Understanding the energetics of biomolecules on an atomic level is of interest to many fields from physics to medicine. Towards that goal, we present work on three areas of interest. A statistical mechanical algorithm, MDMC, for increasing the efficiency of equilibrium calculations of a rigid polymer (e.g. a globular protein) in solution is developed and rigorously proven to yield the correct canonical results.; The difference between hydrophobic hydration of infinite hydrophobic slabs and finite edge slabs is investigated to test the validity of approximating macromolecular surfaces as infinite surfaces. A ‘mesoscale effect’ is identified, whereby water near a hydrophobic surface is observed to have a different structure if it is in contact with the bulk than if it is not. The implications of this result to intracellular processes, such as protein folding and enzyme docking are discussed.; The calculation of the long-range terms in ionic solutions between infinite surfaces is discussed, and a method for efficient calculation of these interactions is developed for systems of slab and pore geometries. A possible approach to three dimensional systems is also discussed.
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