Fig. 3.
Chains of nontrivial topology and their typical conformations in strong confinement. (A) A schematic representation of the slowly evolving topology of circular chromosome during replication. (Note: not to be confused with actual polymer conformations.) (B) Results of two stages of the replication process, indicated by the vertical gray bar in A, namely, the asymmetric and symmetric figure-θ conformations, respectively. For each case, a snapshot of a typical conformation is shown (top of each image) and the spatial distribution of the midpoints of the colored segments (blue, red, and gray) around their average position (bottom of each image). (C) The conformation of a figure-eight chain consisting of a total of 2,047 beads (>120 times the width D of the box) in a rod-shaped box of aspect ratio 6. Note the mirror-like, linear ordering of the chain within the rod-shaped geometry, although each bead shows a positional fluctuation comparable with the size of the confinement width D.