Protein motors induced enhanced diffusion in intracellular transport

Diffusion of transported particles in the intracellular medium is described by means of a generalized diffusion equation containing forces due to the cytoskeleton network and to the protein motors. We find that the enhanced diffusion observed in experiments depends on the nature of the force exerted by the protein motors and on parameters characterizing the intracellular medium which is described in terms of a generalized Debye spectrum for the noise density of states.     

A molecular dynamics study of uranyl hydration

Molecular dynamics calculations were carried out in order to investigate the hydration structure of uranyl in aqueous solution. The CF1 model of flexible water molecules is used. This model allows one to investigate a hydrolysis reaction for water molecules in the first uranyl hydration shell. Charge redistribution effects on hydrolysis products are also taken into account. We found five ligands in uranyl hydration shell, which is of bipyramidal pentacoordinated structure. The charge redistribution effects resulted in ligands of four water molecules and one hydroxyl, which was found closer to uranium than the other ligands.     

基于接触数引导的迭代多组独立分子动力学模拟实现配体-蛋白质结合与解离过程

配体的结合与解离过程在蛋白质实现其生物学功能方面非常关键,因此对这些高度动态过程的研究变得非常重要. 尽管已有实验方法可以确定蛋白质-配体复合物的三维结构,但一般仅可获得静态图片. 随着计算机算力的快速提高以及算法的优化,分子动力学模拟在探索配体的结合与解离过程方面具有诸多优势. 然而,当系统变得足够大时,分子动力学模拟的时间和空间尺度成为了巨大的挑战. 本工作提出了一种研究配体-蛋白质结合与解离的增强采样工具,它基于配体和蛋白质之间形成的接触数来引导迭代多组独立分子动力学模拟. 在腺苷酸激酶的模拟结果中,观测到配体的结合和解离过程,而使用传统分子动力学模拟在同一时间尺度下则无法实现这一过程.     

Mechanical properties of kirigami phosphorene via molecular dynamics simulation

The newly discovered two-dimensional phosphorene suffers low stretchability which limits its application in flexible devices. Herein we employ kirigami technique to overcome this limitation. Molecular dynamics simulation is employed to investigate the mechanical properties of kirigami-phosphorene under shear and tensile loadings. Our simulation results show that loading type, intrinsic structural anisotropy, and the height of middle cuts are three key factors that govern the mechanical response of kirigami-phosphorene. Under the tensile loading along the armchair direction, phosphorene exhibits a considerable increase in its tensile strain. By contrast, phosphorene is too weak to stand any structural modification induced by kirigami in the zigzag direction. Under shear loading, there is merely no improvement in the shear properties of kirigami-phosphorene. Our results demonstrate the prospective applications of kirigami-phosphorene along the armchair direction in modern wearable, and stretchable electronics and optoelectronics devices.     

Canonical ensemble and nonequilibrium states by molecular dynamics

We present a new technique to simulate the contact of a molecular dynamics system with a thermal wall. A canonical ensemble is obtained, and its statistical and thermodynamic fluctuations are studied. The values of the specific heat found by simulation agree with the experimental data. By means of thermal walls at different temperatures, thermal gradients are obtained. The values of the thermal conductivity are consistent with the experimental data.This work was supported in part by the Commissariat à l'Énergie Atomique (France).     

Calculation of diffusion coefficient of long chain molecules using molecular dynamics

Molecular dynamics (MD) is a powerful tool for calculating several thermo-physical properties of wide range of materials. In this study, the diffusivities (D) of two widely used long chain molecules MHA and ODT are calculated at various temperatures using MD simulations coupled with Einstein relationship. Four different kinds of forcefields COMPASS, UFF, CVFF and PCFF are employed in the MD simulation and the results are compared. Diffusivity values are evaluated in a humid environment in presence of water molecules.     

System size and trajectory length dependence of the static structure factor and the diffusion coefficient as calculated from molecular dynamics simulations: The case of SPC/E water

The effect of the applied trajectory length on the convergence of the self-diffusion coefficient was examined for the SPC/E water model in the NVT ensemble with different system sizes at 293 K. Temperature dependence and isotope effects, via using D₂O instead of H₂O, were also investigated. A simulation for the polarizable SWM4-DP model was also carried out to compare the effect of different potential models. Radial distribution functions and the neutron weighted structure factor were also calculated; they were found to be insensitive to changing the system size in the range of 216 to 16,000 molecules. On the other hand, the diffusion coefficient is rather sensitive to the applied trajectory length, system size and the method of calculation. The diffusion coefficient is therefore not appropriate for assessing, and distinguishing between, potential models of water, whereas the structure factor could serve as a more stable measure.     

一种描述金属界面原子扩散的加速分子动力学方法

传统分子动力学(MD)的纳秒级时间尺度限制了对固体界面原子的深层扩散、渗透以及相形成等长时动力学性质的模拟研究.在Voter的超动力学框架内,提出了一种更为简单的偏移势的构建方法.该方法通过在偏移势中引入一个加速因子,抬高了原势阱,从而加速了原子的跃迁,将MD模拟的时间尺度提高了若干个数量级.更为重要的是,该方法不需要预知体系势能的势阱及鞍点分布,还能够将原势能曲面的特性完全保留.以Mg/Zn界面扩散为例,选取简单的Lennard-Jones双体势,考察了不同加速因子对界面原子扩散速度的影响.结果显示,该 关键词： 超动力学 加速因子 原子扩散 金属界面     

Peculiar diffusion behavior of AlCl_4 intercalated in graphite from nanosecond-long molecular dynamics simulations

The diffusion property of the intercalated species in the graphite materials is at the heart of the rate performance of graphite-based metal-ion secondary battery. Here we study the diffusion process of a AlCl_4 molecule within graphite — a key component of a recently reported aluminum ion battery with excellent performance — via molecular dynamics(MD) simulations. Both ab-initio MD(AIMD) and semiempirical tight-binding MD simulations show that the diffusion process of the intercalated AlCl_4 molecule becomes rather inhomogeneous, when the simulation time exceeds approximately 100 picoseconds. Specifically, during its migration in between graphene layers, the intercalated AlCl_4 molecule may become stagnant occasionally, and then recovers its normal(fast) diffusion behavior after halting for a while. When this phenomenon occurs, the linear relationship of the mean squared displacement(MSD) versus the duration time is not fulfilled. We interpret this peculiar behavior as a manifestation of inadequate sampling of rare event(the stagnation of the molecule), which does not yet appear in short-time MD simulations. We further check the influence of strains present in graphite intercalated compounds(GIC) on the diffusion properties of AlCl_4, and find that their presence in general slows down the diffusion of the intercalated molecule, and is detrimental to the rate performance of the GIC-based battery.     

Surface diffusion of Si,Ge and C adatoms on Si （001） substrate studied the molecular dynamics simulation

Depositions of Si, Ge and C atoms onto a preliminary Si (001) substrate at different temperatures are investigated by using the molecular dynamics method. The mechanism of atomic self-assembling occurring locally on the flat terraces between steps is suggested. Diffusion and arrangement patterns of adatoms at different temperatures are observed. At 900 K, the deposited atoms are more likely to form dimers in the perpendicular [110] direction due to the more favourable movement along the perpendicular [110] direction. C adatoms are more likely to break or reconstruct the dimers on the substrate surface and have larger diffusion distances than Ge and Si adatoms. Exchange between C adatoms and substrate atoms are obvious and the epitaxial thickness is small. Total potential energies of adatoms and substrate atoms involved in the simulation cell are computed. When a newly arrived adatom reaches the stable position, the potential energy of the system will decrease and the curves turns into a ladder-like shape. It is found that C adatoms can lead to more reduction of the system energy and the potential energy of the system will increase as temperature increases.     

空位在金刚石近(001)表面扩散的分子动力学模拟

用分子动力学方法模拟了空位在金刚石近(001)表面的扩散过程,研究了温度对空位扩散的影响.结果表明,当温度为1000K左右时,位于近表面第二层上的空位开始向表面运动;当温度在1400—2000K时,空位完全扩散到表面.这与实验结果和其他计算结果符合得很好.同时发现,温度为1400—1800K时,空位的扩散经历了两次迁移运动,其分别对应了均方位移图中的两个极大值.在不施加任何约束的条件下得到了空位的动态扩散路径,空位在金刚石近(001)表面的扩散势垒约为042eV.并探讨了一定温度下空位数目增多及其不同排列 关键词： 金刚石 空位 扩散 分子动力学     

Verification of the inverted temperature gradient condition via molecular dynamics simulation

We perform molecular dynamics simulations to verify the critical condition for the existence of an inverted temperature profile in the vapor between two liquid slabs at slightly different temperatures. Reasonable agreement is found between the kinetic theory based condition and simulations. The deviation from theory can be explained by deviation from ideal gas behavior on which the kinetic condition is based and by deviation in the MD from diffuse boundary conditions, which are used in deriving the kinetic condition.     

Vibrations of single- and double-walled carbon nanotubes with layerwise boundary conditions: A molecular dynamics study

In the present work, the vibration characteristics of single- and double-walled carbon nanotubes under various layerwise boundary conditions at different lengths are investigated. This is accomplished by the use of molecular dynamics simulations based on the Tersoff-Brenner and Lennard-Jones potential energy functions. The effects of initial tensile and compressive strains on the resonant frequency of carbon nanotubes are also taken into consideration. From the results generated, it is observed that the natural frequency of carbon nanotubes is strongly dependent on their boundary conditions especially when tubes are shorter in length. The natural frequency and its dependence on tube end conditions reduce by increasing the tube length. The natural frequency of DWCNTs lies between those of the constituent inner and outer SWCNTs and is nearer to those of the outer one. It is further observed that the natural frequency is highly sensitive to tensile and compressive strains. The frequency shift occurring in the presence of small initial strains is positive for tensile strains and negative for compressive strains. The results obtained provide valuable information for calibrating the small scaling parameter of the nonlocal models for the vibration problem of carbon nanotubes.     

Cu(111)三维表面岛对表面原子扩散影响的分子动力学研究

采用嵌入原子方法的原子间相互作用势，利用分子动力学方法计算了同质外延生长中不同层数的三维Cu(111)表面岛上表面原子扩散激活能，分析了三维表面岛的层数对表面原子交换扩散和跳跃扩散势垒的影响. 研究结果表明，二维Enrilich-Schwoebel(ES)势垒小于三维ES势垒，且三维ES势垒不随表面岛层数的增加而显著变化. 对于侧向表面为(100)的表面岛，表面原子沿〈011〉方向上的扩散行为，随表面岛层数增加而逐渐变化；在表面岛层数达到3层时，扩散路径上的势垒变化趋于稳定，表面原子扩散以下坡扩散为主. 对于侧面取向为(111)的表面岛，当表面岛层数大于3层后，开始呈现上坡扩散的可能. 关键词： 表面原子 扩散 分子动力学模拟     

分子动力学方法研究金属Ti中He小团簇的迁移

采用分子动力学方法模拟了不同温度下He原子及He团簇在金属Ti中的迁移特性,并计算了扩散前系数和激活能. 研究发现这种扩散的各向异性非常显著,具体表现在He原子及He团簇在不同方向上扩散系数的前系数完全不同,但它们的激活能却相同. 研究表明:在预测金属中He的扩散行为时,必须采用动态模拟方法才能得到准确的前系数,仅仅考虑势垒的静态模拟方法是不行的. 另外,还发现一个不同于直觉的现象,即较低温度下He二聚物的扩散系数比单个He原子的扩散系数大;此外,在所模拟的温度范围内Arrhenius方程能够很好地描述它们的扩散. 这说明动力学模拟对预测金属中He的扩散行为具有重要的意义. 关键词： 分子动力学 扩散系数 各向异性 氦     

Mechanical properties of defective single-layered graphene sheets via molecular dynamics simulation

In this paper, the effects of two main types of structural defects, i.e. Stone–Wales and single vacancy, on the mechanical properties of single-layered graphene sheets (SLGSs) are investigated. To this end, molecular dynamics simulations based on the Tersoff–Brenner potential function and Nose–Hoover thermostat technique are implemented. The results obtained have revealed that the presence of defects significantly reduces the failure strain and the intrinsic strength of SLGSs, while it has a slight effect on Young’s modulus. Furthermore, the examination of loading in both armchair and zigzag directions demonstrated that SLGSs are slightly stronger in the armchair direction and defects have lower effect in this direction. Considering the fracture mechanism, the failure process of defective and perfect graphene sheets is also presented.     

Heat conductivity of three periodic Hard Disks via nonequilibrium molecular dynamics

We use a driving field, of the type first suggested by Evans, to generate a steady heat current in the simplest possible system, a two-dimensional periodic fluid of three hard disks. Hard-disk motion equations can be conveniently derived from repulsive constant-force or linear-force potentials by considering the infinitely repulsive limit of these potentials. We show that the isoenergetic and isokinetic forms of the nonequilibrium equations of motion generate steady-state heat conductivities differing by terms of order 1/N, whereN is the number of particles. The resulting conductivities appear to vary as the logarithm of the driving field strength. Even at low fields, the three-body periodic-system results lie well below Enskog's infinite-system prediction.     

Introducing dislocation climb by bulk diffusion in discrete dislocation dynamics

We report a method to incorporate dislocation climb controlled by bulk diffusion in a three-dimensional discrete dislocation dynamics (DDD) simulation for fcc metals. In this model we couple the vacancy diffusion theory to the DDD in order to obtain the climb rate of the dislocation segments. The capability of the model to reproduce the motion of climbing dislocations is examined by calculating several test-cases of pure climb-related phenomena and comparing the results with existing analytical predictions and experimental observations. As test-cases, the DDD is used to study the activation of Bardeen–Herring sources upon the application of an external stress or under vacancy supersaturation. Loop shrinkage and expansion due to vacancy emission or absorption is shown to be well described by our model. In particular, the model naturally describes the coarsening of a population of loops having different sizes.