Abstract
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.
| Original language | English |
|---|---|
| Article number | 074102 |
| Journal | Journal of Chemical Physics |
| Volume | 126 |
| Issue number | 7 |
| DOIs | |
| State | Published - Feb 28 2007 |
Fingerprint
ASJC Scopus subject areas
- Atomic and Molecular Physics, and Optics
Cite this
K -leap method for accelerating stochastic simulation of coupled chemical reactions. / Cai, Xiaodong; Xu, Zhouyi.
In: Journal of Chemical Physics, Vol. 126, No. 7, 074102, 28.02.2007.Research output: Contribution to journal › Article
}
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.
UR - http://www.scopus.com/inward/record.url?scp=33847220720&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33847220720&partnerID=8YFLogxK
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 -