The Mechanical Genome in Regulation and Infection

Author: Chen, Yi-Ju

Year: 2015

Degree: Dissertation (Ph.D.)

Advisor: Phillips, Robert B.

Committee Members: Politzer, Hugh David; Roukes, Michael Lee; Cai, Long; Phillips, Robert B.

Option: Physics

DOI: 10.7907/Z9PC308X

Abstract

Biological information storage and retrieval is a dynamic process that requires the genome to undergo dramatic structural rearrangements. Recent advances in single-molecule techniques have allowed precise quantification of the nano-mechanical properties of DNA [1, 2], and direct in vivo observation of molecules in action [3]. In this work, we will examine elasticity in protein-mediated DNA looping, whose structural rearrangement is essential for transcriptional regulation in both prokaryotes and eukaryotes. We will look at hydrodynamics in the process of viral DNA ejection, which mediates information transfer and exchange and has prominent implications in evolution. As in the case of Kepler's laws of planetary motion leading to Newton's gravitational theory, and the allometric scaling laws in biology revealing the organizing principles of complex networks [4], experimental data collapse in these biological phenomena has guided much of our studies and urged us to find the underlying physical principles.

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