ReaDDy

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.

Installation

The preferred way of installing the software is by using the conda package manager:

# add conda-forge channel
conda config --add channels conda-forge

# optional: create environment for readdy, switch to that environment
conda create -n readdy python=3
source activate readdy

# install readdy
conda install -c readdy readdy

Documentation

A documentation and a few examples are provided at https://readdy.github.io/.

Core features

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
- aggregation
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