A three-dimensional numerical simulation of flow in patterned microchannel with alternate layers of hydrophilic and hydrophobic surfaces at the bottom wall is studied here. Surface characteristics of the microchannel are accounted by specifying the contact angle and the surface tension of the fluid. Meniscus profiles with varying amplitude and shapes are obtained under the different specified surface conditions. Flow instability increases as the fluid at the bottom wall traverses alternately from hydrophilic region to hydrophobic region. To understand the surface tension effect of the side walls, a two-dimensional numerical study has also been carried out for the microchannel and the results are compared with three-dimensional simulation. The surface tension effect of the side walls enhances the capillary effect for three-dimensional case.

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