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Ben Walker – Applied GMA Seminar
February 3, 2020 @ 4:00 pm - 5:00 pm
Title: Emergent Clustering from Pairwise Interactions in Polymer Genome Models
Abstract: The physical organization of chromosomes is known to be vital to cell function. Highly efficient compaction is achieved through various means, including histones, loop extrusion, and crosslinking. Prior work using a polymer bead-chain model of the nucleolus found that rapid crosslinking created multiscale structure, with pairwise bonds creating clusters creating nucleolar compaction and segregation. I explore this relationship, revealing the presence of an additional intermediate timescale that maximizes mixing. I present a network approach for leveraging temporal data to identify spatio-temporal clusters in the data. I further consider the problem of finding an effective energy landscape and temperature to explain the clustering dynamics as transmission over energy barriers. Naive averaging of the random crosslinking overestimates the barrier height; I propose an alternative inverse problem approach, and plan to apply use this technique to obtain estimates of clustering stability in future work.