XPK程序包:扩展唯象动力学方法(XPK)与常规动力学蒙特卡罗(KMC)方法的比较（英文）

在常规的动力学蒙特卡罗方法(KMC)中,扩散过程的速率往往远大于化学反应,因而造成KMC方法在模拟表面化学体系演化时效率非常低下.为了解决这一时间尺度分离问题,本文最近发展了扩展唯象动力学方法(XPK).本文基于加氢反应体系模型,利用新发展的XPK程序包,对XPK方法与常规的KMC方法进行了细致的对比.为了更全面地说明问题,测试中包含了两条不同的势能曲线,以及多种吸附物之间的相互作用.对比的内容包括计算消耗、并行效率以及稳态的收敛行为等.测试结果表明,相比于常规的KMC方法,XPK方法在兼顾精度的同时大大提高了模拟效率.因而可以预期,XPK方法将成为多相催化理论研究的强有力工具.特别是在表面吸附物种相互作用有决定性影响的情况下,XPK方法的优势尤其突出.     

网格上布鲁塞尔体系化学振荡的粗粒化模拟

将一种有效的粗粒化的动力学蒙特卡罗(KMC)方法用于加速模拟二维格气布鲁塞尔体系中的振荡行为．这种方法是将微观网格合并得到粗粒化的网格,并在该粗粒化网格上按粗粒化的反应速率执行KMC,即粗粒化的KMC．数值结果表明,由于非线性三分子反应导致的相邻元胞之间的关联是不能忽略的．通过正确的考虑这一边界效应,引入了所谓的b-LMF方法．大量的数据表明,只要体系的扩散系数不是很小,b-LMF方法能够很好的重现体系的振荡行为．另外,发现该方法所得的结果与KMC的偏离在合适的粗粒化尺度下存在一个接近于0的极小值,这一粗     

基于修正并行光滑粒子动力学方法三维变系数瞬态热传导问题的模拟

为了解决传统光滑粒子动力学(SPH)方法求解三维变系数瞬态热传导方程时出现的精度低、稳定性差和计算效率低的问题,本文首先基于Taylor展开思想拓展一阶对称SPH方法到三维热传导问题的模拟,其次引入稳定化处理的迎风思想,最后基于相邻粒子标记和MPI并行技术,结合边界处理方法得到一种能够准确、高效地求解三维变系数瞬态热传导问题的修正并行SPH方法.通过对带有Direclet和Newmann边界条件的常/变系数三维热传导方程进行模拟,并与解析解进行对比,对提出的方法的精度、收敛性及计算效率进行了分析;随后,运用提出的修正并行SPH方法对三维功能梯度材料中温度变化进行了模拟预测,并与其他数值结果做对比,准确地展现了功能梯度材料中温度变化过程.     

压强对Zr_(67)Ni_(33)非晶合金结构和动力学性能的影响

采用分子动力学的方法模拟Zr_(67)Ni_(33)合金液体在不同压强下快速凝固过程,通过结构分析方法如对分布函数、配位数、Honeycutt-Andersen(HA)键型指数法,以及动力学参数如均方位移、自散射关联函数、非高斯参数研究压强对Zr_(67)Ni_(33)非晶合金局域原子结构和其过冷液体动力学性能的影响.研究结果表明:压强越大,Zr_(67)Ni_(33)非晶合金中Zr-Ni原子间的相互作用越强,体系结构有序性越强,过冷液体中动力学减慢和动力学不均匀现象越显著.     

Molecular Dynamics Simulation on Stability of Insulin on Graphene

通过分子动力学模拟研究了胰岛素与不同尺寸石墨烯的相互作用,并比较了固定的石墨烯与不固定的石墨烯对蛋白质吸附行为及动力学的影响. 通过分析胰岛素蛋白在吸附过程中构象与取向的变化和吸附过程的动力学行为证实了石墨烯对胰岛素蛋白的有效吸附. 通过对蛋白质结构的分析发现蛋白质的三级结构在所有的体系中均有不同程度的破坏,而蛋白质二级结构的稳定性则与体系有关,其中非固定的石墨烯因其具有较大柔性而表现出对蛋白质二级结构的破坏具有一定选择性. 同时还发现石墨烯的尺寸对于胰岛素的吸附动力学过程也有较大影响.     

蛋白质动力学理论研究中的计算机模拟方法

蛋白质是生物体中一种十分重要的高分子物质。蛋白质分子有着自身所特有的化学、物理结构;在溶液中蛋白质分子不仅自身不同部分间存在着相互作用,而且还与溶剂分子间发生着复杂的相互作用,这些都很大程度上影响到分子的结构和演变过程。为了对蛋白质分子进行模拟,很有必要建立适当的描述蛋白质分子结构的模型,引入合理的模型基元间的相互作用,并采用有效的方法进行模拟,本着贴近现实和方便模拟的原则,在本文中我们系统地总结了近年来蛋白质动力学及其物理特性,特别对其模型、势能及模拟方法进行了着重介绍。为了增加一些感性认识,文中还就实验分析、折叠的协作性、搜寻保守残基和动力学过程的熵效应和阻挫效应等几个专题进行了应用介绍。     

基于光滑粒子动力学方法的液滴冲击固壁面问题数值模拟

采用改进的光滑粒子动力学(SPH)方法对液滴冲击固壁面问题进行了数值模拟. 为了提高传统SPH方法的计算精度和数值稳定性, 在传统的SPH方法的基础上对粒子方法中的密度和核梯度进行了修正, 采用了考虑黎曼解法的SPH流体控制方程, 构造了一种新型的粒子间相互作用力(IIF)模型来模拟表面张力的影响. 应用改进的SPH方法对液滴冲击固壁面问题进行了数值模拟. 计算结果表明：新型的IIF 模型能够较好地模拟表面张力的影响, 改进的SPH方法能够精细地描述液滴与固壁面相互作用过程中液滴的内部压力场演变和自由面形态变化, 液滴的铺展因子随初始韦伯数的增大而增大, 数值模拟结果与实验得到的结果基本一致. 关键词： 液滴 固壁面 光滑粒子动力学 表面张力     

基于弱可压与不可压光滑粒子动力学方法的封闭方腔自然对流数值模拟及算法对比

为了对比研究弱可压光滑粒子动力学(WCSPH)方法和不可压光滑粒子动 力学(ISPH)方法在模拟封闭方腔自然对流问题时的特性, 采用粒子位移技术有效地解决了高瑞利数条件下, 拉格朗日型SPH方法模拟封闭方腔自然对流时流体域内的粒子聚集和空穴问题, 将拉格朗日型SPH 方法求解封闭方腔自然对流问题的最高瑞利数提高到了10⁶; 进而通过对比瑞利数分别为10⁴, 10⁵, 10⁶的条件下, 采用拉格朗日型WCSPH、 拉格朗日型ISPH、欧拉型ISPH三种SPH方法模拟得到的封闭方腔速度分布云图、 温度分布云图、壁面努赛尔特数分布曲线和平均努塞尔特数, 分析了三种SPH方法在模拟封闭方腔自然对流时的精度、稳定性和计算效率. 结果表明: 在低瑞利数条件下, 以上三种SPH方法都可以较好地模拟此问题, 在高瑞利数条件下, 欧拉型ISPH方法的模拟结果最为精确; 拉格朗日型WCSPH方法模拟所得结果比拉格朗日型ISPH方法模拟所得结果稍好些. 关键词： 光滑粒子动力学 不可压光滑粒子动力学 粒子位移技术 自然对流     

多纳米粒子穿越磷脂膜

本文采用耗散粒子动力学模拟方法研究了多纳米粒子与溶液中的磷脂膜相互作用. 模拟中选择纳米颗粒的形状分别为球状和柱状，并且在动力学过程中给它们设置了不同的初始速度. 根据纳米粒子穿膜在动力学过程中体现出不同的特性，分别定义了几种粒子穿越磷脂的模式，并且基于粒子之间的相互作用强度和粒子初始速度，描绘了穿膜模式的详细相图. 本文还进一步研究了体系能量、迴旋半径等参数在不同穿越模式中的动力学过程. 研究结果有助于人们理解纳米颗粒穿膜在生命活动过程中的作用.     

在ADC(2)水平上通过从头算非绝热动力学方法模拟硝酸甲酯的光解

在ADC(2)水平上通过轨线面跳跃方法模拟了硝酸甲酯的非绝热动力学. 结果证实该体系存在快速的非绝热动力学过程,导致了体系回到电子基态. 当动力学从S₁和S₂电子态开始时,光解产物是CH₃O+NO₂,这个发现与实验研究的结果以及更高精度的XMS-CASPT2水平上模拟出的结果一致. 在ADC(2)水平上,当动力学从S₃态开始时,光解产物依然是CH₃O+NO₂. 该研究表明：ADC(2)方法可用于研究硝酸甲酯在长波下的光解机理,然而无法用于理解其在短波段下的光解动力学. 本文为在ADC(2)水平上处理类似化合物的光诱导过程提供了有价值的信息.     

Kinetic Monte Carlo simulations of heteroepitaxial growth with an atomistic model of elasticity

We have implemented Kinetic Monte Carlo (KMC) simulations of growth of heteroepitaxial thin films. A simple cubic Solid-on-Solid (SOS) model is used to describe the atomic configurations and nearest neighbor bonds are used to describe the energetics. Elastic effects are modeled using harmonic springs between atoms displaced from their lattice positions. The misfit strain is a consequence of different equilibrium spring lengths for the substrate and film. The consistency of this elastic model with continuum theories for strained surfaces has been shown by performing elastic energy calculations for various morphologies. KMC simulations for submonolayer deposition show scaling behavior in the island size distribution. The resulting island shapes are predominantly square and do not show any shape transitions in the physically relevant range of conditions. This method gives a detailed understanding of elastic interactions and their interplay with surface diffusion in heteroepitaxial systems.     

Multiscale modeling of submonolayer growth for Fe/Mo (110)

We use a multiscale approach to study a lattice-gas model of submonolayer growth of Fe/Mo (110) by Molecular Beam Epitaxy. To begin with, we construct a two-dimensional lattice-gas model of the Fe/Mo (110) system based on our first-principles calculations of the monomer diffusion barrier and adatom-adatom interactions. The model is investigated by equilibrium Monte Carlo (MC) simulations to compute the diffusion coefficients of Fe islands of different sizes. These diffusion coefficients are used as input to the coarse-grained kinetic rate equation (KRE) approach. We also evaluate effects of the range of Fe-Fe interaction, restriction of interaction to third nearest neighbors allowed to develop feasible atomistic kinetic Monte Carlo (KMC) model. We calculate time evolution of the island size distributions by both KMC and KRE methods and find good agreement between the two methods.     

Study of the island morphology at the early stages of Fe/Mo(110) MBE growth

We present theoretical study of morphology of Fe islands grown at Mo(110) surface in submonolayer MBE mode. We utilize atomistic SOS model with bond counting, and interactions of Fe adatom up to third nearest neighbors. We performed KMC simulations for different values of adatom interactions and varying temperatures. We have found that, while for the low temperature islands are fat fractals, for the temperature 500 K islands have faceted rhombic-like shape. For the higher temperature, islands acquire a rounded shape. In order to evaluate qualitatively morphological changes, we measured average aspect ratio of islands. We calculated dependence of the average aspect ratio on the temperature, and on the strength of interactions of an adatom with neighbors.      

Simulation of multilayer Cu/Pd（100） heteroepitaxial growth by pulse laser deposition

The heteroepitaxial growth of multilayer Cu/Pd(100) thin film via pulse laser deposition (PLD) at room temperature is simulated by using kinetic Monte Carlo (KMC) method with realistic physical parameters. The effects of mass transport between interlayers, edge diffusion of adatoms along the islands and instantaneous deposition are considered in the simulation model. Emphasis is placed on revealing the details of multilayer Cu/Pd(100) thin film growth and estimating the Ehrlich--Schwoebel (ES) barrier. It is shown that the instantaneous deposition in the PLD growth gives rise to the layer-by-layer growth mode, persisting up to about 9 monolayers (ML) of Cu/Pd(100). The ES barriers of The heteroepitaxial growth of multilayer Cu/Pd（100） thin film via pulse laser deposition （PLD） at room temperature is simulated by using kinetic Monte Carlo （KMC） method with realistic physical parameters. The effects of mass transport between interlayers, edge diffusion of adatoms along the islands and instantaneous deposition are considered in the simulation model, Emphasis is placed on revealing the details of multilayer Cu/Pd（100） thin film growth and estimating the Ehrlich-Schwoebel （ES） barrier. It is shown that the instantaneous deposition in the PLD growth gives rise to the layer-by-layer growth mode, persisting up to about 9 monolayers （ML） of Cu/Pd（100）. The ES barriers of 0.08 ± 0.01 eV is estimated by comparing the KMC simulation results with the real scanning tunnelling microscopy （STM） measurements,     

Simulation of multilayer homoepitaxial growth on Cu （100） surface

The processes of multilayer thin Cu films grown on Cu (100) surfaces at elevated temperature (250--400\,K) are simulated by mean of kinetic Monte Carlo (KMC) method, where the realistic growth model and physical parameters are used. The effects of small island (dimer and trimer) diffusion, edge diffusion along the islands, exchange of the adatom with an atom in the existing island, as well as mass transport between interlayers are included in the simulation model. Emphasis is placed on revealing the influence of the Ehrlich--Schwoebel (ES) barrier on growth mode and morphology during multilayer thin film growth. We present numerical evidence that the ES barrier does exist for the Cu/Cu(100) system and an ES barrier $E_{\rm B} >0.125$\,eV is estimated from a comparison of the KMC simulation with the realistic experimental images. The transitions of growth modes with growth conditions and the influence of exchange barrier on growth mode are also investigated.     

Kinetic model for a step edge in epitaxial growth

A kinetic theory is formulated for the velocity of a step edge in epitaxial growth. The formulation involves kinetic, mean-field equations for the density of kinks and "edge adatoms" along the step edge. Equilibrium and kinetic steady states, corresponding to zero and nonzero deposition flux, respectively, are derived for a periodic sequence of step edges. The theoretical results are compared to results from kinetic Monte Carlo (KMC) simulations of a simple solid-on-solid model, and excellent agreement is obtained. This theory provides a starting point for modeling the growth of two-dimensional islands in molecular-beam epitaxy through motion of their boundaries, as an alternative to KMC simulations.     

Kinetic Monte-Carlo simulation of the homoepitaxial growth of MgO{001} thin films by molecular deposition

A lattice-based kinetic Monte-Carlo (KMC) code has been developed to investigate the MgO{001} crystal growth from deposition of MgO molecules, as a prototypical case of the growth of oxide thin films. The KMC approach has been designed on the basis of an extensive database including all possible diffusion mechanisms. The corresponding activation energies have been computed through first-principles calculations at zero temperature or from Arrhenius plots of the frequencies obtained by molecular dynamics simulations with empirical potentials. Crystal growth occurs layer by layer, as experimentally observed, and the diffusion of admolecules leads to a high capacity of nucleation, which is enhanced by vacancy diffusion. We have characterized the growth through surface roughness, size distribution and density of the islands, and filling ratios of the growing layers. Moreover, we have analysed the influence of each elementary mechanism on the growth. The best quality of the deposited layers is reached for temperatures larger than 700 K and for pressures smaller than 0.1 Torr. For these conditions, the simulated surface roughness is fully consistent with available experimental results.     

A First-Passage Kinetic Monte Carlo algorithm for complex diffusion–reaction systems

We develop an asynchronous event-driven First-Passage Kinetic Monte Carlo (FPKMC) algorithm for continuous time and space systems involving multiple diffusing and reacting species of spherical particles in two and three dimensions. The FPKMC algorithm presented here is based on the method introduced in Oppelstrup et al. [10] and is implemented in a robust and flexible framework. Unlike standard KMC algorithms such as the n-fold algorithm, FPKMC is most efficient at low densities where it replaces the many small hops needed for reactants to find each other with large first-passage hops sampled from exact time-dependent Green’s functions, without sacrificing accuracy. We describe in detail the key components of the algorithm, including the event-loop and the sampling of first-passage probability distributions, and demonstrate the accuracy of the new method. We apply the FPKMC algorithm to the challenging problem of simulation of long-term irradiation of metals, relevant to the performance and aging of nuclear materials in current and future nuclear power plants. The problem of radiation damage spans many decades of time-scales, from picosecond spikes caused by primary cascades, to years of slow damage annealing and microstructure evolution. Our implementation of the FPKMC algorithm has been able to simulate the irradiation of a metal sample for durations that are orders of magnitude longer than any previous simulations using the standard Object KMC or more recent asynchronous algorithms.     

Spin kinetic Monte Carlo method for nanoferromagnetism and magnetization dynamics of nanomagnets with large magnetic anisotropy

The Kinetic Monte Carlo (KMC) method based on the transition-state theory, powerful and famous for simulating atomic epitaxial growth of thin films and nanostructures, was used recently to simulate the nanoferromagnetism and magnetization dynamics of nanomagnets with giant magnetic anisotropy. We present a brief introduction to the KMC method and show how to reformulate it for nanoscale spin systems. Large enough magnetic anisotropy, observed experimentally and shown theoretically in terms of first-principle calculation, is not only essential to stabilize spin orientation but also necessary in making the transition-state barriers during spin reversals for spin KMC simulation. We show two applications of the spin KMC method to monatomic spin chains and spin-polarized-current controlled composite nanomagnets with giant magnetic anisotropy. This spin KMC method can be applied to other anisotropic nanomagnets and composite nanomagnets as long as their magnetic anisotropy energies are large enough.