Behavior of ring polymers under 1D confinement

Most of the research on polymers under nanoscale confinement have focused on linear polymers, finding that a decrease in entanglement density can accelerate their dynamics. Ring polymers, being more difficult to synthesize and purify, have not been well-studied in similar conditions. However, biophysicists have an interest in the behavior of ring polymers under confinement since they model circular DNA packed tightly inside the nucleus of a cell.

Zhang et al. performed molecular dynamics simulations of ring polymers confined in one dimension to investigate their chain conformations and dynamics. Their results indicate a pronounced chain length dependence in the self-density profile. Compared to their linear counterparts, the ring polymers had a larger maximum self-density that increases with ring size.

The molecular simulations involved slowly compressing the ring polymers within a thin film at a slow rate to ensure stability. The researchers varied the number of monomers per chain as well as the thickness of the confining thin film.

The monomer density near the wall did not show a difference between linear versus ring polymers, nor did it change with a difference in chain length. But for the center-of-mass density profile, the peak adjacent to the walls of linear polymers was much smaller than that of the ring polymers. Also, smaller rings of 50 or 100 monomers per chain exhibit a peak close to the wall, while the density profile flattens out for larger rings. Similar to linear polymers, the ring polymer chains were stretched along the parallel direction and compressed perpendicular to the walls.

The results have potential applications for understanding which genes might be accessible and readily expressed more depending on the configuration of DNA within the nucleus.

Source: “Conformation and dynamics of ring polymers under symmetric thin film confinement,” by Tianren Zhang, Karen I. Winey, and Robert A. Riggleman, Journal of Chemical Physics (2020). The article can be accessed at http://doi.org/10.1063/5.0024729 .