PyRID: A Brownian dynamics simulator for reacting and interacting particles written in Python

Recent technological developments in molecular biology led to large data sets providing new insights into the molecular organisation of cells. To fully exploit their potential, these developments have to be complemented by computer simulations that allow to gain in-depth understanding on molecular principles. We developed the Python-based, reaction-diffusion simulator PyRID, integrating many features for the efficient simulation of molecular biological systems. Amongst others, PyRID is capable of simulating unimolecular and bimolecular reactions as well as pair-interactions to assess the dynamics resulting from individual interacting proteins to polydisperse substrates consisting of many different molecules. Furthermore, PyRID supports mesh-based compartments and surface diffusion of particles, enabling analyses of the interaction between (trans-)membrane proteins with intra- and extracellular proteins. PyRID is written entirely in Python, which is a programming language being known for its readability and easy accessibility, such that the scientific community can easily extend PyRID to its current and future needs.