Use of the Richtmyer-Meshkov instability to infer yield stress at high-energy densities

We use the Richtmyer-Meshkov instability (RMI) at a metal-gas interface to infer the metal's yield stress (Y) under shock loading and release. We first model how Y stabilizes the RMI using hydrodynamics simulations with a perfectly plastic constitutive relation for copper (Cu). The model is then tested with molecular dynamics (MD) of crystalline Cu by comparing the inferred Y from RMI simulations with direct stress-strain calculations, both with MD at the same conditions. Finally, new RMI experiments with solid Cu validate our simulation-based model and infer Y~0.47 GPa for a 36 GPa shock.     

Atomistic investigation of phase transition in solid argon induced by shock wave transmission

A molecular dynamics (MD) simulation is employed to study the phase transition process in argon induced by shock wave transmission. Deriving the relation between the shock and piston velocities, the theoretical equation of state for argon is presented. Also, argon equation of state is obtained by measuring the quantities directly from simulations to be able to detect the phase transitions. The phase transition is also detected by using argon phase diagram and free energy calculations. A comparison shows good agreement between the theoretical and MD results for the phase transitions. Based on these simulations, it is concluded that under a shock wave transmission with suitable energy, the solid argon experiences a phase transition from solid to liquid and another from liquid to supercritical fluid. By reflecting the shock wave back at the end of its passage, the whole argon may reach the supercritical state.     

Origin of unrealistic blunting during atomistic fracture simulations based on MEAM potentials

Atomistic simulations based on interatomic potentials have frequently failed to correctly reproduce the brittle fracture of materials, showing an unrealistic blunting. We analyse the origin of the unrealistic blunting during atomistic simulations by modified embedded-atom method (MEAM) potentials for experimentally well-known brittle materials such as bcc tungsten and diamond silicon. The radial cut-off which has been thought to give no influence on MEAM calculations is found to have a decisive effect on the crack propagation behaviour. Extending both cut-off distance and truncation range can prevent the unrealistic blunting, reproducing many well-known fracture behaviour which have been difficult to reproduce. The result provides a guideline for future atomistic simulations that focus on various fracture-related phenomena including the failure of metallic-covalent bonding material systems using MEAM potentials.     

Numerical Simulation of the Formation of Granular Shock Wave Over Cylindrical Obstacle

A two dimensional (2‐D) stream of granular flow with zero initial granular temperature passing over a cylindrical obstacle is simulated by means of both molecular dynamics (MD) simulation and finite volume method (FVM). In experiments, a bow‐shaped shock wave with higher area fraction forms in front of the obstacle that was reproduced in our simulations. Due to the different circumstances to which particles are subjected, the granular flow is divided in two zones. One is undisturbed where quantities, such as space fraction (volume fraction for 3‐D and area fraction for 2‐D geometries), velocity and granular temperature are uniformly distributed and the other is called the shock wave zone. In this region, the values of the space fraction increases and the velocity of particles changes. From the MD simulation, it is found that the area fraction of the shock wave depends on surface roughness, coefficient of restitution (COR) of particles, the obstacle diameter as well as velocity of the granular stream, and a triangular region forms with almost zero velocity, and granular temperature forms in front of the cylindrical obstacle. The bigger is the size of the obstacle, the more stable this region is. In FVM simulations solid phase velocity and area fraction distributions similar to the MD simulation results are obtained for proper parameters.     

Phase behaviour and interfacial properties of ternary system CO2 + n-butane + n-decane: coarse-grained theoretical modelling and molecular simulations

ABSTRACT

This work illustrates the application of a three-party approach based on theoretical modelling, molecular dynamic (MD) simulations and available experimental data for describing the phase equilibrium and interfacial properties for the ternary system: carbon dioxide + n-butane + n-decane and its corresponding binary sub-systems at 344.3 K. Specifically, a coarse-grained force field is employed for both theoretical predictions and MD. The interfacial region is described by the square gradient theory where the homogenous Helmholtz energy density contribution is provided by the Statistical Associated Fluid Theory equation of state for potentials of variable range for molecules conformed of segments interacting through the Mie potential (SAFT-VR Mie) and MD simulations in the canonical ensemble where the molecules are represented by a coarse-grained Mie force field. The novelty here is that both the theory and the simulations uniquely share the same underlying intermolecular potentials; hence, the experimental data are employed to verify both the theory and simulations. In this schema, the ternary mixture is full predictive as its parameters are only based on pure fluids parameters and binary interactions. It is observed that the phase equilibria and the interfacial properties are equally well represented by the used approach.     

Dynamics of ions in the selectivity filter of the KcsA channel

The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion’s dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force derived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications.     

快速冷却条件下银的比热及玻璃化过程的分子动力学模拟

本文采用以嵌入原子模型为基础的分子动力学方法对液态银快速冷却条件下的比热及玻璃化过程进行了模拟，得到了银的比热及其与温度的关系．同时，对快速冷却条件下银的结构特性以及动力学特性进行模拟和分析，结果表明在所模拟的冷却速率下，银在从 １２００ Ｋ冷却到 １０００ Ｋ的过程中发生了玻璃化转变，其玻璃化温度在 １０００ Ｋ左右．     

Shock waves in high-energy materials: the initial chemical events in nitramine RDX

We extend the reactive force field ReaxFF to describe the high energy nitramine RDX and use it with molecular dynamics (MD) to study its shock-induced chemistry. We studied shock propagation via nonequilibrium MD simulations at various collision velocities. We find that for high impact velocities (>6 km/s) the RDX molecules decompose and react to form a variety of small molecules in very short time scales (<3 ps). These products are consistent with those found experimentally at longer times. For lower velocities only NO2 is formed, also in agreement with experiments.     

Prediction of ion channel transport from Grote—Hynes and Kramers theories

Generalized Langevin equation based Grote—Hynes (GH) theory and Langevin equation based Kramers theory are used to calculate the transmission coefficient for K⁺ diffusion through a model of the biological potassium ion channel IRK1, which contains a high potential barrier in the selectivity filter. The ion friction kernel is determined from a molecular dynamics (MD) simulation of the force on a stationary ion at the barrier top. The GH and Kramers estimates of the transmission coefficient are compared with those obtained from MD simulations of ion diffusion at the barrier top of the IRK1 channel. It is found that the GH estimate agrees with the value determined by rigorous MD, but the Kramers estimate is about 40% too small. The success or failure of GH and Kramers theories for various other systems is discussed and compared with these results.     

Quasi-coarse-grained dynamics: modelling of metallic materials at mesoscales

A computationally efficient modelling method called quasi-coarse-grained dynamics (QCGD) is developed to expand the capabilities of molecular dynamics (MD) simulations to model behaviour of metallic materials at the mesoscales. This mesoscale method is based on solving the equations of motion for a chosen set of representative atoms from an atomistic microstructure and using scaling relationships for the atomic-scale interatomic potentials in MD simulations to define the interactions between representative atoms. The scaling relationships retain the atomic-scale degrees of freedom and therefore energetics of the representative atoms as would be predicted in MD simulations. The total energetics of the system is retained by scaling the energetics and the atomic-scale degrees of freedom of these representative atoms to account for the missing atoms in the microstructure. This scaling of the energetics renders improved time steps for the QCGD simulations. The success of the QCGD method is demonstrated by the prediction of the structural energetics, high-temperature thermodynamics, deformation behaviour of interfaces, phase transformation behaviour, plastic deformation behaviour, heat generation during plastic deformation, as well as the wave propagation behaviour, as would be predicted using MD simulations for a reduced number of representative atoms. The reduced number of atoms and the improved time steps enables the modelling of metallic materials at the mesoscale in extreme environments.     

冲击加载下铝中氦泡和孔洞的塑性变形特征研究

通过分子动力学模拟研究了在相同冲击加载强度下单晶铝中氦泡和孔洞的塑性变形特征,结果发现氦泡和孔洞的塌缩是由发射剪切型位错环引起的,而没有观测到棱锥型位错环发射. 氦泡和孔洞周围的位错优先成核位置基本一致,但是氦泡周围发射的位错环数目比孔洞多,位错环发射速度明显比孔洞快. 且氦泡和孔洞被冲击波先扫过部分比后扫过部分发射位错困难. 通过滑移面上的分解应力分析发现,氦泡和孔洞周围塑性特征的差别是由于氦泡内压引起最大分解应力分布改变造成的. 氦泡和孔洞被冲击波先后扫过部分塑性不对称是因为冲击波扫过时引起形状变化, 关键词： 分子动力学 冲击波 氦泡 孔洞     

Simulation of screw dislocation motion in iron by molecular dynamics simulations

Molecular dynamics (MD) simulations are used to investigate the response of a/2<111> screw dislocation in iron submitted to pure shear strain. The dislocation glides and remains in a (110) plane; the motion occurs exclusively through the nucleation and propagation of double kinks. The critical stress is calculated as a function of the temperature. A new method is developed and used to determine the activation energy of the double kink mechanism from MD simulations. It is shown that the differences between experimental and simulation conditions lead to a significant difference in activation energy. These differences are explained, and the method developed provides the link between MD and mesoscopic simulations.     

基于接触数引导的迭代多组独立分子动力学模拟实现配体-蛋白质结合与解离过程

配体的结合与解离过程在蛋白质实现其生物学功能方面非常关键,因此对这些高度动态过程的研究变得非常重要. 尽管已有实验方法可以确定蛋白质-配体复合物的三维结构,但一般仅可获得静态图片. 随着计算机算力的快速提高以及算法的优化,分子动力学模拟在探索配体的结合与解离过程方面具有诸多优势. 然而,当系统变得足够大时,分子动力学模拟的时间和空间尺度成为了巨大的挑战. 本工作提出了一种研究配体-蛋白质结合与解离的增强采样工具,它基于配体和蛋白质之间形成的接触数来引导迭代多组独立分子动力学模拟. 在腺苷酸激酶的模拟结果中,观测到配体的结合和解离过程,而使用传统分子动力学模拟在同一时间尺度下则无法实现这一过程.     

Power-law slip profile of the moving contact line in two-phase immiscible flows

Large-scale molecular dynamics (MD) simulations on two-phase immiscible flows show that, associated with the moving contact line, there is a very large 1/x partial-slip region where x denotes the distance from the contact line. This power-law partial-slip region is verified in large-scale adaptive continuum calculations based on a local, continuum hydrodynamic formulation, which has proved successful in reproducing MD results at the nanoscale. Both MD simulations and numerical solutions of continuum equations indicate the existence of a universal slip profile in the Stokes-flow regime.     

Structure of a tethered polymer under flow using molecular dynamics and hybrid molecular-continuum simulations

We analyse the structure of a single polymer tethered to a solid surface undergoing a Couette flow. We study the problem using molecular dynamics (MD) and hybrid MD-continuum simulations, wherein the polymer and the surrounding solvent are treated via standard MD, and the solvent flow farther away from the polymer is solved by continuum fluid dynamics (CFD). The polymer represents a freely jointed chain (FJC) and is modelled by Lennard-Jones (LJ) beads interacting through the FENE potential. The solvent (modelled as a LJ fluid) and a weakly attractive wall are treated at the molecular level. At large shear rates the polymer becomes more elongated than predicted by existing theoretical scaling laws. Also, along the normal-to-wall direction the structure observed for the FJC is, surprisingly, very similar to that predicted for a semiflexible chain. Comparison with previous Brownian dynamics simulations (which exclude both solvent and wall potential) indicates that these effects are due to the polymer–solvent and polymer–wall interactions. The hybrid simulations are in perfect agreement with the MD simulations, showing no trace of finite size effects. Importantly, the extra cost required to couple the MD and CFD domains is negligible.     

Diffusion Dynamics of Cux Cluster on Cu(111) Surface

利用分子动力学与修正分析型嵌入原子模型研究了从200K至800 K范围内,Cux (1·x·8)小团簇在(111)面的自扩散动力学行为,计算了Cu小团簇的扩散系数与激活能. 计算结果表明,密排的Cu7团簇的激活能最高,其扩散前因子比单个吸附原子的高3个数量级,这与其他类似金属的实验结果一致. 另外,还定量讨论了薄膜生长与团簇扩散的关系.     

高压下液态硝基甲烷的分子动力学模拟

 对高压下液态硝基甲烷的性质进行经典和基于第一性原理计算的Car-Parrinello分子动力学（CPMD）模拟。利用经典势的分子动力学（MD）模拟研究了高压压缩状态下液态硝基甲烷的结构和热力学性质,得到了高达14.2 GPa压力下的理论Hugoniot数据。对于一些热力学函数,如总能和粒子速度,经典势模拟给出了很好的总趋势,基本特征和实验观测一致。但是在给定的密度下,经典模拟预言的Hugoniot压力偏高。在几个选定的密度下,进行了CPMD模拟,得到了二体相关函数、速度自相关函数、振动光谱和其它的热力学性质,并与经典模拟结果进行了比较。对二体相关函数的分析表明经典势的短程部分的刚性可能太强,从而导致了比实验值高的理论压力值。对于某些二体相关函数,CPMD模拟和经典模拟结果差别很大,可以归结为量子效应。当压力增高时,量子模拟得到的振动光谱向高频部分移动的现象与实验观测相符合。     

Computer simulation study of self-diffusion in Pd(0 0 1) surface

Both the formation energies and the intra- and inter-layer activation energies of self-diffusion of a single vacancy in the first six planes of Pd(0 0 1) surface have been investigated by means of molecular dynamics (MD) in conjunction with the semi-experiential many-body potential of the modified analytical embedded-atom method (MAEAM). The results show that the effect of the surface on the vacancy is only down to the fifth-layer. It is easer for a single vacancy to form and to migrate in the first layer. Furthermore, the vacancy in the second layer is favorable to migrate to the first layer. This is in agreement with the experimental results that the first layer has the highest concentration of the vacancy.     

分析复杂化学及生物体系分子动力学模拟轨迹的聚类方法

Molecular dynamics (MD) simulation has become a powerful tool to investigate the structurefunction relationship of proteins and other biological macromolecules at atomic resolution and biologically relevant timescales. MD simulations often produce massive datasets containing millions of snapshots describing proteins in motion. Therefore, clustering algorithms have been in high demand to be developed and applied to classify these MD snapshots and gain biological insights. There mainly exist two categories of clustering algorithms that aim to group protein conformations into clusters based on the similarity of their shape (geometric clustering) and kinetics (kinetic clustering). In this paper, we review a series of frequently used clustering algorithms applied in MD simulations, including divisive algorithms, agglomerative algorithms (single-linkage, complete-linkage, average-linkage, centroid-linkage and ward-linkage), center-based algorithms (K-Means, K-Medoids, K-Centers, and APM), density-based algorithms (neighbor-based, DBSCAN, density-peaks, and Robust-DB), and spectral-based algorithms (PCCA and PCCA+). In particular, differences between geometric and kinetic clustering metrics will be discussed along with the performances of different clustering algorithms. We note that there does not exist a one-size-fits-all algorithm in the classification of MD datasets. For a specific application, the right choice of clustering algorithm should be based on the purpose of clustering, and the intrinsic properties of the MD conformational ensembles. Therefore, a main focus of our review is to describe the merits and limitations of each clustering algorithm. We expect that this review would be helpful to guide researchers to choose appropriate clustering algorithms for their own MD datasets.     

Matter Effects on Neutrino Oscillations in Different Supernova Models

In recent years,with the development of simulations about supernova explosion,we have a better understanding about the density profiles and the shock waves in supernovae than before.There might be a reverse shock wave,another sudden change of density except the forward shock wave,or even no shock wave,emerging in the supernova.Instead of using the expression of the crossing probability at the high resonance,PH,we have studied the matter effects on neutrino oscillations in different supernova models.In detail,we have calculated the survival probability of νe(P_s)and the conversion probability of ν_x(P_c) in the Schrodinger equation within a simplified two-flavor framework for a certain case,in which the neutrino transfers through the supernova matter from an initial flavor eigenstate located at the core of the supernova.Our calculations was based on the data of density in three different supernova models obtained from simulations.In our work,we do not steepen the density gradient around the border of the shock wave,which differs to what was done in most of the other simulations.It is found that the mass and the density distribution of the supernova do make a difference on the behavior of P_s and P_c.With the results of P_s and P_c,we can estimate the number of νe(and ν_x) remained in the beam after they go through the matter in the supernova.