Monte Carlo simulation of diffusion and reaction in two-dimensional cell structures

Diffusion and reaction processes control the dynamics of many different biological systems. For example, tissue respiration can be limited by the delivery of oxygen to the cells and to the mitochondria. In this case, oxygen is small and travels quickly compared with the mitochondria, which can be considered as immobile reactive traps in the cell cytoplasm. A Monte Carlo theoretical investigation quantifying the interplay of diffusion, reaction, and structure on the reaction rate constant is reported here for diffusible particles in two-dimensional, reactive traps. The placement of traps in overlapping, nonoverlapping, and clustered spatial arrangements can have a large effect on the rate constant when the process is diffusion limited. However, under reaction-limited conditions the structure has little effect on the rate constant. For the same trap fractions and reactivities, nonoverlapping traps have the highest rate constants, overlapping traps yield intermediate rate constants, and clustered traps have the lowest rate constants. An increase in the particle diffusivity in the traps can increase the rate constant by reducing the time required by the particles to reach reactive sites. Various diffusive, reactive, and structural conditions are evaluated here, exemplifying the versatility of the Monte Carlo technique.