气体在水中扩散过程的分子模拟

用分子动力学(MD)模拟法模拟正则系综下氧气、甲烷等4种气体,在水中的扩散过程.计算扩散系数采用微分--区限变分法.结果表明:水分子数目相同下计算不同分子数气体的扩散系数差别较大.与氨基酸相比,其扩散系数模拟值并不总是随着浓度的增加而减小,而是先增大后减小.4种气体在水中的扩散系数与文献值相对比,模拟结果与实验结果吻合较好.研究结果表明采用分子模拟手段可以获得具有工业应用价值的扩散系数,从而有助于计算传质学的发展.     

芳香氨基类化合物对铁缓蚀行为的分子动力学模拟

采用分子动力学模拟方法研究了2种芳香氨基类缓蚀剂（对氨基苯磺酸、2-氨基5-硝基苯甲酸）在Fe（110）表面的吸附行为,计算了吸附能,并对其缓蚀机理进行了深入分析,研究结果表明,芳香氨基类分子的极性端基会吸附在金属表面上,而非极性端基则背离金属表面,并通过自身的扭转形变实现稳定吸附;两种缓蚀剂膜均能有效阻碍溶液中的腐蚀介质向金属铁表面扩散,从而达到延缓金属腐蚀的目的。另从缓蚀剂膜阻碍腐蚀介质粒子（H₃O和H₃O⁺）向金属表面扩散的角度,研究了腐蚀介质粒子在2-氨基5-硝基苯甲酸缓蚀剂膜中的扩散行为,计算其扩散系数,结果表明,缓蚀剂膜能有效抑制腐蚀介质的迁移,削弱其腐蚀能力:与中性H₃O分子对比,缓蚀剂膜对H₃O⁺带电离子的扩散具有更强的抑制效果。     

非平衡分子动力学模拟在炭膜气体分离中的研究进展

叙述了近年来非平衡分子动力学在炭膜气体分离中的研究进展,包括分子模拟方法的选取及非平衡分子动力学模拟的几个主要步骤;综述了气体混合物通过炭膜时传递和分离性能的影响因素(如孔结构及孔径大小、操作压力、温度、组分组成等);并对炭膜研究现状作了简要的概述,提出目前分子模拟在炭膜研究中所存在的问题,一方面是模型建立问题．另一方面是研究膜传递和分离机理性能所考察的影响因素还不够完善,加强对膜传递分离机理的研究,对膜的设计、制备及应用都有重要的指导意义。     

烷烃在分子筛孔中吸附和扩散的分子模拟

用巨正则系综蒙特卡罗(grand canonical monte carlo,GCMC)和构型偏倚蒙特卡罗(configurational-bias monte carlo,CB- MC)相结合的模拟方法,研究300 K下,烷烃(甲烷、乙烷、丙烷、丁烷)在ISV、MEL型分子筛上的吸附,饱和吸附量的大小顺序为:甲烷>乙烷>丙烷>丁烷。模拟甲烷-乙烷、乙烷-丙烷混合物在分子筛(ISV、MOR、MEL型)中的吸附分离,结果甲烷-丙烷比乙烷-丙烷混合物更易分离。采用分子动力学(molecular dynamics,MD)模拟方法,研究甲烷在MEL、MOR分子筛上的扩散系数,分别为2.76-3.86 m~2·s~(-1)、3.14-13.30 m~2·s~(-1),烷烃在分子筛中的扩散与吸附相关,且扩散系数的大小与分子筛的结构有关。模拟所得的有关吸附扩散性质的数据对于化工生产、研发和设计具有指导意义。     

LTA和FAU型分子筛吸附CO2力场的研究

采用巨正则系综的蒙特卡罗法,由通用力场Universal、Pcff、Dreiding和Cvff模拟CO2在LTA(4A和5A)和FAU型(NaX和NaY)分子筛上的吸附行为.计算结果显示,现有的通用力场已不适用于分子筛吸附CO2的体系,需要优化力场.CO2在分子筛上吸附是通过分子间非键能发生作用,而文献中优化力场常用的量子化学计算法,虽然求得的分子内键作用力较为精确,但对分子间作用力却不一定有效,特别是范德华力.而计算结果与实验数据拟合法可以更真实反映分子间作用力,故采用后一种方法优化CO2/LTA型分子筛的力场.所得力场参数既适合CO2与5A分子筛吸附体系又适合CO2在4A分子筛上的吸附,但根据LTA型分子筛得到的优化力场不能正确描述FAU型分子筛的吸附行为.采用拟合实验数据的方法,同样得到1组适合NaY分子筛的优化力场,用于计算NaX分子筛的CO2吸附等温线,结果与实验值相吻合.可见,骨架结构相同的分子筛,可以用相同的力场参数去计算其吸附性质,而不受硅铝比和骨架外阳离子的影响.但不同的骨架结构需要不同的力场参数来描述.     

甲烷、乙烷及其共混物在silicalite-1中吸附的蒙特卡罗模拟

采用TraPPE力场、巨正则系综蒙特卡罗(GCMC)的方法,通过调节部分力场参数,拟合纯组分等温吸附的实验数据,研究了甲烷、乙烷纯组分在silicalite-1中的吸附平衡性及其共混物的分离性。模拟结果和实验的吸附等温线相一致,计算的吸附热与实验值相吻合,说明该计算方法可靠、合理;研究压力范围内silicalite-1中分子吸附的构型,甲烷分子分布均匀,乙烷分子在稍高压力下便向孔道交叉处分布;乙烷对甲烷的选择性,在不同气相摩尔组分变化不明显,分离性能稳定,其选择性系数在21左右。     

用分子模拟方法预测MOFs材料氢吸附的能力

用分子力学力场模拟法预测材料的储氢性能,为实验合成提供理论指导,降低开发成本和时间,有重要的实用意义.本文采用第一性原理推导的分子力学力场及巨正则系综蒙特卡洛模拟(GCMC)法和Feyman-Hibbs有效势计算氢分子在MOF-5体系的吸附曲线,所得不同温度和压力下的超额及绝对吸附曲线均与实验吻合良好,表明模拟法和力场的准确性.于是,预测了一系列不同MOFs材料的储放氢性能后,探讨材料结构和储氢能力.发现化学结构相似的MOFs材料,影响材料储放氢能力的关键因素是材料的自由体积.     

HZSM-5中水吸附行为的实验与分子模拟

利用智能重量分析仪(IGA—003,HIDEN)测定了298K条件下水蒸汽在HZSM-5型分子筛中的吸附等温线。并采用巨正则系综Monte Carlo模拟方法(GCMC)研究了水在HZSM—5型分子筛中的吸附等温线,计算结果与实验结果吻合较好。分子模拟计算得到的水分子的微观吸附性质表明水分子吸附在氢离子和铝原子的周围,这是因为水分子是极性分子,分子筛上的氢在库仑力的作用下会与水分子发生强的相互作用,并导致分子筛骨架上的硅铝比与水分子的吸附量之间存在线性关系。计算结果还表明水的吸附热与H_2O/Al之间存在线性关系。     

分子动力学模拟蛋白质吸附过程中势能函数计算的分组简化

分子水平上理解蛋白质吸附的机理,是目前蛋白质工程、生物材料和生物医学领域中一个基本问题。本文根据蛋白质分子结构的特点,采用刚体模型,在NVT条件下,对聚十赖氨酸分子在固液界面上的吸附过程进行了分子动力学模拟。在计算过程中,通过对原胞内原子进行适当分组的方法改进,以求进一步提高对势能函数的计算速度。研究结果表明,适当分组的方法可以简化分子动力学模拟的计算过程,加快计算速度,而模拟结果反映了吸附过程中蛋白质分子构象变化过程。     

氮化铝陶瓷薄膜热导率的分子动力学模拟

采用平衡分子动力学方法(EMD)研究了平衡温度为300K的氮化铝薄膜的法向热导率.利用Stillinger-Weber势函数以及Green-Kubo线性响应理论计算热导率.计算结果表明,氮化铝薄膜的热导率值显著小于对应大体积材料的实验值,具有明显的尺寸效应.在氮化铝薄膜为1.47～5.39 nm的范围内,氮化铝薄膜的热导率随着薄膜厚度的增加而近似的线性增加.     

Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations

In complex systems with many degrees of freedom such as spin glass and biomolecular systems, conventional simulations in canonical ensemble suffer from the quasi-ergodicity problem. A simulation in generalized ensemble performs a random walk in potential energy space and overcomes this difficulty. From only one simulation run, one can obtain canonical ensemble averages of physical quantities as functions of temperature by the single-histogram and/or multiple-histogram reweighting techniques. In this article we review the generalized ensemble algorithms. Three well-known methods, namely, multicanonical algorithm (MUCA), simulated tempering (ST), and replica-exchange method (REM), are described first. Both Monte Carlo (MC) and molecular dynamics (MD) versions of the algorithms are given. We then present five new generalized-ensemble algorithms which are extensions of the above methods.     

硅的平衡态分子动力学模拟

平衡态分子动力学模拟是研究既定系统向所期望的平衡态演化的一种方法,不仅可预测平衡态的各种性质,还为动力学加载过程提供合理的初始条件.本文主要研究Free、NVT、NVE平衡态分子动力学模拟中系统宏观量的演化过程;并讨论如何根据不同的初始条件,选择恰当的平衡态模拟方法.     

Stochastic boundary conditions for grand-canonical-like molecular dynamics simulations of open systems

In this paper we develop a stochastic boundary conditions (SBC) for event-driven molecular dynamics simulations of a finite volume embedded within an infinite environment. In this method, we first collect the statistics of injection/ejection events in periodic boundary conditions (PBC). Once sufficient statistics are collected, we remove the PBC and turn on the SBC. In the SBC simulations, we allow particles leaving the system to be truly ejected from the simulation, and randomly inject particles at the boundaries by resampling from the injection/ejection statistics collected from the current or previous simulations. With the SBC, we can measure thermodynamic quantities within the grand canonical ensemble, based on the particle number and energy fluctuations. To demonstrate how useful the SBC algorithm is, we simulated a hard disk gas and measured the pair distribution function, the compressibility and the specific heat, comparing them against literature values.     

pH effects on adsorption behavior and self-aggregation of dodecylamine at muscovite/aqueous interfaces

In this work, molecular dynamics simulation was used to examine the effect of solution pH on the adsorption behavior and self-aggregation of dodecylamine hydrochloride (DDA) on the muscovite (0 0 1) surface. The properties of surfactants are assessed in terms of density profiles in the direction perpendicular to the muscovite surface. Results show that although DDA can adsorb at muscovite at all pH we discussed, the self-aggregation of DDA varies significantly at different pH values. At pH 10, a compact hydrophobic monolayer forms on the muscovite surface. At pH 3, hemi-micelle aggregated structure forms with several DDA cations far away from muscovite surface. At pH 12, it has been confirmed that adsorption of DDA neutral molecules occurs with only a few DDA molecules adsorbing on muscovite directly and acting as a bridge linking the rest DDA molecules, which exists nearby muscovite surface irregularly. Density profiles revealed that at pH 10, DDA cations play a dominant role in the interaction between DDA surfactants and muscovite. While DDA molecules have difficulty in forming a hydrogen bond with the oxygen atom on the muscovite surfaces, and they co-adsorb onto muscovite through the electrostatic interactions with muscovite and hydrophobic force with DDA cations. Therefore, the hydrophobization of muscovite in the presence of DDA are higher at pH 10 than that at pH 3 and pH 12. Our results indicate that molecular dynamics simulation can be a power tool in charactering adsorption behavior of surfactants onto mineral surfaces at different pH values.     

Fundamental dynamics of flow through carbon nanotube membranes

The flow of a model non-polar liquid through small carbon nanotubes is studied using non-equilibrium molecular dynamics simulation. We explain how a membrane of small-diameter nanotubes can transport this liquid faster than a membrane consisting of larger-diameter nanotubes. This effect is shown to be back-pressure dependent, and the reasons for this are explored. The flow through the very smallest nanotubes is shown to depend strongly on the depth of the potential inside, suggesting atomic separation can be based on carbon interaction strength as well as physical size. Finally, we demonstrate how increasing the back-pressure can counter-intuitively result in lower exit velocities from a nanotube. Such studies are crucial for optimisation of nanotube membranes.     

Parallel computing of diatomic molecular rarefied gas flows

A parallel algorithm for direct simulation Monte Carlo calculation of diatomic molecular rarefied gas flows is presented. For reliable simulation of such flow, an efficient molecular collision model is required. Using the molecular dynamics method, the collision of N₂ molecules is simulated. For this molecular dynamics simulation, the parameter decomposition method is applied for parallel computing. By using these results, the statistical collision model of diatomic molecule is constructed. For validation this model is applied to the direct simulation Monte Carlo method to simulate the energy distribution at equilibrium condition and the structure of normal shock wave. For this DSMC calculation, the domain decomposition is applied. It is shown that the collision process of diatomic molecules can be calculated precisely and the parallel algorithm can be efficiently implemented on the parallel computer.     

双目标推动下群体行为的元胞自动机模拟

采用元胞自动机对自推动粒子改进模型进行模拟,在此基础上分别探讨无目标与双目标群体行为的演化特征。无目标条件下群体行为的元胞模拟结果显示低密度环境下大部分个体处于动态均衡,高密度环境下大部分个体处于静态均衡,中等密度下两种均衡均存在。基于双目标吸引力的群体行为模拟结果显示当智能体的理性程度较低时系统演化能够产生一定的集聚效应,处于吸引源以外的智能体与吸引源保持一定距离并呈湍流式运动,而当智能体具备小概率全局理性判断能力时,群体行为的演化结果为大部分智能体都聚集在吸引源附近。     

Ptuba: a tool for the visualization of helix surfaces in proteins

Projection of transmembrane helices using a Uniform B-spline Algorithm is a tool for the visualization of interactions between helices in membrane proteins. It allows the user to generate projections of 3D helices, no matter what their deviations from a canonical helix might be. When associated with adapted coloring schemes it facilitates the comprehension of helix-helix interactions. Examples of transmembrane proteins were chosen to illustrate the advantages that this method provides. In the glycophorin A dimer we can easily appreciate the structural features behind homodimerisation. Using the structure of the fumarate reductase we analyze the contact surfaces inside a helical bundle and thanks to structures from a molecular dynamics simulation we see how modifications in structure and electrostatics relate to their interaction. We propose the use of this tool as an aid to the visualization and analysis of transmembrane helix surfaces and properties.     

Fast,automatic character animation pipelines

Humanoid three‐dimensional (3D) models can be easily acquired through various sources, including through online marketplaces. The use of such models within a game or simulation environment requires human input and intervention in order to associate such a model with a relevant set of motions and control mechanisms. In this paper, we demonstrate a pipeline where humanoid 3D models can be incorporated within seconds into an animation system and infused with a wide range of capabilities, such as locomotion, object manipulation, gazing, speech synthesis and lip syncing. We offer a set of heuristics that can associate arbitrary joint names with canonical ones and describe a fast retargeting algorithm that enables us to instill a set of behaviors onto an arbitrary humanoid skeleton on‐the‐fly. We believe that such a system will vastly increase the use of 3D interactive characters due to the ease that new models can be animated.Copyright © 2013 John Wiley & Sons, Ltd.