Semiflexible Polymers: Fundamental Theory and Applications in DNA Packaging

Citation

Spakowitz, Andrew James (2005) Semiflexible Polymers: Fundamental Theory and Applications in DNA Packaging. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/GGY2-SZ67. https://resolver.caltech.edu/CaltechETD:etd-11162004-120143

Abstract

Much is understood about the behavior of perfectly flexible and perfectly rigid polymer chains; however, many polymers, for example DNA, are somewhere in between these two limiting cases. Such polymers are termed semiflexible, and their molecular elasticity can play a significant role in single-chain behavior as well as contribute to collective effects. Using analytical theory and numerical methods, we address several problems that focus on the equilibrium and dynamic behavior of semiflexible polymers to gain a deeper understanding of their fundamental physics. We consider the equilibrium statistical behavior of semiflexible polymers under the influence of external fields, confinement, and the collective influence of a nematic liquid-crystal phase. We then turn to the dynamics of a deformed elastic thread, addressing instances of instability and the subsequent nonlinear relaxation. Once we establish an understanding of these physical effects, we discuss the role that they play in DNA packaging, specifically focusing on the role of twist in DNA packaging in chromatin and the formation of an ordered conformation within a viral capsid.

Thesis Files