Coarse-grained polymer simulations were performed using LAMMPS molecular dynamics software. Chains of identical monomers were simulated using BD with a Langevin thermostat. Each monomer represents a nucleosome core and has mass m = 1. Polymers up to ~150 kbp (1000 monomers) were simulated. Intermonomer bonds were formed between successive monomers using the finitely extensible nonlinear elastic potential

for K = 30.0, R0 = 1.5, ε = 1.0, σ = 1.0, and Δ = 4.0. An LJ potential was used to model pairwise interactions between all monomers and reinforce excluded volume effects

for σ = 1.0, Δ = 4.0, and rc = σ + 1.12246. D and s were modulated by tuning εLJ, the depth of the attractive LJ well potential, between 0 and 2.5. All simulations were first equilibrated, and all mass scaling and contact probability scaling calculations were performed on trajectory files generated by subsequent production runs. Mass scaling was calculated by first counting the number of monomers within a sphere of increasing radius with an origin at the center of mass of the polymer chain and then fitting the resulting relationship between the radius of sphere and mass using linear regression. Two beads were in contact if their coordinates were within a critical distance rcrit of each other in 3D space. Contact probability was calculated by summing up all observed contacts between monomers of a certain distance apart in the 1D linear chain overall 4D trajectories. A linear regression fit to the contact probability decay curve plotted against genomic distance was used to calculate contact probability scaling.

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