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.     

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.     

采用密度泛函理论与分子动力学对聚甲基丙烯酸甲酯双折射性的理论计算

双折射性是各种光学材料的重要性能之一,具有高双折射率的光学材料在诸多研究及工业领域的应用越来越广泛.然而,作为常用的光学薄膜及光波导材料之一的聚合物材料的双折射性通常却很弱,只能通过实验对其双折射率进行大致的表征,缺乏对其双折射率的系统性理论计算,从而限制了提高聚合物双折射性的研究.本文建立了从聚合物的单体分子结构到多分子链的系统性的双折射率理论计算方法,并借助此方法研究了导致聚合物弱双折射性的限制因素.以聚甲基丙烯酸甲酯(PMMA)为研究对象,运用密度泛函理论研究了其本征双折射率,这里的本征双折射率是指分子链完全取向时其单体单元的双折射率.计算结果表明其本征双折射率高达0.0738左右,并且通过计算给出了PMMA单体单元的平均双折射率色散曲线.采用分子动力学方法研究了该聚合物(包含20个分子链)的材料双折射率.理论计算结果表明,尽管该聚合物具有较大的本征双折射率,但是由于聚合物中分子链取向度极低,聚合物材料最终表现出来的双折射率只有0.00052.本文建立的研究方法及研究结果为研究增强聚合物材料双折射性提供了理论依据.     

Analysis of water molecules around GTP in Hras-GTP complex and GDP in Hras-GDP complex by molecular dynamics simulations

We investigate the structures of the Hras-GTP and the Hras-GDP complexes in water solvents in order to understand the mechanism of GTP hydrolysis in the Hras-GTP complex. We performed MD simulations of these complexes in order to study the positions and the orientations of water molecules around the guanosine nucleotides. Using trajectories we calculated the angular distribution of water molecules around the most distant phosphorus from guanosine in our previous work. It was shown that water molecules are distributed evenly in GTP, although unevenly in GDP. This suggests that the trigger of GTP hydrolysis is possibly the attack of water molecule to γ?phosphate from the appropriate direction. In this paper, in order to investigate the role of water molecules in GTP hydrolysis in detail, we calculate the orientation of water molecules. The distribution of the orientation is different between GTP and GDP. In order to investigate the cause of this difference, we examine the hydrogen bonds between water molecules and oxygen atom of the most distant phosphate from guanosine. We find that these hydrogen bonds are formed. We also find that the oxygen atom of hydrogen bond is determined by the position of the water molecule of hydrogen bond.     

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.     

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。     

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。     

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.     

Prediction of flexoelectricity in BaTiO3 using molecular dynamics simulations

Flexoelectric effect, referring to the strain gradient induced polarization, widely exists in dielectric materials, but its molecular dynamics has not been studied so much so far. In this work, the radial distribution function of BaTiO₃ and the phase transition temperatures have been investigated, and the results show that the core-shell potential model is effective and the structure of BaTiO₃ is stable in a temperature range of 10 K-150 K. Molecular dynamics simulated hysteresis loops of BaTiO₃ show that anisotropy can play an important role in the coercive field. Based on the rational simulation process, the effects of cantilever beam bent angle and fixed length on the polarization are analyzed. It is found that the small bent angle of the curved cantilever beam can give a proportional relationship with a fixed end length and a non-linear relationship is presented when the bent angle is much larger. The prediction of flexoelectric coefficient in BaTiO₃ is 18.5 nC/m. This work provides a computational framework for the study of flexoelectric effect by using molecular dynamics.     

Investigation of the dissociative adsorption for cyclopropane on the copper surface by density functional theory and quantum chemical molecular dynamics method

The dissociative adsorption of cyclopropane on the copper surface was studied using quantum chemical molecular dynamics method with “Colors-Excite” code and density functional theory by Amsterdam Density Functional program (ADF2000). The excited state of cyclopropane was used as adsorbate to simulate the dissociated adsorption under an irradiation energy of ca. 10 eV. One of the C-C bonds in cyclopropane was broken and the two new bonds between cyclopropane and copper surface were formed. The electrons transferred from the copper atoms to cyclopropane with a value of about 0.2e. The shorter distances between the carbons and surface copper atoms showed the existence of strong interaction. Consistently, the results indicated metallacyclopentane was the most possible intermediate species in dissociative adsorption by ADF2000 and “Colors-Excite” method.     

Simulation of plasma doping process by using the localized molecular dynamics method

Plasma doping is the candidate for semiconductor doping. Accurate simulation of the doping technology is needed for the advanced integrated circuit manufacturing. In this paper, the plasma doping process simulation is performed by using the localized molecular dynamics method. Models that involve the statistics of the implanted compositions, angles and energies are developed. The effect of the model on simulation results is studied. The simulation results about the doping concentration profile are supported by experimental data.     

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.     

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.     

分子动力学模拟组分对Co_(1415-x)Al_x团簇结构特征的影响

本文采用分子动力学模拟方法结合镶嵌原子势,研究了在200 K时二元(Co Al)1415团簇的结构随Co原子浓度的变化情况.利用径向分布函数、对分析技术和键取向序参数方法研究了微观局部结构情况,研究结果表明:(Co Al)1415团簇的组分对最终冷却结构影响较大,Co原子浓度为100%~70%的团簇表现出不完全的六角密排结构特征;Co原子浓度为50%的团簇具有局部的体心立方体结构特征;Co原子浓度为30%~10%时,表现出部分区域的二十面体和缺陷二十面体结构特征.     

分子动力学模拟组分对Co1415-xAlx团簇结构特征的影响

本文采用分子动力学模拟方法结合镶嵌原子势,研究了在200 K时二元（CoAl）1415团簇的结构随Co原子浓度的变化情况。利用径向分布函数、对分析技术和键取向序参数方法研究了微观局部结构情况,研究结果表明： （CoAl）1415团簇的组分对最终冷却结构影响较大,Co原子浓度为100%~70%的团簇表现出不完全的六角密排结构特征;Co原子浓度为50%的团簇具有局部的体心立方体结构特征;Co原子浓度为30%~10%时,表现出部分区域的二十面体和缺陷二十面体结构特征。     

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.     

Ag309团簇升温过程中结构转变的分子动力学模拟研究

采用分子动力学模拟研究了具有面心立方(fcc)晶格结构的截断八面体Ag309团簇升温过程中结构演变.对团簇的能量曲线变化、快照图演变和键对分析表明:无缺陷截断八面体Ag309团簇在410 K时转变为二十面体,在840 K时熔化;不同缺陷诱导二十面体结构转变温度异常变化,沿晶面滑移缺陷使二十面体转变温度升高,沿晶面旋转缺陷使二十面体结构转变温度降低;不同缺陷对团簇键型和势能产生的影响是使二十面体结构转变温度异常变化的主要诱导因素.这种通过缺陷控制团簇结构转变的研究为新型纳米结构的可控制备提供理论基础.     

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     

Role of oxygen functional groups for structure and dynamics of interfacial water on low rank coal surface: a molecular dynamics simulation

Molecular dynamics simulations were employed to study the effects of oxygen functional groups for structure and dynamics properties of interfacial water molecules on the subbituminous coal surface. Because of complex composition and structure, the graphite surface modified by hydroxyl, carboxyl and carbonyl groups was used to represent the surface model of subbituminous coal according to XPS results, and the composing proportion for hydroxyl, carbonyl and carboxyl is 25:3:5. The hydration energy with ?386.28 kJ/mol means that the adsorption process between water and coal surface is spontaneous. Density profiles for oxygen atoms and hydrogen atoms indicate that the coal surface properties affect the structural and dynamic characteristics of the interfacial water molecules. The interfacial water exhibits much more ordering than bulk water. The results of radial distribution functions, mean square displacement and local self-diffusion coefficient for water molecule related to three oxygen moieties confirmed that the water molecules prefer to absorb with carboxylic groups, and adsorption of water molecules at the hydroxyl and carbonyl is similar.