#28 · Epigenomics

Chromatin and mitotic folding models coupled to measured observables

The dominant thread is coarse-grained mechanistic modeling constrained by experimental data. A chemical-reaction network of cohesin loop-extrusion regulation is fit to in vivo measurements and integrated into polymer simulations of interphase chromatin. A hybrid motorized polymer model of mitotic chromosome folding attributes scaffold formation to condensin II and a helical loop arrangement. A minimal vertex model of epithelial tissue is a separate mechanics case that links cell shape to mechanical energy and shows centroidal Voronoi tiling in rigid regimes, sharing the modeling approach rather than the chromatin system. What is new in the cohesin study is explicit fitting of a mechanistic model to measured observables, rather than simulation alone.