Figure 3.

Simulations reveal local compaction of individual topological domains. Snapshot from the simulation run that provided the data for Figure 1B. One chromatin fragment consisting of two supercoiled topological domains with sizes corresponding to 800 and 400 kb was simulated under periodic boundary conditions. For better visibility, one of the periodic copies of the simulated fragment composed of two supercoiled topological domains is partially ‘extracted’ from highly crowded melt composed of other periodic copies of the same molecule. The image shows eight periodic copies of the actual simulation box. Notice local compaction of individual supercoiled topological domains.