Theoretical studies of chromosome folding as a consequence of molecular motor activity

dc.contributor.advisorThirumalai, Devarajan
dc.contributor.committeeMemberElber, Ron
dc.contributor.committeeMemberLeahy, Daniel J
dc.contributor.committeeMemberMakarov, Dmitrii E
dc.creatorDey, Atreya
dc.date.accessioned2024-03-26T23:19:29Z
dc.date.available2024-03-26T23:19:29Z
dc.date.created2023-12
dc.date.issued2023-12
dc.date.submittedDecember 2023
dc.date.updated2024-03-26T23:19:29Z
dc.description.abstractIn this thesis we develop theoretical models of how the molecular motor condensin folds the mitotic chromosome. In chapter 2 we simple theoretical models to discuss that the protein condensin must be a molecular motor. In chapter 3 we develop a theory for single condensin molecules. By fitting our theory to available experimental data, we predict the ATP hydrolysis rate and the magnitude of structural fluctuations in condensin. In chapter 4 we extend our single molecule theory of condensins, and show that multiple condensin molecules can dynamically come together to create fold the mitotic chromosome structure. We also use a data-driven model to show that mitotic chromosomes are helical with random helix perversions. In chapter 5, we provide a theoretical description of reverse stepping of condensin and predict that one of the states during the loop-extrusion process must involve a catch-bond like state. In chapter 6, we take a turn towards more a general polymer problem. We demonstrate that a deep neural network can approximately reconstruct the structure of a polymer from its contact map. Overall this thesis has derived theoretical and computational principles of chromosome folding.
dc.description.departmentChemistry
dc.format.mimetypeapplication/pdf
dc.identifier.uri
dc.identifier.urihttps://hdl.handle.net/2152/124447
dc.identifier.urihttps://doi.org/10.26153/tsw/51055
dc.language.isoen
dc.subjectDNA
dc.subjectBiophysics
dc.subjectChromosome
dc.subjectMolecular Biology
dc.titleTheoretical studies of chromosome folding as a consequence of molecular motor activity
dc.typeThesis
dc.type.materialtext
thesis.degree.departmentChemistry
thesis.degree.grantorThe University of Texas at Austin
thesis.degree.nameDoctor of Philosophy

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