Simulations of (an)isotropic diffusion on curved biological surfaces.
We present a computational particle method for the simulation of isotropic and anisotropic diffusion on curved biological surfaces that have been reconstructed from image data. The method is capable of handling surfaces of high curvature and complex shape, which are often encountered in biology. The method is validated on simple benchmark problems and is shown to be second-order accurate in space and time and of high parallel efficiency. It is applied to simulations of diffusion on the membrane of endoplasmic reticula (ER) in live cells. Diffusion simulations are conducted on geometries reconstructed from real ER samples and are compared to fluorescence recovery after photobleaching experiments in the same ER samples using the transmembrane protein tsO45-VSV-G, C-terminally tagged with green fluorescent protein. Such comparisons allow derivation of geometry-corrected molecular diffusion constants for membrane components from fluorescence recovery after photobleaching data. The results of the simulations indicate that the diffusion behavior of molecules in the ER membrane differs significantly from the volumetric diffusion of soluble molecules in the lumen of the same ER. The apparent speed of recovery differs by a factor of approximately 4, even when the molecular diffusion constants of the two molecules are identical. In addition, the specific shape of the membrane affects the recovery half-time, which is found to vary by a factor of approximately 2 in different ER samples.
Sbalzarini
Ivo F
IF
Institute of Computational Science, and Institute of Biochemistry, ETH Zürich, Switzerland.
Hayer
Arnold
A
Helenius
Ari
A
Koumoutsakos
Petros
P
D000818:Animals; D016880:Anisotropy; D001703:Biophysics / Q000379:methods*; D002462:Cell Membrane / Q000378:metabolism; D002522:Chlorocebus aethiops; D004247:DNA / Q000737:chemistry; D004058:Diffusion; D004721:Endoplasmic Reticulum / Q000378:metabolism*; D036681:Fluorescence Recovery After Photobleaching; D049452:Green Fluorescent Proteins / Q000737:chemistry; D008853:Microscopy; D008958:Models, Molecular; D008962:Models, Theoretical; D013499:Surface Properties; D013997:Time Factors; D014709:Vero Cells
D049452:Green Fluorescent Proteins; D004247:DNA