Compensating Mass Matrix Potential Constrained Molecular Dynamics
.Jain@jpl.nasa.gov Journal of Computational Physics, Jul, '97 (in press) Subject classification: 65P99, 82A71. KeywordsCompensating Mass Matrix Potential for Constrained Molecular Dynamics Abhinandan Jain Jet: Molecular dynamics, algorithms, simulation. #12; Running head: Compensating Potential for Constrained
Crystal Structure and Pair Potentials: A Molecular-Dynamics Study
M. Parrinello; A. Rahman
1980-01-01
With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.
Molecular dynamics simulations of solutions at constant chemical potential
NASA Astrophysics Data System (ADS)
Perego, C.; Salvalaglio, M.; Parrinello, M.
2015-04-01
Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (C?MD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the C?MD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.
Molecular Dynamics Simulations of Solutions at Constant Chemical Potential
Perego, Claudio; Parrinello, Michele
2015-01-01
Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, that range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, that influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a Grand-Canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work we propose the C$\\mu$MD method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the C$\\mu$MD method to the paradigmatic case of urea crystall...
Molecular Dynamics Simulations of Supported Pt Nanoclusters with Sutton-Chen Potentials
Washington at Seattle, University of - Department of Physics, Electroweak Interaction Research Group
Molecular Dynamics Simulations of Supported Pt Nanoclusters with Sutton-Chen Potentials Jeffrey M2O3 surface. Results are compared to previous density functional theory/molecular dynamics (DFT Density Functional Theory/Molecular Dynamics (DFT/MD) calculations have been implemented previ- ously
New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations
de Groot, Bert
New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations require the modification of the classical nonbonded potential energy terms by applying soft-core potential functions to avoid singularity points. In this work, we propose a novel formulation for a soft
Variable-charge interatomic potentials for molecular-dynamics simulations Shuji Ogataa)
Southern California, University of
Variable-charge interatomic potentials for molecular-dynamics simulations of TiO2 Shuji Ogataa, and Priya Vashishta Concurrent Computing Laboratory for Materials Simulation, Department of Physics. Adhes. Sci. Technol. 8, 853 1994 , in which atomic charges vary dynamically according to the generalized
Mean molecular potentials in a model lipid bilayer: A molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Xiang, Tian-xiang; Anderson, Bradley D.
1995-11-01
Various mean-field potentials in a model lipid bilayer are calculated by means of molecular dynamics (MD) simulation. The bilayer assembly consists of 200 chain molecules. The anisotropic united atom model is employed for nonbonded interactions and is extended to allow bond length to vary with time. The interfacial translational order is systematically varied and found to correlate strongly with the chain orientational order. A new torsional potential is developed and shown to give order parameters in better agreement with experiment than the Padilla-Toxvaerd potential. Nonbonded interaction reduces the trans-gauche and gauche-gauche transition barriers by 0.9—1.5 kcal/mole. The mean trans-gauche energy difference near the chain tail is close to that in liquid hydrocarbons but 0.34 kcal/mol lower than that in the highly ordered chain region. In contrast to the Mar?elja model, both mean intermolecular dispersive and repulsive energies depend exponentially on the chain orientational parameter and the repulsive component has a poor and inverse correlation with the reciprocal of the chain end-to-end displacement along the bilayer normal. Inclusion of spatial heterogeneity effects of the interaction energy, a treatment similar to the Gruen model [Biochim. Biophys Acta 367, 165 (1980)], does not give a better description of the mean intermolecular interaction. A new and unified model for the mean intermolecular interaction energy is developed based on our present MD simulation data. Various possible chain configurations which are responsible for these results are discussed. Finally, our MD results suggest that, consistent with the ``wobble in a cone'' model, a chain molecule can rotate freely within an angular range without being subjected to a strong potential force.
Manabu Satou; Sidney Yip; Katsunori Abe
2002-01-01
Elastic constants of vanadium are obtained by means of molecular dynamics simulation of stress–strain response. Results at finite temperature are compared with experiments to provide validation of the interatomic potential. Previously, experimental elastic constants and lattice parameter, obtained at finite temperature, were used for parameter fitting at 0 K, leading to poor agreement in the temperature variation. In this work
Hiroshi Sakuma; Taku Tsuchiya; Katsuyuki Kawamura; Kenshiro Otsuki
2003-01-01
Mobility of water at the (0001) surfaces of brucite has been studied using a molecular dynamics method. Ab initio model potential for the water–brucite interaction has been obtained by fitting the parameters to ab initio electronic structure data, calculated by means of the first-principles method based on density functional theory. Using this ab initio model potential, molecular dynamics simulations of
Gereben, Orsolya; Pusztai, László
2013-10-28
The liquid structure of tetrachloroethene has been investigated on the basis of measured neutron and X-ray scattering structure factors, applying molecular dynamics simulations and reverse Monte Carlo (RMC) modeling with flexible molecules and interatomic potentials. As no complete all-atom force field parameter set could be found for this planar molecule, the closest matching all-atom Optimized Potentials for Liquid Simulations (OPLS-AA) intra-molecular parameter set was improved by equilibrium bond length and angle parameters coming from electron diffraction experiments [I. L. Karle and J. Karle, J. Chem. Phys. 20, 63 (1952)]. In addition, four different intra-molecular charge distribution sets were tried, so in total, eight different molecular dynamics simulations were performed. The best parameter set was selected by calculating the mean square difference between the calculated total structure factors and the corresponding experimental data. The best parameter set proved to be the one that uses the electron diffraction based intra-molecular parameters and the charges qC = 0.1 and qCl = -0.05. The structure was further successfully refined by applying RMC computer modeling with flexible molecules that were kept together by interatomic potentials. Correlation functions concerning the orientation of molecular axes and planes were also determined. They reveal that the molecules closest to each other exclusively prefer the parallel orientation of both the molecular axes and planes. Molecules forming the first maximum of the center-center distribution have a preference for <30° and >60° axis orientation and >60° molecular plane arrangement. A second coordination sphere at ?11 A? and a very small third one at ?16 A? can be found as well, without preference for any axis or plane orientation. PMID:24182051
Southern California, University of
Interaction potential for silicon carbide: A molecular dynamics study of elastic constants dynamics method, the interaction potential is used to study structural, elastic, and dynamical properties to be 90 GPa. For 3C-SiC, our computed elastic constants C11, C12, and C44 , melting temperature
NASA Astrophysics Data System (ADS)
Starrett, C. E.; Daligault, J.; Saumon, D.
2015-01-01
An approach to simulating warm and hot dense matter that combines density-functional-theory-based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The method, which we call pseudoatom molecular dynamics, can be applied to single-component or multicomponent plasmas. It gives equation of state and self-diffusion coefficients with an accuracy comparable to orbital-free molecular dynamics simulations but is computationally much more efficient.
Christian Bayer; Hakon Hoel; Ashraful Kadir; Petr Plechac; Mattias Sandberg; Anders Szepessy
2015-05-12
The difference of the values of observables for the time-independent Schroedinger equation, with matrix valued potentials, and the values of observables for ab initio Born-Oppenheimer molecular dynamics, of the ground state, depends on the probability to be in excited states and the electron/nuclei mass ratio. The paper first proves an error estimate (depending on the electron/nuclei mass ratio and the probability to be in excited states) for this difference of microcanonical observables, assuming that molecular dynamics space-time averages converge, with a rate related to the maximal Lyapunov exponent. The error estimate is uniform in the number of particles and the analysis does not assume a uniform lower bound on the spectral gap of the electron operator and consequently the probability to be in excited states can be large. A numerical method to determine the probability to be in excited states is then presented, based on Ehrenfest molecular dynamics and stability analysis of a perturbed eigenvalue problem.
Car-Parrinello Molecular Dynamics With A Sinusoidal Time-Dependent Potential Field
Alznauer, Tobias
2012-01-01
A sinusoidal external field is applied in Car-Parrinello molecular dynamics simulations. We present an implementation and discuss first test applications to electron and ion transfers in complex molecular systems.
Seniya, Chandrabhan; Khan, Ghulam Jilani; Uchadia, Kuldeep
2014-01-01
Cholinesterase inhibitors (ChE-Is) are the standard for the therapy of AD associated disorders and are the only class of approved drugs by the Food and Drug Administration (FDA). Additionally, acetylcholinesterase (AChE) is the target for many Alzheimer's dementia drugs which block the function of AChE but have some side effects. Therefore, in this paper, an attempt was made to elucidate cholinesterase inhibition potential of secondary metabolite from Cannabis plant which has negligible or no side effect. Molecular docking of 500 herbal compounds, against AChE, was performed using Autodock 4.2 as per the standard protocols. Molecular dynamics simulations have also been carried out to check stability of binding complex in water for 1000?ps. Our molecular docking and simulation have predicted high binding affinity of secondary metabolite (C28H34N2O6) to AChE. Further, molecular dynamics simulations for 1000?ps suggest that ligand interaction with the residues Asp72, Tyr70-121-334, and Phe288 of AChE, all of which fall under active site/subsite or binding pocket, might be critical for the inhibitory activity of AChE. This approach might be helpful to understand the selectivity of the given drug molecule in the treatment of Alzheimer's disease. The study provides evidence for consideration of C28H34N2O6 as a valuable small ligand molecule in treatment and prevention of AD associated disorders and further in vitro and in vivo investigations may prove its therapeutic potential. PMID:25054066
Atomistic simulations of TeO?-based glasses: interatomic potentials and molecular dynamics.
Gulenko, Anastasia; Masson, Olivier; Berghout, Abid; Hamani, David; Thomas, Philippe
2014-07-21
In this work we present for the first time empirical interatomic potentials that are able to reproduce TeO2-based systems. Using these potentials in classical molecular dynamics simulations, we obtained first results for the pure TeO2 glass structure model. The calculated pair distribution function is in good agreement with the experimental one, which indicates a realistic glass structure model. We investigated the short- and medium-range TeO2 glass structures. The local environment of the Te atom strongly varies, so that the glass structure model has a broad Q polyhedral distribution. The glass network is described as weakly connected with a large number of terminal oxygen atoms. PMID:24905883
Angular dependent potential for ?-boron and large-scale molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Pokatashkin, P.; Kuksin, A.; Yanilkin, A.
2015-06-01
Both quantum mechanical and molecular-dynamics (MD) simulations of ?-boron are done at this work. Angular dependent interatomic potential (ADP) for boron is obtained using force-matching technique. Fitting data are based on ab initio results within???20..100 GPa pressure range and temperatures up to 2000 K. Characteristics of ?-boron, obtained using ADP potential such as bond lengths at equilibrium condition, bulk modulus, pressure-volume relations, Gruneisen coefficient, thermal expansion coefficient are in good agreement with both ab initio data, obtained in this work and known experimental data. As an example of application, the propagation of shock waves through a single crystal of ?-boron is also explored by large-scale MD simulations.
Roger F. Cracknell; David Nicholson; Nicholas Quirke
1995-01-01
A novel nonequilibrium molecular dynamics simulation technique has been developed whereby the flux of particles, flowing between explicitly defined regions of different constant chemical potential, is measured directly by counting particles. The method uses both stochastic and dynamic steps. A linear relationship between flux and concentration gradient (Fick's law) is found for methane in a carbonaceous slit micropore with a
Yongfeng Zhang; Paul C Millett; Michael R Tonks; Xian-Ming Bai; S Bulent Biner
2014-09-01
The intergranular fracture behavior of UO2 was studied using molecular dynamics simulations with a bicrystal model. The anisotropic fracture behavior due to the different grain boundary characters was investigated with the View the MathML source symmetrical tilt S5 and the View the MathML source symmetrical tilt S3 ({1 1 1} twin) grain boundaries. Nine interatomic potentials, seven rigid-ion plus two core–shell ones, were utilized to elucidate possible potential dependence. Initiating from a notch, crack propagation along grain boundaries was observed for most potentials. The S3 boundary was found to be more prone to fracture than the S5 one, indicated by a lower energy release rate associated with the former. However, some potential dependence was identified on the existence of transient plastic deformation at crack tips, and the results were discussed regarding the relevant material properties including the excess energies of metastable phases and the critical energy release rate for intergranular fracture. In general, local plasticity at crack tips was observed in fracture simulations with potentials that predict low excess energies for metastable phases and high critical energy release rates for intergranular fracture.
G. C. Lie; E. Clementi
1986-01-01
The Matsuoka-Clementi-Yoshimine (MCY) configuration interaction potential for rigid water-water interactions has been extended to include the intramolecular vibrations. The extended potential (MCYL), using no empirical parameters other than the atomic masses, electron charge, and Planck constant, is used in a molecular-dynamics simulation study of the static and dynamic properties of liquid water. Among the properties studied are internal energy, heat
Justin R. Gullingsrud; Rosemary Braun; Klaus Schulten
1999-01-01
Atomic force microscopy (AFM) experiments and steered molecular dynamics (SMD) simulations have revealed much about the dynamics of protein-ligand binding and unbinding, as well as the stretching and unfolding of proteins. Both techniques induce ligand unbinding or protein unfolding by applying external mechanical forces to the ligand or stretched protein. However, comparing results from these two techniques, such as the
Kim, Junghan; Iype, Eldhose; Frijns, Arjan J.H.; Nedea, Silvia V.; Steenhoven, Anton A. van
2014-07-01
Molecular dynamics simulations of heat transfer in gases are computationally expensive when the wall molecules are explicitly modeled. To save computational time, an implicit boundary function is often used. Steele's potential has been used in studies of fluid–solid interface for a long time. In this work, the conceptual idea of Steele's potential was extended in order to simulate water–silicon and water–silica interfaces. A new wall potential model is developed by using the electronegativity-equalization method (EEM), a ReaxFF empirical force field and a non-reactive molecular dynamics package PumMa. Contact angle simulations were performed in order to validate the wall potential model. Contact angle simulations with the resulting tabulated wall potentials gave a silicon–water contact angle of 129°, a quartz–water contact angle of 0°, and a cristobalite–water contact angle of 40°, which are in reasonable agreement with experimental values.
Hua Y. Geng
2014-12-19
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model, the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4 fold for a two-level implementation, and can be increased to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of $r_{s}=0.912$.
NASA Astrophysics Data System (ADS)
Geng, Hua Y.
2015-02-01
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model-the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of rs = 0.912.
Wucher, Andreas
silver clusters can now be almost quantitatively modeled by the simulation. © 1996 American Institute on silver clusters as a model system, however, revealed that the EAM potential fit for silver significantlyCluster formation in sputtering: A molecular dynamics study using the MD/MC-corrected effective
NASA Astrophysics Data System (ADS)
Wu, Xiaojie; Li, Xiantao
2015-01-01
Results from molecular dynamics simulations often need to be further processed to understand the physics on a larger scale. This paper considers the definitions of momentum and energy fluxes obtained from a control-volume approach. To assess the validity of these defined quantities, two consistency criteria are proposed. As examples, the embedded atom potential and the Tersoff potential are considered. The consistency is verified using analytical and numerical methods.
Molecular Dynamics Studies of Dislocations in CdTe Crystals from a New Bond Order Potential
2012-01-01
Cd1-xZnxTe (CZT) crystals are the leading semiconductors for radiation detection, but their application is limited by the high cost of detector-grade materials. High crystal costs primarily result from property nonuniformity that causes low manufacturing yield. Although tremendous efforts have been made in the past to reduce Te inclusions/precipitates in CZT, this has not resulted in an anticipated improvement in material property uniformity. Moreover, it is recognized that in addition to Te particles, dislocation cells can also cause electric field perturbations and the associated property nonuniformities. Further improvement of the material, therefore, requires that dislocations in CZT crystals be understood and controlled. Here, we use a recently developed CZT bond order potential to perform representative molecular dynamics simulations to study configurations, energies, and mobilities of 29 different types of possible dislocations in CdTe (i.e., x = 1) crystals. An efficient method to derive activation free energies and activation volumes of thermally activated dislocation motion will be explored. Our focus gives insight into understanding important dislocations in the material and gives guidance toward experimental efforts for improving dislocation network structures in CZT crystals. PMID:22962626
Introduction to Accelerated Molecular Dynamics
Perez, Danny [Los Alamos National Laboratory
2012-07-10
Molecular Dynamics is the numerical solution of the equations of motion of a set of atoms, given an interatomic potential V and some boundary and initial conditions. Molecular Dynamics is the largest scale model that gives unbiased dynamics [x(t),p(t)] in full atomistic detail. Molecular Dynamics: is simple; is 'exact' for classical dynamics (with respect to a given V); can be used to compute any (atomistic) thermodynamical or dynamical properties; naturally handles complexity -- the system does the right thing at the right time. The physics derives only from the interatomic potential.
Sciortino, Francesco
of hexagonal ice (Ih). We focus on (i) the intramolecular and intermolecular structure, a subject of longStructure and dynamics in hexagonal ice: A molecular dynamics simulation with an ab rinifio)]. The collective low frequency modes in the simulated ice are in good agreement with the experimental data in the c
D. C. Rapaport
1999-01-01
The article presents a discussion on molecular dynamics (MD) simulation. MD requires a description of the molecules and the forces that act between them; a well known example is the Lennard-Jones potential, in which spherical particles repel one another at close range but otherwise attract. The MD simulation itself amounts to numerically integrating the equations of motion for systems of
Constant-temperature molecular-dynamics algorithms for mixed hard-core/continuous potentials
Houndonougbo, Yao; Laird, Brian Bostian
2002-07-03
m, K le h e´ # f @ C es di nc I date, simulation studies for such systems have been primarily JOURNAL OF CHEMICAL PHYSICS VOLUME 117, NUMBER 3 15 JULY 2002 This arestricted to Monte Carlo studies due to the lack of a viable molecular-dynamics ~MD... for hy- brid continuous/discontinuous systems. The Collision Verlet algorithm was formulated as a constant energy simulation method, which generates configurations from a microcanoni- cal ~NVE! distribution. However, to mimic experimental conditions most...
D. Toghraie Semiromi; A. R. Azimian
Molecular dynamics simulation of annular flow boiling in a nanochannel is numerically investigated. In this research, an annular\\u000a flow model is developed to predict the superheated flow boiling heat transfer characteristics in a nanochannel. To characterize\\u000a the forced annular boiling flow in a nanochannel, an external driving force $$ \\\\overrightarrow {F}_{\\\\text{ext}} $$ ranging from 1 to 12 PN (PN = pico newton)
Ning Gao; Wen-Sheng Lai
2006-01-01
The calculation of elastic constants of Ag\\/Pd superlattice thin films by molecular dynamics simulations with many-body potentials is presented. It reveals that the elastic constants C11 and C55 increase with decreasing modulation wavelength ? of the films, which is consistent with experiments. However, the change of C11 and C55 with ? is found to be around the values determined by
Guarini, E.; Barocchi, F. [Dipartimento di Fisica, Universita di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino (Italy); CNR-INFM CRS-Soft c/o Dipartimento di Fisica, Universita di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino (Italy); Sampoli, M. [Dipartimento di Energetica, Universita di Firenze, via S. Marta 3, I-50139 Firenze (Italy); CNR-INFM CRS-Soft c/o Dipartimento di Fisica, Universita di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino (Italy); Venturi, G. [CNR-INFM CRS-Soft c/o Dipartimento di Fisica, Universita di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino (Italy); Bafile, U. [Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, via Madonna del Piano 10, I-50019 Sesto Fiorentino (Italy)
2007-10-19
Anisotropic interactions of liquid CD{sub 4} are studied in detail by comparison of inelastic neutron Brillouin scattering data with molecular dynamics simulations using up to four different models of the methane site-site potential. We demonstrate that the experimental dynamic structure factor S(Q,{omega}) acts as a highly discriminating quantity for possible interaction schemes. In particular, the Q evolution of the spectra enables a selective probing of the short- and medium-range features of the anisotropic potentials. We show that the preferential configuration of methane dimers at liquid densities can thus be discerned by analyzing the orientation-dependent model potential curves, in light of the experimental and simulation results.
Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations
Mollica, Luca; Decherchi, Sergio; Zia, Syeda Rehana; Gaspari, Roberto; Cavalli, Andrea; Rocchia, Walter
2015-01-01
Drug discovery is expensive and high-risk. Its main reasons of failure are lack of efficacy and toxicity of a drug candidate. Binding affinity for the biological target has been usually considered one of the most relevant figures of merit to judge a drug candidate along with bioavailability, selectivity and metabolic properties, which could depend on off-target interactions. Nevertheless, affinity does not always satisfactorily correlate with in vivo drug efficacy. It is indeed becoming increasingly evident that the time a drug spends in contact with its target (aka residence time) can be a more reliable figure of merit. Experimental kinetic measurements are operatively limited by the cost and the time needed to synthesize compounds to be tested, to express and purify the target, and to setup the assays. We present here a simple and efficient molecular-dynamics-based computational approach to prioritize compounds according to their residence time. We devised a multiple-replica scaled molecular dynamics protocol with suitably defined harmonic restraints to accelerate the unbinding events while preserving the native fold. Ligands are ranked according to the mean observed scaled unbinding time. The approach, trivially parallel and easily implementable, was validated against experimental information available on biological systems of pharmacological relevance. PMID:26103621
Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations.
Mollica, Luca; Decherchi, Sergio; Zia, Syeda Rehana; Gaspari, Roberto; Cavalli, Andrea; Rocchia, Walter
2015-01-01
Drug discovery is expensive and high-risk. Its main reasons of failure are lack of efficacy and toxicity of a drug candidate. Binding affinity for the biological target has been usually considered one of the most relevant figures of merit to judge a drug candidate along with bioavailability, selectivity and metabolic properties, which could depend on off-target interactions. Nevertheless, affinity does not always satisfactorily correlate with in vivo drug efficacy. It is indeed becoming increasingly evident that the time a drug spends in contact with its target (aka residence time) can be a more reliable figure of merit. Experimental kinetic measurements are operatively limited by the cost and the time needed to synthesize compounds to be tested, to express and purify the target, and to setup the assays. We present here a simple and efficient molecular-dynamics-based computational approach to prioritize compounds according to their residence time. We devised a multiple-replica scaled molecular dynamics protocol with suitably defined harmonic restraints to accelerate the unbinding events while preserving the native fold. Ligands are ranked according to the mean observed scaled unbinding time. The approach, trivially parallel and easily implementable, was validated against experimental information available on biological systems of pharmacological relevance. PMID:26103621
Bauchy, M
2014-07-14
We study a calcium aluminosilicate glass of composition (SiO2)0.60(Al2O3)0.10(CaO)0.30 by means of molecular dynamics. To this end, we conduct parallel simulations, following a consistent methodology, but using three different potentials. Structural and elastic properties are analyzed and compared to available experimental data. This allows assessing the respective abilities of the potentials to produce a realistic glass. We report that, although all these potentials offer a reasonable glass structure, featuring tricluster oxygen atoms, their respective vibrational and elastic predictions differ. This allows us to draw some general conclusions about the crucial role, or otherwise, of the interaction potential in silicate systems. PMID:25028027
Bauchy, M., E-mail: bauchy@mit.edu [Concrete Sustainability Hub, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA and Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095 (United States)
2014-07-14
We study a calcium aluminosilicate glass of composition (SiO{sub 2}){sub 0.60}(Al{sub 2}O{sub 3}){sub 0.10}(CaO){sub 0.30} by means of molecular dynamics. To this end, we conduct parallel simulations, following a consistent methodology, but using three different potentials. Structural and elastic properties are analyzed and compared to available experimental data. This allows assessing the respective abilities of the potentials to produce a realistic glass. We report that, although all these potentials offer a reasonable glass structure, featuring tricluster oxygen atoms, their respective vibrational and elastic predictions differ. This allows us to draw some general conclusions about the crucial role, or otherwise, of the interaction potential in silicate systems.
Kumar, R. Barani; Suresh, M. Xavier; Priya, B. Shanmuga
2015-01-01
Background: The alpha-delta bungartoxin-4 (?-?-Bgt-4) is a potent neurotoxin produced by highly venomous snake species, Bungarus caeruleus, mainly targeting neuronal acetylcholine receptors (nAchRs) and producing adverse biological malfunctions leading to respiratory paralysis and mortality. Objective: In this study, we predicted the three-dimensional structure of ?-?-Bgt-4 using homology modeling and investigated the conformational changes and the key residues responsible for nAchRs inhibiting activity. Materials and Methods: From the selected plants, which are traditionally used for snake bites, the active compounds are taken and performed molecular interaction studies and also used for modern techniques like pharmacophore modeling and mapping and absorption, distribution, metabolism, elimination and toxicity analysis which may increase the possibility of success. Results: Moreover, 100's of drug-like compounds were retrieved and analyzed through computational virtual screening and allowed for pharmacokinetic profiling, molecular docking and dynamics simulation. Conclusion: Finally the top five drug-like compounds having competing level of inhibition toward ?-?-Bgt-4 toxin were suggested based on their interaction with ?-?-Bgt-4 toxin.
Grenier, Romain; To, Quy-Dong; Lara-Castells, María Pilar de; Léonard, Céline
2015-07-01
Global potentials for the interaction between the Ar atom and gold surfaces are investigated and Ar-Au pair potentials suitable for molecular dynamics simulations are derived. Using a periodic plane-wave representation of the electronic wave function, the nonlocal van-der-Waals vdW-DF2 and vdW-OptB86 approaches have been proved to describe better the interaction. These global interaction potentials have been decomposed to produce pair potentials. Then, the pair potentials have been compared with those derived by combining the dispersionless density functional dlDF for the repulsive part with an effective pairwise dispersion interaction. These repulsive potentials have been obtained from the decomposition of the repulsive interaction between the Ar atom and the Au2 and Au4 clusters and the dispersion coefficients have been evaluated by means of ab initio calculations on the Ar+Au2 complex using symmetry adapted perturbation theory. The pair potentials agree very well with those evaluated through periodic vdW-DF2 calculations. For benchmarking purposes, CCSD(T) calculations have also been performed for the ArAu and Ar+Au2 systems using large basis sets and extrapolations to the complete basis set limit. This work highlights that ab initio calculations using very small surface clusters can be used either as an independent cross-check to compare the performance of state-of-the-art vdW-corrected periodic DFT approaches or, directly, to calculate the pair potentials necessary in further molecular dynamics calculations. PMID:26046588
Accelerated molecular dynamics methods
Perez, Danny [Los Alamos National Laboratory
2011-01-04
The molecular dynamics method, although extremely powerful for materials simulations, is limited to times scales of roughly one microsecond or less. On longer time scales, dynamical evolution typically consists of infrequent events, which are usually activated processes. This course is focused on understanding infrequent-event dynamics, on methods for characterizing infrequent-event mechanisms and rate constants, and on methods for simulating long time scales in infrequent-event systems, emphasizing the recently developed accelerated molecular dynamics methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics). Some familiarity with basic statistical mechanics and molecular dynamics methods will be assumed.
NASA Astrophysics Data System (ADS)
Allen, Roland; Jiang, Chen-Wei; Zhang, Xiu-Xing; Fang, Ai-Ping; Li, Hong-Rong; Xie, Rui-Hua; Li, Fu-Li
2015-03-01
It is worthwhile to explore the detailed reaction dynamics of various candidates for molecular switches, in order to understand, e.g., the differences in quantum yields and switching times. Here we report density-functional-based simulations for the rhodopsin-based molecule 4-[4-Methylbenzylidene]-5-p-tolyl-3,4-dihydro-2H-pyrrole (MDP), synthesized by Sampedro et al. We find that the photoisomerization quantum yields are remarkably high: 82% for cis-to-trans, and 68% for trans-to-cis. The lifetimes of the S1 excited state in cis-MDP in our calculations are in the range of 900-1800 fs, with a mean value of 1270 fs, while the range of times required for full cis-to-trans isomerization are 1100-2000 fs, with a mean value of 1530 fs. In trans-MDP, the calculated S1 excited state lifetimes are 860-2140 fs, with a mean value of 1330 fs, and with the full trans-to-cis isomerization completed about 200 fs later. In both cases, the dominant reaction mechanism is rotation around the central C =C bond (connected to the pyrroline ring), and de-excitation occurs at an avoided crossing between the ground state and the lowest singlet state, near the midpoint of the rotational pathway. Research Fund for the Doctoral Program of Higher Education of China; Fundamental Research Funds for the Central Universities; Robert A. Welch Foundation; National Natural Science Foundation of China.
Galliero, Guillaume; Boned, Christian
2008-08-21
In this work, using extensive molecular dynamics simulations of several thermophysical properties, it is proposed to analyze possible relationships (in the corresponding state sense) between monoatomic fluids for which the repulsive interactions are modeled by an inverse n-power form, the Lennard-Jones 12-6 (LJ), or by an exponential one, the exponential-6 (Exp-6). To compare results between them, two possible definitions of Exp-6 potentials "equivalent" to the LJ one are proposed. In pure fluids, for a large range of thermodynamic conditions, the properties computed are the surface tension, liquid/vapor equilibrium densities, one-phase potential energy, pressure, isometric heat capacity, thermal pressure coefficient, self-diffusion, shear viscosity, and thermal conductivity. Additionally, thermodiffusion (Soret effect) has been considered in "isotopic" equimolar mixtures. It is shown that despite similarities exhibited by alike radial distribution functions, differences exist between the thermodynamic properties values provided by the LJ fluid and the two equivalent Exp-6 fluids. Nevertheless, quite surprisingly, when temperature and density are used as inputs, all three direct transport properties are shown to be nearly independent of the choice of the potential tested. Unexpectedly, these similarities hold even for thermodiffusion which is a priori very sensitive to the nature of the interactions. These results indicate that the use of an Exp-6 potential form to describe nonbonded/nonpolar interaction in molecular simulation is an alternative (more physically acceptable) to the LJ potential when dealing simultaneously with thermodynamic and transport properties. However, when only transport properties are considered (including thermodiffusion), the Exp-6 potential form should not lead to any differences compared to the LJ one. PMID:19044782
Bassolino-Klimas, D.; Tejero, R.; Krystek, S. R.; Metzler, W. J.; Montelione, G. T.; Bruccoleri, R. E.
1996-01-01
A new functional representation of NMR-derived distance constraints, the flexible restraint potential, has been implemented in the program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168) for molecular structure generation. In addition, flat-bottomed restraint potentials for representing dihedral angle and vicinal scalar coupling constraints have been introduced into CONGEN. An effective simulated annealing (SA) protocol that combines both weight annealing and temperature annealing is described. Calculations have been performed using ideal simulated NMR constraints, in order to evaluate the use of restrained molecular dynamics (MD) with these target functions as implemented in CONGEN. In this benchmark study, internuclear distance, dihedral angle, and vicinal coupling constant constraints were calculated from the energy-minimized X-ray crystal structure of the 46-amino acid polypeptide crambin (ICRN). Three-dimensional structures of crambin that satisfy these simulated NMR constraints were generated using restrained MD and SA. Polypeptide structures with extended backbone and side-chain conformations were used as starting conformations. Dynamical annealing calculations using extended starting conformations and assignments of initial velocities taken randomly from a Maxwellian distribution were found to adequately sample the conformational space consistent with the constraints. These calculations also show that loosened internuclear constraints can allow molecules to overcome local minima in the search for a global minimum with respect to both the NMR-derived constraints and conformational energy. This protocol and the modified version of the CONGEN program described here are shown to be reliable and robust, and are applicable generally for protein structure determination by dynamical simulated annealing using NMR data. PMID:8845749
Softened electrostatic molecular potentials.
Besalú, Emili; Carbó-Dorca, Ramon
2013-02-01
Electrostatic molecular potentials (EMPs) are studied from two points of view. First, a softened EMP (SEMP) approach is proposed, consisting in the substitution of a positive point charge as the entity with which an electronic density function (DF) interacts electrostatically to generate a classical EMP for a Gaussian charge distribution. Second, the performance of this SEMP approach under the Atomic Shell Approximation (ASA) is described and compared with classical EMP at the same ASA level. Several sample applications are presented to describe the general features of this new method of studying electrostatic interactions in molecules. The net result is a family of SEMPs that encompass EMPs as special cases but do not possess their infinite discontinuities. The features of SEMPs are quite similar to those of EMPs distant from nuclei, and the absence of infinity values makes them good candidates to be employed in molecular similarity calculations. PMID:23220280
Quantum molecular Dynamics Ronnie Kosloff
Kosloff, Ronnie
Quantum molecular Dynamics Ronnie Kosloff The Fritz Haber Center for Molecular Dynamics Hebrew University, Jerusalem Israel. · Lecture 6: · Time dependent Quantum Molecular Dynamics #12;#12;State #12;Quantum molecular Dynamics Ronnie Kosloff The Fritz Haber Center for Molecular Dynamics Hebrew
Larcher, G; Tran, H; Schwell, M; Chelin, P; Landsheere, X; Hartmann, J-M; Hu, S-M
2014-02-28
Room temperature absorption spectra of various transitions of pure CO2 have been measured in a broad pressure range using a tunable diode-laser and a cavity ring-down spectrometer, respectively, in the 1.6 ?m and 0.8 ?m regions. Their spectral shapes have been calculated by requantized classical molecular dynamics simulations. From the time-dependent auto-correlation function of the molecular dipole, including Doppler and collisional effects, spectral shapes are directly computed without the use of any adjusted parameter. Analysis of the spectra calculated using three different anisotropic intermolecular potentials shows that the shapes of pure CO2 lines, in terms of both the Lorentz widths and non-Voigt effects, slightly depend on the used potential. Comparisons between these ab initio calculations and the measured spectra show satisfactory agreement for all considered transitions (from J = 6 to J = 46). They also show that non-Voigt effects on the shape of CO2 transitions are almost independent of the rotational quantum number of the considered lines. PMID:24588170
NASA Astrophysics Data System (ADS)
Boisse, J.; Domain, C.; Becquart, C. S.
2014-12-01
Density Functional Theory calculations and Molecular Dynamics with a recently developed potential for W-He were used to evaluate the thermal stability of helium-vacancy clusters (nHe.mv) as well as pure interstitial helium clusters in tungsten. The stability of such objects results from a competitive process between thermal emission of vacancies, self interstitial atoms (SIAs) and helium, depending on the helium-to-vacancy ratio in mixed clusters or helium number in pure interstitial helium clusters. We investigated in particular the thermodynamics and kinetics of self trapping and trap mutation, i.e. the emission of one SIA along with the creation of one vacancy from a vacancy-helium or pure helium object.
Fu, Yao; Song, Jeong-Hoon
2014-08-01
Hardy stress definition has been restricted to pair potentials and embedded-atom method potentials due to the basic assumptions in the derivation of a symmetric microscopic stress tensor. Force decomposition required in the Hardy stress expression becomes obscure for multi-body potentials. In this work, we demonstrate the invariance of the Hardy stress expression for a polymer system modeled with multi-body interatomic potentials including up to four atoms interaction, by applying central force decomposition of the atomic force. The balance of momentum has been demonstrated to be valid theoretically and tested under various numerical simulation conditions. The validity of momentum conservation justifies the extension of Hardy stress expression to multi-body potential systems. Computed Hardy stress has been observed to converge to the virial stress of the system with increasing spatial averaging volume. This work provides a feasible and reliable linkage between the atomistic and continuum scales for multi-body potential systems. PMID:25106571
Slow dynamics by molecular dynamics
NASA Astrophysics Data System (ADS)
Alder, Berni J.
2002-11-01
We learned early in the computer study of the H-function with particle dynamics that the velocity distribution reaches a local equilibrium (Maxwellian) distribution fast, within a few mean collision times, but that the subsequent structural rearrangement of the particles can be quite slow, particularly if a highly correlated event of many degrees of freedom is involved. During that process potential energy is slowly converted into kinetic energy to reach overall equilibrium. To study processes that are so unlikely that they do not occur within long computer runs (typically less than 10 -8 s of real time) we developed a rare event algorithm. In that calculation the particles are brought adiabatically, that is so slowly that the system is at equilibrium in the presence of the external force at every step, to the rare event configuration (the activated state) and the work to do that is determined. The probability of the event is then calculated by standard reaction rate theory by also determining the transmission coefficient through releasing the constraint near the activated state and observing how often the system goes to the new state relative to how often it falls back to the initial state. The problem with that calculation besides the assumption of adiabaticity is that one needs a model for the activated state, which is often hard to guess. Simulated annealing might aid in the search for an activated state. The other possibility is to speed up particle dynamics and that can be done by direct simulation Monte Carlo, a stochastic particle solution of the Boltzmann equation for a perfect gas. That approach can be extended to higher densities, but the stochastic approach cannot account for the structural features of the medium. However, systems can be followed up to 10 -5 s. We have been able to follow, for example, droplet formation and coalescence by this method. To study even larger systems we have embedded this particle algorithm into a continuum Navier-Stokes algorithm to study the onset of hydrodynamic instabilities. However, the approach cannot deal with the protein folding problem, because the structural aspects dominate the process. One would have to embed molecular dynamics into a continuum, a much more computer intensive problem, in order to even treat water, for example, as a continuum beyond a few molecular layers around a biological molecule.
Ahadi, Elias; Konermann, Lars
2009-05-21
Water nanodroplets charged with excess protons play a central role during electrospray ionization (ESI). In the current study molecular dynamics (MD) simulations were used for gaining insights into the nanodroplet behavior based on classical mechanics. The SPC/E water model was modified to permit the inclusion of protons as highly mobile point charges at minimum computational cost. A spherical trapping potential was assigned to every SPC/E oxygen, thereby allowing the formation of protonated water molecules. Within a tightly packed nanodroplet the individual potential wells merge to form a three-dimensional energy landscape that facilitates rapid proton hopping between water molecules. This approach requires short-range modifications to the standard Coulomb potential for modeling electrostatic proton-water interactions. Simulations on nanodroplets consisting of 1248 water molecules and 10 protons (radius, ca. 21 A) result in a proton diffusion coefficient that is in agreement with the value measured in bulk solution. Radial proton distributions extracted from 1 ns MD runs exhibit a large peak around 14 A, in addition to substantial population density closer to the droplet center. Similar radial distributions were found for nanodroplets charged with Na+ ions. This behavior is dramatically different from that expected on the basis of continuum electrostatic theory, which predicts that excess charge should be confined to a thin layer on the droplet surface. One important contributor to this effect seems to be the ordering of water molecules at the liquid/vacuum interface. This ordering results in an electrical double layer, generating a potential gradient that tends to pull positive charge carriers (such as protons, but also others such as Na+ ions) toward the droplet interior. This deviation from the widely assumed surface charge paradigm could have implications for the mechanism by which protonated analyte ions are formed during ESI. PMID:19388688
Molecular Dynamics: Simulations of Nucleic
Westhof, Eric
as an extension of the crystallographic determinations of nucleic acid structures, often plagued by low resolutionMolecular Dynamics: Simulations of Nucleic Acids Pascal Auffinger and Eric Westhof Institut de mesh Ewald; PMF D potential of mean force; T D thymine; U D uracil. 1 INTRODUCTION Nucleic acids, DNA
Quantum molecular Dynamics Ronnie Kosloff
Kosloff, Ronnie
Quantum molecular Dynamics Ronnie Kosloff The Fritz Haber Center for Molecular Dynamics Hebrew.mpg #12;#12;#12;#12;Quantum molecular Dynamics Ronnie Kosloff The Fritz Haber Center for Molecular Dynamics Hebrew University, Jerusalem Israel. ·Lecture 10: Coherent Control & Summary #12;Coherent Control
Molecular dynamics simulations
Tomas Hansson; Chris Oostenbrink; WilfredF van Gunsteren
2002-01-01
Molecular dynamics simulations have become a standard tool for the investigation of biomolecules. Simulations are performed of ever bigger systems using more realistic boundary conditions and better sampling due to longer sampling times. Recently, realistic simulations of systems as complex as transmembrane channels have become feasible. Simulations aid our understanding of biochemical processes and give a dynamic dimension to structural
Paulo Sergio Branicio; José Pedro Rino; Chee Kwan Gan; Hélio Tsuzuki
2009-01-01
Indium phosphide is investigated using molecular dynamics (MD) simulations and density-functional theory calculations. MD simulations use a proposed effective interaction potential for InP fitted to a selected experimental dataset of properties. The potential consists of two- and three-body terms that represent atomic-size effects, charge-charge, charge-dipole and dipole-dipole interactions as well as covalent bond bending and stretching. Predictions are made for
Paulo Sergio Branicio; José Pedro Rino; Chee Kwan Gan; Hélio Tsuzuki
2009-01-01
Indium phosphide is investigated using molecular dynamics (MD) simulations and density-functional theory calculations. MD simulations use a proposed effective interaction potential for InP fitted to a selected experimental dataset of properties. The potential consists of two- and three-body terms that represent atomic-size effects, charge–charge, charge–dipole and dipole–dipole interactions as well as covalent bond bending and stretching. Predictions are made for
Kat?, Toshiko
2004-01-01
The dissociation and association dynamics of N2O4 [see text] 2NO2 in liquid state are studied by classical molecular dynamics simulations of reactive liquid NO2. An OSPP+LJ potential between NO2 molecules, which is a sum of an orientation-sensitive pairwise potential (OSPP) between N-N atoms proposed in Paper I [J. Chem. Phys. 115, 10852 (2001)] and Lennard-Jones potentials between N-O and O-O atoms, has been used in the simulation. The reaction dynamics is studied as a function of well depth De and anisotropy factors of the OSPP potential: Atheta (0< or =Atheta< or =1) for the rocking angle and Atau (0< or =Atau< or =0.5) for the torsional angle of relative NO2-NO2 orientation. The lifetime tauD of initially prepared NO2 dimers is found to increase as De increases, Atheta increases, and Atau decreases. Dissociation and association dynamics are studied in detail around the extreme limit of pure NO2-dimer liquid: De=0.12 x 10(-18) J, Atheta=0.5, and Atau=0.1, which has been found to reproduce both the observed liquid phase equilibrium properties and Raman band shapes of the dissociation mode very well. The dissociation dynamics from microscopic reaction trajectories is compared with the potential of the mean force (PMF) as a function of the N-N distance R. The PMF of reactive liquid NO2 shows a transition state barrier at R=2.3-2.5 A, and NO2-trimer structure is found to be formed at the barrier. Two types of dissociation of the NO2 dimer-the dissociation by collisional activation of the reactive mode to cross the dissociation limit and the NO2-mediated dissociation via bond transfer-are studied. The latter needs less free energy and is found to be much more probable. The dissociation trajectories and PMF in reactive liquid NO2 are compared with those of a reactive NO2 pair in inert solvent N2O4. PMID:15267919
Abriata, Luciano A; Dal Peraro, Matteo
2015-01-01
Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin's noncovalent dimerization equilibrium to assess the potential of atomistic simulations to reproduce reversible protein-protein binding, by running submicrosecond simulations of systems with multiple copies of the protein at millimolar concentrations. The simulations essentially fail because they lead to aggregates, yet they reproduce some specificity in the binding interfaces as observed in known covalent and noncovalent ubiquitin dimers. Following similar observations in literature we hint at electrostatics and water descriptions as the main liable force field elements, and propose that their optimization should consider observables relevant to multi-protein systems and unfolded proteins. Within limitations, analysis of binding events suggests salient features of protein-protein recognition and binding, to be retested with improved force fields. Among them, that specific configurations of relative direction and orientation seem to trigger fast binding of two molecules, even over 50?Å distances; that conformational selection can take place within surface-to-surface distances of 10 to 40?Å i.e. well before actual intermolecular contact; and that establishment of contacts between molecules further locks their conformations and relative orientations. PMID:26023027
Abriata, Luciano A.; Dal Peraro, Matteo
2015-01-01
Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin’s noncovalent dimerization equilibrium to assess the potential of atomistic simulations to reproduce reversible protein-protein binding, by running submicrosecond simulations of systems with multiple copies of the protein at millimolar concentrations. The simulations essentially fail because they lead to aggregates, yet they reproduce some specificity in the binding interfaces as observed in known covalent and noncovalent ubiquitin dimers. Following similar observations in literature we hint at electrostatics and water descriptions as the main liable force field elements, and propose that their optimization should consider observables relevant to multi-protein systems and unfolded proteins. Within limitations, analysis of binding events suggests salient features of protein-protein recognition and binding, to be retested with improved force fields. Among them, that specific configurations of relative direction and orientation seem to trigger fast binding of two molecules, even over 50?Å distances; that conformational selection can take place within surface-to-surface distances of 10 to 40?Å i.e. well before actual intermolecular contact; and that establishment of contacts between molecules further locks their conformations and relative orientations. PMID:26023027
Substructured multibody molecular dynamics.
Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.
2006-11-01
We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.
Hamed Akbarzadeh; Hadi Abroshan; Farid Taherkhani; Cobra Izanloo; Gholam Abbas Parsafar
2011-01-01
We have investigated the size dependence of a nano-cavity properties produced in a Xe fluid using molecular dynamics simulations. We have created a nano-cavity of different sizes at 170 and 200K (cavities diameters are within 1–10nm). Liquid pressure, vapor pressure and surface tension of the nano-cavity for some given values of diameter are calculated. Within 1–10nm cavity diameter, we have
Lattice Molecular Dynamics: Extending the Scale of Molecular Dynamics
Jeffrey Yepez
1996-01-01
Presented is a lattice molecular dynamics technique for extending the spatial and temporal scales achieved with standard molecular dynamics modelling techniques. In the lattice molecular dyanamics, particle momenta and positions are discrete. Particle dynamics described by a general Hamiltonian are carried out in a fashion that obeys semi-detailed balance. Furthermore, all additive conserved quantities, mass, momentum, and energy, are exactly
NASA Astrophysics Data System (ADS)
Olmsted, David; Hector, Louis, Jr.; Curtin, W. A.
2005-03-01
Magnesium is used as a substitutional alloying agent to improve the formability, and other properties, of aluminum in alloys such as 5xxx aluminum. Serrated flow (Portevin-Le Chatelier effect) in these alloys limit their usefulness in certain automotive applications. These serrated flow effects are believed to be dependent on Mg diffusion. In order to establish both a baseline for and a suitable model in which to study the effect of diffusion on dislocation mobility in Al-Mg alloys we have performed molecular dynamics simulations the motion of a single dislocation in Al with randomly distributed 2.5 and 5.0 at% Mg. For a suitable length of dislocation, on the order of the Labusch length, we compare pinning and de-pinning of the dislocation in the molecular dynamics with a model in which a straight dislocation interacts with single Mg atoms, the small Mg-Mg interactions being ignored. We report on the results of the molecular dynamics simulations and the validation of the one-dimensional energy map model.
Toby W. Allen; Olaf S. Andersen; Benoit Roux
2006-01-01
We investigate methods for extracting the potential of mean force (PMF) governing ion permeation from molecular dynamics simulations (MD) using gramicidin A as a prototypical narrow ion channel. It is possible to obtain well-converged meaningful PMFs using all-atom MD, which predict experimental observables within order-of-magnitude agreement with experimental results. This was possible by careful attention to issues of statistical convergence
Michael Levitt; Miriam Hirshberg; Ruth Sharon; Valerie Daggett
1995-01-01
We present the complete set of energy parameters used in the ENCAD (Energy Calculation and Dynamics) simulation program [J. Mol. Biol. 168 (1983) 595]. Full details are given of the form of the potential, which has been designed for efficient simulation of trajectories of macromolecules in solution. Emphasis is placed on energy conservation and the nonbonded truncation schemes needed to
Sakiyama, Yukinori; Takagi, Shu; Matsumoto, Yoichiro
2005-06-15
We demonstrate a validation of the intermolecular pair potential model of SiH(4), which is constructed from ab initio molecular-orbital calculations and expressed as the sum of the exponential and the London dispersion terms. The saturated liquid densities of SiH(4) are calculated for temperatures from 100 to 225 K by molecular-dynamics (MD) simulation. The average deviation between the experiment and the MD simulation using the present potential model is 3.9%, while the deviations exceed 10% for other well-known potential models such as the five-center Lennard-Jones (LJ) model. Subsequently, the shear viscosity, the thermal conductivity, and the self-diffusion coefficient of liquid SiH(4) are calculated by an equilibrium MD simulation with the Green-Kubo formula from 100 to 225 K. The average deviations from experiment are 11.8% and 13.7% for the shear viscosity and the thermal conductivity, respectively. Comparing the present model with an empirical one-center LJ model, it turns out that the rotational energy transfer through the intermolecular potential energy, which comes from the anisotropic potential energy, plays an important role in the thermal conductivity of liquid SiH(4). These results indicate that the present intermolecular potential model has an ability to give realistic pictures for liquid SiH(4) through molecular simulations. PMID:16008456
Tight binding molecular dynamics
Goedecker, S. [Cornell Univ., Ithaca, NY (United States). Cornell Theory Center; Colombo, L. [Univ. di Milano (Italy). Dipt. di Fisica
1994-12-31
Molecular Dynamics is a widely used method to calculate structural and thermodynamic properties of materials. With a new and intrinsically parallel algorithm for Tight Binding Molecular Dynamics the authors obtain a performance of 3.4 Gigaflops per million dollar on a cluster of 8 Hewlett Packard workstations in a simulation of 216 Silicon atoms. One time step with this new algorithm takes as much time for the 216 atom system as one time step with a conventional algorithm on a NEC-SX3 supercomputer. In addition, the linear scaling of new algorithm allows them to calculate systems of unprecedented size which are not any more accessible by the combination of standard algorithms and vector supercomputers.
Dynamics of charged molecular strands
David C. P. Ellis; Francois Gay-Balmaz; Darryl D. Holm; Vakhtang Putkaradze; Tudor S. Ratiu
2009-01-19
Euler-Poincare equations are derived for the dynamical folding of charged molecular strands (such as DNA) modeled as flexible continuous filamentary distributions of interacting rigid charge conformations. The new feature is that the equations of motion for the dynamics of such molecular strands are nonlocal when the screened Coulomb interactions, or Lennard-Jones potentials between pairs of charges are included. These nonlocal dynamical equations are derived in the convective representation of continuum motion by using modified Euler-Poincare and Hamilton-Pontryagin variational formulations that illuminate the various approaches within the framework of symmetry reduction of Hamilton's principle for exact geometric rods. In the absence of nonlocal interactions, the equations recover the classical Kirchhoff theory of elastic rods in the spatial representation. The motion equations in the convective representation are shown to be affine Euler-Poincare equations relative to a certain cocycle. This property relates the geometry of the molecular strands to that of complex fluids. An elegant change of variables allows a direct passage from the infinite dimensional point of view to the covariant formulation in terms of Lagrange-Poincare equations. In another revealing perspective, the convective representation of the nonlocal equations of molecular strand motion is transformed into quaternionic form.
Abdel-Waged, Khaled [Umm Al-Qura University, Faculty of Applied Science, Physics Department, Makkah Unit 126, P.O. Box 7047 (Saudi Arabia)
2006-09-15
The dependence of spallation neutron production double-differential cross sections on the density of the quantum molecular dynamics potential is investigated in p+Al, Fe, Zr, and Pb reactions at 1.2 GeV. It is shown that the cascade component of the neutron spectra is largely unaffected by the parameters of the density-dependent potential. As for the evaporative part (<20 MeV), some differences are marked only for Pb. Calculated results with a Skyrme-type equation of state of K=300 MeV reproduce the neutron spectra for the reactions under study.
NASA Astrophysics Data System (ADS)
Liu, J.; Lu, W. Q.
2010-03-01
This paper presents the detailed MD simulation on the properties including the thermal conductivities and viscosities of the quantum fluid helium at different state points. The molecular interactions are represented by the Lennard-Jones pair potentials supplemented by quantum corrections following the Feynman-Hibbs approach and the properties are calculated using the Green-Kubo equations. A comparison is made among the numerical results using LJ and QFH potentials and the existing database and shows that the LJ model is not quantitatively correct for the supercritical liquid helium, thereby the quantum effect must be taken into account when the quantum fluid helium is studied. The comparison of the thermal conductivity is also made as a function of temperatures and pressure and the results show quantum effect correction is an efficient tool to get the thermal conductivities.
Multiscale reactive molecular dynamics
NASA Astrophysics Data System (ADS)
Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.
2012-12-01
Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system.
Multiscale reactive molecular dynamics.
Knight, Chris; Lindberg, Gerrick E; Voth, Gregory A
2012-12-14
Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system. PMID:23249062
Multiscale reactive molecular dynamics
Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.
2012-01-01
Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system. PMID:23249062
Interactive molecular dynamics
NASA Astrophysics Data System (ADS)
Schroeder, Daniel V.
2015-03-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in html5 and javascript for running within any modern Web browser, is provided as an online supplement.
Interactive molecular dynamics
Schroeder, Daniel V
2015-01-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in HTML5 and JavaScript for running within any modern Web browser, is provided as an online supplement.
Constant pressure molecular dynamics for molecular systems
Shuichi Nosé; M. L. Klein
1983-01-01
Technical aspects of the constant pressure molecular dynamics (MD) method proposed by Andersen and extended by Parrinello and Rahman to allow changes in the shape of the MD cell are discussed. The new MD method is extended to treat molecular systems and to include long range charge-charge interactions.Results on the conservation laws, the frequency of oscillation of the MD cell,
Jiang, Ludi; Zhang, Xianbao; Chen, Xi; He, Yusu; Qiao, Liansheng; Zhang, Yanling; Li, Gongyu; Xiang, Yuhong
2015-01-01
The metabotropic glutamate subtype 1 (mGluR1), a member of the metabotropic glutamate receptors, is a therapeutic target for neurological disorders. However, due to the lower subtype selectivity of mGluR1 orthosteric compounds, a new targeted strategy, known as allosteric modulators research, is needed for the treatment of mGluR1-related diseases. Recently, the structure of the seven-transmembrane domain (7TMD) of mGluR1 has been solved, which reveals the binding site of allosteric modulators and provides an opportunity for future subtype-selectivity drug design. In this study, a series of computer-aided drug design methods were utilized to discover potential mGluR1 negative allosteric modulators (NAMs). Pharmacophore models were constructed based on three different structure types of mGluR1 NAMs. After validation using the built-in parameters and test set, the optimal pharmacophore model of each structure type was selected and utilized as a query to screen the Traditional Chinese Medicine Database (TCMD). Then, three different hit lists of compounds were obtained. Molecular docking was used based on the latest crystal structure of mGluR1-7TMD to further filter these hits. As a compound with high QFIT and LibDock Score was preferred, a total of 30 compounds were retained. MD simulation was utilized to confirm the stability of potential compounds binding. From the computational results, thesinine-4'-O-?-d-glucoside, nigrolineaxanthone-P and nodakenin might exhibit negative allosteric moderating effects on mGluR1. This paper indicates the applicability of molecular simulation technologies for discovering potential natural mGluR1 NAMs from Chinese herbs. PMID:26184151
Molecular Dynamics Study of Alkali Thiocyanates
M. Ossowski; J. R. Hardy
1997-01-01
Calculations based on an ab initio model developed for intermolecular and intramolecular potentials in ionic molecular solids, performed before on A_2BX4 compounds(H. M. Lu and J. R. Hardy, Phys. Rev. B, 42, 8339 (1990)), are now extended to include a sequence of thiocyanates including NaSCN, KSCN, RbSCN and CsSCN. We performed first-principles static structural relaxation, supercell molecular-dynamics, lattice-dynamical studies and
Stochastic Event-Driven Molecular Dynamics
Aleksandar Donev; Alejandro L. Garcia; Berni J. Alder
2008-01-01
A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. SEDMD combines event-driven molecular dynamics (EDMD) with the Direct Simulation Monte Carlo (DSMC) method. The polymers are represented as chains of hard-spheres tethered by square wells and interact with the solvent particles with hard-core potentials. The algorithm uses EDMD for
Torres, Rodrigo; Swift, Robert V.; Chim, Nicholas; Wheatley, Nicole; Lan, Benson; Atwood, Brian R.; Pujol, Céline; Sankaran, Banu; Bliska, James B.; Amaro, Rommie E.; Goulding, Celia W.
2011-01-01
Human diseases are attributed in part to the ability of pathogens to evade the eukaryotic immune systems. A subset of these pathogens has developed mechanisms to survive in human macrophages. Yersinia pestis, the causative agent of the bubonic plague, is a predominately extracellular pathogen with the ability to survive and replicate intracellularly. A previous study has shown that a novel rip (required for intracellular proliferation) operon (ripA, ripB and ripC) is essential for replication and survival of Y. pestis in postactivated macrophages, by playing a role in lowering macrophage-produced nitric oxide (NO) levels. A bioinformatics analysis indicates that the rip operon is conserved among a distally related subset of macrophage-residing pathogens, including Burkholderia and Salmonella species, and suggests that this previously uncharacterized pathway is also required for intracellular survival of these pathogens. The focus of this study is ripA, which encodes for a protein highly homologous to 4-hydroxybutyrate-CoA transferase; however, biochemical analysis suggests that RipA functions as a butyryl-CoA transferase. The 1.9 Å X-ray crystal structure reveals that RipA belongs to the class of Family I CoA transferases and exhibits a unique tetrameric state. Molecular dynamics simulations are consistent with RipA tetramer formation and suggest a possible gating mechanism for CoA binding mediated by Val227. Together, our structural characterization and molecular dynamic simulations offer insights into acyl-CoA specificity within the active site binding pocket, and support biochemical results that RipA is a butyryl-CoA transferase. We hypothesize that the end product of the rip operon is butyrate, a known anti-inflammatory, which has been shown to lower NO levels in macrophages. Thus, the results of this molecular study of Y. pestis RipA provide a structural platform for rational inhibitor design, which may lead to a greater understanding of the role of RipA in this unique virulence pathway. PMID:21966419
Dynamic fracture toughness determined using molecular dynamics
Swadener, J. G. (John G.); Baskes, M. I. (Michael I.); Nastasi, Michael Anthony,
2004-01-01
Molecular dynamics (MD) simulations of fracture in crystalline silicon are conducted in order to determine the dynamic fracture toughness. The MD simulations show how the potential energy released during fracture is partitioned into surface energy, energy stored in defects and kinetic energy. First, the MD fracture simulations are shown to produce brittle fracture and be in reasonable agreement with experimental results. Then dynamic hcture toughness is calculated as the sum of the surface energy and the energy stored as defects directly from the MD models. Models oriented to produce fracture on either (111) or (101) planes are used. For the (101) fracture orientation, equilibrium crack speeds of greater than 80% of the Rayleigh wave speed are obtained. Crack speeds initially show a steep increase with increasing energy release rate followed by a much more gradual increase. No plateau in crack speed is observed for static energy release rates up to 20 J/m{sup 2}. At the point where the change in crack speed behavior occur, the dynamic fracture toughness (J{sub d}) is still within 10% of two times the surface energy (2{gamma}{sub 0}) and changing very slowly. From these MD simulations, it appears that the change in crack speed behavior is due to a change in the kinetic energy generation during dynamic fracture. In addition, MD simulations of facture in silicon with defects were conducted. The addition of defects increases the inelastic dissipation and the energy stored in defects.
Scalable molecular dynamics with NAMD.
Phillips, James C; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D; Kalé, Laxmikant; Schulten, Klaus
2005-12-01
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu. PMID:16222654
Scalable Molecular Dynamics with NAMD
Phillips, James C.; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D.; Kalé, Laxmikant; Schulten, Klaus
2008-01-01
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This paper, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Next, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, e.g., the Tcl scripting language. Finally, the paper provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu. PMID:16222654
Ghosh, Manik Kumer; Lee, Jooyong; Choi, Cheol Ho; Cho, Minhaeng
2012-09-13
One of the most stringent tests for chemical accuracy of a hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation method would be to directly compare the calculated vibrational spectra with the corresponding experimental results. Here, the applicability of hybrid QM/effective fragment potential (EFP) to the simulations of methanol infrared spectra is investigated in detail. It is demonstrated that the QM/EFP simulations in combination with time correlation function theory yield not only the fundamental transition bands but also the major overtone and combination bands of methanol dissolved in water in both mid- and near-IR regions. This clearly indicates that the QM/EFP-molecular dynamics can be a viable way of obtaining an anharmonic infrared spectrum that provides information on solvatochromic frequency shifts and fluctuations, solute-solvent interaction-induced dephasing, and anharmonic coupling effects on vibrational spectra of aqueous solutions. We anticipate that the computational protocol developed here can be effectively used to simulate both one- and two-dimensional vibrational spectra of biomolecules and chemically reactive systems in condensed phases. PMID:22913548
Virtual Molecular Dynamics Laboratory (VMDL)
NSDL National Science Digital Library
Center for Polymer Studies
The Virtual Molecular Dynamics Laboratory is a software and curriculum package that enables students to work with research quality molecular dynamics simulations. Users can easily visualize atomic motion, manipulate atomic interactions, and quantitatively investigate the resulting macroscopic properties of biological, chemical, and physical systems.
Floating orbital molecular dynamics simulations.
Perlt, Eva; Brüssel, Marc; Kirchner, Barbara
2014-04-21
We introduce an alternative ab initio molecular dynamics simulation as a unification of Hartree-Fock molecular dynamics and the floating orbital approach. The general scheme of the floating orbital molecular dynamics method is presented. Moreover, a simple but sophisticated guess for the orbital centers is provided to reduce the number of electronic structure optimization steps at each molecular dynamics step. The conservation of total energy and angular momentum is investigated in order to validate the floating orbital molecular dynamics approach with and without application of the initial guess. Finally, a water monomer and a water dimer are simulated, and the influence of the orbital floating on certain properties like the dipole moment is investigated. PMID:24600690
Vitaliy Kapko; Dmitry V. Matyushov; C. Austen Angell
2011-06-07
The ability of some liquids to vitrify during supercooling is usually seen as a consequence of the rates of crystal nucleation (and/or crystal growth) becoming small- thus a matter of kinetics. However there is evidence, dating back to the empirics of coal briquetting for maximum trucking efficiency, that ellipsoids pack efficiently when disordered. Noting that key studies of non-spherical object packing have never been followed from hard ellipsoids or spherocylinders (diatomics excepted) into the world of molecules with attractive forces, we have made a molecular dynamics MD study of crystal melting and glass formation on the Gay- Berne (G-B) model of ellipsoidal objects across the aspect ratio range of the hard ellipsoid studies. Here we report that, in the aspect ratio range of maximum ellipsoid packing efficiency, various G-B crystalline states, that cannot be obtained directly from the liquid, disorder spontaneously near 0 K and transform to liquids without any detectable enthalpy of fusion. Without claiming to have proved the existence of single component examples, we use the present observations, together with our knowledge of non-ideal mixing effects, to discuss the probable existence of "ideal glassformers" - single or multicomponent liquids that vitrify before ever becoming metastable with respect to crystals. The existence of crystal-free routes to the glassy state removes any precrystalline fluctuation perspective from the "glass problem". Unexpectedly we find that liquids with aspect ratios in the "crystallophobic" range also behave in an unusual (non-hysteritic) way during temperature cycling through the glass transition. We link this to the highly volume fraction-sensitive ("fragile") behavior observed in recent hard dumbbell studies at similar length/diameter ratios.
Plasticity of metal wires in torsion: Molecular dynamics and dislocation dynamics simulations
Cai, Wei
Brittle and ductile fracture of semiconductor nanowires -- molecular dynamics simulations Keonwook is studied by Molecular Dynamics simulations using sev- eral inter-atomic potential models. While some15, 1121 May 2007, 21692189 #12;Contents 1 Introduction 3 2 Molecular dynamics simulations 4 2
NASA Astrophysics Data System (ADS)
Yang, Xu-qiu; Zhai, Peng-cheng; Liu, Li-sheng; Chen, Gang; Zhang, Qing-jie
2014-06-01
Molecular dynamics simulations have been performed to investigate the effect of nanometer-size pores on the phonon conductivity of single-crystal bulk CoSb3. The cylindrical pores are uniformly distributed along two vertical principal crystallographic directions of a square lattice. Because pore diameter and porosity are two key factors that could affect the performance of the materials, they were varied individually in the ranges a 0-6 a 0 and 0.1-5%, respectively, where a 0 is the lattice constant of CoSb3. The simulation results indicate that the phonon conductivity of nanoporous CoSb3 is significantly lower than that of no-pore CoSb3. The reduction of phonon conductivity in this simulation was consistent with the ballistic-diffusive microscopic effective medium model, demonstrating the ballistic character of phonon transport when the phonon mean-free-path is comparable with or larger than the pore size. Reducing pore diameter or increasing porosity are alternative means of effective reduction of the thermal conductivity of CoSb3. These results are expected to provide a useful basis for the design of high-performance skutterudites.
Discrete Molecular Dynamics Simulation of Biomolecules
NASA Astrophysics Data System (ADS)
Ding, Feng
2011-10-01
Discrete molecular dynamics (DMD) simulation of hard spheres was the first implementation of molecular dynamics (MD) in history. DMD simulations are computationally more efficient than continuous MD simulations due to simplified interaction potentials. However, also due to these simplified potentials, DMD has often been associated with coarse-grained modeling, and hence continuous MD has become the dominant approach used to study the internal dynamics of biomolecules. With the recent advances in DMD methodology, including the development of high-resolution models for biomolecules and approaches to increase DMD efficiency, DMD simulations are emerging as an important tool in the field of molecular modeling, including the study of protein folding, protein misfolding and aggregation, and protein engineering. Recently, DMD methodology has been applied to modeling RNA folding and protein-ligand recognition. With these improvements to DMD methodology and the continuous increase in available computational power, we expect a growing role of DMD simulations in our understanding of biology.
Larcher, G.; Tran, H., E-mail: ha.tran@lisa.u-pec.fr; Schwell, M.; Chelin, P.; Landsheere, X.; Hartmann, J.-M. [Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA, CNRS UMR 7583), Université Paris Est Créteil, Université Paris Diderot, Institut Pierre-Simon Laplace, 94010 Créteil Cedex (France)] [Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA, CNRS UMR 7583), Université Paris Est Créteil, Université Paris Diderot, Institut Pierre-Simon Laplace, 94010 Créteil Cedex (France); Hu, S.-M. [Hefei National Laboratory for Sciences at Microscale, University of Science and Technology of China, 230026 Hefei (China)] [Hefei National Laboratory for Sciences at Microscale, University of Science and Technology of China, 230026 Hefei (China)
2014-02-28
Room temperature absorption spectra of various transitions of pure CO{sub 2} have been measured in a broad pressure range using a tunable diode-laser and a cavity ring-down spectrometer, respectively, in the 1.6 ?m and 0.8 ?m regions. Their spectral shapes have been calculated by requantized classical molecular dynamics simulations. From the time-dependent auto-correlation function of the molecular dipole, including Doppler and collisional effects, spectral shapes are directly computed without the use of any adjusted parameter. Analysis of the spectra calculated using three different anisotropic intermolecular potentials shows that the shapes of pure CO{sub 2} lines, in terms of both the Lorentz widths and non-Voigt effects, slightly depend on the used potential. Comparisons between these ab initio calculations and the measured spectra show satisfactory agreement for all considered transitions (from J = 6 to J = 46). They also show that non-Voigt effects on the shape of CO{sub 2} transitions are almost independent of the rotational quantum number of the considered lines.
Patel, Sonal; Wilding, W Vincent; Rowley, Richard L
2011-12-21
Two-phase molecular dynamics simulations employing a Monte Carlo volume sampling method were performed using an ab initio based force field model parameterized to reproduce quantum-mechanical dimer energies for methanol and 1-propanol at temperatures approaching the critical temperature. The intermolecular potential models were used to obtain the binodal vapor-liquid phase dome at temperatures to within about 10 K of the critical temperature. The efficacy of two all-atom, site-site pair potential models, developed solely from the energy landscape obtained from high-level ab initio pair interactions, was tested for the first time. The first model was regressed from the ab initio landscape without point charges using a modified Morse potential to model the complete interactions; the second model included point charges to separate Coulombic and dispersion interactions. Both models produced equivalent phase domes and critical loci. The model results for the critical temperature, density, and pressure, in addition to the sub-critical equilibrium vapor and liquid densities and vapor pressures, are compared to experimental data. The model's critical temperature for methanol is 77 K too high while that for 1-propanol is 80 K too low, but the critical densities are in good agreement. These differences are likely attributable to the lack of multi-body interactions in the true pair potential models used here. PMID:22191893
NASA Astrophysics Data System (ADS)
Patel, Sonal; Wilding, W. Vincent; Rowley, Richard L.
2011-12-01
Two-phase molecular dynamics simulations employing a Monte Carlo volume sampling method were performed using an ab initio based force field model parameterized to reproduce quantum-mechanical dimer energies for methanol and 1-propanol at temperatures approaching the critical temperature. The intermolecular potential models were used to obtain the binodal vapor-liquid phase dome at temperatures to within about 10 K of the critical temperature. The efficacy of two all-atom, site-site pair potential models, developed solely from the energy landscape obtained from high-level ab initio pair interactions, was tested for the first time. The first model was regressed from the ab initio landscape without point charges using a modified Morse potential to model the complete interactions; the second model included point charges to separate Coulombic and dispersion interactions. Both models produced equivalent phase domes and critical loci. The model results for the critical temperature, density, and pressure, in addition to the sub-critical equilibrium vapor and liquid densities and vapor pressures, are compared to experimental data. The model's critical temperature for methanol is 77 K too high while that for 1-propanol is 80 K too low, but the critical densities are in good agreement. These differences are likely attributable to the lack of multi-body interactions in the true pair potential models used here.
Sheldon Goldstein; Ward Struyve
2014-11-05
Non-relativistic de Broglie-Bohm theory describes particles moving under the guidance of the wave function. In de Broglie's original formulation, the particle dynamics is given by a first-order differential equation. In Bohm's reformulation, it is given by Newton's law of motion with an extra potential that depends on the wave function--the quantum potential--together with a constraint on the possible velocities. It was recently argued, mainly by numerical simulations, that relaxing this velocity constraint leads to a physically untenable theory. We provide further evidence for this by showing that for various wave functions the particles tend to escape the wave packet. In particular, we show that for a central classical potential and bound energy eigenstates the particle motion is often unbounded. This work seems particularly relevant for ways of simulating wave function evolution based on Bohm's formulation of the de Broglie-Bohm theory. Namely, the simulations may become unstable due to deviations from the velocity constraint.
Priya Vashishta; Rajiv K. Kalia; Aiichiro Nakano; José Pedro Rino
2011-01-01
An effective interatomic interaction potential for AlN is proposed. The potential consists of two-body and three-body covalent interactions. The two-body potential includes steric repulsions due to atomic sizes, Coulomb interactions resulting from charge transfer between atoms, charge-induced dipole-interactions due to the electronic polarizability of ions, and induced dipole-dipole (van der Waals) interactions. The covalent characters of the Al-N-Al and N-Al-N
Molecular dynamics simulations of biomolecules
J. Andrew McCammon; Martin Karplus
2002-01-01
Molecular dynamics simulations are important tools for understanding the physical basis of the structure and function of biological macromolecules. The early view of proteins as relatively rigid structures has been replaced by a dynamic model in which the internal motions and resulting conformational changes play an essential role in their function. This review presents a brief description of the origin
Attard, Phil
Stochastic molecular dynamics: A combined Monte Carlo and molecular dynamics technique techniques--Monte Carlo and molecular dynamics--has their own advantage. The molecular dynamics method can to cover the important states of the system in an efficient manner. In recent years the molecular dynamics
Schlegel, H. Bernhard
Ab Initio Molecular Dynamics Bull. Korean Chem. Soc. 2003, Vol. 24, No. 6 1 Ab Initio Molecular February 25, 2003 In ab initio molecular dynamics, whenever information about the potential energy surface advances for both approaches are discussed. Key Words : Ab initio molecular dynamics, Direct classical
Brela, Mateusz Z; Wójcik, Marek J; Boczar, Marek; Witek, ?ukasz; Yasuda, Mitsuru; Ozaki, Yukihiro
2015-06-25
We studied proton dynamics of a hydrogen bonds of the crystalline l-ascorbic acid. Our approach was based on the Car-Parrinello molecular dynamics. The focal point of our study was simulation of the infrared spectra of l-ascorbic acid associated with the O-H stretching modes that are very sensitive to the strength of hydrogen bonding. In the l-ascorbic acid there are four kinds of hydrogen bonds. We calculated their spectra by using anharmonic approximation and the time course of the dipole moment function as obtained from the Car-Parrinello simulation. The quantization of the nuclear motion of the protons was made to perform detailed analysis of strength and properties of hydrogen bonds. We presented double minimum proton potentials with small value of barriers for medium-strong hydrogen bonds. We have also shown the difference character of medium-strong hydrogen bonds compared to weaker hydrogen bonds in the l-ascorbic acid. PMID:26028251
Interatomic potential for Pd and molecular-dynamics simulation of diffusion in Pd\\/Pd(1 1 1) system
N. I Papanicolaou; D. A Papaconstantopoulos
2003-01-01
We present a many-body interatomic potential for Pd within the second-moment approximation of the tight-binding model by fitting to the volume dependence of the total energy of the metal, computed by first-principles linearized augmented plane wave calculations. This potential achieved good accuracy for the elastic constants, phonon spectrum, along with the temperature dependence of the lattice constant of Pd. This
Modeling Molecular Dynamics from Simulations
Hinrichs, Nina Singhal (University of Chicago) [University of Chicago
2009-01-28
Many important processes in biology occur at the molecular scale. A detailed understanding of these processes can lead to significant advances in the medical and life sciences. For example, many diseases are caused by protein aggregation or misfolding. One approach to studying these systems is to use physically-based computational simulations to model the interactions and movement of the molecules. While molecular simulations are computationally expensive, it is now possible to simulate many independent molecular dynamics trajectories in a parallel fashion by using super- or distributed- computing methods such as Folding@Home or Blue Gene. The analysis of these large, high-dimensional data sets presents new computational challenges. In this seminar, I will discuss a novel approach to analyzing large ensembles of molecular dynamics trajectories to generate a compact model of the dynamics. This model groups conformations into discrete states and describes the dynamics as Markovian, or history-independent, transitions between the states. I will discuss why the Markovian state model (MSM) is suitable for macromolecular dynamics, and how it can be used to answer many interesting and relevant questions about the molecular system. I will also discuss many of the computational and statistical challenges in building such a model, such as how to appropriately cluster conformations, determine the statistical reliability, and efficiently design new simulations.
Kumar, R. Barani; Priya, B. Shanmuga; Suresh, M. Xavier
2015-01-01
Objective: Charybdotoxin-C (ChTx-C), from the scorpion Leiurus, quinquestriatus hebraeus blocks the calcium-activated potassium channels and causes hyper excitability of the nervous system. Detailed understanding the structure of ChTx-C, conformational stability, and intermolecular interactions are required to select the potential inhibitors of the toxin. Materials and Methods: The structure of ChTx-C was modeled using Modeller 9v7. The amino acid residues lining the binding site were predicted and used for toxin-ligand docking studies, further, selected toxin-inhibitor complexes were studied using molecular dynamics (MD) simulations. Results: The predicted structure has 91.7% of amino acids in the core and allowed regions of Ramachandran plot. A total of 133 analog compounds of existing drugs for scorpion bites were used for docking. As a result of docking, a list of compounds was shown good inhibiting properties with target protein. By analyzing the interactions, Ser 15, Lys 32 had significant interactions with selected ligand molecules and Val5, which may have hydrophobic interaction with the cyclic group of the ligand. MD simulation studies revealed that the conformation and intermolecular interactions of all selected toxin-inhibitor complexes were stable. Conclusion: The interactions of the ligand and active site amino acids were found out for the best-docked poses in turn helpful in designing potential antitoxins which may further be exploited in toxin based therapies.
Toby W. Allen; Olaf S. Andersen; Benoit Roux
2006-01-01
Ion channels catalyze the permeation of charged molecules across cell membranes and are essential for many vital physiological functions, including nerve and muscle activity. To understand better the mechanisms underlying ion conduction and valence selectivity of narrow ion channels, we have employed free energy techniques to calculate the potential of mean force (PMF) for ion movement through the prototypical gramicidin
Grand Canonical Molecular Dynamics Sharada Boinepalli
Attard, Phil
Grand Canonical Molecular Dynamics Sharada Boinepalli CSSM, University of Adelaide, SA 5005. Phys., 119, 1276912775 (2003)) A hybrid molecular dynamics-Monte Carlo grand canonical simulation of solids, liquids or gases can be simu- lated at the molecular level in two ways, viz., molecular dynamics
Design Challenges for Control of Molecular Dynamics
Peirce, Anthony
Design Challenges for Control of Molecular Dynamics M. Dahleh,A.P. Peirce, and H. Rabitz Molecular is a problem of control over molecular structure, if not dynamics itself. The success- ful introduction, the extemal optical field must literally take over the molecular dynamics, or at least work cooperatively
State-dependent molecular dynamics.
Yang, Ciann-Dong; Weng, Hung-Jen
2014-01-01
This paper proposes a new mixed quantum mechanics (QM)-molecular mechanics (MM) approach, where MM is replaced by quantum Hamilton mechanics (QHM), which inherits the modeling capability of MM, while preserving the state-dependent nature of QM. QHM, a single mechanics playing the roles of QM and MM simultaneously, will be employed here to derive the three-dimensional quantum dynamics of diatomic molecules. The resulting state-dependent molecular dynamics including vibration, rotation and spin are shown to completely agree with the QM description and well match the experimental vibration-rotation spectrum. QHM can be incorporated into the framework of a mixed quantum-classical Bohmian method to enable a trajectory interpretation of orbital-spin interaction and spin entanglement in molecular dynamics. PMID:25302703
How accurate is molecular dynamics?
Christian Bayer; Håkon Hoel; Petr Plechá?; Anders Szepessy; Raúl Tempone
2011-09-20
Born-Oppenheimer dynamics is shown to provide an accurate approximation of time-independent Schr\\"odinger observables for a molecular system with an electron spectral gap, in the limit of large ratio of nuclei and electron masses, without assuming that the nuclei are localized to vanishing domains. The derivation, based on a Hamiltonian system interpretation of the Schr\\"odinger equation and stability of the corresponding Hamilton-Jacobi equation, bypasses the usual separation of nuclei and electron wave functions, includes caustic states and gives a different perspective on the Born-Oppenheimer approximation, Schr\\"odinger Hamiltonian systems and numerical simulation in molecular dynamics modeling at constant energy microcanonical ensembles.
Molecular dynamics and protein function
Karplus, M.; Kuriyan, J.
2005-01-01
A fundamental appreciation for how biological macromolecules work requires knowledge of structure and dynamics. Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled with improvements in methodology makes this an exciting time for the application of simulation to structural biology. In this Perspective we survey two areas, protein folding and enzymatic catalysis, in which simulations have contributed to a general understanding of mechanism. We also describe results for the F1 ATPase molecular motor and the Src family of signaling proteins as examples of applications of simulations to specific biological systems. PMID:15870208
Soliton dynamics in complex potentials
NASA Astrophysics Data System (ADS)
Kominis, Yannis
2015-01-01
Soliton propagation dynamics under the presence of a complex potential are investigated. Cases of both symmetric and non-symmetric potentials are studied in terms of their effect on soliton dynamics. The existence of an invariant of soliton propagation under specific symmetry conditions for the real and the imaginary part of the potential is shown. The rich set of dynamical features of soliton propagation include dynamical trapping, periodic and nonperiodic soliton mass variation and non-reciprocal dynamics. These features are systematically investigated with the utilization of an effective particle phase space approach which is shown in remarkable agreement with direct numerical simulations. The generality of the results enables the consideration of potential applications where the inhomogeneity of the gain and loss is appropriately engineered in order to provide desirable soliton dynamics.
Population Based Reweighting of Scaled Molecular Dynamics
2013-01-01
Molecular dynamics simulation using enhanced sampling methods is one of the powerful computational tools used to explore protein conformations and free energy landscapes. Enhanced sampling methods often employ either an increase in temperature or a flattening of the potential energy surface to rapidly sample phase space, and a corresponding reweighting algorithm is used to recover the Boltzmann statistics. However, potential energies of complex biomolecules usually involve large fluctuations on a magnitude of hundreds of kcal/mol despite minimal structural changes during simulation. This leads to noisy reweighting statistics and complicates the obtainment of accurate final results. To overcome this common issue in enhanced conformational sampling, we propose a scaled molecular dynamics method, which modifies the biomolecular potential energy surface and employs a reweighting scheme based on configurational populations. Statistical mechanical theory is applied to derive the reweighting formula, and the canonical ensemble of simulated structures is recovered accordingly. Test simulations on alanine dipeptide and the fast folding polypeptide Chignolin exhibit sufficiently enhanced conformational sampling and accurate recovery of free energy surfaces and thermodynamic properties. The results are comparable to long conventional molecular dynamics simulations and exhibit better recovery of canonical statistics over methods which employ a potential energy term in reweighting. PMID:23721224
Kapko, Vitaliy; Angell, C Austen
2010-01-01
The ability of some liquids to vitrify during supercooling is usually seen as a consequence of the rates of crystal nucleation (and/or crystal growth) becoming small [1] - thus a matter of kinetics. However there is evidence, dating back to the empirics of coal briquetting for maximum trucking efficiency [2] that some object shapes find little advantage in self- assembly to ordered structures - meaning random packings prevail. Noting that key studies of non-spherical object packing have never been followed from hard ellipsoids [3,4] or spherocylinders [5] into the world of molecules with attractive forces, we have carried out potential tuning MD studies on the behavior of the Gay-Berne (G-B) model [6] at aspect ratios in the range of the hard ellipsoid studies. Here we report that, in the aspect ratio range of maximum ellipsoid packing efficiency, some G-B crystalline states disorder spontaneously near 0 K and transform to liquids without any detectable enthalpy of fusion. Cooling of the liquids in this range...
Allen, Toby W.; Andersen, Olaf S.; Roux, Benoit
2006-01-01
We investigate methods for extracting the potential of mean force (PMF) governing ion permeation from molecular dynamics simulations (MD) using gramicidin A as a prototypical narrow ion channel. It is possible to obtain well-converged meaningful PMFs using all-atom MD, which predict experimental observables within order-of-magnitude agreement with experimental results. This was possible by careful attention to issues of statistical convergence of the PMF, finite size effects, and lipid hydrocarbon chain polarizability. When comparing the modern all-atom force fields of CHARMM27 and AMBER94, we found that a fairly consistent picture emerges, and that both AMBER94 and CHARMM27 predict observables that are in semiquantitative agreement with both the experimental conductance and dissociation coefficient. Even small changes in the force field, however, result in significant changes in permeation energetics. Furthermore, the full two-dimensional free-energy surface describing permeation reveals the location and magnitude of the central barrier and the location of two binding sites for K+ ion permeation near the channel entrance—i.e., an inner site on-axis and an outer site off-axis. We conclude that the MD-PMF approach is a powerful tool for understanding and predicting the function of narrow ion channels in a manner that is consistent with the atomic and thermally fluctuating nature of proteins. PMID:16500984
Adaptive integration of molecular dynamics
Illia Horenko; Martin Weiser
2003-01-01
This article presents a particle method framework for simulating molecular dynamics. For time integration, the implicit trapezoidal rule is employed, where an explicit predictor enables large time steps. Error estimators for both the temporal and spatial discretization are advocated, and facilitate a fully adaptive propagation. The framework is developed and exemplified in the context of the classical Liouville equation, where
Molecular dynamics simulations in biology
Martin Karplus; Gregory A. Petsko
1990-01-01
Molecular dynamics-the science of simulating the motions of a system of particles-applied to biological macromolecules gives the fluctuations in the relative positions of the atoms in a protein or in DNA as a function of time. Knowledge of these motions provides insights into biological phenomena such as the role of flexibility in ligand binding and the rapid solvation of the
Elastic constants of sodium from molecular dynamics
Tahir Çagin; John R. Ray
1988-01-01
We have performed molecular-dynamics calculations of the adiabatic elastic constants of sodium at three different temperatures, T=198, 299, and 349 K. Our method uses fluctuation formulas appropriate for the microcanonical ensemble which contain the elastic constants. In the simulation we have used a first-principles potential to model the interaction between the sodium atoms. The results, including the shear modulus C44,
A molecular dynamics study on iridium
NASA Astrophysics Data System (ADS)
Ferah, Gülen; Colakoglu, Kemal; Ciftci, Yasemin; Ozgen, Soner; Kazanc, Sefa
2007-06-01
In this study, molecular dynamics simulations are performed by using a modified form of Morse potential function in the framework of the Embedded Atom Method (EAM). Temperature-and pressure-dependent behaviours of bulk modulus, second-order elastic constants (SOEC), and the linear-thermal expansion coefficient is calculated and compared with the available experimental data. The melting temperature is estimated from 3 different plots. The obtained results are in agreement with the available experimental findings for iridium.
Hall, G.E.; Prrese, J.M.; Sears, T.J.; Weston, R.E.
1999-05-21
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution high-sensitivity laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular flee radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wavepacket calculations that provide insights into energy flow between the vibrational modes of the molecule.
FPGA Acceleration of Discrete Molecular Dynamics Simulation
Herbordt, Martin
' & $ % FPGA Acceleration of Discrete Molecular Dynamics Simulation Joshua Model Thesis submitted UNIVERSITY COLLEGE OF ENGINEERING Thesis FPGA Acceleration of Discrete Molecular Dynamics Simulation Engineering Third Reader Alexander Taubin, Ph.D. Professor of Electreical and Computer Engineering #12;FPGA
FPGA ACCELERATION OF MOLECULAR DYNAMICS SIMULATIONS
Herbordt, Martin
this problem by creating an explicitly designed FPGA-coprocessor that can be integrated into generic' & $ % FPGA ACCELERATION OF MOLECULAR DYNAMICS SIMULATIONS YONGFENG GU Dissertation submitted;BOSTON UNIVERSITY COLLEGE OF ENGINEERING Dissertation FPGA ACCELERATION OF MOLECULAR DYNAMICS SIMULATIONS
NASA Astrophysics Data System (ADS)
Kiljunen, Toni; Eloranta, Jussi; Kunttu, Henrik
1999-06-01
Ground-state potential-energy curves and distance dependent isotropic hyperfine coupling (IHC) constants for ground-state H-RG (=Ne, Ar, Kr, Xe) are obtained at CCSD(T) (coupled-cluster single double triple) and MP4(SDQ) (fourth-order Moller-Plesset single double quadruple) levels, respectively, with an augmented basis set aug-Stuttgart (RG)/aug-cc-pVQZ (H). The obtained Rm and ? are for NeH: 3.45 Å and -1.36 meV; ArH: 3.65 Å and -3.48 meV; KrH: 3.75 Å and -4.32 meV; XeH: 3.90 Å and -5.22 meV. The computed pair potentials are utilized in classical molecular-dynamics simulations of H-RG lattices. Along the classical trajectory, the many-body perturbation on the H atom hyperfine coupling constant is computed by pair-wise addition of the individual RG-H contributions obtained from the present quantum-chemical calculations. The computed IHC shifts are compared with electron paramagnetic resonance (EPR) spectra obtained in low-temperature matrix isolation experiments. For most cases this theoretical treatment agrees very well with the experiment and confirms the previous site assignments. However, for H-Xe, the theory would suggest stability of both interstitial Oh and substitutional sites, whereas only one site is observed in the experiment. Based on the present calculations this site can be assigned as a nearly undistorted substitutional site.
Structure and dynamics of complex liquid water: Molecular dynamics simulation
NASA Astrophysics Data System (ADS)
S, Indrajith V.; Natesan, Baskaran
2015-06-01
We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.
MDLab: A Molecular Dynamics Simulation Prototyping Environment
Izaguirre, JesÃºs A.
MDLab: A Molecular Dynamics Simulation Prototyping Environment Trevor Cickovski1 ,Santanu level sampling protocols that run several instances of molecular dynamics. For computationally demanding-Eijnden. MDLab is available at http://mdlab.sourceforge.net. Key words: molecular dynamics, sampling, Python
A Fast Recursive Algorithm Molecular Dynamics Simulation
A Fast Recursive Algorithm for Molecular Dynamics Simulation A. Jain Jet Propulsion Laboratory: Molecular dynamics, algorithms, simulation. #12; Running head: A Fast Algorithm for MD Simulation Please Pasadena, CA 91109 2 #12; A Fast Recursive Algorithm for Molecular Dynamics Simulation A. Jain, N. Vaidehi
Saliency Guided Summarization of Molecular Dynamics Simulations
Varshney, Amitabh
Saliency Guided Summarization of Molecular Dynamics Simulations Robert Patro1 , Cheuk Yiu Ip1,ipcy,varshney}@cs.umd.edu Abstract We present a novel method to measure saliency in molecular dynamics simulation data. This saliency exceedingly long timescale molecular dynamics simulations, does not necessarily mean that we are better
Peridynamics as an Upscaling of Molecular Dynamics
Pablo Seleson; Michael L. Parks; Max Gunzburger; Richard B. Lehoucq
2009-01-01
Peridynamics is a formulation of continuum mechanics based on integral equations. It is a nonlocal model, accounting for the effects of long-range forces. Correspondingly, classical molecular dynamics is also a nonlocal model. Peridynamics and molecular dynamics have similar discrete computational structures, as peridynamics computes the force on a particle by summing the forces from surrounding particles, similarly to molecular dynamics.
Wilets, L.; Beck, W.
1991-12-31
classical many body models supplemented by repulsive momentum-dependent potentials to simulate the Pauli and Heisenberg principles have been use with some success for nuclear and atomic bound state and collision problems. They are capable of describing mean ground state properties, hydrodynamics, shocks (if warranted by the physics), viscosity, correlations, clustering, fragmentation, etc. We have become interested in the Feldmeier Gaussian packet formulation since it is based on a variational principle using trial wave functions. We discuss some limitations of the model and discuss further directions of investigation.
Wilets, L.; Beck, W.
1991-01-01
classical many body models supplemented by repulsive momentum-dependent potentials to simulate the Pauli and Heisenberg principles have been use with some success for nuclear and atomic bound state and collision problems. They are capable of describing mean ground state properties, hydrodynamics, shocks (if warranted by the physics), viscosity, correlations, clustering, fragmentation, etc. We have become interested in the Feldmeier Gaussian packet formulation since it is based on a variational principle using trial wave functions. We discuss some limitations of the model and discuss further directions of investigation.
Chapter 21 MOLECULAR DYNAMICS METHOD FOR MICRO/NANO SYSTEMS Shigeo Maruyama
Maruyama, Shigeo
1 Chapter 21 MOLECULAR DYNAMICS METHOD FOR MICRO/NANO SYSTEMS Shigeo Maruyama Department.1. INTRODUCTION 21.2. MOLECULAR DYNAMICS METHOD 21.2.1 Equations of Motion and Potential Functions 21.2.2 Examples and Dynamic Properties 21.2.7 Heat Conduction and Heat Transfer 21.3. MOLECULAR DYNAMICS OF PHASE
Langevin molecular dynamics derived from Ehrenfest dynamics
Anders Szepessy
2011-03-30
Stochastic Langevin molecular dynamics for nuclei is derived from the Ehrenfest Hamiltonian system (also called quantum classical molecular dynamics) in a Kac-Zwanzig setting, with the initial data for the electrons stochastically perturbed from the ground state and the ratio, $M$, of nuclei and electron mass tending to infinity. The Ehrenfest nuclei dynamics is approximated by the Langevin dynamics with accuracy $o(M^{-1/2})$ on bounded time intervals and by $o(1)$ on unbounded time intervals, which makes the small $\\mathcal{O}(M^{-1/2})$ friction and $o(M^{-1/2})$ diffusion terms visible. The initial electron probability distribution is a Gibbs density at low temperture, derived by a stability and consistency argument: starting with any equilibrium measure of the Ehrenfest Hamiltonian system, the initial electron distribution is sampled from the equilibrium measure conditioned on the nuclei positions, which after long time leads to the nuclei positions in a Gibbs distribution (i.e. asymptotic stability); by consistency the original equilibrium measure is then a Gibbs measure.The diffusion and friction coefficients in the Langevin equation satisfy the Einstein's fluctuation-dissipation relation.
Bernd Hartke; Emily A. Carter
1992-01-01
We present an abinitio molecular dynamics algorithm at the generalized valence bond level. It does not need a precalculated potential energy surface or model Hamiltonian; instead the nuclei move according to first principles forces derived from the electronic wave function which in turn follows the movement of the nuclei. This technique includes the dominant static electron correlations, it can treat
Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.
Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A
2012-12-11
It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as "multistate". These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations. PMID:25100924
Computationally Efficient Multiconfigurational Reactive Molecular Dynamics
Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A.
2012-01-01
It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as “multistate”. These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations. PMID:25100924
2015-01-01
Solute sampling of explicit bulk-phase aqueous environments in grand canonical (GC) ensemble simulations suffer from poor convergence due to low insertion probabilities of the solutes. To address this, we developed an iterative procedure involving Grand Canonical-like Monte Carlo (GCMC) and molecular dynamics (MD) simulations. Each iteration involves GCMC of both the solutes and water followed by MD, with the excess chemical potential (?ex) of both the solute and the water oscillated to attain their target concentrations in the simulation system. By periodically varying the ?ex of the water and solutes over the GCMC-MD iterations, solute exchange probabilities and the spatial distributions of the solutes improved. The utility of the oscillating-?ex GCMC-MD method is indicated by its ability to approximate the hydration free energy (HFE) of the individual solutes in aqueous solution as well as in dilute aqueous mixtures of multiple solutes. For seven organic solutes: benzene, propane, acetaldehyde, methanol, formamide, acetate, and methylammonium, the average ?ex of the solutes and the water converged close to their respective HFEs in both 1 M standard state and dilute aqueous mixture systems. The oscillating-?ex GCMC methodology is also able to drive solute sampling in proteins in aqueous environments as shown using the occluded binding pocket of the T4 lysozyme L99A mutant as a model system. The approach was shown to satisfactorily reproduce the free energy of binding of benzene as well as sample the functional group requirements of the occluded pocket consistent with the crystal structures of known ligands bound to the L99A mutant as well as their relative binding affinities. PMID:24932136
Statistical Prediction and Molecular Dynamics Simulation
Cooke, Ben; Schmidler, Scott C.
2008-01-01
We describe a statistical approach to the validation and improvement of molecular dynamics simulations of macromolecules. We emphasize the use of molecular dynamics simulations to calculate thermodynamic quantities that may be compared to experimental measurements, and the use of a common set of energetic parameters across multiple distinct molecules. We briefly review relevant results from the theory of stochastic processes and discuss the monitoring of convergence to equilibrium, the obtaining of confidence intervals for summary statistics corresponding to measured quantities, and an approach to validation and improvement of simulations based on out-of-sample prediction. We apply these methods to replica exchange molecular dynamics simulations of a set of eight helical peptides under the AMBER potential using implicit solvent. We evaluate the ability of these simulations to quantitatively reproduce experimental helicity measurements obtained by circular dichroism. In addition, we introduce notions of statistical predictive estimation for force-field parameter refinement. We perform a sensitivity analysis to identify key parameters of the potential, and introduce Bayesian updating of these parameters. We demonstrate the effect of parameter updating applied to the internal dielectric constant parameter on the out-of-sample prediction accuracy as measured by cross-validation. PMID:18676654
Dynamic strength of molecular adhesion bonds.
Evans, E; Ritchie, K
1997-01-01
In biology, molecular linkages at, within, and beneath cell interfaces arise mainly from weak noncovalent interactions. These bonds will fail under any level of pulling force if held for sufficient time. Thus, when tested with ultrasensitive force probes, we expect cohesive material strength and strength of adhesion at interfaces to be time- and loading rate-dependent properties. To examine what can be learned from measurements of bond strength, we have extended Kramers' theory for reaction kinetics in liquids to bond dissociation under force and tested the predictions by smart Monte Carlo (Brownian dynamics) simulations of bond rupture. By definition, bond strength is the force that produces the most frequent failure in repeated tests of breakage, i.e., the peak in the distribution of rupture forces. As verified by the simulations, theory shows that bond strength progresses through three dynamic regimes of loading rate. First, bond strength emerges at a critical rate of loading (> or = 0) at which spontaneous dissociation is just frequent enough to keep the distribution peak at zero force. In the slow-loading regime immediately above the critical rate, strength grows as a weak power of loading rate and reflects initial coupling of force to the bonding potential. At higher rates, there is crossover to a fast regime in which strength continues to increase as the logarithm of the loading rate over many decades independent of the type of attraction. Finally, at ultrafast loading rates approaching the domain of molecular dynamics simulations, the bonding potential is quickly overwhelmed by the rapidly increasing force, so that only naked frictional drag on the structure remains to retard separation. Hence, to expose the energy landscape that governs bond strength, molecular adhesion forces must be examined over an enormous span of time scales. However, a significant gap exists between the time domain of force measurements in the laboratory and the extremely fast scale of molecular motions. Using results from a simulation of biotin-avidin bonds (Izrailev, S., S. Stepaniants, M. Balsera, Y. Oono, and K. Schulten. 1997. Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys. J., this issue), we describe how Brownian dynamics can help bridge the gap between molecular dynamics and probe tests. Images FIGURE 2 PMID:9083660
Molecular Dynamics for Dense Matter
Toshiki Maruyama; Gentaro Watanabe; Satoshi Chiba
2012-07-05
We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions on the nuclear structure. First we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that the pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With increase of density, a crystalline solid of spherical nuclei change to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss the fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid-gas phase transition is not plausible at lower temperatures.
Rheology via nonequilibrium molecular dynamics
Hoover, W.G.
1982-10-01
The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference.
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)
Better, Cheaper, Faster Molecular Dynamics
NASA Technical Reports Server (NTRS)
Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)
2001-01-01
Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.
A concurrent multiscale micromorphic molecular dynamics
NASA Astrophysics Data System (ADS)
Li, Shaofan; Tong, Qi
2015-04-01
In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation.
A system for interactive molecular dynamics simulation
John E. Stone; Justin Gullingsrud; Klaus Schulten
2001-01-01
We have implemented a system termed Interactive Molecu- lar Dynamics (IMD), which permits manipulation of mole- cules in molecular dynamics simulations with real-time force feedback and graphical display. Communication is achieved through an e cient socket connection between the visual- ization program (VMD) and a molecular dynamics program (NAMD) running on single or multiple machines. A natural force feedback interface
Potential formulation of sleep dynamics.
Phillips, A J K; Robinson, P A
2009-02-01
A physiologically based model of the mechanisms that control the human sleep-wake cycle is formulated in terms of an equivalent nonconservative mechanical potential. The potential is analytically simplified and reduced to a quartic two-well potential, matching the bifurcation structure of the original model. This yields a dynamics-based model that is analytically simpler and has fewer parameters than the original model, allowing easier fitting to experimental data. This model is first demonstrated to semiquantitatively match the dynamics of the physiologically based model from which it is derived, and is then fitted directly to a set of experimentally derived criteria. These criteria place rigorous constraints on the parameter values, and within these constraints the model is shown to reproduce normal sleep-wake dynamics and recovery from sleep deprivation. Furthermore, this approach enables insights into the dynamics by direct analogies to phenomena in well studied mechanical systems. These include the relation between friction in the mechanical system and the timecourse of neurotransmitter action, and the possible relation between stochastic resonance and napping behavior. The model derived here also serves as a platform for future investigations of sleep-wake phenomena from a dynamical perspective. PMID:19391784
High order finite difference algorithms for solving the Schrodinger equation in molecular dynamics
Farantos, Stavros C.
High order finite difference algorithms for solving the Schro¨dinger equation in molecular dynamics¨dinger equation in molecular dynamics. A Morse type potential for iodine molecule is used to compare systems constitutes the aim of quantum molecular dynamics and the way to obtain reli- able quantitative
Molecular Dynamics Simulations to Compute the Bulk Response of Amorphous PMMA
Çagin, Tahir
Molecular Dynamics Simulations to Compute the Bulk Response of Amorphous PMMA S.B. Sane* , T. Cagin of molecular dynamics computations and corresponding values of laboratory measurements are compared to assess computational methods has offered the potential for "molecular dynamics" simulations to predict the mechanical
Unified approach for molecular dynamics and density-functional theory
R. Car; M. Parrinello
1985-01-01
We present a unified scheme that, by combining molecular dynamics and density-functional theory, profoundly extends the range of both concepts. Our approach extends molecular dynamics beyond the usual pair-potential approximation, thereby making possible the simulation of both covalently bonded and metallic systems. In addition it permits the application of density-functional theory to much larger systems than previously feasible. The new
Achieving Energy Conservation in Poisson-Boltzmann Molecular Dynamics
Zhao, Hongkai
1 Achieving Energy Conservation in Poisson-Boltzmann Molecular Dynamics: Accuracy and Precision important for their structures, dynamics, and functions. Efficient molecular dynamics simulation most particles in molecular dynamics are to represent water molecules solvating the target biomolecules
Application of optimal prediction to molecular dynamics
Barber IV, John Letherman
2004-12-01
Optimal prediction is a general system reduction technique for large sets of differential equations. In this method, which was devised by Chorin, Hald, Kast, Kupferman, and Levy, a projection operator formalism is used to construct a smaller system of equations governing the dynamics of a subset of the original degrees of freedom. This reduced system consists of an effective Hamiltonian dynamics, augmented by an integral memory term and a random noise term. Molecular dynamics is a method for simulating large systems of interacting fluid particles. In this thesis, I construct a formalism for applying optimal prediction to molecular dynamics, producing reduced systems from which the properties of the original system can be recovered. These reduced systems require significantly less computational time than the original system. I initially consider first-order optimal prediction, in which the memory and noise terms are neglected. I construct a pair approximation to the renormalized potential, and ignore three-particle and higher interactions. This produces a reduced system that correctly reproduces static properties of the original system, such as energy and pressure, at low-to-moderate densities. However, it fails to capture dynamical quantities, such as autocorrelation functions. I next derive a short-memory approximation, in which the memory term is represented as a linear frictional force with configuration-dependent coefficients. This allows the use of a Fokker-Planck equation to show that, in this regime, the noise is {delta}-correlated in time. This linear friction model reproduces not only the static properties of the original system, but also the autocorrelation functions of dynamical variables.
NASA Astrophysics Data System (ADS)
Duan, Zhenhao; Zhang, Zhigang
2006-05-01
Based on our previous development of the molecular interaction potential for pure H 2O and CO 2 [Zhang, Z.G., Duan, Z.H. 2005a. Isothermal-isobaric molecular dynamics simulations of the PVT properties of water over wide range of temperatures and pressures. Phys. Earth Planet Interiors149, 335-354; Zhang, Z.G., Duan, Z.H. 2005b. An optimized molecular potential for carbon dioxide. J. Chem. Phys.122, 214507] and the ab initio potential surface across CO 2-H 2O molecules constructed in this study, we carried out more than one thousand molecular dynamics simulations of the PVTx properties of the CO 2-H 2O mixtures in the temperature-pressure range from 673.15 to 2573.15 K up to 10.0 GPa. Comparison with extensive experimental PVTx data indicates that the simulated results generally agree with experimental data within 2% in density, equivalent to experimental uncertainty. Even the data under the highest experimental temperature-pressure conditions (up to 1673 K and 1.94 GPa) are well predicted with the agreement within 1.0% in density, indicating that the high accuracy of the simulation is well retained as the temperature and pressure increase. The consistent and stable predictability of the simulation from low to high temperature-pressure and the fact that the molecular dynamics simulation resort to no experimental data but to ab initio molecular potential makes us convinced that the simulation results should be reliable up to at least 2573 K and 10 GPa with errors less than 2% in density. In order to integrate all the simulation results of this study and previous studies [Zhang and Duan, 2005a, 2005b] and the experimental data for the calculation of volumetric properties (volume, density, and excess volume), heat properties, and chemical properties (fugacity, activity, and possibly supercritical phase separation), an equation of state (EOS) is laboriously developed for the CO 2, H 2O, and CO 2-H 2O systems. This EOS reproduces all the experimental and simulated data covering a wide temperature and pressure range from 673.15 to 2573.15 K and from 0 to 10.0 GPa within experimental or simulation uncertainty.
NAMD2: Greater Scalability for Parallel Molecular Dynamics
Laxmikant Kale; Robert Skeel; Milind Bhandarkar; Robert Brunner
1998-01-01
Molecular dynamics programs simulate the behavior of biomolecular systems, leading toinsights and understanding of their functions. However, the computational complexity of suchsimulations is enormous. Parallel machines provide the potential to meet this computationalchallenge. To harness this potential, it is necessary to develop a scalable program. It is alsonecessary that the program be easily modified by application-domain programmers.
Elastic constants of diamond from molecular dynamics simulations
Guangtu Gao; Kevin Van Workum; J. David Schall; Judith A. Harrison
2006-01-01
The elastic constants of diamond between 100 and 1100 K have been calculated for the first time using molecular dynamics and the second-generation, reactive empirical bond-order potential (REBO). This version of the REBO potential was used because it was redesigned to be able to model the elastic properties of diamond and graphite at 0 K while maintaining its original capabilities.
Extended Born-Oppenheimer molecular dynamics.
Niklasson, Anders M N
2008-03-28
A Lagrangian generalization of time-reversible Born-Oppenheimer molecular dynamics Niklasson et al. [Phys. Rev. Lett. 97, 123001 (2006)10.1103/PhysRevLett.97.123001] is proposed. The formulation enables the application of higher-order symplectic or geometric integration schemes that are stable and energy conserving even under incomplete self-consistency convergence. It is demonstrated how the accuracy is improved by over an order of magnitude compared to previous formulations at the same level of computational cost. The proposed Lagrangian includes extended electronic degrees of freedom as auxiliary dynamical variables in addition to the nuclear coordinates and momenta. While the nuclear degrees of freedom propagate on the Born-Oppenheimer potential energy surface, the extended auxiliary electronic degrees of freedom evolve as a harmonic oscillator centered around the adiabatic propagation of the self-consistent ground state. PMID:18517861
Emergent Phenomena via Molecular Dynamics
NASA Astrophysics Data System (ADS)
Rapaport, D. C.
Emergent phenomena are unusual because they are not obvious consequences of the design of the systems in which they appear, a feature no less relevant when they are being simulated. Several systems that exhibit surprisingly rich emergent behavior, each studied by molecular dynamics (MD) simulation, are described: (i) Modeling self-assembly processes associated with virus growth reveals the ability to achieve error-free assembly, where paradoxically, near-maximum yields are due to reversible bond formation. (ii) In fluids studied at the atomistic level, complex hydrodynamic phenomena in rotating and convecting fluids - the Taylor- Couette and Rayleigh-Bénard instabilities - can be reproduced, despite the limited length and time scales accessible by MD. (iii) Segregation studies of granular mixtures in a rotating drum reproduce the expected, but counterintuitive, axial and radial segregation, while for the case of a vertically vibrated layer a novel form of horizontal segregation is revealed.
Optimal prediction in molecular dynamics
Benjamin Seibold
2008-08-22
Optimal prediction approximates the average solution of a large system of ordinary differential equations by a smaller system. We present how optimal prediction can be applied to a typical problem in the field of molecular dynamics, in order to reduce the number of particles to be tracked in the computations. We consider a model problem, which describes a surface coating process, and show how asymptotic methods can be employed to approximate the high dimensional conditional expectations, which arise in optimal prediction. The thus derived smaller system is compared to the original system in terms of statistical quantities, such as diffusion constants. The comparison is carried out by Monte-Carlo simulations, and it is shown under which conditions optimal prediction yields a valid approximation to the original system.
Optimizing molecular dynamics simulations with product lines
Rui C. Silva; João L. Sobral
2011-01-01
This paper presents a case study of using product-lines to address the variability of optimization methods and target platform mappings in high-performance molecular dynamics simulations. We use Feature Oriented Programming to incrementally extend the base algorithm by composing performance enhancement features with the core functionality. Developed features encapsulate common optimization methods in molecular dynamics simulations and target platform mappings. The
Molecular dynamics simulations of lipid bilayers
Scott E. Feller
2000-01-01
Computer simulation methods are becoming increasingly widespread as tools for studying the structure and dynamics of lipid bilayer membranes. The length scale and time scale accessible to atomic-level molecular dynamics simulations are rapidly increasing, providing insight into the relatively slow motions of molecular reorientation and translation and demonstrating that effects due to the finite size of the simulation cell can
Molecular dynamics and phase transitions in alkali azides and thiocyanates
Maciej Ossowski
1998-01-01
Calculations based on an ab initio model developed for the intermolecular and intramolecular potentials in complex ionic solids were performed on selected alkali azides (KNsb3,\\\\ RbNsb3,\\\\ CsNsb3) and thiocyanates (KSCN, RbSCN, CsSCN). With these parameter-free potentials we performed static structural relaxations, supercell molecular dynamics and lattice dynamical studies and predict with reasonable accuracy the temperatures for the onset of the
Radion Potential and Brane Dynamics
L. Mersini
2001-08-30
We examine the cosmology of the Randall-Sundrum model in a dynamic setting where scalar fields are present in the bulk as well as the branes. This generates a mechanism similar to that of Goldberger-Wise for radion stabilization and the recovery of late-cosmology features in the branes. Due to the induced radion dynamics, the inflating branes roll towards the minimum of the radion potential, thereby exiting inflation and reheating the Universe. In the slow roll part of the potential, the 'TeV' branes have maximum inflation rate and energy as their coupling to the radion and bulk modes have minimum suppresion. Hence, when rolling down the steep end of the potential towards the stable point, the radion field (which appears as the inflaton of the effective 4D theory in the branes) decays very fast, reheats the Universe .This process results decayin a decrease of brane's canonical vacuum energy $\\Lambda_4$. However, at the minimum of the potential $\\Lambda_4$ is small but not neccessarily zero and the fine-tuning issue remains .Density perturbation constraints introduce an upper bound when the radion stabilizies. Due to the large radion mass and strong suppression to the bulk modes, moduli problems and bulk reheating do not occur. The reheat temperature and a sufficient number of e-folding constraints for the brane-universe are also satisfied. The model therefore recovers the radiation dominated FRW universe.
An Interacting Particle System Approach for Molecular Dynamics
Del Moral , Pierre
An Interacting Particle System Approach for Molecular Dynamics Mathias Rousset Laboratoire de Particle Sys- tem (IPS) methodology to the field of Molecular Dynamics. This IPS method allows several and free energy differences. Keywords: Canonical distribution, molecular dynamics, simulated an- nealing
Southern California, University of
Molecular dynamics study of structural, mechanical, and vibrational properties of crystalline June 2003 Using an interaction potential scheme, molecular dynamics MD simulations are performed study. Calculated elastic constants show a significant nonlinear dependence on the composition
Stresses and elastic constants of crystalline sodium, from molecular dynamics
Schiferl
1985-01-01
The stresses and the elastic constants of bcc sodium are calculated by molecular dynamics (MD) for temperatures to T = 340K. The total adiabatic potential of a system of sodium atoms is represented by pseudopotential model. The resulting expression has two terms: a large, strictly volume-dependent potential, plus a sum over ion pairs of a small, volume-dependent two-body potential. The
Miller, William H.
Semiclassical molecular dynamics simulations of ultrafast photodissociation dynamics associated methods1,2 to a real molecular system, the ultrafast photodis- sociation dynamics associated of quantum and mixed quantum-classical methods for describing chemical/ molecular dynamics, including full
Kraszewski, Sebastian; Drabik, Dominik; Langner, Marek; Ramseyer, Christophe; Kembubpha, Sineenat; Yasothornsrikul, Sukkid
2015-06-24
Catestatin, a cationic and hydrophobic 21-amino acid fragment of chromogranin A, is known to be a non-competitive nicotinic antagonist acting through nicotinic acetylcholine receptors (nAChRs) to inhibit catecholamine release. Since this receptor is the target of several neuronal and non-neuronal disorder prophylaxes and treatments, this study aims at the elucidation of the binding of human catestatin to the entire nAChR reconstructed in lipid bilayers by means of docking followed by full atomistic molecular dynamics simulations. The obtained results show that the minimum free energy for the binding of the peptide and the receptor attains minimal values for locations at the pore site and in the outer beta subunit. This result is consistent with previous studies showing that catestatin occludes the pore opening. A new finding is an additional even stronger binding seat at the beta subunit and that membrane presence could be an important factor. Specific amino acids involved in catestatin binding have been identified, indicating targets for point mutation studies. In addition to improving the understanding of the interaction between the peptide and muscle-type and even other nAChR subtypes, the results of this study provide directions for future peptidomimetic research. PMID:26079001
First principles molecular dynamics without self-consistent field optimization
Souvatzis, Petros, E-mail: petros.souvatsiz@fysik.uu.se [Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Box 516, SE-75120 Uppsala (Sweden)] [Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Box 516, SE-75120 Uppsala (Sweden); Niklasson, Anders M. N., E-mail: amn@lanl.gov [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)] [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)
2014-01-28
We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations.
Molecular dynamics in amorphous ergocalciferol
NASA Astrophysics Data System (ADS)
Mohamed, Sahra; Thayyil, M. Shahin; Capaccioli, S.
2014-04-01
While developing new pharmaceutical products based on drug substances in their amorphous form, the molecular mobility of amorphous active ingredients have to be characterized in detail. The molecular mobility in the supercooled liquid and glassy states of ergocalciferol is studied using broadband dielectric spectroscopy over wide frequency and temperature ranges. Dielectric studies revealed a number of relaxation process of different molecular origin.
Molecular-Dynamics Study of Phase Transitions in Alkali Thiocyanates
M. M. Ossowski; John R. Hardy; Robert W. Smith
2000-01-01
An account is presented of our studies of the order-disorder phase transitions in KSCN, RbSCN, and CsSCN. These are based on parameter-free interionic potentials based on the Gordon-Kim modified electron gas formalism extended to molecular ions. We performed static structural relaxations and supercell molecular dynamics and predicted with reasonable accuracy the temperatures for the onset of the transitions. In particular,
Molecular-dynamics study of phase transitions in alkali thiocyanates
M. M. Ossowski; J. R. Hardy; R. W. Smith
2000-01-01
An account is presented of our studies of the order-disorder phase transitions in KSCN, RbSCN, and CsSCN. These are based on parameter-free interionic potentials based on the Gordon-Kim modified electron gas formalism extended to molecular ions. We performed static structural relaxations and supercell molecular dynamics and predicted with reasonable accuracy the temperatures for the onset of the transitions. In particular,
Improved simulation of liquid water by molecular dynamics
Frank H. Stillinger; Aneesur Rahman
1974-01-01
Molecular dynamics calculations on a classical model for liquid water have been carried out at mass density 1 g\\/cm3 and at four temperatures. The effective pair potential employed is based on a four-charge model for each molecule and represents a modification of the prior ``BNS'' interaction. Results for molecular structure and thermodynamic properties indicate that the modification improves the fidelity
NASA Astrophysics Data System (ADS)
Hele, Timothy J. H.; Willatt, Michael J.; Muolo, Andrea; Althorpe, Stuart C.
2015-05-01
We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the "Classical Wigner" approximation. Here, we show that the further approximation of this "Matsubara dynamics" gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by discarding (classical) fluctuations around the centroid, and that RPMD is the result of discarding a term in the Matsubara Liouvillian which shifts the frequencies of these fluctuations. These findings are consistent with previous numerical results and give explicit formulae for the terms that CMD and RPMD leave out.
Hele, Timothy J H; Willatt, Michael J; Muolo, Andrea; Althorpe, Stuart C
2015-05-21
We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the "Classical Wigner" approximation. Here, we show that the further approximation of this "Matsubara dynamics" gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by discarding (classical) fluctuations around the centroid, and that RPMD is the result of discarding a term in the Matsubara Liouvillian which shifts the frequencies of these fluctuations. These findings are consistent with previous numerical results and give explicit formulae for the terms that CMD and RPMD leave out. PMID:26001438
Molecular dynamics simulations of ribonuclease T1
A. D. MacKerell Jr; R. Rigler; L. Nilsson; U. Heinemann; W. Saenger
1988-01-01
Molecular dynamics simulations in vacuum and with a water sphere around the active site were performed on the 2'GMP-RNase T1 complex. The presence of water led to the maintenance of the 2'-GMP-RNase T1 interactions as compared to the X-ray structure, including the hydrogen bonds implicated in the enzyme-inhibitor recognition process. The sidechain of His92 in the molecular dynamics water simulation,
Modeling the Hydrogen Bond within Molecular Dynamics
ERIC Educational Resources Information Center
Lykos, Peter
2004-01-01
The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.
Molecular ions, Rydberg spectroscopy and dynamics
NASA Astrophysics Data System (ADS)
Jungen, Ch.
2015-01-01
Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.
Molecular dynamics simulations of microwave heating of water
Niall J. English; J. M. D. MacElroy
2003-01-01
Nonequilibrium molecular dynamics simulations of water in an intense external microwave field have been performed using a rigid\\/polarizable and a flexible\\/nonpolarizable potential model, from ambient conditions to supercriticality. The heating profiles were compared to that predicted from a macroscopic energy balance, and the polarizable model was found to be superior in this regard.
Molecular Dynamics Studies of Ion Permeation in VDAC
Rui, Huan; Lee, Kyu II; Pastor, Richard W.; Im, Wonpil
2011-02-02
, and the mechanisms underlying its electrophysiological properties, we performed a total of 1.77 ?s molecular dynamics simulations of human VDAC isoform 1 in DOPE/DOPC mixed bilayers in 1 M KCl solution with transmembrane potentials of 0, ±25, ±50, ±75, and ±100 m...
Elastic Constants from Molecular Dynamics in the Presence of Microstructure
S. G. Srinivasan; D. A. Dimitrov; T. Lookman; A. Saxena; R. C. Albers; A. R. Bishop
2000-01-01
We calculate second (and third) order elastic constants in the presence of twin and tweed-like microstructure in martensitic and other structural phase transitions using fluctuation formulas and embedded atom method (EAM) and modified (MEAM) potentials in molecular dynamics simulations. We illustrate the results on NiAl alloys. This procedure allows us to study and distinguish the effects of microstructure such as
Quantum molecular dynamics and particle production in heavy ion collisions
S. W. Huang; A. Faessler; G. Q. Li; D. T. Khoa; E. Lehmann; M. A. Matin; N. Ohtsuka; R. K. Puri
1993-01-01
The production of photons, kaons, antikaons and antiprotons in heavy-ion collisions is calculated in the framework of ``quantum'' molecular dynamics (QMD). The Skyrme potentials, with parameters chosen to generate the soft and hard nuclear equations of state(EOS), are used in the propagation of nucleons within QMD. The sensitivity of the production of each type of particle to the EOS is
High Temperature Graphite Simulations Using Molecular Dynamics
NASA Astrophysics Data System (ADS)
Hehr, Brian D.
Graphite, a major structural and moderator material in the proposed Generation IV reactor roadmap, is expected to experience irradiation at temperatures up to 1800 K. In this study, molecular dynamics (MD) is employed to investigate the physical properties of graphite from 0 K to 1800 K. MD applies the classical laws of physics to simulate atomistic-level behavior, and from the observed microscopic data, macroscopic properties may be surmised. For the purposes of this study, a graphite-specific MD code was created and benchmarked against high temperature graphite data. Modifications were introduced into the interatomic potential function as needed to fit experimental measurements. Graphite-specific modifications include a plane-by-plane center of mass velocity correction, an additional potential energy cutoff function for out-of-plane displacements, and temperature-dependent parameterization of the potential function. These adjustments were fitted to high temperature measurements of thermal expansion and mean squared displacement. The refined MD model of graphite was subsequently utilized to examine the threshold displacement energy at temperatures ranging from 300 K to 1800 K. It was found that the threshold energy depends strongly on the knock-on direction, as is expected due to the highly anisotropic nature of graphite. MD calculations of the threshold energy exhibited good agreement with the results of two electron irradiation studies.
Molecular-Dynamics Simulations and Density Functional Theory
Duisburg-Essen, Universität
Molecular-Dynamics Simulations and Density Functional Theory Part 1 - Molecular-Dynamics Simulations 1. Introduction 2. Basics of Molecular-Dynamics Simulations 3. Analyzing the Results 4. Model Simulations of Liquids (Clarendon Press, Oxford 1987). · D. C. Rapaport, The Art of Molecular Dynamics
Ab initio molecular dynamics for liquid metals
G. Kresse
1995-01-01
In recent years, ab initio molecular dynamics (MD) techniques have made a profound impact on the investigation of the structure of the electronic and dynamic properties of liquid and amorphous materials. In this paper, recent developments in this field are reviewed and it is shown that the exact calculation of the electronic groundstate at each MD timestep is feasible using
A Virtual Environment for Steered Molecular Dynamics
Jan F. Prins; Jan Hermans; Geoffrey Mann; Lars S. Nyland; Martin Simons
1999-01-01
A molecular dynamics simulation approximates the motion of atoms in a system of molecules over short intervals of simulated time, typically on the order of picoseconds to nanoseconds. Such simulations may run for days or weeks on a computer when used to investigate the dynamic behavior of small proteins in biological systems. By adding additional restraints, a simulation may be
Osmosis : a molecular dynamics computer simulation study
NASA Astrophysics Data System (ADS)
Lion, Thomas
Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..
Molecular dynamics and time correlation function theories
NASA Astrophysics Data System (ADS)
Devane, Russell H.
The research presented in this thesis makes use of theoretical/computational techniques to calculate nonlinear spectroscopic signals and molecular volumes. These techniques have become more practical with advances in computational resources and now are an integral part of research in these areas. Preliminary results allude to the power of these techniques when applied to relevant problems and suggest that much progress can be made in understanding the complex nature of nonlinear spectroscopic signals and molecular volume contributions. The nonlinear spectroscopy work involves writing the quantum mechanical response functions in terms of classical time correlation functions which are amenable to calculation using classical molecular dynamics. The response functions reported in this thesis include the fifth order response function, probed in the fifth order Raman experiment, and the third order response function probed in the two dimensional infrared experiment. The molecular volume calculations make use of modern algorithms used in molecular dynamics simulations to calculate the full thermodynamic volumes of molecules.
Elastic constants of diamond from molecular dynamics simulations
Guangtu Gao; Kevin Van Workum; J David Schall; Judith A Harrison
2006-01-01
The elastic constants of diamond between 100 and 1100K have been calculated for the first time using molecular dynamics and the second-generation, reactive empirical bond-order potential (REBO). This version of the REBO potential was used because it was redesigned to be able to model the elastic properties of diamond and graphite at 0K while maintaining its original capabilities. The independent
Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code
NASA Astrophysics Data System (ADS)
Davis, Sergio; Loyola, Claudia; González, Felipe; Peralta, Joaquín
2010-12-01
Las Palmeras Molecular Dynamics (LPMD) is a highly modular and extensible molecular dynamics (MD) code using interatomic potential functions. LPMD is able to perform equilibrium MD simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium MD (NEMD) simulations such as shock wave propagation, projectile impacts, cluster collisions, shearing, deformation under load, heat conduction, heterogeneous melting, among others, which involve unusual MD features like non-moving atoms and walls, unstoppable atoms with constant-velocity, and external forces like electric fields. LPMD is written in C++ as a compromise between efficiency and clarity of design, and its architecture is based on separate components or plug-ins, implemented as modules which are loaded on demand at runtime. The advantage of this architecture is the ability to completely link together the desired components involved in the simulation in different ways at runtime, using a user-friendly control file language which describes the simulation work-flow. As an added bonus, the plug-in API (Application Programming Interface) makes it possible to use the LPMD components to analyze data coming from other simulation packages, convert between input file formats, apply different transformations to saved MD atomic trajectories, and visualize dynamical processes either in real-time or as a post-processing step. Individual components, such as a new potential function, a new integrator, a new file format, new properties to calculate, new real-time visualizers, and even a new algorithm for handling neighbor lists can be easily coded, compiled and tested within LPMD by virtue of its object-oriented API, without the need to modify the rest of the code. LPMD includes already several pair potential functions such as Lennard-Jones, Morse, Buckingham, MCY and the harmonic potential, as well as embedded-atom model (EAM) functions such as the Sutton-Chen and Gupta potentials. Integrators to choose include Euler (if only for demonstration purposes), Verlet and Velocity Verlet, Leapfrog and Beeman, among others. Electrostatic forces are treated as another potential function, by default using the plug-in implementing the Ewald summation method. Program summaryProgram title: LPMD Catalogue identifier: AEHG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 509 490 No. of bytes in distributed program, including test data, etc.: 6 814 754 Distribution format: tar.gz Programming language: C++ Computer: 32-bit and 64-bit workstation Operating system: UNIX RAM: Minimum 1024 bytes Classification: 7.7 External routines: zlib, OpenGL Nature of problem: Study of Statistical Mechanics and Thermodynamics of condensed matter systems, as well as kinetics of non-equilibrium processes in the same systems. Solution method: Equilibrium and non-equilibrium molecular dynamics method, Monte Carlo methods. Restrictions: Rigid molecules are not supported. Polarizable atoms and chemical bonds (proteins) either. Unusual features: The program is able to change the temperature of the simulation cell, the pressure, cut regions of the cell, color the atoms by properties, even during the simulation. It is also possible to fix the positions and/or velocity of groups of atoms. Visualization of atoms and some physical properties during the simulation. Additional comments: The program does not only perform molecular dynamics and Monte Carlo simulations, it is also able to filter and manipulate atomic configurations, read and write different file formats, convert between them, evaluate different structural and dynamical properties. Running time: 50 seconds on a 1000-step simulation of 4000 argon atoms, running on a single 2.67 GHz Intel processor.
Kapko, Vitaliy; Zhao, Zuofeng; Matyushov, Dmitry V; Austen Angell, C
2013-03-28
The ability of some liquids to vitrify during supercooling is usually seen as a consequence of the rates of crystal nucleation (and?or crystal growth) becoming small [D. R. Uhlmann, J. Non-Cryst. Solids 7, 337 (1972)]--and thus a matter of kinetics. However, there is evidence dating back to the empirics of coal briquetting for maximum trucking efficiency [D. Frenkel, Physics 3, 37 (2010)] that some object shapes find little advantage in self-assembly to ordered structures--meaning random packings prevail. Noting that key studies of non-spherical object packing have never been followed from hard ellipsoids [A. Donev, F. H. Stillinger, P. M. Chaikin, and S. Torquato, Phys. Rev. Lett. 92, 255506 (2004); A. Donev, I. Cisse, D. Sachs, E. A. Variano, F. H. Stillinger, R. Connelly, S. Torquato, and P. M. Chaikin, Science 303, 990 (2004)] or spherocylinders [S. R. Williams and A. P. Philipse, Phys. Rev. E 67, 051301 (2003)] (diatomics excepted [S.-H. Chong, A. J. Moreno, F. Sciortino, and W. Kob, Phys. Rev. Lett. 94, 215701 (2005)] into the world of molecules with attractive forces, we have made a molecular dynamics study of crystal melting and glass formation on the Gay-Berne (G-B) model of ellipsoidal objects [J. G. Gay and B. J. Berne, J. Chem. Phys. 74, 3316 (1981)] across the aspect ratio range of the hard ellipsoid studies. Here, we report that in the aspect ratio range of maximum ellipsoid packing efficiency, various G-B crystalline states that cannot be obtained directly from the liquid, disorder spontaneously near 0 K and transform to liquids without any detectable enthalpy of fusion. Without claiming to have proved the existence of single component examples, we use the present observations, together with our knowledge of non-ideal mixing effects, to discuss the probable existence of "ideal glassformers"--single or multicomponent liquids that vitrify before ever becoming metastable with respect to crystals. We find evidence that "ideal glassformer" systems might also be highly fragile systems, approaching the "ideal glass" condition. We link this to the high "volume fragility" behavior observed in recent hard dumbbell studies at similar length?diameter ratios [R. Zhang and K. S. Schweitzer, J. Chem. Phys. 133, 104902 (2010)]. The discussion suggests some unusual systems for laboratory study. Using differential scanning calorimetry detection of fusion points T(m), liquidus temperatures T(l), and glass transition temperatures T(g), we describe a system that would seem incapable of crystallizing before glass transition, i.e., an "ideal glassformer." The existence of crystal-free routes to the glassy state will eliminate precrystalline fluctuations as a source of the dynamic heterogeneities that are generally considered important in the discussion of the "glassy state problem [P. W. Anderson, Science 267, 1615 (1995)]." PMID:23556800
Molecular Dynamics Machine: Special-Purpose Computer for Molecular Dynamics Simulations
Tetsu Narumi; Ryutaro Susukita; Toshikazu Ebisuzaki; Geoffrey McNiven; Bruce Elmegreen
1999-01-01
We are now developing Molecular Dynamics Machine (MDM), a special-purpose computer for classical molecular dynamics simulations. It accelerates the calculation of non-bonding force, Coulomb and van der Waals forces, because the calculation cost for Coulomb force dominates the total calculation time when we treat a large system of charged particles without truncating Coulomb force. When we use Ewald method, the
NVU dynamics. III. Simulating molecules at constant potential energy
NASA Astrophysics Data System (ADS)
Ingebrigtsen, Trond S.; Dyre, Jeppe C.
2012-12-01
This is the final paper in a series that introduces geodesic molecular dynamics at constant potential energy. This dynamics is entitled NVU dynamics in analogy to standard energy-conserving Newtonian NVE dynamics. In the first two papers [T. S. Ingebrigtsen, S. Toxvaerd, O. J. Heilmann, T. B. Schrøder, and J. C. Dyre, J. Chem. Phys. 135, 104101 (2011), 10.1063/1.3623585; T. S. Ingebrigtsen, S. Toxvaerd, T. B. Schrøder, and J. C. Dyre, J. Chem. Phys. 135, 104102 (2011), 10.1063/1.3623586], a numerical algorithm for simulating geodesic motion of atomic systems was developed and tested against standard algorithms. The conclusion was that the NVU algorithm has the same desirable properties as the Verlet algorithm for Newtonian NVE dynamics, i.e., it is time-reversible and symplectic. Additionally, it was concluded that NVU dynamics becomes equivalent to NVE dynamics in the thermodynamic limit. In this paper, the NVU algorithm for atomic systems is extended to be able to simulate the geodesic motion of molecules at constant potential energy. We derive an algorithm for simulating rigid bonds and test this algorithm on three different systems: an asymmetric dumbbell model, Lewis-Wahnström o-terphenyl (OTP) and rigid SPC/E water. The rigid bonds introduce additional constraints beyond that of constant potential energy for atomic systems. The rigid-bond NVU algorithm conserves potential energy, bond lengths, and step length for indefinitely long runs. The quantities probed in simulations give results identical to those of Nosé-Hoover NVT dynamics. Since Nosé-Hoover NVT dynamics is known to give results equivalent to those of NVE dynamics, the latter results show that NVU dynamics becomes equivalent to NVE dynamics in the thermodynamic limit also for molecular systems.
NVU dynamics. III. Simulating molecules at constant potential energy.
Ingebrigtsen, Trond S; Dyre, Jeppe C
2012-12-28
This is the final paper in a series that introduces geodesic molecular dynamics at constant potential energy. This dynamics is entitled NVU dynamics in analogy to standard energy-conserving Newtonian NVE dynamics. In the first two papers [T. S. Ingebrigtsen, S. Toxvaerd, O. J. Heilmann, T. B. Schrøder, and J. C. Dyre, J. Chem. Phys. 135, 104101 (2011); T. S. Ingebrigtsen, S. Toxvaerd, T. B. Schrøder, and J. C. Dyre, ibid. 135, 104102 (2011)], a numerical algorithm for simulating geodesic motion of atomic systems was developed and tested against standard algorithms. The conclusion was that the NVU algorithm has the same desirable properties as the Verlet algorithm for Newtonian NVE dynamics, i.e., it is time-reversible and symplectic. Additionally, it was concluded that NVU dynamics becomes equivalent to NVE dynamics in the thermodynamic limit. In this paper, the NVU algorithm for atomic systems is extended to be able to simulate the geodesic motion of molecules at constant potential energy. We derive an algorithm for simulating rigid bonds and test this algorithm on three different systems: an asymmetric dumbbell model, Lewis-Wahnström o-terphenyl (OTP) and rigid SPC/E water. The rigid bonds introduce additional constraints beyond that of constant potential energy for atomic systems. The rigid-bond NVU algorithm conserves potential energy, bond lengths, and step length for indefinitely long runs. The quantities probed in simulations give results identical to those of Nosé-Hoover NVT dynamics. Since Nose?-Hoover NVT dynamics is known to give results equivalent to those of NVE dynamics, the latter results show that NVU dynamics becomes equivalent to NVE dynamics in the thermodynamic limit also for molecular systems. PMID:23277922
T. Kumagai; S. Izumi; S. Hara; S. Sakai
2007-01-01
The Tersoff potential is one of the most widely used interatomic potentials for silicon. However, its poor description of the elastic constants and melting point of diamond silicon is well known. In this research, three bond-order type interatomic potentials have been developed: the first one is fitted to the elastic constants by employing the Tersoff potential function form, the second
Liouville-von Neumann molecular dynamics.
Jakowski, Jacek; Morokuma, Keiji
2009-06-14
We present a novel first principles molecular dynamics scheme, called Liouville-von Neumann molecular dynamics, based on Liouville-von Neumann equation for density matrices propagation and Magnus expansion of the time-evolution operator. The scheme combines formally accurate quantum propagation of electrons represented via density matrices and a classical propagation of nuclei. The method requires a few iterations per each time step where the Fock operator is formed and von Neumann equation is integrated. The algorithm (a) is free of constraint and fictitious parameters, (b) avoids diagonalization of the Fock operator, and (c) can be used in the case of fractional occupation as in metallic systems. The algorithm is very stable, and has a very good conservation of energy even in cases when a good quality conventional Born-Oppenheimer molecular dynamics trajectories is difficult to obtain. Test simulations include initial phase of fullerene formation from gaseous C(2) and retinal system. PMID:19530761
Liouville-von Neumann molecular dynamics
NASA Astrophysics Data System (ADS)
Jakowski, Jacek; Morokuma, Keiji
2009-06-01
We present a novel first principles molecular dynamics scheme, called Liouville-von Neumann molecular dynamics, based on Liouville-von Neumann equation for density matrices propagation and Magnus expansion of the time-evolution operator. The scheme combines formally accurate quantum propagation of electrons represented via density matrices and a classical propagation of nuclei. The method requires a few iterations per each time step where the Fock operator is formed and von Neumann equation is integrated. The algorithm (a) is free of constraint and fictitious parameters, (b) avoids diagonalization of the Fock operator, and (c) can be used in the case of fractional occupation as in metallic systems. The algorithm is very stable, and has a very good conservation of energy even in cases when a good quality conventional Born-Oppenheimer molecular dynamics trajectories is difficult to obtain. Test simulations include initial phase of fullerene formation from gaseous C2 and retinal system.
Understanding Modularity in Molecular Networks Requires Dynamics
NSDL National Science Digital Library
Roger P. Alexander (Yale University; Program in Computational Biology and Bioinformatics REV)
2009-07-28
The era of genome sequencing has produced long lists of the molecular parts from which cellular machines are constructed. A fundamental goal in systems biology is to understand how cellular behavior emerges from the interaction in time and space of genetically encoded molecular parts, as well as nongenetically encoded small molecules. Networks provide a natural framework for the organization and quantitative representation of all the available data about molecular interactions. The structural and dynamic properties of molecular networks have been the subject of intense research. Despite major advances, bridging network structure to dynamics—and therefore to behavior—remains challenging. A key concept of modern engineering that recurs in the functional analysis of biological networks is modularity. Most approaches to molecular network analysis rely to some extent on the assumption that molecular networks are modular—that is, they are separable and can be studied to some degree in isolation. We describe recent advances in the analysis of modularity in biological networks, focusing on the increasing realization that a dynamic perspective is essential to grouping molecules into modules and determining their collective function.
Molecular dynamics simulation of Li surface erosion and bubble formation
Harilal, S. S.
Molecular dynamics simulation of Li surface erosion and bubble formation Z. Insepov *, A. Hassanein Structure and dynamical properties of liquid Li containing He atoms were studied by the Molecular Dynamics devices. Molecular dynamics (MD) method is capable of studying important collision processes and providing
Priya Vashishta; Rajiv K. Kalia; Aiichiro Nakano; José Pedro Rino
2007-01-01
An effective interatomic interaction potential for SiC is proposed. The potential consists of two-body and three-body covalent interactions. The two-body potential includes steric repulsions due to atomic sizes, Coulomb interactions resulting from charge transfer between atoms, charge-induced dipole-interactions due to the electronic polarizability of ions, and induced dipole-dipole (van der Waals) interactions. The covalent characters of the Si-C-Si and C-Si-C
Priya Vashishta; Rajiv K. Kalia; Aiichiro Nakano; Jose´ Pedro Rino
2007-01-01
An effective interatomic interaction potential for SiC is proposed. The potential consists of two-body and three-body covalent interactions. The two-body potential includes steric repulsions due to atomic sizes, Coulomb interactions resulting from charge transfer between atoms, charge-induced dipole-interactions due to the electronic polarizability of ions, and induced dipole-dipole (van der Waals) interactions. The covalent characters of the Si–C–Si and C–Si–C
Damage in Alumina Induced by Hypervelocity Impact System Setup of Molecular Dynamics Simulation
Southern California, University of
Damage in Alumina Induced by Hypervelocity Impact System Setup of Molecular Dynamics Simulation C11 potential is validated against experimental values as follows: Fig. 1: Schematic of the -alumina system Computing and Simulations, USC High Strain Rate Deformation in -Alumina: 540 Million Atom Molecular Dynamics
Neutron Star Crust and Molecular Dynamics Simulation
C. J. Horowitz; J. Hughto; A. Schneider; D. K. Berry
2011-09-23
In this book chapter we review plasma crystals in the laboratory, in the interior of white dwarf stars, and in the crust of neutron stars. We describe a molecular dynamics formalism and show results for many neutron star crust properties including phase separation upon freezing, diffusion, breaking strain, shear viscosity and dynamics response of nuclear pasta. We end with a summary and discuss open questions and challenges for the future.
Symmetry and dynamics of molecular rotors in amphidynamic molecular crystals
Karlen, Steven D.; Reyes, Horacio; Taylor, R. E.; Khan, Saeed I.; Hawthorne, M. Frederick; Garcia-Garibay, Miguel A.
2010-01-01
Rotary biomolecular machines rely on highly symmetric supramolecular structures with rotating units that operate within a densely packed frame of reference, stator, embedded within relatively rigid membranes. The most notable examples are the enzyme FoF1 ATP synthase and the bacterial flagellum, which undergo rotation in steps determined by the symmetries of their rotators and rotating units. Speculating that a precise control of rotational dynamics in rigid environments will be essential for the development of artificial molecular machines, we analyzed the relation between rotational symmetry order and equilibrium rotational dynamics in a set of crystalline molecular gyroscopes with rotators having axial symmetry that ranges from two- to fivefold. The site exchange frequency for these molecules in their closely related crystals at ambient temperature varies by several orders of magnitude, up to ca. 4.46 × 108 s-1. PMID:20689041
Rigid body molecular dynamics with nonholonomic constraints: Molecular thermostat algorithms
NASA Astrophysics Data System (ADS)
Kutteh, Ramzi; Jones, R. B.
2000-03-01
Generalized Euler equations and center of mass equations are derived to describe the motion of a rigid body under general nonholonomic constraints. These equations provide a basis for developing algorithms for rigid body molecular dynamics (MD) simulations with nonholonomic constraints. In particular, two distinct molecular thermostat algorithms for constant temperature rigid body MD simulations are described. Both algorithms ensure satisfaction of the temperature constraint at every MD time step, without introducing additional numerical errors into the center of mass velocities or angular velocities. Results from constant temperature MD simulations of a system of 500 methylene chloride (CH2Cl2) rigid molecules using both thermostats are presented, exhibiting their efficiency and accuracy. Finally, a generalized Gauss's principle of least constraint is derived, to establish a formal connection between the molecular approach described here for incorporating nonholonomic constraints in MD simulations and previous atomistic approaches.
Crystalline molecular machines: Encoding supramolecular dynamics into molecular structure
Garcia-Garibay, Miguel A.
2005-01-01
Crystalline molecular machines represent an exciting new branch of crystal engineering and materials science with important implications to nanotechnology. Crystalline molecular machines are crystals built with molecules that are structurally programmed to respond collectively to mechanic, electric, magnetic, or photonic stimuli to fulfill specific functions. One of the main challenges in their construction derives from the picometric precision required for their mechanic operation within the close-packed, self-assembled environment of crystalline solids. In this article, we outline some of the general guidelines for their design and apply them for the construction of molecular crystals with units intended to emulate macroscopic gyroscopes and compasses. Recent advances in the preparation, crystallization, and dynamic characterization of these interesting systems offer a foothold to the possibilities and help highlight some avenues for future experimentation. PMID:16046543
Structure and dynamics of nonaqueous mixtures of dipolar liquids. II. Molecular dynamics simulations
2000 Molecular dynamics simulations have been used to study mixtures of acetone/methanol, acetonitrile/ methanol, and acetone/acetonitrile over their entire composition range. Using the effective pair potentials in these two papers is on the nonaqueous dipolar liquid mixtures of acetone/methanol, acetonitrile
Langevin Stabilization of Multiscale Mollified Molecular Dynamics
Izaguirre, Jesús A.
Langevin Stabilization of Multiscale Mollified Molecular Dynamics Jes'us A. Izaguirre Department. Langevin Molly (LM) is introduced in this paper. It uses the mollified impulse method for the Newtonian term and the Langevin impulse method for the Langevin term. A parallel version of LM is available
Ion Mobility Analysis of Molecular Dynamics
Clemmer, David E.
structure, gas-phase structure, IMS-IMS Abstract The combination of mass spectrometry and ion mobility in an ion mobility spectrometry experiment Ion mobility spectrometry (IMS): separation method employingIon Mobility Analysis of Molecular Dynamics Thomas Wyttenbach,1 Nicholas A. Pierson,2 David E
Dynamics and Molecular Evolution of Influenza
Goldschmidt, Christina
Dynamics and Molecular Evolution of Influenza Gunnar Sigurðsson Hlynur Sigurgíslason Jón Ingi Sveinbjörnsson #12;The Orthomyxoviridae family Influenza is in the Orthomyxoviridae family. The family contains Influenza A,B,C and the following viruses: Isavirus Infectious salmon anemia virus Atlantic salmon
Crystallographic R Factor Refinement by Molecular Dynamics
Axel T. Brunger; John Kuriyan; Martin Karplus
1987-01-01
Molecular dynamics was used to refine macromolecular structures by incorporating the difference between the observed crystallographic structure factor amplitude and that calculated from an assumed atomic model into the total energy of the system. The method has a radius of convergence that is larger than that of conventional restrained least-squares refinement. Test cases showed that the need for manual corrections
Parallelizing molecular dynamics using spatial decomposition
Terry W. Clark; R. von Hanxleden; J. A. McCammon; L. R. Scott
1994-01-01
Several algorithms have been used for parallel molecular dynamics, including the replicated algorithm and those based on spatial decompositions. The replicated algorithm stores the entire system's coordinates and forces at each processor, and therefore has a low overhead in maintaining the data distribution. Spatial decompositions distribute the data, providing better locality and scalability with respect to memory and computation. We
Molecular dynamics simulation of a phospholipid membrane
Egbert Egberts; Siewert-Jan Marrink; Herman J. C. Berendsen
1994-01-01
We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in future simulations. This goal being reached it is then further
Molecular Dynamics Simulations of Interface Failure
Martina E. Bachlechner; Deng Cao; Robert H. Leonard; Eli T. Owens; Wm. Trevor Swan III; Samuel C. Ducatman
2007-01-01
The mechanical integrity of silicon\\/silicon nitride interfaces is of great importance in their applications in micro electronics and solar cells. Large-scale molecular dynamics simulations are an excellent tool to study mechanical and structural failure of interfaces subjected to externally applied stresses and strains. When pulling the system parallel to the interface, cracks in silicon nitride and slip and pit formation
Molecular Dynamics Simulation of Nucleic Acids
Thomas E. Cheatham III; Peter A. Kollman
2000-01-01
We review molecular dynamics simulations of nucleic acids, including those completed from 1995 to 2000, with a focus on the applications and results rather than the methods. After the introduction, which discusses recent advances in the simulation of nucleic acids in solution, we describe force fields for nucleic acids and then provide a detailed summary of the published literature. We
A molecular dynamics study of polarizable water
Peter Ahlström; Anders Wallqvist; Sven Engström; Bo Jönsson
1989-01-01
We have investigated the effect of adding a point polarizability to a SPC like rigid water model in molecular dynamics simulations. A new algorithm for calculating the induced dipole moments based on a predictive, instead of an iterative scheme, is presented. The predictive scheme considerably reduces the demand on computer time. Both schemes gives identical results for energy, structure and
Pemra Doruker; Ali Rana Atilgan; Ivet Bahar
2000-01-01
The dynamics of a-amylase inhibi- tors has been investigated using molecular dynam- ics (MD) simulations and two analytical approaches, the Gaussian network model (GNM) and anisotropic network model (ANM). MD simulations use a full atomic approach with empirical force fields, while the analytical approaches are based on a coarse- grained single-site-per-residue model with a single- parameter harmonic potential between sufficiently
Molecular understanding of mutagenicity using potential energy methods
Broyde, S.; Shapiro, R.
1992-07-01
Our objective, has been to elucidate on a molecular level, at atomic resolution, the structures of DNAs modified by 2-aminofluorene and its N-acetyl derivative, 2-acetylaminofluorene (AAF). The underlying hypothesis is that DNA replicates with reduced fidelity when its normal right-handed B-structure is altered, and one result is a higher mutation rate. This change in structure may occur normally at a low incidence, for example by the formation of hairpin loops in appropriate sequences, but it may be enhanced greatly after covalent modification by a mutagenic substance. We use computational methods and have been able to incorporate the first data from NMR studies in our calculations. Computational approaches are important because x-ray and spectroscopic studies have not succeeded in producing atomic resolution views of mutagen and carcinogen-oligonucleotide adducts. The specific methods that we employ are minimized potential energy calculations using the torsion angle space molecular mechanics program DUPLEX to yield static views. Molecular dynamics simulations, with full solvent and salt, of the important static structures are carried out with the program AMBER; this yields mobile views in a medium that mimics the natural aqueous environment of the cell as well as can be done with current available computing resources.
Elastic constants of crystalline sodium from molecular dynamics
Sheila K. Schiferl; Duane C. Wallace
1985-01-01
We have used molecular-dynamics simulations to calculate the elastic constants C11, C12, and C44 of bcc sodium based on a pseudopotential model, at approximately zero pressure and for temperatures to near melting. Our procedure requires evaluation of average fluctuations of position and volume derivatives of the ion-ion interaction potential. The agreement with experiment is good for the magnitudes of C11
A molecular dynamics simulation of the plastic phase of hexachloroethane
A. Criado; A. Muñoz
1994-01-01
A molecular dynamics simulation of the plastic phase of the pseudo-octahedral molecule C2Cl6 has been carried out using a 6-exp potential model taken from the literature. A plastic phase has been found for a temperature range which is in good agreement with experiment. The calculated thermal averages of the centre of mass displacements and the orientational cubic harmonics are also
DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations
Filip Lankaš; Ji?í Šponer; Jörg Langowski; Thomas E. Cheatham III
2003-01-01
The sequence-dependent DNA deformability at the basepair step level was investigated using large-scale atomic resolution molecular dynamics simulation of two 18-bp DNA oligomers: d(GCCTATAAACGCCTATAA) and d(CTAGGTGGATGACTCATT). From an analysis of the structural fluctuations, the harmonic potential energy functions for all 10 unique steps with respect to the six step parameters have been evaluated. In the case of roll, three distinct
Numerical methods for molecular dynamics
Skeel, R.D.
1991-01-01
This report summarizes our research progress to date on the use of multigrid methods for three-dimensional elliptic partial differential equations, with particular emphasis on application to the Poisson-Boltzmann equation of molecular biophysics. This research is motivated by the need for fast and accurate numerical solution techniques for three-dimensional problems arising in physics and engineering. In many applications these problems must be solved repeatedly, and the extremely large number of discrete unknowns required to accurately approximate solutions to partial differential equations in three-dimensional regions necessitates the use of efficient solution methods. This situation makes clear the importance of developing methods which are of optimal order (or nearly so), meaning that the number of operations required to solve the discrete problem is on the order of the number of discrete unknowns. Multigrid methods are generally regarded as being in this class of methods, and are in fact provably optimal order for an increasingly large class of problems. The fundamental goal of this research is to develop a fast and accurate numerical technique, based on multi-level principles, for the solutions of the Poisson-Boltzmann equation of molecular biophysics and similar equations occurring in other applications. An outline of the report is as follows. We first present some background material, followed by a survey of the literature on the use of multigrid methods for solving problems similar to the Poisson-Boltzmann equation. A short description of the software we have developed so far is then given, and numerical results are discussed. Finally, our research plans for the coming year are presented.
Communication: nonadiabatic ring-polymer molecular dynamics.
Richardson, Jeremy O; Thoss, Michael
2013-07-21
A new method based on an extension of ring-polymer molecular dynamics is proposed for the calculation of thermal correlation functions in electronically nonadiabatic systems. The ring-polymer dynamics are performed using a continuous-variable representation of the electronic states within the mapping approach, such that the electronic and nuclear degrees of freedom are treated on an equal footing. Illustrative applications of the method show good agreement with exact quantum results for the dynamics over short to moderate times and reveal a systematic improvement over the classical implementation of the mapping approach (single-bead limit). Being based on trajectories, the method scales well with the number of degrees of freedom and will be applicable to simulate certain nonadiabatic processes in complex molecular systems. PMID:23883003
Sanville, Edward J [Los Alamos National Laboratory; Bock, Nicolas [Los Alamos National Laboratory; Challacombe, William M [Los Alamos National Laboratory; Cawkwell, Marc J [Los Alamos National Laboratory; Niklasson, Anders M N [Los Alamos National Laboratory; Dattelbaum, Dana M [Los Alamos National Laboratory; Sheffield, Stephen [Los Alamos National Laboratory; Sewell, Thomas D [UNIV OF MISSOURI
2010-01-01
A set of interatomic potentials for hydrocarbons that are based upon the self-consistent charge transfer tight-binding approximation to density functional theory have been developed and implemented into the quantum molecular dynamics code ''LATTE''. The interatomic potentials exhibit an outstanding level of transferability and have been applied in molecular dynamics simulations of tert-butylacetylene under thermodynamic conditions that correspond to its single-shock Hugoniot. We have achieved precise conservation of the total energy during microcanonical molecular dynamics trajectories under incomplete convergence via the extended Lagrangian Born-Oppenheimer molecular dynamics formalism. In good agreement with the results of a series of flyer-plate impact experiments, our SCC-TB molecular dynamics simulations show that tert-butylactylene molecules polymerize at shock pressures around 6.1 GPa.
Thumm, Uwe
Complete Characterization of Molecular Dynamics in Ultrashort Laser Fields B. Feuerstein,* Th and additionally opens the excit- ing possibility to dynamically modify the potential sur- faces of the molecular dynamics on field-modified molecular potential curves, explaining important strong-field-induced phenomena
Combined molecular dynamics-spin dynamics simulations of bcc iron
Perera, Meewanage Dilina N [ORNL] [ORNL; Yin, Junqi [ORNL] [ORNL; Landau, David P [University of Georgia, Athens, GA] [University of Georgia, Athens, GA; Nicholson, Don M [ORNL] [ORNL; Stocks, George Malcolm [ORNL] [ORNL; Eisenbach, Markus [ORNL] [ORNL; Brown, Greg [ORNL] [ORNL
2014-01-01
Using a classical model that treats translational and spin degrees of freedom on an equal footing, we study phonon-magnon interactions in BCC iron with combined molecular and spin dynamics methods. The atomic interactions are modeled via an empirical many-body potential while spin dependent interactions are established through a Hamiltonian of the Heisenberg form with a distance dependent magnetic exchange interaction obtained from first principles electronic structure calculations. The temporal evolution of translational and spin degrees of freedom was determined by numerically solving the coupled equations of motion, using an algorithm based on the second order Suzuki-Trotter decomposition of the exponential operators. By calculating Fourier transforms of space- and time-displaced correlation functions, we demonstrate that the the presence of lattice vibrations leads to noticeable softening and damping of spin wave modes. As a result of the interplay between lattice and spin subsystems, we also observe additional longitudinal spin wave excitations, with frequencies which coincide with that of the longitudinal lattice vibrations.
Iyengar, Srinivasan S.
Quantum wave packet ab initio molecular dynamics: An approach to study quantum dynamics in large and Toeplitz representation for the discrete free propagator, in conjunction with ab initio molecular dynamics of the methodology, namely, quantum dynamics and ab initio molecular dynamics, are harnessed together using a time
Long time step molecular dynamics using targeted Langevin stabilization
Izaguirre, JesÃºs A.
Long time step molecular dynamics using targeted Langevin stabilization Qun Ma JesÂ´us A. Izaguirre, IN 46556-0309, USA #12;Long time step molecular dynamics using targeted Langevin stabilization Abstract We introduce the B-spline Mollified Impulse (MOLLY) and the Targeted MOLLY (TM) for molecular dynamics (MD). TM
c Robert D. Skeel, 1998 Integration Schemes for Molecular Dynamics
Skeel, Robert
c Robert D. Skeel, 1998 Integration Schemes for Molecular Dynamics and Related Applications1 Robert of integration schemes that are useful for molecular dynamics and a variety of related applications. In partic molecular dynamics (MD) and related applications. This is not a comprehensive survey but more of a sampling
A molecular dynamics simulation of droplet evaporation Lorenzo Consolini 1
Aggarwal, Suresh K.
A molecular dynamics simulation of droplet evaporation Lorenzo Consolini 1 , Suresh K. Aggarwal A molecular dynamics (MD) simulation method is developed to study the evaporation of submicron droplets the ``vaporization'' process. Ó 2003 Elsevier Science Ltd. All rights reserved. Keywords: Molecular dynamics
Scalable Molecular Dynamics with NAMD JAMES C. PHILLIPS,1
Skeel, Robert
Scalable Molecular Dynamics with NAMD JAMES C. PHILLIPS,1 ROSEMARY BRAUN,1 WEI WANG,1 JAMES GUMBART in Wiley InterScience (www.interscience.wiley.com). Abstract: NAMD is a parallel molecular dynamics code introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force
been observed by molecular dynamics simulations is that, once
Thompson, John N.
been observed by molecular dynamics simulations is that, once the interface is removed (by removing microscopy and insights from molecular dynamics simulations are rapidly completing the picture of how clamp as the conformational agility observed by EM and by molecular dynamics simulations. As the role of DNA sliding clamps
Molecular dynamics simulation of thermal conductivity of nanocrystalline composite films
Walker, D. Greg
Molecular dynamics simulation of thermal conductivity of nanocrystalline composite films N numerically using a molecular dynamics simulation. Results indicate that a reduction of 25% in the effective yielding values for ZT 6 1 at room temperature [4]. Using molecular dynamics, the present work explores
Molecular Dynamics Investigation of Spall Fracture A. M. Krivtsov1
Krivtsov, Anton M.
Molecular Dynamics Investigation of Spall Fracture A. M. Krivtsov1 , Y. I. Mescheryakov2 1 St212. ABSTRACT Molecular dynamics investigation of central impact of thin plate impactor to target from the same understanding material kinetics inside the speci- men during shock loading. Using molecular dynamics simulation
Molecular dynamics simulations of protein folding from the transition state
Caflisch, Amedeo
Molecular dynamics simulations of protein folding from the transition state Jo¨ rg Gsponer molecular dynamics (MD) simulations of unfolding. Sixty MD trajectories (for a total of about 7 s) were as in the denatured state. Molecular dynamics (MD) simulations of protein unfolding at high temperature with explicit
Molecular Dynamics simulations of enforced functional protein motions
Gräter, Frauke
Molecular Dynamics simulations of enforced functional protein motions Dissertation zur Erlangung;Contents 1 Introduction 7 2 Theory and Methods 17 2.1 Molecular Dynamics Simulations-Exchange Molecular Dynamics Simulations . . . . . . 25 2.4 Simulating force-induced transitions
MOLECULAR DYNAMICS SIMULATION ON COMMODITY SHAREDMEMORY MULTIPROCESSOR SYSTEMS
Goddard III, William A.
MOLECULAR DYNAMICS SIMULATION ON COMMODITY SHAREDMEMORY MULTIPROCESSOR SYSTEMS WITH LIGHTWEIGHT@cco.caltech.edu {hli, tahir, wag}@wag.caltech.edu Keywords: molecular dynamics simulation, Nbody prob lems, shared molecular dynamics to astrophysics. In all these applications, the basic approach to simulation is the same
A PENALTY FUNCTION METHOD FOR CONSTRAINED MOLECULAR DYNAMICS SIMULATION
A PENALTY FUNCTION METHOD FOR CONSTRAINED MOLECULAR DYNAMICS SIMULATION By Ajith Gunaratne000 A PENALTY FUNCTION METHOD FOR CONSTRAINED MOLECULAR DYNAMICS SIMULATION AJITH GUNARATNE AND ZHIJUN WU FOR MOLECULAR DYNAMICS SIMULATION 1 that the new iterate can satisfy the constraints [3]. Depending
Computing thermomechanical properties of crosslinked epoxy by molecular dynamic simulations
Chen, Wei
Computing thermomechanical properties of crosslinked epoxy by molecular dynamic simulations Shaorui Keywords: Cross-linked epoxy Molecular dynamics simulation Structuralproperty correlation a b s t r a c t This paper reports the use of molecular dynamics simulations to study the thermomechanical properties
Looking Back Molecular-dynamics simulations require numerical methods
Duisburg-Essen, Universität
Looking Back · Molecular-dynamics simulations require numerical methods for the integration, Heun, and Runge-Kutta. However, these methods are not suitable for molecular-dynamics simulations. · Frequently used methods for the integration of the equations in a molecular-dynamics simulation are the Gear
RESEARCH PAPER Molecular dynamics simulations of oscillatory Couette flows
Priezjev, Nikolai V.
RESEARCH PAPER Molecular dynamics simulations of oscillatory Couette flows with slip boundary-periodic flows of monatomic liquids is investigated using non-equilibrium molecular dynamics simulations Molecular dynamics simulation Á Liquid flow Á Nanofluidics Á Slip length 1 Introduction The rational design
TECHNICAL REPORT 022 "Molecular Dynamics Simulation of Vitreous Silica Structures"
Barr, Al
TECHNICAL REPORT 022 1999 "Molecular Dynamics Simulation of Vitreous Silica Structures" N. T. Huff-Crystalline Solids MOLECULAR DYNAMICS SIMULATION OF VITREOUS SILICA STRUCTURES Norman T. Huff*, Owens Corning Science-74), California Institute of Technology, Pasadena, CA 91125 Abstract Molecular dynamics (MD) simulations can
Calculation of elastic constants using isothermal molecular dynamics
John R. Ray; Michael C. Moody; Aneesur Rahman
1986-01-01
A new form of molecular dynamics has been developed whose trajectories generate the isothermal or canonical ensemble of classical statistical physics. We have performed molecular-dynamics calculations of the elastic constants using this new ensemble. We find that the elastic constants, as well as other thermodynamic quantities, may be calculated just as efficiently in the isothermal form of molecular dynamics as
Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears
NASA Technical Reports Server (NTRS)
Srivastava, Deepak; Globus, Al; Han, Jie; Chancellor, Marisa K. (Technical Monitor)
1997-01-01
Dynamics of laser powered carbon nanotube gears is investigated by molecular dynamics simulations with Brenner's hydrocarbon potential. We find that when the frequency of the laser electric field is much less than the intrinsic frequency of the carbon nanotube, the tube exhibits an oscillatory pendulam behavior. However, a unidirectional rotation of the gear with oscillating frequency is observed under conditions of resonance between the laser field and intrinsic gear frequencies. The operating conditions for stable rotations of the nanotube gears, powered by laser electric fields are explored, in these simulations.
Analysis of motion features for molecular dynamics simulation of proteins
NASA Astrophysics Data System (ADS)
Kamada, Mayumi; Toda, Mikito; Sekijima, Masakazu; Takata, Masami; Joe, Kazuki
2011-01-01
Recently, a new method for time series analysis using the wavelet transformation has been proposed by Sakurai et al. We apply it to molecular dynamics simulation of Thermomyces lanuginosa lipase (TLL). Introducing indexes to characterize collective motion of the protein, we have obtained the following two results. First, time evolution of the collective motion involves not only the dynamics within a single potential well but also takes place wandering around multiple conformations. Second, correlation of the collective motion between secondary structures shows that collective motion exists involving multiple secondary structures. We discuss future prospects of our study involving 'disordered proteins'.
A molecular dynamics simulation of the plastic phase of hexachloroethane
NASA Astrophysics Data System (ADS)
Criado, A.; Muñoz, A.
A molecular dynamics simulation of the plastic phase of the pseudo-octahedral molecule C2Cl6 has been carried out using a 6-exp potential model taken from the literature. A plastic phase has been found for a temperature range which is in good agreement with experiment. The calculated thermal averages of the centre of mass displacements and the orientational cubic harmonics are also in good agreement with the experimental values. The calculated atomic orientational probability distribution shows maxima along the [100] and [111] directions for the Cl and C atoms, respectively, and the distribution is isotropic over a wide angular range about the maxima. An analysis of the instantaneous molecular positions shows that the molecules have a larger probability of rotating, and perform sudden reorientations around the [100] crystal directions. It has been found that the molecular C-C axis plays no important role in the molecular dynamics, which is identical to what is found for the plastic phase of the octahedral molecule SF6. A search has been made for the formation of linear clusters of molecules as suggested in the literature but these do not appear in the simulation. A correlated repulsion between molecules and their next-nearest neighbours has been found so that the molecules avoid close contacts of the chlorine atoms along the [100] directions by performing rotations about the [110] crystal directions. The single-molecule rotational potential is calculated and compared with the experimental one, showing that the potential energy barrier for molecular rotations about the [100] directions is considerably lower than for the [110] and [111] rotations. The single-molecule dynamics are also studied and the translational power spectrum reveals a strong translational-rotational coupling whereas the rotational spectrum shows an isotropic rotational diffusion behaviour. The molecules are found to librate around ideal positions for an average residence time of 5·4 ps between consecutive reorientational jumps.
Toni Kiljunen; Jussi Eloranta; Henrik Kunttu
1999-01-01
Ground-state potential-energy curves and distance dependent isotropic hyperfine coupling (IHC) constants for ground-state H-RG (=Ne, Ar, Kr, Xe) are obtained at CCSD(T) (coupled-cluster single double triple) and MP4(SDQ) (fourth-order Moller-Plesset single double quadruple) levels, respectively, with an augmented basis set aug-Stuttgart (RG)\\/aug-cc-pVQZ (H). The obtained Rm and ? are for NeH: 3.45 Å and -1.36 meV; ArH: 3.65 Å and
Hammes-Schiffer, Sharon
Hybrid approach for including electronic and nuclear quantum effects in molecular dynamics profiles. The dynamical effects are studied with the molecular dynamics with quantum transitions MDQT is the use of classical molecular dynamics simulations with molecular mechanical forcefields.7
Molecular profiling of gliomas: potential therapeutic implications.
Alentorn, Agusti; Duran-Peña, Alberto; Pingle, Sandeep C; Piccioni, David E; Idbaih, Ahmed; Kesari, Santosh
2015-08-01
Gliomas are the most common primary malignant brain tumor. Over the last decade, significant advances have been made in the molecular characterization of this tumor group, identifying predictive biomarkers or molecular actionable targets, and paving the way to molecular-based targeted therapies. This personalized therapeutic approach is effective and illustrated in the present review. Among many molecular abnormalities, BRAF mutation and mTOR activation in pilocytic astrocytomas and subependymal giant cell astrocytomas are actionable targets sensitive to vemurafenib and everolimus, respectively. Chromosome arms 1p/19q co-deletion and IDH mutational status are pivotal in driving delivery of early procarbazine, lomustine and vincristine chemotherapy in anaplastic oligodendroglial tumors. Although consensus to assess MGMT promoter methylation is not reached yet, it may be useful in predicting resistance to temozolomide in elderly patients. PMID:26118895
Freedman, Holly; Truong, Thanh N
2005-03-17
An application of the coupled reference interaction site model (RISM)/simulation methodology to the calculation of the potential of mean force (PMF) curve in aqueous solution for the identity nucleophilic substitution reaction Cl(-) + CH(3)Cl is performed. The free energy of activation is calculated to be 27.1 kcal/mol which compares very well with the experimentally determined barrier height of 26.6 kcal/mol. Furthermore, the calculated PMF is almost superimposed with that previously calculated using the computationally rigorous Monte Carlo with importance sampling method (Chandrasekhar, J.; Smith, S. F.; Jorgensen, W. L. J. Am. Chem. Soc. 1985, 107, 154). Using the calculated PMF, a crude estimate of the solvated kinetic transmission coefficient also compares well with that of previous more accurate simulations. These results indicate that the coupled RISM/simulation method provides a cost-effective methodology for studying reactions in solution. PMID:16851554
Molecular dynamic simulation methods for anisotropic liquids.
Aoki, Keiko M; Yoneya, Makoto; Yokoyama, Hiroshi
2004-03-22
Methods of molecular dynamics simulations for anisotropic molecules are presented. The new methods, with an anisotropic factor in the cell dynamics, dramatically reduce the artifacts related to cell shapes and overcome the difficulties of simulating anisotropic molecules under constant hydrostatic pressure or constant volume. The methods are especially effective for anisotropic liquids, such as smectic liquid crystals and membranes, of which the stacks of layers are compressible (elastic in direction perpendicular to the layers) while the layer itself is liquid and only elastic under uniform compressive force. The methods can also be used for crystals and isotropic liquids as well. PMID:15267433
Electron Dynamics during Strong Field Molecular Ionization
NASA Astrophysics Data System (ADS)
Weinacht, Thomas
2014-05-01
Strong Field Ionization plays a central role in the study of ultrafast electron dynamics, both as the first step in attosecond pulse generation and in the launch of electron wave packets in atoms and molecules. This talk will focus on studies of strong field molecular ionization with shaped laser pulses, where the pulse shape dependence yields insight into the electron dynamics during ionization. Coincidence velocity map imaging and close collaboration with theory enable us to examine the role of both neutral and ionic resonances as well as electron correlation. We gratefully acknowledge support from the National Science Foundation under grant number 1205397.
Molecular Dynamics Simulation of Disordered Zircon
Devanathan, Ram; Corrales, Louis R.; Weber, William J.; Chartier, Alain; Meis, Constantin
2004-02-27
The melting of zircon and the amorphous state produced by quenching from the melt were simulated by molecular dynamics using a new partial charge model combined with the Ziegler-Biersack-Littmark potential. The model has been established for the description of the crystalline and aperiodic structures of zircon in order to be used for the simulation of displacement cascades. It provides an excellent fit to the structure, and accounts with convenient precision the mechanical and thermodynamic properties of zircon. The calculated melting temperature is about 2100 K. The activation energy for self-diffusion of ions in the liquid state was determined to be 190-200 kJ/mole. Melt quenching was employed to produce two different disordered states with distinct densities and structures. In the high density disordered state, the zircon structure is intact but the bond angle distributions are broader, 4% of the Si units are polymerized, and the volume swelling is about 8%. In the low density amorphous state, the Zr and Si coordination numbers are lower, and the Zr-O and Si-O bond lengths are shorter than corresponding values for the crystal. In addition, a highly polymerized Si network, with average connectivity of two, is observed in the low density amorphous state. These features have all been experimentally observed in natural metamict zircon. The present findings, when considered in light of experimental radiation effects studies, suggest that the swelling in zircon arises initially from disorder in the zircon crystal, and at high doses the disordered crystal is unable to accommodate the volume expansion and transforms to the amorphous state.
Open quantum system parameters from molecular dynamics
Wang, Xiaoqing; Wüster, Sebastian; Eisfeld, Alexander
2015-01-01
We extract the site energies and spectral densities of the Fenna-Matthews-Olson (FMO) pigment protein complex of green sulphur bacteria from simulations of molecular dynamics combined with energy gap calculations. Comparing four different combinations of methods, we investigate the origin of quantitative differences regarding site energies and spectral densities obtained previously in the literature. We find that different forcefields for molecular dynamics and varying local energy minima found by the structure relaxation yield significantly different results. Nevertheless, a picture averaged over these variations is in good agreement with experiments and some other theory results. Throughout, we discuss how vibrations external- or internal to the pigment molecules enter the extracted quantities differently and can be distinguished. Our results offer some guidance to set up more computationally intensive calculations for a precise determination of spectral densities in the future. These are required to determ...
Molecular dynamics simulation of strongly coupled QCD plasmas
P. Hartmann; Z. Donko; P. Levai; G. J. Kalman
2006-01-06
The properties of a strongly interacting quark plasma are investigated by molecular dynamics method including non-abelian quark-quark potential. Our main goal is to study the thermalization process in this system. We find an interesting resonance-like behaviour: at a characteristic time close to the inverse plasma frequency the quark plasma is heated up substantially via energy transfer from quark potential energy into one particle kinetic energy. Color rotation mechanism enhances the effectivity of this heating process, leading to a very fast thermalization with high temperature.
Molecular dynamics simulation of threshold displacement energies in zircon
Moreira, Pedro A.; Devanathan, Ramaswami; Yu, Jianguo; Weber, William J.
2009-10-15
Molecular-dynamics simulations were used to examine the displacement threshold energy (Ed) surface for Zr, Si and O in zircon using two different interatomic potentials. For each sublattice, the simulation was repeated from different initial conditions to estimate the uncertainty in the calculated value of Ed. The displacement threshold energies vary considerably with crystallographic direction and sublattice. The average displacement energy calculated with a recently developed transferable potential is about 120 and 60 eV for cations and anions, respectively. The oxygen displacement energy shows good agreement with experimental estimates in ceramics.
Improving structure-based function prediction using molecular dynamics
Glazer, Dariya S.; Radmer, Randall J.; Altman, Russ B.
2009-01-01
Summary The number of molecules with solved three-dimensional structure but unknown function is increasing rapidly. Particularly problematic are novel folds with little detectable similarity to molecules of known function. Experimental assays can determine the functions of such molecules, but are time-consuming and expensive. Computational approaches can identify potential functional sites; however, these approaches generally rely on single static structures and do not use information about dynamics. In fact, structural dynamics can enhance function prediction: we coupled molecular dynamics simulations with structure-based function prediction algorithms that identify Ca2+ binding sites. When applied to 11 challenging proteins, both methods showed substantial improvement in performance, revealing 22 more sites in one case and 12 more in the other, with a modest increase in apparent false positives. Thus, we show that treating molecules as dynamic entities improves the performance of structure-based function prediction methods. PMID:19604472
Molecular dynamics simulation: A tool for exploration and discovery
NASA Astrophysics Data System (ADS)
Rapaport, Dennis C.
2009-03-01
The exploratory and didactic aspects of science both benefit from the ever-growing role played by computer simulation. One particularly important simulational approach is the molecular dynamics method, used for studying the nature of matter from the molecular to much larger scales. The effectiveness of molecular dynamics can be enhanced considerably by employing visualization and interactivity during the course of the computation and afterwards, allowing the modeler not only to observe the detailed behavior of the systems simulated in different ways, but also to steer the computations in alternative directions by manipulating parameters that govern the actual behavior. This facilitates the creation of potentially rich simulational environments for examining a multitude of complex phenomena, as well as offering an opportunity for enriching the learning process. A series of relatively advanced examples involving molecular dynamics will be used to demonstrate the value of this approach, in particular, atomistic simulations of spontaneously emergent structured fluid flows (the classic Rayleigh--B'enard and Taylor--Couette problems), supramolecular self-assembly of highly symmetric shell structures (involved in the formation of viral capsids), and that most counterintuitive of phenomena, granular segregation (e.g., axial and radial separation in a rotating cylinder).
Molecular dynamics simulation of nanoscale liquid flows
Yuxiu LiJinliang XuDongqing Li; Jinliang Xu; Dongqing Li
2010-01-01
Molecular dynamics (MD) simulation is a powerful tool to investigate the nanoscale fluid flow. In this article, we review\\u000a the methods and the applications of MD simulation in liquid flows in nanochannels. For pressure-driven flows, we focus on\\u000a the fundamental research and the rationality of the model hypotheses. For electrokinetic-driven flows and the thermal-driven\\u000a flows, we concentrate on the principle
Exploring Transmembrane Diffusion Pathways With Molecular Dynamics
NSDL National Science Digital Library
Yi Wang (University of Illinois at Urbana-Champaign)
2010-06-01
Transmembrane exchange of materials is a fundamental process in biology. Molecular dynamics provides a powerful method to investigate in great detail various aspects of the phenomenon, particularly the permeation of small uncharged molecules, which continues to pose a challenge to experimental studies. We will discuss some of the recent simulation studies investigating the role of lipid-mediated and protein-mediated mechanisms in permeation of water and gas molecules across the membrane.
New faster CHARMM molecular dynamics engine
Hynninen, Antti-Pekka; Crowley, Michael F
2014-01-01
We introduce a new faster molecular dynamics (MD) engine into the CHARMM software package. The new MD engine is faster both in serial (i.e., single CPU core) and parallel execution. Serial performance is approximately two times higher than in the previous version of CHARMM. The newly programmed parallelization method allows the MD engine to parallelize up to hundreds of CPU cores. PMID:24302199
Molecular dynamics simulations of polymer electrolytes
Oleg Alexandrovich Borodin
2000-01-01
Molecular dynamics simulations have been performed on solutions of 12 repeat unit poly(ethylene oxide) (PEO) and diglyme doped LiI at 363 K and 450 K for compositions ether oxygen:Li (EO:Li) = 48:1, 15:1 and 5:1. An explicit atom quantum chemistry based force field developed in our previous works has been used allowing us quantitative predictions of solutions structural properties, polymer
Membrane Electroporation: A Molecular Dynamics Simulation
Mounir Tarek
2005-01-01
We present results of molecular dynamics simulations of lipid bilayers under a high transverse electrical field aimed at investigating their electroporation. Several systems are studied, namely 1), a bare bilayer, 2), a bilayer containing a peptide nanotube channel, and 3), a system with a peripheral DNA double strand. In all systems, the applied transmembrane electric fields (0.5V.nm?1 and 1.0V.nm?1) induce
Learning generative models of molecular dynamics
2012-01-01
We introduce three algorithms for learning generative models of molecular structures from molecular dynamics simulations. The first algorithm learns a Bayesian-optimal undirected probabilistic model over user-specified covariates (e.g., fluctuations, distances, angles, etc). L1 reg-ularization is used to ensure sparse models and thus reduce the risk of over-fitting the data. The topology of the resulting model reveals important couplings between different parts of the protein, thus aiding in the analysis of molecular motions. The generative nature of the model makes it well-suited to making predictions about the global effects of local structural changes (e.g., the binding of an allosteric regulator). Additionally, the model can be used to sample new conformations. The second algorithm learns a time-varying graphical model where the topology and parameters change smoothly along the trajectory, revealing the conformational sub-states. The last algorithm learns a Markov Chain over undirected graphical models which can be used to study and simulate kinetics. We demonstrate our algorithms on multiple molecular dynamics trajectories. PMID:22369071
Control-volume representation of molecular dynamics
E. R. Smith; D. M. Heyes; D. Dini; T. A. Zaki
2012-05-24
A Molecular Dynamics (MD) parallel to the Control Volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood, J. Chem. Phys. 18, 817 (1950) over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds' Transport Theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-Control-Volume (\\CV) conversion function $\\vartheta_{i}$, for each molecule $i$. The \\CV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the Volume Average (VA, Lutsko, J. Appl. Phys 64, 1152 (1988)) techniques and the Method of Planes (MOP, Todd et al, Phys. Rev. E 52, 1627 (1995)) emerges naturally from the treatment. Numerical experiments using the MD CV method are reported for equilibrium and non-equilibrium (start-up Couette flow) model liquids, which demonstrate the advantages of the formulation. The CV formulation of the MD is shown to be exactly conservative, and is therefore ideally suited to obtain macroscopic properties from a discrete system.
Learning generative models of molecular dynamics.
Razavian, Narges Sharif; Kamisetty, Hetunandan; Langmead, Christopher J
2012-01-01
We introduce three algorithms for learning generative models of molecular structures from molecular dynamics simulations. The first algorithm learns a Bayesian-optimal undirected probabilistic model over user-specified covariates (e.g., fluctuations, distances, angles, etc). L1 regularization is used to ensure sparse models and thus reduce the risk of over-fitting the data. The topology of the resulting model reveals important couplings between different parts of the protein, thus aiding in the analysis of molecular motions. The generative nature of the model makes it well-suited to making predictions about the global effects of local structural changes (e.g., the binding of an allosteric regulator). Additionally, the model can be used to sample new conformations. The second algorithm learns a time-varying graphical model where the topology and parameters change smoothly along the trajectory, revealing the conformational sub-states. The last algorithm learns a Markov Chain over undirected graphical models which can be used to study and simulate kinetics. We demonstrate our algorithms on multiple molecular dynamics trajectories. PMID:22369071
Equipartition Principle for Internal Coordinate Molecular Dynamics
Jain, Abhinandan; Park, In-Hee; Vaidehi, Nagarajan
2012-01-01
The principle of equipartition of (kinetic) energy for all-atom Cartesian molecular dynamics states that each momentum phase space coordinate on the average has ½kT of kinetic energy in a canonical ensemble. This principle is used in molecular dynamics simulations to initialize velocities, and to calculate statistical properties such as entropy. Internal coordinate molecular dynamics (ICMD) models differ from Cartesian models in that the overall kinetic energy depends on the generalized coordinates and includes cross-terms. Due to this coupled structure, no such equipartition principle holds for ICMD models. In this paper we introduce non-canonical modal coordinates to recover some of the structural simplicity of Cartesian models and develop a new equipartition principle for ICMD models. We derive low-order recursive computational algorithms for transforming between the modal and physical coordinates. The equipartition principle in modal coordinates provides a rigorous method for initializing velocities in ICMD simulations thus replacing the ad hoc methods used until now. It also sets the basis for calculating conformational entropy using internal coordinates. PMID:23341754
The 2011 Dynamics of Molecular Collisions Conference
Nesbitt, David J. [JILA, NIST
2011-07-11
The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor Yuan T. Lee & Professor George Schatz. Professor Lee’s research has been based on the development & use of advanced chemical kinetics & molecular beams to investigate & manipulate the behavior of fundamental chemical reactions. Lee’s work has been recognized by many awards, including the Nobel Prize for Chemistry in 1986, as well as Sloan Fellow, Dreyfus Scholar, Fellowship in the American Academy of Arts & Sciences, Fellowship in the American Physical Society, Guggenheim Fellow, Member National Academy of Sciences, Member Academia Sinica, E.O. Lawrence Award, Miller Professor, Berkeley, Fairchild Distinguished Scholar, Harrison Howe Award, Peter Debye Award, & the National Medal of Science. Lee also has served as the President of the Academia Sinica in Taiwan (ROC). Professor Schatz’s research group is interested in using theory & computation to describe physical phenomena in a broad range of applications relevant to chemistry, physics, biology & engineering. Among the types of applications that we interested are: optical properties of nanoparticles & nanoparticle assemblies; using theory to model polymer properties; DNA structure, thermodynamics & dynamics; modeling self assembly & nanopatterning; & gas phase reaction dynamics. Among his many awards & distinctions have been appointment as an Alfred P. Sloan Research Fellow, Camille & Henry Dreyfus Teacher-Scholar, the Fresenius Award, Fellow of the American Physical Society, the Max Planck Research Award, Fellowship in the American Association for the Advancement of Science, & election to the International Academy of Quantum Molecular Sciences & the American Academy of Arts & Sciences. Dr Schatz is also lauded for his highly successful work as Editor for the Journal of Physical Chemistry. We requested $10,000 from DOE in support of this meeting. The money was distributed widely among the student & post doctoral fellows & some used to attract the very best scientists in the field. The organizers were committed to encouraging women & minorities as well as encourage the field of Chemical Physics in scientific
Evaluating data mining algorithms using molecular dynamics trajectories.
Tatsis, Vasileios A; Tjortjis, Christos; Tzirakis, Panagiotis
2013-01-01
Molecular dynamics simulations provide a sample of a molecule's conformational space. Experiments on the mus time scale, resulting in large amounts of data, are nowadays routine. Data mining techniques such as classification provide a way to analyse such data. In this work, we evaluate and compare several classification algorithms using three data sets which resulted from computer simulations, of a potential enzyme mimetic biomolecule. We evaluated 65 classifiers available in the well-known data mining toolkit Weka, using 'classification' errors to assess algorithmic performance. Results suggest that: (i) 'meta' classifiers perform better than the other groups, when applied to molecular dynamics data sets; (ii) Random Forest and Rotation Forest are the best classifiers for all three data sets; and (iii) classification via clustering yields the highest classification error. Our findings are consistent with bibliographic evidence, suggesting a 'roadmap' for dealing with such data. PMID:24010266
Molecular dynamics studies of a hexameric purine nucleoside phosphorylase.
Zanchi, Fernando Berton; Caceres, Rafael Andrade; Stabeli, Rodrigo Guerino; de Azevedo, Walter Filgueira
2010-03-01
Purine nucleoside phosphorylase (PNP) (EC.2.4.2.1) is an enzyme that catalyzes the cleavage of N-ribosidic bonds of the purine ribonucleosides and 2-deoxyribonucleosides in the presence of inorganic orthophosphate as a second substrate. This enzyme is involved in purine-salvage pathway and has been proposed as a promising target for design and development of antimalarial and antibacterial drugs. Recent elucidation of the three-dimensional structure of PNP by X-ray protein crystallography left open the possibility of structure-based virtual screening initiatives in combination with molecular dynamics simulations focused on identification of potential new antimalarial drugs. Most of the previously published molecular dynamics simulations of PNP were carried out on human PNP, a trimeric PNP. The present article describes for the first time molecular dynamics simulations of hexameric PNP from Plasmodium falciparum (PfPNP). Two systems were simulated in the present work, PfPNP in ligand free form, and in complex with immucillin and sulfate. Based on the dynamical behavior of both systems the main results related to structural stability and protein-drug interactions are discussed. PMID:19669809
Strak, Pawe?; Krukowski, Stanis?aw
2011-04-21
Determination of shear viscosity of molecular nitrogen (N(2)) by molecular dynamics (MD) in the high density range needs explicit incorporation of the rotational motion and therefore precise knowledge of angular dependence of N(2)-N(2) intermolecular potential. Newly designed Couette flow nonequilibrium molecular dynamic (NEMD) simulation procedure employs corrugated moving boundary, coupling the moving walls to translational and rotational motion exactly. Low density data on nitrogen viscosity show good agreement between MD data and experiment, confirming the radial dependence of the potential derived from quantum mechanical (QM) high precision calculations (coupled-cluster singles-and-doubles with a perturbative triples corrections [CCSD(T)]). Additionally, the angular dependence of the potential is verified using shear viscosity data for high density region, obtained from newly developed molecular dynamics (MD) simulations. It was demonstrated that the corrugated wall flow simulations provide results that are independent of the details of wall potential, fulfilling a basic requirement for application of MD simulations. These results are in good agreement with the equilibrium molecular dynamics (EMD) viscosity, derived from the Green-Kubo formula. Derived analytical dependence of the shear viscosity on the density and temperature shows that the MD data are in good agreement with experiment. Thus, MD simulations indicate that the CCSD(T) potential angular form is sufficiently precise for determination of the viscosity in a wide range of temperature and pressure. PMID:21438507
E, Weinan
Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics; accepted 24 March 2003 We present a ``coarse molecular dynamics'' approach and apply it to studying and trace low-dimensional free energy surfaces. To illustrate the coarse molecular dynamics approach, we
Cellular/Molecular Stimulus History Reliably Shapes Action Potential
Juusola, Mikko
Cellular/Molecular Stimulus History Reliably Shapes Action Potential Waveforms of Cortical Neurons, they participate in synaptic integration, and thus in the probability of generating succeeding action potentials, in a shape-dependent way. Here we test whether the different action potential waveforms produced during
Large scale molecular dynamics simulations of nuclear pasta
NASA Astrophysics Data System (ADS)
Horowitz, C. J.; Berry, D.; Briggs, C.; Chapman, M.; Clark, E.; Schneider, A.
2014-09-01
We report large-scale molecular dynamics simulations of nuclear pasta using from 50,000 to more than 3,000,000 nucleons. We use a simple phenomenological two-nucleon potential that reproduces nuclear saturation. We find a complex ``nuclear waffle'' phase in addition to more conventional rod, plate, and sphere phases. We also find long-lived topological defects involving screw like dislocations that may reduce the electrical conductivity and thermal conductivity of lasagna phases. From MD trajectories we calculate a variety of quantities including static structure factor, dynamical response function, shear modulus and breaking strain. We report large-scale molecular dynamics simulations of nuclear pasta using from 50,000 to more than 3,000,000 nucleons. We use a simple phenomenological two-nucleon potential that reproduces nuclear saturation. We find a complex ``nuclear waffle'' phase in addition to more conventional rod, plate, and sphere phases. We also find long-lived topological defects involving screw like dislocations that may reduce the electrical conductivity and thermal conductivity of lasagna phases. From MD trajectories we calculate a variety of quantities including static structure factor, dynamical response function, shear modulus and breaking strain. Supported in parts by DOE Grants No. DE-FG02-87ER40365 (Indiana University) and No. DE-SC0008808 (NUCLEI SciDAC Collaboration).
Molecular dynamics simulation study of methanesulfonic acid.
Canales, Manel; Alemán, Carlos
2014-03-27
A molecular dynamics simulation study of methanesulfonic acid has been carried out using a reliable force field in a large range of temperatures. Several thermodynamic, structural, and dynamical properties have been calculated and compared with the available experimental data. The density, the shear viscosity, the heat of vaporization, and the melting temperature results, calculated from this force field, are in a good agreement with the experimental data. Analysis of the influence of the hydrogen bonds in structural and dynamical properties has also been performed. The continuous and interrupted methodologies to compute hydrogen bonding lifetimes have been applied. The interrupted hydrogen bond lifetimes values are consistent with the diffusion and viscosity coefficients. The activation energies of the self-diffusion, the reorientational motions, and the hydrogen bonding lifetimes are coincident. PMID:24593036
Molecular dynamics simulations of the elastic moduli of polymer–carbon nanotube composites
Michael Griebel; Jan Hamaekers
2004-01-01
The elastic moduli of polymer–carbon nanotube composites are examined by molecular dynamics simulations of a single-walled carbon nanotube embedded in polyethylene. The overall system is modeled with a many-bond order potential due to Brenner. Alternatively, only the carbon nanotube is modeled with Brenner's potential and the polyethylene matrix is modeled by a united-atom potential. For these systems we perform molecular
On the ionization potential of molecular oxygen
NASA Technical Reports Server (NTRS)
Samson, J. A. R.; Gardner, J. L.
1974-01-01
The ionization potential of O2 was measured by the technique of high resolution photoelectron spectroscopy taking into account the influence of rotational structure on the shape of the vibrational bands. A value of 12.071 + or - .001 eV (1027.1 + or - 0.1 A) was found for the ionization potential. A lowering of the ionization potential caused by a branch-head when delta N = -2 gave an appearance potential for ionization of 12.068 + or - .001 eV (1027.4 + or - 0.1 A).
Southern California, University of
Brittle dynamic fracture of crystalline cubic silicon carbide ,,3C-SiC... via molecular dynamics for three low-index crack surfaces, i.e., 110 , 111 , and 100 , in crystalline cubic silicon carbide 3C-SiC fracture in crystalline cubic silicon carbide 3C-SiC using our interatomic potential. The results exhibit
Computing Molecular Potential Energy Surface with DIET Emmanuel Jeannot
Jeannot, Emmanuel
Computing Molecular Potential Energy Surface with DIET Emmanuel Jeannot LORIA Universit´e Henri tackled this problem using several up-to-date computer science technology such as grid-computing middleware, molecular databases, script interfacing, etc. An example on the optimization of semiem- pirical
MOLECULAR ANALYSIS OF HUMAN SPERMATOZOA: POTENTIAL FOR INFERTILITY RESEARCH
Gordon Research Conference: Mammalian Gametogenesis and Embryogenesis New London, CT, July 1-6, 2000 Molecular Analysis of Human Spermatozoa: Potential for Infertility Research David Miller 1, David Dix2, Robert Reid 3, Stephen A Krawetz 3 1Reproductive ...
NASA Astrophysics Data System (ADS)
Feng, Wei; Ma, Ning; Zhu, Dan
2015-03-01
The improvement of methods for optical clearing agent prediction exerts an important impact on tissue optical clearing technique. The molecular dynamic simulation is one of the most convincing and simplest approaches to predict the optical clearing potential of agents by analyzing the hydrogen bonds, hydrogen bridges and hydrogen bridges type forming between agents and collagen. However, the above analysis methods still suffer from some problem such as analysis of cyclic molecule by reason of molecular conformation. In this study, a molecular effective coverage surface area based on the molecular dynamic simulation was proposed to predict the potential of optical clearing agents. Several typical cyclic molecules, fructose, glucose and chain molecules, sorbitol, xylitol were analyzed by calculating their molecular effective coverage surface area, hydrogen bonds, hydrogen bridges and hydrogen bridges type, respectively. In order to verify this analysis methods, in vitro skin samples optical clearing efficacy were measured after 25 min immersing in the solutions, fructose, glucose, sorbitol and xylitol at concentration of 3.5 M using 1951 USAF resolution test target. The experimental results show accordance with prediction of molecular effective coverage surface area. Further to compare molecular effective coverage surface area with other parameters, it can show that molecular effective coverage surface area has a better performance in predicting OCP of agents.
Tunable Interfacial Thermal Conductance by Molecular Dynamics
NASA Astrophysics Data System (ADS)
Shen, Meng
We study the mechanism of tunable heat transfer through interfaces between solids using a combination of non-equilibrium molecular dynamics simulation (NEMD), vibrational mode analysis and wave packet simulation. We investigate how heat transfer through interfaces is affected by factors including pressure, interfacial modulus, contact area and interfacial layer thickness, with an overreaching goal of developing fundamental knowledge that will allow one to tailor thermal properties of interfacial materials. The role of pressure and interfacial stiffness is unraveled by our studies on an epitaxial interface between two Lennard-Jones (LJ) crystals. The interfacial stiffness is varied by two different methods: (i) indirectly by applying pressure which due to anharmonic nature of bonding, increases interfacial stiffness, and (ii) directly by changing the interfacial bonding strength by varying the depth of the potential well of the LJ potential. When the interfacial bonding strength is low, quantitatively similar behavior to pressure tuning is observed when the interfacial thermal conductance is increased by directly varying the potential-well depth parameter of the LJ potential. By contrast, when the interfacial bonding strength is high, thermal conductance is almost pressure independent, and even slightly decreases with increasing pressure. This decrease can be explained by the change in overlap between the vibrational densities of states of the two crystalline materials. The role of contact area is studied by modeling structures comprised of Van der Waals junctions between single-walled nanotubes (SWCNT). Interfacial thermal conductance between SWCNTs is obtained from NEMD simulation as a function of crossing angle. In this case the junction conductance per unit area is essentially a constant. By contrast, interfacial thermal conductance between multiwalled carbon nanotubes (MWCNTs) is shown to increase with diameter of the nanotubes by recent experimental studies [1]. To elucidate this behavior we studied a simplified model comprised of an interface between two stacks of graphene ribbons to mimic the contact between multiwalled nanotubes. Our results, in agreement with experiment, show that the interfacial thermal conductance indeed increases with the number of graphene layers, corresponding to larger diameter and larger number of walls in MWCNT. The role of interfacial layer thickness is investigated by modeling a system of a few layers of graphene sandwiched between two silicon slabs. We show, by wave packet simulation and by theoretical calculation of a spring-mass model, that the transmission coefficient of individual vibrational modes is strongly dependent on the frequency and the number of graphene layers due to coherent interference effects; by contrast, the interfacial thermal conductance obtained in NEMD simulation, which represents an integral over all phonons, is essentially independent of the number of graphene layers, in agreement with recent experiments. Furthermore, when we heat one atomic layer of graphene directly, the effective interfacial conductance associated with heat dissipation to the silicon substrate is very small. We attribute this to the resistance associated with heat transfer between high and low frequency phonon modes within graphene. Finally, we also replaced graphene layers by a few WSe2 sheets and observed that interfacial thermal resistance of a Si/n-WSe2/Si structure increases linearly with interface thickness at least for 1 < n <= 20, indicating diffusive heat transfer mechanism, in contrast to ballistic behavior of a few graphene layers. The corresponding thermal conductivity (0.048 W m-1 K-1) of a few WSe2 layers is rather small. By comparing phonon dispersion of graphene layers and WSe2 sheets, we attribute the diffusive behavior of a few WSe2 sheets to abundant optical phonons at low and medium frequencies leading to very short mean free path. Our computational studies of effects of pressure and structural properties on interfacial thermal conductance provide fundamental in
Parallel Molecular Dynamics Simulation on Elastic Properties of Solid Argon
Futoshi Shimizu; Hajime Kimizuka; Hideo Kaburaki; Ju Li; Sidney Yip
2000-01-01
Parallel Molecular Dynamics Stencil has been developed to execute effectively large-scale parallel molecular dynamics simulations. The Stencil is adapted to varieties of molecular dy- namics simulations without special attention to parallelization techniques. As an example of large-scale simulation using this Stencil, the adiabatic elastic constants of solid argon in crys- talline and amorphous states, have been evaluated over the temperature
Molecular gas and the dynamics of galaxies
F. Combes
1999-02-01
In this review, I discuss some highlights of recent research on molecular gas in galaxies; large-scale CO maps of nearby galaxies are being made, which extend our knowledge on global properties, radial gradients, and spiral structure of the molecular ISM. Very high resolution are provided by the interferometers, that reveal high velocity gradients in galaxy nuclei, and formation of embedded structures, like bars within bars. Observation of the CO and other lines in starburst galaxies have questioned the H2-to-CO conversion factor. Surveys of dwarfs have shown how the conversion factor depends on metallicity. The molecular content is not deficient in galaxy clusters, as is the atomic gas. Galaxy interactions are very effective to enhance gas concentrations and trigger starbursts. Nuclear disks or rings are frequently observed, that concentrate the star formation activity. Since the density of starbursting galaxies is strongly increasing with redshift, the CO lines are a privileged tool to follow evolution of galaxies and observe the ISM dynamics at high redshift: due to the high excitation of the molecular gas, the stronger high-$J$ CO lines are redshifted into the observable band, which facilitates the detection.
Attosecond VUV Coherent Control of Molecular Dynamics
Ranitovic, P; Riviere, P; Palacios, A; Tong, X M; Toshima, N; Gonzalez-Castrillo, A; Martin, L; Martin, F; Murnane, M M; Kapteyn, H C
2014-01-01
High harmonic light sources make it possible to access attosecond time-scales, thus opening up the prospect of manipulating electronic wave packets for steering molecular dynamics. However, two decades after the birth of attosecond physics, the concept of attosecond chemistry has not yet been realized. This is because excitation and manipulation of molecular orbitals requires precisely controlled attosecond waveforms in the deep ultraviolet, which have not yet been synthesized. Here, we present a novel approach using attosecond vacuum ultraviolet pulse-trains to coherently excite and control the outcome of a simple chemical reaction in a deuterium molecule in a non-Born Oppenheimer regime. By controlling the interfering pathways of electron wave packets in the excited neutral and singly-ionized molecule, we unambiguously show that we can switch the excited electronic state on attosecond timescales, coherently guide the nuclear wave packets to dictate the way a neutral molecule vibrates, and steer and manipula...
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.
Dynamics of Thioether Molecular Rotors: Effects of Surface Interactions and Chain Flexibility
Dynamics of Thioether Molecular Rotors: Effects of Surface Interactions and Chain Flexibility of alkyl chain length but then quickly saturated. Molecular dynamics simulations have also been performed motions of altitudinal molecular rotors using molecular dynamics (MD) computer simulations based
Molecular dynamics simulation: a tool for exploration and discovery using simple models
Rapaport, Dennis C.
Molecular dynamics simulation: a tool for exploration and discovery using simple models D, all studied by molecular dynamics (MD) simulation. The examples are taken from the disparate fields: molecular dynamics simulation, emergent phenomena, atomistic hydrodynamics, granular segregation, molecular
Ad hoc continuum-atomistic thermostat for modeling heat flow in molecular dynamics simulations
Brenner, Donald W.
Ad hoc continuum-atomistic thermostat for modeling heat flow in molecular dynamics simulations J 2004) An ad hoc thermostating procedure that couples a molecular dynamics (MD) simulation without the thermostat. Keywords: Molecular dynamics simulation; Molecular heat flow; Continuum
Molecular Dynamics Simulations of the Lipid Bilayer Edge
Frank Y. Jiang; Yann Bouret; James T. Kindt
2004-01-01
Phospholipid bilayers have been intensively studied by molecular dynamics (MD) simulation in recent years. The properties of bilayer edges are important in determining the structure and stability of pores formed in vesicles and biomembranes. In this work, we use molecular dynamics simulation to investigate the structure, dynamics, and line tension of the edges of bilayer ribbons composed of pure dimyristoylphosphatidylcholine
-Value analysis by molecular dynamics simulations of reversible folding
Caflisch, Amedeo
-Value analysis by molecular dynamics simulations of reversible folding Giovanni Settanni dynamics (MD) simulations (total- ing 0.65 ms) have been performed for a large set of single-point mutants of conformations from the TS ensemble of several proteins (59) and to bias molecular dynamics (MD) trajectories
Molecular Dynamics Simulations of Hydrophobic Residues
NASA Astrophysics Data System (ADS)
Caballero, Diego; Zhou, Alice; Regan, Lynne; O'Hern, Corey
2013-03-01
Molecular recognition and protein-protein interactions are involved in important biological processes. However, despite recent improvements in computational methods for protein design, we still lack a predictive understanding of protein structure and interactions. To begin to address these shortcomings, we performed molecular dynamics simulations of hydrophobic residues modeled as hard spheres with stereo-chemical constraints initially at high temperature, and then quenched to low temperature to obtain local energy minima. We find that there is a range of quench rates over which the probabilities of side-chain dihedral angles for hydrophobic residues match the probabilities obtained for known protein structures. In addition, we predict the side-chain dihedral angle propensities in the core region of the proteins T4, ROP, and several mutants. These studies serve as a first step in developing the ability to quantitatively rank the energies of designed protein constructs. The success of these studies suggests that only hard-sphere dynamics with geometrical constraints are needed for accurate protein structure prediction in hydrophobic cavities and binding interfaces. Molecular recognition and protein-protein interactions are involved in important biological processes. However, despite recent improvements in computational methods for protein design, we still lack a predictive understanding of protein structure and interactions. To begin to address these shortcomings, we performed molecular dynamics simulations of hydrophobic residues modeled as hard spheres with stereo-chemical constraints initially at high temperature, and then quenched to low temperature to obtain local energy minima. We find that there is a range of quench rates over which the probabilities of side-chain dihedral angles for hydrophobic residues match the probabilities obtained for known protein structures. In addition, we predict the side-chain dihedral angle propensities in the core region of the proteins T4, ROP, and several mutants. These studies serve as a first step in developing the ability to quantitatively rank the energies of designed protein constructs. The success of these studies suggests that only hard-sphere dynamics with geometrical constraints are needed for accurate protein structure prediction in hydrophobic cavities and binding interfaces. NSF Grant PHY-1019147
Very-high-temperature molecular dynamics.
Lambert, Flavien; Clérouin, Jean; Zérah, Gilles
2006-01-01
It is shown that a modified scheme of density functional theory, using the Thomas-Fermi kinetic energy functional for the electrons, is well suited to perform very-high-temperature molecular dynamics simulations on high-Z elements. As an example, iron on the principal Hugoniot is simulated up to 5 keV and 5 times the normal density, giving an equation of state in agreement with current models. Ionic structure is obtained and is given to an excellent level of precision by the structure of the one-component plasma computed for a coupling parameter corresponding to Thomas-Fermi ionization. PMID:16486284
Bio-Molecular Dynamics Comes of Age
NSDL National Science Digital Library
Herman J. C. Berendsen (University of Groningen, Netherlands; Department of Biophysical Chemistry and the BIOSON Research Institute)
1996-02-16
Access to the article is free, however registration and sign-in are required. Atomic force microscopy has recently been used to measure the binding force between two biomolecules; complementing the experiments are computational molecular dynamics studies that seek to reveal the details of the binding and unbinding mechanisms. In his Perspective, Berendsen discusses the results reported in the same issue by GrubmÃ¼ller et al. (p. 997) on numerical simulations of the binding and separation of biotin from streptavidin, which show excellent agreement with measurements of the rupture force.
Laser-induced perturbation into molecular dynamics localized in neuronal cell
NASA Astrophysics Data System (ADS)
Hosokawa, Chie; Takeda, Naoko; Kudoh, Suguru N.; Taguchi, Takahisa
2015-03-01
Molecular dynamics at synaptic terminals in neuronal cells is essential for synaptic plasticity and subsequent modulation of cellular functions in a neuronal network. For realizing artificial control of living neuronal network, we demonstrate laser-induced perturbation into molecular dynamics in the neuronal cells. The optical trapping of cellular molecules such as synaptic vesicles or neural cell adhesion molecules labeled with quantum dots was evaluated by fluorescence imaging and fluorescence correlation spectroscopy. The trapping and assembling dynamics was revealed that the molecular motion was constrained at the focal spot of a focused laser beam due to optical trapping force. Our method has a potential to manipulate synaptic transmission at single synapse level.
Molecular dynamics investigation of dynamical properties of phosphatidylethanolamine lipid bilayers
NASA Astrophysics Data System (ADS)
Pitman, Michael C.; Suits, Frank; Gawrisch, Klaus; Feller, Scott E.
2005-06-01
We describe the dynamic behavior of a 1-stearoyl-2-oleoyl-phosphatidylethanolamine (SOPE) bilayer from a 20ns molecular dynamics simulation. The dynamics of individual molecules are characterized in terms of H2 spin-lattice relaxation rates, nuclear overhauser enhancement spectroscopy (NOESY) cross-relaxation rates, and lateral diffusion coefficients. Additionally, we describe the dynamics of hydrogen bonding through an analysis of hydrogen bond lifetimes and the time evolution of clusters of hydrogen bonded lipids. The simulated trajectory is shown to be consistent with experimental measures of internal, intermolecular, and diffusive motion. Consistent with our analysis of SOPE structure in the companion paper, we see hydrogen bonding dominating the dynamics of the interface region. Comparison of H2 T1 relaxation rates for chain methylene segments in phosphatidylcholine and phosphatidylethanolamine bilayers indicates that slower motion resulting from hydrogen bonding extends at least three carbons into the hydrophobic core. NOESY cross-relaxation rates compare well with experimental values, indicating the observed hydrogen bonding dynamics are realistic. Calculated lateral diffusion rates (4±1×10-8cm2/s) are comparable, though somewhat lower than, those determined by pulsed field gradient NMR methods.
Molecular dynamics simulations of phospholipases A2.
Demaret, J P; Brunie, S
1990-12-01
An extensive molecular dynamics study of phospholipases A2 from pancreatic bovine and Crotalus atrox venom has shown that the well-conserved homologous core of the phospholipases A2, including the so called catalytic network, is very stable during the course of the calculations. The fluctuations which occur are located in segments which have significantly different three-dimensional conformations in the two phospholipases A2 studied, suggesting that a particularly stable core conformation gives rise to a large homologous family of similar three-dimensional structure. The calcium ion, which exhibits a crucial structural role in the monomeric phospholipases A2, appears not to be required to stabilize the C.atrox dimer. Moreover, the behaviour of the dimeric structure during the dynamics raises the question of a possible dissociation of the two subunits into functional monomers. PMID:2075191
Higher-order symplectic Born-Oppenheimer molecular dynamics
Niklasson, Anders [Los Alamos National Laboratory; Bock, Nicolas [Los Alamos National Laboratory; Challacombe, Matt [Los Alamos National Laboratory; Odell, Anders [RIT; Delin, Anna [RIT; Johansson, Borje [RIT
2009-01-01
The extended Lagrangian formulation of time-reversible Born-Oppenheimer molecular dynamics (TR-BOMD) enables the use of geometric integrators in the propagation of both the nuclear and the electronic degrees of freedom on the Born-Oppenheimer potential energy surface. Different symplectic integrators up to the 6th order have been adapted and optimized to TR-BOMD in the framework of ab initio self-consistent-field theory. It is shown how the accuracy can be significantly improved compared to a conventional Verlet integration at the same level of computational cost, in particular for the case of very high accuracy requirements.
Molecular Dynamics Computer Simulation Studies of Close-Packed Solids
NASA Astrophysics Data System (ADS)
Moody, Michael Craig
Close-packed (polytypic) structures, found to be metastable during studies of structural phase transformations among close-packed crystalline systems in molecular dynamics computer simulations, are considered in conjunction with the often-used periodic boundary conditions and potential cutoff range. After presenting a denotation of those polytypes compatible with periodic boundary conditions, the computation of the fractional particle coordination numbers exhibited by polytypic structures is discussed and exemplified. The limited structure recognition due to the use of a cutoff range in particle coordination number calculations is noted, and computations of geometrical structure factors as well as a graphical display scheme are used to exemplify complete structure recognition. Some significant consequences of the restraints on the possible structural results in the molecular dynamics simulation method of studying close -packed crystals should be recognized when interpreting the results of employing this method of study. Only the denotation of polytypes compatible with periodic boundary conditions together with their structure recognition are considered; transformations among these structures are not considered in this paper. The molecular dynamics computer simulation method is next utilized to calculate various thermodynamic quantities for both fcc and hcp systems interacting with a specifically parameterized central pair potential. A discussion of the determination of error in the computation of such quantities is included with the results. Order of magnitude agreement with experimental values is found for response functions computed from fluctuation formulas. Finally, the long-standing question of thermodynamic relative stability of fcc and hcp structures is investigated by a direct calculation of their free energy differences using the molecular dynamics simulation method. Making the first known use of a specifically parameterized central pair potential in such a calculation, the entropy contribution to the free energy difference is found to favor the fcc phase, in contrast to the potential energy contribution. At the temperature investigated (T (TURNEQ) 1000 K for Ni), the free energy difference is found to favor hcp, in contrast to experimental findings. The current analysis leaves unresolved however the results of such an analysis at nucleation temperatures.
Thermal conductivity of ionic systems from equilibrium molecular dynamics.
Salanne, Mathieu; Marrocchelli, Dario; Merlet, Céline; Ohtori, Norikazu; Madden, Paul A
2011-03-16
Thermal conductivities of ionic compounds (NaCl, MgO, Mg(2)SiO(4)) are calculated from equilibrium molecular dynamics simulations using the Green-Kubo method. Transferable interaction potentials including many-body polarization effects are employed. Various physical conditions (solid and liquid states, high temperatures, high pressures) relevant to the study of the heat transport in the Earth's mantle are investigated, for which experimental measures are very challenging. By introducing a frequency-dependent thermal conductivity, we show that important coupled thermoelectric effects occur in the energy conduction mechanism in the case of liquid systems. PMID:21335634
Thermal properties of metallic sodium near melt from molecular-dynamics calculations
Straub, G.K.; Swanson, R.E.; Holian, B.L.; Wallace, D.C.
1981-01-01
Molecular dynamics simulations of the thermal properties of metallic sodium were performed in the high temperature anharmonic region near the melting point. The ion-ion interaction potential was derived from pseudopotential theory. From the molecular dynamics results, the anharmonic thermal energy was determined directly without the use of thermodynamic perturbation theory. Comparison of the calculated melting temperature, latent heat of fusion, fluid phase diffusion coefficient, and the atomic distribution function are all in good agreement with experiment.
Boyer, Edmond
1 Dynamic viscosity estimation of hydrogen sulfide using a predictive scheme based on molecular on molecular dynamics results on Lennard-Jones spheres is proposed to model the viscosity of hydrogen sulfide is appropriate for the other species of the mixtures. Keywords: Hydrogen sulfide; Viscosity; Molecular Dynamics
Deformation processes in polycrystalline Zr by molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Lu, Zizhe; Noordhoek, Mark J.; Chernatynskiy, Aleksandr; Sinnott, Susan B.; Phillpot, Simon R.
2015-07-01
Molecular dynamics simulation is used to characterize the deformation behavior of polycrystalline Zr. The predictions of two different potentials, an embedded atom method potential and a charge optimized many body potential are compared. The experimentally observed prismatic dislocations, pyramidal dislocations and twinning behaviors are produced in the simulations of [ 1 1 2 bar 0 ] and [0 0 0 1] textured structures and in fully 3D structure simulations. The relationship between the generalized stacking fault energy and the mechanical properties is discussed. In particular we find that the different shapes of the generalized stacking-fault energy curve for the two different interatomic descriptions of Zr have a significant effect on the deformation mechanisms. The deformation behavior of Zr is compared with analogous simulations of deformation of polycrystalline Mg.
Multiple branched adaptive steered molecular dynamics
NASA Astrophysics Data System (ADS)
Ozer, Gungor; Keyes, Thomas; Quirk, Stephen; Hernandez, Rigoberto
2014-08-01
Steered molecular dynamics, SMD, [S. Park and K. Schulten, J. Chem. Phys. 120, 5946 (2004)] combined with Jarzynski's equality has been used widely in generating free energy profiles for various biological problems, e.g., protein folding and ligand binding. However, the calculated averages are generally dominated by "rare events" from the ensemble of nonequilibrium trajectories. The recently proposed adaptive steered molecular dynamics, ASMD, introduced a new idea for selecting important events and eliminating the non-contributing trajectories, thus decreasing the overall computation needed. ASMD was shown to reduce the number of trajectories needed by a factor of 10 in a benchmarking study of decaalanine stretching. Here we propose a novel, highly efficient "multiple branching" (MB) version, MB-ASMD, which obtains a more complete enhanced sampling of the important trajectories, while still eliminating non-contributing segments. Compared to selecting a single configuration in ASMD, MB-ASMD offers to select multiple configurations at each segment along the reaction coordinate based on the distribution of work trajectories. We show that MB-ASMD has all benefits of ASMD such as faster convergence of the PMF even when pulling 1000 times faster than the reversible limit while greatly reducing the probability of getting trapped in a non-significant path. We also analyze the hydrogen bond breaking within the decaalanine peptide as we force the helix into a random coil and confirm ASMD results with less noise in the numerical averages.
Accelerated molecular dynamics simulations of protein folding.
Miao, Yinglong; Feixas, Ferran; Eun, Changsun; McCammon, J Andrew
2015-07-30
Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies. © 2015 Wiley Periodicals, Inc. PMID:26096263
Exact dynamic properties of molecular motors
NASA Astrophysics Data System (ADS)
Boon, N. J.; Hoyle, R. B.
2012-08-01
Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecular motor walks, a generalized and straightforward graphical method for calculating their dynamic properties is presented. It allows the calculation of the velocity, dispersion, and randomness ratio for any proposed system through analysis of its structure. This article extends work of King and Altman ["A schematic method of deriving the rate laws of enzyme-catalyzed reactions," J. Phys. Chem. 60, 1375-1378 (1956)], 10.1021/j150544a010 on networks of enzymatic reactions by calculating additional dynamic properties for spatially hopping systems. Results for n-state systems are presented: single chain, parallel pathway, divided pathway, and divided pathway with a chain. A novel technique for combining multiple system architectures coupled at a reference state is also demonstrated. Four-state examples illustrate the effectiveness and simplicity of these methods.
Car, R.; Parrinello, M.
1988-01-18
An amorphous silicon structure is obtained with a computer simulation based on a new molecular-dynamics technique in which the interatomic potential is derived from a parameter-free quantum mechanical method. Our results for the atomic structure, the phonon spectrum, and the electronic properties are in excellent agreement with experiment. In addition we study details of the microscopic dynamics which are not directly accessible to experiment. We find in particular that structural defects are associated with weak bonds. These may give rise to low-frequency vibrational modes.
Ten-Microsecond Molecular Dynamics Simulation of a Fast-Folding WW Domain
Peter L. Freddolino; Feng Liu; Martin Gruebele; Klaus Schulten
2008-01-01
All-atom molecular dynamics (MD) simulations of protein folding allow analysis of the folding process at an unprecedented level of detail. Unfortunately, such simulations have not yet reached their full potential both due to difficulties in sufficiently sampling the microsecond timescales needed for folding, and because the force field used may yield neither the correct dynamical sequence of events nor the
Local Behavior of Water Molecules on Brucite, Talc, and Halite Surfaces: A Molecular Dynamics Study
Hiroshi Sakuma; Taku Tsuchiya; Katsuyuki Kawamura; Kenshiro Otsuki
2004-01-01
The structural and dynamic properties of water between brucite (0001), talc (001), and halite (100) surfaces have been calculated by classical molecular dynamics (MD) simulations at ambient conditions. The interaction potential models between water and the minerals have been developed by the energy curves obtained from the ab initio electronic state calculations. Orientational anisotropy of water molecules is almost limited
Proton motion in malonaldehyde: an ab initio molecular dynamics study
NASA Astrophysics Data System (ADS)
Wolf, K.; Mikenda, W.; Nusterer, E.; Schwarz, K.
1998-07-01
A Projector Augmented Wave (PAW) molecular dynamics study of the proton motion and proton transfer in malonaldehyde is presented. Molecular dynamics runs of malonaldehyde were performed at several temperatures between 100 K and 600 K. At elevated temperatures proton transfer is not associated with a well-defined C 2v symmetric transition state, but takes place at largely differing geometric situations. A short Otctdot;O distance is highly favourable for proton transfer to occur, but it is neither a sufficient nor a necessary criterion and a proper description requires many, if not all, 21 internal degrees of freedom. The energetics of the proton motion have been modelled by calculating potential energies along a properly chosen reaction coordinate for single time steps within a 'heavy-light-heavy' approximation. Four different extreme situations can reasonably well be distinguished: (1) 'normal periods', where the proton remains firmly located at one oxygen, and which are characterized by an approximately constant, strongly asymmetric single-minimum potential; (2) 'isolated proton transfer transitions', which start and end with strongly asymmetric single-minimum potentials, but pass through (near-) symmetric double- or single-minimum potentials; (3) 'proton shuttling periods', which include several consecutive transitions and correspond to a stationary proton motion within a symmetric single-minimum potential that remains approximately constant for a longer period of time; and (4) 'near-transitions' where the proton moves towards the opposite oxygen but due to kinetic reasons turns back again. It is shown that the proton motion is governed by both the potential energy along an appropriately chosen proton transfer reaction coordinate and by kinetic effects.
Shock compression of hydrocarbon polymer foam using molecular dynamics
NASA Astrophysics Data System (ADS)
Lane, J. Matthew D.; Grest, Gary S.; Thompson, Aidan P.; Cochrane, Kyle R.; Desjarlais, Michael; Mattsson, Thomas R.
2012-03-01
Organic polymers and nanocomposites are increasingly being subjected to extreme environments. Molecular-scale modeling of these materials offers insight into failure mechanisms and response. In previously published work, we used classical molecular dynamics (MD) and density functional theory (DFT) simulations to determine the principal shock Hugoniot for two hydrocarbon polymers, polyethylene (PE) and poly(4-methyl-1-pentene) (PMP). DFT was in excellent agreement with experiment, and one of four classical MD potentials, ReaxFF, was found to be suitable for studies up to 50 GPa. Here, we extend these results to include low-density polymer foams using NEMD techniques. We find good quantitative agreement with both experiment and hydrocode simulations. Further, we have measured local temperatures to investigate the formation of hot spots and polymer dissociation near foam voids.
Are molecular markers useful predictors of adaptive potential?
Mittell, Elizabeth A; Nakagawa, Shinichi; Hadfield, Jarrod D
2015-08-01
Estimates of molecular genetic variation are often used as a cheap and simple surrogate for a population's adaptive potential, yet empirical evidence suggests they are unlikely to be a valid proxy. However, this evidence is based on molecular genetic variation poorly predicting estimates of adaptive potential rather than how well it predicts true values. As a consequence, the relationship has been systematically underestimated and the precision with which it could be measured severely overstated. By collating a large database, and using suitable statistical methods, we obtain a 95% upper bound of 0.26 for the proportion of variance in quantitative genetic variation explained by molecular diversity. The relationship is probably too weak to be useful, but this conclusion must be taken as provisional: less noisy estimates of quantitative genetic variation are required. In contrast, and perhaps surprisingly, current sampling strategies appear sufficient for characterising a population's molecular genetic variation at comparable markers. PMID:25989024
Ab initio based force field and molecular dynamics simulations of crystalline TATB
Richard H. Gee; Szczepan Roszak; Krishnan Balasubramanian; Laurence E. Fried
2004-01-01
An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular
Classical reactive molecular dynamics implementations: state of the art.
Farah, Karim; Müller-Plathe, Florian; Böhm, Michael C
2012-04-10
Reactive molecular dynamics (RMD) implementations equipped with force field approaches to simulate both the time evolution as well as chemical reactions of a broad class of materials are reviewed herein. We subdivide the RMD approaches developed during the last decade as well as older ones already reviewed in 1995 by Srivastava and Garrison and in 2000 by Brenner into two classes. The methods in the first RMD class rely on the use of a reaction cutoff distance and employ a sudden transition from the educts to the products. Due to their simplicity these methods are well suited to generate equilibrated atomistic or material-specific coarse-grained polymer structures. In connection with generic models they offer useful qualitative insight into polymerization reactions. The methods in the second RMD class are based on empirical reactive force fields and implement a smooth and continuous transition from the educts to the products. In this RMD class, the reactive potentials are based on many-body or bond-order force fields as well as on empirical standard force fields, such as CHARMM, AMBER or MM3 that are modified to become reactive. The aim with the more sophisticated implementations of the second RMD class is the investigation of the reaction kinetics and mechanisms as well as the evaluation of transition state geometries. Pure or hybrid ab initio, density functional, semi-empirical, molecular mechanics, and Monte Carlo methods for which no time evolution of the chemical systems is achieved are excluded from the present review. So are molecular dynamics techniques coupled with quantum chemical methods for the treatment of the reactive regions, such as Car-Parinello molecular dynamics. PMID:22287184
Thermodynamic, dynamic, and structural anomalies for shoulderlike potentials
NASA Astrophysics Data System (ADS)
Barraz, Ney M.; Salcedo, Evy; Barbosa, Marcia C.
2009-09-01
Using molecular dynamic simulations we study a family of continuous core-softened potentials consisting of a hard core, a shoulder at closest distances, and an attractive well at further distance. The repulsive shoulder and the well distances represent two length scales. We show that if the first scale, the shoulder, is repulsive or has a small well, the potential has a region in the pressure-temperature phase diagram with density, diffusion, and structural anomalies. However, if the closest scale becomes a deep well, the regions in the pressure-temperature phase diagram where the three anomalies are present shrink and disappear. This result helps in defining two length scales potentials that exhibit anomalies.
Nonequilibrium molecular dynamics for bulk materials and nanostructures
NASA Astrophysics Data System (ADS)
Dayal, Kaushik; James, Richard D.
2010-02-01
We describe a method of constructing exact solutions of the equations of molecular dynamics in non-equilibrium settings. These solutions correspond to some viscometric flows, and to certain analogs of viscometric flows for fibers and membranes that have one or more dimensions of atomic scale. This work generalizes the method of objective molecular dynamics (OMD) ( Dumitric? and James, 2007). It allows us to calculate viscometric properties from a molecular-level simulation in the absence of a constitutive equation, and to relate viscometric properties directly to molecular properties. The form of the solutions is partly independent of the form of the force laws between atoms, and therefore these solutions have implications for coarse-grained theories. We show that there is an exact reduction of the Boltzmann equation corresponding to one family of OMD solutions. This reduction includes most known exact solutions of the equations of the moments for special kinds of molecules and gives the form of the molecular density function corresponding to such flows. This and other consequences leads us to propose an addition to the principle of material frame indifference, a cornerstone of nonlinear continuum mechanics. The method is applied to the failure of carbon nanotubes at an imposed strain rate, using the Tersoff potential for carbon. A large set of simulations with various strain rates, initial conditions and two choices of fundamental domain (unit cell) give the following unexpected results: Stone-Wales defects play no role in the failure (though Stone-Wales partials are sometimes seen just prior to failure), a variety of failure mechanisms is observed, and most simulations give a strain at failure of 15-20%, except those done with initial temperature above about 1200 K and at the lower strain rates. The latter have a strain at failure of 1-2%.
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Gottwald, Fabian; Ivanov, Sergei D; Kühn, Oliver
2015-01-01
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation (GLE), which can be rigorously derived by means of a linear projection (LP) technique. Within this framework a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here we discuss that this task is most naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importa...
Nerukh, Dmitry
molecular dynamics MD simulations, can shed light on the role of water in protein structure and functionWater network dynamics at the critical moment of a peptide's -turn formation: A molecular dynamics, and dynamics of a protein as determined from experiment and computer simulations. It has been shown
Cecconi, Fabio
A molecular dynamics investigation of the kinetic bottlenecks of the hPin1 WW domain. II molecular dynamics simulations on the WW domain of Pin1 protein. The aim of the work is the reconstruction of Pin1 WW domain, can be related to the absence of angular potentials, which makes the protein
Nordlund, Kai
Fragmentation of clusters sputtered from silver and gold: Molecular dynamics simulations K. O. E January 2005 Using molecular dynamics simulations and the embedded atom method EAM potential we have investi- gated the sputtered atom clusters produced by 15 keV xenon impacts on silver and 20 keV xenon
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.
The Anton 2 Chip: A 2nd Generation ASIC for Molecular Dynamics Simulation Hot Chips 2014
Southern California, University of
The Anton 2 Chip: A 2nd Generation ASIC for Molecular Dynamics Simulation Hot Chips 2014 A Second-Generation ASIC for Molecular Dynamics 1 #12;The Anton 2 Chip: A 2nd Generation ASIC for Molecular Dynamics Generation ASIC for Molecular Dynamics Simulation Hot Chips 2014 Molecular Dynamics (MD) and Why It's Hard
Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field
2015-01-01
Molecular dynamics simulation of the oxygenase component of nitrobenzene dioxygenase (NBDO) system, a member of the naphthalene family of Rieske nonheme iron dioxygenases, has been carried out using the AMBER force field combined with a new set of parameters for the description of the mononuclear nonheme iron center and iron–sulfur Rieske cluster. Simulation results provide information on the structure and dynamics of nitrobenzene dioxygenase in an aqueous environment and shed light on specific interactions that occur in its catalytic center. The results suggest that the architecture of the active site is stabilized by key hydrogen bonds, and Asn258 positions the substrate for oxidation. Analysis of protein–water interactions reveal the presence of a network of solvent molecules at the entrance to the active site, which could be of potential catalytic importance. PMID:24955078
Molecular dynamics simulation of radiation damage cascades in diamond
NASA Astrophysics Data System (ADS)
Buchan, J. T.; Robinson, M.; Christie, H. J.; Roach, D. L.; Ross, D. K.; Marks, N. A.
2015-06-01
Radiation damage cascades in diamond are studied by molecular dynamics simulations employing the Environment Dependent Interaction Potential for carbon. Primary knock-on atom (PKA) energies up to 2.5 keV are considered and a uniformly distributed set of 25 initial PKA directions provide robust statistics. The simulations reveal the atomistic origins of radiation-resistance in diamond and provide a comprehensive computational analysis of cascade evolution and dynamics. As for the case of graphite, the atomic trajectories are found to have a fractal-like character, thermal spikes are absent and only isolated point defects are generated. Quantitative analysis shows that the instantaneous maximum kinetic energy decays exponentially with time, and that the timescale of the ballistic phase has a power-law dependence on PKA energy. Defect recombination is efficient and independent of PKA energy, with only 50% of displacements resulting in defects, superior to graphite where the same quantity is nearly 75%.
Molecular Modeling and Molecular Dynamics Simulations of Recombinase Rad51
Kokabu, Yuichi; Ikeguchi, Mitsunori
2013-01-01
The Rad51 ATPase plays central roles in DNA homologous recombination. Yeast Rad51 dimer structure in the active form of the filament was constructed using homology modeling techniques, and all-atom molecular dynamics (MD) simulations were performed using the modeled structure. We found two crucial interaction networks involving ATP: one is among the ?-phosphate of ATP, K+ ions, H352, and D374; the other is among the adenine ring of ATP, R228, and P379. Multiple MD simulations were performed in which the number of bound K+ ions was changed. The simulated structures suggested that K+ ions are indispensable for the stabilization of the active dimer and resemble the arginine and lysine fingers of other P-loop containing ATPases and GTPases. MD simulations also showed that the adenine ring of ATP mediates interactions between adjacent protomers. Furthermore, in MD simulations starting from a structure just after ATP hydrolysis, the opening motion corresponding to dissociation from DNA was observed. These results support the hypothesis that ATP and K+ ions function as glue between protomers. PMID:23561532
Ion mobility analysis of molecular dynamics.
Wyttenbach, Thomas; Pierson, Nicholas A; Clemmer, David E; Bowers, Michael T
2014-01-01
The combination of mass spectrometry and ion mobility spectrometry (IMS) employing a temperature-variable drift cell or a drift tube divided into sections to make IMS-IMS experiments possible allows information to be obtained about the molecular dynamics of polyatomic ions in the absence of a solvent. The experiments allow the investigation of structural changes of both activated and native ion populations on a timescale of 1-100 ms. Five different systems representing small and large, polar and nonpolar molecules, as well as noncovalent assemblies, are discussed in detail: a dinucleotide, a sodiated polyethylene glycol chain, the peptide bradykinin, the protein ubiquitin, and two types of peptide oligomers. Barriers to conformational interconversion can be obtained in favorable cases. In other cases, solution-like native structures can be observed, but care must be taken in the experimental protocols. The power of theoretical modeling is demonstrated. PMID:24328447
Elastic anomalies of anorthite: Molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Noritake, Fumiya; Kawamura, Katsuyuki; Matsukage, Kyoko N.
2015-07-01
We investigated the elastic anomalies of anorthite using molecular dynamics simulations in which the temperature and pressure induced P 1 bar / I 1 bar phase transitions were reproduced. The resulting changes in structure were investigated as functions of pressure and temperature. It was found that the temperature-induced elastic anomaly is caused by two different thermal expansion behaviors of atomic motion, that is, increased distance between nearest neighbor atoms and increased Si-O-Al angle. Furthermore, the pressure-induced elastic anomaly was found to be caused by a decrease in the Si-O-Al angle in six-membered rings, which is similar to the cases of vitreous silica or acidic silicate liquids.
Ion Mobility Analysis of Molecular Dynamics
NASA Astrophysics Data System (ADS)
Wyttenbach, Thomas; Pierson, Nicholas A.; Clemmer, David E.; Bowers, Michael T.
2014-04-01
The combination of mass spectrometry and ion mobility spectrometry (IMS) employing a temperature-variable drift cell or a drift tube divided into sections to make IMS-IMS experiments possible allows information to be obtained about the molecular dynamics of polyatomic ions in the absence of a solvent. The experiments allow the investigation of structural changes of both activated and native ion populations on a timescale of 1&-100 ms. Five different systems representing small and large, polar and nonpolar molecules, as well as noncovalent assemblies, are discussed in detail: a dinucleotide, a sodiated polyethylene glycol chain, the peptide bradykinin, the protein ubiquitin, and two types of peptide oligomers. Barriers to conformational interconversion can be obtained in favorable cases. In other cases, solution-like native structures can be observed, but care must be taken in the experimental protocols. The power of theoretical modeling is demonstrated.
Symplectic quaternion scheme for biophysical molecular dynamics
NASA Astrophysics Data System (ADS)
Miller, T. F.; Eleftheriou, M.; Pattnaik, P.; Ndirango, A.; Newns, D.; Martyna, G. J.
2002-05-01
Massively parallel biophysical molecular dynamics simulations, coupled with efficient methods, promise to open biologically significant time scales for study. In order to promote efficient fine-grained parallel algorithms with low communication overhead, the fast degrees of freedom in these complex systems can be divided into sets of rigid bodies. Here, a novel Hamiltonian form of a minimal, nonsingular representation of rigid body rotations, the unit quaternion, is derived, and a corresponding reversible, symplectic integrator is presented. The novel technique performs very well on both model and biophysical problems in accord with a formal theoretical analysis given within, which gives an explicit condition for an integrator to possess a conserved quantity, an explicit expression for the conserved quantity of a symplectic integrator, the latter following and in accord with Calvo and Sanz-Sarna, Numerical Hamiltonian Problems (1994), and extension of the explicit expression to general systems with a flat phase space.
Nonequilibrium molecular dynamics: The first 25 years
Hoover, W.G. [Univ. of California, Davis, CA (United States); [Lawrence Livermore National Lab., CA (United States)
1992-08-01
Equilibrium Molecular Dynamics has been generalized to simulate Nonequilibrium systems by adding sources of thermodynamic heat and work. This generalization incorporates microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress, and augments atomistic forces with special boundary, constraint, and driving forces capable of doing work on, and exchanging heat with, an otherwise Newtonian system. The underlying Lyapunov instability of these nonequilibrium equations of motion links microscopic time-reversible deterministic trajectories to macroscopic time-irreversible hydrodynamic behavior as described by the Second Law of Thermodynamics. Green-Kubo linear-response theory has been checked. Nonlinear plastic deformation, intense heat conduction, shockwave propagation, and nonequilibrium phase transformation have all been simulated. The nonequilibrium techniques, coupled with qualitative improvements in parallel computer hardware, are enabling simulations to approximate real-world microscale and nanoscale experiments.
Molecular Dynamics Simulations of Water Evaporation
NASA Astrophysics Data System (ADS)
Wen, Chengyuan; Grest, Gary; Cheng, Shengfeng
2015-03-01
The evaporation of water from the liquid/vapor interface is studied via large-scale molecular dynamics simulations for systems of more than a million atoms at 550K and 600K. The TIP4P-2005 water model whose liquid/vapor surface tension is in excellent agreement with experiments is used. Evaporative cooling at the interface is observed from temperature profiles determined from both translational and rotational kinetic energy. During evaporation, the density of water is slightly enhanced near the liquid-vapor interface. The velocity distribution of water molecules in the vapor phase during evaporation at various distances relative to the interface fit a Maxwell-Boltzmann distribution. While our results indicate an imbalance between evaporating and condensing water molecules, local thermal equilibrium is found to hold in addition to mechanical equilibrium. Department of Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
Simulation of transcritical oxygen droplet vaporization using molecular dynamics
NASA Astrophysics Data System (ADS)
Kaltz, Teresa Lynn
Many aerospace vehicles have spray combustion devices as part of their propulsion system. Knowledge of the fluid dynamic processes that occur prior to combustion is important in determining important system behavior, such as burning rate and combustion stability. In addition, these devices usually operate at very high pressures in order to generate a large amount of thrust. If the pressure is high enough, then one or more of the reactants will be above the thermodynamic critical point, where the distinction between liquid and gas breaks down and many material properties are either zero or undefined. Thus understanding and predicting the phase change occurring during droplet vaporization upstream of the combustion zone has had limited success when at supercritical pressures. This research approaches the problem in a totally new way. Instead of using traditional methods such as the Navier-Stokes equations, the technique used for this research is called 'molecular dynamics'. Molecular dynamics (MD) solves the equations of motion for a system of molecules that interact with each other through an intermolecular potential. Theoretically, provided an accurate intermolecular potential can be found, MD can be used regardless of the phase and thermodynamic state of the system. All calculations are performed from first principles, and thermodynamic and transport properties are results instead of assumptions. Simulations were performed of the complete vaporization of a three dimensional submicron oxygen droplet into both quiescent and convective environments. The environments consisted of oxygen, hydrogen and helium. Environment pressures and temperatures ranged from 2-20 MPa and 200-300 K, respectively. Vaporization rates were obtained along with contour and profile plots of thermodynamic properties. All simulations were performed on the IBM SP-2 parallel computer using the Message Passing Interface for parallel communication. In addition, the validity of extrapolating MD results to macroscopic system sizes by scaling the intermolecular potential parameters was investigated.
Statistical Analysis of Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Atkinson, R. A.
Available from UMI in association with The British Library. Requires signed TDF. This thesis is concerned with the specification and analysis of stochastic models of molecular motion and interaction in simple liquids. Basic chemical terminology is introduced and a brief description is given of the technique of molecular dynamics simulation. Stochastic process theory, in so far as it is relevant to the modelling of molecular trajectories and chemical reaction, is reviewed. First passage densities are shown to be important in the analysis of diffusion controlled chemical reaction. The relationship between first passage densities and flux or flow across the absorbing boundary is given. A formula proposed by Durbin is discussed and shown to be valid for diffusion processes under certain regularity conditions. The simplest integrated diffusion, integrated Brownian motion, is considered and a detailed derivation of McKean's half-winding formula is given. An explicit expression for the return-time density is derived, from which the large time asymptotics can be deduced. Goldman's formula for the density of the hitting-time of positive levels is extended to all real values and a simple intuitive derivation is given. Similar arguments enable the results of Gor'kov to be extended to a wider class of integrated diffusions. First passage time densities are computed numerically using the extension of Goldman's formula and compared with approximations which have been suggested by Hesse. Small drift asymptotics are derived for the escape probability of integrated Brownian motion with drift. A number of results are obtained for the integrated Ornstein -Uhlenbeck process, by using martingale methods. Finally, the empirical observations of Lynden-Bell, Hutchinson and Doyle are analysed. A stochastic model of single-particle motion based on the velocity autocorrelation function is proposed and shown to be in excellent agreement with the computer generated data.
Performance Analysis on Molecular Dynamics Simulation of Protein Using GROMACS
A. D. Astuti; A. B. Mutiara
2009-01-01
Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example of molecular dynamics application developed by Groningen University. This application is a non-commercial and able to work in the operating system Linux. The main
Nanoindentation hardness anisotropy of alumina crystal: A molecular dynamics study
Southern California, University of
Nanoindentation hardness anisotropy of alumina crystal: A molecular dynamics study Kenji Nishimura nanoindentation are studied by molecular dynamics simulations for three surface orientations of alumina crystal Institute of Physics. DOI: 10.1063/1.2913016 Crystalline alumina Al2O3 is a highly insulating, opti- cally
Molecular Dynamics Simulations of Silica Glass Ersan Demiralp 1 , Tahir
Goddard III, William A.
Molecular Dynamics Simulations of Silica Glass Ersan Demiralp 1 , Tahir ¸ Ca~gin 1 , Norman T. Huff temperature (NPT) molecular dynamic (MD) simulations of silica glass to understand the effects 2 and William A. Goddard III 1 1 Materials and Process Simulation Center, Beckman Institute (139
Molecular dynamics and the accuracy of numerically computed averages
Stephen D. Bond; Benedict J. Leimkuhler
2007-01-01
Molecular dynamics is discussed from a mathematical perspective. The re- cent history of method development is briefly surveyed with an emphasis on the use of geometric integration as a guiding principle. The recovery of sta- tistical mechanical averages from molecular dynamics is then introduced, and the use of backward error analysis as a technique for analysing the accuracy of numerical
Nonequilibrium molecular dynamics for bulk materials and nanostructures
Kaushik Dayal; Richard D. James
2010-01-01
We describe a method of constructing exact solutions of the equations of molecular dynamics in non-equilibrium settings. These solutions correspond to some viscometric flows, and to certain analogs of viscometric flows for fibers and membranes that have one or more dimensions of atomic scale. This work generalizes the method of objective molecular dynamics (OMD) (Dumitric? and James, 2007). It allows
Structural properties of polymeric DNA from molecular dynamics simulations
Sudipta Samanta; Supti Mukherjee; Jaydeb Chakrabarti; Dhananjay Bhattacharyya
2009-01-01
Most of the reported DNA structural studies are based on oligonucleotide structures, which have artifacts due to unstable terminal base pairs (bps). We have carried out molecular dynamics simulation of DNA oligonucleotides in such a manner that gives rise to properties of polymeric DNA of infinite length. Molecular dynamics simulation studies of six homo- and heteropolymeric DNA sequences are reported
Gradient-driven diffusion using dual control volume grand canonical molecular dynamics
Thompson, A.M.; Ford, D.M. [Sandia National Labs., Albuquerque, NM (United States). Materials Simulation Science Dept.; Heffelfinger, G.S. [Texas A and M Univ., College Station, TX (United States). Dept. of Chemical Engineering
1998-06-14
The dual control volume grand canonical molecular dynamics (DCV-GCMD) method, designed to enable the dynamic simulation of a system with a steady state chemical potential gradient is first briefly reviewed. A new, novel implementation of the method which enables the establishment of a steady state chemical potential gradient in a multicomponent system without having to insert or delete one of the components is then presented and discussed.
Time-averaged order parameter restraints in molecular dynamics simulations.
Hansen, Niels; Heller, Fabian; Schmid, Nathan; van Gunsteren, Wilfred F
2014-11-01
A method is described that allows experimental S(2) order parameters to be enforced as a time-averaged quantity in molecular dynamics simulations. The two parameters that characterize time-averaged restraining, the memory relaxation time and the weight of the restraining potential energy term in the potential energy function used in the simulation, are systematically investigated based on two model systems, a vector with one end restrained in space and a pentapeptide. For the latter it is shown that the backbone N-H order parameter of individual residues can be enforced such that the spatial fluctuations of quantities depending on atomic coordinates are not significantly perturbed. The applicability to realistic systems is illustrated for the B3 domain of protein G in aqueous solution. PMID:25312596
Isomorphic phase transformation in shocked cerium using molecular dynamics
Dupont, Virginie [Los Alamos National Laboratory; Germann, Timothy C [Los Alamos National Laboratory; Chen, Shao - Ping [Los Alamos National Laboratory
2010-08-12
Cerium (Ce) undergoes a significant ({approx}16%) volume collapse associated with an isomorphic fcc-fcc phase transformation when subject to compressive loading. We present here a new Embedded Atom Method (EAM) potential for Cerium that models two minima for the two fcc phases. We show results from its use in Molecular Dynamics (MD) simulations of Ce samples subjected to shocks with pressures ranging from 0.5 to 25 GPa. A split wave structure is observed, with an elastic precursor followed by a plastic wave. The plastic wave causes the expected fcc-fcc phase transformation. Comparisons to experiments and MD simulations on Cesium (Cs) indicate that three waves could be observed. The construction of the EAM potential may be the source of the difference.
Molecular Dynamics Calculation of the Viscosity of Xenon Gas
NASA Astrophysics Data System (ADS)
Mountain, Raymond D.
2007-02-01
The density variation of the viscosity of xenon gas is determined using molecular dynamics simulation with a semi-empirical pair potential fit to low-density gas properties. The gas states ranged in density from 0.37 to 7.62 mol · dm-3, and varied in temperature from 240 -591 K. The simulation results match the kinetic-theory predictions for the model potential at the lowest density, and systematically lie below the experimental values for higher densities. This indicates the need for many-body interactions to accurately predict the viscosity of xenon gas at even moderate densities. An operational criterion for identifying the density region where kinetic theory is appropriate is proposed.
NASA Astrophysics Data System (ADS)
Bauer, Brad A.; Patel, Sandeep
2010-01-01
We present molecular dynamics simulations of the liquid-vapor interface of 1M salt solutions of nonpolarizable NaCl, NaBr, and NaI in polarizable transferable intermolecular potential 4-point with charge dependent polarizability water [B. A. Bauer et al., J. Chem. Theory Comput. 5, 359 (2009)]; this water model accommodates increased solvent polarizability (relative to the condensed phase) in the interfacial and vapor regions. We employ fixed-charge ion models developed in conjunction with the TIP4P-QDP water model to reproduce ab initio ion-water binding energies and ion-water distances for isolated ion-water pairs. The transferability of these ion models to the condensed phase was validated with hydration free energies computed using thermodynamic integration (TI) and appropriate energy corrections. Density profiles of Cl-, Br-, and I- exhibit charge layering in the interfacial region; anions and cation interfacial probabilities show marked localization, with the anions penetrating further toward the vapor than the cations. Importantly, in none of the cases studied do anions favor the outermost regions of the interface; there is always an aqueous region between the anions and vapor phase. Observed interfacial charge layering is independent of the strength of anion-cation interactions as manifest in anion-cation contact ion pair peaks and solvent separated ion pair peaks; by artificially modulating the strength of anion-cation interactions (independent of their interactions with solvent), we find little dependence on charge layering particularly for the larger iodide anion. The present results reiterate the widely held view of the importance of solvent and ion polarizability in mediating specific anion surface segregation effects. Moreover, due to the higher parametrized polarizability of the TIP4P-QDP condensed phase {1.31 Å3 for TIP4P-QDP versus 1.1 Å3 (TIP4P-FQ) and 0.87 Å3 (POL3) [Ponder and Case, Adv. Protein Chem. 66, 27 (2003)]} based on ab initio calculations of the condensed-phase polarizability reduction in liquid water, the present simulations highlight the role of water polarizability in inducing water molecular dipole moments parallel to the interface normal (and within the interfacial region) so as to favorably oppose the macrodipole generated by the separation of anion and cation charge. Since the TIP4P-QDP water polarizability approaches that of the experimental vapor phase value for water, the present results suggest a fundamental role of solvent polarizability in accommodating the large spatial dipole generated by the separation of ion charges. The present results draw further attention to the question of what exact value of condensed phase water polarizability to incorporate in classical polarizable water force fields.
Molecular beam studies of reaction dynamics
Lee, Yuan T.
1991-03-01
The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.
Molecular beam studies of reaction dynamics
Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)
1993-12-01
The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.
Statistical coarse-graining of molecular dynamics into peridynamics.
Silling, Stewart Andrew; Lehoucq, Richard B.
2007-10-01
This paper describes an elegant statistical coarse-graining of molecular dynamics at finite temperature into peridynamics, a continuum theory. Peridynamics is an efficient alternative to molecular dynamics enabling dynamics at larger length and time scales. In direct analogy with molecular dynamics, peridynamics uses a nonlocal model of force and does not employ stress/strain relationships germane to classical continuum mechanics. In contrast with classical continuum mechanics, the peridynamic representation of a system of linear springs and masses is shown to have the same dispersion relation as the original spring-mass system.
Molecular dynamics simulation of amorphous indomethacin.
Xiang, Tian-Xiang; Anderson, Bradley D
2013-01-01
Molecular dynamics (MD) simulations have been conducted using an assembly consisting of 105 indomethacin (IMC) molecules and 12 water molecules to investigate the underlying dynamic (e.g., rotational and translational diffusivities and conformation relaxation rates) and structural properties (e.g., conformation, hydrogen-bonding distributions, and interactions of water with IMC) of amorphous IMC. These properties may be important in predicting physical stability of this metastable material. The IMC model was constructed using X-ray diffraction data with the force-field parameters mostly assigned by analogy with similar groups in Amber-ff03 and atomic charges calculated with the B3LYP/ccpVTZ30, IEFPCM, and RESP models. The assemblies were initially equilibrated in their molten state and cooled through the glass transition temperature to form amorphous solids. Constant temperature dynamic runs were then carried out above and below the T(g) (i.e., at 600 K (10 ns), 400 K (350 ns), and 298 K (240 ns)). The density (1.312 ± 0.003 g/cm(3)) of the simulated amorphous solid at 298 K was close to the experimental value (1.32 g/cm(3)) while the estimated T(g) (384 K) was ~64 degrees higher than the experimental value (320 K) due to the faster cooling rate. Due to the hindered rotation of its amide bond, IMC can exist in different diastereomeric states. Different IMC conformations were sufficiently sampled in the IMC melt or vapor, but transitions occurred rarely in the glass. The hydrogen-bonding patterns in amorphous IMC are more complex in the amorphous state than in the crystalline polymorphs. Carboxylic dimers that are dominant in ?- and ?-crystals were found to occur at a much lower probability in the simulated IMC glasses while hydrogen-bonded IMC chains were more easily identified patterns in the simulated amorphous solids. To determine molecular diffusivity, a novel analytical method is proposed to deal with the non-Einsteinian behavior, in which the temporal evolution of the apparent diffusivity D(t) is described by a relaxation model such as the KWW function and extrapolated to infinite time. The diffusion coefficient found for water diffusing in amorphous indomethacin at 298 K (2.7 × 10(-9) cm(2)/s) compares favorably to results obtained in experimental IMC glasses (0.9-2.0 × 10(-9) cm(2)/s) and is mechanistically associated with ?-relaxation processes that are dominant in sub-T(g) glasses. PMID:23116319
Modeling Of Blood Vessel Constriction In 2-D Case Using Molecular Dynamics Method
Mohamad Rendi; Suprijadi; Sparisoma Viridi
2013-06-25
Blood vessel constriction is simulated with particle-based method using a molecular dynamics authoring software known as Molecular Workbench (WM). Blood flow and vessel wall, the only components considered in constructing a blood vessel, are all represented in particle form with interaction potentials: Lennard-Jones potential, push-pull spring potential, and bending spring potential. Influence of medium or blood plasma is accommodated in plasma viscosity through Stokes drag force. It has been observed that pressure p is increased as constriction c is increased. Leakage of blood vessel starts at 80 % constriction, which shows existence of maximum pressure that can be overcome by vessel wall.
Modeling Of Blood Vessel Constriction In 2-D Case Using Molecular Dynamics Method
Rendi, Mohamad; Viridi, Sparisoma
2013-01-01
Blood vessel constriction is simulated with particle-based method using a molecular dynamics authoring software known as Molecular Workbench (WM). Blood flow and vessel wall, the only components considered in constructing a blood vessel, are all represented in particle form with interaction potentials: Lennard-Jones potential, push-pull spring potential, and bending spring potential. Influence of medium or blood plasma is accommodated in plasma viscosity through Stokes drag force. It has been observed that pressure p is increased as constriction c is increased. Leakage of blood vessel starts at 80 % constriction, which shows existence of maximum pressure that can be overcome by vessel wall.
Molecular Dynamics Simulations of Polyelectrolyte Solutions
NASA Astrophysics Data System (ADS)
Dobrynin, Andrey
2014-03-01
Polyelectrolytes are polymers with ionizable groups. In polar solvents, these groups dissociate releasing counterions into solution and leaving uncompensated charges on the polymer backbone. Examples of polyelectrolytes include biopolymers such as DNA and RNA, and synthetic polymers such as poly(styrene sulfonate) and poly(acrylic acids). In this talk I will discuss recent molecular dynamics simulations of static and dynamic properties of polyelectrolyte solutions. These simulations show that in dilute and semidilute polyelectrolyte solutions the electrostatic induced chain persistence length scales with the solution ionic strength as I - 1 / 2. This dependence of the chain persistence length is due to counterion condensation on the polymer backbone. In dilute polyelectrolyte solutions the chain size decreases with increasing the salt concentration as R ~ I- 1 / 5. This is in agreement with the scaling of the chain persistence length on the solution ionic strength, lp ~ I- 1 / 2. In semidilute solution regime at low salt concentrations the chain size decreases with increasing polymer concentration, R ~ cp-1 / 4 . While at high salt concentrations one observes a weaker dependence of the chain size on the solution ionic strength, R ~ I- 1 / 8. Analysis of the simulation data throughout the studied salt and polymer concentration ranges shows that there exist general scaling relations between multiple quantities X (I) in salt solutions and corresponding quantities X (I0) in salt-free solutions, X (I) = X (I0) (I /I0) ? . The exponent ? = -1/2 for chain persistence length lp , ? = 1/4 for solution correlation length, ? = -1/5 and ? = -1/8 for chain size R in dilute and semidilute solution regimes respectively. Furthermore, the analysis of the spectrum and of the relaxation times of Rouse modes confirms existence of the single length scale (correlation length) that controls both static and dynamic properties of semidilute polyelectrolyte solutions. These findings confirm predictions of the scaling model of polyelectrolyte solutions. NSF DMR-1004576.
Insect Chitinases: Molecular Biology and Potential Use as Biopesticides
Karl J Kramer; Subbaratnam Muthukrishnan
1998-01-01
Chitin, an insoluble structural polysaccharide that occurs in the exoskeletal and gut linings of insects, is a metabolic target of selective pest control agents. One potential biopesticide is the insect molting enzyme, chitinase, which degrades chitin to low molecular weight, soluble and insoluble oligosaccharides. For several years, our laboratories have been characterizing this enzyme and its gene. Most recently, we
Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu [Department of Mechanical and Aerospace Engineering, University of Missouri, Columbia, Missouri 65211 (United States); Yang, Mo [College of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai 200093 (China)
2013-12-21
The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.
Zhigilei, Leonid V.
Molecular dynamics simulations of thermal conductivity of carbon nanotubes: Resolving the effects of many molecular dynamics (MD) simulation studies reported in the literature. The values of k obtained, atomistic molecular dynamics (MD) simulations present an attractive alternative. Indeed, atomistic
Molecular dynamics in cytochrome c oxidase Moessbauer spectra deconvolution
Bossis, Fabrizio [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari 'Aldo Moro', Bari (Italy)] [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari 'Aldo Moro', Bari (Italy); Palese, Luigi L., E-mail: palese@biochem.uniba.it [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari 'Aldo Moro', Bari (Italy)
2011-01-07
Research highlights: {yields} Cytochrome c oxidase molecular dynamics serve to predict Moessbauer lineshape widths. {yields} Half height widths are used in modeling of Lorentzian doublets. {yields} Such spectral deconvolutions are useful in detecting the enzyme intermediates. -- Abstract: In this work low temperature molecular dynamics simulations of cytochrome c oxidase are used to predict an experimentally observable, namely Moessbauer spectra width. Predicted lineshapes are used to model Lorentzian doublets, with which published cytochrome c oxidase Moessbauer spectra were simulated. Molecular dynamics imposed constraints to spectral lineshapes permit to obtain useful information, like the presence of multiple chemical species in the binuclear center of cytochrome c oxidase. Moreover, a benchmark of quality for molecular dynamic simulations can be obtained. Despite the overwhelming importance of dynamics in electron-proton transfer systems, limited work has been devoted to unravel how much realistic are molecular dynamics simulations results. In this work, molecular dynamics based predictions are found to be in good agreement with published experimental spectra, showing that we can confidently rely on actual simulations. Molecular dynamics based deconvolution of Moessbauer spectra will lead to a renewed interest for application of this approach in bioenergetics.
Accelerated molecular dynamics methods: introduction and recent developments
Uberuaga, Blas Pedro [Los Alamos National Laboratory; Voter, Arthur F [Los Alamos National Laboratory; Perez, Danny [Los Alamos National Laboratory; Shim, Y [UNIV OF TOLEDO; Amar, J G [UNIV OF TOLEDO
2009-01-01
A long-standing limitation in the use of molecular dynamics (MD) simulation is that it can only be applied directly to processes that take place on very short timescales: nanoseconds if empirical potentials are employed, or picoseconds if we rely on electronic structure methods. Many processes of interest in chemistry, biochemistry, and materials science require study over microseconds and beyond, due either to the natural timescale for the evolution or to the duration of the experiment of interest. Ignoring the case of liquids xxx, the dynamics on these time scales is typically characterized by infrequent-event transitions, from state to state, usually involving an energy barrier. There is a long and venerable tradition in chemistry of using transition state theory (TST) [10, 19, 23] to directly compute rate constants for these kinds of activated processes. If needed dynamical corrections to the TST rate, and even quantum corrections, can be computed to achieve an accuracy suitable for the problem at hand. These rate constants then allow them to understand the system behavior on longer time scales than we can directly reach with MD. For complex systems with many reaction paths, the TST rates can be fed into a stochastic simulation procedure such as kinetic Monte Carlo xxx, and a direct simulation of the advance of the system through its possible states can be obtained in a probabilistically exact way. A problem that has become more evident in recent years, however, is that for many systems of interest there is a complexity that makes it difficult, if not impossible, to determine all the relevant reaction paths to which TST should be applied. This is a serious issue, as omitted transition pathways can have uncontrollable consequences on the simulated long-time kinetics. Over the last decade or so, we have been developing a new class of methods for treating the long-time dynamics in these complex, infrequent-event systems. Rather than trying to guess in advance what reaction pathways may be important, we return instead to a molecular dynamics treatment, in which the trajectory itself finds an appropriate way to escape from each state of the system. Since a direct integration of the trajectory would be limited to nanoseconds, while we are seeking to follow the system for much longer times, we modify the dynamics in some way to cause the first escape to happen much more quickly, thereby accelerating the dynamics. The key is to design the modified dynamics in a way that does as little damage as possible to the probability for escaping along a given pathway - i.e., we try to preserve the relative rate constants for the different possible escape paths out of the state. We can then use this modified dynamics to follow the system from state to state, reaching much longer times than we could reach with direct MD. The dynamics within any one state may no longer be meaningful, but the state-to-state dynamics, in the best case, as we discuss in the paper, can be exact. We have developed three methods in this accelerated molecular dynamics (AMD) class, in each case appealing to TST, either implicitly or explicitly, to design the modified dynamics. Each of these methods has its own advantages, and we and others have applied these methods to a wide range of problems. The purpose of this article is to give the reader a brief introduction to how these methods work, and discuss some of the recent developments that have been made to improve their power and applicability. Note that this brief review does not claim to be exhaustive: various other methods aiming at similar goals have been proposed in the literature. For the sake of brevity, our focus will exclusively be on the methods developed by the group.
Molecular Dynamics Simulations of Cyclohexyl Modified Peptide Nucleic Acids (PNA)
Smriti Sharma; Uddhavesh B. Sonavane; Rajendra R. Joshi
2010-01-01
Peptide Nucleic Acids (PNA) that bind sequence specifically to DNA\\/RNA are of major interest in the field of molecular biology and could form the basis for gene-targeted drugs. Molecular dynamics simulations are aimed to characterize the structural and dynamical features to understand the effect of backbone modification on the structure and dynamics along with the stability of the resulting 10mer
Iyengar, Srinivasan S.
as a time-dependent quantum system interacting with the molecular wire device. We also make an assumptionQuantum Wavepacket Ab-initio Molecular Dynamics Formalism for Calculating Electron Transport in Molecular Wires Alexander B. Pacheco and Srinivasan S. Iyengar Department of Chemistry, Indiana University
Modeling and Bio molecular Self-assembly via Molecular Dynamics and Dissipative Particle Dynamics
NASA Astrophysics Data System (ADS)
Rakesh, L.
2009-09-01
Surfactants like materials can be used to increase the solubility of poorly soluble drugs in water and to increase drug bioavailability. A typical case study will be demonstrated using DPD simulation to model the distribution of anti-inflammatory drug molecules. Computer simulation is a convenient approach to understand drug distribution and solubility concepts without much wastage and costly experiments in the laboratory. Often in molecular dynamics (MD) the atoms are represented explicitly and the equation of motion as described by Newtonian dynamics is integrated explicitly. MD has been used to study spontaneous formation of micelles by hydrophobic molecules with amphiphilic head groups in bulk water, as well as stability of pre-configured micelles and membranes. DPD is a state-of the- art mesoscale simulation, it is a more recent molecular dynamics technique, originally developed for simulating complex fluids but lately also applied to membrane dynamics, hemodynamic in biomedical applications. Such fluids pervade industrial research from paints to pharmaceuticals and from cosmetics to the controlled release of drugs. Dissipative particle dynamics (DPD) can provide structural and dynamic properties of fluids in equilibrium, under shear or confined to narrow cavities, at length- and time-scales beyond the scope of traditional atomistic molecular dynamics simulation methods. Mesoscopic particles are used to represent clusters of molecules. The interaction conserves mass and momentum and as a consequence the dynamics is consistent with Navier-Stokes equations. In addition to the conservative forces, stochastic drive and dissipation is introduced to represent internal degrees of freedom in the mesoscopic particles. In this research, an initial study is being conducted using the aqueous solubilization of the nonsteroidal, anti-inflammatory drug is studied theoretically in micellar solution of nonionic (dodecyl hexa(ethylene oxide), C12E6) surfactants possessing the hydrocarbon "tail" and their hydrophilic head groups. We find that, for the surfactants, the aqueous solubility of anti-inflammatory molecules increases linearly with increasing surfactant concentration. In particular, we observed a 10-fold increase in the solubility of anti-inflammatory drugs relative to that in the aqueous buffer upon the addition of 100 mM dodecyltrimethyl ammonium bromide -DTAB.
Semi-grand canonical molecular dynamics simulation of bovine pancreatic trypsin inhibitor
NASA Astrophysics Data System (ADS)
Lynch, Gillian C.; Pettitt, B. Montgomery
2000-08-01
In the quest to understand both the structural and thermodynamic facets of biomolecular-solvent systems semi-grand canonical ensemble molecular dynamics simulations of a protein in solution are performed. In these simulations only the water molecules in the system are allowed to fluctuate; the final number of water molecules is determined by the chemical potential. An unbiased sampling technique is used for the insertion/deletion procedure of the water molecules thereby providing a benchmark grand ensemble simulation of the hydration structure of proteins. Three different chemical potential simulations were carried out offering a direct route to thermodynamic information from a molecular dynamics simulation.
NASA Astrophysics Data System (ADS)
Jiang, Jin-Wu; Wang, Bing-Shen; Rabczuk, Timon
2014-03-01
We study the phonon modes in single-walled MoS2 nanotubes via lattice dynamics calculation and molecular dynamics simulation. The phonon spectra for tubes of arbitrary chiralities are calculated from a dynamical matrix constructed by the combination of an empirical potential with the conserved helical quantum numbers (?, n). In particular, we show that the frequency (?) of the radial breathing mode is inversely proportional to the tube diameter (d) as ? = 665.3/d cm-1. The eigenvectors of the twenty lowest-frequency phonon modes are illustrated. Based on these eigenvectors, we demonstrate that the radial breathing oscillation is initially disturbed by phonon modes of three-fold symmetry, then eventually the tube is squashed by modes of two-fold symmetry . Our study provides fundamental knowledge for further investigations of the thermal and mechanical properties of MoS2 nanotubes.
Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review
Paquet, Eric; Viktor, Herna L.
2015-01-01
Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods. PMID:25785262
Can the ring polymer molecular dynamics method be interpreted as real time quantum dynamics?
Jang, Seogjoo, E-mail: sjang@qc.cuny.edu [Department of Chemistry and Biochemistry, Queens College and the Graduate Center, City University of New York, 65-30 Kissena Boulevard, Flushing, New York 11367 (United States)] [Department of Chemistry and Biochemistry, Queens College and the Graduate Center, City University of New York, 65-30 Kissena Boulevard, Flushing, New York 11367 (United States); Sinitskiy, Anton V.; Voth, Gregory A., E-mail: gavoth@uchicago.edu [Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics and Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637 (United States)
2014-04-21
The ring polymer molecular dynamics (RPMD) method has gained popularity in recent years as a simple approximation for calculating real time quantum correlation functions in condensed media. However, the extent to which RPMD captures real dynamical quantum effects and why it fails under certain situations have not been clearly understood. Addressing this issue has been difficult in the absence of a genuine justification for the RPMD algorithm starting from the quantum Liouville equation. To this end, a new and exact path integral formalism for the calculation of real time quantum correlation functions is presented in this work, which can serve as a rigorous foundation for the analysis of the RPMD method as well as providing an alternative derivation of the well established centroid molecular dynamics method. The new formalism utilizes the cyclic symmetry of the imaginary time path integral in the most general sense and enables the expression of Kubo-transformed quantum time correlation functions as that of physical observables pre-averaged over the imaginary time path. Upon filtering with a centroid constraint function, the formulation results in the centroid dynamics formalism. Upon filtering with the position representation of the imaginary time path integral, we obtain an exact quantum dynamics formalism involving the same variables as the RPMD method. The analysis of the RPMD approximation based on this approach clarifies that an explicit quantum dynamical justification does not exist for the use of the ring polymer harmonic potential term (imaginary time kinetic energy) as implemented in the RPMD method. It is analyzed why this can cause substantial errors in nonlinear correlation functions of harmonic oscillators. Such errors can be significant for general correlation functions of anharmonic systems. We also demonstrate that the short time accuracy of the exact path integral limit of RPMD is of lower order than those for finite discretization of path. The present quantum dynamics formulation also serves as the basis for developing new quantum dynamical methods that utilize the cyclic nature of the imaginary time path integral.
Internal coordinate molecular dynamics: a foundation for multiscale dynamics.
Vaidehi, Nagarajan; Jain, Abhinandan
2015-01-29
Internal coordinates such as bond lengths, bond angles, and torsion angles (BAT) are natural coordinates for describing a bonded molecular system. However, the molecular dynamics (MD) simulation methods that are widely used for proteins, DNA, and polymers are based on Cartesian coordinates owing to the mathematical simplicity of the equations of motion. However, constraints are often needed with Cartesian MD simulations to enhance the conformational sampling. This makes the equations of motion in the Cartesian coordinates differential-algebraic, which adversely impacts the complexity and the robustness of the simulations. On the other hand, constraints can be easily placed in BAT coordinates by removing the degrees of freedom that need to be constrained. Thus, the internal coordinate MD (ICMD) offers an attractive alternative to Cartesian coordinate MD for developing multiscale MD method. The torsional MD method is a special adaptation of the ICMD method, where all the bond lengths and bond angles are kept rigid. The advantages of ICMD simulation methods are the longer time step size afforded by freezing high frequency degrees of freedom and performing a conformational search in the more important low frequency torsional degrees of freedom. However, the advancements in the ICMD simulations have been slow and stifled by long-standing mathematical bottlenecks. In this review, we summarize the recent mathematical advancements we have made based on spatial operator algebra, in developing a robust long time scale ICMD simulation toolkit useful for various applications. We also present the applications of ICMD simulations to study conformational changes in proteins and protein structure refinement. We review the advantages of the ICMD simulations over the Cartesian simulations when used with enhanced sampling methods and project the future use of ICMD simulations in protein dynamics. PMID:25517406
Molecular Dynamics Simulation of Temperature Relaxation in Dense Hydrogen Plasma
NASA Astrophysics Data System (ADS)
Zhao, Zengxiu; Ma, Qian; Dai, Jiayu; Kang, Dongdong; Yuan, Jianmin
2013-10-01
Temperature relaxation between electrons and ions in dense plasma is regarded as an essential factor in understanding the physics process in laser-plasma interactions. Here, we perform molecular dynamics (MD) simulation to investigate the electron-ion temperature relaxation with semi-classical potentials in fully ionized dense hydrogen plasma. We compare the results of different potentials such as HM potential, Yukawa potential and Coulomb potential with an appropriate cutoff, in addition, a simplified scattering model is used in the MD simulation to overcome the negative effect called Coulomb Catastrophe. The MD simulation is performed with a code using velocity Verlet integration in a box cell with periodic boundary and the electron number density changes from to. The tested particle number N is ranging from N = 500 to as many as N = 4000, the results reported here use N = 1372. Statistical uncertainty for each case is estimated by performing the code from 6 samples of the ensemble and then taking the average and standard deviation. Furthermore, the results of theoretical models, such as LS, GMS and BPS, are also used to compare with the MD results.
Fayer, Michael D.
Experiments and Molecular Dynamics Simulations Ilya J. Finkelstein, Anne Goj, Brian L. McClain, Aaron M and molecular dynamics (MD) simulations. In aqueous solution at room temperature, the vibrational dephasing rateUltrafast Dynamics of Myoglobin without the Distal Histidine: Stimulated Vibrational Echo
Superionic behavior of lithium oxide Li2O : A lattice dynamics and molecular dynamics study
Prabhatasree Goel; N. Choudhury; S. L. Chaplot
2004-01-01
We report a cumulative study of lithium oxide in its normal as well as superionic phase using both lattice dynamical and molecular dynamical calculations. Molecular dynamics simulations have been carried out to study the fast ion phase and the diffusion behavior of lithium and oxygen ions. The results obtained for the diffusion constant and the thermal amplitude of lithium are
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.
Spontaneous formation of polyglutamine nanotubes with molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Laghaei, Rozita; Mousseau, Normand
2010-04-01
Expansion of polyglutamine (polyQ) beyond the pathogenic threshold (35-40 Gln) is associated with several neurodegenerative diseases including Huntington's disease, several forms of spinocerebellar ataxias and spinobulbar muscular atrophy. To determine the structure of polyglutamine aggregates we perform replica-exchange molecular dynamics simulations coupled with the optimized potential for effective peptide forcefield. Using a range of temperatures from 250 to 700 K, we study the aggregation kinetics of the polyglutamine monomer and dimer with chain lengths from 30 to 50 residues. All monomers show a similar structural change at the same temperature from ?-helical structure to random coil, without indication of any significant ?-strand. For dimers, by contrast, starting from random structures, we observe spontaneous formation of antiparallel ?-sheets and triangular and circular ?-helical structures for polyglutamine with 40 residues in a 400 ns 50 temperature replica-exchange molecular dynamics simulation (total integrated time 20 ?s). This ˜32 Å diameter structure reorganizes further into a tight antiparallel double-stranded ˜22 Å nanotube with 22 residues per turn close to Perutz' model for amyloid fibers as water-filled nanotubes. This diversity of structures suggests the existence of polymorphism for polyglutamine with possibly different pathways leading to the formation of toxic oligomers and to fibrils.
Large Scale Molecular Dynamics Simulations of Homogeneous Nucleation
Tanaka, Kyoko K
2013-01-01
We present results from large-scale molecular dynamics (MD) simulations of homogeneous vapor-to-liquid nucleation. The simulations contain between one and eight billion Lennard-Jones (LJ) atoms, covering up to 1.2 {\\mu}s (56 million time-steps). They cover a wide range of supersaturation ratios, S=1.55 to 10^4, and temperatures from kT = 0.3 to 1.0 {\\epsilon} (where {\\epsilon} is the depth of the LJ potential, and k the Boltzmann constant). We have resolved nucleation rates as low as 10^{17} cm^{-3} s^{-1} (in the argon system), and critical cluster sizes as large as 100 atoms. Recent argon nucleation experiments probe nucleation rates in an overlapping range, making the first direct comparison between laboratory experiments and molecular dynamics simulations possible: We find very good agreement within the uncertainties, which are mainly due to the extrapolations of argon and LJ saturation curves to very low temperatures. The self-consistent, modified classical nucleation model of Girshick and Chiu [J. Chem....
An Alamethicin Channel in a Lipid Bilayer: Molecular Dynamics Simulations
D. Peter Tieleman; Herman J. C. Berendsen; Mark S. P. Sansom
1999-01-01
We present the results of 2-ns molecular dynamics (MD) simulations of a hexameric bundle of Alm helices in a 1-palmitoyl-2-oleoylphosphatidylcholine bilayer. These simulations explore the dynamic properties of a model of a helix bundle channel in a complete phospholipid bilayer in an aqueous environment. We explore the stability and conformational dynamics of the bundle in a phospholipid bilayer. We also
Gernot A. Heiser; Ramesh C. Shukla; E. R. Cowley
1986-01-01
Molecular-dynamics (MD) and Monte Carlo (MC) calculations of the mean-square displacement (MSD) have been carried out for a fcc nearest-neighbor Lennard-Jones model for a wide range of temperatures and lattice spacings. The lattice-dynamics (LD) calculations of the harmonic and the lowest-order anharmonic (cubic and quartic) contributions to the mean-square displacement were performed for the same potential model as in the
Microsecond molecular dynamics simulations of lipid mixing.
Hong, Chunkit; Tieleman, D Peter; Wang, Yi
2014-10-14
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 ?s. 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
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations.
Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D; Kühn, Oliver
2015-06-28
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom. PMID:26133413
Evaluation of melting point of UO 2 by molecular dynamics simulation
Tatsumi Arima; Kazuya Idemitsu; Yaohiro Inagaki; Yuichi Tsujita; Motoyasu Kinoshita; Eugene Yakub
2009-01-01
The melting point of UO2 has been evaluated by molecular dynamics simulation (MD) in terms of interatomic potential, pressure and Schottky defect concentration. The Born–Mayer–Huggins potentials with or without a Morse potential were explored in the present study. Two-phase simulation whose supercell at the initial state consisted of solid and liquid phases gave the melting point comparable to the experimental
Shaw, David E.
Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide an atomistic description of picosecond and nanosecond fluctuations in protein structure. Molecular dynamics (MD folding, molecular recognition, and catalysis.4 Values of S2 obtained from protein molecular dynamics (MD
Stability of molecular dynamics simulations of classical systems.
Toxvaerd, Søren
2012-12-01
The existence of a shadow Hamiltonian H? for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics. The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ? gives a criterion for the limit of stability h ? 2/?. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD. The method is also used to investigate higher-order central difference algorithms, which are symplectic and also have shadow Hamiltonians, and for which one can also determine the exact criteria for the limit of stability of a single harmonic mode. A fourth-order central difference algorithm gives an improved stability with a factor of 3, but the overhead of computer time is a factor of at least two. The conclusion is that the second-order "Verlet"-algorithm, most commonly used in MD, is superior. It gives the exact dynamics within the limit of the asymptotic expansion and this limit can be estimated either from the conserved shadow energy or from the instantaneous spectrum of harmonic modes. PMID:23231212
Molecular Dynamics Study of Void Growth and Dislocations in Dynamic Fracture of FCC and BCC Metals
Seppala, E T; Belak, J; Rudd, R E
2003-06-17
Void growth with concomitant dislocation formation has been studied in single crystal face-centered-cubic and body-centered-cubic metals using molecular dynamics method with Embedded-Atom and Finnis-Sinclair potentials for copper and tantalum, respectively. We have concentrated on the quantitative analysis of the void shape evolution, on the structure of dislocations, which emerge from the void, and on the continuum measures such as plastic strain. The effects of strain-rate, differences between lattice structures, and loading conditions as uniaxial, biaxial, and triaxial expansion on the shape of the void and on the dislocations have been investigated.
Molecular chaperone-mediated nuclear protein dynamics.
Echtenkamp, Frank J; Freeman, Brian C
2014-05-01
Homeostasis requires effective action of numerous biological pathways including those working along a genome. The variety of processes functioning in the nucleus is considerable, yet the number of employed factors eclipses this total. Ideally, individual components assemble into distinct complexes and serially operate along a pathway to perform work. Adding to the complexity is a multitude of fluctuating internal and external signals that must be monitored to initiate, continue or halt individual activities. While cooperative interactions between proteins of the same process provide a mechanism for rapid and precise assembly, the inherent stability of such organized structures interferes with the proper timing of biological events. Further prolonging the longevity of biological complexes are crowding effects resulting from the high concentration of intracellular macromolecules. Hence, accessory proteins are required to destabilize the various assemblies to efficiently transition between structures, avoid off-pathway competitive interactions, and to terminate pathway activity. We suggest that molecular chaperones have evolved, in part, to manage these challenges by fostering a general and continuous dynamic protein environment within the nucleus. PMID:24694369
Nitrile and thiocyanate IR probes: molecular dynamics simulation studies.
Oh, Kwang-Im; Choi, Jun-Ho; Lee, Joo-Hyun; Han, Jae-Beom; Lee, Hochan; Cho, Minhaeng
2008-04-21
Nitrile- and thiocyanate-derivatized amino acids have been found to be useful IR probes for investigating their local electrostatic environments in proteins. To shed light on the CN stretch frequency shift and spectral lineshape change induced by interactions with hydrogen-bonding solvent molecules, we carried out both classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations for MeCN and MeSCN in water. These QM/MM and conventional force field MD simulation results were found to be inconsistent with the experimental results as well as with the high-level ab initio calculation results of MeCN-water and MeSCN-water potential energies. Thus, a new set of atomic partial charges of MeCN and MeSCN is obtained. By using the MD simulation trajectories and the electrostatic potential model recently developed, the CN and SCN stretching mode frequency trajectories were obtained and used to simulate the IR spectra. The C[Triple Bond]N frequency blueshifts of MeCN and MeSCN in water are estimated to be 9.0 and 1.9 cm(-1), respectively, in comparison with those of gas phase values. These values are found to be in reasonable agreement with the experimentally measured IR spectra of MeCN, MeSCN, beta-cyano-L-alanine, and cyanylated cysteine in water and other polar solvents. PMID:18433232
Nitrile and thiocyanate IR probes: Molecular dynamics simulation studies
NASA Astrophysics Data System (ADS)
Oh, Kwang-Im; Choi, Jun-Ho; Lee, Joo-Hyun; Han, Jae-Beom; Lee, Hochan; Cho, Minhaeng
2008-04-01
Nitrile- and thiocyanate-derivatized amino acids have been found to be useful IR probes for investigating their local electrostatic environments in proteins. To shed light on the CN stretch frequency shift and spectral lineshape change induced by interactions with hydrogen-bonding solvent molecules, we carried out both classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations for MeCN and MeSCN in water. These QM/MM and conventional force field MD simulation results were found to be inconsistent with the experimental results as well as with the high-level ab initio calculation results of MeCN-water and MeSCN-water potential energies. Thus, a new set of atomic partial charges of MeCN and MeSCN is obtained. By using the MD simulation trajectories and the electrostatic potential model recently developed, the CN and SCN stretching mode frequency trajectories were obtained and used to simulate the IR spectra. The C ?N frequency blueshifts of MeCN and MeSCN in water are estimated to be 9.0 and 1.9cm-1, respectively, in comparison with those of gas phase values. These values are found to be in reasonable agreement with the experimentally measured IR spectra of MeCN, MeSCN, ?-cyano-L-alanine, and cyanylated cysteine in water and other polar solvents.
Enhanced molecular dynamics for simulating porous interphase layers in batteries.
Zimmerman, Jonathan A.; Wong, Bryan Matthew; Jones, Reese E.; Templeton, Jeremy Alan; Lee, Jonathan (Rice University, Houston, TX)
2009-10-01
Understanding charge transport processes at a molecular level using computational techniques is currently hindered by a lack of appropriate models for incorporating anistropic electric fields in molecular dynamics (MD) simulations. An important technological example is ion transport through solid-electrolyte interphase (SEI) layers that form in many common types of batteries. These layers regulate the rate at which electro-chemical reactions occur, affecting power, safety, and reliability. In this work, we develop a model for incorporating electric fields in MD using an atomistic-to-continuum framework. This framework provides the mathematical and algorithmic infrastructure to couple finite element (FE) representations of continuous data with atomic data. In this application, the electric potential is represented on a FE mesh and is calculated from a Poisson equation with source terms determined by the distribution of the atomic charges. Boundary conditions can be imposed naturally using the FE description of the potential, which then propagates to each atom through modified forces. The method is verified using simulations where analytical or theoretical solutions are known. Calculations of salt water solutions in complex domains are performed to understand how ions are attracted to charged surfaces in the presence of electric fields and interfering media.
Multiscale molecular dynamics using the matched interface and boundary method
Geng, Weihua; Wei, G.W.
2010-01-01
The Poisson-Boltzmann (PB) equation is an established multiscale model for electrostatic analysis of biomolecules and other dielectric systems. PB based molecular dynamics (MD) approach has a potential to tackle large biological systems. Obstacles that hinder the current development of PB based MD methods are concerns in accuracy, stability, efficiency and reliability. The presence of complex solvent-solute interface, geometric singularities and charge singularities leads to challenges in the numerical solution of the PB equation and electrostatic force evaluation in PB based MD methods. Recently, the matched interface and boundary (MIB) method has been utilized to develop the first second order accurate PB solver that is numerically stable in dealing with discontinuous dielectric coefficients, complex geometric singularities and singular source charges. The present work develops the PB based MD approach using the MIB method. New formulation of electrostatic forces is derived to allow the use of sharp molecular surfaces. Accurate reaction field forces are obtained by directly differentiating the electrostatic potential. Dielectric boundary forces are evaluated at the solvent-solute interface using an accurate Cartesian-grid surface integration method. The electrostatic forces located at reentrant surfaces are appropriately assigned to related atoms. Extensive numerical tests are carried out to validate the accuracy and stability of the present electrostatic force calculation. The new PB based MD method is implemented in conjunction with the AMBER package. MIB based MD simulations of biomolecules are demonstrated via a few example systems. PMID:21088761
Molecular dynamics study of the mechanical loss in amorphous pure and doped silica.
Hamdan, Rashid; Trinastic, Jonathan P; Cheng, H P
2014-08-01
Gravitational wave detectors and other precision measurement devices are limited by the thermal noise in the oxide coatings on the mirrors of such devices. We have investigated the mechanical loss in amorphous oxides by calculating the internal friction using classical, atomistic molecular dynamics simulations. We have implemented the trajectory bisection method and the non-local ridge method in the DL-POLY molecular dynamics simulation software to carry out those calculations. These methods have been used to locate the local potential energy minima that a system visits during a molecular dynamics trajectory and the transition state between any two consecutive minima. Using the numerically calculated barrier height distributions, barrier asymmetry distributions, relaxation times, and deformation potentials, we have calculated the internal friction of pure amorphous silica and silica mixed with other oxides. The results for silica compare well with experiment. Finally, we use the numerical calculations to comment on the validity of previously used theoretical assumptions. PMID:25106591
Pierce, Levi C. T.; Markwick, Phineus R. L.; McCammon, J. Andrew; Doltsinis, Nikos L.
2011-01-01
A biased potential molecular dynamics simulation approach, accelerated molecular dynamics (AMD), has been implemented in the framework of ab initio molecular dynamics for the study of chemical reactions. Using two examples, the double proton transfer reaction in formic acid dimer and the hypothetical adiabatic ring opening and subsequent rearrangement reactions in methylenecyclopropane, it is demonstrated that ab initio AMD can be readily employed to efficiently explore the reactive potential energy surface, allowing the prediction of chemical reactions and the identification of metastable states. An adaptive variant of the AMD method is developed, which additionally affords an accurate representation of both the free-energy surface and the mechanism associated with the chemical reaction of interest and can also provide an estimate of the reaction rate. PMID:21548673
Ab initio molecular dynamics of liquid hydrogen chloride
NASA Astrophysics Data System (ADS)
Dubois, Vincent; Pasquarello, Alfredo
2005-03-01
We carried out an ab initio molecular dynamics simulation of liquid hydrogen chloride (?-HCl) at a temperature of 313 K. Comparison with inelastic neutron scattering data shows that the simulation achieves an overall good description of the structural correlations, improving significantly upon a description based on classical interaction potentials. Despite some minor differences between theory and experiment in the H-H partial structure factor, the simulation gives a description of the hydrogen bonding in impressive agreement with experiment, for both the amount and the bond-length distribution of the bonds. In the simulation, 40% of the molecules are nonbonded, while the hydrogen-bonded chains are short, principally consisting of dimers (25%) and trimers (15%). Neighboring molecules in the simulation are found to form L-shaped arrangements, like in the isolated (HCl)2 dimer and in crystalline phases of HCl. The time correlation of the molecular-axis orientation is found to be characterized by a very short decay time (0.13 ps), consistent with the short length of the hydrogen-bonded chains. Other dynamical properties investigated in this work include the diffusion coefficient and the vibrational density of states. We evaluated the molecular dipole of the HCl molecule in the liquid using a definition based on the coupling of rotational modes to an external electric field. The average dipole moment (1.53 D) derived in this way is found to be considerably larger than for the isolated molecule (1.11 D). Our results show that the dipole moment in ?-HCl undergoes large fluctuations, both in orientation and in modulus. Upon the onset of an external field, such dipole fluctuations concur to reduce the fluctuations of the dielectric response.
Atomistic molecular dynamics simulations of shock compressed quartz.
Farrow, M R; Probert, M I J
2011-07-28
Atomistic non-equilibrium molecular dynamics simulations of shock wave compression of quartz have been performed using the so-called BKS semi-empirical potential of van Beest, Kramer, and van Santen [Phys. Rev. B 43, 5068 (1991)] to construct the Hugoniot of quartz. Our scheme mimics the real world experimental set up by using a flyer-plate impactor to initiate the shock wave and is the first shock wave simulation that uses a geometry optimised system of a polar slab in a three-dimensional system employing periodic boundary conditions. Our scheme also includes the relaxation of the surface dipole in the polar quartz slab which is an essential pre-requisite to a stable simulation. The original BKS potential is unsuited to shock wave calculations and so we propose a simple modification. With this modification, we find that our calculated Hugoniot is in good agreement with experimental shock wave data up to 25 GPa, but significantly diverges beyond this point. We conclude that our modified BKS potential is suitable for quartz under representative pressure conditions of the Earth core, but unsuitable for high-pressure shock wave simulations. We also find that the BKS potential incorrectly prefers the ?-quartz phase over the ?-quartz phase at zero-temperature, and that there is a ? ? ? phase-transition at 6 GPa. PMID:21806139
Masses, luminosities and dynamics of galactic molecular clouds
NASA Technical Reports Server (NTRS)
Solomon, P. M.; Rivolo, A. R.; Mooney, T. J.; Barrett, J. W.; Sage, L. J.
1987-01-01
Star formation in galaxies takes place in molecular clouds and the Milky Way is the only galaxy in which it is possible to resolve and study the physical properties and star formation activity of individual clouds. The masses, luminosities, dynamics, and distribution of molecular clouds, primarily giant molecular clouds in the Milky Way are described and analyzed. The observational data sets are the Massachusetts-Stony Brook CO Galactic Plane Survey and the IRAS far IR images. The molecular mass and infrared luminosities of glactic clouds are then compared with the molecular mass and infrared luminosities of external galaxies.
Dynamics study of $Z^+(4430)$ and X(3872) in molecular picture
Xiang Liu; Yan-Rui Liu; Wei-Zhen Deng
2008-03-24
In this talk, we review our recent work about the dynamical studies of $Z^+(4430)$ and X(3872). $Z^+(4430)$ can not be explained as a $D_1'D^*$ or $D_1D^*$ molecular state only considering one pion exchange potential without the cutoff, which needs to be confirmed by introducing sigma exchange potential and adding the cutoff in the effective potential. One also excludes the possibility of X(3872) as a $DD^*$ molecular state by one pion and one sigma exchanges with the cutoff. Fortunately there exists an S-wave $BB^*$ bound state with $J^{PC}=1^{++}$. we suggest future experiment to search this state.
Diagnosis of inflammatory bowel disease: Potential role of molecular biometrics
M’Koma, Amosy E
2014-01-01
Accurate diagnosis of predominantly colonic inflammatory bowel disease (IBD) is not possible in 30% of patients. For decades, scientists have worked to find a solution to improve diagnostic accuracy for IBD, encompassing Crohn’s colitis and ulcerative colitis. Evaluating protein patterns in surgical pathology colectomy specimens of colonic mucosal and submucosal compartments, individually, has potential for diagnostic medicine by identifying integrally independent, phenotype-specific cellular and molecular characteristics. Mass spectrometry (MS) and imaging (I) MS are analytical technologies that directly measure molecular species in clinical specimens, contributing to the in-depth understanding of biological molecules. The biometric-system complexity and functional diversity is well suited to proteomic and diagnostic studies. The direct analysis of cells and tissues by Matrix-Assisted-Laser Desorption/Ionization (MALDI) MS/IMS has relevant medical diagnostic potential. MALDI-MS/IMS detection generates molecular signatures obtained from specific cell types within tissue sections. Herein discussed is a perspective on the use of MALDI-MS/IMS and bioinformatics technologies for detection of molecular-biometric patterns and identification of differentiating proteins. I also discuss a perspective on the global challenge of transferring technologies to clinical laboratories dealing with IBD issues. The significance of serologic-immunometric advances is also discussed. PMID:25429322
Diagnosis of inflammatory bowel disease: Potential role of molecular biometrics.
M'Koma, Amosy E
2014-11-27
Accurate diagnosis of predominantly colonic inflammatory bowel disease (IBD) is not possible in 30% of patients. For decades, scientists have worked to find a solution to improve diagnostic accuracy for IBD, encompassing Crohn's colitis and ulcerative colitis. Evaluating protein patterns in surgical pathology colectomy specimens of colonic mucosal and submucosal compartments, individually, has potential for diagnostic medicine by identifying integrally independent, phenotype-specific cellular and molecular characteristics. Mass spectrometry (MS) and imaging (I) MS are analytical technologies that directly measure molecular species in clinical specimens, contributing to the in-depth understanding of biological molecules. The biometric-system complexity and functional diversity is well suited to proteomic and diagnostic studies. The direct analysis of cells and tissues by Matrix-Assisted-Laser Desorption/Ionization (MALDI) MS/IMS has relevant medical diagnostic potential. MALDI-MS/IMS detection generates molecular signatures obtained from specific cell types within tissue sections. Herein discussed is a perspective on the use of MALDI-MS/IMS and bioinformatics technologies for detection of molecular-biometric patterns and identification of differentiating proteins. I also discuss a perspective on the global challenge of transferring technologies to clinical laboratories dealing with IBD issues. The significance of serologic-immunometric advances is also discussed. PMID:25429322
Dynamic Instabilities in Assemblies of Molecular Motors with Finite Stiffness
NASA Astrophysics Data System (ADS)
Guérin, T.; Prost, J.; Joanny, J.-F.
2010-06-01
We propose a two-state “soft-motor” model for the collective behavior of molecular motors which takes into account both the internal motor stiffness and the periodic interaction with the filament. As in the Prandtl-Tomlinson model of tribology, the important parameter of the model is the pinning parameter, which compares the stiffness of the motors to the stiffness of the potential. The model predicts dynamic instabilities in two disconnected regions of parameter space. These parameter ranges correspond to two existing theories of motor assemblies, the rigid two-state model and the crossbridge model. The model also predicts a discontinuity of the slope of the force-velocity relation at small velocities.
Molecular Dynamics Simulations of Carbon Nanotubes in Water
NASA Technical Reports Server (NTRS)
Walther, J. H.; Jaffe, R.; Halicioglu, T.; Koumoutsakos, P.
2000-01-01
We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.
Molecular dynamics study of heat conduction in silicon nanowires
NASA Astrophysics Data System (ADS)
Volz, Sebastian; Chen, Gang
1998-03-01
With the advancement of nanofabrication technologies, nanowires may be produced for both fundamental studies and practical applications. While many former works have been carried out to characterize the electronic and optical properties of nanowires, little attention has been paid to the heat conduction mechanisms occurring in these structures. However, a fundamental understanding of heat conduction in these nanodevices is important for a number of technological areas such as electronics and thermoelectrics. In this works, we performed numerical studies based on molecular dynamics technique to simulate heat conduction in silicon nanowires lying in the vacuum. The device cells are arranged according to a diamond single crystal structure and interatomic forces are derived from the Stillinger-Weber potential currently assumed in solid silicon. By computing the time dependent heat flux and temperature field, the effective thermal conductivity of the wire was derived. The dependence of thermal conductivity on transverse dimensions and temperature is also probed.
Nonequilibrium molecular dynamics of liquid sulfur in Couette flow
NASA Astrophysics Data System (ADS)
Rustad, James R.; Yuen, David A.; Spera, Frank J.
1989-09-01
Previous work in nonequilibrium molecular dynamics (NEMD) has been restricted to systems subject only to pair interactions. We use methods of homogenous NEMD to investigate the nature of liquid sulfur under extreme shear using the potential model developed by Stillinger and Weber which involves explicitly three-body interaction. Simulations with up to 2048 particles have been carried out at a temperature of 1583 K and a density of 1.805 g cm-3 for shear rates between 0.005 and 1.75 in reduced units. We find that the fluid separates in sheets alternating from high to low density in planes perpendicular to the velocity gradient. No evidence is seen for the transition to the ``string'' phase as exhibited by two-body systems. The molecules show a tendency to align in the direction of shear. Data are presented describing the magnitude of this effect.
Molecular dynamics simulation of low energy displacement cascades in Cu
NASA Astrophysics Data System (ADS)
King, Wayne E.; Benedek, R.
1983-07-01
Molecular dynamics computer simulations have been performed to study properties of low-energy (< 500 eV) displacement cascades in Cu. Various aspects of the time development of cascades are considered including instantaneous number of Frenkel pairs, partitioning of kinetic and potential energies, distribution of atom kinetic energies, cascade expansion rate, and Frenkel pair distributions. The anisotropy of the threshold energy for Frenkel-pair production is interpreted in terms of "branching". Replacement sequences and the damage function are discussed based on analysis of events corresponding to 18 recoil directions. The damage function exhibits a plateau at v ~ 0.5 Frenkel pairs extending from 25-150 eV; at higher recoil energies the onset of multiple defect production is much slower than predicted by the modified Kinchin-Pease model.
Large nonadiabatic quantum molecular dynamics simulations on parallel computers
NASA Astrophysics Data System (ADS)
Shimojo, Fuyuki; Ohmura, Satoshi; Mou, Weiwei; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya
2013-01-01
We have implemented a quantum molecular dynamics simulation incorporating nonadiabatic electronic transitions on massively parallel computers to study photoexcitation dynamics of electrons and ions. The nonadiabatic quantum molecular dynamics (NAQMD) simulation is based on Casida's linear response time-dependent density functional theory to describe electronic excited states and Tully's fewest-switches surface hopping approach to describe nonadiabatic electron-ion dynamics. To enable large NAQMD simulations, a series of techniques are employed for efficiently calculating long-range exact exchange correction and excited-state forces. The simulation program is parallelized using hybrid spatial and band decomposition, and is tested for various materials.
Bohm's Quantum Potential and the Visualization of Molecular Structure
NASA Technical Reports Server (NTRS)
Levit, Creon; Chancellor, Marisa K. (Technical Monitor)
1997-01-01
David Bohm's ontological interpretation of quantum theory can shed light on otherwise counter-intuitive quantum mechanical phenomena including chemical bonding. In the field of quantum chemistry, Richard Bader has shown that the topology of the Laplacian of the electronic charge density characterizes many features of molecular structure and reactivity. Visual and computational examination suggests that the Laplacian of Bader and the quantum potential of Bohm are morphologically equivalent. It appears that Bohmian mechanics and the quantum potential can make chemistry as clear as they makes physics.
Massive thermostatting in isothermal density functional molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Windiks, René; Delley, Bernard
2003-08-01
This paper demonstrates the excellent temperature control and rapid equipartioning of the kinetic energy of the massive generalized Gaussian moment thermostat (MGGMT, one thermostat is coupled to each degree of freedom) in isothermal density functional molecular dynamics (MD) simulations on the Born-Oppenheimer potential energy surface. The MGGMT is implemented in the DMoL3 approach and, as far as we know, it is the first time in literature that the MGGMT is combined with density functional methods. The performance of the MGGMT approach is illustrated with MD simulations of the iron porphyrin-imidazole-carbon monoxide [FeP(Im)(CO)] complex and compared with constant energy MD simulations on the same system. Both MD approaches lead to similar average structures of the FeP(Im)(CO) complex. The examination of the frequency distribution functions reveals that the structural dynamics are not seriously affected by the dynamics of the parameters introduced by the MGGMT. The equipartitioning rates in the MGGMT simulations are significantly faster than in the constant energy simulation. We recommend the MGGMT approach as an very efficient equilibration technique in MD simulations and it emerges as a useful technique for, e.g., simulated annealing and nonequilibrium MD simulations.
Molecular polarization potential maps of the nucleic acid bases
Alkorta, I. [Instituto de Quimica Medica, Madrid (Spain)] [Instituto de Quimica Medica, Madrid (Spain); Perez, J.J. [ETS d`Enginyers Industrials, Barcelona (Spain)] [ETS d`Enginyers Industrials, Barcelona (Spain)
1996-01-05
Ab initio calculations at the SCF level were carried out to compute the polarization potential map NM of the nucleic acid bases: cytosine, thymine, uracil, adedine, and guanine. For this purpose, the Dunning`s 9s5p basis set contracted to a split-valence, was selected to perform the calculations. The molecular polarization potential (MPP) at each point was evaluated by the difference between the interaction energy of the molecule with a unit point charge and the molecular electrostatic potential (MEP) at that point. MEPS and MPPS for the different molecules were computed with a density of 5 points/{Angstrom}{sup 2} on the van der Waals surface of each molecule, defined using the van der Waals radii. Due to the symmetry of the molecules, only half the points were computed. The total number of points calculated was 558 for cytosine, 621 for thymine, 526 for uracil, 666 for adenine, and 699 for guanine. The results of these calculations are analyzed in terms of their implications on the molecular interactions between pairs of nucleic acid bases. 23 refs., 5 figs., 1 tab.
Molecular Dynamics Simulation of Homogeneous Crystal Nucleation in Polyethylene
Yi, Peng
Using a realistic united-atom force field, molecular dynamics simulations were performed to study homogeneous nucleation of the crystal phase at about 30% supercooling from the melts of n-pentacontahectane (C150) and a ...
Can Dynamic Contact Angle Be Measured Using Molecular Modeling?
Malani, Ateeque A. A. G.
A method is presented for determining the dynamic contact angle at the three-phase contact between a solid, a liquid, and a vapor under an applied force, using molecular simulation. The method is demonstrated using a ...
RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics
Suleimanov, Yu.V.
We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the ...
CHARACTERIZING COUPLED CHARGE TRANSPORT WITH MULTISCALE MOLECULAR DYNAMICS
Swanson, Jessica
2011-08-31
This is the final progress report for Award DE-SC0004920, entitled 'Characterizing coupled charge transport with multi scale molecular dynamics'. The technical abstract will be provided in the uploaded report.
Molecular Dynamics Simulations of Heat Transfer In Nanoscale Liquid Films
Kim, Bo Hung
2010-07-14
Molecular Dynamics (MD) simulations of nano-scale flows typically utilize fixed lattice crystal interactions between the fluid and stationary wall molecules. This approach cannot properly model thermal interactions at the ...
Molecular Dynamics Simulations of Heat Transfer In Nanoscale Liquid Films
Kim, Bo Hung
2010-07-14
Molecular Dynamics (MD) simulations of nano-scale flows typically utilize fixed lattice crystal interactions between the fluid and stationary wall molecules. This approach cannot properly model thermal interactions at the wall-fluid interface...
Conformational dynamics of the molecular chaperone Hsp90.
Krukenberg, Kristin A; Street, Timothy O; Lavery, Laura A; Agard, David A
2011-05-01
The ubiquitous molecular chaperone Hsp90 makes up 1-2% of cytosolic proteins and is required for viability in eukaryotes. Hsp90 affects the folding and activation of a wide variety of substrate proteins including many involved in signaling and regulatory processes. Some of these substrates are implicated in cancer and other diseases, making Hsp90 an attractive drug target. Structural analyses have shown that Hsp90 is a highly dynamic and flexible molecule that can adopt a wide variety of structurally distinct states. One driving force for these rearrangements is the intrinsic ATPase activity of Hsp90, as seen with other chaperones. However, unlike other chaperones, studies have shown that the ATPase cycle of Hsp90 is not conformationally deterministic. That is, rather than dictating the conformational state, ATP binding and hydrolysis only shift the equilibria between a pre-existing set of conformational states. For bacterial, yeast and human Hsp90, there is a conserved three-state (apo-ATP-ADP) conformational cycle; however; the equilibria between states are species specific. In eukaryotes, cytosolic co-chaperones regulate the in vivo dynamic behavior of Hsp90 by shifting conformational equilibria and affecting the kinetics of structural changes and ATP hydrolysis. In this review, we discuss the structural and biochemical studies leading to our current understanding of the conformational dynamics of Hsp90, as well as the roles that nucleotide, co-chaperones, post-translational modification and substrates play. This view of Hsp90's conformational dynamics was enabled by the use of multiple complementary structural methods including, crystallography, small-angle X-ray scattering (SAXS), electron microscopy, Förster resonance energy transfer (FRET) and NMR. Finally, we discuss the effects of Hsp90 inhibitors on conformation and the potential for developing small molecules that inhibit Hsp90 by disrupting the conformational dynamics. PMID:21414251
Performance Analysis on Molecular Dynamics Simulation of Protein Using GROMACS
A. D. Astuti; A. B. Mutiara
2009-01-01
Development of computer technology in chemistry, bring many application of\\u000achemistry. Not only the application to visualize the structure of molecule but\\u000aalso to molecular dynamics simulation. One of them is Gromacs. Gromacs is an\\u000aexample of molecular dynamics application developed by Groningen University.\\u000aThis application is a non-commercial and able to work in the operating system\\u000aLinux. The main
Fast Parallel Algorithms for Short-Range Molecular Dynamics
Steve Plimpton
1995-01-01
Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors
Modeling Chemical Reactions with First-Principle Molecular Dynamics
Artur Michalak; Tom Ziegler
Density functional theory (DFT)-based molecular dynamics (MD) has established itself as a valuable and powerful tool in studies\\u000a of chemical reactions. Thanks to the rapid increase in power of modern computers, ab initio MD has nowadays become practical. Within the Car-Parinello approach, first-principle MD is already quite popular methodology\\u000a in molecular modeling. MD reveals the dynamical effects at finite temperatures
Special issue on ultrafast electron and molecular dynamics
NASA Astrophysics Data System (ADS)
Hishikawa, Akiyoshi; Martin, Fernando; Vrakking, Marc
2013-07-01
Your invitation to submit. Journal of Physics. B: Atomic Molecular and Optical Physics (JPhysB) is delighted to announce a forthcoming special issue on ultrafast electron and molecular dynamics to appear in 2014, and invites you to submit a paper. Within the last decade, a number of novel approaches have emerged, both experimental and theoretical, that allow the investigation of (time-resolved) molecular dynamics in novel ways not anticipated before. Experimentally, the introduction of novel light sources such as high-harmonic generation and XUV/x-ray free electron lasers, and the emergence of novel detection strategies, such as time-resolved electron/x-ray diffraction and the fully coincident detection of electrons and fragment ions in reaction microscopes, has significantly expanded the arsenal of available techniques, and has taken studies of molecular dynamics into new domains of spectroscopic, spatial and temporal resolution, the latter including first explorations into the attosecond domain. Along the way, particular types of molecular dynamics, such as dynamics around conical intersections, have gained an increased prominence, sparked by an emerging realization about the essential role that this dynamics plays in relaxation pathways in important bio-molecular systems. The progress on the theoretical side has been no less impressive. Novel generations of supercomputers and a series of novel computational strategies have allowed nearly exact calculations in small molecules, as well as highly successful approximate calculations in large, polyatomic molecules. Frequent and intensive collaborations involving both theory and experiment have been essential for the progress that has been accomplished. The special issue 'Ultrafast electron and molecular dynamics' seeks to provide an overview of some of the most important developments in the field, while at the same time indicating how studies of (time-resolved) molecular dynamics are likely to evolve in the coming years. You are invited to submit your article by 1 December 2013.
Heat transport in epoxy networks: A molecular dynamics study
Vikas Varshney; Soumya S. Patnaik; Ajit K. Roy; Barry L. Farmer
2009-01-01
In this article, thermal behavior of an epoxy based thermoset polymer has been discussed using atomistic molecular dynamics simulations. The simulations were performed on crosslinked network of EPON-862 and curing agent-W (DETDA) using consistent valence force field (CVFF). Thermal conductivity was calculated using both equilibrium as well as non-equilibrium molecular dynamics approaches and the results were found to be in
Modeling shockwave deformation via molecular dynamics
Holian, B.L.
1987-01-01
Molecular dynamics (MD), where the equations of motion of up to thousands of interacting atoms are solved on the computer, has proven to be a powerful tool for investigating a wide variety of nonequilibrium processes from the atomistic viewpoint. Simulations of shock waves in three-dimensional (3D) solids and fluids have shown conclusively that shear-stress relaxation is achieved through atomic rearrangement. In the case of fluids, the transverse motion is viscous, and the constitutive model of Navier-Stokes hydrodynamics has been shown to be accurate - even on the time and distance scales of MD experiments. For strong shocks in solids, the plastic flow that leads to shear-stress relaxation in MD is highly localized near the shock front, involving a slippage along close-packed planes. For shocks of intermediate strength, MD calculations exhibit an elastic precursor running out in front of the steady plastic wave, where slippage similar in character to that in the very strong shocks leads to shear-stress relaxation. An interesting correlation between the maximum shear stress and the Hugoniot pressure jump is observed for both 3D and fluid shockwave calculations, which may have some utility in modeling applications. At low shock strengths, the MD simulations show only elastic compression, with no permanent transverse atomic strains. The result for perfect 3D crystals is also seen in calculations for 1D chains. It is speculated that, if it were practical, a very large MD system containing dislocations could be expected to exhibit more realistic plastic flow for weak shock waves, too.
Demontis, Pierfranco; Gulín-González, Jorge; Masia, Marco; Sant, Marco; Suffritti, Giuseppe B
2015-06-28
In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130-350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between "fragile" (at higher temperatures) and "strong" (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between "fragile" (at lower temperatures) and "strong" (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T(?) ? 315 ± 5 K, was spotted at T(?) ? 283 K and T(?) ? 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible mechanisms of the two crossovers at molecular level are discussed. PMID:26133441
Molecular dynamics simulations of yttrium-stabilized zirconia
Xiaoyun Li; B. Hafskjold
1995-01-01
The electric conductivity of yttrium-stabilized zirconia exhibits a maximum as a function of dopant (Y3+) cation concentration in isothermal and isobaric conditions. In order to improve the conductivity of this important solid electrolyte, it is essential to understand the ion transport mechanisms at the molecular level. This was investigated by the molecular dynamics simulations method in the present study. The
Elucidation of molecular dynamics of invasive species of rice
Technology Transfer Automated Retrieval System (TEKTRAN)
Cultivated rice fields are aggressively invaded by weedy rice in the U.S. and worldwide. Weedy rice results in loss of yield and seed contamination. The molecular dynamics of the evolutionary adaptive traits of weedy rice are not fully understood. To understand the molecular basis and identify the i...
Point-centered domain decomposition for parallel molecular dynamics simulation
R. Koradi; M. Billeter; P. Güntert
2000-01-01
A new algorithm for molecular dynamics simulations of biological macromolecules on parallel computers, point-centered domain decomposition, is introduced. The molecular system is divided into clusters that are assigned to individual processors. Each cluster is characterized by a center point and comprises all atoms that are closer to its center point than to the center point of any other cluster. The
Nanoindentation response of nickel surface using molecular dynamics simulation
Wen-Yang Chang; Te-Hua Fang; Shiang-Jiun Lin; Jian-Jin Huang
2010-01-01
The mechanisms of dislocation nucleation on a nickel (Ni) (001) surface under nanoindentation behaviours are investigated using molecular dynamics simulation. The characteristic mechanisms include the molecular models of a thermal layer (TL) and thermal with a free layer (TFL), multi-step load\\/unload cycles, tilt angles and shapes of the indenter, and slip vectors. The model of a TL has higher reaction
Tomotsugu Shimokawa; Toshiyasu Kinari; Sukenori Shintaku; Akihiro Nakatani; Hiroshi Kitagawa
2005-01-01
The influence of defects in nanograins, e.g. stacking faults and twinnings, on mechanical properties of nanocrystalline materials is studied by molecular dynamics simulations. Two types of many-body interatomic potential based on aluminium are adopted to investigate the influence of stacking fault energy on the deformation mechanism of nanocrystalline metals: one accurately reproduces the energy value of stacking faults for aluminium;
Molecular Dynamics Modeling of Thermal Properties of Aluminum Near Melting Line
A. V. Karavaev; V. V. Dremov; F. A. Sapozhnikov
2006-01-01
In this work we present results of calculations of thermal properties of solid and liquid phases of aluminum at different densities and temperatures using classical molecular dynamics with EAM potential function. Dependencies of heat capacity CV on temperature and density have been analyzed. It was shown that when temperature increases, heat capacity CV behavior deviates from that by Dulong-Petit law.
Gramicidin A Channel as a Test Ground for Molecular Dynamics Force Fields
Toby W. Allen; Turgut Ba?tu?; Serdar Kuyucak; Shin-Ho Chung
2003-01-01
We use the well-known structural and functional properties of the gramicidin A channel to test the appropriateness of force fields commonly used in molecular dynamics (MD) simulations of ion channels. For this purpose, the high-resolution structure of the gramicidin A dimer is embedded in a dimyristoylphosphatidylcholine bilayer, and the potential of mean force of a K+ ion is calculated along
Multiple Conformational States of Proteins: A Molecular Dynamics Analysis of Myoglobin
R. Elber; M. Karplus
1987-01-01
A molecular dynamics simulation of myoglobin provides the first direct demonstration that the potential energy surface of a protein is characterized by a large number of thermally accessible minima in the neighborhood of the native structure (for example, approximately 2000 minima were sampled in a 300-picosecond trajectory). This is expected to have important consequences for the interpretation of the activity
Emilio Gallicchio; Ronald M. Levy
2004-01-01
We have developed an implicit solvent effective potential (AGBNP) that is suitable for molecular dynamics simulations and high-resolution modeling. It is based on a novel implementation of the pairwise descreening Gener- alized Born model for the electrostatic component and a new nonpolar hydration free energy estimator. The nonpolar term consists of an estimator for the solute-solvent van der Waals dispersion
Surface free energy of platinum nanoparticles at zero pressure: A molecular dynamic study
Hamed Akbarzadeh; Hadi Abroshan; Gholam Abbas Parsafar
2010-01-01
Metallic nanoparticles are interesting because of their use in catalysis and sensors. The surface energy of the FCC platinum nanoparticles are investigated via molecular dynamics simulation using Quantum Sutton–Chen (QSC) potential. We have calculated the Gibbs free energy for the FCC platinum bulk and also for its nanoparticle. All calculations have been carried out at zero pressure. We have used
Jonathan N. Sachs; Hirsh Nanda; Horia I. Petrache; Thomas B. Woolfz
2004-01-01
The association between monovalent salts and neutral lipid bilayers is known to influence global bilayer structural properties such as headgroup conformational fluctuations and the dipole potential. The local influence of the ions, however, has been unknown due to limited structural resolution of experimental methods. Molecular dynamics simulations are used here to elucidate local structural rearrangements upon association of a series
Molecular Dynamics Study of Extraordinary Elastic Deformation Found in Gold Atomic Cluster
Ken-Ichi Saitoh; Yoshiaki Yonekawa
2010-01-01
Inelastic deformation of gold (Au) atomic cluster is investigated by using molecular dynamics (MD) simulations. We performed compression and unloading tests in which silicon (Si) plates approach each other and push single Au cluster of 4 nm diameter in between. Possibility of super-elastic (hyper-elastic) behavior is first discussed in the present study. The potential function of embedded atom method is
Molecular dynamics study on thermo-mechanical properties of bismuth telluride bulk
Yu Tong; Fajun Yi; Lisheng Liu; Pengcheng Zhai; Qingjie Zhang
2010-01-01
Molecular dynamics method is explored to investigate the effects of temperature on the mechanical and thermal properties of single crystal bismuth telluride from 0K to 600K, with potentials developed by Huang et al. The structural properties, lattice constants, linear thermal expansion coefficients, independent elastic constants were all calculated. The lattice constants were estimated by the size of box from the
Molecular dynamics study on size-dependent elastic properties of silicon nanocantilevers
S. H. Park; J. S. Kim; J. H. Park; J. S. Lee; Y. K. Choi; O. M. Kwon
2005-01-01
The motion of nanoscale structures made of pure crystalline silicon with different lattice conditions is simulated in vacuum by applying the molecular dynamics technique with the use of the Tersoff potential. Elastic moduli for various sized specimens are obtained by simulating flexural and longitudinal vibrations as well as simple tension tests. Compared with the bulk silicon, the elastic modulus decreases
B-DNA Under Stress: Over and Untwisting of DNA during Molecular Dynamics Simulations
Srinivasaraghavan Kannan; Kai Kohlhoff; Martin W. Zacharias
2006-01-01
The twist flexibility of DNA is central to its many biological functions. Explicit solvent molecular dynamics simulations in combination with an umbrella sampling restraining potential have been employed to study induced twist deformations in DNA. Simulations allowed us to extract free energy profiles for twist deformations and were performed on six DNA dodecamer duplexes to cover all 10 possible DNA
J. Phys. Chem. 1903, 87, 4277-4201 4277 Molecular Dynamics Study of Ice Crystallite Melting
Stillinger, Frank
J. Phys. Chem. 1903, 87, 4277-4201 4277 Molecular Dynamics Study of Ice Crystallite Melting Thomas been used to examine the melting process for a 250-moleculeice Ih crystallite. The ST2 potential moves inward eventuallyto consumethe entire hexagonal ice crystallite with which the simulation began
Dynamic transition in an atomic glass former: a molecular dynamics evidence
Estelle Pitard; Vivien Lecomte; Frédéric Van Wijland
2011-11-28
We find that a Lennard-Jones mixture displays a dynamic phase transition between an active regime and an inactive one. By means of molecular dynamics simulations and of a finite-size study, we show that the space time dynamics in the supercooled regime coincides with a dynamic first order transition point.
Molecular dynamics simulations of the structural, elastic and thermodynamic properties of cubic BBi
K. Amara; B. Soudini; D. Rached; A. Boudali
2008-01-01
We present the molecular dynamics simulations results of the structural and dynamical properties of the zinc-blende BBi over a wide range of temperature (400–1500K). Our simulations were carried out using the three-body Tersoff potential, which accurately reproduces the lattice and elastic constants of the BBi. A good agreement was found between our calculated results and the available theoretical data of
NASA Astrophysics Data System (ADS)
Curchod, Basile F. E.; Penfold, Thomas J.; Rothlisberger, Ursula; Tavernelli, Ivano
2013-09-01
We review our recent work on ab initio nonadiabatic molecular dynamics, based on linear-response timedependent density functional theory for the calculation of the nuclear forces, potential energy surfaces, and nonadiabatic couplings. Furthermore, we describe how nuclear quantum dynamics beyond the Born-Oppenheimer approximation can be performed using quantum trajectories. Finally, the coupling and control of an external electromagnetic field with mixed quantum/classical trajectory surface hopping is discussed.
The use of molecular dynamics for the thermodynamic properties of simple and transition metals
Straub, G.K.
1987-04-01
The technique of computer simulation of the molecular dynamics in metallic systems to calculate thermodynamic properties is discussed. The nature of a metal as determined by its electronic structure is used to determine the total adiabatic potential. The effective screened ion-ion interaction can then be used in a molecular dynamics simulation. The method for the construction of a molecular dynamics ensemble, its relation to the canonical ensemble, and the definition of thermodynamic functions from the Helmholtz free energy is given. The method for the analysis of the molecular dynamics results from quasiharmonic lattice dynamics and the decomposition in terms of harmonic and anharmonic contributions is given for solids. For fluid phase metals, procedures for calculating the thermodynamics and determining the constant of entropy are presented. The solid-fluid phase boundary as a function of pressure and temperature is determined using the results of molecular dynamics. Throughout, examples and results for metallic sodium are used. The treatment of the transition metal electronic d-states in terms of an effective pair-wise interaction is also discussed and the phonon dispersion curves of Al, Ni, and Cu are calculated.
In situ structure and dynamics of DNA origami determined through molecular dynamics simulations
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
Computations of Standard Binding Free Energies with Molecular Dynamics Simulations
Deng, Yuqing; Roux, Benoît
2013-01-01
An increasing number of studies have reported computations of the absolute binding free energy of small ligands to proteins using molecular dynamics (MD) simulations with results that are in good agreement with experiments. This encouraging progress suggests that physics-based approaches hold the promise of making important contributions to the process of drug discovery and optimization in the near future. Two types of approaches are principally used to compute binding free energies with MD simulations. The most widely known are based on alchemical free energy methods, in which the interaction of the ligand with its surrounding are progressively switched off. An alternative method is to use a potential of mean force (PMF), in which the ligand is physically separated from the protein receptor. For both of these computational approaches, restraining potentials affecting the translational, rotational and conformational freedom of the ligand and protein may be activated and released during the simulations to aid convergence and improve the sampling. Such restraining potentials add bias to the simulations, but their effects can be rigorously removed to yield a binding free energy that is properly unbiased with respect to the standard state. A review of recent results is presented. Examples of computations with T4-lysozyme mutants, FKBP12, SH2 domain, and cytochrome P450 are discussed and compared. Differences in computational methods are discussed and remaining difficulties and challenges are highlighted. PMID:19146384
Westhof, Eric
227 The growing amount of high quality molecular dynamics simulations generated using the latest molecular dynamics MMD multiple molecular dynamics N number of particles constituting the system PME particle-mesh-Ewald rmsd root mean square deviation Introduction Since the first molecular dynamics (MD
Chu, Shih-I; Yao, Guanhua
1993-07-01
We extend our previous study [Chem. Phys. Lett. 197, 413 (1992)] of the molecular stabilization in intense laser fields by considering the dynamical behavior of the H+2 molecules in intense femtosecond short laser pulses ...
Molecular Dynamics in Self-Assembled Monolayers
Jason Bochinski; Derrick Stevens; Mary Scott; Laura Guy; Casey Dedeugd; Laura Clarke
2007-01-01
Silane self-assembled monolayers (SAMs) are an important tool for both scientific research and technological applications. Despite their widespread use, few experimental investigations have addressed molecular motion within these films, which offer a unique and useful physical system for fundamental scientific studies, such as observing dipolar and other glass transitions in two-dimensions. In addition, relaxations such as ``rotator'' phases where molecular
The Art of Molecular Dynamics Simulation (by D. C. Rapaport)
NASA Astrophysics Data System (ADS)
Molner, Stephen P.
1999-02-01
Cambridge University Press: New York, 1996. 400 pp. ISBN 0 521 44561 2. $74.95. This book describes the extremely powerful techniques of molecular dynamics simulation. The techniques involve solving the classical many-body problems in contexts relevant to the study of matter at the atomic level. The method allows the prediction of static and dynamics properties of substances directly from the underlying interactions between molecules. This is, of course, a very broad subject and the author has adopted a dual approach in that the text is partly tutorial and also contains a large number of computer programs for practical use. Rapaport has adopted the attitude of trying the simplest method first. Atoms are modeled as point particles interacting through point potentials. Molecules are represented by atoms with orientation dependent forces, or as extended structures each containing several interaction sites. The molecules may be rigid, flexible, or somewhere in between, and if there are internal degrees of freedom there will be internal forces as well. The intent of the book is not to discuss the design of molecular models, but rather to make use of existing models, and from a pedagogical viewpoint the simpler the model the better. The aim of the book is to demonstrate the general methodology of molecular dynamics simulation by example, not to review the large body of literature covering the many different kinds of models developed for specific applications. The text is partly tutorial, but also contains a large number of computer programs for practical use. This volume will serve as an introduction to the subject for beginners and as a reference manual for the more experienced practitioner. The material covers a wide range of practical methods and real applications and is organized as a series of case studies. The typical case study includes a summary of the theoretical background used for the formulation of the computational approach. That is described by either a complete program listing or a series of modifications or additions to a program from an earlier case study. The initial conditions of the model, organization of the input and output, accuracy, convergence, and efficiency are also addressed for each case and, of course, the results of the computation are given and discussed. The book begins with the simplest case of basic molecular dynamics, a sift-disk fluid. The development is discussed in considerable depth to set the tone of the work. Later chapters extend the basic model in various directions, deal with various types of measurements, improve the computational methods, and introduce new models for more complex problems. These chapters also discuss the methodology for simulating monatomic systems and focus on measuring the thermodynamic and structural properties of systems in equilibrium. Consideration is given to the dynamical properties of equilibrium systems, including transport coefficients and the correlation functions that characterize space- and time-dependent properties. Chapters are devoted to the study of systems under constant temperature and pressure and the dynamics of rigid systems. It is difficult to cover all aspects of such a broad topic as the subject of this book; and the author has not attempted an exhaustive or encyclopedic coverage, but has produced an excellent introduction to the subject. The publisher has made the implementation of the numerous programs essentially painless by making them available via browser and the World Wide Web. The easy availability of the software, written in C, was welcomed by this old Fortran programmer. It is to be hoped that this service is representative of a trend in technical publishing. Overall this work is a pleasure to read and study and would be a valuable addition to the library of both the beginner and the experienced practitioner of the art.
Self Diffusion in Nano Filled Polymer Melts: a Molecular Dynamics Simulation Study
NASA Astrophysics Data System (ADS)
Desai, Tapan; Keblinski, Pawel
2003-03-01
SELF DIFFUSION IN NANO FILLED POLYMER MELTS: A MOLECULAR DYNAMICS SIMULATION STUDY* T. G. Desai,P. Keblinski, Material Science and Engineering Department, Rensselaer Polytechnic Institute, Troy, NY. Using molecular dynamics simulations, we studied the dynamics of the polymeric systems containing immobile and analytically smooth spherical nanoparticles. Each chain consisted of N monomers connected by an anharmonic springs described by the finite extendible nonlinear elastic, FENE potential. The system comprises of 3nanoparticles and the rest by freely rotating but not overlapping chains. The longest chain studied has a Radius of gyration equal to particle size radius and comparable to inter-particle distance. There is no effect on the structural characteristics such as Radius of gyration or end to end distance due to the nanoparticles. Diffusion of polymeric chains is not affected by the presence of either attractive or repulsive nanoparticles. In all cases Rouse dynamics is observed for short chains with a crossover to reptation dynamics for longer chains.
Nonlocalized cluster dynamics and nuclear molecular structure
Bo Zhou; Yasuro Funaki; Hisashi Horiuchi; Zhongzhou Ren; Gerd Röpke; Peter Schuck; Akihiro Tohsaki; Chang Xu; Taiichi Yamada
2013-12-04
A container picture is proposed for understanding cluster dynamics where the clusters make nonlocalized motion occupying the lowest orbit of the cluster mean-field potential characterized by the size parameter $``B"$ in the THSR (Tohsaki-Horiuchi-Schuck-R\\"{o}pke) wave function. The nonlocalized cluster aspects of the inversion-doublet bands in $^{20}$Ne which have been considered as a typical manifestation of localized clustering are discussed. So far unexplained puzzling features of the THSR wave function, namely that after angular-momentum projection for two cluster systems the prolate THSR wave function is almost 100$\\%$ equivalent to an oblate THSR wave function is clarified. It is shown that the true intrinsic two-cluster THSR configuration is nonetheless prolate. The proposal of the container picture is based on the fact that typical cluster systems, 2$\\alpha$, 3$\\alpha$, and $\\alpha$+$^{16}$O, are all well described by a single THSR wave function. It will be shown for the case of linear-chain states with two and three $\\alpha$-clusters as well as for the $\\alpha$+$^{16}$O system that localization is entirely of kinematical origin, that is, due to the inter-cluster Pauli repulsion. It is concluded that this feature is general for nuclear cluster states.
Molecular dynamics of the water liquid-vapor interface
NASA Technical Reports Server (NTRS)
Wilson, M. A.; Pohorille, A.; Pratt, L. R.; MacElroy, R. D. (Principal Investigator)
1987-01-01
The results of molecular dynamics calculations on the equilibrium interface between liquid water and its vapor at 325 K are presented. For the TIP4P model of water intermolecular pair potentials, the average surface dipole density points from the vapor to the liquid. The most common orientations of water molecules have the C2 nu molecular axis roughly parallel to the interface. The distributions are quite broad and therefore compatible with the intermolecular correlations characteristic of bulk liquid water. All near-neighbor pairs in the outermost interfacial layers are hydrogen bonded according to the common definition adopted here. The orientational preferences of water molecules near a free surface differ from those near rigidly planar walls which can be interpreted in terms of patterns found in hexagonal ice 1. The mean electric field in the interfacial region is parallel to the mean polarization which indicates that attention cannot be limited to dipolar charge distributions in macroscopic descriptions of the electrical properties of this interface. The value of the surface tension obtained is 132 +/- 46 dyn/cm, significantly different from the value for experimental water of 68 dyn/cm at 325 K.
Unfixed cryosections of striated muscle to study dynamic molecular events.
Ménétret, J F; Craig, R
1994-01-01
The structures of the actin and myosin filaments of striated muscle have been studied extensively in the past by sectioning of fixed specimens. However, chemical fixation alters molecular details and prevents biochemically induced structural changes. To overcome these problems, we investigate here the potential of cryosectioning unfixed muscle. In cryosections of relaxed, unfixed specimens, individual myosin filaments displayed the characteristic helical organization of detached cross-bridges, but the filament lattice had disintegrated. To preserve both the filament lattice and the molecular structure of the filaments, we decided to section unfixed rigor muscle, stabilized by actomyosin cross-bridges. The best sections showed periodic, angled cross-bridges attached to actin and their Fourier transforms displayed layer lines similar to those in x-ray diffraction patterns of rigor muscle. To preserve relaxed filaments in their original lattice, unfixed sections of rigor muscle were picked up on a grid and relaxed before negative staining. The myosin and actin filaments showed the characteristic helical arrangements of detached cross-bridges and actin subunits, and Fourier transforms were similar to x-ray patterns of relaxed muscle. We conclude that the rigor structure of muscle and the ability of the filament lattice to undergo the rigor-relaxed transformation can be preserved in unfixed cryosections. In the future, it should be possible to carry out dynamic studies of active sacromeres by cryo-electron microscopy. Images FIGURE 2 FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 6 FIGURE 7 FIGURE 8 PMID:7819493
Comparing Molecular Dynamics Models for Electrolyte Solutions in Nanochannels
NASA Astrophysics Data System (ADS)
Lee, Jonathan; Templeton, Jeremy
2012-11-01
In electrolyte modelling, it is common to simplify the solvent using the three-component model (3CM), i.e. a single-site, chargeless Lennard-Jones atom as the solvent component. To account for the dielectric nature of typical solvents, a relative permittivity value is applied to all Coulombic interactions, thus weakening ion-ion interactions as if each ion is surrounded by a solvation shell. Fluid Density Functional Theory, Monte Carlo simulation, and molecular dynamics (MD) simulation all commonly employ the 3CM to facilitate calculations, but the consequences are not well characterized. We used MD to compare the 3CM electrolyte to a molecular solvent model (MSM) where the solvent is a three-site H2O) molecule. Special care was taken to compare cases with the same thermodynamic state by having a quantifiable reference state, and cases covered a range of applied surface charge in a nanochannel configuration. At a glance, the two models give qualitatively similar density profiles. However, we find that many profile features, physical quantities such as electric field and potential, as well as ionic packing structure near the surface evolve quite differently as the load is varied. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the USDoE's National Nuclear Security Administration under contract DE-AC04-94AL85000.
A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole.
Fonner, John M; Schmidt, Christine E; Ren, Pengyu
2010-10-01
Polypyrrole (PPy) is a biocompatible, electrically conductive polymer that has great potential for battery, sensor, and neural implant applications. Its amorphous structure and insolubility, however, limit the experimental techniques available to study its structure and properties at the atomic level. Previous theoretical studies of PPy in bulk are also scarce. Using ab initio calculations, we have constructed a molecular mechanics force field of chloride-doped PPy (PPyCl) and undoped PPy. This model has been designed to integrate into the OPLS force field, and parameters are available for the Gromacs and TINKER software packages. Molecular dynamics (MD) simulations of bulk PPy and PPyCl have been performed using this force field, and the effects of chain packing and electrostatic scaling on the bulk polymer density have been investigated. The density of flotation of PPyCl films has been measured experimentally. Amorphous X-ray diffraction of PPyCl was obtained and correlated with atomic structures sampled from MD simulations. The force field reported here is foundational for bridging the gap between experimental measurements and theoretical calculations for PPy based materials. PMID:21052521
Zhigilei, Leonid V.
Molecular dynamics simulation study of the ejection of polymer molecules and generation 395 McCormick Road, Charlottesville, Virginia 22904-4745 ABSTRACT Coarse-grained molecular dynamics to the complex morphologies observed in polymer films deposited by MAPLE. The effect of dynamic molecular
NASA Astrophysics Data System (ADS)
Wu, Bin
Neutron scattering and fully atomistic molecular dynamics (MD) are employed to investigate the structural and dynamical properties of polyamidoamine (PAMAM) dendrimers with ethylenediamine (EDA) core under various charge conditions. Regarding to the conformational characteristics, we focus on scrutinizing density profile evolution of PAMAM dendrimers as the molecular charge of dendrimer increases from neutral state to highly charged condition. It should be noted that within the context of small angle neutron scattering (SANS), the dendrimers are composed of hydrocarbon component (dry part) and the penetrating water molecules. Though there have been SANS experiments that studied the charge-dependent structural change of PAMAM dendrimers, their results were limited to the collective behavior of the aforementioned two parts. This study is devoted to deepen the understanding towards the structural responsiveness of intra-molecular polymeric and hydration parts separately through advanced contrast variation SANS data analysis scheme available recently and unravel the governing principles through coupling with MD simulations. Two kinds of acids, namely hydrochloric and sulfuric acids, are utilized to tune the pH condition and hence the molecular charge. As far as the dynamical properties, we target at understanding the underlying mechanism that leads to segmental dynamic enhancement observed from quasielstic neutron scattering (QENS) experiment previously. PAMAM dendrimers have a wealth of potential applications, such as drug delivery agency, energy harvesting medium, and light emitting diodes. More importantly, it is regarded as an ideal system to test many theoretical predictions since dendrimers conjugate both colloid-like globular shape and polymer-like flexible chains. This Ph.D. research addresses two main challenges in studying PAMAM dendrimers. Even though neutron scattering is an ideal tool to study this PAMAM dendrimer solution due to its matching temporal and spatial instrumental scales, understanding experimental results involves extensive and difficult data analysis based on liquid theory and condensed matter physics. Therefore, a model that successfully describes the inter- and intra-dendrimer correlations is crucial in obtaining and delivering reliable information. On the other hand, making meaningful comparisons between molecular dynamics and neutron scattering is a fundamental challenge to link simulations and experiments at the nano-scale. This challenge stems from our approach to utilize MD simulation to explain the underlying mechanism of experimental observation. The SANS measurements were conducted on a series of SANS spectrometers including the Extended Q-Range Small-Angle Neutron Scattering Diffractometer (EQ-SANS) and the General-Purpose Small-Angle Neutron Scattering Diffractometer (GP-SANS) at the Oak Ridge National Laboratory (ORNL), and NG7 Small Angle Neutron Scattering Spectrometer at National Institute of Standards (NIST) and Technology in U.S.A., large dynamic range small-angle diffractometer D22 at Institut Laue-Langevin (ILL) in France, and 40m-SANS Spectrometer at Korea Atomic Energy Research Institute (KAERI) in Korea. On the other hand, the Amber molecular dynamics simulation package is utilized to carry out the computational study. In this dissertation, the following observations have been revealed. The previously developed theoretical model for polyelectrolyte dendrimers are adopted to analyze SANS measurements and superb model fitting quality is found. Coupling with advanced contrast variation small angle neutron scattering (CVSANS) data analysis scheme reported recently, the intra-dendrimer hydration and hydrocarbon components distributions are revealed experimentally. The results indeed indicate that the maximum density is located in the molecular center rather than periphery, which is consistent to previous SANS studies and the back-folding picture of PAMAM dendrimers. According to this picture, at neutral condition, the exterior residues folding back into interior would necessarily
Zhang, Jianwei; He, Xiaodong; Yang, Lin; Wu, Guoqiang; Sha, Jianjun; Hou, Chengyu; Yin, Cunlu; Pan, Acheng; Li, Zhongzhou; Liu, Yubai
2013-01-01
The thermal conductivity of monolayer graphene nanoribbons (GNRs) with different tensile strain is investigated by using a nonequilibrium molecular dynamics method. Significant increasing amplitude of the molecular thermal vibration, molecular potential energy vibration and thermal conductivity vibration of stretching GNRs were detected. Some 20%?30% thermal conductivity decay is found in 9%?15% tensile strain of GNR cases. It is explained by the fact that GNR structural ridges scatter some low-frequency phonons which pass in the direction perpendicular to the direction of GNR stretching which was indicated by a phonon density of state investigation. PMID:23881138
D. Sugny; Stéphane Vranckx; Mamadou Ndong; Nathalie Vaeck; Osman Atabek; Michèle Desouter-Lecomte
2014-12-15
The constraint of time-integrated zero-area on the laser field is a fundamental, both theoretical and experimental requirement in the control of molecular dynamics. By using techniques of local and optimal control theory, we show how to enforce this constraint on two benchmark control problems, namely molecular orientation and photofragmentation. The origin and the physical implications on the dynamics of this zero-area control field are discussed.
A Molecular Dynamics Simulation of C60-C60 Collision
NASA Astrophysics Data System (ADS)
Liu, Lei; Chen, Kaitai; Li, Yufen
1993-12-01
The formation process of C120-complex in C60-C60 collision has been clearly demonstrated by a molecular dynamics simulation. The complex, with a peanut-shell-like structure, is in a quite stable dynamical state. The results are consistent with recent observations.
Polymorphic transitions in single crystals: A new molecular dynamics method
M. Parrinello; A. Rahman
1981-01-01
A new Lagrangian formulation is introduced. It can be used to make molecular dynamics (MD) calculations on systems under the most general, externally applied, conditions of stress. In this formulation the MD cell shape and size can change according to dynamical equations given by this Lagrangian. This new MD technique is well suited to the study of structural transformations in
Protein-Folding Dynamics: Overview of Molecular Simulation Techniques
Harold A. Scheraga; Mey Khalili; Adam Liwo
2007-01-01
Molecular dynamics (MD) is an invaluable tool with which to study protein folding in silico. Although just a few years ago the dynamic behavior of a protein molecule could be simulated only in the neighborhood of the experimental conformation (or protein unfolding could be simulated at high temperature), the advent of distributed computing, new techniques such as replica-exchange MD, new
Molecular dynamics investigations of grain boundary phenomena in cubic zirconia
Craig A. J Fisher; Hideaki Matsubara
1999-01-01
Yttria stabilized zirconia (YSZ) is a fast oxide ion conducting ceramic with the cubic fluorite structure that is used in a number of applications, including solid oxide fuel cells (SOFCs). A molecular dynamics (MD) study has been performed on symmetrical tilt grain boundaries with the ?5 (310)\\/[001] ?=36.9° misorientation to investigate the structure and dynamics of interfaces in this technologically
Molecular dynamics study of silicate glass under shock
Luming Shen
2010-01-01
Molecular dynamics (MD) simulations are conducted to study the dynamic responses of silicate glass shocked at velocities from 1 to 19 km\\/s. The simulated pressure and density of the glass under shock increase as the cooling rate increases, although the effect of the cooling rate on the shock wave velocity is limited. It appears the simulation results match well with
Grzybowski, A; Paluch, M; Grzybowska, K; Haracz, S
2010-10-28
In this communication, we provide a recipe for a consistent relation between dynamic scaling and thermodynamic properties well-grounded by the same intermolecular generalized Lennard-Jones potential, which is derived by using an essentially modified Avramov model within the framework of the "thermodynamic scaling" idea. This relation is experimentally verified very well for supercooled van der Waals liquids, and consequently, it can be a good basis for a proper universal description of molecular dynamics and thermodynamics of viscous systems. PMID:21033768
NASA Astrophysics Data System (ADS)
Grzybowski, A.; Paluch, M.; Grzybowska, K.; Haracz, S.
2010-10-01
In this communication, we provide a recipe for a consistent relation between dynamic scaling and thermodynamic properties well-grounded by the same intermolecular generalized Lennard-Jones potential, which is derived by using an essentially modified Avramov model within the framework of the "thermodynamic scaling" idea. This relation is experimentally verified very well for supercooled van der Waals liquids, and consequently, it can be a good basis for a proper universal description of molecular dynamics and thermodynamics of viscous systems.
Reactive Molecular Dynamics Simulations at the Petascale (Invited)
NASA Astrophysics Data System (ADS)
Nakano, A.
2013-12-01
We are developing a divide-conquer-recombine algorithmic framework into a metascalable (or 'design once, scale on new architectures') parallelization scheme to perform large spatiotemporal-scale reactive molecular dynamics simulations. The scheme has achieved parallel efficiency well over 0.9 on 786,432 IBM BlueGene/Q processors for 8.5 trillion-atom molecular dynamics and 1.9 trillion electronic degrees-of-freedom quantum molecular dynamics in the framework of density functional theory. Simulation results reveal intricate interplay between photoexcitation, mechanics, flow, and chemical reactions at the nanoscale. Specifically, we will discuss atomistic mechanisms of: (1) rapid hydrogen production from water using metallic alloy nanoparticles; (2) molecular control of charge transfer, charge recombination, and singlet fission for efficient solar cells; and (3) mechanically enhanced reaction kinetics in nanobubbles and nanojets.
Analysis of the adsorption of methane in silicalite by a simplified molecular dynamics simulation
Hufton, J.R. (Pennsylvania State Univ., University Park (United States))
1991-10-31
Thermodynamic and transport properties of methane adsorbed in the zeolite silicalite have been calculated from a NVT molecular dynamics algorithm. Methane was modeled as a sphere, with potential parameters determined by comparison of theoretical and experimental Henry's constants. The average potential energy and self-diffusion coefficient of the spherical adsorbate agreed with previous MD results of June et al. obtained with a five-point methane model. Agreement was also obtained with experimental data.
Zhong-Li Liu; Xiu-Lu Zhang; Ling-Cang Cai; Xiang-Rong Chen; Qiang Wu; Fu-Qian Jing
2008-01-01
We performed molecular dynamics simulations with the extended Finnis-Sinclair (EFS) potential to investigate thermal equation of state (EOS), and melting and thermoelastic properties of tantalum. The agreement of the obtained thermal EOS with experiments at ambient conditions is reasonably good. The EFS potential with the two-phase method also reproduced very satisfyingly the high-pressure melting curve, excellently consistent with both the
Tenzin Tashi
2009-01-01
Carbon nanostructures have exhibited fascinating mechanical and electrical properties such as high in-plane elastic modulus and thermal conductivity, which implies promising potential applications in electromechanical devices. Using molecular dynamics simulation technique, this thesis explores intrinsic mechanical properties of two representative carbon nanostructures; single-walled carbon nanotube and graphene monolayer. Nanoresonators based on single-walled carbon nanotubes have a potential application in nanoelectromechanical
Bjørnstad, Ottar Nordal
Role of dynamics in tuning fidelity of RNA-dependent RNA polymerase elucidated by molecular dynamics simulation Ibrahim M. Moustafa Department of Biochemistry and Molecular Biology Eberly College fidelity is not clear but suggested to be linked to dynamics of the enzyme [1]. By using molecular dynamics
Free energy calculations using dual-level Born-Oppenheimer molecular dynamics
Retegan, Marius; Martins-Costa, Marilia; Ruiz-Lopez, Manuel F. [Theoretical Chemistry and Biochemistry Group, SRSMC, CNRS, Nancy-University, BP 70239, 54506 Vandoeuvre-les-Nancy (France)
2010-08-14
We describe an efficient and accurate method to compute free energy changes in complex chemical systems that cannot be described through classical molecular dynamics simulations, examples of which are chemical and photochemical reactions in solution, enzymes, interfaces, etc. It is based on the use of dual-level Born-Oppenheimer molecular dynamics simulations. A low-level quantum mechanical method is employed to calculate the potential of mean force through the umbrella sampling technique. Then, a high-level quantum mechanical method is used to estimate a free energy correction on selected points of the reaction coordinate using perturbation theory. The precision of the results is comparable to that of ab initio molecular dynamics methods such as the Car-Parrinello approach but the computational cost is much lower, roughly by two to three orders of magnitude. The method is illustrated by discussing the association free energy of simple organometallic compounds, although the field of application is very broad.
Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics
Trabuco, Leonardo G.; Villa, Elizabeth; Mitra, Kakoli; Frank, Joachim; Schulten, Klaus
2008-01-01
A novel method to flexibly fit atomic structures into electron microscopy (EM) maps using molecular dynamics simulations is presented. The simulations incorporate the EM data as an external potential added to the molecular dynamics force field, allowing all internal features present in the EM map to be used in the fitting process, while the model remains fully flexible and stereochemically correct. The molecular dynamics flexible fitting (MDFF) method is validated for available crystal structures of protein and RNA in different conformations; measures to assess and monitor the fitting process are introduced. The MDFF method is then used to obtain high-resolution structures of the E. coli ribosome in different functional states imaged by cryo-EM. PMID:18462672
Molecular dynamics simulation of interfacial adhesion
Yarovsky, I.; Chaffee, A.L. [BHP Research, Mulgrave (Australia)
1996-12-31
Chromium salts are often used in the pretreatment stages of steel painting processes in order to improve adhesion at the metal oxide/primer interface. Although well established empirically, the chemical basis for the improved adhesion conferred by chromia is not well understood. A molecular level understanding of this behaviour should provide a foundation for the design of materials offering improved adhesion control. Molecular modelling of adhesion involves simulation and analysis of molecular behaviour at the interface between two interacting phases. The present study concerns behaviour at the boundary between the metal coated steel surface (with or without chromium pretreatment) and an organic primer based on a solid epoxide resin produced from bisphenol A and epichlorohydrin. An epoxy resin oligomer of molecular weight 3750 was used as the model for the primer.
NASA Astrophysics Data System (ADS)
Saiz, Enrique; Tarazona, Maria Pilar
1997-11-01
A general approach to Molecular Dynamics procedures (MD), that can be included as a lesson in different parts of a physical chemistry program, is presented. The basic idea that a MD calculation consists on analyzing the evolution with time of the studied sample is presented and the difficulties arising from the amount of data to be analyzed and the computation of atomic coordinates are explained. Newton's equation of motion is integrated for a trivial system formed by just one isolated particle. Next, a system of two interacting particles is used to illustrate the leap frog algorithm employed for the integration in more realistic cases. Finally, the results obtained by performing a real MD calculation on the water molecule are presented, explained and compared with some basic ideas that we all have about this molecule.
Molecular-dynamics study of copper with defects under strain
NASA Astrophysics Data System (ADS)
Heino, P.; Häkkinen, H.; Kaski, K.
1998-07-01
Mechanical properties of copper with various types of defects have been studied with the molecular-dynamics method and the effective-medium theory potential both at room temperature and near zero temperature. The loading has been introduced as constant rate straining and the dynamics of the process region of fracture is purely Newtonian. With the model three types of defects were studied: point defects, grain boundary, and an initial void serving as a crack seed. Point defects were seen to decrease the system strength in terms of fracture stress, fracture strain, and elastic modulus. Due to random microstructure, highly disordered systems turned out to be isotropic, which on the other hand seems to increase the elastic modulus. In the case of a grain boundary, the elastic modulus was found to be significantly less than the bulk value of the system. In addition, the critical strain for crack initiation seems to be less at the grain boundary than in the bulk. In the case of an initial void, we studied stress concentration, dislocation propagation, and crack propagation in thin systems. The stress concentration was found to be in surprisingly good agreement with continuum predictions. Dislocation and crack were propagated with a velocity much below the speed of sound and they preferred the <110> crystal orientation.
Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics
NASA Astrophysics Data System (ADS)
Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott
2015-01-01
We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.
Molecular dynamics simulations on the hydration of fluoroalcohols
NASA Astrophysics Data System (ADS)
Kinugawa, Kenichi; Nakanishi, Koichiro
1988-11-01
Molecular dynamics (MD) calculations have been carried out for aqueous solutions of isopropyl alcohol (IPA) and its fluorinated compounds, 1,1,1-trifluoro-2-propanol (TFIPA) and 1,1,1,3,3,3-hexafluoro-2-propanol (HFIPA). The simulated systems were canonical ensembles containing 216 molecules in each, one of which was alcohol and the temperature was set to 298.15 K. The MCY (Matsuoka-Clementi-Yoshimine) potential was used for water-water interaction, whereas new potential functions were determined for alcohol-water interactions, on the basis of ab initio molecular orbital calculations on more than 1100 different dimeric configurations for each alcohol-water pair. The static properties of solvent water in the vicinity of each functional group of solute were obtained from MD calculations. It is found that the promotion of water structure and the increase of hydrogen bond between water molecules occurs not only near the fluoroalkyl group but also even near hydroxyl group of fluoroalcohols. Furthermore, the alcohol-water interaction is stronger for fluoroalcohols than for aliphatic alcohols, owing to the electronegativity and the electron withdrawing effect of fluorine atoms. The enthalpies of hydration for fluoroalcohols include the contributions from these features of both water-water and alcohol-water interactions. This is not the case for the hydration of aliphatic alcohols, and is the reason for the lack of regular change of enthalpies of hydration with the degree of the substitution of CH3 by the CF3 group. The hydration of IPA is similar to that of other aliphatic alcohols; hydrophobic hydration near the apolar group and the energetic unstabilization of water near the hydroxyl group are observed.
Symbolic dynamics III. Bifurcations in billiards and smooth potentials
Kai T. Hansen
1993-01-19
The singular bifurcations in a dispersive billiard are discussed in terms of symbolic dynamics and is compared to an example of a bifurcation tree in a smooth potential. Possible generalizations to other smooth potentials are discussed.
Zachariah, M; Romanini, M; Tripathi, P; Tamarit, J Ll; Macovez, R
2015-06-28
We probe the ionic conduction and the molecular dynamics in a pure and lithium-salt doped dinitrile molecular plastic crystal. While the diffusion of the Li(+) ions is decoupled from the molecular reorientational dynamics, in the undoped plastic crystal the temperature dependence of the mobility of dinitrile ions and thus of the conductivity is virtually identical to that of on-site molecular rotations. The undoped material is found to obey the Walden and Stokes-Einstein rules typical of ideal liquid electrolytes, implying that an effective viscosity against diffusion can be defined even for a plastic crystalline phase. These surprising results, never reported before in a translationally ordered solid, indicate that in this dinitrile plastic crystalline material the timescale of translational diffusion is perfectly correlated with that of the purely reorientational on-site dynamics. PMID:26028052
Modeling ramp compression experiments using large-scale molecular dynamics simulation.
Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I. (University of California, San Diego); Winey, J. Michael (Washington State University); Gupta, Yogendra Mohan (Washington State University); Lane, J. Matthew D.; Ditmire, Todd (University of Texas at Austin); Quevedo, Hernan J. (University of Texas at Austin)
2011-10-01
Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.
Ab initio molecular dynamics calculations of ion hydration free energies
Leung, Kevin; Rempe, Susan B.; von Lilienfeld, O. Anatole
2009-01-01
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or “?-path” technique to compute the intrinsic hydration free energies of Li+, Cl?, and Ag+ ions. Using the Perdew–Burke–Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (?) contributions, we obtain absolute AIMD hydration free energies (?Ghyd) within a few kcal?mol, or better than 4%, of Tissandier et al.’s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC?E water model ? predictions. The sums of Li+?Cl? and Ag+?Cl? AIMD ?Ghyd, which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag++Ni+?Ag+Ni2+ in water. The predictions for this reaction suggest that existing estimates of ?Ghyd for unstable radiolysis intermediates such as Ni+ may need to be extensively revised. PMID:19485457
Accelerated Molecular Dynamics Simulation on Friction of Incommensurate Interfaces
NASA Astrophysics Data System (ADS)
Kim, Woo Kyun; Falk, Michael
2009-03-01
We apply a molecular dynamics (MD) methodology to study the friction of incommensurate interfaces. While the traditional Tomlinson model assumes a single, repeatable transition, the sliding at the real incommensurate interface is comprised of a multitude of transition modes. This may account for recent Atomic Force Microscope (AFM) experimental results that indicate more complex temperature and velocity dependence of friction that deviate from the Tomlinson predictions. Conventional MD simulations are unable to simulate a wide range of sliding rates due to time scale limitations. In this study, we achieve decreases in the simulated sliding velocity by several orders of magnitude compared with conventional MD simulations using Voter's hyperdynamics scheme. This method uses a biased potential to reduce the barrier heights of the original potential to decrease the simulated time between slip events. The decrease in the sliding velocity makes it possible to see the atomic level processes during sliding speeds much closer to the experimental time scale. We carefully analyze the simulation results to elucidate the transition mechanisms.
Molecular Dynamics Study of the Photodesorption of CO Ice.
van Hemert, Marc C; Takahashi, Junko; van Dishoeck, Ewine F
2015-06-18
Photodesorption of CO ice is suggested to be the main process that maintains a measurable amount of gaseous CO in cold interstellar clouds. A classical molecular dynamics simulation is used to gain insight into the underlying mechanism. Site-site pair potentials were developed on the basis of ab initio calculations for the ground and excited nonrigid CO dimer. Both amorphous and crystalline CO clusters were created and characterized by their densities, expansion coefficients, binding energies, specific heats, and radial distribution functions. Selected CO molecules were electronically excited with 8.7-9.5 eV photons. CO returns to the ground state after a finite lifetime on the excited potential surface. Two desorption mechanisms are found: (1) direct desorption where excited CO itself is released from the cluster after landing on the ground state in an unfavorable orientation; (2) "kick-out" desorption where excited CO kicks out a neighboring CO molecule. These findings are in accord with laboratory experiments. Little dependence on size of the cluster, excitation energy and temperature in the 6-18 K range was found. The predicted photodesorption probability is 4.0 × 10(-3) molecules photon(-1), smaller by a factor of 3-11 than that given by experiments. PMID:26010083
What Molecular Abundances can Tell us about the Dynamics of Star Formation
NASA Astrophysics Data System (ADS)
Tassis, Konstantinos; Willacy, Karen; Yorke, Harold W.; Turner, Neal J.
2014-06-01
Molecular clouds are the sites where new stars form. Spectroscopic observations of different molecular species in these clouds can provide invaluable information regarding the dynamical evolution of star forming sites: first, they provide direct dynamical information (velocities as a function of density); second, they reveal the abundance of various molecules, which in turn depends on the chemodynamical evolutionary stage and history of the observed region. However, the connection between theoretical models of cloud dynamics and astronomical molecular spectroscopy is far from straight forward. The chemistry and dynamics of the clouds are interlinked, and various parameters such as the cloud temperature and its initial elemental abundances affect theoretical predictions, resulting in large model degeneracies: radically different dynamical models can often result in similar molecular abundances. In this talk, I will discuss first results from a massive effort undertaken to overcome this problem. By coupling non-equilibrium chemistry with a large array of different dynamical models of molecular cloud evolution, we are looking for these molecular line observables that are least affected by varying parameters and model degeneracies, and can be used to drastically constrain the possible dynamical histories of observed star-forming regions. To this end, we have studied a variety of dynamical models describing the evolution of pre- stellar molecular cloud cores (the initial phase of star formation) that cover the entire spectrum of proposed mechanisms, including pure hydrodynamical collapse and magnetically mediated collapse at various levels of importance of the magnetic field in the cloud dynamics. These models have been coupled to a network of chemical reactions that follow the relative abundances for ˜100 molecular species, by solving the non- equilibrium chemical reactions for the first time simultaneously with the dynamical equations. I will present highlights from the results of this work, including newly proposed observables with maximal potential for discrimination between different models of cloud evolution and star formation. These results are especially timely as ALMA is able to measure many of these quantities and contribute to the resolution of long-standing questions in star formation, such as the timescale of pre-stellar core evolution, and the relative importance of magnetic field and turbulence in their dynamics.
Fayer, Michael D.
Myoglobin-CO Substate Structures and Dynamics: Multidimensional Vibrational Echoes and Molecular to establishing the relationships between protein structure and protein function.1-5 Protein dynamics occur structural specificity to assign these dynamics to particular atomic motions. Computational tech- niques
Shin-Ho Chung; Toby W. Allen; Serdar Kuyucak
2002-01-01
The mechanisms underlying transport of ions across the potassium channel are examined using electrostatic calculations and three-dimensional Brownian dynamics simulations. We first build open-state configurations of the channel with molecular dynamics simulations, by pulling the transmembrane helices outward until the channel attains the desired interior radius. To gain insights into ion permeation, we construct potential energy profiles experienced by an
Molecular dynamics and phase transitions in alkali azides and thiocyanates
NASA Astrophysics Data System (ADS)
Ossowski, Maciej
Calculations based on an ab initio model developed for the intermolecular and intramolecular potentials in complex ionic solids were performed on selected alkali azides (KNsb3,\\ RbNsb3,\\ CsNsb3) and thiocyanates (KSCN, RbSCN, CsSCN). With these parameter-free potentials we performed static structural relaxations, supercell molecular dynamics and lattice dynamical studies and predict with reasonable accuracy the temperatures for the onset of the order-disorder phase transitions in these materials. Most significantly, we found that the transitions to the high-temperature disordered phases in these systems are driven by rotational disordering of the linear Nsb3sp- and SCNsp- anions. In case of the azides (Nsb3sp- anions) we observed free rotations of the anions about all three crystallographic axes, in all three systems. However, in the thiocyanates (SCNsp- anions) only one system, caesium thiocyanate (CsSCN), yielded free rotations about all the axes. In potassium thiocyanate (KSCN) and rubidium thiocyanate (RbSCN) the order-disorder transition appears rather to involve large amplitude librations of the SCNsp- ions, primarily about the c axis. This reflects the fact that in the azides the center of mass of the Nsb3sp- ions coincides with the geometric center of these anions, whereas in the thiocyanates this is no longer so since the center of mass lies ˜30% of the distance from the central carbon atom to the sulphur atom. Given this asymmetry in SCNsp- it is inevitable that the rotational motion about the center of mass will necessarily be coupled to the translational motion of the center of mass of this ion.
RedMDStream: Parameterization and Simulation Toolbox for Coarse-Grained Molecular Dynamics Models.
Leonarski, Filip; Trylska, Joanna
2015-04-21
Coarse-grained (CG) models in molecular dynamics (MD) are powerful tools to simulate the dynamics of large biomolecular systems on micro- to millisecond timescales. However, the CG model, potential energy terms, and parameters are typically not transferable between different molecules and problems. So parameterizing CG force fields, which is both tedious and time-consuming, is often necessary. We present RedMDStream, a software for developing, testing, and simulating biomolecules with CG MD models. Development includes an automatic procedure for the optimization of potential energy parameters based on metaheuristic methods. As an example we describe the parameterization of a simple CG MD model of an RNA hairpin. PMID:25902423
Dynamics of Molecular Hydrogen in Hypersaline Microbial Mars
NASA Technical Reports Server (NTRS)
Hoehler, Tori M.; Bebout, Brad M.; Visscher, Pieter T.; DesMarais, David J.; DeVincenzi, Donald L. (Technical Monitor)
2000-01-01
Early Earth microbial communities that centered around the anaerobic decomposition of organic molecular hydrogen as a carrier of electrons, regulator of energy metabolism, and facilitator of syntroph'c microbial interactions. The advent of oxygenic photosynthetic organisms added a highly dynamic and potentially dominant term to the hydrogen economy of these communities. We have examined the daily variations of hydrogen concentrations in cyanobacteria-dominated microbial mats from hypersaline ponds in Baja California Sur, Mexico. These mats bring together phototrophic and anaerobic bacteria (along with virtually all other trophic groups) in a spatially ordered and chemically dynamic matrix that provides a good analog for early Earth microbial ecosystems. Hydrogen concentrations in the photic zone of the mat can be three orders of magnitude or more higher than in the photic zone, which are, in turn, an order of magnitude higher than in the unconsolidated sediments underlying the mat community. Within the photic zone, hydrogen concentrations can fluctuate dramatically during the diel (24 hour day-night) cycle, ranging from less than 0.001% during the day to nearly 10% at night. The resultant nighttime flux of hydrogen from the mat to the environment was up to 17% of the daytime oxygen flux. The daily pattern observed is highly dependent on cyanobacterial species composition within the mat, with Lyngbya-dominated systems having a much greater dynamic range than those dominated by Microcoleus; this may relate largely to differing degrees of nitrogen-fixing and fermentative activity in the two mats. The greatest H2 concentrations and fluxes were observed in the absence of oxygen, suggesting an important potential feedback control in the context of the evolution of atmospheric composition. The impact of adding this highly dynamic photosynthetic term to the hydrogen economy of early microbial ecosystems must have been substantial. From an evolutionary standpoint, the H2 generated in mats could have represented a very important new source of electrons and energy - but one that could not be harnessed without substantial adaptation to the highly variable chemistry of the mat surface. In addition, the emergent chemistry of anaerobic communities is often highly dependent on ambient hydrogen concentrations, so that incorporation of these communities into photosynthetic mats could have significantly affected the composition and flux of reduced "biosignature' gases to the environment.
Molecular Dynamics Simulations of a Liquid Droplet in Contact with a Solid Surface
Maruyama, Shigeo
Molecular Dynamics Simulations of a Liquid Droplet in Contact with a Solid Surface Shigeo MARUYAMA to predict the kinetic behavior of interfaces. Hence, an example of the molecular dynamics simulation molecular species, liquid-solid and vapor-solid interfaces of different species. Molecular dynamics
Mavroidis, Constantinos
2008-01-01
, prototyping tools based on molecular dynamics (MD) simulators should be developed in order to understandMicroelectronics Journal 39 (2008) 190201 Prototyping bio-nanorobots using molecular dynamics Abstract This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled
3358 J. Phys. Chem. 1991,95, 3358-3363 Charge Equilibration for Molecular Dynamics Simulations
Goddard III, William A.
3358 J. Phys. Chem. 1991,95, 3358-3363 Charge Equilibration for Molecular Dynamics Simulations and change during molecular dynamics calculations. We indicate how this approach can also be used to predict hy- drogen bonding) in molecular mechanics and molecular dynamics calculations.I4 Unfortunately
NASA Astrophysics Data System (ADS)
Grest, Gary S.
2008-03-01
Twenty years ago at the APS March Meeting, Kurt Kremer and I presented the first numerical evidence from computer simulations that the reptation model of Edwards and de Gennes correctly describes the dynamics of entangled linear polymer melts. For chains longer than the entanglement length Ne, the monomers of a chain move predominantly along their own contour. The distinctive signature of reptation dynamics, which we observed, was that on intermediate time scales, the mean squared displacement of a monomer increases with time as t^ 1/4. Though these early simulations were limited to chains of a few Ne, they demonstrated the potential of computer simulations to contribute to our understanding of polymer dynamics. Here I will review the progress over the past twenty years and present an outlook for the future in modeling entangled polymer melts and networks. With present day computers coupled with efficient parallel molecular dynamics codes, it is now possible to follow the equilibrium dynamics of chains of length 10-20Ne from the early Rouse regime to the long time diffusive regime. Result of these simulations support the earlier results obtained on chains of only a few Ne. Further evidence for the tube models of polymer dynamics has been obtained by identifying the primitive path mesh that characterizes the microscopic topological state of the computer- generated conformations of the chains. In particular, the plateau moduli derived on the basis of this analysis quantitatively reproduce experimental data for a wide spectrum of entangled polymer liquids including semi-dilute theta solutions of synthetic polymers, the corresponding dense melts, and solutions of semi-flexible (bio)polymers such as f-actin or suspensions of rodlike viruses. We also find that in agreement with the reptation model, the stress, end-to-end distance and entanglement length of an entangled melt subjected to uniaxial elongation, all relax on the same time scale.
Two-stage melting of the ice Ih (0001) surface by molecular dynamics: A molecular dynamics study
NASA Astrophysics Data System (ADS)
Kuga, Mizuki; Iyetomi, Hiroshi
2014-03-01
We report a molecular dynamics simulation study of the structure and energetics of Ice Ih with a free basal (0001) surface. Especially we cast a new light on the formation of a quasi-liquid layer (QLL) at the surface prior to the melting of bulk ice. Detailed analysis of functional behavior of the total and potential energies with respect to temperature clearly separates the surface melting process into two stages. As temperature is increased, the outermost bilayer of the ideal surface first starts disordering in a progressive way with detachment of water molecules from the surface. During this first stage of surface melting, the energies show no discontinuous change as a function of temperature. Subsequently to fully developed disordering of the top layer, the surface shows stepwise melting in a narrow temperature range of around 10 K . This second stage of surface melting has first-order phase-transition-like characteristics as demonstrated by structural relaxation from an initial metastable (super-heating) state to the stable state during which the surface is liquefied layer by layer. Accordingly, it turns out that each of the stable QLL states designated by the number of liquefied bilayers has its own branch of the potential energy.
O. B. M. Hardouin Duparc; M. Meyer
1990-01-01
A molecular dynamics simulation of a realistic model of bicyclo-octane [HC(CH2–CH2)3CH] in its plastic phase has been performed at three different temperatures. The interactions between the molecules of the simulated system are calculated with phenomenological exp-6 additive atom–atom potentials. The molecules are considered rigid and their equations of motion are integrated using a method of constraints. A special attention is
NASA Astrophysics Data System (ADS)
Kazanc, S.; Çiftci, Y. Ö.; Çolako?lu, K.; Ozgen, S.
2006-05-01
In this work, molecular dynamics (MD) simulations are performed for copper using the modified form of the Morse potential function in the framework of Embedded Atom Method (EAM). The temperature- and pressure-dependent behaviours of the bulk modulus, linear-thermal expansion coefficients ( ?), second-order elastic constants (SOEC), and phonon frequencies are calculated and compared with the experimental data and the other theoretical works. The obtained results are in good agreement with the available experimental findings.
S. Kazanc; Y. Ö. Çiftci; K. Çolakoglu; S. Ozgen
2006-01-01
In this work, molecular dynamics (MD) simulations are performed for copper using the modified form of the Morse potential function in the framework of Embedded Atom Method (EAM). The temperature- and pressure-dependent behaviours of the bulk modulus, linear-thermal expansion coefficients (?), second-order elastic constants (SOEC), and phonon frequencies are calculated and compared with the experimental data and the other theoretical
Studying interactions by molecular dynamics simulations at high concentration.
Fogolari, Federico; Corazza, Alessandra; Toppo, Stefano; Tosatto, Silvio C E; Viglino, Paolo; Ursini, Fulvio; Esposito, Gennaro
2012-01-01
Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples. PMID:22500085
Studying Interactions by Molecular Dynamics Simulations at High Concentration
Fogolari, Federico; Corazza, Alessandra; Toppo, Stefano; Tosatto, Silvio C. E.; Viglino, Paolo; Ursini, Fulvio; Esposito, Gennaro
2012-01-01
Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples. PMID:22500085
Nitrile and thiocyanate IR probes: Molecular dynamics simulation studies
Kwang-Im Oh; Jun-Ho Choi; Joo-Hyun Lee; Jae-Beom Han; Hochan Lee; Minhaeng Cho
2008-01-01
Nitrile- and thiocyanate-derivatized amino acids have been found to be useful IR probes for investigating their local electrostatic environments in proteins. To shed light on the CN stretch frequency shift and spectral lineshape change induced by interactions with hydrogen-bonding solvent molecules, we carried out both classical and quantum mechanical\\/molecular mechanical (QM\\/MM) molecular dynamics (MD) simulations for MeCN and MeSCN in
Plasticity of metallic nanostructures : molecular dynamics simulations
Healy, Con
2014-11-27
During high speed cutting processes, metals are subject to high strains and strain rates. The dynamic nature of the deformation during high speed cutting makes it difficult to detect atomic scale deformation mechanisms ...
How Dynamic Visualization Technology can Support Molecular Reasoning
NASA Astrophysics Data System (ADS)
Levy, Dalit
2012-11-01
This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and gas. They interact with the visualizations and carry out inquiry activities to make and refine connections between observable phenomena and atomic level processes related to phase change. The explanations proposed by 300 pairs of students in response to pre/post-assessment items have been analyzed using a scale for measuring the level of molecular reasoning. Results indicate that from pretest to posttest, students make progress in their level of molecular reasoning and are better able to connect intermolecular forces and phase change in their explanations. The paper presents the results through the lens of improvement patterns and the metaphor of the "ladder of molecular reasoning," and discusses how this adds to our understanding of the benefits of interacting with dynamic molecular visualizations.
Joaquín Espinosa-García; Cipriano Rangel; Marta Navarrete; José C. Corchado
2004-01-01
A computational approach to calculating potential energy surfaces for reactive systems is presented and tested. This hybrid approach is based on integrated methods where calculations for a small model system are performed by using analytical potential energy surfaces, and for the real system by using molecular orbital or molecular mechanics methods. The method is tested on a hydrogen abstraction reaction
Replica exchange molecular dynamics simulations of amyloid peptide aggregation
NASA Astrophysics Data System (ADS)
Cecchini, M.; Rao, F.; Seeber, M.; Caflisch, A.
2004-12-01
The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant temperature molecular dynamics (CTMD). During the aggregation process the energetic and structural properties are essentially the same in REMD and CTMD. A condensation stage toward disordered aggregates precedes the ?-sheet formation. Two order parameters, borrowed from anisotropic fluid analysis, are used to monitor the aggregation process. The order parameters do not depend on the peptide sequence and length and therefore allow to compare the amyloidogenic propensity of different peptides.
AceCloud: Molecular Dynamics Simulations in the Cloud.
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. PMID:25849093
Population Dynamics and Harvest Potential of Mountain
SANDRA HAMEL; STEEVE D. COTE; MARCO FESTA-BIANCHET
The understanding of population dynamics is a central issue for managing large mammals. Modeling has allowed population ecologists to increase their knowledge about complex systems and better predict population responses to diverse perturbations. Mountain goats (Oreamnos americanus) appear sensitive to harvest, but the relative influence of survival and reproductive rates on their population dynamics are not well understood. Using longitudinal
InterIntra Molecular Dynamics as an Iterated Function System Kunihiko KANEKO
Kaneko, Kunihiko
InterIntra Molecular Dynamics as an Iterated Function System Kunihiko KANEKO Department of Basic function system, Cantor set, interintra molecular dynamics DOI: 10.1143/JPSJ.74.2386 Biological units have novel dynamical states that are not expected when considering only single molecular dynamics (see also
Non-Born-Oppenheimer molecular dynamics of NaFH photodissociation Ahren W. Jaspera
Truhlar, Donald G
Non-Born-Oppenheimer molecular dynamics of Na¯FH photodissociation Ahren W. Jaspera Combustion Molecular dynamics i.e., classical trajectory simula- tions have found widespread use throughout chemistry not dominate the dynamics. There have been several efforts to generalize molecular dynamics simulations
Gähler, Franz
Molecular Dynamics Simulations with IMD Johannes Roth, J¨org Stadler, Marco Brunelli, Franz G Abstract. We describe IMD (ITAP Molecular Dynamics), a software package for classical molecular dynamics dynamics (MD) simulations in two or three dimensions. The basic implementation of IMD and a description
An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations
Langmead, Christopher James
An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations Arvind as molecular dynamics simulations progress. Our representation of MD simulations as a stream of continuously-dimensional structure, dynamics and function is underway. Molecular dynamics (MD) / Monte-Carlo (MC) simulations have
Karthick, T; Balachandran, V; Perumal, S
2015-04-15
Thiophene derivatives have been focused in the past decades due to their remarkable biological and pharmacological activities. In connection with that the conformational stability, spectroscopic characterization, molecular (inter- and intra-) interactions, and molecular docking studies on thiophene-2-carboxylicacid have been performed in this work by experimental FT-IR and theoretical quantum chemical computations. Experimentally recorded FT-IR spectrum in the region 4000-400 cm(-1) has been compared with the scaled theoretical spectrum and the spectral peaks have been assigned on the basis of potential energy distribution results obtained from MOLVIB program package. The conformational stability of monomer and dimer conformers has been examined. The presence of inter- and intramolecular interactions in the monomer and dimer conformers have been explained by natural bond orbital analysis. The UV-Vis spectra of the sample in different solvents have been simulated and solvent effects were predicted by polarisable continuum model with TD-DFT/B3LYP/6-31+G(d,p) method. To test the biological activity of the sample, molecular docking (ligand-protein) simulations have been performed using SWISSDOCK web server. The full fitness (FF) score and binding affinity values revealed that thiophene-2-carboxylicacid can act as potential inhibitor against inflammation. PMID:25677530
Dynamic Nanodevices Based on Protein Molecular Motors
Dan V. Nicolau
Most of the present micro\\/nano biodevices are designed for a single use, as opposed to ‘classical’ non-biodevices (e.g., from\\u000a the steam engine to the microchip). Once their function, be that simple molecular recognition like in microarrays or even\\u000a biomolecular computation as in DNA computation arrays, is fulfilled and the information is passed further to signal and information\\u000a processing systems, the
Exciton Polarons of Molecular Crystal Model. I. Dynamical CPA
Hitoshi Sumi
1974-01-01
Energy spectrum of exciton polaron is studied with the dynamical CPA (coherent potential approximation), which is introduced for inelastic scattering by Einstein phonons at every lattice site. The coherent potential at energy E is determined by the potentials at energies apart from E by integral times the phonon energy. We determine applicability ranges of the concepts used in the limiting