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Abstract
Although it is now common to look at the information carried by the genome as a linear sequence of nucleotides, such representation does not say much about the organization of the genetic information within the cell nucleus. How the genome accommodates the tight packing needed to fit in the cell nucleus and at the same time maintains the accessibility necessary for specific expression is one of the open questions in modern biology. In eukaryotic cells, DNA is wrapped and packaged into chromatin through the binding of histones assembled into nucleosomes. In addition to bundling DNA, the nucleosomes also facilitate communication between distant genomic sites, such as enhancers and promoters found at the ends of protein-mediated loops. In order to understand the physical and chemical basis of such processes, we have begun to investigate chromatin organization and looping. We have developed a mesoscale model of chromatin at a resolution of a single base pair and used Monte Carlo numerical strategies to unders...
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