Analysis of semi-classical potentials for molecular dynamics and Monte Carlo simulations of warm dense matter

Effective, semi-classical potentials may present a powerful tool for the determination of properties of warm dense matter, systems characterized by both moderate coupling and moderate degeneracy. However, this requires the use of these potentials in a regime where the approximations employed in their derivation begin to break down. This work presents a careful analysis of the methodology and approximations used to derive semi-classical potentials for Coulomb systems. Particular attention is paid to the appearance of many-body effects and the techniques that may be used to model them. Analytical arguments and simple examples indicate that the role of many-body effects cannot be ignored in the warm dense matter regime, and those semi-classical Coulomb potentials that focus on the pair interaction do not adequately treat many-body effects.     

Classical molecular dynamics model for coupled two component plasmas

This work is an improved continuation of a previous attempt to use classical molecular dynamics (MD) as a tool for the investigation of hot and dense “real” plasmas. “Real” in this context refers to ions and electrons interacting through Coulomb forces and undergoing ionization/recombination. The objective of designing such a non standard approach to plasma equilibrium is to explore a new way to discuss warm and dense matter with a method able to deal with the whole complexity of a N-body system of ions and electrons. Plasma relaxation times can be investigated up to a picosecond. The resulting equilibrium ion populations, built self consistently, are comparable to those found in literature and, potentially validate access to all the statistical data usually derived from MD simulations.     

Explicit solvent molecular dynamics simulations of chaperonin-assisted rhodanese folding

Chaperonins are known to facilitate the productive folding of numerous misfolded proteins, Despite their established importance, the mechanism of chaperonin-assisted protein folding remains unknown. In the present article, all-atom explicit solvent molecular dynamics (MD) simulations have been performed for the first time on rhodanese folding in a series of cavity-size and cavity-charge chaperonin mutants. A compromise between stability and flexibility of chaperonin structure during the substrate folding has been observed and the key factors affecting this dynamic process are discussed.     

Effective particle size from molecular dynamics simulations in fluids

We report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. This procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks–Chandler–Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be \(\sim 0.75\sigma \), where \(\sigma \) defines the length scale of the force interaction (the LJ diameter). The effective “hydrodynamic” radii determined by this means are distinct from commonly assumed values of \(0.5\sigma \) and \(1.0\sigma \), but agree with a value developed from the atomistic analysis of the viscosity of such systems.     

SEMILLAC: A new hybrid atomic model of hot dense plasmas

SEMILLAC is a fast, yet highly accurate method to calculate ionic population distributions in plasmas at a given electron temperature and density. SEMILLAC solves rate equations for non-relativistic configurations population distributions. It considers electron collisional, radiative and autoionizing atomic processes. The code is designed to be highly versatile so it can be used for modeling a wide range of laboratory plasmas. The population distributions can be calculated for steady state or time dependent conditions, with or without the presence of a radiation field. SEMILLAC is designed to be used as a tool for population distributions calculations and spectroscopic modeling of plasmas. Our aim is to get high accuracy while keeping the code fast enough to be used for standard PC calculations. At the heart of our method, average transitions energies and rate coefficients are calculated for a restricted set of simple non-relativistic ionic configurations using the HULLAC code. We then use this basic set to calculate energies and rates coefficients of more complex, multiply excited configurations.     

Rheology of dense model fluids via nonequilibrium molecular dynamics: Shear thinning and ordering transition

Nonequilibrium molecular dynamics computer simulations are employed to investigate the rheology of dense simple model fluids. Besides the non-Newtonian behavior of the viscosity functions a shear-induced ordering transition is an essential feature of this presentation. Its occurrence in the simulation is supported by a hydrodynamic stability analysis. To illustrate the scenario preceding the instability, density and velocity profiles of the flow are considered as well as the static structure factor which enables a comparison with recent experimental results for dense suspensions. Problems related to experimental evidence of the ordering transition into layers are discussed in light of the derived stability criterion.

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Zusammenfassung Nichtgleichgewichts-Molekulardynamik Computersimulationen werden zur Untersuchung der rheologischen Eigenschaften von dichten einfachen Modell-Fluiden herangezogen. Neben dem nicht-Newtonschen Verhalten der Viskositätsfunktionen steht ein scherinduzierter Ordnungsübergang im Vordergrund der Betrachtungen. Sein Auftreten in der Simulation wird durch eine hydrodynamische Stabilitätsanalyse untermauert. Dichte- und Geschwindigkeitsprofile der Strömung werden zur Veranschaulichung des der Instabilität vorausgehenden Szenarios ebenso herangezogen wie der statische Strukturfaktor, der einen Vergleich mit neuen experimentellen Beobachtungen an dichten Suspensionen ermöglicht. Probleme beim experimentellen Nachweis dieses sich als Schichtenbildung manifestierenden Ordnungsüberganges werden anhand des abgeleiteten Stabilitätskriteriums diskutiert.

     

A Lagrangian-based continuum homogenization approach applicable to molecular dynamics simulations

The continuum notions of effective mechanical quantities as well as the conditions that give meaningful deformation processes for homogenization problems with large deformations are reviewed. A continuum homogenization model is presented and recast as a Lagrangian-based approach for heterogeneous media that allows for an extension to discrete systems simulated via molecular dynamics (MD). A novel constitutive relation for the effective stress is derived so that the proposed Lagrangian-based approach can be used for the determination of the “stress–deformation” behavior of particle systems. The paper is concluded with a careful comparison between the proposed method and the Parrinello–Rahman approach to the determination of the “stress–deformation” behavior for MD systems. When compared with the Parrinello–Rahman method, the proposed approach clearly delineates under what conditions the Parrinello–Rahman scheme is valid.     

金属材料辐照缺陷演化的分子动力学研究进展

辐照条件下,高能粒子在金属材料内部引入稠密的辐照缺陷,导致材料力学性能严重退化,缩短材料服役寿命,是辐照材料研究的关键问题。辐照缺陷多处在纳米尺度,故分子动力学方法是模拟辐照缺陷的有力工具,近年来被广泛用于研究辐照缺陷演化。本文总结了金属材料中辐照缺陷演化的分子动力学研究进展,介绍了级联碰撞、点缺陷、空洞、氦泡、Frank位错环、层错四面体等辐照缺陷,及其与位错、晶界等微结构的相互作用。分子动力学方法揭示的机制与模型,深化了学界对辐照效应的认识,有助于提高辐照材料力学性能和设计耐辐照材料。     

金属材料辐照缺陷演化的分子动力学研究进展

辐照条件下,高能粒子在金属材料内部引人稠密的辐照缺陷,导致材料力学性能严重退化,缩短材料服役寿命,是辐照材料研究的关键问题.辐照缺陷多处在纳米尺度,故分子动力学方法是模拟辐照缺陷的有力工具,近年来被广泛用于研究辐照缺陷演化.论文总结了金属材料中辐照缺陷演化的分子动力学研究进展,介绍了级联碰撞、点缺陷、空洞、氦泡、Frank位错环、层错四面体等辐照缺陷,及其与位错、晶界等微结构的相互作用.分子动力学方法揭示的机制与模型,深化了学界对辐照效应的认识,有助于提高辐照材料力学性能和设计耐辐照材料.     

Investigations into crazing in glassy amorphous polymers through molecular dynamics simulations

In many glassy amorphous polymers, localisation of deformation during loading leads to crazes. Crazes are crack like features whose faces are bridged either by fibrils or a cellular network of voids and fibrils. While formation of crazes is aided by the presence of surface imperfections and embedded dust particles, in this work, we focus on intrinsic crazes that form spontaneously in the volume of the material. We perform carefully designed molecular dynamics simulations on well equilibrated samples of a model polymer with a view to gaining insights into certain incompletely understood aspects of the crazing process. These include genesis of the early nanovoids leading to craze nucleation, mechanisms of stabilising the cellular or fibrillar structure and the competition between chain scission and chain disentanglement in causing the final breakdown of the craze. Additionally, we identify and enumerate clusters of entanglement points with high functionality as effective topological constraints on macromolecular chains. We show that regions with low density of entanglement clusters serve as sites for nanovoid nucleation under high mean stress. Growth occurs by the repeated triggering of cavitation instabilities above a growing void. The growth of the void is aided by disentanglement in and flow of entanglements away from the cavitating region. Finally, for the chain lengths chosen, scission serves to supply short chains to the growing craze but breakdown occurs by complete disentanglement of the chains. In fact, most of the energy supplied to the material seems to be used in causing disentanglements and very little energy is required to create a stable fibril.     

Numerical simulations of energy transfer in counter-streaming plasmas

Collisionless shock formation is investigated with large scale fully electromagnetic two-dimensional Particle-in-Cell numerical simulations. Two plasmas are colliding in the center of mass reference frame at sub-relativistic velocities. Their interaction leads to collisionless stochastic electron heating, ion slowing down and formation of a shock front. We focus here on the initial stage of evolution where electron heating is due to the Weibel-like micro-instability driven by the high-speed ion flow. A two stage process is described in the detailed analysis of our simulation results. Filament generation, followed by turbulent mixing, constitute the dominant mechanism for energy repartition. The global properties are illustrated by examination of single filament evolution in terms of energy/particle density and fields.     

The application of nonlocal theory method in the coarse-grained molecular dynamics simulations of long-chain polylactic acid

The micro-capsules used for drug delivery are fabricated using polylactic acid(PLA),which is a biomedical material approved by the FDA.A coarse-grained model of long-chain PLA was built,and molecular dynamics(MD)simulations of the model were performed using a MARTINI force field.Based on the nonlocal theory,the formula for the initial elastic modulus of polymers considering the nonlocal effect was derived,and the scaling law of internal characteristic length of polymers was proposed,which was used to adjust the cut-off radius in the MD simulations of PLA.The results show that the elastic modulus should be computed using nonlinear regression.The nonlocal effect has a certain influence on the simulation results of PLA.According to the scaling law,the cut-off radius was determined and applied to the MD simulations,the results of which reflect the influence of the molecular weight change on the elastic moduli of PLA,and are in agreement with the experimental outcome.     

A reversible problem in non-equilibrium thermodynamics: Hamiltonian evolution equations for non-equilibrium molecular dynamics simulations

The reversible contribution to contemporary theories of non-equilibrium thermodynamics is reviewed as a methodology for attacking difficult, conservative problems in complex fluid dynamics. Several examples of past successes are discussed, and a new application is addressed: non-equilibrium molecular dynamics (NEMD) simulations. NEMD simulations of fluids are generally based on either a DOLLS or SLLOD tensor algorithm. The former is always considered to be a Hamiltonian system, but not particularly useful in high strain rate flow simulations, while the latter is considered not to be a Hamiltonian system, but much more practical and accurate in flow simulations. We demonstrate herein using non-canonical transformations of the particle momenta of the system that the SLLOD equations, when written in terms of appropriate non-canonical variables, are completely Hamiltonian, whereas the DOLLS equations are not so. A modified set of DOLLS equations in terms of the non-canonical variables which again is completely Hamiltonian is also derived. Both algorithms then lead to a phase space distribution function which is canonical in both the coordinates and momenta.     

On the energy conservation during the active deformation in molecular dynamics simulations

In this paper, we examined the energy conservation for the current schemes of applying active deformation in molecular dynamics (MD) simulations. Specifically, two methods are examined. One is scaling the dimension of the simulation box and the atom positions via an affine transformation, suitable for the periodic system. The other is moving the rigid walls that interact with the atoms in the system, suitable for the non-periodic system. Based on the calculation of the external work and the internal energy change, we present that the atom velocities also need to be updated in the first deformation method; otherwise the energy conservation cannot be satisfied. The classic updating scheme is examined, in which any atom crossing the periodic boundary experiences a velocity delta that is equal to the velocity difference between the opposite boundaries. In addition, a new scheme which scales the velocities of all the atoms according to the strain increment is proposed, which is more efficient and realistic than the classic scheme. It is also demonstrated that the Virial stress instead of its interaction part is the correct stress definition that corresponds to Cauchy stress in the continuum mechanics.     

Energy corrugation in atomic-scale friction on graphite revisited by molecular dynamics simulations

Although atomic stick–slip friction has been extensively studied since its first demonstration on graphite,the physical understanding of this dissipation-dominated phenomenon is still very limited. In this work, we perform molecular dynamics(MD) simulations to study the frictional behavior of a diamond tip sliding over a graphite surface. In contrast to the common wisdom, our MD results suggest that the energy barrier associated lateral sliding(known as energy corrugation) comes not only from interaction between the tip and the top layer of graphite but also from interactions among the deformed atomic layers of graphite. Due to the competition of these two subentries, friction on graphite can be tuned by controlling the relative adhesion of different interfaces.For relatively low tip-graphite adhesion, friction behaves normally and increases with increasing normal load. However,for relatively high tip-graphite adhesion, friction increases unusually with decreasing normal load leading to an effectively negative coefficient of friction, which is consistent with the recent experimental observations on chemically modified graphite. Our results provide a new insight into the physical origins of energy corrugation in atomic scale friction.     

Predicting EXAFS signals from shock compressed iron by use of molecular dynamics simulations

Simulated EXAFS signals from ab initio models and configurational averaging of molecular dynamics (MD) data are compared for α-Fe, and configurationally averaged MD EXAFS signals are compared with experimental data for iron shock compressed to pressures above the α–ε transition pressure. It is shown that molecular dynamics potentials and ab initio models capable of recreating similar vibrational density of states lead to EXAFS signals in good mutual agreement. The effects of the classical nature of the phonon distribution in the MD and the anharmonicity of the potential give rise to noticeable differences between ab initio models and configurational averaging of MD data. However, the greatest influence on the spectra is the form of the potential itself. We discuss the importance of these effects in simulating EXAFS spectra for shock compressed polycrystalline iron. It is shown that EXAFS is an insensitive probe for determining the nature of the close packed product phase in this system.     

The effects of ionization potential depression on the spectra emitted by hot dense aluminium plasmas

Recent experiments at the Linac Coherent Light Source (LCLS) X-ray Free-Electron-Laser (FEL) have demonstrated that the standard model used for simulating ionization potential depression (IPD) in a plasma (the Stewart–Pyatt (SP) model, J.C. Stewart and K.D. Pyatt Jr., Astrophysical Journal 144 (1966) 1203) considerably underestimates the degree of IPD in a solid density aluminium plasma at temperatures up to 200 eV. In contrast, good agreement with the experimental data was found by use of a modified Ecker–Kröll (mEK) model (G. Ecker and W. Kröll, Physics of Fluids 6 (1963) 62–69). We present here detailed simulations, using the FLYCHK code, of the predicted spectra from hot dense, hydrogenic and helium-like aluminium plasmas ranging in densities from 0.1 to 4 times solid density, and at temperatures up to 1000 eV. Importantly, we find that the greater IPDs predicted by the mEK model result in the loss of the n = 3 states for the hydrogenic ions for all densities above ≈0.8 times solid density, and for the helium-like ions above ≈0.65 solid density. Therefore, we posit that if the mEK model holds at these higher temperatures, the temperature of solid density highly-charged aluminium plasmas cannot be determined by using spectral features associated with the n = 3 principal quantum number, and propose a re-evaluation of previous experimental data where high densities have been inferred from the spectra, and the SP model has been used.     

固体塑性实验室时间尺度的分子动力学模拟概述

随着超级计算机软硬件的飞速提升,基于经验势函数的分子动力学模拟在解析固体塑性的微观机制方面发挥着关键作用.但是,由于传统分子动力学基于牛顿运动方程数值积分,积分时间步长通常为飞秒量级,其模拟的时间尺度通常限于纳秒量级,从而为模拟长时间尺度固体塑性机制带来了巨大的挑战.本文从分子动力学模拟的时间尺度限制切入,介绍目前国际...     

Bin size determination for the measurement of mean flow velocity in molecular dynamics simulations

Extracting macroscopic properties from molecular simulation of fluids is required in most of the molecular dynamics problems. However, methods used for this purpose, their accuracy, and their dependence on the sampling and averaging schemes are still ambiguous. Macroscopic properties at any point of a molecular domain can be extracted via sampling and averaging of molecular behavior within a control region around that point, called a bin. The size of this bin has a significant impact on the accuracy of the macroscopic properties' measurement. In this research, we will focus on the measurement of mean flow velocity using ‘binning method’. On the basis of the results of this study, the most appropriate range of the bin size in which mean velocity can be measured accurately is determined. Although this range is determined based on the measurement of mean flow velocity, we believe that it can be used to estimate the proper range for the measurement of other flow quantities as well. Copyright © 2012 John Wiley & Sons, Ltd.