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On the physical and chemical dynamics of chromatin
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Apratim, Manjul. On the physical and chemical dynamics of chromatin. Retrieved from https://doi.org/doi:10.7282/T3P849P8

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TitleOn the physical and chemical dynamics of chromatin
NameApratim, Manjul (author); Sengupta, Anirvan M (chair); Bhanot, Gyan (internal member); Friedan, Daniel H (internal member); Morozov, Alexandre V (internal member); Mehta, Pankaj (outside member); Rutgers University; Graduate School - New Brunswick
Date Created2012
Other Date2012-10 (degree)
SubjectPhysics and Astronomy, Chromatin, Eukaryotic cells--Research
Extentxvii, 225 p. : ill.
DescriptionThe research performed leading to this dissertation is an endeavor to explore two broad classes of developmental phenomena in the chromatin complex in eukaryotic cells --- physical, for instance, long range interactions between enhancers and promoters, and chemical, such as epigenetic chromatin silencing. I begin by introducing the reader to both types of phenomena, and then set the stage for our strategy in the exploration of the physical side of these processes by creating a new machinery from existing pieces of polymer physics. I then make a brief foray into theoretical realms in an attempt to answer the question of what kinds of conformations of polymers dominate in what regimes. Subsequently, I proceed to consider the problem of analyzing and interpreting data from a major technique of probing the behavior of the chromatin complex in vivo --- Chromosome Conformation Capture --- towards which end we have developed and implemented a new and robust algorithm called `G.R.O.M.A.T.I.N.'. Subsequently, I explore how similar ideas may be invoked in the analysis of direct microscopic observations of native chromatin structure via Fluorescence in situ Hybridization. Following this, I look at the problems of epigenetic chromatin silencing domain formation and stability in the presence of titration feedback and of stochastic noise, and demonstrate how the widely accepted polymerization model of silencing is consistent with Chromatin Immunoprecipitation data from silencing domains in budding yeast. I finally conclude with musings on recent evidence pinpointing the need to unify the physical and chemical pictures into one grand formulation.
NotePh.D.
NoteIncludes bibliographical references
NoteIncludes vita
Noteby Manjul Apratim
Genretheses, ETD doctoral
Persistent URLhttps://doi.org/doi:10.7282/T3P849P8
Languageeng
CollectionGraduate School - New Brunswick Electronic Theses and Dissertations
Organization NameRutgers, The State University of New Jersey
RightsThe author owns the copyright to this work.
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