Theoretical and computational studies of bio-molecular systems : structure and dynamics

Abstract

The research presented in this thesis is relevant for the study of structure, function and dynamics of complex bio-molecular systems. The thesis contains two parts related to (1) protein structure prediction, and (2) free energy profile calculations in nano-scale systems. The new contributions reported in this thesis include (1) the development of the Selective Refinement (SR) protocol and the extension of the Molecular Dynamics Ranking (MDR) selection method for protein structure prediction, and (2) the formulation of the generalized FR (GFR) method for calculating the potential of mean force and the determination of the effective dynamics along one dimensional reaction coordinates in bio-molecular systems.