A constrained approach to multiscale stochastic simulation of chemically reacting systems
A constrained approach to multiscale stochastic simulation of chemically reacting systems
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DOI：
10.1063/1.3624333
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发表时间：
2011-09-07
影响因子：
4.4
通讯作者：
Erban, Radek
中科院分区：
文献类型：
--
作者：
Cotter, Simon L.;Zygalakis, Konstantinos C.;Erban, Radek
耦合化学反应的随机模拟通常需要大量的计算，特别是当一个化学系统包含在不同时间尺度上发生的反应时。在本文中，我们引入了一种适合于解决这一问题的多尺度方法，假设系统中慢物种的进化可以很好地近似于朗之万过程。它基于条件随机模拟算法（CSSA），该算法从条件分布中抽取适当定义的快变量，对慢变量给出给定值。在约束多尺度算法（CMA）中，对慢变量的每个值使用CSSA的单个实现来近似有效漂移和扩散项，类似于其他应用（如分子动力学）中的约束平均力计算。然后，我们展示了如何使用随后的福克-普朗克方程近似，我们可以反过来近似随机化学系统的平均开关时间。(C) 2011年美国物理研究所。(doi: 10.1063/1.3624333)
Stochastic simulation of coupled chemical reactions is often computationally intensive, especially if a chemical system contains reactions occurring on different time scales. In this paper, we introduce a multiscale methodology suitable to address this problem, assuming that the evolution of the slow species in the system is well approximated by a Langevin process. It is based on the conditional stochastic simulation algorithm (CSSA) which samples from the conditional distribution of the suitably defined fast variables, given values for the slow variables. In the constrained multiscale algorithm (CMA) a single realization of the CSSA is then used for each value of the slow variable to approximate the effective drift and diffusion terms, in a similar manner to the constrained mean-force computations in other applications such as molecular dynamics. We then show how using the ensuing Fokker-Planck equation approximation, we can in turn approximate average switching times in stochastic chemical systems. (C) 2011 American Institute of Physics. [doi:10.1063/1.3624333]