Ring Polymers: Threadings, Knot Electrophoresis and Topological Glasses

From Bioreactor to Bulk Rheology: Achieving Scalable Production of Highly Concentrated Circular DNA

DNA serves as a model system in polymer physics due to its ability to be obtained as a uniform polymer with controllable topology and nonequilibrium behavior. Currently, a major obstacle in the widespread adoption of DNA is obtaining it on a scale and cost basis that accommodates bulk rheology and high-throughput screening. To address this, recent advancements in bioreactor-based plasmid DNA production is coupled with anion exchange chromatography producing a unified approach to generating gram-scale quantities of monodisperse DNA. With this method, 1.1 grams of DNA is obtained per batch to generate solutions with concentrations up to 116 mg mL-1. This solution of uniform supercoiled and relaxed circular plasmid DNA, is roughly 69 times greater than the overlap concentration. The utility of this method is demonstrated by performing bulk rheology measurements at sample volumes up to 1 mL on DNA of different lengths, topologies, and concentrations. The measured elastic moduli are orders of magnitude larger than those previously reported for DNA and allowed for the construction of a time-concentration superposition curve that spans 12 decades of frequency. Ultimately, these results can provide important insights into the dynamics of ring polymers and the nature of highly condensed DNA dynamics.

Enzymatic cleaving of entangled DNA rings drives scale-dependent rheological trajectories

DNA, which naturally occurs in linear, ring, and supercoiled topologies, frequently undergoes enzyme-driven topological conversion and fragmentation in vivo, enabling it to perform a variety of functions within the cell. In vitro, highly concentrated DNA polymers form entanglements that yield viscoelastic properties dependent on the topologies and lengths of the DNA. Enzyme-driven alterations of DNA size and shape therefore offer a means of designing active materials with programmable viscoelastic properties. Here, we incorporate multi-site restriction endonucleases into dense DNA solutions to linearize and fragment circular DNA molecules. We pair optical tweezers microrheology with differential dynamic microscopy and single-molecule tracking to measure the linear and nonlinear viscoelastic response and transport properties of entangled DNA solutions over a wide range of spatiotemporal scales throughout the course of enzymatic digestion. We show that, at short timescales, relative to the relaxation timescales of the polymers, digestion of these 'topologically-active' fluids initially causes an increase in elasticity and relaxation times followed by a gradual decrease. Conversely, for long timescales, linear viscoelastic moduli exhibit signatures of increasing elasticity. DNA diffusion, likewise, becomes increasingly slowed, in direct opposition to the short-time behavior. We hypothesize that this scale-dependent rheology arises from the population of small DNA fragments, which increases as digestion proceeds, driving self-association of larger fragments via depletion interactions, giving rise to slow relaxation modes of clusters of entangled chains, interspersed among shorter unentangled fragments. While these slow modes likely dominate at long times, they are presumably frozen out in the short-time limit, which instead probes the faster relaxation modes of the unentangled population.

Unraveling the Glass-like Dynamic Heterogeneity in Ring Polymer Melts: From Semiflexible to Stiff Chain

Ring polymers are an intriguing class of polymers with unique physical properties, and understanding their behavior is important for developing accurate theoretical models. In this study, we investigate the effect of chain stiffness and monomer density on the static and dynamic behaviors of ring polymer melts using molecular dynamics simulations. Our first focus is on the non-Gaussian parameter of center-of-mass displacement as a measure of dynamic heterogeneity, which is commonly observed in glass-forming liquids. We find that the non-Gaussianity in the displacement distribution increases with the monomer density and stiffness of the polymer chains, suggesting that excluded volume interactions between centers of mass have a strong effect on the dynamics of ring polymers. We then analyze the relationship between the radius of gyration and monomer density for semiflexible and stiff ring polymers. Our results indicate that the relationship between the two varies with chain stiffness, which can be attributed to the competition between repulsive forces inside the ring and from adjacent rings. Finally, we study the dynamics of bond-breakage virtually connected between the centers of mass of rings to analyze the exchanges of intermolecular networks of bonds. Our results demonstrate that the dynamic heterogeneity of bond-breakage is coupled with the non-Gaussianity in ring polymer melts, highlighting the importance of the bond-breaking method in determining the intermolecular dynamics of ring polymer melts. Overall, our study sheds light on the factors that govern the dynamic behaviors of ring polymers.

Scalable Synthetic Route to PDMS Ring Polymers in High Yields from Commercially Available Materials Using the Piers-Rubinsztajn Reaction

While cyclic polymers have intrigued researchers for their novel set of architecture-driven rheological interactions, the possibility of incorporating them in topological systems has been limited by the availability of large ring polymers. Thus, the need for scalable methods to produce ring polymers has become apparent. Here, a facile method to prepare polysiloxane ring polymers by means of Piers-Rubinsztajn chemistry is presented. The one-pot nature and commercial availability of reagents additionally confirm the applicability of the method for large-scale production. Furthermore, a highly efficient yet simple purification method was developed for the isolation of pure ring polymers without linear side products.

Effect of ring stiffness and ambient pressure on the dynamical slowdown in ring polymers

Using extensive molecular dynamics simulations, we investigate the slowdown of dynamics in a 3D system of ring polymers by varying the ambient pressure and the stiffness of the rings. Our study demonstrates that the stiffness of the rings determines the dynamics of the ring polymers, leading to glassiness at lower pressures for stiffer rings. The threading of the ring polymers, a unique feature that emerges only due to the topological nature of such polymers in three dimensions, is shown to be the determinant feature of dynamical slowdown, albeit only in a certain stiffness range. Our results suggest a possible framework for exploring the phase space spanned by ring stiffness and pressure to obtain spontaneously emerging topologically constrained polymer glasses.

Effects of chain length on Rouse modes and non-Gaussianity in linear and ring polymer melts

The dynamics of ring polymer melts are studied via molecular dynamics simulations of the Kremer-Grest bead-spring model. Rouse mode analysis is performed in comparison with linear polymers by changing the chain length. Rouse-like behavior is observed in ring polymers by quantifying the chain length dependence of the Rouse relaxation time, whereas a crossover from Rouse to reptation behavior is observed in linear polymers. Furthermore, the non-Gaussian parameters of the monomer bead displacement and chain center-of-mass displacement are analyzed. It is found that the non-Gaussianity of ring polymers is remarkably suppressed with slight growth for the center-of-mass dynamics at long chain length, which is in contrast to the growth in linear polymers for both the monomer bead and center-of-mass dynamics.

Topics in the mathematical design of materials

We present a perspective on several current research directions relevant to the mathematical design of new materials. We discuss: (i) design problems for phase-transforming and shape-morphing materials, (ii) epitaxy as an approach of central importance in the design of advanced semiconductor materials, (iii) selected design problems in soft matter, (iv) mathematical problems in magnetic materials, (v) some open problems in liquid crystals and soft materials and (vi) mathematical problems on liquid crystal colloids. The presentation combines topics from soft and hard condensed matter, with specific focus on those design themes where mathematical approaches could possibly lead to exciting progress. This article is part of the theme issue 'Topics in mathematical design of complex materials'.

Conformational behavior and self-assembly of disjoint semi-flexible ring polymers adsorbed on solid substrates

The conformational behavior and spatial organization of self-avoiding semi-flexible ring polymers, that are fully adsorbed on solid substrates, are investigated via systematic coarse-grained molecular dynamics simulations. Our results show that both conformations and spatial organization of the polymers depend strongly on their bending stiffness, κ, and on their areal number density, ρ. For ρ < ρ*, where ρ* is the overlap density, and for low values of κ, thermal fluctuations lead to weakly anisotropic instantaneous conformations of the polymers. The interplay between thermal fluctuations and polymer stiffness leads to a non-monotonic dependence of the polymers elongation on κ with a maximum elongation at some intermediate κ. Regardless of κ, the polymers elongation is almost independent of ρ for ρ ⪅ ρ*, then increases with ρ. At ρ ≈ ρ* and high κ, the almost circularly-shaped polymers self-assemble into a triangular lattice with quasi-long range order. For ρ above ρ* and high κ, crowding of the polymers leads to their self-assembly into liquid-crystalline phases. In particular, for ρ moderately above ρ* and high κ, the polymer conformations are obround and self-assemble into domains with smectic-A-like order. At higher densities, the polymer have a biconcave geometry and self-assemble into domains with smectic-C-like order.

Threading-Induced Dynamical Transition in Tadpole-Shaped Polymers

The relationship between polymer topology and bulk rheology remains a key question in soft matter physics. Architecture-specific constraints (or threadings) are thought to control the dynamics of ring polymers in ring-linear blends, which thus affects the viscosity to range between that of the pure rings and a value larger, but still comparable to, that of the pure linear melt. Here we consider qualitatively different systems of linear and ring polymers, fused together in "chimeric" architectures. The simplest example of this family is a "tadpole"-shaped polymer, a single ring fused to the end of a single linear chain. We show that polymers with this architecture display a threading-induced dynamical transition that substantially slows chain relaxation. Our findings shed light on how threadings control dynamics and may inform design principles for chimeric polymers with topologically tunable bulk rheological properties.

Long-Lived Self-Entanglements in Ring Polymers

The entanglement of ring polymers remains mysterious in many aspects. In this Letter, we use electric fields to induce self-entanglements in circular DNA molecules, which serve as a minimal system for studying chain entanglements. We show that self-threadings give rise to entanglements in ring polymers and can slow down polymer dynamics significantly. We find that strongly entangled circular molecules remain kinetically arrested in a compact state for very long times, thereby providing experimental evidence for the severe topological constraints imposed by threadings.

Statistical Properties of Lasso-Shape Polymers and Their Implications for Complex Lasso Proteins Function

The shape and properties of closed loops depend on various topological factors. One of them is loop-threading, which is present in complex lasso proteins. In this work, we analyze the probability of loop-threading by the tail and its influence on the shape of the loop measured by the radius of gyration, distention, asphericity, and prolateness. In particular, we show that the probability of a trivial lasso for phantom polymer is non-zero even for an infinite structure, as well as that the threading flattens the loop by restricting its motion in one dimension. These results are further used to show that there are fewer non-trivial protein lassos than expected and select potentially functional complex lasso proteins.

Slow Dynamics of Ring Polymer Melts by Asymmetric Interaction of Threading Configuration: Monte Carlo Study of a Dynamically Constrained Lattice Model

Abnormally slower diffusional processes than its internal structure relaxation have been observed in ring polymeric melt systems recently. A key structural feature in ring polymer melts is topological constraints which allow rings to assume a threading configuration in the melt phase. In this work, we constructed a lattice model under the assumption of asymmetric diffusivity between two threading rings, and investigated a link between the structural correlation and its dynamic behavior via Monte Carlo simulations. We discovered that the hierarchical threading configurations render the whole system to exhibit abnormally slow dynamics. By analyzing statistical distributions of timescales of threading configurations, we found that the decoupling between internal structure relaxation and diffusion is crucial to understand the threading effects on the dynamics of a ring melt. In particular, in the limit of small but threaded rings, scaling exponents of the diffusion coefficient D and timescale τ diff with respect to the degree of polymerization N agree well with that of the annealed tree model as well as our mean-field analysis. As N increases, however, the ring diffusion abruptly slows down to the glassy behavior, which is supported by a breakdown of the Stokes⁻Einstein relation.

Threading of Unconcatenated Ring Polymers at High Concentrations: Double-Folded vs Time-Equilibrated Structures

Unconcatenated ring polymers in concentrated solutions and melt are remarkably well described as double-folded conformations on randomly branched primitive trees. This picture though contrasts recent evidence for extensive intermingling between close-by rings in the form of long-lived topological constraints or threadings. Here, we employ the concept of ring minimal surface to quantify the extent of threadings in polymer solutions of the double-folded rings vs rings in equilibrated molecular dynamics computer simulations. Our results show that the double-folded ring polymers are significantly less threaded compared to their counterparts at equilibrium. Second, threadings form through a slow process whose characteristic time-scale is of the same order of magnitude as that of the diffusion of the rings in solution. These findings are robust, being based on universal (model-independent) observables as the average fraction of threaded length or the total penetrations between close-by rings and the corresponding distribution functions.

Conformational statistics of randomly branching double-folded ring polymers

The conformations of topologically constrained double-folded ring polymers can be described as wrappings of randomly branched primitive trees. We extend previous work on the tree statistics under different (solvent) conditions to explore the conformational statistics of double-folded rings in the limit of tight wrapping. In particular, we relate the exponents characterizing the ring statistics to those describing the primitive trees and discuss the distribution functions [Formula: see text] and [Formula: see text] for the spatial distance, [Formula: see text], and tree contour distance, L, between monomers as a function of their ring contour distance, [Formula: see text].