-01

Models of sodium oleate adsorption on siderite, hematite and quartz were investigated by molecular dynamic simulation, respectively. Surface energy was calculated to confirm the cleavage plan of hematite and quartz. Both natural cleavage plane of siderite and calculated plane were used to investigate the flotation of the three minerals. Based on the molecular simulation in solution with water as medium, adsorption quantity and interaction capability of oleate ions on the three minerals indicated that siderite could be collected efficiently by sodium oleate at neutral pH. Results of flotation experiments were further demonstrated by analysis of relative concentration of carbon atoms and oxygen atoms.

The equilibrium properties and folding kinetics of an all-atom Go xAF model of the Trp-cage

NASA Astrophysics Data System (ADS)

Linhananta, Apichart; Boer, Jesse; MacKay, Ian

2005-03-01

The ultrafast-folding 20-residue Trp-cage protein is quickly becoming a new benchmark for molecular dynamics studies. Already several all-atom simulations have probed its equilibrium and kinetic properties. In this work an all-atom Go ¯ model is used to accurately represent the side-chain packing and native atomic contacts of the Trp-cage. The model reproduces the hallmark thermodynamics cooperativity of small proteins. Folding simulations observe that in the fast-folding dominant pathway, partial α-helical structure forms before hydrophobic core collapse. In the slow-folding secondary pathway, partial core collapse occurs before helical structure. The slow-folding rate of the secondary pathway is attributed to the loss of side-chain rotational freedom, due to the early core collapse, which impedes the helix formation. A major finding is the observation of a low-temperature kinetic intermediate stabilized by a salt bridge between residues Asp-9 and Arg-16. Similar observations [R. Zhou, Proc. Natl. Acad. Sci. U.S.A. 100, 13280 (2003)] were reported in a recent study using an all-atom model of the Trp-cage in explicit water, in which the salt-bridge stabilized intermediate was hypothesized to be the origin of the ultrafast-folding mechanism. A theoretical mutation that eliminates the Asp-9-Arg-16 salt bridge, but leaves the residues intact, is performed. Folding simulations of the mutant Trp-cage observe a two-state free-energy landscape with no kinetic intermediate and a significant decrease in the folding rate, in support of the hypothesis.

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

PubMed Central

Yoo, Jejoong; Aksimentiev, Aleksei

2013-01-01

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

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

PubMed

Yoo, Jejoong; Aksimentiev, Aleksei

2013-12-10

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

Shock-induced poration, cholesterol flip-flop and small interfering RNA transfection in a phospholipid membrane: Multimillion atom, microsecond molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Choubey, Amit

Biological cell membranes provide mechanical stability to cells and understanding their structure, dynamics and mechanics are important biophysics problems. Experiments coupled with computational methods such as molecular dynamics (MD) have provided insight into the physics of membranes. We use long-time and large-scale MD simulations to study the structure, dynamics and mechanical behavior of membranes. We investigate shock-induced collapse of nanobubbles in water using MD simulations based on a reactive force field. We observe a focused jet at the onset of bubble shrinkage and a secondary shock wave upon bubble collapse. The jet length scales linearly with the nanobubble radius, as observed in experiments on micron-to-millimeter size bubbles. Shock induces dramatic structural changes, including an ice-VII-like structural motif at a particle velocity of 1 km/s. The incipient ice VII formation and the calculated Hugoniot curve are in good agreement with experimental results. We also investigate molecular mechanisms of poration in lipid bilayers due to shock-induced collapse of nanobubbles. Our multimillion-atom MD simulations reveal that the jet impact generates shear flow of water on bilayer leaflets and pressure gradients across them. This transiently enhances the bilayer permeability by creating nanopores through which water molecules translocate rapidly across the bilayer. Effects of nanobubble size and temperature on the porosity of lipid bilayers are examined. The second research project focuses on cholesterol (CHOL) dynamics in phospholipid bilayers. Several experimental and computational studies have been performed on lipid bilayers consisting of dipalmitoylphosphatidylcholine (DPPC) and CHOL molecules. CHOL interleaflet transport (flip-flop) plays an important role in interleaflet coupling and determining CHOL flip-flop rate has been elusive. Various studies report that the rate ranges between milliseconds to seconds. We calculate CHOL flip-flop rates by

Molecular Dynamics Simulation of Carbon Nanotube Based Gears

NASA Technical Reports Server (NTRS)

Han, Jie; Globus, Al; Jaffe, Richard; Deardorff, Glenn; Chancellor, Marisa K. (Technical Monitor)

1996-01-01

We used molecular dynamics to investigate the properties and design space of molecular gears fashioned from carbon nanotubes with teeth added via a benzyne reaction known to occur with C60. A modified, parallelized version of Brenner's potential was used to model interatomic forces within each molecule. A Leonard-Jones 6-12 potential was used for forces between molecules. One gear was powered by forcing the atoms near the end of the buckytube to rotate, and a second gear was allowed.to rotate by keeping the atoms near the end of its buckytube on a cylinder. The meshing aromatic gear teeth transfer angular momentum from the powered gear to the driven gear. A number of gear and gear/shaft configurations were simulated. Cases in vacuum and with an inert atmosphere were examined. In an extension to molecular dynamics technology, some simulations used a thermostat on the atmosphere while the hydrocarbon gear's temperature was allowed to fluctuate. This models cooling the gears with an atmosphere. Results suggest that these gears can operate at up to 50-100 gigahertz in a vacuum or inert atmosphere at room temperature. The failure mode involves tooth slip, not bond breaking, so failed gears can be returned to operation by lowering temperature and/or rotation rate. Videos and atomic trajectory files in xyz format are presented.

A comparative computational study of coarse-grained and all-atom water models in shock Hugoniot states

NASA Astrophysics Data System (ADS)

Min, Sa Hoon; Berkowitz, Max L.

2018-04-01

We performed molecular dynamics simulations to study how well some of the water models used in simulations describe shocked states. Water in our simulations was described using three different models. One was an often-used all-atom TIP4P/2005 model, while the other two were coarse-grained models used with the MARTINI force field: non-polarizable and polarizable MARTINI water. The all-atom model provided results in good agreement with Hugoniot curves (for data on pressure versus specific volume or, equivalently, on shock wave velocity versus "piston" velocity) describing shocked states in the whole range of pressures (up to 11 GPa) under study. If simulations of shocked states of water using coarse-grained models were performed for short time periods, we observed that data obtained for shocked states at low pressure were fairly accurate compared to experimental Hugoniot curves. Polarizable MARTINI water still provided a good description of Hugoniot curves for pressures up to 11 GPa, while the results for the non-polarizable MARTINI water substantially deviated from the Hugoniot curves. We also calculated the temperature of the Hugoniot states and observed that for TIP4P/2005 water, they were consistent with those from theoretical calculations, while both coarse-grained models predicted much higher temperatures. These high temperatures for MARTINI water can be explained by the loss of degrees of freedom due to coarse-graining procedure.

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.

Molecular Dynamics Modeling and Simulation of Diamond Cutting of Cerium.

PubMed

Zhang, Junjie; Zheng, Haibing; Shuai, Maobing; Li, Yao; Yang, Yang; Sun, Tao

2017-12-01

The coupling between structural phase transformations and dislocations induces challenges in understanding the deformation behavior of metallic cerium at the nanoscale. In the present work, we elucidate the underlying mechanism of cerium under ultra-precision diamond cutting by means of molecular dynamics modeling and simulations. The molecular dynamics model of diamond cutting of cerium is established by assigning empirical potentials to describe atomic interactions and evaluating properties of two face-centered cubic cerium phases. Subsequent molecular dynamics simulations reveal that dislocation slip dominates the plastic deformation of cerium under the cutting process. In addition, the analysis based on atomic radial distribution functions demonstrates that there are trivial phase transformations from the γ-Ce to the δ-Ce occurred in both machined surface and formed chip. Following investigations on machining parameter dependence reveal the optimal machining conditions for achieving high quality of machined surface of cerium.

Molecular Dynamics Modeling and Simulation of Diamond Cutting of Cerium

NASA Astrophysics Data System (ADS)

Zhang, Junjie; Zheng, Haibing; Shuai, Maobing; Li, Yao; Yang, Yang; Sun, Tao

2017-07-01

The coupling between structural phase transformations and dislocations induces challenges in understanding the deformation behavior of metallic cerium at the nanoscale. In the present work, we elucidate the underlying mechanism of cerium under ultra-precision diamond cutting by means of molecular dynamics modeling and simulations. The molecular dynamics model of diamond cutting of cerium is established by assigning empirical potentials to describe atomic interactions and evaluating properties of two face-centered cubic cerium phases. Subsequent molecular dynamics simulations reveal that dislocation slip dominates the plastic deformation of cerium under the cutting process. In addition, the analysis based on atomic radial distribution functions demonstrates that there are trivial phase transformations from the γ-Ce to the δ-Ce occurred in both machined surface and formed chip. Following investigations on machining parameter dependence reveal the optimal machining conditions for achieving high quality of machined surface of cerium.

Molecular dynamics simulations investigating consecutive nucleation, solidification and grain growth in a twelve-million-atom Fe-system

NASA Astrophysics Data System (ADS)

Okita, Shin; Verestek, Wolfgang; Sakane, Shinji; Takaki, Tomohiro; Ohno, Munekazu; Shibuta, Yasushi

2017-09-01

Continuous processes of homogeneous nucleation, solidification and grain growth are spontaneously achieved from an undercooled iron melt without any phenomenological parameter in the molecular dynamics (MD) simulation with 12 million atoms. The nucleation rate at the critical temperature is directly estimated from the atomistic configuration by cluster analysis to be of the order of 1034 m-3 s-1. Moreover, time evolution of grain size distribution during grain growth is obtained by the combination of Voronoi and cluster analyses. The grain growth exponent is estimated to be around 0.3 from the geometric average of the grain size distribution. Comprehensive understanding of kinetic properties during continuous processes is achieved in the large-scale MD simulation by utilizing the high parallel efficiency of a graphics processing unit (GPU), which is shedding light on the fundamental aspects of production processes of materials from the atomistic viewpoint.

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.

Comparison of all atom, continuum, and linear fitting empirical models for charge screening effect of aqueous medium surrounding a protein molecule

NASA Astrophysics Data System (ADS)

Takahashi, Takuya; Sugiura, Junnnosuke; Nagayama, Kuniaki

2002-05-01

To investigate the role hydration plays in the electrostatic interactions of proteins, the time-averaged electrostatic potential of the B1 domain of protein G in an aqueous solution was calculated with full atomic molecular dynamics simulations that explicitly considers every atom (i.e., an all atom model). This all atom calculated potential was compared with the potential obtained from an electrostatic continuum model calculation. In both cases, the charge-screening effect was fairly well formulated with an effective relative dielectric constant which increased linearly with increasing charge-charge distance. This simulated linear dependence agrees with the experimentally determined linear relation proposed by Pickersgill. Cut-off approximations for Coulomb interactions failed to reproduce this linear relation. Correlation between the all atom model and the continuum models was found to be better than the respective correlation calculated for linear fitting to the two models. This confirms that the continuum model is better at treating the complicated shapes of protein conformations than the simple linear fitting empirical model. We have tried a sigmoid fitting empirical model in addition to the linear one. When weights of all data were treated equally, the sigmoid model, which requires two fitting parameters, fits results of both the all atom and the continuum models less accurately than the linear model which requires only one fitting parameter. When potential values are chosen as weighting factors, the fitting error of the sigmoid model became smaller, and the slope of both linear fitting curves became smaller. This suggests the screening effect of an aqueous medium within a short range, where potential values are relatively large, is smaller than that expected from the linear fitting curve whose slope is almost 4. To investigate the linear increase of the effective relative dielectric constant, the Poisson equation of a low-dielectric sphere in a high

The atomic-scale nucleation mechanism of NiTi metallic glasses upon isothermal annealing studied via molecular dynamics simulations.

PubMed

Li, Yang; Li, JiaHao; Liu, BaiXin

2015-10-28

Nucleation is one of the most essential transformation paths in phase transition and exerts a significant influence on the crystallization process. Molecular dynamics simulations were performed to investigate the atomic-scale nucleation mechanisms of NiTi metallic glasses upon devitrification at various temperatures (700 K, 750 K, 800 K, and 850 K). Our simulations reveal that at 700 K and 750 K, nucleation is polynuclear with high nucleation density, while at 800 K it is mononuclear. The underlying nucleation mechanisms have been clarified, manifesting that nucleation can be induced either by the initial ordered clusters (IOCs) or by the other precursors of nuclei evolved directly from the supercooled liquid. IOCs and other precursors stem from the thermal fluctuations of bond orientational order in supercooled liquids during the quenching process and during the annealing process, respectively. The simulation results not only elucidate the underlying nucleation mechanisms varied with temperature, but also unveil the origin of nucleation. These discoveries offer new insights into the devitrification mechanism of metallic glasses.

Introduction of steered molecular dynamics into UNRES coarse-grained simulations package.

PubMed

Sieradzan, Adam K; Jakubowski, Rafał

2017-03-30

In this article, an implementation of steered molecular dynamics (SMD) in coarse-grain UNited RESidue (UNRES) simulations package is presented. Two variants of SMD have been implemented: with a constant force and a constant velocity. The huge advantage of SMD implementation in the UNRES force field is that it allows to pull with the speed significantly lower than the accessible pulling speed in simulations with all-atom representation of a system, with respect to a reasonable computational time. Therefore, obtaining pulling speed closer to those which appear in the atomic force spectroscopy is possible. The newly implemented method has been tested for behavior in a microcanonical run to verify the influence of introduction of artificial constrains on keeping total energy of the system. Moreover, as time dependent artificial force was introduced, the thermostat behavior was tested. The new method was also tested via unfolding of the Fn3 domain of human contactin 1 protein and the I27 titin domain. Obtained results were compared with Gø-like force field, all-atom force field, and experimental results. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

All-atomic simulations on human telomeric G-quadruplex DNA binding with thioflavin T.

PubMed

Luo, Di; Mu, Yuguang

2015-04-16

Ligand-stabilized human telomeric G-quadruplex DNA is believed to be an anticancer agent, as it can impede the continuous elongation of telomeres by telomerase in cancer cells. In this study, five well-established human telomeric G-quadruplex DNA models were probed on their binding behaviors with thioflavin T (ThT) via both conventional molecular dynamics (MD) and well-tempered metadynamics (WT-MetaD) simulations. Novel dynamics and characteristic binding patterns were disclosed by the MD simulations. It was observed that the K(+) promoted parallel and hybridized human telomeric G-quadruplex conformations pose higher binding affinities to ThT than the Na(+) and K(+) promoted basket conformations. It is the end, sandwich, and base stacking driven by π-π interactions that are identified as the major binding mechanisms. As the most energy favorable binding mode, the sandwich stacking observed in (3 + 1) hybridized form 1 G-quadruplex conformation is triggered by reversible conformational change of the G-quadruplex. To further examine the free energy landscapes, WT-MetaD simulations were utilized on G-quadruplex-ThT systems. It is found that all of the major binding modes predicted by the MD simulations are confirmed by the WT-MetaD simulations. The results in this work not only accord with existing experimental findings, but also reinforce our understanding on the dynamics of G-quadruplexes and aid future drug developments for G-quadruplex stabilization ligands.

Evaluating excited state atomic polarizabilities of chromophores† †Electronic supplementary information (ESI) available: Basis set dependence, definition of bond charges, Romberg differentiation, python script to calculate atomic polarizabilities, influence of the cavity radius, atomic polarizabilities of coumarin 153, all tables in atomic units. See DOI: 10.1039/c7cp08549d

PubMed Central

Heid, Esther

2018-01-01

Ground and excited state dipoles and polarizabilities of the chromophores N-methyl-6-oxyquinolinium betaine (MQ) and coumarin 153 (C153) in solution have been evaluated using time-dependent density functional theory (TD-DFT). A method for determining the atomic polarizabilities has been developed; the molecular dipole has been decomposed into atomic charge transfer and polarizability terms, and variation in the presence of an electric field has been used to evaluate atomic polarizabilities. On excitation, MQ undergoes very site-specific changes in polarizability while C153 shows significantly less variation. We also conclude that MQ cannot be adequately described by standard atomic polarizabilities based on atomic number and hybridization state. Changes in the molecular polarizability of MQ (on excitation) are not representative of the local site-specific changes in atomic polarizability, thus the overall molecular polarizability ratio does not provide a good approximation for local atom-specific polarizability changes on excitation. Accurate excited state force fields are needed for computer simulation of solvation dynamics. The chromophores considered in this study are often used as molecular probes. The methods and data reported here can be used for the construction of polarizable ground and excited state force fields. Atomic and molecular polarizabilities (ground and excited states) have been evaluated over a range of functionals and basis sets. Different mechanisms for including solvation effects have been examined; using a polarizable continuum model, explicit solvation and via sampling of clusters extracted from a MD simulation. A range of different solvents have also been considered. PMID:29542743

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

NASA Astrophysics Data System (ADS)

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

2015-08-01

The dynamic properties of liquid B2O3 under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B2O3 shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8).

Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations

NASA Astrophysics Data System (ADS)

Lei, Hongxing; Wu, Chun; Wang, Zhi-Xiang; Zhou, Yaoqi; Duan, Yong

2008-06-01

Reaching the native states of small proteins, a necessary step towards a comprehensive understanding of the folding mechanisms, has remained a tremendous challenge to ab initio protein folding simulations despite the extensive effort. In this work, the folding process of the B domain of protein A (BdpA) has been simulated by both conventional and replica exchange molecular dynamics using AMBER FF03 all-atom force field. Started from an extended chain, a total of 40 conventional (each to 1.0 μs) and two sets of replica exchange (each to 200.0 ns per replica) molecular dynamics simulations were performed with different generalized-Born solvation models and temperature control schemes. The improvements in both the force field and solvent model allowed successful simulations of the folding process to the native state as demonstrated by the 0.80 A˚ Cα root mean square deviation (RMSD) of the best folded structure. The most populated conformation was the native folded structure with a high population. This was a significant improvement over the 2.8 A˚ Cα RMSD of the best nativelike structures from previous ab initio folding studies on BdpA. To the best of our knowledge, our results demonstrate, for the first time, that ab initio simulations can reach the native state of BdpA. Consistent with experimental observations, including Φ-value analyses, formation of helix II/III hairpin was a crucial step that provides a template upon which helix I could form and the folding process could complete. Early formation of helix III was observed which is consistent with the experimental results of higher residual helical content of isolated helix III among the three helices. The calculated temperature-dependent profile and the melting temperature were in close agreement with the experimental results. The simulations further revealed that phenylalanine 31 may play critical to achieve the correct packing of the three helices which is consistent with the experimental observation

Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B.; Jain, Abhinandan; Vaidehi, Nagarajan

2016-01-01

The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential

Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations.

PubMed

Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B; Jain, Abhinandan; Vaidehi, Nagarajan

2016-01-28

The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential

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

Multimillion Atom Simulations of Nanoenergetic Materials

DTIC Science & Technology

2014-12-01

L R E P O R T DTRA-TR-14-46 Multimillion Atom Simulations of Nanoenergetic Materials Distribution Statement A. Approved for public release...December 2009 Multimillion Atom Simulations of Nanoenergetic Materials HDTRA1-07-1-0023 Priya Vashishta Rajiv K. Kalia Aiichiro Nakano Collaboratory for...Technical Report (December 18, 2006—December 17, 2009) Defense Threat Reduction Agency Grant # HDTRA1-07-1-0023 Multimillion Atom Simulations of

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.

Molecular simulations of self-assembly processes in metal-organic frameworks: Model dependence

NASA Astrophysics Data System (ADS)

Biswal, Debasmita; Kusalik, Peter G.

2017-07-01

Molecular simulation is a powerful tool for investigating microscopic behavior in various chemical systems, where the use of suitable models is critical to successfully reproduce the structural and dynamic properties of the real systems of interest. In this context, molecular dynamics simulation studies of self-assembly processes in metal-organic frameworks (MOFs), a well-known class of porous materials with interesting chemical and physical properties, are relatively challenging, where a reasonably accurate representation of metal-ligand interactions is anticipated to play an important role. In the current study, we both investigate the performance of some existing models and introduce and test new models to help explore the self-assembly in an archetypal Zn-carboxylate MOF system. To this end, the behavior of six different Zn-ion models, three solvent models, and two ligand models was examined and validated against key experimental structural parameters. To explore longer time scale ordering events during MOF self-assembly via explicit solvent simulations, it is necessary to identify a suitable combination of simplified model components representing metal ions, organic ligands, and solvent molecules. It was observed that an extended cationic dummy atom (ECDA) Zn-ion model combined with an all-atom carboxylate ligand model and a simple dipolar solvent model can reproduce characteristic experimental structures for the archetypal MOF system. The successful use of these models in extensive sets of molecular simulations, which provide key insights into the self-assembly mechanism of this archetypal MOF system occurring during the early stages of this process, has been very recently reported.

Multimillion atom simulations of dynamics of oxidation of an aluminum nanoparticle and nanoindentation on ceramics.

PubMed

Vashishta, Priya; Kalia, Rajiv K; Nakano, Aiichiro

2006-03-02

We have developed a first-principles-based hierarchical simulation framework, which seamlessly integrates (1) a quantum mechanical description based on the density functional theory (DFT), (2) multilevel molecular dynamics (MD) simulations based on a reactive force field (ReaxFF) that describes chemical reactions and polarization, a nonreactive force field that employs dynamic atomic charges, and an effective force field (EFF), and (3) an atomistically informed continuum model to reach macroscopic length scales. For scalable hierarchical simulations, we have developed parallel linear-scaling algorithms for (1) DFT calculation based on a divide-and-conquer algorithm on adaptive multigrids, (2) chemically reactive MD based on a fast ReaxFF (F-ReaxFF) algorithm, and (3) EFF-MD based on a space-time multiresolution MD (MRMD) algorithm. On 1920 Intel Itanium2 processors, we have demonstrated 1.4 million atom (0.12 trillion grid points) DFT, 0.56 billion atom F-ReaxFF, and 18.9 billion atom MRMD calculations, with parallel efficiency as high as 0.953. Through the use of these algorithms, multimillion atom MD simulations have been performed to study the oxidation of an aluminum nanoparticle. Structural and dynamic correlations in the oxide region are calculated as well as the evolution of charges, surface oxide thickness, diffusivities of atoms, and local stresses. In the microcanonical ensemble, the oxidizing reaction becomes explosive in both molecular and atomic oxygen environments, due to the enormous energy release associated with Al-O bonding. In the canonical ensemble, an amorphous oxide layer of a thickness of approximately 40 angstroms is formed after 466 ps, in good agreement with experiments. Simulations have been performed to study nanoindentation on crystalline, amorphous, and nanocrystalline silicon nitride and silicon carbide. Simulation on nanocrystalline silicon carbide reveals unusual deformation mechanisms in brittle nanophase materials, due to

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

Molecular dynamics simulations of single siloxane dendrimers: Molecular structure and intramolecular mobility of terminal groups

NASA Astrophysics Data System (ADS)

Kurbatov, A. O.; Balabaev, N. K.; Mazo, M. A.; Kramarenko, E. Yu.

2018-01-01

Molecular dynamics simulations of two types of isolated siloxane dendrimers of various generations (from the 2nd to the 8th) have been performed for temperatures ranging from 150 K to 600 K. The first type of dendrimer molecules has short spacers consisting of a single oxygen atom. In the dendrimers of the second type, spacers are longer and comprised of two oxygen atoms separated by a single silicon atom. A comparative analysis of molecular macroscopic parameters such as the gyration radius and the shape factor as well as atom distributions within dendrimer interior has been performed for varying generation number, temperature, and spacer length. It has been found that the short-spacer dendrimers of the 7th and 8th generations have a stressed central part with elongated bonds and deformed valence angles. Investigation of the time evolution of radial displacements of the terminal Si atoms has shown that a fraction of the Si groups have a reduced mobility. Therefore, rather long time trajectories (of the order of tens of nanoseconds) are required to study dendrimer intramolecular dynamics.

Potential energy functions for atomic-level simulations of water and organic and biomolecular systems.

PubMed

Jorgensen, William L; Tirado-Rives, Julian

2005-05-10

An overview is provided on the development and status of potential energy functions that are used in atomic-level statistical mechanics and molecular dynamics simulations of water and of organic and biomolecular systems. Some topics that are considered are the form of force fields, their parameterization and performance, simulations of organic liquids, computation of free energies of hydration, universal extension for organic molecules, and choice of atomic charges. The discussion of water models covers some history, performance issues, and special topics such as nuclear quantum effects.

Structural Interpretation of the Large Slowdown of Water Dynamics at Stacked Phospholipid Membranes for Decreasing Hydration Level: All-Atom Molecular Dynamics

DOE PAGES

Calero, Carles; Stanley, H.; Franzese, Giancarlo

2016-04-27

Hydration water determines the stability and function of phospholipid membranes as well as the interaction of membranes with other molecules. Experiments and simulations have shown that water dynamics slows down dramatically as the hydration decreases, suggesting that the interfacial water that dominates the average dynamics at low hydration is slower than water away from the membrane. Here, based on all-atom molecular dynamics simulations, we provide an interpretation of the slowdown of interfacial water in terms of the structure and dynamics of water–water and water–lipid hydrogen bonds (HBs). We calculate the rotational and translational slowdown of the dynamics of water confinedmore » in stacked phospholipid membranes at different levels of hydration, from completely hydrated to poorly hydrated membranes. For all hydrations, we analyze the distribution of HBs and find that water–lipids HBs last longer than water–water HBs and that at low hydration most of the water is in the interior of the membrane. We also show that water–water HBs become more persistent as the hydration is lowered. We attribute this effect (i) to HBs between water molecules that form, in turn, persistent HBs with lipids; (ii) to the hindering of the H-bonding switching between water molecules due to the lower water density at the interface; and (iii) to the higher probability of water–lipid HBs as the hydration decreases. Lastly, our interpretation of the large dynamic slowdown in water under dehydration is potentially relevant in understanding membrane biophysics at different hydration levels.« less

Crystallized and amorphous vortices in rotating atomic-molecular Bose-Einstein condensates

PubMed Central

Liu, Chao-Fei; Fan, Heng; Gou, Shih-Chuan; Liu, Wu-Ming

2014-01-01

Vortex is a topological defect with a quantized winding number of the phase in superfluids and superconductors. Here, we investigate the crystallized (triangular, square, honeycomb) and amorphous vortices in rotating atomic-molecular Bose-Einstein condensates (BECs) by using the damped projected Gross-Pitaevskii equation. The amorphous vortices are the result of the considerable deviation induced by the interaction of atomic-molecular vortices. By changing the atom-molecule interaction from attractive to repulsive, the configuration of vortices can change from an overlapped atomic-molecular vortices to carbon-dioxide-type ones, then to atomic vortices with interstitial molecular vortices, and finally into independent separated ones. The Raman detuning can tune the ratio of the atomic vortex to the molecular vortex. We provide a phase diagram of vortices in rotating atomic-molecular BECs as a function of Raman detuning and the strength of atom-molecule interaction. PMID:24573303

An undergraduate laboratory activity on molecular dynamics simulations.

PubMed

Spitznagel, Benjamin; Pritchett, Paige R; Messina, Troy C; Goadrich, Mark; Rodriguez, Juan

2016-01-01

Vision and Change [AAAS, 2011] outlines a blueprint for modernizing biology education by addressing conceptual understanding of key concepts, such as the relationship between structure and function. The document also highlights skills necessary for student success in 21st century Biology, such as the use of modeling and simulation. Here we describe a laboratory activity that allows students to investigate the dynamic nature of protein structure and function through the use of a modeling technique known as molecular dynamics (MD). The activity takes place over two lab periods that are 3 hr each. The first lab period unpacks the basic approach behind MD simulations, beginning with the kinematic equations that all bioscience students learn in an introductory physics course. During this period students are taught rudimentary programming skills in Python while guided through simple modeling exercises that lead up to the simulation of the motion of a single atom. In the second lab period students extend concepts learned in the first period to develop skills in the use of expert MD software. Here students simulate and analyze changes in protein conformation resulting from temperature change, solvation, and phosphorylation. The article will describe how these activities can be carried out using free software packages, including Abalone and VMD/NAMD. © 2016 The International Union of Biochemistry and Molecular Biology.

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.

Atomic spectral-product representations of molecular electronic structure: metric matrices and atomic-product composition of molecular eigenfunctions.

PubMed

Ben-Nun, M; Mills, J D; Hinde, R J; Winstead, C L; Boatz, J A; Gallup, G A; Langhoff, P W

2009-07-02

Recent progress is reported in development of ab initio computational methods for the electronic structures of molecules employing the many-electron eigenstates of constituent atoms in spectral-product forms. The approach provides a universal atomic-product description of the electronic structure of matter as an alternative to more commonly employed valence-bond- or molecular-orbital-based representations. The Hamiltonian matrix in this representation is seen to comprise a sum over atomic energies and a pairwise sum over Coulombic interaction terms that depend only on the separations of the individual atomic pairs. Overall electron antisymmetry can be enforced by unitary transformation when appropriate, rather than as a possibly encumbering or unnecessary global constraint. The matrix representative of the antisymmetrizer in the spectral-product basis, which is equivalent to the metric matrix of the corresponding explicitly antisymmetric basis, provides the required transformation to antisymmetric or linearly independent states after Hamiltonian evaluation. Particular attention is focused in the present report on properties of the metric matrix and on the atomic-product compositions of molecular eigenstates as described in the spectral-product representations. Illustrative calculations are reported for simple but prototypically important diatomic (H(2), CH) and triatomic (H(3), CH(2)) molecules employing algorithms and computer codes devised recently for this purpose. This particular implementation of the approach combines Slater-orbital-based one- and two-electron integral evaluations, valence-bond constructions of standard tableau functions and matrices, and transformations to atomic eigenstate-product representations. The calculated metric matrices and corresponding potential energy surfaces obtained in this way elucidate a number of aspects of the spectral-product development, including the nature of closure in the representation, the general redundancy or

Understanding the mechanisms of amorphous creep through molecular simulation

NASA Astrophysics Data System (ADS)

Cao, Penghui; Short, Michael P.; Yip, Sidney

2017-12-01

Molecular processes of creep in metallic glass thin films are simulated at experimental timescales using a metadynamics-based atomistic method. Space-time evolutions of the atomic strains and nonaffine atom displacements are analyzed to reveal details of the atomic-level deformation and flow processes of amorphous creep in response to stress and thermal activations. From the simulation results, resolved spatially on the nanoscale and temporally over time increments of fractions of a second, we derive a mechanistic explanation of the well-known variation of creep rate with stress. We also construct a deformation map delineating the predominant regimes of diffusional creep at low stress and high temperature and deformational creep at high stress. Our findings validate the relevance of two original models of the mechanisms of amorphous plasticity: one focusing on atomic diffusion via free volume and the other focusing on stress-induced shear deformation. These processes are found to be nonlinearly coupled through dynamically heterogeneous fluctuations that characterize the slow dynamics of systems out of equilibrium.

Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations.

PubMed

Gumbart, James C; Beeby, Morgan; Jensen, Grant J; Roux, Benoît

2014-02-01

Bacteria face the challenging requirement to maintain their shape and avoid rupture due to the high internal turgor pressure, but simultaneously permit the import and export of nutrients, chemical signals, and virulence factors. The bacterial cell wall, a mesh-like structure composed of cross-linked strands of peptidoglycan, fulfills both needs by being semi-rigid, yet sufficiently porous to allow diffusion through it. How the mechanical properties of the cell wall are determined by the molecular features and the spatial arrangement of the relatively thin strands in the larger cellular-scale structure is not known. To examine this issue, we have developed and simulated atomic-scale models of Escherichia coli cell walls in a disordered circumferential arrangement. The cell-wall models are found to possess an anisotropic elasticity, as known experimentally, arising from the orthogonal orientation of the glycan strands and of the peptide cross-links. Other features such as thickness, pore size, and disorder are also found to generally agree with experiments, further supporting the disordered circumferential model of peptidoglycan. The validated constructs illustrate how mesoscopic structure and behavior emerge naturally from the underlying atomic-scale properties and, furthermore, demonstrate the ability of all-atom simulations to reproduce a range of macroscopic observables for extended polymer meshes.

Nonlinear effects in defect production by atomic and molecular ion implantation

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

David, C., E-mail: david@igcar.gov.in; Dholakia, Manan; Chandra, Sharat

This report deals with studies concerning vacancy related defects created in silicon due to implantation of 200 keV per atom aluminium and its molecular ions up to a plurality of 4. The depth profiles of vacancy defects in samples in their as implanted condition are carried out by Doppler broadening spectroscopy using low energy positron beams. In contrast to studies in the literature reporting a progressive increase in damage with plurality, implantation of aluminium atomic and molecular ions up to Al{sub 3}, resulted in production of similar concentration of vacancy defects. However, a drastic increase in vacancy defects is observed duemore » to Al{sub 4} implantation. The observed behavioural trend with respect to plurality has even translated to the number of vacancies locked in vacancy clusters, as determined through gold labelling experiments. The impact of aluminium atomic and molecular ions simulated using MD showed a monotonic increase in production of vacancy defects for cluster sizes up to 4. The trend in damage production with plurality has been explained on the basis of a defect evolution scheme in which for medium defect concentrations, there is a saturation of the as-implanted damage and an increase for higher defect concentrations.« less

Analysis of Ligand-Receptor Association and Intermediate Transfer Rates in Multienzyme Nanostructures with All-Atom Brownian Dynamics Simulations.

PubMed

Roberts, Christopher C; Chang, Chia-En A

2016-08-25

We present the second-generation GeomBD Brownian dynamics software for determining interenzyme intermediate transfer rates and substrate association rates in biomolecular complexes. Substrate and intermediate association rates for a series of enzymes or biomolecules can be compared between the freely diffusing disorganized configuration and various colocalized or complexed arrangements for kinetic investigation of enhanced intermediate transfer. In addition, enzyme engineering techniques, such as synthetic protein conjugation, can be computationally modeled and analyzed to better understand changes in substrate association relative to native enzymes. Tools are provided to determine nonspecific ligand-receptor association residence times, and to visualize common sites of nonspecific association of substrates on receptor surfaces. To demonstrate features of the software, interenzyme intermediate substrate transfer rate constants are calculated and compared for all-atom models of DNA origami scaffold-bound bienzyme systems of glucose oxidase and horseradish peroxidase. Also, a DNA conjugated horseradish peroxidase enzyme was analyzed for its propensity to increase substrate association rates and substrate local residence times relative to the unmodified enzyme. We also demonstrate the rapid determination and visualization of common sites of nonspecific ligand-receptor association by using HIV-1 protease and an inhibitor, XK263. GeomBD2 accelerates simulations by precomputing van der Waals potential energy grids and electrostatic potential grid maps, and has a flexible and extensible support for all-atom and coarse-grained force fields. Simulation software is written in C++ and utilizes modern parallelization techniques for potential grid preparation and Brownian dynamics simulation processes. Analysis scripts, written in the Python scripting language, are provided for quantitative simulation analysis. GeomBD2 is applicable to the fields of biophysics, bioengineering

Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

PubMed

Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

2014-10-16

Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of

A model for self-diffusion of guanidinium-based ionic liquids: a molecular simulation study.

PubMed

Klähn, Marco; Seduraman, Abirami; Wu, Ping

2008-11-06

We propose a novel self-diffusion model for ionic liquids on an atomic level of detail. The model is derived from molecular dynamics simulations of guanidinium-based ionic liquids (GILs) as a model case. The simulations are based on an empirical molecular mechanical force field, which has been developed in our preceding work, and it relies on the charge distribution in the actual liquid. The simulated GILs consist of acyclic and cyclic cations that were paired with nitrate and perchlorate anions. Self-diffusion coefficients are calculated at different temperatures from which diffusive activation energies between 32-40 kJ/mol are derived. Vaporization enthalpies between 174-212 kJ/mol are calculated, and their strong connection with diffusive activation energies is demonstrated. An observed formation of cavities in GILs of up to 6.5% of the total volume does not facilitate self-diffusion. Instead, the diffusion of ions is found to be determined primarily by interactions with their immediate environment via electrostatic attraction between cation hydrogen and anion oxygen atoms. The calculated average time between single diffusive transitions varies between 58-107 ps and determines the speed of diffusion, in contrast to diffusive displacement distances, which were found to be similar in all simulated GILs. All simulations indicate that ions diffuse by using a brachiation type of movement: a diffusive transition is initiated by cleaving close contacts to a coordinated counterion, after which the ion diffuses only about 2 A until new close contacts are formed with another counterion in its vicinity. The proposed diffusion model links all calculated energetic and dynamic properties of GILs consistently and explains their molecular origin. The validity of the model is confirmed by providing an explanation for the variation of measured ratios of self-diffusion coefficients of cations and paired anions over a wide range of values, encompassing various ionic liquid classes

Ab initio molecular dynamics simulation study of successive hydrogenation reactions of carbon monoxide producing methanol

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

Pham, Thi Nu; Ono, Shota; Ohno, Kaoru, E-mail: ohno@ynu.ac.jp

Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronicmore » excited state configuration.« less

1984 Bibliography of atomic and molecular processes

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

Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.

1985-04-01

This annotated bibliography includes papers on atomic and molecular processes published during 1984. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

1982 bibliography of atomic and molecular processes

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

Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.

1984-05-01

This annotated bibliography includes papers on atomic and molecular processes published during 1982. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

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.

Charge Inversion by Electrostatic Complexation: Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Faraudo, Jordi; Travesset, Alex

2007-03-01

Ions near interfaces play an important role in many biological and physico-chemical processes and exhibit a fascinating diverse range of phenomena. A relevant example is charge inversion, where interfacial charges attract counterions in excess of their own nominal charge, thus leading to an inversion of the sign of the interfacial charge. In this work, we argue that in the case of amphiphilic interfaces, charge inversion can be generated by complexation, that is, electrostatic complexes containing several counterions bound to amphiphilic molecules. The formation of these complexes require the presence at the interface of groups with conformational degrees of freedom with many electronegative atoms. We illustrate this mechanism by analyzing all atomic molecular dynamics simulations of a DMPA (Dimirystoil-Phosphatidic acid) phospholipid monolayer in contact with divalent counterions. The results are found to be in agreement with recent experimental results on Langmuir monolayers. We also discuss the implications for biological systems, as Phosphatidic acid is emerging as a key signaling phospholipid.

Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations.

PubMed

Wu, Jingheng; Shen, Lin; Yang, Weitao

2017-10-28

Ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation is a useful tool to calculate thermodynamic properties such as potential of mean force for chemical reactions but intensely time consuming. In this paper, we developed a new method using the internal force correction for low-level semiempirical QM/MM molecular dynamics samplings with a predefined reaction coordinate. As a correction term, the internal force was predicted with a machine learning scheme, which provides a sophisticated force field, and added to the atomic forces on the reaction coordinate related atoms at each integration step. We applied this method to two reactions in aqueous solution and reproduced potentials of mean force at the ab initio QM/MM level. The saving in computational cost is about 2 orders of magnitude. The present work reveals great potentials for machine learning in QM/MM simulations to study complex chemical processes.

The characterisation of atomic structure and glass-forming ability of the Zr-Cu-Co metallic glasses studied by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Celtek, M.; Sengul, S.

2018-03-01

In the present work, the glass formation process and structural properties of Zr50Cu50-xCox (0 ≤ x ≤ 50) bulk metallic glasses were investigated by a molecular dynamics simulation with the many body tight-binding potentials. The evolution of structure and glass formation process with temperature were discussed using the coordination number, the radial distribution functions, the volume-temperature curve, icosahedral short-range order, glass transition temperature, Voronoi analysis, Honeycutt-Andersen pair analysis technique and the distribution of bond-angles. Results indicate that adding Co causes similar responses on the nature of the Zr50Cu50-xCox (0 ≤ x ≤ 50) alloys except for higher glass transition temperature and ideal icosahedral type ordered local atomic environment. Also, the differences of the atomic radii play the key role in influencing the atomic structure of these alloys. Both Cu and Co atoms play a significant role in deciding the chemical and topological short-range orders of the Zr50Cu50-xCox ternary liquids and amorphous alloys. The glass-forming ability of these alloys is supported by the experimental observations reported in the literature up to now.

Quantum molecular dynamics simulations of dense matter

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

Collins, L.; Kress, J.; Troullier, N.

1997-12-31

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

Molecular-dynamics simulations of self-assembled monolayers (SAM) on parallel computers

NASA Astrophysics Data System (ADS)

Vemparala, Satyavani

The purpose of this dissertation is to investigate the properties of self-assembled monolayers, particularly alkanethiols and Poly (ethylene glycol) terminated alkanethiols. These simulations are based on realistic interatomic potentials and require scalable and portable multiresolution algorithms implemented on parallel computers. Large-scale molecular dynamics simulations of self-assembled alkanethiol monolayer systems have been carried out using an all-atom model involving a million atoms to investigate their structural properties as a function of temperature, lattice spacing and molecular chain-length. Results show that the alkanethiol chains tilt from the surface normal by a collective angle of 25° along next-nearest neighbor direction at 300K. At 350K the system transforms to a disordered phase characterized by small tilt angle, flexible tilt direction, and random distribution of backbone planes. With increasing lattice spacing, a, the tilt angle increases rapidly from a nearly zero value at a = 4.7A to as high as 34° at a = 5.3A at 300K. We also studied the effect of end groups on the tilt structure of SAM films. We characterized the system with respect to temperature, the alkane chain length, lattice spacing, and the length of the end group. We found that the gauche defects were predominant only in the tails, and the gauche defects increased with the temperature and number of EG units. Effect of electric field on the structure of poly (ethylene glycol) (PEG) terminated alkanethiol self assembled monolayer (SAM) on gold has been studied using parallel molecular dynamics method. An applied electric field triggers a conformational transition from all-trans to a mostly gauche conformation. The polarity of the electric field has a significant effect on the surface structure of PEG leading to a profound effect on the hydrophilicity of the surface. The electric field applied anti-parallel to the surface normal causes a reversible transition to an ordered state

Towards Quantum Simulation with Circular Rydberg Atoms

NASA Astrophysics Data System (ADS)

Nguyen, T. L.; Raimond, J. M.; Sayrin, C.; Cortiñas, R.; Cantat-Moltrecht, T.; Assemat, F.; Dotsenko, I.; Gleyzes, S.; Haroche, S.; Roux, G.; Jolicoeur, Th.; Brune, M.

2018-01-01

The main objective of quantum simulation is an in-depth understanding of many-body physics, which is important for fundamental issues (quantum phase transitions, transport, …) and for the development of innovative materials. Analytic approaches to many-body systems are limited, and the huge size of their Hilbert space makes numerical simulations on classical computers intractable. A quantum simulator avoids these limitations by transcribing the system of interest into another, with the same dynamics but with interaction parameters under control and with experimental access to all relevant observables. Quantum simulation of spin systems is being explored with trapped ions, neutral atoms, and superconducting devices. We propose here a new paradigm for quantum simulation of spin-1 /2 arrays, providing unprecedented flexibility and allowing one to explore domains beyond the reach of other platforms. It is based on laser-trapped circular Rydberg atoms. Their long intrinsic lifetimes, combined with the inhibition of their microwave spontaneous emission and their low sensitivity to collisions and photoionization, make trapping lifetimes in the minute range realistic with state-of-the-art techniques. Ultracold defect-free circular atom chains can be prepared by a variant of the evaporative cooling method. This method also leads to the detection of arbitrary spin observables with single-site resolution. The proposed simulator realizes an X X Z spin-1 /2 Hamiltonian with nearest-neighbor couplings ranging from a few to tens of kilohertz. All the model parameters can be dynamically tuned at will, making a large range of simulations accessible. The system evolution can be followed over times in the range of seconds, long enough to be relevant for ground-state adiabatic preparation and for the study of thermalization, disorder, or Floquet time crystals. The proposed platform already presents unrivaled features for quantum simulation of regular spin chains. We discuss

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

Molecular dynamics simulation of metal nanoislands growth

NASA Astrophysics Data System (ADS)

Kapralov, N. V.; Babich, E. S.; Redkov, A. V.

2017-11-01

We present the atomistic model and the simulation of a self-assembled growth of a silver nanoisland film and small groups of nanoislands on a glass substrate after thermal poling of the glass with a profiled electrode. The calculations were performed in molecular dynamics simulator LAMMPS taking into account the diffusion of the metal atoms towards and along the glass surface and their clustering. Lennard-Jones potential was used to describe metal-metal and metal-glass interaction. The potential parameters were determined to provide qualitative coincidence of the simulated configurations of the metal nanostructures and the experimental ones, such as an isolated nanoisland, a pair and a set of three nanoislands and a “plasmonic molecule”.

Assessing the Efficacy of Poly(N-isopropylacrylamide) for Drug Delivery Applications Using Molecular Dynamics Simulations.

PubMed

Moghadam, Soroush; Larson, Ronald G

2017-02-06

All-atom molecular dynamic simulations (AA-MD) are performed for aqueous solutions of hydrophobic drug molecules (phenytoin) with model polymer excipients, namely, (1) N-isopropylacrylamide, (pNIPAAm), (2) pNIPAAm-co-acrylamide (Am), and (3) pNIPAAm-co-dimethylacrylamide (DMA). After validating the force field parameters using the well-known lower critical solution behavior of pNIPAAm, we simulate the polymer-drug complex in water and its behavior at temperatures below (295 K) and above the LCST (310 K). Using radial distribution functions, we find that there is an optimum comonomer molar fraction of around 20-30% DMA at which interaction with phenytoin drug molecules is strongest, consistent with recent experimental findings. The results provide evidence that molecular simulations are able to provide guidance in the optimization of novel polymer excipients for drug release.

PREFACE: 8th Asian International Seminar on Atomic and Molecular Physics (AISAMP)

NASA Astrophysics Data System (ADS)

Williams, Jim F.; Buckman, Steve; Bieske, Evan J.

2009-09-01

These proceedings arose from the 8th Asian International Seminar on Atomic and Molecular Physics (AISAMP) which was held at the University of Western Australia 24-28 November 2008. The history of AISAMP (Takayanagi and Matsuzawa 2002) recognizes its origin from the Japan-China meeting of 1985, and the first use of the name 'The First Asian International Seminar on Atomic and Molecular Physics (AISAMP)' in 1992. The initial attendees, Japan and China, were joined subsequently by scientists from Korea, Taiwan, India, Australia and recently by Malaysia, Thailand, Vietnam, Turkey Iran, UK and USA. The main purpose of the biennial AISAMP series is to create a wide forum for exchanging ideas and information among atomic and molecular scientists and to promote international collaboration. The scope of the AISAMP8 meeting included pure, strategic and applied research involving atomic and molecular structure and processes in all forms of matter and antimatter. For 2008 the AISAMP conference incorporated the Australian Atomic and Molecular Physics and Quantum Chemistry meeting. The topics for AISAMP8 embraced themes from earlier AISAMP meetings and reflected new interests, in atomic and molecular structures, spectroscopy and collisions; atomic and molecular physics with laser or synchrotron radiation; quantum information processing using atoms and molecules; atoms and molecules in surface physics, nanotechnology, biophysics, atmospheric physics and other interdisciplinary studies. The implementation of the AISAMP themes, as well as the international representation of research interests, is indicated both in the contents list of these published manuscripts as well as in the program for the meeting. Altogether, 184 presentations were made at the 8th AISAMP, including Invited Talks and Contributed Poster Presentations, of which 60 appear in the present Proceedings after review by expert referees in accordance with the usual practice of Journal of Physics: Conference Series of

Ab-Initio Molecular Dynamics Simulation of Graphene Sheet

NASA Astrophysics Data System (ADS)

Kolev, S.; Balchev, I.; Cvetkov, K.; Tinchev, S.; Milenov, T.

2017-01-01

The study of graphene is important because it is a promising material for a variety of applications in the electronic industry. In the present work, the properties of а 2D periodic graphene sheet are studied with the use of ab initio molecular dynamics. DFT in the generalized gradient approximation is used in order to carry out the dynamical simulations. The PBE functional and DZVP-MOLOPT basis set are implemented in the CP2K/Quickstep package. A periodic box, consisting of 288 carbon atoms is chosen for the simulations. After geometry optimization it has dimensions 2964 x 2964 x 1500 pm and form angles of 90, 90, 60 degrees. The dynamical simulation is run for 1 ps in the NPT ensemble, at temperature T = 298.15 K. The radial distribution function shows a first peak at 142 pm, marking the bond length between carbon atoms. The density of states for the periodic systems is simulated as occupied orbitals represent the valence band and unoccupied ones the conduction band. The calculated bandgap, as expected is close to 0 eV.

Continuous all-optical deceleration of molecular beams

NASA Astrophysics Data System (ADS)

Jayich, Andrew; Chen, Gary; Long, Xueping; Wang, Anna; Campbell, Wesley

2014-05-01

A significant impediment to generating ultracold molecules is slowing a molecular beam to velocities where the molecules can be cooled and trapped. We report on progress toward addressing this issue with a general optical deceleration technique for molecular and atomic beams. We propose addressing the molecular beam with a pump and dump pulse sequence from a mode-locked laser. The pump pulse counter-propagates with respect to the beam and drives the molecules to the excited state. The dump pulse co-propagates and stimulates emission, driving the molecules back to the ground state. This cycle transfers 2 ℏk of momentum and can generate very large optical forces, not limited by the spontaneous emission lifetime of the molecule or atom. Importantly, avoiding spontaneous emission limits the branching to dark states. This technique can later be augmented with cooling and trapping. We are working towards demonstrating this optical force by accelerating a cold atomic sample.

Shaping the Atomic-Scale Geometries of Electrodes to Control Optical and Electrical Performance of Molecular Devices.

PubMed

Zhao, Zhikai; Liu, Ran; Mayer, Dirk; Coppola, Maristella; Sun, Lu; Kim, Youngsang; Wang, Chuankui; Ni, Lifa; Chen, Xing; Wang, Maoning; Li, Zongliang; Lee, Takhee; Xiang, Dong

2018-04-01

A straightforward method to generate both atomic-scale sharp and atomic-scale planar electrodes is reported. The atomic-scale sharp electrodes are generated by precisely stretching a suspended nanowire, while the atomic-scale planar electrodes are obtained via mechanically controllable interelectrodes compression followed by a thermal-driven atom migration process. Notably, the gap size between the electrodes can be precisely controlled at subangstrom accuracy with this method. These two types of electrodes are subsequently employed to investigate the properties of single molecular junctions. It is found, for the first time, that the conductance of the amine-linked molecular junctions can be enhanced ≈50% as the atomic-scale sharp electrodes are used. However, the atomic-scale planar electrodes show great advantages to enhance the sensitivity of Raman scattering upon the variation of nanogap size. The underlying mechanisms for these two interesting observations are clarified with the help of density functional theory calculation and finite-element method simulation. These findings not only provide a strategy to control the electron transport through the molecule junction, but also pave a way to modulate the optical response as well as to improve the stability of single molecular devices via the rational design of electrodes geometries. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

STOCK: Structure mapper and online coarse-graining kit for molecular simulations

DOE PAGES

Bevc, Staš; Junghans, Christoph; Praprotnik, Matej

2015-03-15

We present a web toolkit STructure mapper and Online Coarse-graining Kit for setting up coarse-grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, e.g. all-atom, to low, i.e. coarse-grained, resolution. Using a graphical user interface it generates input files, which are compatible with standard coarse-graining packages, e.g. VOTCA and DL_CGMAP. Our second tool generates effective potentials for coarse-grained simulations preserving the structural properties, e.g. radial distribution functions, of the underlying higher resolution model. The required distribution functions can be providedmore » by any simulation package. Simulations are performed on a local machine and only the distributions are uploaded to the server. The applicability of the toolkit is validated by mapping atomistic pentane and polyalanine molecules to a coarse-grained representation. Effective potentials are derived for systems of TIP3P (transferable intermolecular potential 3 point) water molecules and salt solution. The presented coarse-graining web toolkit is available at http://stock.cmm.ki.si.« less

Imaging Multi-Particle Atomic and Molecular Dynamics

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

Landers, Allen

2016-02-12

Final Report for Grant Number: DE- FG02-10ER16146 This grant supported research in basic atomic, molecular and optical physics related to the interactions of atoms and molecules with photons and electrons. The duration of the grant was the 5 year period from 4/1/2010 – 10/31/2015. All of the support from the grant was used to pay salaries of the PI, graduate students, and undergraduates and travel to conferences and meetings. The results were in the form of publications in peer reviewed journals. There were 20 peer reviewed publications over these 5 years with 2 of the publications in Physical Review Lettersmore » and 1 in Nature; all of the other articles were in respected peer reviewed journals (Physical Review A, New Journal of Physics, Journal of Physics B ...).« less

Molecular Simulations in Astrobiology

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.; Schweighofer, Karl; Chipot, Christophe; New, Michael H.

2000-01-01

One of the main goals of astrobiology is to understand the origin of cellular life. The most direct approach to this problem is to construct laboratory models of protocells. Such efforts, currently underway in the NASA Astrobiology Program, are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures that are capable of performing protocellular functions. Many of these functions, such as importing nutrients, capturing energy and responding to changes in the environment, are carried out by proteins bound to membranes. We use computer simulations to address the following questions about these proteins: (1) How do small proteins self-organize into ordered structures at water-membrane interfaces and insert into membranes? (2) How do peptides form membrane-spanning structures (e.g. channels)? (3) By what mechanisms do such structures perform their functions? The simulations are performed using the molecular dynamics method. In this method, Newton's equations of motion for each atom in the system are solved iteratively. At each time step, the forces exerted on each atom by the remaining atoms are evaluated by dividing them into two parts. Short-range forces are calculated in real space while long-range forces are evaluated in reciprocal space, using a particle-mesh algorithm which is of order O(NInN). With a time step of 2 femtoseconds, problems occurring on multi-nanosecond time scales (10(exp 6)-10(exp 8) time steps) are accessible. To address a broader range of problems, simulations need to be extended by three orders of magnitude, which requires algorithmic improvements and codes scalable to a large number of processors. Work in this direction is in progress. Two series of simulations are discussed. In one series, it is shown that nonpolar peptides, disordered in water, translocate to the nonpolar interior of the membrane and fold into helical structures (see Figure). Once in the membrane, the peptides

Atomic and Molecular Systems in Intense Ultrashort Laser Pulses

NASA Astrophysics Data System (ADS)

Saenz, A.

2008-07-01

The full quantum mechanical treatment of atomic and molecular systems exposed to intense laser pulses is a so far unsolved challenge, even for systems as small as molecular hydrogen. Therefore, a number of simplified qualitative and quantitative models have been introduced in order to provide at least some interpretational tools for experimental data. The assessment of these models describing the molecular response is complicated, since a comparison to experiment requires often a number of averages to be performed. This includes in many cases averaging of different orientations of the molecule with respect to the laser field, focal volume effects, etc. Furthermore, the pulse shape and even the peak intensity is experimentally not known with very high precision; considering, e.g., the exponential intensity dependence of the ionization signal. Finally, experiments usually provide only relative yields. As a consequence of all these averagings and uncertainties, it is possible that different models may successfully explain some experimental results or features, although these models disagree substantially, if their predictions are compared before averaging. Therefore, fully quantum-mechanical approaches at least for small atomic and molecular systems are highly desirable and have been developed in our group. This includes efficient codes for solving the time-dependent Schrodinger equation of atomic hydrogen, helium or other effective one- or two-electron atoms as well as for the electronic motion in linear (effective) one-and two-electron diatomic molecules like H_2.Very recently, a code for larger molecular systems that adopts the so-called single-active electron approximation was also successfully implemented and applied. In the first part of this talk popular models describing intense laser-field ionization of atoms and their extensions to molecules are described. Then their validity is discussed on the basis of quantum-mechanical calculations. Finally, some

1978 bibliography of atomic and molecular processes. [Bibliography

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

Not Available

This annotated bibliography lists 2557 works on atomic and molecular processes reported in publications dated 1978. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors.

1979 bibliography of atomic and molecular processes. [Bibliography

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

None

1980-08-01

This annotated bibliography lists 2146 works on atomic and molecular processes reported in publications dated 1979. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory, to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors.

Molecular dynamics simulation of metallic impurity diffusion in liquid lead-bismuth eutectic (LBE)

NASA Astrophysics Data System (ADS)

Gao, Yun; Takahashi, Minoru; Cavallotti, Carlo; Raos, Guido

2018-04-01

Corrosion of stainless steels by lead-bismuth eutectic (LBE) is an important problem which depends, amongst other things, on the diffusion of the steel components inside this liquid alloy. Here we present the results of classical molecular dynamics simulations of the diffusion of Fe and Ni within LBE. The simulations complement experimental studies of impurity diffusion by our group and provide an atomic-level understanding of the relevant diffusion phenomena. They are based on the embedded atom method (EAM) to represent many-body interactions among atoms. The EAM potentials employed in our simulations have been validated against ab initio density functional calculations. We show that the experimental and simulation results for the temperature-dependent viscosity of LBE and the impurity diffusion coefficients can be reconciled by assuming that the Ni and Fe diffuse mainly as nanoscopic clusters below 1300 K. The average Fe and Ni cluster sizes decrease with increasing the temperature and there is essentially single-atom diffusion at higher temperatures.

Molecular Dynamics Simulation Study of the Selectivity of a Silica Polymer for Ibuprofen

PubMed Central

Concu, Riccardo; Cordeiro, M. Natalia D. S.

2016-01-01

In the past few years, the sol-gel polycondensation technique has been increasingly employed with great success as an alternative approach to the preparation of molecularly imprinted materials (MIMs). The main aim of this study was to study, through a series of molecular dynamics (MD) simulations, the selectivity of an imprinted silica xerogel towards a new template—the (±)-2-(P-Isobutylphenyl) propionic acid (Ibuprofen, IBU). We have previously demonstrated the affinity of this silica xerogel toward a similar molecule. In the present study, we simulated the imprinting process occurring in a sol-gel mixture using the Optimized Potentials for Liquid Simulations-All Atom (OPLS-AA) force field, in order to evaluate the selectivity of this xerogel for a template molecule. In addition, for the first time, we have developed and verified a new parameterisation for the Ibuprofen® based on the OPLS-AA framework. To evaluate the selectivity of the polymer, we have employed both the radial distribution functions, interaction energies and cluster analyses. PMID:27399685

Molecular Dynamics Simulation Study of the Selectivity of a Silica Polymer for Ibuprofen.

PubMed

Concu, Riccardo; Cordeiro, M Natalia D S

2016-07-07

In the past few years, the sol-gel polycondensation technique has been increasingly employed with great success as an alternative approach to the preparation of molecularly imprinted materials (MIMs). The main aim of this study was to study, through a series of molecular dynamics (MD) simulations, the selectivity of an imprinted silica xerogel towards a new template-the (±)-2-(P-Isobutylphenyl) propionic acid (Ibuprofen, IBU). We have previously demonstrated the affinity of this silica xerogel toward a similar molecule. In the present study, we simulated the imprinting process occurring in a sol-gel mixture using the Optimized Potentials for Liquid Simulations-All Atom (OPLS-AA) force field, in order to evaluate the selectivity of this xerogel for a template molecule. In addition, for the first time, we have developed and verified a new parameterisation for the Ibuprofen(®) based on the OPLS-AA framework. To evaluate the selectivity of the polymer, we have employed both the radial distribution functions, interaction energies and cluster analyses.

Atomic and Molecular Databases, VAMDC (Virtual Atomic and Molecular Data Centre)

NASA Astrophysics Data System (ADS)

Dubernet, Marie-Lise; Zwölf, Carlo Maria; Moreau, Nicolas; Awa Ba, Yaya; VAMDC Consortium

2015-08-01

The "Virtual Atomic and Molecular Data Centre Consortium",(VAMDC Consortium, http://www.vamdc.eu) is a Consortium bound by an Memorandum of Understanding aiming at ensuring the sustainability of the VAMDC e-infrastructure. The current VAMDC e-infrastructure inter-connects about 30 atomic and molecular databases with the number of connected databases increasing every year: some databases are well-known databases such as CDMS, JPL, HITRAN, VALD,.., other databases have been created since the start of VAMDC. About 90% of our databases are used for astrophysical applications. The data can be queried, retrieved, visualized in a single format from a general portal (http://portal.vamdc.eu) and VAMDC is also developing standalone tools in order to retrieve and handle the data. VAMDC provides software and support in order to include databases within the VAMDC e-infrastructure. One current feature of VAMDC is the constrained environnement of description of data that ensures a higher quality for distribution of data; a future feature is the link of VAMDC with evaluation/validation groups. The talk will present the VAMDC Consortium and the VAMDC e infrastructure with its underlying technology, its services, its science use cases and its etension towards other communities than the academic research community.

Continuum description of solvent dielectrics in molecular-dynamics simulations of proteins

NASA Astrophysics Data System (ADS)

Egwolf, Bernhard; Tavan, Paul

2003-02-01

We present a continuum approach for efficient and accurate calculation of reaction field forces and energies in classical molecular-dynamics (MD) simulations of proteins in water. The derivation proceeds in two steps. First, we reformulate the electrostatics of an arbitrarily shaped molecular system, which contains partially charged atoms and is embedded in a dielectric continuum representing the water. A so-called fuzzy partition is used to exactly decompose the system into partial atomic volumes. The reaction field is expressed by means of dipole densities localized at the atoms. Since these densities cannot be calculated analytically for general systems, we introduce and carefully analyze a set of approximations in a second step. These approximations allow us to represent the dipole densities by simple dipoles localized at the atoms. We derive a system of linear equations for these dipoles, which can be solved numerically by iteration. After determining the two free parameters of our approximate method we check its quality by comparisons (i) with an analytical solution, which is available for a perfectly spherical system, (ii) with forces obtained from a MD simulation of a soluble protein in water, and (iii) with reaction field energies of small molecules calculated by a finite difference method.

Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Translocation into DMPC Bilayers

PubMed Central

2015-01-01

Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide–water and peptide–membrane interactions allow prediction of free energy minima at the bilayer–water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are −2.51, −4.28, and −5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are −0.83, −3.33, and −3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of

Adsorption of Synthetic Cationic Polymers on Model Phospholipid Membranes: Insight from Atomic-Scale Molecular Dynamics Simulations.

PubMed

Kostritskii, Andrei Yu; Kondinskaia, Diana A; Nesterenko, Alexey M; Gurtovenko, Andrey A

2016-10-11

Although synthetic cationic polymers represent a promising class of effective antibacterial agents, the molecular mechanisms behind their antimicrobial activity remain poorly understood. To this end, we employ atomic-scale molecular dynamics simulations to explore adsorption of several linear cationic polymers of different chemical structure and protonation (polyallylamine (PAA), polyethylenimine (PEI), polyvinylamine (PVA), and poly-l-lysine (PLL)) on model bacterial membranes (4:1 mixture of zwitterionic phosphatidylethanolamine (PE) and anionic phosphatidylglycerol (PG) lipids). Overall, our findings show that binding of polycations to the anionic membrane surface effectively neutralizes its charge, leading to the reorientation of water molecules close to the lipid/water interface and to the partial release of counterions to the water phase. In certain cases, one has even an overcharging of the membrane, which was shown to be a cooperative effect of polymer charges and lipid counterions. Protonated amine groups of polycations are found to interact preferably with head groups of anionic lipids, giving rise to formation of hydrogen bonds and to a noticeable lateral immobilization of the lipids. While all the above findings are mostly defined by the overall charge of a polymer, we found that the polymer architecture also matters. In particular, PVA and PEI are able to accumulate anionic PG lipids on the membrane surface, leading to lipid segregation. In turn, PLL whose charge twice exceeds charges of PVA/PEI does not induce such lipid segregation due to its considerably less compact architecture and relatively long side chains. We also show that partitioning of a polycation into the lipid/water interface is an interplay between its protonation level (the overall charge) and hydrophobicity of the backbone. Therefore, a possible strategy in creating highly efficient antimicrobial polymeric agents could be in tuning these polycation's properties through proper

Ultracold-atom quantum simulator for attosecond science

NASA Astrophysics Data System (ADS)

Sala, Simon; Förster, Johann; Saenz, Alejandro

2017-01-01

A quantum simulator based on ultracold optically trapped atoms for simulating the physics of atoms and molecules in ultrashort intense laser fields is introduced. The slowing down by about 13 orders of magnitude allows one to watch in slow motion the tunneling and recollision processes that form the heart of attosecond science. The extreme flexibility of the simulator promises a deeper understanding of strong-field physics, especially for many-body systems beyond the reach of classical computers. The quantum simulator can experimentally straightforwardly be realized and is shown to recover the ionization characteristics of atoms in the different regimes of laser-matter interaction.

Atomic insight into tribochemical wear mechanism of silicon at the Si/SiO2 interface in aqueous environment: Molecular dynamics simulations using ReaxFF reactive force field

NASA Astrophysics Data System (ADS)

Wen, Jialin; Ma, Tianbao; Zhang, Weiwei; Psofogiannakis, George; van Duin, Adri C. T.; Chen, Lei; Qian, Linmao; Hu, Yuanzhong; Lu, Xinchun

2016-12-01

In this work, the atomic mechanism of tribochemical wear of silicon at the Si/SiO2 interface in aqueous environment was investigated using ReaxFF molecular dynamics (MD) simulations. Two types of Si atom removal pathways were detected in the wear process. The first is caused by the destruction of stretched Si-O-Si bonds on the Si substrate surface and is assisted by the attachment of H atoms on the bridging oxygen atoms of the bonds. The other is caused by the rupture of Si-Si bonds in the stretched Si-Si-O-Si bond chains at the interface. Both pathways effectively remove Si atoms from the silicon surface via interfacial Si-O-Si bridge bonds. Our simulations also demonstrate that higher pressures applied to the silica phase can cause more Si atoms to be removed due to the formation of increased numbers of interfacial Si-O-Si bridge bonds. Besides, water plays a dual role in the wear mechanism, by oxidizing the Si substrate surface as well as by preventing the close contact of the surfaces. This work shows that the removal of Si atoms from the substrate is a result of both chemical reaction and mechanical effects and contributes to the understanding of tribochemical wear behavior in the microelectromechanical systems (MEMS) and Si chemical mechanical polishing (CMP) process.

Convergence of Molecular Dynamics Simulation of Protein Native States: Feasibility vs Self-Consistency Dilemma.

PubMed

Sawle, Lucas; Ghosh, Kingshuk

2016-02-09

All-atom molecular dynamics simulations need convergence tests to evaluate the quality of data. The notion of "true" convergence is elusive, and one can only hope to satisfy self-consistency checks (SCC). There are multiple SCC criteria, and their assessment of all-atom simulations of the native state for real globular proteins is sparse. Here, we present a systematic study of different SCC algorithms, both in terms of their ability to detect the lack of self-consistency and their computational demand, for the all-atom native state simulations of four globular proteins (CSP, CheA, CheW, and BPTI). Somewhat surprisingly, we notice some of the most stringent SCC criteria, e.g., the criteria demanding similarity of the cluster probability distribution between the first and the second halves of the trajectory or the comparison of fluctuations between different blocks using covariance overlap measure, can require tens of microseconds of simulation even for proteins with less than 100 amino acids. We notice such long simulation times can sometimes be associated with traps, but these traps cannot be detected by some of the common SCC methods. We suggest an additional, and simple, SCC algorithm to quickly detect such traps by monitoring the constancy of the cluster entropy (CCE). CCE is a necessary but not sufficient criteria, and additional SCC algorithms must be combined with it. Furthermore, as seen in the explicit solvent simulation of 1 ms long trajectory of BPTI,1 passing self-consistency checks at an earlier stage may be misleading due to conformational changes taking place later in the simulation, resulting in different, but segregated regions of SCC. Although there is a hierarchy of complex SCC algorithms, caution must be exercised in their application with the knowledge of their limitations and computational expense.

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.

Simulating Picosecond X-ray Diffraction from shocked crystals by Post-processing Molecular Dynamics Calculations

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

Kimminau, G; Nagler, B; Higginbotham, A

2008-06-19

Calculations of the x-ray diffraction patterns from shocked crystals derived from the results of Non-Equilibrium-Molecular-Dynamics (NEMD) simulations are presented. The atomic coordinates predicted by the NEMD simulations combined with atomic form factors are used to generate a discrete distribution of electron density. A Fast-Fourier-Transform (FFT) of this distribution provides an image of the crystal in reciprocal space, which can be further processed to produce quantitative simulated data for direct comparison with experiments that employ picosecond x-ray diffraction from laser-irradiated crystalline targets.

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

PubMed

Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N

2009-05-01

Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function.

An All-atom Structure-Based Potential for Proteins: Bridging Minimal Models with All-atom Empirical Forcefields

PubMed Central

Whitford, Paul C.; Noel, Jeffrey K.; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y.; Onuchic, José N.

2012-01-01

Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Gō) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a Cα structure-based model and an all-atom empirical forcefield. Key findings include 1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature 2) folding mechanisms are robust to variations of the energetic parameters 3) protein folding free energy barriers can be manipulated through parametric modifications 4) the global folding mechanisms in a Cα model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model 5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Since this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035

Molecular Dynamics Simulations Provide Atomistic Insight into Hydrogen Exchange Mass Spectrometry Experiments.

PubMed

Petruk, Ariel A; Defelipe, Lucas A; Rodríguez Limardo, Ramiro G; Bucci, Hernán; Marti, Marcelo A; Turjanski, Adrian G

2013-01-08

It is now clear that proteins are flexible entities that in solution switch between conformations to achieve their function. Hydrogen/Deuterium Exchange Mass Spectrometry (HX/MS) is an invaluable tool to understand dynamic changes in proteins modulated by cofactor binding, post-transductional modifications, or protein-protein interactions. ERK2MAPK, a protein involved in highly conserved signal transduction pathways of paramount importance for normal cellular function, has been extensively studied by HX/MS. Experiments of the ERK2MAPK in the inactive and active states (in the presence or absence of bound ATP) have provided valuable information on the plasticity of the MAPK domain. However, interpretation of the HX/MS data is difficult, and changes are mostly explained in relation to available X-ray structures, precluding a complete atomic picture of protein dynamics. In the present work, we have used all atom Molecular Dynamics simulations (MD) to provide a theoretical framework for the interpretation of HX/MS data. Our results show that detailed analysis of protein-solvent interaction along the MD simulations allows (i) prediction of the number of protons exchanged for each peptide in the HX/MS experiments, (ii) rationalization of the experimentally observed changes in exchange rates in different protein conditions at the residue level, and (iii) that at least for ERK2MAPK, most of the functionally observed differences in protein dynamics are related to what can be considered the native state conformational ensemble. In summary, the combination of HX/MS experiments with all atom MD simulations emerges as a powerful approach to study protein native state dynamics with atomic resolution.

Machine learning molecular dynamics for the simulation of infrared spectra.

PubMed

Gastegger, Michael; Behler, Jörg; Marquetand, Philipp

2017-10-01

Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects - typically neglected by conventional quantum chemistry approaches - we base our machine learning strategy on ab initio molecular dynamics simulations. While these simulations are usually extremely time consuming even for small molecules, we overcome these limitations by leveraging the power of a variety of machine learning techniques, not only accelerating simulations by several orders of magnitude, but also greatly extending the size of systems that can be treated. To this end, we develop a molecular dipole moment model based on environment dependent neural network charges and combine it with the neural network potential approach of Behler and Parrinello. Contrary to the prevalent big data philosophy, we are able to obtain very accurate machine learning models for the prediction of infrared spectra based on only a few hundreds of electronic structure reference points. This is made possible through the use of molecular forces during neural network potential training and the introduction of a fully automated sampling scheme. We demonstrate the power of our machine learning approach by applying it to model the infrared spectra of a methanol molecule, n -alkanes containing up to 200 atoms and the protonated alanine tripeptide, which at the same time represents the first application of machine learning techniques to simulate the dynamics of a peptide. In all of these case studies we find an excellent agreement between the infrared spectra predicted via machine learning models and the respective theoretical and experimental spectra.

Coarse-grained molecular dynamics simulations for giant protein-DNA complexes

NASA Astrophysics Data System (ADS)

Takada, Shoji

Biomolecules are highly hierarchic and intrinsically flexible. Thus, computational modeling calls for multi-scale methodologies. We have been developing a coarse-grained biomolecular model where on-average 10-20 atoms are grouped into one coarse-grained (CG) particle. Interactions among CG particles are tuned based on atomistic interactions and the fluctuation matching algorithm. CG molecular dynamics methods enable us to simulate much longer time scale motions of much larger molecular systems than fully atomistic models. After broad sampling of structures with CG models, we can easily reconstruct atomistic models, from which one can continue conventional molecular dynamics simulations if desired. Here, we describe our CG modeling methodology for protein-DNA complexes, together with various biological applications, such as the DNA duplication initiation complex, model chromatins, and transcription factor dynamics on chromatin-like environment.

Efficient molecular dynamics simulations with many-body potentials on graphics processing units

NASA Astrophysics Data System (ADS)

Fan, Zheyong; Chen, Wei; Vierimaa, Ville; Harju, Ari

2017-09-01

Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones. In the conventional force evaluation algorithm for many-body potentials, the force, virial stress, and heat current for a given atom are accumulated within different loops, which could result in write conflict between different threads in a CUDA kernel. In this work, we provide a new force evaluation algorithm, which is based on an explicit pairwise force expression for many-body potentials derived recently (Fan et al., 2015). In our algorithm, the force, virial stress, and heat current for a given atom can be accumulated within a single thread and is free of write conflicts. We discuss the formulations and algorithms and evaluate their performance. A new open-source code, GPUMD, is developed based on the proposed formulations. For the Tersoff many-body potential, the double precision performance of GPUMD using a Tesla K40 card is equivalent to that of the LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) molecular dynamics code running with about 100 CPU cores (Intel Xeon CPU X5670 @ 2.93 GHz).

European Virtual Atomic And Molecular Data Center - VAMDC

NASA Astrophysics Data System (ADS)

Dimitrijevic, M. S.; Sahal-Brechot, S.; Kovacevic, A.; Jevremovic, D.; Popovic, L. C.

2010-07-01

Reliable atomic and molecular data are of great importance for different applications in astrophysics, atmospheric physics, fusion, environmental sciences, combustion chemistry, and in industrial applications from plasmas and lasers to lighting. Currently, very important resources of such data are highly fragmented, presented in different, nonstandardized ways, available through a variety of highly specialized and often poorly documented interfaces, so that the full exploitation of all their scientific worth is limited, hindering research in many topics like e.g. the characterization of extrasolar planets, understanding the chemistry of our local solar system and of the wider universe, the study of the terrestrial atmosphere and quantification of climate change; the development of the fusion rersearch, etc. The Virtual Atomic and Molecular Data Centre (http://www.vamdc.eu, VAMDC) is an European Union funded FP7 project aiming to build a secure, documented, flexible and interoperable e-science environment-based interface to existing atomic and molecular data. It will also provide a forum for training potential users and dissemination of expertise worldwide. Partners in the Consortium of the Project are: 1) Centre National de Recherche Scientifique - CNRS (Paris, Reims, Grenoble, Bordeaux, Dijon, Toulouse); 2) The Chancellor, Masters and Scholars of the University of Cambridge - CMSUC; 3) University College London - UCL; 4) Open University - OU; (Milton Keynes, England); 5) Universitaet Wien - UNIVIE; 6) Uppsala Universitet - UU; 7) Universitaet zu Koeln - KOLN; 8) Istituto Nazionale di Astrofisica - INAF (Catania, Cagliari); 9) Queen's University Belfast - QUB; 10) Astronomska Opservatorija - AOB (Belgrade, Serbia); 11) Institute of Spectroscopy RAS - ISRAN (Troitsk, Russia); 12) Russian Federal Nuclear Center - All-Russian Institute of Technical Physics - RFNC-VNIITF (Snezhinsk, Chelyabinsk Region, Russia; 13) Institute of Atmospheric Optics - IAO (Tomsk, Russia

Self-Consistent Determination of Atomic Charges of Ionic Liquid through a Combination of Molecular Dynamics Simulation and Density Functional Theory.

PubMed

Ishizuka, Ryosuke; Matubayasi, Nobuyuki

2016-02-09

A self-consistent scheme is developed to determine the atomic partial charges of ionic liquid. Molecular dynamics (MD) simulation was conducted to sample a set of ion configurations, and these configurations were subject to density functional theory (DFT) calculations to determine the partial charges. The charges were then averaged and used as inputs for the subsequent MD simulation, and MD and DFT calculations were repeated until the MD results are not altered any more. We applied this scheme to 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl) imide ([C1mim][NTf2]) and investigated its structure and dynamics as a function of temperature. At convergence, the average ionic charges were ±0.84 e at 350 K due to charge transfer among ions, where e is the elementary charge, while the reduced ionic charges do not affect strongly the density of [C1mim][NTf2] and radial distribution function. Instead, major effects are found on the energetics and dynamics, with improvements of the overestimated heat of vaporization and the too slow motions of ions observed in MD simulations using commonly used force fields.

TMFF-A Two-Bead Multipole Force Field for Coarse-Grained Molecular Dynamics Simulation of Protein.

PubMed

Li, Min; Liu, Fengjiao; Zhang, John Z H

2016-12-13

Coarse-grained (CG) models are desirable for studying large and complex biological systems. In this paper, we propose a new two-bead multipole force field (TMFF) in which electric multipoles up to the quadrupole are included in the CG force field. The inclusion of electric multipoles in the proposed CG force field enables a more realistic description of the anisotropic electrostatic interactions in the protein system and, thus, provides an improvement over the standard isotropic two-bead CG models. In order to test the accuracy of the new CG force field model, extensive molecular dynamics simulations were carried out for a series of benchmark protein systems. These simulation studies showed that the TMFF model can realistically reproduce the structural and dynamical properties of proteins, as demonstrated by the close agreement of the CG results with those from the corresponding all-atom simulations in terms of root-mean-square deviations (RMSDs) and root-mean-square fluctuations (RMSFs) of the protein backbones. The current two-bead model is highly coarse-grained and is 50-fold more efficient than all-atom method in MD simulation of proteins in explicit water.

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale.

PubMed

Parton, Daniel L; Grinaway, Patrick B; Hanson, Sonya M; Beauchamp, Kyle A; Chodera, John D

2016-06-01

The rapidly expanding body of available genomic and protein structural data provides a rich resource for understanding protein dynamics with biomolecular simulation. While computational infrastructure has grown rapidly, simulations on an omics scale are not yet widespread, primarily because software infrastructure to enable simulations at this scale has not kept pace. It should now be possible to study protein dynamics across entire (super)families, exploiting both available structural biology data and conformational similarities across homologous proteins. Here, we present a new tool for enabling high-throughput simulation in the genomics era. Ensembler takes any set of sequences-from a single sequence to an entire superfamily-and shepherds them through various stages of modeling and refinement to produce simulation-ready structures. This includes comparative modeling to all relevant PDB structures (which may span multiple conformational states of interest), reconstruction of missing loops, addition of missing atoms, culling of nearly identical structures, assignment of appropriate protonation states, solvation in explicit solvent, and refinement and filtering with molecular simulation to ensure stable simulation. The output of this pipeline is an ensemble of structures ready for subsequent molecular simulations using computer clusters, supercomputers, or distributed computing projects like Folding@home. Ensembler thus automates much of the time-consuming process of preparing protein models suitable for simulation, while allowing scalability up to entire superfamilies. A particular advantage of this approach can be found in the construction of kinetic models of conformational dynamics-such as Markov state models (MSMs)-which benefit from a diverse array of initial configurations that span the accessible conformational states to aid sampling. We demonstrate the power of this approach by constructing models for all catalytic domains in the human tyrosine kinase

Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

NASA Astrophysics Data System (ADS)

Matsushita, Y.; Murakawa, T.; Shimamura, K.; Oishi, M.; Ohyama, T.; Kurita, N.

2015-02-01

The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

Lightweight computational steering of very large scale molecular dynamics simulations

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

Beazley, D.M.; Lomdahl, P.S.

1996-09-01

We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show howmore » this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages.« less

PREFACE: 7th Asian International Seminar on Atomic and Molecular Physics

NASA Astrophysics Data System (ADS)

Deshmukh, Pranawa C.; Chakraborty, Purushottam; Williams, Jim F.

2007-09-01

, Molecular and Optical Physics. We received extensive support from the Journal of Physics: Conference Series staff; Graham Douglas, in particular, has been of tremendous help. The 7th AISAMP was very well attended and was sponsored primarily by the host Indian Institute of Technology, Madras (Chennai), the Board of Research in Nuclear Sciences, (Department of Atomic Energy, Government of India), the Department of Science and Technology, (Government of India), and the Asian Office of Aerospace Research and Development (AOARD) of the US Air Force. There was support from various quarters—each was invaluable and added to the success of the 7th AISAMP. We are very grateful to all the sponsors. It is superfluous to add that guidance and active participation from several colleagues within the host Institute was the primary source of strength for the actual organization of the conference and the multitude of arrangements for the organization came from the young graduate students at the IIT-Madras. We hope that this volume of Journal of Physics: Conference Series will be referenced widely and that it will strengthen ties between various countries in the region in and around Asia, and also of course to all scientists in this field the world over. Pranawa C Deshmukh, Purushottam Chakraborty and Jim F Williams Editors Conference photograph

Molecular Beam Studies of Hot Atom Chemical Reactions: Reactive Scattering of Energetic Deuterium Atoms

DOE R&D Accomplishments Database

Continetti, R. E.; Balko, B. A.; Lee, Y. T.

1989-02-01

A brief review of the application of the crossed molecular beams technique to the study of hot atom chemical reactions in the last twenty years is given. Specific emphasis is placed on recent advances in the use of photolytically produced energetic deuterium atoms in the study of the fundamental elementary reactions D + H{sub 2} -> DH + H and the substitution reaction D + C{sub 2}H{sub 2} -> C{sub 2}HD + H. Recent advances in uv laser and pulsed molecular beam techniques have made the detailed study of hydrogen atom reactions under single collision conditions possible.

Mechanism Responsible for Intercalation of Dimethyl Sulfoxide in Kaolinite: Molecular Dynamics Simulations.

PubMed

Zhang, Shuai; Liu, Qinfu; Cheng, Hongfei; Gao, Feng; Liu, Cun; Teppen, Brian J

2018-01-01

Intercalation is the promising strategy to expand the interlayer region of kaolinite for their further applications. Herein, the adaptive biasing force (ABF) accelerated molecular dynamics simulations were performed to calculate the free energies involved in the kaolinite intercalation by dimethyl sulfoxide (DMSO). Additionally, the classical all atom molecular dynamics simulations were carried out to calculate the interfacial interactions between kaolinite interlayer surfaces and DMSO with the aim at exploring the underlying force that drives the DMSO to enter the interlayer space. The results showed that the favorable interaction of DMSO with both kaolinite interlayer octahedral surface and tetrahedral surface can help in introducing DMSO enter kaolinite interlayer. The hydroxyl groups on octahedral surface functioned as H-donors attracting the S=O groups of DMSO through hydrogen bonding interaction. The tetrahedral surface featuring hydrophobic property attracted the methyl groups of DMSO through hydrophobic interaction. The results provided a detailed picture of the energetics and interlayer structure of kaolinite-DMSO intercalate.

Molecular dynamics simulations through GPU video games technologies

PubMed Central

Loukatou, Styliani; Papageorgiou, Louis; Fakourelis, Paraskevas; Filntisi, Arianna; Polychronidou, Eleftheria; Bassis, Ioannis; Megalooikonomou, Vasileios; Makałowski, Wojciech; Vlachakis, Dimitrios; Kossida, Sophia

2016-01-01

Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements of atoms and molecules is molecular dynamics (MD). MD is an in silico method to simulate the physical motions of atoms and molecules under certain conditions. This has become a state strategic technique and now plays a key role in many areas of exact sciences, such as chemistry, biology, physics and medicine. Due to their complexity, MD calculations could require enormous amounts of computer memory and time and therefore their execution has been a big problem. Despite the huge computational cost, molecular dynamics have been implemented using traditional computers with a central memory unit (CPU). A graphics processing unit (GPU) computing technology was first designed with the goal to improve video games, by rapidly creating and displaying images in a frame buffer such as screens. The hybrid GPU-CPU implementation, combined with parallel computing is a novel technology to perform a wide range of calculations. GPUs have been proposed and used to accelerate many scientific computations including MD simulations. Herein, we describe the new methodologies developed initially as video games and how they are now applied in MD simulations. PMID:27525251

Interfacial water on crystalline silica: a comparative molecular dynamics simulation study

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

Ho, Tuan A.; Argyris, Dimitrios; Papavassiliou, Dimitrios V.

2011-03-03

All-atom molecular dynamics simulations were conducted to study the dynamics of aqueous electrolyte solutions confined in slit-shaped silica nanopores of various degrees of protonation. Five degrees of protonation were prepared by randomly removing surface hydrogen atoms from fully protonated crystalline silica surfaces. Aqueous electrolyte solutions containing NaCl or CsCl salt were simulated at ambient conditions. In all cases, the ionic concentration was 1 M. The results were quantified in terms of atomic density distributions within the pores, and the self-diffusion coefficient along the direction parallel to the pore surface. We found evidence for ion-specific properties that depend on ion surface,more » water ion, and only in some cases ion ion correlations. The degree of protonation strongly affects the structure, distribution, and the dynamic behavior of confined water and electrolytes. Cl ions adsorb on the surface at large degrees of protonation, and their behavior does not depend significantly on the cation type (either Na+ or Cs+ ions are present in the systems considered). The cations show significant ion-specific behavior. Na+ ions occupy different positions within the pore as the degree of protonation changes, while Cs+ ions mainly remain near the pore center at all conditions considered. For a given degree of protonation, the planar self-diffusion coefficient of Cs+ is always greater than that of Na+ ions. The results are useful for better understanding transport under confinement, including brine behavior in the subsurface, with important applications such as environmental remediation.« less

Dynamics of Nanoscale Grain-Boundary Decohesion in Aluminum by Molecular-Dynamics Simulation

NASA Technical Reports Server (NTRS)

Yamakov, V.; Saether, E.; Phillips, D. R.; Glaessegen, E. H.

2007-01-01

The dynamics and energetics of intergranular crack growth along a flat grain boundary in aluminum is studied by a molecular-dynamics simulation model for crack propagation under steady-state conditions. Using the ability of the molecular-dynamics simulation to identify atoms involved in different atomistic mechanisms, it was possible to identify the energy contribution of different processes taking place during crack growth. The energy contributions were divided as: elastic energy, defined as the potential energy of the atoms in fcc crystallographic state; and plastically stored energy, the energy of stacking faults and twin boundaries; grain-boundary and surface energy. In addition, monitoring the amount of heat exchange with the molecular-dynamics thermostat gives the energy dissipated as heat in the system. The energetic analysis indicates that the majority of energy in a fast growing crack is dissipated as heat. This dissipation increases linearly at low speed, and faster than linear at speeds approaching 1/3 the Rayleigh wave speed when the crack tip becomes dynamically unstable producing periodic dislocation bursts until the crack is blunted.

Molecular Dynamics Simulation of Hydrogen Trapping on Sigma 5 Tungsten Grain Boundaries

NASA Astrophysics Data System (ADS)

Al-Shalash, Aws Mohammed Taha

Tungsten as a plasma facing material is the predominant contender for future Tokamak reactor environments. The interaction between the plasma particles and tungsten is crucial to be studied for successful usage and design of tungsten in the plasma facing components ensuring the reliability and longevity of the fusion reactors. The bombardment of the sigma 5 polycrystalline tungsten was modeled using the molecular dynamics simulation through the large-scale atomic/molecular massively parallel simulator (LAMMPS) code and Tersoff type interatomic potential. By simulating the operational conditions of the Tokamak reactors, the hydrogen trapping rate, implantation distribution, and bubble formation was investigated at various temperatures (300-1200 K) and various hydrogen incident energy (20-100 eV). The substrate's temperature increases the deflected H atoms, and increases the penetration depth for the ones that go through. As well, the lower temperature tungsten substrates retain more H atoms. Increasing the bombarded hydrogen's energy increases the trapping and retention rate and the depth of penetration. Another experiments were conducted to determine whether the Sigma5 grain boundary's (GB) location affects the trapping profiles in H. The findings are ranges from small effect on deflection rates at low H energies to no effect at high H energies. However, there is a considerable effect on shifting the trapping depth profile upward toward the surface when raising the GB closer to the surface. Hydrogen atoms are highly mobile on tungsten substrate, yet no bubble formation was witnessed.

Molecular dynamics study of the melting of a supported 887-atom Pd decahedron.

PubMed

Schebarchov, D; Hendy, S C; Polak, W

2009-04-08

We employ classical molecular dynamics simulations to investigate the melting behaviour of a decahedral Pd(887) cluster on a single layer of graphite (graphene). The interaction between Pd atoms is modelled with an embedded-atom potential, while the adhesion of Pd atoms to the substrate is approximated with a Lennard-Jones potential. We find that the decahedral structure persists at temperatures close to the melting point, but that just below the melting transition, the cluster accommodates to the substrate by means of complete melting and then recrystallization into an fcc structure. These structural changes are in qualitative agreement with recently proposed models, and they verify the existence of an energy barrier preventing softly deposited clusters from 'wetting' the substrate at temperatures below the melting point.

Committee on Atomic, Molecular and Optical Sciences

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

Lancaster, James

The Committee on Atomic, Molecular, and Optical Sciences (CAMOS) is a standing activity of the National Research Council (NRC) that operates under the auspices of the Board on Physics and Astronomy. CAMOS is one of five standing committees of the BPA that are charged with assisting it in achieving its goals—monitoring the health of physics and astronomy, identifying important new developments at the scientific forefronts, fostering interactions with other fields, strengthening connections to technology, facilitating effective service to the nation, and enhancing education in physics. CAMOS provides these capabilities for the atomic, molecular and optical (AMO) sciences.

Molecular dynamics for near melting temperatures simulations of metals using modified embedded-atom method

NASA Astrophysics Data System (ADS)

Etesami, S. Alireza; Asadi, Ebrahim

2018-01-01

Availability of a reliable interatomic potential is one of the major challenges in utilizing molecular dynamics (MD) for simulations of metals at near the melting temperatures and melting point (MP). Here, we propose a novel approach to address this challenge in the concept of modified-embedded-atom (MEAM) interatomic potential; also, we apply the approach on iron, nickel, copper, and aluminum as case studies. We propose adding experimentally available high temperature elastic constants and MP of the element to the list of typical low temperature properties used for the development of MD interatomic potential parameters. We show that the proposed approach results in a reasonable agreement between the MD calculations of melting properties such as latent heat, expansion in melting, liquid structure factor, and solid-liquid interface stiffness and their experimental/computational counterparts. Then, we present the physical properties of mentioned elements near melting temperatures using the new MEAM parameters. We observe that the behavior of elastic constants, heat capacity and thermal linear expansion coefficient at room temperature compared to MP follows an empirical linear relation (α±β × MP) for transition metals. Furthermore, a linear relation between the tetragonal shear modulus and the enthalpy change from room temperature to MP is observed for face-centered cubic materials.

Hybrid statistics-simulations based method for atom-counting from ADF STEM images.

PubMed

De Wael, Annelies; De Backer, Annick; Jones, Lewys; Nellist, Peter D; Van Aert, Sandra

2017-06-01

A hybrid statistics-simulations based method for atom-counting from annular dark field scanning transmission electron microscopy (ADF STEM) images of monotype crystalline nanostructures is presented. Different atom-counting methods already exist for model-like systems. However, the increasing relevance of radiation damage in the study of nanostructures demands a method that allows atom-counting from low dose images with a low signal-to-noise ratio. Therefore, the hybrid method directly includes prior knowledge from image simulations into the existing statistics-based method for atom-counting, and accounts in this manner for possible discrepancies between actual and simulated experimental conditions. It is shown by means of simulations and experiments that this hybrid method outperforms the statistics-based method, especially for low electron doses and small nanoparticles. The analysis of a simulated low dose image of a small nanoparticle suggests that this method allows for far more reliable quantitative analysis of beam-sensitive materials. Copyright © 2017 Elsevier B.V. All rights reserved.

vmdICE: a plug-in for rapid evaluation of molecular dynamics simulations using VMD.

PubMed

Knapp, Bernhard; Lederer, Nadja; Omasits, Ulrich; Schreiner, Wolfgang

2010-12-01

Molecular dynamics (MD) is a powerful in silico method to investigate the interactions between biomolecules. It solves Newton's equations of motion for atoms over a specified period of time and yields a trajectory file, containing the different spatial arrangements of atoms during the simulation. The movements and energies of each single atom are recorded. For evaluating of these simulation trajectories with regard to biomedical implications, several methods are available. Three well-known ones are the root mean square deviation (RMSD), the root mean square fluctuation (RMSF) and solvent accessible surface area (SASA). Herein, we present a novel plug-in for the software "visual molecular dynamics" (VMD) that allows an interactive 3D representation of RMSD, RMSF, and SASA, directly on the molecule. On the one hand, our plug-in is easy to handle for inexperienced users, and on the other hand, it provides a fast and flexible graphical impression of the spatial dynamics of a system for experts in the field. © 2010 Wiley Periodicals, Inc.

Equilibration and analysis of first-principles molecular dynamics simulations of water

NASA Astrophysics Data System (ADS)

Dawson, William; Gygi, François

2018-03-01

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

Equilibration and analysis of first-principles molecular dynamics simulations of water.

PubMed

Dawson, William; Gygi, François

2018-03-28

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

The effect of betaine on the foam stability: Molecular simulation

NASA Astrophysics Data System (ADS)

Gao, Fengfeng; Liu, Guokui; Yuan, Shiling

2017-06-01

Zwitterionic betaines are widely used as foam boosters due to these can enhance the stability of foam films. In this paper, mechanistic insights of betaine to improve the stability of alkyl-polyoxyethylene carboxylate (AEC) foam are provided by molecular simulation. In the simulation, we observe the electropositive nitrogen atoms in betaine interact with the electronegative sulfur atoms, an electrostatic structure is formed at the air/water interface. Interaction energies of the mixed surfactants are calculated by the quantum chemistry methods. The calculations show betaine-AEC and betaine-betaine possess attractive interaction, and that AEC-AEC has repulsion to each other. In the other words, the repulsion between the headgroups of anionic surfactants is relaxed by betaine. Additionally, the influence of concentration of betaine on the stability of foam films is also simulated. The RDF and coordination numbers show that the electrostatic structures become denser with the increasing concentration of betaine. Therefore, entry barrier is enhanced accordingly. The SMD simulation also demonstrates the same variation tendency of entry barrier. The simulation details provide vital supplements to experiments.

Secondary ion emission from phosphatidic acid sandwich films under atomic and molecular primary ion bombardment

NASA Astrophysics Data System (ADS)

Stapel, D.; Benninghoven, A.

2001-11-01

Secondary ion yields increase considerably when changing from atomic to molecular primary ions. Since secondary ion emission from deeper layers could result in a pronounced yield increase, the secondary ion emission depth of molecular fragments was investigated. A phosphatidic acid Langmuir-Blodgett (LB) sandwich system was applied. The well-defined layer structure of the applied sample allows the assignment of different depths of origin to the selected fragment ions. At least 93% of the detected characteristic molecular fragment ions originate from the first and second layers. This holds true for all applied atomic and molecular primary ions.

Modeling the nanoscale viscoelasticity of fluids by bridging non-Markovian fluctuating hydrodynamics and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Voulgarakis, Nikolaos K.; Satish, Siddarth; Chu, Jhih-Wei

2009-12-01

A multiscale computational method is developed to model the nanoscale viscoelasticity of fluids by bridging non-Markovian fluctuating hydrodynamics (FHD) and molecular dynamics (MD) simulations. To capture the elastic responses that emerge at small length scales, we attach an additional rheological model parallel to the macroscopic constitutive equation of a fluid. The widely used linear Maxwell model is employed as a working choice; other models can be used as well. For a fluid that is Newtonian in the macroscopic limit, this approach results in a parallel Newtonian-Maxwell model. For water, argon, and an ionic liquid, the power spectrum of momentum field autocorrelation functions of the parallel Newtonian-Maxwell model agrees very well with those calculated from all-atom MD simulations. To incorporate thermal fluctuations, we generalize the equations of FHD to work with non-Markovian rheological models and colored noise. The fluctuating stress tensor (white noise) is integrated in time in the same manner as its dissipative counterpart and numerical simulations indicate that this approach accurately preserves the set temperature in a FHD simulation. By mapping position and velocity vectors in the molecular representation onto field variables, we bridge the non-Markovian FHD with atomistic MD simulations. Through this mapping, we quantitatively determine the transport coefficients of the parallel Newtonian-Maxwell model for water and argon from all-atom MD simulations. For both fluids, a significant enhancement in elastic responses is observed as the wave number of hydrodynamic modes is reduced to a few nanometers. The mapping from particle to field representations and the perturbative strategy of developing constitutive equations provide a useful framework for modeling the nanoscale viscoelasticity of fluids.

Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water

NASA Astrophysics Data System (ADS)

Reinhardt, Aleks; Doye, Jonathan P. K.; Noya, Eva G.; Vega, Carlos

2012-11-01

We present a local order parameter based on the standard Steinhardt-Ten Wolde approach that is capable both of tracking and of driving homogeneous ice nucleation in simulations of all-atom models of water. We demonstrate that it is capable of forcing the growth of ice nuclei in supercooled liquid water simulated using the TIP4P/2005 model using over-biassed umbrella sampling Monte Carlo simulations. However, even with such an order parameter, the dynamics of ice growth in deeply supercooled liquid water in all-atom models of water are shown to be very slow, and so the computation of free energy landscapes and nucleation rates remains extremely challenging.

Atomic structure and transport properties of Cu50Zr45Al5 metallic liquids and glasses: Molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Zhang, Y.; Mattern, N.; Eckert, J.

2011-11-01

We have simulated the atomic structure and the transport properties of Cu50Zr45Al5 metallic liquids and glasses within a wide cooling temperature range from 2000 to 300 K, using molecular dynamics simulations. High fractions of Cu- and Al-centered full icosahedra and Zr-centered icosahedra-like clusters have been detected in both supercooled liquids and glasses. The heat capacity and linear thermal expansion coefficients of both liquids and glasses are also calculated, which have not been reported for this off-eutectic composition previously. The critical temperature (Tc) of Cu50Zr45Al5 liquids is determined to be 874.7 K by investigating the self-diffusivity using the mode coupling theory. A dynamics cross-over is detected in the vicinity of Tc, which can be reflected by different diffusion mechanisms and a remarkable deviation from the Einstein-Stokes relation. The results further suggest a fragile to strong transition of Cu50Zr45Al5 liquids between 1500 K and 1300 K upon cooling, which may result from a drastic increase of stable clusters within this temperature range.

A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein-protein interaction with an all-atom model in explicit solvent

NASA Astrophysics Data System (ADS)

Higo, Junichi; Umezawa, Koji; Nakamura, Haruki

2013-05-01

We propose a novel generalized ensemble method, a virtual-system coupled multicanonical molecular dynamics (V-McMD), to enhance conformational sampling of biomolecules expressed by an all-atom model in an explicit solvent. In this method, a virtual system, of which physical quantities can be set arbitrarily, is coupled with the biomolecular system, which is the target to be studied. This method was applied to a system of an Endothelin-1 derivative, KR-CSH-ET1, known to form an antisymmetric homodimer at room temperature. V-McMD was performed starting from a configuration in which two KR-CSH-ET1 molecules were mutually distant in an explicit solvent. The lowest free-energy state (the most thermally stable state) at room temperature coincides with the experimentally determined native complex structure. This state was separated to other non-native minor clusters by a free-energy barrier, although the barrier disappeared with elevated temperature. V-McMD produced a canonical ensemble faster than a conventional McMD method.

Computing the Rotational Diffusion of Biomolecules via Molecular Dynamics Simulation and Quaternion Orientations.

PubMed

Chen, Po-Chia; Hologne, Maggy; Walker, Olivier

2017-03-02

Rotational diffusion (D rot ) is a fundamental property of biomolecules that contains information about molecular dimensions and solute-solvent interactions. While ab initio D rot prediction can be achieved by explicit all-atom molecular dynamics simulations, this is hindered by both computational expense and limitations in water models. We propose coarse-grained force fields as a complementary solution, and show that the MARTINI force field with elastic networks is sufficient to compute D rot in >10 proteins spanning 5-157 kDa. We also adopt a quaternion-based approach that computes D rot orientation directly from autocorrelations of best-fit rotations as used in, e.g., RMSD algorithms. Over 2 μs trajectories, isotropic MARTINI+EN tumbling replicates experimental values to within 10-20%, with convergence analyses suggesting a minimum sampling of >50 × τ theor to achieve sufficient precision. Transient fluctuations in anisotropic tumbling cause decreased precision in predictions of axisymmetric anisotropy and rhombicity, the latter of which cannot be precisely evaluated within 2000 × τ theor for GB3. Thus, we encourage reporting of axial decompositions D x , D y , D z to ease comparability between experiment and simulation. Where protein disorder is absent, we observe close replication of MARTINI+EN D rot orientations versus CHARMM22*/TIP3p and experimental data. This work anticipates the ab initio prediction of NMR-relaxation by combining coarse-grained global motions with all-atom local motions.

Physics through the 1990s: Atomic, molecular and optical physics

NASA Technical Reports Server (NTRS)

1986-01-01

The volume presents a program of research initiatives in atomic, molecular, and optical physics. The current state of atomic, molecular, and optical physics in the US is examined with respect to demographics, education patterns, applications, and the US economy. Recommendations are made for each field, with discussions of their histories and the relevance of the research to government agencies. The section on atomic physics includes atomic theory, structure, and dynamics; accelerator-based atomic physics; and large facilities. The section on molecular physics includes spectroscopy, scattering theory and experiment, and the dynamics of chemical reactions. The section on optical physics discusses lasers, laser spectroscopy, and quantum optics and coherence. A section elucidates interfaces between the three fields and astrophysics, condensed matter physics, surface science, plasma physics, atmospheric physics, and nuclear physics. Another section shows applications of the three fields in ultra-precise measurements, fusion, national security, materials, medicine, and other topics.

Homology modeling, molecular docking and MD simulation studies to investigate role of cysteine protease from Xanthomonas campestris in degradation of Aβ peptide.

PubMed

Dhanavade, Maruti J; Jalkute, Chidambar B; Barage, Sagar H; Sonawane, Kailas D

2013-12-01

Cysteine protease is known to degrade amyloid beta peptide which is a causative agent of Alzheimer's disease. This cleavage mechanism has not been studied in detail at the atomic level. Hence, a three-dimensional structure of cysteine protease from Xanthomonas campestris was constructed by homology modeling using Geno3D, SWISS-MODEL, and MODELLER 9v7. All the predicted models were analyzed by PROCHECK and PROSA. Three-dimensional model of cysteine protease built by MODELLER 9v7 shows similarity with human cathepsin B crystal structure. This model was then used further for docking and simulation studies. The molecular docking study revealed that Cys17, His87, and Gln88 residues of cysteine protease form an active site pocket similar to human cathepsin B. Then the docked complex was refined by molecular dynamic simulation to confirm its stable behavior over the entire simulation period. The molecular docking and MD simulation studies showed that the sulfhydryl hydrogen atom of Cys17 of cysteine protease interacts with carboxylic oxygen of Lys16 of Aβ peptide indicating the cleavage site. Thus, the cysteine protease model from X. campestris having similarity with human cathepsin B crystal structure may be used as an alternate approach to cleave Aβ peptide a causative agent of Alzheimer's disease. © 2013 Elsevier Ltd. All rights reserved.

Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

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

Mansbach, Rachael A.; Ferguson, Andrew L.

Self-assembled aggregates of peptides containing aromatic groups possess optoelectronic properties that make them attractive targets for the fabrication of biocompatible electronics. Molecular-level understanding of how the microscopic peptide chemistry influences the properties of the aggregates is vital for rational peptide design. We construct a coarse-grained model of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp (DFAG-OPV3-GAFD) peptides containing OPV3 (distyrylbenzene) π-conjugated cores explicitly parameterized against all-atom calculations and perform molecular dynamics simulations of the self-assembly of hundreds of molecules over hundreds of nanoseconds. We observe a hierarchical assembly mechanism wherein ~2-8 peptides assemble into stacks with aligned aromatic cores that subsequently form elliptical aggregates and ultimately amore » branched network with a fractal dimensionality of ~1.5. The assembly dynamics are well described by a Smoluchowski coagulation process for which we extract rate constants from the molecular simulations to both furnish insight into the microscopic assembly kinetics and extrapolate our aggregation predictions to time and length scales beyond the reach of molecular simulation. Lastly, this study presents new molecular-level understanding of the morphology and dynamics of the spontaneous self-assembly of DFAG-OPV3-GAFD peptides and establishes a systematic protocol to develop coarse-grained models of optoelectronic peptides for the exploration and design of π-conjugated peptides with tunable optoelectronic properties.« less

Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

DOE PAGES

Mansbach, Rachael A.; Ferguson, Andrew L.

2017-02-10

Self-assembled aggregates of peptides containing aromatic groups possess optoelectronic properties that make them attractive targets for the fabrication of biocompatible electronics. Molecular-level understanding of how the microscopic peptide chemistry influences the properties of the aggregates is vital for rational peptide design. We construct a coarse-grained model of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp (DFAG-OPV3-GAFD) peptides containing OPV3 (distyrylbenzene) π-conjugated cores explicitly parameterized against all-atom calculations and perform molecular dynamics simulations of the self-assembly of hundreds of molecules over hundreds of nanoseconds. We observe a hierarchical assembly mechanism wherein ~2-8 peptides assemble into stacks with aligned aromatic cores that subsequently form elliptical aggregates and ultimately amore » branched network with a fractal dimensionality of ~1.5. The assembly dynamics are well described by a Smoluchowski coagulation process for which we extract rate constants from the molecular simulations to both furnish insight into the microscopic assembly kinetics and extrapolate our aggregation predictions to time and length scales beyond the reach of molecular simulation. Lastly, this study presents new molecular-level understanding of the morphology and dynamics of the spontaneous self-assembly of DFAG-OPV3-GAFD peptides and establishes a systematic protocol to develop coarse-grained models of optoelectronic peptides for the exploration and design of π-conjugated peptides with tunable optoelectronic properties.« less

Watching proteins function with picosecond X-ray crystallography and molecular dynamics simulations.

NASA Astrophysics Data System (ADS)

Anfinrud, Philip

2006-03-01

Time-resolved electron density maps of myoglobin, a ligand-binding heme protein, have been stitched together into movies that unveil with < 2-å spatial resolution and 150-ps time-resolution the correlated protein motions that accompany and/or mediate ligand migration within the hydrophobic interior of a protein. A joint analysis of all-atom molecular dynamics (MD) calculations and picosecond time-resolved X-ray structures provides single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin following ligand dissociation reproduce the direction, amplitude, and timescales of crystallographically-determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories, which identify and structurally characterize a conformational switch that directs dissociated ligands to one of two nearby protein cavities. This unique combination of simulation and experiment unveils functional protein motions and illustrates at an atomic level relationships among protein structure, dynamics, and function. In collaboration with Friedrich Schotte and Gerhard Hummer, NIH.

Multiscale Molecular Dynamics Simulations of Beta-Amyloid Interactions with Neurons

NASA Astrophysics Data System (ADS)

Qiu, Liming; Vaughn, Mark; Cheng, Kelvin

2012-10-01

Early events of human beta-amyloid protein interactions with cholesterol-containing membranes are critical to understanding the pathogenesis of Alzheimer's disease (AD) and to exploring new therapeutic interventions of AD. Atomistic molecular dynamics (AMD) simulations have been extensively used to study the protein-lipid interaction at high atomic resolutions. However, traditional MD simulations are not efficient in sampling the phase space of complex lipid/protein systems with rugged free energy landscapes. Meanwhile, coarse-grained MD (CGD) simulations are efficient in the phase space sampling but suffered from low spatial resolutions and from the fact that the energy landscapes are not identical to those of the AMD. Here, a multiscale approach was employed to simulate the protein-lipid interactions of beta-amyloid upon its release from proteolysis residing in the neuronal membranes. We utilized a forward (AMD to CGD) and reverse (CGD-AMD) strategy to explore new transmembrane and surface protein configuration and evaluate the stabilization mechanisms by measuring the residue-specific protein-lipid or protein conformations. The detailed molecular interactions revealed in this multiscale MD approach will provide new insights into understanding the early molecular events leading to the pathogenesis of AD.

Structural properties of CuAu nanoparticles with different type. Molecular dynamic simulations

NASA Astrophysics Data System (ADS)

Chepkasov, I. V.; Baidyshev, V. S.; Baev, A. Y.

2018-05-01

The paper is devoted to the thermal stability of a CuAu nanoparticles structure (D=5 nm) of various type (binary alloy, core-shell, "Janus" type) and of various percentage of copper atoms. The simulation was carried out with molecular dynamics, using the embedded atom potential. The authors defined the most preferable structural options from the standpoint of thermodynamics, as well as studied in detail the influence of different temperatures on the structural stability of CuAu nanoparticles.

Atomic and molecular adsorption on Au(111)

DOE PAGES

Santiago-Rodriguez, Yohaselly; Herron, Jeffrey A.; Curet-Arana, Maria C.; ...

2014-05-02

Periodic self-consistent density functional theory (DFT-GGA) calculations were used to study the adsorption of several atomic species, molecular species and molecular fragments on the Au(111) surface with a coverage of 1/4 monolayer (ML). Binding geometries, binding energies, and diffusion barriers were calculated for 27 species. Furthermore, we calculated the surface deformation energy associated with the binding events. The binding strength for all the analyzed species can be ordered as follows: NH 3 < NO < CO < CH 3 < HCO < NH 2 < COOH < OH < HCOO < CNH 2 < H < N < NH atomic species preferred to bind at the three-fold fcc site, no tendency was observed in site preference for the molecular species and fragments. The intramolecular and adsorbate-surface vibrational frequencies were calculated for all the adsorbates on their most energetically stable adsorption site. Most of the theoretical binding energies and frequencies agreed with experimental values reported in the literature. In general, the values obtained with the PW91 functional are more accurate than RPBE in reproducing these experimental binding energies. The energies of the adsorbed species were used to calculate the thermochemical potential energy surfaces for decomposition of CO, NO, N 2, NH 3 and CH 4, oxidation of CO, and hydrogenation of CO, CO 2 and NO, giving insight into the thermochemistry of these reactions on gold nanoparticles. As a result, these potential energy surfaces demonstrated that: the decomposition of species is not energetically favorable on Au(111); the desorption of NH 3, NO and CO are more favorable than their decomposition; the oxidation of CO and hydrogenation of CO and NO on Au(111) to form HCO and HNO, respectively, are also thermodynamically favorable.« less

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.

Classical molecular dynamics simulations for non-equilibrium correlated plasmas

NASA Astrophysics Data System (ADS)

Ferri, S.; Calisti, A.; Talin, B.

2017-03-01

A classical molecular dynamics model was recently extended to simulate neutral multi-component plasmas where various charge states of the same atom and electrons coexist. It is used to investigate the plasma effects on the ion charge and on the ionization potential in dense plasmas. Different simulated statistical properties will show that the concept of isolated particles is lost in such correlated plasmas. The charge equilibration is discussed for a carbon plasma at solid density and investigation on the charge distribution and on the ionization potential depression (IPD) for aluminum plasmas is discussed with reference to existing experiments.

All-Atom Molecular-Level Computational Analyses of Polyurea/Fused-Silica Interfacial Decohesion Caused by Impinging Tensile Stress-Waves

DTIC Science & Technology

2014-01-01

glass, the polyhedron -center atoms are all silicon and each silicon atom is surrounded by four oxygen atoms (while each oxygen atom is connected to...of non-bridging (connected to only a single network forming cation) oxygen atoms per network polyhedron and takes on a zero value in the case of...network polyhedron and takes on a value of 4.0 in the case of fused silica. In addition to the three parameters mentioned above, the “seemingly

Determination of mechanical behavior of nanoscale materials using molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Heo, Seongjun

It is important to understand the mechanical properties of nanometer-scale materials for use in such applications as microelectromechanical systems (MEMS) and nanoelectromechanical systems (NEMS). These properties are difficult to measure directly using experimental methods due to their small sizes. Computational simulations provide important insights that complement experimental data and lead to improved understanding of the mechanical properties of nanometer-scale systems. Molecular dynamics (MD) simulations, which are used to investigate the properties of materials at the atomic scale, is used in my research to determine (1) best thermostat managing way for acceptable mechanical behavior of nanoscale systems; (2) filling effect on the bending and compressive properties of carbon nanotubes (CNTs); (3) vibrational behavior of bridged and cantilevered CNT bombarded by external fluid atoms; (4) frictional behavior of filled CNT bundles and the effect of external molecules on friction; (5) effect of sliding orientations on the tribological properties of polyethylene (PE). In all the simulations the reactive empirical bond-order (REBO) potential combined with the Lennard Jones potential is applied to control inter-atomic interactions. During the MD simulations, thermostats are used to maintain the system temperature at a constant value. Tests indicate that the simulations describe the mechanical behavior of CNTs differently depending on the type of thermostat used, and the relative fraction of the system to which the thermostat is applied. The results indicate that Langevin and velocity rescaling thermostats are more reliable for temperature control than the Nose-Hoover thermostat. In examining CNT bending and compression, the simulations predict filled CNTs are more resistant to external bending and compressive forces than hollow CNTs. The mechanical properties deteriorate with increases in temperature and number of CNT wall defects. MD simulations of the vibrational

Advancing Efficient All-Electron Electronic Structure Methods Based on Numeric Atom-Centered Orbitals for Energy Related Materials

NASA Astrophysics Data System (ADS)

Blum, Volker

This talk describes recent advances of a general, efficient, accurate all-electron electronic theory approach based on numeric atom-centered orbitals; emphasis is placed on developments related to materials for energy conversion and their discovery. For total energies and electron band structures, we show that the overall accuracy is on par with the best benchmark quality codes for materials, but scalable to large system sizes (1,000s of atoms) and amenable to both periodic and non-periodic simulations. A recent localized resolution-of-identity approach for the Coulomb operator enables O (N) hybrid functional based descriptions of the electronic structure of non-periodic and periodic systems, shown for supercell sizes up to 1,000 atoms; the same approach yields accurate results for many-body perturbation theory as well. For molecular systems, we also show how many-body perturbation theory for charged and neutral quasiparticle excitation energies can be efficiently yet accurately applied using basis sets of computationally manageable size. Finally, the talk highlights applications to the electronic structure of hybrid organic-inorganic perovskite materials, as well as to graphene-based substrates for possible future transition metal compound based electrocatalyst materials. All methods described here are part of the FHI-aims code. VB gratefully acknowledges contributions by numerous collaborators at Duke University, Fritz Haber Institute Berlin, TU Munich, USTC Hefei, Aalto University, and many others around the globe.

Molecular Dynamic Simulation Insights into the Normal State and Restoration of p53 Function

PubMed Central

Fu, Ting; Min, Hanyi; Xu, Yong; Chen, Jianzhong; Li, Guohui

2012-01-01

As a tumor suppressor protein, p53 plays a crucial role in the cell cycle and in cancer prevention. Almost 50 percent of all human malignant tumors are closely related to a deletion or mutation in p53. The activity of p53 is inhibited by over-active celluar antagonists, especially by the over-expression of the negative regulators MDM2 and MDMX. Protein-protein interactions, or post-translational modifications of the C-terminal negative regulatory domain of p53, also regulate its tumor suppressor activity. Restoration of p53 function through peptide and small molecular inhibitors has become a promising strategy for novel anti-cancer drug design and development. Molecular dynamics simulations have been extensively applied to investigate the conformation changes of p53 induced by protein-protein interactions and protein-ligand interactions, including peptide and small molecular inhibitors. This review focuses on the latest MD simulation research, to provide an overview of the current understanding of interactions between p53 and its partners at an atomic level. PMID:22949826

A real-time all-atom structural search engine for proteins.

PubMed

Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F

2014-07-01

Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new "designability"-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license).

Simulated quantum computation of molecular energies.

PubMed

Aspuru-Guzik, Alán; Dutoi, Anthony D; Love, Peter J; Head-Gordon, Martin

2005-09-09

The calculation time for the energy of atoms and molecules scales exponentially with system size on a classical computer but polynomially using quantum algorithms. We demonstrate that such algorithms can be applied to problems of chemical interest using modest numbers of quantum bits. Calculations of the water and lithium hydride molecular ground-state energies have been carried out on a quantum computer simulator using a recursive phase-estimation algorithm. The recursive algorithm reduces the number of quantum bits required for the readout register from about 20 to 4. Mappings of the molecular wave function to the quantum bits are described. An adiabatic method for the preparation of a good approximate ground-state wave function is described and demonstrated for a stretched hydrogen molecule. The number of quantum bits required scales linearly with the number of basis functions, and the number of gates required grows polynomially with the number of quantum bits.

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.

Continuum description of ionic and dielectric shielding for molecular-dynamics simulations of proteins in solution

NASA Astrophysics Data System (ADS)

Egwolf, Bernhard; Tavan, Paul

2004-01-01

We extend our continuum description of solvent dielectrics in molecular-dynamics (MD) simulations [B. Egwolf and P. Tavan, J. Chem. Phys. 118, 2039 (2003)], which has provided an efficient and accurate solution of the Poisson equation, to ionic solvents as described by the linearized Poisson-Boltzmann (LPB) equation. We start with the formulation of a general theory for the electrostatics of an arbitrarily shaped molecular system, which consists of partially charged atoms and is embedded in a LPB continuum. This theory represents the reaction field induced by the continuum in terms of charge and dipole densities localized within the molecular system. Because these densities cannot be calculated analytically for systems of arbitrary shape, we introduce an atom-based discretization and a set of carefully designed approximations. This allows us to represent the densities by charges and dipoles located at the atoms. Coupled systems of linear equations determine these multipoles and can be rapidly solved by iteration during a MD simulation. The multipoles yield the reaction field forces and energies. Finally, we scrutinize the quality of our approach by comparisons with an analytical solution restricted to perfectly spherical systems and with results of a finite difference method.

Highly Efficient Computation of the Basal kon using Direct Simulation of Protein-Protein Association with Flexible Molecular Models.

PubMed

Saglam, Ali S; Chong, Lillian T

2016-01-14

An essential baseline for determining the extent to which electrostatic interactions enhance the kinetics of protein-protein association is the "basal" kon, which is the rate constant for association in the absence of electrostatic interactions. However, since such association events are beyond the milliseconds time scale, it has not been practical to compute the basal kon by directly simulating the association with flexible models. Here, we computed the basal kon for barnase and barstar, two of the most rapidly associating proteins, using highly efficient, flexible molecular simulations. These simulations involved (a) pseudoatomic protein models that reproduce the molecular shapes, electrostatic, and diffusion properties of all-atom models, and (b) application of the weighted ensemble path sampling strategy, which enhanced the efficiency of generating association events by >130-fold. We also examined the extent to which the computed basal kon is affected by inclusion of intermolecular hydrodynamic interactions in the simulations.

Molecular electronics: insight from first-principles transport simulations.

PubMed

Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads

2010-01-01

Conduction properties of nanoscale contacts can be studied using first-principles simulations. Such calculations give insight into details behind the conductance that is not readily available in experiments. For example, we may learn how the bonding conditions of a molecule to the electrodes affect the electronic transport. Here we describe key computational ingredients and discuss these in relation to simulations for scanning tunneling microscopy (STM) experiments with C60 molecules where the experimental geometry is well characterized. We then show how molecular dynamics simulations may be combined with transport calculations to study more irregular situations, such as the evolution of a nanoscale contact with the mechanically controllable break-junction technique. Finally we discuss calculations of inelastic electron tunnelling spectroscopy as a characterization technique that reveals information about the atomic arrangement and transport channels.

Statistical study of defects caused by primary knock-on atoms in fcc Cu and bcc W using molecular dynamics

NASA Astrophysics Data System (ADS)

Warrier, M.; Bhardwaj, U.; Hemani, H.; Schneider, R.; Mutzke, A.; Valsakumar, M. C.

2015-12-01

We report on molecular Dynamics (MD) simulations carried out in fcc Cu and bcc W using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code to study (i) the statistical variations in the number of interstitials and vacancies produced by energetic primary knock-on atoms (PKA) (0.1-5 keV) directed in random directions and (ii) the in-cascade cluster size distributions. It is seen that around 60-80 random directions have to be explored for the average number of displaced atoms to become steady in the case of fcc Cu, whereas for bcc W around 50-60 random directions need to be explored. The number of Frenkel pairs produced in the MD simulations are compared with that from the Binary Collision Approximation Monte Carlo (BCA-MC) code SDTRIM-SP and the results from the NRT model. It is seen that a proper choice of the damage energy, i.e. the energy required to create a stable interstitial, is essential for the BCA-MC results to match the MD results. On the computational front it is seen that in-situ processing saves the need to input/output (I/O) atomic position data of several tera-bytes when exploring a large number of random directions and there is no difference in run-time because the extra run-time in processing data is offset by the time saved in I/O.

Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample

NASA Technical Reports Server (NTRS)

Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)

2001-01-01

Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.

Classical Molecular Dynamics Simulation of Nuclear Fuel

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

Devanathan, Ram; Krack, Matthias; Bertolus, Marjorie

2015-10-10

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

A low Earth orbit molecular beam space simulation facility

NASA Technical Reports Server (NTRS)

Cross, J. B.

1984-01-01

A brief synopsis of the low Earth orbit (LEO) satellite environment is presented including neutral and ionic species. Two ground based atomic and molecular beam instruments are described which are capable of simulating the interaction of spacecraft surfaces with the LEO environment and detecting the results of these interactions. The first detects mass spectrometrically low level fluxes of reactively and nonreactively surface scattered species as a function of scattering angle and velocity while the second ultrahigh velocity (UHV) molecular beam, laser induced fluorescence apparatus is capable of measuring chemiluminescence produced by either gas phase or gas-surface interactions. A number of proposed experiments are described.

High Fidelity Simulation of Atomization in Diesel Engine Sprays

DTIC Science & Technology

2015-09-01

ARL-RP-0555 ● SEP 2015 US Army Research Laboratory High Fidelity Simulation of Atomization in Diesel Engine Sprays by L Bravo...ARL-RP-0555 ● SEP 2015 US Army Research Laboratory High Fidelity Simulation of Atomization in Diesel Engine Sprays by L...Simulation of Atomization in Diesel Engine Sprays 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) L Bravo, CB Ivey, D

Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences.

PubMed

Best, Robert B; Mittal, Jeetain

2011-04-01

Although it is now possible to fold peptides and miniproteins in molecular dynamics simulations, it is well appreciated that force fields are not all transferable to different proteins. Here, we investigate the influence of the protein force field and the solvent model on the folding energy landscape of a prototypical two-state folder, the GB1 hairpin. We use extensive replica-exchange molecular dynamics simulations to characterize the free-energy surface as a function of temperature. Most of these force fields appear similar at a global level, giving a fraction folded at 300 K between 0.2 and 0.8 in all cases, which is a difference in stability of 2.8 kT, and are generally consistent with experimental data at this temperature. The most significant differences appear in the unfolded state, where there are different residual secondary structures which are populated, and the overall dimensions of the unfolded states, which in most of the force fields are too collapsed relative to experimental Förster Resonance Energy Transfer (FRET) data.

Molecular Simulations in Astrobiology

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.; Schweighofer, Karl; Chipot, Christophe; New, Michael H.; Vincenzi, Donald L. (Technical Monitor)

2001-01-01

One of the main goals of astrobiology is to understand the origin of cellular life. In the absence of any record of the earliest ancestors of contemporary cells, protocells, the most direct way to test our understanding of their characteristics is to construct laboratory models of protocells. Such efforts, currently underway in the NASA Astrobiology Program, are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs of molecules that are capable of performing protocellular functions. Many of these functions, such as importing nutrients, capturing and storing energy, and responding to changes in the environment, are carried out by proteins bound to membranes. We use computer simulations to address the following, questions about these proteins: (1) How do small proteins (peptides) organize themselves into ordered structures at water-membrane interfaces and insert into membranes? (2) How do peptides aggregate to form membrane-spannin(y structures (e.g., channels)? (3) By what mechanisms do such aggregates perform their functions? The simulations are performed using the molecular dynamics (MD) method. In this method, Newton's equations of motion for each atom in the system are solved iteratively. At each time step, the forces exerted on each atom by the remaining atoms are evaluated by dividing them into two parts. Short-range forces are calculated directly in real space while long-range forces are evaluated in reciprocal space, usually using a particle-mesh algorithm which is of order O(NlnN). Currently, a time step of 2 femtoseconds is typically used, thereby making studies of problems occurring on multi-nanosecond time scales (10(exp 6) - 10(exp 8) time steps) accessible. To address a broader range of problems, simulations need to be extended by three orders of magnitude. Such an extension requires both algorithmic improvements and codes scalable to a large number of parallel

Molecular dynamic simulation for nanometric cutting of single-crystal face-centered cubic metals.

PubMed

Huang, Yanhua; Zong, Wenjun

2014-01-01

In this work, molecular dynamics simulations are performed to investigate the influence of material properties on the nanometric cutting of single crystal copper and aluminum with a diamond cutting tool. The atomic interactions in the two metallic materials are modeled by two sets of embedded atom method (EAM) potential parameters. Simulation results show that although the plastic deformation of the two materials is achieved by dislocation activities, the deformation behavior and related physical phenomena, such as the machining forces, machined surface quality, and chip morphology, are significantly different for different materials. Furthermore, the influence of material properties on the nanometric cutting has a strong dependence on the operating temperature.

Effective Particle Size From Molecular Dynamics Simulations in Fluids

DOE PAGES

Ju, Jianwei; Welch, Paul Michael Jr.; Rasmussen, Kim Orskov; ...

2017-12-08

Here, we report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. Thismore » procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks–Chandler–Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ~0.75σ, where σ defines the length scale of the force interaction (the LJ diameter). The effective “hydrodynamic” radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ, but agree with a value developed from the atomistic analysis of the viscosity of such systems.« less

Effective particle size from molecular dynamics simulations in fluids

NASA Astrophysics Data System (ADS)

Ju, Jianwei; Welch, Paul M.; Rasmussen, Kim Ø.; Redondo, Antonio; Vorobieff, Peter; Kober, Edward M.

2018-04-01

We report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. This procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks-Chandler-Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ˜ 0.75σ , where σ defines the length scale of the force interaction (the LJ diameter). The effective "hydrodynamic" radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ , but agree with a value developed from the atomistic analysis of the viscosity of such systems.

Effective Particle Size From Molecular Dynamics Simulations in Fluids

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

Ju, Jianwei; Welch, Paul Michael Jr.; Rasmussen, Kim Orskov

Here, we report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. Thismore » procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks–Chandler–Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ~0.75σ, where σ defines the length scale of the force interaction (the LJ diameter). The effective “hydrodynamic” radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ, but agree with a value developed from the atomistic analysis of the viscosity of such systems.« less

Effective particle size from molecular dynamics simulations in fluids

NASA Astrophysics Data System (ADS)

Ju, Jianwei; Welch, Paul M.; Rasmussen, Kim Ø.; Redondo, Antonio; Vorobieff, Peter; Kober, Edward M.

2017-12-01

We report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. This procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks-Chandler-Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ˜ 0.75σ , where σ defines the length scale of the force interaction (the LJ diameter). The effective "hydrodynamic" radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ , but agree with a value developed from the atomistic analysis of the viscosity of such systems.

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.

Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

PubMed Central

2012-01-01

Implicit solvation is a mean force approach to model solvent forces acting on a solute molecule. It is frequently used in molecular simulations to reduce the computational cost of solvent treatment. In the first instance, the free energy of solvation and the associated solvent–solute forces can be approximated by a function of the solvent-accessible surface area (SASA) of the solute and differentiated by an atom–specific solvation parameter σiSASA. A procedure for the determination of values for the σiSASA parameters through matching of explicit and implicit solvation forces is proposed. Using the results of Molecular Dynamics simulations of 188 topologically diverse protein structures in water and in implicit solvent, values for the σiSASA parameters for atom types i of the standard amino acids in the GROMOS force field have been determined. A simplified representation based on groups of atom types σgSASA was obtained via partitioning of the atom–type σiSASA distributions by dynamic programming. Three groups of atom types with well separated parameter ranges were obtained, and their performance in implicit versus explicit simulations was assessed. The solvent forces are available at http://mathbio.nimr.mrc.ac.uk/wiki/Solvent_Forces. PMID:23180979

Molecular dynamics simulations of structural transformation of perfluorooctane sulfonate (PFOS) at water/rutile interfaces.

PubMed

He, Guangzhi; Zhang, Meiyi; Zhou, Qin; Pan, Gang

2015-09-01

Concentration and salinity conditions are the dominant environmental factors affecting the behavior of perfluorinated compounds (PFCs) on the surfaces of a variety of solid matrices (suspended particles, sediments, and natural minerals). However, the mechanism has not yet been examined at molecular scales. Here, the structural transformation of perfluorooctane sulfonate (PFOS) at water/rutile interfaces induced by changes of the concentration level of PFOS and salt condition was investigated using molecular dynamics (MD) simulations. At low and intermediate concentrations all PFOS molecules directly interacted with the rutile (110) surface mainly by the sulfonate headgroups through electrostatic attraction, yielding a typical monolayer structure. As the concentration of PFOS increased, the molecules aggregated in a complex multi-layered structure, where an irregular assembling configuration was adsorbed on the monolayer structure by the van der Waals interactions between the perfluoroalkyl chains. When adding CaCl2 to the system, the multi-layered structure changed to a monolayer again, indicating that the addition of CaCl2 enhanced the critical concentration value to yield PFOS multilayer assemblies. The divalent Ca(2+) substituted for monovalent K(+) as the bridging counterion in PFOS adsorption. MD simulation may trigger wide applications in study of perfluorinated compounds (PFCs) from atomic/molecular scale. Copyright © 2015 Elsevier Ltd. All rights reserved.

Towards the simulation of molecular collisions with a superconducting quantum computer

NASA Astrophysics Data System (ADS)

Geller, Michael

2013-05-01

I will discuss the prospects for the use of large-scale, error-corrected quantum computers to simulate complex quantum dynamics such as molecular collisions. This will likely require millions qubits. I will also discuss an alternative approach [M. R. Geller et al., arXiv:1210.5260] that is ideally suited for today's superconducting circuits, which uses the single-excitation subspace (SES) of a system of n tunably coupled qubits. The SES method allows many operations in the unitary group SU(n) to be implemented in a single step, bypassing the need for elementary gates, thereby making large computations possible without error correction. The method enables universal quantum simulation, including simulation of the time-dependent Schrodinger equation, and we argue that a 1000-qubit SES processor should be capable of achieving quantum speedup relative to a petaflop supercomputer. We speculate on the utility and practicality of such a simulator for atomic and molecular collision physics. Work supported by the US National Science Foundation CDI program.

Nanoscale deicing by molecular dynamics simulation.

PubMed

Xiao, Senbo; He, Jianying; Zhang, Zhiliang

2016-08-14

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

Comparing selected morphological models of hydrated Nafion using large scale molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Knox, Craig K.

Experimental elucidation of the nanoscale structure of hydrated Nafion, the most popular polymer electrolyte or proton exchange membrane (PEM) to date, and its influence on macroscopic proton conductance is particularly challenging. While it is generally agreed that hydrated Nafion is organized into distinct hydrophilic domains or clusters within a hydrophobic matrix, the geometry and length scale of these domains continues to be debated. For example, at least half a dozen different domain shapes, ranging from spheres to cylinders, have been proposed based on experimental SAXS and SANS studies. Since the characteristic length scale of these domains is believed to be ˜2 to 5 nm, very large molecular dynamics (MD) simulations are needed to accurately probe the structure and morphology of these domains, especially their connectivity and percolation phenomena at varying water content. Using classical, all-atom MD with explicit hydronium ions, simulations have been performed to study the first-ever hydrated Nafion systems that are large enough (~2 million atoms in a ˜30 nm cell) to directly observe several hydrophilic domains at the molecular level. These systems consisted of six of the most significant and relevant morphological models of Nafion to-date: (1) the cluster-channel model of Gierke, (2) the parallel cylinder model of Schmidt-Rohr, (3) the local-order model of Dreyfus, (4) the lamellar model of Litt, (5) the rod network model of Kreuer, and (6) a 'random' model, commonly used in previous simulations, that does not directly assume any particular geometry, distribution, or morphology. These simulations revealed fast intercluster bridge formation and network percolation in all of the models. Sulfonates were found inside these bridges and played a significant role in percolation. Sulfonates also strongly aggregated around and inside clusters. Cluster surfaces were analyzed to study the hydrophilic-hydrophobic interface. Interfacial area and cluster volume

Atomistic Molecular Dynamics Simulations of the Electrical Double

NASA Astrophysics Data System (ADS)

Li, Zifeng; Milner, Scott; Fichthorn, Kristen

2015-03-01

The electrical double layer (EDL) near the polymer/water interface plays a key role in the colloidal stability of latex paint. To elucidate the structure of the EDL at the molecular level, we conducted an all-atom molecular dynamics simulations. We studied two representative surface charge groups in latex, the ionic surfactant sodium dodecyl sulfate (SDS) and the grafted short polyelectrolyte charged by dissociated methyl methacrylic acid (MAA) monomers. Our results confirm that the Poisson-Boltzmann theory works well outside the Stern layer. Our calculated electrostatic potential at the Outer Helmholtz Plane (OHP) is close to the zeta potential measured experimentally, which suggests that the potential at the OHP is a good estimate of the zeta potential. We found that the position of the OHP for the MAA polyelectrolyte system extends much further into the aqueous phase than that in the SDS system, resulting in a Stern layer that is twice as thick. This model will allow for future investigations of the interactions of the surface with different surfactants and rheology modifiers, which may serve as a guide to tune the rheology of latex formulations. We thank Dow Chemical Company for financial support.

Improved Simulations of Astrophysical Plasmas: Computation of New Atomic Data

NASA Technical Reports Server (NTRS)

Gorczyca, Thomas W.; Korista, Kirk T.

2005-01-01

Our research program is designed to carry out state-of-the-art atomic physics calculations crucial to advancing our understanding of fundamental astrophysical problems. We redress the present inadequacies in the atomic data base along two important areas: dielectronic recombination and inner-shell photoionization and multiple electron ejection/Auger fluorescence therefrom. All of these data are disseminated to the astrophysical community in the proper format for implementation in spectral simulation code.

Elucidation of atomic scale mechanisms for polytetrafluoroethylene tribology using molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Barry, Peter R.

Polytetrafluoroethylene (PTFE) is a polymer that has been widely exploited commercially as a result of its low friction, 'non-stick' properties. The polymer has found usage as 'non-stick,' chemically resistant coatings for bearings, valves, rollers and pipe linings with applications in industries ranging from food and chemical processing to construction, automotive and aerospace. The major drawback of PTFE in low friction applications involves its excessive wear rate. For decades, scientists and engineers have sought to improve the polymer's wear resistance while maintaining its low sliding friction by reinforcing the polymer matrix with a host of filler materials ranging from fibril to particulate. In this study, a different approach is taken in which the atomic scale phenomena between two crystalline PTFE surfaces in sliding contact are examined. The goal is to obtain atomic-level insights into PTFE's low friction and high wear rate to aid in the designing of effective polymer based tribological composites for extreme condition applications. To accomplish this, several tribological conditions were varied. These included sliding direction of the two polymer surfaces with respect to their chain alignment, sliding velocity, degree of crystalline phase rigidity, interfacial contact pressure, sample temperature and the presence of fluorocarbon fluids between the two crystalline PTFE surfaces. From these studies, it was found that crystalline PTFE-PTFE sliding demonstrates friction anisotropy. Low friction and molecular wear was observed when sliding in the direction of the chain alignment with high friction and wear behavior dominating when sliding in a direction perpendicular to the chain alignment. For the range of cross-link density (average linear density of 6.2 to 11.1 A) and sliding rate (5 m/s to 20 m/s) explored, a significant change in friction behavior or wear mechanisms was not observed. Under conditions of increased normal load or low temperature however

Molecular dynamics simulations on PGLa using NMR orientational constraints.

PubMed

Sternberg, Ulrich; Witter, Raiker

2015-11-01

NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.

NARROW Na AND K ABSORPTION LINES TOWARD T TAURI STARS: TRACING THE ATOMIC ENVELOPE OF MOLECULAR CLOUDS

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

Pascucci, I.; Simon, M. N.; Edwards, S.

2015-11-20

We present a detailed analysis of narrow Na i and K i absorption resonance lines toward nearly 40 T Tauri stars in Taurus with the goal of clarifying their origin. The Na i λ5889.95 line is detected toward all but one source, while the weaker K i λ7698.96 line is detected in about two-thirds of the sample. The similarity in their peak centroids and the significant positive correlation between their equivalent widths demonstrate that these transitions trace the same atomic gas. The absorption lines are present toward both disk and diskless young stellar objects, which excludes cold gas within themore » circumstellar disk as the absorbing material. A comparison of Na i and CO detections and peak centroids demonstrates that the atomic gas and molecular gas are not co-located, the atomic gas being more extended than the molecular gas. The width of the atomic lines corroborates this finding and points to atomic gas about an order of magnitude warmer than the molecular gas. The distribution of Na i radial velocities shows a clear spatial gradient along the length of the Taurus molecular cloud filaments. This suggests that absorption is associated with the Taurus molecular cloud. Assuming that the gradient is due to cloud rotation, the rotation of the atomic gas is consistent with differential galactic rotation, whereas the rotation of the molecular gas, although with the same rotation axis, is retrograde. Our analysis shows that narrow Na i and K i absorption resonance lines are useful tracers of the atomic envelope of molecular clouds. In line with recent findings from giant molecular clouds, our results demonstrate that the velocity fields of the atomic and molecular gas are misaligned. The angular momentum of a molecular cloud is not simply inherited from the rotating Galactic disk from which it formed but may be redistributed by cloud–cloud interactions.« less

Multimillion Atom Reactive Simulations of Nanostructured Energetic Materials

DTIC Science & Technology

2007-08-01

code) 2007 Reprint Aug 2006-Aug 2007 Multimillion Atom Reactive Simulations of Nanostructured Energetic Materials W911NF-04-1-0178 sub 2781-USC-DOA...Priya Vashishta 213 821 2663 Reset Multimillion Atom Reactive Simulations of Nanostructured Energetic Materials Priya Vashishta,∗ Rajiv K. Kalia...function of the particle velocity that drives the shock [18]. The MD and experimental data agree very well. Furthermore, the simulation shows a sudden

Interactions between Ether Phospholipids and Cholesterol as Determined by Scattering and Molecular Dynamics Simulations

PubMed Central

Pan, Jianjun; Cheng, Xiaolin; Heberle, Frederick A.; Mostofian, Barmak; Kučerka, Norbert; Drazba, Paul; Katsaras, John

2012-01-01

Cholesterol and ether lipids are ubiquitous in mammalian cell membranes, and their interactions are crucial in ether lipid mediated cholesterol trafficking. We report on cholesterol’s molecular interactions with ether lipids as determined using a combination of small-angle neutron and X-ray scattering, and all-atom molecular dynamics (MD) simulations. A scattering density profile model for an ether lipid bilayer was developed using MD simulations, which was then used to simultaneously fit the different experimental scattering data. From the analysis of the data the various bilayer structural parameters were obtained. Surface area constrained MD simulations were also performed to reproduce the experimental data. This iterative analysis approach resulted in good agreement between the experimental and simulated form factors. The molecular interactions taking place between cholesterol and ether lipids were then determined from the validated MD simulations. We found that in ether membranes, cholesterol primarily hydrogen bonds with the lipid headgroup phosphate oxygen, while in their ester membrane counterparts, cholesterol hydrogen bonds with the backbone ester carbonyls. This different mode of interaction between ether lipids and cholesterol induces cholesterol to reside closer to the bilayer surface, dehydrating the headgroup’s phosphate moiety. Moreover, the three-dimensional lipid chain spatial density distribution around cholesterol indicates anisotropic chain packing, causing cholesterol to tilt. These insights lend a better understanding of ether lipid mediated cholesterol trafficking and the roles that the different lipid species have in determining the structural and dynamical properties of membrane associated biomolecules. PMID:23199292

Atomic and molecular adsorption on Fe(110)

DOE PAGES

Xu, Lang; Kirvassilis, Demetrios; Bai, Yunhai; ...

2017-09-12

Iron is the principal catalyst for the ammonia synthesis process and the Fischer–Tropsch process, as well as many other heterogeneously catalyzed reactions. It is thus of fundamental importance to understand the interactions between the iron surface and various reaction intermediates. Here in this paper, we present a systematic study of atomic and molecular adsorption behavior over Fe(110) using periodic, self-consistent density functional theory (DFT-GGA) calculations. The preferred binding sites, binding energies, and the corresponding surface deformation energies of five atomic species (H, C, N, O, and S), six molecular species (NH 3, CH 4, N 2, CO, HCN, and NO),more » and eleven molecular fragments (CH, CH 2, CH 3, NH, NH 2, OH, CN, COH, HCO, NOH, and HNO) were determined on the Fe(110) surface at a coverage of 0.25 monolayer. The binding strengths calculated using the PW91 functional decreased in the following order: C> CH > N > O > S > NH > COH > CN > CH2 > NOH > OH > HNO > HCO > NH2 > H > NO > HCN > CH 3 > CO > N 2 > NH 3. No stable binding structures were observed for CH 4. The estimated diffusion barriers and pathways, as well as the adsorbate-surface and intramolecular vibrational modes of all the adsorbates at their preferred binding sites, were identified. Using the calculated adsorption energetics, we constructed the potential energy surfaces for a few surface reactions including the decomposition of methane, ammonia, dinitrogen, carbon monoxide, and nitric oxide. These potential energy surfaces provide valuable insight into the ability of Fe(110) to catalyze common elementary steps.« less

How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?

PubMed

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

2017-05-01

We provide a critical assessment of explicit-solvent atomistic molecular dynamics (MD) simulations of RNA and protein/RNA complexes, written primarily for non-specialists with an emphasis to explain the limitations of MD. MD simulations can be likened to hypothetical single-molecule experiments starting from single atomistic conformations and investigating genuine thermal sampling of the biomolecules. The main advantage of MD is the unlimited temporal and spatial resolution of positions of all atoms in the simulated systems. Fundamental limitations are the short physical time-scale of simulations, which can be partially alleviated by enhanced-sampling techniques, and the highly approximate atomistic force fields describing the simulated molecules. The applicability and present limitations of MD are demonstrated on studies of tetranucleotides, tetraloops, ribozymes, riboswitches and protein/RNA complexes. Wisely applied simulations respecting the approximations of the model can successfully complement structural and biochemical experiments. WIREs RNA 2017, 8:e1405. doi: 10.1002/wrna.1405 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.

A Real-Time All-Atom Structural Search Engine for Proteins

PubMed Central

Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F.

2014-01-01

Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designability”-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license). PMID:25079944

Molecular dynamics simulations and photoluminescence measurements of annealed ZnO surfaces

NASA Astrophysics Data System (ADS)

Min, Tjun Kit; Yoon, Tiem Leong; Ling, Chuo Ann; Mahmud, Shahrom; Lim, Thong Leng; Saw, Kim Guan

2017-06-01

The effect of thermal annealing on wurtzite ZnO, terminated by two surfaces, (000 1 bar) (which is oxygen-terminated) and (0 0 0 1) (which is Zn-terminated), is investigated via molecular dynamics simulation using reactive force field (ReaxFF). As a result of annealing at a threshold temperature range of 700 K atoms begin to sublimate from the (000 1 bar) surface, while no atom leaves the (0 0 0 1) surface. The ratio of oxygen leaving the surface increases with temperature T (for T ≥Tt). The relative luminescence intensity of the secondary peak in the photoluminescence (PL) spectra, interpreted as a measurement of amount of vacancies on the sample surfaces, qualitatively agrees with the threshold behavior as found in the MD simulations. Our simulations have also revealed the formation of oxygen dimers on the surface and evolution of partial charge distribution during the annealing process. Our MD simulation based on the ReaxFF is consistent with experimental observations.