Perspective: Stochastic algorithms for chemical kinetics
Perspective: Stochastic algorithms for chemical kinetics
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DOI：
10.1063/1.4801941
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发表时间：
2013-05-07
影响因子：
4.4
通讯作者：
Petzold, Linda R.
中科院分区：
文献类型：
--
作者：
Gillespie, Daniel T.;Hellander, Andreas;Petzold, Linda R.
我们概述了我们的观点随机化学动力学，特别注意数值模拟算法。我们首先集中在稀释，充分混合的系统，其描述使用常微分方程已作为传统的化学动力学的基础，在过去的150年。对于这样的系统，我们回顾了离散随机方法的物理和数学原理，以及为了重新获得传统的连续确定性描述而需要进行的近似。接下来，我们注意到一些更有前途的策略，用于处理刚性系统，罕见事件和敏感性分析的随机性。最后，我们回顾了最近的一些努力，以适应和扩展的离散随机方法的系统，没有很好的混合。在目前正在发展的领域，我们主要集中在细分成良好的混合子体积的系统的战略，然后模拟相邻子体积之间的反应物分子的扩散转移连同子体积内的化学反应。(C)2013 AIP Publishing LLC.
We outline our perspective on stochastic chemical kinetics, paying particular attention to numerical simulation algorithms. We first focus on dilute, well-mixed systems, whose description using ordinary differential equations has served as the basis for traditional chemical kinetics for the past 150 years. For such systems, we review the physical and mathematical rationale for a discrete-stochastic approach, and for the approximations that need to be made in order to regain the traditional continuous-deterministic description. We next take note of some of the more promising strategies for dealing stochastically with stiff systems, rare events, and sensitivity analysis. Finally, we review some recent efforts to adapt and extend the discrete-stochastic approach to systems that are not well-mixed. In that currently developing area, we focus mainly on the strategy of subdividing the system into well-mixed subvolumes, and then simulating diffusional transfers of reactant molecules between adjacent subvolumes together with chemical reactions inside the subvolumes. (C) 2013 AIP Publishing LLC.