ON THE PHYSICAL AND CHEMICAL DYNAMICS OF CHROMATIN By

The research performed leading to this dissertation is an endeavor to explore two broad classes of developmental phenomena in the chromatin complex in eukaryotic cells — phys-ical, 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 pro-ceed 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 in-voked 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 feedbac