Abstract:
Biological cells are crowded environments where macromolecular crowders significantly influence the conformation and dynamics of biopolymers, such as DNA and RNA. The conformations of polymers are not clearly understood in the presence of surface and crowders of various sizes. Motivated by this problem, we use coarse-grained molecular dynamics simulations to investigate the behavior of bead-spring polymers (ring vs linear) confined within an explicit bead-based wall in the presence of crowders of varying sizes and volume fractions (ϕ). Our results reveal stark, topology-dependent phenomena. We find that small crowders generate strong depletion forces that drive ring polymers into a sharply defined, flattened, and compacted state adsorbed onto the wall, even at moderate crowding fractions. In contrast, linear polymers exhibit a significantly higher threshold for adsorption, only gradually adhering to the wall at high crowder concentrations in the presence of free ends. Furthermore, large crowders create caging effects that sterically hinder mobility and suppress stable wall adsorption for both topologies. These findings demonstrate how crowder size and polymer topology synergistically regulate biopolymer compaction and surface localization. The distinct conformational states observed, such as the flattened adsorption of ring polymers, have significant biological implications.