ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics.

ABSTRACT: Interacting-particle reaction dynamics (iPRD) combines the simulation of dynamical trajectories of interacting particles as in molecular dynamics (MD) simulations with reaction kinetics, in which particles appear, disappear, or change their type and interactions based on a set of reaction rules. This combination facilitates the simulation of reaction kinetics in crowded environments, involving complex molecular geometries such as polymers, and employing complex reaction mechanisms such as breaking and fusion of polymers. iPRD simulations are ideal to simulate the detailed spatiotemporal reaction mechanism in complex and dense environments, such as in signalling processes at cellular membranes, or in nano- to microscale chemical reactors. Here we introduce the iPRD software ReaDDy 2, which

SUBMITTER: Hoffmann M 

PROVIDER: S-EPMC6413953 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature