Abstract/Details

Dynamics of gene networks with time delays


2009 2009

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Abstract (summary)

The study of time delays and their influence on gene network dynamics is the central topic of this thesis. Three different gene models with delay are studied: (1) a single gene-mRNA-protein model; (2) a multiple gene network model; (3) a continuous gene network model.

Chapters 2 and 3 present a brief introduction to the fields of gene regulatory networks and delay differential equations, respectively. Previous results relevant for this thesis are presented and a friendly overview with figures and examples is given. The purpose of these two chapters is to present a self-contained introduction of the main ideas to the rest of the thesis.

Chapter 4 presents a linear and nonlinear analysis of (1) a single gene-mRNA-protein system given by [special characters omitted]The study of this model is divided into three cases: Case 1: Perturbation Methods with Constant Delay; Case 2 : Center Manifold Reduction with Constant Delay; Case 3: Perturbation Methods with State-Dependent Delay.

Theoretical proof that the model exhibits oscillatory behavior of mRNA and protein expressions was found. The final outcome results in closed form expressions for the limit cycle amplitude and frequency of oscillation. An important result of these findings is the theoretical evidence that delays can drive oscillations in gene activity.

Chapter 5 presents a study of a network model of N coupled gene units. This analysis is the natural extension of a single-gene model by considering multiple gene-mRNA-protein units interconnected. Two different cases are studied and theoretical and numerical results are presented.

Chapter 6 presents a study of a continuous network model. The model takes the form [special characters omitted]where m = m(x, t), p = p(x, t), pd() = p(x¯, t − T), H is a Hill function, and where K(x − x¯) is a weighting function. We choose K(x − x¯ ) in two different ways K(x − x¯ ) = 1 and K(x − x¯) = e-|x−x¯ | which we name uniform and exponential weighting, respectively. Both of these cases are studied by either theoretical or numerical analysis, and a detailed stability study of the steady states is given. Closed form expressions for the critical delay Tcr and associated frequency ω are found. Finally, confirmation of our results are presented by discretizing the continuous system into an N-dimensional system and showing that the discrete results in Chapter 5 approach the continuous results as N→∞.

Indexing (details)


Subject
Genetics;
Mathematics
Classification
0369: Genetics
0405: Mathematics
Identifier / keyword
Pure sciences; Biological sciences; Bifurcation; Delays; Dynamics; Gene networks; Hopf
Title
Dynamics of gene networks with time delays
Author
Verdugo, Anael
Number of pages
171
Publication year
2009
Degree date
2009
School code
0058
Source
DAI-B 70/06, Dissertation Abstracts International
Place of publication
Ann Arbor
Country of publication
United States
ISBN
9781109231021
Advisor
Rand, Richard
University/institution
Cornell University
University location
United States -- New York
Degree
Ph.D.
Source type
Dissertations & Theses
Language
English
Document type
Dissertation/Thesis
Dissertation/thesis number
3363546
ProQuest document ID
304876643
Copyright
Database copyright ProQuest LLC; ProQuest does not claim copyright in the individual underlying works.
Document URL
http://search.proquest.com/docview/304876643/abstract
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