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.

We used molecular dynamics simulations to investigate the self-entanglements of the collapsed linear catenanes. We found two different types of topologically complex states. First, we observed numerous long-lived knotting events of the catenane backbone. However, comparison with conventional polymers reveals that knots are suppressed in catenanes. Next, we observed topologically complex states with no analogue in polymers, where a concatenated ring was threaded by other near or distal rings sliding through it. Differently from knots, these threaded states can disentangle by becoming fully tightened. A detailed thermodynamic and microscopic analysis is employed to rationalize the persistence of threaded states, which can survive significant internal reorganizations of the entire catenane. We finally discuss the broader implications of these previously unreported types of entanglements for other systems, such as noncollapsed and interacting catenanes.

We used molecular dynamics simulations to investigate the statics and dynamics of poly[n]catenanes for different bending rigidities of the constituent rings. We show that stiffer rings yield catenanes with more extended and, at the same time, more flexible backbones. The softening of the backbone reflects the decreasing steric interactions of catenated rings as their shape becomes more oblate due to increased rigidity. The internal dynamics of catenanes is affected too. Going from flexible to rigid rings causes a several-fold slowing of different processes, from segmental rotations and size fluctuations to Rouse modes. Finally, by considering the statics and dynamics of crowded solutions of catenanes, we isolate another emergent property controlled by the rigidity of the rings. Specifically, we show that catenanes with rigid rings hinder each other’s motion more than those with flexible rings. Thus, in equally crowded solutions, the diffusion coefficient is smaller for catenanes with stiffer rings.

We use MD simulations to study the pore translocation properties of a pseudoknotted viral RNA. We consider the 71-nucleotide-long xrRNA from the Zika virus and establish how it responds when driven through a narrow pore by static or periodic forces applied to either of the two termini. Unlike the case of fluctuating homopolymers, the onset of translocation is significantly delayed with respect to the application of static driving forces. Because of the peculiar xrRNA architecture, activation times can differ by orders of magnitude at the two ends. Instead, translocation duration is much smaller than activation times and occurs on time scales comparable at the two ends. Periodic forces amplify significantly the differences at the two ends, for both activation times and translocation duration. Finally, we use a waiting-times analysis to examine the systematic slowing downs in xrRNA translocations and associate them to the hindrance of specific secondary and tertiary elements of xrRNA. The findings provide a useful reference to interpret and design future theoretical and experimental studies of RNA translocation.

We study the large deviations of the distribution P(Wτ) of the work associated with the propulsion of individual active Brownian particles in a time interval τ, in the region of the phase diagram where macroscopic phase separation takes place. P(Wτ) is characterised by two peaks, associated to particles in the gaseous and in the clusterised phases, and two separate non-convex branches. Accordingly, the generating function of Wτ's cumulants displays a double singularity. We discuss the origin of such non-convex branches in terms of the peculiar dynamics of the system phases, and the relation between the observation time τ and the typical persistence times of the particles in the two phases.