Figure 1. Illustration of the residue-level coarse-grained explicit ion model for chromatin simulations.

The left panel presents a snapshot for the simulation box of a 147 bp nucleosome in a solution of 100 mM NaCl and 0.5 mM MgCl₂. The nucleosomal DNA and histone proteins are colored in red and white, respectively. The zoom-in on the right highlights the condensation of ions around the nucleosome, with Na⁺ in cyan and Mg²⁺ in yellow. Negative residues of the histone proteins are colored in pink.