title: Are assumptions about the model type necessary in reaction-diffusion modeling? A FRAP application.
abstract: At present, fluorescence recovery after photobleaching (FRAP) data are interpreted using various types of reaction-diffusion (RD) models: the model type is usually fixed first, and corresponding model parameters are inferred subsequently. In this article, we describe what we believe to be a novel approach for RD modeling without using any assumptions of model type or parameters. To the best of our knowledge, this is the first attempt to address both model-type and parameter uncertainties in inverting FRAP data. We start from the most general RD model, which accounts for a flexible number of molecular fractions, all mobile, with different diffusion coefficients. The maximal number of possible binding partners is identified and optimal parameter sets for these models are determined in a global search of the parameter-space using the Simulated Annealing strategy. The numerical performance of the described techniques was assessed using artificial and experimental FRAP data. Our general RD model outperformed the standard RD models used previously in modeling FRAP measurements and showed that intracellular molecular mobility can only be described adequately by allowing for multiple RD processes. Therefore, it is important to search not only for the optimal parameter set but also for the optimal model type.
authors.affiliation: Department of Computational Hydrosystems, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany. juliane.mai@ufz.de
authors.forename: Juliane
authors.initials: J
authors.lastname: Mai
authors.forename: Saskia
authors.initials: S
authors.lastname: Trump
authors.forename: Rizwan
authors.initials: R
authors.lastname: Ali
authors.forename: R Louis
authors.initials: RL
authors.lastname: Schiltz
authors.forename: Gordon
authors.initials: G
authors.lastname: Hager
authors.forename: Thomas
authors.initials: T
authors.lastname: Hanke
authors.forename: Irina
authors.initials: I
authors.lastname: Lehmann
authors.forename: Sabine
authors.initials: S
authors.lastname: Attinger
mesh_terms: D000465:Algorithms; D004058:Diffusion; D036681:Fluorescence Recovery After Photobleaching; D007700:Kinetics; D008954:Models, Biological; D035501:Uncertainty