A reaction–subdiffusion model of fluorescence recovery after photobleaching (FRAP)

DOI10.1088/1742-5468/2014/11/P11014zbMATH Open1456.92068arXiv1407.8226MaRDI QIDQ3301797FDOQ3301797

Authors: Katja Lindenberg, S. B. Yuste, Enrique Abad 

Publication date: 11 August 2020

Published in: Journal of Statistical Mechanics: Theory and Experiment (Search for Journal in Brave)

Abstract: Anomalous diffusion, in particular subdiffusion, is frequently invoked as a mechanism of motion in dense biological media, and may have a significant impact on the kinetics of binding/unbinding events at the cellular level. In this work we incorporate anomalous diffusion in a previously developed model for FRAP experiments. Our particular implementation of subdiffusive transport is based on a continuous time random walk (CTRW) description of the motion of fluorescent particles, as CTRWs lend themselves particularly well to the inclusion of binding/unbinding events. In order to model switching between bound and unbound states of fluorescent subdiffusive particles, we derive a fractional reaction-subdiffusion equation of rather general applicability. Using suitable initial and boundary conditions, this equation is then incorporated in the model describing two-dimensional kinetics of FRAP experiments. We find that this model can be used to obtain excellent fits to experimental data. Moreover, recovery curves corresponding to different radii of the circular bleach spot can be fitted by a single set of parameters. While not enough evidence has been collected to claim with certainty that CTRW is the underlying transport mechanism in FRAP experiments, the compatibility of our results with experimental data fuels the discussion as to whether normal diffusion or anomalous diffusion is the appropriate model, and as to whether anomalous diffusion effects are important to fully understand the outcomes of FRAP experiments. On a more technical side, we derive explicit analytic solutions of our model in certain limits.

Full work available at URL: https://arxiv.org/abs/1407.8226

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Mathematics Subject Classification ID

Applications of Brownian motions and diffusion theory (population genetics, absorption problems, etc.) (60J70) Biochemistry, molecular biology (92C40) Classical flows, reactions, etc. in chemistry (92E20)

Cites Work

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Cited In (17)

• Nonlinear theory of anomalous diffusion and application to fluorescence correlation spectroscopy
• A general framework for fractional order compartment models
• Modeling subdiffusion using reaction diffusion systems
• Generalized continuous time random walks, master equations, and fractional Fokker-Planck equations
• An integral relationship for a fractional one-phase Stefan problem
• Extrapolating for attaining high precision solutions for fractional partial differential equations
• Expanding the scope of quantitative FRAP analysis
• Mathematical modelling of subdiffusion-reaction systems
• Fractional diffusion equations coupled by reaction terms
• Fractional order compartment models
• Principles of modeling the fluorescence spectral dynamics of dye molecules in solutions
• Anomalous diffusion with an irreversible linear reaction and sorption-desorption process
• Computational modeling of fluorescence loss in photobleaching
• A class of exact solutions for biomacromolecule diffusion-reaction in live cells
• Experiment Setups and Parameter Estimation in Fluorescence Recovery After Photobleaching Experiments: A Review of Current Practice
• A hidden Markov model approach to characterizing the photo-switching behavior of fluorophores
• A data-driven alternative to the fractional Fokker-Planck equation

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