Nested stochastic simulation algorithms for chemical kinetic systems with multiple time scales
Nested stochastic simulation algorithms for chemical kinetic systems with multiple time scales
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DOI：
10.1016/j.jcp.2006.06.019
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发表时间：
2007-01-20
影响因子：
4.1
通讯作者：
Vanden-Eijnden, Eric
中科院分区：
文献类型：
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作者：
Weinan, E.;Liu, Di;Vanden-Eijnden, Eric
我们提出了一种有效的数值算法来模拟多时间尺度的化学动力学系统。该算法是传统随机模拟算法（SSA）的改进，也称为 Gillespie 算法。它采用嵌套 SSA 的形式，并使用外部 SSA 来模拟慢速反应，其速率是根据模拟快速反应的内部 SSA 的实现计算得出的。该算法本身非常通用且无缝，相当于对原始 SSA 的一个小修改。我们对此类多尺度化学动力学系统的分析使我们能够识别系统中的慢变量，得出慢时间尺度上的有效动力学，并为嵌套 SSA 提供误差估计。使用这些误差估计来讨论嵌套 SSA 的效率，并通过几个数值示例进行说明。 (c) 2006 Elsevier Inc. 保留所有权利。
We present an efficient numerical algorithm for simulating chemical kinetic systems with multiple time scales. This algorithm is an improvement of the traditional stochastic simulation algorithm (SSA), also known as Gillespie's algorithm. It is in the form of a nested SSA and uses an outer SSA to simulate the slow reactions with rates computed from realizations of inner SSAs that simulate the fast reactions. The algorithm itself is quite general and seamless, and it amounts to a small modification of the original SSA. Our analysis of such multi-scale chemical kinetic systems allows us to identify the slow variables in the system, derive effective dynamics on the slow time scale, and provide error estimates for the nested SSA. Efficiency of the nested SSA is discussed using these error estimates, and illustrated through several numerical examples. (c) 2006 Elsevier Inc. All rights reserved.