D-leaping: Accelerating stochastic simulation algorithms for reactions with delays

Bayati, B., Chatelain, P., Koumoutsakos P., Journal of Computational Physics, 228, 5909-5918, 2009


We propose a novel, accelerated algorithm for the approximate stochastic simulation of biochemical systems with delays.  The present work extends existing accelerated algorithms by distributing, in a time adaptive fashion, the delayed reactions so as to minimize the computational effort while preserving their accuracy.  The accuracy of the present algorithm is assessed by comparing its results to those of the corresponding delay differential equations for a representative biochemical system.  In addition, the fluctuations produced from the present algorithm are comparable to those from an exact stochastic simulation with delays.  The algorithm is used to simulate biochemical systems that model oscillatory gene expression.  The results indicate that the present algorithm is competitive with existing works for several benchmark problems while it is orders of magnitude faster for certain systems of biochemical reactions.