The N-leap method for stochastic simulation of coupled chemical reactions.

Numerical simulation of the time evolution of a spatially homogeneous chemical system is always of great interest. Gillespie first developed the exact stochastic simulation algorithm (SSA), which is accurate but time-consuming. Recently, many approximate schemes of the SSA are proposed to speed up simulation. Presented here is the N-leap method, which guarantees the validity of the leap condition and at the same time keeps the efficiency. In many cases, N-leap has better performance than the widely-used τ-leap method. The details of the N-leap method are described and several examples are presented to show its validity.

[1]  Anne Auger,et al.  R-leaping: accelerating the stochastic simulation algorithm by reaction leaps. , 2006, The Journal of chemical physics.

[2]  K. Burrage,et al.  Binomial leap methods for simulating stochastic chemical kinetics. , 2004, The Journal of chemical physics.

[3]  Hong Li,et al.  Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. , 2004, The Journal of chemical physics.

[4]  Jürgen Pahle,et al.  Biochemical simulations: stochastic, approximate stochastic and hybrid approaches , 2008, Briefings Bioinform..

[5]  Muruhan Rathinam,et al.  Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method , 2003 .

[6]  Yang Cao,et al.  Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems , 2005 .

[7]  Linda R Petzold,et al.  Efficient step size selection for the tau-leaping simulation method. , 2006, The Journal of chemical physics.

[8]  Xiaodong Cai,et al.  Unbiased tau-leap methods for stochastic simulation of chemically reacting systems. , 2008, The Journal of chemical physics.

[9]  彭新俊,et al.  L-leap: accelerating the stochastic simulation of chemically reacting systems , 2007 .

[10]  D. Gillespie.  Approximate accelerated stochastic simulation of chemically reacting systems , 2001 .

[11]  Linda R. Petzold,et al.  Improved leap-size selection for accelerated stochastic simulation , 2003 .

[12]  Xiaodong Cai,et al.  K-leap method for accelerating stochastic simulation of coupled chemical reactions. , 2007, The Journal of chemical physics.

[13]  D. Gillespie,et al.  Accelerated stochastic simulation of the stiff enzyme-substrate reaction. , 2005, The Journal of chemical physics.

[14]  D. Gillespie,et al.  Avoiding negative populations in explicit Poisson tau-leaping. , 2005, The Journal of chemical physics.

[15]  Linda R. Petzold,et al.  Accuracy limitations and the measurement of errors in the stochastic simulation of chemically reacting systems , 2006, J. Comput. Phys..

[16]  D. Gillespie.  Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[17]  Michael A. Gibson,et al.  Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels , 2000 .