title: Diffusion in inhomogeneous media: theory and simulations applied to whole cell photobleach recovery.
abstract: A continuum description for diffusion in a simple model for an inhomogeneous but isotropic media is derived and implemented numerically. The locally averaged density of diffusible marker is input from experiment to define the sample. Then a single additional parameter, the effective diffusion constant, permits the quantitative simulation of diffusive relaxation from any initial condition. Using this simulation, it is possible to model the recovery of a fluorescently tagged protein in the endoplasmic reticulum (ER) after photobleaching a substantial region of a live cell, and fit an effective diffusion constant which is a property both of the geometry of the ER and the marker. Such quantitative measurements permit inferences about the topology and internal organization of this organelle.
authors.affiliation: Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399, USA. siggia@eds1.rockefeller.edu
authors.forename: E D
authors.initials: ED
authors.lastname: Siggia
authors.forename: J
authors.initials: J
authors.lastname: Lippincott-Schwartz
authors.forename: S
authors.initials: S
authors.lastname: Bekiranov
mesh_terms: D000465:Algorithms; D000818:Animals; D055592:Biophysical Phenomena; D001703:Biophysics; D002477:Cells / Q000378:metabolism*; D004058:Diffusion; D004721:Endoplasmic Reticulum / Q000378:metabolism; D049452:Green Fluorescent Proteins; D007425:Intracellular Membranes / Q000378:metabolism; D008164:Luminescent Proteins / Q000378:metabolism; D008565:Membrane Proteins / Q000378:metabolism; D008954:Models, Biological; D011993:Recombinant Fusion Proteins / Q000378:metabolism
chemical_list: D008164:Luminescent Proteins; D008565:Membrane Proteins; D011993:Recombinant Fusion Proteins; D049452:Green Fluorescent Proteins