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 tog...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 rn, 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.展开更多
基金This work was supported by the National Natural Science Foundation of China （No.11205002）. Chuansheng Shen was also supported by the Key Scientific Research Fund of Anhui Provincial Education Department （No.KJ2012A189）.
文摘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 rn, 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.
