Theoretical studies of biomolecular self-assembly near equilibrium and far from equilibrium

The physical sciences have played a pre-eminent role in the advance of biology not only by providing advanced techniques, but also by providing simple concepts for navigating through the complexity of biological systems. One area where simple physics concepts help understanding complicated biological phenomena is the study of protein folding. By presenting the framework of a simple funneled energy landscape, folding is no longer a paradox from the physics point of view. In the following chapters, we present the investigations of both thermodynamics (predicting native structure) and kinetics (predicting phi -values) of protein folding on the basis of energy landscape theory. On the other hand, the discovery of assembly using biological molecular machinery presents new challenges to statistical mechanics combining the aspects of complexity and far-from-nonequilibrium behavior. In the fifth chapter, a study of nonequilibrium dynamic assembly inspired by microtubule dynamics in cell is presented. The theory provide a general scheme for studying nonequilibrium assembly in one dimension. Chapter 2 is based on the material as it appears in Biochemistry 45: 6458-6466 (2006). The dissertation author was the primary investigator and author of this paper. Chapter 3 is based on the material as it appears in Proc. Natl. Acad. Sci. 104: 3159-3164 (2007). The dissertation author was the primary investigator and author of this paper. Chapter 4 is based on the material as it appears in J. Am. Chem. Soc. 128: 5168-5176 (2006). The dissertation author was the primary investigator and author of this paper. Chapter 5 is based on the material as it appears in Physical Biology, 3: 83-92 (2006). The dissertation author was the primary investigator and author of this pape