Efficiently Solving the Stochastic Reaction-Diffusion Master Equation in C++ with the COMSOL Multiphysics® Software

L. A. Widmer [1], J. Stelling [1],
[1] Department of Biosystems Science and Engineering, ETH Zürich and Swiss Institute of Bioinformatics, Basel, Switzerland
Veröffentlicht in 2016

We demonstrate a simulation engine using COMSOL® and MATLAB® software that is able to simulate stochastic reaction-diffusion models in the reaction-diffusion master equation framework. We use this engine to construct models of budding yeast cells with embedded microtubules, interfacing stochastic microtubule dynamics with spatiotemporal signaling networks acting during mitosis. Our simulation engine can then be used together with our previously-published virtual microscope to conduct in silico experiments, allowing us to link the model results to experimental observations made with fluorescence microscopy. Finally, we achieve a two-fold speedup compared to a state-of-the art solver.