A study on dissociation of sII krypton hydrate and the effect of hydrocarbon guest molecules as stabilizer by molecular dynamics simulation

In this paper, the characteristics of structure II krypton hydrate are studied by molecular dynamics simulation under isobaric-isothermal (NPT) ensemble condition. The dissociation process of the hydrate is simulated and the effect of krypton (Kr) and various types of hydrocarbon guest molecules (HGMs) on the stability of the hydrate structure is investigated during the simulation time of 1 ns. The studied HGMs are propane, isobutane, neopentane, cyclopropane, cyclobutane, cyclopentane and cyclopentene. The structural change of the Kr-hydrate is analyzed with the radial distribution function, mean square displacement and diffusion coefficient. As temperature increases, the obtained results indicate a gradual increase in the Kr-hydrate cell size, which leads to distortion of the hydrate lattice and escaping of the encapsulated Kr molecules from the hydrate structure to form small bubbles of Kr aggregated in the aqueous solution.     

Molecular dynamics simulations of pure methane and carbon dioxide hydrates: lattice constants and derivative properties

ABSTRACT

We report extensive molecular dynamics simulation results of pure methane and carbon dioxide hydrates at pressure and temperature conditions that are of interest to various practical applications. We focus on the calculation of the lattice constants of the two pure hydrates and their dependence on pressure and temperature. The calculated lattice constants are correlated using second order polynomials which are functions of either temperature or pressure. Finally, the obtained correlations are used in order to calculate two derivative properties, namely the isothermal compressibility and the isobaric thermal expansion coefficient. The current simulation results are also compared against reported experimental measurements and other simulation studies and good agreement is found for the case of isothermal compressibility. On the other hand, for the case of isobaric thermal expansion coefficient good agreement is found only with other simulation studies, while the simulation studies are in disagreement with experiments, particularly at low temperatures.     

Lattice dynamics study of low energy guest-host coupling in clathrate hydrate

Our lattice dynamics simulation of Xe-hydrate with four-site TIP4P oxygen-shell model can accurately reproduce each peak position in the inelastic incoherent neutron scattering spectrum at the acoustic band （below 15 meV） and yield correct relative intensity. Based on the results, the uncertain profile at ～6 meV is assigned to anharmonic guest modes coupled strongly to small cages. Blue shift is proposed in phonon dispersion sheet in the case of anticrossing and found to be an evident signal for guest-host coupling that explains the anomalous thermal conductivity of clathrate hydrate.     

Molecular dynamics simulations of carbon dioxide hydrate growth in electrolyte solutions of NaCl and MgCl2

Molecular dynamics simulations are performed to study the growth of carbon dioxide (CO₂) hydrate in electrolyte solutions of NaCl and MgCl₂. The kinetic behaviour of the hydrate growth is examined in terms of cage content, density profile, and mobility of ions and water molecules, and how these properties are influenced by added NaCl and MgCl₂. Our simulation results show that both NaCl and MgCl₂ inhibit the CO₂ hydrate growth. With a same mole concentration or ion density, MgCl₂ exhibits stronger inhibition on the growth of CO₂ hydrate than NaCl does. The growth rate of the CO₂ hydrate in NaCl and MgCl₂ solutions decreases slightly with increasing pressure. During the simulations, the Na⁺, Mg²⁺, and Cl^? ions are mostly excluded by the growing interface front. We find that these ions decrease the mobility of their surrounding water molecules, and thus reduce the opportunity for these water molecules to form cage-like clusters toward hydrate formation. We also note that during the growth processes, several 5¹²6³ cages appear at the hydrate/solution interface, although they are finally transformed to tetrakaidecahedral (5¹²6²) cages. Structural defects consisting of one water molecule trapped in a cage with its hydrogen atoms being attracted by two Cl^? ions have also been observed.     

Molecular dynamics study of mosaic structure in the Ni-based single-crystal superalloy

The mosaic structure in a Ni-based single-crystal superalloy is simulated by molecular dynamics using a potential employed in a modified analytic embedded atom method. From the calculated results we find that a closed three-dimensional misfit dislocation network, with index of $\langle 011\rangle${\{}100{\}} and the side length of the mesh 89.6\,{\AA}, is formed around a cuboidal $\gamma '$ precipitate. Comparing the simulation results of the different mosaic models, we find that the side length of the mesh only depends on the lattice parameters of the $\gamma $ and $\gamma '$ phases as well as the $\gamma $/$\gamma '$ interface direction, but is independent of the size and number of the cuboidal $\gamma '$ precipitate. The density of dislocations is inversely proportional to the size of the cuboidal $\gamma '$ precipitate, i.e.~the amount of the dislocation is proportional to the total area of the $\gamma $/$\gamma '$ interface, which may be used to explain the relation between the amount of the fine $\gamma '$ particles and the creep rupture life of the superalloy. In addition, the closed three-dimensional networks assembled with the misfit dislocations can play a significant role in improving the mechanical properties of superalloys.     

Molecular dynamics simulations on the melting of gold nanoparticles

Molecular dynamics is employed to study the melting of bulk gold and gold nanoparticles. PCFF, Sutton-Chen and COMPASS force fields are adopted to study the melting point of bulk gold and we find out that the Sutton-Chen force field is the most accurate model in predicting the melting point of bulk gold. Consequently, the Sutton-Chen force field is applied to study the melting points of spherical gold nanoparticles with different diameters. Variations of diffusion coefficient, potential energy and translational order parameter with temperature are analyzed. The simulated melting points of gold nanoparticles are between 615～1115 K, which are much lower than that of bulk gold (1336 K). As the diameter of gold nanoparticle drops, the melting point also descends. The melting mechanism is also analyzed for gold nanoparticles.     

Molecular dynamics study of helium bubble pressure in titanium

In this paper,the pressure state of the helium bubble in titanium is simulated by a molecular dynamics(MD) method.First,the possible helium/vacancy ratio is determined according to therelation between the bubble pressure and helium/vacancy ratio;then the dependences of the helium bubble pressure on the bubble radius at different temperatures are studied.It is shown that the product of the bubble pressure and the radius is approximately a constant,a result justifying the pressure-radius relation predicted by thermodynamics-based theory for gas bubble.Furthermore,a state equation of the helium bubble is established based on the MD calculations.Comparison between the results obtained by the state equation and corresponding experimental data shows that the state equation can describe reasonably the state of helium bubble and thus could be used for Monte Carlo simulations of the evolution of helium bubble in metals.     

低温下Au959团簇负载于MgO(100)表面后结构变化的分子动力学研究

采用基于Chen-Mbius反演方法,从金属/金属氧化物界面第一性原理计算的粘结能结果中推导出的Au/MgO原子间相互作用势的正则系综(NVT)分子动力学,模拟了在10 K条件下,Au959团簇负载于MgO(100)表面后团簇结构的变化.根据原子对分析技术和对分布函数的分析表明,由于团簇界面处原子间距与载体原子间距相匹配,置于载体上的Au团簇经过一个变形过程后,较其孤立自由表面时的团簇体积变大.     

低温下Cu13团簇负载于Cu(001)表面上结构变化的分子动力学研究

应用分子动力学方法研究温度为10和50 K时具有二十面体结构的Cu13团簇以不同接触条件与Cu(001)表面结合后的结构变化,原子间的相互作用势采用Johnson的嵌入原子方法模型.通过基于原子密度分布函数的分析表明,负载团簇与表面的结合能主要受团簇与载体相接触的最低层原子数及这些原子所具有的不同几何构型影响,同时更高层的原子呈现出不同的几何结构.温度为10 K时,负载团簇的初始位置对团簇几何结构和结合能影响较大.     

超临界Lennard-Jones流体结构特性分子动力学研究

研究超临界流体在不同压力和温度的结构特征有助于深刻理解并有效利用超临界流体.本文采用分子动力学方法模拟超临界压力、拟临界温度附近流体的结构及密度波动曲线的排列熵,分析状态参数变化的影响.结果表明,定压下,径向分布函数随温度升高,第一峰值位置逐渐向右移动,但右移幅度随着压力偏离临界点距离的增大而减弱,近临界压力时,出现峰值最高点的工况和等温压缩系数的极值点位置一致,压力增大,该现象消失.低压力拟临界点时易出现面积大、相对集中且分布稳定的高/低密度区,无明显嵌套现象.静态结构因子存在一定发散行为,发散的最大值和等温压缩系数极值点所处工况符合.低压力时密度时间序列的波动幅度最大,类周期现象较明显.在分子间势能、等温压缩系数和热运动效应的共同作用下,当压力(P)为1.1倍的临界压力(Pc)时,排列熵在0.99倍的拟临界温度(Tpc)达到最小值,P = 1.3Pc和1.5Pc时,最小排列熵与等温压缩系数的最大值工况点保持一致,压力继续增大,各模拟工况密度和排列熵的波动减弱,流体均匀性增强.     

Molecular dynamics study of biomembrane/local anesthetics interactions

It is still controversial how local anesthetics (LAs) act upon the nervous system and how the membrane contributes to this process, since probably the most important active site of the LAs is located in the sodium channels, a trans-membrane protein. An important role of the bio-membrane would be the stabilization and orientation of local anesthetics molecules, reducing their translational and rotational degrees of freedom, which could reinforce the mechanisms which interrupt the nervous impulse. This study aims to perform a computational analysis of the LAs behaviour in the membrane, and the effect of the water/membrane interface on their stabilization and orientation. Analysis by molecular dynamics (MD) showed that the charged form of these drugs are oriented at the interface, while the neutral form can easily cross the interface, entering the membrane, in agreement with the most recent experimental results in the literature. In contrast, it is here suggested that benzocaine (BZC), which exists only in its uncharged form in physiological media, behaves like the charged anesthetics, remaining stabilized and oriented at the interface. This could explain the similar anesthetic effect of BZC and the charged forms of tetracaine (TTC) and lidocaine (LDC).     

Molecular dynamics simulation of an argon cluster filled inside carbon nanotubes

The effects of the diameters of single-walled carbon nanotubes （SWCNTs） （7.83A to 27.40A） and temperature （20 K-45 K） on the equilibrium structure of an argon cluster are systematically studied by molecular dynamics simulation with consideration of the SWCNTs to be fixed. Since the diameters of SWCNTs with different chiralities increase when temperature is fixed at 20 K, the equilibrium structures of the argon cluster transform from monoatomic chains to helical and then to multishell coaxial cylinders. Chirality has almost no noticeable influence on these cylindrosymmetric structures. The effects of temperature and a non-equilibrium sudden heating process on the structures of argon clusters in SWCNTs are also studied by molecular dynamics simulation.     

Molecular dynamics study on water self-diffusion in aqueous mixtures of methanol,ethylene glycol and glycerol: investigations from the point of view of hydrogen bonding

Molecular dynamics simulations have been performed to investigate the aqueous binary mixtures of alcohols, including methanol, ethylene glycol (EG) and glycerol of molalities ranging from 1 to 5 m at the temperatures of 273, 288 and 298 K, respectively. The primary purpose of this paper is to investigate the mechanism of water self-diffusion in water-alcohol mixtures from the point of view of hydrogen bonding. The effects of temperature and concentration on water self-diffusion coefficient are evaluated quantitatively in this work. Temperature and concentration to some extent affect the hydrogen bonding statistics and dynamics of the binary mixtures. It is shown that the self-diffusion coefficient of water molecules decreases as the concentration increases or the temperature decreases. Moreover, calculations of mean square displacements of water molecules initially with different number n of H-bonds indicate that the water self-diffusion coefficient decreases as n increases. We also studied the aggregation of alcohol molecules by the hydrophobic alkyl groups. The largest cluster size of the alkyl groups clearly increases as the concentration increases, implying the emergence of a closely connected network of water and alcohols. The clusters of water and alcohol that interacted could block the movement of water molecules in binary mixtures. These findings provide insight into the mechanisms of water self-diffusion in aqueous binary mixtures of methanol, EG and glycerol.     

Molecular dynamics study of thermal stress and heat propagation in tungsten under thermal shock

Using molecular dynamics （MD） simulation, we study the thermal shock behavior of tungsten （W）, which has been used for the plasma facing material （PFM） of tokamaks. The thermo-elastic stress wave, corresponding to the collective displacement of atoms, is analyzed with the Lagrangian atomic stress method, of which the reliability is also analyzed. The stress wave velocity corresponds to the speed of sound in the material, which is not dependent on the thermal shock energy. The peak pressure of a normal stress wave increases with the increase of thermal shock energy. We analyze the temperature evolution of the thermal shock region according to the Fourier transformation. It can be seen that the “obvious” velocity of heat propagation is less than the velocity of the stress wave; further, that the thermo-elastic stress wave may contribute little to the transport of kinetic energy. The heat propagation can be described properly by the heat conduction equation. These results may be useful for understanding the process of the thermal shock of tungsten.     

Influence of water on HFO-1234yf oxidation pyrolysis via ReaxFF molecular dynamics simulation

ABSTRACT

The effect of water molecules on HFO-1234yf oxidation pyrolysis was investigated by ReaxFF-molecular dynamics simulation from 1900 to 4200?K. The initial pyrolysis of HFO-1234yf starts around 2500?K and the water molecules participate in chemical reactions at 2800?K when the reactants pyrolysis reached the highest reaction rate. The primary products including HF, COF₂ and CO₂ are observed at 2600, 2700 and 2900?K, respectively. The influence of water molecules on products is mainly reflected in the promotion activity on the conversion from COF₂ to CO₂ and the generation of HF molecules. Four formation pathways are observed and calculated to further elucidate the procedure of pyrolysis. The main conversion process from H₂O to HF is the ?F?+?H₂O?=?HF+?OH reaction, and the paths from H₂O to ?OH radical and COF₂ to ?CFO radical which are promoted by ?F and ?H radical, respectively, have relatively low energy barriers of 10.44 and 40.29?kJ/mol, and both reaction processes released HF molecules.     

Molecular dynamics study for the melting curve of MgO at high pressure

Shell-model molecular dynamics method is used to study the melting temperatures of MgO at elevated temperatures and high pressures using interaction potentials. Equations of state for MgO simulated by molecular dynamics are in good agreement with available experimental data. The pressure dependence of the melting curve of MgO has been calculated. The surface melting and superheating are considered in the correction of experimental data and the calculated values, respectively. The results of corrections are compared with those of previous work. The corrected melting temperature of MgO is consistent with corrected experimental measurements. The melting temperature of MgO up to 140GPa is calculated.     

Molecular dynamics study for the thermal conductivity of diatomic liquid

The thermal conductivity of diatomic liquids was analyzed using a nonequilibrium molecular dynamics (NEMD) method. Five liquids, namely, O₂, CO, CS₂, Cl₂ and Br₂, were assumed. The two-center Lennard-Jones (2CLJ) model was used to express the intermolecular potential acting on liquid molecules. First, the equation of state of each liquid was obtained using MD simulation, and the critical temperature, density and pressure of each liquid were determined. Heat conduction of each liquid at various liquid states [metastable (ρ=1.9ρ_cr), saturated (ρ=2.1ρ_cr), and stable (ρ=2.3ρ_cr)] at T=0.7T_cr was simulated and the thermal conductivity was estimated. These values were compared with experimental results and it was confirmed that the simulated results were consistent with the experimental data within 10%. Obtained thermal conductivities at saturated state were reduced by the critical temperature, density and mass of molecules and these values were compared with each other. It was found that the reduced thermal conductivity increased with the increase in the molecular elongation. Detailed analysis of the molecular contribution to the thermal conductivity revealed that the contribution of the heat flux caused by energy transport and by translational energy transfer to the thermal conductivity is independent of the molecular elongation while the contribution of the heat flux caused by rotational energy transfer to the thermal conductivity increases with the increase in the molecular elongation. Moreover, by comparing the reduced thermal conductivity at various states, it was found that the increase of thermal conductivity with the increase in the density, or pressure, was caused by the increase of the contribution of energy transfer due to molecular interaction.     

层错四面体对单晶铜层裂行为影响的分子动力学研究

层错四面体是一种典型的三维空位型缺陷,广泛存在于受辐照后的面心立方金属材料中,对材料的力学性能有显著的影响.目前,关于层错四面体对辐照材料层裂行为的影响还缺乏深入系统的研究.本文使用分子动力学方法模拟了含有层错四面体的单晶铜在不同冲击速度下的层裂行为,对整个冲击过程中的自由表面速度及微结构演化等进行了深入的分析.研究发现,层错四面体在冲击波作用下会发生坍塌,并进一步诱导材料产生位错、层错等缺陷.在中低速度加载下,层错四面体坍塌引起的缺陷快速向周围扩展,为孔洞提供了更宽的形核区域,促进了孔洞的异质成核,造成材料层裂强度大幅度减小.当冲击速度较高时,层错四面体坍塌导致的局部缺陷对材料的层裂强度不再有明显影响.