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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

Compensating Mass Matrix Potential Constrained Molecular Dynamics

molecular systems. The prohibitive complexity of computing the metric tensor potential and its gradient has Propulsion Laboratory/California Institute of Technology 4800 Oak Grove Drive, Pasadena, CA 91109 Abhinandan.Jain@jpl.nasaï¿½326 4800 Oak Grove Drive Pasadena, CA 91109 Abhinandan.Jain@jpl.nasa.gov Fax: (818) 393ï¿½4440 2 #12

3

combined with an on-the-fly interpolation scheme, allows us to determine the quantum dynamical interactionComputational Improvements to Quantum Wave Packet ab Initio Molecular Dynamics Using a Potential between quantum wave packet dynamics and ab initio molecular dynamics. Atom-centered density

Iyengar, Srinivasan S.

4

Local bias potential in hyper molecular dynamics method X.M. Duan b,1

Local bias potential in hyper molecular dynamics method X.M. Duan b,1 , X.G. Gong a; accepted 16 June 2002 Abstract The hyper molecular dynamics method (Hyper-MD) with a local bias potential. In this paper, we demonstrate the validity of the local bias potential in simulation of various systems

Gong, Xingao

5

New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations

New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations accurate free energy calculations based on molecular dynamics simulations. A thermodynamic integration scheme is often used to calculate changes in the free energy of a system by integrating the change

de Groot, Bert

6

The mechanical elongation of a finite gold nanowire has been studied by molecular dynamics simulations using different semiempirical potentials for transition metals. These potentials have been widely used to study the mechanical properties of finite metal clusters. Combining with density functional theory calculations along several atomic-configuration trajectories predicted by different semiempirical potentials, the authors conclude that the second-moment approximation of

Qing Pu; Yongsheng Leng; Leonidas Tsetseris; Harold S. Park; Sokrates T. Pantelides; Peter T. Cummings

2007-01-01

7

Molecular dynamics simulation of water properties using RWK2 potential: From clusters to bulk water

The accuracy of the two-body potential of Reimers et al. (RWK2, 1982) for water was evaluated by molecular dynamics simulation. As a test of this potential's ability to describe microscopic properties, the predicted structure, binding energy, and vibrational frequencies of clusters of various sizes are shown to agree remarkably well with available measurements and results calculated from first principle methods.

Zhenhao Duan; Nancy Møller; John H. Wears

1995-01-01

8

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

Ladd, A.J.C.

1988-08-01

9

A method for promoting reaction events in ab initio molecular dynamics simulations that is explicitly based on the electronic structure is developed. The technique uses a bias potential that is added to the regular potential and is constructed from the HOMO–LUMO gap of the system. This bias potential is tested along predetermined reaction coordinates and through molecular dynamics simulations for

Nicholas J. Mosey; Anguang Hu; Tom K. Woo

2003-01-01

10

In this work we have developed a polarizable potential to study Cm(III) forming complexes with carbonate anions in liquid water. The potential was developed by employing an extension of the procedure that we used to study the hydration of lanthanoids(III) and actinoids(III). Force field performances were benchmarked against DFT results obtained by both geometry optimization and Car-Parrinello molecular dynamics. With this polarizable potential, we run extended molecular dynamics simulations in liquid water from which we were able to identify structural and dynamical properties of such systems. In particular, water exchange dynamics were analyzed in detail. We obtained an average of three water molecules in the first shell of Cm(III) that show a relatively fast exchange dynamic (faster than for bare ions). Summarizing these results, we were able to draw an analogy to the results from the lanthanoid(III) series. In particular, it seems that Cm(III) behaves more like Nd(III) than Gd(III), as one would expect based on the recent hydration results and on f orbital occupancy. PMID:25086768

Spezia, Riccardo; Jeanvoine, Yannick; Vuilleumier, Rodolphe

2014-08-01

11

We present a method of DPD simulation based on a coarse-grained effective pair potential obtained from the DRISM-KH molecular theory of solvation. The theory is first used to calculate the radial distribution functions of all-atom solute monomers in all-atom solvent and then to invert them into an effective pair potential between coarse-grained beads such that their fluid without solvent accounts for molecular specificities and solvation effects in the all-atom system. Bonded interactions are sampled in relatively short MD of the all-atom system and modeled with best multi-Gaussian fit. Replacing the heuristically defined conservative force potential in DPD, the coarse-grained effective pair potential is free from the artificial restrictions on potential range and shape and on equal volume of solute and solvent blobs inherent in standard DPD. The procedure is flexible in specifying coarse-grained mapping and enormously increases computational efficiency by eliminating solvent. The method is validated on polystyrene chains of various length in toluene at finite concentrations for room and polystyrene glass transition temperature. It yields the chain elastic properties and diffusion coefficient in good agreement with experiment and all-atom MD simulations. DPD with coarse-grained effective pair potential is capable of predicting both structural and dynamic properties of polymer solutions and soft matter with high accuracy and computational efficiency. PMID:25162701

Kobryn, Alexander E; Nikoli?, Dragan; Lyubimova, Olga; Gusarov, Sergey; Kovalenko, Andriy

2014-10-16

12

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

13

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

14

NASA Astrophysics Data System (ADS)

Empirical potentials have a strong effect on the hybridization and structure of amorphous carbon and are of great importance in molecular dynamics (MD) simulations. In this work, amorphous carbon at densities ranging from 2.0 to 3.2 g/cm3 was modeled by a liquid quenching method using Tersoff, 2nd REBO, and ReaxFF empirical potentials. The hybridization, structure and radial distribution function G(r) of carbon atoms were analyzed as a function of the three potentials mentioned above. The ReaxFF potential is capable to model the change of the structure of amorphous carbon and MD results are in a good agreement with experimental results and density function theory (DFT) at low density of 2.6 g/cm3 and below. The 2nd REBO potential can be used when amorphous carbon has a very low density of 2.4 g/cm3 and below. Considering the computational efficiency, the Tersoff potential is recommended to model amorphous carbon at a high density of 2.6 g/cm3 and above. In addition, the influence of the quenching time on the hybridization content obtained with the three potentials is discussed.

Li, Longqiu; Xu, Ming; Song, Wenping; Ovcharenko, Andrey; Zhang, Guangyu; Jia, Ding

2013-12-01

15

A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new method, which we call pseudoatom molecular dynamics (PAMD), can be applied to single or multi-component plasmas. It gives equation of state and self-diffusion coefficients with an accuracy comparable to ab-initio simulations but is computationally much more efficient.

Starrett, C E; Saumon, D

2014-01-01

16

High-precision molecular dynamics simulation of UO2-PuO2: pair potentials comparison

Our series of articles is devoted to high-precision molecular dynamics simulation of mixed actinide-oxide (MOX) fuel in the rigid ions approximation using high-performance graphics processors (GPU). In the first article we assess 10 most relevant interatomic sets of pair potentials (SPP) by reproduction of solid phase properties of uranium dioxide (UO2) - temperature dependences of the lattice constant, bulk modulus, enthalpy and heat capacity. Measurements were performed with 1K accuracy in a wide temperature range from 300K up to melting point. The best results are demonstrated by two recent SPPs MOX-07 and Yakub-09, which both had been fitted to the recommended thermal expansion in the range of temperatures 300-3100K. Compared with them, the widely used SPPs Basak-03 and Morelon-03 reproduce the experimental data noticeably worse at temperatures above 2500K.

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

2011-01-01

17

Intermolecular interaction energy data for the methane dimer have been calculated at a spectroscopic accuracy and employed to construct an ab initio potential energy surface (PES) for molecular dynamics (MD) simulations of fluid methane properties. The full potential curves of the methane dimer at 12 symmetric conformations were calculated by the supermolecule counterpoise-corrected second-order Møller-Plesset (MP2) perturbation theory. Single-point coupled cluster with single and double and perturbative triple excitations [CCSD(T)] calculations were also carried out to calibrate the MP2 potentials. We employed Pople's medium size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (cc-pVXZ and aug-cc-pVXZ, X = D, T, Q). For each conformer, the intermolecular carbon-carbon separation was sampled in a step 0.1 A for a range of 3-9 A, resulting in a total of 732 configuration points calculated. The MP2 binding curves display significant anisotropy with respect to the relative orientations of the dimer. The potential curves at the complete basis set (CBS) limit were estimated using well-established analytical extrapolation schemes. A 4-site potential model with sites located at the hydrogen atoms was used to fit the ab initio potential data. This model stems from a hydrogen-hydrogen repulsion mechanism to explain the stability of the dimer structure. MD simulations using the ab initio PES show quantitative agreements on both the atom-wise radial distribution functions and the self-diffusion coefficients over a wide range of experimental conditions. PMID:19090563

Chao, Shih-Wei; Li, Arvin Huang-Te; Chao, Sheng D

2009-09-01

18

We describe a molecular-dynamics framework for the direct calculation of the short-ranged structural forces underlying grain-boundary premelting and grain coalescence in solidification. The method is applied in a comparative study of (i) a Sigma9115120 degrees twist and (ii) a Sigma9110{411} symmetric tilt boundary in a classical embedded-atom model of elemental Ni. Although both boundaries feature highly disordered structures near the melting point, the nature of the temperature dependence of the width of the disordered regions in these boundaries is qualitatively different. The former boundary displays behavior consistent with a logarithmically diverging premelted layer thickness as the melting temperature is approached from below, while the latter displays behavior featuring a finite grain-boundary width at the melting point. It is demonstrated that both types of behavior can be quantitatively described within a sharp-interface thermodynamic formalism involving a width-dependent interfacial free energy, referred to as the disjoining potential. The disjoining potential for boundary (i) is calculated to display a monotonic exponential dependence on width, while that of boundary (ii) features a weak attractive minimum. The results of this work are discussed in relation to recent simulation and theoretical studies of the thermodynamic forces underlying grain-boundary premelting. PMID:20365741

Fensin, Saryu J; Olmsted, David; Buta, Dorel; Asta, Mark; Karma, Alain; Hoyt, J J

2010-03-01

19

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

20

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

21

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

22

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

23

. For a review of the relatively large amount of related work, which has appeared in the literature, the reader, Pennsylvania 16802 Received 4 April 1996; accepted 25 June 1996 We report on a molecular dynamics simulation-workers. For the specific case of silver as a sample target material, it is shown that this potential allows a much more

Wucher, Andreas

24

Using full-potential linear-muffin-tin-orbital molecular-dynamics method, we have studied the geometric and electronic structures of short possible silicon nanotube consisting of silicon rings. All atoms in the ring structures have fourfold coordination. The stacked tubes are stable.

Bao-xing Li; Pei-lin Cao

2004-01-01

25

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

26

Docking and molecular dynamics studies of new potential inhibitors of the human epidermal receptor 2

Compounds similar to lapatinib and gefitinib have been investigated as potential inhibitors of the intracellular receptor tyrosine kinase (RTK) domain of the human epidermal receptor 2 (HER2), which is a promising molecular target to the drug design of new chemotherapies for breast, lung, ovarian and colorectal cancers. In this study, we have searched potential HER2 inhibitors used for treatment of

Wilian Augusto Cortopassi; Rafael José Cavalieri Feital; Diogo de Jesus Medeiros; Teobaldo Ricardo Cuya Guizado; Tanos Celmar Costa França; André Silva Pimentel

2012-01-01

27

The high-temperature behavior of a high-angle twist grain boundary, a free surface, and planar arrays of voids of various sizes, all on the (001) plane in copper, are studied through molecular-dynamics simulation using an embedded-atom-method potential. Independently, we determine the thermodynamic melting point, {ital T}{sub {ital m}} of this potential through an analysis of the free energies of a perfect

J. F. Lutsko; D. Wolf; S. R. Phillpot; S. Yip

1989-01-01

28

Introduction to Accelerated Molecular Dynamics

Molecular Dynamics is the numerical solution of the equations of motion of a set of atoms, given an interatomic potential V and some boundary and initial conditions. Molecular Dynamics is the largest scale model that gives unbiased dynamics [x(t),p(t)] in full atomistic detail. Molecular Dynamics: is simple; is 'exact' for classical dynamics (with respect to a given V); can be used to compute any (atomistic) thermodynamical or dynamical properties; naturally handles complexity -- the system does the right thing at the right time. The physics derives only from the interatomic potential.

Perez, Danny [Los Alamos National Laboratory

2012-07-10

29

A molecular dynamics simulation performed with the GROMOS molecular dynamics program of the tripeptide L-tryptophan, N-[N-(5-oxo-L-prolyl)-L-leucyl]-methyl ester (Glp-Leu-Trp-OCH3) was fully analyzed. The computation of dynamical nonlinear techniques to describe a potential energy time series, based on recurrence plot methodology, highlighted otherwise hidden features of the molecular dynamics in the equilibration phase.

Alessandro Giuliani; Cesare Manetti

1996-01-01

30

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

Jiyao Wang; Yuqing Deng; Benoît Roux

2006-01-01

31

NASA Astrophysics Data System (ADS)

A major advance in electronic structure calculations was the combination of local-density techniques with molecular dynamics by Car and Parrinello seven years ago. Unfortunately, application of the Car-Parrinello scheme has been limited essentially to sp materials because only in the plane-wave pseudopotential method forces are trivial to calculate. We present a systematic approach to derive force theorems with desired characteristics within complicated basis sets, which are applicable to all elements of the periodic table equally well. Application to the LMTO basis set yields an accurate force theorem, quite distinct from the Hellman-Feynman form, which is exceptionally insensitive to errors in the trial density. The forces were implemented in a new full-potential LMTO method which is suited to arbitrary geometries. First results for ab-initio molecular dynamics and simulated annealing runs are shown for some random small molecules and small clusters of silver atoms.

Methfessel, M.; van Schilfgaarde, M.

32

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

33

Molecular dynamics simulations of the ceramic compound zirconolite (CaZrTi?O?), a potential crystalline wasteform host for plutonium, were carried out for ideal and experimental crystalline forms and a simulated molten ...

Rich, Sarah Celeste

2008-01-01

34

We present a continuous pseudo-hard-sphere potential based on a cut-and-shifted Mie (generalized Lennard-Jones) potential with exponents (50, 49). Using this potential one can mimic the volumetric, structural, and dynamic properties of the discontinuous hard-sphere potential over the whole fluid range. The continuous pseudo potential has the advantage that it may be incorporated directly into off-the-shelf molecular-dynamics code, allowing the user to capitalise on existing hardware and software advances. Simulation results for the compressibility factor of the fluid and solid phases of our pseudo hard spheres are presented and compared both to the Carnahan-Starling equation of state of the fluid and published data, the differences being indistinguishable within simulation uncertainty. The specific form of the potential is employed to simulate flexible chains formed from these pseudo hard spheres at contact (pearl-necklace model) for m(c) = 4, 5, 7, 8, 16, 20, 100, 201, and 500 monomer segments. The compressibility factor of the chains per unit of monomer, m(c), approaches a limiting value at reasonably small values, m(c) < 50, as predicted by Wertheim's first order thermodynamic perturbation theory. Simulation results are also presented for highly asymmetric mixtures of pseudo hard spheres, with diameter ratios of 3:1, 5:1, 20:1 over the whole composition range. PMID:23061853

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

2012-10-14

35

NASA Astrophysics Data System (ADS)

Molecular dynamics simulation of annular flow boiling in a nanochannel is numerically investigated. In this research, an annular flow model is developed to predict the superheated flow boiling heat transfer characteristics in a nanochannel. To characterize the forced annular boiling flow in a nanochannel, an external driving force overrightarrow {F}_{{ext}} ranging from 1 to 12 PN (PN = pico newton) is applied along the flow direction to inlet fluid particles during the simulation. Based on an annular flow model analysis, it is found that saturation condition and superheat degree have great influences on the liquid-vapor interface. Also, the results show that due to the relatively strong influence of the surface tension in small channels, the interface between the liquid film and the vapor core is fairly smooth, and the mean velocity along the stream-wise direction does not change anymore. Also, it is found that the heat flux values depend on the boundary conditions. Finally, the Green-Kubo formula is used to calculate the thermal conductivity of liquid Argon. The simulations predict thermal conductivity of liquid Argon quite well.

Semiromi, D. Toghraie; Azimian, A. R.

2012-01-01

36

Biological activity, functionality, and synthesis of (fluoro)quinolones is closely related to their precursors (for instance 3-fluoroanilinoethylene derivatives) (i.e., their functional groups, conformational behavior, and/or electronic structure). Herein, the theoretical study of 3-fluoroanilinoethylene derivatives is presented. Impact of substituents (acetyl, methyl ester, and ethyl ester) on the conformational analysis and the spectral behavior is investigated. The B3LYP/6-311++G** computational protocol is utilized. It is found that the intramolecular hydrogen bond N-H···O is responsible for the energetic preference of anti (a) conformer (anti position of 3-fluoroanilino group with respect to the C?C double bond). The Boltzmann ratios of the conformers are related to the differences of the particular dipole moments and/or their dependence on the solvent polarity. The studied acetyl, ethyl ester, and methyl ester substituted fluoroquinolone precursors prefer in the solvent either EZa, ZZa, or both conformers equally, respectively. In order to understand the degree of freedom of rotation of the trans ethyl ester group, B3LYP/6-311G** molecular dynamic simulations were carried out. Vibrational frequencies, electron transitions, as well as NMR spectra are analyzed with respect to conformational analysis, including the effect of the substituent. X-ray structures of the precursors are presented and compared with the results of the conformational analysis. PMID:25188903

Dorotíková, Sandra; Plevová, Kristína; Bu?inský, Lukáš; Mal?ek, Michal; Herich, Peter; Kucková, Lenka; Bobeni?ová, Miroslava; Soralová, Stanislava; Kožíšek, Jozef; Fronc, Marek; Milata, Viktor; Dvoranová, Dana

2014-10-01

37

NASA Astrophysics Data System (ADS)

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

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

2013-10-01

38

NASA Astrophysics Data System (ADS)

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

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

2012-04-01

39

A new functional representation of NMR-derived distance constraints, the flexible restraint potential, has been implemented in the program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168) for molecular structure generation. In addition, flat-bottomed restraint potentials for representing dihedral angle and vicinal scalar coupling constraints have been introduced into CONGEN. An effective simulated annealing (SA) protocol that combines both weight annealing and temperature annealing is described. Calculations have been performed using ideal simulated NMR constraints, in order to evaluate the use of restrained molecular dynamics (MD) with these target functions as implemented in CONGEN. In this benchmark study, internuclear distance, dihedral angle, and vicinal coupling constant constraints were calculated from the energy-minimized X-ray crystal structure of the 46-amino acid polypeptide crambin (ICRN). Three-dimensional structures of crambin that satisfy these simulated NMR constraints were generated using restrained MD and SA. Polypeptide structures with extended backbone and side-chain conformations were used as starting conformations. Dynamical annealing calculations using extended starting conformations and assignments of initial velocities taken randomly from a Maxwellian distribution were found to adequately sample the conformational space consistent with the constraints. These calculations also show that loosened internuclear constraints can allow molecules to overcome local minima in the search for a global minimum with respect to both the NMR-derived constraints and conformational energy. This protocol and the modified version of the CONGEN program described here are shown to be reliable and robust, and are applicable generally for protein structure determination by dynamical simulated annealing using NMR data. PMID:8845749

Bassolino-Klimas, D.; Tejero, R.; Krystek, S. R.; Metzler, W. J.; Montelione, G. T.; Bruccoleri, R. E.

1996-01-01

40

NASA Astrophysics Data System (ADS)

Typically, short range potential only depends on neighbouring atoms and its parameters function can be categorized into bond stretching, angle bending and bond rotation potential. In this paper, we present our work called Angle Bending (AB) potential, whereas AB potential is the extension of our previous work namely Bond Stretching (BS) potential. Basically, potential will tend to zero after truncated region, potential in specific region can be represented by different piecewise polynomial. We proposed the AB piecewise potential which is possible to solve a system involving three atoms. AB potential able to handle the potential of covalent bonds for three atoms as well as two atoms cases due to its degeneracy properties. Continuity for the piecewise polynomial has been enforced by coupling with penalty methods. There are still plenty of improvement spaces for this AB potential. The improvement for three atoms AB potential will be studied and further modified into torsional potential which are the ongoing current research.

Ping, Tan Ai; Hoe, Yeak Su

2014-07-01

41

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

NASA Astrophysics Data System (ADS)

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

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

2011-05-01

42

Hardy stress definition has been restricted to pair potentials and embedded-atom method potentials due to the basic assumptions in the derivation of a symmetric microscopic stress tensor. Force decomposition required in the Hardy stress expression becomes obscure for multi-body potentials. In this work, we demonstrate the invariance of the Hardy stress expression for a polymer system modeled with multi-body interatomic potentials including up to four atoms interaction, by applying central force decomposition of the atomic force. The balance of momentum has been demonstrated to be valid theoretically and tested under various numerical simulation conditions. The validity of momentum conservation justifies the extension of Hardy stress expression to multi-body potential systems. Computed Hardy stress has been observed to converge to the virial stress of the system with increasing spatial averaging volume. This work provides a feasible and reliable linkage between the atomistic and continuum scales for multi-body potential systems. PMID:25106571

Fu, Yao; Song, Jeong-Hoon

2014-08-01

43

NASA Astrophysics Data System (ADS)

Hardy stress definition has been restricted to pair potentials and embedded-atom method potentials due to the basic assumptions in the derivation of a symmetric microscopic stress tensor. Force decomposition required in the Hardy stress expression becomes obscure for multi-body potentials. In this work, we demonstrate the invariance of the Hardy stress expression for a polymer system modeled with multi-body interatomic potentials including up to four atoms interaction, by applying central force decomposition of the atomic force. The balance of momentum has been demonstrated to be valid theoretically and tested under various numerical simulation conditions. The validity of momentum conservation justifies the extension of Hardy stress expression to multi-body potential systems. Computed Hardy stress has been observed to converge to the virial stress of the system with increasing spatial averaging volume. This work provides a feasible and reliable linkage between the atomistic and continuum scales for multi-body potential systems.

Fu, Yao; Song, Jeong-Hoon

2014-08-01

44

Molecular modeling of hydrate-clathrates via ab initio, cell potential, and dynamic methods

High level ab initio quantum mechanical calculations were used to determine the intermolecular potential energy surface between argon and water, corrected for many- body interactions, to predict monovariant and invariant ...

Anderson, Brian, Ph. D. Massachusetts Institute of Technology

2005-01-01

45

Aggregation is a common hurdle faced during the development of antibody therapeutics. In this study, we explore the potential aggregation liabilities of the Fab (fragment antigen-binding) from a human IgG1? antibody via multiple elevated temperature molecular dynamic simulations, analogous to accelerated stability studies performed during formulation development. Deformation and solvent exposure changes in response to thermal stress were monitored for individual structural domains (V(H), V(L), C(H)1 and C(L)), their interfaces (V(H):V(L) and C(H)1:C(L)), edge beta-strands and sequence-predicted aggregation-prone regions (APRs). During simulations, domain interfaces deformed prior to the unfolding of individual domains. However, interfacial beta-strands retained their secondary structure and remained solvent protected longer than all other strands or loops. Thus, APRs located in interfacial beta-strands are effectively blocked from self-association. Structural deformations were also observed in complementarity-determining regions, edge beta-strands and adjoining framework beta-strands, which increased their solvent-accessible surface area and exposed APRs in these regions. From the analysis of these structural changes, two potential aggregation liabilities were identified in the V(H) domain of this Fab. Insights gained from this investigation should be useful in devising a rational structure-based strategy for the design and selection of antibody candidates with high potency and improved developability. PMID:23188804

Buck, Patrick M; Kumar, Sandeep; Singh, Satish K

2013-03-01

46

In this work, we have developed a polarizable classical interaction potential to study actinoids(III) in liquid water. This potential has the same analytical form as was recently used for lanthanoid(III) hydration [M. Duvail, P. Vitorge, and R. Spezia, J. Chem. Phys. 130, 104501 (2009)]. The hydration structure obtained with this potential is in good agreement with the experimentally measured ion-water distances and coordination numbers for the first half of the actinoid series. In particular, the almost linearly decreasing water-ion distance found experimentally is replicated within the calculations, in agreement with the actinoid contraction behavior. We also studied the hydration of the last part of the series, for which no structural experimental data are available, which allows us to provide some predictive insights on these ions. In particular we found that the ion-water distance decreases almost linearly across the series with a smooth decrease of coordination number from nine to eight at the end. PMID:21806134

Duvail, Magali; Martelli, Fausto; Vitorge, Pierre; Spezia, Riccardo

2011-07-28

47

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

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

Paolo Valentini; Thomas E. Schwartzentruber; Ioana Cozmuta

2011-01-01

48

Molecular electrostatic potentials by systematic molecular fragmentation

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. [Research School of Chemistry, Australian National University, Canberra, ACT 0200 (Australia)] [Research School of Chemistry, Australian National University, Canberra, ACT 0200 (Australia)

2013-11-14

49

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. PMID:24073401

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

2013-01-01

50

NASA Astrophysics Data System (ADS)

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

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

2012-11-01

51

NASA Astrophysics Data System (ADS)

Molecular dynamics (MD) is an important research tool extensively applied in materials science. Running MD on a graphics processing unit (GPU) is an attractive new approach for accelerating MD simulations. Currently, GPU implementations of MD usually run in a one-host-process-one-GPU (OHPOG) scheme. This scheme may pose a limitation on the system size that an implementation can handle due to the small device memory relative to the host memory. In this paper, we present a one-host-process-multiple-GPU (OHPMG) implementation of MD with embedded-atom-model or semi-empirical tight-binding many-body potentials. Because more device memory is available in an OHPMG process, the system size that can be handled is increased to a few million or more atoms. In comparison with the serial CPU implementation, in which Newton's third law is applied to improve the computational efficiency, our OHPMG implementation has achieved a 28.9x-86.0x speedup in double precision, depending on the system size, the cut-off ranges and the number of GPUs. The implementation can also handle a group of small simulation boxes in one run by combining the small boxes into a large box. This approach greatly improves the GPU computing efficiency when a large number of MD simulations for small boxes are needed for statistical purposes.

Hou, Qing; Li, Min; Zhou, Yulu; Cui, Jiechao; Cui, Zhenguo; Wang, Jun

2013-09-01

52

Substructured multibody molecular dynamics.

We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

2006-11-01

53

Molecular dynamics simulations.

Molecular dynamics simulations have become a standard tool for the investigation of biomolecules. Simulations are performed of ever bigger systems using more realistic boundary conditions and better sampling due to longer sampling times. Recently, realistic simulations of systems as complex as transmembrane channels have become feasible. Simulations aid our understanding of biochemical processes and give a dynamic dimension to structural data; for example, the transformation of harmless prion protein into the disease-causing agent has been modeled. PMID:11959496

Hansson, Tomas; Oostenbrink, Chris; van Gunsteren, WilfredF

2002-04-01

54

On Molecular Dynamics Algorithms

The step errors (the local errors, called also the truncation errors) of algorithms used in molecular dynamics simulations result in errors of thermodynamic properties of simulated systems. The simulations on the Lennard-Jones (L-J) liquid showed that in the case of the Verlet algorithm the values of the errors are noticeable even if we apply Beeman's technique. For the time step

Marek Litniewski

2003-01-01

55

A major advance in electronic structure calculations was the combination of local-density techniques with molecular dynamics by Car and Parrinello seven years ago. Unfortunately, application of the Car-Parrinello scheme has been limited essentially to sp materials because only in the plane-wave pseudopotential method forces are trivial to calculate. We present a systematic approach to derive force theorems with desired characteristics

M. Methfessel; M. van Schilfgaarde

1993-01-01

56

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

57

Molecular dynamics simulations: insight into molecular phenomena at interfaces.

Molecular dynamics simulations, when aptly devised, can enhance our fundamental understanding of a system, set up a platform for testing theoretical predictions, and provide insight and a framework for further experimental studies. This feature article highlights the importance of molecular dynamics simulations in understanding interfacial phenomena using three case studies involving liquid-liquid and solid-liquid interfaces. After briefly reviewing molecular dynamics methods, we discuss velocity slip at a liquid-liquid interface, the coalescence of liquid drops in suspension and in free space, and the behavior of colloidal nanoparticles at a liquid-liquid interface. We emphasize the utility of simple intermolecular potentials and generic liquids. The case studies exemplify the significant insight gained through the molecular modeling approach regarding the interfacial phenomena studied. We conclude the highlight with a brief discussion illustrating potential shortcomings and pitfalls of molecular dynamics simulations. PMID:24684531

Razavi, Sepideh; Koplik, Joel; Kretzschmar, Ilona

2014-09-30

58

Adaptive integration of molecular dynamics.

This article presents a particle method framework for simulating molecular dynamics. For time integration, the implicit trapezoidal rule is employed, where an explicit predictor enables large time steps. Error estimators for both the temporal and spatial discretization are advocated, and facilitate a fully adaptive propagation. The framework is developed and exemplified in the context of the classical Liouville equation, where Gaussian phase-space packets are used as particles. Simplified variants are discussed briefly. The concept is illustrated by numerical examples for one-dimensional dynamics in double well potential. PMID:14515374

Horenko, Illia; Weiser, Martin

2003-11-30

59

Differential elastic scattering cross sections of metastable He(21S) and He(23S) with Ne and Ar were measured at thermal collision energies by the crossed molecular beam method. The interaction potentials of these systems are found to be similar to those of alkali-rare gas systems. The excitation transfer from He(21S) to Ne and the Penning and associative ionization processes in He(21S,23S) and

C. H. Chen; H. Haberland; Y. T. Lee

1974-01-01

60

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

M Warrier; P Pahari; S Chaturvedi

2012-01-01

61

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

62

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

63

NASA Astrophysics Data System (ADS)

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

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

2012-07-01

64

Human diseases are attributed in part to the ability of pathogens to evade the eukaryotic immune systems. A subset of these pathogens has developed mechanisms to survive in human macrophages. Yersinia pestis, the causative agent of the bubonic plague, is a predominately extracellular pathogen with the ability to survive and replicate intracellularly. A previous study has shown that a novel rip (required for intracellular proliferation) operon (ripA, ripB and ripC) is essential for replication and survival of Y. pestis in postactivated macrophages, by playing a role in lowering macrophage-produced nitric oxide (NO) levels. A bioinformatics analysis indicates that the rip operon is conserved among a distally related subset of macrophage-residing pathogens, including Burkholderia and Salmonella species, and suggests that this previously uncharacterized pathway is also required for intracellular survival of these pathogens. The focus of this study is ripA, which encodes for a protein highly homologous to 4-hydroxybutyrate-CoA transferase; however, biochemical analysis suggests that RipA functions as a butyryl-CoA transferase. The 1.9 Å X-ray crystal structure reveals that RipA belongs to the class of Family I CoA transferases and exhibits a unique tetrameric state. Molecular dynamics simulations are consistent with RipA tetramer formation and suggest a possible gating mechanism for CoA binding mediated by Val227. Together, our structural characterization and molecular dynamic simulations offer insights into acyl-CoA specificity within the active site binding pocket, and support biochemical results that RipA is a butyryl-CoA transferase. We hypothesize that the end product of the rip operon is butyrate, a known anti-inflammatory, which has been shown to lower NO levels in macrophages. Thus, the results of this molecular study of Y. pestis RipA provide a structural platform for rational inhibitor design, which may lead to a greater understanding of the role of RipA in this unique virulence pathway. PMID:21966419

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

65

Human diseases are attributed in part to the ability of pathogens to evade the eukaryotic immune systems. A subset of these pathogens has developed mechanisms to survive in human macrophages. Yersinia pestis, the causative agent of the bubonic plague, is a predominately extracellular pathogen with the ability to survive and replicate intracellularly. A previous study has shown that a novel rip (required for intracellular proliferation) operon (ripA, ripB and ripC) is essential for replication and survival of Y. pestis in postactivated macrophages, by playing a role in lowering macrophage-produced nitric oxide (NO) levels. A bioinformatics analysis indicates that the rip operon is conserved among a distally related subset of macrophage-residing pathogens, including Burkholderia and Salmonella species, and suggests that this previously uncharacterized pathway is also required for intracellular survival of these pathogens. The focus of this study is ripA, which encodes for a protein highly homologous to 4-hydroxybutyrate-CoA transferase; however, biochemical analysis suggests that RipA functions as a butyryl-CoA transferase. The 1.9 Å X-ray crystal structure reveals that RipA belongs to the class of Family I CoA transferases and exhibits a unique tetrameric state. Molecular dynamics simulations are consistent with RipA tetramer formation and suggest a possible gating mechanism for CoA binding mediated by Val227. Together, our structural characterization and molecular dynamic simulations offer insights into acyl-CoA specificity within the active site binding pocket, and support biochemical results that RipA is a butyryl-CoA transferase. We hypothesize that the end product of the rip operon is butyrate, a known anti-inflammatory, which has been shown to lower NO levels in macrophages. Thus, the results of this molecular study of Y. pestis RipA provide a structural platform for rational inhibitor design, which may lead to a greater understanding of the role of RipA in this unique virulence pathway. PMID:21966419

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

2011-01-01

66

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

67

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

68

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. PMID:16222654

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

69

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

2014-01-01

70

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

71

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

72

Variational Molecular Dynamics

We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. We show that within this framework it is possible to simulate on a small computer cluster conformational reactions as complex as protein folding, using state-of-the-art all-atom force fields in explicit solvent. The same approach also yields the potential of mean-force for reaction coordinates, the reaction rate and transition path time. For illustration and validation purposes, we test this method against the results of protein folding MD simulations which were obtained on the Anton supercomputer, using the same all-atom force field. We find that our approach yields consistent results at a computational cost which is many orders of magnitude smaller than that required by standard MD simulations.

S. a Beccara; P. Faccioli

2014-05-23

73

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 × 10(6) 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. PMID:22605995

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

2012-01-01

74

Non-relativistic de Broglie-Bohm theory describes particles moving under the guidance of the wave function. In de Broglie's original formulation, the particle dynamics is given by a first-order differential equation. In Bohm's reformulation, it is given by Newton's law of motion with an extra potential that depends on the wave function--the quantum potential--together with a constraint on the possible velocities. It was recently argued, mainly by numerical simulations, that relaxing this velocity constraint leads to a physically untenable theory. We provide further evidence for this by showing that for various wave functions the particles tend to escape the wave packet. In particular, we show that for a central classical potential and bound energy eigenstates the particle motion is often unbounded. This work seems particularly relevant for ways of simulating wave function evolution based on Bohm's formulation of the de Broglie-Bohm theory. Namely, the simulations may become unstable due to deviations from the velocity constraint.

Sheldon Goldstein; Ward Struyve

2013-12-06

75

Uncertainty quantification in molecular dynamics

NASA Astrophysics Data System (ADS)

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

Rizzi, Francesco

76

NASA Astrophysics Data System (ADS)

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

Zhang, Yan; Lin, Hai

2009-05-01

77

Reactive Force Field & Molecular Dynamics Simulations

: Parallel reactive molecular dynamics (MD) RMD ReaxFF Â· Applications: 1. Combustion of aluminum Â· Large scale (multimillion atoms) Â· Long time (nanosecond) #12;Reactive force field (RMD & ReaxFF (ReaxFF) #12;Classification of ReaxFF Potential Bonded Non-bonded E = Elp + Eover + Eunder + Ebond

Southern California, University of

78

NASA Astrophysics Data System (ADS)

This paper reports an advanced study of the excited ionic states of the gas-phase nitrogen molecule in the binding-energy region of 22-34 eV, combining ultrahigh-resolution resonant photoemission (RPE) and ab initio configuration-interaction calculations. The RPE spectra are recorded for nine photon energies within the N 1s??* absorption resonance of N2 by using a photon bandwidth that is considerably smaller than lifetime broadening, and the dependence on excitation energy of the decay spectra is analyzed and used for the first assignment of 12 highly overlapped molecular states. The effect on the RPE profile of avoided curve crossings between the final N2+ ionic states is discussed, based on theoretical simulations that account for vibronic coupling, and compared with the experimental data. By use of synchrotron radiation with high spectral brightness, it is possible to selectively promote the molecule to highly excited vibrational sublevels of a core-excited electronic state, thereby controlling the spatial distribution of the vibrational wave packets, and to accurately image the ionic molecular potentials. In addition, the mapping of the vibrational wave functions of the core-excited states using the bound final states with far-from-equilibrium bond lengths has been achieved experimentally for the first time. Theoretical analysis has revealed the rich femtosecond nuclear dynamics underlying the mapping phenomenon.

Kimberg, V.; Lindblad, A.; Söderström, J.; Travnikova, O.; Nicolas, C.; Sun, Y. P.; Gel'mukhanov, F.; Kosugi, N.; Miron, C.

2013-01-01

79

interaction potential models for pure alkanes D. K. Dysthe,a) A. H. Fuchs, and B. Rousseau Laboratoire de of the fluid.7 We therefore find it timely to evaluate the alkane models that are most frequently used and most

Dysthe, Dag Kristian

80

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

81

NASA Astrophysics Data System (ADS)

The structures of self-assembled monolayers (SAMs) of short (methyl) and long (hexyl) chain alkyl thiols on the clean gold (111) surface were modelled using for the Au-S interactions either the reactive ReaxFF potential or the well known non-reactive Morse potential, while for the Au-Au interactions either the ReaxFF potential or an embedded-atom method (EAM). Analysis of the MD trajectories of possible SAM structures suggests that disordering of interfacial Au atoms is definitely driven by the gold-sulphur interactions. Our MD results reveal a novel structure where two methanethiol molecules are bound to a gold adatom that has been lifted from the surface at 300 K, and the same kind of RS-Au-SR motif was also observed for hexanethiol at 600 K but not at 300 K. What is more, the above motif is only observed for the reactive ReaxFF potential. Moreover, these results are in clear agreement with recent experiments and more costly first principles-based MD simulations. These findings strongly support the use of reactive potentials such as ReaxFF for gathering an accurate description of Au-S interactions in inexpensive classical MD simulations.

Vasumathi, V.; Cordeiro, Maria Natalia D. S.

2014-03-01

82

State-dependent molecular dynamics.

This paper proposes a new mixed quantum mechanics (QM)-molecular mechanics (MM) approach, where MM is replaced by quantum Hamilton mechanics (QHM), which inherits the modeling capability of MM, while preserving the state-dependent nature of QM. QHM, a single mechanics playing the roles of QM and MM simultaneously, will be employed here to derive the three-dimensional quantum dynamics of diatomic molecules. The resulting state-dependent molecular dynamics including vibration, rotation and spin are shown to completely agree with the QM description and well match the experimental vibration-rotation spectrum. QHM can be incorporated into the framework of a mixed quantum-classical Bohmian method to enable a trajectory interpretation of orbital-spin interaction and spin entanglement in molecular dynamics. PMID:25302703

Yang, Ciann-Dong; Weng, Hung-Jen

2014-01-01

83

Ion channels catalyze the permeation of charged molecules across cell membranes and are essential for many vital physiological functions, including nerve and muscle activity. To understand better the mechanisms underlying ion conduction and valence selectivity of narrow ion channels, we have employed free energy techniques to calculate the potential of mean force (PMF) for ion movement through the prototypical gramicidin

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

2006-01-01

84

Population Based Reweighting of Scaled Molecular Dynamics

Molecular dynamics simulation using enhanced sampling methods is one of the powerful computational tools used to explore protein conformations and free energy landscapes. Enhanced sampling methods often employ either an increase in temperature or a flattening of the potential energy surface to rapidly sample phase space, and a corresponding reweighting algorithm is used to recover the Boltzmann statistics. However, potential energies of complex biomolecules usually involve large fluctuations on a magnitude of hundreds of kcal/mol despite minimal structural changes during simulation. This leads to noisy reweighting statistics and complicates the obtainment of accurate final results. To overcome this common issue in enhanced conformational sampling, we propose a scaled molecular dynamics method, which modifies the biomolecular potential energy surface and employs a reweighting scheme based on configurational populations. Statistical mechanical theory is applied to derive the reweighting formula, and the canonical ensemble of simulated structures is recovered accordingly. Test simulations on alanine dipeptide and the fast folding polypeptide Chignolin exhibit sufficiently enhanced conformational sampling and accurate recovery of free energy surfaces and thermodynamic properties. The results are comparable to long conventional molecular dynamics simulations and exhibit better recovery of canonical statistics over methods which employ a potential energy term in reweighting. PMID:23721224

2013-01-01

85

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

86

FPGA ACCELERATION OF MOLECULAR DYNAMICS SIMULATIONS

this problem by creating an explicitly designed FPGA-coprocessor that can be integrated into generic' & $ % FPGA ACCELERATION OF MOLECULAR DYNAMICS SIMULATIONS YONGFENG GU Dissertation submitted;BOSTON UNIVERSITY COLLEGE OF ENGINEERING Dissertation FPGA ACCELERATION OF MOLECULAR DYNAMICS SIMULATIONS

Herbordt, Martin

87

Molecular dynamics simulation of zirconia melting

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

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

2010-01-01

88

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

89

The singlet-triplet transformation and molecular dissociation of ozone (O(3)) gas is investigated by performing quasi-classical molecular dynamics (MD) simulations on an ab initio potential energy surface (PES) with visible and near-infrared excitations. MP4(SDQ) level of theory with the 6-311g(2d,2p) basis set is executed for three different electronic spin states (singlet, triplet, and quintet). In order to simplify the potential energy function, an approximation is adopted by ignoring the spin-orbit coupling and allowing the molecule to switch favorably and instantaneously to the spin state that is more energetically stable (lowest in energy among the three spin states). This assumption has previously been utilized to study the SiO(2) system as reported by Agrawal et al. (J. Chem. Phys. 2006, 124 (13), 134306). The use of such assumption in this study probably makes the upper limits of computed rate coefficients the true rate coefficients. The global PES for ozone is constructed by fitting 5906 ab initio data points using a 60-neuron two-layer feed-forward neural network. The mean-absolute error and root-mean-squared error of this fit are 0.0446 eV (1.03 kcal/mol) and 0.0756 eV (1.74 kcal/mol), respectively, which reveal very good fitting accuracy. The parameter coefficients of the global PES are reported in this paper. In order to identify the spin state with high confidence, we propose the use of a pattern-recognition neural network, which is trained to predict the spin state of a given configuration (with a prediction accuracy being 95.6% on a set of testing data points). To enhance the prediction effectiveness, a buffer series of five points are validated to confirm the spin state during the MD process to gain better confidence. Quasi-classical MD simulations from 1.2 to 2.4 eV of total internal energy (including zero-point energy) result in rate coefficients of singlet-triplet transformation in the range of 0.027 ps(-1) to 1.21 ps(-1). Also, we find very low dissociation probability up to 2.4 eV of internal energy during the investigating period (5 ps), which suggests that dissociation does not occur directly from the singlet ground-state, but it involves the excited triplet-state as an intermediate step and requires more reaction time to occur. PMID:21888438

Le, Hung M; Dinh, Thach S; Le, Hieu V

2011-10-13

90

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

91

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

92

of the methodology, namely, quantum dynamics and ab initio molecular dynamics, are harnessed together using a time-dependent self-consistent field-like coupling procedure. The quantum wave packet dynamics is made computationally. This approach, when combined with full quantum or semiclassical dynamics schemes, has the potential to treat

Iyengar, Srinivasan S.

93

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

94

Molecular dynamics: deciphering the data.

The dynamic behaviour of molecules is important in determining their activity. Molecular dynamics (MD) simulations give a detailed description of motion, from small fluctuations to conformational transitions, and can include solvent effects. However, extracting useful information about conformational motion from a trajectory is not trivial. We have used digital signal-processing techniques to characterise the motion in MD simulations, including: calculating the frequency distribution, applying filtering functions, and extraction of vectors defining the characteristic motion for each frequency in an MD simulation. We describe here some typical results obtained for peptides and proteins. The nature of the low-frequency modes of motion, as obtained from MD and normal mode (NM) analysis, of Ace-(Ala)31-Nma and of a proline mutant is discussed. Low-frequency modes extracted from the MD trajectories of Rop protein and phospholipase A2 reveal characteristic motions of secondary structure elements, as well as concerned motions that are of significance to the protein's biological activity. MD simulations are also used frequently as a tool for conformational searches and for investigating protein folding/unfolding. We have developed a novel method that uses time-domain filtering to channel energy into conformational motion and thus enhance conformational transitions. The selectively enhanced molecular dynamics method is tested on the small molecule hexane. PMID:8808735

Dauber-Osguthorpe, P; Maunder, C M; Osguthorpe, D J

1996-06-01

95

Fast dynamics of molecular bridges

NASA Astrophysics Data System (ADS)

We address the dynamics of open quantum systems, in which complex finite time initial conditions, an ensuing rapid non-equilibrium transient, quantum interferences and their attenuation play important roles. To study all these phenomena in conditions of general non-equilibrium, open systems are represented by a simple structure of a molecular island between two leads. We treat this model using the non-equilibrium Green functions (NGF) method for a finite initial condition. We demonstrate that the non-interacting molecular bridge model captures well many features of general open quantum systems. Three stages of its non-equilibrium evolution, the first described by the full NGF description, the second ruled by the asymptotically exact generalized master equation and the third governed by a Markovian master equation, are delineated and related to each other.

Špi?ka, V.; Kalvová, A.; Velický, B.

2012-11-01

96

Molecular Dynamics Simulation of Shock Induced Detonation

NASA Astrophysics Data System (ADS)

This research focuses on molecular dynamics (MD) simulation of shock induced detonation in Fe2O3+Al thermite mixtures. A MD model is developed to simulate non-equilibrium stress-induced reactions. The focus is on establishing a criterion for reaction initiation, energy content and rate of energy release as functions of mixture and reinforcement characteristics. A cluster functional potential is proposed for this purpose. The potential uses the electronegativity equalization to account for changes in the charge of different species according to local environment. Parameters in the potential are derived to fit to the properties of Fe, Al, Fe2O3, and Al2O3. NPT MD simulations are carried out to qualitatively check the energetics of the forward (Fe2O3+Al) as well as backward (Al2O3+Fe) thermite reactions. The results show that the potential can account for the energetics of thermite reactions.

Tomar, Vikas; Zhou, Min

2004-07-01

97

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

98

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

99

The rotation of F1Fo-ATP synthase is powered by the proton motive force across the energy-transducing membrane. The protein complex functions like a turbine; the proton flow drives the rotation of the c-ring of the transmembrane Fo domain, which is coupled to the ATP-producing F1 domain. The hairpin-structured c-protomers transport the protons by reversible protonation/deprotonation of a conserved Asp/Glu at the outer transmembrane helix (TMH). An open question is the proton transfer pathway through the membrane at atomic resolution. The protons are thought to be transferred via two half-channels to and from the conserved cAsp/Glu in the middle of the membrane. By molecular dynamics simulations of c-ring structures in a lipid bilayer, we mapped a water channel as one of the half-channels. We also analyzed the suppressor mutant cP24D/E61G in which the functional carboxylate is shifted to the inner TMH of the c-protomers. Current models concentrating on the “locked” and “open” conformations of the conserved carboxylate side chain are unable to explain the molecular function of this mutant. Our molecular dynamics simulations revealed an extended water channel with additional water molecules bridging the distance of the outer to the inner TMH. We suggest that the geometry of the water channel is an important feature for the molecular function of the membrane part of F1Fo-ATP synthase. The inclination of the proton pathway isolates the two half-channels and may contribute to a favorable clockwise rotation in ATP synthesis mode. PMID:22942277

Gohlke, Holger; Schlieper, Daniel; Groth, Georg

2012-01-01

100

Radiation in molecular dynamic simulations

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

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

2008-10-13

101

Molecular dynamics simulation of zirconia melting

NASA Astrophysics Data System (ADS)

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

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

2010-10-01

102

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

103

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

104

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

105

Fiber lubrication: A molecular dynamics simulation study

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

Hongyi Liu

2009-01-01

106

Molecular dissolution processes in lipid bilayers: A molecular dynamics simulation

NASA Astrophysics Data System (ADS)

A thorough understanding of the effects of chain ordering on solute partitioning and transport across biomembranes requires a detailed account of various dissolution processes in lipid bilayers. In this study, the dissolution properties and related molecular processes for noble gases in the alkyl chain region of lipid bilayers were obtained by means of molecular dynamics simulation. The excess chemical potential exhibits a plateau value in the ordered peripheral region followed by a steep decline near the center of the bilayer. The strong entropic effects as manifested by the larger Barclay-Butler constants than commonly encountered in hydrocarbon solvents indicate that solute partitioning into membranes is driven primarily by changes of lipid chain conformation or/and an extra confinement of solute in the bilayer interior. Solute partitioning into lipid bilayers is analyzed in terms of two contributions: (1) the free energy for cavity creation to accommodate a solute, which is analyzed by scaled particle theory; and (2) the interaction energy between the inserted solute and surrounding molecules in the bilayer. The unfavorable free energy for cavity creation is found to be primarily responsible for the substantial decrease of solubility into the membranes from that into a hydrocarbon solvent (dodecane) when the solute size is increased. The observed linear decrease of the excess chemical potential with solute surface area arises from linear but opposite dependencies of the reversible work for cavity creation and the intermolecular interaction energy on solute surface area and may be described by an anisotropic surface-tension model.

Xiang, Tian-xiang; Anderson, Bradley D.

1999-01-01

107

Quantum Spin Dynamics in Molecular Magnets

The detailed theoretical understanding of quantum spin dynamics in various molecular magnets is an important step on the roadway to technological applications of these systems. Quantum effects in both ferromagnetic and antiferromagnetic molecular clusters are, by now, theoretically well understood. Ferromagnetic molecular clusters allow one to study the interplay of incoherent quantum tunneling and thermally activated transitions between states with

Michael N. Leuenberger; Florian Meier; Daniel Loss

2002-01-01

108

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

109

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

110

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

111

Stochastic molecular dynamics: A combined Monte Carlo and molecular dynamics technique for isothermal simulations Phil Attard Ian Wark Research Institute, University of South Australia, Mawson Lakes dynamics technique is developed that gives equations of motion for an isothermal system. Test results

Attard, Phil

112

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

113

Phonostat: Thermostatting phonons in molecular dynamics simulations

Thermostat algorithms in a molecular dynamics simulation maintain an average temperature of a system by regulating the atomic velocities rather than the internal degrees of freedom. Herein, we present a “phonostat” algorithm ...

Raghunathan, Rajamani

114

Quantum Spin Dynamics in Molecular Magnets

Summary. ?The detailed theoretical understanding of quantum spin dynamics in various molecular magnets is an important step on the\\u000a roadway to technological applications of these systems. Quantum effects in both ferromagnetic and antiferromagnetic molecular\\u000a clusters are, by now, theoretically well understood. Ferromagnetic molecular clusters allow one to study the interplay of\\u000a incoherent quantum tunneling and thermally activated transitions between states with

Michael N. Leuenberger; Florian Meier; Daniel Loss

2003-01-01

115

Molecular dynamics of a bilayer membrane

A molecular dynamics simulation was carried out for a bilayer of 2 × 64 decane molecules as a model for a biological membrane. Two dimensional periodic conditions were used and head groups were subjected to a simple mean force interaction. Four runs at two different temperatures and head group densities were executed, each over 80 ps. Molecular order parameters were

P. van der Ploeg; H. J. C. Berendsen

1983-01-01

116

NASA Astrophysics Data System (ADS)

A new parallel computing environment, called as ``Parallel Molecular Dynamics Stencil'', has been developed to carry out a large-scale short-range molecular dynamics simulation of solids. The stencil is written in C language using MPI for parallelization and designed successfully to separate and conceal parts of the programs describing cutoff schemes and parallel algorithms for data communication. This has been made possible by introducing the concept of image atoms. Therefore, only a sequential programming of the force calculation routine is required for executing the stencil in parallel environment. Typical molecular dynamics routines, such as various ensembles, time integration methods, and empirical potentials, have been implemented in the stencil. In the presentation, the performance of the stencil on parallel computers of Hitachi, IBM, SGI, and PC-cluster using the models of Lennard-Jones and the EAM type potentials for fracture problem will be reported.

Shimizu, Futoshi; Kimizuka, Hajime; Kaburaki, Hideo

2002-08-01

117

A Combined Molecular Dynamics and Diffusion Model of Single Proton Conduction through Gramicidin

We develop a model for proton conduction through gramicidin based on the molecular dynamics simulations of Pomès and Roux (Biophys. J. 72:A246, 1997). The transport of a single proton through the gramicidin pore is described by a potential of mean force and diffusion coefficient obtained from the molecular dynamics. In addition, the model incorporates the dynamics of a defect in

Mark F. Schumaker; Régis Pomès; Benoît Roux

2000-01-01

118

Multiple time step integrators in ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

Luehr, Nathan; Markland, Thomas E.; Martínez, Todd J.

2014-02-01

119

Thermal transport properties of uranium dioxide by molecular dynamics simulations

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

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

2008-01-01

120

Programming an interpreter using molecular dynamics

PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of dynamic data structures in pro- gramming. We consider the programming of an interpreter for a program notation that is close to existing

Jan A. Bergstra; C. A. Middelburg

2008-01-01

121

Confinement of conjugated polymers into soft nanoparticles: molecular dynamics simulations

NASA Astrophysics Data System (ADS)

The structure and dynamics of conjugated polymers confined into soft nanoparticles (SNPs) have been studies by molecular dynamic simulations. This new class of tunable luminescent SNPs exhibits an immense potential as bio-markers as well as targeted drug delivery agents where tethering specific groups to the surface particles offers a means to target specific applications. Of particular interest are SNPs that consist of non- crosslinked polymers, decorated with polar groups. These SNPs are potentially tunable through the dynamics of the polymer chains, whereas the polar entity serves as internal stabilizer and surface encore. Confinement of a polymer whose inherent conformation is extended impacts not only their dynamics and as a result their optical properties. Here we will present insight into the structure and dynamics of dialkyl poly para phenylene ethynylene (PPE), decorated by a carboxylate groups, confined into a soft particle. The conformation and dynamics of polymer within SNP will be discussed and compared with that of the linear chain in solution.

Wijesinghe, Sidath; Perahia, Dvora; Grest, Gary S.

2013-03-01

122

Molecular dynamics modelling of radiation defects in ferromagnetic ?-iron

NASA Astrophysics Data System (ADS)

The need to perform large-scale molecular dynamics simulations of radiation defects in ferritic steels has stimulated the recent development of a 'magnetic' interatomic potential for body-centred cubic ?-iron [1,2]. Here we describe the first application of the new method to molecular dynamics modelling of radiation defects. We investigate the magneto-elastic fields of defects and study their thermally activated migration. We propose that the origin of the low-temperature ( T ? 120 K) resistivity recovery stages in irradiated ?-iron is associated with clustering of self-interstitial atoms.

Dudarev, S. L.; Derlet, P. M.

2007-08-01

123

A Review of Wave Packet Molecular Dynamics

Warm dense matter systems created in the laboratory are highly dynamical. In such cases electron dynamics is often needed to accurately simulate the evolution and properties of the system. Large systems force one to make simple approximations enabling computationally feasibility. Wave packet molecular dynamics (WPMD) provides a simple framework for simulating time-dependent quantum plasmas. Here, this method is reviewed. The different variants of WPMD are shown and compared and their validity is discussed.

Paul E. Grabowski

2014-08-09

124

A Review of Wave Packet Molecular Dynamics

Warm dense matter systems created in the laboratory are highly dynamical. In such cases electron dynamics is often needed to accurately simulate the evolution and properties of the system. Large systems force one to make simple approximations enabling computationally feasibility. Wave packet molecular dynamics (WPMD) provides a simple framework for simulating time-dependent quantum plasmas. Here, this method is reviewed. The different variants of WPMD are shown and compared and their validity is discussed.

Grabowski, Paul E

2014-01-01

125

The ability of some liquids to vitrify during supercooling is usually seen as a consequence of the rates of crystal nucleation (and?or crystal growth) becoming small [D. R. Uhlmann, J. Non-Cryst. Solids 7, 337 (1972)]--and thus a matter of kinetics. However, there is evidence dating back to the empirics of coal briquetting for maximum trucking efficiency [D. Frenkel, Physics 3, 37 (2010)] that some object shapes find little advantage in self-assembly to ordered structures--meaning random packings prevail. Noting that key studies of non-spherical object packing have never been followed from hard ellipsoids [A. Donev, F. H. Stillinger, P. M. Chaikin, and S. Torquato, Phys. Rev. Lett. 92, 255506 (2004); A. Donev, I. Cisse, D. Sachs, E. A. Variano, F. H. Stillinger, R. Connelly, S. Torquato, and P. M. Chaikin, Science 303, 990 (2004)] or spherocylinders [S. R. Williams and A. P. Philipse, Phys. Rev. E 67, 051301 (2003)] (diatomics excepted [S.-H. Chong, A. J. Moreno, F. Sciortino, and W. Kob, Phys. Rev. Lett. 94, 215701 (2005)] into the world of molecules with attractive forces, we have made a molecular dynamics study of crystal melting and glass formation on the Gay-Berne (G-B) model of ellipsoidal objects [J. G. Gay and B. J. Berne, J. Chem. Phys. 74, 3316 (1981)] across the aspect ratio range of the hard ellipsoid studies. Here, we report that in the aspect ratio range of maximum ellipsoid packing efficiency, various G-B crystalline states that cannot be obtained directly from the liquid, disorder spontaneously near 0 K and transform to liquids without any detectable enthalpy of fusion. Without claiming to have proved the existence of single component examples, we use the present observations, together with our knowledge of non-ideal mixing effects, to discuss the probable existence of "ideal glassformers"--single or multicomponent liquids that vitrify before ever becoming metastable with respect to crystals. We find evidence that "ideal glassformer" systems might also be highly fragile systems, approaching the "ideal glass" condition. We link this to the high "volume fragility" behavior observed in recent hard dumbbell studies at similar length?diameter ratios [R. Zhang and K. S. Schweitzer, J. Chem. Phys. 133, 104902 (2010)]. The discussion suggests some unusual systems for laboratory study. Using differential scanning calorimetry detection of fusion points T(m), liquidus temperatures T(l), and glass transition temperatures T(g), we describe a system that would seem incapable of crystallizing before glass transition, i.e., an "ideal glassformer." The existence of crystal-free routes to the glassy state will eliminate precrystalline fluctuations as a source of the dynamic heterogeneities that are generally considered important in the discussion of the "glassy state problem [P. W. Anderson, Science 267, 1615 (1995)]." PMID:23556800

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

2013-03-28

126

Quasiclassical molecular dynamics for the dilute Fermi gas at unitarity

NASA Astrophysics Data System (ADS)

We study the dilute Fermi gas at unitarity using molecular dynamics with an effective quantum potential constructed to reproduce the quantum two-body density matrix at unitarity. Results for the equation of state, the pair-correlation function, and the shear viscosity are presented. These quantities are well understood in the dilute, high-temperature limit. Using molecular dynamics we determine higher-order corrections in the diluteness parameter n?3, where n is the density and ? is the thermal de Broglie wavelength. In the case of the contact density, which parameterizes the short distance behavior of the correlation function, we find that the results of molecular dynamics interpolate between the truncated second- and third-order virial expansion and are in excellent agreement with existing T-matrix calculations. For the shear viscosity we reproduce the expected scaling behavior at high temperature, ?˜1/?3, and we determine the leading density-dependent correction to this result.

Dusling, K.; Schäfer, T.

2012-12-01

127

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. PMID:22253857

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

2012-01-01

128

NASA Astrophysics Data System (ADS)

Background: Of the two sources of nonlocality in nucleon-nucleus and nucleus-nucleus interactions, knock-on exchange and dynamically generated, almost all papers referring to nonlocality mention only the first. Purpose: Our purpose is threefold: to demonstrate a method for including dynamical nonlocality, for which a simple prescription (like the Perey factor for exchange nonlocality) is unknown, within distorted wave Born approximation (DWBA) calculations; to identify signatures of dynamic nonlocality and illuminate the extent to which the presence of such nonlocality can influence the extraction of spectroscopic information from direct reactions, and more generally, to increase our understanding of nucleus-nucleus interactions. Methods: After reviewing existing indications of dynamically induced nonlocality, DWBA transfer calculations are presented which compare results involving dynamically nonlocal potentials with those involving their local equivalents. The dynamical nonlocal potentials are generated in situ by the presence of channel coupling and the local equivalents are generated by inversion of the corresponding coupled channel elastic S matrix. This method obviates the need for solving integro-differential equations for including nonlocal potentials in DWBA. Results: The coupling of nucleons to collective states of the target nucleus induces dynamical nonlocality in the nucleon-nucleus interaction that has a significant effect on (p ,d) reactions at energies relevant to spectroscopic studies. Conclusions: A method for studying the contribution of dynamically induced nonlocality in nuclear interactions has been demonstrated. Dynamically induced nonlocality should not be overlooked in the analysis of direct reactions. The method can also be applied to dynamic nonlocality due to projectile excitation.

Keeley, N.; Mackintosh, R. S.

2014-10-01

129

Molecular dynamics simulation of polycrystalline copper

NASA Astrophysics Data System (ADS)

An approach for molecular dynamics simulation of the formation of polycrystalline materials from a melt during its cooling is proposed. Atomic configurations of copper corresponding to polycrystals with the mean grain size from 2 to 16 nm are obtained. Isothermal uniaxial tension and compression of these polycrystals is studied by the molecular dynamics method. For the mean grain size of polycrystalline copper being smaller than 10 nm, it is shown that Young's modulus and yield stress decrease as the grain size decreases. Shock adiabats for polycrystalline copper are constructed. For a material with the grain size approximately equal to 2 nm, the temperature behind the shock wave front is demonstrated to be 10% higher than that in a polycrystal with the grain size greater than 10 nm. Molecular dynamics calculations predict the presence of copper with a body-centered cubic lattice behind the shock wave front at pressures ranging from 100 to 200 GPa.

Bolesta, A. V.; Fomin, V. M.

2014-09-01

130

Water transport in aquaporins: molecular dynamics simulations.

Aquaporins and aquaglyceroporins are membrane channel proteins that selectively transport water and small molecules such as glycerol across biological membranes. Molecular dynamics simulations have made substantial contributions toward understanding the permeation mechanisms of aquaporins in atomic detail. Osmotic pressure is the driving force of the transport by aquaporins. The osmotic water permeability of aquaporins can be estimated from equilibrium molecular dynamics simulations by using linear response theory. The relationship between osmotic permeability and channel structure was investigated by the recently proposed pf-matrix method. In addition to the water transport, other functions of aquaporins and aquaglyceroporins, i.e., glycerol permeation, proton blockage, and gating, have also been extensively studied by molecular dynamics simulations. PMID:19273130

Ikeguchi, Mitsunori

2009-01-01

131

Molecular dynamic simulations of ocular tablet dissolution.

Small tablets for implantation into the subconjunctival space in the eye are being developed to inhibit scarring after glaucoma filtration surgery (GFS). There is a need to evaluate drug dissolution at the molecular level to determine how the chemical structure of the active may correlate with dissolution in the nonsink conditions of the conjunctival space. We conducted molecular dynamics simulations to study the dissolution process of tablets derived from two drugs that can inhibit fibrosis after GFS, 5-fluorouracil (5-FU) and the matrix metalloprotease inhibitor (MMPi), ilomastat. The dissolution was simulated in the presence of simple point charge (SPC) water molecules, and the liquid turnover of the aqueous humor in the subconjunctival space was simulated by removal of the dissolved drug molecules at regular intervals and replacement by new water molecules. At the end of the simulation, the total molecular solvent accessible surface area of 5-FU tablets increased by 60 times more than that of ilomastat as a result of tablet swelling and release of molecules into solution. The tablet dissolution pattern shown in our molecular dynamic simulations tends to correlate with experimental release profiles. This work indicates that a series of molecular dynamic simulations can be used to predict the influence of the molecular properties of a drug on its dissolution profile and could be useful during preformulation where sufficient amounts of the drug are not always available to perform dissolution studies. PMID:24073784

Ru, Qian; Fadda, Hala M; Li, Chung; Paul, Daniel; Khaw, Peng T; Brocchini, Steve; Zloh, Mire

2013-11-25

132

Understanding Modularity in Molecular Networks Requires Dynamics

The era of genome sequencing has produced long lists of the molecular parts from which cellular machines are constructed. A fundamental goal in systems biology is to understand how cellular behavior emerges from the interaction in time and space of genetically encoded molecular parts, as well as non-genetically encoded small molecules. Networks provide a natural framework for the organization and quantitative representation of all the available data about molecular interactions. The structural and dynamic properties of molecular networks have been the subject of intense research. Despite major advances, bridging network structure to dynamics – and therefore to behavior – remains challenging. A key concept of modern engineering that recurs in the functional analysis of biological networks is modularity. Most approaches to molecular network analysis rely to some extent on the assumption that molecular networks are modular – that is, they are separable and can be studied to some degree in isolation. We describe recent advances in the analysis of modularity in biological networks, focusing on the increasing realization that a dynamic perspective is essential to grouping molecules into modules and determining their collective function. PMID:19638611

Alexander, Roger P.; Kim, Philip M.; Emonet, Thierry; Gerstein, Mark B.

2014-01-01

133

Understanding Modularity in Molecular Networks Requires Dynamics

NSDL National Science Digital Library

The era of genome sequencing has produced long lists of the molecular parts from which cellular machines are constructed. A fundamental goal in systems biology is to understand how cellular behavior emerges from the interaction in time and space of genetically encoded molecular parts, as well as nongenetically encoded small molecules. Networks provide a natural framework for the organization and quantitative representation of all the available data about molecular interactions. The structural and dynamic properties of molecular networks have been the subject of intense research. Despite major advances, bridging network structure to dynamics—and therefore to behavior—remains challenging. A key concept of modern engineering that recurs in the functional analysis of biological networks is modularity. Most approaches to molecular network analysis rely to some extent on the assumption that molecular networks are modular—that is, they are separable and can be studied to some degree in isolation. We describe recent advances in the analysis of modularity in biological networks, focusing on the increasing realization that a dynamic perspective is essential to grouping molecules into modules and determining their collective function.

Roger P. Alexander (Yale University;Program in Computational Biology and Bioinformatics REV); Philip M. Kim (University of Toronto;Terrence Donnelly Centre for Cellular and Biomolecular Research REV); Thierry Emonet (Yale University;Program in Computational Biology and Bioinformatics REV); Mark B. Gerstein (Yale University;Program in Computational Biology and Bioinformatics REV)

2009-07-28

134

Molecular Scale Dynamics of Large Ring Polymers

NASA Astrophysics Data System (ADS)

We present neutron scattering data on the structure and dynamics of melts from polyethylene oxide rings with molecular weights up to ten times the entanglement mass of the linear counterpart. The data reveal a very compact conformation displaying a structure approaching a mass fractal, as hypothesized by recent simulation work. The dynamics is characterized by a fast Rouse relaxation of subunits (loops) and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture.

Gooßen, S.; Brás, A. R.; Krutyeva, M.; Sharp, M.; Falus, P.; Feoktystov, A.; Gasser, U.; Pyckhout-Hintzen, W.; Wischnewski, A.; Richter, D.

2014-10-01

135

Molecular scale dynamics of large ring polymers.

We present neutron scattering data on the structure and dynamics of melts from polyethylene oxide rings with molecular weights up to ten times the entanglement mass of the linear counterpart. The data reveal a very compact conformation displaying a structure approaching a mass fractal, as hypothesized by recent simulation work. The dynamics is characterized by a fast Rouse relaxation of subunits (loops) and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture. PMID:25361284

Gooßen, S; Brás, A R; Krutyeva, M; Sharp, M; Falus, P; Feoktystov, A; Gasser, U; Pyckhout-Hintzen, W; Wischnewski, A; Richter, D

2014-10-17

136

Multifractal and complex network analyses of protein molecular dynamics

Based on protein molecular dynamics, we analyze fractal properties of energy, pressure and volume time series using the multifractal detrended fluctuations analysis (MF-DFA); and investigate the topological and multifractal properties of their visibility graph (complex network) representations. The energy terms of proteins we considered are bonded potential, angle potential, dihedral potential, improper potential, kinetic energy, Van der Waals potential, electrostatic potential, total energy and potential energy. Results of MF-DFA show that these time series are multifractal. The numerical values of the exponent $h(2)$ of MF-DFA which is related to Hurst exponent $H$ show that the series of total energy and potential energy are non-stationary and anti-persistent; other kinds of time series are stationary and persistent apart from series of pressure which has the weakest memorability with $H\\approx 0.5$. Results of complex networks analysis based on visibility graph algorithm show that these visibility graphs ...

Zhou, Yuan-Wu; Yu, Zu-Guo; Zhao, Zhi-Qin; Anh, Vo

2014-01-01

137

Engineered bacteriorhodopsin: a molecular scale potential switch.

Bacteriorhodopsin, BR, is a natural, photoresponsive, biomolecule that has potential application in data storage, imaging and sensing. Being membrane-bound, however, it is coupled with metallic electronic surfaces only with some difficulty. We report herein a facile method to generate uniformly orientated, anchored and active monolayers of BR on metallic electrodes. In the present study, the cytoplasmic side of the BR is equipped with an engineered cysteine to achieve largely lipid-free, orientation-specific, highly stable, covalent immobilization on gold surfaces. By using non-invasive Kelvin probe force microscopy, it is possible to measure the light-induced proton accumulation at the extracellular protein surface at truly molecular scales. The intimate probe-BR interaction possible on lipid removal facilitates the detection of photoinduced surface potential switching substantially larger ((20.4 ± 7.5) mV) with functional single delipidated mutant BR trimers than for the wild-type protein. The proton pumping detected is also notably highly unidirectional with the orientated protein. PMID:22454208

Patil, Amol V; Premaraban, Thenuhan; Berthoumieu, Olivia; Watts, Anthony; Davis, Jason J

2012-04-27

138

Molecular dynamics study of electromigration

NASA Astrophysics Data System (ADS)

A software package has been assembled (written and adapted from commercial sources) that allows three dimensional atomic level modeling, simulation and visualization of polycrystalline samples subjected to various stresses. Sample preparation, is accomplished with a commercial software package, ADESH, that allows initial atomic coordinates to be prepared conveniently for submission to the dynamics portion of the code. The code, mdem. exe, that traces the atom motions was written in the C programming language for convenient portability across computing platforms. On an Intel 486/66 class machine, it can provide 10 ps of history for a system containing 1896 atoms in approximately 62 hours of computing time. Temperature control is provided by a thermostat function known to preserve the statistical integrity of the dynamic variables. Several techniques have been developed for visualization of the output data. Preliminary results demonstrating thermal expansion, specific heat, self-diffusion and annealing behavior have been published.

Helbig, Herbert F.

1994-11-01

139

A test of the random network model of water using molecular dynamics simulation data

NASA Astrophysics Data System (ADS)

Time-averaged molecular dynamics simulations based on the ST2 potential model are used to test the ideas of the random network model of water proposed by Sceats and Rice. The agreement between the predictions of the random network model and the tune-averaged molecular dynamics simulations is very good.

Belch, Alan C.; Rice, Stuart A.; Sceats, Mark G.

1981-02-01

140

Molecular to fluid dynamics: The consequences of stochastic molecular motion Stefan Heinz*

Molecular to fluid dynamics: The consequences of stochastic molecular motion Stefan Heinz) The derivation of fluid dynamic equations from molecular equations is considered. This is done on the basis equations. The stochastic model is used to derive fluid dynamic equations where the molecular stress tensor

Heinz, Stefan

141

Reaction dynamics in polyatomic molecular systems

The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)

1993-12-01

142

Performance dissection of a Molecular Dynamics code

this direction. At the same time, the hardware technology has also evolved, i.e., from the Tesla to the Kepler-source molecular dynamics code. I. INTRODUCTION Programming tools and technologies have been continu- ously and steadily evolving in the GPU community. The CUDA programming language and NVIDIA technology have been

Taufer, Michela

143

Hybrid Molecular Dynamics for Lattice Supersymmetry

We present the first results obtained with a Hybrid Molecular Dynamics algorithm applied to an $N=1$ SU(2) Super-Yang--Mills on the lattice. We derive the Hamilton equations of motion for the system with Wilson gluinos and present preliminary results on small lattices.

A. Donini; M. Guagnelli

1996-05-10

144

Molecular beam studies of reaction dynamics

The major thrust of this research project is to elucidate detailed dynamics of simple reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free

1990-01-01

145

Molecular beam studies of reaction dynamics

The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a

Yuan T. Lee; Yuan T

1991-01-01

146

Mathematical Modeling and Analysis Molecular Dynamics

Mathematical Modeling and Analysis Molecular Dynamics Simulations of Peptide Nucleic Acid in Lipid- tant bio-molecule is peptide nucleic acids (PNA). PNA is a lab-created analogue of DNA, in which water-insoluble or nonpo- lar compounds of biological origin. The simplest lipids are linear fatty acids

Kurien, Susan

147

MDLab: A molecular dynamics simulation prototyping environment

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

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

2010-01-01

148

ras-p21 protein binds to the son-of-sevenless (SOS) guanine nucleotide-exchange promoter that allows it to exchange GDP for GTP. Previously, we performed molecular dynamics calculations on oncogenic (Val 12-) and wild-type ras-p21 bound to SOS. By superimposing the average structures of these two complexes, we identified four domains (residues 631-641, 676-691, 718-729, and 994-1004) in SOS that change conformation and were candidates for being effector domains. These calculations were performed in the absence of three crystallographically undefined loops (i.e., residues 591-596, 654-675, and 742-751). We have now modeled these loops into the SOS structure and have re-performed the dynamics calculations. We find that all three loop domains undergo large changes in conformation that involve mostly changes in their positioning and not their individual conformations. We have also identified another potential effector domain (i.e., residues 980-989). Overall, our current results suggest that SOS interactions with oncogenic ras-p21 may enhance ras-p21 mitogenic signaling through prolonging its activation by maintaining its binding to GTP and by allowing its effector domains to interact with intracellular targets. PMID:15200053

Duncan, Thomas; Chen, James M; Friedman, Fred K; Hyde, Mark; Chie, Lyndon; Pincus, Matthew R

2004-04-01

149

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 electromechanical analog of this process. The resultant molecular-dynamics 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 modeling tool to bridge theoretical studies and eventual laboratory experiments at the true molecular scale.

Husman, M.; Schwieters, C.; Littman, M.; Rabitz, H.

1991-11-01

150

Nanoindentation hardness anisotropy of alumina crystal: A molecular dynamics study

Nanoindentation hardness anisotropy of alumina crystal: A molecular dynamics study Kenji Nishimura nanoindentation are studied by molecular dynamics simulations for three surface orientations of alumina crystal metallurgical engineering to opto- and microelectronics. Nanoindentation is widely used to examine mechanical

Southern California, University of

151

Relationship between nanocrystalline and amorphous microstructures by molecular dynamics simulation

A recently developed molecular-dynamics simulation method for the growth of fully dense nanocrystalline materials by crystallization from the melt was used together with the Stillinger-Weber three-body potential to synthesize nanocrystalline silicon with a grain size up to 75Å. The structures of the highly-constrained grain boundaries (GBs), triple lines and point grain junctions were found to be highly disordered and similar

P. Keblinski; S. R. Phillpot; D. Wolf; H. Gleiter

1997-01-01

152

Molecular dynamics study of methane in water: diffusion and structure

We present molecular dynamics simulation results for the diffusion coefficients and structure of water–methane mixtures in constant NPT ensembles, at T = 270, 300 K and P = 8.104 × 10 Pa. The systems we have studied consist of one, four and eight CH4 molecules and varying H2O molecules per unit cell, which correspond to methane concentration of 0.081, 0.324 and 0.643 mol\\/l, respectively. The intermolecular potentials used in

J. Zhang; S. Piana; R. Freij-Ayoub; M. Rivero; S. K. Choi

2006-01-01

153

Grand Canonical Molecular Dynamic Simulations For Polar Systems

The purely molecular dynamical formulation of grand canonical ensemble of Pettitt and co-workers was extended to implement the Nosé-Hoover thermostat and introduce multiple fractional particles. The algorithm was applied to simulation of ?VT ensembles of TIP4P water and methanol molecules at 298 K. The procedure reproduced the experimental density of water for input chemical potential of ?24.0 kJ\\/mol, as well that of

Tatyana Kuznetsova; Bjørn Kvamme

2005-01-01

154

Combined molecular dynamics-spin dynamics simulations of bcc iron

NASA Astrophysics Data System (ADS)

Using a classical model that treats translational and spin degrees of freedom on an equal footing, we study phonon-magnon interactions in BCC iron with combined molecular and spin dynamics methods. The atomic interactions are modeled via an empirical many-body potential while spin dependent interactions are established through a Hamiltonian of the Heisenberg form with a distance dependent magnetic exchange interaction obtained from first principles electronic structure calculations. The temporal evolution of translational and spin degrees of freedom was determined by numerically solving the coupled equations of motion, using an algorithm based on the second order Suzuki-Trotter decomposition of the exponential operators. By calculating Fourier transforms of space- and time-displaced correlation functions, we demonstrate that the the presence of lattice vibrations leads to noticeable softening and damping of spin wave modes. As a result of the interplay between lattice and spin subsystems, we also observe additional longitudinal spin wave excitations, with frequencies which coincide with that of the longitudinal lattice vibrations.

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

2014-03-01

155

A set of interatomic potentials for hydrocarbons that are based upon the self-consistent charge transfer tight-binding approximation to density functional theory have been developed and implemented into the quantum molecular dynamics code ''LATTE''. The interatomic potentials exhibit an outstanding level of transferability and have been applied in molecular dynamics simulations of tert-butylacetylene under thermodynamic conditions that correspond to its single-shock Hugoniot. We have achieved precise conservation of the total energy during microcanonical molecular dynamics trajectories under incomplete convergence via the extended Lagrangian Born-Oppenheimer molecular dynamics formalism. In good agreement with the results of a series of flyer-plate impact experiments, our SCC-TB molecular dynamics simulations show that tert-butylactylene molecules polymerize at shock pressures around 6.1 GPa.

Sanville, Edward J [Los Alamos National Laboratory; Bock, Nicolas [Los Alamos National Laboratory; Challacombe, William M [Los Alamos National Laboratory; Cawkwell, Marc J [Los Alamos National Laboratory; Niklasson, Anders M N [Los Alamos National Laboratory; Dattelbaum, Dana M [Los Alamos National Laboratory; Sheffield, Stephen [Los Alamos National Laboratory; Sewell, Thomas D [UNIV OF MISSOURI

2010-01-01

156

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. PMID:22035460

2011-01-01

157

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

158

Molecular understanding of mutagenicity using potential energy methods

Our objective, has been to elucidate on a molecular level, at atomic resolution, the structures of DNAs modified by 2-aminofluorene and its N-acetyl derivative, 2-acetylaminofluorene (AAF). The underlying hypothesis is that DNA replicates with reduced fidelity when its normal right-handed B-structure is altered, and one result is a higher mutation rate. This change in structure may occur normally at a low incidence, for example by the formation of hairpin loops in appropriate sequences, but it may be enhanced greatly after covalent modification by a mutagenic substance. We use computational methods and have been able to incorporate the first data from NMR studies in our calculations. Computational approaches are important because x-ray and spectroscopic studies have not succeeded in producing atomic resolution views of mutagen and carcinogen-oligonucleotide adducts. The specific methods that we employ are minimized potential energy calculations using the torsion angle space molecular mechanics program DUPLEX to yield static views. Molecular dynamics simulations, with full solvent and salt, of the important static structures are carried out with the program AMBER; this yields mobile views in a medium that mimics the natural aqueous environment of the cell as well as can be done with current available computing resources.

Broyde, S.; Shapiro, R.

1992-07-01

159

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

160

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

161

Density-Functional Molecular Dynamics Simulations of Shocked Molecular Liquids

NASA Astrophysics Data System (ADS)

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, and O2) undergo a continuous transition from a molecular to a partially dissociated fluid containing a mixture of atoms and molecules.

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

2002-07-01

162

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

163

Molecular dynamics simulation of membrane proteins.

Membrane proteins play crucial roles in a range of biological processes. High resolution structures provide insights into the functional mechanisms of membrane proteins, but detailed biophysical characterization of membrane proteins is difficult. Complementary to experimental techniques, molecular dynamics simulations is a powerful tool in providing more complete description of the dynamics and energetics of membrane proteins with high spatial-temporal resolution. In this chapter, we provide a survey of the current methods and technique issues for setting up and running simulations of membrane proteins. The recent progress in applying simulations to understanding various biophysical properties of membrane proteins is outlined. PMID:24446367

Weng, Jingwei; Wang, Wenning

2014-01-01

164

Exploring Transmembrane Diffusion Pathways With Molecular Dynamics

NSDL National Science Digital Library

Transmembrane exchange of materials is a fundamental process in biology. Molecular dynamics provides a powerful method to investigate in great detail various aspects of the phenomenon, particularly the permeation of small uncharged molecules, which continues to pose a challenge to experimental studies. We will discuss some of the recent simulation studies investigating the role of lipid-mediated and protein-mediated mechanisms in permeation of water and gas molecules across the membrane.

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

2010-06-01

165

Isothermal isobaric molecular dynamics simulation of water

A series of isothermal isobaric molecular dynamics simulation are carried out on a system made up of 210 molecules at normal temperature and pressure (T=298K, P=1bar) and at high pressure (T=298K, P=2.1kbar). The physical model is based upon the tetrahedral cluster architecture composed of one central molecule (20% of the sample) and four outer molecules (80%). This theoretical approach of

M. Amrani; D. Bendeddouch; D. Bormann; A. Krallafa

2008-01-01

166

Molecular dynamics simulation of nanoscale liquid flows

Molecular dynamics (MD) simulation is a powerful tool to investigate the nanoscale fluid flow. In this article, we review\\u000a the methods and the applications of MD simulation in liquid flows in nanochannels. For pressure-driven flows, we focus on\\u000a the fundamental research and the rationality of the model hypotheses. For electrokinetic-driven flows and the thermal-driven\\u000a flows, we concentrate on the principle

Yuxiu LiJinliang XuDongqing Li; Jinliang Xu; Dongqing Li

2010-01-01

167

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. PMID:20551228

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

2010-06-01

168

Control-volume representation of molecular dynamics.

A molecular dynamics (MD) parallel to the control volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood [J. Chem. Phys. 18, 817 (1950)] over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds' transport theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-control-volume (LCV) conversion function ?(i) for each molecule i. The LCV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the volume average [Lutsko, J. Appl. Phys. 64, 1152 (1988)] techniques and the method of planes [Todd et al., Phys. Rev. E 52, 1627 (1995)] emerges naturally from the treatment. Numerical experiments using the MD CV method are reported for equilibrium and nonequilibrium (start-up Couette flow) model liquids, which demonstrate the advantages of the formulation. The CV formulation of the MD is shown to be exactly conservative and is, therefore, ideally suited to obtain macroscopic properties from a discrete system. PMID:23004901

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

2012-05-01

169

Control-volume representation of molecular dynamics

A Molecular Dynamics (MD) parallel to the Control Volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood, J. Chem. Phys. 18, 817 (1950) over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds' Transport Theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-Control-Volume (\\CV) conversion function $\\vartheta_{i}$, for each molecule $i$. The \\CV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the Volume Average (VA, Lutsko, J. Appl. Phys 64, 1152 (1988)) techniques and the Method of Planes (MOP, Todd et al, Phys. Rev. E 52, 1627 (1995)) emerges naturally from the treatment. Numerical experiments using the MD CV method are reported for equilibrium and non-equilibrium (start-up Couette flow) model liquids, which demonstrate the advantages of the formulation. The CV formulation of the MD is shown to be exactly conservative, and is therefore ideally suited to obtain macroscopic properties from a discrete system.

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

2012-03-12

170

The dynamical origin of the zeta potential

NASA Astrophysics Data System (ADS)

By using evanescent waves, we study equilibrium and dynamical properties of liquid-solid interfaces in the Debye layer for hydrophilic and hydrophobic surfaces. We measure velocity profiles and nanotracer concentration and diffusion profiles between 20 and 300 nm from the walls in pressure-driven and electroosmotic flows. We extract electrostatic and zeta potentials and determine hydrodynamic slip lengths with 10 nm accuracy. The spectacular amplification of the zeta potential resulting from hydrodynamic slippag allows to clarify for the first time the dynamic origin of this potential.

Tabeling, Patrick

2009-03-01

171

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

The main 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, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.

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

2012-05-29

172

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

173

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 PMID:8994588

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

1997-01-01

174

Molecular dynamics at low time resolution

NASA Astrophysics Data System (ADS)

The internal dynamics of macromolecular systems is characterized by widely separated time scales, ranging from fraction of picoseconds to nanoseconds. In ordinary molecular dynamics simulations, the elementary time step ?t used to integrate the equation of motion needs to be chosen much smaller of the shortest time scale in order not to cut-off physical effects. We show that in systems obeying the overdamped Langevin equation, it is possible to systematically correct for such discretization errors. This is done by analytically averaging out the fast molecular dynamics which occurs at time scales smaller than ?t, using a renormalization group based technique. Such a procedure gives raise to a time-dependent calculable correction to the diffusion coefficient. The resulting effective Langevin equation describes by construction the same long-time dynamics, but has a lower time resolution power, hence it can be integrated using larger time steps ?t. We illustrate and validate this method by studying the diffusion of a point-particle in a one-dimensional toy model and the denaturation of a protein.

Faccioli, P.

2010-10-01

175

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

176

Electron and molecular dynamics: Penning ionization and molecular charge transport

NASA Astrophysics Data System (ADS)

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

Madison, Tamika Arlene

177

Visual verification and analysis of cluster detection for molecular dynamics.

A current research topic in molecular thermodynamics is the condensation of vapor to liquid and the investigation of this process at the molecular level. Condensation is found in many physical phenomena, e.g. the formation of atmospheric clouds or the processes inside steam turbines, where a detailed knowledge of the dynamics of condensation processes will help to optimize energy efficiency and avoid problems with droplets of macroscopic size. The key properties of these processes are the nucleation rate and the critical cluster size. For the calculation of these properties it is essential to make use of a meaningful definition of molecular clusters, which currently is a not completely resolved issue. In this paper a framework capable of interactively visualizing molecular datasets of such nucleation simulations is presented, with an emphasis on the detected molecular clusters. To check the quality of the results of the cluster detection, our framework introduces the concept of flow groups to highlight potential cluster evolution over time which is not detected by the employed algorithm. To confirm the findings of the visual analysis, we coupled the rendering view with a schematic view of the clusters' evolution. This allows to rapidly assess the quality of the molecular cluster detection algorithm and to identify locations in the simulation data in space as well as in time where the cluster detection fails. Thus, thermodynamics researchers can eliminate weaknesses in their cluster detection algorithms. Several examples for the effective and efficient usage of our tool are presented. PMID:17968118

Grottel, Sebastian; Reina, Guido; Vrabec, Jadran; Ertl, Thomas

2007-01-01

178

Thermal Transport in Carbon Nanotubes using Molecular Dynamics

NASA Astrophysics Data System (ADS)

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

Moore, Andrew; Khatun, Mahfuza

2011-10-01

179

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

180

(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

181

SUPERADIABATIC TRANSITIONS IN QUANTUM MOLECULAR DYNAMICS

crossing of two electronic energy levels, for one nuclear degree of freedom. We derive the general form. In turn, the nuclear quantum dynamical motion is determined by an effective potential given by the energy electronic energy levels at an avoided crossing. We treat a two-level system with one nuclear degree

Betz, Volker

182

Molecular dynamics simulations of structure and dynamics of organic molecular crystals.

A set of model compounds covering a range of polarity and flexibility have been simulated using GAFF, CHARMM22, OPLS and MM3 force fields to examine how well classical molecular dynamics simulations can reproduce structural and dynamic aspects of organic molecular crystals. Molecular structure, crystal structure and thermal motion, including molecular reorientations and internal rotations, found from the simulations have been compared between force fields and with experimental data. The MM3 force field does not perform well in condensed phase simulations, while GAFF, CHARMM and OPLS perform very similarly. Generally molecular and crystal structure are reproduced well, with a few exceptions. The atomic displacement parameters (ADPs) are mostly underestimated in the simulations with a relative error of up to 70%. Examples of molecular reorientation and internal rotation, observed in the simulations, include in-plane reorientations of benzene, methyl rotations in alanine, decane, isopropylcyclohexane, pyramidal inversion of nitrogen in amino group and rotation of the whole group around the C-N bond. Frequencies of such dynamic processes were calculated, as well as thermodynamic properties for reorientations in benzene and alanine. We conclude that MD simulations can be used for qualitative analysis, while quantitative results should be taken with caution. It is important to compare the outcomes from simulations with as many experimental quantities as available before using them to study or quantify crystal properties not available from experiment. PMID:20944862

Nemkevich, Alexandra; Bürgi, Hans-Beat; Spackman, Mark A; Corry, Ben

2010-12-01

183

Electronic continuum model for molecular dynamics simulations

NASA Astrophysics Data System (ADS)

A simple model for accounting for electronic polarization in molecular dynamics (MD) simulations is discussed. In this model, called molecular dynamics electronic continuum (MDEC), the electronic polarization is treated explicitly in terms of the electronic continuum (EC) approximation, while the nuclear dynamics is described with a fixed-charge force field. In such a force-field all atomic charges are scaled to reflect the screening effect by the electronic continuum. The MDEC model is rather similar but not equivalent to the standard nonpolarizable force-fields; the differences are discussed. Of our particular interest is the calculation of the electrostatic part of solvation energy using standard nonpolarizable MD simulations. In a low-dielectric environment, such as protein, the standard MD approach produces qualitatively wrong results. The difficulty is in mistreatment of the electronic polarizability. We show how the results can be much improved using the MDEC approach. We also show how the dielectric constant of the medium obtained in a MD simulation with nonpolarizable force-field is related to the static (total) dielectric constant, which includes both the nuclear and electronic relaxation effects. Using the MDEC model, we discuss recent calculations of dielectric constants of alcohols and alkanes, and show that the MDEC results are comparable with those obtained with the polarizable Drude oscillator model. The applicability of the method to calculations of dielectric properties of proteins is discussed.

Leontyev, I. V.; Stuchebrukhov, A. A.

2009-02-01

184

Electronic continuum model for molecular dynamics simulations.

A simple model for accounting for electronic polarization in molecular dynamics (MD) simulations is discussed. In this model, called molecular dynamics electronic continuum (MDEC), the electronic polarization is treated explicitly in terms of the electronic continuum (EC) approximation, while the nuclear dynamics is described with a fixed-charge force field. In such a force-field all atomic charges are scaled to reflect the screening effect by the electronic continuum. The MDEC model is rather similar but not equivalent to the standard nonpolarizable force-fields; the differences are discussed. Of our particular interest is the calculation of the electrostatic part of solvation energy using standard nonpolarizable MD simulations. In a low-dielectric environment, such as protein, the standard MD approach produces qualitatively wrong results. The difficulty is in mistreatment of the electronic polarizability. We show how the results can be much improved using the MDEC approach. We also show how the dielectric constant of the medium obtained in a MD simulation with nonpolarizable force-field is related to the static (total) dielectric constant, which includes both the nuclear and electronic relaxation effects. Using the MDEC model, we discuss recent calculations of dielectric constants of alcohols and alkanes, and show that the MDEC results are comparable with those obtained with the polarizable Drude oscillator model. The applicability of the method to calculations of dielectric properties of proteins is discussed. PMID:19256627

Leontyev, I V; Stuchebrukhov, A A

2009-02-28

185

Molecular dynamics simulations of F1-ATPase.

F1-ATPase is a rotary motor enzyme. Despite many theoretical and experimental studies, the molecular mechanism of the motor rotation is still not fully understood. However, plenty of available data provide a clue as to how this molecular motor rotates: with nucleotide perturbations, the catalytically active ? subunit propagates its structural changes to the entire ?3?3 complex via both sides of the subunits, resulting that asymmetry is created in the ?3?3 hexamer ring. In the sequential reaction step, the structure of the asymmetrical ?3?3 complex changes from one state to the other due to the nucleotide perturbations, and the ? subunit axis follows the sequentially changing ?3?3 structure. Therefore, there are mainly two essential elements for motor rotation: the conformational change of the ? subunit and the asymmetrical structure of the ?3?3 subunit complex. Therefore, this chapter reports a series of studies focused on these two elements via combinational approaches of molecular dynamics (MD) simulations and experimental or other theoretical studies. In addition to the motor rotation factors, the combined study also revealed other important elements of F1-ATPase, such as torque transmission and the chemical reaction pathway, which is described in the later part of this chapter. All of these results provide insight into the rotational mechanism and deepen the understanding of this molecular motor. PMID:24446371

Ito, Yuko; Ikeguchi, Mitsunori

2014-01-01

186

DYNAMICAL ANALYSIS OF HIGHLY EXCITED MOLECULAR SPECTRA

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

Michael E. Kellman

2005-06-17

187

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

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

Dang, Liem X.; Chang, Tsun-Mei

2012-01-19

188

Exploring Hamiltonian dielectric solvent molecular dynamics

NASA Astrophysics Data System (ADS)

Hamiltonian dielectric solvent (HADES) is a recent method [7,25], which enables Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric continua. Sample simulations of an ?-helical decapeptide with and without explicit solvent demonstrate the high efficiency of HADES-MD. Addressing the folding of this peptide by replica exchange MD we study the properties of HADES by comparing melting curves, secondary structure motifs and salt bridges with explicit solvent results. Despite the unoptimized ad hoc parametrization of HADES, calculated reaction field energies correlate well with numerical grid solutions of the dielectric Poisson equation.

Bauer, Sebastian; Tavan, Paul; Mathias, Gerald

2014-09-01

189

Microscale swimming: The molecular dynamics approach

The self-propelled motion of microscopic bodies immersed in a fluid medium is studied using molecular dynamics simulation. The advantage of the atomistic approach is that the detailed level of description allows complete freedom in specifying the swimmer design and its coupling with the surrounding fluid. A series of two-dimensional swimming bodies employing a variety of propulsion mechanisms -- motivated by biological and microrobotic designs -- is investigated, including the use of moving limbs, changing body shapes and fluid jets. The swimming efficiency and the nature of the induced, time-dependent flow fields are found to differ widely among body designs and propulsion mechanisms.

D. C. Rapaport

2007-05-11

190

Analysis of molecular diffusion in resist polymer films simulated by molecular dynamics

NASA Astrophysics Data System (ADS)

The diffusion process of acids plays important roles in chemically amplified resists. Polymer matrices from the diffusion path, and the structure significantly influences the behavior of the acid diffusion. We have simulated the diffusions of molecules in polymer matrices by molecular dynamics in order to analyze the diffusion mechanism in chemically amplified resist syste. To represent bulk state conditions of the polymer film, we prepared the molecular structures under the 3D periodic boundary conditions utilizing the molecular simulation. This amorphous cell contained three chains of methacrylate polymers such as poly(methacrylate), poly(tert-butylmethacrylate), poly(isobornylmethacrylate) and one diffusion molecule such as oxygen and methanesulfonic acid. The structure was energy-minimized and equilibrated under stable conditions. The free volumes in the system were estimated as the volumes enclosed by the iso-potential surfaces around the polymer using the Gusev-Suter method. The average size of the free volumes in the poly(methylmethacrylate) system was obtained as 3.7 angstrom3 with large standard deviation of 11.1 angstrom3, which indicates the large width of the size- distribution of free volumes scattered at random in the system. Molecular diffusion in the energy-minimized cell was simulated for 50 picoseconds by the molecular dynamics. The time dependence of the mean-square displacements of diffusing molecules was obtained from the dynamics treatments and it determined the diffusion constant in the resist systems. It is shown that the molecules do not always rapidly diffuse with larger free volumes, but the diffusions also depend upon the interaction with the polymer, and that the computer simulation tools provide the potentia for the molecular level study of resists chemistry.

Toriumi, Minoru; Ohfuji, Takeshi; Endo, Masayuki; Morimoto, Hiroaki

1999-06-01

191

Molecular Dynamics Simulations of the Lipid Bilayer Edge

Phospholipid bilayers have been intensively studied by molecular dynamics (MD) simulation in recent years. The properties of bilayer edges are important in determining the structure and stability of pores formed in vesicles and biomembranes. In this work, we use molecular dynamics simulation to investigate the structure, dynamics, and line tension of the edges of bilayer ribbons composed of pure dimyristoylphosphatidylcholine

Frank Y. Jiang; Yann Bouret; James T. Kindt

2004-01-01

192

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. PMID:24913987

Kessler, Ji?í; Bou?, Petr

2014-08-01

193

Dynamic Mechanism of E2020 Binding to Acetylcholinesterase: A Steered Molecular Dynamics Simulation

Dynamic Mechanism of E2020 Binding to Acetylcholinesterase: A Steered Molecular Dynamics Simulation site gorge of Torpedo californica acetylcholinesterase (TcAChE) was studied by using steered molecular

Sussman, Joel L.

194

Pressure derivatives in the classical molecular-dynamics ensemble

NASA Astrophysics Data System (ADS)

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

Meier, Karsten; Kabelac, Stephan

2006-02-01

195

Molecular dynamics algorithms and hydrodynamic screening

NASA Astrophysics Data System (ADS)

In this paper molecular dynamics simulations of a system of Brownian particles in an explicit bath of solvent particles are considered. Generalized algorithms (Langevin simulations), in which both the Brownian particles and the solvent particles are artificially coupled to a heat bath, are analyzed for their dynamical properties on long length scales. Although such a dynamic is clearly unphysical, its analysis is useful for two reasons: The Langevin algorithm is frequently applied in an ad hoc fashion, and the deviation of its dynamical properties from the physical Hamiltonian case can be made arbitrarily small by choosing a sufficiently weak coupling to the heat bath. By a direct application of the Mori-Zwanzig projection operator formalism it is shown that the violation of global momentum conservation results in an artificial screening of the hydrodynamic interactions, with a screening length proportional to the inverse square root of the friction constant of the algorithm. The result is formally similar to expressions given in phenomenological theories of hydrodynamic screening in semidilute polymer solutions.

Dünweg, Burkhard

1993-11-01

196

Attosecond VUV Coherent Control of Molecular Dynamics

High harmonic light sources make it possible to access attosecond time-scales, thus opening up the prospect of manipulating electronic wave packets for steering molecular dynamics. However, two decades after the birth of attosecond physics, the concept of attosecond chemistry has not yet been realized. This is because excitation and manipulation of molecular orbitals requires precisely controlled attosecond waveforms in the deep ultraviolet, which have not yet been synthesized. Here, we present a novel approach using attosecond vacuum ultraviolet pulse-trains to coherently excite and control the outcome of a simple chemical reaction in a deuterium molecule in a non-Born Oppenheimer regime. By controlling the interfering pathways of electron wave packets in the excited neutral and singly-ionized molecule, we unambiguously show that we can switch the excited electronic state on attosecond timescales, coherently guide the nuclear wave packets to dictate the way a neutral molecule vibrates, and steer and manipulate the ionization and dissociation channels. Furthermore, through advanced theory, we succeed in rigorously modeling multi-scale electron and nuclear quantum control in a molecule for the first time. The observed richness and complexity of the dynamics, even in this very simplest of molecules, is both remarkable and daunting, and presents intriguing new possibilities for bridging the gap between attosecond physics and attochemistry.

P. Ranitovic; C. W. Hogle; P. Riviere; A Palacios; X. M. Tong; N. Toshima; A. Gonzalez-Castrillo; L. Martin; F. Martin; M. M. Murnane; H. C. Kapteyn

2013-12-30

197

Molecular dynamics of the excitatory synapse.

Molecular dynamics of synapses are one of the most important factors that control the remodeling of synaptic connection and efficacy of transmission. This chapter focuses on the dynamics of postsynaptic molecular machinery and describes the imaging technologies important for quantitative analyses of synapses, their application to the postsynaptic molecules, and the insights obtained from these analyses. New visualization techniques, such as super-resolution microscopy, will become an indispensable approach to reveal submicron changes of synaptic molecules. New methods of monitoring protein interactions will also be integrated with experimental paradigms of synaptic plasticity. Cell biological analyses, together with cutting-edge imaging technologies, have been applied to the studies of nascent synapse formation, synapse maintenance, and activity-dependent synapse remodeling. From these studies, a variety of new concepts emerged, such as local assembly of postsynaptic scaffolds, presence of "transport packets" of postsynaptic receptors, heterogeneity of actin movement within spines, and activity-free fluctuation of PSD/spine sizes. These new concepts are useful in understanding specific properties of postsynaptic functions and should be integrated in future to build a realistic model of the postsynaptic organization that can explain its remarkable stability and tunability. PMID:22351054

Okabe, Shigeo

2012-01-01

198

Exact dynamic properties of molecular motors

NASA Astrophysics Data System (ADS)

Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecular motor walks, a generalized and straightforward graphical method for calculating their dynamic properties is presented. It allows the calculation of the velocity, dispersion, and randomness ratio for any proposed system through analysis of its structure. This article extends work of King and Altman ["A schematic method of deriving the rate laws of enzyme-catalyzed reactions," J. Phys. Chem. 60, 1375-1378 (1956)], 10.1021/j150544a010 on networks of enzymatic reactions by calculating additional dynamic properties for spatially hopping systems. Results for n-state systems are presented: single chain, parallel pathway, divided pathway, and divided pathway with a chain. A novel technique for combining multiple system architectures coupled at a reference state is also demonstrated. Four-state examples illustrate the effectiveness and simplicity of these methods.

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

2012-08-01

199

ls1 mardyn: The massively parallel molecular dynamics code for large systems

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

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

2014-01-01

200

ls1 mardyn: The massively parallel molecular dynamics code for large systems

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

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

2014-08-20

201

On electronic representations in molecular reaction dynamics

NASA Astrophysics Data System (ADS)

For many decades, the field of chemical reaction dynamics has utilized computational methods that rely on potential energy surfaces that are constructed using stationary-state calculations. These methods are typically devoid of dynamical couplings between the electronic and nuclear degrees of freedom, a fact that can result in incorrect descriptions of dynamical processes. Often, non-adiabatic coupling expressions are included in these methodologies. The Electron-Nuclear Dynamics (END) formalism, in contrast, circumvents these deficiencies by calculating all intermolecular forces directly at each time step in the dynamics and by explicitly maintaining all electronic-nuclear couplings. The purpose of this work is to offer two new frameworks for implementing electronic representations in dynamical calculations. Firstly, a new schema is proposed for developing atomic basis sets that are consistent with dynamical calculations. Traditionally, basis sets have been designed for use in stationary-state calculations of the structures and properties of molecules in their ground states. As a consequence of common construction techniques that utilize energy optimization methods, the unoccupied orbitals bear little resemblance to physical virtual atomic orbitals. We develop and implement a method for basis set construction that relies upon physical properties of atomic orbitals and that results in meaningful virtual orbitals. These basis sets are shown to provide a significant improvement in the accuracy of calculated dynamical properties such as charge transfer probabilities. Secondly, the theoretical framework of END is expanded to incorporate a multi-configurational representation for electrons. This formalism, named Vector Hartree-Fock, is based in the theory of vector coherent states and utilizes a complete active space electronic representation. The Vector Hartree-Fock method is fully disclosed, with derivation of the equations of motion. The expressions for the equation of motion are derived in full and a plan for implementing the Vector Hartree-Fock formalism within the current ENDyne computer code is given.

Killian, Benjamin J.

202

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

203

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

2014-01-01

204

Reaching biological timescales with all-atom molecular dynamics simulations.

Molecular dynamics (MD) simulations can provide atomically detailed views of protein motions, sampling multiple timescales ranging from femtoseconds to nanoseconds on typical computing resources. The 'reach' of these computer simulations toward biologically relevant timescales (microseconds and beyond) has been improving with advances in hardware and software, as well as the development of enhanced sampling techniques. This review outlines these advances, focusing on techniques that also provide realistic, unperturbed kinetics. These longer-timescale MD simulations can provide detailed insights into the mechanisms of biological events, potentially aiding the design of pharmaceuticals. PMID:20934381

Zwier, Matthew C; Chong, Lillian T

2010-12-01

205

Shock compression and spallation of tantalum: Molecular dynamics simulations

NASA Astrophysics Data System (ADS)

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

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

2011-06-01

206

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

207

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

NASA Technical Reports Server (NTRS)

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

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

2007-01-01

208

Identification of Allosteric Mechanisms in Thrombin through Molecular Dynamics Simulations.

??Molecular dynamics (MD) simulation, an established method for investigating the internal motions of biomolecules, is applied to thrombin protein, a critical blood coagulation cascade protease… (more)

Gasper, Paul M.

2013-01-01

209

Molecular dynamics simulation of a water/metal interface

NASA Astrophysics Data System (ADS)

First results of a molecular dynamics study of a water/metal interface, lasting 3.3 ps at an average temperature of 294 K, are reported. The basic periodic box contains 216 water molecules and a crystal slab of 550 platinum atoms with (100) surface planes. A combination of a Lennard-Jones potential between centers of mass and a Coulomb potential arising from dielectric interactions of the water charge distribution with the metal is employed for the water-wall interaction, the ST2 model for the water-water, and a nearest-neighbour harmonic potential for the platinum-platinum interactions. Considerable adsorption at the interface together with a drastic change of the water structure is observed.

Spohr, E.; Heinzinger, K.

1986-01-01

210

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. PMID:23226688

Abrams, Cameron F.; Vanden-Eijnden, Eric

2012-01-01

211

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

212

A scheme to combine molecular dynamics and dislocation dynamics

NASA Astrophysics Data System (ADS)

Many engineering challenges occur on multiple interacting length scales, e.g. during fracture atoms separate on the atomic scale while plasticity develops on the micrometer scale. To investigate the details of these events, a concurrent multiscale model is required which studies the problem at appropriate length- and time-scales: the atomistic scale and the dislocation dynamics scale. The AtoDis multiscale model is introduced, which combines atomistics and dislocation dynamicsinto a fully dynamic model that is able to simulate deformation mechanisms at finite temperature. The model uses point forces to ensure mechanical equilibrium and kinematic continuity at the interface. By resolving each interface atom analytically, and not numerically, the framework uses a coarse FEM mesh and intrinsically filters out atomistic vibrations. This multiscale model allows bi-directional dislocation transition at the interface of both models with no remnant atomic disorder. Thereby, the model is able to simulate a larger plastic zone than conventional molecular dynamics while reducing the need for constitutive dislocation dynamics equations. This contribution studies dislocation nucleation at finite temperature and investigates the absorption of dislocations into the crack wake.

Brinckmann, Steffen; Mahajan, Dhiraj K.; Hartmaier, Alexander

2012-06-01

213

NMR Experiments and Molecular Dynamics Simulations of the Segmental Dynamics of Polystyrene

NMR Experiments and Molecular Dynamics Simulations of the Segmental Dynamics of Polystyrene Yiyong experiments and molecular dynamics (MD) computer simulations on atactic polystyrene (a-PS). The segmental the segmental dynamics of atactic polystyrene (a-PS) obtained from NMR experiments and MD simulations. Atactic

Utah, University of

214

Heterogeneous dynamics of ionic liquids from molecular dynamics simulations.

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

Habasaki, J; Ngai, K L

2008-11-21

215

How Dynamic Visualization Technology Can Support Molecular Reasoning

ERIC Educational Resources Information Center

This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…

Levy, Dalit

2013-01-01

216

MOLECULAR DYNAMICS SIMULATIONS OF CARBON NANOTUBE-BASED OSCILLATORS

MOLECULAR DYNAMICS SIMULATIONS OF CARBON NANOTUBE-BASED OSCILLATORS HAVING TOPOLOGICAL DEFECTSÃ?Wales defects on the oscillatory behavior of (5,5)/(10,10) carbon nanotube-based oscillator are studied using NVE molecular dynamics simulations. Results show that defects reduce stability of the oscillators. E

Bhattacharya, Baidurya

217

...........................................................16 2.2.1.3.2 Morse Charge Equilibration (MS-Q) Force Field...............21 2.2.2 Ensembles .......................................................................................22 2.2.3 Types of Molecular Dynamics................................................................................................24 Table 3. Diagonal Morse type Van der Waals potential...................................................37 Table 4. Off-diagonal Morse type Van der Waals potential.............................................38 Table 5. Lattice parameters...

Atilhan, Selma

2009-05-15

218

Fractal and complex network analyses of protein molecular dynamics

NASA Astrophysics Data System (ADS)

Based on protein molecular dynamics, we investigate the fractal properties of energy, pressure and volume time series using the multifractal detrended fluctuation analysis (MF-DFA) and the topological and fractal properties of their converted horizontal visibility graphs (HVGs). The energy parameters of protein dynamics we considered are bonded potential, angle potential, dihedral potential, improper potential, kinetic energy, Van der Waals potential, electrostatic potential, total energy and potential energy. The shape of the h(q) curves from MF-DFA indicates that these time series are multifractal. The numerical values of the exponent h(2) of MF-DFA show that the series of total energy and potential energy are non-stationary and anti-persistent; the other time series are stationary and persistent apart from series of pressure (with H?0.5 indicating the absence of long-range correlation). The degree distributions of their converted HVGs show that these networks are exponential. The results of fractal analysis show that fractality exists in these converted HVGs. For each energy, pressure or volume parameter, it is found that the values of h(2) of MF-DFA on the time series, exponent ? of the exponential degree distribution and fractal dimension dB of their converted HVGs do not change much for different proteins (indicating some universality). We also found that after taking average over all proteins, there is a linear relationship between

Zhou, Yuan-Wu; Liu, Jin-Long; Yu, Zu-Guo; Zhao, Zhi-Qin; Anh, Vo

2014-12-01

219

Molecular beam studies of reaction dynamics

The major thrust of this research project is to elucidate detailed dynamics of simple reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation. 34 refs.

Lee, Y.T.

1990-03-01

220

Molecular beam studies of reaction dynamics

The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.

Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)

1993-12-01

221

The dynamic structure and potential energy surface of adenine...thymine and guanine...cytosine base pairs and their methylated analogues interacting with a small number (from 1 to 16 molecules) of organic solvents (methanol, dimethylsulfoxide, and chloroform) were investigated by various theoretical approaches starting from simple empirical methods employing the Cornell et al. force field to highly accurate ab initio quantum chemical calculations (MP2 and particularly CCSD(T) methods). After the simple molecular dynamics simulation, the molecular dynamics in combination with quenching technique was also used. The molecular dynamics simulations presented here have confirmed previous experimental and theoretical results from the bulk solvents showing that, whereas in chloroform the base pairs create hydrogen-bonded structures, in methanol, stacked structures are preferred. While methanol (like water) can stabilize the stacked structures of the base pairs by a higher number of hydrogen bonds than is possible in hydrogen-bonded pairs, the chloroform molecule lacks such a property, and the hydrogen-bonded structures are preferred in this solvent. The large volume of the dimethylsulfoxide molecule is an obstacle for the creation of very stable hydrogen-bonded and stacked systems, and a preference for T-shaped structures, especially for complexes of methylated adenine...thymine base pairs, was observed. These results provide clear evidence that the preference of either the stacked or the hydrogen-bonded structures of the base pairs in the solvent is not determined only by bulk properties or the solvent polarity but rather by specific interactions of the base pair with a small number of the solvent molecules. These conclusions obtained at the empirical level were verified also by high-level ab initio correlated calculations. PMID:17302446

Zendlová, Lucie; Hobza, Pavel; Kabelác, Martin

2007-03-15

222

Time-averaged order parameter restraints in molecular dynamics simulations.

A method is described that allows experimental [Formula: see text] order parameters to be enforced as a time-averaged quantity in molecular dynamics simulations. The two parameters that characterize time-averaged restraining, the memory relaxation time and the weight of the restraining potential energy term in the potential energy function used in the simulation, are systematically investigated based on two model systems, a vector with one end restrained in space and a pentapeptide. For the latter it is shown that the backbone N-H order parameter of individual residues can be enforced such that the spatial fluctuations of quantities depending on atomic coordinates are not significantly perturbed. The applicability to realistic systems is illustrated for the B3 domain of protein G in aqueous solution. PMID:25312596

Hansen, Niels; Heller, Fabian; Schmid, Nathan; van Gunsteren, Wilfred F

2014-11-01

223

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

2010-08-12

224

Statistical coarse-graining of molecular dynamics into peridynamics.

This paper describes an elegant statistical coarse-graining of molecular dynamics at finite temperature into peridynamics, a continuum theory. Peridynamics is an efficient alternative to molecular dynamics enabling dynamics at larger length and time scales. In direct analogy with molecular dynamics, peridynamics uses a nonlocal model of force and does not employ stress/strain relationships germane to classical continuum mechanics. In contrast with classical continuum mechanics, the peridynamic representation of a system of linear springs and masses is shown to have the same dispersion relation as the original spring-mass system.

Silling, Stewart Andrew; Lehoucq, Richard B.

2007-10-01

225

Hydration Effect on Temperature Dependence of Protein Dynamics Studied by Molecular Dynamics Simulation of Crystalline Protein Yasumasa JOTI and Akio KITAO Institute of Molecular and Cellular Biosciences, University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 1. Introduction Proteins are molecular

Katsumoto, Shingo

226

Molecular dynamics in cytochrome c oxidase Moessbauer spectra deconvolution

Research highlights: {yields} Cytochrome c oxidase molecular dynamics serve to predict Moessbauer lineshape widths. {yields} Half height widths are used in modeling of Lorentzian doublets. {yields} Such spectral deconvolutions are useful in detecting the enzyme intermediates. -- Abstract: In this work low temperature molecular dynamics simulations of cytochrome c oxidase are used to predict an experimentally observable, namely Moessbauer spectra width. Predicted lineshapes are used to model Lorentzian doublets, with which published cytochrome c oxidase Moessbauer spectra were simulated. Molecular dynamics imposed constraints to spectral lineshapes permit to obtain useful information, like the presence of multiple chemical species in the binuclear center of cytochrome c oxidase. Moreover, a benchmark of quality for molecular dynamic simulations can be obtained. Despite the overwhelming importance of dynamics in electron-proton transfer systems, limited work has been devoted to unravel how much realistic are molecular dynamics simulations results. In this work, molecular dynamics based predictions are found to be in good agreement with published experimental spectra, showing that we can confidently rely on actual simulations. Molecular dynamics based deconvolution of Moessbauer spectra will lead to a renewed interest for application of this approach in bioenergetics.

Bossis, Fabrizio [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari 'Aldo Moro', Bari (Italy)] [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari 'Aldo Moro', Bari (Italy); Palese, Luigi L., E-mail: palese@biochem.uniba.it [Department of Medical Biochemistry, Medical Biology and Medical Physics (DIBIFIM), University of Bari 'Aldo Moro', Bari (Italy)

2011-01-07

227

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu [Department of Mechanical and Aerospace Engineering, University of Missouri, Columbia, Missouri 65211 (United States); Yang, Mo [College of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai 200093 (China)

2013-12-21

228

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

229

Can the ring polymer molecular dynamics method be interpreted as real time quantum dynamics?

NASA Astrophysics Data System (ADS)

The ring polymer molecular dynamics (RPMD) method has gained popularity in recent years as a simple approximation for calculating real time quantum correlation functions in condensed media. However, the extent to which RPMD captures real dynamical quantum effects and why it fails under certain situations have not been clearly understood. Addressing this issue has been difficult in the absence of a genuine justification for the RPMD algorithm starting from the quantum Liouville equation. To this end, a new and exact path integral formalism for the calculation of real time quantum correlation functions is presented in this work, which can serve as a rigorous foundation for the analysis of the RPMD method as well as providing an alternative derivation of the well established centroid molecular dynamics method. The new formalism utilizes the cyclic symmetry of the imaginary time path integral in the most general sense and enables the expression of Kubo-transformed quantum time correlation functions as that of physical observables pre-averaged over the imaginary time path. Upon filtering with a centroid constraint function, the formulation results in the centroid dynamics formalism. Upon filtering with the position representation of the imaginary time path integral, we obtain an exact quantum dynamics formalism involving the same variables as the RPMD method. The analysis of the RPMD approximation based on this approach clarifies that an explicit quantum dynamical justification does not exist for the use of the ring polymer harmonic potential term (imaginary time kinetic energy) as implemented in the RPMD method. It is analyzed why this can cause substantial errors in nonlinear correlation functions of harmonic oscillators. Such errors can be significant for general correlation functions of anharmonic systems. We also demonstrate that the short time accuracy of the exact path integral limit of RPMD is of lower order than those for finite discretization of path. The present quantum dynamics formulation also serves as the basis for developing new quantum dynamical methods that utilize the cyclic nature of the imaginary time path integral.

Jang, Seogjoo; Sinitskiy, Anton V.; Voth, Gregory A.

2014-04-01

230

NASA Astrophysics Data System (ADS)

In this work we studied the temperature-induced changes in the structural and dynamical properties of liquid Ag using molecular dynamics (DM) computer simulation. The atomic interactions are modeled through a semiempirical potential function which incorporates n-body effects and is based on the second moments approximation of the density of states of a tight-binding Hamiltonian. The caloric curve was used to calculate the latent heat of fusion and the pair distribution function, g(r), was calculated from a set of atomic configurations collected at several time-steps. The dynamical properties are studied through the velocity autocorrelation function and the mean-square displacement. The self-diffusion coefficient and its behavior with the temperature, obtained from our simulations, shows the typical behavior of the simple liquids. Our results are compared to available experimental data.

Banuelos, E. U.; Amarillas, A. P.

2004-02-01

231

We study the phonon modes in single-walled MoS? 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 MoS? nanotubes. PMID:24531058

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

2014-03-14

232

Kinetic theory molecular dynamics and hot dense matter: Theoretical foundations

NASA Astrophysics Data System (ADS)

Electrons are weakly coupled in hot, dense matter that is created in high-energy-density experiments. They are also mildly quantum mechanical and the ions associated with them are classical and may be strongly coupled. In addition, the dynamical evolution of plasmas under these hot, dense matter conditions involve a variety of transport and energy exchange processes. Quantum kinetic theory is an ideal tool for treating the electrons but it is not adequate for treating the ions. Molecular dynamics is perfectly suited to describe the classical, strongly coupled ions but not the electrons. We develop a method that combines a Wigner kinetic treatment of the electrons with classical molecular dynamics for the ions. We refer to this hybrid method as "kinetic theory molecular dynamics," or KTMD. The purpose of this paper is to derive KTMD from first principles and place it on a firm theoretical foundation. The framework that KTMD provides for simulating plasmas in the hot, dense regime is particularly useful since current computational methods are generally limited by their inability to treat the dynamical quantum evolution of the electronic component. Using the N-body von Neumann equation for the electron-proton plasma, three variations of KTMD are obtained. Each variant is determined by the physical state of the plasma (e.g., collisional versus collisionless). The first variant of KTMD yields a closed set of equations consisting of a mean-field quantum kinetic equation for the electron one-particle distribution function coupled to a classical Liouville equation for the protons. The latter equation includes both proton-proton Coulombic interactions and an effective electron-proton interaction that involves the convolution of the electron density with the electron-proton Coulomb potential. The mean-field approach is then extended to incorporate equilibrium electron-proton correlations through the Singwi-Tosi-Land-Sjolander (STLS) ansatz. This is the second variant of KTMD. The STLS contribution produces an effective electron-proton interaction that involves the electron-proton structure factor, thereby extending the usual mean-field theory to correlated but near equilibrium systems. Finally, a third variant of KTMD is derived. It includes dynamical electrons and their correlations coupled to a MD description for the ions. A set of coupled equations for the one-particle electron Wigner function and the electron-electron and electron-proton correlation functions are coupled to a classical Liouville equation for the protons. This latter variation has both time and momentum dependent correlations.

Graziani, F. R.; Bauer, J. D.; Murillo, M. S.

2014-09-01

233

Modeling Of Blood Vessel Constriction In 2-D Case Using Molecular Dynamics Method

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.

Mohamad Rendi; Suprijadi; Sparisoma Viridi

2013-06-25

234

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

235

Modeling Of Blood Vessel Constriction In 2-D Case Using Molecular Dynamics Method

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.

Rendi, Mohamad; Viridi, Sparisoma

2013-01-01

236

Microsecond molecular dynamics simulations of lipid mixing.

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

Hong, Chunkit; Tieleman, D Peter; Wang, Yi

2014-10-14

237

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

The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA’s activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM’s unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand’s binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs. PMID:22761821

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

2012-01-01

238

Huge-scale Molecular Dynamics Simulation of Multibubble Nuclei

We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can b...

Watanabe, Hiroshi; Ito, Nobuyasu

2012-01-01

239

Molecular dynamics simulation of amorphous SiO2 nanoparticles.

Molecular dynamics simulation of amorphous SiO2 spherical nanoparticles has been carried out in a model with different sizes, 2, 4, and 6 nm, under non-periodic boundary conditions. We use the pair interatomic potentials which have weak Coulomb interaction and Morse type short-range interaction. Models have been obtained by cooling from the melt via molecular dynamics (MD) simulation. Structural properties of amorphous nanoparticles obtained at 350 K have been studied via partial radial distribution functions (PRDFs), mean interatomic distances, coordination numbers, and bond-angle distributions, which are compared with those observed in the bulk. Calculations of the radial density profile in nanoparticles show the tendency of oxygen to concentrate at the surface as observed previously in other amorphous clusters or thin films. Size effects on structure of nanosized models are significant. The calculations show that if the size is larger than 4 nm, amorphous SiO2 nanoparticles have a distorted tetrahedral network structure with the mean coordination number ZSi-O approximately 4.0 and ZO-Si approximately 2.0 like those observed in the bulk. Surface structure, surface energy, and glass transition temperature of SiO2 nanoparticles have been obtained and presented. PMID:17944505

Hoang, Vo Van

2007-11-01

240

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

241

Molecular dynamics simulations of compressed liquid hydrogen.

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations have been performed for highly compressed fluid hydrogen in the density and temperature regime of recent shock-compression experiments. Both density functional and tight-binding electronic structure techniques have been used to describe interatomic forces. A new tight-binding model of hydrogen has been developed with a single s orbital on each atom that reproduces properties of the dimer, of various crystalline structures, and of the fluid. The simulations give pressures and electrical conductivities in general agreement with the measured values. The pressures are also compared with recent quantum Monte Carlo results. This analysis provides a firm foundation for exploring the origins of the rapid change in electrical conductivity with temperature and density observed in the experiments. The simulations indicate that the conductivity in fluid hydrogen in this regime arises both from: (1) closing of the band gap due to thermal effects and compression; (2) electron hopping facilitated by the dissociated atoms (monomers) with the latter process the most important. Finally, the authors find that the internal structure of cool, dense hydrogen has a pronounced time-dependent nature with molecules (dimers) constantly dissociating and atoms (monomers) constantly associating all of the time.

Lenosky, T. J.; Kress, J. D.; Collins, L. A.; Kwon, I.

1997-12-01

242

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

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

2011-05-12

243

Enhanced molecular dynamics for simulating porous interphase layers in batteries.

Understanding charge transport processes at a molecular level using computational techniques is currently hindered by a lack of appropriate models for incorporating anistropic electric fields in molecular dynamics (MD) simulations. An important technological example is ion transport through solid-electrolyte interphase (SEI) layers that form in many common types of batteries. These layers regulate the rate at which electro-chemical reactions occur, affecting power, safety, and reliability. In this work, we develop a model for incorporating electric fields in MD using an atomistic-to-continuum framework. This framework provides the mathematical and algorithmic infrastructure to couple finite element (FE) representations of continuous data with atomic data. In this application, the electric potential is represented on a FE mesh and is calculated from a Poisson equation with source terms determined by the distribution of the atomic charges. Boundary conditions can be imposed naturally using the FE description of the potential, which then propagates to each atom through modified forces. The method is verified using simulations where analytical or theoretical solutions are known. Calculations of salt water solutions in complex domains are performed to understand how ions are attracted to charged surfaces in the presence of electric fields and interfering media.

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

2009-10-01

244

Multiscale molecular dynamics using the matched interface and boundary method

The Poisson-Boltzmann (PB) equation is an established multiscale model for electrostatic analysis of biomolecules and other dielectric systems. PB based molecular dynamics (MD) approach has a potential to tackle large biological systems. Obstacles that hinder the current development of PB based MD methods are concerns in accuracy, stability, efficiency and reliability. The presence of complex solvent-solute interface, geometric singularities and charge singularities leads to challenges in the numerical solution of the PB equation and electrostatic force evaluation in PB based MD methods. Recently, the matched interface and boundary (MIB) method has been utilized to develop the first second order accurate PB solver that is numerically stable in dealing with discontinuous dielectric coefficients, complex geometric singularities and singular source charges. The present work develops the PB based MD approach using the MIB method. New formulation of electrostatic forces is derived to allow the use of sharp molecular surfaces. Accurate reaction field forces are obtained by directly differentiating the electrostatic potential. Dielectric boundary forces are evaluated at the solvent-solute interface using an accurate Cartesian-grid surface integration method. The electrostatic forces located at reentrant surfaces are appropriately assigned to related atoms. Extensive numerical tests are carried out to validate the accuracy and stability of the present electrostatic force calculation. The new PB based MD method is implemented in conjunction with the AMBER package. MIB based MD simulations of biomolecules are demonstrated via a few example systems.

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

2011-01-20

245

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations varying the molecular mass distribution in linear molecules are performed to search for a direct test of Hubbard relations for liquid state dynamics. Results are obtained for series of models with different moments of inertia and the same multipoles and molecular length. The intermolecular potential is composed of different contributions including a nonpolar term. This potential allows for a steady variation of moment of inertia. Correlation times are directly checked with Hubbard relations and a nearly quantitative agreement found. Nonpreviously reported relationships between single correlation times and transport coefficients versus molecular moment of inertia are shown.

Calero, S.; Lago, S.; Garzón, B.

1999-09-01

246

. A semiclassical, finite temperature, quantum dynamics scheme based on the use of classical time correlation funcAdiabatic path integral molecular dynamics methods. II. Algorithms J. Cao Department of Chemistry approximations to quantum dynamics both of which require trajectories generated on potentials of mean force

Cao, Jianshu

247

Multipole Algorithms for Molecular Dynamics Simulation on High Performance Computers.

NASA Astrophysics Data System (ADS)

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

Elliott, William Dewey

1995-01-01

248

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. PMID:24266910

2013-01-01

249

Molecular Dynamics Simulations of Temperature Equilibration in Dense Hydrogen

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

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

2008-02-14

250

Effective interactions in molecular dynamics simulations of lysozyme solutions

NASA Astrophysics Data System (ADS)

In this article we explore a problem of effective interactions between two rotationally restrained lysozyme molecules forming a crystal contact in aqueous solution. We perform non-equilibrium molecular dynamics simulations in order to estimate the interaction energy as a function of the distance between the two proteins obtained from direct application of the Jarzynski equality (JE), and compare it with that calculated by means of another non-equilibrium approach (Forward-Reverse method) and constrained force methods. The performance of the JE equality when applied to solvated protein interactions is discussed. All of the equilibrium and non-equilibrium methods show clear evidence that the potentials of mean force (PMF) are short-ranged, do not exceed few kTs, and that there is an accumulation of anions in the presence of hydrophobic surfaces.

Pellicane, Giuseppe; Sarkisov, Lev

2014-09-01

251

Quasi-Ab initio molecular dynamic study of Fe melting

We have investigated the melting of hcp Fe at high pressure by employing molecular dynamics simulations in conjunction with the full potential linear muffin tin orbital method. Apart from being of fundamental value, the melting of iron at high pressure is also important for our understanding of the Earth. The subject of iron melting at high pressures is controversial. The experimental data for the iron melting temperature can be separated into two regions, "low" and "high." Here we present an ab initio simulated iron melting curve which is in agreement with the low temperatures at lower pressures, but is in excellent agreement with the high-mostly shockwave-temperatures at high pressures. A comparison with available data lends support to the presented iron melting curve. PMID:11019165

Belonoshko; Ahuja; Johansson

2000-04-17

252

Relationship between nanocrystalline and amorphous microstructures by molecular dynamics simulation

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

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

1996-08-01

253

Surface Diffusion of Single Polymer Chain Using Molecular Dynamics SIMULATION*

NASA Astrophysics Data System (ADS)

Results of recent experiments on polymer chains adsorbed from dilute solution at solid-liquid interface show the power scaling law dependence of the chain diffusivity, D, as a function of the degree of polymerization, N, D ˜ N^3/2. By contrast, DNA molecules bound to fluid cationic lipid bilayers follows Rouse dynamics with D ˜ N^1. We used molecular dynamics simulations to gain an understanding of these dissimilar scaling behaviors. Our model systems contain chains comprised of N monomers connected by anharmonic springs described by the finite extendible nonlinear elastic, FENE potential, embedded into a solvent of N=1 monomers. Two types of simulations we performed: (i) the chain is confined to two dimensions, (ii) the three dimensional chain in the solvent is confined between two solids plates. With randomly placed impenetrable obstacles on the surface, the diffusion of 2D chains exhibits, D ˜ N^3/2 behavior, when the chain radius of gyration, Rg, is larger than half the distance between obstacles, and D ˜ N^1 for shorter chains. In the presence of an athermal solvent, the scaling exponent is 0.75 due to hydrodynamic forces, for the two-dimensional system. We will also discuss the nature of dynamic adsorption transition and effects of hydrodynamics forces on chain diffusion for the three-dimensional simulations.

Desai, Tapan; Keblinski, Pawel; Kumar, Sanat; Granick, Steve

2004-05-01

254

Molecular Dynamics Simulations of Heat Transfer In Nanoscale Liquid Films

Molecular Dynamics (MD) simulations of nano-scale flows typically utilize fixed lattice crystal interactions between the fluid and stationary wall molecules. This approach cannot properly model thermal interactions at the wall-fluid interface...

Kim, Bo Hung

2010-07-14

255

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

256

Constant pressure hybrid Molecular Dynamics-Monte Carlo simulations

New hybrid Molecular Dynamics-Monte Carlo methods are proposed to increase the efficiency of constant-pressure simulations. Two variations of the isobaric Molecular Dynamics component of the algorithms are considered. In the first, we use the extended-ensemble method of Andersen [H. C. Andersen, J. Chem. Phys. 72, 2384 (1980)]. In the second, we arrive at a new constant-pressure Monte Carlo technique based

Roland Faller; Juan J. de Pablo

2002-01-01

257

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

258

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. PMID:23298176

2013-01-01

259

Molecular dynamics simulations of oil components at geological conditions

Modern methods of computational chemistry, including molecular dynamics and quantum mechanics of molecular systems, allow one to obtain accurate values of structural parameters and physicochemical properties of complex systems for a wide range of temperatures and pressures without resorting to experiment. In this work, we explore the effects of physical conditions on densities and viscosities of typical petroleum components, including

Jason Ho; Sarah Reimer; Noham Weinberg

2009-01-01

260

Diagnosis of inflammatory bowel disease: Potential role of molecular biometrics

Accurate diagnosis of predominantly colonic inflammatory bowel disease (IBD) is not possible in 30% of patients. For decades, scientists have worked to find a solution to improve diagnostic accuracy for IBD, encompassing Crohn’s colitis and ulcerative colitis. Evaluating protein patterns in surgical pathology colectomy specimens of colonic mucosal and submucosal compartments, individually, has potential for diagnostic medicine by identifying integrally independent, phenotype-specific cellular and molecular characteristics. Mass spectrometry (MS) and imaging (I) MS are analytical technologies that directly measure molecular species in clinical specimens, contributing to the in-depth understanding of biological molecules. The biometric-system complexity and functional diversity is well suited to proteomic and diagnostic studies. The direct analysis of cells and tissues by Matrix-Assisted-Laser Desorption/Ionization (MALDI) MS/IMS has relevant medical diagnostic potential. MALDI-MS/IMS detection generates molecular signatures obtained from specific cell types within tissue sections. Herein discussed is a perspective on the use of MALDI-MS/IMS and bioinformatics technologies for detection of molecular-biometric patterns and identification of differentiating proteins. I also discuss a perspective on the global challenge of transferring technologies to clinical laboratories dealing with IBD issues. The significance of serologic-immunometric advances is also discussed.

M’Koma, Amosy E

2014-01-01

261

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

262

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

Johnston, Jennifer M.

2014-01-01

263

GPU acceleration of cutoff pair potentials for molecular modeling applications

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

Christopher I. Rodrigues; David J. Hardy; John E. Stone; Klaus Schulten; Wen-mei W. Hwu

2008-01-01

264

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

2013-01-01

265

Chemical dynamics by molecular beam methods

The described research is classified in three separate categories: (a) theoretical analysis of glory scattering experiments; (b) measurements of kinetic energy thresholds (at very high energy resolution) for ion-pair production from molecular collisions, with subsequent derivation of molecular binding energies and electron affinities; and (c) formation of negative ions from high energy collisions of molecules with Cs. References to comprehensive

E. W. Rothe

1974-01-01

266

Bohm's Quantum Potential and the Visualization of Molecular Structure

NASA Technical Reports Server (NTRS)

David Bohm's ontological interpretation of quantum theory can shed light on otherwise counter-intuitive quantum mechanical phenomena including chemical bonding. In the field of quantum chemistry, Richard Bader has shown that the topology of the Laplacian of the electronic charge density characterizes many features of molecular structure and reactivity. Visual and computational examination suggests that the Laplacian of Bader and the quantum potential of Bohm are morphologically equivalent. It appears that Bohmian mechanics and the quantum potential can make chemistry as clear as they makes physics.

Levit, Creon; Chancellor, Marisa K. (Technical Monitor)

1997-01-01

267

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

We use the well-known structural and functional properties of the gramicidin A channel to test the appropriateness of force fields commonly used in molecular dynamics (MD) simulations of ion channels. For this purpose, the high-resolution structure of the gramicidin A dimer is embedded in a dimyristoylphosphatidylcholine bilayer, and the potential of mean force of a K+ ion is calculated along

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

2003-01-01

268

The association between monovalent salts and neutral lipid bilayers is known to influence global bilayer structural properties such as headgroup conformational fluctuations and the dipole potential. The local influence of the ions, however, has been unknown due to limited structural resolution of experimental methods. Molecular dynamics simulations are used here to elucidate local structural rearrangements upon association of a series

Jonathan N. Sachs; Hirsh Nanda; Horia I. Petrache; Thomas B. Woolfz

2004-01-01

269

Mg2SiO4 liquid under high pressure from molecular dynamics Omar Adjaoud a

the sinking velocity of a solid sphere through a liquid can be related to viscosity by Stokes' law (Kushiro Thermodynamics Diffusivity Viscosity We use a flexible potential model to perform large-scale molecular dynamics pressure. At high pressure viscosity is measured most directly by the "falling sphere" method, in which

Steinle-Neumann, Gerd

270

In this paper, we present decomposition mechanism studies of energetic molecules using HOMO and LUMO orbital energy gap driven molecular dynamics (MD) method. Under frozen orbital approximation, this is an `electronic excitation' MD, where electrons is excited from HOMO to LUMO orbitals Meanwhile, the HOMO and LUMO orbital energy gap is taken as a biasing potential to accelerate chemical reactions,

Yanhua Dong; Yanfeng Song; Hakima Abou-Rachid

2009-01-01

271

Molecular dynamics simulation of helium-vacancy interaction in plutonium

NASA Astrophysics Data System (ADS)

The formation energies of small He nV m clusters ( n and m denote the number of He atoms and vacancy, respectively) in Pu have been calculated with molecular dynamics (MD) simulations using the embedded atom method (EAM) potential, the Mores potential and the Lennard-Jones potential for describing the interactions of Pu-Pu, Pu-He and He-He, respectively. The binding energies of an interstitial He atom, an isolated vacancy and a self-interstitial Pu atom to a He nV m cluster are also obtained from the calculated formation energies of the clusters. All the binding energies mainly depend on the He-vacancy ratio ( n/ m) of clusters rather than the clusters size. With the increase of the n/ m ratio, the binding energies of a He atom and a Pu atom to a He nV m cluster decrease with the ratio, and the binding energy of a vacancy to a He nV m cluster increases. He atoms act as a catalyst for the formation of He nV m clusters.

Ao, Bingyun; Wang, Xiaolin; Hu, Wangyu; Yang, Jianyu

2009-03-01

272

Molecular dynamics investigation of water permeation through nanopores

NASA Astrophysics Data System (ADS)

Molecular dynamics (MD) simulations are carried out to investigate the permeation of nanometer-sized cylindrical pores connecting two reservoirs, by water molecules and by a reference Lennard-Jones fluid. Water molecules penetrate a channel of fixed length only beyond a minimum radius. Near threshold, permeation is found to be intermittent and sensitive to other physical parameters, including the polarizability of the medium (e.g., a cell membrane) embedding the channel. Once the molecules fill the pore, the confined water exhibits properties (mean density, diffusivity, hydrogen bonding) surprisingly close to those of the bulk. The intermittent behavior near the threshold is analyzed in terms of a Landau-like grand potential regarded as a function of the pore occupancy. The grand potential, which is determined using a biased sampling technique, generally exhibits two minima, associated with the ``empty'' and ``filled'' states, separated by a potential barrier (transition state). No intermittent filling of identical pores is observed in the possible case of the reference Lennard-Jones fluid over a wide range of physical conditions, pointing to the specific role of hydrogen bonding for intermittent behavior. A careful analysis of the MD-generated configurations shows that the filled state nucleates around a chain of hydrogen-bonded molecules spanning the pore.

Allen, Rosalind; Hansen, Jean-Pierre; Melchionna, Simone

2003-08-01

273

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.

2013-01-01

274

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

275

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

276

Protein-Folding Dynamics: Overview of Molecular Simulation Techniques

Molecular dynamics (MD) is an invaluable tool with which to study protein folding in silico. Although just a few years ago the dynamic behavior of a protein molecule could be simulated only in the neighborhood of the experimental conformation (or protein unfolding could be simulated at high temperature), the advent of distributed computing, new techniques such as replica-exchange MD, new

Harold A. Scheraga; Mey Khalili; Adam Liwo

2007-01-01

277

Ion clustering in molecular dynamics simulations of sodium iodide solutions

Model systems of sodium iodide dissolved in dimethyl ether or 1,2-dimethoxyethane (glyme) were studied in order to investigate the structural and dynamic properties of ionic solutions in small and polymeric ethers. Full molecular dynamics simulations were performed at a range of different salt concentrations. An algorithm was designed which assigns ions to clusters and then calculates all the terms which

Vilia Ann Payne; Jian-Hua Xu; Maria Forsyth; Mark A. Ratner; Duward F. Shriver; Simon W. de Leeuw

1995-01-01

278

Multiple ionization and fragmentation dynamics of molecular iodine studied in

Multiple ionization and fragmentation dynamics of molecular iodine studied in IRï¿½XUV pump The ionization and fragmentation dynamics of iodine molecules (I2) are traced using very intense ($1014 W cmï¿½2 ) ultra-short ($60 fs) light pulses with 87 eV photons of the Free- electron LASer at Hamburg (FLASH

Kling, Matthias

279

Grain boundary migration in metals: Molecular dynamics simulations

Grain boundary migration is key to materials microstructural processes such as grain growth and recrystallization. Quantitative boundary dynamic data is difficult to obtain, yet important for quantitative prediction of microstructural evolution and understanding migration fundamentals. Our molecular dynamics simulations first focus on curvature driven grain boundary migration to extract the reduced mobility and activation energy for migration as a function

Hao Zhang

2005-01-01

280

Molecular dynamics simulations of the mechanical properties of monoclinic hydroxyapatite.

Inorganic biomedical materials are of great interest in the biomedical field. One such material, hydroxyapatite (HAP), is the main inorganic substance in the hard tissue of bones and teeth in the human body. Until recently, studies of the mechanical properties of HAP by uniaxial tension testing and compression molecular dynamics (MD) simulation had remained difficult. In addition, electric charges used in such simulations alter the molecular structure of HAP. Here, we present the mechanical properties and new charges of the monoclinic form of HAP using the self-consistent charge equilibration (QEq) scheme proposed by Rappé and Goddard in 1991 (J Phys Chem 95:3358-3363), and a successful MD simulation of the uniaxially tensile and compressive properties of monoclinic HAP. Also presented is the change in potential energy in the cell and how temperature and strain rate affect the uniaxial tension and compressive properties of HAP. Additionally, we compare the mechanical properties of this substance along different directions, and some conclusions useful for further studies of the mechanical properties of HAP composite materials are discussed. PMID:25352517

Ou, Xiang; Han, Qiang

2014-11-01

281

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

282

NASA Astrophysics Data System (ADS)

The constraint of time-integrated zero area on the laser field is a fundamental requirement, both theoretically and experimentally, in the control of molecular dynamics. By using techniques of local and optimal control theory, we show how to enforce this constraint in two benchmark control problems, namely, molecular orientation and photofragmentation. The origin and the physical implications for the dynamics of this zero-area control field are discussed.

Sugny, Dominique; Vranckx, Stéphane; Ndong, Mamadou; Vaeck, Nathalie; Atabek, Osman; Desouter-Lecomte, Michèle

2014-11-01

283

Molecular dynamics simulations of proteins in lipid bilayers.

With recent advances in X-ray crystallography of membrane proteins promising many new high-resolution structures, molecular dynamics simulations will become increasingly valuable for understanding membrane protein function, as they can reveal the dynamic behavior concealed in the static structures. Dramatic increases in computational power, in synergy with more efficient computational methodologies, now allow us to carry out molecular dynamics simulations of any structurally known membrane protein in its native environment, covering timescales of up to 0.1 micros. At the frontiers of membrane protein simulations are ion channels, aquaporins, passive and active transporters, and bioenergetic proteins. PMID:16043343

Gumbart, James; Wang, Yi; Aksimentiev, Alekseij; Tajkhorshid, Emad; Schulten, Klaus

2005-08-01

284

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

285

GROMACS: A message-passing parallel molecular dynamics implementation

NASA Astrophysics Data System (ADS)

A parallel message-passing implementation of a molecular dynamics (MD) program that is useful for bio(macro)molecules in aqueous environment is described. The software has been developed for a custom-designed 32-processor ring GROMACS (GROningen MAchine for Chemical Simulation) with communication to and from left and right neighbours, but can run on any parallel system onto which a a ring of processors can be mapped and which supports PVM-like block send and receive calls. The GROMACS software consists of a preprocessor, a parallel MD and energy minimization program that can use an arbitrary number of processors (including one), an optional monitor, and several analysis tools. The programs are written in ANSI C and available by ftp (information: gromacs@chem.rug.nl). The functionality is based on the GROMOS (GROningen MOlecular Simulation) package (van Gunsteren and Berendsen, 1987; BIOMOS B.V., Nijenborgh 4, 9747 AG Groningen). Conversion programs between GROMOS and GROMACS formats are included. The MD program can handle rectangular periodic boundary conditions with temperature and pressure scaling. The interactions that can be handled without modification are variable non-bonded pair interactions with Coulomb and Lennard-Jones or Buckingham potentials, using a twin-range cut-off based on charge groups, and fixed bonded interactions of either harmonic or constraint type for bonds and bond angles and either periodic or cosine power series interactions for dihedral angles. Special forces can be added to groups of particles (for non-equilibrium dynamics or for position restraining) or between particles (for distance restraints). The parallelism is based on particle decomposition. Interprocessor communication is largely limited to position and force distribution over the ring once per time step.

Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R.

1995-09-01

286

Dynamical analysis of highly excited molecular spectra

The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.

Kellman, M.E. [Univ. of Oregon, Eugene (United States)

1993-12-01

287

Molecular Diagnosis of Diarrhea: Current Status and Future Potential

Determining the microbiologic etiology of enteric infection remains an elusive goal. Conventional approaches, including culture, microscopy, and antigen-based tests have significant limitations such as limit of detection and the need for multiple procedures. Molecular diagnostics, especially PCR based tests, are rapidly changing research and practice in infectious diseases. Diarrheal disease, with its broad range of potential infectious etiologies, is well suited for multiplex molecular testing. This review highlights examples of currently employed molecular tests, as well as ways in which these tests can be applied in the future. The absence of a gold standard for the microbiologic cause of diarrhea means that the clinical significance of detected organisms may not always be clear. Conventional wisdom is that there should be one main pathogen causing diarrhea, however our thinking is challenged by increased detection of mixed infections. Thus, the successful incorporation of molecular diagnostics for diarrheal disease into practice will require both a careful understanding of the technical aspects and research to define their clinical utility. PMID:22116640

Platts-Mills, James A; Operario, Darwin J

2011-01-01

288

i-PI: A Python interface for ab initio path integral molecular dynamics simulations

Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high pressure water.

Ceriotti, Michele; Manolopoulos, David E

2014-01-01

289

The molecular tweezers (1, 2) and clips (3-7) containing naphthalene and benzene spacer units can be synthesized via repetitive Diels-Alder reactions by the use of a molecular "Lego" set consisting of bisdienophiles (8, 9, 14) and dienes (10, 13). The new receptors selectively bind electron-deficient neutral and cationic substrates in solution. Only the benzene-spaced tweezers form complexes with aliphatic substrates, whereas the other receptors bind aromatic substrates preferentially. HPLC studies with 1 and 2 chemically bonded to stationary phases give similar results for the heterogeneous systems. The formation of stable complexes between the water-soluble clip 5g and N-alkylpyridinium cations, such as N-methylnicotinamide and NAD(+), in aqueous solution illustrates the importance of the hydrophobic effect for arene-arene interactions. The dynamics of the complex formation and substrate mobility were investigated by the use of temperature-dependent liquid- and solid-state NMR spectroscopy. The electrostatic potential surface (EPS) of 1-7 is calculated to be surprisingly negative on the concave side of each molecule and, hence, complementary to the EPS of the electron-deficient substrates, suggesting that the attractive receptor-substrate interaction is here of predominantly electrostatic nature. PMID:14674783

Klärner, Frank-Gerrit; Kahlert, Björn

2003-12-01

290

Accelerated Molecular Dynamics Simulation on Friction of Incommensurate Interfaces

NASA Astrophysics Data System (ADS)

We apply a molecular dynamics (MD) methodology to study the friction of incommensurate interfaces. While the traditional Tomlinson model assumes a single, repeatable transition, the sliding at the real incommensurate interface is comprised of a multitude of transition modes. This may account for recent Atomic Force Microscope (AFM) experimental results that indicate more complex temperature and velocity dependence of friction that deviate from the Tomlinson predictions. Conventional MD simulations are unable to simulate a wide range of sliding rates due to time scale limitations. In this study, we achieve decreases in the simulated sliding velocity by several orders of magnitude compared with conventional MD simulations using Voter's hyperdynamics scheme. This method uses a biased potential to reduce the barrier heights of the original potential to decrease the simulated time between slip events. The decrease in the sliding velocity makes it possible to see the atomic level processes during sliding speeds much closer to the experimental time scale. We carefully analyze the simulation results to elucidate the transition mechanisms.

Kim, Woo Kyun; Falk, Michael

2009-03-01

291

Flooding in GROMACS: accelerated barrier crossings in molecular dynamics.

The major bottleneck of today's atomistic molecular dynamics (MD) simulations is that because of the enormous computational effort involved, only processes at nanoseconds to microseconds time scales or faster can be studied directly. Unfortunately, apart from a few exceptions, relevant processes, such as chemical reactions or many large scale conformational transitions in proteins, occur at slower time scales and therefore are currently far out of reach for conventional MD. The flooding technique addresses this problem by inclusion of a flooding potential into the force field. This flooding potential locally destabilizes the educt state and thereby significantly accelerates the escape from the initial energy well without affecting the reaction pathway. Here, we summarize the theory and method for the computational chemistry community and detail the implementation within the official version 3.3 of the freely available MD program package GROMACS. Two examples shall demonstrate the application of flooding to accelerate conformational transitions and chemical reactions. The second example was carried out within a QM/MM framework. PMID:16900489

Lange, Oliver F; Schäfer, Lars V; Grubmüller, Helmut

2006-11-15

292

Molecular dynamics studies of radiation effects in silicon carbide

We discuss results of molecular dynamics computer simulation studies of 3 keV and 5 keV displacement cascades in {beta}-SIC, and compare them to results of 5 keV cascades in pure silicon. The SiC simulations are performed with the Tersoff potential. For silicon we use the Stillinger-Weber potential. Simulations were carried out for Si recoils in 3 dimensional cubic computational cells With periodic boundary conditions and up to 175,616 atoms. The cascade lifetime in SiC is found to be extremely short. This, combined with the high melting temperature of SiC, precludes direct lattice amorphization during the cascade. Although large disordered regions result, these retain their basic crystalline structure. These results are in contrast with observations in pure silicon where direct-impact amorphization from the cascade is seen to take place. The SiC results also show anisotropy in the number of Si and C recoils as well as in the number of replacements in each sublattice. Details of the damage configurations obtained will be discussed.

Diaz de la Rubia, T.; Caturla, M.J.; Tobin, M.

1995-01-01

293

NASA Astrophysics Data System (ADS)

MDMC2 is a parallel code for performing molecular dynamics simulations on multiply charged clusters. It is a valuable complement to MCMC2, a Monte Carlo program devoted to Monte Carlo simulations of multiply charged clusters in the NVT ensemble (Bonhommeau and Gaigeot, 2013). Both MCMC2 and MDMC2 codes employ a mesoscopic coarse-grained simplified representation of the clusters (or droplets): these clusters are composed of neutral and charged spherical particles/grains that may be polarisable. One grain can be either neutral or charged. The interaction potential is a sum of 2-body Lennard-Jones potentials (main cohesive contribution) and electrostatic terms (repulsive contribution), possibly supplemented by N-body polarisation interactions. There is no restriction imposed on the values of the particle charges and/or polarisabilities. An external field can also be applied to the whole system. The derivatives of the potential energy-surface are determined analytically which ensures an accurate integration of classical equations of motion by a velocity Verlet algorithm. Conservation rules, such as energy conservation or centre-of-mass linear momentum conservation, can be steadily checked during the simulation. The program also provides some statistical information on the run and configuration files that can be used for data post-treatment. MDMC2 is provided with a serial conjugate gradient program, called CGMC2, that uses the same analytical derivatives as MDMC2 and was found useful to probe the minima of the energy landscape explored during Monte Carlo or molecular dynamics simulations performed on multiply charged clusters.

Bonhommeau, David A.; Gaigeot, Marie-Pierre

2014-02-01

294

Massively parallel molecular dynamics simulations of two-dimensional materials at high strain rates

NASA Astrophysics Data System (ADS)

Large scale molecular dynamics simulations on a massively parallel computer are performed to investigate the mechanical behavior of 2-dimensional materials. A pair potential and a model embedded atom many-body potential are examined, corresponding to 'brittle' and 'ductile' materials, respectively. A parallel molecular dynamics (MD) algorithm is developed to exploit the architecture of the Connection Machine, enabling simulations of greater than 10(exp 6) atoms. A model spallation experiment is performed on a 2-D triagonal crystal with a well-defined nanocrystalline defect on the spall plane. The process of spallation is modeled as a uniform adiabatic expansion. The spall strength is shown to be proportional to the logarithm of the applied strain rate and a dislocation dynamics model is used to explain the results. Good predictions for the onset of spallation in the computer experiments is found from the simple model. The nanocrystal defect affects the propagation of the shock front and failure is enhanced along the grain boundary.

Wagner, N. J.; Holian, B. L.

1992-11-01

295

Scaling of the Local Dynamics and the Intermolecular Potential

The experimental fact that relaxation times, tau, of supercooled liquids and polymers are uniquely defined by the quantity TV^g, where T is temperature, V specific volume, and g a material constant, leads to a number of interpretations and predictions concerning the dynamics of vitrification. Herein we examine means to determine the scaling exponent g apart from the usual superpositioning of relaxation data. If the intermolecular potential can be approximated by an inverse power law, as implied by the TV^g scaling, various equations are derived relating g to the Gruneisen parameter and to a common expression for the pressure derivative of the glass temperature. In addition, without assumptions, g can be obtained directly from pressure-volume-temperature data. These methods for determining g from molecular or thermodynamic properties are useful because they enable the P- and V-dependences of tau to be obtained, and thereby various analyses of the dynamics to be explored, without the need to carry out relaxation measurements beyond ambient pressure.

C. M. Roland; J. L. Feldman; R. Casalini

2006-02-06

296

Modeling ramp compression experiments using large-scale molecular dynamics simulation.

Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.

Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I. (University of California, San Diego); Winey, J. Michael (Washington State University); Gupta, Yogendra Mohan (Washington State University); Lane, J. Matthew D.; Ditmire, Todd (University of Texas at Austin); Quevedo, Hernan J. (University of Texas at Austin)

2011-10-01

297

NASA Astrophysics Data System (ADS)

Molecular dynamics (MD) simulations of united atom models for alkane melts are compared with a recently developed theory for calculating the memory functions of flexible polymers. The theory is based upon an approximate solution of the diffusion equation without hydrodynamic interactions. The polymer dynamics are described by using time correlation functions which are expressed in terms of a set of equilibrium averages and the approximate eigenvalues and eigenfunctions of the diffusion operator. For flexible enough chains with sufficiently high molecular weight, the hydrodynamic interactions are screened, and the simplified solvent model used by the theory is expected to be adequate. The only parameter not defined by the MD simulations is the bead friction coefficient ?. In the limit of weak hydrodynamic interactions (Rouse dynamics), ? can be determined from the molecular diffusion coefficient by applying the Rouse relation D=kT/N?R. Given this choice of ?R, the time correlation functions computed from the theory are compared with those obtained directly from the MD simulations. Excellent agreement with the simulations is found for all correlation functions and all times for the decane dynamics, provided the theory employs one scale factor to increase ?R and, hence, to compensate for the inadequacy of the Rouse relation. The same picture holds for hexadecane and triacontane (C30H62) but with smaller scale factors. Scaling becomes unnecessary for C44H90 which is long enough for the crossover to Rouse dynamics for D to be almost complete. Very good agreement (after appropriate scaling of ?R) also emerges between theory and simulations for several branched alkanes with carbon numbers C25-C30. Computations for hexadecane at different temperatures show that the scale factors may be weakly temperature dependent.

Kostov, Konstantin S.; Freed, Karl F.; Webb, Edmund B.; Mondello, Maurizio; Grest, Gary S.

1998-06-01

298

NASA Astrophysics Data System (ADS)

Twenty years ago at the APS March Meeting, Kurt Kremer and I presented the first numerical evidence from computer simulations that the reptation model of Edwards and de Gennes correctly describes the dynamics of entangled linear polymer melts. For chains longer than the entanglement length Ne, the monomers of a chain move predominantly along their own contour. The distinctive signature of reptation dynamics, which we observed, was that on intermediate time scales, the mean squared displacement of a monomer increases with time as t^ 1/4. Though these early simulations were limited to chains of a few Ne, they demonstrated the potential of computer simulations to contribute to our understanding of polymer dynamics. Here I will review the progress over the past twenty years and present an outlook for the future in modeling entangled polymer melts and networks. With present day computers coupled with efficient parallel molecular dynamics codes, it is now possible to follow the equilibrium dynamics of chains of length 10-20Ne from the early Rouse regime to the long time diffusive regime. Result of these simulations support the earlier results obtained on chains of only a few Ne. Further evidence for the tube models of polymer dynamics has been obtained by identifying the primitive path mesh that characterizes the microscopic topological state of the computer- generated conformations of the chains. In particular, the plateau moduli derived on the basis of this analysis quantitatively reproduce experimental data for a wide spectrum of entangled polymer liquids including semi-dilute theta solutions of synthetic polymers, the corresponding dense melts, and solutions of semi-flexible (bio)polymers such as f-actin or suspensions of rodlike viruses. We also find that in agreement with the reptation model, the stress, end-to-end distance and entanglement length of an entangled melt subjected to uniaxial elongation, all relax on the same time scale.

Grest, Gary S.

2008-03-01

299

Molecular dynamics simulations are performed on the atomic origin of the evolution of residual stress in tetrahedral amorphous\\u000a carbon (ta-C) film using the empirical Tersoff potential. The densities of and residual stresses in the amorphous films generated\\u000a by molecular dynamics simulations were found to be in good agreement with the corresponding experimental results. A radial\\u000a distribution function analysis shows that

Kyung-Soo Kim; Seung-Hyeob Lee; Yoo-Chan Kim; Seung-Cheol Lee; Pil-Ryung Cha; Kwang-Ryeol Lee

2008-01-01

300

Dynamics of Molecular Hydrogen in Hypersaline Microbial Mars

NASA Technical Reports Server (NTRS)

Early Earth microbial communities that centered around the anaerobic decomposition of organic molecular hydrogen as a carrier of electrons, regulator of energy metabolism, and facilitator of syntroph'c microbial interactions. The advent of oxygenic photosynthetic organisms added a highly dynamic and potentially dominant term to the hydrogen economy of these communities. We have examined the daily variations of hydrogen concentrations in cyanobacteria-dominated microbial mats from hypersaline ponds in Baja California Sur, Mexico. These mats bring together phototrophic and anaerobic bacteria (along with virtually all other trophic groups) in a spatially ordered and chemically dynamic matrix that provides a good analog for early Earth microbial ecosystems. Hydrogen concentrations in the photic zone of the mat can be three orders of magnitude or more higher than in the photic zone, which are, in turn, an order of magnitude higher than in the unconsolidated sediments underlying the mat community. Within the photic zone, hydrogen concentrations can fluctuate dramatically during the diel (24 hour day-night) cycle, ranging from less than 0.001% during the day to nearly 10% at night. The resultant nighttime flux of hydrogen from the mat to the environment was up to 17% of the daytime oxygen flux. The daily pattern observed is highly dependent on cyanobacterial species composition within the mat, with Lyngbya-dominated systems having a much greater dynamic range than those dominated by Microcoleus; this may relate largely to differing degrees of nitrogen-fixing and fermentative activity in the two mats. The greatest H2 concentrations and fluxes were observed in the absence of oxygen, suggesting an important potential feedback control in the context of the evolution of atmospheric composition. The impact of adding this highly dynamic photosynthetic term to the hydrogen economy of early microbial ecosystems must have been substantial. From an evolutionary standpoint, the H2 generated in mats could have represented a very important new source of electrons and energy - but one that could not be harnessed without substantial adaptation to the highly variable chemistry of the mat surface. In addition, the emergent chemistry of anaerobic communities is often highly dependent on ambient hydrogen concentrations, so that incorporation of these communities into photosynthetic mats could have significantly affected the composition and flux of reduced "biosignature' gases to the environment.

Hoehler, Tori M.; Bebout, Brad M.; Visscher, Pieter T.; DesMarais, David J.; DeVincenzi, Donald L. (Technical Monitor)

2000-01-01

301

Hydrolysis of Al3+ from constrained molecular dynamics

NASA Astrophysics Data System (ADS)

We investigated the hydrolysis reactions of Al3+ in AlCl3 aqueous solution using the constrained molecular dynamics based on the Car-Parrinello molecular-dynamics method. By employing the proton-aluminum coordination number as a reaction coordinate in the constrained molecular dynamics the deprotonation as well as dehydration processes are successfully realized. From our free-energy difference of ?G0~=8.0 kcal mol-1 the hydrolysis constant pKa1 is roughly estimated as 5.8, comparable to the literature value of 5.07. We show that the free-energy difference for the hydrolysis of Al3+ in acidic conditions is at least 4 kcal mol-1 higher than that in neutral condition, indicating that the hydrolysis reaction is inhibited by the presence of excess protons located around the hydrated ion, in agreement with the change of the predominant species by pH.

Ikeda, Takashi; Hirata, Masaru; Kimura, Takaumi

2006-02-01

302

Polarizability anisotropy relaxation in liquid ethanol: A molecular dynamics study

Molecular dynamics simulation is used to study the relaxation of the polarizability anisotropy in liquid ethanol at temperatures of 298 and 348 K. Ethanol molecules are represented by a four-site semi-flexible model in which the internal degree of freedom, corresponding to the torsional motion around the C-O bond, is taken into consideration. The molecular polarizability is calculated using an interaction-site

Marco Paolantoni; Branka M. Ladanyi

2002-01-01

303

Population Dynamics and Harvest Potential of Mountain

The understanding of population dynamics is a central issue for managing large mammals. Modeling has allowed population ecologists to increase their knowledge about complex systems and better predict population responses to diverse perturbations. Mountain goats (Oreamnos americanus) appear sensitive to harvest, but the relative influence of survival and reproductive rates on their population dynamics are not well understood. Using longitudinal

SANDRA HAMEL; STEEVE D. COTE; MARCO FESTA-BIANCHET

304

Dynamic Assessment in Educational Settings: Realising Potential.

ERIC Educational Resources Information Center

Makes the case for dynamic assessment, in which individualized instruction and feedback are built into the testing process. Urges the use of dynamic approaches to help psychologists and teachers collaborate on classroom-based interventions. Calls for studies to examine the utility of approaches. An appendix identifies target group, nature, and…

Elliott, Julian

2003-01-01

305

NASA Astrophysics Data System (ADS)

The Fokker-Planck (FP) equation describing the dynamics of a single Brownian particle near a fixed external surface is derived using the multiple-time-scales perturbation method, previously used by Cukier and Deutch and Nienhuis in the absence of any external surfaces, and Piasecki et al. for two Brownian spheres in a hard fluid. The FP equation includes an explicit expression for the (time-independent) particle friction tensor in terms of the force autocorrelation function and equilibrium average force on the particle by the surrounding fluid and in the presence of a fixed external surface, such as an adsorbate. The scaling and perturbation analysis given here also shows that the force autocorrelation function must decay rapidly on the zeroth-order time scale ? 0, which physically requires N Kn?1, where N Kn is the Knudsen number (ratio of the length scale for fluid intermolecular interactions to the Brownian particle length scale). This restricts the theory given here to liquid systems where N Kn?1. For a specified particle configuration with respect to the external surface, equilibrium canonical molecular dynamics (MD) calculations are conducted, as shown here, in order to obtain numerical values of the friction tensor from the force autocorrelation expression. Molecular dynamics computations of the friction tensor for a single spherical particle in the absence of a fixed external surface are shown to recover Stokes' law for various types of fluid molecule-particle interaction potentials. Analytical studies of the static force correlation function also demonstrate the remarkable principle of force-time parity whereby the particle friction coefficient is nearly independent of the fluid molecule-particle interaction potential. Molecular dynamics computations of the friction tensor for a single spherical particle near a fixed external spherical surface (adsorbate) demonstrate a breakdown in continuum hydrodynamic results at close particle-surface separation distances on the order of several molecular diameters.

Peters, Michael H.

1999-02-01

306

Femtosecond molecular dynamics studied with vacuum ultraviolet pulse pairs

NASA Astrophysics Data System (ADS)

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

Allison, Thomas K., III

307

Driving ordering processes in molecular-dynamics simulations.

Self-organized criticality describes the emergence of complexity in dynamical nonequilibrium systems. In this paper we introduce a unique approach whereby a driven energy conversion is utilized as a sampling bias for ordered arrangements in molecular dynamics simulations of atomic and molecular fluids. This approach gives rise to dramatically accelerated nucleation rates, by as much as 30 orders of magnitude, without the need of predefined order parameters, which commonly employed rare-event sampling methods rely on. The measured heat fluxes suggest how the approach can be generalized. PMID:24877946

Dittmar, Harro; Kusalik, Peter G

2014-05-16

308

Driving Ordering Processes in Molecular-Dynamics Simulations

NASA Astrophysics Data System (ADS)

Self-organized criticality describes the emergence of complexity in dynamical nonequilibrium systems. In this paper we introduce a unique approach whereby a driven energy conversion is utilized as a sampling bias for ordered arrangements in molecular dynamics simulations of atomic and molecular fluids. This approach gives rise to dramatically accelerated nucleation rates, by as much as 30 orders of magnitude, without the need of predefined order parameters, which commonly employed rare-event sampling methods rely on. The measured heat fluxes suggest how the approach can be generalized.

Dittmar, Harro; Kusalik, Peter G.

2014-05-01

309

State-to-state dynamics of molecular energy transfer

The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.

Gentry, W.R.; Giese, C.F. [Univ. of Minnesota, Minneapolis (United States)

1993-12-01

310

Review on Molecular and Therapeutic Potential of Thymoquinone in Cancer

Thymoquinone (TQ) is the predominant bioactive constituent present in black seed oil (Nigella sativa) and has been tested for its efficacy against cancer. Here, we summarize the literature about TQ’s molecular mechanism of action and its ability to induce apoptosis and inhibit tumor growth in preclinical models. TQ has anti-inflammatory effects, and it inhibits tumor cell proliferation through modulation of apoptosis signaling, inhibition of angiogenesis, and cell cycle arrest. Chemosensitization by TQ is mostly limited to in vitro studies, and it has potential in therapeutic strategy for cancer. The results favor efficacy and enhancement of therapeutic benefit against tumor cells resistant to therapy based on cellular targets that are molecular determinants for cancer cell survival and progression. There have been attempts to synthesize novel analogs of TQ directed toward superior effects in killing tumor cells with more enhanced chemosensitizing potential than parent TQ compound. Based on published reports, we believe that further in-depth studies are warranted including investigation of its bioavailability and Phase I toxicity profiling in human subjects. The results from such studies will be instrumental in advancing this field in support of initiating clinical trials for testing the effects of this ancient agent in cancer therapy. PMID:20924969

Banerjee, Sanjeev; Padhye, Subhash; Azmi, Asfar; Wang, Zhiwei; Philip, Philip A.; Kucuk, Omer; Sarkar, Fazlul H.; Mohammad, Ramzi M.

2014-01-01

311

VUV studies of molecular photofragmentation dynamics

State-resolved, photoion and photoelectron methods are used to study the neutral fragmentation and ionization dynamics of small molecules relevant to atmospheric and combustion chemistry. Photodissociation and ionization are initiated by coherent VUV radiation and the fragmentation dynamics are extracted from measurements of product rovibronic state distributions, kinetic energies and angular distributions. The general aim of these studies is to investigate the multichannel interactions between the electronic and nuclear motions which determine the evolution of the photoexcited {open_quotes}complex{close_quotes} into the observed asymptotic channels.

White, M.G. [Brookhaven National Laboratory, Upton, NY (United States)

1993-12-01

312

NASA Astrophysics Data System (ADS)

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

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

2011-09-01

313

Imaging the molecular dynamics of dissociative electron attachment to water

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

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

2009-10-19

314

Electron trapping in amorphous silicon: A quantum molecular dynamics study

Quantum molecular dynamics (QMD) simulations provide the real-time dynamics of electrons and ions through numerical solutions of the time-dependent Schrodinger and Newton equations, respectively. Using the QMD approach we have investigated the localization behavior of an excess electron in amorphous silicon at finite temperatures. For time scales on the order of a few picoseconds, we find the excess electron is localized inside a void of radius {approximately}3 {Angstrom} at finite temperatures. 12 refs.

Yang, Lin H.; Kalia, R.K.; Vashishta, P.

1990-12-01

315

Molecular Dynamics Simulation of Amyloid ? Dimer Formation

Recent experiments with amyloid ? (A?) peptide indicate that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of A? oligomers depends on their structure, which is governed by assembly dynamics. Due to limitations of current experimental techniques, a detailed knowledge of oligomer structure at the atomic level is missing. We introduce

B. Urbanc; L. Cruz; F. Ding; D. Sammond; S. Khare; S. V. Buldyrev; H. E. Stanley; N. V. Dokholyany

2004-01-01

316

Dynamic molecular processes mediate cellular mechanotransduction

Cellular responses to mechanical forces are crucial in embryonic development and adult physiology, and are involved in numerous diseases, including atherosclerosis, hypertension, osteoporosis, muscular dystrophy, myopathies and cancer. These responses are mediated by load-bearing subcellular structures, such as the plasma membrane, cell-adhesion complexes and the cytoskeleton. Recent work has demonstrated that these structures are dynamic, undergoing assembly, disassembly and movement,

Brenton D. Hoffman; Carsten Grashoff; Martin A. Schwartz

2011-01-01

317

Dynamic Deformation of Multiwall Nanotubes and Ropes by Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Dynamic deformation of single- and multi-wall nanotubes and nanotube ropes have been studied through large scale molecular dynamics simulations using the Brenner many-body potential for carbon-carbon interactions. Intertube interactions are modeled with additional two-body long-range interactions which keep the tube separation to about 3.5A until the deforming forces become too large. Multiwall nanotube and rope deformation are studied for compressive, bending and torsional strains. ( D.Srivastava and S. T. Barnard, Super Computing 97 (1997)) For bending and torsional strains we find that multiwall tubes are stiffer than the comparative single wall nanotubes. For compressive strains, a more complex behavior is observed. All tubes show well defined structural instabilities when subjected to dynamic deformations which are analyzed as a function of the applied strain. Finally, a nanotube rope is deformed through similar mechanisms and an estimation is made of the longitudinal and transverse strains needed to split a rope into the constituent nanotubes.

Srivastava, Deepak; Barnard, Stephen T.

1998-03-01

318

Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes

Triclocarban and triclosan, two potent antibacterial molecules present in many consumer products, have been subject to growing debate on a number of issues, particularly in relation to their possible role in causing microbial resistance. In this computational study, we present molecular-level insights into the interaction between these antimicrobial agents and hydrated phospholipid bilayers (taken as a simple model for the cell membrane). Simulations are conducted by a novel ‘dual-resolution’ molecular dynamics approach which combines accuracy with efficiency: the antimicrobials, modelled atomistically, are mixed with simplified (coarse-grain) models of lipids and water. A first set of calculations is run to study the antimicrobials' transfer free energies and orientations as a function of depth inside the membrane. Both molecules are predicted to preferentially accumulate in the lipid headgroup–glycerol region; this finding, which reproduces corresponding experimental data, is also discussed in terms of a general relation between solute partitioning and the intramembrane distribution of pressure. A second set of runs involves membranes incorporated with different molar concentrations of antimicrobial molecules (up to one antimicrobial per two lipids). We study the effects induced on fundamental membrane properties, such as the electron density, lateral pressure and electrical potential profiles. In particular, the analysis of the spontaneous curvature indicates that increasing antimicrobial concentrations promote a ‘destabilizing’ tendency towards non-bilayer phases, as observed experimentally. The antimicrobials' influence on the self-assembly process is also investigated. The significance of our results in the context of current theories of antimicrobial action is discussed. PMID:21131331

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

2011-01-01

319

Molecular dynamics modelling of radiation damage in zircon

NASA Astrophysics Data System (ADS)

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

Grechanovsky, A. E.

2009-04-01

320

NASA Astrophysics Data System (ADS)

Oxidation of a flat aluminum (111) surface and the reactive wetting of the aluminum (Al) droplet on a flat alumina (alpha-Al2O 3) surface are investigated by using parallel molecular-dynamics simulations with dynamic charge transfer among atoms on a microscopic length scale. The interatomic potential, based on the formalism of Streitz and Mintmire, allows atoms to vary their charges dynamically between anions and cations, when atoms move and their local environment is altered. We investigate the oxidation thickness as a function of time and the oxygen density which is 10--40 times that of the normal state (1 atm and 300 K). Stable amorphous oxide scales form around 51 A at 4.42 ns, 2.862 ns, and 2.524 ns, respectively, and molecular oxygen density 10--40 times the normal state. We also study structural correlations in the resulting final oxide scale. The structure of final oxide scales depend on depth, where density of aluminum (Al) and oxygen (0) atoms change. Reactive wetting of aluminum nanodroplet on alumina surface is also studied using parallel MD. We study heat transfer, diffusion within droplet, and the structure of the inter-metallic phases in the liquid-solid interface. Oxygen (0) atoms diffuse into the spherical aluminum (Al) droplet and form an interface between the flat solid substrate and the Al droplet. This diffusion of oxygen atoms may be the main source of adhesion between the Al drop and the flat alpha-Al 2O3 substrate. The temperature in the flat alpha-Al 2O3 bulk substrate rises from OK to 200 K at the end of the simulation, 8.5 ps, but the temperature becomes much higher at the reactive interface. We have examined which oxygen atoms from the substrate participate in the wetting and the formation of a solder joint at the Al/alpha-Al 2O3 interface.

Aral, Gurcan

321

Employing nonequilibrium molecular dynamics simulations, a comprehensive computational study of the photoinduced conformational dynamics of a photoswitchable bicyclic azobenzene octapeptide is presented. The calculation of time-dependent probability distributions along various global and local reaction coordinates reveals that the conformational rearrangement of the peptide is rather complex and occurs on at least four timescales: 1) After photoexcitation, the azobenzene unit of the molecule undergoes nonadiabatic photoisomerization within 0.2 ps. 2) On the picosecond timescale, the cooling (13 ps) and the stretching (14 ps) of the photoexcited peptide is observed. 3) Most reaction coordinates exhibit a 50–100 ps component reflecting a fast conformational rearrangement. 4) The 500–1000 ps component observed in the simulation accounts for the slow diffusion-controlled conformational equilibration of the system. The simulation of the photoinduced molecular processes is in remarkable agreement with time-resolved optical and infrared experiments, although the calculated cooling as well as the initial conformational rearrangements of the peptide appear to be somewhat too slow. Based on an ab initio parameterized vibrational Hamiltonian, the time-dependent amide I frequency shift is calculated. Both intramolecular and solvent-induced contributions to the frequency shift were found to change by \\documentclass[10pt]{article} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\pagestyle{empty} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} \\begin{equation*}{\\lesssim}2{\\mathrm{cm}}^{-1}\\end{equation*}\\end{document}, in reasonable agreement with experiment. The potential of transient infrared spectra to characterize the conformational dynamics of peptides is discussed in some detail. PMID:16731560

Nguyen, Phuong H.; Gorbunov, Roman D.; Stock, Gerhard

2006-01-01

322

NASA Astrophysics Data System (ADS)

Molecular dynamics (MD) simulations were used to examine elastic shock wave propagation in aluminum single crystals along [100], [110] and [111] directions using four different embedded-atom method potentials. Continuum variables extracted from MD results show that stresses, densities, and temperatures for [100] shock propagation are significantly different for the various potentials, while the results for [110] and [111] propagation are similar for three of the four potentials. Overall, the recent potential by Winey, Kubota and Gupta [MSMSE 17, 055004 (2009)] provides the best agreement with nonlinear elastic calculations that include elastic constants up to fourth order. Our MD-continuum approach provides a key step in establishing the applicability of classical MD potentials for dynamic compression. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Zimmerman, J. A.; Winey, J. M.; Gupta, Y. M.

2011-06-01

323

Large-Scale Molecular Dynamics Simulation of Polyolefin Blends

NASA Astrophysics Data System (ADS)

Molecular dynamics (MD) simulations were carried out on the binary blends of five polyolefins: head-to-tail isotactic (iPP) and syndiotactic (sPP) polypropylene, head-to-head polypropylene (hhPP), polyisobutylene (PIB), and polyethylene (PE). These polyolefins were modeled at the united atom level at 453K using the TRaPPE potential between pairs of sites. Surprisingly, the heat of mixing for all the blends was found to depend not only on the intermolecular van der Waals contributions, but also on intramolecular van der Waals, angular bending, and torsional components. The i parameters from the simulations were estimated from the structure factors using the random phase approximation (RPA) in analogy with neutron scattering (SANS) experiments. The MD simulations predicted temperature dependent i parameters in good agreement with SANS measurements previously reported on hhPP/PIB, hhPP/PP, and hhPP/PE. Intermolecular pair correlation functions were used to compare chain packing in the melts and blends.

Jaramillo, Eugenio; Grest, Gary S.; Curro, John G.; Wu, David T.

2003-03-01

324

Molecular dynamics study of melting of the hcp metal Mg

NASA Astrophysics Data System (ADS)

We present molecular dynamics simulations of the melting transition of Mg, an hcp metal, using the potential developed by Sun This study was motivated by the question of whether the hierarchy of premelting phenomena, found to occur between different facets of metals with an fcc or bcc structure, is also present in hcp metals. We first determined the structural and energetic properties of the effectively infinite solid with no boundaries. We then investigated the low-index surfaces of Mg, namely the c (0001), a (101¯0), and s (101¯1) facets. We found that as the temperature increases, the (101¯0) surface disorders first, followed by the (101¯1) surface, while the (0001) surface remains stable up to the melting temperature. The disorder spreads from the surface into the bulk, establishing a thin quasiliquid film in the surface region. We conclude that the effect of premelting phenomena is inversely proportional to the surface atomic density, being most pronounced at the a (101¯0) facet which has the lowest density. This conclusion is in line with the behavior found for fcc and bcc metals.

Bavli, P.; Polturak, E.; Adler, Joan

2011-12-01

325

Helium diffusion in tungsten: A molecular dynamics study

NASA Astrophysics Data System (ADS)

The diffusion process of He in W is simulated by a molecular dynamics (MD) method with self-developed W-H-He analytic bond-order potentials. The mean squared displacement (MSD) method is employed to determine diffusivity at different temperatures, and then the diffusivity-temperature (D-T) relationship is fitted by the Arrhenius equation to obtain the prefactor and the diffusion barrier. We show the diffusivity of He and the corresponding prefactor and diffusion barrier are different at different temperature ranges. The diffusivities are 9.50 × 10-9 exp(-0.021 eV/kT) m2/s in the temperature range of 50-300 K, 3.61 × 10-8 exp(-0.057 eV/kT) m2/s in 300-1500 K, and 8.562 × 10-8 exp(-0.157 eV/kT) m2/s in 1500-3000 K, respectively, which correspond to different diffusion mechanisms. At a lower temperature, He diffuses directly from one tetrahedral interstitial site (TIS) to another TIS through the diagonal interstitial site with a lower diffusion barrier, while it can diffuse from one TIS to other TIS through the octahedral interstitial site with higher barrier at higher temperature.

Shu, Xiaolin; Tao, Peng; Li, Xiaochun; Yu, Yi

2013-05-01

326

Tight-binding molecular dynamic study of silver clusters

Tight-binding molecular dynamics (TBMD) is used to study the structural and electronic properties of silver clusters. The ground state structures of Ag clusters up to 21 atoms are optimized via TBMD combined with genetic algorithm (GA). The detailed comparison with {\\em ab initio} results on small Ag$_n$ clusters (n=3-9) proves the validity of the tight-bind model. The clusters are found to undergo a transition from ``electronic order'' to ``atomic order'' at n=10. This is due to s-d mixing at such size. The size dependence of electronic properties such as density of states (DOS), s-d band separation, HOMO-LUMO gap, and ionization potentials are discussed. Magic number behavior at Ag$_2$, Ag$_8$, Ag$_{14}$, Ag$_{18}$, Ag$_{20}$ is obtained, in agreement with the prediction of electronic ellipsoid shell model. It is suggested that both the electronic and geometrical shell exist in the coinage metal clusters and they play a significant role in determining cluster properties.

Zhao, J

1999-01-01

327

Molecular dynamics model of carbon nanotubes in EPON 862/DETDA polymer

NASA Astrophysics Data System (ADS)

The aerospace industry is interested in increasing the strength while reducing the weight of carbon fiber composite materials. Adding single walled carbon nanotubes (SWCNT) to a polymer matrix can achieve that goal by improving delamination properties of the composite. Due to the complexity of polymer molecules and the curing process, few 3-D Molecular Dynamics simulations of a polymer-SWCNT composite have been run. Our model runs on the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), with a COMPASS (Condensed phase Optimized Molecular Potential for Atomistic Simulations Studies) potential to represent the interactions between the atoms of the polymer and the SWCNT. This potential includes non-bonded interactions (9-6 Lennard-Jones), bond interaction (class2), angles (class2) and dihedrals (class2) to create a molecular dynamics model for single-walled carbon nanotubes and EPON 862/DETDA (Diethyltoluenediamine) polymer matrix. Two simulations were performed in order to test the implementation of the potential. The first one is a tensile test on a SWCNT, leading to a Young's modulus of 1.4 TPa at 300K. The second one is a pull-out test of a SWCNT from an originally uncured EPON 862/DETDA matrix.

Ingvason, Guttormur Arnar

328

Molecular dynamic simulations of self-interstitials in silicon

NASA Astrophysics Data System (ADS)

Ab initio molecular-dynamics simulations in periodic supercells containing 64 up to 216 Si host atoms were used to study the static and dynamic properties of neutral self-interstitial aggregates, I n, in silicon. The lowest energy configurations for In, n < 5, have been identified. Each of I and I 2 has one local minimum, while the potential energy surface for aggregates of three or more I's have 2 several local minima, leading to a range of metastable configurations. Constant temperature runs show that I2 and the most stable Ia3 clusters are highly mobile. In these complexes, all the self-interstitials are located around a single bond centered site, a feature that greatly facilitates exchange process and is responsible for the rapid diffusion. Simulations of Ib3 show that the three I's exchange sites with each other, but the center of the defect remains at the same place. Simulations of I and I4 show no diffusion or exchange on the same time scale. Next, the highly mobile Ia3 'units' are assumed to be the building blocks for self-interstitial precipitates. We study the interactions Ia3+Iae?I 6 and I6+Ia3?I9 by bringing an Ia3 toward either Ia3 or I6 along various crystalline directions in 216 host silicon atoms supercells. The calculations show that these reactions occur at a substantial gain in energy and that the stacking along some directions is energetically preferred over others. The results suggest that precipitation mechanisms involving rapidly moving self-interstitial clusters could play an important role in the formation of extended defects.

Gharaibeh, Maen Ahmed

329

RPMDRATE: Bimolecular chemical reaction rates from ring polymer molecular dynamics

NASA Astrophysics Data System (ADS)

We present RPMDRATE, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH4, OH+CH4 and H+C2H6 reactions. Catalogue identifier: AENW_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AENW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: MIT license No. of lines in distributed program, including test data, etc.: 94512 No. of bytes in distributed program, including test data, etc.: 1395674 Distribution format: tar.gz Programming language: Fortran 90/95, Python (version 2.6.x or later, including any version of Python 3, is recommended). Computer: Not computer specific. Operating system: Any for which Python, Fortran 90/95 compiler and the required external routines are available. Has the code been vectorized or parallelized?: The program can efficiently utilize 4096+ processors, depending on problem and available computer. At low temperatures, 110 processors are reasonable for a typical umbrella integration run with an analytic potential energy function and gradients on the latest x86-64 machines.

Suleimanov, Yu. V.; Allen, J. W.; Green, W. H.

2013-03-01

330

The collapsing bubble in a liquid by molecular dynamics simulations

Molecular dynamics simulations have been made of a collapsing bubble or cavity in a simple liquid. Simulations of a Lennard-Jones liquid reveal that the collapsing process takes place in a series of stages. First, the ‘hottest’ molecules from the high kinetic energy tail in the Maxwell—Boltzmann distribution diffuse into the empty cavity. This is followed by a gradual filling in

C. XIAO; D. M. HEYES; J. G. POWLES

2002-01-01

331

The collapsing bubble in a liquid by molecular dynamics simulations

Molecular dynamics simulations have been made of a collapsing bubble or cavity in a simple liquid. Simulations of a Lennard-Jones liquid reveal that the collapsing process takes place in a series of stages. First, the 'hottest' molecules from the high kinetic energy tail in the Maxwell-Boltzmann distribution diffuse into the empty cavity. This is followed by a gradual filling in

C. Xiao; D. M. Heyes; J. G. Powles

2002-01-01

332

Lightweight computational steering of very large scale molecular dynamics simulations

We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can

David M. Beazley; Peter S. Lomdahl

1996-01-01

333

Microscale Swimming: The Molecular Dynamics Approach D. C. Rapaport*

, unlike other approaches, hydrodynamic correlations emerge naturally. A selection of self-propelled bodies is a compari- son of the efficiency of the alternative body designs and propulsion techniques. The MD approachMicroscale Swimming: The Molecular Dynamics Approach D. C. Rapaport* Physics Department, Bar

Rapaport, Dennis C.

334

Study of the electrostatics treatment in molecular dynamics simulations

This article considers the treat- ment of long-range interactions in molecular dynam- ics simulations. We investigate the effects of using different cutoff distances, constant versus distance- dependent dielectric, and different smoothing meth- ods. In contrast to findings of earlier studies, we find that increasing the cutoff over 8 Å does not signifi- cantly improve the accuracy (Arnold and Ornstein, Proteins

Robert Garemyr; Arne Elofsson

1999-01-01

335

Molecular dynamics with coupling to an external bath

In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties in nonequilibrium MD. A method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling. The method is easily

H. J. C. Berendsen; J. P. M. Postma; W. F. van Gunsteren; A. DiNola; J. R. Haak

1984-01-01

336

Constant pressure molecular dynamics simulation: The Langevin piston method

A new method for performing molecular dynamics simulations under constant pressure is presented. In the method, which is based on the extended system formalism introduced by Andersen, the deterministic equations of motion for the piston degree of freedom are replaced by a Langevin equation; a suitable choice of collision frequency then eliminates the unphysical ‘‘ringing’’ of the volume associated with

Scott E. Feller; Yuhong Zhang; Richard W. Pastor; Bernard R. Brooks

1995-01-01

337

DNA deformability and hydration studied by molecular dynamics simulation

DNA tetramer sequences AATT and TTAA are known to be conformationally more rigid and flexible, respectively. In this study, we carry out molecular dynamics (MD) simulations of these two sequences and investigate the characteristic hydration pattern. The rigid AATT is found to be more likely to construct the hydration spine in the minor groove, than the flexible TTAA. The result

Y. Yonetani; H. Kono; S. Fujii; A. Sarai; N. Go

2007-01-01

338

Molecular Dynamics Simulations of Hydrophilic Pores in Lipid Bilayers

Hydrophilic pores are formed in peptide free lipid bilayers under mechanical stress. It has been proposed that the transport of ionic species across such membranes is largely determined by the existence of such meta-stable hydrophilic pores. To study the properties of these structures and understand the mechanism by which pore expansion leads to membrane rupture, a series of molecular dynamics

Hari Leontiadou; Alan E. Mark; Siewert J. Marrink

2004-01-01

339

DNA and its counterions: a molecular dynamics study

The behaviour of mobile counterions, Na+ and K+, was analysed around a B-DNA double helix with the sequence CCATGCGCTGAC in aqueous solution dur- ing two 50 ns long molecular dynamics trajectories. The movement of both monovalent ions remains dif- fusive in the presence of DNA. Ions sample the com- plete space available during the simulation time, although individual ions sample

Peter Varnai; Krystyna Zakrzewska

2004-01-01

340

Cationic DMPC\\/DMTAP Lipid Bilayers: Molecular Dynamics Study

Cationic lipid membranes are known to form compact complexes with DNA and to be effective as gene delivery agents both in vitro and in vivo. Here we employ molecular dynamics simulations for a detailed atomistic study of lipid bilayers consisting of a mixture of cationic dimyristoyltrimethylammonium propane (DMTAP) and zwitterionic dimyristoylphosphatidylcholine (DMPC). Our main objective is to examine how the

Andrey A. Gurtovenko; Michael Patra; Mikko Karttunen; Ilpo Vattulainen

2004-01-01

341

Molecular dynamics simulation of the inverted temperature gradient phenomenon

A molecular dynamics simulation of the temperature profile between two liquid surfaces kept at slightly different temperatures, with evaporation from the hot surface and condensation on the cold surface, is presented. The more than 30 years old theoretical prediction of an inverted temperature gradient by gas-kinetic calculations has still not been proven experimentally. However, the inverted temperature gradient phenomenon is

Roar Meland

2003-01-01

342

Thermodiffusion in model nanofluids by molecular dynamics simulations

1 Thermodiffusion in model nanofluids by molecular dynamics simulations G. Galliero1,2,* , S. Volz3-Jones fluids and for model nanofluids (spherical non-metallic nanoparticles + Lennard-Jones fluid) where concentration. Then, in nanofluids in the liquid state, by changing the nature of the nanoparticle (size, mass

Paris-Sud XI, UniversitÃ© de

343

OPTIMAL CONTROL OF ATOMIC, MOLECULAR AND ELECTRON DYNAMICS

to be able to observe in a passive way, but in fact also to actively control quantum mechanical processesChapter 9 OPTIMAL CONTROL OF ATOMIC, MOLECULAR AND ELECTRON DYNAMICS WITH TAILORED FEMTOSECOND Am Hubland, 97074 WÃ¼rzburg, Germany Matthias Wollenhaupt and Thomas Baumert Institute of Physics

Kassel, UniversitÃ¤t

344

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

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

Brad Holian; Dennis Grady

1988-01-01

345

A FULLERENE FORMATION MODEL PROPOSED FROM MOLECULAR DYNAMICS SIMULATIONS

A FULLERENE FORMATION MODEL PROPOSED FROM MOLECULAR DYNAMICS SIMULATIONS Yasutaka Yamaguchi distributed carbon atoms was simulated. A C60 imperfect fullerene obtained in the simulation was kept at 2500 in the clustering simulation. Through successive pentagon-migration transformations, the perfect fullerene structure

Maruyama, Shigeo

346

A molecular dynamics study on the formation of metallofullerene

method similar to our simulations of prefect C60 and C70 formation [1,2]. In order to model the metal-8656, Japan The growth process of metal-containing fullerenes is studied by using the molecular dynamics is not experimentally assigned to be encapsulated in the fullerene cage so far, were also applied as shown in Fig. 2

Maruyama, Shigeo

347

Thermal decomposition of RDX from reactive molecular dynamics Alejandro Strachana)

field ReaxFF with molecular dynamics to study thermal induced chemistry in RDX cyclic- CH2N NO2 fields FFs that can describe chemical reactions in a computationally efficient way.3Â5 ReaxFF4 is a new

Goddard III, William A.

348

Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques

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

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

2009-01-01

349

Molecular dynamics of 16000 Lennard-Jones particles

NASA Astrophysics Data System (ADS)

We report a molecular-dynamics simulation of very large two-dimensional Lennard-Jones systems (up to 16383 particles). The simulation was carried out on a special-purpose processor built by Bakker. The processor's principal features and possibilities are described. Preliminary results of measurements along the isochore ? ? = 0.94 are presented.

Bakker, A. F.; Bruin, C.; van Dieren, F.; Hilhorst, H. J.

1982-12-01

350

Stationary nonequilibrium states by molecular dynamics. II. Newton's law

We present molecular-dynamics results for a dense Lennard-Jones fluid near the triple point subjected to the Couette flow. The method is based on the introduction of stochastic boundary conditions to simulate the contact with a moving thermal wall. The method allows the simulation of bulk properties of the system and the study of the local thermodynamical equilibrium. Furthermore, it gives

Carlo Trozzi; Giovanni Ciccotti

1984-01-01

351

Anton, a special-purpose machine for molecular dynamics simulation

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

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

2007-01-01

352

Anton, a special-purpose machine for molecular dynamics simulation

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

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

2007-01-01

353

Dynamics of Molecular Motors in Reversible Burnt-Bridge Models

Dynamic properties of molecular motors whose motion is powered by interactions with specific lattice bonds are studied theoretically with the help of discrete-state stochastic "burnt-bridge" models. Molecular motors are depicted as random walkers that can destroy or rebuild periodically distributed weak connections ("bridges") when crossing them, with probabilities $p_1$ and $p_2$ correspondingly. Dynamic properties, such as velocities and dispersions, are obtained in exact and explicit form for arbitrary values of parameters $p_1$ and $p_2$. For the unbiased random walker, reversible burning of the bridges results in a biased directed motion with a dynamic transition observed at very small concentrations of bridges. In the case of backward biased molecular motor its backward velocity is reduced and a reversal of the direction of motion is observed for some range of parameters. It is also found that the dispersion demonstrates a complex, non-monotonic behavior with large fluctuations for some set of parameters. Complex dynamics of the system is discussed by analyzing the behavior of the molecular motors near burned bridges.

Maxim N. Artyomov; Alexander Yu. Morozov; Anatoly B. Kolomeisky

2009-11-22

354

Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine

Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine D 2009; published 30 April 2009 A nanoscale-sized Stirling engine with an atomistic working fluid has s : 02.70.Ns, 05.70.Ln, 47.61. k The Stirling engine, an external combustion engine in- vented almost two

Rapaport, Dennis C.

355

Molecular dynamics in arbitrary geometries: Parallel evaluation of pair forces

A new algorithm for calculating intermolecular pair forces in molecular dynamics (MD) simulations on a distributed parallel computer is presented. The arbitrary interacting cells algorithm (AICA) is designed to operate on geometrical domains defined by an unstructured, arbitrary polyhedral mesh that has been spatially decomposed into irregular portions for parallelisation. It is intended for nano scale fluid mechanics simulation by

Graham B. Macpherson; Jason M. Reese

2008-01-01

356

Molecular Cell Dynamic DNA Helicase-DNA Polymerase

Molecular Cell Article Dynamic DNA Helicase-DNA Polymerase Interactions Assure Processive-associated DNA polymerases can exchange with free DNA polymerase without affecting processivity (Johnson et al DNA poly- merase and DNA helicase advance the replica- tion fork with a processivity greater than 17

357

GPU accelerated molecular dynamics simulation of thermal conductivities

Molecular dynamics (MD) simulations have become a powerful tool for elucidating complex physical phenomena. However, MD method is very time-consuming. This paper presents a method to accelerate computation of MD simulation. The acceleration is achieved by take advantage of modern graphics processing units (GPU). As an example, the thermal conductivities of solid argon were calculated with the GPU-based MD algorithm.

Juekuan Yang; Yujuan Wang; Yunfei Chen

2007-01-01

358

A Formulation of the Ring Polymer Molecular Dynamics

The exact formulation of the path integral centroid dynamics is extended to include composites of the position and momentum operators. We present the generalized centroid dynamics (GCD), which provides a basis to calculate Kubo-transformed correlation functions by means of classical averages. We define various types of approximate GCD, one of which is equivalent to the ring polymer molecular dynamics (RPMD). The RPMD and another approximate GCD are tested in one-dimensional harmonic system, and it is shown that the RPMD works better in the short time region.

Atsushi Horikoshi

2014-01-04

359

A Formulation of the Ring Polymer Molecular Dynamics

The exact formulation of the path integral centroid dynamics is extended to include composites of the position and momentum operators. We present the generalized centroid dynamics (GCD), which provides a basis to calculate Kubo-transformed correlation functions by means of classical averages. We define various types of approximate GCD, one of which is equivalent to the ring polymer molecular dynamics (RPMD). The RPMD and another approximate GCD are tested in one-dimensional harmonic system, and it is shown that the RPMD works better in the short time region.

Horikoshi, Atsushi

2014-01-01

360

NASA Astrophysics Data System (ADS)

A bistable, dipolar stator-rotor molecular system-candidate for molecular electronics is investigated. We demonstrate that it is possible to control the intramolecular torsional states and dynamics in this system by applying an appropriate additional electric field (instead of biasing one), achieving fine tuning and modulation of the relevant properties. The electric field effects on the quantities responsible for torsional dynamics (potential energy surface, potential barrier height, quantum and classical transition probabilities, correlation time, HOMO-LUMO gap) are studied from first principles. Our results indicate that it is possible to artificially stabilize the metastable conformational state of the studied molecule. The importance of this is evident, as the current-voltage characteristics of the metastable state are clearly distinguishable from the current-voltage characteristics of the two stable states. We report for the first time exact calculations related to the possibilities to control the thermally induced stochastic switching, and reduce the noise in a practical application. Thus, we believe that the molecule studied in this paper could operate as a field-switchable molecular device under real conditions.

Petreska, Irina; Pejov, Ljup?o; Kocarev, Ljup?o

2011-01-01

361

This paper presents studies on the characteristics of gas molecular mean free path in nanopores by molecular dynamics simulation. Our study results indicate that the mean free path of all molecules in nanopores depend on both the radius of the nanopore and the gas-solid interaction strength. Besides mean free path of all molecules in the nanopore, this paper highlights the gas molecular mean free path at different positions of the nanopore and the anisotropy of the gas molecular mean free path at nanopores. The molecular mean free path varies with the molecule’s distance from the center of the nanopore. The least value of the mean free path occurs at the wall surface of the nanopore. The present paper found that the gas molecular mean free path is anisotropic when gas is confined in nanopores. The radial gas molecular mean free path is much smaller than the mean free path including all molecular collisions occuring in three directions. Our study results also indicate that when gas is confined in nanopores the gas molecule number density does not affect the gas molecular mean free path in the same way as it does for the gas in unbounded space. These study results may bring new insights into understanding the gas flow’s characteristic at nanoscale. PMID:25046745

Liu, Qixin; Cai, Zhiyong

2014-01-01

362

Molecular thermometers for potential applications in thermal ablation procedures

NASA Astrophysics Data System (ADS)

Thermal ablation is a promising minimally invasive method for treating tumors without surgical intervention. Thermal ablation uses thermal sources such as lasers, radiowaves or focused ultrasound to increase the temperature of the tumor to levels lethal to cancer cells. This treatment based on heat therapy may be problematic as the temperature of the operation site is unknown. To address this problem, we developed optical molecular thermometers that can potentially measure the temperature on a molecular scale and be compatible with in vivo measurements. The thermometers are centered on a combination of two fluorophores emitting in two distinct spectral ranges and having different temperature-dependent emission properties. In this design, a fluorophore with relatively insensitive temperature-dependent fluorescence serves as a reference while another sensitive fluorophore serves as a sensor. We have demonstrated the feasibility of this approach using a coumarin-rhodamine conjugate. The sensitivity of the construct to the clinically relevant ablation temperatures (20-85 °C) was demonstrated in vitro.

Zhegalova, Natalia G.; Aydt, Alex; Wang, Steven T.; Berezin, Mikhail Y.

2013-02-01

363

Molecular dynamics simulation of primary irradiation defect formation in Fe 10%Cr alloy

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations of displacement cascades in Fe and Fe-10%Cr have been performed for primary knock-on energies from 1 to 20 keV using two different Finnis-Sinclair style interatomic potentials. The different potentials were fit to describe the extremes of positive (attractive) and negative (repulsive) binding between substitutional Cr atoms and Fe self-interstitial atoms. As expected, the effect of Cr on the collisional stage of cascade evolution and on the number of point defects and point defect clusters produced is quite minimal. However, the quantity of mixed Fe-Cr dumbbells produced is sensitive to the choice of potential.

Shim, Jae-Hyeok; Lee, Hyon-Jee; Wirth, Brian D.

2006-06-01

364

Molecular dynamics studies of shock initiation in a model energetic material

NASA Astrophysics Data System (ADS)

In this paper we report the results of molecular dynamics simulations of shock initiation in an energetic material. An Abell-Tersoff potential has been used to represent a lattice of diatomic molecules capable of undergoing an exothermic reaction. This model system has been employed to investigate the critical conditions for, initiation of a chemically sustained shock wave. The effect of shock pulses of differing amplitude and duration have been studied, and some variations in the potential parameters have been considered to examine the influence of potential barriers on the initiation thresholds. Finally the results of these simulations are compared with the classical picture of initiation in homogeneous explosives.

Haskins, P. J.; Cook, M. D.

1994-07-01

365

Stability Mechanisms of a Thermophilic Laccase Probed by Molecular Dynamics

Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD) was applied to a Trametes versicolor laccase in response to variable ionic strengths, temperatures, and glycosylation status. Near-physiological conditions provided excellent agreement with the crystal structure (average RMSD ?0.92 Å) and residual agreement with experimental B-factors. The persistence of backbone hydrogen bonds was identified as a key descriptor of structural response to environment, whereas solvent-accessibility, radius of gyration, and fluctuations were only locally relevant. Backbone hydrogen bonds decreased systematically with temperature in all simulations (?9 per 50 K), probing structural changes associated with enthalpy-entropy compensation. Approaching Topt (?350 K) from 300 K, this change correlated with a beginning “unzipping” of critical ?-sheets. 0 M ionic strength triggered partial denucleation of the C-terminal (known experimentally to be sensitive) at 400 K, suggesting a general salt stabilization effect. In contrast, F? (but not Cl?) specifically impaired secondary structure by formation of strong hydrogen bonds with backbone NH, providing a mechanism for experimentally observed small anion destabilization, potentially remedied by site-directed mutagenesis at critical intrusion sites. N-glycosylation was found to support structural integrity by increasing persistent backbone hydrogen bonds by ?4 across simulations, mainly via prevention of F? intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical ?-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes. PMID:23658618

Christensen, Niels J.; Kepp, Kasper P.

2013-01-01

366

Gramicidin A (gA) channels provide an ideal system to test molecular dynamics (MD) simulations of membrane proteins. The peptide backbone lines a cation-selective pore, and due to the small channel size, the average structure and extent of fluctuations of all atoms in the peptide will influence ion permeation. This raises the question of how well molecular mechanical force fields used in MD simulations and potential of mean force (PMF) calculations can predict structure and dynamics as well as ion permeation. To address this question, we undertook a comparative study of nuclear magnetic resonance (NMR) observables predicted by fully atomistic MD simulations on a gA dimer embedded in a sodium dodecyl sulfate (SDS) micelle with measurements of the gA dimer backbone and tryptophan side chain dynamics using solution-state (15)N NMR on gA dimers in SDS micelles (Vostrikov, V. V.; Gu, H.; Ingo?lfsson, H. I.; Hinton, J. F.; Andersen, O. S.; Roux, B.; Koeppe, R. E., II. J. Phys. Chem. B2011, DOI 10.1021/jp200906y , accompanying article). This comparison enables us to examine the robustness of the MD simulations done using different force fields as well as their ability to predict important features of the gA channel. We find that MD is able to predict NMR observables, including the generalized order parameters (S(2)), the (15)N spin-lattice (T(1)) and spin-spin (T(2)) relaxation times, and the (1)H-(15)N nuclear Overhauser effect (NOE), with remarkable accuracy. To examine further how differences in the force fields can affect the channel conductance, we calculated the PMF for K(+) and Na(+) permeation through a gA channel in a dimyristoylphosphatidylcholine (DMPC) bilayer. In this case, we find that MD is less successful in quantitatively predicting the single-channel conductance. PMID:21574563

Ingólfsson, Helgi I; Li, Yuhui; Vostrikov, Vitaly V; Gu, Hong; Hinton, James F; Koeppe, Roger E; Roux, Benoît; Andersen, Olaf S

2011-06-01

367

Drugs That Target Dynamic Microtubules: A New Molecular Perspective

Microtubules have long been considered an ideal target for anticancer drugs because of the essential role they play in mitosis, forming the dynamic spindle apparatus. As such, there is a wide variety of compounds currently in clinical use and in development that act as antimitotic agents by altering microtubule dynamics. Although these diverse molecules are known to affect microtubule dynamics upon binding to one of the three established drug domains (taxane, vinca alkaloid, or colchicine site), the exact mechanism by which each drug works is still an area of intense speculation and research. In this study, we review the effects of microtubule-binding chemotherapeutic agents from a new perspective, considering how their mode of binding induces conformational changes and alters biological function relative to the molecular vectors of microtubule assembly or disassembly. These “biological vectors” can thus be used as a spatiotemporal context to describe molecular mechanisms by which microtubule-targeting drugs work. PMID:21381049

Stanton, Richard A.; Gernert, Kim M.; Nettles, James H.; Aneja, Ritu

2011-01-01

368

Influence of conformational molecular dynamics on matter wave interferometry

We investigate the influence of thermally activated internal molecular dynamics on the phase shifts of matter waves inside a molecule interferometer. While de Broglie physics generally describes only the center-of-mass motion of a quantum object, our experiment demonstrates that the translational quantum phase is sensitive to dynamic conformational state changes inside the diffracted molecules. The structural flexibility of tailor-made hot organic particles is sufficient to admit a mixture of strongly fluctuating dipole moments. These modify the electric susceptibility and through this the quantum interference pattern in the presence of an external electric field. Detailed molecular dynamics simulations combined with density functional theory allow us to quantify the time-dependent structural reconfigurations and to predict the ensemble-averaged square of the dipole moment which is found to be in good agreement with the interferometric result. The experiment thus opens a new perspective on matter wave interfe...

Gring, Michael; Eibenberger, Sandra; Nimmrichter, Stefan; Berrada, Tarik; Arndt, Markus; Ulbricht, Hendrik; Hornberger, Klaus; Müri, Marcel; Mayor, Marcel; Böckmann, Marcus; Doltsinis, Nikos

2014-01-01

369

Molecular dynamics saddle search adaptive kinetic Monte Carlo

NASA Astrophysics Data System (ADS)

A method for accelerating molecular dynamics simulations in rare event systems is described. From each new state visited, high temperature molecular dynamics trajectories are used to discover the set of escape mechanisms and rates. This event table is provided to the adaptive kinetic Monte Carlo algorithm to model the evolution of the system from state to state. Importantly, an estimator for the completeness of the calculated rate table in each state is derived. The method is applied to three model systems: adatom diffusion on Al(100); island diffusion on Pt(111); and vacancy cluster ripening in bulk Fe. Connections to the closely related temperature accelerated dynamics method of Voter and co-workers is discussed.

Chill, Samuel T.; Henkelman, Graeme

2014-06-01

370

The electric field dependence of the structure and dynamics of water at 77 K, i.e., below the glass transition temperature (136 K), is investigated using molecular dynamics simulations. Transitions are found at two critical field strengths, denoted E1 and E2. The transition around E1 3.5 V/nm is characterized by the onset of significant structural disorder, a rapid increase in the orientational polarization, and a maximum in the dynamical fluctuations. At E2 40 V/nm, the system crystallizes in discrete steps into a body-centered-cubic unit cell that minimizes the potential energy by simultaneous superpolarization of the water molecular dipoles and maximization of the intermolecular hydrogen bonds. The stepwise and discontinuous increase of the orientational polarization with the increasing electric field indicates that the dipole relaxation in the electric field is highly cooperative.

Hu, Xiaohu [ORNL; Elghobashi-Meinhardt, Nadia [Karlsruhe Institute of Technology, Karlsruhe, Germany; Gembris, Daniel [Bruker Bio-Spin MRI GmbH, Ettling, Germany; Smith, Jeremy C [ORNL

2011-01-01

371

Piezoelectric coefficients by molecular dynamics simulations in the constant stress ensemble Abstract Piezoelectric (strain) coefficients dij of quartz are calculated in terms of molecular dynamics is employed suppressing significantly stochastic fluctuations of the estimators for piezoelectric coefficients

Mueser, Martin

372

Adaptive-boost molecular dynamics simulation of carbon diffusion in iron

We have developed an accelerated molecular dynamics (MD) method to model atomic-scale rare events. In this method, a smooth histogram of collective variables is first estimated by canonical ensemble molecular dynamics ...

Ishii, Akio

373

Applications of Langevin and Molecular Dynamics methods

Computer simulation of complex nonlinear and disordered phenomena from materials science is rapidly becoming an active and new area serving as guide for experiments and for testing of theoretical concepts. This is especially true when novel massively parallel computer systems and techniques are used on these problems. In particular the Langevin dynamics simulation technique has proven useful in situations where the time evolution of a system in contact with a heat bath is to be studied. The traditional way to study systems in contact with a heat bath has been via the Monte Carlo method. While this method has indeed been used successfully in many applications, it has difficulty addressing true dynamical questions. Large systems of coupled stochastic ODEs (or Langevin equations) are commonly the end result of a theoretical description of higher dimensional nonlinear systems in contact with a heat bath. The coupling is often local in nature, because it reflects local interactions formulated on a lattice, the lattice for example represents the underlying discreteness of a substrate of atoms or discrete k-values in Fourier space. The fundamental unit of parallelism thus has a direct analog in the physical system the authors are interested in. In these lecture notes the authors will illustrate the use of Langevin stochastic simulation techniques on a number of nonlinear problems from materials science and condensed matter physics that have attracted attention in recent years. First, the authors will review the idea behind the fluctuation-dissipation theorem which forms that basis for the numerical Langevin stochastic simulation scheme. The authors then show applications of the technique to various problems from condensed matter and materials science.

Lomdahl, P.S.

1994-12-31

374

Reflection coefficients for carbon atoms and hydrocarbon molecules on a carbon surface are critically needed for plasma–surface interaction analysis of carbon surfaces. These coefficients have been calculated with a molecular dynamics code using the Brenner hydrocarbon potential. The surface was prepared by bombarding a pure graphite lattice with energetic hydrogen, until a saturation was reached at ?0.42 H:C. Carbon atoms

Darren A. Alman; D.N. Ruzic

2003-01-01

375

Molecular dynamics study of shock-induced chemistry in small condensed-phase hydrocarbons

Molecular dynamics simulations using an empirical bond order potential have been performed to investigate shock-induced chemistry in solid acetylene, ethylene, and methane. Acetylene was found to undergo significant polymerization reactions for flyer plate impact speeds above 10 km\\/s. These conditions are similar to those which would be experienced upon planetary impact of comets, which are known to contain condensed-phase acetylene.

M. L. Elert; S. V. Zybin; C. T. White

2003-01-01

376

Molecular-dynamics study of lattice-defect-nucleated melting in silicon

The high-temperature behavior of both a high-angle twist grain boundary and a free surface on the (110) plane of silicon are investigated using molecular dynamics and the Stillinger-Weber potential. It is found that, above the thermodynamic melting point, melting is nucleated at the grain boundary or surface and propagates through the system with a velocity that increases with temperature. We

S. R. Phillpot; J. F. Lutsko; D. Wolf; S. Yip

1989-01-01

377

Molecular-dynamics simulations using the Stillinger-Weber three-body potential are used to synthesize fully dense nanocrystalline silicon with a grain size up to 7.3 nm by crystallization from the melt. The structures of the highly-constrained grain boundaries, triple lines and point grain junctions are found to be highly disordered and similar to the structure of amorphous silicon. These results suggest that nanocrystalline

P. Keblinski; S. R. Phillpot; D. Wolf; H. Gleiter

1997-01-01

378

Recent experiments have shown that liquid crystals can be used to image mammalian cell membranes and to amplify structural reorganization in phospholipid-laden liquid crystal-aqueous interfaces. In this work, molecular dynamics simulations were employed to explore the interactions between commonly used liquid crystal-forming molecules and phospholipid bilayers. In particular, umbrella sampling was used to obtain the potential of mean force of

Evelina B. Kim; Nathan Lockwood; Manan Chopra; Orlando Guzmán; Nicholas L. Abbott; Juan J. de Pablo

2005-01-01

379

Thermal conductivity of metal-organic framework 5 (MOF-5): Part I. Molecular dynamics simulations

The phonon thermal conductivity of MOF-5, a metal-organic framework crystal with a phenylene bridge, is predicted between temperatures of 200K and 400K using molecular dynamics simulations and the Green–Kubo method. The simulations are performed using interatomic potentials obtained using ab initio calculations and experimental results. The predicted thermal conductivity of MOF-5 is low for a crystal, 0.31W\\/mK at a temperature

B. L. Huang; A. J. H. McGaughey; M. Kaviany

2007-01-01

380

Vibrational spectra and thermal properties of a two-dimensional triangular lattice, where first-neighbor atoms interact with a Lennard-Jones potential, are calculated using both classical molecular dynamics (MD) and leading-order anharmonic perturbation theory (PT). The phonon quasiparticle spectra (QPS), obtained nonperturbatively through MD, depend linearly on T at low temperatures and are in good agreement with the QPS calculated by PT. However,

Tao Sun; Xiao Shen; Philip B. Allen

2010-01-01

381

Initiation of PETN decomposition under shock compression: Reactive molecular dynamics simulation

The initial physical and chemical response of energetic materials under mechanical shock has been investigated for PETN by molecular dynamics method with ReaxFF reactive force field parameterized from first-principles calculations. We study the propagation of a shock wave and shock-induced chemical reactions created by moving piston mimicked by a potential wall. We simulate both the continuous and impulsive piston loading

Peng Xu; Sergey Zybin; Aidan Thompson; Joanne Budzien; William Goddard III

2009-01-01

382

The initial physical and chemical response of energetic materials under mechanical shock or shear loading has been investigated for RDX, PETN and HMX by molecular dynamics method with ReaxFF reactive force field parameterized from first-principles calculations. We study the propagation of a shock wave and shock-induced chemical reactions created by moving piston mimicked by a potential wall. We simulate both

Sergey Zybin; Peng Xu; Adri van Duin; William Goddard

2007-01-01

383

Molecular Dynamics Approach to Aggregation of Polymer Chains with Monomers Connected by Rigid Bonds

We use molecular dynamics simulation to study the aggregation of polymer chains in the environment with or without Lennard-Jones (L-J) fluid consisting of L-J molecules. The neighboring monomers of a polymer chain are connected by rigid bonds and have small or zero bending- and torsion-angle dependent potentials. When the fluid is present, a small number of ``linker'' sites along a

Wen-Jong Ma; Chin-Kun Hu

2010-01-01

384

Our objective has been to elucidate on a molecular level, at atomic resolution, the structures of DNAs modified by highly mutagenic aromatic amines and hydrocarbons. The underlying hypothesis is that DNA replicates with reduced fidelity when its normal right-handed B-structure is altered, and one result is a higher mutation rate. This change in structure may occur normally at a low incidence but it may be enhanced greatly after covalent modification by a mutagenic substance. The methods that we use to elucidate structures are computational, but we keep in close contact with experimental developments, and we incorporate data from NMR studies in our calculations when they are available. X-ray and low resolution spectroscopic studies have not succeeded in producing atomic resolution views of mutagen and carcinogen-oligonucleotide adducts. Even the high resolution NMR method cannot alone yield molecular views, though it does so in combination with our computations. The specific methods that we employ are minimized potential energy calculations using the torsion angle space molecular mechanics program DUPLEX to yield static views. Molecular dynamics simulations of static structures with solvent and salt can be carried out with the program AMBER; this yields mobile views in a medium that mimics aspects of the natural aqueous environment of the cell.

Broyde, S.; Shapiro, R.

1993-09-01

385

GAS PHASE MOLECULAR DYNAMICS: HIGH-RESOLUTION SPECTROSCOPIC PROBES OF CHEMICAL DYNAMICS.

This research is carried out as part of the Gas Phase Molecular Dynamics group program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopic tools are developed and applied to problems in chemical dynamics. Recent topics have included the state-resolved studies of collision-induced electronic energy transfer, dynamics of barrierless unimolecular reactions, and the kinetics and spectroscopy of transient species.

HALL, G.E.

2006-05-30

386

Special issue on ultrafast electron and molecular dynamics

NASA Astrophysics Data System (ADS)

In the last few years, the advent of novel experimental and theoretical approaches has made possible the investigation of (time-resolved) molecular dynamics in ways not anticipated before. Experimentally, the introduction of novel light sources such as high-harmonic generation (HHG) 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, thus opening completely new avenues for imaging electronic and nuclear dynamics in molecules. Along the way, particular types of molecular dynamics, e.g., dynamics around conical intersections, have gained an increased prominence, sparked by the realization of the essential role that this dynamics plays in relaxation pathways in important bio-molecular systems. In the short term, this will allow one to uncover and control the dynamics of elementary chemical processes such as, e.g., ultrafast charge migration, proton transfer, isomerization or multiple ionization, and to address new key questions about the role of attosecond coherent electron dynamics in chemical reactivity. 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, including biomolecules. 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 the current developments, as well as new concepts that are emerging in this field when studying molecular dynamics at attosecond or few-femtosecond time-scales. It also aims at indicating how such studies are likely to evolve in the coming years. In this context, the present special issue contains contributions from recognized experts on HHG, free electron lasers, attosecond and femtosecond pump-probe spectroscopy, electron and x-ray diffraction methods, photoionization and theoretical methods specially designed for the analysis of experiments in this field. Seven review articles report on the present status of some selected topics, namely, table-top and free-electron lasers operating in the XUV and x-ray wavelength regimes to investigate ultrafast molecular dynamics, imaging methods to visualize electron and nuclear dynamics, nonlinear optics applications, and recent theoretical developments. These and other topics are covered by 32 research papers, in which new exciting results show the path for future developments in this field.

Martin, Fernando; Hishikawa, Akiyoshi; Vrakking, Marc

2014-06-01

387

Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.

We consider the convergence behavior of replica-exchange molecular dynamics (REMD) [Sugita and Okamoto, Chem. Phys. Lett. 314, 141 (1999)] based on properties of the numerical integrators in the underlying isothermal molecular dynamics (MD) simulations. We show that a variety of deterministic algorithms favored by molecular dynamics practitioners for constant-temperature simulation of biomolecules fail either to be measure invariant or irreducible, and are therefore not ergodic. We then show that REMD using these algorithms also fails to be ergodic. As a result, the entire configuration space may not be explored even in an infinitely long simulation, and the simulation may not converge to the desired equilibrium Boltzmann ensemble. Moreover, our analysis shows that for initial configurations with unfavorable energy, it may be impossible for the system to reach a region surrounding the minimum energy configuration. We demonstrate these failures of REMD algorithms for three small systems: a Gaussian distribution (simple harmonic oscillator dynamics), a bimodal mixture of Gaussians distribution, and the alanine dipeptide. Examination of the resulting phase plots and equilibrium configuration densities indicates significant errors in the ensemble generated by REMD simulation. We describe a simple modification to address these failures based on a stochastic hybrid Monte Carlo correction, and prove that this is ergodic. PMID:19045252

Cooke, Ben; Schmidler, Scott C

2008-10-28

388

A molecular dynamics study of polymer/graphene interfacial systems

NASA Astrophysics Data System (ADS)

Graphene based polymer nanocomposites are hybrid materials with a very broad range of technological applications. In this work, we study three hybrid polymer/graphene interfacial systems (polystyrene/graphene, poly(methyl methacrylate)/graphene and polyethylene/graphene) through detailed atomistic molecular dynamics (MD) simulations. Density profiles, structural characteristics and mobility aspects are being examined at the molecular level for all model systems. In addition, we compare the properties of the hybrid systems to the properties of the corresponding bulk ones, as well as to theoretical predictions.

Rissanou, Anastassia N.; Harmandaris, Vagelis

2014-05-01

389

Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps

Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND) protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa. PMID:24688701

Ruggerone, Paolo; Vargiu, Attilio V.; Collu, Francesca; Fischer, Nadine; Kandt, Christian

2013-01-01

390

Stretching siloxanes: An ab initio molecular dynamics study

NASA Astrophysics Data System (ADS)

We present an ab initio molecular dynamics study of siloxane elastomers placed under tensile stress for comparison with single molecule AFM experiments. Of particular interest is stress-induced chemical bond breaking in the high force regime, where a description of the molecular electronic structure is essential to determine the rupture mechanism. We predict an ionic mechanism for the bond breaking process with a rupture force of 4.4 nN for an isolated siloxane decamer pulled at a rate of 27.3 m/s and indicate lower values at experimental polymer lengths and pulling rates.

Lupton, E. M.; Nonnenberg, C.; Frank, I.; Achenbach, F.; Weis, J.; Bräuchle, C.

2005-10-01

391

Background SG2NA is a member of the striatin sub-family of WD-40 repeat proteins. Striatin family members have been associated with diverse physiological functions. SG2NA has also been shown to have roles in cell cycle progression, signal transduction etc. They have been known to interact with a number of proteins including Caveolin and Calmodulin and also propagate the formation of a multimeric protein unit called striatin-interacting phosphatase and kinase. As a pre-requisite for such interaction ability, these proteins are known to be unstable and primarily disordered in their arrangement. Earlier we had identified that it has multiple isoforms (namely 35, 78, 87 kDa based on its molecular weight) which are generated by alternative splicing. However, detailed structural information of SG2NA is still eluding the researchers. Results This study was aimed towards three-dimensional molecular modeling and characterization of SG2NA protein and its isoforms. One structure out of five was selected for each variant having the least value for C score. Out of these, m35 kDa with a C score value of ?3.21was the most poorly determined structure in comparison to m78 kDa and m87 kDa variants with C scores of ?1.16 and ?1.97 respectively. Further evaluation resulted in about 61.6% residues of m35 kDa, 76.6% residues of m78 kDa and 72.1% residues of m87 kDa falling in the favorable regions of Ramchandran Plot. Molecular dynamics simulations were also carried out to obtain biologically relevant structural models and compared with previous atomic coordinates. N-terminal region of all variants was found to be highly disordered. Conclusion This study provides first-hand detailed information to understand the structural conformation of SG2NA protein variants (m35 kDa, m78 kDa and m87 kDa). The WD-40 repeat domain was found to constitute antiparallel strands of ?-sheets arranged circularly. This study elucidates the crucial structural features of SG2NA proteins which are involved in various protein-protein interactions and also reveals the extent of disorder present in the SG2NA structure crucial for excessive interaction and multimeric protein complexes. The study also potentiates the role of computational approaches for preliminary examination of unknown proteins in the absence of experimental information. PMID:25015106

2014-01-01

392

THEORETICAL AND NUMERICAL COMPARISON OF SOME SAMPLING METHODS FOR MOLECULAR DYNAMICS

THEORETICAL AND NUMERICAL COMPARISON OF SOME SAMPLING METHODS FOR MOLECULAR DYNAMICS By Eric Canc AND NUMERICAL COMPARISON OF SOME SAMPLING METHODS FOR MOLECULAR DYNAMICS Eric CANC`ES1, 2 , FrÂ´edÂ´eric LEGOLL3)) dqdp, (2) Keywords and phrases: Sampling methods, canonical ensemble, Molecular Dynamics. 1 CERMICS

393

Molecular-statics and molecular-dynamics study of diffusion along [001] tilt grain boundaries in Ag

Self-diffusion parameters of Ag along [Sigma]5(310)[001] and [Sigma]13(320)[001] tilt grain boundaries are determined using both molecular-statics (MS) and molecular-dynamics (MD) techniques with a Ag potential based on the embedded-atom method. The MS calculations provide the diffusion energetics in the low-temperature regime for possible diffusion paths along the grain boundaries, while the MD simulations provide information on the effect of temperature on the diffusion parameters. The MD results indicate that diffusion mechanisms change from low temperatures to high temperatures. In the low-temperature regime, interstitial-related diffusion mechanisms are dominant. Vacancy-related diffusion mechanisms, while unimportant at low temperatures, become dominant at high temperatures due to increased vacancy concentration and mobility. These observations are supported by changing slopes in the Arrhenius plots for both our simulation results and experimental data. The calculated diffusion parameters are in satisfactory agreement with available experimental results.

Liu, C. (Solid State Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830 (United States)); Plimpton, S.J. (Sandia National Laboratories, Albuquerque, New Mexico 87185 (United States))

1995-02-15

394

Nonadiabatic excited-state molecular dynamics: numerical tests of convergence and parameters.

Nonadiabatic molecular dynamics simulations, involving multiple Born-Oppenheimer potential energy surfaces, often require a large number of independent trajectories in order to achieve the desired convergence of the results, and simulation relies on different parameters that should be tested and compared. In addition to influencing the speed of the simulation, the chosen parameters combined with the frequently reduced number of trajectories can sometimes lead to unanticipated changes in the accuracy of the simulated dynamics. We have previously developed a nonadiabatic excited state molecular dynamics methodology employing Tully's fewest switches surface hopping algorithm. In this study, we seek to investigate the impact of the number of trajectories and the various parameters on the simulation of the photoinduced dynamics of distyrylbenzene (a small oligomer of polyphenylene vinylene) within our developed framework. Various user-defined parameters are analyzed: classical and quantum integration time steps, the value of the friction coefficient for Langevin dynamics, and the initial seed used for stochastic thermostat and hopping algorithms. Common approximations such as reduced number of nonadiabatic coupling terms and the classical path approximation are also investigated. Our analysis shows that, at least for the considered molecular system, a minimum of ~400 independent trajectories should be calculated in order to achieve statistical averaging necessary for convergence of the calculated relaxation timescales. PMID:22320726

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

2012-02-01

395

Ab initio molecular dynamics simulations of overlapping recoil events in ThO2

NASA Astrophysics Data System (ADS)

Ab initio molecular dynamics is used to study defect production and interactions from overlapping atomic recoil events in thoria. The pre-existing defects, charge redistribution, and structural distortion from an initial recoil event significantly affect the dynamics of defect production processes that occur from a subsequent overlapping recoil event. The final defect configurations and increase in system energy are dependent on the incident directions and sequence of the recoils. A linear relationship between system potential energy and charge transfer at the distance of closest approach between the recoil and atomic nuclei demonstrates the important role of charge transfer in the response of thoria to single and overlapping recoils.

Liu, B.; Xiao, H. Y.; Zhang, Y.; Weber, W. J.

2013-10-01

396

Molecular dynamics simulation of proton transport near the surface of a phospholipid membrane.

The structural and dynamical properties of a hydrated proton near the surface of DMPC membrane were studied using a molecular dynamics simulation. The proton transport between water molecules was modeled using the second generation multistate empirical valence bond model. The proton diffusion was found to be inhibited at the membrane surface. The potential of mean force for the proton adsorption to the membrane surface and its release back into the bulk water was also determined, yielding a small barrier in each direction. An efficient algorithm for Ewald summation calculations for the multistate empirical valence bond model is also introduced. PMID:11867461

Smondyrev, Alexander M; Voth, Gregory A

2002-01-01

397

Molecular dynamics study of ferroelectric 90 degree domain walls in lead titanate

NASA Astrophysics Data System (ADS)

Molecular dynamics (MD) simulations were carried out to study the 90^o domain wall dynamics of PbTiO3 under mechanical strain. By using a well-parameterized interatomic potential, the rate of formation of new 90^o domains at different temperatures and strain states were extracted. Due to faster stress relaxation, the nucleation rate is slower and the critical nucleus larger at higher temperature. Furthermore, alternative stress relief mechanisms are studied. The critical nucleation size is found to be small. A simple mathematical model describing the relationship between rate and strain is formulated.

Qi, Tingting; Colbert, Jacob; Chen, I.-Wei; Rappe, Andrew

2010-03-01

398

Dynamical Casimir-Polder potentials in non-adiabatic conditions

NASA Astrophysics Data System (ADS)

In this paper we review different aspects of the dynamical Casimir-Polder potential between a neutral atom and a perfectly conducting plate under nonequilibrium conditions. In order to calculate the time evolution of the atom-wall Casimir-Polder potential, we solve the Heisenberg equations describing the dynamics of the coupled system using an iterative technique. Different nonequilibrium initial states are considered, such as bare and partially dressed states. The partially dressed states considered are obtained by a sudden change of a physical parameter of the atom or of its position relative to the conducting plate. Experimental feasibility of detecting the considered dynamical effects is also discussed.

Messina, Riccardo; Passante, Roberto; Rizzuto, Lucia; Spagnolo, Salvatore; Vasile, Ruggero

2014-04-01

399

Probing protein aggregation using simplified models and discrete molecular dynamics

Understanding the role of biomolecular dynamics in cellular processes leading to human diseases and the ability to rationally manipulate these processes is of fundamental importance in scientific research. The last decade has witnessed significant progress in probing biophysical behavior of proteins. However, we are still limited in understanding how changes in protein dynamics and inter-protein interactions occurring in short length- and time-scales lead to aberrations in their biological function. Bridging this gap in biology probed using computer simulations marks a challenging frontier in computational biology. Here we examine hypothesis-driven simplified protein models in conjunction with discrete molecular dynamics in the study of protein aggregation, implicated in series of neurodegenerative diseases, such as Alzheimer's and Huntington's diseases. Discrete molecular dynamics simulations of simplified protein models have emerged as a powerful methodology with its ability to bridge the gap in time and length scales from protein dynamics to aggregation, and provide an indispensable tool for probing protein aggregation. PMID:18508545

Sharma, Shantanu; Ding, Feng; Dokholyan, Nikolay V.

2008-01-01

400

Finite Temperature Quasicontinuum: Molecular Dynamics without all the Atoms

Using a combination of statistical mechanics and finite-element interpolation, the authors develop a coarse-grained (CG) alternative to molecular dynamics (MD) for crystalline solids at constant temperature. The new approach is significantly more efficient than MD and generalizes earlier work on the quasi-continuum method. The method is validated by recovering equilibrium properties of single crystal Ni as a function of temperature. CG dynamical simulations of nanoindentation reveal a strong dependence on temperature of the critical stress to nucleate dislocations under the indenter.

Dupuy, L; Tadmor, E B; Miller, R E; Phillips, R

2005-02-02

401

Human Lactate Dehydrogenase A Inhibitors: A Molecular Dynamics Investigation

Lactate dehydrogenase A (LDHA) is an important enzyme in fermentative glycolysis, generating most energy for cancer cells that rely on anaerobic respiration even under normal oxygen concentrations. This renders LDHA a promising molecular target for the treatment of various cancers. Several efforts have been made recently to develop LDHA inhibitors with nanomolar inhibition and cellular activity, some of which have been studied in complex with the enzyme by X-ray crystallography. In this work, we present a molecular dynamics (MD) study of the binding interactions of selected ligands with human LDHA. Conventional MD simulations demonstrate different binding dynamics of inhibitors with similar binding affinities, whereas steered MD simulations yield discrimination of selected LDHA inhibitors with qualitative correlation between the in silico unbinding difficulty and the experimental binding strength. Further, our results have been used to clarify ambiguities in the binding modes of two well-known LDHA inhibitors. PMID:24466056

Shi, Yun; Pinto, B. Mario

2014-01-01

402

Constant pressure hybrid Molecular Dynamics-Monte Carlo simulations

NASA Astrophysics Data System (ADS)

New hybrid Molecular Dynamics-Monte Carlo methods are proposed to increase the efficiency of constant-pressure simulations. Two variations of the isobaric Molecular Dynamics component of the algorithms are considered. In the first, we use the extended-ensemble method of Andersen [H. C. Andersen, J. Chem. Phys. 72, 2384 (1980)]. In the second, we arrive at a new constant-pressure Monte Carlo technique based on the reversible generalization of the weak-coupling barostat [H. J. C. Berendsen et al., J. Chem. Phys. 81, 3684 (1984)]. This latter technique turns out to be highly effective in equilibrating and maintaining a target pressure. It is superior to the extended-ensemble method, which in turn is superior to simple volume-rescaling algorithms. The efficiency of the proposed methods is demonstrated by studying two systems. The first is a simple Lennard-Jones fluid. The second is a mixture of polyethylene chains of 200 monomers.

Faller, Roland; de Pablo, Juan J.

2002-01-01

403

Long Timestep Molecular Dynamics on the Graphical Processing Unit

Molecular dynamics (MD) simulations now play a key role in many areas of theoretical chemistry, biology, physics, and materials science. In many cases, such calculations are significantly limited by the massive amount of computer time needed to perform calculations of interest. Herein, we present Long Timestep Molecular Dynamics (LTMD), a method to significantly speed MD simulations. In particular, we discuss new methods to calculate the needed terms in LTMD as well as issues germane to a GPU implementation. The resulting code, implemented in the OpenMM MD library, can achieve a significant 6-fold speed increase, leading to MD simulations on the order of 5 ?s/day using implicit solvent models. PMID:24436689

Sweet, James C.; Nowling, Ronald J.; Cickovski, Trevor; Sweet, Christopher R.; Pande, Vijay S.; Izaguirre, Jesus A.

2013-01-01

404

Molecular Dynamics Simulations of Olivine-Silicate Melt Interfaces

NASA Astrophysics Data System (ADS)

Partially molten rocks are important constituents of the Earth's crust and mantle. Their properties depend not only on the chemistry and mineralogy but also on the fraction and distribution of melt or fluid. Partially molten rocks strongly influence the chemical transport in the Earth and geodynamics. We model a partially molten rock on the atomic scale by confining a silicate melt of MgSiO3 composition between Mg2SiO4 olivine crystals. Molecular dynamics simulation is used to study the atomic scale structure and respective transport properties at the interfaces. To represent the atomic interaction, we use an advanced ionic model that accounts for anion polarization and shape deformations (Jahn and Madden, 2007). We construct interfaces between silicate melt layers of different thickness (1.85nm & 3.7nm) and mineral surfaces with different crystal orientations ((010), (001) and (100)). From the particle trajectories we derive various properties like charge density, cation coordination, connectivity of SiO4 tetrahedra and self diffusion coefficients. By adding some (Al, Ca) impurities to the system, the response to different chemical compositions is studied. To obtain a stable solid-melt interface, a temperature of 2000K is chosen. Simulations are performed at ambient pressure. We examine how the chemical composition and the self-diffusion coefficients vary across the interface. Our results indicate that with increase of surface energy, the self-diffusion coefficients of the various species decrease. This may be related to the stronger interaction of the crystal surface with the melt when the surface energy is high, which leads to more structured melt close to the interface. In conclusion, our simulations provide insight into the relation between atomic scale structure and transport properties in partially molten rocks. References S. Jahn and P.A. Madden (2007) Modeling Earth materials from crustal to lower mantle conditions: A transferable set of interaction potentials for the CMAS system. Phys. Earth Planet. Int. 162, 129-139.

Gurmani, Samia; Jahn, Sandro; Brasse, Heinrich; Schilling, Frank R.

2010-05-01

405

Mechanical characterization of nanoindented graphene via molecular dynamics simulations

The mechanical behavior of graphene under various indentation depths, velocities, and temperatures is studied using molecular dynamics analysis. The results show that the load, elastic and plastic energies, and relaxation force increased with increasing indentation depth and velocity. Nanoindentation induced pile ups and corrugations of the graphene. Resistance to deformation decreased at higher temperature. Strong adhesion caused topological defects and vacancies during the unloading process. PMID:21813011

2011-01-01

406

Mechanical characterization of nanoindented graphene via molecular dynamics simulations.

The mechanical behavior of graphene under various indentation depths, velocities, and temperatures is studied using molecular dynamics analysis. The results show that the load, elastic and plastic energies, and relaxation force increased with increasing indentation depth and velocity. Nanoindentation induced pile ups and corrugations of the graphene. Resistance to deformation decreased at higher temperature. Strong adhesion caused topological defects and vacancies during the unloading process. PMID:21813011

Fang, Te-Hua; Wang, Tong Hong; Yang, Jhih-Chin; Hsiao, Yu-Jen

2011-01-01

407

Mechanical characterization of nanoindented graphene via molecular dynamics simulations

NASA Astrophysics Data System (ADS)

The mechanical behavior of graphene under various indentation depths, velocities, and temperatures is studied using molecular dynamics analysis. The results show that the load, elastic and plastic energies, and relaxation force increased with increasing indentation depth and velocity. Nanoindentation induced pile ups and corrugations of the graphene. Resistance to deformation decreased at higher temperature. Strong adhesion caused topological defects and vacancies during the unloading process.

Fang, Te-Hua; Wang, Tong Hong; Yang, Jhih-Chin; Hsiao, Yu-Jen

2011-08-01

408

Deformation twinning in nanocrystalline Al by molecular-dynamics simulation

We use a recently developed, massively parallel molecular-dynamics code for the simulation of polycrystal plasticity to elucidate the intricate interplay between dislocation and GB processes during room-temperature plastic deformation of model nanocrystalline-Al microstructures. Our simulations reveal that under relatively high stresses (of 2.5 GPa) and large plastic strains (of ~12%), extensive deformation twinning takes place, in addition to deformation by

V. Yamakov; D. Wolf; S. R. Phillpot; H. Gleiter; Forschungszentrum Karlsruhe

2002-01-01

409

Molecular Dynamics Simulations of Lipid Vesicle Fusion in Atomic Detail

The fusion of a membrane-bounded vesicle with a target membrane is a key step in intracellular trafficking, exocytosis, and drug delivery. Molecular dynamics simulations have been used to study the fusion of small unilamellar vesicles composed of a dipalmitoyl-phosphatidylcholine (DPPC)\\/palmitic acid 1:2 mixture in atomic detail. The simulations were performed at 350–370K and mimicked the temperature- and pH-induced fusion of

Volker Knecht; Siewert-Jan Marrinky

2007-01-01

410

Molecular-Dynamics Simulations of Carbon Nanotubes as Gigahertz Oscillators

Recently Zheng and Jiang [PRL 88, 045503 (2002)], based on static models,\\u000ahave proposed that multiwalled carbon nanotubes could be the basis for a new\\u000ageneration of nanooscilators in the several gigahertz range. In this work we\\u000apresent the first molecular dynamics simulation for these systems. Different\\u000ananotube types were considered in order to verify the reliability of such\\u000adevices

S. B. Legoas; V. R. Coluci; S. F. Braga; P. Z. Coura; S. O. Dantas; D. Galvão

2003-01-01

411

Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine

NASA Astrophysics Data System (ADS)

A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

Rapaport, D. C.

2009-04-01

412

Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine

A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

Rapaport, D C

2009-01-01

413

Molecular dynamics simulation of chains mobility in polyethylene crystal

The mobility of polymer chains in perfect polyethylene (PE) crystal was calculated as a function of temperature and chain length through Molecular dynamics (MD) in united atom approximation. The results demonstrate that the chain mobility drastically increases in the vicinity of the phase transition from the orthorhombic to quasi-hexagonal phase. In the quasi-hexagonal phase, the chain mobility is almost independent on temperature and inversely proportional to the chain length.

V. I. Sultanov; V. V. Atrazhev; D. V. Dmitriev; S. F. Burlatsky

2014-01-17

414

Tight-binding molecular-dynamics simulation of buckyball collisions

The collisions between C[sub 60] molecules are studied by tight-binding molecular-dynamics simulations. We observe three different regimes of behavior as the collisions become more and more energetic: bouncing, fusion, and fragmentation. The critical energies for fusion and fragmentation as well as details of the energy transfer during the collision process for the bouncing regime are investigated. The collisions at several

B. L. Zhang; C. Z. Wang; C. T. Chan; K. M. Ho

1993-01-01

415

Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.

A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency. PMID:19518394

Rapaport, D C

2009-04-01

416

Reactive Molecular Dynamics Study of TATB Detonation Products

Under shock conditions 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) reacts to form primarily gaseous N2, H2O, CO2 and CO as well as solid carbon. In a previous study of TATB thermal decomposition based on molecular dynamics (MD) simulations using the ReaxFF reactive force field, we observed a large amount of amorphous (graphite-like) carbon but no diamond structures, even at high pressures. In the current

Jason Quenneville; Thomas D. Sewell; Timothy C. Germann; M. Sam Shaw

2009-01-01

417

Fragmentation dynamics of molecular hydrogen in strong ultrashort laser pulses

NASA Astrophysics Data System (ADS)

We present the results of a systematic experimental study of dissociation and Coulomb explosion of molecular hydrogen induced by intense ultrashort (7-25 fs) laser pulses. Using coincident recoil-ion momentum spectroscopy we can distinguish the contributions from dissociation and double ionization even if they result in the same kinetic energies of the fragments. The dynamics of all fragmentation channels drastically depends on the pulse duration, and for 7 fs pulses becomes extremely sensitive to the pulse shape.

Rudenko, A.; Feuerstein, B.; Zrost, K.; de Jesus, V. L. B.; Ergler, T.; Dimopoulou, C.; Schröter, C. D.; Moshammer, R.; Ullrich, J.

2005-03-01

418

Molecular Dynamics Simulation of Shear Moduli for Coulomb Crystals

Torsional (shear) oscillations of neutron stars may have been observed in quasiperiodic oscillations of Magnetar Giant Flares. The frequencies of these modes depend on the shear modulus of neutron star crust. We calculate the shear modulus of Coulomb crystals from molecular dynamics simulations. We find that electron screening reduces the shear modulus by about 10% compared to previous Ogata et al. results. Our MD simulations can be extended to calculate the effects of impurities and or polycrystalline structures on the shear modulus.

C. J. Horowitz; J. Hughto

2008-12-15

419

Annealing twins in nanocrystalline fcc metals: A molecular dynamics simulation

NASA Astrophysics Data System (ADS)

We report fully three-dimensional atomistic molecular dynamics studies of grain growth kinetics in nanocrystalline Cu of 5nm average grain size. We observe the formation of annealing twins as part of the grain growth process. The grain size and energy evolution was monitored as a function of time for various temperatures, yielding an activation energy for the process. The atomistic mechanism of annealing twin formation from the moving boundaries is described.

Farkas, Diana; Bringa, Eduardo; Caro, Alfredo

2007-05-01

420

Molecular dynamics study of BBO crystal growth melts

The crystalline and molten states of ?-BaB2O4, and the melts of its crystal-growth solutions have been studied by molecular dynamics simulations. The simulations on BBO crystalline and molten states gave the crystalline-structure data close to the experimental values, and showed that the pair distribution functions of molten state were in fair agreement with the total radial distribution function curve obtained

Zhaonian Cheng; Yu Lei; Dingyuan Tang

1998-01-01

421

Molecular genetics of adrenocortical tumor formation and potential pharmacologic targets

Abnormalities in the cAMP/PKA signaling pathway have been linked to the formation of benign adrenal tumors, as well as a possible predisposition to adrenocortical cancer. Mutations in the G-protein coupled receptor are associated with McCune-Albright syndrome and ACTH-independent macronodular adrenal hyperplasia, while defects in cAMP-dependent protein kinase A can lead to the development of Carney’s complex, as well as primary pigmented nodular adrenocortical disease (PPNAD), and micronodular adrenocortical hyperplasia (MAH). Defects in phosphodiesterases, which regulate cAMP levels, have also been demonstrated in PPNAD and MAH. The Wnt signaling pathway, which is involved in oncogenesis in a variety of tumors, has also been implicated in adrenocortical tumorigenesis. MicroRNA profiling has added to the our understanding of the signaling pathways involved in tumor formation in the adrenal cortex. Will this all lead to the development of specific targets for pharmacologic therapies? In this article, we review the molecular genetics of adrenocortical tumors and refer to potential targets for pharmacologic therapy. PMID:22691887

Rauschecker, Mitra; Stratakis, Constantine A.

2014-01-01

422

Molecular and Phenotypic Characterization of Potentially New Shigella dysenteriae Serotype

From September 1997 to November 1998, the French National Center for Salmonella and Shigella received 22 Shigella isolates recovered from 22 different patients suffering from dysentery. None of these isolates reacted with any of the antisera used to identify established Shigella serotypes, but all of them agglutinated in the presence of antisera to a previously described potentially new Shigella dysenteriae serotype (represented by strain 96–204) primarily isolated from stool cultures of imported diarrheal cases in Japan. All French isolates, as well as strain 96–204, showed biochemical reactions typical of S. dysenteriae and gave positive results in a PCR assay for detection of the plasmid ipaH gene coding for invasiveness. No Shiga toxin gene was detected by PCR. These isolates were indistinguishable by molecular analysis of ribosomal DNA (ribotyping) and seemed to be related to S. dysenteriae serotypes 3 and 12. However, further characterization by restriction of the amplified O-antigen gene cluster clearly distinguished this new serotype from all other Shigella or Escherichia coli serotypes. PMID:11158117

Coimbra, Roney S.; Lenormand, Pascal; Grimont, Francine; Bouvet, Philippe; Matsushita, Shigeru; Grimont, Patrick A. D.

2001-01-01

423

Molecular Alterations in Pediatric Sarcomas: Potential Targets for Immunotherapy

Purpose/results/discussion. Recurrent chromosomal translocations are common features of many human malignancies. While such translocations often serve as diagnostic markers, molecular analysis of these breakpoint regions and the characterization of the affected genes is leading to a greater understanding of the causal role such translocations play in malignant transformation. A common theme that is emerging from the study of tumor-associated translocations is the generation of chimeric genes that, when expressed, frequently retain many of the functional properties of the wild-type genes from which they originated. Sarcomas, in particular, harbor chimeric genes that are often derived from transcription factors, suggesting that the resulting chimeric transcription factors contribute to tumorigenesis. The tumor-specific expression of the fusion proteins make them likely candidates for tumor-associated antigens (TAA) and are thus of interest in the development of new therapies. The focus of this review will be on the translocation events associated with Ewing's sarcomas/PNETs (ES), alveolar rhabdomyosarcoma (ARMS), malignant melanoma of soft parts (MMSP) (clear cell sarcoma), desmoplastic small round cell tumor (DSRCT), synovial sarcoma (SS), and liposarcoma (LS), and the potential for targeting the resulting chimeric proteins in novel immunotherapies. PMID:18521238

Goletz, Theresa J.; Mackall, Crystal L.; Berzofsky, Jay A.

1998-01-01

424

Electronic continuum model for molecular dynamics simulations of biological molecules

Electronic polarizability is an important factor in molecular interactions. In the conventional force fields such as AMBER or CHARMM, however, there is inconsistency in how the effect of electronic dielectric screening of Coulombic interactions, inherent for the condensed phase media, is treated. Namely, the screening appears to be accounted for via effective charges only for neutral moieties, whereas the charged residues are treated as if they were in vacuum. As a result, the electrostatic interactions between ionized groups are exaggerated in molecular simulations by the factor of about 2. The discussed here MDEC (Molecular Dynamics in Electronic Continuum) model provides a theoretical framework for modification of the standard non-polarizable force fields to make them consistent with the idea of uniform electronic screening of partial atomic charges. The present theory states that the charges of ionized groups and ions should be scaled; i.e. reduced by a factor of about 0.7. In several examples, including the interaction between Na+ ions, which is of interest for ion-channel simulations, and the dynamics of an important salt-bride in Cytochrome c Oxidase, we compared the standard non-polarizable MD simulations with MDEC simulations, and demonstrated that MDEC charge scaling procedure results in more accurate interactions. The inclusion of electronic screening for charged moieties is shown to result in significant changes in protein dynamics and can give rise to new qualitative results compared with the traditional non-polarizable force fields simulations.

Leontyev, I. V.; Stuchebrukhov, A. A.

2010-01-01

425

Solitary wave dynamics in time-dependent potentials

The long time dynamics of solitary wave solutions of the nonlinear Schroedinger equation in time-dependent external potentials is rigorously studied. To set the stage, the well-posedness of the Cauchy problem for a generalized nonautonomous nonlinear Schroedinger equation with time-dependent nonlinearities and potential is established. Afterward, the dynamics of NLS solitary waves in time-dependent potentials is studied. It is shown that in the space-adiabatic regime where the external potential varies slowly in space compared to the size of the soliton, the dynamics of the center of the soliton is described by Hamilton's equations, plus terms due to radiation damping. Finally, two physical applications are discussed: the first is adiabatic transportation of solitons and the second is the Mathieu instability of trapped solitons due to time-periodic perturbations.

Abou Salem, Walid K. [Department of Mathematics, University of Toronto, Toronto, Ontario, M5S 2E4 (Canada)

2008-03-15

426

Dynamic covalent chemistry approaches toward macrocycles, molecular cages, and polymers.

The current research in the field of dynamic covalent chemistry includes the study of dynamic covalent reactions, catalysts, and their applications. Unlike noncovalent interactions utilized in supramolecular chemistry, the formation/breakage of covalent bonding has slower kinetics and usually requires the aid of a catalyst. Catalytic systems that enable efficient thermodynamic equilibrium are thus essential. In this Account, we describe the development of efficient catalysts for alkyne metathesis, and discuss the application of dynamic covalent reactions (mainly imine, olefin, and alkyne metathesis) in the development of organic functional materials. Alkyne metathesis is an emerging dynamic covalent reaction that offers robust and linear acetylene linkages. By introducing a podand motif into the catalyst ligand design, we have developed a series of highly active and robust alkyne metathesis catalysts, which, for the first time, enabled the one-step covalent assembly of ethynylene-linked functional molecular cages. Imine chemistry and olefin metathesis are among the most well-established reversible reactions, and have also been our main synthetic tools. Various shape-persistent macrocycles and covalent organic polyhedrons have been efficiently constructed in one-step through dynamic imine chemistry and olefin metathesis. The geometrical features and solubilizing groups of the building blocks as well as the reaction kinetics have significant effect on the outcome of a covalent assembly process. More recently, we explored the orthogonality of imine and olefin metatheses, and successfully synthesized heterosequenced macrocycles and molecular cages through one-pot orthogonal dynamic covalent chemistry. In addition to discrete molecular architectures, functional polymeric materials can also be accessed through dynamic covalent reactions. Defect-free solution-processable conjugated polyaryleneethynylenes and polydiacetylenes have been prepared through alkyne metathesis polymerization. We prepared imine- or ethynylene-linked porous polymer networks, which exhibit permanent porosity with high specific surface areas. Our most recent contribution is the discovery of a recyclable polyimine material whose self-healing can be activated simply by heating or water treatment. The facile access to complex functional organic molecules through dynamic covalent chemistry has allowed us to explore their exciting applications in gas adsorption/separation, host-guest chemistry, and nanocomposite fabrication. It is clear that there are significant opportunities for improved dynamic covalent systems and their more widespread applications in materials science. PMID:24739018

Jin, Yinghua; Wang, Qi; Taynton, Philip; Zhang, Wei

2014-05-20

427

Aquaporins (AQPs) are a family of integral membrane proteins, which facilitate the rapid and yet highly selective flux of\\u000a water and other small solutes across biological membranes. Molecular dynamics (MD) simulations contributed substantially to\\u000a the understanding of the molecular mechanisms that underlie this remarkable efficiency and selectivity of aquaporin channels.\\u000a This chapter reviews the current state of MD simulations of

Jochen S. Hub; Helmut Grubmüller; Bert L. Groot

428

This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.

Hall, G.E.

2011-05-31

429

NASA Astrophysics Data System (ADS)

Photofragmentation dynamics of molecular iodine was studied as a response to the joint illumination with femtosecond 800 nm near-infrared and 13 nm extreme ultraviolet (XUV) pulses delivered by the free-electron laser facility FLASH. The interaction of the molecular target with two light pulses of different wavelengths but comparable pulse energy elucidates a complex intertwined electronic and nuclear dynamics. To follow distinct pathways out of a multitude of reaction channels, the recoil of created ionic fragments is analyzed. The delayed XUV pulse provides a way of following molecular photodissociation of I2 with a characteristic time-constant of (55 +/- 10) fs after the laser-induced formation of antibonding states. A preceding XUV pulse, on the other hand, preferably creates a 4d-1 inner-shell vacancy followed by the fast Auger cascade with a revealed characteristic time constant ?A2=(23+/-11) fs for the second Auger decay transition. Some fraction of molecular cationic states undergoes subsequent Coulomb explosion, and the evolution of the launched molecular wave packet on the repulsive Coulomb potential was accessed by the laser-induced postionization. A further unexpected photofragmentation channel, which relies on the collective action of XUV and laser fields, is attributed to a laser-promoted charge transfer transition in the exploding molecule.

Krikunova, Maria; Maltezopoulos, Theophilos; Wessels, Philipp; Schlie, Moritz; Azima, Armin; Wieland, Marek; Drescher, Markus

2011-01-01

430

3-Hydroxy-3-methylglutaryl coenzyme-A reductase (HMGR) is generally regarded as targets for the treatment of hypercholesterolemia. HMGR inhibitors (more commonly known as statins) are discovered as plasma cholesterol lowering molecules. In this work, 120 atorvastatin analogues were studied using a combination of molecular modeling techniques including three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamics (MD) simulation. The results show that the best CoMFA (comparative molecular field analysis) model has q(2)=0.558 and r(2)=0.977, and the best CoMSIA (comparative molecular similarity indices analysis) model has q(2)=0.582 and r(2)=0.919. Molecular docking and MD simulation explored the binding relationship of the ligand and the receptor protein. The calculation results indicated that the hydrophobic and electrostatic fields play key roles in QSAR model. After MD simulation, we found four vital residues (Lys735, Arg590, Asp690 and Asn686) and three hydrophobic regions in HMGR binding site. The calculation results show that atorvastatin analogues obtained by introduction of F atoms or gem-difluoro groups could obviously improve the inhibitory activity. The new HMGR inhibitor analogues design in this Letter had been submitted which is being currently synthesized by our laboratories. PMID:25022881

Wang, Zhi; Cheng, Liping; Kai, Zhenpeng; Wu, Fanhong; Liu, Zhuoyu; Cai, Minfeng

2014-08-15

431

Footprinting molecular electrostatic potential surfaces for calculation of solvation energies.

A liquid is composed of an ensemble of molecules that populate a large number of different states, so calculation of the solvation energy of a molecule in solution requires a method for summing the interactions with the environment over all of these states. The surface site interaction model for the properties of liquids at equilibrium (SSIMPLE) simplifies the surface of a molecule to a discrete number of specific interaction sites (SSIPs). The thermodynamic properties of these interaction sites can be characterised experimentally, for example, through measurement of association constants for the formation of simple complexes that feature a single H-bonding interaction. Correlation of experimentally determined solution phase H-bond parameters with gas phase ab initio calculations of maxima and minima on molecular electrostatic potential surfaces (MEPS) provides a method for converting gas phase calculations on isolated molecules to parameters that can be used to estimate solution phase interaction free energies. This approach has been generalised using a footprinting technique that converts an MEPS into a discrete set of SSIPs (each described by a polar interaction parameter, ?i). These SSIPs represent the molecular recognition properties of the entire surface of the molecule. For example, water is described by four SSIPs, two H-bond donor sites and two H-bond acceptor sites. A liquid mixture is described as an ensemble of SSIPs that represent the components of the mixture at appropriate concentrations. Individual SSIPs are assumed to be independent, so speciation of SSIP contacts can be calculated based on properties of the individual SSIP interactions, which are given by the sum of a polar (?i?j) and a non-polar (E(vdW)) interaction term. Results are presented for calculation the free energies of transfer of a range of organic molecules from the pure liquid into water, from the pure liquid into n-hexadecane, from n-hexadecane into water, from n-octanol into water, and for the transfer of water from pure water into a range of organic liquids. The agreement with experiment is accurate to within 1.6-3.9 kJ mol(-1) root mean square difference, which suggests that the SSIMPLE approach is a promising method for estimation of solvation energies in more complex systems. PMID:24064723

Calero, Christian Solis; Farwer, Jochen; Gardiner, Eleanor J; Hunter, Christopher A; Mackey, Mark; Scuderi, Serena; Thompson, Stuart; Vinter, Jeremy G

2013-11-01

432

Structural properties of CHAPS micelles, studied by molecular dynamics simulations.

Detergents are essential tools to study biological membranes, and they are frequently used to solubilize lipids and integral membrane proteins. Particularly the nondenaturing zwitterionic detergent usually named CHAPS was designed for membrane biochemistry and integrates the characteristics of the sulfobetaine-type detergents and bile salts. Despite the available experimental data little is known about the molecular structure of its micelles. In this work, molecular dynamics simulations were performed to study the aggregation in micelles of several numbers of CHAPS (? 18) starting from a homogeneous water dilution. The force field parameters to describe the interactions of the molecule were developed and validated. After 50 ns of simulation almost all the systems result in the formation of stable micelles. The molecular shape (gyration radii, volume, surface) and the molecular structure (RDF, salt bridges, H-bonds, SAS) of the micelles were characterized. It was found that the main interactions that lead to the stability of the micelles are the electrostatic ones among the polar groups of the tails and the OH's from the ring moiety. Unlike micelles of other compounds, CHAPS show a grainlike heterogeneity with hydrophobic micropockets. The results are in complete agreement with the available experimental information from NMR, TEM, and SAXS studies, allowing the modeling of the molecular structure of CHAPS micelles. Finally, we hope that the new force field parameters for this detergent will be a significant contribution to the knowledge of such an interesting molecule. PMID:24650115

Herrera, Fernando E; Garay, A Sergio; Rodrigues, Daniel E

2014-04-10

433

Classical free energies for the cage and prism isomers of water hexamer computed by the self- consistent phonons (SCP) method and reversible scaling (RS) method are presented for several flexible water potentials. Both methods have been augmented with a rotational correction for improved accuracy when working with clusters. Comparison of the SCP results with the RS results suggests a fairly broad temperature range over which the SCP approximation can be expected to give accurate results for systems of water clusters, and complements a previously reported assessment of SCP. Discrepancies between the SCP and RS results presented here, and recently published replica exchange molecular dynamics (REMD) results bring into question the convergence of the REMD and accompanying replica exchange path integral molecular dynamics results. In addition to the ever-present specter of unconverged results, several possible sources for the discrepancy are explored based on inherent characteristics of the methods used.

Brown, Sandra E

2014-01-01

434

A multiscale modeling technique for bridging molecular dynamics with finite element method

NASA Astrophysics Data System (ADS)

In computational mechanics, molecular dynamics (MD) and finite element (FE) analysis are well developed and most popular on nanoscale and macroscale analysis, respectively. MD can very well simulate the atomistic behavior, but cannot simulate macroscale length and time due to computational limits. FE can very well simulate continuum mechanics (CM) problems, but has the limitation of the lack of atomistic level degrees of freedom. Multiscale modeling is an expedient methodology with a potential to connect different levels of modeling such as quantum mechanics, molecular dynamics, and continuum mechanics. This study proposes a new multiscale modeling technique to couple MD with FE. The proposed method relies on weighted average momentum principle. A wave propagation example has been used to illustrate the challenges in coupling MD with FE and to verify the proposed technique. Furthermore, 2-Dimensional problem has also been used to demonstrate how this method would translate into real world applications.

Lee, Yongchang; Basaran, Cemal

2013-11-01

435

Assessment of the convergence of molecular dynamics simulations of lipopolysaccharide membranes

The outer membrane of Gram-negative bacteria is composed of a phospholipid inner leaflet and a lipopolysaccharide outer leaflet. The chemical structure of lipopolysaccharide confers an asymmetric character to outer membranes that has been shown to play an important role in the in the electrical properties of porins, low permeability and intrinsic antibiotic resistance of Gram-negative bacteria. In the present work, atomistic molecular dynamics simulations of two different configurations of the outer membrane of Pseudomonas aeruginosa under periodic boundary conditions were carried out in order to i) validate model-derived properties against the available experimental data, ii) identify the properties whose dynamics can be sampled on nanosecond timescales, and iii) evaluate the dependence of the convergence of structural and dynamical properties on the initial configuration of the system, within the chosen force field and simulation conditions. Because the relaxation times associated with the motions of individual LPS monomers in outer membranes is very slow, the two initial configurations do not converge to a common ensemble of configuration on the nanosecond time scale. However, a number of properties of the outer membrane that will significantly impact the structural and internal dynamics of transmembrane proteins, most notably the electrostatic potential and molecular density, do converge within the simulated time scale. For these properties, a good agreement with the available experimental data was found. Such molecular model, capable of accounting for the high asymmetry and low fluidity characteristics of outer membranes, will certainly benefit future atomistic simulations of outer membrane proteins.

Soares, Thereza A.; Straatsma, TP

2008-03-01

436

Topoisomerase IB (Top1) inhibitors, such as camptothecin (CPT), stabilize the Top1-DNA cleavage complex in a DNA sequence-dependent manner. The sequence selectivity of Top1 inhibitors is important for targeting specific genomic sequences of therapeutic value. However, the molecular mechanisms underlying this selectivity remain largely unknown. We performed molecular dynamics simulations to delineate structural, dynamic and energetic features that contribute to the differential sequence selectivity of the Top1 inhibitors. We found the sequence selectivity of CPT to be highly correlated with the drug binding energies, dynamic and structural properties of the linker domain. Chemical insights, gained by per-residue binding energy analysis revealed that the non-polar interaction between CPT and nucleotide at the +1 position of the cleavage site was the major (favorable) contributor to the total binding energy. Mechanistic insights gained by a potential of mean force analysis implicated that the drug dissociation step was associated with the sequence selectivity. Pharmaceutical insights gained by our molecular dynamics analyses explained why LMP-776, an indenoisoquinoline derivative under clinical development at the National Institutes of Health, displays different sequence selectivity when compared with camptothecin and its clinical derivatives. PMID:24021629

Siu, Fung-Ming; Pommier, Yves

2013-01-01

437

NASA Astrophysics Data System (ADS)

The thermodynamic scaling of molecular dynamic properties of rotation and thermodynamic parameters in a nematic phase was investigated by a molecular dynamic simulation using the Gay-Berne potential. A master curve for the relaxation time of flip-flop motion was obtained using thermodynamic scaling, and the dynamic property could be solely expressed as a function of TV??, where T and V are the temperature and volume, respectively. The scaling parameter ?? was in excellent agreement with the thermodynamic parameter ?, which is the logarithm of the slope of a line plotted for the temperature and volume at constant P2. This line was fairly linear, and as good as the line for p-azoxyanisole or using the highly ordered small cluster model. The equivalence relation between ? and ?? was compared with results obtained from the highly ordered small cluster model. The possibility of adapting the molecular model for the thermodynamic scaling of other dynamic rotational properties was also explored. The rotational diffusion constant and rotational viscosity coefficients, which were calculated using established theoretical and experimental expressions, were rescaled onto master curves with the same scaling parameters. The simulation illustrates the universal nature of the equivalence relation for liquid crystals.

Satoh, Katsuhiko

2013-08-01

438

Topoisomerase IB (Top1) inhibitors, such as camptothecin (CPT), stabilize the Top1-DNA cleavage complex in a DNA sequence-dependent manner. The sequence selectivity of Top1 inhibitors is important for targeting specific genomic sequences of therapeutic value. However, the molecular mechanisms underlying this selectivity remain largely unknown. We performed molecular dynamics simulations to delineate structural, dynamic and energetic features that contribute to the differential sequence selectivity of the Top1 inhibitors. We found the sequence selectivity of CPT to be highly correlated with the drug binding energies, dynamic and structural properties of the linker domain. Chemical insights, gained by per-residue binding energy analysis revealed that the non-polar interaction between CPT and nucleotide at the +1 position of the cleavage site was the major (favorable) contributor to the total binding energy. Mechanistic insights gained by a potential of mean force analysis implicated that the drug dissociation step was associated with the sequence selectivity. Pharmaceutical insights gained by our molecular dynamics analyses explained why LMP-776, an indenoisoquinoline derivative under clinical development at the National Institutes of Health, displays different sequence selectivity when compared with camptothecin and its clinical derivatives. PMID:24021629

Siu, Fung-Ming; Pommier, Yves

2013-12-01

439

Molecular dynamics studies of interfacial water at the alumina surface.

Interfacial water properties at the alumina surface were investigated via all-atom equilibrium molecular dynamics simulations at ambient temperature. Al-terminated and OH-terminated alumina surfaces were considered to assess the structural and dynamic behavior of the first few hydration layers in contact with the substrates. Density profiles suggest water layering up to {approx}10 {angstrom} from the solid substrate. Planar density distribution data indicate that water molecules in the first interfacial layer are organized in well-defined patterns dictated by the atomic terminations of the alumina surface. Interfacial water exhibits preferential orientation and delayed dynamics compared to bulk water. Water exhibits bulk-like behavior at distances greater than {approx}10 {angstrom} from the substrate. The formation of an extended hydrogen bon