Conventional fluid mechanics (Navier–Stokes equations with linear constitutive relations) is, on the whole, applicable for simulating very small scale liquid and gas systems. This changes (for simple fluids) only in the vicinity of solid surfaces (approximately 5 molecular diameters for liquids, or one mean free path for gases) or under very high temperature or velocity gradients. It is shown that typical experimental conditions in practical systems do not give rise to gradients of this magnitude. Therefore, only surface effects cause significant deviation from results expected by conventional fluid mechanics. In micro and nano systems, however, large surface area to volume ratio means that the detail of boundary conditions and near surface dynamics can dominate the flow characteristics. In this paper, the use of non–equilibrium molecular dynamics (NEMD) to study these fluid mechanics problems in an engineering simulation context is discussed. The extent of systems that can be studied by NEMD, given current computational capabilities, is demonstrated. Methods for reducing computational cost, such as hybridisation with continuum based fluid mechanics and extracting information from a small representative systems are also discussed. Non–equilibrium surface effects in gas micro systems may also been studied using NEMD. These occur at boundaries in the form of discontinuities (velocity slip and temperature jump) and within approximately one mean free path of a surface, in the form of a Knudsen layer. The distributions of molecular velocities, free path between collisions and time spent in collision have been calculated for an unbounded equilibrium fluid. The influence of a solid surface on the state of a fluid or flow can be investigated by measuring how these fundamental properties are affected.

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