A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection-diffusion-reaction problems.

ABSTRACT: We have developed a new algorithm which merges discrete stochastic simulation, using the spatial stochastic simulation algorithm (sSSA), with the particle based fluid dynamics simulation framework of smoothed dissipative particle dynamics (SDPD). This hybrid algorithm enables discrete stochastic simulation of spatially resolved chemically reacting systems on a mesh-free dynamic domain with a Lagrangian frame of reference. SDPD combines two popular mesoscopic techniques: smoothed particle hydrodynamics and dissipative particle dynamics (DPD), linking the macroscopic and mesoscopic hydrodynamics effects of these two methods. We have implemented discrete stochastic simulation using the reaction-diffusion master equations (RDME) formalism, and deterministic reaction-diffusion equations based o

SUBMITTER: Brian D 

PROVIDER: S-EPMC6481948 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature