The Brownian dynamics simulator PyRID for reacting and interacting particles written in Python.

Abstract

Recent advances in molecular biology have led to large-scale datasets providing new insights into the molecular organization of cells. To fully exploit their potential, computer simulations are essential to gain in-depth understanding of molecular principles. We developed the Python reaction interaction diffusion simulator (PyRID), a Python-based reaction-diffusion simulator designed for the efficient simulation of molecular biological systems. PyRID incorporates unimolecular and bimolecular reactions as well as pair interactions and simulation of individual interacting proteins to polydisperse molecular assemblies. It supports mesh-based compartments and surface diffusion of particles, enabling analyses of interactions between (trans)membrane proteins with intra- and extracellular proteins. Distinctively, PyRID uses hierarchical grids for polydisperse systems, supports rigid bead models, and calculates diffusion tensors internally. Validation against theoretical results and established models confirms PyRID's accuracy in reproducing key physical properties. PyRID is written entirely in Python, making it accessible to the broader scientific community, facilitating customization and integration into diverse research workflows.