Stochastic simulation of biochemical reactions with partial-propensity and rejection-based approaches

摘要

Highlights ? A new fast exact stochastic simulation algorithm is developed. ? The search time complexity of the algorithm is scaled with the number of species. ? The updates of the algorithm are skipped and performed only as needed. Abstract We present in this paper a new exact algorithm for improving performance of exact stochastic simulation algorithm. The algorithm is developed on concepts of the partial-propensity and the rejection-based approaches. It factorizes the propensity bounds of reactions and groups factors by common reactant species for selecting next reaction firings. Our algorithm provides favorable computational advantages for simulating of biochemical reaction networks by reducing the cost for selecting the next reaction firing to scale with the number of chemical species and avoiding expensive propensity updates during the simulation. We present the details of our new algorithm and benchmark it on concrete biological models to demonstrate its applicability and efficiency. ]]>