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Entropic repulsion between DNA ring polymers under confinement is the keymechanism governing the spatial segregation of bacterial chromosomes, althoughit remains incompletely understood how proteins aid the process of entropicsegregation. Here we establish that `internal' loops within a modified-ringpolymer architecture enhances entropic repulsion between two overlappingpolymers confined in a cylinder. Moreover it also induces entropy-drivenspatial organization of polymer segments as seen in-vivo. To that end, wedesign polymers of different architectures in our simulations, by introducing aminimal number of cross-links between particular monomers along the chaincontour. This helps us to identify the underlying mechanisms which lead tofaster segregation of spatially overlapping polymers as well as localization ofspecific polymer segments. The observed segregation dynamics of overlappingpolymers is aided in our simulations by the frequent release of topologicalconstraints, implemented by allowing chains to cross each at regular intervals.Additionally, we compare the segregation dynamics timescales with that ofself-avoiding polymers and thereby highlight the significance of Topoisomerasein biological systems where DNA-strands are allowed to occasionally passthrough each other. We use the blob model to provide a theoreticalunderstanding of why or how certain architectures lead to enhanced entropicrepulsive forces between loops, which in turn leads to the positionalorganization of segments relative to each other in confined environments.Lastly, we establish a correspondence between the C.crescentus bacterialspecies and our results for one particular polymer architecture.

The role of polymer architecture in the entropy driven segregation and spatial organization of bacterial chromosomes