Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes

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.Meredys provides a powerful and versatile way to run accurate simulations of molecular and sub-cellular systems, that complement existing multi-agent simulation systems. Meredys is a Free Software and the source code is available at http://meredys.sourceforge.net/ webcite.The influence of geometry and space on the functioning of cellular processes, the vast quantity of potential interactions due to molecular complex formation, and the stochasticity caused by low copy numbers of molecular species are all recognised features of many biological systems [1-3]. Within the field of computational biology these systems are best modelled using a particle-based stochastic approach [4]. Here we present Meredys (MEsoscopic REaction DYnamics Simulator), a stochastic, particle-based simulation software designed to model and simulate reaction-diffusion systems at the mesoscopic level. The software is derived from an idea initially developed by Dan Mossop and Fred Howell in the Abstracted Protein Simulator (APS) [5]. It is implemented in the Java programming language and uses Java3D as visualization framework for rendering to the screen. The input to the software is a model of a reaction diffusion system encoded in a Meredys specific implementation of the N