Monte Carlo simulation study of diffusion controlled reactions in three dimensional crowded media

Abstract

Published data reveal that the rate coefficients of diffusion controlled reactions taking place in crowded media are time dependent. Within this study we have performed on lattice 3D Monte Carlo simulations concerning Michaelis-Menten enzymatic reactions in crowded media, such as the cyto- plasmatic region of the cells. We have considered the same size and mobility of the reactant particles and different crowding conditions using distinct concentrations and sizes of the immobile obstacles. The results we have obtained indicate a fractal like kinetics with the degree of fractality that changes with the concentration and dimension of the obstacles. The simulation data also reflect that, depending on the temporal scale, molecular crowding can bring positive or negative effects on reaction kinetics. Comparing the cases studied, for short periods of time the value of the initial rate constant generally increases with the degree of crowding. For longer periods of time and larger distances, molecular crowding slows down the reaction kinetics in every case, due to smaller diffusion coefficients of the reactants, having a more intense effect for the cases with higher degree of crowding.