电场环境下纳米通道内水分子传输行为的MD模拟研究

纳米通道内的水分子传输是近年来分子动力学(MD)模拟研究的热点之一。本文综述了电场对纳米通道中水分子传输行为影响的研究成果,主要介绍了三种施加电场的方法:在通道附近加电荷、在通道两侧的水相中加离子或带电荷的氨基酸以及对纳米通道直接施加电场。并报道了各类电场对纳米通道内水的填充平衡及相变行为、水分子偶极取向、水流量、水扩散速率等产生的影响,以及加电场的各种相关应用,如水流开关、信号传输、水泵及存储器等。最后,剖析了电场环境下MD模拟研究中尚待解决的问题。

Molecular Simulations of Adsorption and Diffusion Behaviors of Benzene Molecules in NaY Zeolite

In the article the Grand Canonical Monte Carlo （GCMC）, molecular dynamics（MD）, and kinetic Monte Carlo （KMC） simulations with particular focus on ascertaining the loading dependence of benzene diffusion in the zeolite were performed. First, a realistic representation of the structure of the sorbate-sorbent system was obtained based on GCMC simulation. The simulation clearly shows the characteristics of the adsorption sites of the benzene-NaY system, from which two kinds of preferably adsorbing sites for benzene molecules, called SⅡ and W sites, are identified. The structure thus obtained was then used as a basis for KMC and MD simulations. A compara-tive study by introducing and comparing two different mechanisms underlying jump diffusion in the zeolite of in-terest shows that the.MS diffusivity values predicted by the KMC and MD methods are fairly close to each other,leading to the conclusion that for benzene diffusion in NaY, the SⅡ→W→SⅡ jumps of benzene molecules are dominated,while the W→Wjumps do not exist in the process. These findings provide further support to our previous conclusion about the absence of the W→W jumps in the process of benzene diffusion in NaY. Finally, to relations, for predicting the self-and MS difthsivities were derived and found to be in fair agreement with the KMC and MD simulations.

Simulation of Liquid Argon Flow along a Nanochannel： Effect of Applied Force

Liquid argon flow along a nanochannel is studied using molecular dynamics (MD) simulation in this work.Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is used as the MD simulator.The effects of reduced forces at 0.5,1.0 and 2.0 on argon flow on system energy in the form of system potential energy,pressure and velocity profile are described.Output in the form of three-dimensional visualization of the system at steady-state condition using Visual Molecular Dynamics (VMD) is provided to describe the dynamics of the argon atoms.The equilibrium state is reached after 16000 time steps.The effects on system energy,pressure and velocity profile due to reduced force of 2.0 (F2) are clearly distinguishable from the other two lower forces where sufficiently high net force along the direction of the nanochannel for F2 renders the attractive and repulsive forces between the argon atoms virtually non-existent.A reduced force of 0.5 (F0.5) provides liquid argon flow that approaches Poiseuille (laminar) flow as clearly shown by the n-shaped average velocity profile.The extension of the present MD model to a more practical application affords scientists and engineers a good option for simulation of other nanofluidic dynamics processes.

The Phase Transition during Post Annealing

We have studied why PA （post-annealing） takes a long time to restore damaged crystallinity, which corresponds to repeat 10 10 times of lattice vibrations. Using a MD （molecular dynamics） simulation, we monitored the time-series of the LRO （long-range order） parameter as LRO pattern, in the case of a type IIa diamond, from the beginning of ion impact by a sub-keV N2 beam implantation to a few nanoseconds, i.e., close to the feasible time limit for MD simulations. Due to the ion impact, the LRO parameter changed gradually from ＂LRO = 1＂ （crystal） to ＂LRO = 0＂ （amorphous）, showing the so-called critical slowing-down phenomenon. However, since PA was started the LRO pattern was not unique. The LRO patterns were grouped into more than three types of phases and the transition between them was also found. From the viewpoint of statistical dynamics, such chaotic variations in the LRO pattern may present that the system is a GCM （globally coupled map） of a complex system in a closed system. A GCM composed of coupled oscillators develops slowly to exhibit several different phases or ‘chaotic itinerancy＇ over time. Therefore, the long duration required for PA may be attributable to the nature of a complex system.

Stochastically driven vibrations of single-layered graphene sheets

Thermal vibration of single-layered graphene sheets (SLGSs) is investigated using plate model together with the law of equi-partition of energy and the molecular dynamics (MD) method based on the condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies (COMPASS) force field.The in-plane stiffness and Poisson ratio of SLGSs are calculated by stretching SLGSs.The effective thickness of SLGSs is obtained by the MD simulations for the thermal vibration of SLGSs through the natural frequency.The root-mean-squared (RMS) amplitudes for SLGSs of differing temperatures and boundary conditions are calculated by the MD,and are compared with the results calculated by the thin plate model together with the law of equi-partition of energy.At the center of SLGSs,the thin plate theory can predict the MD results reasonably well.For the difference of bonding structure of the edge atoms,the deviation between the MD results and plate theory becomes more readily apparent near the edges of SLGSs.

Molecular simulation study of dynamical properties of room temperature ionic liquids with carbon pieces

Room temperature ionic liquids(RTILs) with dispersed carbon pieces exhibit distinctive physiochemical properties. To explore the molecular mechanism, RTILs/carbon pieces mixture was investigated by molecular dynamics(MD) simulation in this work. Rigid and flexible carbon pieces in the form of graphene with different thicknesses and carbon nanotubes in different sizes were dispersed in a representative RTIL 1-butyl-3-methyl-imidazolium dicyanamide([Bmim][DCA]). This study demonstrated that the diffusion coefficients of RTILs in the presence of flexible carbons are similar to those of bulk RTILs at varying temperatures, which is in contrast to the decreased diffusion of RTILs in the presence of rigid carbons. In addition, interfacial ion number density at rigid carbon surfaces was higher than that at flexible ones, which is correlated with the accessible external surface area of carbon pieces. The life time of cation-anion pair in the presence of carbon pieces also exhibited a dependence on carbon flexibility. RTILs with dispersed rigid carbon pieces showed longer ion pair life time than those with flexible ones, in consistence with the observation in diffusion coefficients. This work highlights the necessity of including the carbon flexibility when performing MD simulation of RTILs in the presence of dispersed carbon pieces in order to obtain the reliable dynamical and interfacial structural properties.