TY - JOUR

T1 - K -leap method for accelerating stochastic simulation of coupled chemical reactions

AU - Cai, Xiaodong

AU - Xu, Zhouyi

PY - 2007/2/28

Y1 - 2007/2/28

N2 - Leap methods are very promising for accelerating stochastic simulation of a well stirred chemically reacting system, while providing acceptable simulation accuracy. In Gillespie's τ -leap method [D. Gillespie, J. Phys. Chem. 115, 1716 (2001)], the number of firings of each reaction channel during a leap is a Poisson random variable, whose sample values are unbounded. This may cause large changes in the populations of certain molecular species during a leap, thereby violating the leap condition. In this paper, we develop an alternative leap method called the K -leap method, in which we constrain the total number of reactions occurring during a leap to be a number K calculated from the leap condition. As the number of firings of each reaction channel during a leap is upper bounded by a properly chosen number, our K -leap method can better satisfy the leap condition, thereby improving simulation accuracy. Since the exact stochastic simulation algorithm (SSA) is a special case of our K -leap method when K=1, our K -leap method can naturally change from the exact SSA to an approximate leap method during simulation, whenever the leap condition allows to do so.

AB - Leap methods are very promising for accelerating stochastic simulation of a well stirred chemically reacting system, while providing acceptable simulation accuracy. In Gillespie's τ -leap method [D. Gillespie, J. Phys. Chem. 115, 1716 (2001)], the number of firings of each reaction channel during a leap is a Poisson random variable, whose sample values are unbounded. This may cause large changes in the populations of certain molecular species during a leap, thereby violating the leap condition. In this paper, we develop an alternative leap method called the K -leap method, in which we constrain the total number of reactions occurring during a leap to be a number K calculated from the leap condition. As the number of firings of each reaction channel during a leap is upper bounded by a properly chosen number, our K -leap method can better satisfy the leap condition, thereby improving simulation accuracy. Since the exact stochastic simulation algorithm (SSA) is a special case of our K -leap method when K=1, our K -leap method can naturally change from the exact SSA to an approximate leap method during simulation, whenever the leap condition allows to do so.

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U2 - 10.1063/1.2436869

DO - 10.1063/1.2436869

M3 - Article

AN - SCOPUS:33847220720

VL - 126

JO - Journal of Chemical Physics

JF - Journal of Chemical Physics

SN - 0021-9606

IS - 7

M1 - 074102

ER -