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Diffusion processes in the lumen as well as on the membrane of the endoplasmic reticulum of tissue derived cells are investigated using a computational approach based on particle methods. A simulation code is presented that can handle arbitrary geometries as found in real cells, sources, sinks, separator planes and full anisotropic and spatially dependent diffusion. Using this tool it is possible to simulate fluorescence recovery after photobleaching (FRAP) in different geometries and dimensions in order to compare the results. Dependences of the apparent diffusion constant determined in experiments on geometrical factors such as dimensionality of space, surface shape or tube distribution can be addressed. Considerations about 3D shape reconstruction and fractal properties of the endoplasmic reticulum conclude this work.

On protein diffusion in the endoplasmic reticulum: a computational approach using particle simulations