Conventional computational methods available today for studying macromolecules and their complexes are limited to simulating short time frames and are insufficient to study processes of interest related to their function that usually occur In nature on longer time scales. Alternative methods that extend our capabilities continue to be proposed, and most often involve some kind of reduction In complexity or representation in order to simulate these biological processes on longer time and length scales. The ability to investigate through simulation the structural and functional properties of protein macromolecular complexes IS of particular importance in the field of bionanotechnology, whose goal IS to harness nanoscale devices made from or inspired by biological counterparts. Clearly then, methods are needed that can capture the large changes seen In macromoleculat assemblies to elucidate important principles of their structure and function and apply these to the nanomachines envisaged in bionanotechnology. At the forefront of this field lie the nanomotors, whose biological counterparts, the molecular protein motors, are used in cells to drive a host of essential processes with an amazing degree of efficiency and precision. The work in this thesis describes the development of a hierarchic modeling paradigm applied toward simulating the processi ve movement of the molecular myos m motor protein along an actin filament track. In the hierarchic model, three different levels of protein structure resolution are represented, with the level of detail changing according to the degree of interaction among the molecules, the integrity of which is maintained using a tree of spatially organized bounding volumes. Although applied to an acto-myosin system, the hierarchic framework is general enough so that it may easily be adapted to a number of other biomolecular systems of interest within the bionanotechnology field.