Parallelization of particle-based reaction-diffusion simulations using MPI.

ABSTRACT: Particle-based reaction-diffusion models offer a high-resolution alternative to the continuum reaction-diffusion approach, capturing the discrete and volume-excluding nature of molecules undergoing stochastic dynamics. These methods are thus uniquely capable of simulating explicit self-assembly of particles into higher-order structures like filaments, spherical cages, or heterogeneous macromolecular complexes, which are ubiquitous across living systems and in materials design. The disadvantage of these high-resolution methods is their increased computational cost. Here we present a parallel implementation of the particle-based NERDSS software using the Message Passing Interface (MPI) and spatial domain decomposition, achieving close to linear scaling for up to 96 processors in the largest

SUBMITTER: Guo S 

PROVIDER: S-EPMC11661114 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature