ReaDDy is an open source Java library for particle based Reaction Diffusion Dynamics.
It unites explicit time, explicit space diffusion simulations with a reaction engine, bridging the gap between mesoscopic molecular dynamics simulations (MD) and event based reaction kinetics simulations. This especially allows the investigation of crowding and spatial effects in cellular environments. It can either be used as a stand alone simulation toolkit to run simulations or as a library within your code.
- Programming Language: Java
- License: BSD/3-clause
- Supported Platforms: Windows, Linux, Mac, with Java Version 6 or later
The runtime of ReaDDy scales linearly with the number of particles involved in the system. At 10% occupied volume density, integrating the dynamics for 1000 particles for one timesteps takes 7.7 ms in 3D and 2.5 ms in 2D systems on a single core CPU.
In explicit reaction diffusion simulations, most of the computing time is spent on calculating the diffusional displacements of the particles. For that reason, the reaction module of ReaDDy is separated from its diffusion engine and both only communicate via a small lightweight interface. This design is intended to facilitate the implementation of a faster, parallelized ReaDDy core or its replacement by a fast third party particle diffusion engine to speed up simulations in the future.
The development of ReaDDy is part of the Ph.D. thesis of Johannes Schöneberg under supervision of Prof. Frank Noé. Started in June 2011, it took about 1.5 years to complete version 1.0 in December 2012, resulting in about 35k lines of code in 313 files, including 118 unit tests.