Python / C++ based particle reaction-diffusion simulator

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.

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

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
    • aggregation
  • particle complexes via harmonic

     

     

     

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