ReaDDy: High-performance simulator for reaction-diffusion dynamics with interacting particles. Suitable for modeling cellular signal transduction, chemical microreactors, soft matter systems, membrane mechanics, virus assembly etc. Previous version was Java-based. New version currently developed with software abstraction layers: (i) Python user API, (ii) C++ API, (iii) Multithreading/CUDA/MPI kernels for execution of different platforms.

Code: github.com/readdy/readdy
Languages: C++ (70%) CUDA (20%) Python (10%)
Usage: ca. 1,000 downloads
License: Lesser GPL (open-source)
Releases: 1.0 (Java),  v1.0.0 (C++)
Platforms: Linux, Mac
DOI: 10.1371/journal.pone.0074261
DOI: 10.1016/j.bpj.2014.12.025

Our 1-week ReaDDy summer school in July is open to students and researchers. For information on the upcoming summer school see here.