Multi-Grid Reaction-Diffusion Master Equation: Applications to Morphogen Gradient Modelling
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...
| Autors principals: | , |
|---|---|
| Format: | Journal article |
| Idioma: | English |
| Publicat: |
Springer
2024
|
| _version_ | 1826315396691525632 |
|---|---|
| author | Erban, R Winkelmann, S |
| author_facet | Erban, R Winkelmann, S |
| author_sort | Erban, R |
| collection | OXFORD |
| description | 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. |
| first_indexed | 2024-12-09T03:25:00Z |
| format | Journal article |
| id | oxford-uuid:f54ded7f-90b0-4f3d-a58b-6e90b40dfead |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-12-09T03:25:00Z |
| publishDate | 2024 |
| publisher | Springer |
| record_format | dspace |
| spelling | oxford-uuid:f54ded7f-90b0-4f3d-a58b-6e90b40dfead2024-11-27T20:10:31ZMulti-Grid Reaction-Diffusion Master Equation: Applications to Morphogen Gradient ModellingJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:f54ded7f-90b0-4f3d-a58b-6e90b40dfeadEnglishJisc Publications RouterSpringer2024Erban, RWinkelmann, SThe 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. |
| spellingShingle | Erban, R Winkelmann, S Multi-Grid Reaction-Diffusion Master Equation: Applications to Morphogen Gradient Modelling |
| title | Multi-Grid Reaction-Diffusion Master Equation: Applications to Morphogen Gradient Modelling |
| title_full | Multi-Grid Reaction-Diffusion Master Equation: Applications to Morphogen Gradient Modelling |
| title_fullStr | Multi-Grid Reaction-Diffusion Master Equation: Applications to Morphogen Gradient Modelling |
| title_full_unstemmed | Multi-Grid Reaction-Diffusion Master Equation: Applications to Morphogen Gradient Modelling |
| title_short | Multi-Grid Reaction-Diffusion Master Equation: Applications to Morphogen Gradient Modelling |
| title_sort | multi grid reaction diffusion master equation applications to morphogen gradient modelling |
| work_keys_str_mv | AT erbanr multigridreactiondiffusionmasterequationapplicationstomorphogengradientmodelling AT winkelmanns multigridreactiondiffusionmasterequationapplicationstomorphogengradientmodelling |