一种用于化学反应动力学多尺度建模的“分区跳跃”方法。

A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics.

作者信息

Harris Leonard A, Clancy Paulette

机构信息

School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, USA.

出版信息

J Chem Phys. 2006 Oct 14;125(14):144107. doi: 10.1063/1.2354085.

DOI:10.1063/1.2354085

PMID:17042579

Abstract

We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" methodologies into a single partitioned leaping algorithmic framework. The technique correctly accounts for stochastic noise at significantly reduced computational cost, requires the definition of only three model-independent parameters, and is particularly well suited for simulating systems containing widely disparate species populations. We present the theoretical foundations of partitioned leaping, discuss various options for its practical implementation, and demonstrate the utility of the method via illustrative examples.

摘要

我们提出了一种用于对化学反应网络中的随机性进行建模的新型多尺度模拟方法。该方法将精确随机方法和“跳跃”方法无缝集成到一个单一的分区跳跃算法框架中。该技术以显著降低的计算成本正确地考虑了随机噪声，只需要定义三个与模型无关的参数，并且特别适合于模拟包含差异极大的物种数量的系统。我们阐述了分区跳跃的理论基础，讨论了其实际实现的各种选项，并通过示例演示了该方法的实用性。