Binomial leap methods for simulating stochastic chemical kinetics

Binomial leap methods for simulating stochastic chemical kinetics.

This paper discusses efficient simulation methods for stochastic chemical kinetics. Based on the tau-leap and midpoint tau-leap methods of Gillespie [D. T. Gillespie, J. Chem. Phys. 115, 1716 (2001)], binomial random variables are used in these leap methods rather than Poisson random variables. The motivation for this approach is to improve the efficiency of the Poisson leap methods by using la...

Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics.

In cell biology, cell signaling pathway problems are often tackled with deterministic temporal models, well mixed stochastic simulators, and/or hybrid methods. But, in fact, three dimensional stochastic spatial modeling of reactions happening inside the cell is needed in order to fully understand these cell signaling pathways. This is because noise effects, low molecular concentrations, and spa...

Implicit Simulation Methods for Stochastic Chemical Kinetics

In biochemical systems some of the chemical species are present with only small numbers of molecules. In this situation discrete and stochastic simulation approaches are more relevant than continuous and deterministic ones. The fundamental Gillespie’s stochastic simulation algorithm (SSA) accounts for every reaction event, which occurs with a probability determined by the configuration of the s...

Numerical Solution Methods in Stochastic Chemical Kinetics

Stochastic projective methods for simulating stiff chemical reacting systems

Article history: Received 27 September 2011 Received in revised form 15 February 2012 Accepted 16 February 2012 Available online 22 February 2012