An efficient multi-scale Green's function reaction dynamics scheme.

Molecular Dynamics-Green's Function Reaction Dynamics (MD-GFRD) is a multiscale simulation method for particle dynamics or particle-based reaction-diffusion dynamics that is suited for systems involving low particle densities. Particles in a low-density region are just diffusing and not interacting. In this case, one can avoid the costly integration of microscopic equations of motion, such as molecular dynamics (MD), and instead turn to an event-based scheme in which the times to the next particle interaction and the new particle positions at that time can be sampled. At high (local) concentrations, however, e.g., when particles are interacting in a nontrivial way, particle positions must still be updated with small time steps of the microscopic dynamical equations. The efficiency of a multiscale simulation that uses these two schemes largely depends on the coupling between them and the decisions when to switch between the two scales. Here we present an efficient scheme for multi-scale MD-GFRDsimulations. It has been shownthatMD-GFRDschemes are more efficient than brute-force molecular dynamics simulations up to a molar concentration of 10² µM. In this paper, we showthat the choice of the propagation domains has a relevant impact on the computational performance. Domains are constructed using a local optimization of their sizes and a minimal domain size is proposed. The algorithm is shown to be more efficient than brute-force Brownian dynamics simulations up to a molar concentration of 10³ µM and is up to an order of magnitude more efficient compared with previous MD-GFRD schemes. [ABSTRACT FROM AUTHOR]