On hydrophobic surfaces, roughness may lead to a transition to a superhydrophobic state, where gas bubbles at the surface can have a strong impact on a detected slip. We present two-phase lattice Boltzmann simulations of a Couette flow over structured surfaces with attached gas bubbles. Even though the bubbles add slippery surfaces to the channel, they can cause negative slip to appear due to the increased roughness. The simulation method used allows the bubbles to deform due to viscous stresses. We find a decrease of the detected slip with increasing shear rate which is in contrast to some recent experimental results implicating that bubble deformation cannot account for these experiments. Possible applications of bubble surfaces in microfluidic devices are discussed.

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.

Capillary penetration of a wetting liquid in a microtomographic image of paper board, whose linear dimension was close to the average length of wood fibers, was simulated by the lattice-Boltzmann method. In spite of the size of the system not being large with respect to the size of structural inhomogeneities in the sample, for unidirectional penetration the simulated behavior was described well by that of the Lucas-Washburn equation, while for radial penetration a radial capillary equation described the behavior. In both cases the average penetration depth of the liquid front as a function of time followed a power law over many orders of magnitude. Capillary penetration of small droplets of liquid was also simulated in the same three-dimensional image of paper. In this case the simulation results could be described by a generalized form of the radial-penetration equation.

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