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1

Massively parallel molecular dynamics simulations with EAM potentials

Molecular dynamics of cascades in pure iron and iron-copper alloys using embedded atom method type of interatomic potentials are presented. Reliable simulations of radiation damage at the atomic scale with high energy Primary Knocked Atoms (PKA) need systems with large numbers of particles and very long computational time. To perform the simulation in a reasonable amount of time high-performance computer

C. S. Becquart; K. M. Decker; J. Ruste; Y. Souffez; J. C. Turbatte; J. C. van Duysen

1997-01-01

2

Molecular Dynamics Simulation of ZnS using Interatomic Potentials

NASA Astrophysics Data System (ADS)

Constant temperature molecular dynamics simulations have been performed on ZnS at different temperatures ranging from 300 K to 1400 K with the objective of establishing and validating the temperature dependent structural and thermodynamic properties. The simulations were carried out in canonical ensemble (NVT) using Lennard-Jones pair potential. Radial distribution functions have been calculated. RDF peaks are found to be broadened and decrease in heights with increasing temperature, reflecting enhanced atomic motions. Energy temperature graph does not show any break, however a break in the specific heat curve and a ? type transformation are observed indicating second order phase transformation. Mean Square Displacement (MSD) for Zn and S atoms separately have been measured and almost identical graph were obtained. The MSD curve exhibits the existence of maximum disorderness at 1100 K and 1400 K which indicates phase transformations around them.

Khan, M. Ajmal; Sultan, Badriah S. A.; Bouarissa, Nadir; Wahab, M. A.

2011-10-01

3

Massively parallel molecular dynamics simulations with EAM potentials

NASA Astrophysics Data System (ADS)

Molecular dynamics of cascades in pure iron and iron-copper alloys using embedded atom method type of interatomic potentials are presented. Reliable simulations of radiation damage at the atomic scale with high energy Primary Knocked Atoms (PKA) need systems with large numbers of particles and very long computational time. To perform the simulation in a reasonable amount of time high-performance computer systems such as massively parallel machines need to be used. This paper presents the parallelisation strategy applied to a serial classical Molecular Dynamics code: DYMOKA. The original sequential Fortran code CDCMD from the University of Connecticut was first improved algorithmically by applying a link cell method for the neighbour list construction of the Verlet list, resulting in a fully linear algorithm. The parallelisation strategy adopted is a multidimensional domain decomposition of the simulation box using a link cell method and a Verlet list method for each subdomain independently. The program paradigm is based on explicit message passing, and the standard Message-Passing Interface (MPI) was chosen in order to achieve portability. First measurements have demonstrated that the simulation of a system of 2.000.000 (750.000) atoms on 128 (32) processors costs 2.5 (10.) ?s per atom per step. The current implementation has proven good scalability up to 32 processors on a NEC Cenju-3 machine. To study the effects of irradiation on copper segregation, simulations with up to 1.000.000 atoms in iron and iron-copper were performed with PKA energies up to 20 keV.

Becquart, C. S.; Decker, K. M.; Domain, C.; Ruste, J.; Souffez, Y.; Turbatte, J. C.; van Duysen, J. C.

4

Molecular Dynamics Study of Protein Folding: Potentials and Mechanisms

NASA Astrophysics Data System (ADS)

This paper is concerned with the investigations of the protein folding problem by molecular dynamics simulations performed with minimal protein models. We briefly review some of the recently presented off-lattice protein models. In detail description is given for a particular model which uses spherical beads placed at the positions of C?s to represent amino acid residues. Then we turn to discussing some of the algorithms available presently for efficient simulations of protein models. In particular we concentrate on the non-iterative multicanonical algorithm. Finally we demonstrate the usage of the models and computational methods by investigating thermodynamics and kinetics of a short ?-sheet protein motif. From thermodynamical point of view we determine the temperatures of three basic phase transitions that take place in the present model: collapse, folding and glass transition. Kinetically we show that folding reaction of the employed model is well described by a diffusion-equation formula.

Baumketner, A.; Hiwatari, Y.

2003-04-01

5

The basic methodology of equilibrium molecular dynamics is described. Examples from the literature are used to illustrate how molecular dynamics has been used to resolve theoretical controversies, provide data to test theories, and occasionally to discover new phenomena. The emphasis is on the application of molecular dynamics to an understanding of the microscopic physics underlying the transport properties of simple fluids. 98 refs., 4 figs.

Ladd, A.J.C.

1988-08-01

6

Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently Plattner et al. [J. Chem. Phys. 135, 134111 (2011)] proposed a method to implement infinite swapping REMD in practice. Here we introduce a natural modification of this method that involves molecular dynamics simulations over a mixture potential. This modification is both simple to implement in practice and provides a better, energy based understanding of how to choose the temperatures in REMD to optimize efficiency. It also has implications for generalizations of REMD in which the swaps involve other parameters than the temperature. PMID:23464138

Lu, Jianfeng; Vanden-Eijnden, Eric

2013-02-28

7

Five bulk properties of liquid hydrogen fluoride were obtained by a molecular dynamics simulation at five temperatures between 203 and 273 K. The rigid-body interaction potential was designed with emphasis on the electrostatic contribution. The potential was expanded in spherical tensor multipole moments, and its corresponding Ewald summations, containing all possible interaction up to L=5 (i.e., monopole-hexadecapole, dipole-octopole, quadrupole-quadrupole). The

S. Y. Liem; P. L. A. Popelier

2003-01-01

8

Validation of potential models for Li2O in classical molecular dynamics simulation

NASA Astrophysics Data System (ADS)

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

Oda, Takuji; Oya, Yasuhisa; Tanaka, Satoru; Weber, William J.

2007-08-01

9

Validation of Potential Models for Li2O in Classical Molecular Dynamics Simulation

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

Oda, Takuji; Oya, Yasuhisa; Tanaka, Satoru; Weber, William J.

2007-08-01

10

Anisotropic interactions of liquid CD4 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. PMID:17995296

Guarini, E; Sampoli, M; Venturi, G; Bafile, U; Barocchi, F

2007-10-19

11

Molecular dynamics simulations of Si F surface chemistry with improved interatomic potentials

NASA Astrophysics Data System (ADS)

Molecular dynamics results using an improved Tersoff-Brenner style interatomic potential for Si-F (denoted by TB-HG) are presented. In simulations of F/Ar+, F+, and SiF_{3}^{+} etching of silicon, the TB-HG potential predicts different behaviour from that of Stillinger and Weber (SW). With the SW potential, F atoms do not mix into Si surfaces, creating instead a roughened surface with F on the outside. With the TB-HG potential, F atoms are able to mix into Si, leading to higher F uptake and Si etch rate in all cases. The TB-HG potential is compared to the modified SW potential of Weakliem et al (SW-WWC) in simulations of F+ etching of Si. The quantitative values of steady-state F uptake and Si etch rate for the (SW-WWC and TB-HG) potentials are nearly identical, but surface structure and etch product distributions are qualitatively different. Evidence of spurious energetic barriers in the SW potential form is given.

Humbird, David; Graves, David B.

2004-08-01

12

Structural and dynamic properties of cristobalite silica have been studied using molecular dynamics simulations based on a charge transfer three-body potential model. In this potential model, the directional covalent bonding of SiO2 is characterized by a charge transfer function of the interatomic distance between Si and O atoms, and in the form of Si-O-Si and O-Si-O three-body interactions. The dynamic

Liping Huang; John Kieffer

2003-01-01

13

NASA Astrophysics Data System (ADS)

We compare the molecular dynamics Green-Kubo and direct methods for calculating thermal conductivity ?, using as a test case crystalline silicon at temperatures T in the range 500-1000 K (classical regime). We pay careful attention to the convergence with respect to simulation size and duration and to the procedures used to fit the simulation data. We show that in the Green-Kubo method the heat current autocorrelation function is characterized by three decay processes, of which the slowest lasts several tens of picoseconds so that convergence requires several tens of nanoseconds of data. Using the Stillinger-Weber potential we find excellent agreement between the two methods. We also use the direct method to calculate ?(T) for the Tersoff potential and find that the magnitude and the temperature-dependence are different for the two potentials and that neither potential agrees with experimental data. We argue that this implies that using the Stillinger-Weber or Tersoff potentials to predict trends in kappa as some system parameter is varied may yield results which are specific to the potential but not intrinsic to Si.

Howell, P. C.

2012-12-01

14

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

G. C. Lie; E. Clementi

1986-01-01

15

NSDL National Science Digital Library

The EJS Molecular Dynamics model is constructed using the Lennard-Jones potential truncated at a distance of 3 molecular diameters. The motion of the molecules is governed by Newton's laws, approximated using the Verlet algorithm with the indicated time step. For sufficiently small time steps dt, the system's total energy should be approximately conserved. The Molecular Dynamics model was created using the Easy Java Simulations (Ejs) modeling tool. It is distributed as a ready-to-run (compiled) Java archive. Double clicking the ejs_stp_md_MolecularDynamics.jar file will run the program if Java is installed. Ejs is a part of the Open Source Physics Project and is designed to make it easier to access, modify, and generate computer models. Additional Ejs models for classical mechanics are available. They can be found by searching ComPADRE for Open Source Physics, OSP, or Ejs.

Christian, Wolfgang

2008-11-16

16

The absolute (standard) binding free energy of eight FK506-related ligands to FKBP12 is calculated using free energy perturbation molecular dynamics (FEP/MD) simulations with explicit solvent. A number of features are implemented to improve the accuracy and enhance the convergence of the calculations. First, the absolute binding free energy is decomposed into sequential steps during which the ligand-surrounding interactions as well as various biasing potentials restraining the translation, orientation, and conformation of the ligand are turned "on" and "off." Second, sampling of the ligand conformation is enforced by a restraining potential based on the root mean-square deviation relative to the bound state conformation. The effect of all the restraining potentials is rigorously unbiased, and it is shown explicitly that the final results are independent of all artificial restraints. Third, the repulsive and dispersive free energy contribution arising from the Lennard-Jones interactions of the ligand with its surrounding (protein and solvent) is calculated using the Weeks-Chandler-Andersen separation. This separation also improves convergence of the FEP/MD calculations. Fourth, to decrease the computational cost, only a small number of atoms in the vicinity of the binding site are simulated explicitly, while all the influence of the remaining atoms is incorporated implicitly using the generalized solvent boundary potential (GSBP) method. With GSBP, the size of the simulated FKBP12/ligand systems is significantly reduced, from approximately 25,000 to 2500. The computations are very efficient and the statistical error is small ( approximately 1 kcal/mol). The calculated binding free energies are generally in good agreement with available experimental data and previous calculations (within approximately 2 kcal/mol). The present results indicate that a strategy based on FEP/MD simulations of a reduced GSBP atomic model sampled with conformational, translational, and orientational restraining potentials can be computationally inexpensive and accurate. PMID:16844742

Wang, Jiyao; Deng, Yuqing; Roux, Benoît

2006-07-14

17

The temperature and density dependence of the structure and polarization properties of bulk water were systematically investigated using the ab initio MCYna potential [Li et al., J. Chem. Phys. 127, 154509 (2007)], which includes nonadditive contributions to intermolecular interactions. Molecular dynamics simulations were conducted for isochores of 1, 0.8, and 0.6 g/cm^{3} and temperatures from 278 to 750 K. Special attention was paid to the structural change of water in the range from the normal boiling point to supercritical temperatures. At temperatures below the normal boiling temperature, water exhibits a tetrahedral structure along the 0.8 and 0.6 g/cm^{3} isochores. A significant collapse of the hydrogen bonding network was observed at temperatures of 450, 550, and 650 K. The MCYna potential was able to successfully reproduce the experimental dielectric constant. The dielectric constant and average dipole moments decrease with increasing temperature and decreasing density due to weakened polarization. A comparison is also made with SPC-based models. PMID:23004769

Shvab, I; Sadus, Richard J

2012-05-30

18

NASA Astrophysics Data System (ADS)

The temperature and density dependence of the structure and polarization properties of bulk water were systematically investigated using the ab initio MCYna potential [Li , J. Chem. Phys.JCPSA60021-960610.1063/1.2786449 127, 154509 (2007)], which includes nonadditive contributions to intermolecular interactions. Molecular dynamics simulations were conducted for isochores of 1, 0.8, and 0.6 g/cm3 and temperatures from 278 to 750 K. Special attention was paid to the structural change of water in the range from the normal boiling point to supercritical temperatures. At temperatures below the normal boiling temperature, water exhibits a tetrahedral structure along the 0.8 and 0.6 g/cm3 isochores. A significant collapse of the hydrogen bonding network was observed at temperatures of 450, 550, and 650 K. The MCYna potential was able to successfully reproduce the experimental dielectric constant. The dielectric constant and average dipole moments decrease with increasing temperature and decreasing density due to weakened polarization. A comparison is also made with SPC-based models.

Shvab, I.; Sadus, Richard J.

2012-05-01

19

Introduction to Accelerated Molecular Dynamics

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.

Perez, Danny [Los Alamos National Laboratory

2012-07-10

20

Molecular dynamics of liquids modelled by '2-Lennard-Jones' pair potentials

NASA Astrophysics Data System (ADS)

Mori's continued fraction method has been applied with closure at the second level to the velocity and angular momentum autocorrelation functions (acf) and with closure at the third level to the orientational acfs

Detyna, E.; Singer, K.; Singer, J. V. L.; Taylor, A. J.

21

Molecular dynamics of liquids modelled by '2-Lennard-Jones centres' pair potentials

NASA Astrophysics Data System (ADS)

The molecular dynamics study based on two-Lennard-Jones (12-6) centres pair potentials, with reduced bond lengths in the range 0·5 ?l/??0&(s)breve;d8, and with ?, ?-parameters simulating liquid F2, Cl2, Br2 and CO2 (14) is extended to time correlation functions. The calculated properties include: translational velocity and force self correlation functions; orientational self-correlation functions

Singer, K.; Singer, J. V. L.; Taylor, A. J.

22

The absolute (standard) binding free energy of eight FK506-related ligands to FKBP12 is calculated using free energy perturbation molecular dynamics (FEP\\/MD) simulations with explicit solvent. A number of features are implemented to improve the accuracy and enhance the convergence of the calculations. First, the absolute binding free energy is decomposed into sequential steps during which the ligand-surrounding interactions as well

Jiyao Wang; Yuqing Deng; Benoît Roux

2006-01-01

23

An interatomic potential model for Si-Br systems has been developed for performing classical molecular dynamics (MD) simulations. This model enables us to simulate atomic-scale reaction dynamics during Si etching processes by Br{sup +}-containing plasmas such as HBr and Br{sub 2} plasmas, which are frequently utilized in state-of-the-art techniques for the fabrication of semiconductor devices. Our potential form is based on the well-known Stillinger-Weber potential function, and the model parameters were systematically determined from a database of potential energies obtained from ab initio quantum-chemical calculations using GAUSSIAN03. For parameter fitting, we propose an improved linear scheme that does not require any complicated nonlinear fitting as that in previous studies [H. Ohta and S. Hamaguchi, J. Chem. Phys. 115, 6679 (2001)]. In this paper, we present the potential derivation and simulation results of bombardment of a Si(100) surface using a monoenergetic Br{sup +} beam.

Ohta, H.; Iwakawa, A.; Eriguchi, K.; Ono, K. [Department of Aeronautics and Astronautics, Graduate School of Engineering, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501 (Japan)

2008-10-01

24

The structural, adhesive, and electronic properties of Cu\\/alpha-cristobalite SiO2 interfaces with various interface terminations are investigated with molecular dynamics simulations using the charge-optimized many-body (COMB) potential. We predict that the Cu\\/alpha-cristobalite interface exhibits the largest adhesion energy for the oxygen-richest condition. The trend of the adhesion energies is consistent with that determined from density functional theory (DFT) calculations. We also

Tzu-Ray Shan; Bryce D. Devine; Simon R. Phillpot; Susan B. Sinnott

2011-01-01

25

To evaluate the adsorption sites of hydrogen atom on buckybowl-like molecule (C36H12), which is a model fragment structure of zeolite-templated carbon (ZTC), we have performed path integral molecular dynamics (PIMD) simulation including thermal and nuclear quantum fluctuations under the semi-empirical PM3 potential. Here we have picked up ten carbons as the adsorption sites of additional hydrogen atom (H*), which are

Kimichi Suzuki; Megumi Kayanuma; Masanori Tachikawa; Hiroshi Ogawa; Hirotomo Nishihara; Takashi Kyotani; Umpei Nagashima

2011-01-01

26

This work provides a generalization of Evans' homogeneous nonequilibrium method for estimating thermal conductivity to molecular systems that are described by general multibody potentials. A perturbed form of the usual Nose-Hoover equations of motion is formally constructed and is shown to satisfy the requirements of Evans' original method. These include adiabatic incompressibility of phase space, equivalence of the dissipative and heat fluxes, and momentum preservation. PMID:19905491

Mandadapu, Kranthi K; Jones, Reese E; Papadopoulos, Panayiotis

2009-10-29

27

NASA Astrophysics Data System (ADS)

This work provides a generalization of Evans’ homogeneous nonequilibrium method for estimating thermal conductivity to molecular systems that are described by general multibody potentials. A perturbed form of the usual Nose-Hoover equations of motion is formally constructed and is shown to satisfy the requirements of Evans’ original method. These include adiabatic incompressibility of phase space, equivalence of the dissipative and heat fluxes, and momentum preservation.

Mandadapu, Kranthi K.; Jones, Reese E.; Papadopoulos, Panayiotis

2009-10-01

28

We present results addressing properties of a polarizable force field for hexane based on the fluctuating charge (FQ) formalism and developed in conjunction with the Chemistry at Harvard Molecular Mechanics (CHARMM) potential function. Properties of bulk neat hexane, its liquid-vapor interface, and its interface with a polarizable water model (TIP4P-FQ) are discussed. The FQ model is compared to a recently

Sandeep A. Patel; Charles L. Brooks

2006-01-01

29

Accelerated molecular dynamics methods

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.

Perez, Danny [Los Alamos National Laboratory

2011-01-04

30

Comparison of model potentials for molecular-dynamics simulations of silica

NASA Astrophysics Data System (ADS)

Structural, thermomechanical, and dynamic properties of pure silica SiO2 are calculated with three different model potentials, namely, the potential suggested by van Beest, Kramer, and van Santen (BKS) [Phys. Rev. Lett. 64, 1955 (1990)], the fluctuating-charge potential with a Morse stretch term for the short-range interactions proposed by Demiralp, Cagin, and Goddard (DCG)[Phys. Rev. Lett. 82, 1708 (1999)], and a polarizable force field proposed by Tangney and Scandolo (TS) [J. Chem. Phys. 117, 8898 (2002)]. The DCG potential had to be modified due to flaws in the original treatment. While BKS reproduces many thermomechanical properties of different polymorphs rather accurately, it also shows qualitatively wrong trends concerning the phononic density of states, an absence of the experimentally observed anomaly in the c/a ratio at the quartz ?-? transition, pathological instabilities in the ?-cristobalite phase, and a vastly overestimated transition pressure for the stishovite I-->II transition. These shortcomings are only partially remedied by the modified DCG potential but greatly improved by the TS potential. DCG and TS both reproduce a pressure-induced transition from ?-quartz to quartz II, predicted theoretically based on the BKS potential.

Herzbach, Daniel; Binder, Kurt; Müser, Martin H.

2005-09-01

31

Accelerating Molecular Dynamics Simulations

In contrast with the converging length scales of atomistic simulations and experimental nanoscience, large time scale discrepancies still remain, due to the time-scale limitations of molecular dynamics. We briefly review two recently devel- oped methods, derived from transition state theory, for accel- erating molecular dynamics simulations of infrequent-event processes. These techniques, parallel replica dynamics and hyperdynamics, can reach simulation times

Timothy C. Germann; Arthur F. Voter

32

We present an atomistic potential for BiFeO(3) based on the principles of bond-valence (BV) and bond-valence vector (BVV) conservation. The validity of this model potential is tested for both canonical ensemble (NVT) and isobaric-isothermal ensemble (NPT) molecular dynamics (MD) simulations. The model reproduces the ferroelectric-to-paraelectric phase transition in both NVT and NPT MD simulations and the temperature dependence of the local structure in BiFeO(3). The calculated domain wall energies for 71°, 109°and 180° walls agree well with density functional theory results. The success of our simple model potential for BiFeO(3) indicates that BV and BVV conservation provides a firm basis for the development of accurate atomistic potentials for complex oxides. PMID:23399759

Liu, Shi; Grinberg, Ilya; Rappe, Andrew M

2013-02-12

33

NASA Astrophysics Data System (ADS)

Interpolated potential energy surfaces (PESs) have been used for performing reliable molecular dynamics (MD) simulations of small molecular reactions. In this article, we extend this method to MD simulations in condensed phase and show that the same scheme can also be feasibly used when it is supplemented with additional terms for describing intermolecular interactions. We then apply the approach for studying the resolvation process of coumarin 153 in a number of polar solvents. We find that the interpolated surface actually reproduces experimentally found features much better than the conventional force field based potential especially in terms of both dynamics Stokes shift in the short time limit and solute vibrational decoherence. This shows that the solute vibrational effect is important to some degree along the resolvation and should be modeled properly for accurate description of the related dynamics. The stability issue of trajectories on the interpolated PESs is also discussed, in regard to the goal of reliably performing long time simulations. Operational limitations of the present scheme are also discussed.

Park, Jae Woo; Kim, Hyun Woo; Song, Chang-Ik; Rhee, Young Min

2011-07-01

34

NASA Astrophysics Data System (ADS)

We present a continuous pseudo-hard-sphere potential based on a cut-and-shifted Mie (generalized Lennard-Jones) potential with exponents (50, 49). Using this potential one can mimic the volumetric, structural, and dynamic properties of the discontinuous hard-sphere potential over the whole fluid range. The continuous pseudo potential has the advantage that it may be incorporated directly into off-the-shelf molecular-dynamics code, allowing the user to capitalise on existing hardware and software advances. Simulation results for the compressibility factor of the fluid and solid phases of our pseudo hard spheres are presented and compared both to the Carnahan-Starling equation of state of the fluid and published data, the differences being indistinguishable within simulation uncertainty. The specific form of the potential is employed to simulate flexible chains formed from these pseudo hard spheres at contact (pearl-necklace model) for mc = 4, 5, 7, 8, 16, 20, 100, 201, and 500 monomer segments. The compressibility factor of the chains per unit of monomer, mc, approaches a limiting value at reasonably small values, mc < 50, as predicted by Wertheim's first order thermodynamic perturbation theory. Simulation results are also presented for highly asymmetric mixtures of pseudo hard spheres, with diameter ratios of 3:1, 5:1, 20:1 over the whole composition range.

Jover, J.; Haslam, A. J.; Galindo, A.; Jackson, G.; Müller, E. A.

2012-10-01

35

NASA Astrophysics Data System (ADS)

We report on large-scale nonequilibrium molecular dynamics simulations of shock wave compression in tantalum single crystals. Two new embedded atom method interatomic potentials of Ta have been developed and optimized by fitting to experimental and density functional theory data. The potentials reproduce the isothermal equation of state of Ta up to 300 GPa. We examined the nature of the plastic deformation and elastic limits as functions of crystal orientation. Shock waves along (100), (110), and (111) exhibit elastic-plastic two-wave structures. Plastic deformation in shock compression along (110) is due primarily to the formation of twins that nucleate at the shock front. The strain-rate dependence of the flow stress is found to be orientation dependent, with (110) shocks exhibiting the weaker dependence. Premelting at a temperature much below that of thermodynamic melting at the shock front is observed in all three directions for shock pressures above about 180 GPa.

Ravelo, R.; Germann, T. C.; Guerrero, O.; An, Q.; Holian, B. L.

2013-10-01

36

NASA Astrophysics Data System (ADS)

Using coarse-grained molecular dynamics simulations based on Gay-Berne potential model, we have simulated the cooling process of liquid n-butanol. A new set of GB parameters are obtained by fitting the results of density functional theory calculations. The simulations are carried out in the range of 290-50 K with temperature decrements of 10 K. The cooling characteristics are determined on the basis of the variations of the density, the potential energy and orientational order parameter with temperature, whose slopes all show discontinuity. Both the radial distribution function curves and the second-rank orientational correlation function curves exhibit splitting in the second peak. Using the discontinuous change of these thermodynamic and structure properties, we obtain the glass transition at an estimate of temperature Tg=120±10 K, which is in good agreement with experimental results 110±1 K.

Xie, Gui-long; Zhang, Yong-hong; Huang, Shi-ping

2012-04-01

37

Molecular Dynamics Replicated Data Model

NSDL National Science Digital Library

The Molecular Dynamics Replicated Data Model is a parallel computer simulation that uses a 3D Lennard-Jones potential truncated at a distance of three molecular diameters. Each thread computes a portion of the force on each atom and these contributions are summed to compute the total acceleration using the Verlet ODE algorithm. Allocating memory for each thread's avoids the problem of parallel threads simultaneously writing to array elements. The Molecular Dynamics Replicated Data Model was developed using the Easy Java Simulations (EJS) modeling tool. It is distributed as a ready-to-run (compiled) Java archive.

Christian, Wolfgang

2013-08-30

38

NASA Astrophysics Data System (ADS)

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 bonds are described by the three-body potential. The proposed three-body interaction potential is a modification of the Stillinger-Weber form proposed to describe Si. Using the molecular dynamics method, the interaction potential is used to study structural, elastic, and dynamical properties of crystalline and amorphous states of AlN for several densities and temperatures. The structural energy for wurtzite (2H) structure has the lowest energy, followed zinc-blende and rock-salt (RS) structures. The pressure for the structural transformation from wurtzite-to-RS from the common tangent is found to be 24 GPa. For AlN in the wurtzite phase, our computed elastic constants (C11, C12, C13, C33, C44, and C66), melting temperature, vibrational density-of-states, and specific heat agree well with the experiments. Predictions are made for the elastic constant as a function of density for the crystalline and amorphous phase. Structural correlations, such as pair distribution function and neutron and x-ray static structure factors are calculated for the amorphous and liquid state.

Vashishta, Priya; Kalia, Rajiv K.; Nakano, Aiichiro; Rino, José Pedro; Collaboratory For Advanced Computing; Simulations

2011-02-01

39

Molecular Dynamics modeling of O2/Pt(111) gas-surface interaction using the ReaxFF potential

NASA Astrophysics Data System (ADS)

We studied adsorption dynamics of O2 on Pt(111) using Molecular Dynamics (MD) simulations with the ab initio based reactive force field ReaxFF. We found good quantitative agreement with the experimental data at low incident energies. Specifically, our simulations reproduce the characteristic minimum of the trapping probability at kinetic incident energies around 0.1 eV. This feature is determined by the presence of a physisorption well in the ReaxFF Potential Energy Surface (PES) and the progressive suppression of a steering mechanism as the translational kinetic energy (or the molecule's rotational energy) is increased. In the energy range between 0.1 eV and 0.4 eV, the sticking probability increases, similarly to molecular beam sticking data. For very energetic impacts (above 0.4 eV), ReaxFF predicts sticking probabilities lower than experimental sticking data by almost a factor of 3, due to an overall less attractive ReaxFF PES compared to experiments and DFT.

Valentini, Paolo; Schwartzentruber, Thomas E.; Cozmuta, Ioana

2011-05-01

40

Nonequilibrium molecular dynamics

The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. 14 refs., 8 figs.

Hoover, W.G. (California Univ., Davis, CA (USA). Dept. of Applied Science Lawrence Livermore National Lab., CA (USA))

1990-11-01

41

Molecular dynamics simulation of potential sputtering on a LiF surface by slow highly charged ions

NASA Astrophysics Data System (ADS)

Potential sputtering on the lithium fluoride (LiF) (100) surface by slow highly charged ions (HCI) has been studied via molecular dynamics (MD) simulations. A model that is different from the conventional MD is formulated to include partially the electronic degrees of freedom. In this model, electrons are allowed to be in the ground state as well as in low-lying excited states. The interatomic potential energy function of each state is obtained by extensive first-principles calculations based on a high-level quantum chemistry method. In the MD simulations, various initial conditions of the LiF surface are assumed and the resulting sputtering patterns are analyzed fully. The results demonstrate that the so-called defect-mediated sputtering model provides a qualitatively correct physical picture. The simulations provide quantitative descriptions in which neutral particles dominate the sputtering yield, in agreement with the experimental observations for HCI-LiF surface bombardment. Dynamical consequences, surface modification, and angular distributions of sputtering yields are also discussed with a full, comprehensive analysis of structure and energetics.

Wang, Lin-Lin; Perera, Ajith; Cheng, Hai-Ping

2003-09-01

42

NASA Astrophysics Data System (ADS)

For several liquid states of CF4 and SF4, the shear and the bulk viscosity as well as the thermal conductivity were determined by equilibrium molecular dynamics (MD) calculations. Lennard-Jones four- and six-center pair potentials were applied, and the method of constraints was chosen for the MD. The computed Green-Kubo integrands show a steep time decay, and no particular longtime behavior occurs. The molecule number dependence of the results is found to be small, and 3×105 integration steps allow an accuracy of about 10% for the shear viscosity and the thermal conductivity coefficient. Comparison with experimental data shows a fair agreement for CF4, while for SF6 the transport coefficients fall below the experimental ones by about 30%.

Hoheisel, C.

1989-01-01

43

Potential of hydrogen bond is the function which relates its energy to geometrical parameters of hydrogen bridge: its length R(O…O) and angles between direction O…O and OH group [? (H-O…O)] and/or lone pair of proton accepting oxygen atom [?(-O…O)]. Previously we have suggested an approach to design such potentials based on the approximate numerical solution of a reverse problem of the spectrum band shape in the frames of the fluctuation theory of hydrogen bonding. In the given work this method is applied to construction of the two-parameter potentials that depend on parameters {R(O…O), ? (H-O…O} or {? (H-O…O), ? (-O…O)}. Using them, the spectra of OH vibrations of HOD molecules in a liquid phase are calculated theoretically in good agreement with experiment in the temperature range up to 200 °C. Distributions of angles P(?, T), P(?, T), and energies P(E) are calculated also. The same distributions and spectra are independently calculated on the basis of the geometrical parameters of the hydrogen bridges obtained from molecular dynamics models of water. The shapes of the spectral contours and their temperature evolution calculated for computer models turned out to be similar to experimental ones only for the potential that includes the length of H-bond R(O…O). PMID:21190891

Efimov, Yuri Ya; Naberukhin, Yuri I

2010-12-07

44

NASA Astrophysics Data System (ADS)

We have constructed a polarizable potential model for benzene using molecular dynamics techniques. The atomic site polarizabilities for carbon and hydrogen were taken from the recent work of Applequist [J. Phys. Chem. 97, 6016 (1993)], which reproduced the experimental molecular polarizability of the benzene molecule very accurately. Our model describes well the available experimental data such as the structure and thermodynamic properties of liquid benzene and the equilibrium properties of the liquid/vapor interface of benzene. The lowest minimum-energy structure of the benzene dimer predicted by our model has a T-shape with a potential energy of -2.5 kcal/mol. This value agrees with the experimentally obtained value (-2.4+/-0.4 kcal/mol), which was determined from a high-precision ionization measurement. The cyclic minimum-energy structures are found for both the benzene trimer and tetramer clusters. The computed density profile shows that the interface is not sharp at a microscopic level and has a thickness about 5 Ĺ at 300 K. The calculated surface tension is 25+/-2 dyn/cm, which is in excellent agreement with the experimentally obtained value of 28 dyn/cm. The results of our model also compare well with the corresponding results for benzene obtained by Jorgensen and Severance [J. Am. Chem. Soc. 112, 4768 (1990)], who used nonpolarizable potential parameters. We also report the details of our study of K+(C6H6)n=1-6 clusters. We found that the polarization effects were quite significant in these systems.

Dang, Liem X.

2000-07-01

45

Second-moment interatomic potential for gold and its application to molecular-dynamics simulations

We have obtained a new interatomic potential for Au in the framework of the second-moment approximation to the tight-binding model by fitting the total energy of the metal as a function of the volume computed by first-principles calculations. The scheme was validated by calculating the bulk modulus, elastic constants, vacancy formation energy and relaxed surface energies of Au, which were

H. Chamati; N. I. Papanicolaou

2004-01-01

46

Substructured multibody molecular dynamics.

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.

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

47

NASA Astrophysics Data System (ADS)

In analytic theories as well as binary collision simulations the attractive forces between the surface atoms and a recoil leaving the target are described by a surface potential. While in an isotropic model the recoil only suffers energy loss, in the more commonly used planar model refraction or reflection of the recoil also occur. In this work I discuss the limitations of these models, including a generalized model containing the isotropic and planar models as special cases, by comparing molecular dynamics (MD) and binary collision (BC) simulations of atom ejection from (1 0 0)-Si surfaces. It is shown that a surface potential close to planar best describes the MD results. However, in the BC simulations (i) emission yields are systematically too high at low ejection energies, (ii) discrepancies with respect to MD are larger for the ejection of atoms from sub-surface layers, and (iii) the emission yield for top-layer atoms does not increase during erosion of the top layer as suggested by MD. Possible reasons for these deficiencies are discussed. It is concluded that BC results are seriously in question when the effect under investigation depends on the fate of low-energy recoils at the surface.

Hobler, G.

2013-05-01

48

Molecular Dynamics modeling of O2\\/Pt(111) gas-surface interaction using the ReaxFF potential

We studied adsorption dynamics of O2 on Pt(111) using Molecular Dynamics (MD) simulations with the ab initio based reactive force field ReaxFF. We found good quantitative agreement with the experimental data at low incident energies. Specifically, our simulations reproduce the characteristic minimum of the trapping probability at kinetic incident energies around 0.1 eV. This feature is determined by the presence

Paolo Valentini; Thomas E. Schwartzentruber; Ioana Cozmuta

2011-01-01

49

Softened electrostatic molecular potentials.

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

Besalú, Emili; Carbó-Dorca, Ramon

2012-11-02

50

NASA Astrophysics Data System (ADS)

The structure of molten AgCl, AgI, and their eutectic mixture Ag(Cl0.43I0.57) is studied by means of molecular dynamics simulations of polarizable ion model potentials. The corresponding static coherent structure factors reproduce quite well the available neutron scattering data. The qualitative behavior of the simulated partial structure factors and radial distribution functions for molten AgCl and AgI is that predicted by the reverse Monte Carlo modeling of the experimental data. The AgI results are also in qualitative agreement with those calculated from ab initio molecular dynamics.

Alcaraz, Olga; Bitrián, Vicente; Trullŕs, Joaquim

2011-01-01

51

The structure of molten AgCl, AgI, and their eutectic mixture Ag(Cl(0.43)I(0.57)) is studied by means of molecular dynamics simulations of polarizable ion model potentials. The corresponding static coherent structure factors reproduce quite well the available neutron scattering data. The qualitative behavior of the simulated partial structure factors and radial distribution functions for molten AgCl and AgI is that predicted by the reverse Monte Carlo modeling of the experimental data. The AgI results are also in qualitative agreement with those calculated from ab initio molecular dynamics. PMID:21219005

Alcaraz, Olga; Bitrián, Vicente; Trullŕs, Joaquim

2011-01-01

52

In this work, we used molecular dynamics techniques and mean force approaches to compute the ion transfer free energy for the water/dichloromethane liquid-liquid interface. We used polarizable potential models to describe the interactions among the species, and both forward and reverse directions were carried out to estimate the error bar of the computed free energy results. Based on the results of our calculations, we have proposed a mechanism that describes the transport of a chlorine ion across the interface. The computed ion transfer free energy is 14 & No.177; 2 kcal/mol, which is in reasonable agreement with the experimentally reported value of 10 kcal/mol. A smooth transition from the aqueous phase to the non-aqueous phase on the free energy profile clearly indicates that the ion transfer mechanism is a nonactivated process. The computed hydration number for the chlorine ion indicates that some water molecules are associated with the ion inside the non-aqueous phase. This result is in excellent agreement with the experimental interpretation of the ion transfer mechanism reported recently by Osakai et al. (J. Phys. Chem. 1997, 101, 8341).

Dang, Liem X. (BATTELLE (PACIFIC NW LAB))

2001-02-01

53

NASA Astrophysics Data System (ADS)

A new analytical potential energy surface (PES) based on new density functional theory data is constructed for the interaction of atomic hydrogen with both a clean and an H-preadsorbed ?-cristobalite (001) surface. For the atomic interaction, six adsorption sites have been considered, the Si site (T1') being the most stable one. The PES was developed as a sum of pairwise atom-atom interactions between the gas-phase hydrogen atoms and the Si and O atoms of the ?-cristobalite surface. A preliminary molecular dynamics semiclassical study of the different heterogeneous processes (e.g., H2 formation via Eley-Rideal reaction, H adsorption) that occur when H collides with an H-preadsorbed ?-cristobalite (001) surface was carried out. The calculations were performed for collisional energy in the range (0.06 <= Ekin <= 3.0 eV), normal incidence and a surface temperature Tsurf = 1000 K. The recombination probability reaches its maximum value of approximately 0.1 for collisional energies in the range 0.3 <= Ekin <= 0.8 eV. The H2 molecules are formed in medium-lying vibrational levels, while the energy exchanged with the surface in the recombination process is very low.

Gamallo, P.; Rutigliano, M.; Orlandini, S.; Cacciatore, M.; Sayós, R.

2012-11-01

54

In our presented research, we made an attempt to predict the 3D model for cysteine synthase (A2GMG5_TRIVA) using homology-modeling approaches. To investigate deeper into the predicted structure, we further performed a molecular dynamics simulation for 10?ns and calculated several supporting analysis for structural properties such as RMSF, radius of gyration, and the total energy calculation to support the predicted structured model of cysteine synthase. The present findings led us to conclude that the proposed model is stereochemically stable. The overall PROCHECK G factor for the homology-modeled structure was ?0.04. On the basis of the virtual screening for cysteine synthase against the NCI subset II molecule, we present the molecule 1-N, 4-N-bis [3-(1H-benzimidazol-2-yl) phenyl] benzene-1,4-dicarboxamide (ZINC01690699) having the minimum energy score (?13.0?Kcal/Mol) and a log?P value of 6 as a potential inhibitory molecule used to inhibit the growth of T. vaginalis infection.

Singh, Satendra; Singh, Atul Kumar; Gautam, Budhayash

2013-01-01

55

In the present study, we have performed combined molecular dynamics (MD) and potential of mean force (PMF) simulations to determine the enzyme-substrate (ES) binding pathway and the corresponding free energy profiles for wild-type butyrylcholinesterase (BChE) binding with (?)/(+)-cocaine and for the A328W/Y332G mutant binding with (?)-cocaine. According to the PMF simulations, for each ES binding system, the substrate first binds with the enzyme at a peripheral anionic site around the entrance of the active site gorge to form the first ES complex (ES1-like) during the binding process. Further evolution from the ES1-like complex to the nonprereactive ES complex is nearly barrierless, with a free energy barrier being lower than 1.0 kcal/mol. So, the nonprereactive ES binding process should be very fast. The rate-determining step of the entire ES binding process is the subsequent evolution from the nonprereactive ES complex to the prereactive ES complex. Further accounting for the entire ES binding process, the PMF-based simulations qualitatively reproduced the relative order of the experimentally-derived binding free energies (?Gbind), although the simulations systematically overestimated the magnitude of the binding affinity and systematically underestimated the differences between the ?Gbind values. The obtained structural and energetic insights into the entire ES binding process provide a valuable base for future rational design of high-activity mutants of BChE as candidates of an enzyme therapy for cocaine overdose and abuse.

Huang, Xiaoqin; Zheng, Fang; Zhan, Chang-Guo

2011-01-01

56

Scalable molecular dynamics with NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomo- lecular 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

James C. Phillips; Rosemary Braun; Wei Wang; James Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D. Skeel; Laxmikant V. Kalé; Klaus Schulten

2005-01-01

57

The combined molecular dynamics (MD) and potential of mean force (PMF) simulations have been performed to determine the free energy profiles for the binding process of (?)-cocaine interacting with wild-type cocaine esterase (CocE) and its mutants (T172R/G173Q and L119A/L169K/G173Q). According to the MD simulations, the general protein-(?)-cocaine binding mode is not affected by the mutations, e.g. the benzoyl group of (?)-cocaine is always bound in a sub-site composed of aromatic residues W151, W166, F261, and F408 and hydrophobic residue L407, while the carbonyl oxygen on the benzoyl group of (?)-cocaine is hydrogen-bonded with the oxyanion-hole residues Y44 and Y118. According to the PMF-calculated free energy profiles for the binding process, the binding free energies for (?)-cocaine with the wild-type, T172R/G173Q, and L119A/L169K/G173Q CocEs are predicted to be ?6.4, ?6.2, and ?5.0 kcal/mol, respectively. The computational predictions are supported by experimental kinetic data, as the calculated binding free energies are in good agreement with the experimentally-derived binding free energies, i.e. ?7.2, ?6.7, and ?4.8 kcal/mol for the wild-type, T172R/G173Q, and L119A/L169K/G173Q, respectively. The reasonable agreement between the computational and experimental data suggests that the PMF simulations may be used as a valuable tool in new CocE mutant design that aims to decrease the Michaelis-Menten constant of the enzyme for (?)-cocaine.

Huang, Xiaoqin; Zhao, Xinyun; Zheng, Fang; Zhan, Chang-Guo

2012-01-01

58

Multiscale reactive molecular dynamics

NASA Astrophysics Data System (ADS)

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.

Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.

2012-12-01

59

Molecular-dynamics simulations of gold clusters

Structural stability and energetics of gold microclusters Aun (n=313,19–555) have been investigated by molecular-dynamics simulations. A model potential energy function has been parametrized for the gold element by using the dimer interaction potential energy profile of the Au2, which is calculated by relativistic density functional method. Stable structures of the microclusters for (n=3–13) have been determined by a molecular-dynamics simulation.

Takeshi Mukoyama; Masaru Hirata; Sven Varga; Burkhard Fricke; Sakir Erkoç

2000-01-01

60

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

Toby W. Allen; Olaf S. Andersen; Benoit Roux

2006-01-01

61

NASA Astrophysics Data System (ADS)

Path-integral molecular dynamics simulations for the HCl(H 2O) 4 cluster have been performed on the ground-state potential energy surface directly obtained on-the-fly from semiempirical PM3-MAIS molecular orbital calculations. It is found that the HCl(H 2O) 4 cluster has structural rearrangement above the temperature of 300 K showing a liquid-like behavior. Quantum mechanical fluctuation of hydrogen nuclei plays a significant role in structural arrangement processes in this cluster.

Takayanagi, Toshiyuki; Takahashi, Kenta; Kakizaki, Akira; Shiga, Motoyuki; Tachikawa, Masanori

2009-04-01

62

The parameter sets of the ReaxFF potential distributed with the open source, Large-scale Atomic\\/Molecular Massively Parallel Simulator (LAMMPS) code, is validated for simulating crystal RDX. These parameters are used to model crystal RDX and obtain its unit cell size and bulk modulus. It is seen that the parameters supplied with LAMMPS (5-April, 2011 release) do not reproduce the unit cell

M Warrier; P Pahari; S Chaturvedi

2012-01-01

63

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 the elastic constants as a function of density and temperature, the generalized stacking fault energy and the low-index surface energies. PMID:21817375

Branicio, Paulo Sergio; Rino, José Pedro; Gan, Chee Kwan; Tsuzuki, Hélio

2009-01-29

64

NASA Astrophysics Data System (ADS)

The parameter sets of the ReaxFF potential distributed with the open source, Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code, is validated for simulating crystal RDX. These parameters are used to model crystal RDX and obtain its unit cell size and bulk modulus. It is seen that the parameters supplied with LAMMPS (5-April, 2011 release) do not reproduce the unit cell size and bulk modulus of crystal RDX as reported by experiments and by other simulations using the ReaxFF potential. The simulation method and relevant parts of the LAMMPS code implementing the method has been earlier validated for Cu. We conclude that either the parameter sets provided with the LAMMPS distribution or its implementation of the ReaxFF potential are not suitable for modeling crystal RDX.

Warrier, M.; Pahari, P.; Chaturvedi, S.

2012-07-01

65

Molecular dynamics simulations

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

Alder, B.J.

1985-07-01

66

NASA Astrophysics Data System (ADS)

The molecular dynamics method is applied to simulate the recrystallization of an amorphous/crystalline silicon interface. The atomic structure of the amorphous material is constructed with the method of Wooten, Winer, and Weaire. The amorphous on crystalline stack is annealed afterward on a wide range of temperature and time using five different interatomic potentials: Stillinger-Weber, Tersoff, EDIP, SW115, and Lenosky. The simulations are exploited to systematically extract the recrystallization velocity. A strong dependency of the results on the interatomic potential is evidenced and explained by the capability of some potentials (Tersoff and SW115) to correctly handle the amorphous structure, while other potentials (Stillinger-Weber, EDIP, and Lenosky) lead to the melting of the amorphous. Consequently, the interatomic potentials are classified according to their ability to simulate the solid or the liquid phase epitaxy.

Krzeminski, C.; Brulin, Q.; Cuny, V.; Lecat, E.; Lampin, E.; Cleri, F.

2007-06-01

67

Molecular dynamics simulations of silicon wafer bonding

Molecular dynamics simulations based on a modified Stillinger-Weber potential are used to investigate the elementary steps of bonding two Si(0 0 1) wafers. The energy dissipation and thus the dynamic bonding behaviour are controlled by the transfer rates for the kinetic energy. The applicability of the method is demonstrated by studying the interaction of perfect wafer surfaces (UHV conditions). First

D. Conrad; K. Scheerschmidt; U. Gösele

1995-01-01

68

Reactive molecular dynamics simulations of shocked PETN

NASA Astrophysics Data System (ADS)

We have performed molecular dynamics simulations of PETN crystals subjected to shock along the [100] direction. Using the reactive forcefield, ReaxFF, and the molecular dynamics code, GRASP, allows us to track the chemical reactions that occur as both a function of time and position. By simulating larger systems, we can observe the formation of both primary and secondary products to make comparisons with experiments. Composition profiles of these products will be shown along with profiles of stress, temperature, and potential energy.

Budzien, Joanne; Thompson, Aidan P.; Zybin, Sergey V.

2008-03-01

69

Scalable Molecular Dynamics with NAMD

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.

Phillips, James C.; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D.; Kale, Laxmikant; Schulten, Klaus

2008-01-01

70

Scalable molecular dynamics with NAMD.

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

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

71

NASA Astrophysics Data System (ADS)

We develop a general theoretical framework for the analytical description of the interaction of a model diatomic molecular system with an intense, arbitrarily polarized monochromatic laser field. The model molecule comprises an electron in the field of two zero-range potentials separated by the internuclear distance. This model has an exact analytical solution within the theoretical framework of the quasistationary quasienergy (Floquet) approach. In addition to the development of this general framework, we also present a detailed analysis of the weak-field limit, within which we obtain both the frequency-dependent polarizability and the angle-resolved photodetachment cross section for the model system. These fundamental properties are analyzed for both homonuclear and heteronuclear molecular systems in a linearly polarized laser field, for both ground and excited electronic states, and for arbitrary orientation of the molecular axis relative to the polarization vector of the laser field. The analytical expressions for the polarizability and angle-resolved photoelectron spectra exhibit characteristic double-slit interference patterns, allowing one to study their dependence on the parameters of the problem beyond the level of the Born approximation.

Borzunov, S. V.; Frolov, M. V.; Ivanov, M. Yu.; Manakov, N. L.; Marmo, S. S.; Starace, Anthony F.

2013-09-01

72

NASA Astrophysics Data System (ADS)

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.

Liu, J.; Lu, W. Q.

2010-03-01

73

Fermion molecular dynamics in atomic, molecular, and optical physics

NASA Astrophysics Data System (ADS)

Classical dynamics, often called 'molecular dynamics' when applied to atoms and molecules, is much easier than solving the many-body Schrodinger equation for a number of reasons. In particular, correlation and rearrangement are simple in classical dynamics. Fermion molecular dynamics (FMD) is a quasi-classical method for treating quantum-mechanical systems using classical equations of motion with momentum-dependent model potentials added to the usual Hamiltonian. These model potentials constrain the motion to satisfy the Heisenberg uncertainty and the Pauli exclusion principles. We discuss the foundations of the FMD model and its applications to atomic and molecular structure, ion-atom collisions, stopping powers, formation of antiprotonic atoms, and multiple ionization of atoms in strong laser fields.

Wilets, Lawrence; Cohen, James S.

1998-03-01

74

Efficient molecular simulation of chemical potentials

This paper evaluates methods of estimating chemical potential: actually fugacity coefficient: from molecular simulations. These methods are based on formulas given by Widom, by Bennett, and by Shing and Gubbins. They are tested with molecular dynamics simulations of Lennard-Jones liquids along the isotherm kT\\/epsilon = 1.2 for densities from 0.65sigmaâ»Âł to 0.90sigmaâ»Âł. A new test molecule sampling method, excluded volume

G. L. Deitrick; L. E. Scriven; H. T. Davis

1989-01-01

75

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 Ĺ 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.

Torres, Rodrigo; Swift, Robert V.; Chim, Nicholas; Wheatley, Nicole; Lan, Benson; Atwood, Brian R.; Pujol, Celine; Sankaran, Banu; Bliska, James B.; Amaro, Rommie E.; Goulding, Celia W.

2011-01-01

76

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 Ĺ 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

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

2011-09-26

77

Molecular dynamics with quantum fluctuations

A quantum dynamics approach, called Gaussian molecular dynamics, is introduced. As in the centroid molecular dynamics, the N-body quantum system is mapped to an N-body classical system with an effective Hamiltonian arising within the variational Gaussian wave-packet approximation. The approach is exact for the harmonic oscillator and for the high-temperature limit, accurate in the short-time limit and is computationally very efficient.

Georgescu, Ionut; Mandelshtam, Vladimir A. [Chemistry Department, University of California at Irvine, Irvine, California 92697 (United States)

2010-09-01

78

Using an integrated computational approach involving homology modelling, pharmacophore/structure-based virtual screening, molecular dynamics simulations and per-residue energy contribution, 10 compounds were proposed as potential TB inhibitors. Via validated docking calculations, binding free energy calculations showed that the proposed compounds presented better binding affinity with DNA gyrase B when compared to novobiocin. The compiled in silico approach employed in this study may serve as a useful tool in the process of the design and development of drugs, not only against TB, but also for a wide range of biological systems. PMID:23614896

Maharaj, Yushir; Soliman, Mahmoud E S

2013-08-01

79

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

Ghosh, Manik Kumer; Lee, Jooyong; Choi, Cheol Ho; Cho, Minhaeng

2012-08-30

80

NASA Astrophysics Data System (ADS)

Characterization of the potential energy surface is one of the essential problems to understand the mechanism of the ion conduction in glasses. In this work, ion dynamics in several lithium silicate glasses are examined by using molecular dynamics simulations. The number of ion sites, site energy, and the respective structures were examined for both fast (diffusive) and slow (localized) ions. We have visualized ion sites using the molecular dynamics simulation data and obtained the number of sites without being affected by a cut off value. The number obtained for the Li2SiO3 glass is 8 10% larger than that of ions. The value is reasonable to explain the diffusion mechanism by cooperative jumps, since rapid decrease of transport property in cooperative dynamics is expected if the number of the sites is too small while the cooperative jumps may be scarcely observed when the number of the vacancy is too large. The percentage of the available sites for the Li4SiO4 in the glassy state was found to be almost the same as that for Li2SiO3, while the diffusion coefficient of Li in Li4SiO4 is larger than Li2SiO3. Increase of the diffusion coefficient with increasing alkali contents is easily explained by the contribution of the cooperative jumps but not by a simple mobile vacancy mechanism. Besides the characteristic sites for each slow (type A) and fast (type B) ions, many common sites for both type of ions are found, while the steepest descent energy distribution for these types of ions is quite similar. On the other hand, the partial pair correlation function, g(r) of A-A pairs is found to be quite different from that of B-B pairs. Therefore, microstructures related to the density fluctuation of the Li ions are important for the difference of slow and fast dynamics.

Habasaki, Junko; Hiwatari, Yasuaki

2004-04-01

81

Uncertainty quantification in molecular dynamics

NASA Astrophysics Data System (ADS)

This dissertation focuses on uncertainty quantification (UQ) in molecular dynamics (MD) simulations. The application of UQ to molecular dynamics is motivated by the broad uncertainty characterizing MD potential functions and by the complexity of the MD setting, where even small uncertainties can be amplified to yield large uncertainties in the model predictions. Two fundamental, distinct sources of uncertainty are investigated in this work, namely parametric uncertainty and intrinsic noise. Intrinsic noise is inherently present in the MD setting, due to fluctuations originating from thermal effects. Averaging methods can be exploited to reduce the fluctuations, but due to finite sampling, this effect cannot be completely filtered, thus yielding a residual uncertainty in the MD predictions. Parametric uncertainty, on the contrary, is introduced in the form of uncertain potential parameters, geometry, and/or boundary conditions. We address the UQ problem in both its main components, namely the forward propagation, which aims at characterizing how uncertainty in model parameters affects selected observables, and the inverse problem, which involves the estimation of target model parameters based on a set of observations. The dissertation highlights the challenges arising when parametric uncertainty and intrinsic noise combine to yield non-deterministic, noisy MD predictions of target macroscale observables. Two key probabilistic UQ methods, namely Polynomial Chaos (PC) expansions and Bayesian inference, are exploited to develop a framework that enables one to isolate the impact of parametric uncertainty on the MD predictions and, at the same time, properly quantify the effect of the intrinsic noise. Systematic applications to a suite of problems of increasing complexity lead to the observation that an uncertain PC representation built via Bayesian regression is the most suitable model for the representation of uncertain MD predictions of target observables in the presence of intrinsic noise and parametric uncertainty. The dissertation is organized in successive, self-contained problems of increasing complexity aimed at investigating the target UQ challenge in a progressive fashion.

Rizzi, Francesco

82

Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics.

National Technical Information Service (NTIS)

Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycos...

M. C. Donnamaira E. I. Howard J. R. Grigera

1992-01-01

83

Molecular photoionization dynamics

This program seeks to develop both physical insight and quantitative characterization of molecular photoionization processes. Progress is briefly described, and some publications resulting from the research are listed. (WHK)

Dehmer, J.L.

1982-01-01

84

Symmetry Reduced Dynamics of Charged Molecular Strands

The equations of motion are derived for the dynamical folding of charged molecular strands (such as DNA) modeled as flexible\\u000a continuous filamentary distributions of interacting rigid charge conformations. The new feature is that these equations are\\u000a nonlocal when the screened Coulomb interactions, or Lennard–Jones potentials between pairs of charges, are included. The nonlocal\\u000a dynamics is derived in the convective representation

David C. P. Ellis; François Gay-Balmaz; Darryl D. Holm; Vakhtang Putkaradze; Tudor S. Ratiu

2010-01-01

85

Chitinolytic ?-N-acetyl-d-hexosaminidases, as a class of chitin hydrolysis enzyme in insects, are a potential species-specific target for developing environmentally-friendly pesticides. Until now, pesticides targeting chitinolytic ?-N-acetyl-d-hexosaminidase have not been developed. This study demonstrates a combination of different theoretical methods for investigating the key structural features of this enzyme responsible for pesticide inhibition, thus allowing for the discovery of novel small molecule inhibitors. Firstly, based on the currently reported crystal structure of this protein (OfHex1.pdb), we conducted a pre-screening of a drug-like compound database with 8 × 106 compounds by using the expanded pesticide-likeness criteria, followed by docking-based screening, obtaining 5 top-ranked compounds with favorable docking conformation into OfHex1. Secondly, molecular docking and molecular dynamics simulations are performed for the five complexes and demonstrate that one main hydrophobic pocket formed by residues Trp424, Trp448 and Trp524, which is significant for stabilization of the ligand–receptor complex, and key residues Asp477 and Trp490, are respectively responsible for forming hydrogen-bonding and ?–? stacking interactions with the ligands. Finally, the molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) analysis indicates that van der Waals interactions are the main driving force for the inhibitor binding that agrees with the fact that the binding pocket of OfHex1 is mainly composed of hydrophobic residues. These results suggest that screening the ZINC database can maximize the identification of potential OfHex1 inhibitors and the computational protocol will be valuable for screening potential inhibitors of the binding mode, which is useful for the future rational design of novel, potent OfHex1-specific pesticides.

Liu, Jianling; Liu, Mengmeng; Yao, Yao; Wang, Jinan; Li, Yan; Li, Guohui; Wang, Yonghua

2012-01-01

86

Modeling Molecular Dynamics from Simulations

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.

Hinrichs, Nina Singhal (University of Chicago)

2009-01-28

87

NASA Astrophysics Data System (ADS)

Testosterone hydroxylation is a prototypical reaction of human cytochrome P450 3A4, which metabolizes about 50% of oral drugs on the market. Reaction dynamics calculations were carried out for the testosterone 6?-hydrogen abstraction and the 6?-d1-testosterone 6?-duterium abstraction employing a model that consists of the substrate and the active oxidant compound I. The calculations were performed at the level of canonical variational transition state theory with multidimensional tunneling and were based on a semiglobal full-dimensional potential energy surface generated by the multiconfiguration molecular mechanics technique. The tunneling coefficients were found to be around 3, indicating substantial contributions by quantum tunneling. However, the tunneling made only modest contributions to the kinetic isotope effects. The kinetic isotope effects were computed to be about 2 in the doublet spin state and about 5 in the quartet spin state.

Zhang, Yan; Lin, Hai

2009-05-01

88

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

Patel, Sonal; Wilding, W Vincent; Rowley, Richard L

2011-12-21

89

Second-moment interatomic potential for Al, Ni and Ni–Al alloys, and molecular dynamics application

We present an interatomic potential for Al, Ni and Ni–Al ordered alloys within the second-moment approximation of the tight-binding theory. The potential was obtained by fitting to the total energy of these materials computed by first-principles augmented-plane-wave calculations as a function of the volume. The scheme was validated by calculating the bulk modulus and the elastic constants of the pure

N. I Papanicolaou; H Chamati; G. A Evangelakis; D. A Papaconstantopoulos

2003-01-01

90

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.

Hall, G.E.; Prrese, J.M.; Sears, T.J.; Weston, R.E.

1999-05-21

91

Adaptive integration of molecular dynamics

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

Illia Horenko; Martin Weiser

2003-01-01

92

A recently proposed electronic structure-based force field called the explicit polarization (X-Pol) potential is used to study many-body electronic polarization effects in a protein, in particular by carrying out a molecular dynamics (MD) simulation of bovine pancreatic trypsin inhibitor (BPTI) in water with periodic boundary conditions. The primary unit cell is cubic with dimensions ~54 × 54 × 54 Ĺ(3), and the total number of atoms in this cell is 14281. An approximate electronic wave function, consisting of 29026 basis functions for the entire system, is variationally optimized to give the minimum Born-Oppenheimer energy at every MD step; this allows the efficient evaluation of the required analytic forces for the dynamics. Intramolecular and intermolecular polarization and intramolecular charge transfer effects are examined and are found to be significant; for example, 17 out of 58 backbone carbonyls differ from neutrality on average by more than 0.1 electron, and the average charge on the six alanines varies from -0.05 to +0.09. The instantaneous excess charges vary even more widely; the backbone carbonyls have standard deviations in their fluctuating net charges from 0.03 to 0.05, and more than half of the residues have excess charges whose standard deviation exceeds 0.05. We conclude that the new-generation X-Pol force field permits the inclusion of time-dependent quantum mechanical polarization and charge transfer effects in much larger systems than was previously possible. PMID:20490369

Xie, Wangshen; Orozco, Modesto; Truhlar, Donald G; Gao, Jiali

2009-02-17

93

Population based reweighting of scaled molecular dynamics.

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

Sinko, William; Miao, Yinglong; de Oliveira, César Augusto F; McCammon, J Andrew

2013-07-11

94

Population Based Reweighting of Scaled Molecular Dynamics

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.

2013-01-01

95

Multibaric-multithermal ensemble molecular dynamics simulations.

We present new generalized-ensemble molecular dynamics simulation algorithms, which we refer to as the multibaric-multithermal molecular dynamics. We describe three algorithms based on (1) the Nosé thermostat and the Andersen barostat, (2) the Nosé-Poincaré thermostat and the Andersen barostat, and (3) the Gaussian thermostat and the Andersen barostat. The multibaric-multithermal simulations perform random walks widely both in the potential-energy space and in the volume space. Therefore, one can calculate isobaric-isothermal ensemble averages in wide ranges of temperature and pressure from only one simulation run. We test the effectiveness of the multibaric-multithermal algorithm by applying it to a Lennard-Jones 12-6 potential system. PMID:16381079

Okumura, Hisashi; Okamoto, Yuko

2006-02-01

96

Molecular dynamics simulation of zirconia melting

The melting point for the tetragonal and cubic phases of zirconia (ZrO2) was computed using Z-method microcanonical molecular dynamics simulations for two different interaction models: the empirical\\u000a Lewis-Catlow potential versus the relatively new reactive force field (ReaxFF) model. While both models reproduce the stability of the cubic phase over\\u000a the tetragonal phase at high temperatures, ReaxFF also gives approximately the

Sergio Davis; Anatoly B. Belonoshko; Anders Rosengren; Adri C. T. van Duin; Börje Johansson

2010-01-01

97

WHAT MAKES MOLECULAR DYNAMICS WORK?*

The equations of motion for deterministic molecular dynamics (MD) are chaotic, creating problems for their numerical treatment due to the exponential growth of error with time. Indeed, modeling and computational errors overwhelm numerical trajectories in typical simulations. Consequently, accuracy is expected only in a statistical sense, based on random initial conditions. Of great interest then is the relationship between errors in the dynamics and their effects on the accuracy of statistical quantities, specifically, expectations. This article provides a formula for the effect of a perturbation on an ensemble average, which explains the accuracy of such calculations. It also provides a formula for the effect of a perturbation on a time correlation function, which, however, fails to explain accuracy for these calculations. Additionally, this article clarifies the relationships among various dynamical properties of MD and provides an extension to a theory of non-Hamiltonian MD.

SKEEL, ROBERT D.

2009-01-01

98

We have explored the degree to which an intermolecular potential for the explosive hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX) is transferable for predictions of crystal structures (within the approximation of rigid molecules) of a similar chemical system,in this case, polymo...

99

Molecular to fluid dynamics: The consequences of stochastic molecular motion

The derivation of fluid dynamic equations from molecular equations is considered. This is done on the basis of a stochastic model for the molecular motion which can be obtained by a projection of underlying deterministic equations. The stochastic model is used to derive fluid dynamic equations where the molecular stress tensor and heat flux appear as unknowns. However, the stochastic

Stefan Heinz

2004-01-01

100

Potential energy landscape contribution to the dynamic heat capacity

NASA Astrophysics Data System (ADS)

The dynamic heat capacity of a simple polymeric, model glass former was computed using molecular dynamics simulations by sinusoidally driving the temperature and recording the resultant energy. The underlying potential energy landscape of the system was probed by taking a time series of particle positions and quenching them. The resulting dynamic heat capacity demonstrates that the long time relaxation is the direct result of dynamics resulting from the potential energy landscape.

McCoy, John; Brown, Jonathan

2013-03-01

101

Molecular dynamics simulations of dipolar dusty plasmas

The authors use molecular dynamics (MD) simulation methods to investigate dusty plasma crystal structure in an external potential, with the grains subject to both a spherically symmetric Debye-Hueckel potential and a cylindrically symmetric dipole interaction. The dipole contribution models the experimentally important effects of ion flow or intrinsic grain polarization. They find that the addition of a small dipole term changes the crystal structure from bct to one in which the grains are aligned vertically, consistent with experiments as well as recent theoretical calculations.

Hammerberg, J.E.; Holian, B.L.; Murillo, M.S.; Winske, D.

1998-12-31

102

Rheology via nonequilibrium molecular dynamics

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.

Hoover, W.G.

1982-10-01

103

Accelerated molecular dynamics: Theory, implementation and applications

NASA Astrophysics Data System (ADS)

Accelerated molecular dynamics (aMD) is an enhanced-sampling method that improves the conformational space sampling by reducing energy barriers separating different states of a system. Since it was first proposed by Hamelberg et al. (J. Chem. Phys., 120:11919, 2004), the method has been applied to study a variety of biological and chemical problems. AMD is now available in several major molecular dynamics programs and its applications range from protein and lipid conformational sampling to ab initio and free energy calculations. Here we briefly review the development of the aMD method, focusing on its theory, implementation and applications. Through discussions of several examples, we also comment on potential directions of future development of the aMD method.

Wang, Yi; McCammon, J. Andrew

2012-06-01

104

Potential formulation of sleep dynamics

NASA Astrophysics Data System (ADS)

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.

Phillips, A. J. K.; Robinson, P. A.

2009-02-01

105

Sets of self-consistent oxygen-rare earth (RE = La, Y, Lu, Sc) interatomic potential parameters are derived using a force-matching procedure and utilized in molecular dynamics (MD) simulations for exploring the structures of RE2O3-Al2O3-SiO2 glasses that feature a fixed molar ratio nAl/nSi = 1 but variable RE contents. The structures of RE aluminosilicate (AS) glasses depend markedly on the RE(3+) cation field strength (CFS) over both short and intermediate length-scales. We explore these dependencies for glasses incorporating the cations La(3+), Y(3+), Lu(3+) and Sc(3+), whose CFSs increase due to the concomitant shrinkage of the ionic radii: RLa > RY > RLu > RSc. This trend is mirrored in decreasing average RE(3+) coordination numbers (Z[combining macron]RE) from Z[combining macron]La = 6.4 to Z[combining macron]Sc = 5.4 in the MD-derived data. However, overall the effects from RE(3+) CFS elevations on the local glass structures are most pronounced in the O and {Al([4]), Al([5]), Al([6])} speciations. The former display minor but growing populations of O([0]) ("free oxygen ion") and O([3]) ("oxygen tricluster") moieties. The abundance of AlO5 polyhedra increases significantly from ?10% in La-based glasses to ?30% in their Sc counterparts at the expense of the overall dominating AlO4 tetrahedra, whereas the amounts of AlO6 groups remain <5% throughout. We also discuss the Si([4])/Al([p]) (p = 4, 5, 6) intermixing and the nature of their oxygen bridges, where the degree of edge-sharing increases together with the RE(3+) CFS. PMID:23925792

Okhotnikov, Kirill; Stevensson, Baltzar; Edén, Mattias

2013-08-21

106

Radiation in molecular dynamic simulations

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

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

2008-10-13

107

Molecular dynamics simulations with many-body interactions were carried out to understand the bulk and interfacial absorption of gases in 1-butyl-3-methylimidazolium tetrafluoroborate (BMIMBF4). A new polarizable molecular model was developed for BMIMBF4, which was found to give the correct liquid density, but also had good agreement with experiment for its surface tension and X-ray reflectivity. The potential of mean force of CO2 and SO2 were calculated across the air-BMIMBF4 interface, and the bulk free energies were calculated with the free energy perturbation method. A new polarizable model was also developed for CO2. The air-BMIMBF4 interface had enhanced BMIM density, which was mostly related to its butyl group, followed by enhanced BF4 density a few angstroms towards the liquid bulk. The density profiles were observed to exhibit oscillations between high BMIM and BF4 density, indicating the presence of surface layering induced by the interface. The potential of mean force for CO2 and SO2 showed more negative free energies in regions of enhanced BF4 density, while more positive free energies in regions of high BMIM density. Moreover, these gases showed free energy minimums at the interface, where the BMIM alkyl groups were found to be most prevalent. Our results show the importance of ionic liquid interfacial ordering for understanding gas solvation in them. This work was supported by the US Department of Energy Basic Energy Sciences' Chemical Sciences, Geosciences & Biosciences Division. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

Wick, Collin D.; Chang, Tsun-Mei; Dang, Liem X.

2010-11-25

108

Molecular Dynamics Simulation of Substituted Polyacetylenes.

National Technical Information Service (NTIS)

Molecular mechanics and molecular dynamics calculations have been applied to several substituted polyacetylenes. Results for the barrier height for single bond rotation for polyacetylene were compared to experimental values and quantum mechanics results f...

X. F. Sun S. B. Clough S. K. Tripathy G. L. Baker

1991-01-01

109

Molecular dynamics simulation of zirconia melting

NASA Astrophysics Data System (ADS)

The melting point for the tetragonal and cubic phases of zirconia (ZrO2) was computed using Z-method microcanonical molecular dynamics simulations for two different interaction models: the empirical Lewis-Catlow potential versus the relatively new reactive force field (ReaxFF) model. While both models reproduce the stability of the cubic phase over the tetragonal phase at high temperatures, ReaxFF also gives approximately the correct melting point, around 2900 K, whereas the Lewis-Catlow estimate is above 6000 K.

Davis, Sergio; Belonoshko, Anatoly B.; Rosengren, Anders; van Duin, Adri C. T.; Johansson, Börje

2010-10-01

110

Molecular dynamics simulation of chiral chromatography

NASA Astrophysics Data System (ADS)

Molecular dynamics (MD) has been used to simulate the liquid chromatography process. The flow speed was arbitrarily increased to save computer time. Then the average translational motion is still relatively slow and does not perturb the interaction of the solute with the stationary phase. The CHFClBr molecule was used as model chiral system, with water as a solvent. The MD technique with a standard potential provided realistic all-atomic simulations of the separation ratios and enabled to test the sensitivity of the process to solvent polarity and temperature. Low temperature and non-polar solvent favored the separation.

Šebestík, Jaroslav; Bou?, Petr

2008-01-01

111

An optimized molecular potential for carbon dioxide.

An optimized molecular potential model for carbon dioxide is presented in this paper. Utilizing the established techniques of molecular-dynamics and histogram reweighting grand canonical Monte Carlo simulations, this model is demonstrated to show excellent predictability for thermodynamic, transport, and liquid structural properties in a wide temperature-pressure range with remarkable accuracies. The average deviations of this new model from experimental data for the saturated liquid densities, vapor densities, vapor pressures, and heats of vaporization are around 0.1%, 2.3%, 0.7%, and 1.9%, respectively. The calculated critical point is almost pinpointed by the new model. The experimental radial distribution functions ranging from 240.0 to 473.0 K are well reproduced as compared to neutron-diffraction measurements. The predicted self-diffusion coefficients are in good agreement with the nuclear-magnetic-resonance measurements. The previously published potential models for CO2 are also systematically evaluated, and our proposed new model is found to be superior to the previous models in general. PMID:15974754

Zhang, Zhigang; Duan, Zhenhao

2005-06-01

112

Dynamics and Potential Energy Landscape of Supercooled Water

We present molecular dynamics simulations of the SPC\\/E model of water to explore the connection between dynamic properties and the potential energy landscape. We calculate the configurational entropy and instantaneous normal mode (or local potential energy curvature) spectrum in the same region of the phase diagram where the dynamics are well-described by the predictions of the mode-coupling theory. We find

Francis W. Starr; Emilia Lanave; Antonio Scala; Francesco Sciortino; H. Eugene Stanley

2000-01-01

113

Application of optimal prediction to molecular dynamics

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.

Barber IV, John Letherman

2004-12-01

114

Fragment recognition in molecular dynamics

We investigate the properties of three methods of fragment recognition in microscopic simulations of molecular dynamics. They are (a) the early cluster recognition algorithm (ECRA) which looks for the most bound partitions in phase space, (b) the minimum spanning tree in two particle energy space (MSTE) which looks for those simply connected partitions in which each particle is bound to, at least, one other member of the cluster to which it belongs, and (c) the standard minimum spanning tree (MST) in configuration space. It is found that, if the objective of a given calculation is to study the time evolution of properties related to the fragment distribution, the MST should be discarded, MSTE results will be valid for not too short times, and ECRA results will give the most complete description of such properties. {copyright} {ital 1997} {ital The American Physical Society}

Strachan, A.; Dorso, C.O. [Departamento de Fisica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellon I, Ciudad Universitaria, Nunez (1428), Buenos Aires (Argentina)

1997-08-01

115

Molecular Dynamics Studies of Superionic Conductor CaF2

In the molecular dynamics study of the superionic conductor CaF2, the ionic soft-core system, of which the pair potential consists of the Coulombic and soft-core potentials, is investigated. The influence of the potential, especially of the softness of the soft-core repulsion, on the distribution of anions and diffusion paths is studied. We also study the dynamics of the diffusion in

Yutaka Kaneko; Akira Ueda

1988-01-01

116

The rotation of F1Fo-ATP synthase is powered by the proton motive force across the energy-transducing membrane. The protein complex functions like a turbine; the proton flow drives the rotation of the c-ring of the transmembrane Fo domain, which is coupled to the ATP-producing F1 domain. The hairpin-structured c-protomers transport the protons by reversible protonation/deprotonation of a conserved Asp/Glu at the outer transmembrane helix (TMH). An open question is the proton transfer pathway through the membrane at atomic resolution. The protons are thought to be transferred via two half-channels to and from the conserved cAsp/Glu in the middle of the membrane. By molecular dynamics simulations of c-ring structures in a lipid bilayer, we mapped a water channel as one of the half-channels. We also analyzed the suppressor mutant cP24D/E61G in which the functional carboxylate is shifted to the inner TMH of the c-protomers. Current models concentrating on the “locked” and “open” conformations of the conserved carboxylate side chain are unable to explain the molecular function of this mutant. Our molecular dynamics simulations revealed an extended water channel with additional water molecules bridging the distance of the outer to the inner TMH. We suggest that the geometry of the water channel is an important feature for the molecular function of the membrane part of F1Fo-ATP synthase. The inclination of the proton pathway isolates the two half-channels and may contribute to a favorable clockwise rotation in ATP synthesis mode.

Gohlke, Holger; Schlieper, Daniel; Groth, Georg

2012-01-01

117

The rotation of F(1)F(o)-ATP synthase is powered by the proton motive force across the energy-transducing membrane. The protein complex functions like a turbine; the proton flow drives the rotation of the c-ring of the transmembrane F(o) domain, which is coupled to the ATP-producing F(1) domain. The hairpin-structured c-protomers transport the protons by reversible protonation/deprotonation of a conserved Asp/Glu at the outer transmembrane helix (TMH). An open question is the proton transfer pathway through the membrane at atomic resolution. The protons are thought to be transferred via two half-channels to and from the conserved cAsp/Glu in the middle of the membrane. By molecular dynamics simulations of c-ring structures in a lipid bilayer, we mapped a water channel as one of the half-channels. We also analyzed the suppressor mutant cP24D/E61G in which the functional carboxylate is shifted to the inner TMH of the c-protomers. Current models concentrating on the "locked" and "open" conformations of the conserved carboxylate side chain are unable to explain the molecular function of this mutant. Our molecular dynamics simulations revealed an extended water channel with additional water molecules bridging the distance of the outer to the inner TMH. We suggest that the geometry of the water channel is an important feature for the molecular function of the membrane part of F(1)F(o)-ATP synthase. The inclination of the proton pathway isolates the two half-channels and may contribute to a favorable clockwise rotation in ATP synthesis mode. PMID:22942277

Gohlke, Holger; Schlieper, Daniel; Groth, Georg

2012-08-31

118

Molecular dynamics of membrane proteins.

Understanding the dynamics of the membrane protein rhodopsin will have broad implications for other membrane proteins and cellular signaling processes. Rhodopsin (Rho) is a light activated G-protein coupled receptor (GPCR). When activated by ligands, GPCRs bind and activate G-proteins residing within the cell and begin a signaling cascade that results in the cell's response to external stimuli. More than 50% of all current drugs are targeted toward G-proteins. Rho is the prototypical member of the class A GPCR superfamily. Understanding the activation of Rho and its interaction with its Gprotein can therefore lead to a wider understanding of the mechanisms of GPCR activation and G-protein activation. Understanding the dark to light transition of Rho is fully analogous to the general ligand binding and activation problem for GPCRs. This transition is dependent on the lipid environment. The effect of lipids on membrane protein activity in general has had little attention, but evidence is beginning to show a significant role for lipids in membrane protein activity. Using the LAMMPS program and simulation methods benchmarked under the IBIG program, we perform a variety of allatom molecular dynamics simulations of membrane proteins.

Woolf, Thomas B. (Johns Hopkins University School of Medicine, Baltimore, MD); Crozier, Paul Stewart; Stevens, Mark Jackson

2004-10-01

119

Symmetry Reduced Dynamics of Charged Molecular Strands

NASA Astrophysics Data System (ADS)

The equations of motion 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 these equations are nonlocal when the screened Coulomb interactions, or Lennard-Jones potentials between pairs of charges, are included. The nonlocal dynamics is derived in the convective representation of continuum motion by using modified Euler-Poincaré 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. The motion equations in the convective representation are shown to arise by a classical Lagrangian reduction associated to the symmetry group of the system. This approach uses the process of affine Euler-Poincaré reduction initially developed for complex fluids. On the Hamiltonian side, the Poisson bracket of the molecular strand is obtained by reduction of the canonical symplectic structure on phase space. A change of variables allows a direct passage from this classical point of view to the covariant formulation in terms of Lagrange-Poincaré equations of field theory. In another revealing perspective, the convective representation of the nonlocal equations of molecular strand motion is transformed into quaternionic form.

Ellis, David C. P.; Gay-Balmaz, François; Holm, Darryl D.; Putkaradze, Vakhtang; Ratiu, Tudor S.

2010-09-01

120

Reactive molecular dynamics simulations of shocked PETN

We have performed molecular dynamics simulations of PETN crystals subjected to shock along the [100] direction. Using the reactive forcefield, ReaxFF, and the molecular dynamics code, GRASP, allows us to track the chemical reactions that occur as both a function of time and position. By simulating larger systems, we can observe the formation of both primary and secondary products to

Joanne Budzien; Aidan P. Thompson; Sergey V. Zybin

2008-01-01

121

Efficient molecular simulation of chemical potentials

This paper evaluates methods of estimating chemical potential: actually fugacity coefficient: from molecular simulations. These methods are based on formulas given by Widom, by Bennett, and by Shing and Gubbins. They are tested with molecular dynamics simulations of Lennard-Jones liquids along the isotherm kT/epsilon = 1.2 for densities from 0.65sigma/sup -3/ to 0.90sigma/sup -3/. A new test molecule sampling method, excluded volume map sampling, is found to be as much as 2 orders of magnitude more efficient than uniform test molecule sampling; it is more efficient and reliable than restricted umbrella sampling proposed by Shing and Gubbins. Several difficulties of estimating the variance of the fugacity coefficient estimates are surmounted by novel application of standard statistical methods. The statistical analysis shows that Bennett's method yields estimates with the least variance and Widom's method yields estimates with the greatest variance although all methods are consistent to within statistical error. Pressure and fugacity coefficient estimates obey the Gibbs--Duhem equation along the chosen isotherm up to densities of 0.75sigma/sup -3/ for 108-molecule, 0.8sigma/sup -3/ for 200-molecule, and 0.9sigma/sup -3/ for 500-molecule simulations.

Deitrick, G.L.; Scriven, L.E.; Davis, H.T.

1989-02-15

122

Molecular dynamics simulation of condensed-phase chiral molecular propellers.

Molecular dynamics simulations were performed for an axial-chiral liquid crystalline (LC) monolayer under trans-monolayer gas flow. The rotational dynamics of the monolayer chiral LC molecule along its long-molecular axis were analyzed at the molecular level. We found a precise correspondence between the flow-driven molecular rotation direction and molecular chirality as well as between the rotation direction and the trans-monolayer flow direction. The rotational direction exactly corresponded to what was expected in the proposed chiral molecular propeller model (Tabe, Y.; Yokoyama, H. Nat. Mater. 2003, 2, 806). Among the four trans-monolayer gas species we investigated, we found argon to be the most efficient at driving the chiral molecular propeller and helium the least efficient. PMID:20536201

Yoneya, M; Tabe, Y; Yokoyama, H

2010-07-01

123

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

Many interesting dynamic properties of biological molecules cannot be simulated directly using molecular dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy minima with high free energy barriers for large numbers of computational steps. The dynamic evolution of many molecular systems occurs through a series of rare events as the system moves from one potential

Donald Hamelberg; John Mongan; J. Andrew McCammon

2004-01-01

124

Molecular dynamics investigation on tin

NASA Astrophysics Data System (ADS)

Laser-produced tin (Sn) plasma has been considered as one of main candidates for extreme ultraviolet (EUV) light source used in EUV lithography. In order to increase conversion efficiency and to mitigate energetic ions and neutral from laser-produced Sn plasma, fundamental investigation is necessary. Theoretical study by means of hydrodynamic simulation is expected to guide us to optimize Sn target and pumping conditions. Equation of state of materials is an inevitable ingredient of all hydrodynamic simulations. However, the early stages of the laser-matter interaction process, equation of state at phase transition, for example, liquid-vapor transition, and the ejection of particles are remain unexplored. The aim of this research is to report the simulated properties of Sn over wide physical conditions by means of Materials Studio code and a 3D homemade molecular dynamics code developed for this purpose. Results have shown transient effects on the phase transitions. The simulation results are compared to experimental data obtained by pulsed laser ablation of Sn. Velocity distributions of evaporated particles from the Sn are discussed as a function of laser fluence. Also, the equation of state has been tabulated in warm dense region.

Masnavi, M.; Parchamy Araghy, H.; Ghoranneviss, M.; Nakajima, M.; Endo, A.; Horioka, K.

2010-11-01

125

NAMD2: Greater Scalability for Parallel Molecular Dynamics

Molecular dynamics programs simulate the behavior of biomolecular systems, leading to understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this potential, it is necessary to develop a scalable program. It is also necessary that the program be easily modified by application–domain programmers. The

Laxmikant Kalé; Robert Skeel; Milind Bhandarkar; Robert Brunner; Attila Gursoy; Neal Krawetz; James Phillips; Aritomo Shinozaki; Krishnan Varadarajan; Klaus Schulten

1999-01-01

126

Molecular dynamics study of tantalum spallation

NASA Astrophysics Data System (ADS)

We present in this paper a molecular dynamics study of tantalum spallation. The spallation is the final stage of the damaging caused by a series of shock and rarefaction waves. This complex process is due to the nucleation, the growth and the coalescence of pores within a thin zone corresponding to the crossing of two rarefaction waves. Various experimental works allowed a partial description of this process. We present here a complementary analysis based on large classical molecular dynamics simulations in single and polycristal of tantalum. We use a rather sophisticated potential function (MEAM) associated with multi-million particle samples. The simulations were made on the TERA 10 computer of CEA-DAM, and needed several hundred processors. We examine at various times the apparition and the evolution of pores, and provide their spatio-temporal distribution. The one dimensional (in the hydrodynamics sense) and 3D cases are considered in order to understand the effects of lateral rarefaction waves in the spallation phenomenon. Comparisons with experimental data are shown.

Soulard, Laurent; Bontaz, Joelle

2007-06-01

127

Time-Dependent Molecular Reaction Dynamics

This paper is a brief review of a time-dependent, direct, nonadiabatic theory of molecular processes called Electron Nuclear Dynamics (END). This approach to the study of molecular reaction dynamics is a hierarchical theory that can be applied at various levels of approximation. The simplest level of END uses classical nuclei and represents all electrons by a single, complex, determinantal wave function. The wave function parameters such as average nuclear positions and momenta, and molecular orbital coefcients carry the time dependence and serve as dynamical variables. Examples of application are given of the simplest level of END to ion-atom and ion-molecule reactions.

Oehrn, Yngve [QTP, Departments of Chemistry and Physics, University of Florida, Gainesville, FL, 32611-8435 (United States)

2007-11-29

128

DNA translocation through a molecular nanopore: A molecular dynamics study

In this thesis, the experimental and modeling techniques are discussed that were applied to thread a DNA molecule through a molecular nanopore. In a forced probe molecular dynamic simulation, a single-stranded (ss)DNA molecule was threaded through a beta-cyclodextrin (CD) ring at different constant speeds. Forces of friction between the molecular ring and each nucleotide were computed. These forces were plotted

Shahid Qamar

2009-01-01

129

NASA Astrophysics Data System (ADS)

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.

Duan, Zhenhao; Zhang, Zhigang

2006-05-01

130

Molecular dynamics investigation of dynamical properties of phosphatidylethanolamine lipid bilayers

We describe the dynamic behavior of a 1-stearoyl-2-oleoyl-phosphatidylethanolamine (SOPE) bilayer from a 20 ns molecular dynamics simulation. The dynamics of individual molecules are characterized in terms of 2H 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

Michael C. Pitman; Frank Suits; Klaus Gawrisch; Scott E. Feller

2005-01-01

131

Molecular dynamics studies of superionic conductors

Structural and dynamical properties of superionic conductors AgI and CuI are studied using molecular dynamics (MD) techniques. Our model of these superionic conductors is based on the use of effective pair potentials. To determine the constants in these potentials, cohesive energy and bulk modulus are used as input; in addition one uses notions of ionic size based on the known crystal structure. Salient features of the MD technique are outlined. Methods of treating long range Coulomb forces are discussed in detail. This includes the manner of doing Ewald sum for MD cells of arbitrary shape. Features which can be incorporated to expedite the MD calculations are also discussed. A novel MD technique which allows for a dynamically controlled variation of the shape and size of the MD cell is described briefly. The development of this novel technique has made it possible to study structural phase transitions in super-ionic conductors. For ..cap alpha..-AgI, among the structural properties we have studied are: partial pair correlation functions, mean square displacements of iodines, cation density maps, Havens ratio, etc. The dynamical properties examined include cation self-diffusion, nature of cation jumps, bias in successive jumps, velocity auto correlation functions, current-current correlation functions. In CuI, we have examined the microscopic nature of ..gamma --> cap alpha.. transition. It is found that at about 700 K the copper ions undergo an order-disorder transformation leading to a specific heat anomaly. The nature of the first-order transition and its precursor effects are also analyzed. In AgI the ..cap alpha.. reversible ..beta.. transition is studied. In our model, upon heating ..beta..-AgI, the iodines undergo hcp..-->..bcc transformation and the silver ions become mobile, whereas the reverse transformation is observed on cooling ..cap alpha..-AgI.

Rahman, A.; Vashishta, P.

1980-01-01

132

Molecular Dynamic Shock Wave Studies in Solids.

National Technical Information Service (NTIS)

Molecular dynamics is the technique of using a computer to solve Newton's equations of motion for a number of interacting atoms. Computer programs were developed which simulated shock waves moving in three dimensional solids. The pressure, density and tem...

A. Paskin

1976-01-01

133

Spinodal decomposition in nuclear molecular dynamics.

National Technical Information Service (NTIS)

Unstable zero-sound waves and cluster formation are studied in the framework of molecular dynamics approaches based on Gaussian single particle wave packets. It was observed that zero-sound properties are significantly affected when the Gaussian width tak...

M. Colonna P. Chomaz

1997-01-01

134

Ab initio non-adiabatic molecular dynamics.

Adiabatic nuclear potential energy surfaces (PESs) defined via the Born-Oppenheimer (BO) approximation are a fundamental concept underlying chemical reactivity theory. For a wide range of excited-state phenomena such as radiationless decay, energy and charge transfer, and photochemical reactions, the BO approximation breaks down due to strong couplings between two or more BO PESs. Non-adiabatic molecular dynamics (NAMD) is the method of choice to model these processes. We review new developments in quantum-classical dynamics, analytical derivative methods, and time-dependent density functional theory (TDDFT) which have lead to a dramatic expansion of the scope of ab initio NAMD simulations for molecular systems in recent years. We focus on atom-centered Gaussian basis sets allowing highly efficient simulations for molecules and clusters, especially in conjunction with hybrid density functionals. Using analytical derivative techniques, forces and derivative couplings can be obtained with machine precision in a given basis set, which is crucial for accurate and stable dynamics. We illustrate the performance of surface-hopping TDDFT for photochemical reactions of the lowest singlet excited states of cyclohexadiene, several vitamin D derivatives, and a bicyclic cyclobutene. With few exceptions, the calculated quantum yields and excited state lifetimes agree qualitatively with experiment. For systems with ?50 atoms, the present Turbomole implementation allows NAMD simulations with 0.2-0.4 ns total simulation time using hybrid density functionals and polarized double zeta valence basis sets on medium-size compute clusters. We close by discussing open problems and future directions. PMID:24068257

Tapavicza, Enrico; Bellchambers, Gregory D; Vincent, Jordan C; Furche, Filipp

2013-10-01

135

Molecular rheology of perfluoropolyether lubricant via nonequilibrium molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Molecular rheology of perfluoropolyether (PFPE) systems is particularly important in designing effective lubricants that control the friction and wear in tribological applications. Using the coarse-grained, bead-spring model, equilibrium molecular dynamics based on the Langevin equation in a quiescent flow was first employed to examine the nanostructure of PFPE. Further, by integrating the modified Langevin equation and imposing the Lees-Edwards boundary condition, nonequilibrium molecular dynamics of steady shear was investigated. We observe that the shear viscosity of PFPE system depends strongly on molecular architecture (e.g., molecular weight and endgroup functionality) and external conditions (e.g., temperature and shear rate). Our study of the flow activation energy/entropy and their correlations with nanostructure visualization showed that the PFPE structure was substantially modified.

Guo, Qian; Chung, Pil Seung; Chen, Haigang; Jhon, Myung S.

2006-04-01

136

Fermionic Molecular Dynamics for Nuclear Dynamics and Thermodynamics

NASA Astrophysics Data System (ADS)

A new Fermionic Molecular Dynamics (FMD) model based on a Skyrme functional is proposed in this paper. After introducing the basic formalism, some first applications to nuclear structure and nuclear thermodynamics are presented.

Hasnaoui, K. H. O.; Chomaz, Ph; Gulminelli, F.

137

Molecular Dynamics Simulations of Simple Liquids

ERIC Educational Resources Information Center

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

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

2004-01-01

138

Modeling the Hydrogen Bond within Molecular Dynamics

ERIC Educational Resources Information Center

|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.|

Lykos, Peter

2004-01-01

139

For the first time, the binding of ropinirole hydrochloride (ROP) and aspirin (ASA) to human holo-transferrin (hTf) has been investigated by spectroscopic approaches (fluorescence quenching, synchronous fluorescence, time-resolved fluorescence, three-dimensional fluorescence, UV-vis absorption, circular dichroism, resonance light scattering), as well as zeta potential and molecular modeling techniques, under simulated physiological conditions. Fluorescence analysis was used to estimate the effect of the ROP and ASA drugs on the fluorescence of hTf as well as to define the binding and quenching properties of binary and ternary complexes. The synchronized fluorescence and three-dimensional fluorescence spectra demonstrated some micro-environmental and conformational changes around the Trp and Tyr residues with a faint red shift. Thermodynamic analysis displayed the van der Waals forces and hydrogen bonds interactions are the major acting forces in stabilizing the complexes. Steady-state and time-resolved fluorescence data revealed that the fluorescence quenching of complexes are static mechanism. The effect of the drugs aggregating on the hTf resulted in an enhancement of the resonance light scattering (RLS) intensity. The average binding distance between were computed according to the forster non-radiation energy transfer theory. The circular dichroism (CD) spectral examinations indicated that the binding of the drugs induced a conformational change of hTf. Measurements of the zeta potential indicated that the combination of electrostatic and hydrophobic interactions between ROP, ASA and hTf formed micelle-like clusters. The molecular modeling confirmed the experimental results. This study is expected to provide important insight into the interaction of hTf with ROP and ASA to use in various toxicological and therapeutic processes. PMID:22410420

Kabiri, Mona; Amiri-Tehranizadeh, Zeinab; Baratian, Ali; Saberi, Mohammad Reza; Chamani, Jamshidkhan

2012-03-12

140

High Temperature Graphite Simulations Using Molecular Dynamics

NASA Astrophysics Data System (ADS)

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.

Hehr, Brian D.

141

Modeling and Dynamical Analysis of Molecular Networks

NASA Astrophysics Data System (ADS)

One of major challenges for post-genomic biology is to understand how molecules dynamically interact to form networks which facilitate sophisticated biological functions. Instead of analyzing individual molecules, systems biology is to study dynamical networks of interacting molecules which give rise to life. In recent years, many progress have been made in systematic approaches and high-throughput technologies for systematic studying complex molecular networks. Analyzing these networks provides novel insights in understanding not only complicated cellular phenomena but also the essential principles or fundamental mechanisms behind the phenomena at system level. This paper presents a brief survey on recent developments on modeling and analyzing complex molecular networks mainly from global and dynamical properties of complex molecular networks. Some recent developments and perspectives of analysis on molecular networks are also discussed.

Wang, Ruiqi; Zhao, Xing-Ming; Liu, Zengrong

142

Potential impact of molecular imaging in oncology.

Despite all progress in molecular imaging methods, the actual number of validated new markers is still limited. The breakthrough of individual efforts is often hampered by lack of critical mass of resources. To overcome these shortcomings a "network" of multidisciplinary experts is indispensable. Focusing on cancer therapy, molecular imaging has a high potential impact in (a) early therapy monitoring and (b) prediction of therapeutic response. Novel molecular markers with high diagnostic potential reflecting apoptosis, proliferation and glucose metabolism are currently used in clinical trials for monitoring of tumor response to therapy. A further innovative approach for supporting individualized cancer therapy may be the application of radio-labelled therapeutic drugs at tracer concentrations in order to estimate their individual uptake in the tumor tissue. To meet this challenge, our group initiated a research project focusing on radio-labelling of selected molecules with proven therapeutic potential. PMID:16033107

Klutmann, Susanne; Clausen, Malte

143

Fragmentation of water clusters: Molecular-dynamics simulation study

NASA Astrophysics Data System (ADS)

The fragmentation of water clusters, [(H2O)n;n = 2-8], have been investigated by using molecular-dynamics simulation method. In the simulations a polarizable-dissociable potential energy function for water has been used. Particular attention has bee paid to investigate the effect of structural properties and cluster size on the fragmentation.

Erkoç, ?.; Kökten, H.; Güvenç, Z.

2001-02-01

144

Thermal transport properties of uranium dioxide by molecular dynamics simulations

The thermal conductivities of single crystal and polycrystalline UO2 are calculated using molecular dynamics simulations, with interatomic interactions described by two different potential models. For single crystals, the calculated thermal conductivities are found to be strongly dependent on the size of the simulation cell. However, a scaling analysis shows that the two models predict essentially identical values for the thermal

Taku Watanabe; Susan B. Sinnott; James S. Tulenko; Robin W. Grimes; Patrick K. Schelling; Simon R. Phillpot

2008-01-01

145

Thermal Decomposition of RDX from Reactive Molecular Dynamics.

National Technical Information Service (NTIS)

We use the recently developed reactive force field ReaxFF with molecular dynamics to study thermal induced chemistry in RDX cyclic- CH2N(NO2)(3) at various temperatures and densities. We find that the time evolution of the potential energy can be describe...

A. Strachan E. M. Kober A. C. Van Duin J. Oxgaard I. W. Goddard

2005-01-01

146

Thermodynamics and quantum corrections from molecular dynamics for liquid water

In principle, given the potential energy function, the values of thermodynamic variables can be computed from statistical mechanics for a system of molecules. In practice for the liquid state, however, two barriers must be overcome. This paper treats the first problem, how to quantum correct the classical mechanical thermodynamic values available from molecular dynamics, Monte Carlo, perturbation, or integral methods

Peter H. Berens; Donald H. J. Mackay; Gary M. White; Kent R. Wilson

1983-01-01

147

Trillion-atom molecular dynamics becomes a reality

By utilizing the molecular dynamics code SPaSM on Livermore's BlueGene/L architecture, consisting of 212 992 IBM PowerPC440 700 MHz processors, a molecular dynamics simulation was run with one trillion atoms. To demonstrate the practicality and future potential of such ultra large-scale simulations, the onset of the mechanical shear instability occurring in a system of Lennard-Jones particles arranged in a simple cubic lattice was simulated. The evolution of the instability was analyzed on-the-fly using the in-house developed massively parallel graphical object-rendering code MD{_}render.

Kadau, Kai [Los Alamos National Laboratory; Germann, Timothy C [Los Alamos National Laboratory

2008-01-01

148

Operator Dynamics in Molecular Biology.

National Technical Information Service (NTIS)

Recent development of molecular biology revealed some mathematical nature of the structure of genes. Basic elements of genes are DNA, which are (double helixed) sequences consisted by four bases, X=(A,T,G,C). A primary structure of genes is just a finite ...

T. Kato

2001-01-01

149

NVU dynamics. III. Simulating molecules at constant potential energy.

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. Schrřder, and J. C. Dyre, J. Chem. Phys. 135, 104101 (2011); T. S. Ingebrigtsen, S. Toxvaerd, T. B. Schrřder, 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

Ingebrigtsen, Trond S; Dyre, Jeppe C

2012-12-28

150

Nonequilibrium molecular dynamics simulations of aluminum oxynitride

NASA Astrophysics Data System (ADS)

Aluminum oxynitride, or AlON, is a polycrystalline ceramic material, whose transparency and high strength make it a potentially useful material for many structural engineering applications. The structure of AlON is cubic spinel, with anions forming a close-packed structure, and aluminum atoms occupying the tetrahedral and octahedral interstitial sites, with one site remaining vacant. However, the location of the vacancy is not unique, nor are the positions of the nitrogen atoms, which replace oxygen atoms in the close-packed structure. We have developed an interatomic potential based on the Buckingham model for use in classical molecular dynamics (MD) simulations of AlON. Using this model, and crystal structures determined from first principles calculations, we have calculated a number of material properties and we compare these to experimental values. We present the results of nonequilibrium MD simulations of single crystal AlON under applied tension, with a discussion of the yield and failure mechanisms of this material.

Weingarten, N. Scott; Batyrev, Iskander G.; Rice, Betsy M.

2012-03-01

151

Nonequilibrium molecular dynamics simulations of aluminum oxynitride

NASA Astrophysics Data System (ADS)

Aluminum oxynitride, or AlON, is a crystalline ceramic material, whose transparency and high strength make it a potentially useful material for many structural engineering applications. The structure of AlON is cubic spinel, with anions forming a close-packed structure, and aluminum atoms occupying the tetrahedral and octahedral interstitial sites, with one site remaining vacant. However, the location of the vacancy is not unique, nor are the positions of the nitrogen atoms, which replace oxygen atoms in the close-packed structure. We have developed an interatomic potential based on the Buckingham model for use in classical molecular dynamics (MD) simulations of AlON. Using this model, and crystal structures determined from first principles calculations, we have calculated a number of material properties and we compare these to experimental values. We present the results of nonequilibrium MD simulations of single crystal and bicrystal AlON systems under applied tension and compression, with a discussion of the yield and failure mechanisms of this material. Finally, we present preliminary observations of shock simulations, with comparisons to simulations of other crystalline ceramic material.

Weingarten, N. Scott; Batyrev, Iskander G.; Rice, Betsy M.

2011-06-01

152

Surface Phenomena of Molecular Clusters by Molecular Dynamics Method

Liquid droplets of water and argon surrounded by their vapor have been simulated by the molecular dynamics method. To explore the surface phenomena of clusters, each molecule is classified into 'liquid', 'surface', or 'vapor' with respect to the number of neighbor molecules. The contribution of a 'surface' molecule of the water cluster to the far infrared spectrum is almost the

Shigeo MARUYAMA; Sohei MATSUMOTO; Akihiro OGITA

1994-01-01

153

NASA Astrophysics Data System (ADS)

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 Tm, liquidus temperatures Tl, and glass transition temperatures Tg, 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)].''

Kapko, Vitaliy; Zhao, Zuofeng; Matyushov, Dmitry V.; Austen Angell, C.

2013-03-01

154

Homogeneous Nucleation in Superheated Crystal. Molecular Dynamics Simulation

Molecular dynamics method is used for the study of homogeneous nucleation in superheated model crystal. Fcc-lattice of N particles interacting via U=?(sigma\\/r)^n potential is simulated with periodic boundary conditions. In this case system properties depend only on a single parameter X rhosigma^3(?\\/k_BT)^3\\/n, where rho - density, T - temperature. This potential was used for simulation of liquid and solid

Guenri Norman; Vladimir Stegailov; Maxim Krivoguz

2002-01-01

155

Molecular Cores in Taurus: Evolution and Dynamics

NASA Astrophysics Data System (ADS)

The evolution and dynamics of the molecular cores traced by 13CO J = 1 ? 0 emission in the Taurus molecular cloud are studied. We performed a systematic examination of the distribution and dynamic state of cores in a large contiguous region, as well as the core ages, which lie between 106 and 107 years. The core velocity dispersion (CVD), which is the variance of the core velocity difference ? v, exhibits a power-law behavior as a function of the apparent separation L, i.e. CVD (km/s) ? L (pc)0.7, with similarities to Larson's law for the velocity dispersion of the gas.

Qian, Lei; Li, Di; Goldsmith, Paul

2013-03-01

156

Relativistic versus nonrelativistic quantum molecular dynamics

NASA Astrophysics Data System (ADS)

One of the most successful models to describe heavy ion reactions on the microscopic level is the Quantum Molecular Dynamics (QMD). At relativistic energies a covariant generalization of this model, the Relativistic Quantum Molecular Dynamics (RQMD), is available. We compare results concerning the time evolution of the phase space and particle production obtained by both methods at the intermediate energy range looking for relativistic effects in heavy ion collisions at these energies. now at I.N.F.N., Via Docecaneso 33, 16146 Genova, Italy

Lehmann, E.; Puri, R. K.; Faessler, A.; Maruyama, T.; Li, G. Q.; Ohtsuka, N.; Huang, S. W.; Khoa, D. T.; Matin, M. A.

157

Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code

NASA Astrophysics Data System (ADS)

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.

Davis, Sergio; Loyola, Claudia; González, Felipe; Peralta, Joaquín

2010-12-01

158

Quantum dynamics of light-driven chiral molecular motors.

The results of theoretical studies on quantum dynamics of light-driven molecular motors with internal rotation are presented. Characteristic features of chiral motors driven by a non-helical, linearly polarized electric field of light are explained on the basis of symmetry argument. The rotational potential of the chiral motor is characterized by a ratchet form. The asymmetric potential determines the directional motion: the rotational direction is toward the gentle slope of the asymmetric potential. This direction is called the intuitive direction. To confirm the unidirectional rotational motion, results of quantum dynamical calculations of randomly-oriented molecular motors are presented. A theoretical design of the smallest light-driven molecular machine is presented. The smallest chiral molecular machine has an optically driven engine and a running propeller on its body. The mechanisms of transmission of driving forces from the engine to the propeller are elucidated by using a quantum dynamical treatment. The results provide a principle for control of optically-driven molecular bevel gears. Temperature effects are discussed using the density operator formalism. An effective method for ultrafast control of rotational motions in any desired direction is presented with the help of a quantum control theory. In this method, visible or UV light pulses are applied to drive the motor via an electronic excited state. A method for driving a large molecular motor consisting of an aromatic hydrocarbon is presented. The molecular motor is operated by interactions between the induced dipole of the molecular motor and the electric field of light pulses. PMID:19290336

Yamaki, Masahiro; Nakayama, Shin-ichiro; Hoki, Kunihito; Kono, Hirohiko; Fujimura, Yuichi

2009-01-30

159

Molecular dynamics studies on nanoscale gas transport

NASA Astrophysics Data System (ADS)

Three-dimensional molecular dynamics (MD) simulations of nanoscale gas flows are studied to reveal surface effects. A smart wall model that drastically reduces the memory requirements of MD simulations for gas flows is introduced. The smart wall molecular dynamics (SWMD) represents three-dimensional FCC walls using only 74 wall Molecules. This structure is kept in the memory and utilized for each gas molecule surface collision. Using SWMD, fluid behavior within nano-scale confinements is studied for argon in dilute gas, dense gas, and liquid states. Equilibrium MD method is employed to resolve the density and stress variations within the static fluid. Normal stress calculations are based on the Irving-Kirkwood method, which divides the stress tensor into its kinetic and virial parts. The kinetic component recovers pressure based on the ideal gas law. The particle-particle virial increases with increased density, while the surface-particle virial develops due to the surface force field effects. Normal stresses within nano-scale confinements show anisotropy induced primarily by the surface force-field and local variations in the fluid density near the surfaces. For dilute and dense gas cases, surface-force field that extends typically 1nm from each wall induces anisotropic normal stress. For liquid case, this effect is further amplified by the density fluctuations that extend beyond the three field penetration region. Outside the wall force-field penetration and density fluctuation regions the normal stress becomes isotropic and recovers the thermodynamic pressure, provided that sufficiently large force cut-off distances are utilized in the computations. Next, non-equilibrium SWMD is utilized to investigate the surface-gas interaction effects on nanoscale shear-driven gas flows in the transition and free molecular flow regimes. For the specified surface properties and gas-surface pair interactions, density and stress profiles exhibit a universal behavior inside the wall force penetration region at different flow conditions. Shear stress results are utilized to calculate the tangential momentum accommodation coefficient (TMAC) between argon gas and FCC walls. The TMAC value is shown to he independent of the now properties and Knudsen number in all simulations. Velocity profiles show distinct deviations from the kinetic theory based solutions inside the wall force penetration depth, while they match the linearized Boltzmann equation solution outside these zones. Afterwards, surface effects are studied as a function of the surface-gas potential strength ratio (epsilon wf/epsilonff) for the shear driven argon gas flows in the early transition and tree molecular flow regimes. Results show that increased epsilonwf/epsilon ff results in increased gas density, leading towards monolayer adsorption on surfaces. The near wall velocity profile shows reduced gas slip, and eventually velocity stick with increased epsilonwf/epsilon ff. Similarly, using MD predicted shear stress values and kinetic theory, TMAC are calculated as a function of epsilonwf/epsilon ff and TMAC values are shown to be independent of the Knudsen number. Results indicate emergence of the wall force field penetration depth as an additional length scale for gas flows in nano-channels, breaking the dynamic similarity between rarefied and nano-scale gas flows solely based on the Knudsen and Mach numbers.

Barisik, Murat

160

Molecular dynamic simulation of transmembrane pore growth.

A molecular dynamic approach was applied for simulation of dynamics of pore formation and growth in a phospholipid bilayer in the presence of an external electric field. Processing the simulation results permitted recovery of the kinetic coefficients used in the Einstein-Smoluchowski equation describing the dynamics of pore evolution. Two different models of the bilayer membrane were considered: membrane consisting of POPC and POPE lipids. The simulations permitted us to find nonempirical values of the pore energy parameters, which are compared with empirical values. It was found that the parameters are sensitive to membrane type. PMID:23660813

Deminsky, M; Eletskii, A; Kniznik, A; Odinokov, A; Pentkovskii, V; Potapkin, B

2013-05-10

161

Molecular Dynamics Simulations of Thermal Properties of Solid Uranium Dioxide

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations are performed with the recently developed empirical interaction potential by Morelon et al. Thermodynamics properties of solid UO2 that have been assessed include melt point, density, enthalpy, heat capacity, lattice parameter variation with temperature, mean-square-displacement and diffusion coefficients of oxygen ion. The results are compared with the data in literature and it is suggested that the rigid ionic potential provides perfect results below the superionic range. The data showing thermodynamics properties will become unacceptable when the temperature is higher than 2500 K. Compared with the previous empirical potentials, the empirical potential developed by Morelon et al. improves the agreement of these data with the recommend ones.

Li, Jiu-Kai; Tian, Xiao-Feng

2010-03-01

162

Formation and Classification of Amorphous Carbon by Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

By using molecular dynamics simulation, the formation mechanisms of amorphous carbon in a particular sp3-rich structure were researched. The problem that reactive empirical bond order potential cannot represent amorphous carbon properly was resolved in the transition process from graphite to diamond by a high pressure and the deposition of amorphous carbon thin films. Moreover, a new potential model, which is based on the electron distribution simplified as a point charge, was developed by using the downfolding method. As a result, the molecular dynamics simulation with the new potential could demonstrate the transition from graphite to diamond at the pressure of 15 GPa, which agrees with an experimental report and the deposition of sp3-rich amorphous carbon.

Ito, Atsushi M.; Takayama, Arimichi; Saito, Seiki; Nakamura, Hiroaki

2013-01-01

163

Numerical methods for molecular dynamics

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.

Skeel, R.D.

1991-01-01

164

MDLab: A molecular dynamics simulation prototyping environment

Molecular dynamics (MD) simulation involves solving Newton's equations of motion for a system of atoms, by calculating forces and updating atomic positions and ve- locities over a timestept. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep re- quired for propagation, and the expensive algorithm for computing pairwise

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

2010-01-01

165

Molecular beam studies of reaction dynamics

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

Yuan T. Lee; Yuan T

1991-01-01

166

Molecular beam studies of reaction dynamics

The major thrust of this research project is to elucidate detailed dynamics of simple 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

1990-01-01

167

Molecular Dynamics Simulation of Elliptical Vibration Cutting

For better understanding of the essential removal mechanisms of brittle material and stress distribution at high speed and ultrasonic elliptical vibration assisted cutting conditions at the atomic level, the single crystal silicon, expected as a next generation semiconductor material for wide band cap, high-voltage and low-loss power devices, MEMS components and so on, is analyzed by molecular dynamics computer simulation

Yingchun Liang; Degang Li; Qingshun Bai; Shumei Wang; Mingjun Chen

2006-01-01

168

A molecular dynamics study of polarizable water

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

Peter Ahlström; Anders Wallqvist; Sven Engström; Bo Jönsson

1989-01-01

169

Molecular Dynamics Simulations of Coulomb Explosion.

National Technical Information Service (NTIS)

A swift ion creates a track of electronic excitations in the target material. A net repulsion inside the track can cause a 'Coulomb Explosion', which can lead to damage and sputtering of the material. Here we report results from molecular-dynamics (MD) si...

E. M. Bringa

2002-01-01

170

Molecular dynamics simulations of xDNA.

xDNA is a modified DNA, which contains natural as well as expanded bases. Expanded bases are generated by the addition of a benzene spacer to the natural bases. A set of AMBER force-field parameters were derived for the expanded bases and the structural dynamics of the xDNA decamer (xT5' G xT A xC xG C xA xG T3').(xA5' C T xG C G xT A xC A3') was explored using a 22 ns molecular dynamics simulation in explicit solvent. During the simulation, the duplex retained its Watson-Crick base-pairing and double helical structure, with deviations from the starting B-form geometry towards A-form; the deviations are mainly in the backbone torsion angles and in the helical parameters. The sugar pucker of the residues were distributed among a variety of modes; C2' endo, C1' exo, O4' endo, C4' exo, C2' exo, and C3' endo. The enhanced stacking interactions on account of the modification in the bases could help to retain the duplex nature of the helix with minor deviations from the ideal geometry. In our simulation, the xDNA showed a reduced minor groove width and an enlarged major groove width in comparison with the NMR structure. Both the grooves are larger than that of standard B-DNA, but major groove width is larger than that of A-DNA with almost equal minor groove width. The enlarged groove widths and the possibility of additional hydration in the grooves makes xDNA a potential molecule for various applications. PMID:19137576

Varghese, Mathew K; Thomas, Renjith; Unnikrishnan, N V; Sudarsanakumar, C

2009-05-01

171

Structural and dynamic properties of calcium aluminosilicate melts: A molecular dynamics study

NASA Astrophysics Data System (ADS)

The structural and dynamic properties of calcium aluminosilicate (CaO-Al2O3)1-x(SiO2)x melts with low silica content, namely, along the concentration ratio R = 1 are studied by classical molecular dynamics. An empirical potential has been developed here on the basis of our previous ab initio molecular dynamics. The new potential gives a description of the structural as well as the dynamics with a good accuracy. The self-intermediate scattering function and associated ?-relaxation times are analyzed within the mode-coupling theory. Our results indicate a decrease of the fragility whose structural origin is a reduction of the number of fivefold coordinated Al atoms and non-bridging oxygen.

Bouhadja, M.; Jakse, N.; Pasturel, A.

2013-06-01

172

MDMovie: a molecular dynamics viewing tool.

The graphics program MDMovie (Molecular Dynamics Movie), written in C using IRIS GL graphics library calls, is designed to facilitate the visualization and interpretation of empirical force field data. MDMovie was created and initially adapted in accord with the needs of physical chemists and thereafter became an expandable analysis tool. Capabilities include the display of chemical structure, animation of molecular dynamics and Monte Carlo trajectories, and the visual representation of various vector and scalar dynamical properties. In addition to being a research tool, MDMovie has features for creating presentation videos and hardcopy output. A library is also available for linking to Fortran simulation codes running on a remote machine and connecting to MDMovie via a socket connection. MDMovie continues to be an ongoing research project and new features are actively being added in collaboration with various research groups. Future plans include porting to OpenGL and the design of an XII-based user interface. PMID:9097234

Greenberg, J P

1996-10-01

173

By means of molecular dynamics simulations of 15 pairs of molecules selected to model the interactions of nonpolar, nonpolar and polar, nonpolar and charged, polar, and polar and charged side chains in water, we determined the potentials of mean force (PMFs) of pairs of interacting molecules in water as functions of distance between the interacting particles or their distance and orientations at three temperatures: 283, 323, and 373 K, respectively. The systems were found to fall into the following four categories as far as the temperature dependence of the PMF is concerned: (i) pairs for which association is entropy-driven, (ii) pairs for which association is energy-driven, (iii) pairs of positively charged solute molecules, for which association is energy-driven with unfavorable entropy change, and (iv) the remaining systems for which temperature dependence is weak. For each pair of PMFs, entropic and energetic contributions have been discussed. PMID:22475198

Sobolewski, Emil; O?dziej, Stanis?aw; Wi?niewska, Marta; Liwo, Adam; Makowski, Mariusz

2012-04-16

174

Dynamic Potentials in Gyrotropic Plasmas.

National Technical Information Service (NTIS)

Wave equations are derived for the scalar and vector potentials of guided electromagnetic waves propagating in a laterally bounded magnetized plasma along the axis of the static magnetic field. Solutions are given in the Coulomb and the Lorentz gauge. The...

V. Bevc

1969-01-01

175

Crystalline molecular machines: Encoding supramolecular dynamics into molecular structure

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.

Garcia-Garibay, Miguel A.

2005-01-01

176

Rigid body molecular dynamics with nonholonomic constraints: Molecular thermostat algorithms

NASA Astrophysics Data System (ADS)

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.

Kutteh, Ramzi; Jones, R. B.

2000-03-01

177

We study the influence that the choice of the electron correlation calculation method has on the thermodynamic, electrical, and structural properties of liquid hydrogen fluoride (HF) as obtained by Quantum Mechanics\\/Molecular Mechanics methods (QM\\/MM). We consider also the influence of the basis set and Lennard–Jones parameters. In our study we applied a non-traditional QM\\/MM method that makes use of the

A. Muńoz Losa; I. Fdez. Galván; M. E. Mart??n; M. A. Aguilar

2003-01-01

178

We present a novel and efficient method to integrate chemical reactions into molecular dynamics to simulate chemical reaction systems. We have dubbed this method RTAMD, an acronym for reaction time accelerating molecular dynamics. The methodology we propose here requires no more than the knowledge of the empirical intermolecular potentials for the species at play as well as the elementary reaction

Hiromitsu Takaba; Shigekazu Hayashi; Huifeng Zhong; Hema Malani; Ai Suzuki; Riadh Sahnoun; Michihisa Koyama; Hideyuki Tsuboi; Nozomu Hatakeyama; Akira Endou; Momoji Kubo; Carlos A. Del Carrpio; Akira Miyamoto

2008-01-01

179

Molecular dynamics simulation of layered double hydroxides

The interlayer structure and the dynamics of Cl{sup {minus}} ions and H{sub 2}O molecules in the interlayer space of two typical LDH [Layered Double Hydroxide] phases were investigated by molecular dynamics computer simulations. The simulations of hydrocalumite, [Ca{sub 2}Al(OH){sub 6}]Cl{center_dot}2H{sub 2}O reveal significant dynamic disorder in the orientations of interlayer water molecules. The hydration energy of hydrotalcite, [Mg{sub 2}Al(0H){sub 6}]Cl{center_dot}nH{sub 2}O, is found to have a minimum at approximately n = 2, in good agreement with experiment. The calculated diffusion coefficient of Cl{sup {minus}} as an outer-sphere surface complex is almost three times that of inner-sphere Cl{sup {minus}}, but is still about an order of magnitude less than that of Cl{sup {minus}} in bulk solution. The simulations demonstrate unique capabilities of combined NMR and molecular dynamics studies to understand the structure and dynamics of surface and interlayer species in mineral/water systems.

KALINICHEV,ANDREY G.; WANG,JIANWEI; KIRKPATRICK,R. JAMES; CYGAN,RANDALL T.

2000-05-19

180

Adaptive Multiscale Molecular Dynamics of Macromolecular Fluids

NASA Astrophysics Data System (ADS)

Until now, adaptive atomistic-coarse-grain (A/CG) molecular dynamics simulations have had very limited applicability because the on-the-fly CG?A transformation is problematic for all but those molecules whose CG representation consists of a single particle. Here, we solve this problem by combining a transitional healing region with a rotational dynamics of rigid atomistic fragments in the CG region. Error control is obtained by analysis of the A?CG energy flow. We illustrate the method with adaptive multiscale simulations of liquid hexane and of a dilute polymer solution in a theta solvent.

Nielsen, Steven O.; Moore, Preston B.; Ensing, Bernd

2010-12-01

181

Complete Characterization of Molecular Dynamics in Ultrashort Laser Fields

Reaction Microscope-based, complete, and time-resolved Coulomb explosion imaging of vibrating and dissociating D{sub 2}{sup +} molecules with femtosecond time-resolution allowed us to perform an internuclear distance (R-)dependent Fourier analysis of the corresponding wave packets. Calculations demonstrate that the obtained two-dimensional R-dependent frequency spectra enable the complete characterization of the wave packet dynamics and directly visualize the field-modified molecular potential curves in intense, ultrashort laser pulses.

Feuerstein, B.; Ergler, Th.; Rudenko, A.; Zrost, K.; Schroeter, C. D.; Moshammer, R.; Ullrich, J.; Niederhausen, T.; Thumm, U. [Max-Planck-Institut fuer Kernphysik, D-69029 Heidelberg (Germany); James R. Macdonald Laboratory, Kansas State University, Manhattan, Kansas 66506-2604 (United States)

2007-10-12

182

A molecular dynamics investigation of surface reconstruction on magnetite (001)

Molecular dynamics calculations using analytical potential functions with polarizable oxygen ions have been used to identify a novel mode of reconstruction on the half-occupied tetrahedral layer termination of the magnetite (Fe3O4) (001) surface. In the proposed reconstruction, the twofold coordinated iron ion in the top monolayer rotates downward to occupy a vacant half-octahedral site in the plane of the second-layer

J. R. Rustad; E. Wasserman; A. R. Felmy

1999-01-01

183

Quantum molecular dynamics and particle production in heavy ion collisions

NASA Astrophysics Data System (ADS)

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 discussed. The mechanisms of production processes are studied. The theoretical results are compared with the available experimental data.

Huang, S. W.; Faessler, A.; Li, G. Q.; Khoa, D. T.; Lehmann, E.; Matin, M. A.; Ohtsuka, N.; Puri, R. K.

184

Molecular dynamics studies and neutron scattering experiments on methylene chloride

NASA Astrophysics Data System (ADS)

Molecular dynamics (MD) simulations of methylene chloride (CH2Cl2) with two different potentials are used to calculate the intermolecular static structure factor inter(q) for a series of isotopic substituted mixtures CX2Cl2. The intermolecular structure factors are compared with corresponding experimental data obtained from neutron diffraction. We discuss the validity of the rigid molecule approximation in the MD simulation and show that the quantitative comparison of the static structure factors of molecular liquids obtained from neutron diffraction experiments and MD simulation must be considered with some care for molecules containing hydrogen atoms with low effective masses.

Kneller, Gerald R.; Geiger, Alfons

185

Relativistic all-electron molecular dynamics simulations.

The scalar-relativistic Douglas-Kroll-Hess method is implemented in the Born-Oppenheimer molecular dynamics simulation package CP2K. Using relativistic densities in a nonrelativistic gradient routine is found to be a valid approximation of relativistic gradients. An excellent agreement between optimized structures and geometries obtained from numerical gradients is observed with an error smaller than 0.02 pm. Hydrogen halide dimers [(HX)(2), with X = F, Cl, Br, I] serve as small test systems for first-principles molecular dynamics simulations. Relativistic effects are observed. That is, the amplitude of motion is larger, the frequency of motion is smaller, and the distances are larger in the relativistic picture. Several localization schemes are evaluated for different interatomic and intermolecular distances. The errors of these localization schemes are small for geometries which are similar to the equilibrium structure. They become larger for smaller distances, introducing a slight bias toward closed packed configurations. PMID:19334804

Thar, Jens; Kirchner, Barbara

2009-03-28

186

Classical molecular dynamics in a nutshell.

This chapter provides an overview of the various techniques that are commonly used in classical molecular dynamics simulations. It describes suitable algorithms for the integration of Newton's equation of motion over many time steps for systems containing a large number of particles, different choices of boundary conditions as well as available force fields for biological systems, that is, the mathematical description of the interactions of atoms and molecules with each other. It also illustrates algorithms used to simulate systems at constant temperature and/or pressure and discusses their advantages and disadvantages. It presents a few methods to save CPU time and a summary of popular software for biomolecular molecular dynamics simulations. PMID:23034748

Hug, Susanna

2013-01-01

187

Molecular dynamics studies of polyurethane nanocomposite hydrogels

NASA Astrophysics Data System (ADS)

Polyurethane PEO-based hydrogels have a broad range of biomedical applicability. They are attractive for drug-controlled delivery systems, surgical implants and wound healing dressings. In this study, a PEO based polyurethane hydrogels containing Cloisite® 30B, an organically modified clay mineral, was synthesized. Structure of nanocomposite hydrogels was determined using XRD technique. Its molecular dynamics was studied by means of NMR spectroscopy, DMA and DSC analysis. The mechanical properties and thermal stability of the systems were improved by incorporation of clay and controlled by varying the clay content in polymeric matrix. Molecular dynamics of polymer chains depends on interaction of Cloisite® 30B nanoparticles with soft segments of polyurethanes. The characteristic nanosize effect is observed.

Strankowska, J.; Piszczyk, ?.; Strankowski, M.; Danowska, M.; Szutkowski, K.; Jurga, S.; Kwela, J.

2013-10-01

188

Dynamic surface tension effects from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

We will present results of our recent large scale molecular dynamics simulations of dynamic surface tension behaviour in the case of a liquid-gas interface. We will demonstrate the mechanism of surface tension relaxation from a non-equilibrium state in several representative cases: long-chain flexible molecules with Lennard-Jones beads connected by FENE springs and binary Lennard-Jones mixtures (Kob-Andersen model). The methodology of the surface tension evaluation has been successfully tested against the Laplace law in all the cases.

Lukyanov, Alex; Likhtman, Alexei

2011-11-01

189

Molecular dynamics simulation of ribosome jam

NASA Astrophysics Data System (ADS)

We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models.

Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu

2011-09-01

190

Exploring Transmembrane Diffusion Pathways with Molecular Dynamics

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.

Wang, Yi; Shaikh, Saher A.; Tajkhorshid, Emad

2013-01-01

191

A Molecular Dynamics Study of Thermal Ablation

The bio-heat transfer problem and the thermal ablation in bio-tissue require general solutions for the control of the external heating power. An algorithm based on the molecular dynamics (MD) and the GROMACS protein data bank is developed to solve the bio-heat transfer problem. The value of the thermal conductivity of alanine is calculated from the autocorrelation function of the Green-Kubo

D. T. W. Lin; Yuh-Chung Hu

2006-01-01

192

Exploring Transmembrane Diffusion Pathways With Molecular Dynamics

NSDL National Science Digital Library

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.

Yi Wang (University of Illinois at Urbana-Champaign); Saher Shaikh (University of Illinois at Urbana-Champaign); Emad Tajkhorshid (University of Illinois at Urbana-Champaign)

2010-06-01

193

Unravelling Prion Diseases Using Molecular Dynamics Simulations

Human prion diseases such as Creutzfeldl-Jakob disease are neurodegenerative diseases and present as infectious, sporadic and genetic disorders. Association of bovine spongiform encephalopathy (BSE) or 'mad cow disease' with human variant Creutzfeldt-Jakob disease (vCJD) have increased the attention on these diseases. Here we review and summarizes the use of molecular dynamics simulation to investigate the possible conformational transformation pathways of

Mohd Shahir Shamsir; Zeti Azura Hussein; Johan Sharif

2008-01-01

194

Molecular dynamics simulation of nanoscale liquid flows

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

Yuxiu LiJinliang XuDongqing Li; Jinliang Xu; Dongqing Li

2010-01-01

195

Direct formation of "Janus"-particles via molecular dynamics simulations

NASA Astrophysics Data System (ADS)

The binary nucleation of phase separated Lennard-Jones nanoclusters was observed using Molecular Dynamics (MD) simulations. MD provides insight into the structure as well as the dynamics of the inhomogeneous clusters formed. Modification of the potential parameters allows control of the transition from homogeneously coated clusters to "Janus"-particles, with two distinct regions combined within the same particle. From the analysis of the intermolecular behavior we learned which parameters to tune for future, direct syntheses of these inhomogeneous nanoparticles by nucleation processes from the gas phase.

Wittmann, Jan-Hubert; Strey, Reinhard

2013-05-01

196

Molecular Dynamics Simulation of Disordered Zircon

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.

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

2004-02-27

197

Equipartition Principle for Internal Coordinate Molecular Dynamics.

The principle of equipartition of (kinetic) energy for all-atom Cartesian molecular dynamics states that each momentum phase space coordinate on the average has ˝kT 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

Jain, Abhinandan; Park, In-Hee; Vaidehi, Nagarajan

2012-07-01

198

Equipartition Principle for Internal Coordinate Molecular Dynamics

The principle of equipartition of (kinetic) energy for all-atom Cartesian molecular dynamics states that each momentum phase space coordinate on the average has ˝kT 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.

Jain, Abhinandan; Park, In-Hee; Vaidehi, Nagarajan

2012-01-01

199

A molecular dynamics simulation of sulphur hexafluoride

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations are performed for the six-centre Lennard-Jones model of SF6 over a temperature range from 225 to 398 K and density from 1·3 to 1·9 g cm-3. The results of simulations are in good agreement with experimental data for the translational diffusion coefficient and correlation times for molecular reorientation and angular momentum, except for the highest temperature where small discrepancies between the simulated and experimental values for the diffusion coefficients are observed. Theoretical models for time correlation functions of molecular reorientations are compared with computer simulation results. It is found that the J-diffusion model reproduces the rotational correlation function of SF6 more satisfactorily than other models.

Brodka, A.; Zerda, T. W.

200

Learning generative models of molecular dynamics.

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

Razavian, Narges Sharif; Kamisetty, Hetunandan; Langmead, Christopher J

2012-01-17

201

Control-volume representation of molecular dynamics.

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 (LCV) conversion function ?(i) for each molecule i. The LCV 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 [Lutsko, J. Appl. Phys. 64, 1152 (1988)] techniques and the method of planes [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 nonequilibrium (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. PMID:23004901

Smith, E R; Heyes, D M; Dini, D; Zaki, T A

2012-05-22

202

Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics

The goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods.

Yu, H.G.; Muckerman, J.T.

2010-06-01

203

Dynamic Maintenance and Visualization of Molecular Surfaces

Molecular surface computations are often necessary in order to perform synthetic drug design. A critical step in this process is the computation and update of an exact boundary representation for the molecular surface (e.g. the Lee-Richards surface). In this paper they introduce efficient techniques for computing a molecular surface boundary representation as a set of NURBS (non-uniform rational B-splines) patches. This representation introduces for molecules the same geometric data structure used in the solid modeling community and enables immediate access to a wide range of modeling operations and techniques. Furthermore, this allows the use of any general solid modeling or visualization system as a molecular modeling interface. However, using such a representation in a molecular modeling environment raises several efficiency and update constraints, especially in a dynamic setting. For example, changes in the probe radius result in both geometric and topological changes to the set of patches. The techniques provide the option of trading accuracy of the representation for the efficiency of the computation, while still tracking the changes in the set of patches. In particular, they discuss two main classes of dynamic updates: one that keeps the topology of the molecular configuration fixed, and a more complicated case where the topology may be updated continuously. In general the generated output surface is represented in a format that can be loaded into standard solid modeling systems. It can also be directly triangulated or rendered, possibly at different levels of resolution, by a standard graphics library such as OpenGL without any additional effort.

Bajaj, C L; Pascucci, V; Shamir, A; Holt, R J; Netravali, A N

2004-12-16

204

Improving structure-based function prediction using molecular dynamics

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.

Glazer, Dariya S.; Radmer, Randall J.; Altman, Russ B.

2009-01-01

205

Potential energy surfaces and reaction dynamics of polyatomic molecules

A simple empirical valence bond (EVB) model approach is suggested for constructing global potential energy surfaces for reactions of polyatomic molecular systems. This approach produces smooth and continuous potential surfaces which can be directly utilized in a dynamical study. Two types of reactions are of special interest, the unimolecular dissociation and the unimolecular isomerization. For the first type, the molecular dissociation dynamics of formaldehyde on the ground electronic surface is investigated through classical trajectory calculations on EVB surfaces. The product state distributions and vector correlations obtained from this study suggest very similar behaviors seen in the experiments. The intramolecular hydrogen atom transfer in the formic acid dimer is an example of the isomerization reaction. High level ab initio quantum chemistry calculations are performed to obtain optimized equilibrium and transition state dimer geometries and also the harmonic frequencies.

Chang, Yan-Tyng

1991-11-01

206

On the dynamics of molecular conformation

Understanding the mechanism of fast transitions between conformed states of large biomolecules is central to reconciling the dichotomy between the relatively high speed of metabolic processes and slow (random-walk based) estimates on the speed of biomolecular processes. Here we use the dynamical systems approach to suggest that the reduced time of transition between different conformations is due to features of the dynamics of molecules that are a consequence of their structural features. Long-range and local effects both play a role. Long-range molecular forces account for the robustness of final states and nonlinear processes that channel localized, bounded disturbances into collective, modal motions. Local interconnections provide fast transition dynamics. These properties are shared by a class of networked systems with strong local interconnections and long-range nonlinear forces that thus exhibit flexibility and robustness at the same time.

Mezic, Igor

2006-01-01

207

DENSITY-FUNCTIONAL MOLECULAR DYNAMICS SIMULATIONS OF SHOCKED MOLECULAR LIQUIDS

Molecular dynamics (MD) simulations have been performed for highly compressed fluid deuterium, nitrogen, and oxygen, in the density and temperature regime of shock-compression experiments, using density functional (DF) electronic structure techniques to describe the interatomic forces. The Hugoniots derived from the calculated equation-of-state for deuterium does not exhibit the large compression predicted by the recently reported laser-driven experiments. However, the Hugoniot derived for nitrogen and oxygen agree well with explosively-driven and gas-gun experiments. The nature of the fluid along the Hugoniot, as calculated with DF-MD, has been analyzed. All three species (D2, N2, amd 02) undergo a continuous transition from a molecular to a partially dissociated fluid containing a mixture of atoms and molecules.

Kress, J. D. (Joel D.); Mazevet, S. (Stephane); Collins, L. A. (Lee A.)

2001-01-01

208

Thermal conductivities of molecular liquids by reverse nonequilibrium molecular dynamics.

The reverse nonequilibrium molecular dynamics method for thermal conductivities is adapted to the investigation of molecular fluids. The method generates a heat flux through the system by suitably exchanging velocities of particles located in different regions. From the resulting temperature gradient, the thermal conductivity is then calculated. Different variants of the algorithm and their combinations with other system parameters are tested: exchange of atomic velocities versus exchange of molecular center-of-mass velocities, different exchange frequencies, molecular models with bond constraints versus models with flexible bonds, united-atom versus all-atom models, and presence versus absence of a thermostat. To help establish the range of applicability, the algorithm is tested on different models of benzene, cyclohexane, water, and n-hexane. We find that the algorithm is robust and that the calculated thermal conductivities are insensitive to variations in its control parameters. The force field, in contrast, has a major influence on the value of the thermal conductivity. While calculated and experimental thermal conductivities fall into the same order of magnitude, in most cases the calculated values are systematically larger. United-atom force fields seem to do better than all-atom force fields, possibly because they remove high-frequency degrees of freedom from the simulation, which, in nature, are quantum-mechanical oscillators in their ground state and do not contribute to heat conduction. PMID:16852906

Zhang, Meimei; Lussetti, Enrico; de Souza, Luís E S; Müller-Plathe, Florian

2005-08-11

209

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.

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

210

Molecular dynamics investigation of dynamical properties of phosphatidylethanolamine lipid bilayers.

We describe the dynamic behavior of a 1-stearoyl-2-oleoyl-phosphatidylethanolamine (SOPE) bilayer from a 20 ns molecular dynamics simulation. The dynamics of individual molecules are characterized in terms of (2)H 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 (2)H T(1) 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 x 10(-8) cm(2)s) are comparable, though somewhat lower than, those determined by pulsed field gradient NMR methods. PMID:16035801

Pitman, Michael C; Suits, Frank; Gawrisch, Klaus; Feller, Scott E

2005-06-22

211

Molecular dynamics investigation of dynamical properties of phosphatidylethanolamine lipid bilayers

NASA Astrophysics Data System (ADS)

We describe the dynamic behavior of a 1-stearoyl-2-oleoyl-phosphatidylethanolamine (SOPE) bilayer from a 20 ns molecular dynamics simulation. The dynamics of individual molecules are characterized in terms of 2H 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 2H 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+/-1×10-8 cm2/s) are comparable, though somewhat lower than, those determined by pulsed field gradient NMR methods.

Pitman, Michael C.; Suits, Frank; Gawrisch, Klaus; Feller, Scott E.

2005-06-01

212

DYNAMICAL ANALYSIS OF HIGHLY EXCITED MOLECULAR SPECTRA

Spectra and internal dynamics of highly excited molecules are essential to understanding processes of fundamental importance for combustion, including intramolecular energy transfer and isomerization reactions. The goal of our program is to develop new theoretical tools to unravel information about intramolecular dynamics encoded in highly excited experimental spectra. We want to understand the formations of ''new vibrational modes'' when the ordinary normal modes picture breaks down in highly excited vibrations. We use bifurcation analysis of semiclassical versions of the effective Hamiltonians used by spectroscopists to fit complex experimental spectra. Specific molecular systems are of interest for their relevance to combustion and the availability of high-quality experimental data. Because of its immense importance in combustion, the isomerizing acetylene/vinylidene system has been the object of long-standing experimental and theoretical research. We have made significant progress in systematically understanding the bending dynamics of the acetylene system. We have begun to make progress on extending our methodology to the full bend-stretch vibrational degrees of freedom, including dynamics with multiple wells and above barrier motion, and time-dependent dynamics. For this, development of our previous methods using spectroscopic fitting Hamiltonians is needed, for example, for systems with multiple barriers.

Michael E. Kellman

2005-06-17

213

Molecular dynamics simulation of the melting of uranium dioxide nanocrystals

NASA Astrophysics Data System (ADS)

The melting of vacuum-isolated uranium dioxide (UO2) nanocrystals is studied by molecular dynamics simulation using the approximation of pair potentials and point ions. The size dependences of the melting temperature, the heat of melting, and the density jump of cubic crystals up to 1000 nm3 in size are measured for the ten most relevant sets of pair potentials. The linear and parabolic extrapolations of these dependences to macroscopic sizes are considered, and the parabolic extrapolation is found to be better for analyzing data on the melting temperature and heat.

Boyarchenkov, A. S.; Potashnikov, S. I.; Nekrasov, K. A.; Kupryazhkin, A. Ya.

2012-08-01

214

Molecular dynamics simulation of threshold displacement energies in zircon

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.

Moreira, Pedro A.; Devanathan, Ramaswami; Yu, Jianguo; Weber, William J.

2009-10-15

215

Conformational analysis of nucleosides may have direct applications to the structure–activity relationship (SAR) studies and in the design of new drug candidates. Although conformational analysis may be accessed in many different ways, in this work it was performed using molecular dynamics (MD) simulation in order to study the dynamic behavior of a nucleoside derivative of 1,4-dihydro-4-oxoquinoline-3-carboxylic acid, synthesized by our

Julliane Diniz Yoneda; Magaly Girăo Albuquerque; Kátia Zaccur Leal; Peter R. Seidl; Ralph A. Wheeler; Scott E. Boesch; Ricardo Bicca de Alencastro; Maria Cecília B. V. de Souza; Vitor F. Ferreira

2006-01-01

216

Ab initio molecular dynamics on the electronic Boltzmann equilibrium distribution

NASA Astrophysics Data System (ADS)

We prove that for a combined system of classical and quantum particles, it is possible to describe a dynamics for the classical particles that incorporates in a natural way the Boltzmann equilibrium population for the quantum subsystem. In addition, these molecular dynamics (MD) do not need to assume that the electrons immediately follow the nuclear motion (in contrast to any adiabatic approach) and do not present problems in the presence of crossing points between different potential energy surfaces (conical intersections or spin-crossings). A practical application of this MD to the study of the effect of temperature on molecular systems presenting (nearly) degenerate states—such as the avoided crossing in the ring-closure process of ozone—is presented.

Alonso, J. L.; Castro, A.; Echenique, P.; Polo, V.; Rubio, A.; Zueco, D.

2010-08-01

217

Molecular dynamics equation of state for nonpolar geochemical fluids

NASA Astrophysics Data System (ADS)

Remarkable agreement between molecular dynamics simulations and experimental measurements has been obtained for methane for a large range of intensive variables, including those corresponding to liquid/vapor coexistence. Using a simple Lennard-Jones potential the simulations not only predict the PVT properties up to 2000°C and 20,000 bar with errors less than 1.5%, but also reproduce phase equilibria well below 0°C with accuracy close to experiment. This two-parameter molecular dynamics equation of state (EOS) is accurate for a much larger range of temperatures and pressures than our previously published EOS with a total fifteen parameters or that of Angus et al. (1978) with thirty-three parameters. By simple scaling, it is possible to predict PVT and phase equilibria of other nonpolar and weakly polar species.

Duan, Zhenhao; Mřller, Nancy; Weare, John H.

1995-04-01

218

Evaluating data mining algorithms using molecular dynamics trajectories.

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

Tatsis, Vasileios A; Tjortjis, Christos; Tzirakis, Panagiotis

2013-01-01

219

Molecular dynamics simulations of a helicase.

Helicases are ubiquitous enzymes involved in nucleic acid metabolism. The PcrA DNA helicase is an essential bacterial protein involved in rolling circle plasmid replication and DNA repair. Recent crystal structures of PcrA bound to DNA indicate that a flexible loop mediates a functionally important rigid-body-domain rotation. In this study, we report stochastic boundary molecular dynamics simulations focused on this region for wild-type and mutants designed to increase the rigidity of the region. Residues in the region that were helix-disfavoring, such as glycine, threonine, and others, were mutated to alanine. The simulated dynamics, analyzed with a variety of measures of structure and mobility, indicate that a few point mutations will substantially increase helix formation in this region. Subnanosecond stochastic boundary molecular dynamics simulations at several temperatures offer a rapid protocol for assessing large numbers of mutants and provides a novel strategy for the design of experiments to test the role of this flexible loop region in the function of PcrA. PMID:12833548

Cox, Katherine; Watson, Tim; Soultanas, Panos; Hirst, Jonathan D

2003-08-01

220

Electron and molecular dynamics: Penning ionization and molecular charge transport

NASA Astrophysics Data System (ADS)

An understanding of fundamental reaction dynamics is an important problem in chemistry. In this work, experimental and theoretical methods are combined to study the dynamics of fundamental chemical reactions. Molecular collision and dissociation dynamics are explored with the Penning ionization of amides, while charge transfer reactions are examined with charge transport in organic thin film devices. Mass spectra from the Penning ionization of formamide by He*, Ne*, and Ar* were measured using molecular beam experiments. When compared to 70eV electron ionization spectra, the He* and Ne* spectra show higher yields of fragments resulting from C--N and C--H bond cleavage, while the Ar* spectrum only shows the molecular ion, H-atom elimination, and decarbonylation. The differences in yields and observed fragments are attributed to the differences in the dynamics of the two ionization methods. Fragmentation in the Ar* spectrum was analyzed using quantum chemistry and RRKM calculations. Calculated yields for the Ar* spectrum are in excellent agreement with experiment and show that 15% and 50% of the yields for decarbonylation and H-atom elimination respectively are attributed to tunneling. The effects of defects, traps, and electrostatic interactions on charge transport in imperfect organic field effect transistors were studied using course-grained Monte Carlo simulations with explicit introduction of defect and traps. The simulations show that electrostatic interactions dramatically affect the field and carrier concentration dependence of charge transport in the presence of a significant number of defects. The simulations also show that while charge transport decreases linearly as a function of neutral defect concentration, it is roughly unaffected by charged defect concentration. In addition, the trap concentration dependence on charge transport is shown to be sensitive to the distribution of trap sites. Finally, density functional theory calculations were used to study how charge localization affects the orbital energies of positively charged bithiophene clusters. These calculations show that the charge delocalizes over at least seven molecules, is more likely to localize on "tilted" molecules due to polarization effects, and affects molecules anisotropically. These results suggest that models for charge transport in organic semiconductors should be modified to account for charge delocalization and intermolecular interactions.

Madison, Tamika Arlene

221

Dynamical evolution of substucture in molecular clouds

NASA Astrophysics Data System (ADS)

There is abundant and diverse evidence that clumping is a common feature of molecular clouds. These observations have motivated a dynamical model of molecular clouds which views them as an ensemble of interacting clumps of gas. The primitive forms of clump interaction were studied through the technique of hydrodynamical simulation. The simplest interaction is that of a single clump plowing through an ambient medium. Plowing clumps in both subsonic and supersonic regimes were studied with particular emphasis on the physics of shock compression and rarefaction, vorticity, and drag. The infrared emission spectra of the shock-heated gas associated with supersonic clumps was also calculated. It is found that an ensemble of clumps will emit radiation, primarily in clump wake, sufficient to be observable. The observation of this infrared radiation is proposed as a consistency test of clumpy models of molecular clouds. Gravitational instability and clump coalescence were studied in simulations of clump collisions. The thermal stability of molecular gas was also studied, and unstable condensation modes in secularly cooling gas were found. These modes damp before reaching nonlinearity, but provide a continual source of acoustic perturbation.

Gilden, D. L.

1982-03-01

222

Molecular dynamics simulation of hydration in myoglobin

This study was carried out to evaluate the stability of the 89 bound water molecules that were observed in the neutron diffraction study of CO myoglobin. The myoglobin structure derived from the neutron analysis was used as the starting point in the molecular dynamics simulation using the software package CHARMM. After salvation of the protein, energy minimization and equilibration of the system, 50 pico seconds of Newtonian dynamics was performed. This data showed that only 4 water molecules are continously bound during the length of this simulation while the other solvent molecules exhibit considerable mobility and are breaking and reforming hydrogen bonds with the protein. At any instant during the simulation, 73 of the hydration sites observed in the neutron structure are occupied by water.

Gu, Wei [New Mexico Univ., Albuquerque, NM (United States). Dept. of Biochemistry; Schoenborn, B.P. [Los Alamos National Lab., NM (United States)

1995-09-01

223

Molecular beam studies of reaction dynamics

Purpose of this research project is two-fold: (1) to elucidate detailed dynamics of simple elementary reactions which are theoretically important and to unravel the mechanism of complex chemical reactions or photo chemical processes which play an important role in many macroscopic processes and (2) to determine the energetics of polyatomic free radicals using microscopic experimental methods. Most of the information is derived from measurement of the product fragment translational energy and angular distributions using unique molecular beam apparati designed for these purposes.

Lee, Y.T.

1987-03-01

224

Molecular dynamics simulations on distributed memory machines

NASA Astrophysics Data System (ADS)

We have developed an efficient method of performing large scale molecular dynamics simulations on a distributed memory parallel computer. A novel strategy has been used to calculate interaction forces across processors which avoids redundant calculation of forces and incurs relatively low communication overheads. The method uses the link-cell technique to increase computational efficiency. Spatial decomposition is used to map the particles in the fluid system onto different slave processors. As a result, the algorithm exhibits good scaling characteristics and high efficiency which makes it particular suitable for large scale simulations on a many processor network.

Liem, S. Y.; Brown, D.; Clarke, J. H. R.

1991-12-01

225

[Oligoglycine surface structures: molecular dynamics simulation].

The full-atomic molecular dynamics (MD) simulation of adsorption mode for diantennary oligoglycines [H-Gly4-NH(CH2)5]2 onto graphite and mica surface is described. The resulting structure of adsorption layers is analyzed. The peptide second structure motives have been studied by both STRIDE (structural identification) and DSSP (dictionary of secondary structure of proteins) methods. The obtained results confirm the possibility of polyglycine II (PGII) structure formation in diantennary oligoglycine (DAOG) monolayers deposited onto graphite surface, which was earlier estimated based on atomic-force microscopy measurements. PMID:21063448

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

226

Quantum thermal transport from classical molecular dynamics.

Using a generalized Langevin equation of motion, quantum thermal transport is obtained from classical molecular dynamics. This is possible because the heat baths are represented by random noises obeying quantum Bose-Einstein statistics. The numerical method gives asymptotically exact results in both the low-temperature ballistic transport regime and the high-temperature strongly nonlinear classical regime. The method is a quasiclassical approximation to the quantum transport problem. A one-dimensional quartic on-site model is used to demonstrate the crossover from ballistic to diffusive thermal transport. PMID:17995230

Wang, Jian-Sheng

2007-10-15

227

Implementing peridynamics within a molecular dynamics code

NASA Astrophysics Data System (ADS)

Peridynamics (PD) is a continuum theory that employs a nonlocal model to describe material properties. In this context, nonlocal means that continuum points separated by a finite distance may exert force upon each other. A meshless method results when PD is discretized with material behavior approximated as a collection of interacting particles. This paper describes how PD can be implemented within a molecular dynamics (MD) framework, and provides details of an efficient implementation. This adds a computational mechanics capability to an MD code, enabling simulations at mesoscopic or even macroscopic length and time scales.

Parks, Michael L.; Lehoucq, Richard B.; Plimpton, Steven J.; Silling, Stewart A.

2008-12-01

228

Dynamical nucleus-nucleus potential at short distances

The dynamical nucleus-nucleus potentials for fusion reactions {sup 40}Ca+{sup 40}Ca, {sup 48}Ca+{sup 208}Pb, and {sup 126}Sn+{sup 130}Te are studied with the improved quantum molecular dynamics model together with the extended Thomas-Fermi approximation for the kinetic energies of nuclei. The obtained fusion barrier for {sup 40}Ca+{sup 40}Ca is in good agreement with the extracted fusion barrier from the measured fusion excitation function, and the depths of the fusion pockets are close to the results of time-dependent Hartree-Fock calculations. The energy dependence of the fusion barrier is also investigated. The fusion pocket becomes shallow for a heavy fusion system and almost disappears for heavy nearly symmetric systems, and the obtained potential at short distances is higher than the adiabatic potential.

Jiang Yongying; Wang Ning [Department of Physics, Guangxi Normal University, Guilin 541004 (China); Li Zhuxia [China Institute of Atomic Energy, Beijing 102413 (China); Scheid, Werner [Institute for Theoretical Physics, Justus-Liebig-University, D-35392 Giessen (Germany)

2010-04-15

229

NASA Astrophysics Data System (ADS)

The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio.

Capar, M. Ilk; Nar, A.; Ferrarini, A.; Frezza, E.; Greco, C.; Zakharov, A. V.; Vakulenko, A. A.

2013-03-01

230

Bohmian Dynamics on Multiple Potential Energy Surfaces

The coupled Schrodinger equations that describe nonadiabatic dynamics on multiple potential energy surfaces are recast using the Bohm formulation of quantum mechanics. The resulting coupled Bohm equations are exact; i.e., numerical solutions are identical to those obtained from the original coupled Schrodinger equations by wave packet propagation. The classical limit of the coupled Bohm equations is derived. It corresponds to

John Burant; John Tully

2001-01-01

231

Thermal Transport in Carbon Nanotubes using Molecular Dynamics

NASA Astrophysics Data System (ADS)

We will present results of thermal transport phenomena in Carbon Nanotube (CNT) structures. CNTs have many interesting physical properties, and have the potential for device applications. Specifically, CNTs are robust materials with high thermal conductance and excellent electrical conduction properties. A review of electrical and thermal conduction of the structures will be discussed. The research requires analytical analysis as well as simulation. The major thrust of this study is the usage of the molecular dynamics (MD) simulator, LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). A significant investigation using the LAMMPS code is conducted on the existing Beowulf Computing Cluster at BSU. NanoHUB, an open online resource to the entire nanotechnology community developed by the researchers of Purdue University, is used for further supplementary resources. Results will include the time-dependence of temperature, kinetic energy, potential energy, heat flux correlation, and heat conduction.

Moore, Andrew; Khatun, Mahfuza

2011-10-01

232

Potential profile across a biased molecular wire

NASA Astrophysics Data System (ADS)

The potential profile across a biased molecular junction is calculated within two approaches: (1) a classical Thomas-Fermi type screening model and (2) a Hartree-Fock calculation for a tight-binding model with a three-dimensional electron distribution where the finite length of the molecule is accounted for by image charges. As an important result we find that the lateral width of the charge density strongly influences the potential profile thus underlining the need for a three-dimensional calculation. In addition to the classical model, the quantum calculation yields pronounced Friedel oscillations that can be related to the breaking of electron-hole symmetry. The quantum mechanical results are further used to calculate the current-voltage characteristics for weak contacts within the Landauer formalism. It is found that the Coulomb interaction partially compensates the localization of the induced charges and thus tends to suppress zones of negative differential resistance. [1] A. Nitzan et al., arXiv:physics/0207124, to appear in J. Chem. Phys. (2002) [2] S. Pleutin et al., arXiv:physics/0209091, to appear in J. Chem. Phys. (2003)

Ingold, G.-L.; Galperin, M.; Grabert, H.; Nitzan, A.; Pleutin, Stephane

2003-03-01

233

Dynamic transitions in molecular dynamics simulations of supercooled silicon

NASA Astrophysics Data System (ADS)

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

Mei, Xiaojun; Eapen, Jacob

2013-04-01

234

Heterogeneous dynamics of ionic liquids from molecular dynamics simulations.

Molecular dynamics simulations have been performed to study the complex and heterogeneous dynamics of ions in ionic liquids. The dynamics of cations and anions in 1-ethyl-3-methyl imidazolium nitrate (EMIM-NO(3)) are characterized by van Hove functions and the corresponding intermediate scattering functions F(s)(k,t) and elucidated by the trajectories augmented by the use of singular spectrum analysis (SSA). Several time regions are found in the mean squared displacement of the ions. Change in the slope in a plot of the diffusion coefficient against temperature is found at around 410 K in the simulation. Heterogeneous dynamics with the presence of both localized ions and fast ions capable of successive jumps were observed at long time scales in the self-part of the van Hove functions and in the trajectories. Non-Gaussian dynamics are evidenced by the self-part of the van Hove functions and wave number dependence of F(s)(k,t) and characterized as Levy flights. Successive motion of some ions can continue even after several nanoseconds at 370 K, which is longer than the onset time of diffusive motion, t(dif). Structure of the long time dynamics of fast ions is clarified by the phase space plot of the successive motion using the denoised data by SSA. The continual dynamics are shown to have a long term memory, and therefore local structure is not enough to explain the heterogeneity. The motion connecting localized regions at about 370 K is jumplike, but there is no typical one due to local structural changes during jump motion. With the local motion, mutual diffusion between cation and anion occurs. On decreasing temperature, mutual diffusion is suppressed, which results in slowing down of the dynamics. This "mixing effect of cation and anion" is compared with the "mixed alkali effect" found in the ionics in the ionically conducting glasses, where the interception of paths by different alkali metal ions causes the large reduction in the dynamics [J. Habasaki and K. L. Ngai, Phys. Chem. Chem. Phys. 9, 4673 (2007), and references herein]. Although a similar mechanism of the slowing down is observed, strong coupling of the motion of cation and anion prevents complete interception unless deeply supercooled, and this explains the wide temperature region of the existence of the liquid and supercooled liquid states in the ionic liquid. PMID:19026060

Habasaki, J; Ngai, K L

2008-11-21

235

Flow and plasticity via nonequilibrium molecular dynamics

The viscous flow of fluids and the plastic flow of solids, such as metals, are interesting from both the practical and the theoretical points of view. Atomistic molecular dynamics simulations provide a way of visualizing and understanding these flows in a detailed microscopic way. Simulations are necessarily carried out at relatively high rates of strain. For this reason they are ideally suited to the study of nonlinear flow phenomena: normal stresses induced by shear deformation, stress rotation, and the coupling of stress with heat flow, for instance. The simulations require appropriate boundary conditions, forces, and equations of motion. Newtonian mechanics is relatively inefficient for this simulation task. A modification, Nonequilibrium Molecular Dynamics, has been developed to simulate nonequilibrium flows. By now, many high-strain-rate rheological studies of flowing (viscous) fluids and (plastic) solids have been carried out. Here I describe the new methods used in the simulations and some results obtained in this way. A three-body shear-flow exercise is appended to make these ideas more concrete.

Hoover, W.G.

1984-06-11

236

Exact dynamic properties of molecular motors

NASA Astrophysics Data System (ADS)

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)] 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.

Boon, N. J.; Hoyle, R. B.

2012-08-01

237

Molecular dynamics simulation of radiation damage in bcc tungsten

NASA Astrophysics Data System (ADS)

Molecular dynamics (MD) simulations are performed to assess the primary damage due to high-energy neutron irradiation in bcc tungsten. For short-range interactions two different universal potentials are used, while for long-range interactions, two empirical embedded atom method (EAM) tungsten potentials are used. The short-range and long-range potentials are smoothly connected. Additionally, truncation of the electron density function at low distances is used. Statistically meaningful Frenkel pairs (FP) are counted and interstitial dumbbell orientations and interstitial or vacancy cluster counts are obtained. In addition, an approach to assess the volume influenced by the cascades based on a standard deviation ellipsoid is presented. A critical review of present and existing MD results is performed, and an attempt is made to clarify the roles played by the empirical potentials and by the temperature.

Fikar, J.; Schaeublin, R.

2007-02-01

238

Pressure derivatives in the classical molecular-dynamics ensemble.

The calculation of thermodynamic state variables, particularly derivatives of the pressure with respect to density and temperature, in conventional molecular-dynamics simulations is considered in the frame of the comprehensive treatment of the molecular-dynamics ensemble by Lustig [J. Chem. Phys. 100, 3048 (1994)]. This paper improves the work of Lustig in two aspects. In the first place, a general expression for the basic phase-space functions in the molecular-dynamics ensemble is derived, which takes into account that a mechanical quantity G is, in addition to the number of particles, the volume, the energy, and the total momentum of the system, a constant of motion. G is related to the initial position of the center of mass of the system. Secondly, the correct general expression for volume derivatives of the potential energy is derived. This latter result solves a problem reported by Lustig [J. Chem. Phys. 109, 8816 (1998)] and Meier [Computer Simulation and Interpretation of the Transport Coefficients of the Lennard-Jones Model Fluid (Shaker, Aachen, 2002)] and enables the correct calculation of the isentropic and isothermal compressibilities, the speed of sound, and, in principle, all higher pressure derivatives. The derived equations are verified by calculations of several state variables and pressure derivatives up to second order by molecular-dynamics simulations with 256 particles at two state points of the Lennard-Jones fluid in the gas and liquid regions. It is also found that it is impossible for systems of this size to calculate third- and higher-order pressure derivatives due to the limited accuracy of the algorithm employed to integrate the equations of motion. PMID:16483193

Meier, Karsten; Kabelac, Stephan

2006-02-14

239

Atomistic molecular dynamic simulations of multiferroics.

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

Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L

2012-08-08

240

Atomistic Molecular Dynamic Simulations of Multiferroics

NASA Astrophysics Data System (ADS)

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

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

2012-08-01

241

Electron-nuclear corellations for photoinduced dynamics in molecular dimers

NASA Astrophysics Data System (ADS)

Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by dynamic reorganization of of inter- and intra- molecular nuclear configuration modelled by quantized nuclear degree of freedom [1]. The dynamics of the electronic population and nuclear coherence is analyzed with help of both numerical solution of the chain of coupled differential equations for mean coordinate, population inversion, electronic-vibrational correlation etc.[2] and by propagating the Gaussian wavepackets in relevant adiabatic potentials. Intriguing results were obtained in the approximation of small energy difference and small change of nuclear equilibrium configuration for excited electronic states. In the limiting case of resonance between electronic states energy difference and frequency of the nuclear mode these results have been justified by comparison to exactly solvable Jaynes-Cummings model. It has been found that the photoinduced processes in dimer are arranged according to their time scales:(i) fast scale of nuclear motion,(ii) intermediate scale of dynamical redistribution of electronic population between excited states as well as growth and dynamics of electronic -nuclear correlation,(iii) slow scale of electronic population approaching to the quasiequilibrium distribution, decay of electronic-nuclear correlation, and diminishing the amplitude of mean coordinate oscillations, accompanied by essential growth of the nuclear coordinate dispersion associated with the overall nuclear wavepacket width. Demonstrated quantum-relaxational features of photoinduced vibronic dinamical processess in molecular dimers are obtained by simple method, applicable to large biological systems with many degrees of freedom. [1] J. A. Cina, D. S. Kilin, T. S. Humble, J. Chem. Phys. (2003) in press. [2] O. V. Prezhdo, J. Chem. Phys. 117, 2995 (2002).

Kilin, Dmitri S.; Pereversev, Yuryi V.; Prezhdo, Oleg V.

2003-03-01

242

Molecular dynamics simulations of retinoblastoma protein.

Tumor suppressor proteins play a crucial role in cell cycle regulation. Retinoblastoma protein (pRB) is one among them which regulates G1-S transition by binding with transcription factors. The activity of pRB is deregulated by cyclin dependent kinases-mediated hyper-phosphorylation and also due to cancer-derived mutations. In addition, it is also deactivated by binding of viral onco-proteins such as large T antigen, E1A, and E7. These viral proteins initially recognize pRB through their conserved LxCxE motif and facilitate dissociation of preexisting pRB-E2F complex. Based on these features, molecular dynamics (MD) simulation is performed for four different states of pRB for which the crystal structure is available. The unliganded/apo form and complex forms with E2F and E7 peptides reveal the molecular mechanism behind the activation and inactivation of pRB. In addition, the ternary complex of pRB with both E7 and E2F (for which no crystal structure is available) is modeled and simulated to understand the influence of binding of one ligand on the other. The variations in the three major factors such as conformational changes, inter- and intra-molecular interactions, and binding free energies between the apo and complex forms confirm the possibility for designing a small molecule inhibitor to inhibit pRB-E7 interactions without altering the prebound E2F. The present study deals with the molecular modeling and MD simulations of pRB in free and ligand-bound forms and confirms that pRB could be a valid target for the anticancer drug design when the cancer is induced by the viral onco-proteins and forms a clear base for designing E7 antagonists. PMID:23157310

Ramakrishnan, C; Subramanian, V; Balamurugan, K; Velmurugan, D

2012-11-19

243

Potential molecular targets for Ewing's sarcoma therapy

Ewing's sarcoma (ES) is a highly malignant tumor of children and young adults. Modern therapy for Ewing's sarcoma combines high-dose chemotherapy for systemic control of disease, with advanced surgical and/or radiation therapeutic approaches for local control. Despite optimal management, the cure rate for localized disease is only approximately 70%, whereas the cure rate for metastatic disease at presentation is less than 30%. Patients who experience long-term disease-free survival are at risk for significant side-effects of therapy, including infertility, limb dysfunction and an increased risk for second malignancies. The identification of new targets for innovative therapeutic approaches is, therefore, strongly needed for its treatment. Many new pharmaceutical agents have been tested in early phases of clinical trials in ES patients who have recurrent disease. While some agents led to partial response or stable disease, the percentages of drugs eliciting responses or causing an overall effect have been minimal. Furthermore, of the new pharmaceuticals being introduced to clinical practice, the most effective agents also have dose-limiting toxicities. Novel approaches are needed to minimize non-specific toxicity, both for patients with recurrence and at diagnosis. This report presents an overview of the potential molecular targets in ES and highlights the possibility that they may serve as therapeutic targets for the disease. Although additional investigations are required before most of these approaches can be assessed in the clinic, they provide a great deal of hope for patients with Ewing's sarcoma.

Jully, Babu; Rajkumar, Thangarajan

2012-01-01

244

Molecular mechanism of gas adsorption into ionic liquids: A molecular dynamics study

Room temperature ionic liquids (RTILs) have been shown to be versatile and tunable solvents that can be used in many chemical applications. In this study, we developed a dynamical, molecular-scale picture of the gas dissolution and interfacial processes in RTILs using molecular simulations. These simulations can provide the free energies associated with transporting a gas solute across various RTIL interfaces and physical insights into the interfacial properties and transport molecular mechanism of gas sorption processes. For CO2 sorption, the features in the potential of mean force (PMF) of CO2 using both polarizable and non-polarizable force fields are similar qualitatively. However, we observed some quantitative differences, and we describe the causes of these differences in this paper. We also show the significant impact of ionic-liquid chemical structures on the gas sorption process, and we discuss their influence on the H2O transport mechanism.

Dang, Liem X.; Chang, Tsun-Mei

2012-01-19

245

Molecular-dynamics simulation of thermal conductivity in amorphous silicon

NASA Astrophysics Data System (ADS)

The temperature-dependent thermal conductivity ?(T) of amorphous silicon has been calculated from equilibrium molecular-dynamics simulations using the time correlations of the heat flux operator in which anharmonicity is explicitly incorporated. The Stillinger-Weber two- and three-body Si potential and the Wooten-Weaire-Winer a-Si model were utilized. The calculations correctly predict an increasing thermal conductivity at low temperatures (below 400 K). The ?(T), for T>400 K, is affected by the thermally generated coordination-defect states. Comparisons to both experiment and previous calculations will be described.

Lee, Young Hee; Biswas, R.; Soukoulis, C. M.; Wang, C. Z.; Chan, C. T.; Ho, K. M.

1991-03-01

246

State-to-state collision dynamics of molecular free radicals

State-to-state collision dynamics of molecular radicals were investigated by the laser-induced fluorescence technique in a pulsed, crossed-beam apparatus. Dramatically different product state distributions were observed for two prototypical radicals, NCO({tilde X}{sup 2}{product}) and CH(X{sup 2}{product}). Based on a quantum scattering formalism and general considerations of the potential energy surfaces these observations were interpreted as generic features for the inelastic scattering of {sup 2}{product} radicals. The differences observed for NCO and CH are the results of well-known Hund's coupling classification of linear molecules.

Macdonald, R.G.; Liu, K.

1992-01-01

247

State-to-state collision dynamics of molecular free radicals

State-to-state collision dynamics of molecular radicals were investigated by the laser-induced fluorescence technique in a pulsed, crossed-beam apparatus. Dramatically different product state distributions were observed for two prototypical radicals, NCO({tilde X}{sup 2}{product}) and CH(X{sup 2}{product}). Based on a quantum scattering formalism and general considerations of the potential energy surfaces these observations were interpreted as generic features for the inelastic scattering of {sup 2}{product} radicals. The differences observed for NCO and CH are the results of well-known Hund`s coupling classification of linear molecules.

Macdonald, R.G.; Liu, K.

1992-02-01

248

Thermal conductivity of ionic systems from equilibrium molecular dynamics.

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

Salanne, Mathieu; Marrocchelli, Dario; Merlet, Céline; Ohtori, Norikazu; Madden, Paul A

2011-02-18

249

Molecular dynamics simulations of oxide memory resistors (memristors).

Reversible bipolar nanoswitches that can be set and read electronically in a solid-state two-terminal device are very promising for applications. We have performed molecular dynamics simulations that mimic systems with oxygen vacancies interacting via realistic potentials and driven by an external bias voltage. The competing short- and long-range interactions among charged mobile vacancies lead to density fluctuations and short-range ordering, while illustrating some aspects of observed experimental behavior, such as memristor polarity inversion. The simulations show that the 'localized conductive filaments' and 'uniform push/pull' models for memristive switching are actually two extremes of the one stochastic mechanism. PMID:21572187

Savel'ev, S E; Alexandrov, A S; Bratkovsky, A M; Williams, R Stanley

2011-05-16

250

Molecular dynamics calculations for sodium using pseudopotential theory

The equation of state of sodium is studied using the molecular dynamics technique whereby the classical motion of a system of ions is solved with the aid of computers. The interaction potential between pairs of sodium ions consists of Coulomb and Born-Mayer repulsion terms and an effective ion-ion interaction derived from pseudopotential theory. This theory includes the effects of electron gas screening, exchange, and correlation. A model pseudopotential with parameters fit to experimental low-temperature data is used. By using this technique, an atomic description of a simple metal proceeds to the calculation of macroscopic thermodynamic properties.

Swanson, R.E.

1981-06-01

251

Statistical Molecular Dynamics study of displacement energies in diamond

NASA Astrophysics Data System (ADS)

Molecular Dynamics simulations in bulk diamond using AIREBO potential have been used to calculate minimum displacement energy. A statistical approach has been applied calculating displacement probability curves along the main crystallographic directions. With these curves a minimum displacement energy of around 30 eV can be obtained, and a weighted average energy of around 70 eV. This value has been estimated as more accurate for its use in BCA displacement equations to obtain Frenkel pairs at moderate temperatures. This work also includes a study of defect states whose analysis reveals interesting results concerning the evolution of primary damage at higher PKA energies.

Delgado, Diego; Vila, Rafael

2011-12-01

252

Shock compression and spallation of tantalum: Molecular dynamics simulations

NASA Astrophysics Data System (ADS)

We perform large-scale molecular dynamics simulations of shock wave compression and spallation of Ta single crystals with different potentials including embedded-atom method (EAM), first-principles-based EAM (qEAM) and reactive forcefield (ReaxFF). Shock loading is applied along <100 >, <110> and <111>. Hugoniot states are obtained from direct shock or Hugoniostat simulations. Anisotropic behaviors are observed in plasticity (including twinning) during compression/tension and in spallation. We present detailed analysis of dislocations, twins and void nucleation and growth, and their implications for the mechanisms of plasticity and spall damage in Ta.

Luo, S. N.; An, Q.; Ravelo, R.; Germann, T. C.; Tonks, D. L.; Goddard, W. A., III

2011-06-01

253

Growth of carbon nanotubes: a molecular dynamics study

NASA Astrophysics Data System (ADS)

Molecular dynamics with realistic many-body atomic potentials was used to study the growth of carbon nanotubes. Analysis of the bond switching and ring migration processes has led to an identification of tube growth mechanisms. Wide tubes, initially open, were found to grow straight maintaining an all-hexagonal structure, while narrow tubes were found to develop permanent pentagonal rings that lead to tube closure upon further deposition. Continued deposition on the top of a closed tube yields a disordered cap structure, implying that open tubes are critical for defect-free growth.

Brabec, C. J.; Maiti, A.; Roland, C.; Bernholc, J.

1995-04-01

254

Properties of oxidized phospholipid monolayers: An atomistic molecular dynamics study

NASA Astrophysics Data System (ADS)

Non-saturated lipids in the lung surfactant are prone to oxidation by oxidative species present in air. In this Letter, oxidized monolayers of dioleoylphosphatidylcholine (DOPC) were studied by means of both molecular dynamics and potential of mean force calculations. Structural changes of the monolayer following oxidation were revealed, including orientational reversal of oxidized chains. Accumulation of oxidized lipids in the monolayer is observed for moderate oxidation ratios, whereas removal of the short-chain oxidation product is predicted at long timescales. Massive oxidation leads to the loss of the well-ordered monolayer structure and partial solubilization of the oxidized lipids in the aqueous subphase.

Khabiri, Morteza; Roeselova, Martina; Cwiklik, Lukasz

2012-01-01

255

Enhanced thermal characterization of silica aerogels through molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Porous structures of silica aerogels are generated using classical molecular dynamics, with the Tersoff potential, which has been re-parametrized for modeling silicon dioxides. This work demonstrates that this potential is superior to the widely used BKS potential in terms of characterizing the thermal conductivities of amorphous silica, by comparing the vibrational density of states with previous experimental studies. Aerogel samples of increasing densities are obtained through an expanding, heating and quenching process. Reverse non-equilibrium molecular dynamics is applied at each density to determine the thermal conductivity. A power-law fit of the results is found to accurately reflect the power-law variation found in experimental bulk aerogels. The results are also of the same order of magnitude as experimental bulk aerogels, but they are consistently higher. By analyzing the pore size distribution on different simulation length scales, we show that such a disparity is due to finite sizes of pores that can be represented, where increasing simulation length scales lead to an increase in the largest pore size that can be modeled.

Yeo, J. J.; Liu, Z. S.; Ng, T. Y.

2013-10-01

256

Molecular understanding of mutagenicity using potential energy methods

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.

Broyde, S.; Shapiro, R.

1992-07-01

257

Nonequilibrium molecular dynamics: The first 25 years

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.

Hoover, W.G. [Univ. of California, Davis, CA (United States)]|[Lawrence Livermore National Lab., CA (United States)

1992-08-01

258

Hsp70 chaperone dynamics and molecular mechanism.

The chaperone functions of heat shock protein (Hsp)70 involve an allosteric control mechanism between the nucleotide-binding domain (NBD) and polypeptide substrate-binding domain (SBD): ATP binding and hydrolysis regulates the affinity for polypeptides, and polypeptide binding accelerates ATP hydrolysis. These data suggest that Hsp70s exist in at least two conformational states. Although structural information on the conformation with high affinity for polypeptides has been available for several years, the conformation with an open polypeptide binding cleft was elucidated only recently. In addition, other biophysical studies have revealed a more dynamic picture of Hsp70s, shedding light on the molecular mechanism by which Hsp70s assist protein folding. In this review recent insights into the structure and mechanism of Hsp70s are discussed. PMID:24012426

Mayer, Matthias P

2013-09-05

259

Accelerated Molecular Dynamics Simulation of Thermal Desorption

NASA Astrophysics Data System (ADS)

Thermal desorption has been the focus of much surface science research recently. Alkane desorption experiments on graphite [1] show a prefactor that is constant with chain length, while experiments on magnesium oxide [2] show a prefactor that increases with chain length. We utilize an all-atom model to study alkane desorption from graphite. Transition state theory is used to obtain rate constants from the simulation. Accelerated molecular dynamics techniques are used to extend the simulations to experimentally relevant temperatures. Our results provide an explanation [3] for this seemingly contradictory functionality of the prefactor. We also examine the effect that film structure has on the rate of desorption and the shape of the desorption profile through varying coverage. [1] K.R. Paserba and A.J. Gellman, J. Chem. Phys. 115, 6737 (2001). [2] S.L. Tait et al., J. Chem. Phys. 122, 164707 (2005). [3] K.E. Becker and K.A. Fichthorn, J. Chem. Phys. 125, 184706 (2006).

Becker, Kelly; Fichthorn, Kristen

2007-03-01

260

Molecular dynamics simulations of bending behavior of tubular graphite cones

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations are performed to investigate the bending behavior of tubular graphite cones (TGCs). The second-generation reactive bond-order potential and four different van der Waals potentials are used to describe bonding and nonbonding atomic interactions, respectively. It is shown that the bending behavior is insensitive to the choice of the van der Waals potentials. An increase in the cone apex angle of TGCs moderately improves the bending stiffness due to the low shear resistance between the nanotube walls. A TGC with a high cone apex angle is preferred to a TGC with a low cone apex angle in terms of bending stiffness and stress level. It is also shown that an increase in the diameter of the innermost nanotube effectively increases the bending stiffness of TGCs.

Liu, P.; Zhang, Y. W.; Lu, C.

2004-09-01

261

Molecular Dynamics Study of Temperature Effects on Water Structure and Kinetics

For a system of 216 water molecules, molecular dynamics calculations have been carried out at two temperatures in addition to the one studied and reported previously. As before, the Ben-Naim and Stillinger effective pair potential was used for these calculations. The results document the breakdown of hydrogen-bond order and the rapid increase in the freedom of molecular motions that accompany

Frank H. Stillinger; Aneesur Rahman

1972-01-01

262

Combining optimal control theory and molecular dynamics for protein folding.

A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamics (MD). In the first step of the method, optimal control theory is employed to compute the force field and the optimal folding trajectory for the C? atoms of a Coarse-Grained (CG) protein model. The solution of this CG optimization provides an harmonic approximation of the true potential energy surface around the native state. In the next step CG optimization guides the MD simulation by specifying the optimal target positions for the C? atoms. In turn, MD simulation provides an all-atom conformation whose C? positions match closely the reference target positions determined by CG optimization. This is accomplished by Targeted Molecular Dynamics (TMD) which uses a bias potential or harmonic restraint in addition to the usual MD potential. Folding is a dynamical process and as such residues make different contacts during the course of folding. Therefore CG optimization has to be reinitialized and repeated over time to accomodate these important changes. At each sampled folding time, the active contacts among the residues are recalculated based on the all-atom conformation obtained from MD. Using the new set of contacts, the CG potential is updated and the CG optimal trajectory for the C? atoms is recomputed. This is followed by MD. Implementation of this repetitive CG optimization-MD simulation cycle generates the folding trajectory. Simulations on a model protein Villin demonstrate the utility of the method. Since the method is founded on the general tools of optimal control theory and MD without any restrictions, it is widely applicable to other systems. It can be easily implemented with available MD software packages. PMID:22238629

Arkun, Yaman; Gur, Mert

2012-01-06

263

The pathways and dynamics of molecular decomposition

NASA Astrophysics Data System (ADS)

Molecular decompositions often control complex chemical reactions by producing a highly reactive fragment that determines the subsequent chemistry. Despite the importance of such processes, there is little detailed information available for testing theoretical models and guiding the analysis of practical systems. This report describes experiments that produce, characterize, and dissociate highly energized molecules in order to uncover the details of molecular decomposition. These experiments create highly energized molecules either by vibrational overtone excitation or electronic excitation and detect the products either by a state-resolved laser detection technique, such as laser induced fluorescence, or by energy-selective ionization using vacuum ultraviolet photons. The state-resolved measurements probe the decomposition dynamics by determining the quantum state populations in the products and their appearance rates. These data provide a particularly good point of comparison with theoretical models and are a test of the applicability of statistical theories. The energy-selective ionization studies can also provide rate information but are most valuable as a means of identifying the primary dissociation products and their recoil energies. The use of vacuum ultraviolet photons makes our apparatus very sensitive. We have proven the technique on electronic photodissociation of a series of nitroalkanes and on nitrobenzene.

Crim, F. F.

1991-12-01

264

Molecular Dynamic Simulation of Failure of Ettringite

NASA Astrophysics Data System (ADS)

Ettringite is an important component in the hydration products of cement paste. To better understand the failure modes under tensile loading of cement-based materials, mechanical properties of each individual hydration product needs to be evaluated at atomic scale. This paper presents a molecular dynamic (MD) method to characterize and understand the mechanical properties of ettringite and its failure modes. The molecular structure of ettringite is established using ReaxFF force field package in LAMMPS. To characterize the atomic failure modes of cement paste, MD simulations were conducted by applying tensile strain load and shear strain load, respectively. In each MD failure simulation, the stress-strain relationship was plotted to quantify the mechanical properties at atomic scale. Then elastic constants of the ettringite crystal structure were calculated from these stress-strain relationships. MD simulations were validated by comparing the mechanical properties calculated from LAMMPS and those acquired from experiments. Future research should be performed on bridging-relationships of mechanical properties between atomic scale and macroscale to provide insights into further understanding the influence of mechanical properties at atomic scale on the performance of cement-based materials at macroscale.

Sun, W.; Wang, D.; Wang, L.

2013-03-01

265

Molecular reactivity dynamics in a confined environment.

Time evolution of various reactivity parameters viz. hardness, electrophilicity, chemical potential, polarizability, etc. in a confined environment has been studied through quantum fluid density functional theory formalism during time dependent processes such as proton-molecule collisions and molecule-field interaction. A Dirichlet type boundary condition has been incorporated to confine the systems. Responses in the reactivity parameters of the diatomic molecules, in the dynamical context, in ground state as well as in excited state, have been reported. Harmonic spectra are generated in the cases of the external laser field interacting with H2 and N2 molecules. PMID:23471169

Khatua, Munmun; Chattaraj, Pratim Kumar

2013-04-21

266

Statistical Analysis of Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

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.

Atkinson, R. A.

267

Oxidation dynamics of nanophase aluminum clusters : a molecular dynamics study.

Oxidation of an aluminum nanocluster (252,158 atoms) of radius 100{angstrom} placed in gaseous oxygen (530,727 atoms) is investigated by performing molecular-dynamics simulations on parallel computers. The simulation takes into account the effect of charge transfer between Al and O based on the electronegativity equalization principles. We find that the oxidation starts at the surface of the cluster and the oxide layer grows to a thickness of {approximately}28{angstrom}. Evolutions of local temperature and densities of Al and O are investigated. The surface oxide melts because of the high temperature resulting from the release of energy associated with Al-O bondings. Amorphous surface-oxides are obtained by quenching the cluster. Vibrational density-of-states for the surface oxide is analyzed through comparisons with those for crystalline Al, Al nanocluster, and {alpha}-Al{sub 2}O{sub 3}.

Ogata, S.

1998-01-27

268

Gas-Phase Molecular Dynamics: Vibrational Dynamics of Polyatomic Molecules

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 and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high- temperature, flow-tube reaction kinetics studies with mass-spectrometic sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wavepacket calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics.

Muckerman, J.T.

1999-05-21

269

GAS-PHASE MOLECULAR DYNAMICS: VIBRATIONAL DYNAMICS OF POLYATOMIC MOLECULES

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 and properties of short-lived chemical intermediates. 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 free radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wavepacket calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics.

MUCKERMAN,J.T.

1999-06-09

270

Molecular beam studies of reaction dynamics

The major thrust of this research project is to elucidate detailed dynamics of simple 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. 34 refs.

Lee, Y.T.

1990-03-01

271

Molecular dynamics simulation in virus research

Virus replication in the host proceeds by chains of interactions between viral and host proteins. The interactions are deeply influenced by host immune molecules and anti-viral compounds, as well as by mutations in viral proteins. To understand how these interactions proceed mechanically and how they are influenced by mutations, one needs to know the structures and dynamics of the proteins. Molecular dynamics (MD) simulation is a powerful computational method for delineating motions of proteins at an atomic-scale via theoretical and empirical principles in physical chemistry. Recent advances in the hardware and software for biomolecular simulation have rapidly improved the precision and performance of this technique. Consequently, MD simulation is quickly extending the range of applications in biology, helping to reveal unique features of protein structures that would be hard to obtain by experimental methods alone. In this review, we summarize the recent advances in MD simulations in the study of virus–host interactions and evolution, and present future perspectives on this technique.

Ode, Hirotaka; Nakashima, Masaaki; Kitamura, Shingo; Sugiura, Wataru; Sato, Hironori

2012-01-01

272

Molecular beam studies of reaction dynamics

NASA Astrophysics Data System (ADS)

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.

Lee, Yuan T.

1991-03-01

273

Deformation in Silica via Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Molecular Dynamics (MD) simulations probing the atomistic aspects of dynamic fracture in amorphous silica (a-SiO2) reveal nanometer scale cavities nucleating, augmenting, and coalescing with one another up to 20 nm ahead of the crack tip [1, 2]. After which these cavities were seen to merge with the advancing crack to cause mechanical failure. This scenario was also observed experimentally during stress corrosion ultra-slow fracture of glass using Atomic Force Microscopy (AFM) [3, 4]. In order to characterize the irreversible changes in structure taking place within the process zone (i.e. the zone ahead of the crack tip where pores are opening), a variety of simulations have been carried out using 1) cyclic loading and unloading in hydrostatic pressure and 2) cyclic loading and unloading in shear. Structural changes revealed by these simulations have been analyzed in various ways (static structure factor, analysis of the ring structure, evolution of the fabric tensor). [1] C.L. Rountree, et. al. Annual Review of Materials Research. 2002. 32:377-400. [2] L.Van Brutzel, et. al. Mat. Res. Soc. Symp. Proc. 2002. 703:V3.9.1- V3.9.6. [4] F. Celarie, et. al.. Phys. Rev. Lett. Vol. 90 (2003), 075504/1-4. [5] S. Prades, et. al. Int. J. Sol. Struct. Vol. 42 (2005), 637-645.

Rountree, Cindy; Talamali, Mehdi; Bonamy, Daniel; Vandembroucq, Damien; Roux, Stephane; Bouchaud, Elisabeth

2007-03-01

274

Potential of Molecular Markers in Plant Biotechnology

During the last few decades, the use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in plant biotechnology and their genetics studies. There are different types of markers viz. morphological, biochemical and DNA based molecular markers. These DNA based markers are differentiates in two types first non PCR based (RFLP) and second is

P. Kumar; V. K. Gupta; A. K. Misra; D. R. Modi; B. K. Pandey

2009-01-01

275

Structure factor and rheology of chain molecules from molecular dynamics

NASA Astrophysics Data System (ADS)

Equilibrium and non-equilibrium molecular dynamics were performed to determine the relationship between the static structure factor, the molecular conformation, and the rheological properties of chain molecules. A spring-monomer model with Finitely Extensible Nonlinear Elastic and Lennard-Jones force field potentials was used to describe chain molecules. The equations of motion were solved for shear flow with SLLOD equations of motion integrated with Verlet's algorithm. A multiple time scale algorithm extended to non-equilibrium situations was used as the integration method. Concentric circular patterns in the structure factor were obtained, indicating an isotropic Newtonian behavior. Under simple shear flow, some peaks in the structure factor were emerged corresponding to an anisotropic pattern as chains aligned along the flow direction. Pure chain molecules and chain molecules in solution displayed shear-thinning regions. Power-law and Carreau-Yasuda models were used to adjust the generated data. Results are in qualitative agreement with rheological and light scattering experiments.

Castrejón-González, Omar; Castillo-Tejas, Jorge; Manero, Octavio; Alvarado, Juan F. J.

2013-05-01

276

MPSA effects on copper electrodeposition investigated by molecular dynamics simulations.

In superconformal filling of copper-chip interconnects, organic additives are used to fill high-aspect-ratio trenches or vias from the bottom up. In this study we report on the development of intermolecular potentials and use molecular dynamics simulations to provide insight into the molecular function of an organic additive (3-mercaptopropanesulfonic acid or MPSA) important in superconformal electrodeposition. We also investigate how the presence of sodium chloride affects the surface adsorption and surface action of MPSA as well as the charge distribution in the system. We find that NaCl addition decreases the adsorption strength of MPSA at a simulated copper surface and attenuates the copper-ion association with MPSA. The model also was used to simulate induced-charge effects and adsorption on a nonplanar electrode surface. PMID:18247991

Guymon, Clint G; Harb, John N; Rowley, Richard L; Wheeler, Dean R

2008-01-28

277

MPSA effects on copper electrodeposition investigated by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

In superconformal filling of copper-chip interconnects, organic additives are used to fill high-aspect-ratio trenches or vias from the bottom up. In this study we report on the development of intermolecular potentials and use molecular dynamics simulations to provide insight into the molecular function of an organic additive (3-mercaptopropanesulfonic acid or MPSA) important in superconformal electrodeposition. We also investigate how the presence of sodium chloride affects the surface adsorption and surface action of MPSA as well as the charge distribution in the system. We find that NaCl addition decreases the adsorption strength of MPSA at a simulated copper surface and attenuates the copper-ion association with MPSA. The model also was used to simulate induced-charge effects and adsorption on a nonplanar electrode surface.

Guymon, Clint G.; Harb, John N.; Rowley, Richard L.; Wheeler, Dean R.

2008-01-01

278

BEYOND BORN-OPPENHEIMER: Molecular Dynamics Through a Conical Intersection

NASA Astrophysics Data System (ADS)

Nonadiabatic effects play an important role in many areas of physics and chemistry. The coupling between electrons and nuclei may, for example, lead to the formation of a conical intersection between potential energy surfaces, which provides an efficient pathway for radiationless decay between electronic states. At such intersections the Born-Oppenheimer approximation breaks down, and unexpected dynamical processes result, which can be observed spectroscopically. We review the basic theory required to understand and describe conical, and related, intersections. A simple model is presented, which can be used to classify the different types of intersections known. An example is also given using wavepacket dynamics simulations to demonstrate the prototypical features of how a molecular system passes through a conical intersection.

Worth, Graham A.; Cederbaum, Lorenz S.

2004-01-01

279

Molecular Dynamics Simulation on Stability of Insulin on Graphene

NASA Astrophysics Data System (ADS)

The adsorption dynamics of a model protein (the human insulin) onto graphene surfaces with different sizes was investigated by molecular dynamics simulations. During the adsorption, it has different effect on the stability of the model protein in the fixed and non-fixed graphene systems. The tertiary structure of the protein was destroyed or partially destroyed, and graphene surfaces shows the selective protection for some ?-helices in non-fixed systems but not in fixed systems by reason of the flexibility of graphene. As indicated by the interaction energy curve and trajectory animation, the conformation and orientation selection of the protein were induced by the properties and the texture of graphene surfaces. The knowledge of protein adsorption on graphene surfaces would be helpful to better understand stability of protein on graphene surfaces and facilitate potential applications of graphene in biotechnology.

Liang, Li-jun; Wang, Qi; Wu, Tao; Shen, Jia-wei; Kang, Yu

2009-12-01

280

A Hands-On Introduction to Molecular Dynamics

NASA Astrophysics Data System (ADS)

We present an introduction to the chemical and computational aspects of the molecular dynamics (MD) simulation technique. Using just a few elementary ideas from classical mechanics and numerical analysis, and linear chains of identical particles as example systems, we take the reader through the steps required for the design and analysis of a simple molecular dynamics experiment. We employ the Hooke's law model for the interactions between the particles since its visualization in terms of masses and springs provides a natural model for chemical bonds. We derive the classical equations of motion in detail for the three-particle chain. We then introduce two simple methods for numerically integrating the equations of motion, one based on Euler's method for differential equations, and the other a more accurate algorithm developed by Verlet. We analyze the dynamics of the three-particle system in terms of its normal modes of vibration. Finally, exploiting the closed-form solution admitted by the Hooke's law potential, we compare the errors generated by the two integration algorithms. As supplemental material, we provide a basic MD implementation using the Euler algorithm in both Fortran and C and a set of suggested exercises.

Lamberti, Vincent E.; Fosdick, Lloyd D.; Jessup, Elizabeth R.; Schauble, Carolyn J. C.

2002-05-01

281

Camdas: An automated conformational analysis system using molecular dynamics

We present an automated conformational analysis program, CAMDAS (Conformational Analyzer with Molecular Dynamics And Sampling). CAMDAS performs molecular dynamics (MD) calculations for a target molecule and samples conformers from the trajectory of the MD. The program then evaluates the similarities between each of the sampled conformers in terms of the root- mean-square deviations of the atomic positions, clusters similar conformers,

Hideki Tsujishita; Shuichi Hirono

1997-01-01

282

Ultrafast dynamics in isolated molecules and molecular clusters

During the past decade the understanding of photo-induced ultrafast dynamics in molecular systems has improved at an unforeseen speed and a wealth of detailed insight into the fundamental processes has been obtained. This review summarizes our present knowledge on ultrafast dynamics in isolated molecules and molecular clusters evolving after excitation with femtosecond pulses as studied by pump-probe analysis in real

I. V. Hertel; W. Radloff

2006-01-01

283

A Hands-On Introduction to Molecular Dynamics

We present an introduction to the chemical and computational aspects of the molecular dynamics (MD) simulation technique. Using just a few elementary ideas from classical mechanics and numerical analysis, and linear chains of identical particles as example systems, we take the reader through the steps required for the design and analysis of a simple molecular dynamics experiment. We employ the

Vincent E. Lamberti; Lloyd D. Fosdick; Elizabeth R. Jessup; Carolyn J. C. Schauble

2002-01-01

284

The structures of the adducts of (+)- and (-)trans-7,8,dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo (a)pyrene (anti-BPDE) formed by trans addition to N[sup 2] of guanine have been of great interest because the high biological activity of BPDE in mammalian mutagenesis and tumorigenesis has been attributed to the predominant (+)-adduct, while the (-)-adduct is inactive. Molecular mechanics and dynamics calculations have been employed to elucidate the structural difference between this mirror image adduct pair in a duplex dodecamer, d(5' GCGCGCG-(BPDE)CGCGC3') [center dot] d(5'GCGCGCGCGCGC3'). Minimized potential energy calculations using the program DUPLEX were employed to locate starting structures for the dynamics. Three types of structures were found in the energy minimized conformation space searches for each enantiomer: pyrenyl moiety in the minor groove of a Watson-Crick base paired B-DNA duplex, pyrenyl moiety in the major groove of a B-DNA duplex with syn guanine and Hoogsteen base pairs at the modification site, and intercalation type structures. The minor groove structure is energetically preferred for the (+) enantiomer while both minor groove and major groove structures are favored and of comparable energy in the (-) enantiomer. These energy-minimized duplex dodecamers, as well as an unmodified B-DNA control of the same sequence, were subjected to 100 ps molecular dynamics simulations with solvent and salt with the program AMBER. The duplex dodecamer, d(CGCGAATTCGCG)[sub 2], was subjected to a similar simulation using the crystal structure as starting coordinates. Detailed analysis of the dynamic evolution of the conformational and the helical parameters of all the dodecamer simulations were carried out with Molecular Dynamics Analysis Toolchest.

Singh, S.B.

1992-01-01

285

Modeling and Bio molecular Self-assembly via Molecular Dynamics and Dissipative Particle Dynamics

NASA Astrophysics Data System (ADS)

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.

Rakesh, L.

2009-09-01

286

Statistical coarse-graining of molecular dynamics into peridynamics.

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.

Silling, Stewart Andrew; Lehoucq, Richard B.

2007-10-01

287

Dynamics and Potential Energy Landscape of Supercooled Water

NASA Astrophysics Data System (ADS)

We present molecular dynamics simulations of the SPC/E model of water to explore the connection between dynamic properties and the potential energy landscape. We calculate the configurational entropy and instantaneous normal mode (or local potential energy curvature) spectrum in the same region of the phase diagram where the dynamics are well-described by the predictions of the mode-coupling theory. We find a strong correlation between the diffusion constant and the configurational entropy, in the sprit of the Adam-Gibbs hypothesis. We also find that the diffusion constant has monotonic dependence on the fraction of negatively curved directions sampled in the landscape. We further show that a roughly linear relation exists between the number of minima and the connectivity of the minima (i.e. the number of negatively curved directions). These results suggest that the behavior described by MCT captures the slowing of liquid dynamics caused by the ruggedness of the energy landscape, where barrier hopping does not play a role.

Starr, Francis W.; Lanave, Emilia; Scala, Antonio; Sciortino, Francesco; Stanley, H. Eugene

2000-03-01

288

Plasticity of metal wires in torsion: Molecular dynamics and dislocation dynamics simulations

The orientation dependent plasticity in metal nanowires is investigated using molecular dynamics and dislocation dynamics simulations. Molecular dynamics simulations show that the orientation of single crystal metal wires controls the mechanisms of plastic deformation. For wires oriented along ?110?, dislocations nucleate along the axis of the wire, making the deformation homogeneous. These wires also maintain most of their strength after

Christopher R. Weinberger; Wei Cai

2010-01-01

289

He6 breakup dynamic polarization potential reexamined

NASA Astrophysics Data System (ADS)

The dynamic polarization potential contribution to the effective interaction between He6 and Pb208 at 27 MeV, due to breakup channels, is recalculated exploiting a recently developed improved model for He6. The most general features of the long-range attractive and absorptive components remain the same as were found in an earlier study, but the asymptotic magnitudes are reduced by factors of about 2.5 and 4.5, respectively. We draw conclusions from these results, as well as from further calculations at 22 MeV, closer to the Coulomb barrier, and at 32 MeV.

Mackintosh, R. S.; Keeley, N.

2009-01-01

290

Molecular-dynamics simulation of a ceramide bilayer

NASA Astrophysics Data System (ADS)

Ceramide is the simplest lipid in the biologically important class of glycosphingolipids. Ceramide is an important signaling molecule and a major component of the strateum corneum layer in the skin. In order to begin to understand the biophysical properties of ceramide, we have carried out a molecular-dynamics simulation of a hydrated 16:0 ceramide lipid bilayer at 368 K (5° above the main phase transition). In this paper we describe the simulation and present the resulting properties of the bilayer. We compare the properties of the simulated ceramide bilayer to an earlier simulation of 18:0 sphingomyelin, and we discuss the results as they relate to experimental data for ceramide and other sphingolipids. The most significant differences arise at the lipid/water interface, where the lack of a large ceramide polar group leads to a different electron density and a different electrostatic potential but, surprisingly, not a different overall ``dipole potential,'' when ceramide is compared to sphingomyelin.

Pandit, Sagar A.; Scott, H. Larry

2006-01-01

291

Isomorphic phase transformation in shocked cerium using molecular dynamics

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.

Dupont, Virginie [Los Alamos National Laboratory; Germann, Timothy C [Los Alamos National Laboratory; Chen, Shao - Ping [Los Alamos National Laboratory

2010-01-01

292

A molecular dynamics simulation study of defect production in vanadium

We performed molecular dynamics simulations to investigate the process of defect production in pure vanadium. The interaction of atoms was described by the EAM interatomic potential modified at short range to merge smoothly with the universal potential for description of the high energy recoils in cascades. The melting point of this EAM model of vanadium was found to be consistent with the experimental melting temperature. The threshold energies of displacement events in the model system are also consistent with experimental minimum threshold in vanadium, and its average was found to be 44 eV. We evaluated the efficiencies of defect production in the displacement events initiated by recoils with kinetic energy up to 5 keV, and found that the probability of cluster formation is smaller than that of simulated events in fcc metals reported in the literature.

Morishita, K. [Lawrence Livermore National Lab., CA (United States)]|[Univ. of Tokyo (Japan); Diaz de la Rubia, T. [Lawrence Livermore National Lab., CA (United States)

1995-01-23

293

Ion pairing and dissociation at liquid\\/liquid interfaces: Molecular dynamics and continuum models

The thermodynamics and dynamics of NaCl ion-pair dissociation at the water\\/1,2-dichloroethane liquid\\/liquid interface are examined using a continuum electrostatic model, molecular dynamics free energy calculations, and nonequilibrium dynamic trajectory calculations. The continuum model shows increased stability of the ion pair relative to that in bulk water and strong dependence of the potential of mean force on the orientation and location

Karl Schweighofer; Ilan Benjamin

2000-01-01

294

Molecular dynamics simulations were carried out for Pd-Pt , Pd-Rh , and Pd-Cu nanoclusters supported on a static graphite substrate using the quantum Sutton-Chen potential for the metal-metal interactions. The graphite substrate was represented as layers of fixed carbons sites and modeled with the Lennard-Jones potential model. Metal-graphite interaction potentials obtained by fitting experimental cohesive energies were utilized. Monte Carlo

Subramanian K. R. S. Sankaranarayanan; Venkat R. Bhethanabotla; Babu Joseph

2005-01-01

295

(Molecular understanding of mutagenicity using potential energy methods)

The objective of our work has been, for many year, to elucidate on a molecular level at atomic resolution the structures of DNAs modified by highly mutagenic polycyclic aromatic amines and hydrocarbons, and their less mutagenic chemically related analogs and unmodified DNAs, as controls. The ultimate purpose of this undertaking is to obtain an understanding of the relationship DNA structures and mutagenicity. Our methods for elucidating structures are computational, but we keep in close contact with experimental developments, and have, very recently, been able to incorporate the first experimental information from NMR studies by other workers in our calculations. The specific computational methods we employ are minimized potential energy calculations using the torsion angle space program DUPLEX, developed and written by Dr. Brain Hingerty to yield static views. Molecular dynamics simulations of the important static structures with full solvation and salt are carried out with the program AMBER; this yields mobile views in a milieu that best mimics the natural environment of the cell. In addition, we have been developing new strategies for searching conformation space and building DNA duplexes from favored subunit structures. 30 refs., 12 figs.

Broyde, S.

1990-01-01

296

Phonostat: thermostatting phonons in molecular dynamics simulations.

Thermostat algorithms in a molecular dynamics simulation maintain an average temperature of a system by regulating the atomic velocities rather than the internal degrees of freedom. Herein, we present a "phonostat" algorithm that can regulate the total energy in a given internal degree of freedom. In this algorithm, the modal energies are computed at each time step using a mode-tracking scheme and then the system is driven by an external driving force of desired frequency and amplitude. The rate and amount of energy exchange between the phonostat and the system is controlled by two distinct damping parameters. Two different schemes for controlling the external driving force amplitude are also presented. In order to test our algorithm, the method is applied initially to a simple anharmonic oscillator for which the role of various phonostat parameters can be carefully tested. We then apply the phonostat to a more realistic (10,0) carbon nanotube system and show how such an approach can be used to regulate energy of highly anharmonic modes. PMID:21663354

Raghunathan, Rajamani; Greaney, P Alex; Grossman, Jeffrey C

2011-06-01

297

Molecular Dynamics Simulations of Ferroelectric Phase Transitions

NASA Astrophysics Data System (ADS)

Based on an analysis of the wavevector dependence of the lattice instabilities in KNbO_3, we proposed a real-space chain-like instability and a scenario of sequential freezing out or onset of coherence of these instabilities, which qualitatively explains the sequence of observed temperature-dependent ferroelectric phases.(R. Yu and H. Krakauer, Phys. Rev. Lett. 74), 4067 (1995). We suggested that this chain-like instability should also be found in BaTiO_3, and this has been subsequently confirmed by Ghosez et al.(P. Ghosez et al.), Proc. 4th Williamsburg Workshop on First-Principles Calculations for Ferroelectrics, to be published We will present molecular dynamics simulations on BaTiO_3, using effective Hamiltonians constructed from first-principles calculations,(W. Zhong, D. Vanderbilt, and K. M. Rabe, Phys. Rev. Lett. 73), 1861 (1994). that reproduce the essential features of diffuse x-ray scattering measurements in the cubic, tetragonal, orthorhombic, and rhombohedral phases. The good agreement supports the interpretation of real-space chain-formation. Simulations for KNbO3 may also be reported.

Yu, Rici; Krakauer, Henry

1997-03-01

298

Molecular Dynamics Simulations of Biotin Carboxylase†

Biotin carboxylase catalyzes the ATP-dependent carboxylation of biotin, and is one component of the multienzyme complex acetyl-CoA carboxylase that catalyzes the first committed step in fatty acid synthesis in all organisms. Biotin carboxylase from Escherichia coli, whose crystal structures with and without ATP bound have been determined, has served as a model system for this component of the acetyl-CoA carboxylase complex. The two crystal structures revealed a large conformational change of one domain relative to the other domains when ATP is bound. Unfortunately, the crystal structure with ATP bound was obtained with an inactive site-directed mutant of the enzyme. As a consequence the structure with ATP bound lacked key structural information such as for the Mg2+ ions and contained altered conformations of key active site residues. Therefore, nanosecond molecular dynamics studies of the wild-type biotin carboxylase were undertaken to supplant and amend the results of the crystal structures. Specifically, the protein-metal interactionsof the two catalytically critical Mg2+ ions bound in the active site are presented along with a reevaluation of the conformations of active site residues bound to ATP. In addition, the regions of the polypeptide chain that serve as hinges for the large conformational change were identified. The results of the hinge analysis complemented a covariance analysis that identified the individual structural elements of biotin carboxylase that change their conformation in response to ATP binding.

Lill, Sten O. Nilsson; Gao, Jiali; Waldrop, Grover L.

2009-01-01

299

We have studied the melting properties of magic number Pd clusters with sizes up to several thousand atoms using classical molecular dynamics employing embedded atom potentials. These sizes correspond to cluster diameters of up to 10 nm. The potentials used do not only qualitatively predict the size dependent behavior but are also found to reveal some interesting results about the

Najeh Jisrawi; Saja Abdulhadi; Astrid Pundt

2007-01-01

300

Elastic electron scattering from molecular potentials

Fink and co-workers have reported a molecular electron density function for the nitrogen molecule which was derived from an experimental differential electron scattering cross section. The transformation of the data was accomplished by assuming that the first Born approximation could be used to describe the scattering process. This procedure is analyzed by considering a higher order treatment of the elastic

D. A. Kohl; M. M. Arvedson

1980-01-01

301

Thermomechanical anomalies and polyamorphism in B2O3 glass: A molecular dynamics simulation study

Molecular dynamics (MD) simulations, based on a new coordination-dependent charge-transfer potential, were used to study the behavior of B2O3 in response to various thermal and mechanical constraints. This interaction potential allows for the charges on atoms to redistribute upon the formation and rupture of chemical bonds, and dynamically adjusts to multiple coordination states for a given species. Our simulations reveal

Liping Huang; John Kieffer

2006-01-01

302

Study of the dynamical potential barriers in heavy ion collisions

NASA Astrophysics Data System (ADS)

The nucleus-nucleus interaction potentials for the fusion reactions 16O + 208Pb, 64Ni + 64Ni, 58Ni + 58Ni and 16O + 154Sm are extracted from the improved isospin-dependent quantum molecular dynamics model. The shell correction effects are discussed. The negative shell correction energies lower potential barriers of a certain reaction. The incident energy dependence of the potential barrier is investigated for each system. A complex phenomenon of energy dependence is observed. It is also found that incident energy dependence of the barrier radius and barrier height shows opposite behaviors. The Coulomb potential shows weak energy dependence when distance of two colliding nuclei is lower than the touching distance. The isospin effects of the potential barrier are investigated. The orientation effects of the potential barrier is also discussed for the system 16O + 154Sm. The fusion cross sections that correspond to the equatorial orientation of 154Sm are very low in sub-barrier region because of the high fusion barriers and the shallow potential pockets.

Zhu, Long; Su, Jun; Xie, Wen-Jie; Zhang, Feng-Shou

2013-10-01

303

Nonadiabatic dynamics generally defines the entire evolution of electronic excitations in optically active molecular materials. It is commonly associated with a number of fundamental and complex processes such as intraband relaxation, energy transfer, and light harvesting influenced by the spatial evolution of excitations and transformation of photoexcitation energy into electrical energy via charge separation (e.g., charge injection at interfaces). To treat ultrafast excited-state dynamics and exciton/charge transport we have developed a nonadiabatic excited-state molecular dynamics (NA-ESMD) framework incorporating quantum transitions. Our calculations rely on the use of the Collective Electronic Oscillator (CEO) package accounting for many-body effects and actual potential energy surfaces of the excited states combined with Tully's fewest switches algorithm for surface hopping for probing nonadiabatic processes. This method is applied to model the photoinduced dynamics of distyrylbenzene (a small oligomer of polyphenylene vinylene, PPV). Our analysis shows intricate details of photoinduced vibronic relaxation and identifies specific slow and fast nuclear motions that are strongly coupled to the electronic degrees of freedom, namely, torsion and bond length alternation, respectively. Nonadiabatic relaxation of the highly excited mA(g) state is predicted to occur on a femtosecond time scale at room temperature and on a picosecond time scale at low temperature. PMID:21218841

Nelson, Tammie; Fernandez-Alberti, Sebastian; Chernyak, Vladimir; Roitberg, Adrian E; Tretiak, Sergei

2011-01-10

304

The results of experimental studies of the valence electronic structure of 1-butene by means of electron momentum spectroscopy (EMS) have been reinterpreted on the basis of molecular dynamical simulations in conjunction with the classical MM3 force field. The computed atomic trajectories demonstrate the importance of thermally induced nuclear dynamics in the electronic neutral ground state, in the form of significant deviations from stationary points on the potential energy surface and considerable variations of the C-C-C-C dihedral angle. These motions are found to have a considerable influence on the computed spectral bands and outer-valence electron momentum distributions. Euclidean distances between spherically averaged electron momentum densities confirm that thermally induced nuclear motions need to be fully taken into account for a consistent interpretation of the results of EMS experiments on conformationally flexible molecules. PMID:23902590

Shojaei, S H Reza; Vandenbussche, Jelle; Deleuze, Michael S; Bultinck, Patrick

2013-08-22

305

On the electrostatic potential profile in biased molecular wires

NASA Astrophysics Data System (ADS)

The potential profile across a biased molecular junction is calculated within the framework of a simple Thomas-Fermi-type screening model. In particular, the relationship between this profile and the lateral molecular cross section is examined. We find that a transition from a linear potential profile to a potential that drops mainly near the molecule-metal contacts occurs with increasing cross-section width, in agreement with numerical quantum calculations.

Nitzan, Abraham; Galperin, Michael; Ingold, Gert-Ludwig; Grabert, Hermann

2002-12-01

306

Ab initio molecular dynamics — Applications to the molecular and solid state physics of phosphorus

Summary We review combined molecular dynamics (MD) and density functional (DF) simulations and their applicability in chemistry and physics. This method (also termedab initio MD, “first principles” MD or “Car-Parrinello” method) exhibits characteristic strengths and weaknesses, and we demonstrate both in a set of typical example applications from molecular physics (phosphorus clusters) and solid state physics\\/chemistry (liquid phosphorus). Dynamical, finite

D. Hohl

1995-01-01

307

Molecular Dynamics Studies of Dynamical High-Pressure Phase Transitions in Rare-Gas Solids

NASA Astrophysics Data System (ADS)

The phase diagram of pair potential models of rare-gases was studied with respect to the effect of the choice of potential on the nature of the phase diagram. In particular the existence of a high-pressure bcc phase is shown to be potential sensitive. We show using molecular dynamics that the fcc-bcc phase transition cannot be reproduced with the Lennard-Jones (12-6) pair potential, though it is reproduced with the Buckingham pair potential. We propose a simple analytical technique, based on the Einstein theory of a harmonic solid, for predicting an fcc-bcc phase transition in a given system. Using the atomic volume and the pair potential as input, we were able to predict the transition temperature. These findings agree with an earlier work by A. B. Belonoshko et al., Phys. Rev. Lett. 87, 165505 (2001). Additionally, shock wave simulations of several model systems were conducted. The structure of shock wave in this model was examined as a function of shock strength and the existence of a dynamic phase transition was explored.

Pechenik, Eugene; Makov, Guy

2006-03-01

308

Molecular Dynamics Simulation of Binary Fluid in a Nanochannel

This paper presents the results from a molecular dynamics simulation of binary fluid (mixture of argon and krypton) in the nanochannel flow. The computational software LAMMPS is used for carrying out the molecular dynamics simulations. Binary fluids of argon and krypton with varying concentration of atom species were taken for two densities 0.65 and 0.45. The fluid flow takes place between two parallel plates and is bounded by horizontal walls in one direction and periodic boundary conditions are imposed in the other two directions. To drive the flow, a constant force is applied in one direction. Each fluid atom interacts with other fluid atoms and wall atoms through Week-Chandler-Anderson (WCA) potential. The velocity profile has been looked at for three nanochannel widths i.e for 12{sigma}, 14{sigma} and 16{sigma} and also for the different concentration of two species. The velocity profile of the binary fluid predicted by the simulations agrees with the quadratic shape of the analytical solution of a Poiseuille flow in continuum theory.

Mullick, Shanta; Ahluwalia, P. K. [Department of Physics, Himachal Pradesh University, SummerHill, Shimla - 171005 (India); Pathania, Y. [Chitkara University, Atal Shiksha Kunj, Atal Nagar, Barotiwala, Dist Solan, Himachal Pradesh - 174103 (India)

2011-12-12

309

Molecular Dynamics Simulations Suggest Ligand's Binding to Nicotinamidase/Pyrazinamidase

The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA’s activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM’s unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand’s binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.

Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing

2012-01-01

310

Spontaneous formation of polyglutamine nanotubes with molecular dynamics simulations

NASA Astrophysics Data System (ADS)

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 A? diameter structure reorganizes further into a tight antiparallel double-stranded ~22 A? 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.

Laghaei, Rozita; Mousseau, Normand

2010-04-01

311

Graphical User Interfaces for Molecular Dynamics--Quo Vadis?

In the past years an increasing number of graphical user interfaces for Molecular Dynamics (MD) were presented and concomitantly, more and more Molecular Dynamics studies were published. With the easier application of MD software packages the field runs the risk however, of being pervaded with unreliable results. Therefore, possible benefits and caveats have to be carefully balanced. Here we outline in which respects a broader access of MD via graphical user interfaces may help to increase the usability of Molecular Dynamics simulations while maintaining their quality.

Knapp, B.; Schreiner, W.

2009-01-01

312

Stresses and elastic constants of crystalline sodium, from molecular dynamics

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 stresses and the elastic constants are given as strain derivatives of the Helmholtz free energy. The resulting expressions involve canonical ensemble averages (and fluctuation averages) of the position and volume derivatives of the potential. An ensemble correction relates the results to MD equilibrium averages. Evaluation of the potential and its derivatives requires the calculation of integrals with infinite upper limits of integration, and integrand singularities. Methods for calculating these integrals and estimating the effects of integration errors are developed. A method is given for choosing initial conditions that relax quickly to a desired equilibrium state. Statistical methods developed earlier for MD data are extended to evaluate uncertainties in fluctuation averages, and to test for symmetry. 45 refs., 10 figs., 4 tabs.

Schiferl, S.K.

1985-02-01

313

Part I. Molecular dynamics simulation of organometallic reaction dynamics. To study the interplay of solute and solvent dynamics, large-scale molecular dynamics simulations were employed. Lennard-Jones and electrostatic models of potential energies from solvent-only studies were combined with solute potentials generated from ab-initio calculations. Radial distribution functions and other measures revealed the polar solvent's response to solute dynamics following CO dissociation.

Sheryl Dee Mebane

2004-01-01

314

Molecular dynamics study of the flagella inside the carbon torus.

We propose a system that avoids the open ends of the nanotube, we used a device consisting of flagellum (FLA) inside a nanotorus (NT) formed by carbon atoms. The flagellum consists of a C20 nanosphere with fixed size of tail within the NT. The full system consists of a closed loop drive and static nanotubes and nanospheres not static with different sizes of flagella released inside the nanotube, with each simulation, allows the relaxation between (internal and external NT). The nanospheres result in a system that provides movement of Van der Waals. The simulations were done by well-known classic molecular dynamics with standard parameterization. We calculate thermodynamic properties of these devices as heat capacity and molar entropy variation. For this system were obtained properties such as: the speed of nanospheres plagued the efficiency of molecular motor versus time, the kinetic energy, potential energy and total energy in each of the simulations. In our calculations, this system has a number of carbon atoms ranging from (2721 until 2728) with up to almost 10 ps simulation. These facts can be useful for the construction of new molecular machines. PMID:21456164

Neto, Antonio M J C; Santos, Júlio C S; Santos, Elson C

2011-02-01

315

Ab initio based force field and molecular dynamics simulations of crystalline TATB

NASA Astrophysics Data System (ADS)

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 dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally.

Gee, Richard H.; Roszak, Szczepan; Balasubramanian, Krishnan; Fried, Laurence E.

2004-04-01

316

Multiscale molecular dynamics using the matched interface and boundary method

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.

Geng Weihua [Department of Mathematics, Michigan State University, East Lansing, MI 48824 (United States); Wei, G.W., E-mail: wei@math.msu.ed [Department of Mathematics, Michigan State University, East Lansing, MI 48824 (United States); Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824 (United States)

2011-01-20

317

Enhanced molecular dynamics for simulating porous interphase layers in batteries.

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.

Zimmerman, Jonathan A.; Wong, Bryan Matthew; Jones, Reese E.; Templeton, Jeremy Alan; Lee, Jonathan (Rice University, Houston, TX)

2009-10-01

318

Molecular Dynamics Simulations of Ordering of Polydimethylsiloxane Under Uniaxial Extension.

National Technical Information Service (NTIS)

Molecular dynamics simulations of a bulk melts of polydimethylsiloxane (PDMS) are utilized to study chain conformation and ordering under constant uniaxial tension. We find that large extensions induce chain ordering in the direction of applied tension. W...

N. M. Lacevic R. H. Gee

2005-01-01

319

Molecular dynamics simulations of the C70-graphite interaction

NASA Astrophysics Data System (ADS)

The collisions of low-energy C70 clusters with a graphite (0001) surface have been investigated by molecular dynamics simulations with Tersoff potential an a Lennard-Jones potential. The dynamic process of the collisions and the energy transfer are calculated. During the interaction process, the C70 cluster behaves as a deformable but stable hollow cage. The collisions are highly inelastic processes. These results are compared to similar interaction of C60 molecule with graphite surface. At the low energy region (up to 2.5eV/atom), no significant differences are observed between the C70-graphite interaction and the C60-graphite interaction. Our simulation results are in accordance with the experimental findings. This may be interpretable in terms of the unique cage structures of the fullerenes. However, the anisotropic feature of the C70 structure implies that difference might arise when different initial orientations as well as positions of the C70 with respect to the surface are considered.

Man, Zhenyong; Pan, Zhengying; Xie, Jun; Ho, Yukun

1998-02-01

320

Molecular Dynamics Studies of Molten AgI. I. Structure and Dynamical Properties

NASA Astrophysics Data System (ADS)

The structural and dynamical properties of molten AgI are investigated using molecular dynamics calculations and pair potentials originally given by Parrinello et al. and modified by authors. The total pair distribution functions, thus obtained, are in good agreement with experimental results by Takahashi et al. and with theoretical results by Stafford and Silbert. The wave-number-dependent static dielectric function \\varepsilon(\\mbi{k}) is also calculated with use of the charge correlation function in the both ?- and molten phases. In the ?-phase, \\varepsilon(\\mbi{k}) is negative for small wave numbers and approaches zero at special wave numbers, which correspond to the positions of the Debye lines in the reciprocal lattice space. \\varepsilon(\\mbi{k}) in the molten phase shows the forerunning phenomenon to the crystalization, which is a very similar behavior to that in the strongly coupled one component plasma.

Shimojo, Fuyuki; Kobayashi, Michisuke

1991-11-01

321

Relationship between nanocrystalline and amorphous microstructures by molecular dynamics simulation

A recent molecular dynamics simulation method for growth of fully dense nanocrystalline materials crystallized from melt was used with the Stillinger-Weber three-body potential to synthesize nanocrystalline Si with a grain size up to 75{Angstrom}. Structures of the highly constrained grain boundaries (GBs), triple lines, and point grain junctions were found to be highly disordered and similar to the structure of amorphous Si. These and earlier results for fcc metals suggest that a nanocrystalline microstructure may be viewed as a two-phase system, namely an ordered crystalline phase in the grain interiors connected by an amorphous, intergranular, glue-like phase. Analysis of the structures of bicrystalline GBs in the same materials reveals the presence of an amorphous intergranular equilibrium phase only in the high-energy but not the low-energy GBs, suggesting that only high-energy boundaries are present in nanocrystalline microstructures.

Keblinski, P.; Phillpot, S.R.; Wolf, D. [Argonne National Lab., IL (United States); Gleiter, H. [Forschungszentrum Karlsruhe GmbH Technik und Umwelt (Germany)

1996-08-01

322

Molecular-Dynamics Simulations of Droplets on a Solid Surface

NASA Astrophysics Data System (ADS)

By using a semi-empirical Lennard-Jones embedded-atom-method potential, we study the influence of many-body forces and atomic size mismatch on the wetting behavior of nano droplets on a solid surface. With molecular dynamics simulations, we find that the contact angle decreases with increasing many-body forces. The increase of atomic size mismatch between solid and liquid results in the decrease of contact angles. Our calculation also shows that the interface structure is strongly affected by the interaction between liquid and solid as well as the atomic size mismatch. For weak solid-liquid interaction, the interface layer of the droplet nearest to the solid exhibits a typical simple liquid structure regardless of the size mismatch. For strong solid-liquid interaction, evident ordering in the interface layer is observed for well matched cases.

Gao, Yu-Feng; Sun, De-Yan

2010-06-01

323

Erbium Implantation in Silica Studied by Molecular Dynamics Simulations

Defect formation induced by erbium implantation in silica glass and cristobalite was studied using molecular dynamics simulations employing a partial charge model in combination with the ZBL potential. The results show that the number of displaced atoms generated at the same PKA energy is similar in silica and cristobalite but the number of coordination defects created is much lower in the cristobalite than in silica glass. In both cases, the erbium ion is able to create an optimal coordination environment at the end of the collision cascade. Subsequent thermal annealing causes the relaxation of the silicon oxygen network structure along with a reduction of silicon and oxygen defects. This research is supported by the Divisions of Materials Sciences and Engineering and Chemical Science, Office of Basic Energy Sciences, U.S. Department of Energy. The Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

Du, Jincheng; Corrales, Louis R.

2007-02-01

324

Molecular Dynamics of Hot Dense Plasmas: New Horizons

NASA Astrophysics Data System (ADS)

We describe the status of a new time-dependent simulation capability for hot dense plasmas. The backbone of this multi-institutional computational and experimental effort---the Cimarron Project---is the massively parallel molecular dynamics (MD) code ``ddcMD''. The project's focus is material conditions such as exist in inertial confinement fusion experiments, and in many stellar interiors: high temperatures, high densities, significant electromagnetic fields, mixtures of high- and low-Z elements, and non-Maxwellian particle distributions. Of particular importance is our ability to incorporate into this classical MD code key atomic, radiative, and nuclear processes, so that their interacting effects under non-ideal plasma conditions can be investigated. This talk summarizes progress in computational methodology, discusses strengths and weaknesses of quantum statistical potentials as effective interactions for MD, explains the model used for quantum events possibly occurring in a collision and highlights some significant results obtained to date.

Graziani, Frank

2011-11-01

325

Molecular dynamics simulation of martensitic transformations in NiAl

Both thermally induced and stress-induced coherent nucleation and growth of an L1{sub 0} martensitic phase have been examined and analyzed at the atomic level in molecular dynamics (MD) computer simulations of an ordered B2 NiAl lattice array using embedded atom method (EAM) interatomic potentials. Both heterogeneous and homogeneous nucleation are observed, the latter requiring an applied stress. The heterogeneous process occurs at ledge corners on stepped free surfaces and can be analyzed in terms of localized soft modes. The homogeneous nucleation can be understood as resulting from a strain spinodal instability which produces a morphology reminiscent of chemical spinodal decomposition. Self-accommodating martensite variants appear very early in the growth process, and all interfaces remain coherent with no detectable presence of dislocations in these early stages.

Shao, Y.; Clapp, P.C.; Rifkin, J.A. [Univ. of Connecticut, Storrs, CT (United States)

1996-06-01

326

Dynamic instabilities in assemblies of molecular motors with finite stiffness.

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. PMID:20867339

Guérin, T; Prost, J; Joanny, J-F

2010-06-16

327

Molecular dynamics simulations of temperature equilibration in dense hydrogen

NASA Astrophysics Data System (ADS)

The temperature equilibration rate between electrons and protons in dense hydrogen has been calculated with molecular dynamics simulations for temperatures between 10 and 600eV and densities between 1020cm-3to1024cm-3 . Careful attention has been devoted to convergence of the simulations, including the role of semiclassical potentials. We find that for Coulomb logarithms L?1 , a model by Gericke-Murillo-Schlanges (GMS) [D. O. Gericke , Phys. Rev. E 65, 036418 (2002)] based on a T -matrix method and the approach by Brown-Preston-Singleton [L. S. Brown , Phys. Rep. 410, 237 (2005)] agrees with the simulation data to within the error bars of the simulation. For smaller Coulomb logarithms, the GMS model is consistent with the simulation results. Landau-Spitzer models are consistent with the simulation data for L>4 .

Glosli, J. N.; Graziani, F. R.; More, R. M.; Murillo, M. S.; Streitz, F. H.; Surh, M. P.; Benedict, L. X.; Hau-Riege, S.; Langdon, A. B.; London, R. A.

2008-08-01

328

Dynamic Instabilities in Assemblies of Molecular Motors with Finite Stiffness

NASA Astrophysics Data System (ADS)

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.

Guérin, T.; Prost, J.; Joanny, J.-F.

2010-06-01

329

Molecular Dynamics Simulations of Temperature Equilibration in Dense Hydrogen

The temperature equilibration rate in dense hydrogen (for both T{sub i} > T{sub e} and T{sub i} < T{sub e}) has been calculated with large-scale molecular dynamics simulations for temperatures between 10 and 300 eV and densities between 10{sup 20}/cc to 10{sup 24}/cc. Careful attention has been devoted to convergence of the simulations, including the role of semiclassical potentials. We find that for Coulomb logarithms L {approx}> 1, Brown-Preston-Singleton [Brown et al., Phys. Rep. 410, 237 (2005)] with the sub-leading corrections and the fit of Gericke-Murillo-Schlanges [Gericke et al., PRE 65, 036418 (2003)] to the T-matrix evaluation of the collision operator, agrees with the MD data to within the error bars of the simulation. For more strongly-coupled plasmas where L {approx}< 1, our numerical results are consistent with the fit of Gericke-Murillo-Schlanges.

Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M; Benedict, L; Hau-Riege, S; Langdon, A; London, R

2008-02-14

330

Molecular Dynamics Simulations: Difficulties, Solutions and Strategies for Treating Metalloenzymes

\\u000a The application of molecular dynamics (MD) simulations is now firmly established as a strategy to help understanding the activity\\u000a of biological systems, being routinely applied to investigate the structure, dynamics and thermodynamics of biological molecules\\u000a and their complexes. Commonly available biomolecular force fields like AMBER, CHARMM, OPLS, and GROMOS contain sets of molecular\\u000a mechanical parameters for the 20 natural amino

Sérgio F. Sousa; Pedro A. Fernandes; Maria Joăo Ramos

331

Parallel Molecular Dynamics Simulations of Biomolecular Systems

. We describe a general purpose parallel molecular dynamicscode, for simulations of arbitrary mixtures of flexible molecules in solution.The program allows us to simulate molecular systems describedby standard force fields like AMBER, GROMOS or CHARMM, containingterms for short-range interactions of the Lennard-Jones type,electrostatic interactions, covalent bonds, covalent angles and torsionalangles and a few other optional terms. The state-of-the-art molecular dynamicstechniques

Alexander Lyubartsev; Aatto Laaksonen

1998-01-01

332

Epitaxial growth of silicon: A molecular-dynamics simulation

NASA Astrophysics Data System (ADS)

We have studied the epitaxial growth of silicon using molecular-dynamics techniques. The model consists of a temperature-controlled Si(111) substrate, with the Si atoms projected towards the substrate as is done in the laboratory. The atoms interact via a potential developed by Stillinger and Weber to simulate the bulk properties of Si. We find that at low substrate temperatures the growth is not well ordered; this is in accordance with experimental observation. It is precisely the opposite of what occurs in spherically symmetric potentials that were used to simulate the growth of metallic films. At higher substrate temperatures the growth is into properly stacked, crystalline Si layers. In contrast to the growth of metals (spherically symmetric potentials), the atomic mobility on the growing surface and the thermal conductivity of the system are much lower for Si; the results of this simulation and those of our previous work are in agreement with experimental observations showing, as expected, that a major determining factor in epitaxial growth of films is the nature of the interaction potential.

Schneider, M.; Schuller, Ivan K.; Rahman, A.

1987-07-01

333

Atomistic molecular dynamics simulations of shock compressed quartz

NASA Astrophysics Data System (ADS)

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.

Farrow, M. R.; Probert, M. I. J.

2011-07-01

334

Molecular Dynamics Simulations of Protein Dynamics and their relevance to drug discovery

Molecular dynamics simulations have become increasingly useful in studying biological systems of biomedical interest, and not just in the study of model or toy systems. In this article, the methods and principles of all-atom molecular dynamics will be elucidated with several examples provided of their utility to investigators interested on drug discovery.

Salsbury, Freddie R.

2010-01-01

335

NASA Astrophysics Data System (ADS)

Born-Oppenheimer molecular dynamics (BOMD) based on density functional theory offers a very accurate quantum mechanical approach to atomistic simulations that is more reliable and general compared to classical MD. Unfortunately, BOMD simulations are often limited by a high computational cost or by problems such as unbalanced phase space trajectories, numerical instabilities and a systematic long-term energy drift. These problems become particularly severe in combination with reduced complexity or linear scaling algorithms that are necessary for the study of large systems. We have recently taken some steps toward a new generation of first principles MD, which combines some of the best features of regular BOMD and Car-Parrinello MD, while avoiding their most serious shortcomings. The new dynamics is given in terms of an extended Lagrangian (XL), where auxiliary extended electronic degrees of freedom are added to the nuclear part. Our framework enables accurate geometric integration of both the nuclear and electronic degrees of freedom that provide a time-reversible and energy conserving dynamics on the ground state BO potential energy surface that is stable also under approximate SCF convergence. XL-BOMD provides a surprisingly simple and general framework for atomistic simulations

Niklasson, Anders; Cawkwell, Marc

2012-02-01

336

Visual Verification and Analysis of Cluster Detection for Molecular Dynamics

A current research topic in molecular thermodynamics is the condensation of vapor to liquid and the investigation of this process at the molecular level. Condensation is found in many physical phenomena, e.g. the formation of atmospheric clouds or the processes inside steam turbines, where a detailed knowledge of the dynamics of condensation processes will help to optimize energy efficiency and

Sebastian Grottel; Guido Reina; Jadran Vrabec; Thomas Ertl

2007-01-01

337

Molecular dynamics simulations of freezing of water and salt solutions

Results of extensive molecular dynamics simulations of freezing of neat water and aqueous sodium chloride solutions are reported. The process of water freezing in contact with an ice patch is analyzed at a molecular level and a robust simulation protocol within the employed force field is established. Upon addition of a small amount of NaCl brine rejection from the freezing

Luboš Vrbka; Pavel Jungwirth

2007-01-01

338

NASA Astrophysics Data System (ADS)

This special section of Comments on Atomic, Molecular and Optical Physics (CAMOP) in Physica Scripta collects some of the papers that have been presented at the 18th European Conference on Dynamics of Molecular Systems MOLEC 2010 held in September 2010 in Curia, Portugal, as part of a series of biennial MOLEC conferences. This started in 1976 in Trento, Italy, and has continued, visiting 17 cities in 11 countries, namely Denmark, The Netherlands, Israel, France, Italy, Germany, Czech Republic, Spain, United Kingdom, Turkey and Russia. Following the MOLEC tradition, the scientific programme of the Curia meeting focused on experimental and theoretical studies of molecular interactions, collision dynamics, spectroscopy, and related fields. It included invited speakers from 22 countries, who were asked to summarize the problems reported in their presentations with the objective of revealing the current thinking of leading researchers in atomic, molecular and optical physics. It is hoped that their authoritative contributions presented in this CAMOP special section will also appeal to non-specialists through their clear and broad introductions to the field as well as references to the accessible literature. This CAMOP special section comprises ten contributions, which cover theoretical studies on the electronic structure of molecules and clusters as well as dynamics of elastic, inelastic and reactive encounters between atoms, molecules, ions, clusters and surfaces. Specifically, it includes electronic structure calculations using the traditional coupled-cluster method (Barreto et al 028111), the electron-attached equation-of-motion coupled cluster method (Hansen et al 028110), the diffusion Monte Carlo method (López-Durán et al 028107) and the path-integral Monte Carlo method (Barragán et al 028109). The contributions on molecular dynamics include on-the-fly quasi-classical trajectories on a five-atom molecule (Yu 028104), quantum reaction dynamics on triatomics (Bovino et al 028103, and Hankel et al 028102) and statistical reaction dynamics using a model based on the long-range interaction potential (McCarroll 028106). A contribution on gas-surface interactions is also included (Sahoo et al 028105) as well as first-principles ab initio calculations to explore the hydrogen-graphene interaction (Irving et al 028108). These articles reflect the recent progress made in this field and constructively build on work described in the previous three MOLEC special sections of CAMOP published in Physica Scripta. I thank, on behalf of the scientific organizing committee of MOLEC, all the authors who contributed and Physica Scripta for providing a platform for the publication of this special section dedicated to MOLEC 2010. A special thanks goes to the CAMOP Editor, Harold Linarz, for the excellent guidance in handling the editorial work. I hope that the articles catalyze the attention of the readers towards the topics covered and contribute in attracting them to attend MOLEC 2012 in Oxford, UK.

Varandas, A. J. C.

2011-08-01

339

The majority of biological processes mediated by G Protein-Coupled Receptors (GPCRs) take place on timescales that are not conveniently accessible to standard molecular dynamics (MD) approaches, notwithstanding the current availability of specialized parallel computer architectures, and efficient simulation algorithms. Enhanced MD-based methods have started to assume an important role in the study of the rugged energy landscape of GPCRs by providing mechanistic details of complex receptor processes such as ligand recognition, activation, and oligomerization. We provide here an overview of these methods in their most recent application to the field. PMID:24158803

Johnston, Jennifer M; Filizola, Marta

2014-01-01

340

Molecular dynamics modelling of an electrical-driven linear nanopump

The dynamics of an electrical-driven linear nanopump, consisting of a carbon nanotube, a C60 molecule and a graphene sheet, has been simulated via the application of the molecular dynamics method. In this nanopump, the nanotube and the graphene sheet are used as the sleeve of the pump and the boundary between the two sides of the nanopump, respectively. By exposing

A. Lohrasebi; N. Nouri

2012-01-01

341

Molecular dynamics study of silicate glass under shock

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

Luming Shen

2010-01-01

342

The Art of Molecular Dynamics Simulation (by D. C. Rapaport)

NASA Astrophysics Data System (ADS)

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.

Molner, Stephen P.

1999-02-01

343

Constant pH Molecular Dynamics with Proton Tautomerism

The current article describes a new two-dimensional ?-dynamics method to include proton tautomerism in continuous constant pH molecular dynamics (CPHMD) simulations. The two-dimensional ?-dynamics framework is used to devise a tautomeric state titration model for the CPHMD simulations involving carboxyl and histidine residues. Combined with the GBSW implicit solvent model, the new method is tested on titration simulations of blocked

Jana Khandogin; Charles L. Brooks

2005-01-01

344

Anesthetic Interaction with Ketosteroid Isomerase: Insights from Molecular Dynamics Simulations

The nature and the sites of interactions between anesthetic halothane and homodimeric ?5-3-ketosteroid isomerase (KSI) are characterized by flexible ligand docking and confirmed by 1H-15N NMR. The dynamics consequence of halothane interaction and the implication of the dynamic changes to KSI function are studied by multiple 5-ns molecular dynamics simulations in the presence and absence of halothane. Both docking and

Michael J. Yonkunas; Yan Xu; Pei Tang

2005-01-01

345

A molecular modeling study on dihydrofolate reductase (DHFR) inhibitors was carried out. By combining molecular dynamics simulations with semiempirical (PM6), ab initio, and density functional theory (DFT) calculations, a simple and generally applicable procedure to evaluate the binding energies of DHFR inhibitors interacting with the human enzyme is reported here, providing a clear picture of the binding interactions of these ligands from both structural and energetic viewpoints. A reduced model for the binding pocket was used. This approach allows us to perform more accurate quantum mechanical calculations as well as to obtain a detailed electronic analysis using the quantum theory of atoms in molecules (QTAIM) technique. Thus, molecular aspects of the binding interactions between inhibitors and the DHFR are discussed in detail. A significant correlation between binding energies obtained from DFT calculations and experimental IC?? values was obtained, predicting with an acceptable qualitative accuracy the potential inhibitor effect of nonsynthesized compounds. Such correlation was experimentally corroborated synthesizing and testing two new inhibitors reported in this paper. PMID:23834278

Tosso, Rodrigo D; Andujar, Sebastian A; Gutierrez, Lucas; Angelina, Emilio; Rodríguez, Ricaurte; Nogueras, Manuel; Baldoni, Héctor; Suvire, Fernando D; Cobo, Justo; Enriz, Ricardo D

2013-07-24

346

Oxidation of aluminum nanoclusters is investigated with a parallel molecular-dynamics approach based on dynamic charge transfer among atoms. Structural and dynamic correlations reveal that significant charge transfer gives rise to large negative pressure in the oxide which dominates the positive pressure due to steric forces. As a result, aluminum moves outward and oxygen moves towards the interior of the cluster

Timothy Campbell; Rajiv K. Kalia; Aiichiro Nakano; Priya Vashishta; Shuji Ogata; Stephen Rodgers

1999-01-01

347

New all-atom force field for molecular dynamics simulation of an AlPO(4)-34 molecular sieve.

A force field of the triclinic framework of AlPO(4)-34, important in methanol-hydrocarbon conversion reactions, was developed using an empirical potential function. Molecular dynamics simulation of an AlPO(4)-34 triclinic framework segment of 1216 atoms, containing the template molecules isopropylamine and water, was performed with explicit consideration of atomic charges. The average RMS difference between instantaneous positions of the framework atoms during 1 ns simulation and their positions in the structure determined from single crystal X-ray diffraction was calculated, and the average structure of the flexible framework was determined. The computed Debye-Waller factors and simulated FTIR spectra are in good agreement with the experimental data. The new force field permits detailed molecular dynamics simulations of flexible, charged aluminophosphate molecular sieves which should lead to a better understanding of the catalytic processes and the crucial role played by templating molecules. PMID:17546676

Praprotnik, Matej; Hocevar, Stanko; Hodoscek, Milan; Penca, Matej; Janezic, Dusanka

2008-01-15

348

Molecular dynamics simulation of yttria-stabilized zirconia (YSZ) crystalline and amorphous solids

An empirically fitted atomic potential allows a classical molecular dynamics study of the static and dynamic properties of both crystalline and amorphous yttria-stabilized zirconia (YSZ) with typical dilute Y2O3 concentrations (i.e. 3.0-12.0 mol% Y2O3) in the temperature range 300-1400 K. Based on the rigid ion model approximation, we find, regardless of the distinctly different geometries, that the oxygen ionic conductivity

Kah Chun Lau; Brett I. Dunlap

2011-01-01

349

A molecular dynamics study of superionic Ag/sub 2/Se

Structural and dynamical correlations in supersonic Ag/sub 2/Se are studied with the molecular dynamics method using an effective interatomic potential which incorporates the short-range repulsion, charge-dipole and the long-range Coulomb interactions. We focus on the behavior of the pair-correlation functions, partial static structure factors, the temperature dependence of the constant of self diffusion for Ag, and Haven's ratio. The results compare favorably with experimental measurements. 27 refs., 5 figs., 2 tabs.

Rino, J.P.; Hornos, Y.M.M.; Antonio, G.A.; Ebbsjo, I.; Kalia, R.K.; Vashishta, P.

1988-09-01

350

The use of molecular dynamics for the thermodynamic properties of simple and transition metals

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.

Straub, G.K.

1987-04-01

351

Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes

Triclocarban and triclosan, two potent antibacterial molecules present in many consumer products, have been subject to growing debate on a number of issues, particularly in relation to their possible role in causing microbial resistance. In this computational study, we present molecular-level insights into the interaction between these antimicrobial agents and hydrated phospholipid bilayers (taken as a simple model for the cell membrane). Simulations are conducted by a novel ‘dual-resolution’ molecular dynamics approach which combines accuracy with efficiency: the antimicrobials, modelled atomistically, are mixed with simplified (coarse-grain) models of lipids and water. A first set of calculations is run to study the antimicrobials' transfer free energies and orientations as a function of depth inside the membrane. Both molecules are predicted to preferentially accumulate in the lipid headgroup–glycerol region; this finding, which reproduces corresponding experimental data, is also discussed in terms of a general relation between solute partitioning and the intramembrane distribution of pressure. A second set of runs involves membranes incorporated with different molar concentrations of antimicrobial molecules (up to one antimicrobial per two lipids). We study the effects induced on fundamental membrane properties, such as the electron density, lateral pressure and electrical potential profiles. In particular, the analysis of the spontaneous curvature indicates that increasing antimicrobial concentrations promote a ‘destabilizing’ tendency towards non-bilayer phases, as observed experimentally. The antimicrobials' influence on the self-assembly process is also investigated. The significance of our results in the context of current theories of antimicrobial action is discussed.

Orsi, Mario; Noro, Massimo G.; Essex, Jonathan W.

2011-01-01

352

A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole.

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

Fonner, John M; Schmidt, Christine E; Ren, Pengyu

2010-10-01

353

Implementation of force distribution analysis for molecular dynamics simulations

Background The way mechanical stress is distributed inside and propagated by proteins and other biopolymers largely defines their function. Yet, determining the network of interactions propagating internal strain remains a challenge for both, experiment and theory. Based on molecular dynamics simulations, we developed force distribution analysis (FDA), a method that allows visualizing strain propagation in macromolecules. Results To be immediately applicable to a wide range of systems, FDA was implemented as an extension to Gromacs, a commonly used package for molecular simulations. The FDA code comes with an easy-to-use command line interface and can directly be applied to every system built using Gromacs. We provide an additional R-package providing functions for advanced statistical analysis and presentation of the FDA data. Conclusions Using FDA, we were able to explain the origin of mechanical robustness in immunoglobulin domains and silk fibers. By elucidating propagation of internal strain upon ligand binding, we previously also successfully revealed the functionality of a stiff allosteric protein. FDA thus has the potential to be a valuable tool in the investigation and rational design of mechanical properties in proteins and nano-materials.

2011-01-01

354

Fermion Molecular Dynamics for Rearrangement Collisions with Simple Molecules

NASA Astrophysics Data System (ADS)

The Fermion Molecular Dynamics (FMD) method enables an all-electron treatment of reactive scattering using quasiclassical theory.(J.S. Cohen, Phys. Rev. A 54), 573 (1996); 56, 3583 (1997). It has previously been applied to ion-atom collisions and to atoms in strong laser fields. Here it is extended to molecular targets. A simple effective potential is found to provide a useful quasiclassical description of the hydrogen molecule. In particular, it is applied to capture of negative particles (barp and ?^-) by the hydrogen molecule. In contrast to the case with the same atomic targets, strong effects of the target isotope and projectile mass have been found. Negative particles having kinetic energies up to 100 eV are captured while the atomic capture cross sections cut off rapidly above 14 eV (in the c.m. system). The difference is due to the influence of ro-vibrational excitation, in addition to the electronic excitation also possible for atomic targets. Angular scattering distributions, needed for designing a proposed experiment, have been evaluated.

Cohen, J. S.

1998-05-01

355

Unfixed cryosections of striated muscle to study dynamic molecular events.

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

Menetret, J F; Craig, R

1994-01-01

356

Molecular dynamics of the water liquid-vapor interface.

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. PMID:11539733

Wilson, M A; Pohorille, A; Pratt, L R

1987-01-01

357

Molecular Dynamics of Hot Dense Plasmas: New Horizons

NASA Astrophysics Data System (ADS)

We describe the status of a new time-dependent simulation capability for hot dense plasmas. The backbone of this multi-institutional computational and experimental effort---the Cimarron Project---is the massively parallel molecular dynamics (MD) code ``ddcMD''. The project's focus is material conditions such as exist in inertial confinement fusion experiments, and in many stellar interiors: high temperatures, high densities, significant electromagnetic fields, mixtures of high- and low-Z elements, and non-Maxwellian particle distributions. Of particular importance is our ability to incorporate into this classical MD code key atomic, radiative, and nuclear processes, so that their interacting effects under non-ideal plasma conditions can be investigated. This talk summarizes progress in computational methodology, discusses strengths and weaknesses of quantum statistical potentials as effective interactions for MD, explains the model used for quantum events possibly occurring in a collision and highlights some significant results obtained to date. We will also discuss a new idea called kinetic theory MD which now being explored to deal more efficiently with the very disparate dynamical timescales that arise in fusion plasmas. We discuss how this approach can be derived rigorously from the n-body quantum Wigner equation and illustrate the approach with an example.

Graziani, Frank

2011-06-01

358

Energy conservation in molecular dynamics simulations of classical systems.

Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete "Verlet" algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence of a "shadow Hamiltonian" H [S. Toxvaerd, Phys. Rev. E 50, 2271 (1994)], i.e., a Hamiltonian close to the original H with the property that the discrete positions of the Verlet algorithm for H lie on the analytic trajectories of H. The shadow Hamiltonian can be obtained from H by an asymptotic expansion in the time step length. Here we use the first non-trivial term in this expansion to obtain an improved estimate of the discrete values of the energy. The investigation is performed for a representative system with Lennard-Jones pair interactions. The simulations show that inclusion of this term reduces the standard deviation of the energy fluctuations by a factor of 100 for typical values of the time step length. Simulations further show that the energy is conserved for at least one hundred million time steps provided the potential and its first four derivatives are continuous at the cutoff. Finally, we show analytically as well as numerically that energy conservation is not sensitive to round-off errors. PMID:22713035

Toxvaerd, Sřren; Heilmann, Ole J; Dyre, Jeppe C

2012-06-14

359

Energy conservation in molecular dynamics simulations of classical systems

NASA Astrophysics Data System (ADS)

Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete ``Verlet'' algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence of a ``shadow Hamiltonian'' H~ [S. Toxvaerd, Phys. Rev. E 50, 2271 (1994)], i.e., a Hamiltonian close to the original H with the property that the discrete positions of the Verlet algorithm for H lie on the analytic trajectories of H~. The shadow Hamiltonian can be obtained from H by an asymptotic expansion in the time step length. Here we use the first non-trivial term in this expansion to obtain an improved estimate of the discrete values of the energy. The investigation is performed for a representative system with Lennard-Jones pair interactions. The simulations show that inclusion of this term reduces the standard deviation of the energy fluctuations by a factor of 100 for typical values of the time step length. Simulations further show that the energy is conserved for at least one hundred million time steps provided the potential and its first four derivatives are continuous at the cutoff. Finally, we show analytically as well as numerically that energy conservation is not sensitive to round-off errors.

Toxvaerd, Sřren; Heilmann, Ole J.; Dyre, Jeppe C.

2012-06-01

360

Molecular Dynamics Simulations of Dislocation Mobility in Aluminum

NASA Astrophysics Data System (ADS)

Dislocation mobility in Al is studied using molecular dynamics with embedded atom method potentials. The motion of an edge dislocation is simulated for temperatures ranging from 10 K to 200 K and for stresses up to 5 GPa. At sufficiently low levels of applied shear stress (i.e. below the Peierls stress) the dislocation velocity is nominally zero. At somewhat higher stresses the dislocation velocity decreases with increasing temperature, as expected for drag due to thermal phonons. While a linear viscous drag relation is not obtained, an approximate dislocation drag inferred from the simulations is comparable to that reported by others based on ultrasonic attenuation experiments. At still higher stresses the dislocation moves at a sub-sonic limiting velocity that is essentially temperature independent. The limiting velocity is shown to be predicted by a two-dimensional lattice-dynamics analysis. This critical velocity is shown to be a velocity at which the phase velocity and group velocity are equal. At still higher shear stresses the dislocation travels with a transonic velocity equal to ? 2 times the relevant shear wave speed. This speed is one at which radiation from the moving dislocation vanishes according to linear elasticity theory.

Bhate, Nitin; Clifton, Rodney J.; Phillips, Robert

2001-06-01

361

Constrained molecular dynamics simulations were carried out to investigate the lithium chloride ionic associations in dilute aqueous solutions over a wide temperature range. Solvent mediated potentials of mean force have been carefully calculated at different thermodynamic conditions. Two intermediate states of ionic association can be well identified with an energy barrier from the oscillatory free energy profile. Clear pictures for

Zhigang Zhang; Zhenhao Duan

2004-01-01

362

In recent years, short pulsed laser materials interaction has attracted considerable attention owing to the rapid development of short pulsed lasers and their potential applications in laser-material processing. In this work, molecular dynamics (MD) simulations are conducted to study the thermal and thermomechanical phenomena induced by picosecond laser heating. The generation and propagation of the stress wave are calculated and

Xinwei Wang; Xianfan Xu

2003-01-01

363

The melting of structure I methane clathrate hydrate has been investigated using NVT molecular dynamics simulations, for a number of potential energy models for water and methane. The equilibrated hydrate crystal has been heated carefully from 270 K, in steps of 5 K, until a well defined phase instability appears. At a density of 0s92 g cm-3, an upper bound

Ole Kr. Forrisdahl

1996-01-01

364

Molecular dynamics study of mechanical and thermodynamic properties of pentaerythritol tetranitrate

We present in this paper the results of molecular dynamics simulation based on a three-body potential, for mechanical and thermodynamic properties of pentaerythritol tetranitrate (PETN). Elastic constants and melting point obtained are in good agreement with available theoretical and experimental works. Various predictive quantities including longitudinal and transversal velocities, frequencies of the elastic wave, Debye temperature and heat capacity are

A. Zaoui; W Sekkal

2001-01-01

365

A Molecular Dynamics Study of the Vibrational Spectra of Silica Polyamorphs

The vibrational spectra (inelastic neutron scattering, infrared absorption and Raman scattering) of fused silica in the amorphous and in the liquid state are investigated by molecular dynamics simulation in using the TTAM interionic potential (Tsuneyuki et al., Phys. Rev. Lett., 61, 869 (1988)). The simulation predicts in the low frequency region a boson peak, quite similar to the one observed

Bertrand Guillot; Yves Guissani

1997-01-01

366

Thermodynamical properties of a two-dimensional quasi-crystal from molecular dynamics calculations

We propose a simple decoration of the Penrose tiling to produce a two-dimensional quasi-crystalline model. We have used molecular dynamics simulation to invesigate the stability and the phase transitions of this system. Stable with pair potentials, it undergoes a first-order transition to the liquid phase. Its enthalpy is below the enthalpy of the quenched glassy state.

F. Lançon; L. Billard; P. Chaudhari

1986-01-01

367

Gramicidin A Channel as a Test Ground for Molecular Dynamics Force Fields

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

Toby W. Allen; Turgut Ba?tu?; Serdar Kuyucak; Shin-Ho Chung

2003-01-01

368

Non-equilibrium molecular dynamics simulations of structured molecules

NASA Astrophysics Data System (ADS)

Corresponding-states theories fail to predict the large difference observed between n-butane and isobutane viscosities at similar reduced conditions. To investigate the molecular cause of these structural effects upon viscosity, nonequilibrium molecular dynamics simulations of Lennard-Jones site-site models representing n-butane and isobutane are performed over much of the density range for which experimental data are available. Simulated viscosities at zero shear agree very well with experimental data over the entire density range. Site size, non-equilibrium molecular alignment and molecular geometry are the primary factors causing both the similarities and differences between the isomers' viscosity and rheology.

Rowley, Richard L.; Ely, James F.

369

Dynamic Structure of a Molecular Liquid S0.5Cl0.5: Ab initio Molecular-Dynamics Simulations

NASA Astrophysics Data System (ADS)

The static and dynamic structures of a molecular liquid S0.5Cl0.5 consisting of Cl--S--S--Cl (S2Cl2) type molecules are studied by means of ab initio molecular dynamics simulations. Both the calculated static and dynamic structure factors are in good agreement with experimental results. The dynamic structures are discussed based on van-Hove distinct correlation functions, molecular translational mean-square displacements (TMSD) and rotational mean-square displacements (RMSD). In the TMSD and RMSD, there are ballistic and diffusive regimes in the sub-picosecond and picosecond time regions, respectively. These time scales are consistent with the decay time observed experimentally. The interaction between molecules in the liquid is also discussed in comparison with that in another liquid chalcogen--halogen system Se0.5Cl0.5.

Ohmura, Satoshi; Shimakura, Hironori; Kawakita, Yukinobu; Shimojo, Fuyuki; Yao, Makoto

2013-07-01

370

Molecular dynamics study of one dimensional nanoscale Si/SiO2 interfaces

NASA Astrophysics Data System (ADS)

Classical molecular dynamics (CMD) simulations were carried out to optimizesilicon oxide interfaces with (100), (111), and (110) silicon surfaces. A three body interatomic potential (modified version of Stillinger-Weber) was used to model the interactions between the species. The resulting overall stress energies and average bond lengths and angles from CDM calculations were compared to previous density functional theory(DFT) calculations. The comparison yields similar trends in the stress energy and shows a good agreement for the bond lengths and angles. Perspectives for large scale molecular dynamics simulations on these systems are discussed.

Castro-Palacio, Juan Carlos; Velázquez-Abad, Luisberis; Fernández, Michael; Cuador-Gil, José Quint?n

2013-05-01

371

Hydrogen bond lifetime for water in classic and quantum molecular dynamics

NASA Astrophysics Data System (ADS)

The lifetime of hydrogen bonds in water at T = 298 K and p = 0.1 MPa is computed by means of classic molecular dynamics with eight different potentials of pair lifetime interaction and Car-Parinello molecular dynamics. The results obtained using various computational techniques for hydrogen bond life-times are compared. It is shown that they can differ from one another by several times. The dependence for the hydrogen bond lifetime computed in our numerical experiment upon the method of its determination is found.

Antipova, M. L.; Petrenko, V. E.

2013-07-01

372

Charge-transfer water potential for solvated protein dynamics

NASA Astrophysics Data System (ADS)

Water plays a critical role in simulations of complex structure-function relationships such as the mechanochemistry of molecular motor proteins, wherein solvating water molecules interact with divalent cations such as Mg^+2, salt bridges, and polar or charged amino acids. Existing fixed-charge and fluctuating charge water models are inadequate in these environments, since they do not support reactive charge transfer with proper long-range dissociation behavior. The charge-transfer embedded atom method (CT-EAM) potential of Valone and Atlas was developed to address these challenges. It includes charge-polarized and ionic embedding terms that describe many-body atomistic interactions as a statistical ensemble of integer-charge excitations; background embedding densities are functions of local pseudoatom electron density distributions that integrate to non-integer charges and evolve dynamically under chemical potential equalization. Here we report first results from simulations of water using the CT-EAM potential of [1] and compare with characteristic properties of the liquid as determined via conventional force fields. [1] K. Muralidharan, S. M. Valone, and S.R. Atlas. arXiv:cond-mat/0705.0857v1, submitted.

Janardhanam, Vijay; Amo-Kwao, Godwin; Atlas, Susan R.

2010-03-01

373

Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber

We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multi-time steps (up to 20 fs) to enable simulation of large biomolecules. The method has been implemented in the Amber molecular modeling package, and is illustrated here on alanine dipeptide and protein G.

Luchko, Tyler; Gusarov, Sergey; Roe, Daniel R.; Simmerling, Carlos; Case, David A.; Tuszynski, Jack; Kovalenko, Andriy

2010-01-01

374

MOLECULAR DYNAMICS: Biomolecules See the Light

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. Detailed knowledge of the dynamics of biomolecules is crucial for the treatment of human diseases, but is often hard to come by. In his Perspective, Pratt highlights the report of Dian et al., who have developed a method for manipulating the populations of different conformational states of small biomolecules that allows distinct folding pathways to be distinguished. If the method can be extended to larger molecules, it should provide important insights into their dynamics.

David W. Pratt (University of Pittsburgh;Department of Chemistry)

2002-06-28

375

Molecular dynamics study of C60-graphite interaction

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations are performed for the collision of C60 with a graphite (0001) surface. TLHT model potential combined with Lennard-Jones potential has been used to describe the interaction between carbon atoms. The impact energy of C60, Ein, ranges from 10 to 60eV, stimulated by the fact that interesting experimental results in this energy region were obtained recently. It is shown that in this energy region, the recoiled C60 is nearly nondeformed. Its internal excitation energy is found to be much lower than that at the medium impact energy (100-300eV, ME). Furthermore, the rebounding energy is found to be dependent on the impact energy of C60. This behavior is quite different from that at ME. Our simulation results are in good agreement with the recent experimental observations. These rebounding characteristics can be explained by the energy partition in a two-step collision model. This study is of significance in exploring the C60 scattering features.

Man, Zhenyong; Pan, Zhengying; Ho, Yukun; Zhu, Wenjun

1999-06-01

376

Accelerated Molecular Dynamics Simulation on Friction of Incommensurate Interfaces

NASA Astrophysics Data System (ADS)

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.

Kim, Woo Kyun; Falk, Michael

2009-03-01

377

Ab initio molecular dynamics calculations of ion hydration free energies

We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or '{lambda}-path' technique to compute the intrinsic hydration free energies of Li{sup +}, Cl{sup -}, and Ag{sup +} ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential ({phi}) contributions, we obtain absolute AIMD hydration free energies ({Delta}G{sub hyd}) 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 {phi} predictions. The sums of Li{sup +}/Cl{sup -} and Ag{sup +}/Cl{sup -} AIMD {Delta}G{sub hyd}, 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{sup +}+Ni{sup +}{yields}Ag+Ni{sup 2+} in water. The predictions for this reaction suggest that existing estimates of {Delta}G{sub hyd} for unstable radiolysis intermediates such as Ni{sup +} may need to be extensively revised.

Leung, Kevin [Department of Surface and Interface Sciences, MS 1415, Sandia National Laboratories, Albuquerque, New Mexico 87185 (United States); Rempe, Susan B. [Department of Nanobiology, MS 0895, Sandia National Laboratories, Albuquerque, New Mexico 87185 (United States); Lilienfeld, O. Anatole von [Department of Multiscale Dynamic Materials Modeling, MS 1322, Sandia National Laboratories, Albuquerque, New Mexico 87185 (United States)

2009-05-28

378

Molecular pathways and potential therapeutic targets in glioblastoma multiforme.

Glioblastoma multiforme (GBM) is the most common primary brain malignancy. The current standard of therapy consists of surgical resection followed by concurrent chemoradiotherapy with temozolomide. Despite steady advances in all therapeutic modalities, clinical improvements have been slow and the prognosis remains poor. Utilizing powerful large-scale molecular techniques, several key pathways implicated in gliomagenesis have recently been identified and confirmed. These represent potential therapeutic targets, and by developing novel methods to specifically manipulate these pathways, we may achieve a meaningful and substantial improvement in the way we treat GBM. Here, we present and discuss the current status of research into the molecular pathways and potential therapeutic targets in GBM. PMID:24168050

Wardak, Zabi; Choe, Kevin S

2013-11-01

379

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

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.

Trabuco, Leonardo G.; Villa, Elizabeth; Mitra, Kakoli; Frank, Joachim; Schulten, Klaus

2008-01-01

380

Free energy calculations using dual-level Born-Oppenheimer molecular dynamics

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.

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

381

Femtosecond molecular dynamics studied with vacuum ultraviolet pulse pairs

NASA Astrophysics Data System (ADS)

Atoms and molecules have most of their oscillator strength in the vacuum ultraviolet (VUV) and extreme ultraviolet (XUV), between the wavelengths of 200 nm and 30 nm. However, most femtosecond spectroscopy has been restricted to the visible and infrared due to a lack of sufficiently intense VUV and XUV femtosecond light sources. This thesis discusses extensions of pump/probe spectroscopy to the VUV and XUV, and its application to the dynamics of ethylene and oxygen molecules excited at 161 nm. I begin with a detailed discussion of the short wavelength light source used in this work. The source is based on the high order harmonics of a near infrared laser and can deliver > 1010 photons per shot in femtosecond pulses, corresponding to nearly 10 MW peak power in the XUV. Measurements of the harmonic yields as a function of the generation conditions reveal the roles of phase matching and ionization gating in the high order harmonic generation process. Pump/probe measurements are conducted using a unique VUV interferometer, capable of combining two different harmonics at a focus with variable delay. Measurements of VUV multiphoton ionization allows for characterization of the source and the interferometer. In molecules, time resolved measurements of fragment ion yields reveal the femtosecond dynamics of the system. The range of wavelengths available for pump and probe allows the dynamics to be followed from photo-excitation all the way to dissociation without detection window effects. The dynamics in ethylene upon pi ? pi* excitation are protypical of larger molecules and have thus served as an important test case for advanced ab initio molecular dynamics theories. Femtosecond measurements to date, however, have been extremely lacking. In the present work, through a series of pump probe experiments using VUV and XUV pulses, time scales for the non-adiabatic relaxation of the electronic excitation, hydrogen migration across the double bond, and H2 molecule elimination are measured and compared to theory. In the simpler oxygen molecule, excitation in the Schuman-Runge continuum leads to direct dissociation along the B S-u3 potential energy curve. The time resolved photoion spectra show that the total photoionization cross section of the molecule resembles two oxygen atoms within 50 fs after excitation.

Allison, Thomas K., III

382

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.

Zhang, Jianwei; He, Xiaodong; Yang, Lin; Wu, Guoqiang; Sha, Jianjun; Hou, Chengyu; Yin, Cunlu; Pan, Acheng; Li, Zhongzhou; Liu, Yubai

2013-01-01

383

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

Zhang, Jianwei; He, Xiaodong; Yang, Lin; Wu, Guoqiang; Sha, Jianjun; Hou, Chengyu; Yin, Cunlu; Pan, Acheng; Li, Zhongzhou; Liu, Yubai

2013-07-22

384

Energy Level Crossings in Molecular Dynamics

Energy level crossings are the landmarks that separate classical from quantum mechanical modeling of molecular systems. They\\u000a induce non-adiabatic transitions between the otherwise adiabatically decoupled electronic level spaces. This review covers\\u000a results on the analysis of propagation through level crossings of codimension two, a mathematical justification of surface\\u000a hopping algorithms, and a spectral study of a linear isotropic system.

Folkmar Bornemann; Caroline Lasser; Torben Swart

385

Diffusion of a vacancy on Fe(1 0 0): A molecular-dynamics study

The diffusion of a surface vacancy on Fe(100) has been studied at various temperatures by means of molecular-dynamics simulations in conjunction with a many body potential in the context of the embedded atom method. This interatomic potential was recently constructed by fitting its parameters to both experimental and first-principles results. From the analysis of the vacancy jumps, three main diffusion

N. I. Papanicolaou; H. Chamati

2009-01-01

386

Constructing ab initio force fields for molecular dynamics simulations

We explore and discuss several important issues concerning the derivation of many-body force fields from ab initio quantum chemical data. In particular, we seek a general methodology for constructing ab initio force fields that are “chemically accurate” and are computationally efficient for large-scale molecular dynamics simulations. We investigate two approaches for modeling many-body interactions in extended molecular systems. The interactions

Yi-Ping Liu; Kyungsun Kim; B. J. Berne; Richard A. Friesner; Steven W. Rick

1998-01-01

387

Constructing ab initio force fields for molecular dynamics simulations

We explore and discuss several important issues concerning the derivation of many-body force fields from ab initio quantum chemical data. In particular, we seek a general methodology for constructing ab initio force fields that are ``chemically accurate'' and are computationally efficient for large-scale molecular dynamics simulations. We investigate two approaches for modeling many-body interactions in extended molecular systems. The interactions

Yi-Ping Liu; Kyungsun Kim; B. J. Berne; Richard A. Friesner; Steven W. Rick

1998-01-01

388

Studying Interactions by Molecular Dynamics Simulations at High Concentration

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.

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

2012-01-01

389

Energy conserving, linear scaling Born-Oppenheimer molecular dynamics

NASA Astrophysics Data System (ADS)

Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces.

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

2012-10-01

390

Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.

Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces. PMID:23039583

Cawkwell, M J; Niklasson, Anders M N

2012-10-01

391

The modulation of the properties and function of cell membranes by small volatile substances is important for many biomedical applications. Despite available experimental results, molecular mechanisms of action of inhalants and organic solvents, such as acetone, on lipid membranes remain not well understood. To gain a better understanding of how acetone interacts with membranes, we have performed a series of molecular dynamics (MD) simulations of a POPC bilayer in aqueous solution in the presence of acetone, whose concentration was varied from 2.8 to 11.2 mol%. The MD simulations of passive distribution of acetone between a bulk water phase and a lipid bilayer show that acetone favors partitioning into the water-free region of the bilayer, located near the carbonyl groups of the phospholipids and at the beginning of the hydrocarbon core of the lipid membrane. Using MD umbrella sampling, we found that the permeability barrier of ~0.5 kcal/mol exists for acetone partitioning into the membrane. In addition, a Gibbs free energy profile of the acetone penetration across a bilayer demonstrates a favorable potential energy well of -3.6 kcal/mol, located at 15-16? from the bilayer center. The analysis of the structural and dynamics properties of the model membrane revealed that the POPC bilayer can tolerate the presence of acetone in the concentration range of 2.8-5.6 mol%. The accumulation of the higher acetone concentration of 11.2 mol% results, however, in drastic disordering of phospholipid packing and the increase in the membrane fluidity. The acetone molecules push the lipid heads apart and, hence, act as spacers in the headgroup region. This effect leads to the increase in the average headgroup area per molecule. In addition, the acyl tail region of the membrane also becomes less dense. We suggest, therefore, that the molecular mechanism of acetone action on the phospholipid bilayer has many common features with the effects of short chain alcohols, DMSO, and chloroform. PMID:23764528

Posokhov, Yevgen O; Kyrychenko, Alexander

2013-05-07

392

NASA Astrophysics Data System (ADS)

The molecular dynamics (MD) simulations, based on a realistic atom-atom interaction potentials were performed on 4-heptyloxy-4?-cyanobiphenyl (7OCB) and 4-hexyloxy-benzylidene-4?-amino-benzonitrile (HBAB) in nematic phase. The set of the order parameters (OPs) S2L (L = 1, 2, 3), rotational self-diffusion (RSD) coefficient D?, rotational ?i (i = 1, 2) and Leslie ?i (i = 1, … , 6) viscosity coefficients, the set of the orientational correlation times ?j0i (i = 1, 2; j = 0, 1) for 7OCB and HBAB in the nematic phase are calculated. Reasonable agreement between the calculated and the experimentally obtained data on S2, ?001, and ?1 has been obtained.

Ilk Capar, M.; Cebe, E.; Zakharov, A. V.

2011-09-01

393

Estimation of tangential momentum accommodation coefficient using molecular dynamics simulation

NASA Astrophysics Data System (ADS)

The Tangential Momentum Accommodation Coefficient (TMAC) is used to improve the accuracy of fluid flow calculations in the slip flow regime. Under such conditions the continuum assumption that a fluid velocity at a solid surface is equal to the surface velocity is inaccurate because relatively significant fluid "slip" occurs at the surface. In this work, Molecular Dynamics techniques are used to study the impacts of individual gas atoms upon solid surfaces to understand how approach velocity, crystal geometry and interatomic forces affect the scattering of the gas atoms, specifically from the perspective of tangential momentum. The gas - solid impacts were modeled using Lennard Jones potentials. Solid surfaces were modeled with approximately 3 atoms wide by 3 atoms deep by 40 or more atoms long. The crystal surface was modeled as a Face Centered Cubic (100). The gas was modeled as individual free gas atoms. Gas approach angles were varied from 10° to 70° from normal. Gas speed was either specified directly or by way of a ratio relationship with the Lennard-Jones energy potential (Energy Ratio). For each impact the initial and final tangential momenta were determined and after a series of many impacts, a value of TMAC was calculated for those conditions. The modeling was validated with available experimental data for He gas atoms at 1770 m/s impacting Cu over angles ranging from 10° to 70°. The model agreed within 3% of the experimental values and correctly predicted that the coefficient changes with angle of approach. Molecular Dynamics results estimate TMAC values from a high of 1.2 to a low of 0.25, generally estimating a higher coefficient at the smaller angles. TMAC values above 1.0 indicate backscattering, which has been experimentally observed in numerous instances. Increasing the Energy Ratio above a value of 5 tends to decrease the coefficient at all angles. Adsorbed layers atop a surface influence the coefficient similar to their Energy Ratio. The results provide encouragement to develop the model further, so as to be able in the future to evaluate TMAC for gas flows with Maxwell temperature distributions involving numerous impact angles simultaneously.

Finger, George Wayne

394

Imaging the molecular dynamics of dissociative electron attachment to water

Momentum imaging experiments on dissociative electron attachment to the water molecule are combined with ab initio theoretical calculations of the angular dependence of the quantum mechanical amplitude for electron attachment to provide a detailed picture of the molecular dynamics of dissociation attachment via the two lowest energy Feshbach resonances. The combination of momentum imaging experiments and theory can reveal dissociation dynamics for which the axial recoil approximation breaks down and thus provides a powerful reaction microscope for DEA to polyatomics.

Adaniya, Hidihito; Rudek, B.; Osipov, Timur; Haxton, Dan; Weber, Thorsten; Rescigno, Thomas N.; McCurdy, C.W.; Belkacem, Ali

2009-10-19

395

Constrained molecular dynamics simulations of atomic ground states

The constrained molecular dynamics model, previously introduced for nuclear dynamics, has been extended to the atomic structure and collision calculations. Quantum effects, corresponding to the Pauli and Heisenberg principles, are enforced by constraints, following the idea of the Lagrange multiplier method. Our calculations for a small atomic system, H, He, Li, Be, and F reproduce the ground-state binding energies reasonably, compared with the experimental data. We discuss also the shell splitting due to e-e correlation.

Kimura, Sachie; Bonasera, Aldo [Laboratorio Nazionale del Sud, INFN, via Santa Sofia, 62, 95123 Catania (Italy)

2005-07-15

396

Mesoscopic Dynamics of Biopolymers and Protein Molecular Machines

NASA Astrophysics Data System (ADS)

The dynamics of biopolymers in solution and in crowded molecular environments, which mimic some features of the interior of a biochemical cell, will be discussed. In particular, the dynamics of protein machines that utilize chemical energy to effect cyclic conformational changes to carry out their catalytic functions will be described. The investigation of the dynamics of such complex systems requires knowledge of the time evolution on physically relevant long distance and time scales. This often necessitates a coarse grained or mesoscopic treatment of the dynamics. A hybrid particle-based mesoscopic dynamical method, which combines molecular dynamics for a coarse-grain model of the proteins with multiparticle collision dynamics for the solvent, will be described and utilized to study the dynamics of such systems. See, C. Echeverria, Y. Togashi, A. S. Mikhailov, and R. Kapral, Phys. Chem. Chem. Phys 13, 10527 (2011); C. Echeverria and R. Kapral, Phys. Chem. Chem. Phys., 14, 6755 (2012); J. M. Schofield, P. Inder and R. Kapral, J. Chem. Phys. 136, 205101 (2012).

Kapral, Raymond

2013-03-01

397

Molecular wire of urea in carbon nanotube: a molecular dynamics study

NASA Astrophysics Data System (ADS)

We perform molecular dynamics simulations of narrow single-walled carbon nanotubes (SWNTs) in aqueous urea to investigate the structure and dynamical behavior of urea molecules inside the SWNT. Even at low urea concentrations (e.g., 0.5 M), we have observed spontaneous and continuous filling of SWNT with a one-dimensional urea wire (leaving very few water molecules inside the SWNT). The urea wire is structurally ordered, both translationally and orientationally, with a contiguous hydrogen-bonded network and concerted urea's dipole orientations. Interestingly, despite the symmetric nature of the whole system, the potential energy profile of urea along the SWNT is asymmetric, arising from the ordering of asymmetric urea partial charge distribution (or dipole moment) in confined environment. Furthermore, we study the kinetics of confined urea and find that the permeation of urea molecules through the SWNT decreases significantly (by a factor of ~20) compared to that of water molecules, due to the stronger dispersion interaction of urea with SWNT than water, and a maximum in urea permeation happens around a concentration of 5 M. These findings might shed some light on the better understanding of unique properties of molecular wires (particularly the wires formed by polar organic small molecules) confined within both artificial and biological nanochannels, and are expected to have practical applications such as the electronic devices for signal transduction and multiplication at the nanoscale.We perform molecular dynamics simulations of narrow single-walled carbon nanotubes (SWNTs) in aqueous urea to investigate the structure and dynamical behavior of urea molecules inside the SWNT. Even at low urea concentrations (e.g., 0.5 M), we have observed spontaneous and continuous filling of SWNT with a one-dimensional urea wire (leaving very few water molecules inside the SWNT). The urea wire is structurally ordered, both translationally and orientationally, with a contiguous hydrogen-bonded network and concerted urea's dipole orientations. Interestingly, despite the symmetric nature of the whole system, the potential energy profile of urea along the SWNT is asymmetric, arising from the ordering of asymmetric urea partial charge distribution (or dipole moment) in confined environment. Furthermore, we study the kinetics of confined urea and find that the permeation of urea molecules through the SWNT decreases significantly (by a factor of ~20) compared to that of water molecules, due to the stronger dispersion interaction of urea with SWNT than water, and a maximum in urea permeation happens around a concentration of 5 M. These findings might shed some light on the better understanding of unique properties of molecular wires (particularly the wires formed by polar organic small molecules) confined within both artificial and biological nanochannels, and are expected to have practical applications such as the electronic devices for signal transduction and multiplication at the nanoscale. Electronic supplementary information (ESI) available. See DOI: 10.1039/c1nr10793c

Xiu, Peng; Tu, Yusong; Tian, Xingling; Fang, Haiping; Zhou, Ruhong

2012-01-01

398

Molecular-dynamics studies and neutron-scattering experiments on methylene chloride

NASA Astrophysics Data System (ADS)

We calculate inelastic neutron-scattering intensities of methylene chloride for cold neutrons from molecular-dynamics (MD) simulations and compare them with experimental data. To obtain realistic scattering intensities, the effect of multiple scattering is taken into account by a Monte Carlo (MC) simulation, using the dynamic structure factor calculated from our MD simulations as input. The MD simulations of methylene chloride are performed with the same potentials as in Part I of this work. The dynamic structure factor is calculated using fast correlation algorithm (FCA), which is based on the fast-Fourier-transform (FFT) algorithm and the Wiener-Khinchin theorem for discrete functions.

Kneller, Gerald R.; Geiger, Alfons

399

Molecular Mechanotransduction: how forces trigger cytoskeletal dynamics

NASA Astrophysics Data System (ADS)

Mechanical stresses elicit cellular reactions mediated by chemical signals. Defective responses to forces underlie human medical disorders, such as cardiac failure and pulmonary injury. Despite detailed knowledge of the cytoskeleton's structure, the specific molecular switches that convert mechanical stimuli into chemical signals have remained elusive. Here we identify the actin-binding protein, filamin A (FLNa) as a central mechanotransduction element of the cytoskeleton by using Fluorescence Loss After photoConversion (FLAC), a novel high-speed alternative to FRAP. We reconstituted a minimal system consisting of actin filaments, FLNa and two FLNa-binding partners: the cytoplasmic tail of ß-integrin, and FilGAP. Integrins form an essential mechanical linkage between extracellular and intracellular environments, with ß integrin tails connecting to the actin cytoskeleton by binding directly to filamin. FilGAP is a FLNa-binding GTPase-activating protein specific for Rac, which in vivo regulates cell spreading and bleb formation. We demonstrate that both externally-imposed bulk shear and myosin II driven forces differentially regulate the binding of integrin and FilGAP to FLNa. Consistent with structural predictions, strain increases ß-integrin binding to FLNa, whereas it causes FilGAP to dissociate from FLNa, providing a direct and specific molecular basis for cellular mechanotransduction. These results identify the first molecular mechanotransduction element within the actin cytoskeleton, revealing that mechanical strain of key proteins regulates the binding of signaling molecules. Moreover, GAP activity has been shown to switch cell movement from mesenchymal to amoeboid motility, suggesting that mechanical forces directly impact the invasiveness of cancer.

Ehrlicher, Allen

2012-02-01

400

Molecular beam studies of reaction dynamics

Thrust was to elucidate simple elementary reactions and to unravel mechanism of complex/photochemical reactions. Molecular beams are used to study reactions between molecules or to monitor photodissociation events in a collision-free environment. Recent activities centered on reactions involving oxygen atoms with unsaturated hydrocarbons, endothermic substitution reactions, dependence of reactivity of excited atoms on alignment of excited orbitals, photochemical reactions of polyatomic, energy transfer, free radicals in combustion processes, infrared absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation.

Lee, Yuan T.

1993-03-01

401

GPU Acceleration of Cutoff Pair Potentials for Molecular Modeling Applications

The advent of systems biology requires the simulation of ever- larger biomolecular systems, demanding a commensurate growth in computational power. This paper examines the use of the NVIDIA Tesla C870 graphics card programmed through the CUDA toolkit to accelerate the calculation of cutoff pair potentials, one of the most prevalent computations required by many different molecular modeling applications. We present

Christopher I. Rodrigues; David J. HardyÜ; Wen-Mei W. Hwu

402

Molecularly imprinted polymers—potential and challenges in analytical chemistry

Among the variety of biomimetic recognition schemes utilizing supramolecular approaches molecularly imprinted polymers (MIPs) have proven their potential as synthetic receptors in numerous applications ranging from liquid chromatography to assays and sensor technology. Their inherent advantages compared to biochemical\\/biological recognition systems include robustness, storage endurance and lower costs. However, until recently only few contributions throughout the relevant literature describe quantitative

J. O. Mahony; K. Nolan; M. R. Smyth; B. Mizaikoff

2005-01-01

403

A dynamical stabilization of the radion potential

NASA Astrophysics Data System (ADS)

Large extra-dimensional theories attempt to solve the hierarchy problem by assuming that the fundamental scale of the theory is at the electroweak scale. This requires the size of the extra dimensions to be stabilized at a scale which is determined by the effective four-dimensional Planck mass and the number of extra dimensions. In this Letter we concentrate upon the dynamical reasons to stabilize them by providing a running mass to the radion field. We show that it is possible to maintain the size of the extra dimensions once it is stabilized throughout the dynamics of inflation.

Mazumdar, A.; Pérez-Lorenzana, A.

2001-05-01

404

Molecular simulation of protein dynamics in nanopores. II. Diffusion.

A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model of proteins, is used to carry out long (several microsecond) simulations in order to study transport of proteins in nanopores. We simulated single-domain proteins with the alpha-helical native structure. Both attractive and repulsive interaction potentials between the proteins and the pores' walls are considered. The diffusivity D of the proteins is computed not only under the bulk conditions but also as a function of their "length" (the number of the amino-acid groups), temperature T, pore size, and interaction potentials with the walls. Compared with the experimental data, the computed diffusivities under the bulk conditions are of the correct order of magnitude. The diffusivities both in the bulk and in the pores follow a power law in the length [script-l] of the proteins and are larger in pores with repulsive walls. D(+)/D(-), the ratio of the diffusivities in pores with attractive and repulsive walls, exhibits two local maxima in its dependence on the pore size h, which are attributed to the pore sizes and protein configurations that induce long-lasting simultaneous interactions with both walls of the pores. Far from the folding temperature T(f), D increases about linearly with T, but due to the thermal fluctuations and their effect on the proteins' structure near T(f), the dependence of D on T in this region is nonlinear. We propose a novel and general "phase diagram," consisting of four regions, that describes qualitatively the effect of h, T, and interaction potentials with the walls on the diffusivity D of a protein. PMID:19256630

Javidpour, Leili; Tabar, M Reza Rahimi; Sahimi, Muhammad

2009-02-28

405

We have carried out molecular-dynamics simulations on fully flexible all-atom models of the protein lysozyme immersed in trehalose, an effective biopreservative, with the purpose of exploring the nature and extent of the dynamical coupling between them. Our study shows a strong coupling over a wide range of temperatures. We found that the onset of anharmonic behavior was dictated by changes

Taner E. Dirama; Joseph E. Curtis; Gustavo A. Carri; Alexei P. Sokolov

2006-01-01

406

Mechanical and dynamical behavior of carbon nanotube with defects: A molecular dynamics simulation

In this paper, molecular dynamics simulation is carried out to investigate the mechanical properties and dynamic behaviors of carbon nanotubes with vacancies and related defects. We have shown the Yang's modulus and tensile strength of nanotubes with vacancy-related defects are dependent on the characteristics of vacancies. Meanwhile, the phonon density of state (DOS) are used to study the vibration properties

Jenn-Sen Lin; Shin-Pon Ju; Shih-Wen Yung; Wen-Shian Wu; Meng-Hsiung Weng; Wen-Jay Lee

2009-01-01

407

Molecular dynamics modelling of radiation damage in zircon

NASA Astrophysics Data System (ADS)

Zircon (ZrSiO4) is among actinide-bearing phases which has been proposed as a crystalline confinement matrix for nuclear waste management, especially for weapon-grade plutonium and UO2 spent fuel in the USA. Zircon is also widely used in geochronology. But, with accumulating ?-decay damage, zircon undergoes a radiation induced transition to an amorphous (or metamict) state. So, in the present work molecular dynamics simulations (MD simulations) of zircon structure have been performed to study radiation damage in zircon. In this technique, one simulates the propagation of an energetic particle in a system of atoms interacting via model potentials, by integrating the Newton equations of motion. Author has used version 3.09 of the DL_POLY molecular simulation package. Zircon structure containing 181944 atoms (19x19x21 unit cells) was equilibrated at 300 K for 10 ps, and one Zr atom (usually called the primary knock-on atom, PKA) was given a velocity corresponding to an implantation energy of about 20 keV. MD simulations were performed in the microcanonical ensemble that is under conditions of constant particle number, volume and energy. Results of the MD simulations show that the number of interstitials is equal to 840 atoms. This is very close (4000-5000 atoms for 70 keV recoil atom 234Th) to what is measured in the diffuse x-ray scattering and NMR experiments on amorphous metamict samples (damaged by natural irradiation) of geological age. It has been shown that the damaged structure contains several depleted regions with characteristic sized up to 2,5 nm after single event and up to 4,5 nm after three overlapping events. Furthermore, these events produce channels of depleted matter between the overlapping damaged regions. These channels provide a high-diffusivity path for radiogenic Pb (percolation effect). Loss of radiogenic Pb may result in to incorrect dating of rocks.

Grechanovsky, A. E.

2009-04-01

408

Numerical methods for molecular dynamics. Progress report

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.

Skeel, R.D.

1991-12-31

409

Newtonian molecular dynamics in general curvilinear internal coordinates

A simple formulation of Newtonian molecular dynamics in general internal coordinates is given. Our equation for the internal acceleration does not require the transformation matrix from internal to Cartesian coordinates, only the much simpler first and second-order transformation from Cartesians to internals. The formulation has a simple, common general expression for the centrifugal\\/Coriolis contribution to the internal acceleration. The method

P. Pulay; B. Paizs

2002-01-01

410

Thermodynamics and quantum corrections from molecular dynamics for liquid water

This paper treats the first problem, how to quantum correct the classical mechanical thermodynamic values available from molecular dynamics, Monte Carlo, perturbation, or integral methods in order to compare with experimental quantum reality. A subsequent paper will focus on the second difficulty, the effective computation of free energy and entropy. A simple technique, derived from spectral analysis of the atomic

P. H. Berens; D. H. J. Mackay; G. M. White; K. R. Wilson

1982-01-01

411

Ab Initio Molecular Dynamics of Metallic Hydrogen at High Densities

The fully ionized (metallic) hydrogen plasma is studied by ab initio molecular dynamics simulations, for classical protons and fully degenerate electrons, in the strong coupling regime of the protons. The calculated ion-electron pair distribution function signals the breakdown of linear screening with decreasing density while the melting temperature of the proton crystal drops rapidly. The simulations reveal the remarkable persistence

Jorge Kohanoff; Jean-Pierre Hansen

1995-01-01

412

Cycles and communicating classes in membrane systems and molecular dynamics

We are considering sequential membrane systems and molecular dynamics from the view- point of Markov chain theory. The configuration space of thes e systems (including the tran- sitions) is a special kind of directed graph, called pseudo- lattice digraph, which is closely related to the stoichiometric matrix. Taking advantage of the monoidal structure of this space, we introduce the algebraic

Michael Muskulus; Daniela Besozzi; Robert Brijder; Paolo Cazzaniga; Sanne Houweling; Dario Pescini; Grzegorz Rozenberg

2007-01-01

413

A Molecular Dynamics Simulation for the Formation Mechanism of Fullerene

The formation mechanism of fullerene, a new type of carbon molecule with a hollow caged structure, was studied using a molecular dynamics method. In order to simulate the basic reaction process observed in the arc-discharge or the laser vaporization fullerene generation, we have calculated the clustering process starting from randomly located isolated carbon atoms. Here, an empirical many- body carbon

Shigeo MARUYAMA; Yasutaka YAMAGUCHI; T. Takagi; S. Matsumoto

1994-01-01

414

Molecular dynamics studies of protein folding and aggregation

This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation. Most small proteins fold into their native states via a first-order-like phase transition with a major free energy barrier between the folded and unfolded states. A set of protein conformations corresponding to the free energy barrier, Delta G >> kBT, are the

Feng Ding

2004-01-01

415

A Molecular Dynamics Simulation of Bubble Nucleation on Solid Surface

A heterogeneous nucleation of a vapor bubble on a solid surface was simulated by the molecular dynamics method. Liquid argon between parallel solid surfaces was gradually expanded, until a vapor bubble was nucleated. Argon liquid was represented by 5488 Lennard-Jones molecules and each surface was represented by three layers of harmonic molecules with the constant temperature heat bath model. With

Shigeo MARUYAMA; Tatsuto KIMURA

2000-01-01

416

Molecular Dynamics Simulation of Adhesion Forces in a Dipalmitoylphosphatidylcholine Membrane

Adhesion forces of Dipalmitoylphosphatidylcholine (DPPC) membrane in the gel phase are investigated by molecular dynamics (MD) simulation. In the simulations, individual DPPC molecules are pulled out of DPPC membranes with different rates and we get the maximum adhesion forces of DPPC membrane. We find that the maximum adhesion forces increase with pull rate, from about 400 to 700 pN when

Jun Yin; Ya-Pu Zhao

2007-01-01

417

MOLECULAR DYNAMICS SIMULATION OF THERMAL CONDUCTION IN NANOPOROUS THIN FILMS

Molecular dynamics simulations of thermal conduction in nanoporous thin films are performed. Thermal conductivity displays an inverse temperature dependence for films with small pores and a much less pronounced dependence for larger pores. Increasing porosity reduces thermal conductivity, while pore shape has little effect except in the most anisotropic cases. The pores separate the film into local regions with distinctly

Jennifer R Lukes; C. L. Tien

2004-01-01

418

Molecular Dynamics Simulation of Sonoluminescence: Modeling, Algorithms and Simulation Results

Sonoluminescence is the phenomena of light emission from a collapsing gas bubble in a liquid. Theoretical explanations of this extreme energy focusing are controversial and difficult to validate experimentally. We propose to use molecular dynamics simulations of the collapsing gas bubble to clarify the energy focusing mechanism, and provide insight into the mechanism of light emission. In this paper, we

Steven J. Ruuth; Seth Putterman; Barry Merriman

2001-01-01

419

Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques

Molecular dynamics modeling has provided a powerful tool for simulating and understanding diverse systems – ranging from materials processes to biophysical phenomena. Parallel formulations of these methods have been shown to be among the most scalable scientific computing applications. Many instances of this class of methods rely on a static bond structure for molecules, rendering them infeasible for reactive systems.

Hasan Metin Aktulga; Joseph C. Fogarty; Sagar A. Pandit; Ananth Y Grama

2009-01-01

420

Reasoning with Atomic-Scale Molecular Dynamic Models

ERIC Educational Resources Information Center

|The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies…

Pallant, Amy; Tinker, Robert F.

2004-01-01

421

Quantum molecular dynamics: Propagating wavepackets and density operators using the

Quantum molecular dynamics describe the time-evolution of a chem- ical system at the atomic level by directly solving the Schrodinger equation. Time-dependent methods, exemplied by wavepacket prop- agation, are by now developed to a point where they provide an impor- tant insight into the mechanism of many fundamental processes. Of these methods, the most versatile and ecien t is probably

Hans-Dieter Meyer; Graham A. Worthy

422

Molecular dynamics simulation of fast ion impact on cluster atoms

Fragmentation and ion scattering in a fast ion impact on cluster atoms were researched with molecular dynamics simulation methods. The atom evaporation was caused after the incident particle was impacted into the cluster. It has been found from simulation results that the fragmentation distributions have not a large dependence on the energy of the incident particle in the range of

F. Sato; T. Kagawa; S. Sakabe; K. Imasaki; T. Iida

2001-01-01

423

Fragmentation by molecular dynamics: The microscopic ''big bang''

We propose and test a new molecular-dynamics method to study fragmentation of condensed matter under homogeneous adiabatic expansion. Our atomistic simulations give significant insight into the nature of fragment distributions. We also find that a simple continuum model based on energy balance gives a reasonably good estimate of the average fragment mass.

Brad Holian; Dennis Grady

1988-01-01

424

Superionicity in Na3 PO4 : A molecular dynamics simulation

Fast ionic conduction in solid Na3PO4 is studied by use of molecular dynamics simulation based on the modified Lu -Hardy approach. We obtain reasonable agreement with experiment for the structural transition and diffusion of the sodium ions. All the sodium ions are found to contribute comparably to the high ionic conductivity. The results of the simulation are discussed in terms

Wei-Guo Yin; Jianjun Liu; Chun-Gang Duan; Wai-Ning Mei; Robert W. Smith; John R. Hardy

2004-01-01

425

Ab initio molecular dynamics simulation of liquid hydrogen fluoride

We have performed an ab initio molecular dynamics (MD) simulation of the structure of liquid hydrogen fluoride. Our results exhibit a strong contraction of the hydrogen bond in going from the gas to the liquid phase. The local structure of the liquid resembles that of the solid with the appearance of short lived hydrogen-bonded zig-zag chains. We have also studied

Ursula Röthlisberger; Michele Parrinello

1997-01-01

426

Brine Rejection from Freezing Salt Solutions: A Molecular Dynamics Study

The atmospherically and technologically very important process of brine rejection from freezing salt solutions is investigated with atomic resolution using molecular dynamics simulations. The present calculations allow us to follow the motion of each water molecule and salt ion and to propose a microscopic mechanism of brine rejection, in which a fluctuation (reduction) of the ion density in the vicinity

Lubos Vrbka; Pavel Jungwirth

2005-01-01

427

Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences

Weintroduce the Bayesian skyline plot,anew method for estimating past population dynamics throughtime from asample of molecular sequences without dependence on a prespecified parametric model of demographic history. We describe a Markov chain Monte Carlo sampling procedure that efficiently samples a variant of the generalized skyline plot, given sequence data, and combines these plots to generate a posterior distribution of effective

A. J. Drummond; A. Rambaut; B. Shapiro; O. G. Pybus

2005-01-01

428

Molecular Dynamics Studies of the Primary State of Radiation Damage.

National Technical Information Service (NTIS)

This paper summarizes recent progress in the understanding of energetic displacement cascades in metals achieved with the molecular-dynamics (MD) simulation technique. Recoil events with primary-knock-on-atom (PKA) energies up to 5 keV were simulated in C...

T. Diaz de la Rubia R. S. Averback I. M. Robertson R. Benedek

1988-01-01

429

Liapunov exponents and the reversibility of molecular dynamics algorithms

NASA Astrophysics Data System (ADS)

We study the phenomenon of lack of reversibility in molecular dynamics algorithms for the case of Wilson's lattice QCD. We demonstrate that the classical equations of motion that are employed in these algorithms are chaotic in nature. The leading Liapunov exponent is determined in a range of coupling parameters. We consider the consequences of the breakdown of reversibility due to round-off errors.

Liu, Chuan; Jaster, Andreas; Jansen, Karl

1998-08-01

430

A Parallel Engine for Graphical Interactive Molecular Dynamics Simulations

The current work proposes a parallel implementation for interactive molecular dynamics simulations (MD). The interactive capability is modeled by finite automata that are executed in the processing nodes. Any interaction implies in a communication between the user interface and the finite automata. The ADKS, an interactive sequential MD code that provides graphical output was chosen as a case study. A

Eduardo Rocha Rodrigues; Airam Jonatas Preto; Stephan Stephany

2004-01-01

431

Methodological considerations on molecular dynamics simulations of DNA oligonucleotides

Methodological aspects of solvent effects, simulation protocol, analysis and visualization of results, accuracy, and sensitivity of results to force field parametrization are discussed for molecular dynamics simulation on oligonucleotides. Recent results comparing AMBER, CHARMM and GROMOS force fields are included. The calculation of build-up curves for the nuclear Overhauser effect from simulations is also described.

D. L. Beveridge; S. Swaminathan; G. Ravishanker; J. Withka; J. Srinivasan; C. Prévost; S. Louise-May; F. M. Dicapua; P. H. Bolton

1991-01-01

432

Methodological considerations on molecular dynamics simulations of DNA oligonucleotides

NASA Astrophysics Data System (ADS)

Methodological aspects of solvent effects, simulation protocol, analysis and visualization of results, accuracy, and sensitivity of results to force field parametrization are discussed for molecular dynamics simulation on oligonucleotides. Recent results comparing AMBER, CHARMM and GROMOS force fields are included. The calculation of build-up curves for the nuclear Overhauser effect from simulations is also described.

Beveridge, D. L.; Swaminathan, S.; Ravishanker, G.; Withka, J.; Srinivasan, J.; Prévost, C.; Louise-May, S.; Dicapua, F. M.; Bolton, P. H.

1991-10-01

433

Anton, a special-purpose machine for molecular dynamics simulation

The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macro- molecules could in principle provide answers to some of the most important currently outstanding questions in the fields of biology, chemistry and medicine. A wide range of biologically interesting phenomena, however, occur over time scales on the order of a millisecond—about three orders of

David E. Shaw; Martin M. Deneroff; Ron O. Dror; Jeffrey Kuskin; Richard H. Larson; John K. Salmon; Cliff Young; Brannon Batson; Kevin J. Bowers; Jack C. Chao; Michael P. Eastwood; Joseph Gagliardo; J. P. Grossman; Richard C. Ho; Doug Ierardi; István Kolossváry; John L. Klepeis; Timothy Layman; Christine Mcleavey; Mark A. Moraes; Rolf Mueller; Edward C. Priest; Yibing Shan; Jochen Spengler; Michael Theobald; Brian Towles; Stanley C. Wang

2007-01-01