论文标题

通过有限状态扩展对随机化学动力学的改进估计

Improved estimations of stochastic chemical kinetics by finite state expansion

论文作者

Waizmann, Tabea, Bortolussi, Luca, Vandin, Andrea, Tribastone, Mirco

论文摘要

随机反应网络是描述与随机波动相关的物种之间相互作用的基本模型。主方程提供了由每个物种人口计数组成的离散状态空间中概率分布的演变。但是,由于其确切的解决方案通常是难以捉摸的,因此已经提出了几种分析近似。确定性速率方程(DRE)给出了宏观近似,作为一个紧凑的微分方程系统,可估计每个物种的平均种群,但在非线性相互作用动力学的情况下可能是不准确的。在这里,我们提出了有限状态扩展(FSE),这是一种分析方法,该方法通过将离散状态空间所选子集的主方程动力学与DRE的平均种群动力学偶联,通过将随机反应网络的显微镜解释和宏观解释进行了介导。一种算法将网络转化为一个扩展的网络,其中每个离散状态被表示为另一个不同的物种。这种翻译完全保留了随机动力学,但是扩展的网络的DRE可以解释为对原始网络的校正。由于内在的噪声,多规模的人群和多稳定性,挑战最新技术的模型中证明了FSE的有效性。

Stochastic reaction networks are a fundamental model to describe interactions between species where random fluctuations are relevant. The master equation provides the evolution of the probability distribution across the discrete state space consisting of vectors of population counts for each species. However, since its exact solution is often elusive, several analytical approximations have been proposed. The deterministic rate equation (DRE) gives a macroscopic approximation as a compact system of differential equations that estimate the average populations for each species, but it may be inaccurate in the case of nonlinear interaction dynamics. Here we propose finite state expansion (FSE), an analytical method mediating between the microscopic and the macroscopic interpretations of a stochastic reaction network by coupling the master equation dynamics of a chosen subset of the discrete state space with the mean population dynamics of the DRE. An algorithm translates a network into an expanded one where each discrete state is represented as a further distinct species. This translation exactly preserves the stochastic dynamics, but the DRE of the expanded network can be interpreted as a correction to the original one. The effectiveness of FSE is demonstrated in models that challenge state-of-the-art techniques due to intrinsic noise, multi-scale populations, and multi-stability.

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