Non-equilibrium molecular dynamics of nanojet injection in a high pressure environment

Nanojet injection in a high pressure environment was simulated using non-equilibrium molecular dynamics. To maintain constant gas pressure, the periodic-shell boundary condition, which can produce a continuous gas flow with constant temperature and velocity, was used. The breakup characteristics of the jet were compared from vacuum to supercritical conditions. Comparing the previous results from vacuum, high pressure effects generally accelerated jet breakup and droplet vaporization processes. Typical supercritical phenomena such as the disappearance of phase interface caused by drastic reduction of surface tension were also observed. At the supercritical state where both pressure and temperature exceed the critical values, a continuous phase transition becomes dominant without droplet formation.     

双酚A型聚碳酸酯形变行为的MD模拟

采用分子动力学方法(MD),计算了双酚A型聚碳酸酯的应力应/变关系、能量/应变关系.研究中采用了COMPASS力场和NPT系综.应力-应变曲线的研究结果显示,应变εXX≤0.05为"弹性区域",在这一区域,应力-应变有很好的线性关系.在εXX=0.14处出现"屈服点",经过"屈服点",在0.15<εXX<1.0的区域出现应力脉动,应变εXX>1.0后发生了应变硬化.能量-应力关系的研究结果显示,在应力-应变呈线性关系的"弹性区域",体系的总势能及各势能分量随应变增大发生不规则的波动,在"屈服点"附近,Etot与Ebs的变化均产生突跃性的局部高点,而EVW在"屈服点"附近的变化刚好与前两者相反;当体系在经历"屈服区域"时,随着应变的增加,各能量项并不发生明显的变化;当体系处于"应变硬化"阶段时,Etot、Ebs和Ebe会随着应变的增大而继续增大.在整个拉伸过程中,Eto均没有发生明显的变化.对拉伸过程的分子链快照进行分析发现,材料在εXX≤0.16时发生均匀的形变,并维持初始的链结构,同时伴随了一些空穴的生成,在εXX>0.6时,可以清楚地看到密度变得不均匀.在εXX>1.0的应变硬化的初始阶段,新的网络结构生成了,长的直链与缠绕链形成的团簇相连.     

超(近)临界水溶剂特性的分子动力学模拟

采用分子动力学模拟,从溶解度参数的角度考察水在不同条件下的溶剂特性。计算结果表明水的溶解度参数1与温度成反比,但当温度高及723.15 K时,变化趋于平缓;2与压力成正比,在临界点(647.45 k,22 MPa)附近对压力特别敏感;超临界水的溶解度参数与密度有良好的线性关系。     

近程作用分子动力学模拟的两级并行

分子动力学作为一种重要的计算手段在许多领域有着广泛的应用，由于它的计算量比较庞大，因此并行计算方法被越来越多地引入到分子动力学的模拟中。本文在目前常见的SMP集群系统上，根据系统的结构特点，针对分子动力学的三种并行算法：区域分解法、原子分解法和力分解法，利用MPI Pthread的混合编程模型，采用节点间消息传递模式以及节点内部共享存储的编程模式，实现了近程作用分子动力学的两级并行计算。计算结果表明，不同的算法采用了两级并行的方式和原来只有消息传递的并行方式相比，具有不同的计算效率，但是从总体来说采用两级并行的计算方式可以利用更多的计算资源，从而有助于提高计算能力。     

氨水溶液汽液界面微观结构的分子模拟

为研究吸收式制冷机常用工质对氨水溶液的微观形态,采用分子动力学方法:蛙跳法积分运动方程,Ewald加和方法计算库仑相互作用,分别对不同摩尔浓度的氨水溶液的汽液界面的微观结构、密度分布、界面厚度、界面张力进行r分析与计算,并拟合出界面厚度随氨水溶液摩尔浓度变化的线性关系式.结果表明:氨分子比水分子更容易吸附于汽液界面处,随着氨水溶液摩尔浓度的增加,汽液界面厚度增加,汽液界面张力减小,变化趋势与实验一致.界面张力的计算值从计算结果的量级和数量上看,与实验值接近.     

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.     

丁二酰亚胺类分散剂在伪烟炱表面吸附行为的分子动力学模拟

丁二酰亚胺类分散剂是一种典型的用于各种润滑油中的无灰分散剂。由于烟炱颗粒结构的复杂性,从实验研究的角度对分散剂的作用机理尚未给出满意的解释。本文应用分子动力学模拟方法,研究了丁二酰亚胺类分散剂模型分子在伪烟炱表面的吸附行为。模拟结果可以为分散剂的分子设计提供参考。     

GPU并行计算集群上的LAMMPS分子动力学模拟性能测试

近年来GPU作为一种具有极强运算能力的多核处理器,得到了快速的发展,成为高性能计算领域的主要发展方向。各种分子动力学模拟的主流软件也纷纷使用GPU技术,其中LAMMPS较早地开发出了通用的并行GPU版本。本文利用nVIDIA公司最新Femi架构的Tesla C2050 GPU搭建了小型的基于LAMMPS的分子动力学模拟GPU并行计算集群,通过氩原子熔化的算例对集群性能进行了测试,测试的内容包括CPU集群、单节点单GPU、单节点多GPU以及多节点GPU集群。比较了各种情况的加速倍数并对造成性能改变的原因进行了讨论,分析了用于MD模拟的GPU并行计算集群性能的瓶颈所在,提出可能的解决方法,搭建集群时,充分考虑PCI总线的承受能力,对于集群效率的提高有很大好处。测试结果表明,集群的性能较高,相对于以往的单机以及CPU集群,计算的规模大大提高了,加速比也在20倍以上。可以预测,在未来一段时间内,多GPU并行是分子动力学模拟的发展方向。     

短程力分子模拟在Hadoop上的实现及优化

在Hadoop开源云计算平台上运行分子模拟程序,具有节省软硬件投资、缩短模拟时间等研究意义。然而,该平台并不擅长科学计算类应用中所涉及的快速迭代和子任务间通信。为此,在原子分解法基础上提出了三种解决方案并利用"读写HDFS同步法"实现短程作用力有效的分子动力学模拟的并行算法。在一个Hadoop集群上测试和分析了程序的可扩展性、加速比和各部分耗时情况,结果表明在大规模体系模拟中有较好的效果,最高取得了28倍的加速比。实验证明,Hadoop并行技术在分子模拟中有着较高的经济价值和实用价值。     

分子动力学模拟HEWL晶体在不同环境中的动力学行为

简要阐述分子动力学模拟的原理及步骤,介绍研究溶菌酶的一般方法和优缺点。在Ubuntu操作系统环境下,利用Gromacs软件和其自带的Gromos96力场,通过分子动力学模拟(MD)鸡蛋清溶菌酶晶体(chicken egg-whitelysozyme,HEWL)溶液,考察真空、水溶液和加入NaCl 3种不同环境条件对溶菌酶晶体构象动力学行为的影响,发现无论从均方根位移(rmsd)、回旋半径、还是从B因子值的轨迹图分析,HEWL在水溶液特别是加入抗衡离子(Na~+,Cl~-)的水溶液的环境下的结构更稳定、合理,与(protein data bank)数据库的真实情况相符。原因是Cl~-与溶菌酶晶体在界面处发生了吸附现象,局部形成溶菌酶-Cl~-复合物,抑制了蛋白-水合物中水分子在相邻水合位置间的跳跃,从而使单晶体在离子液态中更加稳定。模拟结果表明,在pH值6.5,等电位点13.1,总电荷7.999 6的体系下,影响HEWL的吸附位点为123号残基(色氨酸),对从分子水平上解释HEWL晶体的动力学吸附行为具有重要指导意义。     

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。     

非平衡分子动力学在炭膜气体分离CH4/CO2中的模拟研究

通过建立单孔狭缝模型,采用非平衡分子动力学方法研究CH_4/CO_2二元气体混合物通过管状炭膜的传递和分离特性,考察了系统温度、气体组成和膜孔径对通量的影响。模拟过程中将膜低势,区压力取为更符合实际情况的非零值(大于零)。研究结果表明,在温度为20℃～160℃范围内,随温度升高,CH_4的通量增加,CO_2的通量则先降低后升高(80℃出现最低值);随混合气中CH_4组成的增加,CO_2通量下降、CH_4通量升高;随膜孔径增大,CH_4通量先增后减(9.77 (?)时出现最大值)、CO_2通量则呈下降趋势。以上模拟结果与实验数据相比较,吻合良好。在此基础上,本文还考察了跨膜压差对过程的影响,发现CH_4和CO_2的通量均随跨膜压差的增大而增大,膜的分离性能则随之降低。本研究结果充分表明,所建模型能够正确地描述CH_4/CO_2气体混合物的炭膜分离过程。     

Scalability study of molecular dynamics simulation on Godson-T many-core architecture

Molecular dynamics (MD) simulation has broad applications, and an increasing amount of computing power is needed to satisfy the large scale of the real world simulation. The advent of the many-core paradigm brings unprecedented computing power, but it remains a great challenge to harvest the computing power due to MD’s irregular memory-access pattern. To address this challenge, this paper presents a joint application/architecture study to enhance the scalability of MD on Godson-T-like many-core architecture. First, a preprocessing approach leveraging an adaptive divide-and-conquer framework is designed to exploit locality through memory hierarchy with software controlled memory. Then three incremental optimization strategies–a novel data-layout to improve data locality, an on-chip locality-aware parallel algorithm to enhance data reuse, and a pipelining algorithm to hide latency to shared memory–are proposed to enhance on-chip parallelism for Godson-T many-core processor. Experiments on Godson-T simulator exhibit strong-scaling parallel efficiency of 0.99 on 64 cores, which is confirmed by a field-programmable gate array emulator. Also the performance per watt of MD on Godson-T is much higher than MD on a 16-cores Intel core i7 symmetric multiprocessor (SMP) and 26 times higher than MD on an 8-core 64-thread Sun T2 processor. Detailed analysis shows that optimizations utilizing architectural features to maximize data locality and to enhance data reuse benefit scalability most. Furthermore, a hierarchical parallelization scheme is designed to map the MD algorithm to Godson-T many-core cluster and a simple performance model is derived, which suggests that the optimization scheme is likely to scale well toward exascale. Certain architectural features are found essential for these optimizations, which could guide future hardware developments.     

双芘环荧光体Pyrene-diIL-Pyrene荧光特性的分子动力学研究

采用分子动力学模拟方法研究双芘环荧光体Pyrene-diIL-Pyrene(PDP)在水和甲醇中荧光改变的机制.结果表明,平衡时(1)该荧光体当分子中的芘环中心间距小于6 A时,芘环在甲醇中比在水中的排列无序;(2)最近邻芘环中心间距从约4 1 A处移到了6.0 A处,降低了芘分子形成芘激子的概率,进而表明该荧光体的激...     

Exploiting hierarchy parallelism for molecular dynamics on a petascale heterogeneous system

Heterogeneous systems with nodes containing more than one type of computation units, e.g., central processing units (CPUs) and graphics processing units (GPUs), are becoming popular because of their low cost and high performance. In this paper, we have developed a Three-Level Parallelization Scheme (TLPS) for molecular dynamics (MD) simulation on heterogeneous systems. The scheme exploits multi-level parallelism combining (1) inter-node parallelism using spatial decomposition via message passing, (2) intra-node parallelism using spatial decomposition via dynamically scheduled multi-threading, and (3) intra-chip parallelism using multi-threading and short vector extension in CPUs, and employing multiple CUDA threads in GPUs. By using a hierarchy of parallelism with optimizations such as communication hiding intra-node, and memory optimizations in both CPUs and GPUs, we have implemented and evaluated a MD simulation on a petascale heterogeneous supercomputer TH-1A. The results show that MD simulations can be efficiently parallelized with our TLPS scheme and can benefit from the optimizations.     

分子动力学模拟蛋白质溶液吸附过程构象的变化

计算机模拟作为一种工具在药物分子设计、蛋白质工程、药物筛选等方面逐渐广泛应用起来。为了从分子水平上理解蛋白质吸附的机理，本文采用了刚体模型对聚十赖氨酸在固体表面吸附进行了分子动力学模拟。采用立方周期性边界条件，模拟在NVT条件下进行，各刚体的起始速度按Maxwell取样。初步研究了模拟过程中蛋白质构象的变化，跟踪了吸附过程中二面角φ和ψ的变化。研究结果表明，吸附过程中蛋白质二级结构发生了变化，C末端二级结构的变化最为明显。     

黄粉虫α-淀粉酶与抑制剂相互作用的分子动力学模拟

α-淀粉酶与抑制剂相互作用一直受到人们关注。本文利用hyperchem 7.5软件,在opls力场下,选择分子动力学方法,模拟了不同温度条件下,黄粉虫的α-淀粉酶与抑制剂相互作用。通过对势能数据分析,结果显示在280 K左右黄粉虫的α-淀粉酶与抑制剂相互作用最强。这与实验得出的最适温度较为吻合。     

Computational and statistical study on the molecular interaction between antigen and antibody

Monoclonal antibodies are one of the most successful bio-molecules utilized in the clinical scene of today. It is important to clarify general characteristics of the interaction between antigen and antibody and to draw a guide for enhancing their binding affinity in rational design of antibody drugs. In this study, we carried out molecular dynamics simulations for 20 kinds of antigen–antibody complexes. From the statistical analysis of the calculation results, the following findings were deduced. At complementarity determining regions (CDRs) of the antibodies, the rates for the presence of serine (Ser) and tyrosine (Tyr) are high. The amino residues involved in direct hydrogen bonds between antigens and antibodies were examined by counting the numbers of the hydrogen bonds from the respective residues. The contribution of Tyr to the direct hydrogen bonding was the highest and that of Ser was the fourth. Furthermore, the short-distance hydrogen bonds, which is assumed to be so-called “low-barrier hydrogen bond”, were observed at CDRs in three complexes. Interestingly, Ser is involved in the short-distance hydrogen bonding in two cases out of the three. This result suggests that these two unchanged polar amino acid residues play an important role for recognition of antigen. In almost all of the complexes (18/20), the contribution of the electrostatic energy (ΔE_ele) to the binding free energy was calculated to be larger than that of the van der Waals energy (ΔE_vdw). This dominance of the electrostatic energy is in contrast to the case that low molecular-weight compounds are bound to their targets. The findings of this study will be helpful to design an antibody with a high specificity and a high affinity to the antigen.     

The effect of interatomic potentials on the molecular dynamics simulation of nanometric machining

One of the major tasks in a molecular dynamics (MD) simulation is the selection of adequate potential functions, from which forces are derived. If the potentials do not model the behaviour of the atoms correctly, the results produced from the simulation would be useless. Three popular potentials, namely, Lennard-Jones (LJ), Morse, and embedded-atom method (EAM) potentials, were employed to model copper workpiece and diamond tool in nanometric machining. From the simulation results and further analysis, the EAM potential was found to be the most suitable of the three potentials. This is because it best describes the metallic bonding of the copper atoms; it demonstrated the lowest cutting force variation, and the potential energy is most stable for the EAM.     

复合推进剂颗粒填充模型的分子动力学模拟方法

将复合推进剂看作是颗粒与基体组成的复合材料,应用分子动力学模拟方法生成推进剂颗粒在基体中随机分布的填充模型。研究表明,分子动力学模拟方法,指定与颗粒直径成比例的增长率可有效地生成颗粒大小不等的填充模型,为分析推进剂细观力学性能和燃烧性能奠定基础。