Biochemical reactions can happen on different time scales and also the abundance of species in these reactions can be very different from each other. Classical approaches, such as deterministic or stochastic approach fail to account for or to exploit this multi-scale nature, respectively. In this paper, we propose a jumpdiffusion approximation for multi-scale Markov jump processes that couples the two modeling approaches. An error bound of the proposed approximation is derived and used to partition the reactions into fast and slow sets, where the fast set is simulated by a stochastic differential equation and the slow set is modeled by a discrete chain. The error bound leads to a very efficient dynamic partitioning algorithm which has been implemented for several multi-scale reaction systems. The gain in computational efficiency is illustrated by a realistically sized model of a signal transduction cascade coupled to a gene expression dynamics.MSC 2010 subject classifications: 60H30, 60J28, 92B05
Stochastic reaction systems with discrete particle numbers are usually described by a continuous-time Markov process. Realizations of this process can be generated with the stochastic simulation algorithm, but simulating highly reactive systems is computationally costly because the computational work scales with the number of reaction events. We present a new approach which avoids this drawback and increases the efficiency considerably at the cost of a small approximation error. The approach is based on the fact that the time-dependent probability distribution associated to the Markov process is explicitly known for monomolecular, autocatalytic and certain catalytic reaction channels. More complicated reaction systems can often be decomposed into several parts some of which can be treated analytically. These subsystems are propagated in an alternating fashion similar to a splitting method for ordinary differential equations. We illustrate this approach by numerical examples and prove an error bound for the splitting error.Keywords Stochastic simulation algorithm · discrete stochastic reaction systems · splitting methods · analytic solution formulas · error bounds · chemical master equation
Mathematics Subject Classification (2000)
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.