Fig. 1: Polymer model based on experimentally obtained inputs and biologically relevant dynamics.

a The initial polymer strand is constructed using inputs from experimentally obtained sequencing data. The histone ChIP-seq data (through ChromHMM⁶¹) or Hi-C data are used to label the initial configuration of the polymer. We assign all repressed states to heterochromatin (red) and active states to euchromatin (blue) beads. b Lennard‒Jones pairwise potentials are defined for each pair of beads based on their epigenetic marking. \({\epsilon }_{{EE}},\,{\epsilon }_{{EH}}{and}{\epsilon }_{{HH}}\) are the euchromatin-euchromatin, euchromatin-heterochromatin and heterochromatin-heterochromatin bead interaction potential strengths, respectively. For all simulations in the manuscript, we choose \({\epsilon }_{{EE}}=0.3\) and \({\epsilon }_{{EH}}=1.0\). c The system is relaxed (bottom) from a random initial configuration (top) via Langevin dynamics. d Mean spatial distance vs. mean genomic distance obtained after polymer relaxation is plotted with the experimental data¹⁸. Simulation data presented as mean;+/− SD across 10 runs. e The simulated Hi-C map (upper triangle) shows the characteristic checkerboard pattern, which is observed in the experimental Hi-C map (lower triangle)³. f Diffusion of the nucleoplasm (water) is accounted for implicitly via Brownian dynamics. g Diffusion of epigenetic marks is modeled via an energy-based metropolis criterion for exchanging epigenetic marks between spatially neighboring beads. h Epigenetic reactions of acetylation (through the action of histone demethylase (HDM) and histone acetyltransferase (HAT)) and methylation (through the action of histone deacetylase (HDAC) and histone methyltransferase (HMT)) are modeled as Monte Carlo-based epigenetic reassignment processes.