NERDSS: A Nonequilibrium Simulator for Multibody Self-Assembly at the Cellular Scale.

ABSTRACT: Currently, a significant barrier to building predictive models of cellular self-assembly processes is that molecular models cannot capture minutes-long dynamics that couple distinct components with active processes, whereas reaction-diffusion models cannot capture structures of molecular assembly. Here, we introduce the nonequilibrium reaction-diffusion self-assembly simulator (NERDSS), which addresses this spatiotemporal resolution gap. NERDSS integrates efficient reaction-diffusion algorithms into generalized software that operates on user-defined molecules through diffusion, binding and orientation, unbinding, chemical transformations, and spatial localization. By connecting the fast processes of binding with the slow timescales of large-scale assembly, NERDSS integrates molecular resol

SUBMITTER: Varga MJ 

PROVIDER: S-EPMC7300348 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature