Mass fluctuation kinetics:: Capturing stochastic effects in systems of chemical reactions through coupled mean-variance computations
Mass fluctuation kinetics:: Capturing stochastic effects in systems of chemical reactions through coupled mean-variance computations
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DOI：
10.1063/1.2408422
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发表时间：
2007-01-14
影响因子：
4.4
通讯作者：
Verghese, George C.
中科院分区：
文献类型：
--
作者：
Gomez-Uribe, Carlos A.;Verghese, George C.
化学反应中的内在随机效应，特别是在生化网络中，可能会导致与确定性质量作用动力学（MAK）预测的行为显着不同的行为。然而，分析随机效应通常是计算繁重和复杂的。作者在这里描述了他们所谓的质量波动动力学（MFK）的推导和应用，这是一组确定性方程，用于跟踪系统中化学物质浓度的均值、方差和协方差。这些方程通过近似化学主方程的第一和第二时刻的动力学而获得。除了需要系统卷的知识之外，MFK描述只需要用于指定MAK模型的相同信息，并且写下来或应用起来并不困难。当波动的影响可以忽略不计时，MFK描述通常简化为MAK。MFK方程能够比MAK方程更好地描述网络的平均行为，因为它们包含了波动对均值演化的影响。它们还考虑了均值对方差和协方差演变的影响，以在平均行为周围产生相当准确的不确定性带。MFK计算，虽然近似，是显着快于蒙特卡洛方法计算化学反应系统中的第一和第二时刻。因此，它们可以被用来，也许沿着与一些样品状态轨迹的蒙特卡罗模拟，以有效地提供一个化学系统的行为的详细图片。(c)2007年，美国物理学会。
The intrinsic stochastic effects in chemical reactions, and particularly in biochemical networks, may result in behaviors significantly different from those predicted by deterministic mass action kinetics (MAK). Analyzing stochastic effects, however, is often computationally taxing and complex. The authors describe here the derivation and application of what they term the mass fluctuation kinetics (MFK), a set of deterministic equations to track the means, variances, and covariances of the concentrations of the chemical species in the system. These equations are obtained by approximating the dynamics of the first and second moments of the chemical master equation. Apart from needing knowledge of the system volume, the MFK description requires only the same information used to specify the MAK model, and is not significantly harder to write down or apply. When the effects of fluctuations are negligible, the MFK description typically reduces to MAK. The MFK equations are capable of describing the average behavior of the network substantially better than MAK, because they incorporate the effects of fluctuations on the evolution of the means. They also account for the effects of the means on the evolution of the variances and covariances, to produce quite accurate uncertainty bands around the average behavior. The MFK computations, although approximate, are significantly faster than Monte Carlo methods for computing first and second moments in systems of chemical reactions. They may therefore be used, perhaps along with a few Monte Carlo simulations of sample state trajectories, to efficiently provide a detailed picture of the behavior of a chemical system. (c) 2007 American Institute of Physics.