Multi-grid reaction-diffusion master equation: applications to morphogen gradient modelling
Abstract
The multi-grid reaction-diffusion master equation (mgRDME) provides a generalization of stochastic compartment-based reaction-diffusion modelling described by the standard reaction-diffusion master equation (RDME). By enabling different resolutions on lattices for biochemical species with different diffusion constants, the mgRDME approach improves both accuracy and efficiency of compartment-based reaction-diffusion simulations. The mgRDME framework is examined through its application to morphogen gradient formation in stochastic reaction-diffusion scenarios, using both an analytically tractable first-order reaction network and a model with a second-order reaction. The results obtained by the mgRDME modelling are compared with the standard RDME model and with the (more detailed) particle-based Brownian dynamics simulations. The dependence of error and numerical cost on the compartment sizes is defined and investigated through a multi-objective optimization problem.
Cite
@article{arxiv.2405.02117,
title = {Multi-grid reaction-diffusion master equation: applications to morphogen gradient modelling},
author = {Radek Erban and Stefanie Winkelmann},
journal= {arXiv preprint arXiv:2405.02117},
year = {2024}
}