This is a two-part project for the study of biomolecular dynamics using computer simulation. In the first part the time-dependence of the molecular motion of a protein in the multi-nanosecond range will be simulated using a multiple time step Langevin dynamics alogorithm to model experiments which measure how proteins move on time scales varying from a few nanoseconds to many tens of nanoseconds. NMR measurements and fast optical spectroscopy measurements following a laser pulse which gives the protein a shock will be considered. In the second part of the project, protein folding will be examined by fixing the beginning (unfolded) and ending (folded) conformations and examining various reaction paths leading from the unfolded to the folded conformation. The aim of the research is to study the kinds of folding trajectories which occur as the number of time steps allowed between the unfolded and folded states is increased.
