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1

Molecular potentials and relaxation dynamics

The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. Recent calculations of the X/sup 1/..sigma../sup +/ and a/sup 3/..sigma../sup +/ states of LiH, NaH, KH, RbH, and CsH and the X/sup 2/..sigma../sup +/ states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, higly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm/sup -1/ over most of the potential curves) with the difference curves being considerably more accurate. In the method of computer molecular dynamics, the force acting on each particle is the resultant of all interactions with other atoms in the neighborhood and is obtained as the derivative of an effective many-body potential. Exploiting the pseudopotential approach, in obtaining the appropriate potentials may be very fruitful in the future. In the molecular dynamics example considered here, the conventional sum-of-pairwise-interatomic-potentials (SPP) approximation is used with the potentials derived either from experimental spectroscopic data or from Hartree-Fock calculations. The problem is the collisional de-excitation of vibrationally excited molecular hydrogen at an Fe surface. The calculations have been carried out for an initial vibrotational state v = 8, J = 1 and a translational temperature corresponding to a gas temperature of 500/sup 0/K. Different angles of approach and different initial random impact points on the surface have been selected. For any given collision with the wall, the molecule may pick up or lose vibrotatonal and translational energy.

Karo, A.M.

1981-05-18

2

Molecular Potentials and Relaxation Dynamics.

National Technical Information Service (NTIS)

The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativist...

A. M. Karo

1981-01-01

3

Molecular potentials and relaxation dynamics

The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. As an example, recent calculations of the chi/sup 1/..sigma../sup +/ and a/sup 3/..sigma../sup +/ states of LiH, NaH, KH, RbH, and CsH and the chi/sup 2/..sigma../sup +/ states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, highly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm/sup -1/ over most of the potential curves) with the difference curves being considerably more accurate.

Karo, A.M.

1981-03-27

4

Analytic Potentials and Molecular Dynamics Simulations

NSDL National Science Digital Library

This tutorial, created by Donald W. Brenner at North Carolina State University, explains the role of "atomistic simulation in enabling nanotechnology." The tutorial is divided into six sections: "Case Study: Fullene Nanogear," "Molecular Dynamics," "Historical Perspective," "The Nuts and Bolts," "Potential Energy Functions," and "More Examples." Simply click the "forward" and "back" buttons to navigate the tutorial. Images, equations, and graphs help visitors along in understanding the material. This is a useful resource for teachers to use in the classroom or as part of an assignment, and for students studying nanotechnology and nanofabrication.

Brenner, Donald W.

2008-08-27

5

First-Principles Molecular Dynamics at a Constant Electrode Potential

NASA Astrophysics Data System (ADS)

A simulation scheme for performing first-principles molecular dynamics at a constant electrode potential is presented, opening the way for a more realistic modeling of voltage-driven devices. The system is allowed to exchange electrons with a reservoir at fixed potential, and dynamical equations for the total electronic charge are derived by using the potential energy of the extended system. In combination with a thermostat, this potentiostat scheme reproduces thermal fluctuations of the charge with the correct statistics, implying a realistic treatment of the potential as a control variable. Practically, the dynamics of the charge are decoupled from the electronic structure calculations, making the scheme easily implementable in existing first-principles molecular dynamics codes. Our approach is demonstrated on a test system by considering various test cases.

Bonnet, Nicéphore; Morishita, Tetsuya; Sugino, Osamu; Otani, Minoru

2012-12-01

6

First-principles molecular dynamics at a constant electrode potential.

A simulation scheme for performing first-principles molecular dynamics at a constant electrode potential is presented, opening the way for a more realistic modeling of voltage-driven devices. The system is allowed to exchange electrons with a reservoir at fixed potential, and dynamical equations for the total electronic charge are derived by using the potential energy of the extended system. In combination with a thermostat, this potentiostat scheme reproduces thermal fluctuations of the charge with the correct statistics, implying a realistic treatment of the potential as a control variable. Practically, the dynamics of the charge are decoupled from the electronic structure calculations, making the scheme easily implementable in existing first-principles molecular dynamics codes. Our approach is demonstrated on a test system by considering various test cases. PMID:23368585

Bonnet, Nicéphore; Morishita, Tetsuya; Sugino, Osamu; Otani, Minoru

2012-12-28

7

National Technical Information Service (NTIS)

The subject of the thesis is: lattice dynamics calculations on molecular crystals and physically adsorbed molecular layers. The methods used are the standard harmonic method for the solids with larger molecules (chlorinated benzenes and tetracyanoethyene)...

T. H. M. van den Berg

1991-01-01

8

Electron transfer across ?-helical peptides: Potential influence of molecular dynamics

NASA Astrophysics Data System (ADS)

Three hydrophobic leucine-rich peptides Fc18L, Ac18L and 18LAc were prepared. These peptides are equipped with a cystein sulfhydryl group which enables the formation of thin films on gold surfaces. Using these peptides, two types of films of ?-helical peptides have been prepared, in which the redox-active peptide Fc18L is diluted by Ac18L ( SAM1) or by a mixture of Ac18L and 18LAc ( SAM2). In SAM1, the dipole moments of the peptides are aligned in the same direction, whereas in SAM2, they are opposite. Reflection absorption infrared spectroscopy (RAIRS) revealed that the peptides are more vertically oriented in SAM2 compared to those in SAM1. The interaction among the macroscopic helix dipoles gives tighter packing of the peptides in SAM2. Importantly, the electron transfer properties in the two films are significantly different, which is rationalized by differences in the molecular dynamics of the two films.

Mandal, Himadri S.; Kraatz, Heinz-Bernhard

2006-07-01

9

We present computational aspects of Molecular Dynamics calculations of thermal properties of diamond using the Brenner potential. Parallelization was essential in order to carry out these calculations on samples of suitable sizes. Our implementation uses MPI on a multi-processor machine such as the IBM SP2. Three aspects of parallelization of the Brenner potential are discussed in depth. These are its

Irina Rosenblum; Joan Adler; Simon Brandon

1999-01-01

10

ERRATUM: A `magnetic' interatomic potential for molecular dynamics simulations.

NASA Astrophysics Data System (ADS)

Our colleagues pointed out that the format of numerical values given in table 3 of our paper may cause confusion and lead to an error in the numerical implementation of the potential. Below we list the values given in table 3 of our original paper, this time using conventional decimal notations. These values correspond to the same choice of parameter ?c=1. Please see the pdf for table 3

L, Dudarev S.; M, Derlet P.

2007-06-01

11

Potential energy surface and molecular dynamics simulation of gold(I) in liquid nitromethane

Potential energy functions for Au(I)-nitromethane (NM, CH3NO2) and NM–NM interactions were calculated by fitting analytical expressions to quantum chemically derived energies. These functions were then used in a molecular dynamics simulation of one Au(I) cation in 499 nitromethane molecules in the NVT ensemble at room temperature. A comparative simulation with a generic NM–NM potential energy function was also performed for

Natcha Injan; Tünde Megyes; Tamas Radnai; Imre Bako; Szabolcz Balint; Jumras Limtrakul; Daniel Spangberg; Michael Probst

2009-01-01

12

NASA Astrophysics Data System (ADS)

The liquid structure of tetrachloroethene has been investigated on the basis of measured neutron and X-ray scattering structure factors, applying molecular dynamics simulations and reverse Monte Carlo (RMC) modeling with flexible molecules and interatomic potentials. As no complete all-atom force field parameter set could be found for this planar molecule, the closest matching all-atom Optimized Potentials for Liquid Simulations (OPLS-AA) intra-molecular parameter set was improved by equilibrium bond length and angle parameters coming from electron diffraction experiments [I. L. Karle and J. Karle, J. Chem. Phys. 20, 63 (1952)]. In addition, four different intra-molecular charge distribution sets were tried, so in total, eight different molecular dynamics simulations were performed. The best parameter set was selected by calculating the mean square difference between the calculated total structure factors and the corresponding experimental data. The best parameter set proved to be the one that uses the electron diffraction based intra-molecular parameters and the charges qC = 0.1 and qCl = -0.05. The structure was further successfully refined by applying RMC computer modeling with flexible molecules that were kept together by interatomic potentials. Correlation functions concerning the orientation of molecular axes and planes were also determined. They reveal that the molecules closest to each other exclusively prefer the parallel orientation of both the molecular axes and planes. Molecules forming the first maximum of the center-center distribution have a preference for <30° and >60° axis orientation and >60° molecular plane arrangement. A second coordination sphere at ~11 A? and a very small third one at ~16 A? can be found as well, without preference for any axis or plane orientation.

Gereben, Orsolya; Pusztai, László

2013-10-01

13

The liquid structure of tetrachloroethene has been investigated on the basis of measured neutron and X-ray scattering structure factors, applying molecular dynamics simulations and reverse Monte Carlo (RMC) modeling with flexible molecules and interatomic potentials. As no complete all-atom force field parameter set could be found for this planar molecule, the closest matching all-atom Optimized Potentials for Liquid Simulations (OPLS-AA) intra-molecular parameter set was improved by equilibrium bond length and angle parameters coming from electron diffraction experiments [I. L. Karle and J. Karle, J. Chem. Phys. 20, 63 (1952)]. In addition, four different intra-molecular charge distribution sets were tried, so in total, eight different molecular dynamics simulations were performed. The best parameter set was selected by calculating the mean square difference between the calculated total structure factors and the corresponding experimental data. The best parameter set proved to be the one that uses the electron diffraction based intra-molecular parameters and the charges qC = 0.1 and qCl = -0.05. The structure was further successfully refined by applying RMC computer modeling with flexible molecules that were kept together by interatomic potentials. Correlation functions concerning the orientation of molecular axes and planes were also determined. They reveal that the molecules closest to each other exclusively prefer the parallel orientation of both the molecular axes and planes. Molecules forming the first maximum of the center-center distribution have a preference for <30° and >60° axis orientation and >60° molecular plane arrangement. A second coordination sphere at ?11 A? and a very small third one at ?16 A? can be found as well, without preference for any axis or plane orientation. PMID:24182051

Gereben, Orsolya; Pusztai, László

2013-10-28

14

The evolution of irradiation damage cascades in a metal has been simulated by molecular dynamics, using a many-body potential. Over 100 cascades have been produced with random knock-on directions and primary knock-on atom (PKA) energies ranging from 60 to 2 keV. The cascade evolution has been followed for times typically up to about 10ps and in some cases up to

A. J. E. Foreman; W. J. Phythian; C. A. English

1992-01-01

15

Molecular dynamics simulations allow detailed study of the experimentally inaccessible liquid state of supercooled water below its homogeneous nucleation temperature and the characterization of the glass transition. Simple, nonpolarizable intermolecular potentials are commonly used in classical molecular dynamics simulations of water and aqueous systems due to their lower computational cost and their ability to reproduce a wide range of properties. Because the quality of these predictions varies between the potentials, the predicted glass transition of water is likely to be influenced by the choice of potential. We have thus conducted an extensive comparative investigation of various three-, four-, five-, and six-point water potentials in both the NPT and NVT ensembles. The T(g) predicted from NPT simulations is strongly correlated with the temperature of minimum density, whereas the maximum in the heat capacity plot corresponds to the minimum in the thermal expansion coefficient. In the NVT ensemble, these points are instead related to the maximum in the internal pressure and the minimum of its derivative, respectively. A detailed analysis of the hydrogen-bonding properties at the glass transition reveals that the extent of hydrogen-bonds lost upon the melting of the glassy state is related to the height of the heat capacity peak and varies between water potentials. PMID:24467489

Kreck, Cara A; Mancera, Ricardo L

2014-02-20

16

Cholinesterase inhibitors (ChE-Is) are the standard for the therapy of AD associated disorders and are the only class of approved drugs by the Food and Drug Administration (FDA). Additionally, acetylcholinesterase (AChE) is the target for many Alzheimer's dementia drugs which block the function of AChE but have some side effects. Therefore, in this paper, an attempt was made to elucidate cholinesterase inhibition potential of secondary metabolite from Cannabis plant which has negligible or no side effect. Molecular docking of 500 herbal compounds, against AChE, was performed using Autodock 4.2 as per the standard protocols. Molecular dynamics simulations have also been carried out to check stability of binding complex in water for 1000?ps. Our molecular docking and simulation have predicted high binding affinity of secondary metabolite (C28H34N2O6) to AChE. Further, molecular dynamics simulations for 1000?ps suggest that ligand interaction with the residues Asp72, Tyr70-121-334, and Phe288 of AChE, all of which fall under active site/subsite or binding pocket, might be critical for the inhibitory activity of AChE. This approach might be helpful to understand the selectivity of the given drug molecule in the treatment of Alzheimer's disease. The study provides evidence for consideration of C28H34N2O6 as a valuable small ligand molecule in treatment and prevention of AD associated disorders and further in vitro and in vivo investigations may prove its therapeutic potential.

Seniya, Chandrabhan; Khan, Ghulam Jilani; Uchadia, Kuldeep

2014-01-01

17

Cholinesterase inhibitors (ChE-Is) are the standard for the therapy of AD associated disorders and are the only class of approved drugs by the Food and Drug Administration (FDA). Additionally, acetylcholinesterase (AChE) is the target for many Alzheimer's dementia drugs which block the function of AChE but have some side effects. Therefore, in this paper, an attempt was made to elucidate cholinesterase inhibition potential of secondary metabolite from Cannabis plant which has negligible or no side effect. Molecular docking of 500 herbal compounds, against AChE, was performed using Autodock 4.2 as per the standard protocols. Molecular dynamics simulations have also been carried out to check stability of binding complex in water for 1000?ps. Our molecular docking and simulation have predicted high binding affinity of secondary metabolite (C28H34N2O6) to AChE. Further, molecular dynamics simulations for 1000?ps suggest that ligand interaction with the residues Asp72, Tyr70-121-334, and Phe288 of AChE, all of which fall under active site/subsite or binding pocket, might be critical for the inhibitory activity of AChE. This approach might be helpful to understand the selectivity of the given drug molecule in the treatment of Alzheimer's disease. The study provides evidence for consideration of C28H34N2O6 as a valuable small ligand molecule in treatment and prevention of AD associated disorders and further in vitro and in vivo investigations may prove its therapeutic potential. PMID:25054066

Seniya, Chandrabhan; Khan, Ghulam Jilani; Uchadia, Kuldeep

2014-01-01

18

Atomistic simulations of TeO2-based glasses: interatomic potentials and molecular dynamics.

In this work we present for the first time empirical interatomic potentials that are able to reproduce TeO2-based systems. Using these potentials in classical molecular dynamics simulations, we obtained first results for the pure TeO2 glass structure model. The calculated pair distribution function is in good agreement with the experimental one, which indicates a realistic glass structure model. We investigated the short- and medium-range TeO2 glass structures. The local environment of the Te atom strongly varies, so that the glass structure model has a broad Q polyhedral distribution. The glass network is described as weakly connected with a large number of terminal oxygen atoms. PMID:24905883

Gulenko, Anastasia; Masson, Olivier; Berghout, Abid; Hamani, David; Thomas, Philippe

2014-07-21

19

The electrostatic properties of lipid membranes are of profound importance as they are directly associated with membrane potential and, consequently, with numerous membrane-mediated biological phenomena. Here we address a number of methodological issues related to the computation of the electrostatic potential from atomic-scale molecular dynamics simulations of lipid bilayers. We discuss two slightly different forms of Poisson equation that are normally used to calculate the membrane potential: (i) a classical form when the potential and the electric field are chosen to be zero on one of the sides of a simulation box and (ii) an alternative form, when the potential is set to be the same on the opposite sides of a simulation box. Both forms differ by a position-dependent correction term, which has been shown to be proportional to the overall dipole moment of a bilayer system (for neutral systems). For symmetric bilayers we demonstrate that both approaches give essentially the same potential profiles, provided that simulations are long enough (a production run of at least 100 ns is required) and that fluctuations of the center of mass of a bilayer are properly accounted for. In contrast, for asymmetric lipid bilayers, the second approach is no longer appropriate due to a nonzero net dipole moment across a simulation box with a single asymmetric bilayer. We demonstrate that in this case the electrostatic potential can adequately be described by the classical form of Poisson equation, provided that it is employed in conjunction with tin-foil boundary conditions, which exactly balance a nonzero surface charge of a periodically replicated multibilayer system. Furthermore, we show that vacuum boundary conditions give qualitatively similar potential profiles for asymmetric lipid bilayers as compared to the conventional periodic boundaries, but accurate determination of the transmembrane potential difference is then hindered due to detachment of some water dipoles from bulk aqueous solution to vacuum. PMID:19508106

Gurtovenko, Andrey A; Vattulainen, Ilpo

2009-06-01

20

NASA Astrophysics Data System (ADS)

An application of combined molecular dynamics method which uses classical mechanics equations and quantum-mechanical potential (which is calulated on each time step) to describe atom-atomic interactions to investigation in shock induced chemical reactions in energetic materials has been considered. Semiempirical quantum chemistry computer code MOPAC has bee used to calculate energy surface. Calculations have been carried out on the example of nitromethane molecules system containing several molecules. In this approach the system of molecules is considered as one supermolecule. The processes of energy pumping into internal degrees of freedom and dependence of these processes upon mutual orientation of the molecules have been investigated. The special features of dissociation reactions undergoing at various mutual orientations and effect of neighbor molecules have also been explored. This makes the results of calculation useful for understanding the reaction mechanisms in condensed matter.

Dremov, Vladimir; Vorob'eva, Marina

1999-06-01

21

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

22

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

2012-05-01

23

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

24

Molecular Dynamics Demonstration Model

NSDL National Science Digital Library

The EJS Molecular Dynamics Demonstration 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. Users can select various initial configurations using the drop down menu. Ejs Molecular Dynamics Demonstration 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 js_stp_md_MolecularDynamicsDemo.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 statistical mechanics are available. They can be found by searching ComPADRE for Open Source Physics, OSP, or Ejs.

Christian, Wolfgang

2008-11-15

25

Implementing molecular dynamics on hybrid high performance computers—Three-body potentials

NASA Astrophysics Data System (ADS)

The use of coprocessors or accelerators such as graphics processing units (GPUs) has become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid high-performance computers, defined as machines with nodes containing more than one type of floating-point processor (e.g. CPU and GPU), are now becoming more prevalent due to these advantages. Although there has been extensive research into methods to use accelerators efficiently to improve the performance of molecular dynamics (MD) codes employing pairwise potential energy models, little is reported in the literature for models that include many-body effects. 3-body terms are required for many popular potentials such as MEAM, Tersoff, REBO, AIREBO, Stillinger-Weber, Bond-Order Potentials, and others. Because the per-atom simulation times are much higher for models incorporating 3-body terms, there is a clear need for efficient algorithms usable on hybrid high performance computers. Here, we report a shared-memory force-decomposition for 3-body potentials that avoids memory conflicts to allow for a deterministic code with substantial performance improvements on hybrid machines. We describe modifications necessary for use in distributed memory MD codes and show results for the simulation of water with Stillinger-Weber on the hybrid Titan supercomputer. We compare performance of the 3-body model to the SPC/E water model when using accelerators. Finally, we demonstrate that our approach can attain a speedup of 5.1 with acceleration on Titan for production simulations to study water droplet freezing on a surface.

Brown, W. Michael; Yamada, Masako

2013-12-01

26

Implementing Molecular Dynamics on Hybrid High Performance Computers - Three-Body Potentials

The use of coprocessors or accelerators such as graphics processing units (GPUs) has become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power re- quirements. Hybrid high-performance computers, defined as machines with nodes containing more than one type of floating-point processor (e.g. CPU and GPU), are now becoming more prevalent due to these advantages. Although there has been extensive research into methods to efficiently use accelerators to improve the performance of molecular dynamics (MD) employing pairwise potential energy models, little is reported in the literature for models that include many-body effects. 3-body terms are required for many popular potentials such as MEAM, Tersoff, REBO, AIREBO, Stillinger-Weber, Bond-Order Potentials, and others. Because the per-atom simulation times are much higher for models incorporating 3-body terms, there is a clear need for efficient algo- rithms usable on hybrid high performance computers. Here, we report a shared-memory force-decomposition for 3-body potentials that avoids memory conflicts to allow for a deterministic code with substantial performance improvements on hybrid machines. We describe modifications necessary for use in distributed memory MD codes and show results for the simulation of water with Stillinger-Weber on the hybrid Titan supercomputer. We compare performance of the 3-body model to the SPC/E water model when using accelerators. Finally, we demonstrate that our approach can attain a speedup of 5.1 with acceleration on Titan for production simulations to study water droplet freezing on a surface.

Brown, W Michael [ORNL] [ORNL; Yamada, Masako [GE Global Research] [GE Global Research

2013-01-01

27

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations of heat transfer in gases are computationally expensive when the wall molecules are explicitly modeled. To save computational time, an implicit boundary function is often used. Steele's potential has been used in studies of fluid-solid interface for a long time. In this work, the conceptual idea of Steele's potential was extended in order to simulate water-silicon and water-silica interfaces. A new wall potential model is developed by using the electronegativity-equalization method (EEM), a ReaxFF empirical force field and a non-reactive molecular dynamics package PumMa. Contact angle simulations were performed in order to validate the wall potential model. Contact angle simulations with the resulting tabulated wall potentials gave a silicon-water contact angle of 129°, a quartz-water contact angle of 0°, and a cristobalite-water contact angle of 40°, which are in reasonable agreement with experimental values.

Kim, Junghan; Iype, Eldhose; Frijns, Arjan J. H.; Nedea, Silvia V.; van Steenhoven, Anton A.

2014-07-01

28

Molecular Dynamics Studies of Dislocations in CdTe Crystals from a New Bond Order Potential

Cd1-xZnxTe (CZT) crystals are the leading semiconductors for radiation detection, but their application is limited by the high cost of detector-grade materials. High crystal costs primarily result from property nonuniformity that causes low manufacturing yield. Although tremendous efforts have been made in the past to reduce Te inclusions/precipitates in CZT, this has not resulted in an anticipated improvement in material property uniformity. Moreover, it is recognized that in addition to Te particles, dislocation cells can also cause electric field perturbations and the associated property nonuniformities. Further improvement of the material, therefore, requires that dislocations in CZT crystals be understood and controlled. Here, we use a recently developed CZT bond order potential to perform representative molecular dynamics simulations to study configurations, energies, and mobilities of 29 different types of possible dislocations in CdTe (i.e., x = 1) crystals. An efficient method to derive activation free energies and activation volumes of thermally activated dislocation motion will be explored. Our focus gives insight into understanding important dislocations in the material and gives guidance toward experimental efforts for improving dislocation network structures in CZT crystals.

2012-01-01

29

Parallel molecular dynamics simulations for short-ranged many-body potentials

A new method is described that permits the efficient execution of parallel molecular dynamics simulations for irregular problems with several thousands of atoms on Single-Instruction Multiple-Data computers. The approach is based on a data-parallel atomic decomposition scheme and has overall time-complexity O(N) , where N is the size of the system. The method has been implemented on a MasPar MP-1

C. F. Cornwell; L. T. Wille

2000-01-01

30

?-Hemolysin of Staphylococcus aureus is a self-assembling toxin that forms a water-filled transmembrane channel upon oligomerization in a lipid membrane. Apart from being one of the best-studied toxins of bacterial origin, ?-hemolysin is the principal component in several biotechnological applications, including systems for controlled delivery of small solutes across lipid membranes, stochastic sensors for small solutes, and an alternative to conventional technology for DNA sequencing. Through large-scale molecular dynamics simulations, we studied the permeability of the ?-hemolysin/lipid bilayer complex for water and ions. The studied system, composed of ?300,000 atoms, included one copy of the protein, a patch of a DPPC lipid bilayer, and a 1 M water solution of KCl. Monitoring the fluctuations of the pore structure revealed an asymmetric, on average, cross section of the ?-hemolysin stem. Applying external electrostatic fields produced a transmembrane ionic current; repeating simulations at several voltage biases yielded a current/voltage curve of ?-hemolysin and a set of electrostatic potential maps. The selectivity of ?-hemolysin to Cl? was found to depend on the direction and the magnitude of the applied voltage bias. The results of our simulations are in excellent quantitative agreement with available experimental data. Analyzing trajectories of all water molecule, we computed the ?-hemolysin's osmotic permeability for water as well as its electroosmotic effect, and characterized the permeability of its seven side channels. The side channels were found to connect seven His-144 residues surrounding the stem of the protein to the bulk solution; the protonation of these residues was observed to affect the ion conductance, suggesting the seven His-144 to comprise the pH sensor that gates conductance of the ?-hemolysin channel.

Aksimentiev, Aleksij; Schulten, Klaus

2005-01-01

31

NASA Astrophysics Data System (ADS)

Path integral molecular dynamics simulations for the H6+ and D6+ cluster cations have been carried out in order to understand the floppy nature of their molecular structure due to quantum-mechanical fluctuation. A full-dimensional analytical potential energy surface for the ground electronic state of H6+ has been developed on the basis of accurate ab initio electronic structure calculations at the CCSD(T)/cc-pVTZ level. It is found that the outer H 2(D 2) nuclei rotate almost freely and that the probability density distributions of the central H 2(D 2) nuclei show strong spatial delocalization.

Kakizaki, Akira; Takayanagi, Toshiyuki; Shiga, Motoyuki

2007-11-01

32

Molecular-dynamics study of 2-D melting: long-range potentials

Melting of a two-dimensional electron lattice and a two-dimensional dipolar solid are studied using molecular-dynamics techniques. The existence of hysteresis and latent heat of melting are observed, and the melting transitions in the two cases are found to be first order. For an electron lattice the melting occurs between GAMMA=129 +- 3 whereas in the dipolar solid it is between GAMMA=62 +- 3, with a transition entropy of 0.3 k/sub B/ per particle for both the systems.

Kalia, R.K.; Vashishta, P.

1981-01-01

33

Anisotropic interactions of liquid CD{sub 4} are studied in detail by comparison of inelastic neutron Brillouin scattering data with molecular dynamics simulations using up to four different models of the methane site-site potential. We demonstrate that the experimental dynamic structure factor S(Q,{omega}) acts as a highly discriminating quantity for possible interaction schemes. In particular, the Q evolution of the spectra enables a selective probing of the short- and medium-range features of the anisotropic potentials. We show that the preferential configuration of methane dimers at liquid densities can thus be discerned by analyzing the orientation-dependent model potential curves, in light of the experimental and simulation results.

Guarini, E.; Barocchi, F. [Dipartimento di Fisica, Universita di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino (Italy); CNR-INFM CRS-Soft c/o Dipartimento di Fisica, Universita di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino (Italy); Sampoli, M. [Dipartimento di Energetica, Universita di Firenze, via S. Marta 3, I-50139 Firenze (Italy); CNR-INFM CRS-Soft c/o Dipartimento di Fisica, Universita di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino (Italy); Venturi, G. [CNR-INFM CRS-Soft c/o Dipartimento di Fisica, Universita di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino (Italy); Bafile, U. [Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, via Madonna del Piano 10, I-50019 Sesto Fiorentino (Italy)

2007-10-19

34

Equilibrium Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Molecular dynamics (MD) is a widely used atomistic simulation method due to the detailed information it can provide, often with a relatively small computational investment. The most distinguishing attribute of MD among molecular simulation methods is that it provides a means to monitor the time evolution of a system of particles (usually atoms) in phase space, thus allowing for an atomic-level view of the dynamics of a material in a given equilibrium or nonequilibrium thermodynamic state. This is particularly appealing for those in the energetic materials (EM) community since such a detailed description could reveal the fundamental mechanisms controlling the initiation of an energetic material to detonation, a phenomenon for which direct experimental measurement is in short Superscriptply due to the small time and spatial scales involved and the accompanying large rates of chemical energy release. MD is not affected by any of these factors; rather, its main limitations are the description of interatomic interactions (potential energy functions) used in the simulations and the viability of using classical mechanics to study molecular-scale phenomena. MD is receiving increased use in condensed-phase EM research as interaction potentials emerge that "realistically" describe the chemistry associated with initiation of an EM. However, MD is not limited to studying nonequilibrium dynamic events only; it has proven to be extremely useful for predicting thermodynamic equilibrium properties in the condensed phase.

Rice, Betsy M.; Sewell, Thomas D.

35

NASA Astrophysics Data System (ADS)

We present the first molecular-dynamics study of the amorphization of a crystalline alloy (NiZr2) induced by chemical disorder. We used a n-body potential in conjunction with isobaric-isothermal molecular dynamics. The behavior of the pair distribution function suggests that the instability leading to the amorphous state is a first-order phase transformation.

Massobrio, C.; Pontikis, V.; Martin, G.

1989-03-01

36

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

37

NASA Astrophysics Data System (ADS)

Because the geodesic pathways that a liquid follows through its potential energy landscape govern its slow, diffusive motion, we suggest that these pathways are logical candidates for the title of a liquid's "inherent dynamics." Like their namesake "inherent structures," these objects are simply features of the system's potential energy surface and thus provide views of the system's structural evolution unobstructed by thermal kinetic energy. This paper shows how these geodesic pathways can be computed for a liquid of linear molecules, allowing us to see precisely how such molecular liquids mix rotational and translational degrees of freedom into their dynamics. The ratio of translational to rotational components of the geodesic path lengths, for example, is significantly larger than would be expected on equipartition grounds, with a value that scales with the molecular aspect ratio. These and other features of the geodesics are consistent with a picture in which molecular reorientation adiabatically follows translation—molecules largely thread their way through narrow channels available in the potential energy landscape.

Jacobson, Daniel; Stratt, Richard M.

2014-05-01

38

Homology modeling of G protein-coupled receptors is becoming a widely used tool in drug discovery. However, unrefined models built using the bovine rhodopsin crystal structure as the template, often have binding sites that are too small to accommodate known ligands. Here, we present a novel systematic method to refine model active sites based on a pressure-guided molecular dynamics simulation. A distinct advantage of this approach is the ability to introduce systematic perturbations in model backbone atoms in addition to side chain adjustments. The method is validated on two test cases: (1) docking of retinal into an MD-relaxed structure of opsin and (2) docking of known ligands into a homology model of the CCR2 receptor. In both cases, we show that the MD expansion algorithm makes it possible to dock the ligands in poses that agree with the crystal structure or mutagenesis data. PMID:18175323

Kimura, S Roy; Tebben, Andrew J; Langley, David R

2008-06-01

39

We study a calcium aluminosilicate glass of composition (SiO2)0.60(Al2O3)0.10(CaO)0.30 by means of molecular dynamics. To this end, we conduct parallel simulations, following a consistent methodology, but using three different potentials. Structural and elastic properties are analyzed and compared to available experimental data. This allows assessing the respective abilities of the potentials to produce a realistic glass. We report that, although all these potentials offer a reasonable glass structure, featuring tricluster oxygen atoms, their respective vibrational and elastic predictions differ. This allows us to draw some general conclusions about the crucial role, or otherwise, of the interaction potential in silicate systems. PMID:25028027

Bauchy, M

2014-07-14

40

NASA Astrophysics Data System (ADS)

The primary state of damage obtained in molecular dynamics (MD) simulations of displacement cascades in ?-Fe, particularly the fraction of point-defects in clusters, depends on the interatomic potential used to describe the atomic interactions. The differences may influence the microstructural evolution predicted in damage accumulation models which use results from MD cascade simulations as input. In this work, a number of displacement cascades of energy ranging from 5 to 40 keV have been simulated using the same procedure with four different interatomic potentials for ?-Fe, each of them providing, among other things, varying descriptions of self-interstitial atoms (SIA) in this metal. The behaviour of the cascades at their different phases and the final surviving defect population have been studied and compared applying the same cascade analysis criteria for all potentials. The outcome is discussed trying to identify the characteristics of the potential that have the largest influence on the predicted primary state of damage.

Terentyev, D.; Lagerstedt, C.; Olsson, P.; Nordlund, K.; Wallenius, J.; Becquart, C. S.; Malerba, L.

2006-06-01

41

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

2013-03-13

42

The folding process of the 20 residue Trp-cage mini-protein was investigated using standard temperature replica exchange molecular dynamics (T-RexMD) simulation and a biasing potential RexMD (BP-RexMD) method. In contrast to several conventional molecular dynamics simulations, both RexMD methods sampled conformations close to the native structure after 10–20 ns simulation time as the dominant conformational states. In contrast, to T-RexMD involving 16 replicas the BP-RexMD method achieved very similar sampling results with only five replicas. The result indicates that the BP-RexMD method is well suited to study folding processes of proteins at a significantly smaller computational cost, compared to T-RexMD. Both RexMD methods sampled not only similar final states but also agreed on the sampling of intermediate conformations during Trp-cage folding. The analysis of the sampled potential energy contributions indicated that Trp-cage folding is favored by both van der Waals and to a lesser degree electrostatic contributions. Folding does not introduce any significant sterical strain as reflected by similar energy distributions of bonded energy terms (bond length, bond angle and dihedral angle) of folded and unfolded Trp-cage structures.

Kannan, Srinivasaraghavan; Zacharias, Martin

2009-01-01

43

NASA Astrophysics Data System (ADS)

A charge-optimized many-body (COMB) potential is proposed for the zirconium-zirconium oxide-zirconium hydride system. This potential is developed to describe the energetics of the interactions of oxygen and hydrogen with zirconium metal. We perform classical molecular dynamics simulations showing the initial corrosion behavior of three low-index zirconium surfaces via the deposition of O2 and H2O molecules. The basal (0 0 0 1) surface shows greater resistance to oxygen diffusion than the prism (1 0 1bar 0) and (1 1 2bar 0) surfaces. We suggest ways in which the surface structure has a unique role in the experimentally observed enhanced corrosion of the prism surfaces.

Noordhoek, Mark J.; Liang, Tao; Chiang, Tsu-Wu; Sinnott, Susan B.; Phillpot, Simon R.

2014-09-01

44

NASA Astrophysics Data System (ADS)

A new pair-potential energy function of ammonia has been determined via the inversion of reduced viscosity collision integrals and fitted to obtain a Hartree-Fock dispersion (HFD)-like potential form. The pair-potential reproduces the second virial coefficient, viscosity, thermal conductivity, and self-diffusion coefficient of ammonia in a good accordance with experimental data over wide ranges of temperatures. Molecular dynamics (MD) simulation has been also performed to obtain pressure, self-diffusion coefficient, and radial distribution function of fluid ammonia at different temperatures and densities using the calculated HFD-like pair-potential. To take higher-body forces into account, three-body potential of Hauschild and Prausnitz (1993) [19] extended as a function of density and temperature and used with the HFD-like potential to improve the prediction of the pressures of fluid ammonia without requiring an expensive three-body calculation. The results are in a good agreement with experiment and literature values.

Abbaspour, Mohsen

2011-11-01

45

In this work, using extensive molecular dynamics simulations of several thermophysical properties, it is proposed to analyze possible relationships (in the corresponding state sense) between monoatomic fluids for which the repulsive interactions are modeled by an inverse n-power form, the Lennard-Jones 12-6 (LJ), or by an exponential one, the exponential-6 (Exp-6). To compare results between them, two possible definitions of Exp-6 potentials "equivalent" to the LJ one are proposed. In pure fluids, for a large range of thermodynamic conditions, the properties computed are the surface tension, liquid/vapor equilibrium densities, one-phase potential energy, pressure, isometric heat capacity, thermal pressure coefficient, self-diffusion, shear viscosity, and thermal conductivity. Additionally, thermodiffusion (Soret effect) has been considered in "isotopic" equimolar mixtures. It is shown that despite similarities exhibited by alike radial distribution functions, differences exist between the thermodynamic properties values provided by the LJ fluid and the two equivalent Exp-6 fluids. Nevertheless, quite surprisingly, when temperature and density are used as inputs, all three direct transport properties are shown to be nearly independent of the choice of the potential tested. Unexpectedly, these similarities hold even for thermodiffusion which is a priori very sensitive to the nature of the interactions. These results indicate that the use of an Exp-6 potential form to describe nonbonded/nonpolar interaction in molecular simulation is an alternative (more physically acceptable) to the LJ potential when dealing simultaneously with thermodynamic and transport properties. However, when only transport properties are considered (including thermodiffusion), the Exp-6 potential form should not lead to any differences compared to the LJ one. PMID:19044782

Galliero, Guillaume; Boned, Christian

2008-08-21

46

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.

Junko Habasaki; Yasuaki Hiwatari

2004-01-01

47

NASA Astrophysics Data System (ADS)

Mechanism of heat conduction in copper-argon nanofluids is studied by molecular dynamics simulation and the thermal conductivity was obtained using the Green-Kubo method. While the interatomic potential between argon atoms is described using the well-known Lennard-Jones (L-J) potential, a more accurate embedded atom method (EAM) potential is used in describing the interatomic interaction between copper atoms. It is found that the heat current autocorrelation function obtained using L-J potential to describe the copper-copper interatomic interaction fluctuates periodically due to periodic oscillation of the instantaneous microscopic heat fluxes. Thermal conductivities of nanofluids using EAM potentials were calculated with different volume fractions but the same nanoparticle size. The results show that thermal conductivity of nanofluids are almost a linear function of the volume fraction and slightly higher than the results predicted by the conventional effective media theory for a well-dispersed solution. A solid-like base fluid liquid layer with a thickness of 0.6 nm was found in the simulation and this layer is believed to account for the small discrepancy between the results of MD simulation and the conventional effective media theory.

Kang, Hongbo; Zhang, Yuwen; Yang, Mo

2011-06-01

48

Molecular Dynamics Replicated Data Model

NSDL National Science Digital Library

The Molecular Dynamics Replicated Data Model implements a parallel computer program 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

49

NASA Astrophysics Data System (ADS)

Room temperature absorption spectra of various transitions of pure CO2 have been measured in a broad pressure range using a tunable diode-laser and a cavity ring-down spectrometer, respectively, in the 1.6 ?m and 0.8 ?m regions. Their spectral shapes have been calculated by requantized classical molecular dynamics simulations. From the time-dependent auto-correlation function of the molecular dipole, including Doppler and collisional effects, spectral shapes are directly computed without the use of any adjusted parameter. Analysis of the spectra calculated using three different anisotropic intermolecular potentials shows that the shapes of pure CO2 lines, in terms of both the Lorentz widths and non-Voigt effects, slightly depend on the used potential. Comparisons between these ab initio calculations and the measured spectra show satisfactory agreement for all considered transitions (from J = 6 to J = 46). They also show that non-Voigt effects on the shape of CO2 transitions are almost independent of the rotational quantum number of the considered lines.

Larcher, G.; Tran, H.; Schwell, M.; Chelin, P.; Landsheere, X.; Hartmann, J.-M.; Hu, S.-M.

2014-02-01

50

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

51

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

52

NASA Astrophysics Data System (ADS)

Density Functional Theory calculations and Molecular Dynamics with a recently developed potential for W-He were used to evaluate the thermal stability of helium-vacancy clusters (nHe.mv) as well as pure interstitial helium clusters in tungsten. The stability of such objects results from a competitive process between thermal emission of vacancies, self interstitial atoms (SIAs) and helium, depending on the helium-to-vacancy ratio in mixed clusters or helium number in pure interstitial helium clusters. We investigated in particular the thermodynamics and kinetics of self trapping and trap mutation, i.e. the emission of one SIA along with the creation of one vacancy from a vacancy-helium or pure helium object.

Boisse, J.; Domain, C.; Becquart, C. S.

2014-12-01

53

In this chapter, an introduction to ab initio molecular dynamics (AIMD) has been given. Many of the basic concepts, like the Hellman-Feynman forces, the difference between the Car-Parrinello molecular dynamics and AIMD, have been explained. Also a very versatile AIMD code, the CP2K, has been introduced. On the application, the emphasis was on the aqueous systems and chemical reactions. The biochemical applications have not been discussed in depth. PMID:23034744

Laasonen, Kari

2013-01-01

54

NASA Astrophysics Data System (ADS)

Based on the approach of Gruhn and Monson [Phys. Rev. E 63, 061106 (2001)], we present a new method for deriving the collisions dynamics for particles that interact via discontinuous potentials. By invoking the conservation of the extended Hamiltonian, we generate molecular dynamics (MD) algorithms for simulating the hard-sphere and square-well fluids within the isothermal-isobaric (NpT) ensemble. Consistent with the recent rigorous reformulation of the NpT ensemble partition function, the equations of motion impose a constant external pressure via the introduction of a shell particle of known mass [M. J. Uline and D. S. Corti, J. Chem. Phys. 123, 164101 (2005); 123, 164102 (2005)], which serves to define uniquely the volume of the system. The particles are also connected to a temperature reservoir through the use of a chain of Nosé-Hoover thermostats, the properties of which are not affected by a hard-sphere or square-well collision. By using the Liouville operator formalism and the Trotter expansion theorem to integrate the equations of motion, the update of the thermostat variables can be decoupled from the update of the positions of the particles and the momentum changes upon a collision. Hence, once the appropriate collision dynamics for the isobaric-isenthalpic (NpH) equations of motion is known, the adaptation of the algorithm to the NpT ensemble is straightforward. Results of MD simulations for the pure component square-well fluid are presented and serve to validate our algorithm. Finally, since the mass of the shell particle is known, the system itself, and not a piston of arbitrary mass, controls the time scales for internal pressure and volume fluctuations. We therefore consider the influence of the shell particle algorithm on the dynamics of the square-well fluid.

Uline, Mark J.; Corti, David S.

2008-07-01

55

Based on the approach of Gruhn and Monson [Phys. Rev. E 63, 061106 (2001)], we present a new method for deriving the collisions dynamics for particles that interact via discontinuous potentials. By invoking the conservation of the extended Hamiltonian, we generate molecular dynamics (MD) algorithms for simulating the hard-sphere and square-well fluids within the isothermal-isobaric (NpT) ensemble. Consistent with the recent rigorous reformulation of the NpT ensemble partition function, the equations of motion impose a constant external pressure via the introduction of a shell particle of known mass [M. J. Uline and D. S. Corti, J. Chem. Phys. 123, 164101 (2005); 123, 164102 (2005)], which serves to define uniquely the volume of the system. The particles are also connected to a temperature reservoir through the use of a chain of Nose-Hoover thermostats, the properties of which are not affected by a hard-sphere or square-well collision. By using the Liouville operator formalism and the Trotter expansion theorem to integrate the equations of motion, the update of the thermostat variables can be decoupled from the update of the positions of the particles and the momentum changes upon a collision. Hence, once the appropriate collision dynamics for the isobaric-isenthalpic (NpH) equations of motion is known, the adaptation of the algorithm to the NpT ensemble is straightforward. Results of MD simulations for the pure component square-well fluid are presented and serve to validate our algorithm. Finally, since the mass of the shell particle is known, the system itself, and not a piston of arbitrary mass, controls the time scales for internal pressure and volume fluctuations. We therefore consider the influence of the shell particle algorithm on the dynamics of the square-well fluid. PMID:18624470

Uline, Mark J; Corti, David S

2008-07-01

56

We have studied portability, efficiency and accuracy of a standard Molecular Dynamics simulation on the SIMD parallel computer APE100. Computing speed performance and physical system size range have been analyzed and compared with those of a conventional computer. Short range and long range potentials have been considered, and the comparative advantage of different simulation approaches has been assessed. For long

Luciano Maria Barone; Riccardo Simonazzi; Alexander Tenenbaum

1995-01-01

57

An advanced implicit solvent model of water-proton bath for protein simulations at constant pH is presented. The implicit water-proton bath model approximates the potential of mean force of a protein in water solvent in a presence of hydrogen ions. Accurate and fast computational implementation of the implicit water-proton bath model is developed using the continuum electrostatic Poisson equation model for calculation of ionization equilibrium and the corrected MSR6 generalized Born model for calculation of the electrostatic atom-atom interactions and forces. Molecular dynamics (MD) method for protein simulation in the potential of mean force of water-proton bath is developed and tested on three proteins. The model allows to run MD simulations of proteins at constant pH, to calculate pH-dependent properties and free energies of protein conformations. The obtained results indicate that the developed implicit model of water-proton bath provides an efficient way to study thermodynamics of biomolecular systems as a function of pH, pH-dependent ionization-conformation coupling, and proton transfer events. PMID:22278814

Vorobjev, Yury N

2012-03-30

58

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

59

NASA Astrophysics Data System (ADS)

We have investigated the size dependence of a nano-cavity properties produced in a Xe fluid using molecular dynamics simulations. We have created a nano-cavity of different sizes at 170 and 200 K (cavities diameters are within 1-10 nm). Liquid pressure, vapor pressure and surface tension of the nano-cavity for some given values of diameter are calculated. Within 1-10 nm cavity diameter, we have observed two opposite behavior for dependency of surface tension on the cavity diameter: for the range of 1-5 nm, it increases with the diameter, while, for the range of 5-10 nm remains constant. Also, the value of liquid pressure becomes less negative, when the size of cavity increases. Vapor pressure in the cavity was found to be independent of cavity size. In this paper, we have also studied the effects of Lennard-Jones potential parameters on the surface tension (while temperature and cavity radius are held constant).

Akbarzadeh, Hamed; Abroshan, Hadi; Taherkhani, Farid; Izanloo, Cobra; Parsafar, Gholam Abbas

2011-03-01

60

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

61

NASA Astrophysics Data System (ADS)

Previously we demonstrated the effectiveness of the recently developed q-jumping molecular dynamics simulation method (q-jumping MD) in vacuo for fast conformational searches and optimization purposes. In this work we attempt to further investigate the conformational searching capability of this new scheme by applying it to folding problems of helical peptides containing fully charged side chains in an implicit water. With a slightly modified q-jumping MD method using the all-atom empirical force field and its generalized Born solvation model, the current simulations at T=300 K all lead to fast helix folding with broad potential energy fluctuations, starting from their extended (linear) conformations. The present study demonstrates that this new MD scheme greatly enhances the rate of conformational changes, making it possible to explore low energy conformations of peptides in aqueous environments in a reasonably short time. Therefore, the all-atom based theoretical prediction of native solution structures of more challenging systems, such as helix bundles, ?-sheets, and even small proteins may be a realistic possibility.

Pak, Youngshang; Jang, Soonmin; Shin, Seokmin

2002-04-01

62

A molecular dynamics calculation on aqueous solution of urea has been carried out using constant temperature technique. The total number of molecules was 216, one of which was urea and the temperature was set to 298.15 K and an experimental value was used for the density. For water–water interaction, the MCY (Matsuoka–Clementi–Yoshimine) potential was used, whereas a new potential function

Hideki Tanaka; Hidekazu Touhara; Koichiro Nakanishi; Nobuatsu Watanabe

1984-01-01

63

Lattice Molecular Dynamics: Extending the Scale of Molecular Dynamics

Presented is a lattice molecular dynamics technique for extending the spatial and temporal scales achieved with standard molecular dynamics modelling techniques. In the lattice molecular dyanamics, particle momenta and positions are discrete. Particle dynamics described by a general Hamiltonian are carried out in a fashion that obeys semi-detailed balance. Furthermore, all additive conserved quantities, mass, momentum, and energy, are exactly

Jeffrey Yepez

1996-01-01

64

NSDL National Science Digital Library

The NVT-Molecular Dynamics Model performs molecular dynamics simulations at constant temperature of 32, 108, 256 or 500 molecules interacting through the Lennard-Jones potential, in a wide range of densities and temperatures covering liquid, vapor and solid states. Thermodynamic properties, radial and speed distribution functions, velocity autocorrelation functions (vcf's) and their Fourier spectra, and mean square displacements (msd's) are calculated and displayed. Self-diffusion coefficients are worked out from the vcf's and msd's. Self space-time correlation functions (sstcf's) are estimated and compared with the Gaussian approximation. The 3D molecular motions can also be visualized. The motion equations are integrated by two methods, at user's choice: the damped-force with leap-frog Verlet's algorithm, and the "ad-hoc" rescaling with the velocity Verlet algorithm. The model allows to assess the role of the potential cut-off distance, the number of steps in equilibration runs, the time-step and the gap between time origins for vcf's, msd's and sstcf's. The NVT-Molecular Dynamics Model was developed using the Easy Java Simulations (EJS) modeling tool. It is distributed as a ready-to-run (compiled) Java archive. Double clicking the jar file will run the program if Java is installed. You can modify this simulation if you have EJS installed by right-clicking within the map and selecting "Open Ejs Model" from the pop-up menu item.

Fernandes, Fernando S.; Freitas, Filomena; Christian, Wolfgang

2013-05-19

65

Molecular dynamics simulations

NASA Astrophysics Data System (ADS)

A tutorial introduction to the technique of molecular dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is discussed, and the basic MD algorithms are described. The sampling of intensive variables (temperature T, pressure p) in runs carried out in the microcanonical (NV E) ensemble (N = particle number, V = volume, E = energy) is discussed, as well as the realization of other ensembles (e.g. the NV T ensemble). For a typical application example, molten SiO2, the estimation of various transport coefficients (self-diffusion constants, viscosity, thermal conductivity) is discussed. As an example of non-equilibrium molecular dynamics, a study of a glass-forming polymer melt under shear is mentioned.

Binder, Kurt; Horbach, Jürgen; Kob, Walter; Paul, Wolfgang; Varnik, Fathollah

2004-02-01

66

Evaluating the Force Matrix constitutes the most computationally intensive part of a Classical Molecular Dynamics (MD) simulation. In three-body MD simulations, the total energy of the system is determined by the energy of every unique triple in the system and the force matrix is three-dimensional. The execution time of a three-body MD algorithm is thus proportional to the cube of

J. V. Sumanth; David R. Swanson; Hong Jiang

2007-01-01

67

Ab initio molecular dynamics study of the potential energy surface for the CH 3 Cl+F ? reaction

The non-minimum energy profile of the reaction CH3Cl+F? has been studied byab initio molecular dynamics. In the framework of the Car Parrinello method both statistical and impact trajectory studies have been\\u000a carried out. Out of the C3v\\u000a symmetry axis a hydrogen bonded structure has been identified and characterized evaluating the charge transfer by Natural\\u000a Population Analysis and Atom In Molecules

Martina Mugnai; Gianni Cardini; Vincenzo Schettino

2004-01-01

68

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

69

NAMD Scalable Molecular Dynamics

NSDL National Science Digital Library

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using switched fast ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms.

70

Molecular Dynamics of Acetylcholinesterase

Molecular dynamics simulations are leading to a deeper understanding of the activity of the enzyme acetylcholinesterase. Simulations have shown how breathing motions in the enzyme facilitate the displacement of substrate from the surface of the enzyme to the buried active site. The most recent work points to the complex and spatially extensive nature of such motions and suggests possible modes of regulation of the activity of the enzyme.

Shen, T Y.; Tai, Kaihsu; Henchman, Richard H.; Mccammon, Andy

2002-06-01

71

Molecular electrostatic potentials by systematic molecular fragmentation

NASA Astrophysics Data System (ADS)

A simple method is presented for estimating the molecular electrostatic potential in and around molecules using systematic molecular fragmentation. This approach estimates the potential directly from the electron density. The accuracy of the method is established for a set of organic molecules and ions. The utility of the approach is demonstrated by estimating the binding energy of a water molecule in an internal cavity in the protein ubiquitin.

Reid, David M.; Collins, Michael A.

2013-11-01

72

Protein farnesyltransferase (FTase) is an important target in many research fields, more markedly so in cancer investigation since several proteins known to be involved in human cancer development are thought to serve as substrates for FTase and to require farnesylation for proper biological activity. Several FTase inhibitors (FTIs) have advanced into clinical testing. Nevertheless, despite the progress in the field several functional and mechanistic doubts on the FTase catalytic activity have persisted. This work provides some crucial information on this important enzyme by describing the application of molecular dynamics simulations using specifically designed molecular mechanical parameters for a variety of 22 CaaX peptides known to work as natural substrates or inhibitors for this enzyme. The study involves a comparative analysis of several important molecular aspects, at the mechanistic level, of the behavior of substrates and inhibitors at the dynamic level, including the behavior of the enzyme and peptides, as well as their interaction, together with the effect of the solvent. Properties evaluated include the radial distribution function of the water molecules around the catalytically important zinc metal atom and cysteine sulfur of CaaX, the conformations of the substrate and inhibitor and the corresponding RMSF values, critical hydrogen bonds, and several catalytically relevant distances. These results are discussed in light of recent experimental and computational evidence that provides new insights into the activity of this enzyme. PMID:23011608

Sousa, Sérgio F; Coimbra, João T S; Paramos, Diogo; Pinto, Rita; Guimarães, Rodrigo S; Teixeira, Vitor; Fernandes, Pedro A; Ramos, Maria J

2013-02-01

73

Statistical properties of fermionic molecular dynamics.

National Technical Information Service (NTIS)

Statistical properties of Fermionic Molecular Dynamics are studied. It is shown that, although the centroids of the single-particle wave-packets follow classical trajectories in the case of a harmonic oscillator potential, the equilibrium properties of th...

J. Schnack H. Feldmeier

1995-01-01

74

Aqueous solutions of a light (Nd3+), a middle (Gd3+), and a heavy (Yb3+) lanthanide ion were studied using ab initio based flexible and polarizable analytical potentials in classical molecular dynamics simulations to describe their thermodynamic, structural, and dynamic features. To avoid the spurious demise of O-H bonds, it was necessary to reparametrize an existing water model, which resulted in an improved description of pure water. The good agreement of the results from the simulations with the experimental hydration enthalpies, the Ln(III)-water radial distribution functions, and the water-exchange rates validated the potentials, though the r(Ln-Ow) distances were 6% longer than the experimentally determined values. A nona-coordinated state was found for Nd3+ in 95% of the simulation, with a tricapped trigonal prism (TCTP) geometry; the corresponding water-exchange mechanism was found to be of dissociative interchange (Id) character through a short-lived octa-coordinated transition state in a square antiprism (SQA) geometry. An octa-coordinated state in SQA geometry was found for Yb3+ in 99% of the simulation, and the observed exchange events exhibited characteristics of an interchange (I) mechanism. For Gd3+ an equilibrium was observed between 8-fold SQA and 9-fold TCTP coordinated states that was maintained by the frequent exchange of a water molecule from the first hydration shell with the bulk, thus producing significant deviations from the ideal geometries, and a fast exchange rate. Though strong water-water interactions prevented a full alignment of the dipoles to the ion's electric field, the screening was found large enough as to limit its range to 5 A; water molecules further apart from the ion were found to have the same dipole as the molecules in the bulk, and a random orientation. The interplay among the water-ion and the water-water interactions determined the different coordination numbers and the different dynamics of the water exchange in the first hydration shell for each ion. PMID:19402691

Villa, Alessandra; Hess, Berk; Saint-Martin, Humberto

2009-05-21

75

The 3D intramolecular dynamics of the N2H+ molecular ion in its electronic ground state is reported. A potential energy surface (PES) is numerically calculated by a multireference configuration interaction method. Employing this PES we calculated the bound-state eigenvalue spectrum of the N2H+ ion by applying the three-dimensional time-dependent wavepacket (WP) method for the total angular momentum J=0. The spectrum is

S. Mahapatra; R. Vetter; C. Zuhrt; H. T Nguyen; T. Ritschel; L. Zulicke

1998-01-01

76

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

77

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

78

The nonequilibrium molecular dynamics

NASA Astrophysics Data System (ADS)

Molecular dynamics is generalized in order to simulate a variety of nonequilibrium systems. This generalization was achieved by adopting microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress. Some of the problems already treated include rapid plastic deformation, intense heat conduction, strong shockwaves simulation, and far-from-equilibrium phase transformations. Continuing advances in technique and in the modeling of interatomic forces, coupled with qualitative improvements in computer hardware, are enabling such simulations to approximate real-world microscale and nanoscale experiments.

Hoover, W. G.

1992-03-01

79

Fast method for quantum mechanical molecular dynamics

NASA Astrophysics Data System (ADS)

As the processing power available for scientific computing grows, first-principles Born-Oppenheimer molecular dynamics simulations are becoming increasingly popular for the study of a wide range of problems in materials science, chemistry, and biology. Nevertheless, the computational cost of Born-Oppenheimer molecular dynamics still remains prohibitively large for many potential applications. Here we show how to avoid a major computational bottleneck: the self-consistent-field optimization prior to force calculations. The optimization-free quantum mechanical molecular dynamics method gives trajectories that are almost indistinguishable from an “exact” microcanonical Born-Oppenheimer molecular dynamics simulation even when low-prefactor linear scaling sparse matrix algebra is used. Our findings show that the computational gap between classical and quantum mechanical molecular dynamics simulations can be significantly reduced.

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

2012-11-01

80

NASA Astrophysics Data System (ADS)

Over the years, many techniques for studying molecular reaction dynamics have been developed and fine-tuned to probe chemical dynamics at an ever-increasing level of detail. Unfortunately, this progress has frequently come at the price of high experimental cost and great complexity. In this regard experiments employing direct absorption have a distinct advantage in that they are comparatively simple in setup and they probe nascent product distributions directly. Even though the low product number densities in molecular-beam experiments put severe constraints on the noise and sensitivity requirements of detectors, Nesbitt and co-workers [J. Chem. Phys. 86, 3151 (1987); Rev. Sci. Instrum. 58, 807 (1987); J. Chem. Phys. 85, 4890 (1986); J. Chem. Phys. 107, 5661 (1997); Chem. Phys. Lett. 258, 207 (1996)] have demonstrated the use of direct infrared absorption in a variety of molecular reaction dynamics studies. In analogous experiments, this article explores the use of millimeter- and submillimeter-wavelength radiation in direct absorption experiments in a molecular beam. The comparatively simple and inexpensive setup demonstrates the utility of combining new commercial solid-state millimeter/submillimeter-wavelength sources with hot-electron bolometer detectors to directly probe parent and product hyperfine rovibronic levels and their Doppler-resolved velocity distributions in a molecular beam. For example, in open-shell products with nuclear spin, the ultrahigh energy resolution of the rotational spectroscopy easily resolves nuclear quadrupole hyperfine structure and lambda doublets in both ground and excited spin-orbit states as well as in ground and excited vibrational levels. Two molecular beam examples are given: (1) detection of ``hyper-rovibronic'' structure in ClO (2??=3/2,1/2, ?=0-8, J=112-712, ?,F) following the mode-specific photodissociation of OClO (A2A2<--X2B1, ?1=14-15), and (2) coherent transient absorption of HCN following the 266 nm photodissociation of sym-triazine/argon clusters.

Duffy, Liam M.

2005-09-01

81

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

2009-03-01

82

NASA Astrophysics Data System (ADS)

We demonstrate a validation of the intermolecular pair potential model of SiH4, which is constructed from ab initio molecular-orbital calculations and expressed as the sum of the exponential and the London dispersion terms. The saturated liquid densities of SiH4 are calculated for temperatures from 100 to 225 K by molecular-dynamics (MD) simulation. The average deviation between the experiment and the MD simulation using the present potential model is 3.9%, while the deviations exceed 10% for other well-known potential models such as the five-center Lennard-Jones (LJ) model. Subsequently, the shear viscosity, the thermal conductivity, and the self-diffusion coefficient of liquid SiH4 are calculated by an equilibrium MD simulation with the Green-Kubo formula from 100 to 225 K. The average deviations from experiment are 11.8% and 13.7% for the shear viscosity and the thermal conductivity, respectively. Comparing the present model with an empirical one-center LJ model, it turns out that the rotational energy transfer through the intermolecular potential energy, which comes from the anisotropic potential energy, plays an important role in the thermal conductivity of liquid SiH4. These results indicate that the present intermolecular potential model has an ability to give realistic pictures for liquid SiH4 through molecular simulations.

Sakiyama, Yukinori; Takagi, Shu; Matsumoto, Yoichiro

2005-06-01

83

We demonstrate a validation of the intermolecular pair potential model of SiH(4), which is constructed from ab initio molecular-orbital calculations and expressed as the sum of the exponential and the London dispersion terms. The saturated liquid densities of SiH(4) are calculated for temperatures from 100 to 225 K by molecular-dynamics (MD) simulation. The average deviation between the experiment and the MD simulation using the present potential model is 3.9%, while the deviations exceed 10% for other well-known potential models such as the five-center Lennard-Jones (LJ) model. Subsequently, the shear viscosity, the thermal conductivity, and the self-diffusion coefficient of liquid SiH(4) are calculated by an equilibrium MD simulation with the Green-Kubo formula from 100 to 225 K. The average deviations from experiment are 11.8% and 13.7% for the shear viscosity and the thermal conductivity, respectively. Comparing the present model with an empirical one-center LJ model, it turns out that the rotational energy transfer through the intermolecular potential energy, which comes from the anisotropic potential energy, plays an important role in the thermal conductivity of liquid SiH(4). These results indicate that the present intermolecular potential model has an ability to give realistic pictures for liquid SiH(4) through molecular simulations. PMID:16008456

Sakiyama, Yukinori; Takagi, Shu; Matsumoto, Yoichiro

2005-06-15

84

Molecular Dynamics Calculations

NASA Technical Reports Server (NTRS)

The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two winning videos in a competition held at the meeting of the American Physical Society's Division of Fluid Dynamics, held in Atlanta, Georgia, in November 1994. Of great interest was the result that in every shock there were a few high-speed precursor particles racing ahead of the shock, carrying information about its impending arrival. Most recently, Dr. Woo has been applying molecular dynamics techniques to the problem of determining the drag produced by the space station truss structure as it flies through the thin residual atmosphere of low-Earth orbit. This problem is made difficult by the complex structure of the truss and by the extreme supersonic nature of the flow. A fully filled section of the truss has already been examined, and drag predictions have been made. Molecular dynamics techniques promise to make realistic drag calculations possible even for very complex partially filled truss segments flying at arbitrary angles.

1996-01-01

85

NASA Astrophysics Data System (ADS)

We have performed molecular dynamics (MD) simulation to obtain pressure, internal energy, radial distribution function, and self-diffusion coefficient of fluid oxygen using effective two-site Lennard-Jones (2SLJ) and two-body Hartree-Fock dispersion (HFD)-like potentials. To take higher-body forces into account, we have used three-body potentials of Hauschild and Prausnitz [T. Hauschild, J.M. Prausnitz, Molec. Simul. 11 (1993) 177] and Miyano [Y. Miyano, Fluid Phase Equilib. 104 (1995) 71] with the two-body HFD-like potential. We have also considered the spin correction in our simulation which improved our energy results. The significance of this work is that the three-body potential of Hauschild and Prausnitz extended as a function of density and temperature and can be used with the HFD-like potential to improve the prediction of the pressures of fluid oxygen without requiring an expensive three-body calculation. The molecular dynamics simulation of oxygen has been also used to determine a new equation of state.

Ghahremani, Hosein; Abbaspour, Mohsen

2010-11-01

86

NASA Astrophysics Data System (ADS)

This paper reports molecular dynamics simulations on the diffusion of sulfur hexafluoride SF6 molecules in one-dimensional zeolite ZSM-22 pores. In particular, the simulations explored the effects of the periodic boundary conditions of the ZSM-22 pores and the SF6-SF6 molecular interactions on the time (t) dependence of the mean square displacement (d) of the SF6 molecules. The simulation results clearly indicate that, with time, the molecules undergo three types of diffusions in sequence: a projectile diffusion regime with d~t2, a single-file diffusion regime with d~t0.5, and a normal diffusion regime with d~t1. The time for the transition from the single-file diffusion to the normal diffusion increases with the length of the pores. When the interaction between the SF6 molecules is sufficiently strong, there exists also a suppressed single-file (SSF) diffusion regime in between the single-file and normal diffusion regimes that is characterized by d~t? with ?<0.5. The intermolecule interaction also substantially affects the durations of the single-file diffusion and the SSF diffusion, as well as the time for the transition to the normal diffusion state. A detailed discussion is provided that compares the results from this work with those from previous simulation and experimental works.

Yang, Xiaofeng; Wu, Mingzhong; Qin, Zhangfeng; Wang, Jianguo; Wen, Tindun

2009-10-01

87

Configurational constant pressure molecular dynamics.

We propose two new algorithms for generating isothermal-isobaric molecular dynamics. The algorithms are based on an extended phase space dynamics where two extra degrees of freedom, representing the thermostat and the barostat, are included. These new methods adopt a totally different approach towards molecular dynamics simulation in the isothermal-isobaric ensemble. They are fully configurational in the sense that only the particle positions are required in the control of the system temperature and pressure. Following on from the works of Delhommelle and Evans [Mol. Phys., 99, 1825 (2001)] and of Braga and Travis [J. Chem. Phys., 123, 134101 (2005)] concerning configurational canonical dynamics, these new algorithms can be seen as a natural extension to the isothermal-isobaric ensemble. We have validated both of our new configurational isothermal-isobaric schemes by conducting molecular dynamics simulations of a Lennard-Jones fluid and comparing the static and dynamic properties for a single state point. We find that both schemes generate similar results compared with schemes which use kinetic temperature and pressure control. We have also monitored the response of the system to a series of isothermal compressions and isobaric quenches. We find that the configurational schemes performed at least as well as the kinetic based scheme in bringing the system temperature and pressure into line with the set point values of these variables. These new methods will potentially play a significant role in simulations where the calculation of the kinetic temperature and pressure can be problematic. A well known example resides in the field of nonequilibrium simulations where the kinetic temperature and pressure require a knowledge of the streaming velocity of the fluid in order to calculate the true peculiar velocities (or momenta) that enter into their definitions. These are completely avoided by using our configurational thermostats and barostats, since these are independent of momenta. By extending the analysis of Kusnezov et al. [Ann. Phys., 204, 155 (1990)] in order to derive a set of generalized Nose-Hoover equations of motion which can generate isothermal-isobaric dynamics in a number of different ways, we are able to show that both of our new configurational barostats and Hoover's kinetic isothermal-isobaric scheme are special cases of this more general set of equations. This generalization can be very powerful in generating constant pressure dynamics for a variety of systems. PMID:16542063

Braga, Carlos; Travis, Karl P

2006-03-14

88

Human diseases are attributed in part to the ability of pathogens to evade the eukaryotic immune systems. A subset of these pathogens has developed mechanisms to survive in human macrophages. Yersinia pestis, the causative agent of the bubonic plague, is a predominately extracellular pathogen with the ability to survive and replicate intracellularly. A previous study has shown that a novel rip (required for intracellular proliferation) operon (ripA, ripB and ripC) is essential for replication and survival of Y. pestis in postactivated macrophages, by playing a role in lowering macrophage-produced nitric oxide (NO) levels. A bioinformatics analysis indicates that the rip operon is conserved among a distally related subset of macrophage-residing pathogens, including Burkholderia and Salmonella species, and suggests that this previously uncharacterized pathway is also required for intracellular survival of these pathogens. The focus of this study is ripA, which encodes for a protein highly homologous to 4-hydroxybutyrate-CoA transferase; however, biochemical analysis suggests that RipA functions as a butyryl-CoA transferase. The 1.9 Å X-ray crystal structure reveals that RipA belongs to the class of Family I CoA transferases and exhibits a unique tetrameric state. Molecular dynamics simulations are consistent with RipA tetramer formation and suggest a possible gating mechanism for CoA binding mediated by Val227. Together, our structural characterization and molecular dynamic simulations offer insights into acyl-CoA specificity within the active site binding pocket, and support biochemical results that RipA is a butyryl-CoA transferase. We hypothesize that the end product of the rip operon is butyrate, a known anti-inflammatory, which has been shown to lower NO levels in macrophages. Thus, the results of this molecular study of Y. pestis RipA provide a structural platform for rational inhibitor design, which may lead to a greater understanding of the role of RipA in this unique virulence pathway.

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

89

Stochastic Event-Driven Molecular Dynamics

A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. SEDMD combines event-driven molecular dynamics (EDMD) with the Direct Simulation Monte Carlo (DSMC) method. The polymers are represented as chains of hard-spheres tethered by square wells and interact with the solvent particles with hard-core potentials. The algorithm uses EDMD for

Aleksandar Donev; Alejandro L. Garcia; Berni J. Alder

2008-01-01

90

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

91

Virtual Molecular Dynamics Laboratory (VMDL)

NSDL National Science Digital Library

The Virtual Molecular Dynamics Laboratory is a software and curriculum package that enables students to work with research quality molecular dynamics simulations. Users can easily visualize atomic motion, manipulate atomic interactions, and quantitatively investigate the resulting macroscopic properties of biological, chemical, and physical systems.

Studies, Center F.

92

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

93

Molecular Dynamics (MD) Gas Module

NSDL National Science Digital Library

This simulation consists of a single-component system of particles that interact as either ideal gas particles with no intermolecular potential or as Lennard-Jones Particles . The system runs NVT Molecular Dynamics utilizing the Berendsen Thermostat. The number of particles, volume and temperature are all user-modifiable variables. Additionally, one can select between non-interacting ideal gas particles or particles that interact via the Lennard-Jones Potential. The system can be changed between Argon and Krypton based on reduced unit variables. The average temperature and pressure are displayed on the screen. Additional information is also provided such simulation model/method description, detailed instructions for running the simulation, tutorials, sample questions, literature examples, and links to other relevant data.

Iacovella, Christopher R.; Glotzer, Sharon C.

2007-12-10

94

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

95

NASA Astrophysics Data System (ADS)

In an experiment performed by P. Armentrout (Int. Rev. Phys. Chem. 1990, 9, 115), the Al^+ cation was accelerated into the various isotopic combinations of H2 to form AlH^+ and AlD^+. It was found that the product-forming reactions proceed very inefficiently. The experiments also showed a reduction of ˜29% in the threshold for the formation of AlD^+ from the HD reactant whereas all other AlH^+ and AlD^+ products formed at the same energetic threshold. Four previous theoretical attempts at capturing this unusual phenomenon have not been successful. The lowest energy singlet surfaces for the reaction of Al^+ with H2 have been calculated at the multi-reference configuration interaction (MRCI) level of theory. The real/imaginary boundary of the symmetry-breaking b2 vibrational mode was examined in three dimensions using Hessian matrices computed at a multi-configurational self-consistent field (MCSCF) level of theory. Molecular dynamic simulations numbering on the order of 10^7 were performed, sampling initial conditions reflective of the experiments. The simulations were run until they reached the location where the b2 vibrational mode became unbound. A dissociation model was applied at these greatly compressed geometries to model the dissociation into AlH^+ and AlD^+ products.

Brewer, Nathan

2008-04-01

96

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations have been performed to investigate the effect of nanometer-size pores on the phonon conductivity of single-crystal bulk CoSb3. The cylindrical pores are uniformly distributed along two vertical principal crystallographic directions of a square lattice. Because pore diameter and porosity are two key factors that could affect the performance of the materials, they were varied individually in the ranges a 0-6 a 0 and 0.1-5%, respectively, where a 0 is the lattice constant of CoSb3. The simulation results indicate that the phonon conductivity of nanoporous CoSb3 is significantly lower than that of no-pore CoSb3. The reduction of phonon conductivity in this simulation was consistent with the ballistic-diffusive microscopic effective medium model, demonstrating the ballistic character of phonon transport when the phonon mean-free-path is comparable with or larger than the pore size. Reducing pore diameter or increasing porosity are alternative means of effective reduction of the thermal conductivity of CoSb3. These results are expected to provide a useful basis for the design of high-performance skutterudites.

Yang, Xu-qiu; Zhai, Peng-cheng; Liu, Li-sheng; Chen, Gang; Zhang, Qing-jie

2014-06-01

97

Scalable Software for Quantum Molecular Dynamics.

National Technical Information Service (NTIS)

The objective of this project was to develop highly scalable quantum molecular dynamics software for the DoD CHSSI Initiative. Parallel versions of path integral Molecular Dynamics (PIMD) and centroid Molecular Dynamics (CMD) codes for homogeneous systems...

G. A. Voth

2001-01-01

98

A series of diphenyl ether derivatives were developed and showed promising potency for inhibiting InhA, an essential enoyl acyl carrier protein reductase involved in mycolic acid biosynthesis, leading to the lysis of Mycobacterium tuberculosis. To understand the structural basis of diphenyl ether derivatives for designing more potent inhibitors, molecular dynamics (MD) simulations were performed. Based on the obtained results, the dynamic behaviour in terms of flexibility, binding free energy, binding energy decomposition, conformation, and the inhibitor-enzyme interaction of diphenyl ether inhibitors were elucidated. Phe149, Tyr158, Met161, Met199, Val203 and NAD+ are the key residues for binding of diphenyl ether inhibitors in the InhA binding pocket. Our results could provide the structural concept to design new diphenyl ether inhibitors with better enzyme inhibitory activity against M. tuberculosis InhA. The present work facilitates the design of new and potentially more effective anti-tuberculosis agents. PMID:24785640

Kamsri, P; Koohatammakun, N; Srisupan, A; Meewong, P; Punkvang, A; Saparpakorn, P; Hannongbua, S; Wolschann, P; Prueksaaroon, S; Leartsakulpanich, U; Pungpo, P

2014-06-01

99

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

100

Molecular dynamics simulations of metals

NASA Astrophysics Data System (ADS)

This dissertation describes the development and testing of modified embedded atom method (MEAM) interatomic potentials for Al, Si, Mg, Cu, Fe, and their alloys, with primary concentration on Mg-Al system. We performed the density functional theory (DFT) based ab initio calculations to determine the structural and elastic properties of element pairs that are impractical to obtain from experimental measurements. Specifically, we estimated the cohesive energy, equilibrium atomic volume, bulk modulus, and elastic moduli of every element pair in the NaCl reference structure. Based on the results of DFT calculations, MEAM parameters for each element pair were constructed. We extensively tested the new MEAM potential for Mg-Al alloy system. The new Mg-Al MEAM potential was compared with DFT calculations, previously published semi-empirical interatomic potentials, and experiments. Applicability of the new MEAM potential to atomistic modeling was demonstrated by calculating stress-strain responses from molecular dynamics (MD) simulations of Mg and Al systems in a variety of configurations. The effects of alloying, porosity, and strain rate conditions on the stress-strain response were quantified. The underlying mechanisms for tension-compression asymmetry observed in the macroscale experiments of Mg alloys were investigated at the nanoscale. This work presents a contribution to the task of bridging quantum-mechanical and classical atomistic scale simulations. Information from ab initio electronic structure calculations was used to construct parameters of semi-empirical MEAM potentials for large-scale atomistic simulations of alloys. The results of the new MEAM models compare extremely well to those from other published interatomic potentials. The applicability of the new MEAM potential to investigate nanoscale mechanisms of the deformation and fracture for Al, Mg and Mg-Al alloys was demonstrated. It has been shown that the MEAM provides a single universal formalism for classical atomistic simulations of a wide range of elements and their alloys.

Jelinek, Bohumir

101

Si: A Molecular Dynamics Study

NASA Astrophysics Data System (ADS)

The mechanical properties of single-crystal bulk Mg2Si have been investigated using the molecular dynamics simulation method, in which a many-body potential energy function including bond and angle interactions is adopted to predict the mechanical properties. Virtual tension tests of specimens under different conditions, including Mg vacancy and temperature effects, were carried out by controlling the strain along the principal crystallographic direction. The simulation results show that single-crystal bulk Mg2Si exhibits a nonlinear elastic stress-strain response and the mechanical properties degrade significantly with increasing vacancy content. Moreover, the effect of temperature on the mechanical properties of single-crystal bulk Mg2Si is also discussed in detail.

Yu, Rui; Yang, Shuyong; Chen, Gang; Zhai, Pengcheng; Liu, Lisheng

2014-06-01

102

Molecular dynamics simulations of biomolecules

Molecular dynamics simulations are important tools for understanding the physical basis of the structure and function of biological macromolecules. The early view of proteins as relatively rigid structures has been replaced by a dynamic model in which the internal motions and resulting conformational changes play an essential role in their function. This review presents a brief description of the origin

J. Andrew McCammon; Martin Karplus

2002-01-01

103

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

104

Molecular Dynamics Study of Liquid Water

A sample of water, consisting of 216 rigid molecules at mass density 1 gm\\/cm3, has been simulated by computer using the molecular dynamics technique. The system evolves in time by the laws of classical dynamics, subject to an effective pair potential that incorporates the principal structural effects of many-body interactions in real water. Both static structural properties and the kinetic

Aneesur Rahman; Frank H. Stillinger

1971-01-01

105

NASA Astrophysics Data System (ADS)

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.

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

2011-12-01

106

National Technical Information Service (NTIS)

An experiment that tests a novel method for deflecting molecular beams using inhomogeneous resonance fields is described. If an electric field rotates at the same frequency as a molecule placed in it, the field and molecule remain aligned and the dipole m...

R. M. Hill T. F. Gallagher

1974-01-01

107

Time-reversible ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Time-reversible ab initio molecular dynamics based on a lossless multichannel decomposition for the integration of the electronic degrees of freedom [Phys. Rev. Lett. 97, 123001 (2006)] is explored. The authors present a lossless time-reversible density matrix molecular dynamics scheme. This approach often allows for stable Hartree-Fock simulations using only one single self-consistent field cycle per time step. They also present a generalization, introducing an additional ``forcing'' term, that in a special case includes a hybrid Lagrangian, i.e., Car-Parrinello-type, method, which can systematically be constrained to the Born-Oppenheimer potential energy surface by using an increasing number of self-consistency cycles in the nuclear force calculations. Furthermore, in analog to the reversible and symplectic leapfrog or velocity Verlet schemes, where not only the position but also the velocity is propagated, the authors propose a Verlet-type density velocity formalism for time-reversible Born-Oppenheimer molecular dynamics.

Niklasson, Anders M. N.; Tymczak, C. J.; Challacombe, Matt

2007-04-01

108

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 Å(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

109

Dynamic molecular graphs: "hopping" structures.

This work aims to contribute to the discussion about the suitability of bond paths and bond-critical points as indicators of chemical bonding defined within the theoretical framework of the quantum theory of atoms in molecules. For this purpose, we consider the temporal evolution of the molecular structure of [Fe{C(CH2 )3 }(CO)3 ] throughout Born-Oppenheimer molecular dynamics (BOMD), which illustrates the changing behaviour of the molecular graph (MG) of an electronic system. Several MGs with significant lifespans are observed across the BOMD simulations. The bond paths between the trimethylenemethane and the metallic core are uninterruptedly formed and broken. This situation is reminiscent of a "hopping" ligand over the iron atom. The molecular graph wherein the bonding between trimethylenemethane and the iron atom takes place only by means of the tertiary carbon atom has the longest lifespan of all the considered structures, which is consistent with the MG found by X-ray diffraction experiments and quantum chemical calculations. In contrast, the ?(4) complex predicted by molecular-orbital theory has an extremely brief lifetime. The lifespan of different molecular structures is related to bond descriptors on the basis of the topology of the electron density such as the ellipticities at the Fe?CH2 bond-critical points and electron delocalisation indices. This work also proposes the concept of a dynamic molecular graph composed of the different structures found throughout the BOMD trajectories in analogy to a resonance hybrid of Lewis structures. It is our hope that the notion of dynamic molecular graphs will prove useful in the discussion of electronic systems, in particular for those in which analysis on the basis of static structures leads to controversial conclusions. PMID:24692252

Cortés-Guzmán, Fernando; Rocha-Rinza, Tomas; Guevara-Vela, José Manuel; Cuevas, Gabriel; Gómez, Rosa María

2014-05-01

110

Molecular dynamics simulations in biology

Molecular dynamics-the science of simulating the motions of a system of particles-applied to biological macromolecules gives the fluctuations in the relative positions of the atoms in a protein or in DNA as a function of time. Knowledge of these motions provides insights into biological phenomena such as the role of flexibility in ligand binding and the rapid solvation of the

Martin Karplus; Gregory A. Petsko

1990-01-01

111

Using integrated in-silico computational techniques, including homology modeling, structure-based and pharmacophore-based virtual screening, molecular dynamic simulations, per-residue energy decomposition analysis and atom-based 3D-QSAR analysis, we proposed ten novel compounds as potential CCR5-dependent HIV-1 entry inhibitors. Via validated docking calculations, binding free energies revealed that novel leads demonstrated better binding affinities with CCR5 compared to maraviroc, an FDA-approved HIV-1 entry inhibitor and in clinical use. Per-residue interaction energy decomposition analysis on the averaged MD structure showed that hydrophobic active residues Trp86, Tyr89 and Tyr108 contributed the most to inhibitor binding. The validated 3D-QSAR model showed a high cross-validated rcv2 value of 0.84 using three principal components and non-cross-validated r2 value of 0.941. It was also revealed that almost all compounds in the test set and training set yielded a good predicted value. Information gained from this study could shed light on the activity of a new series of lead compounds as potential HIV entry inhibitors and serve as a powerful tool in the drug design and development machinery. PMID:24762964

Moonsamy, Suri; Dash, Radha Charan; Soliman, Mahmoud E S

2014-01-01

112

classical many body models supplemented by repulsive momentum-dependent potentials to simulate the Pauli and Heisenberg principles have been use with some success for nuclear and atomic bound state and collision problems. They are capable of describing mean ground state properties, hydrodynamics, shocks (if warranted by the physics), viscosity, correlations, clustering, fragmentation, etc. We have become interested in the Feldmeier Gaussian packet formulation since it is based on a variational principle using trial wave functions. We discuss some limitations of the model and discuss further directions of investigation.

Wilets, L.; Beck, W.

1991-12-31

113

classical many body models supplemented by repulsive momentum-dependent potentials to simulate the Pauli and Heisenberg principles have been use with some success for nuclear and atomic bound state and collision problems. They are capable of describing mean ground state properties, hydrodynamics, shocks (if warranted by the physics), viscosity, correlations, clustering, fragmentation, etc. We have become interested in the Feldmeier Gaussian packet formulation since it is based on a variational principle using trial wave functions. We discuss some limitations of the model and discuss further directions of investigation.

Wilets, L.; Beck, W.

1991-01-01

114

Photomechanical spallation of molecular and metal targets: molecular dynamics study

Microscopic mechanisms of photomechanical spallation are investigated in a series of large-scale molecular dynamics simulations performed for molecular and metal targets. A mesoscopic breathing sphere model is used in simulations of laser interaction with molecular targets. A coupled atomistic-continuum model that combines a molecular dynamics method with a continuum description of the laser excitation and subsequent relaxation of the conduction

E. Leveugle; D. S. Ivanov; L. V. Zhigilei

2004-01-01

115

Uroporphyrinogen decarboxylase (UROD) has been suggested as a protectant against radiation for head and neck cancer (HNC). In this study, we employed traditional Chinese medicine (TCM) compounds from TCM Database@Taiwan (http://tcm.cmu.edu.tw/) to screen for drug-like candidates with potential UROD inhibition characteristics using virtual screening techniques. Isopraeroside IV, scopolin, and nodakenin exhibited the highest Dock Scores, and were predicted to have good Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) properties. Two common moieties, 2H-chromen-2-one and glucoside, were observed among the top TCM candidates. Cross comparison of the docking poses indicated that candidates formed stable interactions with key binding and catalytic residues of UROD through these two moieties. The 2H-chromen-2-one moiety enabled pi-cation interactions with Arg37 and H-bonds with Tyr164. The glucoside moiety was involved in forming H-bonds with Arg37 and Asp86. From our computational results, we propose isopraeroside IV, scopolin, and nodakenin as ligands that might exhibit drug-like inhibitory effects on UROD. The glucoside and 2H-chromen-2-one moieties may potentially be used for designing inhibitors of UROD.

Lin, Hung-Che; Chang, Su-Sen; Chen, Calvin Yu-Chian

2012-01-01

116

Monte Carlo simulation in molecular gas dynamics

In the Monte Carlo simulation in the molecular gas dynamics, the behaviors of molecules are probabilistically simulated based on the Boltzmann equation assumptions, i.e., binary molecular collisions, molecular chaos, and vanishingly short time and small physical space for molecular collisions; the simulated molecules are probabilistically followed using random numbers on a computer through the molecular motions the molecular collisions, and

K. Koura

1983-01-01

117

Path-Integral Molecular Dynamics Calculations of Electron Plasma

NASA Astrophysics Data System (ADS)

We introduce a first-principles molecular dynamics method based on the discretized path integral representation of quantum particles. Fermi statistics is automatically generated by an effective exchange potential. This path-integral molecular dynamics method is able to simulate exchange in electron plasmas at the border of the degenerate regime with a satisfactory level of accuracy.

Oh, Ki-Dong; Deymier, P. A.

1998-10-01

118

National Technical Information Service (NTIS)

We have explored the degree to which an intermolecular potential for theexplosive 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 sy...

D. C. SOrescu D. L. Thompson B. M. Rice

1998-01-01

119

A molecular dynamics study on iridium

NASA Astrophysics Data System (ADS)

In this study, molecular dynamics simulations are performed by using a modified form of Morse potential function in the framework of the Embedded Atom Method (EAM). Temperature-and pressure-dependent behaviours of bulk modulus, second-order elastic constants (SOEC), and the linear-thermal expansion coefficient is calculated and compared with the available experimental data. The melting temperature is estimated from 3 different plots. The obtained results are in agreement with the available experimental findings for iridium.

Ferah, Gülen; Colakoglu, Kemal; Ciftci, Yasemin Oztekin; Ozgen, Soner; Kazanc, Sefa

2007-06-01

120

Molecular dynamics simulation of dense fluid methane

A molecular dynamics study of methane in the liquid and gaseous states is reported. Systems studied consists of 108 and 500 particles interacting with a site-site exp-6 potential due to Williams. Thermodynamic properties (configurational energy, pressure and specific heat), mean-squared force, mean-squared torque, self-diffusion coefficient, site-site correlation functions (gcc, gch, ghh), partial structure factors (Scc, Sch, Shh) and total structure

S. Murad; D. J. Evans; K. E. Gubbins; W. B. Streett; D. J. Tildesley

1979-01-01

121

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 which also had good agreement with experiment for its surface tension and X-ray reflectivity. The potential of mean force of CO(2) and SO(2) was 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 CO(2). The air-BMIMBF4 interface had enhanced BMIM density, which was mostly related to its butyl group, followed by enhanced BF4 density a few angstroms toward 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 CO(2) and SO(2) showed more negative free energies in regions of enhanced BF4 density, while more positive free energies were found 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. PMID:20882993

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

2010-11-25

122

Molecular Dynamics Performance JS Model

NSDL National Science Digital Library

The Molecular Dynamics Performance JavaScript Model computes the trajectory of particles acted on by a Lennard-Jones force. This simulation was designed to test the speed of JavaScript for a computationally intensive model. The user can vary the number of particles, the number of frames per second displayed on the computer monitor, and the requested number of Verlet steps between frames. The actual number of Verlet steps per frame is shown. This number will be less than the requested number of steps on slow processors. The Molecular Dynamics Performance JS Model was developed using the Easy Java Simulations (EJS) version 5. It is distributed as a ready-to-run html page and requires only a browser with JavaScript support.

Christian, Wolfgang; Franciscouembre

2013-09-06

123

Peridynamics as an Upscaling of Molecular Dynamics

Peridynamics is a formulation of continuum mechanics based on integral equations. It is a nonlocal model, accounting for the effects of long-range forces. Correspondingly, classical molecular dynamics is also a nonlocal model. Peridynamics and molecular dynamics have similar discrete computational structures, as peridynamics computes the force on a particle by summing the forces from surrounding particles, similarly to molecular dynamics.

Pablo Seleson; Michael L. Parks; Max Gunzburger; Richard B. Lehoucq

2009-01-01

124

Molecular dynamics on vector computers

NASA Astrophysics Data System (ADS)

An algorithm called the method of lights (MOL) has been developed for the computerized simulation of molecular dynamics. The MOL, implemented on the CYBER 205 computer, is based on sorting and reformulating the manner in which neighbor lists are compiled, and it uses data structures compatible with specialized vector statements that perform parallel computations. The MOL is found to reduce running time over standard methods in scalar form, and vectorization is shown to produce an order-of-magnitude reduction in execution time.

Sullivan, F.; Mountain, R. D.; Oconnell, J.

1985-10-01

125

From molecular dynamics to Brownian dynamics

Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analysing multi-scale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane.

Erban, Radek

2014-01-01

126

Molecular Dynamics Adiabatic Piston Model

NSDL National Science Digital Library

The Molecular Dynamics Adiabatic Piston model shows two gas samples within a horizontal cylinder that is divided by an insulated piston that moves without friction. It is a supplemental simulation for the article by Eric Gislason and has been approved by the authors and the AJP editor. Initially the piston is held (locked) in place, and the pressures of the gases on each side of the piston are different. When the piston is released it undergoes oscillations that are damped due to collisions of the particles with the piston, and it finally ends up at rest. The final pressures of the two gases are equal, but the final temperatures are typically different. All particles in the Molecular Dynamics Adiabatic Piston model have unit mass and interact through pairwise Leonard-Jones forces. Gas particles interact with the container walls via a spring (Hooke's law) force and this particle-wall interaction is used to move the piston and to compute the pressure. The temperature is computed from the average kinetic energy. The piston position and the temperature and pressure are shown as functions of time in additional windows. The Molecular Dynamics Adiabatic Piston 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_md_AdiabaticPiston.jar file will run the program if Java is installed.

Christian, Wolfgang

2010-07-13

127

Molecular dynamics simulation of dynamic response of beryllium

NASA Astrophysics Data System (ADS)

The response of beryllium to dynamic loading has been extensively studied, both experimentally and theoretically, due to its importance in several technological areas. Compared to other metals, it is quite challenging to accurately represent the various anomalous behaviors of beryllium using classical interatomic potentials. We have used large-scale classical molecular dynamics simulations to study the response of single-crystal beryllium to high-strain rate uniaxial loading. We compare results from two different types of interatomic potential. A MEAM potential was constructed to reproduce properties of beryllium at ambient conditions. A potential based on the recently-developed GAP approach was fit to quantum simulations of solid and liquid beryllium phases near the shock-melting line.

Thompson, Aidan P.; Lane, J. Matthew D.; Desjarlais, Michael P.; Bartok, Albert P.; Csanyi, Gabor

2011-06-01

128

Molecular dynamics for dense matter

NASA Astrophysics Data System (ADS)

We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid-gas phase transition is not plausible at lower temperatures.

Maruyama, Toshiki; Watanabe, Gentaro; Chiba, Satoshi

2012-08-01

129

Potential molecular wires and molecular alligator clips

NASA Astrophysics Data System (ADS)

The synthesis of oligo(2-ethylphenylene-ethynylene)s, oligo(2-(0957-4484/7/4/023/img1-ethylheptyl)phenylene-ethynylene)s, and oligo(3-ethylthiophene-ethynylene)s is described via an iterative divergent convergent approach. Synthesized were the monomer, dimer, tetramer, octamer and 16-mer of the oligo(3-ethylthiophene-ethynylene)s and oligo(2-0957-4484/7/4/023/img1-ethylheptyl)phenylene-ethynylene)s. The 16-mers are 100 Å and 128 Å long, respectively. At each stage in the iteration, the length of the framework doubles. Only three sets of reaction conditions are needed for the entire iterative synthetic sequence; an iodination, a protodesilylation, and a Pd/Cu-catalyzed cross coupling. The oligomers were characterized spectroscopically and by mass spectrometry. The optical properties are presented which show the stage of optical absorbance saturation. The size exclusion chromatography values for the number average weights, relative to polystyrene, illustrate the tremendous differences in the hydrodynamic volume of these rigid rod oligomers versus the random coils of polystyrene. These differences become quite apparent at the octamer stage. The preparation of thiol-protected end groups is described. These may serve as molecular alligator clips for adhesion to gold surfaces. These oligomers may act as molecular wires in molecular electronic devices and they also serve as useful models for understanding related bulk polymers.

Schumm, Jeffry S.; Pearson, Darren L.; Jones, LeRoy, II; Hara, Ryuichiro; Tour, James M.

1996-12-01

130

NASA Astrophysics Data System (ADS)

Ground-state potential-energy curves and distance dependent isotropic hyperfine coupling (IHC) constants for ground-state H-RG (=Ne, Ar, Kr, Xe) are obtained at CCSD(T) (coupled-cluster single double triple) and MP4(SDQ) (fourth-order Moller-Plesset single double quadruple) levels, respectively, with an augmented basis set aug-Stuttgart (RG)/aug-cc-pVQZ (H). The obtained Rm and ? are for NeH: 3.45 Å and -1.36 meV; ArH: 3.65 Å and -3.48 meV; KrH: 3.75 Å and -4.32 meV; XeH: 3.90 Å and -5.22 meV. The computed pair potentials are utilized in classical molecular-dynamics simulations of H-RG lattices. Along the classical trajectory, the many-body perturbation on the H atom hyperfine coupling constant is computed by pair-wise addition of the individual RG-H contributions obtained from the present quantum-chemical calculations. The computed IHC shifts are compared with electron paramagnetic resonance (EPR) spectra obtained in low-temperature matrix isolation experiments. For most cases this theoretical treatment agrees very well with the experiment and confirms the previous site assignments. However, for H-Xe, the theory would suggest stability of both interstitial Oh and substitutional sites, whereas only one site is observed in the experiment. Based on the present calculations this site can be assigned as a nearly undistorted substitutional site.

Kiljunen, Toni; Eloranta, Jussi; Kunttu, Henrik

1999-06-01

131

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

132

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

133

Molecular dynamics simulations of classical stopping power.

Molecular dynamics can provide very accurate tests of classical kinetic theory; for example, unambiguous comparisons can be made for classical particles interacting via a repulsive 1/r potential. The plasma stopping power problem, of great interest in its own right, provides an especially stringent test of a velocity-dependent transport property. We have performed large-scale (~10(4)-10(6) particles) molecular dynamics simulations of charged-particle stopping in a classical electron gas that span the weak to moderately strong intratarget coupling regimes. Projectile-target coupling is varied with projectile charge and velocity. Comparisons are made with disparate kinetic theories (both Boltzmann and Lenard-Balescu classes) and fully convergent theories to establish regimes of validity. We extend these various stopping models to improve agreement with the MD data and provide a useful fit to our results. PMID:24313494

Grabowski, Paul E; Surh, Michael P; Richards, David F; Graziani, Frank R; Murillo, Michael S

2013-11-22

134

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

135

Molecular Dynamics Simulator for Optimal Control of Molecular Motion.

National Technical Information Service (NTIS)

In recognition of recent interest in developing optimal control techniques for manipulating molecular motion, this paper introduces a computer-driven electro-mechanical analog of this process. The resultant Molecular Dynamic Simulator (MDS) is centered ar...

H. Rabitz

1990-01-01

136

Molecular dynamics simulation of oxides with ionic–covalent bonds

A “semi-classical” method was developed for molecular dynamics simulation of a system with ionic–covalent bonds like silica. The ionic charges were calculated by minimization of the potential energy on each step of molecular dynamics simulation. Ionic–covalent potential was used in modeling of SiO2 molecule, non-crystalline silica, and calcium metasilicate. The internal energy of a system includes energies of silicon ionization,

D. K Belashchenko; O. I Ostrovski

2001-01-01

137

Molecular dynamics calculation (MD) has been carried out for an aqueous solution of urea at 298.15 K and with experimental density value at ordinary pressure by the use of constant temperature technique developed previously. The total number of molecules is 216, of which 17 are urea. The mole fraction of urea in the solution is thus 0.078. For water–water and

Hideki Tanaka; Koichiro Nakanishi; Hidekazu Touhara

1985-01-01

138

Recently, a controversy has come to light in literature regarding the structure of water in nonambient conditions. Disagreement is evident between the site-site pair correlation functions of water derived from neutron diffraction and those obtained by computer simulations which employ effective pairwise potentials to express the intermolecular interactions. In this paper the SCFMI method (self-consistent field for molecular interaction) followed

Antonino Famulari; Roberto Specchio; Maurizio Sironi; Mario Raimondi

1998-01-01

139

Potential of mean force (PMF) profiles of a single Na+ or K+ ion passing through a cyclic peptide nanotube, cyclo[-(D-Ala-Glu-D-Ala-Gln)2-], in water are calculated to provide insight into ion transport and to understand the conductance difference between these two ions. The PMF profiles are obtained by performing steered molecular dynamics (SMD) simulations that are based on the Jarzynski equality. The computed PMF profiles for both ions show barriers of around 2.4 kcal/mol at the channel entrances and exits and energy wells in the middle of the tube. The energy barriers, so-called dielectric energy barriers, arise due to the desolvation of water molecules when ions move across the nanotube, and the energy wells appear as a result of attractive interactions between the cations and negatively charged carbonyl oxygens on the backbone of the tube. We find more and deeper energy wells in the PMF profile for Na+ than for K+, which suggests that Na+ ions have a longer residence time inside the nanotube and that permeation of Na+ ions is reduced compared to K+ ions. Calculations of the radial distribution functions (RDF) between the ions and oxygens in the water molecules and in carbonyl groups on the tube and an investigation of the orientations of the carbonyl groups show that, in contrast with the dynamic carbonyl groups observed in the selectivity filter of the KcsA ion channel, the carbonyl groups in the cyclic peptide nanotube are relatively rigid, with only slight reorientation of the carbonyl groups as the cations pass through. The rigidity of the carbonyl groups in the cyclic peptide nanotube can be attributed to their role in hydrogen bonding, which is responsible for the tube structure. Comparison of the PMF profiles with the electrostatic energy profiles calculated from the Poisson-Boltzmann (PB) equation, a dielectric continuum model, reveals that the dielectric continuum model breaks down in the confined region within the tube that governs ion transport. PMID:17181305

Hwang, Hyonseok; Schatz, George C; Ratner, Mark A

2006-12-28

140

The "Collisions Cube" Molecular Dynamics Simulator.

ERIC Educational Resources Information Center

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

Nash, John J.; Smith, Paul E.

1995-01-01

141

Molecular dynamics simulations in drug design.

This minireview focuses on recent developments in the application of molecular dynamics to drug design. Recent applications of endpoint free-energy computational methods such as molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and generalized Born surface area (MM-GBSA) and linear response methods are described. Recent progress in steered molecular dynamics applied to drug design is reviewed. PMID:23568466

Kerrigan, John E

2013-01-01

142

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

143

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

144

Hybrid molecular dynamics simulations of living filaments

NASA Astrophysics Data System (ADS)

We propose a hybrid molecular dynamics/multi-particle collision dynamics model to simulate a set of self-assembled semiflexible filaments and free monomers. Further, we introduce a Monte Carlo scheme to deal with single monomer addition (polymerization) or removal (depolymerization), satisfying the detailed balance condition within a proper statistical mechanical framework. This model of filaments, based on the wormlike chain, aims to represent equilibrium polymers with distinct reaction rates at both ends, such as self-assembled adenosine diphosphate-actin filaments in the absence of adenosine triphosphate (ATP) hydrolysis and other proteins. We report the distribution of filament lengths and the corresponding dynamical fluctuations on an equilibrium trajectory. Potential generalizations of this method to include irreversible steps like ATP-actin hydrolysis are discussed.

Caby, Mathieu; Hardas, Priscilla; Ramachandran, Sanoop; Ryckaert, Jean-Paul

2012-03-01

145

Molecular model potentials: Combination of atomic boxes

A new Combination of Atomic Boxes (CAB) molecular orbital model is introduced, having the following characteristics:1)Atomic model potentials are one-dimensional potential boxes of finite depth UA and of length LA, the box-parameters being chosen to give valence electron ionization energies.2)Explicit molecular model potentials are constructed by combining all the model potentials of the atoms in the molecule.3)A minimum computational effort

László v. Szentpály

1979-01-01

146

Molecular dynamic simulations with radiation

NASA Astrophysics Data System (ADS)

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 validations of the models used for describing 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 first attempt at 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.

2009-05-01

147

Molecular dynamics of interface rupture

NASA Technical Reports Server (NTRS)

Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.

Koplik, Joel; Banavar, Jayanth R.

1993-01-01

148

Protocol for MM/PBSA Molecular Dynamics Simulations of Proteins

Continuum solvent models have been employed in past years for understanding processes such as protein folding or biomolecular association. In the last decade, several attempts have been made to merge atomic detail molecular dynamics simulations with solvent continuum models. Among continuum models, the Poisson-Boltzmann solvent accessible surface area model is one of the oldest and most fundamental. Notwithstanding its wide usage for simulation of biomolecular electrostatic potential, the Poisson-Boltzmann equation has been very seldom used to obtain solvation forces for molecular dynamics simulation. We propose here a fast and reliable methodology to implement continuum forces in standard molecular mechanics and dynamics algorithms. Results for a totally unrestrained 1 ns molecular dynamics simulation of a small protein are quantitatively similar to results obtained by explicit solvent molecular dynamics simulations.

Fogolari, Federico; Brigo, Alessandro; Molinari, Henriette

2003-01-01

149

Protocol for MM/PBSA molecular dynamics simulations of proteins.

Continuum solvent models have been employed in past years for understanding processes such as protein folding or biomolecular association. In the last decade, several attempts have been made to merge atomic detail molecular dynamics simulations with solvent continuum models. Among continuum models, the Poisson-Boltzmann solvent accessible surface area model is one of the oldest and most fundamental. Notwithstanding its wide usage for simulation of biomolecular electrostatic potential, the Poisson-Boltzmann equation has been very seldom used to obtain solvation forces for molecular dynamics simulation. We propose here a fast and reliable methodology to implement continuum forces in standard molecular mechanics and dynamics algorithms. Results for a totally unrestrained 1 ns molecular dynamics simulation of a small protein are quantitatively similar to results obtained by explicit solvent molecular dynamics simulations. PMID:12829472

Fogolari, Federico; Brigo, Alessandro; Molinari, Henriette

2003-07-01

150

Time-reversible ab initio molecular dynamics.

Time-reversible ab initio molecular dynamics based on a lossless multichannel decomposition for the integration of the electronic degrees of freedom [Phys. Rev. Lett. 97, 123001 (2006)] is explored. The authors present a lossless time-reversible density matrix molecular dynamics scheme. This approach often allows for stable Hartree-Fock simulations using only one single self-consistent field cycle per time step. They also present a generalization, introducing an additional "forcing" term, that in a special case includes a hybrid Lagrangian, i.e., Car-Parrinello-type, method, which can systematically be constrained to the Born-Oppenheimer potential energy surface by using an increasing number of self-consistency cycles in the nuclear force calculations. Furthermore, in analog to the reversible and symplectic leapfrog or velocity Verlet schemes, where not only the position but also the velocity is propagated, the authors propose a Verlet-type density velocity formalism for time-reversible Born-Oppenheimer molecular dynamics. PMID:17444697

Niklasson, Anders M N; Tymczak, C J; Challacombe, Matt

2007-04-14

151

Bead-Fourier path integral molecular dynamics.

Molecular dynamics formulation of Bead-Fourier path integral method for simulation of quantum systems at finite temperatures is presented. Within this scheme, both the bead coordinates and Fourier coefficients, defining the path representing the quantum particle, are treated as generalized coordinates with corresponding generalized momenta and masses. Introduction of the Fourier harmonics together with the center-of-mass thermostating scheme is shown to remove the ergodicity problem, known to pose serious difficulties in standard path integral molecular dynamics simulations. The method is tested for quantum harmonic oscillator and hydrogen atom (Coulombic potential). The simulation results are compared with the exact analytical solutions available for both these systems. Convergence of the results with respect to the number of beads and Fourier harmonics is analyzed. It was shown that addition of a few Fourier harmonics already improves the simulation results substantially, even for a relatively small number of beads. The proposed Bead-Fourier path integral molecular dynamics is a reliable and efficient alternative to simulations of quantum systems. PMID:16241383

Ivanov, Sergei D; Lyubartsev, Alexander P; Laaksonen, Aatto

2003-06-01

152

Bead-Fourier path integral molecular dynamics

NASA Astrophysics Data System (ADS)

Molecular dynamics formulation of Bead-Fourier path integral method for simulation of quantum systems at finite temperatures is presented. Within this scheme, both the bead coordinates and Fourier coefficients, defining the path representing the quantum particle, are treated as generalized coordinates with corresponding generalized momenta and masses. Introduction of the Fourier harmonics together with the center-of-mass thermostating scheme is shown to remove the ergodicity problem, known to pose serious difficulties in standard path integral molecular dynamics simulations. The method is tested for quantum harmonic oscillator and hydrogen atom (Coulombic potential). The simulation results are compared with the exact analytical solutions available for both these systems. Convergence of the results with respect to the number of beads and Fourier harmonics is analyzed. It was shown that addition of a few Fourier harmonics already improves the simulation results substantially, even for a relatively small number of beads. The proposed Bead-Fourier path integral molecular dynamics is a reliable and efficient alternative to simulations of quantum systems.

Ivanov, Sergei D.; Lyubartsev, Alexander P.; Laaksonen, Aatto

2003-06-01

153

Ab initio molecular dynamics for liquid metals

We present ab initio quantum-mechanical molecular-dynamics calculations based on the calculation of the electronic ground state and of the Hellmann-Feynman forces in the local-density approximation at each molecular-dynamics step. This is possible using conjugate-gradient techniques for energy minimization, and predicting the wave functions for new ionic positions using subspace alignment. This approach avoids the instabilities inherent in quantum-mechanical molecular-dynamics calculations

G. Kresse; J. Hafner

1993-01-01

154

An optimized replica exchange molecular dynamics method.

We introduce a new way to perform swaps between replicas in replica exchange molecular dynamics simulations. The method is based on a generalized canonical probability distribution function and flattens the potential of mean force along the temperature coordinate, such that a random walk in temperature space is achieved. Application to a Go model of protein A showed that the method is more efficient than conventional replica exchange. The method results in a constant probability distribution of the replicas over the thermostats, yields a minimum round-trip time between extremum temperatures, and leads to faster ergodic convergence. PMID:19239315

Kamberaj, Hiqmet; van der Vaart, Arjan

2009-02-21

155

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

2012-10-19

156

NASA Astrophysics Data System (ADS)

Path-integral molecular dynamics simulations for the hydrogen-bonded glycine·(H 2O) n ( n = 1-7) clusters have been carried out using an on-the-fly direct dynamics technique at the semi-empirical PM6 level of theory. In the case of smaller clusters with n = 1-3, the simulations show that the cluster structure takes exclusively the hydrogen-bonded complex between a canonical neutral glycine and a water cluster moiety. In contrast, it was found that proton-exchange processes effectively occur between the COOH carboxylic group and water cluster moiety for n = 4-6 clusters although the overall structures are the complex between a neutral glycine and water clusters. In the case of the n = 7 cluster, glycine preferentially takes a zwitterionic form having NH3+ and COO - functional groups.

Yoshikawa, Takehiro; Motegi, Haruki; Kakizaki, Akira; Takayanagi, Toshiyuki; Shiga, Motoyuki; Tachikawa, Masanori

2009-11-01

157

Fragment recognition in molecular dynamics

NASA Astrophysics Data System (ADS)

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.

Strachan, A.; Dorso, C. O.

1997-08-01

158

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)] [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

159

Molecular dynamics of liquid lead near its melting point

The molecular dynamics of liquid lead is simulated at T = 613 K using the following three models of an interparticle interaction potential: the Dzugutov pair potential and two multiparticle potentials (the 'glue' potential and the Gupta potential). One of the purposes of this work is to determine the optimal model potential of the interatomic interaction in liquid lead. The calculated structural static and dynamic characteristics are compared with the experimental data on X-ray and neutron scattering. On the whole, all three model potentials adequately reproduce the experimental data. The calculations using the Dzugutov pair potential are found to reproduce the structural properties and dynamics of liquid lead on the nanoscale best of all. The role of a multiparticle contribution to the glue and Gupta potentials is studied, and its effect on the dynamic properties of liquid lead in nanoregions is revealed. In particular, the neglect of this contribution is shown to noticeably decrease the acoustic-mode frequency.

Khusnutdinov, R. M.; Mokshin, A. V., E-mail: avm@kazan-spu.ru; Yul'met'ev, R. M. [Kazan State University (Russian Federation)

2009-03-15

160

The development of SrtA inhibitors targeting the biothreat organism namely Bacillus anthracis was achieved by the combined approach of pharmacophore modeling, binding interactions, electron transferring capacity, ADME, and Molecular dynamics studies. In this study, experimentally reported Ba-SrtA inhibitors (pyridazinone and pyrazolethione derivatives) were considered for the development of enhanced pharmacophoric model. The obtained AAAHR hypothesis was a pure theoretical concept that accounts for common molecular interaction network present in experimentally active pyridazinone and pyrazolethione derivatives. Pharmacophore-based screening of AAAHR hypothesis provides several new compounds, and those compounds were treated with four phases of docking protocols with combined Glide-QPLD docking approach. In this approach, scoring and charge accuracy variations were seen to be dominated by QM/MM approach through the allocation of partial charges. Finally, we reported the best compounds from binding db, Chembridge db, and Toslab based on scoring values, energy parameters, electron transfer reaction, ADME, and cell adhesion inhibition activity. The dynamic state of interaction and binding energy assess that new compounds are more active inside the binding pocket and these compounds on experimental validations will survive as better inhibitors for targeting the cell adhesion mechanism of Ba-SrtA. PMID:23869520

Selvaraj, Chandrabose; Singh, Sanjeev Kumar

2014-08-01

161

Unified approach for molecular dynamics and density-functional theory

We present a unified scheme that, by combining molecular dynamics and density-functional theory, profoundly extends the range of both concepts. Our approach extends molecular dynamics beyond the usual pair-potential approximation, thereby making possible the simulation of both covalently bonded and metallic systems. In addition it permits the application of density-functional theory to much larger systems than previously feasible. The new

R. Car; M. Parrinello

1985-01-01

162

Binding of transcription factors to DNA is a dynamic process allowing for spatial- and sequence-specificity. Many methods for determination of DNA-protein structures do not allow for identification of dynamics of the search process, but provide only a single snapshot of the most stable binding. In order to better understand the dynamics of DNA binding as a protein encounters its cognate site, we have created a computer-based DNA scanning array macro that sequentially inserts a high affinity DNA consensus binding site at all possible locations in a predicted protein-DNA interface. We show, using short molecular dynamic simulations at each location in the interface, that energy minimized states and decreased movement of evolutionary conserved amino acids can be readily observed and used to predict the consensus binding site. The macro was applied to SNAIL class C2H2 zinc finger family proteins. The analysis suggests that (1) SNAIL binds to the E-box in multiple states during its encounter with its cognate site; (2) several different amino acids contribute to the E-box binding in each state; (3) the linear array of zinc fingers contributes differentially to overall folding and base-pair recognition; and (4) each finger may be specialized for stability and sequence specificity. Moreover, the macromolecular movement observed using this dynamic approach may allow the NH2-terminal finger to bind without sequence specificity yet result in higher binding energy. This macro and overall approach could be applicable to many evolutionary conserved transcription factor families and should help to better elucidate the varied mechanisms used for DNA sequence-specific binding. PMID:23708613

Prokop, Jeremy W; Liu, Yuanjie; Milsted, Amy; Peng, Hongzhuang; Rauscher, Frank J

2013-09-01

163

RedMD--reduced molecular dynamics package.

We developed a software package (RedMD) to perform molecular dynamics simulations and normal mode analysis of reduced models of proteins, nucleic acids, and their complexes. With RedMD one can perform molecular dynamics simulations in a microcanonical ensemble, with Berendsen and Langevin thermostats, and with Brownian dynamics. We provide force field and topology generators which are based on the one-bead per residue/nucleotide elastic network model and its extensions. The user can change the force field parameters with the command line options that are passed to generators. Also, the generators can be modified, for example, to add new potential energy functions. Normal mode analysis tool is available for elastic or anisotropic network models. The program is written in C and C++ languages and the structure/topology of a molecule is based on an XML format. OpenMP technology for shared-memory architectures was used for code parallelization. The code is distributed under GNU public licence and available at http://bionano.icm.edu.pl/software/. PMID:19247989

Górecki, Adam; Szypowski, Marcin; D?ugosz, Maciej; Trylska, Joanna

2009-11-15

164

Molecular dynamics simulation by atomic mass weighting

A molecular dynamics-based simulation method in which atomic masses are weighted is described. Results from this method showed that the capability for conformation search in molecular dynamics simulation of a short peptide (FMRF-amide) is significantly increased by mass weighting.

Mao, Boryeu; Friedman, Alan R.

1990-01-01

165

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

166

Dynamic Shear Modulus of Polymers from Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

In this work we describe the methodology for using equilibrium molecular dynamics simulations (MD) simulations to obtain the viscoelastic properties of polymers in the glassy regime. Specifically we show how the time dependent shear stress modulus and frequency dependent complex shear modulus in the high-frequency regime can be determined from the off-diagonal terms of the stress-tensor autocorrelation function obtained from MD trajectories using the Green-Kubo method and appropriate Fourier transforms. In order to test the methodology we have performed MD simulations of a low-molecular-weight polybutadiene system using quantum chemistry based potential functions. Values of the glassy modulus and the maximum loss frequency were found to be in good agreement with experimental data for polybutadiene at 298 K.

Byutner, Oleksiy; Smith, Grant

2001-03-01

167

Steered molecular dynamics investigations of protein function

Molecular recognition and mechanical properties of proteins govern molecular processes in the cell that can cause disease and can be targeted for drug design. Single molecule measurement techniques have greatly advanced knowledge but cannot resolve enough detail to be interpreted in terms of protein structure. We seek to complement the observations through so-called Steered Molecular Dynamics (SMD) simulations that link

Barry Isralewitz; Jerome Baudry; Justin Gullingsrud; Dorina Kosztin; Klaus Schulten

2001-01-01

168

Langevin stabilization of molecular dynamics

NASA Astrophysics Data System (ADS)

In this paper we show the possibility of using very mild stochastic damping to stabilize long time step integrators for Newtonian molecular dynamics. More specifically, stable and accurate integrations are obtained for damping coefficients that are only a few percent of the natural decay rate of processes of interest, such as the velocity autocorrelation function. Two new multiple time stepping integrators, Langevin Molly (LM) and Brünger-Brooks-Karplus-Molly (BBK-M), are introduced in this paper. Both use the mollified impulse method for the Newtonian term. LM uses a discretization of the Langevin equation that is exact for the constant force, and BBK-M uses the popular Brünger-Brooks-Karplus integrator (BBK). These integrators, along with an extrapolative method called LN, are evaluated across a wide range of damping coefficient values. When large damping coefficients are used, as one would for the implicit modeling of solvent molecules, the method LN is superior, with LM closely following. However, with mild damping of 0.2 ps-1, LM produces the best results, allowing long time steps of 14 fs in simulations containing explicitly modeled flexible water. With BBK-M and the same damping coefficient, time steps of 12 fs are possible for the same system. Similar results are obtained for a solvated protein-DNA simulation of estrogen receptor ER with estrogen response element ERE. A parallel version of BBK-M runs nearly three times faster than the Verlet-I/r-RESPA (reversible reference system propagator algorithm) when using the largest stable time step on each one, and it also parallelizes well. The computation of diffusion coefficients for flexible water and ER/ERE shows that when mild damping of up to 0.2 ps-1 is used the dynamics are not significantly distorted.

Izaguirre, Jesús A.; Catarello, Daniel P.; Wozniak, Justin M.; Skeel, Robert D.

2001-02-01

169

Molecular dynamics in amorphous ergocalciferol

NASA Astrophysics Data System (ADS)

While developing new pharmaceutical products based on drug substances in their amorphous form, the molecular mobility of amorphous active ingredients have to be characterized in detail. The molecular mobility in the supercooled liquid and glassy states of ergocalciferol is studied using broadband dielectric spectroscopy over wide frequency and temperature ranges. Dielectric studies revealed a number of relaxation process of different molecular origin.

Mohamed, Sahra; Thayyil, M. Shahin; Capaccioli, S.

2014-04-01

170

Hydration dynamics in water clusters via quantum molecular dynamics simulations

NASA Astrophysics Data System (ADS)

We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of the non-cavity type model. Relaxation associated with cavity collapse presents, however, unique dynamical signatures.

Turi, László

2014-05-01

171

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

172

Transport Coefficients and Molecular Dynamics: Alternatives.

National Technical Information Service (NTIS)

The task of using molecular dynamics to determine the shear viscosity and the thermal conductivity of a model fluid is examined in detail for the Lennard-Jones fluid. The equilibrium time correlation function approach is compared with three nonequilibrium...

R. D. Mountain

2004-01-01

173

The classical reaction dynamics of a four-body, bimolecular reaction on a neural network (NN) potential-energy surface (PES) fitted to a database obtained solely from ab initio MP2/6-311G(d,p) calculations are reported. The present work represents the first reported application of ab initio NN methods to a four-body, bimolecular, gas-phase reaction where bond extensions reach 8.1 A for the BeH + H(2) --> BeH(2) + H reaction. A modified, iterative novelty sampling method is used to select data points based on classical trajectories computed on temporary NN surfaces. After seven iterations, the sampling process is found to converge after selecting 9604 configurations. Incorporation of symmetry increases this to 19 208 BeH(3) configurations. The analytic PES for the system is obtained from the ensemble average of a five-member (6-60-1) NN committee. The mean absolute error (MAE) for the committee is 0.0046 eV (0.44 kJ mol(-1)). The total energy range of the BeH(3) database is 147.0 kJ mol(-1). Therefore, this MAE represents a percent energy error of 0.30%. Since it is the gradient of the PES that constitutes the most important quantity in molecular dynamics simulations, the paper also reports mean absolute error for the gradient. This result is 0.026 eV A(-1) (2.51 kJ mol(-1) A(-1)). Since the gradient magnitudes span a range of 15.32 eV A(-1) over the configuration space tested, this mean absolute gradient error represents a percent error of 0.17%. The mean percent absolute relative gradient error is 4.67%. The classically computed reaction cross sections generally increase with total energy. They vary from 0.007 to 0.030 A(2) when H(2) is at ground state, and from 0.05 to 0.10 A(2) when H(2) is in the first excited state. Trajectory integration is very fast using the five-member NN PES. The average trajectory integration time is 1.07 s on a CPU with a clock speed of 2.4 GHz. Zero angular momentum collisions are also investigated and compared with previously reported quantum dynamics on the same system. The quantum reaction probabilities exhibit pronounced resonance effects that are absent in the classical calculations. The magnitudes of quantum and classical results are in fair accord with the classical results being about 30-40% higher due to the lack of quantum restrictions on the zero-point vibrational energy. PMID:19852450

Le, Hung M; Raff, Lionel M

2010-01-14

174

We discuss dissipative particle dynamics as a thermostat to molecular dynamics, and highlight some of its virtues: (i) universal applicability irrespective of the interatomic potential; (ii) correct and unscreened reproduction of hydrodynamic correlations; (iii) stabilization of the numerical integration of the equations of motion; and (iv) the avoidance of a profile bias in boundary-driven nonequilibrium simulations of shear flow. Numerical

Thomas Soddemann; Burkhard Dünweg; Kurt Kremer

2003-01-01

175

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

176

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

177

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.

178

Laser Coulomb explosion imaging of molecular dynamics

NASA Astrophysics Data System (ADS)

The goal of this dissertation project was to study the dynamics of nuclear motion in diatomic (H2, N2, O2, CO) and triatomic (CO2) molecules initiated by the ionization and/or excitation of these molecules with near-IR few-cycle laser pulses. This dynamics includes vibrational and rotational motion on the electronic potential surfaces of the molecules and their molecular ions. The experimental techniques used included the pump-probe approach, laser Coulomb explosion imaging and the COLTRIMS technique. The results are presented in four chapters. A study of rotational and vibrational nuclear dynamics in H2 and D2 molecules and ions initiated by 8 fs near-IR pulses is presented in Chapter 4. Transient alignment of the neutral molecules was observed and simulated; rotational frequency components contributing to the rotational wavepacket dynamics were recovered. Chapter 5 is dedicated to revealing the contribution of excited dissociative states of D2+ ions to the process of fragmentation by electron recollision. It was shown that it is possible to isolate the process of resonant excitation and estimate the individual contributions of the 2Sigmau+ and 2? u states. In Chapter 6 the subject of investigation is the nuclear dynamics of N2, O2 and CO molecules initiated by ionization of a neutral molecule by a short intense laser pulse. It was shown that the kinetic energy release of the Coulomb explosion fragments, measured as a function of the delay time between pump and probe pulses, reveals the behavior of nuclear wave packet evolution on electronic states of the molecular ions. It was shown that information on the dissociation and excitation pathways can be extracted from the experimental spectra and the relative contributions of particular electronic states can be estimated. Chapter 7 is focused on studying the fragmentation of CO2 following the interaction of this molecule with the laser field. The most important result of this study was that it presented direct experimental evidence of charge-resonant enhanced ionization (CREI), a phenomenon well-studied for diatomic molecules and predicted theoretically for triatomic molecules. The critical internuclear distance, the relevant ionic charge state and a pair of charge-resonant states responsible for the CREI were also found.

Bocharova, Irina A.

179

Reactive Molecular Dynamics of Detonating Petn

We investigate the initial chemical events sustaining a detonation in shock-compressed PETN resulting from intermolecular collisions behind the shock wave using first-principles reactive molecular dynamics. The reaction dynamics of bimolecular collisions was studied as a function of collision velocities and crystallographic orientations. For each orientation, threshold collision velocities of reaction, and products of decomposition were determined. The timescale of reaction

A. C. Landerville; I. I. Oleynik; C. T. White

2009-01-01

180

REACTIVE MOLECULAR DYNAMICS OF DETONATING PETN

We investigate the initial chemical events sustaining a detonation in shock-compressed PETN resulting from intermolecular collisions behind the shock wave using first-principles reactive molecular dynamics. The reaction dynamics of bimolecular collisions was studied as a function of collision velocities and crystallographic orientations. For each orientation, threshold collision velocities of reaction, and products of decomposition were determined. The timescale of reaction

A. C. Landerville; I. I. Oleynik; C. T. White

2009-01-01

181

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.

182

Molecular dynamics investigation of tracer diffusion in a simple liquid.

National Technical Information Service (NTIS)

Extensive Molecular-Dynamics (MD) simulations have been carried out for a model trace-solvent system made up of 100 solvent molecules and 8 tracer molecules interacting through truncated Lennard-Jones potentials. The influence of the size ratio between so...

F. Ould-Kaddour J. L. Barrat

1991-01-01

183

Molecular dynamics calculations of point defect diffusion coefficients in vanadium

NASA Astrophysics Data System (ADS)

Diffusion coefficients for vacancies and self-interstitial atoms (SIA) in vanadium at several temperatures have been calculated by the molecular dynamics method using EAM potential proposed by Foiles and Adams. Apart from the migration energy the preexponential factor was an object of interest. Simulation results show that the SIA in vanadium exists in a <111>-dumbbell configuration and migrates exceptionally along <111> directions.

Minashin, A. M.; Ryabov, V. A.

1996-10-01

184

Molecular Dynamics Calculations for Sodium using Pseudopotential Theory.

National Technical Information Service (NTIS)

We study the equation of state of sodium 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...

R. E. Swanson

1981-01-01

185

Molecular Dynamics Calculations for Sodium Using Pseudopotential Theory.

National Technical Information Service (NTIS)

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-May...

R. E. Swanson

1981-01-01

186

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. Program summaryProgram title: LPMD Catalogue identifier: AEHG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 509 490 No. of bytes in distributed program, including test data, etc.: 6 814 754 Distribution format: tar.gz Programming language: C++ Computer: 32-bit and 64-bit workstation Operating system: UNIX RAM: Minimum 1024 bytes Classification: 7.7 External routines: zlib, OpenGL Nature of problem: Study of Statistical Mechanics and Thermodynamics of condensed matter systems, as well as kinetics of non-equilibrium processes in the same systems. Solution method: Equilibrium and non-equilibrium molecular dynamics method, Monte Carlo methods. Restrictions: Rigid molecules are not supported. Polarizable atoms and chemical bonds (proteins) either. Unusual features: The program is able to change the temperature of the simulation cell, the pressure, cut regions of the cell, color the atoms by properties, even during the simulation. It is also possible to fix the positions and/or velocity of groups of atoms. Visualization of atoms and some physical properties during the simulation. Additional comments: The program does not only perform molecular dynamics and Monte Carlo simulations, it is also able to filter and manipulate atomic configurations, read and write different file formats, convert between them, evaluate different structural and dynamical properties. Running time: 50 seconds on a 1000-step simulation of 4000 argon atoms, running on a single 2.67 GHz Intel processor.

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

2010-12-01

187

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

188

Statistical Coarse-Graining of Molecular Dynamics into Peridynamics.

National Technical Information Service (NTIS)

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 scale...

R. B. Lehoucq S. A. Silling

2007-01-01

189

Molecular Rheology of Perfluoropolyether Lubricant via Nonequilibrium Molecular Dynamics Simulation

Rheological properties of perfluoropolyether (PFPE) systems can be particularly important in designing effective lubricants that control the friction and wear in their tribological applications. Using equilibrium\\/nonequilibrium molecular dynamics (MD) simulation, we examined the rheological properties of PFPE lubricant, such as viscosity and viscoelastic properties, by observing the time-dependent system in shear motion. Strong dependence of PFPE bulk viscosity on PFPE

Hyoung Jin Choi; Qian Guo; Pil S. Chung; Myung S. Jhon

2007-01-01

190

Histone variants are used by the cell to build specialized nucleosomes, replacing canonical histones and generating functionally specialized chromatin domains. Among many other processes, the specialization imparted by histone H2A (H2A.X and H2A.Z) variants to the nucleosome core particle constitutes the earliest response to DNA damage in the cell. Consequently, chromatin-based genotoxicity tests have been developed in those cases where enough information pertaining chromatin structure and dynamics is available (i.e., human and mouse). However, detailed chromatin knowledge is almost absent in most organisms, specially protostome animals. Molluscs (which represent sentinel organisms for the study of pollution) are not an exception to this lack of knowledge. In the present work we first identified the existence of functionally differentiated histone H2A.X and H2A.Z variants in the mussel Mytilus galloprovincialis (MgH2A.X and MgH2A.Z), a marine organism widely used in biomonitoring programs. Our results support the functional specialization of these variants based on: a) their active expression in different tissues, as revealed by the isolation of native MgH2A.X and MgH2A.Z proteins in gonad and hepatopancreas; b) the evolutionary conservation of different residues encompassing functional relevance; and c) their ability to confer specialization to nucleosomes, as revealed by nucleosome reconstitution experiments using recombinant MgH2A.X and MgH2A.Z histones. Given the seminal role of these variants in maintaining genomic integrity and regulating gene expression, their preliminary characterization opens up new potential applications for the future development of chromatin-based genotoxicity tests in pollution biomonitoring programs.

Gonzalez-Romero, Rodrigo; Rivera-Casas, Ciro; Frehlick, Lindsay J.; Mendez, Josefina; Ausio, Juan; Eirin-Lopez, Jose M.

2012-01-01

191

NVU dynamics. III. Simulating molecules at constant potential energy

NASA Astrophysics Data System (ADS)

This is the final paper in a series that introduces geodesic molecular dynamics at constant potential energy. This dynamics is entitled NVU dynamics in analogy to standard energy-conserving Newtonian NVE dynamics. In the first two papers [T. S. Ingebrigtsen, S. Toxvaerd, O. J. Heilmann, T. B. Schrøder, and J. C. Dyre, J. Chem. Phys. 135, 104101 (2011); T. S. Ingebrigtsen, S. Toxvaerd, T. B. Schrøder, and J. C. Dyre, ibid. 135, 104102 (2011)], a numerical algorithm for simulating geodesic motion of atomic systems was developed and tested against standard algorithms. The conclusion was that the NVU algorithm has the same desirable properties as the Verlet algorithm for Newtonian NVE dynamics, i.e., it is time-reversible and symplectic. Additionally, it was concluded that NVU dynamics becomes equivalent to NVE dynamics in the thermodynamic limit. In this paper, the NVU algorithm for atomic systems is extended to be able to simulate the geodesic motion of molecules at constant potential energy. We derive an algorithm for simulating rigid bonds and test this algorithm on three different systems: an asymmetric dumbbell model, Lewis-Wahnström o-terphenyl (OTP) and rigid SPC/E water. The rigid bonds introduce additional constraints beyond that of constant potential energy for atomic systems. The rigid-bond NVU algorithm conserves potential energy, bond lengths, and step length for indefinitely long runs. The quantities probed in simulations give results identical to those of Nosé-Hoover NVT dynamics. Since Nosé-Hoover NVT dynamics is known to give results equivalent to those of NVE dynamics, the latter results show that NVU dynamics becomes equivalent to NVE dynamics in the thermodynamic limit also for molecular systems.

Ingebrigtsen, Trond S.; Dyre, Jeppe C.

2012-12-01

192

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. Schrøder, and J. C. Dyre, J. Chem. Phys. 135, 104101 (2011); T. S. Ingebrigtsen, S. Toxvaerd, T. B. Schrøder, and J. C. Dyre, ibid. 135, 104102 (2011)], a numerical algorithm for simulating geodesic motion of atomic systems was developed and tested against standard algorithms. The conclusion was that the NVU algorithm has the same desirable properties as the Verlet algorithm for Newtonian NVE dynamics, i.e., it is time-reversible and symplectic. Additionally, it was concluded that NVU dynamics becomes equivalent to NVE dynamics in the thermodynamic limit. In this paper, the NVU algorithm for atomic systems is extended to be able to simulate the geodesic motion of molecules at constant potential energy. We derive an algorithm for simulating rigid bonds and test this algorithm on three different systems: an asymmetric dumbbell model, Lewis-Wahnström o-terphenyl (OTP) and rigid SPC/E water. The rigid bonds introduce additional constraints beyond that of constant potential energy for atomic systems. The rigid-bond NVU algorithm conserves potential energy, bond lengths, and step length for indefinitely long runs. The quantities probed in simulations give results identical to those of Nosé-Hoover NVT dynamics. Since Nose?-Hoover NVT dynamics is known to give results equivalent to those of NVE dynamics, the latter results show that NVU dynamics becomes equivalent to NVE dynamics in the thermodynamic limit also for molecular systems. PMID:23277922

Ingebrigtsen, Trond S; Dyre, Jeppe C

2012-12-28

193

Atomic and molecular quantum mechanics by the path integral molecular dynamics method

NASA Astrophysics Data System (ADS)

The quantum path integral molecular dynamics method was applied to studies of excess electron localization by a Na + ion and by a NaCl molecule. Spatial and energetic characterization of the ground state of the excess electron compare favorably with results of model potential calculations for Na and with SCF Cl calculations for NaCl -.

Scharf, Dafna; Jortner, Joshua; Landman, Uzi

1986-10-01

194

Molecular Dynamics Simulation Methods including Quantum Effects

\\u000a The progress of computational chemistry in the treatment of liquid systems is outlined, and the combination of the statistical\\u000a methods (in particular molecular dynamics) with quantum mechanics as the main foundation of this progress is emphasised. The\\u000a difficulties of experimental studies of liquid systems without having obtained sophisticated theoretical models describing\\u000a the structural entities and the dynamical behaviour of these

THOMAS S. HOFER; BERNHARD R. RANDOLF; BERND M. RODE

195

Molecular dynamics simulation of nanoporous silica

The micro-structure and dynamical properties of nanoporous silica are investigated using the molecular dynamics simulation method. The porous silica obtained have densities down to 0.7 g\\/ml and a mass fractal dimension of 2.6 or higher. The specific surface of the porous silica is calculated and found to be in agreement with adsorption experiments. The vibrational and dielectric power spectra show

J. V. L. Beckers; S. W. de Leeuw

2000-01-01

196

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

2009-03-21

197

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

198

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

2013-11-01

199

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

Stewart Andrew Silling; Richard B. Lehoucq

2007-01-01

200

Shell-model molecular dynamics calculations of modified silicate glasses

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations of pure silica, sodium silicate, and soda-lime silicate glasses have been carried out using a developed potential that includes polarization effects through the shell model (SM). The potential has been validated using available experimental and ab initio structural data, such as density, radial and angular distributions, coordination environments, and network connectivity. In addition, Car-Parrinello molecular dynamics simulations of the soda-lime silicate glass have been carried out to obtain reference data for this system. The performances of the SM and of a rigid-ion potential have been compared with experimental and ab initio data, showing that the inclusion of polarization effects improves the description of the intertetrahedral structure and of the local environment surrounding modifier Na and Ca cations; significant improvements are also obtained in the Qn distribution of the sodium silicate glass. This shows that the inclusion of polarization effects in the potential, even at the approximate level of the shell model, is essential for a reliable modeling of modified bulk glasses. Moreover, the accurate reproduction of the glass density and the direct representation of polarization effects are important requisites that should enable the application of the potential to molecular dynamics simulations of modified glass surfaces.

Tilocca, Antonio; de Leeuw, Nora H.; Cormack, Alastair N.

2006-03-01

201

Molecular Dynamics: Application to Liquid Sodium.

National Technical Information Service (NTIS)

Molecular dynamics (M.D.) and Monte Carlo (M.C.) computer simulation methods have become important tools for the study of equilibrium and transport properties of model condensed matter systems. In the present study the alternate M.D. technique has been us...

K. Yaldram A. Sadiq S. Murad

1989-01-01

202

Crystallographic R Factor Refinement by Molecular Dynamics

Molecular dynamics was used to refine macromolecular structures by incorporating the difference between the observed crystallographic structure factor amplitude and that calculated from an assumed atomic model into the total energy of the system. The method has a radius of convergence that is larger than that of conventional restrained least-squares refinement. Test cases showed that the need for manual corrections

Axel T. Brunger; John Kuriyan; Martin Karplus

1987-01-01

203

Molecular Dynamics Simulations of Graphene Oxide Frameworks

We use quantum mechanical calculations to develop a full set of force field parameters in order to perform molecular dynamics simulations to understand and optimize the molecular storage properties inside Graphene Oxide Frameworks (GOFs). A set of boron-related parameters for commonly used empirical force fields is determined to describe the non-bonded and bonded interactions between linear boronic acid linkers and graphene sheets of GOF materials. The transferability of the parameters is discussed and their validity is quantified by comparing quantum mechanical and molecular mechanical structural and vibrational properties. The application of the model to the dynamics of water inside the GOFs reveals significant variations in structural flexibility of GOF depending on the linker density, which is shown to be usable as a tuning parameter for desired diffusion properties.

Zhu, Pan [Rensselaer Polytechnic Institute (RPI)] [Rensselaer Polytechnic Institute (RPI); Sumpter, Bobby G [ORNL] [ORNL; Meunier, V. [Rensselaer Polytechnic Institute (RPI)] [Rensselaer Polytechnic Institute (RPI); Nicolai, Adrien [Rensselaer Polytechnic Institute (RPI)] [Rensselaer Polytechnic Institute (RPI)

2013-01-01

204

Symmetry and dynamics of molecular rotors in amphidynamic molecular crystals

Rotary biomolecular machines rely on highly symmetric supramolecular structures with rotating units that operate within a densely packed frame of reference, stator, embedded within relatively rigid membranes. The most notable examples are the enzyme FoF1 ATP synthase and the bacterial flagellum, which undergo rotation in steps determined by the symmetries of their rotators and rotating units. Speculating that a precise control of rotational dynamics in rigid environments will be essential for the development of artificial molecular machines, we analyzed the relation between rotational symmetry order and equilibrium rotational dynamics in a set of crystalline molecular gyroscopes with rotators having axial symmetry that ranges from two- to fivefold. The site exchange frequency for these molecules in their closely related crystals at ambient temperature varies by several orders of magnitude, up to ca. 4.46 × 108 s-1.

Karlen, Steven D.; Reyes, Horacio; Taylor, R. E.; Khan, Saeed I.; Hawthorne, M. Frederick; Garcia-Garibay, Miguel A.

2010-01-01

205

Ab Initio Molecular Dynamics Simulations of Molecular Collisions of Nitromethane

Ab initio molecular dynamics simulations of bimolecular collisions of nitromethane, and collisions of one nitromethane molecule into a cluster of 12 nitromethane molecules have been performed. For the bimolecular simulations we have examined a variety of collision orientations and collision velocities between 6.5 and 12.0 km\\/s. The lowest dissociation threshold velocity found was 7.0 km\\/s for an anti-parallel collision orientation.

Dongqing Wei; Fan Zhang; Tom K. Woo

2002-01-01

206

Dynamics of Ag clusters on complex surfaces: Molecular dynamics simulations

We study the diffusion of silver nanoparticles on self-assembled monolayers (SAMs). Silver clusters Agn of sizes n=55 , 147, and 1289 were evolved in contact with an alkanethiol (12 carbon, dodecanethiol) SAM deposited on a gold (111) surface. Analysis based on classical molecular dynamics simulations reveals that these systems exhibit a rich variety of behaviors, from superdiffusive for the lightest

S. Alkis; J. L. Krause; J. N. Fry; H.-P. Cheng

2009-01-01

207

We examine the effect of different model potential parameters on several structural and dynamical properties of a liquid–liquid (L\\/L) interface by molecular dynamics (MD) simulations. Additionally, the influence of the particle masses is explored. The L\\/L system consists of two-model Lennard–Jones (LJ) species (called Ar1 and Ar2). It was investigated for four different variations of either the ?- or ?-parameter

Jörn B. Buhn; Philippe A. Bopp; Manfred J. Hampe

2006-01-01

208

Molecular Dynamics Simulation of Point Defect Diffusion in Polycrystalline Metals

NASA Astrophysics Data System (ADS)

The dynamics and interactions of point defects at metallic grain boundaries are of critical importance in understanding the mechanisms governing electromigration in semiconductor device interconnects. We have performed dynamical simulations of point defect diffusion and metal atom self-diffusion at Al grain boundaries, using a parallel molecular dynamics simulation code which can accomodate a variety of atomistic potential models, including embedded atom method (EAM) and iteratively-refined cluster potentials. The construction of the cluster potentials from first principles calculations will be described, and we will discuss the importance of including nonlocal effects at both the electronic and atomic levels of the theory, in light of the strong inhomogenieties in electron density present in these systems.

Atlas, Susan R.

1997-03-01

209

Molecular dynamics and tunnelling in supramolecular complexes

NASA Astrophysics Data System (ADS)

Inelastic neutron scattering has been used to study molecular tunnelling and intramolecular vibrational modes in several inclusion complexes of calixarenes. In methyl-containing guest molecules the free rotor limit is approached, and the splitting of the librational modes appears to be very sensitive to the details of the particle motion. The experimental spectra are interpreted in the framework of different models, and the potential barriers obtained are compared with molecular mechanics calculations.

Caciuffo, R.; Amoretti, G.; Carlile, C. J.; Ferrero, C.; Geremia, S.; Paci, B.; Prager, M.; Ugozzoli, F.

1997-02-01

210

Rational prediction with molecular dynamics for hit identification.

Although the motions of proteins are fundamental for their function, for pragmatic reasons, the consideration of protein elasticity has traditionally been neglected in drug discovery and design. This review details protein motion, its relevance to biomolecular interactions and how it can be sampled using molecular dynamics simulations. Within this context, two major areas of research in structure-based prediction that can benefit from considering protein flexibility, binding site detection and molecular docking, are discussed. Basic classification metrics and statistical analysis techniques, which can facilitate performance analysis, are also reviewed. With hardware and software advances, molecular dynamics in combination with traditional structure-based prediction methods can potentially reduce the time and costs involved in the hit identification pipeline. PMID:23110535

Nichols, Sara E; Swift, Robert V; Amaro, Rommie E

2012-01-01

211

Molecular dynamics simulator for optimal control of molecular motion

NASA Astrophysics Data System (ADS)

In recognition of recent interest in developing optimal control techniques for manipulating molecular motion, this paper introduces a computer-driven electro-mechanical analog of this process. The resultant Molecular Dynamic Simulator (MDS) is centered around a linear air track for which the atoms of the controlled molecule are simulated as nearly frictionless carts on the track. Bonds in the simulated molecule are described by precision springs, and the interaction with an external optical field is simulated through a computer-based linear driver. When the MDS is operated in the harmonic regime, it can be used as an exact analog of molecular scale quantum systems through Ehrenfest's Theorem, or equivalently as a classical set of coupled oscillators. The tools of optimal control theory currently being applied at the molecular scale are used to design the forcing function for the MDS. Optical encoders are used to measure bond distances for graphic representation of the MDS behavior. Bond breaking can also be simulated by bond-length sensitive trigger-release mechanisms. The MDS is especially useful as a modelling tool to bridge theoretical studies and eventual laboratory experiments at the true molecular scale.

Rabitz, Herschel

1990-12-01

212

Molecular dynamics simulation in RNA interference.

RNA interference (RNAi) is a mechanism that utilizes small RNA molecules to silence gene expression after the gene has been transcribed. To understand the mechanisms of small RNA biogenesis, target nucleic acid recognition and cleavage, and how they are influenced by other regulators, one needs to know the structures and dynamics of the proteins or/and nucleic acids in these processes. Molecular dynamics (MD) simulation is a powerful tool for understanding motions and dynamics of macro-biomolecules at an atomic-scale via theoretical and empirical principles in physical chemistry. With its application to RNAi, an excellent overview of structural and dynamical mechanistic of RNAi processes has already emerged. In this review, we summarize the recent advances in MD simulations in the study of functional modules and their assemblies and target recognition and cleavage in RNAi processes. Additionally, we also present some perspectives on this technique. PMID:24350843

Wang, Xia; Wang, Yonghua; Zheng, Lei; Chen, Jianxin

2014-06-01

213

Reactive Molecular Dynamics of Detonating Petn

NASA Astrophysics Data System (ADS)

We investigate the initial chemical events sustaining a detonation in shock-compressed PETN resulting from intermolecular collisions behind the shock wave using first-principles reactive molecular dynamics. The reaction dynamics of bimolecular collisions was studied as a function of collision velocities and crystallographic orientations. For each orientation, threshold collision velocities of reaction, and products of decomposition were determined. The timescale of reaction was evaluated and used to understand whether these initial chemical events are largely driven by reaction dynamics, or temperature. Bond dissociation energies were calculated and used to rationalize the outcome of the chemical events in the course of the reaction dynamics. Finally, the relationship between orientation dependent sensitivities and steric factors is discussed.

Landerville, A. C.; Oleynik, I. I.; White, C. T.

2009-12-01

214

This dissertation examines two of the most important behaviors of amorphous polymers: the glass transition and plastic deformation. These phenomena are examined using atomic-scale molecular dynamics simulations, in which the atomic interactions are described through empirical bonded and non-bonded interatomic potentials representing amorphous polyethylene. Molecular dynamics simulations were performed to elucidate the effects of temperature and thermodynamic constraints on the

Liu Yang

1997-01-01

215

Molecular dynamics simulations and drug discovery

This review discusses the many roles atomistic computer simulations of macromolecular (for example, protein) receptors and their associated small-molecule ligands can play in drug discovery, including the identification of cryptic or allosteric binding sites, the enhancement of traditional virtual-screening methodologies, and the direct prediction of small-molecule binding energies. The limitations of current simulation methodologies, including the high computational costs and approximations of molecular forces required, are also discussed. With constant improvements in both computer power and algorithm design, the future of computer-aided drug design is promising; molecular dynamics simulations are likely to play an increasingly important role.

2011-01-01

216

Molecular Dynamics and Electron Density Studies of Siderophores and Peptides.

NASA Astrophysics Data System (ADS)

The dissertation comprises three separate studies of siderophores and peptides. In the first of these studies the relative potential energies for a series of diastereomers of a siderophore neocoprogen I are evaluated with molecular mechanics force field methods. Charges on the hydroxamate moiety are determined with a synthetic model siderophore compound using valence population refinements, and alternatively, with the theoretical ab initio/ESP calculations. The single diastereomer found in the crystal structure is among four characterized by the low potential energy, while prevalence of Delta vs. Lambda configuration about the iron is found to be a property of the entire series. In the second study the crystal structure of a ferrichrome siderophore ferrirhodin is reported. The crystal structure conformation of the molecular backbone as well as the iron coordination geometry compare well with other ferrichrome structures. The differences between the acyl groups of ferrirubin and ferrirhodin are explored using the methods of molecular mechanics. The third study a 300 ps, 300 K, in vacuo molecular dynamics simulation of didemnin A and B yields distinct molecular conformers, which are different from the one found in the crystal structure or modeled in solution, using the Nuclear Overhauser Effect data. Evaluations of the relative potential energy are performed with short 10 ps simulations in solution. Didemnins are natural depsipeptides isolated from a Caribbean tunicate and characterized by particularly potent antiproliferative and immunomodulatory activity. Conformationally rigid and flexible regions of the molecule are described. A short review of the molecular mechanics methodology is given in the introduction.

Fidelis, Krzysztof Andrzej

1990-08-01

217

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

218

Molecular Dynamics Computer Simulation Studies of Close-Packed Solids

Close-packed (polytypic) structures, found to be metastable during studies of structural phase transformations among close-packed crystalline systems in molecular dynamics computer simulations, are considered in conjunction with the often-used periodic boundary conditions and potential cutoff range. After presenting a denotation of those polytypes compatible with periodic boundary conditions, the computation of the fractional particle coordination numbers exhibited by polytypic structures

Michael Craig Moody

1985-01-01

219

Molecular dynamics study for the thermal conductivity of diatomic liquid

The thermal conductivity of diatomic liquids was analyzed using a nonequilibrium molecular dynamics (NEMD) method. Five liquids, namely, O2, CO, CS2, Cl2 and Br2, were assumed. The two-center Lennard-Jones (2CLJ) model was used to express the intermolecular potential acting on liquid molecules. First, the equation of state of each liquid was obtained using MD simulation, and the critical temperature, density

Takashi Tokumasu; Kenjiro Kamijo

2004-01-01

220

Variational path integral molecular dynamics study of a water molecule

NASA Astrophysics Data System (ADS)

In the present study, a variational path integral molecular dynamics method developed by the author [Chem. Phys. Lett. 482, 165 (2009)] is applied to a water molecule on the adiabatic potential energy surface. The method numerically generates an exact wavefunction using a trial wavefunction of the target system. It has been shown that even if a poor trial wavefunction is employed, the exact quantum distribution is numerically extracted, demonstrating the robustness of the variational path integral method.

Miura, Shinichi

2013-08-01

221

Molecular dynamics calculations for sodium using pseudopotential theory

NASA Astrophysics Data System (ADS)

We study the equation of state of sodium 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. We use a model pseudopotential with parameters fit to experimental low-temperature data. By using this technique, we are able to begin with an atomic description of a simple metal and proceed to calculate its macroscopic thermodynamic properties. We calculate equation-of-state points consisting of the total internal energy in volume and temperature space. We illustrate the unique capabilities of the molecular dynamics technique by inducing a dynamic bcc-to-hcp martensitic phase change. The results of this study demonstrate that the molecular dynamics technique, coupled with an interaction potential that adequately describes the ion-ion interaction in a simple metal, can be used to calculate the macroscopic properties of such systems.

Swanson, R. E.

1981-04-01

222

A random rotor molecule: Vibrational analysis and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Molecular structures that permit intramolecular rotational motion have the potential to function as molecular rotors. We have employed density functional theory and vibrational frequency analysis to study the characteristic structure and vibrational behavior of the molecule (4',4''''-(bicyclo[2,2,2]octane-1,4-diyldi-4,1-phenylene)-bis-2,2':6',2''-terpyridine. IR active vibrational modes were found that favor intramolecular rotation. To demonstrate the rotor behavior of the isolated single molecule, ab initio molecular dynamics simulations at various temperatures were carried out. This molecular rotor is expected to be thermally triggered via excitation of specific vibrational modes, which implies randomness in its direction of rotation.

Li, Yu; Zhang, Rui-Qin; Shi, Xing-Qiang; Lin, Zijing; Van Hove, Michel A.

2012-12-01

223

Locally disrupted synchronization in Langevin molecular dynamics.

Stochastic thermostats commonly used in molecular dynamics trajectories are known, under certain conditions, to exhibit a synchronization effect whereby trajectories initialized at different points in phase space synchronize to a single master trajectory if they are subjected to the same sequence of random forces. We investigate the spatiotemporal robustness of this effect analytically and with molecular dynamics simulations in one and three dimensions in the strong coupling limit. We first investigate the response of the system to a time- and spacewise local perturbation and show that desynchronization behaves diffusively at long times for infinite systems. We then explore the behavior of temporally persistent but spatially local perturbations and observe strikingly different behaviors as a function of dimensionality: in one dimension, the desynchronization propagates through the whole lattice and grows with time, while in three dimensions, the desynchronization remains localized in the neighborhood of the perturbation. PMID:23005878

Georgescu, Andreea I; Denny, Samuel J; Joly, Emilien; Chen, Grace; Perez, Danny; Voter, Arthur F

2012-08-01

224

MOLECULAR DYNAMICS SIMULATION OF NANOMETRIC CUTTING

Molecular Dynamics (MD) simulations of nanometric cutting of single-crystal copper were conducted to predict cutting forces and investigate the mechanism of chip formation at the nano-level. The MD simulations were conducted at a conventional cutting speed of 5 m\\/s and different depths of cut (0.724–2.172 nm), and cutting forces and shear angle were predicted. The effect of tool rake angles and depths

Rapeepan Promyoo; Hazim El-Mounayri; Xiaoping Yang

2010-01-01

225

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

226

Molecular crowding and protein enzymatic dynamics.

The effects of molecular crowding on the enzymatic conformational dynamics and transport properties of adenylate kinase are investigated. This tridomain protein undergoes large scale hinge motions in the course of its enzymatic cycle and serves as prototype for the study of crowding effects on the cyclic conformational dynamics of proteins. The study is carried out at a mesoscopic level where both the protein and the solvent in which it is dissolved are treated in a coarse grained fashion. The amino acid residues in the protein are represented by a network of beads and the solvent dynamics is described by multiparticle collision dynamics that includes effects due to hydrodynamic interactions. The system is crowded by a stationary random array of hard spherical objects. Protein enzymatic dynamics is investigated as a function of the obstacle volume fraction and size. In addition, for comparison, results are presented for a modification of the dynamics that suppresses hydrodynamic interactions. Consistent with expectations, simulations of the dynamics show that the protein prefers a closed conformation for high volume fractions. This effect becomes more pronounced as the obstacle radius decreases for a given volume fraction since the average void size in the obstacle array is smaller for smaller radii. At high volume fractions for small obstacle radii, the average enzymatic cycle time and characteristic times of internal conformational motions of the protein deviate substantially from their values in solution or in systems with small density of obstacles. The transport properties of the protein are strongly affected by molecular crowding. Diffusive motion adopts a subdiffusive character and the effective diffusion coefficients can change by more than an order of magnitude. The orientational relaxation time of the protein is also significantly altered by crowding. PMID:22476233

Echeverria, Carlos; Kapral, Raymond

2012-04-01

227

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 ½kT of kinetic energy in a canonical ensemble. This principle is used in molecular dynamics simulations to initialize velocities, and to calculate statistical properties such as entropy. Internal coordinate molecular dynamics (ICMD) models differ from Cartesian models in that the overall kinetic energy depends on the generalized coordinates and includes cross-terms. Due to this coupled structure, no such equipartition principle holds for ICMD models. In this paper we introduce non-canonical modal coordinates to recover some of the structural simplicity of Cartesian models and develop a new equipartition principle for ICMD models. We derive low-order recursive computational algorithms for transforming between the modal and physical coordinates. The equipartition principle in modal coordinates provides a rigorous method for initializing velocities in ICMD simulations thus replacing the ad hoc methods used until now. It also sets the basis for calculating conformational entropy using internal coordinates.

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

2012-01-01

228

Analysis of motion features for molecular dynamics simulation of proteins

NASA Astrophysics Data System (ADS)

Recently, a new method for time series analysis using the wavelet transformation has been proposed by Sakurai et al. We apply it to molecular dynamics simulation of Thermomyces lanuginosa lipase (TLL). Introducing indexes to characterize collective motion of the protein, we have obtained the following two results. First, time evolution of the collective motion involves not only the dynamics within a single potential well but also takes place wandering around multiple conformations. Second, correlation of the collective motion between secondary structures shows that collective motion exists involving multiple secondary structures. We discuss future prospects of our study involving 'disordered proteins'.

Kamada, Mayumi; Toda, Mikito; Sekijima, Masakazu; Takata, Masami; Joe, Kazuki

2011-01-01

229

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

230

Application of two dimensional periodic molecular dynamics to interfaces.

NASA Astrophysics Data System (ADS)

We have applied two-dimensional molecular dynamics to the surface of a crystalline aspartame and the interface between the crystal face and a solvent (water). This has allowed us to look at the dynamic processes at the surface. Understanding the surface structure and properties are important to controlling the crystal morphology. The thermodynamic ensemble was constant Number, surface Area and Temperature (NAT). The calculations have been carried out using a 2D Ewald summation and 2D periodic boundary conditions for the short range potentials. The equations of motion integration has been carried out using the standard velocity Verlet algorithm.

Gay, David H.; Slater, Ben; Catlow, C. Richard A.

1997-08-01

231

Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears

NASA Technical Reports Server (NTRS)

Dynamics of laser powered carbon nanotube gears is investigated by molecular dynamics simulations with Brenner's hydrocarbon potential. We find that when the frequency of the laser electric field is much less than the intrinsic frequency of the carbon nanotube, the tube exhibits an oscillatory pendulam behavior. However, a unidirectional rotation of the gear with oscillating frequency is observed under conditions of resonance between the laser field and intrinsic gear frequencies. The operating conditions for stable rotations of the nanotube gears, powered by laser electric fields are explored, in these simulations.

Srivastava, Deepak; Globus, Al; Han, Jie; Chancellor, Marisa K. (Technical Monitor)

1997-01-01

232

Molecular dynamics integration meets standard theory of molecular vibrations.

An iterative SISM (split integration symplectic method) for molecular dynamics (MD) integration is described. This work explores an alternative for the internal coordinate system prediction in the SISM introduced by JaneZic et al. (J. Chem. Phys. 2005, 122, 174101). The SISM, which employs a standard theory of molecular vibrations, analytically resolves the internal high-frequency molecular vibrations. This is accomplished by introducing a translating and rotating internal coordinate system of a molecule and calculating normal modes of an isolated molecule only. The Eckart frame, which is usually used in the standard theory of molecular vibrations as an internal coordinate system of a molecule, is adopted to be used within the framework of the second order generalized leapfrog scheme. In the presented MD integrator the internal coordinate frame at the end of the integration step is predicted halfway through the integration step using a predictor-corrector type iterative approach thus ensuring the method's time reversibility. The iterative SISM, which is applicable to any system of molecules with one equilibrium configuration, was applied here to perform all-atom MD simulations of liquid CO2 and SO2. The simulation results indicate that for the same level of accuracy, this algorithm allows significantly longer integration time steps than the standard second-order leapfrog Verlet (LFV) method. PMID:16309256

Praprotnik, Matej; Janezic, Dusanka

2005-01-01

233

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

234

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

235

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

236

Molecular Dynamics in Cyclic Olefin Copolymer

NASA Astrophysics Data System (ADS)

Nuclear magnetic resonance, broadband dielectric spectroscopy and dynamic-mechanical thermal analysis were employed to study molecular dynamics of ethylene-norbornene copolymer. The analysis of experimental data indicates existence of three motional processes denoted as ?, ?, and ? in order of decreasing temperature. The? relaxation is related to the dynamic glass transition, while the? relaxation, observed only for the untreated sample, is assigned to short range segmental motions involving norbornene units. The ? relaxation is due to very local motions of ethylene units e.g. trans-gauche isomerization, similar to those responsible for ? relaxation in polyethylene. The rate of motion accountable for ? process, follows the Vogel-Fulcher-Tammann equation, similarly to ? transition, indicating cooperative nature of the motion.

Makrocka-Rydzyk, M.; Orozbaev, B.; Nowaczyk, G.; G?owinkowski, S.; Jurga, S.

2006-08-01

237

Molecular Dynamics Study of Single Conjugated Polymers Confined to Nanoparticles

NASA Astrophysics Data System (ADS)

Optically active polymers confined into nanoparticles are highly fluorescent and have potential applications in intracellular fluorescence imaging, bio-sensors and other optoelectronic devices. Internal conformation and dynamics of the polymers determines their optical properties. Using molecular dynamics (MD) simulations, we have explored the structure and dynamics of nanoparticles formed by conjugated polymers in a collapsed conformation, which is not the most stable conformation of the polymer. Nanoparticles were formed in a collapsed conformation and followed as the function of time in both poor and good solvents. We found that these nanoparticles are stable and remain collapsed in a poor solvent but rapidly expands and unraveled in a good solvent. The lengths of the side chains affect the internal packing of the side chains which in turn affect the size of the nanoparticles. S(q,t) was measured to characterize the internal dynamics of the collapsed nanoparticles.

Maskey, Sabina; Pierce, Flint; Perahia, Dvora; Grest, Gary

2011-03-01

238

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

239

NASA Astrophysics Data System (ADS)

The tight-binding model is presented as a successful theory for describing cohesion. It allows for rapid, but accurate, evaluation of electronic properties, total energies, and forces, while being simple enough to allow insight into the nature of bonding. The problem of applying this model to very large systems by diagonalizing the Hamiltonian matrix is discussed. Moments methods provide an efficient way to evaluate energies and forces from the Hamiltonian, even for large systems. However, for systems with sharp features in a broad density of states, many moments are required to achieve convergence. By reference to a moments method [the bond-order potential (BOP)] and a cluster-based method [cluster recursion (CR)], the origin of the need for many moments is explained. In particular, it is found that the inclusion of an exact description of the first-neighbor shell is important for obtaining accurate forces. For strongly covalent systems it also improves the energy convergence. Whereas CR gives rapid convergence with respect to number of levels, BOP is found to give more rapid convergence with respect to CPU time.

Horsfield, A. P.; Bratkovsky, A. M.; Pettifor, D. G.; Aoki, M.

1996-01-01

240

First principles molecular dynamics of molten NaCl

NASA Astrophysics Data System (ADS)

First principles Hellmann-Feynman molecular dynamics (HFMD) results for molten NaCl at a single state point are reported. The effect of induction forces on the structure and dynamics of the system is studied by comparison of the partial radial distribution functions and the velocity and force autocorrelation functions with those calculated from classical MD based on rigid-ion and shell-model potentials. The first principles results reproduce the main structural features of the molten salt observed experimentally, whereas they are incorrectly described by both rigid-ion and shell-model potentials. Moreover, HFMD Green-Kubo self-diffusion coefficients are in closer agreement with experimental data than those predicted by classical MD. A comprehensive discussion of MD results for molten NaCl based on different ab initio parametrized polarizable interionic potentials is also given.

Galamba, N.; Costa Cabral, B. J.

2007-03-01

241

Molecular Dynamics of a Protein Surface: Ion-Residues Interactions

Time-resolved measurements indicated that protons could propagate on the surface of a protein or a membrane by a special mechanism that enhanced the shuttle of the proton toward a specific site. It was proposed that a suitable location of residues on the surface contributes to the proton shuttling function. In this study, this notion was further investigated by the use of molecular dynamics simulations, where Na+ and Cl? are the ions under study, thus avoiding the necessity for quantum mechanical calculations. Molecular dynamics simulations were carried out using as a model a few Na+ and Cl? ions enclosed in a fully hydrated simulation box with a small globular protein (the S6 of the bacterial ribosome). Three independent 10-ns-long simulations indicated that the ions and the protein's surface were in equilibrium, with rapid passage of the ions between the protein's surface and the bulk. However, it was noted that close to some domains the ions extended their duration near the surface, thus suggesting that the local electrostatic potential hindered their diffusion to the bulk. During the time frame in which the ions were detained next to the surface, they could rapidly shuttle between various attractor sites located under the electrostatic umbrella. Statistical analysis of the molecular dynamics and electrostatic potential/entropy consideration indicated that the detainment state is an energetic compromise between attractive forces and entropy of dilution. The similarity between the motion of free ions next to a protein and the proton transfer on the protein's surface are discussed.

Friedman, Ran; Nachliel, Esther; Gutman, Menachem

2005-01-01

242

Attractor dynamics of inflationary monomial potentials

NASA Astrophysics Data System (ADS)

We study the attractors solutions of the dynamical system of a scalar field endowed with monomial potentials of the form V(?)~?2n. The evolution equations of the system are written as a dynamical system, and the critical points represent solutions of physical interest. It is easy to find curves that conect the critical points, some of which behave as attractor inflationary trajectories in phase space.

Reyes-Ibarra, Mayra J.; Arturo Ureña-López, L.

2010-07-01

243

Local Refinements in Classical Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Quantum mechanics provide a detailed description of the physical and chemical behavior of molecules. However, with increasing size of the system the complexity rises exponentially, which is prohibitive for efficient dynamical simulation. In contrast, classical molecular dynamics procure a coarser description by using less degrees of freedom. Thus, it seems natural to seek for an adequate trade-off between accurateness and computational feasibility in the simulation of molecules. Here, we propose a novel method, which combines classical molecular simulations with quantum mechanics for molecular systems. For this we decompose the state space of the respective molecule into subsets, by employing a meshfree partition of unity. We show, that this partition allows us to localize an empirical force field and to run locally constrained classical trajectories. Within each subset, we compute the energy on the quantum level for a fixed number of spatial states (ab initio points). With these energy values from the ab initio points we have a local scattered data problem, which can be solved by the moving least squares method.

Fackeldey, Konstantin; Weber, Marcus

2014-03-01

244

NASA Astrophysics Data System (ADS)

An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.

Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi

2004-01-01

245

An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system. PMID:15267291

Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi

2004-01-01

246

Classical molecular dynamics simulations are used to investigate the nuclear motions associated with photoinduced electron transfer in plastocyanin. The blue copper protein is modeled using a molecular mechanics potential; potential parameters for the copper-protein interactions are determined using an x-ray crystallographic structure and absorption and resonance Raman spectra. Molecular dynamics simulations yield a variety of information about the ground (oxidized) and optically excited (charge-transfer) states: 1) The probability distribution of the potential difference between the states, which is used to determine the coordinate and energy displacements, places the states well within the Marcus inverted region. 2) The two-time autocorrelation function of the difference potential in the ground state and the average of the difference potential after instantaneous excitation to the excited state are very similar (confirming linear response in this system); their decay indicates that vibrational relaxation occurs in about 1 ps in both states. 3) The spectral densities of various internal coordinates begin to identify the vibrations that affect the optical transition; the spectral density of the difference potential correlation function should also prove useful in quantum simulations of the back electron transfer. 4) Correlation functions of the protein atomic motions with the difference potential show that the nuclear motions are correlated over a distance of more than 20 A, especially along proposed electron transport paths. Images FIGURE 1 FIGURE 7

Ungar, L W; Scherer, N F; Voth, G A

1997-01-01

247

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

248

Annihilation of craters: Molecular dynamic simulations on a silver surface

The ability of silver cluster ions containing 13 atoms to fill in a preexisting crater with a radius of about 28 A ring on a silver (001) target has been investigated using molecular dynamics simulations and the molecular-dynamics-Monte Carlo corrected effective medium potential. The largest lateral distance r between crater and ion was about three times the radius of the preexisting crater, namely, 75 A ring . The results reveal that when r<20 A ring and r>60 A ring the preexisting crater is partially filled in, and for other distances there is a net growth of the crater. The lattice damage created by the cluster ions, the total sputtering yield, the cluster sputtering yield, and simulated transmission electron microscopy images of the irradiated targets are also presented.

Henriksson, K. O. E.; Nordlund, K.; Keinonen, J. [Royal Institute of Technology, Department of Reactor Physics, S-10691 Stockholm (Sweden); Accelerator Laboratory, P.O. Box 43, FI-00014 University of Helsinki (Finland)

2007-12-15

249

Tunable Interfacial Thermal Conductance by Molecular Dynamics

NASA Astrophysics Data System (ADS)

We study the mechanism of tunable heat transfer through interfaces between solids using a combination of non-equilibrium molecular dynamics simulation (NEMD), vibrational mode analysis and wave packet simulation. We investigate how heat transfer through interfaces is affected by factors including pressure, interfacial modulus, contact area and interfacial layer thickness, with an overreaching goal of developing fundamental knowledge that will allow one to tailor thermal properties of interfacial materials. The role of pressure and interfacial stiffness is unraveled by our studies on an epitaxial interface between two Lennard-Jones (LJ) crystals. The interfacial stiffness is varied by two different methods: (i) indirectly by applying pressure which due to anharmonic nature of bonding, increases interfacial stiffness, and (ii) directly by changing the interfacial bonding strength by varying the depth of the potential well of the LJ potential. When the interfacial bonding strength is low, quantitatively similar behavior to pressure tuning is observed when the interfacial thermal conductance is increased by directly varying the potential-well depth parameter of the LJ potential. By contrast, when the interfacial bonding strength is high, thermal conductance is almost pressure independent, and even slightly decreases with increasing pressure. This decrease can be explained by the change in overlap between the vibrational densities of states of the two crystalline materials. The role of contact area is studied by modeling structures comprised of Van der Waals junctions between single-walled nanotubes (SWCNT). Interfacial thermal conductance between SWCNTs is obtained from NEMD simulation as a function of crossing angle. In this case the junction conductance per unit area is essentially a constant. By contrast, interfacial thermal conductance between multiwalled carbon nanotubes (MWCNTs) is shown to increase with diameter of the nanotubes by recent experimental studies [1]. To elucidate this behavior we studied a simplified model comprised of an interface between two stacks of graphene ribbons to mimic the contact between multiwalled nanotubes. Our results, in agreement with experiment, show that the interfacial thermal conductance indeed increases with the number of graphene layers, corresponding to larger diameter and larger number of walls in MWCNT. The role of interfacial layer thickness is investigated by modeling a system of a few layers of graphene sandwiched between two silicon slabs. We show, by wave packet simulation and by theoretical calculation of a spring-mass model, that the transmission coefficient of individual vibrational modes is strongly dependent on the frequency and the number of graphene layers due to coherent interference effects; by contrast, the interfacial thermal conductance obtained in NEMD simulation, which represents an integral over all phonons, is essentially independent of the number of graphene layers, in agreement with recent experiments. Furthermore, when we heat one atomic layer of graphene directly, the effective interfacial conductance associated with heat dissipation to the silicon substrate is very small. We attribute this to the resistance associated with heat transfer between high and low frequency phonon modes within graphene. Finally, we also replaced graphene layers by a few WSe2 sheets and observed that interfacial thermal resistance of a Si/n-WSe2/Si structure increases linearly with interface thickness at least for 1 < n <= 20, indicating diffusive heat transfer mechanism, in contrast to ballistic behavior of a few graphene layers. The corresponding thermal conductivity (0.048 W m-1 K-1) of a few WSe2 layers is rather small. By comparing phonon dispersion of graphene layers and WSe2 sheets, we attribute the diffusive behavior of a few WSe2 sheets to abundant optical phonons at low and medium frequencies leading to very short mean free path. Our computational studies of effects of pressure and structural properties on interfacial thermal conductance provide fundamental in

Shen, Meng

250

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

251

Wigner's pseudo-particle relativistic dynamics in external potential field

NASA Astrophysics Data System (ADS)

The Wigner's pseudo-particle formalism has been generalized to describe quantum dynamics of relativistic particle in external potential field. As a simplest application of the developed formalism the time evolution of the 1D relativistic quantum harmonic oscillator been considered. Due to the complex structure of the evolution equation for Wigner function, the only numerical treatment is possible by combining Monte Carlo and molecular dynamics methods. Relativistic dynamics results in appearance of the new physical effects as opposed to non-relativistic case. Interesting is the complete changing of the shape of the momentum and coordinate distribution functions as well as formation of ‘unexpected’ protuberances. To analyze the influence of relativistic effects on average values of quantum operators, the dependencies on time of average momentum, position, their dispersions and energy have been compared for the non-relativistic and relativistic dynamics.

Larkin, A. S.; Filinov, V. S.

2014-05-01

252

Cholangiociliopathies: genetics, molecular mechanisms and potential therapies

Purpose of review The present review summarizes recent knowledge on polycystic liver diseases (PCLDs), mechanisms of hepatic cystogenesis and potential therapies for these conditions. Recent findings PCLD may be classified as cholangiociliopathies. In PCLD associated with polycystic kidney disease, cell proliferation is one of the major mechanisms of cystogenesis, whereas in isolated PCLD (autosomal dominant polycystic liver disease), disrupted cell adhesion may be more important in cyst progression. In cystic cholangiocytes, overexpression of ion transporters and water channels facilitates fluid secretion into the cystic lumen, and growth factors, estrogens and cytokines promote cholangiocyte proliferation. With age, cholangiocytes lining liver cysts acquire features of mesenchymal cells contributing to hepatic fibrocystogenesis. A novel mechanism of liver cyst expansion in PCLD involves microRNA regulatory pathways. Hyperproliferation of cystic cholangiocytes is linked to abnormalities in cell cycle progression and microRNA expression. Decreased levels of miR-15a are coupled to upregulation of its target – the cell cycle regulator, Cdc25A. Cholangiocyte cilia in liver cysts are structurally abnormal. Somatostatin analogues and sirolimus reduce liver cyst volume in PCLD patients. Summary Clarification of molecular mechanisms of hepatic cystogenesis provides an opportunity for the development of targeted therapeutic options in PCLD.

Masyuk, Tatyana; Masyuk, Anatoliy; LaRusso, Nicholas

2013-01-01

253

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

254

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

255

Implementing peridynamics within a molecular dynamics code.

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.

Lehoucq, Richard B.; Silling, Stewart Andrew; Plimpton, Steven James; Parks, Michael L.

2007-12-01

256

Bio-Molecular Dynamics Comes of Age

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. Atomic force microscopy has recently been used to measure the binding force between two biomolecules; complementing the experiments are computational molecular dynamics studies that seek to reveal the details of the binding and unbinding mechanisms. In his Perspective, Berendsen discusses the results reported in the same issue by GrubmÃÂ¼ller et al. (p. 997) on numerical simulations of the binding and separation of biotin from streptavidin, which show excellent agreement with measurements of the rupture force.

Herman J. C. Berendsen (University of Groningen, Netherlands;Department of Biophysical Chemistry and the BIOSON Research Institute)

1996-02-16

257

A fast recursive algorithm for molecular dynamics simulation

In this paper, we develop a recursive algorithm for solving the dynamical equations of motion for molecular systems. We make use of internal variable models which have been shown to reduce the computation times of molecular dynamics simulations by an order of magnitude when compared with Cartesian models. The O(N) algorithm described in this paper for solving the equations of motion provides additional significant improvements in computational speed. We make extensive use of the spatial operator methods which have been developed recently for the analysis and simulation of the dynamics of multibody systems. The spatial operators are used to derive the equations of motion and obtain an operator expression for the system mass matrix. An alternative square factorization of the mass matrix leads to a closed form expression for its inverse. From this follows the recursive algorithm for computing the generalized accelerations. The computational cost of this algorithm grows only linearly with the number of degrees of freedom. This is in contrast to conventional constrained dynamics algorithms whose cost is a cubic function of the number of degrees of freedom. For the case of a polypeptide molecule with 400 residues, the O(N) algorithm provides computational speedup by a factor of 450 over the conventional O(N[sup 3]) algorithm. We also describe a simplified method for computing and handling the potential function gradients within the dynamics computations. 21 refs., 3 figs.

Jain, A.; Vaidehi, N.; Rodriguez, G. (California Institute of Technology, Pasadena (United States))

1993-06-01

258

Molecular dynamics with helical periodic boundary conditions.

Helical symmetry is often encountered in nature and thus also in molecular dynamics (MD) simulations. In many cases, an approximation based on infinite helical periodicity can save a significant amount of computer time. However, standard simulations with the usual periodic boundary conditions (PBC) are not easily compatible with it. In the present study, we propose and investigate an algorithm comprising infinitely propagated helicity, which is compatible with commonly used MD software. The helical twist is introduced as a parametric geometry constraint, and the translational PBC are modified to allow for the helical symmetry via a transitional solvent volume. The algorithm including a parallel code was implemented within the Tinker software. The viability of the helical periodic boundary conditions (HPBC) was verified in test simulations including ?-helical and polyproline II like peptide structures. For an insulin-based model, the HPBC dynamics made it possible to simulate a fibrillar structure, otherwise not stable within PBC. © 2014 Wiley Periodicals, Inc. PMID:24913987

Kessler, Ji?í; Bou?, Petr

2014-08-01

259

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

260

Kink's dynamics for a deformable substrate potential

We study the static and dynamic properties of a kink in a chain of harmonically coupled atoms subjected to a deformable double-well substrate potential. We treat intrinsically the lattice discreteness without approximation and show that in some deformation-parameter ranges each period of the PN (Peierls-Nabarro) potential consists of two wells whose minima are located respectively on a lattice site and

P. Tchofo Dinda; C. R. Willis

1994-01-01

261

Polarizable molecular dynamics simulations of aqueous dipeptides.

Molecular dynamics simulations were carried out for concentrated aqueous solutions of three dipeptides: Gly-Ala, Gly-Pro, and Ala-Pro. The simulations were performed using both polarizable and nonpolarizable force fields, as a method of assessing the effects of polarization in a well-characterized biomolecular system, and to determine whether the models are adequate to reproduce observed aggregation behavior. The structure and dynamics of both solute and solvent were analyzed and the results compared to experiment, including neutron diffraction measurements of peptide aggregation. The polarizable water is depolarized in concentrated peptide solutions, reflecting its ability to adapt to heterogeneous electrostatic environments. Significant differences between the polarizable and nonpolarizable models are found in terms of both the structure and the dynamics of water as a solvent. Although the water shows more realistic structure and dynamics in the polarizable simulations, consistent with enhanced peptide-water interaction, the peptide aggregation behavior agrees less well with the experiment. Neither model successfully reproduces the experimentally observed dipeptide aggregation behavior. PMID:22747103

Kucukkal, Tugba G; Stuart, Steven J

2012-08-01

262

Structural dynamics of photoinduced molecular switching in the solid state

NASA Astrophysics Data System (ADS)

A recent investigation by 100 ps X-ray diffraction of the structural dynamics in multifunctional spin-crossover materials, which are prototypes of molecular bistability, is presented. This illustrates how the dynamics of molecular photoswitching between low-spin and high-spin states follows a complex pathway from molecular to material scales through a sequence of processes.

Cailleau, H.; Lorenc, M.; Guerin, L.; Servol, M.; Collet, E.; Cointe, M. Buron-Le

2010-03-01

263

Quantum Molecular Dynamics Simulations of Shocked Molecular Liquids

NASA Astrophysics Data System (ADS)

Quantum Molecular Dynamics (QMD) simulations provide an extremely penetrating probe of a variety of enviroments in which dense matter at elevated temperatures plays a significant role, including solids, fluids, gases, plasmas, and especially mixtures of these various states of matter. In many circumstances, a quantum treatment of the interaction between electrons and ions provides the only reliable procedure for gaining information and understanding on the state and interaction of matter in these extreme conditions in which experiments remain difficult. We shall discuss several applications of QMD including the equation of state and electrical and optical properties of fluid deuterium, the equation of state of oxygen and the shock compression of hydrocarbons. This work was supported under the auspices of the U. S. Department of Energy by Los Alamos and Lawrence Livermore National Laboratories.

Kress, J. D.; Mazevet, S.; Collins, L. A.; Lenosky, T. J.

2001-06-01

264

Molecular-dynamics study of liquid nickel above and below the melting point.

We have investigated the structural and dynamic properties of liquid nickel by means of large-scale molecular-dynamics simulations, using an effective-pair potential derived from the second-order pseudopotential perturbation theory. The model of interactions is assessed on the single-atom as well as collective dynamic properties. The short-range order in the stable and undercooled liquids is also examined. We show that the present model potential gives a description of the local structure in both states in close agreement with first-principles molecular-dynamics simulations. PMID:16396554

Jakse, Noël; Pasturel, Alain

2005-12-22

265

NASA Astrophysics Data System (ADS)

The spectral density of quantum mechanical Frenkel Kontorova chains moving in disordered, external potentials is investigated by means of path-integral molecular dynamics. If the second moment of the embedding potential is well defined (roughness exponent H=0), there is one regime in which the chain is pinned (large masses m of chain particles) and one in which it is unpinned (small m). If the embedding potential can be classified as a random walk on large length scales ( H=1/2), then the chain is always pinned irrespective of the value of m. For H=1/2, two phonon-like branches appear in the spectra.

Krajewski, Florian R.; Müser, Martin H.

2005-07-01

266

Role of wave packet width in quantum molecular dynamics in fusion reactions near barrier

NASA Astrophysics Data System (ADS)

The dynamical fusion process of 48Ca + 144Sm with different impact parameters near barrier is studied by an extended quantum molecular dynamics (EQMD) model, where width of wavepacket is dynamically treated based on variational principle. The time evolution of different energy components such as potential energy, kinetic energy, Coulomb energy and Pauli potential are analyzed when dynamical or fixed width is assumed in calculation. It is found that the dynamical wavepacket width can enhance the dissipation of incident energy and the fluctuations, which are important to form compound nuclei. Moreover, we compare the fusion barrier dependence on the incident energy when it is determined by both dynamical and fixed wavepacket width.

Cao, X. G.; Ma, Y. G.; Zhang, G. Q.; Wang, H. W.; Anastasi, A.; Curciarello, F.; De Leo, V.

2014-05-01

267

Molecular Dynamics Simulations of Hydrophobic Residues

NASA Astrophysics Data System (ADS)

Molecular recognition and protein-protein interactions are involved in important biological processes. However, despite recent improvements in computational methods for protein design, we still lack a predictive understanding of protein structure and interactions. To begin to address these shortcomings, we performed molecular dynamics simulations of hydrophobic residues modeled as hard spheres with stereo-chemical constraints initially at high temperature, and then quenched to low temperature to obtain local energy minima. We find that there is a range of quench rates over which the probabilities of side-chain dihedral angles for hydrophobic residues match the probabilities obtained for known protein structures. In addition, we predict the side-chain dihedral angle propensities in the core region of the proteins T4, ROP, and several mutants. These studies serve as a first step in developing the ability to quantitatively rank the energies of designed protein constructs. The success of these studies suggests that only hard-sphere dynamics with geometrical constraints are needed for accurate protein structure prediction in hydrophobic cavities and binding interfaces.

Caballero, Diego; Zhou, Alice; Regan, Lynne; O'Hern, Corey

2013-03-01

268

Molecular dynamics simulation of adsorption in electric double layers

NASA Astrophysics Data System (ADS)

Classical molecular dynamics is used to model the structure and dynamics of electric double layers that form when a metal electrode is in contact with an aqueous electrolyte solution containing simple ions and neutral organics. First attention is focused on the distribution of ions and neutrals next to an uncharged electrode. The electric field and potential across the system are calculated. The iodide ion adsorbs from neutral solution and causes a negative shift in the potential of zero charge (PZC) relative to fluoride. Adsorbed benzene causes a small positive shift of the PZC. Benzene desorbs when the metal electrode is charged and the surface electric field causes a layer of localized and oriented water to form next to the electrode. Non contact adsorbed hydrated sodium ions are more effective than contact adsorbed chloride in desorbing benzene.

Philpott, Michael R.; Glosli, James N.; Zhu, Sheng-Bai

1995-07-01

269

Molecular Dynamics Simulation of Carbon Nanotube Based Gears

NASA Technical Reports Server (NTRS)

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

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

1996-01-01

270

We have performed a systematic study of lithium hydride in the warm-dense-matter regime for a density range from one to four times ambient solid and for temperatures from 2 to 6 eV using both finite-temperature density-functional theory quantum molecular dynamics (QMD) and orbital-free molecular dynamics (OFMD) with a focus on dynamical properties such as diffusion and viscosity. The validity of various mixing rules, especially those utilizing pressure, were checked for composite properties determined from QMD/OFMD simulations of the pure species against calculations on the fully interacting mixture. These rules produce pressures within about 10% of the full-mixture values but mutual-diffusion coefficients as different as 50%. We found very good agreement overall between the QMD, employing a three-electron pseudopotential, and the OFMD in the local-density approximation, especially at the higher temperatures and densities.

Horner, D. A.; Kress, J. D.; Collins, L. A. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Lambert, F. [CEA, DAM, DIF, F-91297 Arpajon (France)

2009-07-01

271

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

2012-08-10

272

Molecular interferometer to decode attosecond electron-nuclear dynamics.

Understanding the coupled electronic and nuclear dynamics in molecules by using pump-probe schemes requires not only the use of short enough laser pulses but also wavelengths and intensities that do not modify the intrinsic behavior of the system. In this respect, extreme UV pulses of few-femtosecond and attosecond durations have been recognized as the ideal tool because their short wavelengths ensure a negligible distortion of the molecular potential. In this work, we propose the use of two twin extreme UV pulses to create a molecular interferometer from direct and sequential two-photon ionization processes that leave the molecule in the same final state. We theoretically demonstrate that such a scheme allows for a complete identification of both electronic and nuclear phases in the wave packet generated by the pump pulse. We also show that although total ionization yields reveal entangled electronic and nuclear dynamics in the bound states, doubly differential yields (differential in both electronic and nuclear energies) exhibit in addition the dynamics of autoionization, i.e., of electron correlation in the ionization continuum. Visualization of such dynamics is possible by varying the time delay between the pump and the probe pulses. PMID:24591647

Palacios, Alicia; González-Castrillo, Alberto; Martín, Fernando

2014-03-18

273

Isothermal--isobaric molecular dynamics simulation of liquid water

Results of the first isothermal--isobaric molecular dynamics simulation of water are reported. Water molecules are assumed to be flexible and to interact via a sum of pairwise interatomic potentials. Extensive runs for 256 molecules at 298 and 373 K and 1 bar give satisfactory agreement with observed properties of liquid water as diverse as density, internal energy, heat capacity, compressibility, pair correlation functions, diffusion coefficient, vibrational spectrum, relative permittivity, and dielectric relaxation spectra. The nonlinear dependence of the relative permittivity on the electric field is also computed by means of fluctuation--dissipation relations.

Ruff, I.; Diestler, D.J. (Department of Chemistry, Purdue University, West Lafayette, Indiana 47907 (USA))

1990-08-01

274

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

2011-03-16

275

Molecular dynamics calculations for sodium using pseudopotential theory

NASA Astrophysics Data System (ADS)

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

276

Higher-order symplectic Born-Oppenheimer molecular dynamics

The extended Lagrangian formulation of time-reversible Born-Oppenheimer molecular dynamics (TR-BOMD) enables the use of geometric integrators in the propagation of both the nuclear and the electronic degrees of freedom on the Born-Oppenheimer potential energy surface. Different symplectic integrators up to the 6th order have been adapted and optimized to TR-BOMD in the framework of ab initio self-consistent-field theory. It is shown how the accuracy can be significantly improved compared to a conventional Verlet integration at the same level of computational cost, in particular for the case of very high accuracy requirements.

Niklasson, Anders [Los Alamos National Laboratory; Bock, Nicolas [Los Alamos National Laboratory; Challacombe, Matt [Los Alamos National Laboratory; Odell, Anders [RIT; Delin, Anna [RIT; Johansson, Borje [RIT

2009-01-01

277

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

278

Molecular dynamics, spin dynamics study of phonon-magnon interactions in BCC iron

NASA Astrophysics Data System (ADS)

By combining an atomistic many-body potential (Finnis-Sinclair) with a classical Heisenberg-like spin Hamiltonian, we perform combined molecular and spin dynamics simulations to investigate phonon-magnon interactions in BCC iron. The coupling between atomic and spin degrees of freedom is established via a distance dependent exchange interaction derived from first principles electronic structure calculations. Coupled equations of motion are integrated using a second order Suzuki-Trotter decomposition of the exponential time evolution operator. To investigate the effect of lattice vibrations on spin wave spectrum, we calculate spin-spin and density-density dynamic structure factors S(q, ?), and compare that to the results obtained from pure spin dynamics simulations performed on a rigid lattice. In the presence of lattice vibrations, we observe an additional peak in the longitudinal spin-spin dynamic structure factor which coincides with the peak position in density-density dynanmic structure factor.

Perera, Dilina; Landau, David P.; Stocks, G. Malcolm; Nicholson, Don; Eisenbach, Markus; Yin, Junqi

2013-03-01

279

Molecular dynamics (MD) calculation has been carried out for a dilute aqueous solution of tert-butyl alcohol (TBA) at 298.15 K and with experimental density value by the use of constant temperature technique developed previously. The total number of molecule is 216, seven of which are TBA. The mole fraction of TBA is thus 0.032. For water–water and TBA–water interactions, the

Hideki Tanaka; Koichiro Nakanishi; Hidekazu Touhara

1984-01-01

280

Extended Lagrangian free energy molecular dynamics.

Extended free energy Lagrangians are proposed for first principles molecular dynamics simulations at finite electronic temperatures for plane-wave pseudopotential and local orbital density matrix-based calculations. Thanks to the extended Lagrangian description, the electronic degrees of freedom can be integrated by stable geometric schemes that conserve the free energy. For the local orbital representations both the nuclear and electronic forces have simple and numerically efficient expressions that are well suited for reduced complexity calculations. A rapidly converging recursive Fermi operator expansion method that does not require the calculation of eigenvalues and eigenfunctions for the construction of the fractionally occupied density matrix is discussed. An efficient expression for the Pulay force that is valid also for density matrices with fractional occupation occurring at finite electronic temperatures is also demonstrated. PMID:22047232

Niklasson, Anders M N; Steneteg, Peter; Bock, Nicolas

2011-10-28

281

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

282

Discrete molecular dynamics simulations of peptide aggregation

NASA Astrophysics Data System (ADS)

We study the aggregation of peptides using the discrete molecular dynamics simulations. Specifically, at temperatures above the ?-helix melting temperature of a single peptide, the model peptides aggregate into a multilayer parallel ?-sheet structure. This structure has an interstrand distance of 4.8 Å and an intersheet distance of 10 Å, which agree with experimental observations. Our model explains these results as follows: hydrogen-bond interactions give rise to the interstrand spacing in ? sheets, while G? interactions between side chains make ? strands parallel to each other and allow ? sheets to pack into layers. An important feature of our results is that the aggregates contain free edges, which may allow for further aggregation of model peptides to form elongated fibrils.

Peng, S.; Ding, F.; Urbanc, B.; Buldyrev, S. V.; Cruz, L.; Stanley, H. E.; Dokholyan, N. V.

2004-04-01

283

Fiber lubrication: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Molecular and mesoscopic level description of friction and lubrication remains a challenge because of difficulties in the phenomenological understanding of to the behaviors of solid-liquid interfaces during sliding. Fortunately, there is the computational simulation approach opens an opportunity to predict and analyze interfacial phenomena, which were studied with molecular dynamics (MD) and mesoscopic dynamics (MesoDyn) simulations. Polypropylene (PP) and cellulose are two of most common polymers in textile fibers. Confined amorphous surface layers of PP and cellulose were built successfully with xenon crystals which were used to compact the polymers. The physical and surface properties of the PP and cellulose surface layers were investigated by MD simulations, including the density, cohesive energy, volumetric thermal expansion, and contact angle with water. The topology method was employed to predict the properties of poly(alkylene glycol) (PAG) diblock copolymers and Pluronic triblock copolymers used as lubricants on surfaces. Density, zero shear viscosity, shear module, cohesive energy and solubility parameter were predicted with each block copolymer. Molecular dynamics simulations were used to study the interaction energy per unit contact area of block copolymer melts with PP and cellulose surfaces. The interaction energy is defined as the ratio of interfacial interaction energy to the contact area. Both poly(proplene oxide) (PPO) and poly(ethylene oxide) (PEO) segments provided a lipophilic character to both PP and cellulose surfaces. The PPO/PEO ratio and the molecular weight were found to impact the interaction energy on both PP and cellulose surfaces. In aqueous solutions, the interaction energy is complicated due to the presence of water and the cross interactions between the multiple molecular components. The polymer-water-surface (PWS) calculation method was proposed to calculate such complex systems. In a contrast with a vacuum condition, the presence of water increases the attractive interaction energy of the diblock copolymer on the cellulose surface, compared with that on the PP surface. Water decreases the interaction energy of the triblock copolymer on the cellulose surface, compared with that on the PP surface. MesoDyn was adopted to investigate the self-assembled morphology of the triblock copolymer, in aqueous solution, confined and sheared at solid-liquid interfaces. In a bulk aqueous solution, when the polymer concentration reached 10% v/v, micelles were observed with PPO blocks in the core and PEO blocks in the shell of the micelles. At the concentrations of 25% and 50%, worm-like micelles and irregular cylinders were observed in solutions, respectively. The micelles were formed faster in aqueous solutions confined by cellulose surfaces than that in the bulk. The formed micelles were broken under shearing, which led to a depletion of polymers at the interfaces. During the shearing on the PP surfaces, the polymers were adsorbed on the surfaces protecting the PP surfaces. This simulation study in the fiber lubrication was in good agreement with the experimental results and so provided an approach to visualize the polymer configuration at the liquid-solid interface, predict the lubricant-surface systems, and theoretically guide the experiments of designing new/efficient lubricants for fibers.

Liu, Hongyi

284

Normal-mode analysis without the Hessian: A driven molecular-dynamics approach

NASA Astrophysics Data System (ADS)

We point out that normal modes and frequencies of molecules and molecular complexes can be obtained directly from a harmonically driven molecular dynamics calculation. We illustrate this approach for HOD and H5O2+ and then discuss its potential advantages over the standard Hessian-based approach for large molecules.

Bowman, Joel M.; Zhang, Xiubin; Brown, Alex

2003-07-01

285

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

286

Molecular dynamics simulations of microscale fluid transport

Recent advances in micro-science and technology, like Micro-Electro-Mechanical Systems (MEMS), have generated a group of unique liquid flow problems that involve characteristic length scales of a Micron. Also, in manufacturing processes such as coatings, current continuum models are unable to predict microscale physical phenomena that appear in these non-equilibrium systems. It is suspected that in these systems, molecular-level processes can control the interfacial energy and viscoelastic properties at the liquid/solid boundary. A massively parallel molecular dynamics (MD) code has been developed to better understand microscale transport mechanisms, fluid-structure interactions, and scale effects in micro-domains. Specifically, this MD code has been used to analyze liquid channel flow problems for a variety of channel widths, e.g. 0.005-0.05 microns. This report presents results from MD simulations of Poiseuille flow and Couette flow problems and addresses both scaling and modeling issues. For Poiseuille flow, the numerical predictions are compared with existing data to investigate the variation of the friction factor with channel width. For Couette flow, the numerical predictions are used to determine the degree of slip at the liquid/solid boundary. Finally, the results also indicate that shear direction with respect to the wall lattice orientation can be very important. Simulation results of microscale Couette flow and microscale Poiseuille flow for two different surface structures and two different shear directions will be presented.

Wong, C.C.; Lopez, A.R.; Stevens, M.J.; Plimpton, S.J.

1998-02-01

287

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

288

Ewing Sarcoma: Molecular Characterization and Potential Molecular Therapeutic Targets

\\u000a Ewing sarcoma (ES) is the second most common sarcoma affecting children and young adults. Emerging evidence indicates that\\u000a ES is likely the result of spontaneous genetic translocation and the fusion gene EWS-FLI-1 drives ES pathogenesis. ES can\\u000a be reliably diagnosed on tissue by cytology, histology, and immunohistochemistry. However, molecular confirmation and characterization\\u000a are important. Tumor stage is still the most

Marilyn M. Bui; Paul J. Zhang

289

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

290

Molecular-dynamics study of phase transitions in alkali azides

NASA Astrophysics Data System (ADS)

An account is presented of our studies of the order-disorder phase transitions in KN3, RbN3, and CsN3. These are based on parameter-free interionic potentials based on the Gordon-Kim modified electron-gas formalism extended to molecular ions. We performed static structural relaxations and supercell molecular dynamics and predicted with reasonable accuracy the temperatures for the onset of the transitions. In particular, we address the question of how the N-3 ions reorient to yield the transitions. We found the existence of NaCl-type high-temperature phases in disordered KN3 and RbN3 and argue that this restructuring is preempted by melting in these two systems.

Ossowski, M. M.; Hardy, J. R.; Smith, R. W.

1999-12-01

291

Molecular Dynamics Simulations of Non-accreting Neutron Star Crusts

NASA Astrophysics Data System (ADS)

Neutron stars which do not accrete material can still have impurities in their crust, due to nuclear reactions in the crust. These impurities in the crust could affect the mechanical properties of the neutron star crust. In order to investigate the properties of the crust of a non-accreting neutron star we are performing molecular dynamic simulations of the crust. We are using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), where simulations are run at fixed energy and volume, with the isotopes interacting via a repulsive Yukawa potential. Here we are presenting the preliminary results of the equilibrium structure of the solid neutron star crust using abundances of a non-accreting source.

Hoffman, Kelsey L.; Heyl, J. S.

2010-02-01

292

Molecular Modeling and Molecular Dynamics Simulations of Recombinase Rad51

The Rad51 ATPase plays central roles in DNA homologous recombination. Yeast Rad51 dimer structure in the active form of the filament was constructed using homology modeling techniques, and all-atom molecular dynamics (MD) simulations were performed using the modeled structure. We found two crucial interaction networks involving ATP: one is among the ?-phosphate of ATP, K+ ions, H352, and D374; the other is among the adenine ring of ATP, R228, and P379. Multiple MD simulations were performed in which the number of bound K+ ions was changed. The simulated structures suggested that K+ ions are indispensable for the stabilization of the active dimer and resemble the arginine and lysine fingers of other P-loop containing ATPases and GTPases. MD simulations also showed that the adenine ring of ATP mediates interactions between adjacent protomers. Furthermore, in MD simulations starting from a structure just after ATP hydrolysis, the opening motion corresponding to dissociation from DNA was observed. These results support the hypothesis that ATP and K+ ions function as glue between protomers.

Kokabu, Yuichi; Ikeguchi, Mitsunori

2013-01-01

293

Classical reactive molecular dynamics implementations: state of the art.

Reactive molecular dynamics (RMD) implementations equipped with force field approaches to simulate both the time evolution as well as chemical reactions of a broad class of materials are reviewed herein. We subdivide the RMD approaches developed during the last decade as well as older ones already reviewed in 1995 by Srivastava and Garrison and in 2000 by Brenner into two classes. The methods in the first RMD class rely on the use of a reaction cutoff distance and employ a sudden transition from the educts to the products. Due to their simplicity these methods are well suited to generate equilibrated atomistic or material-specific coarse-grained polymer structures. In connection with generic models they offer useful qualitative insight into polymerization reactions. The methods in the second RMD class are based on empirical reactive force fields and implement a smooth and continuous transition from the educts to the products. In this RMD class, the reactive potentials are based on many-body or bond-order force fields as well as on empirical standard force fields, such as CHARMM, AMBER or MM3 that are modified to become reactive. The aim with the more sophisticated implementations of the second RMD class is the investigation of the reaction kinetics and mechanisms as well as the evaluation of transition state geometries. Pure or hybrid ab initio, density functional, semi-empirical, molecular mechanics, and Monte Carlo methods for which no time evolution of the chemical systems is achieved are excluded from the present review. So are molecular dynamics techniques coupled with quantum chemical methods for the treatment of the reactive regions, such as Car-Parinello molecular dynamics. PMID:22287184

Farah, Karim; Müller-Plathe, Florian; Böhm, Michael C

2012-04-10

294

(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

295

A novel combined Event-Driven\\/Time-Driven (ED\\/TD) algorithm to speed-up the Molecular Dynamics simulation of rarefied gases using realistic spherically symmetric soft potentials is presented. Due to the low density regime, the proposed method correctly identifies the time that must elapse before the next interaction occurs, similarly to Event-Driven Molecular Dynamics. However, each interaction is treated using Time-Driven Molecular Dynamics, thereby integrating

Paolo Valentini; Thomas E. Schwartzentruber

2009-01-01

296

Reversible peptide folding in solution by molecular dynamics simulation.

Long-standing questions on how peptides fold are addressed by the simulation at different temperatures of the reversible folding of a peptide in solution in atomic detail. Molecular dynamics simulations correctly predict the structure that is thermodynamically stable at 298 K, irrespective of the initial peptide conformation. The rate of folding and the free energy of folding at different temperatures are estimated. Although the conformational space potentially accessible to the peptide is extremely large, very few conformers (10(1) to 10(2)) are significantly populated at 20 K above the melting temperature. This implies that the search problem in peptide (or even protein) folding is surmountable using dynamics simulations. PMID:9671560

Daura, X; Jaun, B; Seebach, D; van Gunsteren, W F; Mark, A E

1998-07-31

297

On-the-fly free energy parameterization via temperature accelerated molecular dynamics

We discuss a method for parametric calculation of free energy functions in arbitrary collective variables using molecular simulations. The method uses a variant of temperature accelerated molecular dynamics to evolve on-the-fly the parameters of the free energy function to their optimum values by minimization of a cumulative gradient error. We illustrate how the method performs using simple examples and discuss its application in the derivation of effective pairwise potentials for multiscale molecular simulations.

Abrams, Cameron F.; Vanden-Eijnden, Eric

2012-01-01

298

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

299

Electric Double Layer Structures near Rough Surfaces: Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

S. S. Dukhin in Surface and Colloid Science (1974) mentioned both the possibility of increase in zeta potential due to surface roughness and the possibility of decrease, depending on Debye length relative to surface roughness. In this work we report our results of molecular dynamic (MD) simulations on electric double layer structures near solid surfaces having roughness with the order of magnitude of Debye length. For computational simplicity only counter-ions are present. We computed static and dynamics properties including density profiles of water and ions, electrostatic potential distributions due to ions, polarization density profiles and self-diffusivities of water and ions. We also performed nonequilibrium MD to simulate electroosmotic flows. From electrostatic potential distributions and slip plane locations, we computed zeta potential and found that it decreases with surface roughness. It also showed a dependency on the spatial frequency of surface roughness. For comparison we used the Helmholtz-Smoluchowski relation and found the same trend. Currently we are studying pressure-driven flows, a computational counterpart to streaming current experiments. One of the purposes is to find more exact locations of slip planes by fitting to Poiseuille flow solutions. We are also simulating model systems with co-ions to investigate the possibility of charge inversion and other effects.

Kim, Daejoong; Darve, Eric

2006-03-01

300

Seven-helix bundles: molecular modeling via restrained molecular dynamics.

Simulated annealing via restrained molecular dynamics (SA/MD) has been used to model compact bundles of seven approximately (anti)parallel alpha-helices. Seven such helix bundles occur, e.g., in bacteriorhodopsin, in rhodopsin, and in the channel-forming N-terminal domain of Bacillus thuringiensis delta-endotoxin. Two classes of model are considered: (a) those consisting of seven Ala20 peptide chains; and (b) those containing a single polypeptide chain, made up of seven Ala20 helices linked by GlyN interhelix loops (where N = 5 or 10). Three different starting C alpha templates for SA/MD are used, in which the seven helices are arranged (a) on a left-handed circular template, (b) on a bacteriorhodopsin-like template, or (c) on a zig-zag template. The ensembles of models generated by SA/MD are analyzed in terms of their geometry and energetics, and the most stable structures from each ensemble are examined in greater detail. Structures resembling bacteriorhodopsin and structures resembling delta-endotoxin are both represented among the most stable structures. delta-Endotoxin-like structures arise from both circular and bacteriorhodopsin-like C alpha templates. A third helix-packing mode occurs several times among the stable structures, regardless of the C alpha template and of the presence or absence of interhelix loops. It is characterized by a "4 + 1" core, in which four helices form a distorted left-handed supercoil around a central, buried helix. The remaining two helices pack onto the outside of the core. This packing mode is comparable with that proposed for rhodopsin on the basis of two-dimensional electron crystallographic and sequence analysis studies. Images FIGURE 1 FIGURE 4 FIGURE 6

Sansom, M S; Son, H S; Sankararamakrishnan, R; Kerr, I D; Breed, J

1995-01-01

301

Molecular Dynamics Simulations on Commodity GPUs with CUDA

Molecular dynamics simulations are a common and often repeated task in molecular biology. The need for speeding up this treatment\\u000a comes from the requirement for large system simulations with many atoms and numerous time steps. In this paper we present\\u000a a new approach to high performance molecular dynamics simulations on graphics processing units. Using modern graphics processing\\u000a units for high

Weiguo Liu; Bertil Schmidt; Gerrit Voss; Wolfgang Müller-wittig

2007-01-01

302

PROTOTYPING BIO-NANOROBOTS USING MOLECULAR DYNAMIC SIMULATION

This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality techniques for intuitive bio-nanorobotic prototyping. Using molecular dynamic simulations the operator can design, characterize and prototype the behavior of bio-nanorobotic components and structures. The main novelty of the proposed simulations is based on the characterization of stiffness performances of passive joints-based deca-alanine protein

Mustapha Hamdi; Gaurav Sharma; Antoine Ferreira; Constantinos Mavroidis

2005-01-01

303

Thermal conductivity of molecular chains with asymmetric potentials of pair interactions.

We provide molecular-dynamics simulation of heat transport in one-dimensional molecular chains with different interparticle pair potentials. We show that the thermal conductivity is finite in the thermodynamic limit in chains with the potentials that allow for bond dissociation. The Lennard-Jones, Morse, and Coulomb potentials are such potentials. The convergence of the thermal conductivity is provided by phonon scattering on the locally strongly stretched loose interatomic bonds at low temperature and by the many-particle scattering at high temperature. On the other hand, chains with a confining pair potential, which does not allow for bond dissociation, possess anomalous thermal conductivity, diverging with the chain length. We emphasize that chains with a symmetric or asymmetric Fermi-Pasta-Ulam potential or with combined potentials, containing a parabolic and/or a quartic confining potential, all exhibit anomalous heat transport. PMID:24730785

Savin, Alexander V; Kosevich, Yuriy A

2014-03-01

304

Accelerated molecular dynamics methods: introduction and recent developments

A long-standing limitation in the use of molecular dynamics (MD) simulation is that it can only be applied directly to processes that take place on very short timescales: nanoseconds if empirical potentials are employed, or picoseconds if we rely on electronic structure methods. Many processes of interest in chemistry, biochemistry, and materials science require study over microseconds and beyond, due either to the natural timescale for the evolution or to the duration of the experiment of interest. Ignoring the case of liquids xxx, the dynamics on these time scales is typically characterized by infrequent-event transitions, from state to state, usually involving an energy barrier. There is a long and venerable tradition in chemistry of using transition state theory (TST) [10, 19, 23] to directly compute rate constants for these kinds of activated processes. If needed dynamical corrections to the TST rate, and even quantum corrections, can be computed to achieve an accuracy suitable for the problem at hand. These rate constants then allow them to understand the system behavior on longer time scales than we can directly reach with MD. For complex systems with many reaction paths, the TST rates can be fed into a stochastic simulation procedure such as kinetic Monte Carlo xxx, and a direct simulation of the advance of the system through its possible states can be obtained in a probabilistically exact way. A problem that has become more evident in recent years, however, is that for many systems of interest there is a complexity that makes it difficult, if not impossible, to determine all the relevant reaction paths to which TST should be applied. This is a serious issue, as omitted transition pathways can have uncontrollable consequences on the simulated long-time kinetics. Over the last decade or so, we have been developing a new class of methods for treating the long-time dynamics in these complex, infrequent-event systems. Rather than trying to guess in advance what reaction pathways may be important, we return instead to a molecular dynamics treatment, in which the trajectory itself finds an appropriate way to escape from each state of the system. Since a direct integration of the trajectory would be limited to nanoseconds, while we are seeking to follow the system for much longer times, we modify the dynamics in some way to cause the first escape to happen much more quickly, thereby accelerating the dynamics. The key is to design the modified dynamics in a way that does as little damage as possible to the probability for escaping along a given pathway - i.e., we try to preserve the relative rate constants for the different possible escape paths out of the state. We can then use this modified dynamics to follow the system from state to state, reaching much longer times than we could reach with direct MD. The dynamics within any one state may no longer be meaningful, but the state-to-state dynamics, in the best case, as we discuss in the paper, can be exact. We have developed three methods in this accelerated molecular dynamics (AMD) class, in each case appealing to TST, either implicitly or explicitly, to design the modified dynamics. Each of these methods has its own advantages, and we and others have applied these methods to a wide range of problems. The purpose of this article is to give the reader a brief introduction to how these methods work, and discuss some of the recent developments that have been made to improve their power and applicability. Note that this brief review does not claim to be exhaustive: various other methods aiming at similar goals have been proposed in the literature. For the sake of brevity, our focus will exclusively be on the methods developed by the group.

Uberuaga, Blas Pedro [Los Alamos National Laboratory; Voter, Arthur F [Los Alamos National Laboratory; Perez, Danny [Los Alamos National Laboratory; Shim, Y [UNIV OF TOLEDO; Amar, J G [UNIV OF TOLEDO

2009-01-01

305

Elastic Constants from Molecular Dynamics in the Presence of Microstructure

NASA Astrophysics Data System (ADS)

We calculate second (and third) order elastic constants in the presence of twin and tweed-like microstructure in martensitic and other structural phase transitions using fluctuation formulas and embedded atom method (EAM) and modified (MEAM) potentials in molecular dynamics simulations. We illustrate the results on NiAl alloys. This procedure allows us to study and distinguish the effects of microstructure such as twin or tweed on various elastic constants. In addition, it provides direct microscopic input to determine the expansion coefficients in the mesoscopic Ginzburg-Landau free energy description, which can then be validated against measured elastic constants in a single crystal of NiAl. The procedure can be readily applied to other alloys of interest, e.g. AuCd and FePd with appropriate choice of MEAM potentials.

Srinivasan, S. G.; Dimitrov, D. A.; Lookman, T.; Saxena, A.; Albers, R. C.; Bishop, A. R.

2000-03-01

306

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

307

The MOLDY short-range molecular dynamics package

NASA Astrophysics Data System (ADS)

We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy. Program summaryProgram title: MOLDY Catalogue identifier: AEJU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 382 881 No. of bytes in distributed program, including test data, etc.: 6 705 242 Distribution format: tar.gz Programming language: Fortran 95/OpenMP Computer: Any Operating system: Any Has the code been vectorised or parallelized?: Yes. OpenMP is required for parallel execution RAM: 100 MB or more Classification: 7.7 Nature of problem: Moldy addresses the problem of many atoms (of order 10 6) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as measuring thermodynamic properities, diffusion, radiation damage, fracture, twinning deformation, nucleation and growth of phase transitions, sputtering etc. In the vast majority of materials, the interactions are non-pairwise, and the code must be able to deal with many-body forces. Solution method: Molecular dynamics involves integrating Newton's equations of motion. MOLDY uses verlet (for good energy conservation) or predictor-corrector (for accurate trajectories) algorithms. It is parallelised using open MP. It also includes a static minimisation routine to find the lowest energy structure. Boundary conditions for surfaces, clusters, grain boundaries, thermostat (Nose), barostat (Parrinello-Rahman), and externally applied strain are provided. The initial configuration can be either a repeated unit cell or have all atoms given explictly. Initial velocities are generated internally, but it is also possible to specify the velocity of a particular atom. A wide range of interatomic force models are implemented, including embedded atom, Morse or Lennard-Jones. Thus the program is especially well suited to calculations of metals. Restrictions: The code is designed for short-ranged potentials, and there is no Ewald sum. Thus for long range interactions where all particles interact with all others, the order- N scaling will fail. Different interatomic potential forms require recompilation of the code. Additional comments: There is a set of associated open-source analysis software for postprocessing and visualisation. This includes local crystal structure recognition and identification of topological defects. Running time: A set of test modules for running time are provided. The code scales as order N. The parallelisation shows near-linear scaling with number of processors in a shared memory environment. A typical run of a few tens of nanometers for a few nanoseconds will run on a timescale of days on a multiprocessor desktop.

Ackland, G. J.; D'Mellow, K.; Daraszewicz, S. L.; Hepburn, D. J.; Uhrin, M.; Stratford, K.

2011-12-01

308

NASA Astrophysics Data System (ADS)

We study the phonon modes in single-walled MoS2 nanotubes via lattice dynamics calculation and molecular dynamics simulation. The phonon spectra for tubes of arbitrary chiralities are calculated from a dynamical matrix constructed by the combination of an empirical potential with the conserved helical quantum numbers (?, n). In particular, we show that the frequency (?) of the radial breathing mode is inversely proportional to the tube diameter (d) as ? = 665.3/d cm-1. The eigenvectors of the twenty lowest-frequency phonon modes are illustrated. Based on these eigenvectors, we demonstrate that the radial breathing oscillation is initially disturbed by phonon modes of three-fold symmetry, then eventually the tube is squashed by modes of two-fold symmetry . Our study provides fundamental knowledge for further investigations of the thermal and mechanical properties of MoS2 nanotubes.

Jiang, Jin-Wu; Wang, Bing-Shen; Rabczuk, Timon

2014-03-01

309

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

310

Algorithm optimization in molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Establishing the neighbor list to efficiently calculate the inter-atomic forces consumes the majority of computation time in molecular dynamics (MD) simulation. Several algorithms have been proposed to improve the computation efficiency for short-range interaction in recent years, although an optimized numerical algorithm has not been provided. Based on a rigorous definition of Verlet radius with respect to temperature and list-updating interval in MD simulation, this paper has successfully developed an estimation formula of the computation time for each MD algorithm calculation so as to find an optimized performance for each algorithm. With the formula proposed here, the best algorithm can be chosen based on different total number of atoms, system average density and system average temperature for the MD simulation. It has been shown that the Verlet Cell-linked List (VCL) algorithm is better than other algorithms for a system with a large number of atoms. Furthermore, a generalized VCL algorithm optimized with a list-updating interval and cell-dividing number is analyzed and has been verified to reduce the computation time by 30˜60% in a MD simulation for a two-dimensional lattice system. Due to similarity, the analysis in this study can be extended to other many-particle systems.

Wang, Di-Bao; Hsiao, Fei-Bin; Chuang, Cheng-Hsin; Lee, Yung-Chun

2007-10-01

311

Molecular chaperone-mediated nuclear protein dynamics.

Homeostasis requires effective action of numerous biological pathways including those working along a genome. The variety of processes functioning in the nucleus is considerable, yet the number of employed factors eclipses this total. Ideally, individual components assemble into distinct complexes and serially operate along a pathway to perform work. Adding to the complexity is a multitude of fluctuating internal and external signals that must be monitored to initiate, continue or halt individual activities. While cooperative interactions between proteins of the same process provide a mechanism for rapid and precise assembly, the inherent stability of such organized structures interferes with the proper timing of biological events. Further prolonging the longevity of biological complexes are crowding effects resulting from the high concentration of intracellular macromolecules. Hence, accessory proteins are required to destabilize the various assemblies to efficiently transition between structures, avoid off-pathway competitive interactions, and to terminate pathway activity. We suggest that molecular chaperones have evolved, in part, to manage these challenges by fostering a general and continuous dynamic protein environment within the nucleus. PMID:24694369

Echtenkamp, Frank J; Freeman, Brian C

2014-05-01

312

Integrating influenza antigenic dynamics with molecular evolution

Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1, B/Victoria and B/Yamagata, we determine patterns of antigenic drift across viral lineages, showing that A/H3N2 evolves faster and in a more punctuated fashion than other influenza lineages. We also show that year-to-year antigenic drift appears to drive incidence patterns within each influenza lineage. This work makes possible substantial future advances in investigating the dynamics of influenza and other antigenically-variable pathogens by providing a model that intimately combines molecular and antigenic evolution. DOI: http://dx.doi.org/10.7554/eLife.01914.001

Bedford, Trevor; Suchard, Marc A; Lemey, Philippe; Dudas, Gytis; Gregory, Victoria; Hay, Alan J; McCauley, John W; Russell, Colin A; Smith, Derek J; Rambaut, Andrew

2014-01-01

313

Integrating influenza antigenic dynamics with molecular evolution.

Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1, B/Victoria and B/Yamagata, we determine patterns of antigenic drift across viral lineages, showing that A/H3N2 evolves faster and in a more punctuated fashion than other influenza lineages. We also show that year-to-year antigenic drift appears to drive incidence patterns within each influenza lineage. This work makes possible substantial future advances in investigating the dynamics of influenza and other antigenically-variable pathogens by providing a model that intimately combines molecular and antigenic evolution. DOI: http://dx.doi.org/10.7554/eLife.01914.001. PMID:24497547

Bedford, Trevor; Suchard, Marc A; Lemey, Philippe; Dudas, Gytis; Gregory, Victoria; Hay, Alan J; McCauley, John W; Russell, Colin A; Smith, Derek J; Rambaut, Andrew

2014-01-01

314

Fracture simulations via massively parallel molecular dynamics

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

Holian, B.L. [Los Alamos National Lab., NM (United States); Abraham, F.F. [IBM Research Div., San Jose, CA (United States). Almaden Research Center; Ravelo, R. [Texas Univ., El Paso, TX (United States)

1993-09-01

315

The structure and the thermal motion of ions in liquid rubidium are simulated for six states including the critical point along the saturated vapour-pressure curve using the molecular dynamics method. The effective pair potential between rubidium ions in expanded liquid states is calculated by extrapolating the optimised model potential parameters proposed by Cowley (1976) and the screening parameters of Singwi

M. Tanaka

1980-01-01

316

MOLECULAR ANALYSIS OF HUMAN SPERMATOZOA: POTENTIAL FOR INFERTILITY RESEARCH

Gordon Research Conference: Mammalian Gametogenesis and Embryogenesis New London, CT, July 1-6, 2000 Molecular Analysis of Human Spermatozoa: Potential for Infertility Research David Miller 1, David Dix2, Robert Reid 3, Stephen A Krawetz 3 1Reproductive ...

317

Molecular Electrostatic Potentials as Indicators of Covalent Radii.

National Technical Information Service (NTIS)

Through nonlocal density functional calculations (B/LYP/6 -31C**), we show that the minimum of the molecular electrostatic potential along an internuclear axis provides a more realistic boundary point between two bonded atoms than does the electronic dens...

J. J. Wiener M. E. Grice J. S. Murray P. Politzer

1996-01-01

318

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

319

We utilize accelerated molecular dynamics to simulate alkane desorption from the basal plane of graphite. Eight different molecules, ranging from n-pentane to n-hexadecane, are studied in the low coverage limit. Acceleration of the molecular dynamics simulations is achieved using two different methods: temperature acceleration and a compensating potential scheme. We find that the activation energy for desorption increases with increasing

Kelly E. Becker; Kristen A. Fichthorn

2006-01-01

320

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

2013-09-01

321

NASA Astrophysics Data System (ADS)

We present molecular dynamics simulations of the liquid-vapor interface of 1M salt solutions of nonpolarizable NaCl, NaBr, and NaI in polarizable transferable intermolecular potential 4-point with charge dependent polarizability water [B. A. Bauer et al., J. Chem. Theory Comput. 5, 359 (2009)] this water model accommodates increased solvent polarizability (relative to the condensed phase) in the interfacial and vapor regions. We employ fixed-charge ion models developed in conjunction with the TIP4P-QDP water model to reproduce ab initio ion-water binding energies and ion-water distances for isolated ion-water pairs. The transferability of these ion models to the condensed phase was validated with hydration free energies computed using thermodynamic integration (TI) and appropriate energy corrections. Density profiles of Cl-, Br-, and I- exhibit charge layering in the interfacial region; anions and cation interfacial probabilities show marked localization, with the anions penetrating further toward the vapor than the cations. Importantly, in none of the cases studied do anions favor the outermost regions of the interface; there is always an aqueous region between the anions and vapor phase. Observed interfacial charge layering is independent of the strength of anion-cation interactions as manifest in anion-cation contact ion pair peaks and solvent separated ion pair peaks; by artificially modulating the strength of anion-cation interactions (independent of their interactions with solvent), we find little dependence on charge layering particularly for the larger iodide anion. The present results reiterate the widely held view of the importance of solvent and ion polarizability in mediating specific anion surface segregation effects. Moreover, due to the higher parametrized polarizability of the TIP4P-QDP condensed phase {1.31 A?3 for TIP4P-QDP versus 1.1 A?3 (TIP4P-FQ) and 0.87 A?3 (POL3) [Ponder and Case, Adv. Protein Chem. 66, 27 (2003)]} based on ab initio calculations of the condensed-phase polarizability reduction in liquid water, the present simulations highlight the role of water polarizability in inducing water molecular dipole moments parallel to the interface normal (and within the interfacial region) so as to favorably oppose the macrodipole generated by the separation of anion and cation charge. Since the TIP4P-QDP water polarizability approaches that of the experimental vapor phase value for water, the present results suggest a fundamental role of solvent polarizability in accommodating the large spatial dipole generated by the separation of ion charges. The present results draw further attention to the question of what exact value of condensed phase water polarizability to incorporate in classical polarizable water force fields.

Bauer, Brad A.; Patel, Sandeep

2010-01-01

322

We present molecular dynamics simulations of the liquid-vapor interface of 1M salt solutions of nonpolarizable NaCl, NaBr, and NaI in polarizable transferable intermolecular potential 4-point with charge dependent polarizability water [B. A. Bauer et al., J. Chem. Theory Comput. 5, 359 (2009)]; this water model accommodates increased solvent polarizability (relative to the condensed phase) in the interfacial and vapor regions. We employ fixed-charge ion models developed in conjunction with the TIP4P-QDP water model to reproduce ab initio ion-water binding energies and ion-water distances for isolated ion-water pairs. The transferability of these ion models to the condensed phase was validated with hydration free energies computed using thermodynamic integration (TI) and appropriate energy corrections. Density profiles of Cl(-), Br(-), and I(-) exhibit charge layering in the interfacial region; anions and cation interfacial probabilities show marked localization, with the anions penetrating further toward the vapor than the cations. Importantly, in none of the cases studied do anions favor the outermost regions of the interface; there is always an aqueous region between the anions and vapor phase. Observed interfacial charge layering is independent of the strength of anion-cation interactions as manifest in anion-cation contact ion pair peaks and solvent separated ion pair peaks; by artificially modulating the strength of anion-cation interactions (independent of their interactions with solvent), we find little dependence on charge layering particularly for the larger iodide anion. The present results reiterate the widely held view of the importance of solvent and ion polarizability in mediating specific anion surface segregation effects. Moreover, due to the higher parametrized polarizability of the TIP4P-QDP condensed phase {1.31 A(3) for TIP4P-QDP versus 1.1 A(3) (TIP4P-FQ) and 0.87 A(3) (POL3) [Ponder and Case, Adv. Protein Chem. 66, 27 (2003)]} based on ab initio calculations of the condensed-phase polarizability reduction in liquid water, the present simulations highlight the role of water polarizability in inducing water molecular dipole moments parallel to the interface normal (and within the interfacial region) so as to favorably oppose the macrodipole generated by the separation of anion and cation charge. Since the TIP4P-QDP water polarizability approaches that of the experimental vapor phase value for water, the present results suggest a fundamental role of solvent polarizability in accommodating the large spatial dipole generated by the separation of ion charges. The present results draw further attention to the question of what exact value of condensed phase water polarizability to incorporate in classical polarizable water force fields. PMID:20095700

Bauer, Brad A; Patel, Sandeep

2010-01-14

323

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

324

Stability of molecular dynamics simulations of classical systems

NASA Astrophysics Data System (ADS)

The existence of a shadow Hamiltonian H~ for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics. The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ? gives a criterion for the limit of stability h <= 2/?. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD. The method is also used to investigate higher-order central difference algorithms, which are symplectic and also have shadow Hamiltonians, and for which one can also determine the exact criteria for the limit of stability of a single harmonic mode. A fourth-order central difference algorithm gives an improved stability with a factor of 3, but the overhead of computer time is a factor of at least two. The conclusion is that the second-order ``Verlet''-algorithm, most commonly used in MD, is superior. It gives the exact dynamics within the limit of the asymptotic expansion and this limit can be estimated either from the conserved shadow energy or from the instantaneous spectrum of harmonic modes.

Toxvaerd, Søren

2012-12-01

325

Stability of molecular dynamics simulations of classical systems.

The existence of a shadow Hamiltonian H? for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics. The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ? gives a criterion for the limit of stability h ? 2/?. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD. The method is also used to investigate higher-order central difference algorithms, which are symplectic and also have shadow Hamiltonians, and for which one can also determine the exact criteria for the limit of stability of a single harmonic mode. A fourth-order central difference algorithm gives an improved stability with a factor of 3, but the overhead of computer time is a factor of at least two. The conclusion is that the second-order "Verlet"-algorithm, most commonly used in MD, is superior. It gives the exact dynamics within the limit of the asymptotic expansion and this limit can be estimated either from the conserved shadow energy or from the instantaneous spectrum of harmonic modes. PMID:23231212

Toxvaerd, Søren

2012-12-01

326

Atomistic modeling and molecular dynamic simulation of binary metallic glasses

NASA Astrophysics Data System (ADS)

Bulk metallic glasses (BMGs) have great potentials because of their unique outstanding mechanical and physical properties. However, the fundamental principles guiding the discovery of new BMGs have not been systematically developed. In this work, the glass forming ability (GFA) of binary metallic systems has been investigated by using molecular dynamic simulations. A series of interatomic potentials representing different atomic size ratios and chemical bonding of the constituent atoms were constructed to demonstrate the effects of the size ratio, concentration of the minority atoms and compositional short range order (CSRO) on the GFA. The phase diagrams of glass transition were built to represent the glass formation in the quenching process. We found that when the atomic size ratio should be limited in a range to form a binary metallic glasses. The addition of the solute atoms always improves the GFA of the modeling system. The size ratio factor, defined as the product of the size mismatch and the minimum concentration of the solute atoms, has been used to quantitatively describe the GFA. CSRO, introduced by applying the repulsive potential between small sized atoms, improves glass formability, and makes small atoms have slower dynamics and lower diffusivity than large atoms. Al-Ni binary system was studied with Finnis-Sinclair potential to describe atomic interactions. We investigated the transitions of Al80Ni20 systems at two cooling rates, and found that there exist octahedral local clusters in the amorphous AlNi alloys. The strong Al-Ni interaction and weak Ni-Ni interaction leads to preferred Al atoms neighborhood for Ni atoms. This type of the chemical bonding is similar to the CSRO introduced in the modeling system. The studies of the relaxation time reveal that the small sized Ni atoms actually have slower dynamics than Al atoms. It is in agreement with that of the modeling system and suggests that the size mismatch and CSRO play key roles in determining the GFA of BMG materials.

Chen, Hao

327

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

328

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

329

IBIsCO: a molecular dynamics simulation package for coarse-grained simulation.

IBIsCO is a parallel molecular dynamics simulation package developed specially for coarse-grained simulations with numerical potentials derived by the iterative Boltzmann inversion (IBI) method (Reith et al., J Comput Chem 2003, 24, 1624). In addition to common features of molecular dynamics programs, the techniques of dissipative particle dynamics (Groot and Warren, J Chem Phys 1997, 107, 4423) and Lowe-Andersen dynamics (Lowe, Europhys Lett 1999, 47, 145) are implemented, which can be used both as thermostats and as sources of friction to compensate the loss of degrees of freedom by coarse-graining. The reverse nonequilibrium molecular dynamics simulation method (Müller-Plathe, Phys Rev E 1999, 59, 4894) for the calculation of viscosities is also implemented. Details of the algorithms, functionalities, implementation, user interfaces, and file formats are described. The code is parallelized using PE_MPI on PowerPC architecture. The execution time scales satisfactorily with the number of processors. PMID:21425295

Karimi-Varzaneh, Hossein Ali; Qian, Hu-Jun; Chen, Xiaoyu; Carbone, Paola; Müller-Plathe, Florian

2011-05-01

330

Virus-like particles (VLPs) are highly organized nanoparticles that have great potential in vaccinology, gene therapy, drug delivery, and materials science. However, the application of VLPs is hindered by obstacles in their design and production due to low efficiency of self-assembly. In the present study, all-atom (AA) molecular dynamics (MD) simulations coupled with the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method are utilized to examine the molecular interactions in the capsomere of a murine polyomavirus (MPV) VLP. It is found that both low ionic strength and the intracapsomere disulfide bonds are favorable for maintaining a stable capsomere. Simulation results examining the effects of solution conditions on the stabilization of a capsomere were verified by calorimetry experiments. Simulation results of free energy decomposition indicate that hydrophobic interaction is favorable for the formation of a capsomere, whereas electrostatic interaction is unfavorable. With increasing ionic strength, the dominant interaction for the stabilization of a capsomere changes from hydrophobic to electrostatic. By comprehensive analyses, the key amino acid residues (hot spots) in VP1 protein aiding formation of a capsomere in different solution conditions have been identified. These results provide molecular insights into the stabilization of building blocks for VLP and are expected to have implications in their partitioning between the correct and off-pathway reactions in VLP assembly. PMID:23586433

Zhang, Lin; Tang, Ronghong; Bai, Shu; Connors, Natalie K; Lua, Linda H L; Chuan, Yap P; Middelberg, Anton P J; Sun, Yan

2013-05-01

331

Molecular dynamics simulation of radiation damage in bcc tungsten

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations of collision cascades in pure tungsten are performed to assess the primary damage due to irradiation. For short-range interaction the universal potential is used [J.F. Ziegler, J.P. Biersack, U. Littmark, The Stopping and Range of Ions in Solids, Pergamon Press, 1985, p. 41], while for long-range interaction, three different embedded atom method potentials [M.W. Finnis, J.E. Sinclair, Phil. Mag. A 50 (1984) 45; G.J. Ackland, R. Thetford, Phil. Mag. A 56 (1987) 15; P.M. Derlet, D. Nguyen-Manh, S.L. Dudarev, Phys. Rev. B 76 (2007) 054107] are used, namely, Finnis-Sinclair, Ackland-Thetford and Derlet-Nguyen-Manh-Dudarev, the latter providing a more accurate formation energy for the <1 1 0> interstitial. The short-range and long-range potentials are smoothly connected. A new approach improving the reliability of such potential fits at short distances is presented. These potentials are then evaluated on the basis of displacement threshold, point defect formation and migration energies, thermal expansion and temperature of melting. Differences in the damage resulting from collision cascades are discussed.

Fikar, J.; Schäublin, R.

2009-04-01

332

Molecular-dynamics (MD) and Monte Carlo (MC) calculations of the mean-square displacement (MSD) have been carried out for a fcc nearest-neighbor Lennard-Jones model for a wide range of temperatures and lattice spacings. The lattice-dynamics (LD) calculations of the harmonic and the lowest-order anharmonic (cubic and quartic) contributions to the mean-square displacement were performed for the same potential model as in the

Gernot A. Heiser; Ramesh C. Shukla; E. R. Cowley

1986-01-01

333

National Technical Information Service (NTIS)

A molecular simulation method to study the dynamics of chemically reacting mixtures is presented. The method uses a combination of stochastic and dynamic simulation steps, allowing for the simulation of both thermodynamic and transport properties. The met...

J. K. Brennan M. Lisal K. E. Gubbins B. M. Rice

2006-01-01

334

Large nonadiabatic quantum molecular dynamics simulations on parallel computers

NASA Astrophysics Data System (ADS)

We have implemented a quantum molecular dynamics simulation incorporating nonadiabatic electronic transitions on massively parallel computers to study photoexcitation dynamics of electrons and ions. The nonadiabatic quantum molecular dynamics (NAQMD) simulation is based on Casida's linear response time-dependent density functional theory to describe electronic excited states and Tully's fewest-switches surface hopping approach to describe nonadiabatic electron-ion dynamics. To enable large NAQMD simulations, a series of techniques are employed for efficiently calculating long-range exact exchange correction and excited-state forces. The simulation program is parallelized using hybrid spatial and band decomposition, and is tested for various materials.

Shimojo, Fuyuki; Ohmura, Satoshi; Mou, Weiwei; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

2013-01-01

335

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; Wei, G.W.

2010-01-01

336

Molecular dynamics of dopamine at the D2 receptor.

A three-dimensional model of the dopamine D2 receptor, assumed to be a target of antipsychotic drug action, was constructed from its amino acid sequence. The model was based on structural similarities within the super-family of guanine nucleotide-binding regulatory (G) protein-coupled neuroreceptors and has seven alpha-helical transmembrane segments that form a central core with a putative ligand-binding site. The space between two residues postulated to be involved in agonist binding, Asp-80 and Asn-390, perfectly accommodated an anti-dopamine molecule. Molecular electrostatic potentials were mainly negative on the synaptic side of the receptor model and around aspartate residues lining the central core and positive in the cytoplasmic domains. The docking of dopamine into a postulated binding site was examined by molecular dynamics simulation. The protonated amino group became oriented toward negatively charged aspartate residues in helix 2 and helix 3, whereas the dopamine molecule fluctuated rapidly between different anti and gauche conformations during the simulation. The receptor model suggests that protonated ligands are attracted to the binding site by electrostatic forces and that protonated agonists may induce conformational changes in the receptor, leading to G-protein activation, by increasing the electrostatic potentials near Asp-80. Images

Dahl, S G; Edvardsen, O; Sylte, I

1991-01-01

337

Modeling of blood vessel constriction in 2-D case using molecular dynamics method

NASA Astrophysics Data System (ADS)

Blood vessel constriction is simulated with particle-based method using a molecular dynamics authoring software known as Molecular Workbench (WM). Blood flow and vessel wall, the only components considered in constructing a blood vessel, are all represented in particle form with interaction potentials: Lennard-Jones potential, push-pull spring potential, and bending spring potential. Influence of medium or blood plasma is accommodated in plasma viscosity through Stokes drag force. It has been observed that pressure p is increased as constriction c is increased. Leakage of blood vessel starts at 80% constriction, which shows existence of maximum pressure that can be overcome by vessel wall.

A. S., M. Rendi; Suprijadi, Viridi, S.

2014-03-01

338

Dynamic behavioural interpretation of cervical intraepithelial neoplasia with molecular biomarkers

The microscopic phenotype of cervical intraepithelial neoplasia (CIN) reflects a fine balance between factors that promote or reduce CIN development. A shortcoming of the current grading system is its reliance on static morphology and microscopic haematoxylin–eosin features of the epithelium alone. In reality, CIN is a dynamic process, and the epithelium may exhibit differing results over time. Functional biomarkers p16, Ki?67, p53, retinoblastoma protein cytokeratin (CK)14 and CK13, help in the assessment of an individual CIN's lesion's potential for progression and regression. The aggregate information provided by these biomarkers exceeds the value of the classic grading system. Consequently, many more CINs that will either regress or progress can be accurately identified. These findings agree with known molecular interactions between HPV and the host. For accurate interpretation of a CIN, it is essential that these biomarkers be determined quantitatively and separately in the superficial, middle and deep layers of the epithelium. Such geography?specific epithelial evaluations of quantitative biomarkers emphasise the dynamic nature of a particular CIN lesion, thereby changing the art of static morphology grading into dynamic interpretation of the diseased tissue, with a strong prognostic effect.

Baak, J P A; Kruse, A-J; Robboy, S J; Janssen, E A M; van Diermen, B; Skaland, I

2006-01-01

339

Trefoil knotting revealed by molecular dynamics simulations of supercoiled DNA.

Computer simulations of the supercoiling of DNA, largely limited to stochastic search techniques, can offer important information to complement analytical models and experimental data. Through association of an energy function, minimum-energy supercoiled conformations, fluctuations about these states, and interconversions among forms may be sought. In theory, the observation of such large-scale conformational changes is possible, but modeling and numerical considerations limit the picture obtained in practice. A new computational approach is reported that combines an idealized elastic energy model, a compact B-spline representation of circular duplex DNA, and deterministic minimization and molecular dynamics algorithms. A trefoil knotting result, made possible by a large time-step dynamics scheme, is described. The simulated strand passage supports and details a supercoiled-directed knotting mechanism. This process may be associated with collective bending and twisting motions involved in supercoiling propagation and interwound branching. The results also demonstrate the potential effectiveness of the Langevin/implicit-Euler dynamics scheme for studying biomolecular folding and reactions over biologically interesting time scales. PMID:1509261

Schlick, T; Olson, W K

1992-08-21

340

Trefoil Knotting Revealed by Molecular Dynamics Simulations of Supercoiled DNA

NASA Astrophysics Data System (ADS)

Computer simulations of the supercoiling of DNA, largely limited to stochastic search techniques, can offer important information to complement analytical models and experimental data. Through association of an energy function, minimum-energy supercoiled conformations, fluctuations about these states, and interconversions among forms may be sought. In theory, the observation of such large-scale conformational changes is possible, but modeling and numerical considerations limit the picture obtained in practice. A new computational approach is reported that combines an idealized elastic energy model, a compact B-spline representation of circular duplex DNA, and deterministic minimization and molecular dynamics algorithms. A trefoil knotting result, made possible by a large time-step dynamics scheme, is described. The simulated strand passage supports and details a supercoiled-directed knotting mechanism. This process may be associated with collective bending and twisting motions involved in supercoiling propagation and interwound branching. The results also demonstrate the potential effectiveness of the Langevin/implicit-Euler dynamics scheme for studying biomolecular folding and reactions over biologically interesting time scales.

Schlick, Tamar; Olson, Wilma K.

1992-08-01

341

Linear Scaling First-Principles Molecular Dynamics with Controlled Accuracy

In our quest for accurate linear scaling first-principles molecular dynamics methods for pseudopotential DFT calculations, we investigate the accuracy of real-space grid approaches, with finite differences and spherical localization regions. We examine how the positions of the localization centers affect the accuracy and the convergence rate of the optimization process. In particular we investigate the accuracy of the atomic forces computation compared to the standard O(N{sup 3}) approach. We show the exponential decay of the error on the energy and forces with the size of the localization regions for a variety of realistic physical systems. We propose a new algorithm to automatically adapt the localization centers during the ground state computation which allows for molecular dynamics simulations with diffusion processes. The combination of algorithms proposed lead to a genuine linear scaling First-Principles Molecular Dynamics method with controlled accuracy. We illustrate our approach with examples of microcanonical molecular dynamics with localized orbitals.

Gygi, F; Fattebert, J

2004-03-10

342

Comparison of Molecular-Dynamics Calculations with Observed Initiation Phenomena.

National Technical Information Service (NTIS)

A large number of molecular dynamics calculations of the effects of the interaction of shock waves with condensed systems representing chemical explosives have been completed and the microscopic effects of material characteristics known to cause changes i...

F. E. Walker A. M. Karo J. R. Hardy

1981-01-01

343

Molecular dynamics simulations of protein targets identified in Mycobacterium tuberculosis.

Application of molecular dynamics simulation technique has become a conventional computational methodology to calculate significant processes at the molecular level. This computational methodology is particularly useful for analyzing the dynamics of protein-ligand systems. Several uses of molecular dynamics simulation makes possible evaluation of important structural features found at interface between a ligand and a protein, such as intermolecular hydrogen bonds, contact area and binding energy. Considering structure-based virtual screening, molecular dynamics simulations play a pivotal role in understanding the features that are important for ligand-binding affinity. This information could be employed to select higher-affinity ligands obtained in screening processes. Many protein targets such as enoyl-[acyl-carrier-protein] reductase (InhA), purine nucleoside phosphorylase (PNP), and shikimate kinase have been submitted to these simulations and will be analyzed here. All command files used in this review are available for download at http://azevedolab.net/md_75.html. PMID:21366529

de Azevedo, W F

2011-01-01

344

Modeling and Computer Simulation: Molecular Dynamics and Kinetic Monte Carlo.

National Technical Information Service (NTIS)

This article describes the atomistic modeling techniques of molecular dynamics (MD) and kinetic Monte Carlo (KMC), and an example of their application to radiation damage production and accumulation in metals. It is important to note at the outset that th...

B. D. Wirth M. J. Caturla T. Diaz de la Rubia

2000-01-01

345

Predicting large area surface reconstructions using molecular dynamics methods.

In this paper we discuss a new simulation method that can be used to predict preferred surface reconstructions of model systems by Molecular Dynamics (MD). The method overcomes the limitations imposed by periodic boundary conditions for finite boundary MD simulations which can normally prevent reconstructions. By simulating only the reconstructed surface layer and by removing the periodic boundary effects and the free energy barriers to reconstruction, the method allows surfaces to reconstruct to a preferred structure. We test the method on three types of surfaces: (i) the Au(100) and Pt(100) hexagonally reconstructed surface, (ii) the Au(111) herringbone surfaces, and (iii) the triangularly reconstructed Ag surface layer on a Pt(111) substrate and find the method readily finds lower surface energy reconstructions as preferred by the potential. PMID:24511962

Grochola, Gregory; Snook, Ian K; Russo, Salvy P

2014-02-01

346

Molecular Dynamics Simulations of Carbon Nanotubes in Water

NASA Technical Reports Server (NTRS)

We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.

Walther, J. H.; Jaffe, R.; Halicioglu, T.; Koumoutsakos, P.

2000-01-01

347

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

348

Molecular Dynamics Simulation on Mechanics of Mg2Si Nanofilm

NASA Astrophysics Data System (ADS)

Molecular dynamics simulation has been carried out to study the mechanical properties of Mg2Si nanofilm. For the binary thermoelectric material Mg2Si with antifluorite crystal structure, a modified Morse potential energy function in which the bond-angle deformation has been taken into account is developed and employed to describe the atomic interactions to shed light on its mechanical properties. In the simulation, the radial distribution function of Mg2Si nanofilm is computed to validate its crystal structure, and the stress-strain responses of the nanofilm are examined at room temperature. It is found that the mechanical properties of Mg2Si nanofilm are quite different from those of bulk Mg2Si due to the impact of surface atoms of the nanostructures. The size effect and the temperature effect on the mechanical properties of Mg2Si nanofilm are discussed in detail.

Yu, Rui; Yang, Shuyong; Zhai, Pengcheng; Liu, Lisheng

2013-07-01

349

Substrate recognition by norovirus polymerase: microsecond molecular dynamics study.

Molecular dynamics simulations of complexes between Norwalk virus RNA dependent RNA polymerase and its natural CTP and 2dCTP (both containing the O5'-C5'-C4'-O4' sequence of atoms bridging the triphosphate and sugar moiety) or modified coCTP (C5'-O5'-C4'-O4'), cocCTP (C5'-O5'-C4'-C4'') substrates were produced by means of CUDA programmable graphical processing units and the ACEMD software package. It enabled us to gain microsecond MD trajectories clearly showing that similar nucleoside triphosphates can bind surprisingly differently into the active site of the Norwalk virus RNA dependent RNA polymerase. It corresponds to their different modes of action (CTP-substrate, 2dCTP-poor substrate, coCTP-chain terminator, cocCTP-inhibitor). Moreover, extremely rare events-as repetitive pervasion of Arg182 into a potentially reaction promoting arrangement-were captured. PMID:23619980

Malá?, Kamil; Barvík, Ivan

2013-04-01

350

Insights into Buforin II Membrane Translocation from Molecular Dynamics Simulations

Buforin II is a histone-derived antimicrobial peptide that readily translocates across lipid membranes without causing significant membrane permeabilization. Previous studies showed that mutating the sole proline of buforin II dramatically decreases its translocation. As well, researchers have proposed that the peptide crosses membranes in a cooperative manner through forming transient toroidal pores. This paper reports molecular dynamics simulations designed to investigate the structure of buforin II upon membrane entry and evaluate whether the peptide is able to form toroidal pore structures. These simulations showed a relationship between protein-lipid interactions and increased structural deformations of the buforin N-terminal region promoted by proline. Moreover, simulations with multiple peptides show how buforin II can embed deeply into membranes and potentially form toroidal pores. Together, these simulations provide structural insight into the translocation process for buforin II in addition to providing more general insight into the role proline can play in antimicrobial peptides.

Elmore, Donald E.

2012-01-01

351

Study on C-W interactions by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

By means of molecular dynamics simulations using bond-order potential (BOP), we have investigated the interactions between carbon (C) atoms and bcc tungsten (W). At finite temperature ( T = 300 K) with incident energy of C atoms ranging from 0.5 to 100 eV at normal incidence, the projected range distribution as a function of incident energy and the average depth have been depicted. The properties of vacancy, vacancy migration, interstitial and substitutional C atoms in W have been determined. The most stable configuration for an interstitial C atom in W is in octahedral position and the lattice distortion around the C atom in octahedral interstitial configuration occurs along <1 0 0> and <1 1 0> directions. The mutual interaction between a vacancy and near interstitial C atom is also studied.

Yang, Zhongshi; Xu, Q.; Liao, Junqi; Li, Q.; Lu, G.-H.; Luo, G.-N.

2009-09-01

352

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

2010-06-18

353

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

354

Molecular dynamics simulation of displacement cascades in UO2

NASA Astrophysics Data System (ADS)

The primary damage induced within a uranium dioxide matrix subjected to a flux of energetic ions was investigated by classical molecular dynamics. UO2 was modeled using the set of empirical potentials based on a rigid ion model. Displacement cascades were initiated by accelerating a uranium primary knock-on atom to a kinetic energy up to 100 keV. It was first shown that the estimated RID a-thermal coefficient is well below those which are deemed relevant for spent nuclear fuels. Cascades were then purposely overlapped within the same simulation box so as to study the response of the material to increasing damage levels. During cascade overlap sequences, the growth of nanometric voids was observed. Obtained results evidenced a radiation damage controlled heterogeneous mechanism for insoluble fission product segregation in UO2.

Martin, Guillaume; Garcia, Philippe; Sabathier, Catherine; Palancher, Hervé; Maillard, Serge

2014-06-01

355

Predicting large area surface reconstructions using molecular dynamics methods

NASA Astrophysics Data System (ADS)

In this paper we discuss a new simulation method that can be used to predict preferred surface reconstructions of model systems by Molecular Dynamics (MD). The method overcomes the limitations imposed by periodic boundary conditions for finite boundary MD simulations which can normally prevent reconstructions. By simulating only the reconstructed surface layer and by removing the periodic boundary effects and the free energy barriers to reconstruction, the method allows surfaces to reconstruct to a preferred structure. We test the method on three types of surfaces: (i) the Au(100) and Pt(100) hexagonally reconstructed surface, (ii) the Au(111) herringbone surfaces, and (iii) the triangularly reconstructed Ag surface layer on a Pt(111) substrate and find the method readily finds lower surface energy reconstructions as preferred by the potential.

Grochola, Gregory; Snook, Ian K.; Russo, Salvy P.

2014-02-01

356

Atomistic molecular dynamics simulations of shock compressed quartz.

Atomistic non-equilibrium molecular dynamics simulations of shock wave compression of quartz have been performed using the so-called BKS semi-empirical potential of van Beest, Kramer, and van Santen [Phys. Rev. B 43, 5068 (1991)] to construct the Hugoniot of quartz. Our scheme mimics the real world experimental set up by using a flyer-plate impactor to initiate the shock wave and is the first shock wave simulation that uses a geometry optimised system of a polar slab in a three-dimensional system employing periodic boundary conditions. Our scheme also includes the relaxation of the surface dipole in the polar quartz slab which is an essential pre-requisite to a stable simulation. The original BKS potential is unsuited to shock wave calculations and so we propose a simple modification. With this modification, we find that our calculated Hugoniot is in good agreement with experimental shock wave data up to 25 GPa, but significantly diverges beyond this point. We conclude that our modified BKS potential is suitable for quartz under representative pressure conditions of the Earth core, but unsuitable for high-pressure shock wave simulations. We also find that the BKS potential incorrectly prefers the ?-quartz phase over the ?-quartz phase at zero-temperature, and that there is a ? ? ? phase-transition at 6 GPa. PMID:21806139

Farrow, M R; Probert, M I J

2011-07-28

357

Masses, luminosities and dynamics of galactic molecular clouds

NASA Technical Reports Server (NTRS)

Star formation in galaxies takes place in molecular clouds and the Milky Way is the only galaxy in which it is possible to resolve and study the physical properties and star formation activity of individual clouds. The masses, luminosities, dynamics, and distribution of molecular clouds, primarily giant molecular clouds in the Milky Way are described and analyzed. The observational data sets are the Massachusetts-Stony Brook CO Galactic Plane Survey and the IRAS far IR images. The molecular mass and infrared luminosities of glactic clouds are then compared with the molecular mass and infrared luminosities of external galaxies.

Solomon, P. M.; Rivolo, A. R.; Mooney, T. J.; Barrett, J. W.; Sage, L. J.

1987-01-01

358

Nonadiabatic Molecular Dynamics and Orthogonality Constrained Density Functional Theory

NASA Astrophysics Data System (ADS)

The exact quantum dynamics of realistic, multidimensional systems remains a formidable computational challenge. In many chemical processes, however, quantum effects such as tunneling, zero-point energy quantization, and nonadiabatic transitions play an important role. Therefore, approximate approaches that improve on the classical mechanical framework are of special practical interest. We propose a novel ring polymer surface hopping method for the calculation of chemical rate constants. The method blends two approaches, namely ring polymer molecular dynamics that accounts for tunneling and zero-point energy quantization, and surface hopping that incorporates nonadiabatic transitions. We test the method against exact quantum mechanical calculations for a one-dimensional, two-state model system. The method reproduces quite accurately the tunneling contribution to the rate and the distribution of reactants between the electronic states for this model system. Semiclassical instanton theory, an approach related to ring polymer molecular dynamics, accounts for tunneling by the use of periodic classical trajectories on the inverted potential energy surface. We study a model of electron transfer in solution, a chemical process where nonadiabatic events are prominent. By representing the tunneling electron with a ring polymer, we derive Marcus theory of electron transfer from semiclassical instanton theory after a careful analysis of the tunneling mode. We demonstrate that semiclassical instanton theory can recover the limit of Fermi's Golden Rule rate in a low-temperature, deep-tunneling regime. Mixed quantum-classical dynamics treats a few important degrees of freedom quantum mechanically, while classical mechanics describes affordably the rest of the system. But the interface of quantum and classical description is a challenging theoretical problem, especially for low-energy chemical processes. We therefore focus on the semiclassical limit of the coupled nuclear-electronic dynamics. We show that the time-dependent Schrodinger equation for the electrons employed in the widely used fewest switches surface hopping method is applicable only in the limit of nearly identical classical trajectories on the different potential energy surfaces. We propose a short-time decoupling algorithm that restricts the use of the Schrodinger equation only to the interaction regions. We test the short-time approximation on three model systems against exact quantum-mechanical calculations. The approximation improves the performance of the surface hopping approach. Nonadiabatic molecular dynamics simulations require the efficient and accurate computation of ground and excited state potential energy surfaces. Unlike the ground state calculations where standard methods exist, the computation of excited state properties is a challenging task. We employ time-independent density functional theory, in which the excited state energy is represented as a functional of the total density. We suggest an adiabatic-like approximation that simplifies the excited state exchange-correlation functional. We also derive a set of minimal conditions to impose exactly the orthogonality of the excited state Kohn-Sham determinant to the ground state determinant. This leads to an efficient, variational algorithm for the self-consistent optimization of the excited state energy. Finally, we assess the quality of the excitation energies obtained by the new method on a set of 28 organic molecules. The new approach provides results of similar accuracy to time-dependent density functional theory.

Shushkov, Philip Georgiev

359

Water flow in micro- and nanochannels. Molecular dynamics simulations

NASA Astrophysics Data System (ADS)

The flow in carbon nanotube is analysed using mathematical model that accounts for a depletion layer with reduced viscosity near the wall. The model by the author of the paper [Myers T G 2011 Microfluid Nanofluid 10 1141] is corrected. Moreover, the structure of the water flow inside 1 nm diameter and 1.5 nm length nanotubes is examined using molecular dynamics simulations. Molecular dynamics simulations of water flow velocity and flow rate though carbon nanotubes are reported too.

Podolska, N. I.; Zhmakin, A. I.

2013-08-01

360

Special issue on ultrafast electron and molecular dynamics

NASA Astrophysics Data System (ADS)

Your invitation to submit. Journal of Physics. B: Atomic Molecular and Optical Physics (JPhysB) is delighted to announce a forthcoming special issue on ultrafast electron and molecular dynamics to appear in 2014, and invites you to submit a paper. Within the last decade, a number of novel approaches have emerged, both experimental and theoretical, that allow the investigation of (time-resolved) molecular dynamics in novel ways not anticipated before. Experimentally, the introduction of novel light sources such as high-harmonic generation and XUV/x-ray free electron lasers, and the emergence of novel detection strategies, such as time-resolved electron/x-ray diffraction and the fully coincident detection of electrons and fragment ions in reaction microscopes, has significantly expanded the arsenal of available techniques, and has taken studies of molecular dynamics into new domains of spectroscopic, spatial and temporal resolution, the latter including first explorations into the attosecond domain. Along the way, particular types of molecular dynamics, such as dynamics around conical intersections, have gained an increased prominence, sparked by an emerging realization about the essential role that this dynamics plays in relaxation pathways in important bio-molecular systems. The progress on the theoretical side has been no less impressive. Novel generations of supercomputers and a series of novel computational strategies have allowed nearly exact calculations in small molecules, as well as highly successful approximate calculations in large, polyatomic molecules. Frequent and intensive collaborations involving both theory and experiment have been essential for the progress that has been accomplished. The special issue 'Ultrafast electron and molecular dynamics' seeks to provide an overview of some of the most important developments in the field, while at the same time indicating how studies of (time-resolved) molecular dynamics are likely to evolve in the coming years. You are invited to submit your article by 1 December 2013.

Hishikawa, Akiyoshi; Martin, Fernando; Vrakking, Marc

2013-07-01

361

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

NASA Technical Reports Server (NTRS)

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

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

2001-01-01

362

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

??-Microglobulin has been a model system for the study of fibril formation for 20 years. The experimental study of ??-microglobulin structure, dynamics, and thermodynamics in solution, at atomic detail, along the pathway leading to fibril formation is difficult because the onset of disorder and aggregation prevents signal resolution in Nuclear Magnetic Resonance experiments. Moreover, it is difficult to characterize conformers in exchange equilibrium. To gain insight (at atomic level) on processes for which experimental information is available at molecular or supramolecular level, molecular dynamics simulations have been widely used in the last decade. Here, we use molecular dynamics to address three key aspects of ??-microglobulin, which are known to be relevant to amyloid formation: (1) 60 ns molecular dynamics simulations of ??-microglobulin in trifluoroethanol and in conditions mimicking low pH are used to study the behavior of the protein in environmental conditions that are able to trigger amyloid formation; (2) adaptive biasing force molecular dynamics simulation is used to force cis-trans isomerization at Proline 32 and to calculate the relative free energy in the folded and unfolded state. The native-like trans-conformer (known as intermediate 2 and determining the slow phase of refolding), is simulated for 10 ns, detailing the possible link between cis-trans isomerization and conformational disorder; (3) molecular dynamics simulation of highly concentrated doxycycline (a molecule able to suppress fibril formation) in the presence of ??-microglobulin provides details of the binding modes of the drug and a rationale for its effect. PMID:21287627

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

2011-03-01

363

Background An important mechanism of endocrine activity is chemicals entering target cells via transport proteins and then interacting with hormone receptors such as the estrogen receptor (ER). ?-Fetoprotein (AFP) is a major transport protein in rodent serum that can bind and sequester estrogens, thus preventing entry to the target cell and where they could otherwise induce ER-mediated endocrine activity. Recently, we reported rat AFP binding affinities for a large set of structurally diverse chemicals, including 53 binders and 72 non-binders. However, the lack of three-dimensional (3D) structures of rat AFP hinders further understanding of the structural dependence for binding. Therefore, a 3D structure of rat AFP was built using homology modeling in order to elucidate rat AFP-ligand binding modes through docking analyses and molecular dynamics (MD) simulations. Methods Homology modeling was first applied to build a 3D structure of rat AFP. Molecular docking and Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) scoring were then used to examine potential rat AFP ligand binding modes. MD simulations and free energy calculations were performed to refine models of binding modes. Results A rat AFP tertiary structure was first obtained using homology modeling and MD simulations. The rat AFP-ligand binding modes of 13 structurally diverse, representative binders were calculated using molecular docking, (MM-GBSA) ranking and MD simulations. The key residues for rat AFP-ligand binding were postulated through analyzing the binding modes. Conclusion The optimized 3D rat AFP structure and associated ligand binding modes shed light on rat AFP-ligand binding interactions that, in turn, provide a means to estimate binding affinity of unknown chemicals. Our results will assist in the evaluation of the endocrine disruption potential of chemicals.

2013-01-01

364

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

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

Yoo, Jejoong; Aksimentiev, Aleksei

2013-01-01

365

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

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

Yoo, Jejoong; Aksimentiev, Aleksei

2013-12-10

366

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.

Johnston, Jennifer M.

2014-01-01

367

National Technical Information Service (NTIS)

We have studied the electron irradiation-induced amorphization of the ordered intermetallic compound NiZr(sub 2) by molecular dynamics simulations in conjunction with embedded-atom potentials. Randomly chosen Frenkel pairs and chemical disorder were intro...

R. Devanathan N. Q. Lam P. R. Okamoto M. Meshii

1992-01-01

368

Potential energy surfaces describing ion complexes containing molecular hydrogen

High-level abinitio molecular orbital calculations have been carried out to describe the potential energy surfaces for a series of systems corresponding formally to dimer ions of molecular hydrogen with an inert-gas atom or a first- or second-row hydride [X???H2]˙ +, where X=He, Ne, Ar, Kr, HF, HCl, H2O, H2S, NH3, and PH3. Of the [XH2]˙ + ion complexes, [Ne???H2]˙ +,

Josef Ischtwan; Brian J. Smith; Michael A. Collins; Leo Radom

1992-01-01

369

Syntheses of new functionalized azobenzenes for potential molecular electronic devices

New non-symmetrical azobenzene derivatives have been synthesized as potential molecular electronic switching device candidates. The Oxone® mediated oxidation of anilines provided nitroso-functionalized arenes, which were then condensed with substituted anilines to provide a series of azobenzene derivatives that could be further converted into oligo(phenylene ethynylene)s or diazonium salts. The resulting thiolacetates, thiols, or diazonium salts are capable of forming molecular

Byung-Chan Yu; Yasuhiro Shirai; James M. Tour

2006-01-01

370

begincenter Large ``On the fly'' localization of electronic orbitals in Car-Parrinello molecular dynamics: Toward a linear scaling ab initio molecular dynamics algorithm center begincenter Mark E. Tuckerman Department of Chemistry and Courant Institute of Mathematical Sciences New York University, New York, NY 10003 center Ab initio molecular dynamics (AIMD), the technique that generates finite temperature dynamics using forces obtained from

Mark Tuckerman

2004-01-01

371

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. PMID:20971684

Salsbury, Freddie R

2010-12-01

372

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

373

Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations

Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.

2013-01-01

374

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

375

The non-relativistic quantum dynamics of nuclei and electrons is solved within the framework of quantum hydrodynamics using the adiabatic representation of the electronic states. An on-the-fly trajectory-based nonadiabatic molecular dynamics algorithm is derived, which is also able to capture nuclear quantum effects that are missing in the traditional trajectory surface hopping approach based on the independent trajectory approximation. The use of correlated trajectories produces quantum dynamics, which is in principle exact and computationally very efficient. The method is first tested on a series of model potentials and then applied to study the molecular collision of H with H(2) using on-the-fly TDDFT potential energy surfaces and nonadiabatic coupling vectors. PMID:21264437

Curchod, Basile F E; Tavernelli, Ivano; Rothlisberger, Ursula

2011-02-28

376

Probing Transport Mechanisms in Nanofluids by Molecular Dynamics Simulations

Enhanced thermal conduction in nanofluids is an observed phenomenon for which the underlying mechanistic processes are still being debated. We perform molecular dynamics (MD) simulations of the time-dependent heat current correlation to obtain the systematic, dynamical details at the atomistic level. Using a model system of Xe base fluid and Pt nanoparticles, we obtain the enhancement effects which show qualitatively

Jacob Eapen; Ju Li; Sidney Yip

377

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

378

Nonequilibrium molecular dynamics simulation of a photoswitchable peptide

Femtosecond time-resolved experiments on photoswitchable peptides provide a new and promising way to study the folding and unfolding of biomolecules in real time and unprecedented detail. To obtain an appropriate theoretical description of these experiments, a computational strategy is presented that aims to extend well-established molecular dynamics simulation techniques to the description of photoinduced conformational dynamics in peptides. Adopting a

Phuong H. Nguyen; Gerhard Stock

2006-01-01

379

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

380

Extracting Experimental Measurables from Molecular Dynamics Simulations of Membranes

Atomistic molecular dynamics (MD) simulations are a powerful computational tool for probing the atomic-scale details of phospholipid bilayer structure and dynamics. Careful validation of the simulations is a critical step if the simulator is to establish productive contact with the experimentalist. The most fruitful approach is to directly compare simulated properties that correspond to primary experimental data, rather than to

Anthony R. Braun; Jonathan N. Sachs

2011-01-01

381

The Computer Simulation of Liquids by Molecular Dynamics.

ERIC Educational Resources Information Center

Proposes a mathematical computer model for the behavior of liquids using the classical dynamic principles of Sir Isaac Newton and the molecular dynamics method invented by other scientists. Concludes that other applications will be successful using supercomputers to go beyond simple Newtonian physics. (CW)

Smith, W.

1987-01-01

382

NASA Astrophysics Data System (ADS)

Neutron scattering and fully atomistic molecular dynamics (MD) are employed to investigate the structural and dynamical properties of polyamidoamine (PAMAM) dendrimers with ethylenediamine (EDA) core under various charge conditions. Regarding to the conformational characteristics, we focus on scrutinizing density profile evolution of PAMAM dendrimers as the molecular charge of dendrimer increases from neutral state to highly charged condition. It should be noted that within the context of small angle neutron scattering (SANS), the dendrimers are composed of hydrocarbon component (dry part) and the penetrating water molecules. Though there have been SANS experiments that studied the charge-dependent structural change of PAMAM dendrimers, their results were limited to the collective behavior of the aforementioned two parts. This study is devoted to deepen the understanding towards the structural responsiveness of intra-molecular polymeric and hydration parts separately through advanced contrast variation SANS data analysis scheme available recently and unravel the governing principles through coupling with MD simulations. Two kinds of acids, namely hydrochloric and sulfuric acids, are utilized to tune the pH condition and hence the molecular charge. As far as the dynamical properties, we target at understanding the underlying mechanism that leads to segmental dynamic enhancement observed from quasielstic neutron scattering (QENS) experiment previously. PAMAM dendrimers have a wealth of potential applications, such as drug delivery agency, energy harvesting medium, and light emitting diodes. More importantly, it is regarded as an ideal system to test many theoretical predictions since dendrimers conjugate both colloid-like globular shape and polymer-like flexible chains. This Ph.D. research addresses two main challenges in studying PAMAM dendrimers. Even though neutron scattering is an ideal tool to study this PAMAM dendrimer solution due to its matching temporal and spatial instrumental scales, understanding experimental results involves extensive and difficult data analysis based on liquid theory and condensed matter physics. Therefore, a model that successfully describes the inter- and intra-dendrimer correlations is crucial in obtaining and delivering reliable information. On the other hand, making meaningful comparisons between molecular dynamics and neutron scattering is a fundamental challenge to link simulations and experiments at the nano-scale. This challenge stems from our approach to utilize MD simulation to explain the underlying mechanism of experimental observation. The SANS measurements were conducted on a series of SANS spectrometers including the Extended Q-Range Small-Angle Neutron Scattering Diffractometer (EQ-SANS) and the General-Purpose Small-Angle Neutron Scattering Diffractometer (GP-SANS) at the Oak Ridge National Laboratory (ORNL), and NG7 Small Angle Neutron Scattering Spectrometer at National Institute of Standards (NIST) and Technology in U.S.A., large dynamic range small-angle diffractometer D22 at Institut Laue-Langevin (ILL) in France, and 40m-SANS Spectrometer at Korea Atomic Energy Research Institute (KAERI) in Korea. On the other hand, the Amber molecular dynamics simulation package is utilized to carry out the computational study. In this dissertation, the following observations have been revealed. The previously developed theoretical model for polyelectrolyte dendrimers are adopted to analyze SANS measurements and superb model fitting quality is found. Coupling with advanced contrast variation small angle neutron scattering (CVSANS) data analysis scheme reported recently, the intra-dendrimer hydration and hydrocarbon components distributions are revealed experimentally. The results indeed indicate that the maximum density is located in the molecular center rather than periphery, which is consistent to previous SANS studies and the back-folding picture of PAMAM dendrimers. According to this picture, at neutral condition, the exterior residues folding back into interior would necessarily

Wu, Bin

383

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

384

Potential Dynamical Mechanisms Behind Global Mantle Events

NASA Astrophysics Data System (ADS)

By numerical models we have investigated three potential mechanisms behind global mantle events. Plumes, originating in the thermal boundary layers of the mantle convection system can exhibit a significant episodicity, once a strong temperature-dependence of the viscosity of the mantle material is taken into account. An increase of the viscosity with pressure, as sometimes believed to suppress plumes, acts in fact to focus buoyancy into a few strong upwellings, which are potentially able to generate events on global scale. Plumes originating self- consistently from a thermal boundary layer, transport mostly material from their source region, while they entrain only little material during ascent. Compositionally dense material at the Core-mantle boundary has been proposed to explain seismological observed anomalies. The stability of such heterogeneities against entrainment by the overlying mantle-flow is determined by a complex set of properties, rather than by the density difference alone. Model calculations, taking into account a combined dependence of viscosity on temperature, pressure and , as mostly neglected; on composition, demonstrate, that under such conditions the D", can function as an isolated reservoir form some time, that however the destruction of the compositionally distinct layer, shielding the Earth'core can take place rapidly., with a profound effect also on the surface heat flow.. Finally we observe that episodic mobilization events of the surface are dynamically plausible for appropriate rheologies. A combination of temperature- and stress-dependent viscosity leads to an intermittent type of temporal behavior, where periods showing no surface motion (stagnant lid) are interrupted by phases with strong plate motions at the top. It seems at least possible that plate motion is not a continuously operating process.

Hansen, U.; Loddoch, A.; Stein, C.

2007-05-01

385

Molecular dynamics driven by ultrashort laser pulses: Interference effects due to rescattering

A time-dependent Schrödinger equation is integrated numerically to investigate the dynamics of a model molecular system driven\\u000a by a high-intensity ultrashort laser pulse. Two-dimensional photoelectron momentum distributions are analyzed. Highly nonmonotonic\\u000a electron angular distributions are obtained that cannot be explained by diffraction in the double-well potential of a molecular\\u000a ion. The nonmonotonicity is also demonstrated for atomic ionization and is

I. A. Burenkov; E. A. Volkova; A. M. Popov; O. V. Tikhonova

2009-01-01

386

Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations.

A computational method is developed to allow molecular dynamics simulations of biomembrane systems under realistic ionic gradients and asymmetric salt concentrations while maintaining the conventional periodic boundary conditions required to minimize finite-size effects in an all-atom explicit solvent representation. The method, which consists of introducing a nonperiodic energy step acting on the ionic species at the edge of the simulation cell, is first tested with illustrative applications to a simple membrane slab model and a phospholipid membrane bilayer. The nonperiodic energy-step method is then used to calculate the reversal potential of the bacterial porin OmpF, a large cation-specific ?-barrel channel, by simulating the I-V curve under an asymmetric 10:1 KCl concentration gradient. The calculated reversal potential of 28.6 mV is found to be in excellent agreement with the values of 26-27 mV measured from lipid bilayer experiments, thereby demonstrating that the method allows realistic simulations of nonequilibrium membrane transport with quantitative accuracy. As a final example, the pore domain of Kv1.2, a highly selective voltage-activated K(+) channel, is simulated in a lipid bilayer under conditions that recreate, for the first time, the physiological K(+) and Na(+) concentration gradients and the electrostatic potential difference of living cells. PMID:24081985

Khalili-Araghi, Fatemeh; Ziervogel, Brigitte; Gumbart, James C; Roux, Benoît

2013-10-01

387

Thermostat artifacts in replica exchange molecular dynamics simulations.

We explore the effects of thermostats in replica exchange molecular dynamics (REMD) simulations. For thermostats that do not produce a canonical ensemble, REMD simulations are found to distort the configuration-space distributions. For bulk water, we find small deviations of the average potential energies, the buildup of tails in the potential energy distributions, and artificial correlations between the energies at different temperatures. If a solute is present, as in protein folding simulations, its conformational equilibrium can be altered. In REMD simulations of a helix-forming peptide with a weak-coupling (Berendsen) thermostat, we find that the folded state is overpopulated by about 10% at low temperatures, and underpopulated at high temperatures. As a consequence, the enthalpy of folding deviates by almost 3 kcal/mol from the correct value. The reason for this population shift is that non-canonical ensembles with narrowed potential energy fluctuations artificially bias toward replica exchanges between low-energy folded structures at the high temperature and high-energy unfolded structures at the low temperature. We conclude that REMD simulations should only be performed in conjunction with thermostats that produce a canonical ensemble. PMID:20046980

Rosta, Edina; Buchete, Nicolae-Viorel; Hummer, Gerhard

2009-01-01

388

Mobilities of NO+ drifting in helium: A molecular dynamics study

NASA Astrophysics Data System (ADS)

A new molecular dynamics (MD) method is introduced, and used to study NO+ ions drifting in helium under the influence of a uniform electric field. Mobilities, average values of squared velocities, and self-diffusion coefficients parallel and perpendicular to the electric field are reported for two recent ab initio potential surfaces: a coupled cluster singles-doubles with perturbative treatment of triple excitations [CCSD(T)] surface [S. K. Pogrebnya et al., Int. J. Mass Spectrom. Ion Processes 149/150, 207 (1995)] and a MP4SDTQ/6-311+G(2df,p) surface [L. A. Viehland et al., Chem. Phys. 211, 1 (1996)]. Average values of angular momentum and alignment parameters are also reported and compared. In all cases, no significant differences were found in the calculated values for the two different potential surfaces. Finally, mobility values are compared with experimental measurements [J. A. de Gouw et al., J. Chem. Phys. 105, 10398 (1996)] and good agreement is obtained for both potential surfaces.

Baranowski, R.; Thachuk, M.

1999-06-01

389

Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations

A computational method is developed to allow molecular dynamics simulations of biomembrane systems under realistic ionic gradients and asymmetric salt concentrations while maintaining the conventional periodic boundary conditions required to minimize finite-size effects in an all-atom explicit solvent representation. The method, which consists of introducing a nonperiodic energy step acting on the ionic species at the edge of the simulation cell, is first tested with illustrative applications to a simple membrane slab model and a phospholipid membrane bilayer. The nonperiodic energy-step method is then used to calculate the reversal potential of the bacterial porin OmpF, a large cation-specific ?-barrel channel, by simulating the I-V curve under an asymmetric 10:1 KCl concentration gradient. The calculated reversal potential of 28.6 mV is found to be in excellent agreement with the values of 26–27 mV measured from lipid bilayer experiments, thereby demonstrating that the method allows realistic simulations of nonequilibrium membrane transport with quantitative accuracy. As a final example, the pore domain of Kv1.2, a highly selective voltage-activated K+ channel, is simulated in a lipid bilayer under conditions that recreate, for the first time, the physiological K+ and Na+ concentration gradients and the electrostatic potential difference of living cells.

Khalili-Araghi, Fatemeh; Ziervogel, Brigitte; Gumbart, James C.

2013-01-01

390

Molecular Dynamics Study of Thermal Properties of Intermetallic Alloys

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations of bulk copper, gold pure metals and their ordered intermetallics alloys of Cu3Au(L12) and CuAu3(L12) have been carried out between above 0 K and below the their melting points of the materials for predicting their temperature-dependent thermophysical properties. The effects of temperature and concentration on the physical properties such as enthalpy, volume, heat capacity, thermal expansion and density of CuxAu1-x are studied. Especially, temperature-dependent polynomial functions of enthalpy, volume and density are obtained. Sutton-Chen (SC) and Quantum Sutton-Chen (Q-SC) many-body potentials are used in the constant enthalpy-constant pressure ensemble (HPN) and constant pressure-constant temperature ensemble (TPN). Three important properties such as the coefficient of thermal volume expansion, heat capcity and density are correctly found to increase with temperature. Q-SC potential parameter results are usually closer to experimental values than the ones predicted from SC potential parameters.

Kart, H. H.; Tomak, Mehmet; Ça?in, Tahír

2006-07-01

391

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

An increasing number of studies have reported computations of the absolute binding free energy of small ligands to proteins using molecular dynamics (MD) simulations with results that are in good agreement with experiments. This encouraging progress suggests that physics-based approaches hold the promise of making important contributions to the process of drug discovery and optimization in the near future. Two types of approaches are principally used to compute binding free energies with MD simulations. The most widely known are based on alchemical free energy methods, in which the interaction of the ligand with its surrounding are progressively switched off. An alternative method is to use a potential of mean force (PMF), in which the ligand is physically separated from the protein receptor. For both of these computational approaches, restraining potentials affecting the translational, rotational and conformational freedom of the ligand and protein may be activated and released during the simulations to aid convergence and improve the sampling. Such restraining potentials add bias to the simulations, but their effects can be rigorously removed to yield a binding free energy that is properly unbiased with respect to the standard state. A review of recent results is presented. Examples of computations with T4-lysozyme mutants, FKBP12, SH2 domain, and cytochrome P450 are discussed and compared. Differences in computational methods are discussed and remaining difficulties and challenges are highlighted.

Deng, Yuqing; Roux, Benoit

2013-01-01

392

Optimal control of molecular motion expressed through quantum fluid dynamics

NASA Astrophysics Data System (ADS)

A quantum fluid-dynamic (QFD) control formulation is presented for optimally manipulating atomic and molecular systems. In QFD the control quantum system is expressed in terms of the probability density ? and the quantum current j. This choice of variables is motivated by the generally expected slowly varying spatial-temporal dependence of the fluid-dynamical variables. The QFD approach is illustrated for manipulation of the ground electronic state dynamics of HCl induced by an external electric field.

Dey, Bijoy K.; Rabitz, Herschel; Askar, Attila

2000-04-01

393

Molecular dynamics simulation of pervaporation in zeolite membranes

NASA Astrophysics Data System (ADS)

The pervaporation separation of liquid mixtures of water/ethanol and water/methanol using three zeolite (Silicalite, NaA and Chabazite) membranes has been examined using the method of molecular dynamics. The main goal of this study was to identify intermolecular interactions between water, methanol, ethanol and the membrane surface that play a critical role in the separations. This would then allow better membranes to be designed more efficiently and systematically than the trial-and-error procedures often being used. Our simulations correctly exhibited all the qualitative experimental observations for these systems, including the hydrophobic or hydrophilic behaviour of zeolite membranes. The simulations showed that, for Silicalite zeolite, the separation is strongly influenced by the selective adsorption of ethanol. The separation factor, as a consequence, increases almost exponentially as the ethanol composition decreases. For ethanol dehydration in NaA and Chabazite, pore size was found to play a very important role in the separation; very high separation factors were therefore possible. Simulations were also used to investigate the effect of pore structure, feed compositions and operating conditions on the pervaporation efficiency. Finally, our simulations also demonstrated that molecular simulations could serve as a useful screening tool to determine the suitability of a membrane for potential pervaporation separation applications. Simulations can cost only a small fraction of an experiment, and can therefore be used to design experiments most likely to be successful.

Jia, W.; Murad, S.

394

Molecular dynamics of the water liquid-vapor interface

NASA Technical Reports Server (NTRS)

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.

Wilson, M. A.; Pohorille, A.; Pratt, L. R.; MacElroy, R. D. (Principal Investigator)

1987-01-01

395

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

396

Structural dynamics of photoinduced molecular switching in the solid state.

Fast and ultra-fast time-resolved diffraction is a fantastic tool for directly observing the structural dynamics of a material rearrangement during the transformation induced by an ultra-short laser pulse. The paper illustrates this ability using the dynamics of photoinduced molecular switching in the solid state probed by 100 ps X-ray diffraction. This structural information is crucial for establishing the physical foundations of how to direct macroscopic photoswitching in materials. A key feature is that dynamics follow a complex pathway from molecular to material scales through a sequence of processes. Not only is the pathway indirect, the nature of the dynamical processes along the pathway depends on the timescale. This dictates which types of degrees of freedom are involved in the subsequent dynamics or kinetics and which are frozen or statistically averaged. We present a recent investigation of the structural dynamics in multifunctional spin-crossover materials, which are prototypes of molecular bistability in the solid state. The time-resolved X-ray diffraction results show that the dynamics span from subpicosecond molecular photoswitching followed by volume expansion (on a nanosecond timescale) and additional thermoswitching (on a microsecond timescale). PMID:20164642

Cailleau, Hervé; Lorenc, Maciej; Guérin, Laurent; Servol, Marina; Collet, Eric; Buron-Le Cointe, Marylise

2010-03-01

397

A molecular dynamics study of round and flattened carbon nanotube structures

NASA Astrophysics Data System (ADS)

Large diameter single wall carbon nanotubes exist with both round right cylinder and barbell-like flattened cross sections. Using an adaptive intermolecular reactive bond order potential, we examine the characteristics of both configurations by using molecular dynamics simulations. We then continue to examine the dynamical transition from the flattened to round state by charge injection. Predictions based on these simulations provide a basis for the design of active fluid transport devices, and nanoscale mechanical systems/motors.

Liu, Henry J.; Cho, Kyeongjae

2004-08-01

398

Self Diffusion in Nano Filled Polymer Melts: a Molecular Dynamics Simulation Study

NASA Astrophysics Data System (ADS)

SELF DIFFUSION IN NANO FILLED POLYMER MELTS: A MOLECULAR DYNAMICS SIMULATION STUDY* T. G. Desai,P. Keblinski, Material Science and Engineering Department, Rensselaer Polytechnic Institute, Troy, NY. Using molecular dynamics simulations, we studied the dynamics of the polymeric systems containing immobile and analytically smooth spherical nanoparticles. Each chain consisted of N monomers connected by an anharmonic springs described by the finite extendible nonlinear elastic, FENE potential. The system comprises of 3nanoparticles and the rest by freely rotating but not overlapping chains. The longest chain studied has a Radius of gyration equal to particle size radius and comparable to inter-particle distance. There is no effect on the structural characteristics such as Radius of gyration or end to end distance due to the nanoparticles. Diffusion of polymeric chains is not affected by the presence of either attractive or repulsive nanoparticles. In all cases Rouse dynamics is observed for short chains with a crossover to reptation dynamics for longer chains.

Desai, Tapan; Keblinski, Pawel

2003-03-01

399

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

400

Multiple Conformational States of Proteins: A Molecular Dynamics Analysis of Myoglobin

A molecular dynamics simulation of myoglobin provides the first direct demonstration that the potential energy surface of a protein is characterized by a large number of thermally accessible minima in the neighborhood of the native structure (for example, approximately 2000 minima were sampled in a 300-picosecond trajectory). This is expected to have important consequences for the interpretation of the activity

R. Elber; M. Karplus

1987-01-01

401

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

402

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, Søren; Heilmann, Ole J; Dyre, Jeppe C

2012-06-14

403

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, Søren; Heilmann, Ole J.; Dyre, Jeppe C.

2012-06-01

404

Ab initio molecular dynamics calculations to study catalysis

The modern versions of the density functional theory (DFT), especially those using the generalized gradient approximation (GGA), have reached (almost) chemical accuracy and thus can be applied to study problems of real chemical interest such as catalysis. The important equations for the DFT, the local density approximation (LDA), and GGA are given. The full-potential linearized augmented plane wave method (LAPW) is used to check the accuracy of GGA in solids. The basic concepts of the ab initio molecular dynamics (MD) method by Car and Parrinello and its recent implementation using the projector augmented Wave (PAW) method which use a similar augmentation as LAPW are described. PAW applications to ferrocene and beryllocene are summarized, which illustrate that vibrational or fluxional behavior are well described. Sodalite, an aluminosilicate, is discussed as a generic zeolite in comparison with gmelinite. A study of the dynamics of such a system allows the determination of e.g., the proton stretch vibrations of the acid site in silicon-rich sodalite. With this methodology, we are able to study the interaction of methanol trapped inside the cage structure of silicon-rich sodalite and to gain new insight into crucial steps of catalytic reactions, namely, the hydrogen-bonding and the possible protonation in this system, or a proton-exchange reaction. The strategies for parallelizing the PAW code are outlined. 36 refs., 8 figs.

Schwarz, K.; Nusterer, E. [Technische Universitaet Wien, Vienna (Austria)] [Technische Universitaet Wien, Vienna (Austria); Margl, P. [Univ. of Calgary, Alberta (Canada)] [Univ. of Calgary, Alberta (Canada); Bloechl, P.E. [Zurich Research Lab., Rueschlikon (Switzerland)] [Zurich Research Lab., Rueschlikon (Switzerland)

1997-01-20

405

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

406

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

407

Molecular properties, functions, and potential applications of NAD kinases

NADPH biosynthesis. Coenzymes such as NAD(H) and NADP(H) are known for their important functions. Recent studies have partially demonstrated that NAD kinase plays a crucial role in the regulation of NAD(H)\\/ NADP(H) conversion. Here, the molecular properties, physiologic functions, and potential applications of NAD kinase are discussed.

Feng Shi; Yongfu Li; Y. Li; X. Wang

2009-01-01

408

Ion photofragment spectroscopy: Potential surfaces of molecular ions

Techniques of ion photofragment spectroscopy have been used to investigate the structure and dissociation of molecular ions. For this research, a unique laser-ion coaxial beams spectrometer was constructed, allowing substantially improved sensitivity and resolution. The rare gas dimer ions were studied in detail, resulting in the determination of potential curves, absorption and photodissociation cross sections, and photofragment angular distributions for

J. T. Moseley; P. C. Cosby; J. R. Peterson

1979-01-01

409

Mixtures of protic ionic liquids and molecular cosolvents: A molecular dynamics simulation.

In this work, the effect of molecular cosolvents (water, ethanol, and methanol) on the structure of mixtures of these compounds with a protic ionic liquid (ethylammonium nitrate) is analyzed by means of classical molecular dynamics simulations. Included are as-yet-unreported measurements of the densities of these mixtures, used to test our parameterized potential. The evolution of the structure of the mixtures throughout the concentration range is reported by means of the calculation of coordination numbers and the fraction of hydrogen bonds in the system, together with radial and spatial distribution functions for the various molecular species and molecular ions in the mixture. The overall picture indicates a homogeneous mixing process of added cosolvent molecules, which progressively accommodate themselves in the network of hydrogen bonds of the protic ionic liquid, contrarily to what has been reported for their aprotic counterparts. Moreover, no water clustering similar to that in aprotic mixtures is detected in protic aqueous mixtures, but a somehow abrupt replacing of [NO3](-) anions in the first hydration shell of the polar heads of the ionic liquid cations is registered around 60% water molar concentration. The spatial distribution functions of water and alcohols differ in the coordination type, since water coordinates with [NO3](-) in a bidentate fashion in the equatorial plane of the anion, while alcohols do it in a monodentate fashion, competing for the oxygen atoms of the anion. Finally, the collision times of the different cosolvent molecules are also reported by calculating their velocity autocorrelation functions, and a caging effect is observed for water molecules but not in alcohol mixtures. PMID:24908021

Docampo-Álvarez, Borja; Gómez-González, Víctor; Méndez-Morales, Trinidad; Carrete, Jesús; Rodríguez, Julio R; Cabeza, Oscar; Gallego, Luis J; Varela, Luis M

2014-06-01

410

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

411

Dynamical exchange-correlation potentials beyond the local density approximation

NASA Astrophysics Data System (ADS)

Approximations for the static exchange-correlation (xc) potential of density functional theory (DFT) have reached a high level of sophistication. By contrast, time-dependent xc potentials are still being treated in a local (although velocity-dependent) approximation [G. Vignale, C. A. Ullrich and S. Conti, PRL 79, 4879 (1997)]. Unfortunately, one of the assumptions upon which the dynamical local approximation is based appears to break down in the important case of d.c. transport. Here we propose a new approximation scheme, which should allow a more accurate treatment of molecular transport problems. As a first step, we separate the exact adiabatic xc potential, which has the same form as in the static theory and can be treated by a generalized gradient approximation (GGA) or a meta-GGA. In the second step, we express the high-frequency limit of the xc stress tensor (whose divergence gives the xc force density) in terms of the exact static xc energy functional. Finally, we develop a perturbative scheme for the calculation of the frequency dependence of the xc stress tensor in terms of the ground-state Kohn-Sham orbitals and eigenvalues.

Tao, Jianmin; Vignale, Giovanni

2006-03-01

412

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 th