C60—石墨表面散射的计算机模拟研究：两种相互作用模型的比较

本文用分子动力学模拟方法在原子层次研究了低能Ｃ６０在石墨表面的非弹性散射过程。Ｃ６０的轰击能量为９０和１５０ｅＶ。Ｃ原子是的相互作用由两种半经验多体势描述。本文的模拟计算观察到了Ｃ６０分子在石墨表面散射中先发生高度形变，然后在反弹过程中逐渐恢复到接近球形的结构。     

Growth of Ag nanometre-sized particles in solution: molecular dynamics simulations

This work focuses on the growth of nanometre-sized Ag clusters in solution. Molecular dynamics simulations have been employed to gain the necessary detail on the dynamics of solute species and to study the mechanistic features of the processes governing the association of solute atoms in aggregates. Supersaturated liquid solutions of Ag in tetrachloromethane have been considered. A systematic variation of the concentration of Ag atoms in solution permitted us to show the different mechanistic scenarios responsible for the growth processes of solid Ag clusters. It is shown that such processes are limited by the thermal diffusion of solute in the solution bulk at relatively low supersaturation degrees, whereas the growth is limited by interfacial effects at relatively high supersaturation degrees.     

Molecular dynamics investigation to indicate facet effects on coalescence processes of two copper clusters with different structures

Molecular dynamics simulations have been conducted to investigate facet effects on coalescence processes of Cu₅₅ and Cu₄₂₉ clusters respectively having icosahedral (Ih) and faced center cubic (FCC) geometries. It is shown that taking into account initial positions of the two clusters, structural changes of two coalescing clusters present different patterns. Simulation results establish the pathway of the structural evolution during coalescing by using shrinkage factors, average energy per atom, mean square displacements as well as atom packing configurations. The coalescence process can be separated into three stages including an approaching stage, a coalescing stage, and a coalesced stage. In the four coalescence processes, the structural transformations mainly occur in the Cu₅₅ clusters. The simulations show that the contact crystallization orientation plays an important role in the coalescing processes and resultant structures.     

Effect of particle shape on domino wave propagation: a perspective from 3D,anisotropic discrete element simulations

A fundamental understanding of the underlying physics of granular systems is not only of academic interest, but is also relevant for industrial applications. One specific aspect that is currently only poorly understood is the effect of particle shape on the dynamics of such systems. In this work the effect of particle shape on domino wave propagation was studied using 3D, anisotropic discrete element simulations. The dominoes were modelled using the three-dimensional super-quadric equation and very good agreement between the intrinsic collision speeds predicted by the simulations and the corresponding experimental data was observed. Furthermore, the influence of particle blockiness on the collision dynamics of dominoes was investigated numerically using particle shapes ranging from ellipsoids to almost cuboid particles. It was found that the intrinsic collision speed increased with increasing particle blockiness. It was also shown that a higher initial contact point favours the transmission of kinetic energy in the direction of the wave propagation, leading to a higher intrinsic collision speed for dominoes of higher blockiness.     

Disordering of the Pb (110) surface

Molecular dynamics simulations incorporating a many-body glue model potential (GM) have been used to investigate the atomic structure and dynamics of the Pb (1 1 0) surface in the range from room temperature up to the bulk melting point. The main features of the surface disordering process include: generation of vacancies and the formation of an adlayer, the formation of so-called “local steps” and further their proliferation including wandering, creation and propagation of a quasiliquid surface film. These processes are illustrated by the use of a modern visualization technique.     

Melting of Ni and Fe nanoparticles: a molecular dynamics study with application to carbon nanotube synthesis

Molecular dynamics simulations with many-body interatomic potentials are used to study melting of Ni and Fe nanoparticles with diameters that range between 2 and 12 nm. Two different embedded-atom method interatomic potentials are used for each element. The capability of each interatomic potential to model (i) size-dependent melting in nanoparticles and (ii) the bulk melting temperature of Ni or Fe is explored. In agreement with existing theory, molecular dynamics simulations show that the melting temperature of non-supported nanoparticles decreases with decreasing nanoparticle size, displaying a linear relationship with the inverse of nanoparticle diameter. However, molecular dynamics simulations using the interatomic potentials considered in this work provide a lower estimate than existing theory for the sensitivity of the melting temperature to nanoparticle size (slope of linear relationship). Molecular dynamics simulations demonstrate that melting is surface initiated and that a finite temperature range exists in which partial melting of the nanoparticle occurs. This observation is very important in the development of advanced vapor-liquid-solid models for catalyst-assisted single-walled carbon nanotube synthesis.     

Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS

Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.     

分子动力学方法模拟GaN薄膜生长

采用分子动力学模拟方法,应用Buckingham经验势模型,模拟纤锌矿相GaN的薄膜晶格生长.研究了GaN薄膜生长的早期阶段的形貌特点、生长规律、表面结构及动力学特性.模拟发现,N原子与Ga原子按照晶格特征吸附在衬底上,作层状分布趋势并且薄膜层从下到上晶态特征逐渐减弱.观察每层沉积原子数、空位比、沉积原子团簇质心高度与沉积原子均方位移随时间的变化规律,发现了随着时间步数增加,原子团簇逐渐达到稳定,在5000步时前3层都达到了较稳定状态,且N原子比Ga原子能更快地找到平衡位置.     

Molecular dynamics simulation of microcrystalline Si deposition processes by silane plasmas

Molecular dynamics (MD) simulations have been performed to examine enhanced surface diffusion of Si adatoms during silane(SiH₄)-based plasma enhanced chemical vapor deposition (PECVD) processes. Such high surface diffusion, if it actually takes place, has been known to account for the growth of microcrystalline silicon(μc-Si) in the PECVD process. Focused in the present study is the motion of a silicon (Si) adatom on a hydrogenated Si surface and the surface diffusion coefficient of Si adatoms on the fully hydrogenated (111) Si surface at 600 K was evaluated from MD simulations. The obtained diffusion coefficient is much larger than those of typical clean Si surfaces known in the literature. The interatomic potential functions for Si-H systems used for the simulations, which we have developed for this study based on ab initio calculations of the interatomic energies, are also presented.     

Collision cascades in pure δ -plutonium

Molecular dynamics simulations of the formation and annealing of large collision cascades in delta-phase plutonium are presented. The defect evolution is followed with time up to 2 ns. Simulations are performed with the MEAM potential at three different temperatures; at 600 K where the pure delta phase is thermodynamically stable; at 300 K where the delta phase can only be maintained in a metastable state with minor additions of gallium or aluminum; and at 180 K where plutonium should transform to the alpha phase. It is found in all three cases that the atomic structure within the cascade evolves through a glass-like state. At 600 K, this structure recovers very slowly; at 300 K it persist up to 2 ns with no discernable trend to recover eventually; and at 180 K the amorphous structure initiated by the collision cascade spreads through the entire crystal and converts it to a glass-like structure.     

Synthesis and properties of novel materials at high pressure and temperature—molecular dynamics simulation studies

Molecular dynamics simulations, in combination with lattice dynamics studies, based on semiempirical interatomic potentials, have been very useful in the study of properties of complex novel materials at high temperature and pressure. Various properties such as the equation of state, elastic and thermodynamic properties, phase transitions and melting have been studied. These studies help in understanding the synthesis of important new and novel materials, especially the amorphous materials, compounds with unusually coordinated atoms, (e.g. with five-coordinated silicon atoms), materials with controlled thermal expansion, etc. A few examples will be discussed from our recent studies.     

Multiscale simulations: application to the heat transfer simulation of sliding solids

Molecular dynamics is a powerful tool allowing the simulation of matter behaviour at the atomic scale. Due to computation time, it is clearly not possible to use molecular dynamics to simulate a forming process. However, atomistic simulations can be used to study and understand the physical phenomena that occur during matter deformation. As an example, heat transfer between the contacting solids in forming processes is one of the important physics phenomena that have to be taken into account in order to do realistic simulations. A multiscale analysis of heat transfer is presented. This analysis leads to two kinds of models: a macroscopic model which can be used for the simulation of the process itself and a microscopic model that is used to determine the parameters of the macroscopic model. In this microscopic model, the friction heat generation phenomena has to be described quite accurately. Friction heat is mainly due to plastic and elastic deformation and adhesion. Thus, to understand the underlying friction heat generation phenomena, atomistic simulations using molecular dynamics are carried out. It is shown that friction heat is the transformation of mechanical work given to the system at the macroscopic scale into potential energy during elastic deformation. This potential energy which is stored in the system is finally transformed into atomic kinetic energy (friction heat) during plastic transformation.     

Evaluation of the drag force on single-walled carbon nanotubes in rarefied gases

The drag force on carbon nanotubes (CNTs) in dilute gases has been previously derived. However, the drag force formulae involve collision integrals, which are complex functions of the gas-CNT interaction potential. The unavailability of the collision integrals and interaction potential makes the application of the theoretical drag force laws impossible. In this work, we develop a potential model for the interaction between a gas and single-walled CNT. The collision integrals are then calculated based on the potential and empirical expressions are proposed. Finally, the drag force is computed directly through molecular dynamics simulations and compared with the theoretical predictions.     

Event driven algorithms applied to a high energy ball mill simulation

In the physics community, event driven molecular dynamics simulations have been successfully applied to typical physical topics, such as granular gases. In contrast, in the engineering sciences, event driven algorithms have not become as popular, even though they can be far more efficient for special systems. In this paper, we present an event driven simulation of a high energy ball mill, where the motion and energy transfer of the grinding balls during operation are simulated. Stable numerical algorithms for collision detection and collision response are developed and several possible pitfalls are discussed. Furthermore, an improved event list handling technique and a specialized space subdivision method is presented. The performance of the partitioning is demonstrated by experiments. It is shown that the scaling rules usually applied are oversimplified. A new way of scaling the process parameters to obtain a higher production yield using iso-impact diagrams is presented.     

Molecular dynamics simulation approaches to K channels: conformational flexibility and physiological function

Molecular modeling and simulations enable extrapolation for the structure of bacterial potassium channels to the function of their mammalian homologues. Molecular dynamics simulations have revealed the concerted single-file motion of potassium ions and water molecules through the selectivity filter of K channels and the role of filter flexibility in ion permeation and in "fast gating." Principal components analysis of extended K channel simulations suggests that hinge-bending of pore-lining M2 (or S6) helices plays a key role in K channel gating. Based on these and other simulations, a molecular model for gating of inward rectifier K channel gating is presented.     

Molecular dynamics simulation of a DNA containing a single strand break

Molecular dynamics simulations were performed for a dodecamer DNA containing a single strand break (SSB), which has been represented by a 3'-OH deoxyribose and 5'-OH phosphate in the middle of the strand. Molecular force field parameters of the 5'-OH phosphate region were determined from an ab initio calculation at the HF/6-31G level using the program package GAMESS. The DNA was placed in a periodic boundary box with water molecules and Na+ counter-ions to produce a neutralised system. After minimisation, the system was heated to 300 K, equilibrated and a production run at constant NTP was executed for 1 ns using AMBER 4.1. Snapshots of the SSB-containing DNA and a detailed analysis of the equilibrated average structure revealed surprisingly small conformational changes compared to normal DNA. However, dynamic properties calculated using the essential dynamics method showed some features that may be important for the recognition of this damage by repair enzymes.     

MD simulations of amorphous SiO2 thin film formation in reactive sputtering deposition processes

Silicon Dioxide (SiO₂) thin film deposition processes were studied with the use of classical Molecular Dynamics (MD) simulations combined with Monte Carlo (MC) simulations. The MC simulations are shown to efficiently emulate thermal relaxation processes during deposition. Dependence of deposited film properties on the incident kinetic energies is examined from the numerical simulations.     

Evaluation of a grid based molecular dynamics approach for polypeptide simulations

Molecular dynamics is very important for biomedical research because it makes possible simulation of the behavior of a biological macromolecule in silico. However, molecular dynamics is computationally rather expensive: the simulation of some nanoseconds of dynamics for a large macromolecule such as a protein takes very long time, due to the high number of operations that are needed for solving the Newton's equations in the case of a system of thousands of atoms. In order to obtain biologically significant data, it is desirable to use high-performance computation resources to perform these simulations. Recently, a distributed computing approach based on replacing a single long simulation with many independent short trajectories has been introduced, which in many cases provides valuable results. This study concerns the development of an infrastructure to run molecular dynamics simulations on a grid platform in a distributed way. The implemented software allows the parallel submission of different simulations that are singularly short but together bring important biological information. Moreover, each simulation is divided into a chain of jobs to avoid data loss in case of system failure and to contain the dimension of each data transfer from the grid. The results confirm that the distributed approach on grid computing is particularly suitable for molecular dynamics simulations thanks to the elevated scalability.     

A numerical study of the growth process of Au nanometre-sized particles in liquid phases

Molecular dynamics simulations have been employed to study the growth of faceted and spherical gold (Au) nanometre-sized particles in undercooled Au melts and supersaturated Kr-, Xe-?and Rn-based liquid solutions at different degrees of undercooling and supersaturation. Different mechanisms have been observed depending on the chemical environment and temperature. At relatively high temperatures, surface adsorption is shown to critically depend on the dynamics of surface species with low coordination number. At low temperatures, adsorption occurs instead with no selective feature. Dendritic structures are formed at the particle surface at high adsorption rates.     

Collision cascades in pure <Emphasis Type="Italic">δ</Emphasis>-plutonium

Molecular dynamics simulations of the formation and annealing of large collision cascades in delta-phase plutonium are presented. The defect evolution is followed with time up to 2 ns. Simulations are performed with the MEAM potential at three different temperatures; at 600 K where the pure delta phase is thermodynamically stable; at 300 K where the delta phase can only be maintained in a metastable state with minor additions of gallium or aluminum; and at 180 K where plutonium should transform to the alpha phase. It is found in all three cases that the atomic structure within the cascade evolves through a glass-like state. At 600 K, this structure recovers very slowly; at 300 K it persist up to 2 ns with no discernable trend to recover eventually; and at 180 K the amorphous structure initiated by the collision cascade spreads through the entire crystal and converts it to a glass-like structure.