Figure 2.

Snapshots of chromatin configurations and the corresponding contact probabilities between k^th neighbor nucleosomes (I(k)) in the absence (NHP−) and presence (NHP+) of DNA-bending nonhistone proteins (NHPs) that bind along linker DNA regions. The results are presented for four cases, as follows: case 1: simulations with no NHPs and no electrostatic interactions (left column of (a), and (b)); case 2: no NHPs but with electrostatic interactions (right column of (a), and (c)); case 3: with NHPs and no electrostatic interactions (left column of (d), and (e)); case 4: with NHPs and with electrostatic interactions (right column of (d), and (f)). All the results are presented for three different strengths of LJ (ɛ) interaction potentials (see text for details).