A hybrid molecular dynamics/multiparticle collision dynamics algorithm was constructed to model the pressure-driven flow of a compressible fluid through a nanoscopic channel of square cross-sectional area, as well as the effect of this flow on the configuration of a polymer chain that was tethered to the surface of this nanochannel. In the process of simulating channel flow, a new adiabatic partial slip boundary condition was created as well as a modified source/sink inlet and outlet boundary condition that could maintain a specified pressure gradient across the channel without the large entrance effects typically associated with these algorithms. The results of the flow simulations were contrasted with the results from a series solution to the Navier-Stokes equation for isothermal compressible flow, and showed excellent agreement with the results from the series solution when slip-boundary conditions were applied. A finitely extendible non-linear elastic spring and bead polymer chain was used to simulate the effect of flow on the polymer chain configuration under poor solvent and θ solvent conditions. Under θ solvent conditions, the cyclical dynamics that have been previousy observed for tethered polymer chains in pure shear flows were noted, however they were restricted to the end of the polymer chain. Under poor solvent conditions, the polymer adopted a metastable helix configuration as it collapsed to a globule state. The study also examined interchain and intrachain entanglements in polymers using the granny knot and overhand knot. The mechanisms by which these tangles untied themselves were determined. At low flow rates, the tangles unravelled by the end of the chain migrating through the loops of the tangle. At high flow rates, the tangles behaved like an entrained object as they reptated towards the end of the chain.

A hybrid molecular dynamics/multiparticle collision dynamics algorithm was constructed to model the pressure-driven flow of a compressible fluid through a nanoscopic channel of square cross-sectional area, as well as the effect of this flow on the configuration of a polymer chain that was tethered to the surface of this nanochannel. In the process of simulating channel flow, a new adiabatic partial slip boundary condition was created as well as a modified source/sink inlet and outlet boundary condition that could maintain a specified pressure gradient across the channel without the large entrance effects typically associated with these algorithms. The results of the flow simulations were contrasted with the results from a series solution to the Navier-Stokes equation for isothermal compressible flow, and showed excellent agreement with the results from the series solution when slip-boundary conditions were applied. A finitely extendible non-linear elastic spring and bead polymer chain was used to simulate the effect of flow on the polymer chain configuration under poor solvent and θ solvent conditions. Under θ solvent conditions, the cyclical dynamics that have been previousy observed for tethered polymer chains in pure shear flows were noted, however they were restricted to the end of the polymer chain. Under poor solvent conditions, the polymer adopted a metastable helix configuration as it collapsed to a globule state. The study also examined interchain and intrachain entanglements in polymers using the granny knot and overhand knot. The mechanisms by which these tangles untied themselves were determined. At low flow rates, the tangles unravelled by the end of the chain migrating through the loops of the tangle. At high flow rates, the tangles behaved like an entrained object as they reptated towards the end of the chain.