  Entropic repulsion between DNA ring polymers under confinement is the key
mechanism governing the spatial segregation of bacterial chromosomes, although
it remains incompletely understood how proteins aid the process of entropic
segregation. Here we establish that `internal' loops within a modified-ring
polymer architecture enhances entropic repulsion between two overlapping
polymers confined in a cylinder. Moreover it also induces entropy-driven
spatial organization of polymer segments as seen in-vivo. To that end, we
design polymers of different architectures in our simulations, by introducing a
minimal number of cross-links between particular monomers along the chain
contour. This helps us to identify the underlying mechanisms which lead to
faster segregation of spatially overlapping polymers as well as localization of
specific polymer segments. The observed segregation dynamics of overlapping
polymers is aided in our simulations by the frequent release of topological
constraints, implemented by allowing chains to cross each at regular intervals.
Additionally, we compare the segregation dynamics timescales with that of
self-avoiding polymers and thereby highlight the significance of Topoisomerase
in biological systems where DNA-strands are allowed to occasionally pass
through each other. We use the blob model to provide a theoretical
understanding of why or how certain architectures lead to enhanced entropic
repulsive forces between loops, which in turn leads to the positional
organization of segments relative to each other in confined environments.
Lastly, we establish a correspondence between the C.crescentus bacterial
species and our results for one particular polymer architecture.
