Polymer Concepts in Biophysics

Title of dissertation: POLYMER CONCEPTS IN BIOPHYSICS Gregory Morrison, Doctor of Philosophy, 2008 Dissertation directed by: Devarajan Thirumalai Department of Chemistry and Biochemsitry The recent advent of experimental techniques that study biological systems on the level of a single molecule have lead to a number of exciting new results. These experiments have a variety of applications in understanding both the kinetics and equilibrium properties of biomolecules. By applying the concepts of polymer physics to these single molecule experiments, we are able to more fully understand the physical picture underlying a number of experimental observations. In this thesis, we use a variety of polymer models to develop a better understanding of many single molecule experiments. We show that the kinetics of loop formation in biopolymers can be generally understood as a combination of an equilibrium and dynamic part for a number of different polymer models. We study the extension of a homopolymer as a function of applied tension, and develop a simple theoretical framework for determining the effect of interactions on the stretching of the chain. We show that the measured hopping rates in a laser optical tweezer experiment are necessarily altered by the experimental setup, and suggest a method to accurately infer the correct hopping rates using accurately measured free energy profiles. We show that the effect of the experimental setup can be understood using a novel polymer model. Finally, we propose a Hamiltonian-based method to study the properties of spherically confined wormlike chains, which accurately determines the equilibrium properties of the system for strongly confined chains. In these studies, we are able to better understand the behavior of many disparate systems using relatively simple arguments from polymer theory. POLYMER CONCEPTS IN BIOPHYSICS