| In this thesis, the application of classical molecular dynamics to a variety of molecular problems is described. Specifically, the application of MD to three disparate problems; equilibrium versus non-equilibrium treatments of the solvent response to chlorine dioxide photoexcitation, the dissociation of single-strand DNA from carbon nanotubes, and catch-slip bond transition in biological adhesion, is discussed. We see a strong similarity in results when comparing the equilibrium to the non-equilibrium results for the solvent response to chlorine dioxide photoexcitation. In addition, the non-equilibrium results also support the conclusion that this response is dominated by short-ranged mechanical forces. The MD studies of the single-strand DNA and carbon-nanotube complexes provide a description of a dissociation mechanism. We simulated the dissociation of biological adhesion for p-selectin/PSGL-1 complexes using steered molecular dynamics. The resulting trajectories, along with solutions of a two-pathway analytical model, offer support for a sliding-rebinding model that describes the catch-slip bond transition behavior observed experimentally. Through this work, we find that classical molecular dynamics is powerful and versatile in its ability to study a wide range of molecular systems. |
