随机反应扩散格气模型上钙动力学的粗粒化模拟

发展了一种基于随机格气模型的粗粒化方法,该方法能有效模拟内质网表面钙动力学信息. 首先将相邻的微观节点合并成粗粒化节点,再根据局域平均场近似推导出粗粒化反应速率,然后执行粗粒化动力学蒙特卡洛模拟. 发现粗粒化动力学蒙特卡洛模拟结果和微观模拟结果非常吻合. 有趣的是,存在一个最佳的粗粒化比m,使得粗粒化模拟与微观模拟的相变点偏差最小. 固定m,发现临界点随体系尺度增加而单调增加,而且相变点的偏差与体系尺度存在一个标度关系.此外,该粗粒化方法大大地加快了蒙特卡洛模拟速率,并且与微观模拟直接相关. 该方法可以广泛用来研究体系尺度效应,而节省大量计算时间.     

Coarse-graining Calcium Dynamics on Stochastic Reaction-diffusion Lattice Model

We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and deriving CG reaction rates using local mean field approximation, we perform CG kinetic Monte Carlo (kMC) simulations and find the results of CG-kMC simulations are in excellent agreement with that of the microscopic ones. Strikingly, there is an appropriate range of coarse proportion m, corresponding to the minimal deviation of the phase transition point compared to the microscopic one. For fixed m, the critical point increases monotonously as the system size increases, especially, there exists scaling law between the deviations of the phase transition point and the system size. Moreover, the CG approach provides significantly faster Monte Carlo simulations which are easy to implement and are directly related to the microscopics, so that one can study the system size effects at the cost of reasonable computational time.     

Kinetic equation in the kinetic region of the dilute and nonuniform electron plasma

Mori's scaling method is used to derive the kinetic equation for a dilute, nonuniform electron plasma in the kinetic region where the space-time cutoff (b, t _c) satisfies _Dbl _f , _D t _{c f} , with _D the Debye length, _D ^–1= _p the plasma frequency, andl _f and _f the mean free path and time, respectively. The kinetic equation takes account of the nonuniformity of the order ofl _f and _D for the single-and the two-particle distribution function, respectively. Thus the Vlasov term associated with the two-particle distribution function is retained. This kinetic equation is deduced from the kinetic equation in the coherent region obtained by Morita, Mori, and Tokuyama, where the space-time cutoff of the coherent region satisfies _Dbr ₀, _Dt _{c 0}, withr ₀ the Landau length and ₀ the corresponding time scale.     

A path integral method for coarse-graining noise in stochastic differential equations with multiple time scales

We present a new path integral method to analyze stochastically perturbed ordinary differential equations with multiple time scales. The objective of this method is to derive from the original system a new stochastic differential equation describing the system’s evolution on slow time scales. For this purpose, we start from the corresponding path integral representation of the stochastic system and apply a multi-scale expansion to the associated path integral kernel of the corresponding Lagrangian. As a concrete example, we apply this expansion to a system that arises in the study of random dispersion fluctuations in dispersion-managed fiber-optic communications. Moreover, we show that, for this particular example, the new path integration method yields the same result at leading order as an asymptotic expansion of the associated Fokker-Planck equation.     

Coarse-grained atomistic simulation of dislocations

This paper presents a new methodology for coarse-grained atomistic simulation of dislocation dynamics. The methodology combines an atomistic formulation of balance equations and a modified finite element method employing rhombohedral-shaped 3D solid elements suitable for fcc crystals. With significantly less degrees of freedom than that of a fully atomistic model and without additional constitutive rules to govern dislocation activities, this new coarse-graining (CG) method is shown to be able to reproduce key phenomena of dislocation dynamics for fcc crystals, including dislocation nucleation and migration, formation of stacking faults and Lomer-Cottrell locks, and splitting of stacking faults, all comparable with fully resolved molecular dynamics simulations. Using a uniform coarse mesh, the CG method is then applied to simulate an initially dislocation-free submicron-sized thin Cu sheet. The results show that the CG simulation has captured the nucleation and migration of large number of dislocations, formation of multiple stacking fault ribbons, and the occurrence of complex dislocation phenomena such as dislocation annihilation, cutting, and passing through the stacking faults. The distinctions of this method from existing coarse-graining or multiscale methods and its potential applications and limitations are also discussed.     

Ginzburg-Landau theory for higher order phase transition

Ginzburg-Landau theory for studying phase transitions of higher order has been derived using coarse graining and lattice formulation within Ehrenfest thermodynamics. Our developed Hamiltonian leads directly to the functional of the system. We studied the evolution of the order parameter using our developed model equations for third and fourth order phase transitions. The periodic nature of the system can be likened to spatially varying periodic soliton/antisoliton lattice of holes in condensate. This is different from what one observes for any conventional solitary wave in the second order phase regime.     

A scaling method for deriving kinetic equations from the BBGKY hierarchy

On the basis of the scale covariance of correlation functions under a coarsegraining in space and time, the Boltzmann equation for neutral gases, the Balescu-Lenard-Boltzmann-Landau equation for dilute plasmas, and linear equations for the variances of fluctuations are derived from the BBGKY hierarchy equations with no short-range correlations at the initial time. This is done by using Mori's scaling method in an extended form. Thus it is shown that the scale invariance of macroscopic features affords a useful principle in nonequilibrium statistical mechanics. It is also shown that there existtwo kinds of correlation functions, one describing the interlevel correlations of the kinetic level with its sublevels and the other representing the fluctuations in the kinetic level.Partially financed by the Scientific Research Fund of the Ministry of Education.     

Theory of Phase Separation in Finite-Lifetime Systems

We study the phase separation dynamics in finite lifetime systems. Particles created by the external fields are unstable and decay within the finite lifetime. Effects of the particle lifetime and the interparticle interaction for the phase separation dynamics are discussed. In our theory, the formulation is based on the coarse-grained lattice gas model. As a result, effects of the finite lifetime are that the phase separation is restrained and that the finite size of domains remain finally at t = X .