Effect of excluded volume on 2D discrete stochastic chemical kinetics

✍ Scribed by Sotiria Lampoudi; Dan T. Gillespie; Linda R. Petzold

• Book ID: 104021928
• Publisher: Elsevier Science
• Year: 2009
• Tongue: English
• Weight: 714 KB
• Volume: 228
• Category: Article
• ISSN: 0021-9991
• DOI: 10.1016/j.jcp.2009.02.002

✦ Synopsis

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.