Diffusion in inhomogeneous media: theory and simulations applied to whole cell photobleach recovery

Biophys J. 2000 Oct;79(4):1761-70. doi: 10.1016/S0006-3495(00)76428-9.


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.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Animals
  • Biophysical Phenomena
  • Biophysics
  • Cells / metabolism*
  • Diffusion
  • Endoplasmic Reticulum / metabolism
  • Green Fluorescent Proteins
  • Intracellular Membranes / metabolism
  • Luminescent Proteins / metabolism
  • Membrane Proteins / metabolism
  • Models, Biological*
  • Recombinant Fusion Proteins / metabolism


  • Luminescent Proteins
  • Membrane Proteins
  • Recombinant Fusion Proteins
  • Green Fluorescent Proteins