Abstract/Details

An improved short-DNA elasticity theory and a model of the dynamics of biological signaling networks


2010 2010

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Abstract (summary)

This thesis mainly focuses on three topics in mathematical biology. (1) A DNA elasticity theory for relatively short molecules. Single-molecule experiments rely on a model of the polymer force-extension behavior to calibrate the experiments. The worm-like chain (WLC) theory agrees well with experiments for long molecules. Recent single-molecule experiments use shorter molecules for which the WLC does not agree well. The finite worm-like chain (FWLC) theory takes into account boundary conditions and bead rotational fluctuations, which are important for relatively short molecules. (2) DNA entropic elasticity with a bend. Single-molecule experiments have studied the elasticity of DNA with helix-deforming proteins, including proteins that bend DNA. Previous theoretical work on bent DNA has examined a long DNA molecule with many non-specifically binding proteins. Recent experiments used relatively short DNA molecules with a single, well-defined bend site. This work predicts how the DNA force-extension relation changes due to the formation of a single permanent bend. (3) Dynamics of regulatory and signaling networks. Biological networks are generally robust to changes in genotype and environment. This work on networks addresses how network topology affects the network dynamics. Using a simple model of genes/proteins which interact with and regulate each other, this project addresses how network properties such as connection density and topology affect the ability of the network to show signaling dynamics.

Indexing (details)


Subject
Applied Mathematics;
Biophysics
Classification
0364: Applied Mathematics
0786: Biophysics
Identifier / keyword
Applied sciences; Biological sciences; Biological networks; DNA bend modelling; Mathematical biology; Signaling networks and dynamics; Single molecule experiments; Wagner's model; Worm-like chain theory
Title
An improved short-DNA elasticity theory and a model of the dynamics of biological signaling networks
Author
Li, Jinyu
Number of pages
124
Publication year
2010
Degree date
2010
School code
0051
Source
DAI-B 71/06, Dissertation Abstracts International
Place of publication
Ann Arbor
Country of publication
United States
ISBN
9781109780192
Advisor
Betterton, Meredith; Julien, Keith
Committee member
Lladser, Manuel; Perkins, Thomas; Restrepo, Juan
University/institution
University of Colorado at Boulder
Department
Applied Mathematics
University location
United States -- Colorado
Degree
Ph.D.
Source type
Dissertations & Theses
Language
English
Document type
Dissertation/Thesis
Dissertation/thesis number
3403944
ProQuest document ID
521853818
Copyright
Database copyright ProQuest LLC; ProQuest does not claim copyright in the individual underlying works.
Document URL
http://search.proquest.com/docview/521853818
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