Exploring the performance of spatial stochastic simulation algorithms
Since the publication of Gillespies direct method, diverse methods have been developed to improve the performance of stochastic simulation methods and to enter the spatial realm. In this paper we discuss a spatial ?-leaping variant (S?) that extends the basic leap method. S? takes reaction and both outgoing and incoming diffusion events into account when calculating a leap candidate. A performance analysis shall reveal details on the achieved success in balancing speed and accuracy in comparison to other methods. However, performance analysis of spatial stochastic algorithms requires significant effort  it is crucial to choose suitable (benchmark) models and to carefully define model and simulation setups that take problem and simulation design spaces into account.
stochastic simulation spatial ?-leaping ?-leaping performance analysis ssa performance evaluation next sub-volume method gillespie multi-particle method