Mesoscopic modeling of stochastic reaction-diffusion kinetics in the subdiffusive regime

DOI10.1137/15M1013110zbMATH Open1381.35086DBLPjournals/mmas/BlancEHL16arXiv1503.07009OpenAlexW3123331042WikidataQ42378282 ScholiaQ42378282MaRDI QIDQ2806422FDOQ2806422

Emilie Blanc, Per Lötstedt, Stefan Engblom, Andreas Hellander

Publication date: 18 May 2016

Published in: Multiscale Modeling \& Simulation (Search for Journal in Brave)

Abstract: Subdiffusion has been proposed as an explanation of various kinetic phenomena inside living cells. In order to fascilitate large-scale computational studies of subdiffusive chemical processes, we extend a recently suggested mesoscopic model of subdiffusion into an accurate and consistent reaction-subdiffusion computational framework. Two different possible models of chemical reaction are revealed and some basic dynamic properties are derived. In certain cases those mesoscopic models have a direct interpretation at the macroscopic level as fractional partial differential equations in a bounded time interval. Through analysis and numerical experiments we estimate the macroscopic effects of reactions under subdiffusive mixing. The models display properties observed also in experiments: for a short time interval the behavior of the diffusion and the reaction is ordinary, in an intermediate interval the behavior is anomalous, and at long times the behavior is ordinary again.

Full work available at URL: https://arxiv.org/abs/1503.07009

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zbMATH Keywords

fractional derivativecontinuous-time random walksubdiffusionanomalous kineticsmultistate reaction-diffusion system

Mathematics Subject Classification ID

Diffusion processes (60J60) Reaction-diffusion equations (35K57) PDEs in connection with biology, chemistry and other natural sciences (35Q92) Fractional partial differential equations (35R11) Cell biology (92C37) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

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Cited In (11)

• Coupled mesoscopic and microscopic simulation of stochastic reaction-diffusion processes in mixed dimensions
• Subdiffusive Dynamics in Washboard Potentials: Two Different Approaches and Different Universality Classes
• Multiscale modeling of diffusion in a crowded environment
• Multiscale Simulation of Stochastic Reaction-Diffusion Networks
• Encounter-based reaction-subdiffusion model I: surface adsorption and the local time propagator
• Dynamical properties of subdiffusion in the bistable system with aperiodic inputs
• Stability and Strong Convergence for Spatial Stochastic Kinetics
• Effect of mesoscopic conservative phenomena in the dynamics of chemical reactions at the macroscopic scale
• Fractional Euler Limits and their Applications
• A model for reversible reaction in a subdiffusive regime
• Bimolecular reactive transport in a two-dimensional velocity field in disordered media

Uses Software

• SolvOpt
• BioNetGen
• URDME
• PySB
• STEPS
• MesoRD

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