#10 · Epigenomics

Simulations link chromatin accessibility and polymer physics to genome organization

The dominant thread is mechanistic simulation of physical models in which a small set of specific interactions or state variables is distinguished from a larger background of nonspecific effects. In the E. coli study, polymer simulations separate confinement from the fewer than 7% of Hi-C-associated interactions that are specific folding interactions. A lattice and mean-field study shows that surface condensation of ligands on DNA converts small concentration differences into amplified transcriptional sensitivity. A stochastic biophysical model couples loop extrusion motor stepping to chromatin accessibility and nucleosome compaction, yielding non-monotonic speed behavior. The bacterial community study shares the simulation-based approach, combining agent-based simulation with a drift-diffusion model, but addresses ecological rather than genomic scales. What is new across these items is the explicit coupling of physical state variables, such as condensation, compaction, and confinement, to measurable outputs within simulation frameworks.