Untying of Complex Knots on Stretched Polymers in Elongational Fields

Activity-driven polymer knotting for macromolecular topology engineering

Macromolecules can gain special properties by adopting knotted conformations, but engineering knotted macromolecules is a challenging task. Here, we unexpectedly find that knots can be efficiently generated in active polymer systems. When one end of an actively reptative polymer is anchored, it undergoes continual self-knotting as a result of intermittent giant conformation fluctuations and the outward reptative motion. Once a knot is formed, it migrates to the anchoring point due to a nonequilibrium ratchet effect. Moreover, when the active polymer is grafted on a passive polymer, it can function as a self-propelling soft needle to either transfer its own knots or directly braid knots on the passive polymer. We further show that these active needles can create intermolecular bridging knots between two passive polymers. Our finding highlights the nonequilibrium effects in modifying the dynamic pathways of polymer systems, which have potential applications in macromolecular topology engineering.

Topological Entanglement of Linear Catenanes: Knots and Threadings

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.

Diffusion of knots in nanochannel-confined DNA molecules

We used Langevin dynamics simulations without hydrodynamic interactions to probe knot diffusion mechanisms and the time scales governing the evolution and the spontaneous untying of trefoil knots in nanochannel-confined DNA molecules in the extended de Gennes regime. The knot untying follows an "opening up process," wherein the initially tight knot continues growing and fluctuating in size as it moves toward the end of the DNA molecule before its annihilation at the chain end. The mean knot size increases significantly and sub-linearly with increasing chain contour length. The knot diffusion in nanochannel-confined DNA molecules is subdiffusive, with the unknotting time scaling with chain contour length with an exponent of 2.64 ± 0.23 to within a 95% confidence interval. The scaling exponent for the mean unknotting time vs chain contour length, along with visual inspection of the knot conformations, suggests that the knot diffusion mechanism is a combination of self-reptation and knot region breathing for the simulated parameters.

A Trefoil Knot Polymer Chain Translocates through a Funnel-like Channel: A Multi-Particle Collision Dynamics Study

With combining multi-particle collision dynamics (MPCD) for the solvent and molecular dynamics (MD) for the polymer chains, we have studied the conformation and untying behaviors of a trefoil knot polymer chain translocated through a confined funnel-like channel. For the trefoil knot chain, we found that the untying knot behavior mostly happens during the translocation process, and the translocation behavior of linear chains is also simulated as a comparison. Some characteristics of the trefoil knot chain during translocation process, such as average gyration radius and the average end-to-end distances are discussed, and we statistic the scale relations of the translocation time versus the chain length, and that of the chain rigidity. This study may help to understand translocation behaviors of the knotted linear polymer chain in the capillary flow field.

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Topological Disentanglement of Linear Polymers under Tension

We develop a theoretical description of the topological disentanglement occurring when torus knots reach the ends of a semiflexible polymer under tension. These include decays into simpler knots and total unknotting. The minimal number of crossings and the minimal knot contour length are the topological invariants playing a key role in the model. The crossings behave as particles diffusing along the chain and the application of appropriate boundary conditions at the ends of the chain accounts for the knot disentanglement. Starting from the number of particles and their positions, suitable rules allow reconstructing the type and location of the knot moving on the chain Our theory is extensively benchmarked with corresponding molecular dynamics simulations and the results show a remarkable agreement between the simulations and the theoretical predictions of the model.

Free energy of a knotted polymer confined to narrow cylindrical and conical channels

Monte Carlo simulations are used to study the conformational behavior of a semiflexible polymer confined to cylindrical and conical channels. The channels are sufficiently narrow that the conditions for the Odijk regime are marginally satisfied. For cylindrical confinement, we examine polymers with a single knot of topology 3_{1}, 4_{1}, or 5_{1}, as well as unknotted polymers that are capable of forming S loops. We measure the variation of the free energy F with the end-to-end polymer extension length X and examine the effect of varying the polymer topology, persistence length P, and cylinder diameter D on the free-energy functions. Similarly, we characterize the behavior of the knot span along the channel. We find that increasing the knot complexity increases the typical size of the knot. In the regime of low X, where the knot/S-loop size is large, the conformational behavior is independent of polymer topology. In addition, the scaling properties of the free energy and knot span are in agreement with predictions from a theoretical model constructed using known properties of interacting polymers in the Odijk regime. We also examine the variation of F with the position of a knot in conical channels for various values of the cone angle α. The free energy decreases as the knot moves in a direction where the cone widens, and it also decreases with increasing α and with increasing knot complexity. The behavior is in agreement with predictions from a theoretical model in which the dominant contribution to the change in F is the change in the size of the hairpins as the knot moves to the wider region of the channel.

Hydrodynamic interactions in topologically linked ring polymers

Despite decades of interdisciplinary research on topologically linked ring polymers, their dynamics remain largely unstudied. These systems represent a major scientific challenge as they are often subject to both topological and hydrodynamic interactions (HI), which render dynamical solutions either mathematically intractable or computationally prohibitive. Here we circumvent these limitations by preaveraging the HI of linked rings. We show that the symmetry of ring polymers leads to a hydrodynamic decoupling of ring dynamics. This decoupling is valid even for nonideal polymers and nonequilibrium conditions. Physically, our findings suggest that the effects of topology and HI are nearly independent and do not act cooperatively to influence polymer dynamics. We use this result to develop highly efficient Brownian dynamics algorithms that offer enormous performance improvements over conventional methods and apply these algorithms to simulate catenated ring polymers at equilibrium, confirming the independence of topological effects and HI. The methods developed here can be used to study and simulate large systems of linked rings with HI, including kinetoplast DNA, Olympic gels, and poly[n]catenanes.

Conformational State Hopping of Knots in Tensioned Polymer Chains

We use Brownian dynamics simulations to study the conformational states of knots on tensioned chains. Focusing specifically on the 8₁ knot, we observe knot conformational state hopping and show that the process can be described by a two-state kinetic model in the presence of an external force. The distribution of knot conformational states depends on the applied chain tension, which leads to a force-dependent distribution of knot untying pathways. We generalize our findings by considering the untying pathways of other knots and find that the way knots untie is generally governed by the force applied to the chain. From a broader perspective, being able to influence how a knot unties via external force can potentially be useful for applications of single-molecule techniques in which knots are unwanted.

Topological Disentanglement Dynamics of Torus Knots on Open Linear Polymers

We simulate and study the topological disentanglement occurring when torus knots reach the ends of a semiflexible open polymer (decay into simpler knots or unknotting). Through a rescaling procedure and the application of appropriate boundary conditions, we show that the full unknotting process can be understood in terms of point-like particles representing essential crossings, diffusing on the support [0, 1]. We address the bending and configurational free energy drives on the diffusion process, together with the scaling properties of the effective diffusion and friction coefficients. Agreement with simulations suggests universal features for these two model parameters.