Chuan-sheng Shen, Han-shuang Chen. Coarse-graining Calcium Dynamics on Stochastic Reaction-diffusion Lattice Model[J]. Chinese Journal of Chemical Physics , 2013, 26(2): 181-184. doi: 10.1063/1674-0068/26/02/181-184
Citation: Chuan-sheng Shen, Han-shuang Chen. Coarse-graining Calcium Dynamics on Stochastic Reaction-diffusion Lattice Model[J]. Chinese Journal of Chemical Physics , 2013, 26(2): 181-184. doi: 10.1063/1674-0068/26/02/181-184

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

doi: 10.1063/1674-0068/26/02/181-184
Funds:  This work was supported by the National Natural Science Foundation of China (No.11205002). Chuan-sheng Shen was also supported by the Key Scientific Research Fund of Anhui Provincial Education Depart-ment (No.KJ2012A189).
  • Received Date: 2013-01-27
  • 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.
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    沈阳化工大学材料科学与工程学院 沈阳 110142

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

doi: 10.1063/1674-0068/26/02/181-184
Funds:  This work was supported by the National Natural Science Foundation of China (No.11205002). Chuan-sheng Shen was also supported by the Key Scientific Research Fund of Anhui Provincial Education Depart-ment (No.KJ2012A189).

Abstract: 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.

Chuan-sheng Shen, Han-shuang Chen. Coarse-graining Calcium Dynamics on Stochastic Reaction-diffusion Lattice Model[J]. Chinese Journal of Chemical Physics , 2013, 26(2): 181-184. doi: 10.1063/1674-0068/26/02/181-184
Citation: Chuan-sheng Shen, Han-shuang Chen. Coarse-graining Calcium Dynamics on Stochastic Reaction-diffusion Lattice Model[J]. Chinese Journal of Chemical Physics , 2013, 26(2): 181-184. doi: 10.1063/1674-0068/26/02/181-184

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