(A) Dynamics of loop array formation. Left, the fraction of the chromosome extruded into loops (loop coverage, gray) and the mean loop size (black). The time is measured in the units of condensin residence time. Data for each curve was obtained using 10 simulation replicas; the thickness of each line shows the difference between the 10th and 90th percentile at each time point. Right, a phase diagram showing loop coverage vs mean loop length. The curve is averaged over the simulation replicas and colored by log-time. Two stages of dynamics are separated by the two vertical dashed lines corresponding to 95% coverage and 95% of the steady state mean loop length. The distinction between the two stages of compaction is especially easy to see on the phase curve. (B) Dynamics of chromosome morphology. Left: chromosome length (blue) and the mean chromosome diameter (red) shown as a function of time; the thickness of each line shows the difference between the 10th and 90th percentile at each time point. Right, a phase diagram showing chromosome length vs diameter; the curve is averaged over the simulation replicas and colored by log-time. Note that most of chromosome linear compaction is achieved during the first phase, while the second is characterized by widening of the chromosome and further three-fold shortening. (C) Snapshots of polymer simulations. Top row: the conformations of chromosomes at the beginning of simulations (left), slightly before the transition between the loop formation and maturation stages (middle), and in the steady state (right). Color (rainbow: from red to blue) shows positions of individual monomers along the chain and demonstrates that loci in compacted chromosomes are arranged linearly according to their genomic location. Bottom row: same as above, with chromosomes shown in semitransparent gray and condensins as red spheres.