Swagatam Mukhopadhyay

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Maintenance of alternative chromatin states through cell divisions pose some fundamental constraints on the dynamics of histone modifications. In this paper, we study the systems biology of epigenetic inheritance by defining and analyzing general classes of mathematical models. We discuss how the number of modification states involved plays an essential(More)
Long-distance regulatory interactions between enhancers and their target genes are commonplace in higher eukaryotes. Interposed boundaries or insulators are able to block these long-distance regulatory interactions. The mechanistic basis for insulator activity and how it relates to enhancer action-at-a-distance remains unclear. Here we explore the idea that(More)
Action across long distances on chromatin is a hallmark of eukaryotic transcriptional regulation. Although chromatin structure per se can support long-range interactions, the mechanisms of efficient communication between widely spaced DNA modules in chromatin remain a mystery. The molecular simulations described herein suggest that transient binary(More)
Tzu-Chieh Wei, Joseph B. Altepeter, David Branning,* Paul M. Goldbart, D. F. V. James, Evan Jeffrey, Paul G. Kwiat, Swagatam Mukhopadhyay, and Nicholas A. Peters Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3080, USA Theoretical Division, T-4, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA(More)
We introduce and analyze a minimal model of epigenetic silencing in budding yeast, built upon known biomolecular interactions in the system. Doing so, we identify the epigenetic marks essential for the bistability of epigenetic states. The model explicitly incorporates two key chromatin marks, namely H4K16 acetylation and H3K79 methylation, and explores(More)
We use the Allen Gene Expression Atlas (AGEA) and the OMA ortholog dataset to investigate the evolution of mouse-brain neuroanatomy from the standpoint of the molecular evolution of brain-specific genes. For each such gene, using the phylogenetic tree for all fully sequenced species and the presence of orthologs of the gene in these species, we construct(More)
A Landau theory is constructed for the gelation transition in cross-linked polymer systems possessing spontaneous nematic ordering, based on symmetry principles and the concept of an order parameter for the amorphous solid state. This theory is substantiated with help of a simple microscopic model of cross-linked dimers. Minimization of the Landau free(More)
Paul M. Goldbart,1,2 Swagatam Mukhopadhyay,1 and Annette Zippelius2,3 1Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3080, USA 2Kavli Institute for Theoretical Physics, University of California–Santa Barbara, California 93106, USA 3Institut für Theoretische Physik, Universität Göttingen, D-37073 Göttingen, Germany(More)