An effective stepsize selection procedure for discrete simulation of biochemical reaction systems

Abstract

We present an effective procedure for selecting the stepsize in the binomial $\tau$-leap method, which is an efficient technique for the discrete simulation of biochemical reaction systems. We use the difference of the propensity functions to approximate their derivatives, thus giving a derivative-free implementation. We compare the difference between the stepsizes obtained by existing procedures and the new procedure, and compare their relative efficiencies when simulating biochemical reaction systems. Numerical results indicate that the new procedure is very efficient and robust. More importantly, this new procedure is easy to implement and leads one step further towards a general purpose computer program for the efficient simulation of stochastic biochemical reaction systems. References

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