| In this Thesis, physics-based models of protein folding at the secondary and tertiary level are developed to resolve long-standing issues of protein folding kinetics. As discussed in the Introduction, the main objective is to provide fundamental limits on the length and time scales involved in protein folding. Protein folding is also placed within the broader context of macromolecular dynamics, which is extensively studied in the unfolded, folded, and unfolding regimes for the key molecular motifs of cellular biochemistry, including lipids, nucleic acids, and proteins. The effect of the water hydration and temperature are systematically probed to elucidate the crucial role of the environment in macromolecular stability and dynamics. For a wide range of bio-molecular phenomena, the observed collective behavior is shown to arise directly from first principles. Throughout, the emphasis is on analytic results free of tunable parameters, supported by ensemble-converging computational simulations, and corroborated by experimental evidence. |
