Linear Catenanes in Channel Confinement

Abstract

We use Langevin dynamics simulations to investigate the behavior of linear catenanes under channel confinement. We consider model poly[n]catenanes of n = 100 rings, each of m = 40 beads, and present a comprehensive analysis of their statics and dynamics in cylindrical channels of various diameters. To highlight the impact of mechanical bonding, we compare the catenane behavior to an equivalent chain of beads under the same conditions. We show that linear catenanes exhibit various confinement regimes, including a de Gennes one for intermediate channel widths and an overstretching response for strong confinement, which is unique to catenanes. The catenane’s relaxation dynamics also diverge from conventional polymers at strong confinement, presenting much slower modes. Through systematic analysis of the size, shape, and orientation of the concatenated rings and their mechanical bonds, we shed light on the underlying mechanisms driving the catenane’s static and dynamic responses to confinement.

Unraveling the Influence of Topology and Spatial Confinement on Equilibrium and Relaxation Properties of Interlocked Ring Polymers

“…Note also that the longitudinal span relaxation time of the simplest link types has an overall decreasing trend with confinement (Figure S3). This is reminiscent of the same decreasing trend observed for equilibrium relaxation time of the span of confined equilibrated linear Hopf-linked catenanes . However, for complex link types, the decreasing trend is reversed for D ≲ 20σ.…”

“…This is reminiscent of the same decreasing trend observed for equilibrium relaxation time of the span of confined equilibrated linear Hopf-linked catenanes. 68 However, for complex link types, the decreasing trend is reversed for D ≲ 20σ. Such an increase of τ s with confinement appears to be a topological effect; in fact, it typically parallels an analogous increase of τ LK for the more complex topologies ( Figure S3 ).…”

Escape dynamics of active ring polymers in a cylindrical nanochannel

“…The behaviors of polymers confined in a nanochannel have received long-standing academic attention, 1–7 not only concerning the physical properties of polymers when they differ from the free state 8–10 but also about many biological processes, such as the process of chromosome segregation in slender-shaped bacteria, 11,12 the ejection of DNA into cells by phages, 13 and the packaging of genes in phagocytic bacteria. 14 Recently, this issue has been brought into focus again due to the significantly increased possibilities of using nanochannels as a tool for studying and manipulating DNA molecules, e.g.…”

Mixing Linear Polymers with Rings and Catenanes: Bulk and Interfacial Behavior

“…Recent experiments suggest that when digesting the kinetoplasts using enzymes cutting the DNA rings, one first breaks the percolation in the interior of the sheet and is left with the periphery, now being a ring of rings. , Better understanding of such poly­[ n ]­catenanes, , either cyclic or open, presents one of the main challenges for the topological soft materials. Simulations predict that the structure of poly­[ n ]­catenanes in melts is similar to linear chains in the limit of long time scales and length scales but shows a different behavior at the shorter scales, , with a similar relaxation time decoupling being present also in dilute solutions. − However, experimental verifications for some of the simulation predictions are at the moment missing, mainly due to the lack of high-yield synthetic methods leading to high-molar-mass poly­[ n ]­catenanes …”