In the present study, a molecular based scheme has been developed for simulating flows in nano- and micro-channels with roughness. In micro channel flow, there is some difference on the flow friction between roughness and cavitations which is not well studied. The presented approach is based on the molecular dynamics (namely MD) in which different ensemble has been used. For modeling the simulation the classical Newtonian particles are allowed to obey Newtonian mechanics and intermolecular forces are founded by integrating intermolecular potential. Lennard-Jones potential is used to model the interactions between particles. Particles equation of motion is integrated using fifth order Gear predictor-corrector. To ensure rapid sampling of phase space, the time step is made as large as possible. Periodic boundary condition is implemented via minimum image convention. Each atom of the solid wall is anchored at its lattice site by a harmonic restoring force and its temperature has been controlled by utilizing Nose-Hoover thermostat. The roughness is implemented on the lower channel wall. To make a comparison between the effect of roughness and cavitation, the same dimension is used for both for different aspect ratio. To allow comparison with previous results the same fluid density has been used. The effects of surface roughness and cavitation on velocity distribution of hydrophobic and hydrophilic wall undergoing Poiseuille flow are presented.

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