Coarse-grained molecular dynamics simulations of capillary evaporation of water confined in hydrophilic mesopores

Non-equilibrium molecular dynamics (MD) simulations were performed to investigate the capillary evaporation of water confined in hydrophilic mesopores. The electrostatics-based (ELBA) coarse-grained water model was employed to calculate the duration of the time-consuming capillary evaporation process. To evaluate the effect of hydrophilicity of mesopores on the capillary evaporation of water, three types of thin films with a cylindrical mesopore were modelled by tuning the interactions between water and wall atoms. Initially, the cylindrical mesopore was filled with water, and evaporation of the water into vacuum was simulated. The calculation results showed that when capillary evaporation occurred, the desorption rate of water was almost constant in a highly hydrophilic mesopore where a stable water layer was formed on the pore surface, whereas the rate decreased with time in a weakly hydrophilic mesopore where the water layer did not remain stable. As time progressed, the water column shortened and then broke up. The number of water molecules in the mesopores decreased exponentially with time. The difference in the hydrophilicity of the mesopores resulted in different relaxation curves of water desorption from the mesopores.     

Identification of key residues in protein functional movements by using molecular dynamics simulations combined with a perturbation-response scanning method

The realization of protein functional movement is usually accompanied by specific conformational changes, and there exist some key residues that mediate and control the functional motions of proteins in the allosteric process. In the present work, the perturbation-response scanning method developed by our group was combined with the molecular dynamics (MD) simulation to identify the key residues controlling the functional movement of proteins. In our method, a physical quantity that is directly related to protein specific function was introduced, and then based on the MD simulation trajectories, the perturbation-response scanning method was used to identify the key residues for functional motions, in which the residues that highly correlated with the fluctuation of the function-related quantity were identified as the key residues controlling the specific functional motions of the protein. Two protein systems, i.e., the heat shock protein 70 and glutamine binding protein, were selected as case studies to validate the effectiveness of our method. Our calculated results are in good agreement with the experimental results. The location of the key residues in the two proteins are similar, indicating the similar mechanisms behind the performance of their biological functions.     

Molecular kinetic theory of boundary slip on textured surfaces by molecular dynamics simulations

A theoretical model extended from the Frenkel-Eyring molecular kinetic theory (MKT) was applied to describe the boundary slip on textured surfaces. The concept of the equivalent depth of potential well was adopted to characterize the solid-liquid interactions on the textured surfaces. The slip behaviors on both chemically and topographically textured surfaces were investigated using molecular dynamics (MD) simulations. The extended MKT slip model is validated by our MD simulations under various situations, by constructing different complex surfaces and varying the surface wettability as well as the shear stress exerted on the liquid. This slip model can provide more comprehensive understanding of the liquid flow on atomic scale by considering the influence of the solid-liquid interactions and the applied shear stress on the nano-flow. Moreover, the slip velocity shear-rate dependence can be predicted using this slip model, since the nonlinear increase of the slip velocity under high shear stress can be approximated by a hyperbolic sine function.     

基于分子动力学模拟的主链型液晶聚合物的新模型

在传统的Gay-Berne (GB)/Lennard-Jones (LJ)模型的基础上，发展了一种用于模拟半刚性主链型液晶聚合物(LCP)的分子级模型，命名为Solo-LJ-SP-GB 模型.单一的LJ联合体和非线性弹簧被用于描述LCP分子中的间隔体.用分子动力学模拟半刚性主链型LCP系统(该系统由169条分子链组成，每两个刚性体之间的间隔体个数为6)时，该模型所需的计算时间不到传统的GB/LJ 模型所需时间的十分之一，大大地提高了计算效率.通过采用该模型模拟半刚性主链型LCP的相变问题，观察到了与半刚性主链型LCP分子中间隔体个数相关的热力学的奇偶效应以及从等方相到向列相的相转变过程.这些模拟结果与当前的试验结果相当符合，从而表明了该模型可以较为准确地描述出半刚性主链型LCP的结构特性. 关键词： Solo-LJ-SP-GB模型 液晶聚合物 分子动力学模拟     

Molecular dynamics simulations of compressed hydrogen

Abstract

Molecular dynamics simulations have been performed for highly compressed fluid hydrogen in the density and temperature regime of recent shock-compression experiments. Both density functional and tight-binding electronic structure techniques have been used to describe interatomic forces. Two tight-binding models of hydrogen have been developed with a single s-type orbital on each atom that reproduce properties of the dimer, of various crystalline structures, and of the fluid. The simulations indicate that the rapid rise in the electrical conductivity observed in the gas-gun experiments depends critically on the dissociated atoms (monomers). We find that the internal structure of warm, dense hydrogen has a pronounced time-dependent nature with the continual dissociation of molecules (dimers) and association of atoms (monomers). Finally, Hugoniots derived from the equations-of-state of these models do not exhibit the large compressions predicted by the recent laser experiments.     

Novel methodology for the calculation of the enthalpy of enclathration of methane hydrates using molecular dynamics simulations

Methane hydrates are encountered in a plethora of industrial and geological or environmental applications. In the current study, we present a novel methodology which is based on molecular dynamics simulations for the calculation of the enthalpy of enclathration of sI methane hydrates. Simulations are performed along the three-phase (Hydrate – Liquid water – Vapour; H–L_w–V) equilibrium line in the temperature range 274–310?K. The methodology takes into account the two different types of cages that are present in the sI methane hydrate and provides results for the enthalpy of enclathration for both types of cages, while it avoids performing calculations with the metastable, completely empty hydrate lattice. The formulation proposed is general and can be also applied to sII hydrates, while it can be modified/extended appropriately for use in the case of sH hydrates. Comparison is provided with available data from the literature and good agreement is observed.     

High density gas state at water/graphite interface studied by molecular dynamics simulation

In this paper molecular dynamics simulations are performed to study the accumulation behaviour of N2 and H2 at water/graphite interface under ambient temperature and pressure. It finds that both N2 and H2 molecules can accumulate at the interface and form one of two states according to the ratio of gas molecules number to square of graphite surface from our simulation results： gas films （pancake-like） for a larger ratio and nanobubbles for a smaller ratio. In addition, we discuss the stabilities of nanobubbles at different environment temperatures. Surprisingly, it is found that the density of both kinds of gas states can be greatly increased, even comparable with that of the liquid N2 and liquid H2. The present results are expected to be helpful for the understanding of the stable existence of gas film （pancake-like） and nanobubbles.     

Multiscale molecular dynamics simulations of membrane remodeling by Bin/Amphiphysin/Rvs family proteins

Membrane curvature is no longer thought of as a passive property of the membrane; rather, it is considered as an active, regulated state that serves various purposes in the cell such as between cells and organelle definition. While transport is usually mediated by tiny membrane bubbles known as vesicles or membrane tubules, such communication requires complex interplay between the lipid bilayers and cytosolic proteins such as members of the Bin/Amphiphysin/Rvs(BAR) superfamily of proteins. With rapid developments in novel experimental techniques, membrane remodeling has become a rapidly emerging new field in recent years. Molecular dynamics(MD) simulations are important tools for obtaining atomistic information regarding the structural and dynamic aspects of biological systems and for understanding the physics-related aspects. The availability of more sophisticated experimental data poses challenges to the theoretical community for developing novel theoretical and computational techniques that can be used to better interpret the experimental results to obtain further functional insights. In this review, we summarize the general mechanisms underlying membrane remodeling controlled or mediated by proteins. While studies combining experiments and molecular dynamics simulations recall existing mechanistic models, concurrently, they extend the role of different BAR domain proteins during membrane remodeling processes. We review these recent findings, focusing on how multiscale molecular dynamics simulations aid in understanding the physical basis of BAR domain proteins, as a representative of membrane-remodeling proteins.     

Energy flow in thermostatted non-equilibrium molecular dynamics simulations

Energy transfers between internal kinetic and potential energy reservoirs in a simple liquid are studied by setting the temperature of one energy reservoir to a different value from that of the others and computing the resultant energy flows. In the first set of simulations, the x-directional kinetic temperature was artificially raised above the other five, and in the second, the x-directional configurational temperature was artificially raised above the other five. In both cases, external energy flows balanced, but unexpected energy flows between different directional components of the potential energy were observed. Additional simulations showed that these energy flows occurred regardless of the arrangement of thermostats imposed on the six degrees of freedom and the addition of shear. Heat flow between degrees of freedom that were ostensibly at the same temperature was anomalously observed. It was concluded that a different breakdown of the contributions to the configurational energy that is consistent with the definition of the directional configurational temperatures is required.     

氦热力学性质的分子动力学研究

 利用经典分子动力学和第一性原理分子动力学,研究了氦在高压下的熔化曲线、状态方程和非金属-金属转变。得到了氦在温度小于4.5 eV、 密度0.3~5.0 g/cm³范围内的状态方程,并把氦的熔化曲线的压强范围拓展到了50 GPa。氦的能隙宽度曲线表明,温度大大降低了氦的金属化密度。     

双壁碳纳米管电浸润现象的分子动力学模拟

在单壁碳纳米管电浸润现象原子模拟的基础上,对双壁碳纳米管的电浸润现象进行了计算机模拟.运用经典分子动力学方法结合一个宏观的电毛细管模型模拟了双壁碳纳米管在水银中的电浸润过程,对不同内管尺寸情况下的浸润现象作了研究和比较.计算结果表明双壁碳管和单壁碳管的电浸润过程存在很大的不同,双壁碳管的内管在电浸润过程中起到重要的作用：当改变双壁碳管中内管的尺寸时,浸润现象会产生很大的改变. 关键词： 双壁碳纳米管 电浸润 分子动力学     

Studies on the structures and interactions of glutathione in aqueous solution by molecular dynamics simulations and NMR spectroscopy

All-atom molecular simulations and temperature-dependent NMR have been used to investigate the conformations and hydrogen bonds of glutathione (GSH) in aqueous solution. The simulations start from three different initial conformations. The properties are characterized by intramolecular distances, radius of gyration, root-mean-square deviation, and solvent-accessible surface. GSH is highly flexible in aqueous solutions in the simulations. Moreover, conformations can covert between “extended” and “folded” states. Interestingly, the two different hydrogen atoms in cysteine (H_N2) and glycin (H_N3) show different capabilities in forming NH?OW hydrogen bonds. The temperature-dependent NMR results of the different amide hydrogen atoms also show agreements with the MD simulations. Competing formation of GSH hydrogen-bonding interactions in aqueous solutions leads to hydrogen-bonding networks and the distribution of conformations. These changes will affect the activity of GSH under physiological conditions.     

The melting mechanism in binary Pd0.25Ni0.75 nanoparticles: molecular dynamics simulations

The melting mechanism for Pd_0.25Ni_0.75 alloy nanoparticles (NPs) was investigated using molecular dynamics (MD) simulations with quantum Sutton-Chen many-body potentials. NPs of six different sizes ranging from 682 to 22,242 atoms were studied to observe the effect of size on the melting point. The melting temperatures of the NPs were estimated by following the changes in both the thermodynamic and structural quantities such as the total energy, heat capacity and Lindemann index. We also used a thermodynamics model to better estimate the melting point and to check the accuracy of MD simulations. We observed that the melting points of the NPs decreased as their sizes decreased. Although the MD simulations for the bulk system yielded higher melting temperatures because of the lack of a seed for the liquid phase, the melting temperatures determined for both the bulk material and the NPs are in good agreement with those predicted from the thermodynamics model. The melting mechanism proceeds in two steps: firstly, a liquid-like shell is formed in the outer regions of the NP with increasing temperature. The thickness of the liquid-like shell increases with increasing temperature until the shell reaches a critical thickness. Then, the entire Pd–Ni NP including core-related solid-like regions melts at once.     

The influence of changes in the framework on the diffusion in zeolites. Molecular dynamics simulations

Some less known methods are described for the analysis of trajectories of guest molecules in porous solids. Such trajectories can be calculated by Molecular Dynamics (MD) computer simulations in order to analyze the interrelations between the structure and the particle behaviour including collective phenomena. Some results obtained with these methods for diffusing methane in zeolites of type LTA are presented. An analytical potential model for LTA type zeolites is given that make extremely long runs or simulations of large lattice regions for systems with rigid lattice possible. Such runs are necessary e.g. to examine questions as the influence of extented lattice defects or the fractal behaviour of the partical trajectories.     

Notch fatigue of Cu_(50)Zr_(50) metallic glasses under cyclic loading: molecular dynamics simulations

Molecular dynamics simulation is performed to simulate the tension–compression fatigue of notched metallic glasses(MGs), and the notch effect of MGs is explored. The notches will accelerate the accumulation of shear transition zones, leading to faster shear banding around the notches' root causing it to undergo severe plastic deformation. Furthermore, a qualitative investigation of the notched MGs demonstrates that fatigue life gradually becomes shorter with the increase in sharpness until it reaches a critical scale. The fatigue performance of blunt notches is stronger than that of sharp notches. Making the notches blunter can improve the fatigue life of MGs.     

基于分子动力学模拟流体输运性质的稳定性分析

利用线性响应理论对Ar流体输运参数进行了分子动力学模拟,结果发现:导热系数和黏度会随着自相关积分函数积分时间的增加而产生剧烈波动,而扩散系数却相对稳定. 针对积分稳定性这一问题,对导热系数和黏度中的热流密度和应力张量进行了分解分析,发现含分子间作用力项是影响稳定性的最大因素. 从牛顿力学出发对作用力项的影响机理进行了分析,指明减小这种影响的最主要方法是使在体系进行统计输运参数前达到稳定平衡状态,即最小的预平衡步数应该满足使体系达到该状态下熵最大或者能量最低,并尽量减小温度对体系的影响. 同时,还对模拟盒尺寸、统计步长等因素对积分稳定性的影响进行了分析,给出了保持稳定性的建议. 关键词： 分子动力学 输运性质 自相关函数 稳定性     

能量粒子轰击金刚石的计算机模拟

利用Tersoff势和分子动力学方法研究了初始动能为500 eV的硼粒子注入金刚石的微观行为.结果表明：硼注入后产生温度为5000 K的热峰，其寿命为0.18 ps；同时产生半径为0.45 nm局部非晶化区域，三重配位原子数占该区域原子数的7%.薄膜表层原子向内弛豫，近表层原子向外弛豫，表面层与近表层原子的间距减少了15%，表面层表现为压应力.硼原子以B<110>分裂间隙的形式存在于金刚石结构中. 关键词： 分子动力学模拟 金刚石 硼 注入     

双酚A在氧化石墨烯表面吸附的分子动力学模拟

双酚A(bisphenol A,BPA)是一种内分泌干扰物,会对机体多方面产生不良影响,包括生殖系统、神经系统、胚胎发育等.因此,在水环境中如何检测和去除BPA显得尤为重要.实验研究表明,氧化石墨烯(graphene oxide,GO)对BPA具有优异的吸附去除性能,但在分子层面的吸附机制尚不清楚.分子动力学模拟,能提供BPA在GO表面的动态吸附过程以及吸附构象等详细信息,可以弥补实验的不足.本文利用GROMACS分子动力学模拟软件,系统模拟了BPA在含GO的水溶液中的吸附过程,并计算了吸附自由能.结果显示:所有的BPA均被吸附在GO两侧,通过分析BPA的吸附构象以及与GO的相互作用,发现π-π疏水作用对吸附起主导作用,且显示出很好的稳定性,而静电和氢键作用增加了GO的吸附能力.通过自由能计算,BPA在GO表面的结合能达30 k J/mol,远大于水分子的5 k J/mol.这些结果进一步证实GO对BPA具有很强的吸附能力以及GO作为吸附剂在水溶液中去除BPA的可行性.     

Molecular dynamics simulations of displacement cascades in Fe-10%Cr systems

Molecular dynamics simulations of the displacement cascades in Fe-10%Cr systems are used to simulate the primary knocked-on atom events of the irradiation damage at temperatures 300,600,and 750 K with primary knockedon atom energies between 1 and 15 keV.The results indicate that the vacancies produced by the cascade are all in the central region of the displacement cascade.During the cascade,all recoil Fe and Cr atoms combine with each other to form Fe-Cr or Fe-Fe interstitial dumbbells as well as interstitial clusters.The number and the size of interstitial clusters increase with the energy of the primary knocked-on atom and the temperature.A few large clusters consist of a large number of Fe interstitials with a few Cr atoms,the rest are Fe-Cr clusters with small and medium sizes.The interstitial dumbbells of Fe-Fe and Fe-Cr are in the 111 and 110 series directions,respectively.     

Molecular dynamics simulations of displacement cascades in Feben 10%Cr systems

Molecular dynamics simulations of the displacement cascades in Fe-10%Cr systems are used to simulate the primary knocked-on atom events of the irradiation damage at temperatures 300, 600, and 750 K with primary knocked-on atom energies between 1 and 15 keV. The results indicate that the vacancies produced by the cascade are all in the central region of the displacement cascade. During the cascade, all recoil Fe and Cr atoms combine with each other to form Fe-Cr or Fe-Fe interstitial dumbbells as well as interstitial clusters. The number and the size of interstitial clusters increase with the energy of the primary knocked-on atom and the temperature. A few large clusters consist of a large number of Fe interstitials with a few Cr atoms, the rest are Fe-Cr clusters with small and medium sizes. The interstitial dumbbells of Fe-Fe and Fe-Cr are in the lan111ran and lan110ran series directions, respectively.