生化反应系统的建模与分析

很多细胞行为受细胞内基因表达和蛋白质相互作用等生物化学反应的调控.这些细胞内的生化反应表现出明显的随机性,它成为描述细胞行为的可计算建模中不可忽略的因素.该文是关于计算系统生物学中随机模拟的基本理论和新进展的自洽综述.本综述从生化反应系统的基本假设出发,介绍关于生化反应内部噪声、外部随机扰动和包含时间滞后的反应过程的各种数学描述,包括化学主方程、化学福克尔-普朗克方程、化学速率方程、化学郎之万方程等; 还介绍了相关的数值模拟方法,包括随机模拟算法和τ跳跃算法.

The Modeling and Analysis of Biochemical Reaction Systems

Many cellular behaviors are regulated by intracellular biochemical reactions such as gene expression and protein-protein interactions.The kinetics of these biochemical reactions are mostly random,and therefore the stochasticity is essential for the modeling of cellular behaviour in the field of computational biology.This paper is a self contained review trying to provide an overview of stochastic modeling and recent advance in computation biology.This paper starts from basic assumptions in biochemical reaction systems,and introduce mathematical formulations for modeling intrinsic noise,external noise,and reactions systems with delay.Multiple dynamical equations are discussed,including chemical master equation,chemical Fokker-Plank equation,chemical reaction rate equation,and chemical Langevin equation,etc.Several numerical methods are introduced,including the stochastic simulation algorithm(SSA)and the Tau-leaping algorithm.