ReaDDy (Reaction Diffusion Dynamics) is an open source particle based reaction-diffusion simulator that can be configured and run via Python. Currently supported platforms are Mac and Linux.
The preferred way of installing the software is by using the conda package manager:
# optional: create environment for readdy, switch to that environment conda create -n readdy conda activate readdy # add conda-forge channel conda config --env --add channels conda-forge # install readdy with a specified Python version conda install python=3.9 readdy
A documentation and a few examples are provided at https://readdy.github.io/.
- particle based simulation of reaction-diffusion systems in 3D
- particles diffuse via Brownian dynamics
- reactions between single instances of particles (unimolecularly and bimolecularly)
- particle interaction potentials for modeling
- space exclusion
- molecular crowding
- particle complexes via harmonic bonds, angles, and cosine dihedrals for modeling, e.g.,
- domain structure
- polymer chains
- spatially and temporally triggered changes in the particle complexes
- simulation output in a compact hdf5 file
- single-threaded and pthread-parallelized implementations available