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.
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Meredys is distributed under the General Public Licence.
Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexesDominic
P Tolle and Nicolas Le Novère
BMC Systems Biology 2010, 4:24doi:10.1186/1752-0509-4-24