Multiscale simulations of anisotropic particles combining Brownian Dynamics and Green's Function Reaction Dynamics

TL;DR

This paper introduces an extended multiscale simulation method combining Brownian Dynamics and Green's Function Reaction Dynamics to accurately model anisotropic particles with orientational interactions, enabling large-scale biomolecular simulations.

Contribution

The paper develops and validates a novel multiscale algorithm that incorporates rotational dynamics into BD-GFRD for anisotropic particles, advancing simulation capabilities.

Findings

Algorithm successfully models anisotropic particle interactions.

Validation confirms accuracy of the rotational extension.

Performance analysis shows efficiency for large systems.

Abstract

The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic Molecular Dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P.G. Bolhuis and P.R. ten Wolde, J. Chem. Phys. {\bf 43}, 21: 214102 (2015)]. Here we extend this multiscale BD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm we discuss its performance. The rotational BD-GFRD multiscale method will open up the possibility for large scale simulations of e.g. protein signalling networks.