Effects of cross-linking on spatial organization and dynamics of confined associating polymers

We performed Langevin dynamics simulations of two confined polymers containing strongly associating stickers. We investigated the reorganization time scales of polymers cross-linked by sticker aggregates (clusters) and found that strong specific interactions lead to the formation of a polymer gel, with cluster reorganization times growing exponentially with interaction strength. We observed that increasing the strength of specific interactions between stickers promotes segregation and reduces the overlap between the polymers. The relevance of our results to the formation and maintenance of chromatin territories in eukaryotic nuclei is discussed.