Stochastic Modeling of Biochemical Networks

Abstract

In this chapter, we present a stochastic framework for modeling subcellular biochemical reaction networks. In particular, we make an effort to show how the notion of propensity, the chemical master equation (CME), and the stochastic simulation algorithm arise as consequences of the Markov property. We would encourage the reader to pay attention to this, because it is not easy to see this connection when reading the relevant literature in systems biology. We review various analytical approximations of the CME, leaving out stochastic simulation approaches reviewed in [113, 155]. Moreover, we sketch interrelationships between various stochastic approaches. The books [114] and [165] inspired this chapter and can be referred to for further reading.