Dynamical structure functions,collective modes,and energy gap in charged-particle bilayers

The dynamical properties of strongly coupled charged-particle bilayers are investigated by molecular dynamics (MD) simulation and theoretical analysis. The spectra of the current correlation functions show the existence of two (in-phase and out-of-phase) longitudinal and two (in-phase and out-of-phase) transverse collective modes. The out-of-phase modes possess finite frequencies at wave numbers k-->0, confirming the existence of the predicted long-wavelength energy gap in the bilayer system. A theoretical model based on an extended Feynman ansatz for the dynamical structure functions provides predictions on the strength of the collective modes that are verified by the MD experiment.     

在高压诱导蛋白质变性过程中水产生的压缩对它的影响

实验表明水的压缩系数随着压强的改变会发生变化,这种改变将对高压致蛋白质变性的充分含水动力学模拟结果产生直接影响,然而很多高压变性的分子动力学模拟并没有考虑这一点.在温度为300 K,压强为200 MPa、1000 MPa时,利用GROMACS软件包对两种小蛋白Chignolin和Trpcage进行了总计300ns的分子动力学模拟,模拟中考虑了水的压缩系数随压强的改变情况,然后将模拟结果与压缩系数维持在O.1 MPa时的情况进行了比较.结果发现,压缩系数对蛋白质高压变性的影响很大,依据实验数据对不同压强的压缩系数进行调整后,小蛋白Chignolin在高压变性中出现完全去折叠.这为分子动力学模拟研究蛋白质高压变性提供了正确的途径和理论依据.     

Simple theoretical model of shear viscosity in isotopic fluid mixtures

We propose a simple hybrid model for the shear viscosity of isotopic fluid mixtures by coupling the contribution of the Stokes–Einstein relation with the existing linear model of Roults's law for the shear viscosity. The calculated values of shear viscosity using this simple hybrid model are found to be in excellent agreement with the molecular dynamics (MD) simulation results. The calculated value of the shear viscosity obtained from the theoretical model as well as the MD simulation increases with increasing mass ratio.     

Molecular dynamics study of self-diffusion in Zr

We employed a recently developed semi-empirical Zr potential to determine the diffusivities in hcp and bcc Zr via molecular dynamics simulation. The point defect concentration was determined directly from molecular dynamics (MD) simulation rather than from theoretical methods using T = 0 calculations. Our MD simulation indicates that the diffusion proceeds via the interstitial mechanism in hcp Zr, and both vacancy and interstitial mechanisms contribute to diffusivity in bcc Zr. The agreement with the experimental data is excellent for hcp Zr and rather good for bcc Zr at high temperatures, but there is considerable disagreement at low temperatures.     

Void growth via atomistic simulation: will the formation of shear loops still grow a void under different thermo-mechanical constraints?

Abstract

Molecular dynamics (MD) simulations under different mechanical and thermal constraints are carried out with a nanovoid embedded inside a single-crystal, face-centred-cubic copper. The dislocation emission angles measured from MD plots under 0.1 K, uniaxial-strain simulation are in line with the theoretical model. The dislocation density calculated from simulation is qualitatively consistent with the experimental measurement in terms of a saturation feature. The ‘relatively farthest-travelled’ atoms are employed to reflect the correlation between the dislocation structure and the void growth. At a smaller scale, the incomplete shear dislocation loops on the slip plane contribute to the local material transport. At a larger scale, the dislocation structures formed by those incomplete shear loops further facilitate the growth of nanovoid. Compared to the uniaxial-strain case, the void growth under the uniaxial-stress is very limited. The uniaxial-strain loading results in an octahedron void shape. The uniaxial-stress loading turns the nanovoid into a prolate ellipsoid along the loading direction. In the simulation, the largest specimen contains 12 million atoms and the lowest strain rate applied is 2 × 10⁶ s^?1. Under all the different thermomechanical constraints concerned, the formation of incomplete shear dislocation loops are found capable of growing the void.     

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。     

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.     

Assessment of Compatibility in Polypropylene/Poly(lactic acid)/Ethylene Vinyl Alcohol Ternary Blends: Relating Experiments and Molecular Dynamics Simulation Results

Two systems of polypropylene (PP), poly(lactic acid) (PLA) and ethylene vinyl alcohol copolymer (EVOH) ternary blends having different compositions were extruded in a co-rotating twin screw extruder. The first system was PP/PLA (75/25) with various EVOH contents, the second one was PP/EVOH (75/25) having various PLA contents. The effects of composition on the morphology and the tensile and impact properties of the blends were investigated. There were increases in the tensile modulus and tensile strength with an increase in the EVOH and PLA contents in the first and second systems, respectively. A molecular dynamics (MD) simulation was used to investigate the compatibility between the components. Prediction of the miscibility of the blends was carried out by determining the interaction parameters (χ), mixing energies (ΔH_mix), phase diagrams and Gibbs free energies. The MD simulation showed a UCST behavior for the components. Moreover, the simulation results showed a compatibilizer effect for the EVOH component. The experimental values of the dynamic mechanical thermal analysis (DMTA) and mechanical properties were correlated to the MD results. There was a good correlation between the MD and DMTA results. The modulus values using the parallel and Davis models were near to the experimental ones. A good fitting to the mixture law with addition of EVOH confirmed a good compatibilzing effect of it between the PP and PLA components.     

Effect of pressure on the thermal expansion of MgO up to 200~GPa

Constant temperature and pressure molecular dynamics (MD) simulations are performed to investigate the thermal expansivity of MgO at high pressure, by using effective pair-wise potentials which consist of Coulomb, dispersion, and repulsion interactions that include polarization effects through the shell model (SM). In order to take into account non-central forces in crystals, the breathing shell model (BSM) is also introduced into the MD simulation. We present a comparison between the volume thermal expansion coefficient α dependences of pressure P at 300 and 2000~K that are obtained from the SM and BSM potentials and those derived from other experimental and theoretical methods in the case of MgO. Compared with the results obtained by using the SM potentials, the MD results obtained by using BSM potentials are more compressible. In an extended pressure and temperature range, the α value is also predicted. The properties of MgO in a pressure range of 0--200~GPa at temperatures up to 3500~K are summarized.     

相关测速声呐底混响时空相关函数与载体俯仰角的关系

由于载体在运动过程中存在姿态的变化,不考虑载体姿态的理论相关函数会影响相关声呐的测速精确度。考虑载体俯仰角对发射信号海底照射区域的影响,引入不同权重的多阶贝塞尔函数,得到改进后的理论相关函数。同时,根据相关测速声呐发射参数,给出了基于FOM模型的海底回波仿真。仿真结果表明,改进的理论相关函数将相关声呐的测速误差降至1%以下。载体的俯仰角对时空相关函数产生影响。考虑载体俯仰角的理论相关函数更贴近实际情况,与仿真结果的相关系数吻合的较好,能够更加准确的估计载体速度。      

用于α-Al2O3分子动力学模拟的长程Finnis-Sinclair势函数

用金属势函数描述氧化物是实现金属-氧化物界面分子动力学模拟的关键.基于此,通过拟合α-Al₂O₃的晶格能、晶格常数、弹性常数,获得了一套用于描述α-Al₂O₃的长程Finnis-Sinclair（F-S）势.通过与已报道的描述α-Al₂O₃的EAM势、Glue势和modified Matsui（m-Matsui）势的比较,结果达到或优于前人的结果.进而,在300 K的温度下对 关键词： 长程F-S势 2O₃')" href="#">α-Al₂O₃ 2O₃界面')" href="#">Fe-Al₂O₃界面 2O₃界面')" href="#">Al-Al₂O₃界面     

Properties of MgO at high pressures: Shell-model molecular dynamics simulation

Shell-model molecular dynamics (MD) simulation has been performed to investigate the melting of the major Earth-forming mineral: periclase (MgO), at elevated temperatures and high pressures, based on the thermal instability analysis. The interatomic potential is taken to be the sum of pair-wise additive Coulomb, van der Waals attraction, and repulsive interactions. The MD simulation with selected Lewis–Catlow (LC) potential parameters is found to be very successful in describing the melting behavior for MgO, by taking account of the overheating of a crystalline solid at ambient pressure. The thermodynamic melting curve is estimated on the basis of the thermal instability MD simulations and compared with the available experimental data and other theoretical results in the pressure ranges 0–150 GPa. Our simulated melting curve of MgO is consistent with results obtained from Lindemann melting equation and two-phase simulated data at constant pressure by Belonoshko and Dubrovinsky, in the pressure below 20 GPa. The extrapolated melting temperatures in the lower mantle are in good agreement with the results obtained from Wang's empirical model up to 100 GPa. Compared with experimental measurements, our results are substantially higher than that determined by Zerr and Boehler, and the discrepancy between DAC and MD melting temperatures may be well explained with different melting mechanisms. Meanwhile, the radial distribution functions (RDFs) of Mg–Mg, O–Mg, and O–O ion pairs near the melting temperature have been investigated.     

向列相液晶$lt;i$gt;n$lt;/i$gt;CB(4-$lt;i$gt;n$lt;/i$gt;-alkyl-4′-cyanobiphenyls, $lt;i$gt;n$lt;/i$gt;=5—8)的旋转黏度及其奇偶效应的分子动力学模拟

在全原子力场模型的基础上,对向列液晶nCB（4-n-alkyl-4′-cyanobiphenyls, n=5—8）进行了等压等温NPT系综下的分子动力学（MD）模拟.对MD的轨迹分析得到了二阶和四阶序参数以及描述液晶分子翻转运动的取向时间相关函数（TCF）,并通过一个近似的单指函数对TCF拟合得到了相关时间.在此基础上,计算了nCB（n=5—8）的旋转扩散系数（Rotational diffusion coefficient, RDC）.利用基于统计力学模型的Nemtsov-Zakharov方法和Fialkowski方法,分别计算了它们的旋转黏度系数（rotational viscosity coefficient, RVC）,进而分别讨论了RVC,RDC和相关时间的奇偶效应.与文献中的实验结果比较表明,该方法得到了合理的计算结果和一致的奇偶效应. 关键词： 旋转黏度 奇偶效应 分子动力学模拟 向列相液晶     

Statistical fluid theory for associating fluids containing alternating heteronuclear chain molecules

Statistical associating fluid theory of homonuclear dimerized chain fluids and homonuclear monomer-dimer mixture chain fluids are extended to fluids containing alternating heteronuclear chain molecules separately. The proposed models account for the appropriate site-site correlation functions at contact. The modified equations of state show a good agreement with generalized Flory dimer theory and MD simulation data for small and medium size ratio of hard sphere diameters.     

Self-evolving atomistic kinetic Monte?Carlo: fundamentals and applications

The fundamentals of the framework and the details of each component of the self-evolving atomistic kinetic Monte Carlo (SEAKMC) are presented. The strength of this new technique is the ability to simulate dynamic processes with atomistic fidelity that is comparable to molecular dynamics (MD) but on a much longer time scale. The observation that the dimer method preferentially finds the saddle point (SP) with the lowest energy is investigated and found to be true only for defects with high symmetry. In order to estimate the fidelity of dynamics and accuracy of the simulation time, a general criterion is proposed and applied to two representative problems. Applications of SEAKMC for investigating the diffusion of interstitials and vacancies in bcc iron are presented and compared directly with MD simulations, demonstrating that SEAKMC provides results that formerly could be obtained only through MD. The correlation factor for interstitial diffusion in the dumbbell configuration, which is extremely difficult to obtain using MD, is predicted using SEAKMC. The limitations of SEAKMC are also discussed. The paper presents a comprehensive picture of the SEAKMC method in both its unique predictive capabilities and technically important details.     

Micro-hydrodynamics

Micro-hydrodynamics is a term used to describe the search for and study of hydrodynamic phenomena at microscopic scales. The principal method used to accomplish this research is molecular dynamic (MD) simulations. Computational limits on MD models restrict the size of the system and simulation time. Typically, the length scales are on the order of 10–1000 Å and time scales 10–1000 psec (thus the qualifier micro). We review the results of our research in this area. We use MD to model channel flow, flow past a plate, flow past a cylinder, and Rayleigh-Benard convection. In general, we find that the behavior in these models agrees with results obtained from experiment and more traditional theoretical approaches, such as solving the Navier-Stokes equations. In addition to the appearance of spatial and temporal patterns, we observe scaling relations in agreement with those predicted by macroscopic hydrodynamics. In some specific situations, we can see the breakdown of Navier-Stokes theory and estimate its limits.     

The effect of pressure on the elastic constants of Cu, Ag and Au: a molecular dynamics study

This paper describes the effect of pressure on some the mechanical properties of transition metals Cu, Ag, and Au, such as elastic constants and bulk modulus. Using molecular dynamics (MD) simulation, the present study was carried out using the modified many-body Morse potential function expression in the framework of the Embedded Atom Method (EAM). The effect of pressure on equilibrium volume, elastic constants, and bulk modulus were determined, and found to be in agreement with other theoretical calculations and experimental data.     

Applicability of molecular dynamics method to the pressure-driven gas flow in finite length nano-scale slit pores

This study investigates the applicability of the molecular dynamics (MD) method to the pressure-driven gas flow in finite length nano-scale slit pores. The reflecting particle membrane is introduced to induce a pressure difference between the inlet and outlet. The flow properties are compared with those of the Burnett equations. The inlet and outlet pressures, as well as the mass flow rate in these two simulations are maintained the same by adjusting the tangential momentum accommodation coefficient in the Burnett simulation, which is found to be between 0.4 and 0.5. Qualitative and quantitative agreements are observed between the MD and Burnett simulation results in the bulk of the pore for both streamwise distributions and cross-section profiles. The MD simulation shows an advantage in the near-wall region, in which the wall force field dominates flow behaviour. This study indicates that MD simulation can be used to describe the pressure-driven gas flow characteristics in finite length nano-scale slit pores.     

Vibrational spectrum at a water surface: a hybrid quantum mechanics/molecular mechanics molecular dynamics approach

A hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation is applied to the calculation of surface orientational structure and vibrational spectrum (second-order nonlinear susceptibility) at the vapor/water interface for the first time. The surface orientational structure of the QM water molecules is consistent with the previous MD studies, and the calculated susceptibility reproduces the experimentally reported one, supporting the previous results using the classical force field MD simulation. The present QM/MM MD simulation also demonstrates that the positive sign of the imaginary part of the second-order nonlinear susceptibility at the lower hydrogen bonding OH frequency region originates not from individual molecular orientational structure, but from cooperative electronic structure through the hydrogen bonding network.     

Multiscale three-point velocity increment correlation in turbulent flows

The three-point velocity increment correlation function is proposed to represent the multiscale correlations in turbulent flows. The inertial–inertial correlation and the inertial–dissipative correlation are discussed due to their endogenetic properties in turbulence and their roles in large-eddy simulation. The zero-correlation points are then emphasized as equilibrium points between them. The credibility of this theoretical result is numerically verified in both isotropic and anisotropic flows. Results imply the universality of this zero-correlation scaling in different turbulent flows. This work is expected to be a dependable theoretical base for creating multiscale subgrid models in large-eddy simulation.