Work

Multi-Grid Reaction-Diffusion Master Equation: Applications to Morphogen Gradient Modelling

Year: 2024

Type: article

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.

Source: Bulletin of Mathematical Biology

DOI: 10.1007/s11538-024-01377-y

Authors: Radek Erban, Stefanie Winkelmann

Institutions: University of Oxford, Zuse Institute Berlin

Language: English

Topic: Gene Regulatory Network Analysis

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $3,090

Funders: Deutsche Forschungsgemeinschaft, Berlin Mathematics Research Center MATH+, Engineering and Physical Sciences Research Council