readdy 2.0.14

A particle-based reaction-diffusion simulator

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:

# 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

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