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Effect of excluded volume on 2D discrete stochastic chemical kinetics

机译:排除体积对2D离散随机化学动力学的影响

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摘要

The Stochastic Simulation Algorithm (SSA) is widely used in the discrete stochastic simulation of chemical kinetics. The propensity functions which play a central role in this algorithm have been derived under the point-molecule assumption, i.e., that the total volume of the molecules is negligible compared to the volume of the container. It has been shown analytically that for a one dimensional system and the A+A reaction, when the point molecule assumption is relaxed, the propensity function need only be adjusted by replacing the total volume of the system with the free volume of the system. In this paper we investigate via numerical simulations the impact of relaxing the point-molecule assumption in two dimensions. We find that the distribution of times to the first collision is close to exponential in most cases, so that the formalism of the propensity function is still applicable. In addition, we find that the area excluded by the molecules in two dimensions is usually higher than their close-packed area, requiring a larger correction to the propensity function than just the replacement of the total volume by the free volume.
机译:随机模拟算法(SSA)广泛用于化学动力学的离散随机模拟。在该算法中起主要作用的倾向函数是在点分子假设下得出的,即分子的总体积与容器的体积相比可忽略不计。分析地表明,对于一维系统和A + A反应,当放松点分子假设时,仅需通过用系统的自由体积代替系统的总体积来调整倾向函数。在本文中,我们通过数值模拟研究了二维放宽点分子假设的影响。我们发现,在大多数情况下,第一次碰撞的时间分布接近于指数分布,因此倾向函数的形式主义仍然适用。此外,我们发现,分子在二维上排除的面积通常比其密堆积面积高,与仅用自由体积代替总体积相比,需要对倾向函数进行更大的校正。

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