A Convenient Tool for the Stochastic Simulation of Reaction Mechanisms

Abstract

The article introduces the stochastic simulation of chemical reactions with Chemical Kinetics Simulator, CKS, a free, easy-to-use, and powerful program. After familiarizing themselves with the Monte Carlo method of stochastic simulation and CKS, students model reactions with both kinetically and thermodynamically controlled products and study a mechanism where the steady-state approximation gives inaccurate results. Students subsequently model enzyme kinetics, an oscillatory reaction, and the mechanism responsible for the circadian rhythms of cyanobacteria. This computational exercise gives students an opportunity to appreciate the stochastic nature of chemical reactions at the molecular level, stresses the limits of applicability of kinetic approximations, and introduces the modeling of oscillatory reactions.