Molecular dynamics simulations of compressed hydrogen

Abstract

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. Two tight-binding models of hydrogen have been developed with a single s-type orbital on each atom that reproduce properties of the dimer, of various crystalline structures, and of the fluid. The simulations indicate that the rapid rise in the electrical conductivity observed in the gas-gun experiments depends critically on the dissociated atoms (monomers). We find that the internal structure of warm, dense hydrogen has a pronounced time-dependent nature with the continual dissociation of molecules (dimers) and association of atoms (monomers). Finally, Hugoniots derived from the equations-of-state of these models do not exhibit the large compressions predicted by the recent laser experiments.     

Molecular dynamics simulations of one-dimensional Lennard-Jones systems

One-dimensional Lennard-Jones systems are investigated by molecular dynamics simulations. The full Lennard-Jones potential is compared to the repulsive Lennard-Jones potential. It is found that the pair correlation function and the normalized velocity autocorrelation function agree at high densities and high temperature. However, the diffusion coefficient indicates that the attractive potential introduces additional correlations into particle dynamics which are not reflected in the statics. These results are in agreement with three-dimensional studies.     

Molecular dynamics simulations of cytochrome c unfolding in AOT reverse micelles: The first steps

This paper explores the reduced form of horse cytochrome c confined in reverse micelles (RM) of sodium bis-(2-ethylhexyl) sulfosuccinate (AOT) in isooctane by molecular dynamics simulation. RMs of two sizes were constructed at a water content of W _o = [ H_2O ]/[AOT] = 5.5 and 9.1. Our results show that the protein secondary structure and the heme conformation both depend on micellar hydration. At low hydration, the protein structure and the heme moiety remain stable, whereas at high water content the protein becomes unstable and starts to unfold. At W _o = 9.1 , according to the X-ray structure, conformational changes are mainly localized on protein loops and around the heme moiety, where we observe a partial opening of the heme crevice. These findings suggest that within our time window (10ns), the structural changes observed at the heme level are the first steps of the protein denaturation process, previously described experimentally in micellar solutions. In addition, a specific binding of AOT molecules to a few lysine residues of the protein was found only in the small-sized RM.     

Molecular dynamics simulations of electrostatic layer-by-layer self-assembly

Electrostatic assembly of multilayered thin films through sequential adsorption of polyions in layer-by-layer fashion utilizes the strong electrostatic attraction between oppositely charged molecules. We perform molecular dynamics simulations of multilayers of flexible polyelectrolytes around a charged spherical particle. Our simulations establish that the charge reversal after each deposition step is a crucial factor for the steady layer growth. The multilayers appear to be nonequilibrium structures.     

Molecular dynamics simulations on the melting of gold nanoparticles

Molecular dynamics is employed to study the melting of bulk gold and gold nanoparticles. PCFF, Sutton-Chen and COMPASS force fields are adopted to study the melting point of bulk gold and we find out that the Sutton-Chen force field is the most accurate model in predicting the melting point of bulk gold. Consequently, the Sutton-Chen force field is applied to study the melting points of spherical gold nanoparticles with different diameters. Variations of diffusion coefficient, potential energy and translational order parameter with temperature are analyzed. The simulated melting points of gold nanoparticles are between 615～1115 K, which are much lower than that of bulk gold (1336 K). As the diameter of gold nanoparticle drops, the melting point also descends. The melting mechanism is also analyzed for gold nanoparticles.     

Molecular dynamics simulations of phase transition of n-nonadecane under high pressure

The phase transition behavior of n-nonadecane under high pressure was investigated with molecular dynamics (MD) simulations method. A simplified model with amorphous structure and periodic boundary conditions in constant-temperature, constant-pressure ensemble was used in this study. The results showed that the whirling and molecules motion of n-nonadecane chains were restrained by the high pressure. The simulated phase transition temperature of n-nonadecane under high pressure is higher than that under atmospheric pressure. The order parameter of n-nonadecane decreases with the increase in temperature. The simulations reveal that MD is an effective method to understand the phase transition of alkane-based phase change materials on molecular and atomic scale.     

Molecular dynamics simulations of AlN deposition on GaN substrate

ABSTRACT

In this work, we investigated the deposition of AlN film on GaN substrate by using molecular dynamics (MD) simulations. The effects of GaN substrate surface, growth temperature, and injected N: Al flux ratio on the growth of AlN film were simulated and studied. Consequently, the deposited AlN film on the (0001) Ga-terminated GaN surface achieves better surface morphology and crystallinity than that on the (000-1) N-terminated GaN surface due to the different diffusion ability of Al and N adatoms on two GaN surfaces. Furthermore, with the increase of growth temperature, the surface morphology and crystallinity of AlN film were improved owing to the enhanced mobility of adatoms. At the optimised injected N: Al flux ratio of 1, comparatively good surface morphology and crystallinity of deposited AlN films were realised. This method lays a foundation for the follow-up real-time study of defects and stress evolution of AlN on GaN and can be applied to film growth of other materials.     

Molecular dynamics simulations of the nano-droplet impact process on hydrophobic surfaces

Large-scale molecular dynamics simulations are used to study the dynamic processes of a nano-droplet impacting on hydrophobic surfaces at a microscopic level. Both the impact phenomena and the velocity distributions are recorded and analyzed. According to the simulation results, similar phenomena are obtained to those in macro-experiments. Impact velocity affects the spread process to a greater degree than at a level of contact angle when the velocity is relatively high. The velocity distribution along the X axis during spread is wave-like, either W- or M-shaped, and the velocity at each point is oscillatory; while the edges have the highest spread velocity and there are crests in the distribution curve which shift toward the edges over time. The distribution along the Y axis is 〈- or 〉-shaped, and the segments above the middle have the lowest decrease rate in the spreading process and the highest increase rate in the retraction process.     

Molecular kinetic theory of boundary slip on textured surfaces by molecular dynamics simulations

A theoretical model extended from the Frenkel-Eyring molecular kinetic theory (MKT) was applied to describe the boundary slip on textured surfaces. The concept of the equivalent depth of potential well was adopted to characterize the solid-liquid interactions on the textured surfaces. The slip behaviors on both chemically and topographically textured surfaces were investigated using molecular dynamics (MD) simulations. The extended MKT slip model is validated by our MD simulations under various situations, by constructing different complex surfaces and varying the surface wettability as well as the shear stress exerted on the liquid. This slip model can provide more comprehensive understanding of the liquid flow on atomic scale by considering the influence of the solid-liquid interactions and the applied shear stress on the nano-flow. Moreover, the slip velocity shear-rate dependence can be predicted using this slip model, since the nonlinear increase of the slip velocity under high shear stress can be approximated by a hyperbolic sine function.     

Molecular dynamics simulations of jet breakup and ejecta production from a grooved Cu surface under shock loading

Large-scale non-equilibrium molecular dynamics simulations are performed to explore the jet breakup and ejecta production of single crystal Cu with a triangular grooved surface defect under shock loading. The morphology of the jet breakup and ejecta formation is obtained where the ejecta clusters remain spherical after a long simulation time. The effects of shock strength as well as groove size on the steady size distribution of ejecta clusters are investigated. It is shown that the size distribution of ejecta exhibits a scaling power law independent of the simulated shock strengths and groove sizes. This distribution, which has been observed in many fragmentation processes, can be well described by percolation theory.     

Thermal conductivity of multi-walled carbon nanotubes:Molecular dynamics simulations

Heat conduction in single-walled carbon nanotubes(SWCNTs) has been investigated by using various methods, while less work has been focused on multi-walled carbon nanotubes(MWCNTs). The thermal conductivities of the double-walled carbon nanotubes(DWCNTs) with two different temperature control methods are studied by using molecular dynamics(MD) simulations. One case is that the heat baths(HBs) are imposed only on the outer wall, while the other is that the HBs are imposed on both the two walls. The results show that the ratio of the thermal conductivity of DWCNTs in the first case to that in the second case is inversely proportional to the ratio of the cross-sectional area of the DWCNT to that of its outer wall. In order to interpret the results and explore the heat conduction mechanisms, the inter-wall thermal transport of DWCNTs is simulated. Analyses of the temperature profiles of a DWCNT and its two walls in the two cases and the interwall thermal resistance show that in the first case heat is almost transported only along the outer wall, while in the second case a DWCNT behaves like parallel heat transport channels in which heat is transported along each wall independently.This gives a good explanation of our results and presents the heat conduction mechanisms of MWCNTs.     

Molecular dynamics simulations of displacement cascades in Fe-10%Cr systems

Molecular dynamics simulations of the displacement cascades in Fe-10%Cr systems are used to simulate the primary knocked-on atom events of the irradiation damage at temperatures 300,600,and 750 K with primary knockedon atom energies between 1 and 15 keV.The results indicate that the vacancies produced by the cascade are all in the central region of the displacement cascade.During the cascade,all recoil Fe and Cr atoms combine with each other to form Fe-Cr or Fe-Fe interstitial dumbbells as well as interstitial clusters.The number and the size of interstitial clusters increase with the energy of the primary knocked-on atom and the temperature.A few large clusters consist of a large number of Fe interstitials with a few Cr atoms,the rest are Fe-Cr clusters with small and medium sizes.The interstitial dumbbells of Fe-Fe and Fe-Cr are in the 111 and 110 series directions,respectively.     

熔融Cu55团簇在铜块体中凝固过程的分子动力学模拟

应用基于嵌入原子势函数的分子动力学方法,模拟了嵌入在具有面心立方结构同质块体中的熔融Cu55团簇在不同急冷温度下微观结构的演变情况.通过计算熔融Cu55团簇的均方位移和原子平均能量随时间步的变化,并应用键对分析技术,分析了急冷温度对熔融Cu55团簇结构变化的影响.研究结果表明,由于受到块体结构的影响,在所研究的急冷温度范围内,熔融Cu55团簇在凝固过程中形成了以面心立方结构为主的微观结构.结晶过程是原子不断交换其位置的过程,团簇原子位置的重排敏感于温度的变化.随着急冷温度的升高,原子的扩散范围增大.在100,300和500 K三个较低的温度下有利于形成稳定的面心立方结构,但当急冷到100 K时,团簇中的原子在没有找到其最佳位置之前就已经完成晶化.在急冷到500 K时,团簇中的原子在块体中扩散充分,与块体中的原子形成理想的面心立方结构.在700,900和1100 K三个较高的温度上,局域结构表现为随时间步波动性变化.     

The influence of changes in the framework on the diffusion in zeolites. Molecular dynamics simulations

Some less known methods are described for the analysis of trajectories of guest molecules in porous solids. Such trajectories can be calculated by Molecular Dynamics (MD) computer simulations in order to analyze the interrelations between the structure and the particle behaviour including collective phenomena. Some results obtained with these methods for diffusing methane in zeolites of type LTA are presented. An analytical potential model for LTA type zeolites is given that make extremely long runs or simulations of large lattice regions for systems with rigid lattice possible. Such runs are necessary e.g. to examine questions as the influence of extented lattice defects or the fractal behaviour of the partical trajectories.     

Molecular dynamics simulations of pure methane and carbon dioxide hydrates: lattice constants and derivative properties

ABSTRACT

We report extensive molecular dynamics simulation results of pure methane and carbon dioxide hydrates at pressure and temperature conditions that are of interest to various practical applications. We focus on the calculation of the lattice constants of the two pure hydrates and their dependence on pressure and temperature. The calculated lattice constants are correlated using second order polynomials which are functions of either temperature or pressure. Finally, the obtained correlations are used in order to calculate two derivative properties, namely the isothermal compressibility and the isobaric thermal expansion coefficient. The current simulation results are also compared against reported experimental measurements and other simulation studies and good agreement is found for the case of isothermal compressibility. On the other hand, for the case of isobaric thermal expansion coefficient good agreement is found only with other simulation studies, while the simulation studies are in disagreement with experiments, particularly at low temperatures.     

Molecular dynamics of MgSiO3 perovskite melting

The melting curve of MgSiO分子动力学 MgSiO3钙钛矿 熔化温度 高压melting temperature, molecular dynamics, high pressureProject supported by the National Natural Science Foundation of China (Grant Nos 10274055 and 10376021),the Natural Science Foundation of Gansu Province, China (Grant No 3ZS051-A25-027) and the Scientific Research Foundation of Education Bureau of Gansu Province, China (Grant No 0410-01).2005-01-125/8/2005 12:00:00 AMThe melting curve of MgSiO3 perovskite is simulated using molecular dynamics simulations method at high pressure. It is shown that the simulated equation of state of MgSiO3 perovskite is very successful in reproducing accurately the experimental data. The pressure dependence of the simulated melting temperature of MgSiO3 perovskite reproduces the stability of the orthorhombic perovskite phase up to high pressure of 130GPa at ambient temperature, consistent with the theoretical data of the other calculations. It is shown that its transformation to the cubic phase and melting at high pressure and high temperature are in agreement with recent experiments.     

Alchemical molecular dynamics for inverse design

We present a molecular dynamics (MD) implementation of an extended statistical mechanical ensemble that includes ‘alchemical’ degrees of freedom describing particle attributes as thermodynamic variables. We demonstrate the use of this alchemical MD method in inverse design simulations of particles interacting via the Oscillating Pair Potential (OPP) and the Lennard–Jones–Gauss potential (LJG) – two general, previously studied models for which phase diagrams are known. We show that alchemical MD can quickly and efficiently optimise pair potentials for target structures within a specified design space in the low-temperature regime, where internal energy adequately represents the features of the alchemical free energy landscape. We show that alchemical MD can be also used to inversely design pair potentials to achieve target materials properties (here, bulk modulus) directly, without explicit knowledge of the structure–property relationship. Alchemical MD can easily be generalised and applied to any target materials properties or structures and used with any differentiable interaction potential.     

Monte Carlo molecular dynamics simulations for two-dimensional magnets

A combined Monte Carlo molecular dynamics simulation technique is used to study thedynamic structure factor on a square lattice for isotropic Heisenberg and planar classical ferromagnetic spin Hamiltonians.     

Molecular dynamics simulations of the chiral recognition mechanism for a polysaccharide chiral stationary phase in enantiomeric chromatographic separations

We use explicit-solvent fully atomistic molecular dynamics (MD) simulations, permitting all the interactions between the atoms constituting the polymeric chiral stationary phase (CSP), the solvent molecules and the drug molecule enantiomers, to better understand the chiral recognition mechanism that makes chromatographic separation possible. Using amylose tris(3,5-dimethylphenyl carbamate) (ADMPC) as prototype, three solvent systems, and ten racemates as solutes, we seek a molecular dynamics average quantity that could serve as a metric that predicts which of the two enantiomers will elute first and also correlates with the ratio of retention times for enantiomers. To better understand the molecular dynamic chiral recognition that provides the discrimination which results in the separation of enantiomers by high performance liquid chromatography, we examine the differences in hydrogen bonding lifetimes in various donor–acceptor pairs between the drugs and the ADMPC, and map out the differences in ring-ring interactions between the drugs and the ADMPC. Several MD average quantities related to hydrogen-bonding lifetimes correlate with the ratio of retention times for the enantiomers. One of these quantities provides a prediction of the correct elution order 90% of the time, and the ratios of these quantities for the enantiomers provide linear correlation (0.85 coefficient) with experimental separation factors.