Efficient exact and K-skip methods for stochastic simulation of coupled chemical reactions.
Efficient exact and K-skip methods for stochastic simulation of coupled chemical reactions.
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DOI：
10.1063/1.3204422
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发表时间：
2009-08
期刊：
影响因子：
--
通讯作者：
Xiaodong Cai;Ji Wen
中科院分区：
文献类型：
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作者：
Xiaodong Cai;Ji Wen
吉莱斯皮直接法[D.吉莱斯皮，J.Chem.Phys.81，2340（1977）]用于化学反应系统的精确随机模拟已被广泛采用。它易于实现，但对于相对较大的系统需要较大的计算量。近年来，两种更有效的方法，下一反应法（NRM）[M. A.吉布森和J. Bruck，J.Phys.Chem.A105，1876（2000）]和优化的DM（ODM）[Y. Cao等人，J.Chem.Phys.121，4059（2004）]，以提高模拟速度。它已被证明，ODM是最先进的最有效的方法，最实际的反应系统的精确随机模拟。在本文中，我们首先开发了一个精确的随机模拟算法命名为ODMK，这是更有效的比ODM。然后，我们开发了一个近似的方法命名为K-skip方法，以进一步加快模拟。使用两个化学反应系统，我们证明了我们的ODMK和K-skip方法可以节省20%-30%和70%-80%的模拟时间，分别与ODM相比。我们还表明，我们的ODMK和K-skip方法提供了几乎相同的模拟精度的ODM。
Gillespie's direct method (DM) [D. Gillespie, J. Chem. Phys. 81, 2340 (1977)] for exact stochastic simulation of chemical reaction systems has been widely adopted. It is easy to implement but requires large computation for relatively large systems. Recently, two more efficient methods, next reaction method (NRM) [M. A. Gibson and J. Bruck, J. Phys. Chem. A 105, 1876 (2000)] and optimized DM (ODM) [Y. Cao et al., J. Chem. Phys. 121, 4059 (2004)], have been developed to improve simulation speed. It has been demonstrated that the ODM is the state-of-the-art most efficient method for exact stochastic simulation of most practical reaction systems. In this paper, we first develop an exact stochastic simulation algorithm named ODMK that is more efficient than the ODM. We then develop an approximate method named K-skip method to further accelerate simulation. Using two chemical reaction systems, we demonstrate that our ODMK and K-skip method can save 20%-30% and 70%-80% simulation time, respectively, comparing to the ODM. We also show that our ODMK and K-skip method provide almost the same simulation accuracy as the ODM.