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Numerical micropermeametry is performed on three dimensional porous samples having a linear size of approximately 3 mm and a resolution of 7.5 µm. One of the samples is a microtomographic image of Fontainebleau sandstone. Two of the samples are stochastic reconstructions with the same porosity, specific surface area, and two-point correlation function as the Fontainebleau sample. The fourth sample is a physical model which mimics the processes of sedimentation, compaction and diagenesis of Fontainebleau sandstone. The permeabilities of these samples are determined by numerically solving at low Reynolds numbers the appropriate Stokes equations in the pore spaces of the samples. The physical diagenesis model appears to reproduce the permeability of the real sandstone sample quite accurately, while the permeabilities of the stochastic reconstructions deviate from the latter by at least an order of magnitude. This finding confirms earlier qualitative predictions based on local porosity theory. Two numerical algorithms were used in these simulations.One is based on the lattice-Boltzmann method, and the other on conventional finite-difference techniques. The accuracy of these two methods is discussed and compared, also with experiment.

We introduce a new method for mesoscopic modeling of protein diffusion in an entire cell. This method is based on the construction of a three-dimensional digital model cell from confocal microscopy data. The model cell is segmented into the cytoplasm, nucleus, plasma membrane, and nuclear envelope, in which environment protein motion is modeled by fully numerical mesoscopic methods. Finer cellular structures that cannot be resolved with the imaging technique, which significantly affect protein motion, are accounted for in this method by assigning an effective, position-dependent porosity to the cell. This porosity can also be determined by confocal microscopy using the equilibrium distribution of a non-binding fluorescent protein. Distinction can now be made within this method between diffusion in the liquid phase of the cell (cytosol/nucleosol) and the cytoplasm/nucleoplasm. Here we applied the method to analyze fluorescence recovery after photobleach (FRAP) experiments in which the diffusion coefficient of a freely-diffusing model protein was determined for two different cell lines, and to explain the clear difference typically observed between conventional FRAP results and those of fluorescence correlation spectroscopy (FCS). A large difference was found in the FRAP experiments between diffusion in the cytoplasm/nucleoplasm and in the cytosol/nucleosol, for all of which the diffusion coefficients were determined. The cytosol results were found to be in very good agreement with those by FCS.

Crumpling a thin sheet of material into a small volume requires energy for creating a network of deformations such as vertices and ridges. Scaling properties of a single elastic vertex or ridge have been analysed theoretically, and crumpling of a sheet by numerical simulations. Real materials are however elasto-plastic and large local strains induce irreversible plastic deformations. Hence, a numerical model that can be purely elastic or elasto-plastic is introduced. In crumpled elastic sheets, the ridge patterns are found to be similar, independent of the width to thickness (L/h) ratio of the sheet, and the fractal dimension of crumpled sheets is given by scaling properties of the energy and average length of ridges. In crumpled elasto-plastic sheets, such a similarity does not appear as the L/h ratio affects the deformations, and the fractal dimension (Dpl) is thereby reduced. Evidence is also found of Dpl not being universal but dependent on the plastic yield point of the material.