Lattice-based simulations of microscopic reaction-diffusion models in a crowded environment

Abstract: Molecules inside living cells move by diffusion and can react with each other upon collision. Living cells are occupied by macromolecules which limits the available space for the particles to diffuse in. The effect caused by these crowders has been modeled and the accuracy of the models has been evaluated. We investigate two models that follows individual particle trajectories. The more accurate model samples Brownian Dynamics in a continuous space. The second computationally more efficient model, uses discrete space were the particles move on a lattice. The result shows that the lattice model under-estimates the crowding effect on the diffusive behavior. The reaction rates were both increased and decreased depending on the time and amount of crowders when comparing the lattice model to the model using Brownian Dynamics. This also prove the importance to model the particles with realistic sizes when simulating reaction-diffusion in a crowded environment.