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Dynamics of DNA knots and links

Pekoske Fulton, Abby L. (2021) Dynamics of DNA knots and links. Doctoral Dissertation, University of Pittsburgh. (Unpublished)

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The goal of this work is to describe the dynamics of DNA knots and links in an ionized fluid. To do so, we employ three models: 1. The Generalized Immersed Boundary (GIB) method, which is a deterministic method that accounts for the fluid, structure interaction of an immersed DNA molecule in an ionized fluid; 2. The Stochastic Generalized Boundary (SGIB) Method, which is an extension of the GIB method that also takes into account the random thermal fluctuations within the fluid; 3. The Sequence Dependent SGIB method, which is a new extension of the SGIB method that accounts for the elastic properties of a specified DNA sequence. Using the GIB and SGIB methods, we explore the energy landscape of a closed DNA segment in a trefoil knot configuration. We first analyze the symmetry of stable knotted equilibrium configurations, approximate saddle configurations, and examine elastic energy throughout the deterministic process. We then use the SGIB method to model DNA knot dynamics as a continuous time Markov chain. We classify and find boundaries within the energy landscape using Procrustes distance. Finally, we obtain a steady state distribution for the Markov process given a fixed linking number and compare this to the Gibb's distribution from energy estimates obtained from the GIB method. Lastly, using the SD-SGIB method, we also explore the effects of sequence dependence in the formation of kinetoplast DNA (kDNA), which has a chainmail-like linked DNA structure. We do so by finding the distribution of centroid distances of two kDNA minicircles.


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Item Type: University of Pittsburgh ETD
Status: Unpublished
CreatorsEmailPitt UsernameORCID
Pekoske Fulton, Abby L.alp179@pitt.edualp179
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Committee ChairSwigon,
Committee MemberArsuaga,
Committee MemberSchikorra,
Committee MemberVainchtein,
Date: 8 October 2021
Date Type: Publication
Defense Date: 13 July 2021
Approval Date: 8 October 2021
Submission Date: 23 July 2021
Access Restriction: No restriction; Release the ETD for access worldwide immediately.
Number of Pages: 114
Institution: University of Pittsburgh
Schools and Programs: Dietrich School of Arts and Sciences > Mathematics
Degree: PhD - Doctor of Philosophy
Thesis Type: Doctoral Dissertation
Refereed: Yes
Uncontrolled Keywords: DNA dynamics, knotted DNA, linked DNA, Kinetoplast DNA, kDNA, GIB method, SGIB method, sequence dependent SGIB
Date Deposited: 08 Oct 2021 15:51
Last Modified: 08 Oct 2021 15:51

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