Development of the reaction time accelerating molecular dynamics method for simulation of chemical reaction

We present a novel and efficient method to integrate chemical reactions into molecular dynamics to simulate chemical reaction systems. We have dubbed this method RTAMD, an acronym for reaction time accelerating molecular dynamics. The methodology we propose here requires no more than the knowledge of the empirical intermolecular potentials for the species at play as well as the elementary reaction path among them. Bond formation during the simulation is performed by changing the inter-atomic potentials from those of the non-bonded species to those of the bonded ones, and a reaction is deemed to occur by the distance separating the bond forming atoms. In this way the energy barrier for a reaction is no longer considered; the estimation of the reaction rate, however, is possible by introducing the principles of the transition state theory. The simplicity of the present scheme to simulate chemical reactions enables it to be used in large-scale MD simulations involving a large number of simultaneous chemical reactions and to evaluate kinetic parameters. In this paper, the basic theory of the method is presented and application to simple equiatomic reaction system where the reaction rates were estimated was illustrated.     

Kinetic sonication effects in aqueous acetonitrile solutions. Reaction rate levelling by ultrasound

The kinetics of the pH-independent hydrolysis of 4-methoxyphenyl dichloroacetate were investigated with and without ultrasonic irradiation in acetonitrile–water binary mixtures containing 0.008 to 35 wt.% of acetonitrile and the kinetic sonication effects (k_son/k_non) were calculated. Molecular dynamics (MD) simulations of the structure of the solutions were performed with ethyl acetate as the model ester. The ester is preferentially solvated by acetonitrile. The excess of acetonitrile over water in the solvation shell grows fast with an increase in the co-solvent content in the bulk solution. In parallel, the formation of a second solvation shell rich in acetonitrile takes place. Significant kinetic sonication effects for the hydrolysis were explained with facile destruction of the diffuse second solvation shell followed by a rearrangement of the remaining solvent layer under sonication. The rate levelling effect of ultrasound was discussed. In an aqueous-organic binary solvent, independent of the solvent composition, the ultrasonic irradiation evokes changes in the reaction medium which result in an almost identical solvation state of the reagent thus leading to the reaction rate levelling.     

Kinetic and molecular dynamics analysis of carbon diffusion in austenite

A kinetic 10-frequency model for interstitial diffusion via octahedral interstices in the fcc lattice is developed. In this model, the specific role of the transition probabilities during association and dissociation of the first nearest neighbour interstitial pairs through the second nearest neighbour sites is considered. Application of the model is made to carbon diffusion in austenite. Molecular dynamics is used to investigate carbon interstitial diffusion in austenite at low carbon contents. The assumption that carbon atoms can interact with each other only indirectly (via neighbouring iron atoms) is used. The Arrhenius parameters of interstitial carbon jump frequencies consistent with the 10-frequency model are determined. Comparison of the molecular dynamics results with experimental data at 1273?K in the context of the 10-frequency model is performed. It is shown that a small direct repulsion between carbon atoms at first nearest neighbours should be included. It is found that the initial increase (with increasing carbon content) in both the tracer and the chemical diffusion coefficients is shown to be a result of increased rates of dissociation of carbon from first and second nearest neighbour pairs to third nearest neighbour sites.     

分子动力学模拟方法在非线性光学中的应用

有机分子非线性光学材料在频率转换、电光调制和双光子吸收等方面具有重要的应用.介绍了近年来分子动力学模拟方法在有机分子非线性光学性质理论研究中的主要应用,包括电场极化效应、局域场因子、非线性极化率和双光子吸收等.此外,结合最新的科研工作,介绍了分子动力学模拟方法在溶剂效应和聚集效应研究中发挥的重要作用. 关键词： 分子动力学模拟 溶剂效应 聚集效应 双光子吸收     

光与介质作用下的一种分子电流机制

光与介质分子相互作用是一个活跃的研究领域,新的现象、技术和理论不断出现,原有理论对解释某些新的现象遇到困难.本文应用法拉第电磁感应原理研究了分子中电子云与光波之间的相互作用,提出了在光波作用下介质中存在的一种分子电流机制,这种电流的密度随磁场的时间变化率增加而增大,它不同于介质分子的极化电流和磁化电流.这些工作有助于深入认识光波与介质之间的相互作用.     

Methane in carbon nanotube: molecular dynamics simulation

The behaviour of methane molecules inside carbon nanotubes at room temperature is studied using classical molecular dynamics simulations. A methane molecule is represented either by a shapeless super-atom or by a rigid set of five interaction centres localized on atoms. Different loadings of methane molecules ranging from the dense gas density to the liquid density, and the influence of flexibility of the CNT on structural and dynamic properties of confined molecules are considered. The simulation results show the decreases of the diffusion coefficient of methane molecules with density. At higher densities diffusion coefficient values are almost independent of molecular shape, but at low densities one observes faster motion of the super-atom molecule than that for the tetrahedral model of the molecule. For loadings of methane considered here the nanotube flexibility, introduced by the reactive empirical bond order (REBO) potential for interactions between carbon atoms of nanotube, does not have an effect on diffusivity of methane molecules, and its impact on the molecular structure is weak. It is found that methane molecules in the vicinity of the nanotube wall show tripod orientation with respect to the nanotube surface.     

Solvation dynamics in methanol: Experimental and molecular dynamics simulation studies

We have investigated the ultrafast dynamics of methanol by time dependent fluorescent shift experiments and molecular dynamic simulations. The experiments were performed with two different probe molecules, 1-aminonaphthalene and coumarin 153. The molecular dynamic simulations employed these probes as well as small atomic and diatomic solutes. We find a previously unobserved fast decay component in the solvation response of methanol. The molecular dynamics results are in good agreement with this experimental result. The origin of this fast response and the linearity of the solvent response are discussed.     

Kinetic theory of field effects in nonuniform molecular gases

Effects of magnetic and electric fields on transport phenomena in dilute polyatomic gases are reviewed within the framework of first order Enskog theory. The established technique of approximate operator inversion is used to give first order approximations of the transport coefficients. Instead of the customary expansion of polarization into orthogonal polynomials a more general treatment is chosen here so as to accomodate recent experimental observations. The polarizations produced by macroscopic fluxes are assumed to be eigenfunctions of the collision operator within the subspace of functions anisotropic in angular momentum. The formalism is extended to mixtures in a way to let the final expressions assume the same form as for pure gases. The obtained transport coefficients obey several symmetry relations and inequalities. Additional inequalities are now also derived for the matrix describing the saturated field effects.     

Molecular simulation of chemical reaction equilibria by Kinetic Monte Carlo

ABSTRACT

We describe a new algorithm for the molecular simulation of chemical reaction equilibria, which we call the Reactive Kinetic Monte Carlo (ReKMC) algorithm. It is based on the use of the equilibrium Kinetic Monte Carlo (eKMC) method (Ustinov et al., J. Colloid Interface Sci., 2012, 366, 216–223) to generate configurations in the underlying nonreacting system and to calculate the species chemical potentials at essentially zero marginal computational cost. We consider in detail the typical case of specified temperature, T and pressure, P, but extensions to other thermodynamic constraints are straightforward in principle. In the course of this work, we also demonstrate an alternative method for calculating simulation box volume changes in NPT ensemble simulations to achieve the specified P. We consider two sets of example reacting systems previously considered in the literature, and compare the ReKMC results and computational efficiencies with those of different implementations of the REMC algorithm (Turner et al., Molec. Simulation, 2008, 34, 119–146).     

非绝热分子动力学的量子路径模拟

基于近期发展的经典-量子混合模拟非绝热分子动力学的量子路径方案,本文对5个典型势能面模型进行了模拟,包括单交叉模型、双交叉模型、拓展耦合模型、哑铃模型以及双弓模型.由于难以在严格意义上得到退相干速率,数值模拟中,我们比较了三个不同的退相干速率公式,包括冻结高斯波包近似退相干速率、能量分辨速率以及力分辨速率.在模拟过程中,我们恰当地处理了势能面跳跃时的能量守恒和力的反向问题.通过与全量子动力学模拟的精确结果进行对比发现,对于结构较简单的势能面模型,三种退相干速率都能得到较好的结果;然而对于较复杂的势能面模型,由于复杂量子干涉的原因,与其他混合经典-量子动力学方案类似,量子路径方案仍然难以得到较准确的结果.如何发展更加有效的混合经典-量子模拟方案,是未来研究的重要课题.     

DTO体系分子反应动力学

基于DTO分子( 1A1)的氢同位素效应,得到修正的Born-Oppenheimer(B-O)理论下多体展式分析势能函数.用准经典的Monte-Carlo轨迹法研究了D+ TO(0 ,0)和T+ DO(0 ,0)的分子反应动力学过程.结果表明:在碰撞能量较低时( < 209.2 kJ. mol - 1 ),D+ TO(0 ,0)和T+DO(0,0)反应主要生成O+ DT,并且该反应是无阈能的;有少量的交换反应产物DO (TO)生成,并伴有极少量的络合物产生.碰撞能大于209.2kJ . mol - 1后,逐渐出现分子被完全碰散成D,T ,O 原子的情形.反应 D+TO(0 ,0) →OD + T和 T +DO(0 ,0) →OT + D是无热反应但是有阈能存在.由于D和T原子的同位素效应,置换产物轨线存在非一致性.     

Numerical simulation of momentumless turbulent wake dynamics in linearly stratified medium

This paper presents comparison of two numerical models of the momentumless turbulent wake dynamics behind a body of revolution in a linearly stratified medium, namely, the model based on direct (DNS) numerical integration of Navier–Stokes equations in the Oberbeck–Boussinesq approximation and the mathematical model with application of a semi-empirical turbulence model of the third order. The results of calculations by these two models agree with the known experimental data.     

非晶态石英的变电荷分子动力学模拟

基于迭代变电荷方法,用分子动力学模拟了非晶态石英的结构与振动特征.首先利用熔化-猝火方法得到了非晶石英的平衡结构.在此基础上获得了体系不同原子对之间的对关联函数、键角分布函数和振动频谱等,结果与实验数据均符合较好.变电荷方法的计算结果表明,非晶石英体系内粒子的电荷与石英晶体内粒子电荷显著不同,并且出现了较大的涨落. 关键词： 分子动力学 变电荷 非晶石英     

Nonreciprocal effects in light reflection by a moving medium

Nonreciprocal effects in light reflection by a medium moving along an interface are considered in a weakly relativistic approximation. It is found that nonreciprocal effects are anomalously large in the vicinity of the Brewster and the total-internal-reflection (TIR) angles when light is reflected by transparent moving media. These effects exceed considerably (by several orders of magnitude) the ratio of the velocity of the reflecting medium to the velocity of light and can be proportional to rather than to under certain conditions. We show new possibilities for the creation a method for investigation of the structure of nonuniform flows with a very small spatial scale (less than one millimeter). This method is based on measurement of amplitude and phase nonreciprocities in light reflection by these flows.Institute of Applied Physics, Russian Academy of Sciences, Nizhny Novgorod. Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Radiofizika, Vol. 38, No. 11, pp. 1146–1157, November, 1995.     

An investigation of molecular layering at the liquid-solid interface in nanofluids by molecular dynamics simulation

The molecular layering at liquid-solid interface in a nanofluid is investigated by equilibrium molecular dynamics simulation. By tracking the positions of the nanoparticle and the liquid atoms around the spherical nanoparticle, it was found that an absorbed slip layer of liquid is formed at the interface between the nanoparticle and liquid; this thin layer will move with the Brownian motion of the nanoparticle. Through the analysis of the density distribution of the liquid near the nanoparticle it is found that the thickness of the layering is about 0.5 nm under the parameters used in the Letter.     

A molecular dynamics simulation on the convective heat transfer in nanochannels

The understanding of the flow and heat transfer processes for fluid through micro- and nanochannels becomes imperative due to its wide application in micro- and nano-fluidic devices. In this paper, the method to simulate the convective heat transfer process in molecular dynamics is improved based on a previous study. With this method, we simulate a warm dense fluid flowing through a cold parallel-plate nanochannel with constant wall temperature. The characteristics of the velocity and temperature fields are analysed. The temperature difference between the bulk average temperature of fluid and the wall temperature decreases in an exponential form along the flow direction. The Nusselt number for the laminar flow in parallel-plate nanochannel is smaller than its corresponding value at macroscale. It could be attributed to the temperature jump at the fluid–wall interface, which decreases the temperature gradient near the wall. The results also reveal that the heat transfer coefficient is related to the surface wettabilities, which differs from that in the macroscopic condition.     

Alternative ensemble averages in molecular dynamics simulation of hard spheres

ABSTRACT

We consider application to the hard sphere (HS) model of the mapped-averaging framework for generating alternative ensemble averages for thermodynamic properties. Specifically, we develop and examine new formulas for the pressure, the singlet and pair densities, and the cavity-correlation function inside the HS core; the pressure formula in particular is constructed such that it gives an ensemble average that exactly corrects the second-order virial equation of state. The force plays a central role in mapped-averaging expressions, and we write them in a way that accounts for the impulsive, event-driven nature of the HS dynamics. Comparison between results obtained conventionally versus mapped averaging finds that the latter has some advantage at low density, while both perform equally well (in terms of uncertainties for a given amount of sampling) at higher densities.     

Application of shell model in molecular dynamics simulation to MgO

The P－V－T equation of state of MgO has been simulated under high pressure and elevated temperature using the molecular dynamics (MD) method with the breathing shell model (BSM). It is found that the MD simulation with BSM is very successful in reproducing accurately the measured molar volumes of MgO over a wide range of temperature and pressure. In addition, the MD simulation reproduces accurately the measured volume compression data of MgO up to 100GPa at 300K. It is demonstrated that the MD simulated P－V－T equation of state of MgO could be applied as a useful internal pressure calibration standard at elevated temperatures and high pressures.