Stochastic simulation of biochemical reactions with partial-propensity and rejection-based approaches.
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.
['Thanh|Vo Hong|VH|']
D000465:Algorithms D003198:Computer Simulation D008954:Models, Biological D008956:Models, Chemical D013269:Stochastic Processes
Stochastic simulation Computational biology Partial-propensity rejection-based stochastic simulation algorithm