Multiscale stochastic reaction-diffusion modeling: application to actin dynamics in filopodia

DOI10.1007/S11538-013-9844-3MaRDI QIDQ458694zbMATHOpenAlexWikidataFDO

Authors Radek Erban, Mark B. Flegg, Garegin A. Papoian

Publication date 8 October 2014

Published in Bulletin of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/s11538-013-9844-3

Mathematics Subject Classification ID

Systems biology, networks (92C42) Diffusion processes and stochastic analysis on manifolds (58J65)

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Cites work

• An adaptive algorithm for simulation of stochastic reaction-diffusion processes
• Analysis of Brownian dynamics simulations of reversible bimolecular reactions
• Hybrid computations with flux exchange
• Multiscale reaction-diffusion algorithms: PDE-assisted Brownian dynamics
• Simulation of stochastic reaction-diffusion processes on unstructured meshes

Cited in

(14)

• Galerkin finite element method for time-fractional stochastic diffusion equations
• A stochastic analysis of actin polymerization in the presence of twinfilin and gelsolin
• Diffusivity estimation for activator-inhibitor models: theory and application to intracellular dynamics of the actin cytoskeleton
• Flow in filopodia: re-organization and the representation of biological entities as computational objects
• Multi-grid reaction-diffusion master equation: applications to morphogen gradient modelling
• Actin Automata: Phenomenology and Localizations
• Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations
• Actin filament branching and protrusion velocity in a simple 1D model of a motile cell
• Stochastic Turing patterns: analysis of compartment-based approaches
• Reactive boundary conditions as limits of interaction potentials for Brownian and Langevin dynamics
• Protrusion of a virtual model lamellipodium by actin polymerization: A coarse-grained langevin dynamics model
• Mathematical-Computational Simulation of Cytoskeletal Dynamics
• Multiscale stochastic reaction-diffusion algorithms combining Markov chain models with stochastic partial differential equations
• Editorial: Special issue on stochastic modelling of reaction-diffusion processes in biology

Describes a project that uses

Uses Software

• MCELL
• STEPS
• MesoRD

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