| Abstract |
In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex selfassembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. While mean-field rate equations cannot describe such processes, the recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with a Markov State Model (MSM) based on Molecular Dynamics for simulating the system at microscopic scales where reactants are in contact. The new scheme, MSM-GFRD, is generic, and can be used to simulate a plethora of systems relevant in bioenergy, chemistry, and oil reservoirs. |
