Lattice Microbes is a software package for efficiently sampling trajectories from the chemical and reaction-diffusion master equations (CME/RDME) on high performance computing (HPC) infrastructure using both exact and approximate methods.
Meredys (MEsoscopic REaction DYnamics Simulator) is a particle based stochastic simulation software designed to model and simulate reaction-diffusion systems.The input to the software is a model of a reaction diffusion system encoded in a Meredys-specic implementation of the NeuroML model description language.
Meredys allows for the simulation of multi-component, multi-feature state molecular species in two and three dimensions. Several compartments can be defined with different diffusion and boundary properties. The software employs a Brownian dynamics engine to simulate reaction-diffusion systems at the reactive particle level, based on compartment properties, complex structure, and hydro-dynamic radii. Zeroth-, first-, and second order reactions are supported. The molecular complexes have realistic geometries. Reactive species can contain user-defined feature states which can modify reaction rates and outcome. Models are defined in a versatile NeuroML input file. The simulation volume can be split in subvolumes to speed up run-time.
Ilya is a small program for Windows which simulates a reaction-diffusion model based on the Brusselator reaction scheme. Ilya simulates a 2-dimensional rectangular plane with opposite edges connected so that the plane actually forms a torus. The plane is divided up into many small area elements (one area element per screen pixel). The simulation involves computing the rates of change of two chemical species labeled X and Y as a result of both chemical transformations (Brusselator scheme) and diffusion of X and Y to and from adjacent area elements.