When Ends Meet: Circular DNA Stretches Differently in Elongational Flows

Monodisperse Cyclic Polymer Mechanochemistry: Scission Kinetics and the Dynamic Memory Effect with Ultrasonication and Ball-Mill Grinding

A series of monodisperse cyclic and linear poly(d,l-lactide)s (c-PLA and l-PLA, respectively) were prepared with various degrees of polymerization (DP) using an iterative convergent synthesis approach. The absence of a molecular weight distribution provided us a chance to study their mechanochemical reactivity without obstructions arising from the size distribution. Additionally, we prepared l- and c-PLAs with identical DPs, which enabled us to attribute differences in scission rates to the cyclic polymer architecture alone. The polymers were subjected to ultrasonication (US) and ball-mill grinding (BMG), and their degradation kinetics were explored. Up to 9.0 times larger scission rates were observed for l-PLA (compared to c-PLA) with US, but the difference was less than 1.9 times with BMG. Fragmentation requires two backbone scission events for c-PLA, and we were able to observe linear intermediates (formed after a single scission) for the first time. We also developed a new method of studying the dynamic memory effect in US by characterizing and comparing the daughter fragment molecular weight distributions of l- and c-PLAs. These results provide new insights into the influence of the cyclic polymer architecture on mechanochemical reactions as well as differences in reactivity observed with US and BMG.

Unexpected Slow Relaxation Dynamics in Pure Ring Polymers Arise from Intermolecular Interactions

Ring polymers have fascinated scientists for decades, but experimental progress has been challenging due to the presence of linear chain contaminants that fundamentally alter dynamics. In this work, we report the unexpected slow stress relaxation behavior of concentrated ring polymers that arises due to ring-ring interactions and ring packing structure. Topologically pure, high molecular weight ring polymers are prepared without linear chain contaminants using cyclic poly(phthalaldehyde) (cPPA), a metastable polymer chemistry that rapidly depolymerizes from free ends at ambient temperatures. Linear viscoelastic measurements of highly concentrated cPPA show slow, non-power-law stress relaxation dynamics despite the lack of linear chain contaminants. Experiments are complemented by molecular dynamics (MD) simulations of unprecedentedly high molecular weight rings, which clearly show non-power-law stress relaxation in good agreement with experiments. MD simulations reveal substantial ring-ring interpenetrations upon increasing ring molecular weight or local backbone stiffness, despite the global collapsed nature of single ring conformation. A recently proposed microscopic theory for unconcatenated rings provides a qualitative physical mechanism associated with the emergence of strong inter-ring caging which slows down center-of-mass diffusion and long wavelength intramolecular relaxation modes originating from ring-ring interpenetrations, governed by the onset variable N/ND, where the crossover degree of polymerization ND is qualitatively predicted by theory. Our work overcomes challenges in achieving ring polymer purity and by characterizing dynamics for high molecular weight ring polymers. Overall, these results provide a new understanding of ring polymer physics.

Characterisation of hydrodynamic trapping in microfluidic cross-slot devices for high strain rate applications

Hydrodynamic trapping of a particle or cluster of particles based on contact and non-contact approaches has brought prominent insights to micro-nano scale applications. Of the non-contact methods, image-based real-time control in cross-slot microfluidic devices is one of the most promising potential platform for single cellular assays. Here, we report results from experiments conducted in two cross-slot microfluidic channels of different widths, with varying real-time delay of the control algorithm and different magnification. Sustained trapping of 5 μm diameter particles was achieved with high strain rates, of order 10² s^-1, higher than in any previous studies. Our experiments show that the maximum attainable strain rate is a function of the real-time delay of the control algorithm and the particle resolution (pixel/μm). Therefore, we anticipate that with further reduced time delays and enhanced particle resolution, considerably higher strain rates can be attained, opening the platform to single cellular assay studies where very high strain rates are required.

PolyDODT: a macrocyclic elastomer with unusual properties

Reversible Radical Recombination Polymerization (R3P) using triethylamine (TEA), H2O2 and air is a scalable and green method for the synthesis of biodegradable polysulfides.

Transient Electric Birefringence of Linear and Circular DNA: A Comparison of Kinetic Theory Predictions

The use of monodisperse DNA and restriction enzyme modification allows the preparation of model samples of polymer rings and linear chains with a precision that is not possible by conventional synthetic routes. These samples allow direct comparisons of the predictions of polymer kinetic theories. Transient electric birefringence allows rapid imposition or forces (∼100 ns) and monitoring of conformational changes (∼0.7 μs). We determined the relaxation spectra of once-cut linear ΦX-174 (5386 bp), twice-cut linear ΦX-174 (2693 bp), and relaxed ring (5386 bp) ΦX-174 with transient electric birefringence. This allows comparison of the relaxation dynamics of a linear chain and a polymer loop with exactly the same contour length. The relaxed loop and the twice-cut DNA had the longest relaxation times of 1039 and 1076 μs, respectively. The loop was measured both in the native supercoiled state and in the relaxed state. We found the birefringence decayed in agreement with bead-spring (Rouse/Zimm) models for polymer dynamics determined by both a model-independent average relaxation time and deconvolution of the decay into a sum of exponentials. Deconvolution was performed by CONTIN and by the Padé-Laplace method. For both the relaxed ring and the linear fragments, we found the longer time constants τ₁ and τ₂ were discrete and had a spacing that was in agreement with the Rouse model without hydrodynamic interaction (τ₁/τ₂ = 0.25), which would be expected for a chain with 20 statistical segments. The excitation of higher relaxation modes could be observed as the electric field pulse length increased.

Equilibrium Conformation of Catenated DNA Networks in Slitlike Confinement

A kinetoplast is a planar network of catenated DNA rings with topology that resembles that of chain mail armor. In this work, we use single-molecule experiments to probe the conformation of kinetoplasts confined to slits. We find that the in-plane size of kinetoplasts increases with degree of confinement, akin to the slitlike confinement of linear DNA. The change in kinetoplast size with channel height is consistent with the scaling prediction from a Flory-type approach for a 2D polymer. With an increase in extent of confinement, the kinetoplasts appear to unfold and take on more uniform circular shapes, in contrast to the broad range of conformations observed for kinetoplasts in bulk.

The influence of polymer architecture in polymer mechanochemistry

Polymer architecture is an important factor in polymer mechanochemistry. In this Feature Article, we summarize recent developments in utilizing polymer architecture to modulate mechanochemical reactions within polymers, or more specifically, the location and rates of bond scission events that lead to polymer fragmentation or mechanophore activation. Various well-defined architectures have been explored, including those of cyclic, intramolecularly cross-linked, dendritic, star, bottlebrush, and dendronized polymers. We primarily focus on describing the enhancement or suppression of mechanochemical reactivity, with respect to analogous linear polymers, as well as differences in solution- and solid-state behavior.

Nonlinear rheometry of entangled polymeric rings and ring-linear blends

We present a comprehensive experimental rheological dataset for purified entangled ring polystyrenes and their blends with linear chains in nonlinear shear and elongation. In particular, data for shear stress growth coefficient, steady-state shear viscosity, and first and second normal stress differences are obtained and discussed as functions of shear rate as well as molecular parameters (molar mass, blend composition and decreasing molar mass of linear component in blend). Over the extended parameter range investigated, rings do not exhibit clear transient undershoot in shear, in contrast to their linear counterparts and ring-linear blends. For the latter, the size of the undershoot and respective strain appear to increase with shear rate. Universal scaling of strain at overshoot and fractional overshoot (ratio of maximum to steady-state shear stress growth coefficient) indicates subtle differences in the shear-rate dependence between rings and linear polymers or their blends. The shear thinning behaviour of pure rings yields a slope nearly identical to predictions (-4/7) of a recent shear slit model and molecular dynamics simulations. Data for the second normal stress difference are reported for rings and ring-linear blends. While N ₂ is negative and its absolute value stays below that of N ₁ , as for linear polymers, the ratio -N ₂ /N ₁ is unambiguously larger for rings compared to linear polymer solutions with the same number of entanglements (almost by factor of two), in agreement with recent non-equilibrium molecular dynamics simulations. Further, -N ₂ exhibits slightly weaker shear rate dependence compared to N ₁ at high rates, and the respective power-law exponents can be rationalized in view of the slit model (3/7) and simulations (0.6), although further work is needed to unravel the molecular original of the observed behaviour. The comparison of shear and elongational stress growth coefficients for blends reflects the effect of ring-linear threading which leads to significant viscosity enhancement in elongation. Along the same lines, the elongational stress is much larger than the first normal stress in shear, and their ratio is much larger for rings and ring-linear blends compared to linear polymers. This conforms the interlocking scenario of rings and their important role in mechanically reinforcing linear matrices.

Structural and Dynamical Characteristics of Short-Chain Branched Ring Polymer Melts at Interface under Shear Flow

We present a detailed analysis of the interfacial chain structure and dynamics of confined polymer melt systems under shear over a wide range of flow strengths using atomistic nonequilibrium molecular dynamics simulations, paying particular attention to the rheological influence of the closed-loop ring geometry and short-chain branching. We analyzed the interfacial slip, characteristic molecular mechanisms, and deformed chain conformations in response to the applied flow for linear, ring, short-chain branched (SCB) linear, and SCB ring polyethylene melts. The ring topology generally enlarges the interfacial chain dimension along the neutral direction, enhancing the dynamic friction of interfacial chains moving against the wall in the flow direction. This leads to a relatively smaller degree of slip (ds) for the ring-shaped polymers compared with their linear analogues. Furthermore, short-chain branching generally resulted in more compact and less deformed chain structures via the intrinsically fast random motions of the short branches. The short branches tend to be oriented more perpendicular (i.e., aligned in the neutral direction) than parallel to the backbone, which is mostly aligned in the flow direction, thereby enhancing the dynamic wall friction of the moving interfacial chains toward the flow direction. These features afford a relatively lower ds and less variation in ds in the weak-to-intermediate flow regimes. Accordingly, the interfacial SCB ring system displayed the lowest ds among the studied polymer systems throughout these regimes owing to the synergetic effects of ring geometry and short-chain branching. On the contrary, the structural disturbance exerted by the highly mobile short branches promotes the detachment of interfacial chains from the wall at strong flow fields, which results in steeper increasing behavior of the interfacial slip for the SCB polymers in the strong flow regime compared to the pure linear and ring polymers.

Pathologic Shear and Elongation Rates Do Not Cause Cleavage of Von Willebrand Factor by ADAMTS13 in a Purified System

INTRODUCTION

Pathological flows in patients with severe aortic stenosis are associated with acquired von Willebrand syndrome. This syndrome is characterized by excessive cleavage of von Willebrand factor by its main protease, A Disintegrin and Metalloproteinase with a Thrombospondin Type 1 Motif, Member 13 (ADAMTS13) leading to decreased VWF function and mucocutaneous bleeding. Aortic valve replacement and correction of the flow behavior to physiological levels reverses the syndrome, supporting the association between pathological flow and acquired von Willebrand syndrome. We investigated the effects of shear and elongational rates on von Willebrand factor cleavage in the presence of ADAMTS13.

METHODS

We identified acquired von Willebrand syndrome in five patients with severe aortic stenosis. Doppler echography values from these patients were used to develop three computational fluid dynamic (CFD) aortic valve models (normal, mild and severe stenosis). Shear, elongational rates and exposure times identified in the CFD simulations were used as parameters for the design of microfluidic devices to test the effects of pathologic shear and elongational rates on the structure and function of von Willebrand factor.

RESULTS

The shear rates (0-10,000s-1), elongational rates (0-1000 s-1) and exposure times (1-180 ms) tested in our microfluidic designs mimicked the flow features identified in patients with aortic stenosis. The shear and elongational rates tested in vitro did not lead to excessive cleavage or decreased function of von Willebrand factor in the presence of the protease.

CONCLUSIONS

High shear and elongational rates in the presence of ADAMTS13 are not sufficient for excessive cleavage of von Willebrand Factor.

Deformation Response of Catenated DNA Networks in a Planar Elongational Field

A kinetoplast is a complex catenated DNA network that bears resemblance to a two-dimensional polymeric system. In this work, we use single-molecule experiments to study the transient and steady-state deformation of kinetoplasts in a planar elongational field. We demonstrate that kinetoplasts deform in a stagewise manner and undergo transient deformation at large strains, due to conformational rearrangements from an intermediate metastable state. Kinetoplasts in an elongational field achieve a steady-state deformation that depends on strain rate, akin to the deformation of linear polymers. We do not observe an abrupt transition between the nondeformed and deformed states of a kinetoplast, in contrast to the coil-stretch transition for a linear polymer.

Combining particle tracking microrheology and viscometry for the study of DNA aqueous solutions

We use video particle tracking microrheology (VPTMR) in order to investigate the viscoelasticity of salmon DNA and correlate it to its steady-flow shear-thinning viscosity. Aqueous solutions of DNA are tested in a wide concentration range from the dilute to the semidilute unentangled concentration regime. The observed mean squared displacement shows power-law scaling with lag-time which is equivalent to power-law behavior of the complex modulus as a function of frequency that is, |G^* (ω)| = S ∙ ω ^α . The relaxation exponent α changes abruptly with concentration in the semidilute regime from about 1 to about 0.5 which is the exponent predicted by the Rouse model. The quasi-property S follows the scaling of viscosity for uncharged polymers near θ-conditions in the semidilute regime that is, η ∼ c 1 / 3 ν eff - 1 with ν_eff = 0.50 - 0.51. The shear-thinning exponent observed by viscometry increases gradually towards the value of 0.5 which has been predicted for Rouse chains under flow. Our findings are in agreement with recent studies of DNA solutions where DNA is treated as a model polymer and addresses the low-molar mass regime of DNA viscoelasticity. This work demonstrates that the combination of passive particle tracking with viscometry can provide a complete picture on the viscoelasticity of DNA-based biopolymer materials.

Equilibrium structure and deformation response of 2D kinetoplast sheets

The considerable interest in two-dimensional (2D) materials and complex molecular topologies calls for a robust experimental system for single-molecule studies. In this work, we study the equilibrium properties and deformation response of a complex DNA structure called a kinetoplast, a 2D network of thousands of linked rings akin to molecular chainmail. Examined in good solvent conditions, kinetoplasts appear as a wrinkled hemispherical sheet. The conformation of each kinetoplast is dictated by its network topology, giving it a unique shape, which undergoes small-amplitude thermal fluctuations at subsecond timescales, with a wide separation between fluctuation and diffusion timescales. They deform elastically when weakly confined and swell to their equilibrium dimensions when the confinement is released. We hope that, in the same way that linear DNA became a canonical model system on the first investigations of its polymer-like behavior, kinetoplasts can serve that role for 2D and catenated polymer systems.

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.

Ring polymer dynamics and tumbling-stretch transitions in planar mixed flows

The properties of dilute polymer solutions are governed by the conformational dynamics of individual polymers which can be perturbed in the presence of an applied flow. Much of our understanding of dilute solutions comes from studying how flows manipulate the molecular features of polymer chains out of equilibrium, primarily focusing on linear polymer chains. Recently there has been an emerging interest in the dynamics of nonlinear architectures, particularly ring polymers, which exhibit surprising out-of-equilibrium dynamics in dilute solutions. In particular, it has been observed that hydrodynamics can couple to topology in planar elongational and shear flows, driving molecular expansion in the nonflow direction that is not observed for linear chains. In this paper, we extend our understanding of dilute ring polymer dynamics to mixed flows, which represent flow profiles intermediate between simple shear or planar elongation. We map the conformational behaviors at a number of flow geometries and strengths, demonstrating transitions between coiled, tumbling, and stretched regimes. Indeed, these observations are consistent with how linear chains respond to mixed flows. For both linear and ring polymers, we observe a marked first-order-like transition between tumbling and stretched polymers that we attribute to a dynamic energy barrier between the two states. This manifests as bimodal extension distributions in a narrow range of flow strengths and geometries, with the primary difference between rings and linear chains being the presence of molecular expansion in the vorticity direction.

Unexpected Stretching of Entangled Ring Macromolecules

In the melt state at equilibrium, entangled nonconcatenated ring macromolecules adapt more compact conformations compared to their linear analogs and do not form an entanglement network. We show here that, when subjected to uniaxial stretching, they exhibit a unique response, which sets them apart from any other polymer. Remarkably, whereas both linear and ring polymers strain-harden, the viscosity of the rings increases dramatically (the melt thickens) at very low stretch rates due to the unraveling of their conformations along the stretching direction. At high rates, stretching leads to viscosity thinning similar to that of entangled linear polymers, albeit with subtle differences.

Effect of molecular architecture on ring polymer dynamics in semidilute linear polymer solutions

Understanding the dynamics of ring polymers is a particularly challenging yet interesting problem in soft materials. Despite recent progress, a complete understanding of the nonequilibrium behavior of ring polymers has not yet been achieved. In this work, we directly observe the flow dynamics of DNA-based rings in semidilute linear polymer solutions using single molecule techniques. Our results reveal strikingly large conformational fluctuations of rings in extensional flow long after the initial transient stretching process has terminated, which is observed even at extremely low concentrations (0.025 c*) of linear polymers in the background solution. The magnitudes and characteristic timescales of ring conformational fluctuations are determined as functions of flow strength and polymer concentration. Our results suggest that ring conformational fluctuations arise due to transient threading of linear polymers through open ring chains stretching in flow.

Trefoil Knot Hydrodynamic Delocalization on Sheared Ring Polymers

The behavior of unknotted and trefoil-knotted ring polymers under shear flow is here examined by means of mesoscopic simulations. In contrast to most polymers, ring polymers in a hydrodynamic solvent at high shear rates do not get shortened in the vorticity direction. This is a consequence of the backflow produced by the interaction of the sheared solvent with the end-free polymer topology. The extended structures of the ring in the vorticity-flow plane, when they are aligned in a constant velocity plane, favor ring contour fluctuations. This variety of conformations largely suppresses the tank-treading type of rotation with extended conformations in favor of the tumbling type of rotations, where stretched and collapsed conformations alternate. The extension of trefoil knots is also enhanced, so that the knots become delocalized. We anticipate that these effects, which disappear in the absence of hydrodynamic interactions, will have a crucial impact on the rheological properties of concentrated ring solutions, and will also influence the behavior of more complicated systems such as mixtures of polymers with different topologies.

Quantifying Local Molecular Tension Using Intercalated DNA Fluorescence

The ability to measure mechanics and forces in biological nanostructures, such as DNA, proteins and cells, is of great importance as a means to analyze biomolecular systems. However, current force detection methods often require specialized instrumentation. Here, we present a novel and versatile method to quantify tension in molecular systems locally and in real time, using intercalated DNA fluorescence. This approach can report forces over a range of at least ∼0.5-65 pN with a resolution of 1-3 pN, using commercially available intercalating dyes and a general-purpose fluorescence microscope. We demonstrate that the method can be easily implemented to report double-stranded (ds)DNA tension in any single-molecule assay that is compatible with fluorescence microscopy. This is particularly useful for multiplexed techniques, where measuring applied force in parallel is technically challenging. Moreover, tension measurements based on local dye binding offer the unique opportunity to determine how an applied force is distributed locally within biomolecular structures. Exploiting this, we apply our method to quantify the position-dependent force profile along the length of flow-stretched DNA and reveal that stretched and entwined DNA molecules-mimicking catenated DNA structures in vivo-display transient DNA-DNA interactions. The method reported here has obvious and broad applications for the study of DNA and DNA-protein interactions. Additionally, we propose that it could be employed to measure forces in any system to which dsDNA can be tethered, for applications including protein unfolding, chromosome mechanics, cell motility, and DNA nanomachines.

Synthesis and Direct Observation of Thermoresponsive DNA Copolymers

Single-molecule techniques allow for the direct observation of long-chain macromolecules, and these methods can provide a molecular understanding of chemically heterogeneous and stimuli-response polymers. In this work, we report the synthesis and direct observation of thermoresponsive DNA copolymers using single-molecule techniques. DNA-PNIPAM copolymers are synthesized using a two-step strategy based on polymerase chain reaction (PCR) for generating linear DNA backbones containing non-natural nucleotides (dibenzocyclooctyne-dUTP), followed by grafting thermoresponsive side branches (poly(N-isopropylacrylamide), PNIPAM) onto DNA backbones using copper-free click chemistry. Single-molecule fluorescence microscopy is used to directly observe the stretching and relaxation dynamics of DNA-PNIPAM copolymers both below and above the lower critical solution temperature (LCST) of PNIPAM. Our results show that the intramolecular conformational dynamics of DNA-PNIPAM copolymers are affected by temperature, branch density, and branch molecular weight. Single-molecule experiments reveal an underlying molecular heterogeneity associated with polymer stretching and relaxation behavior, which arises in part due to heterogeneous chemical identity on DNA copolymer dynamics.

Knots modify the coil-stretch transition in linear DNA polymers

We perform single-molecule DNA experiments to investigate the relaxation dynamics of knotted polymers and examine the steady-state behavior of knotted polymers in elongational fields. The occurrence of a knot reduces the relaxation time of a molecule and leads to a shift in the molecule's coil-stretch transition to larger strain rates. We measure chain extension and extension fluctuations as a function of strain rate for unknotted and knotted molecules. The curves for knotted molecules can be collapsed onto the unknotted curves by defining an effective Weissenberg number based on the measured knotted relaxation time in the low extension regime, or a relaxation time based on Rouse/Zimm scaling theories in the high extension regime. Because a knot reduces a molecule's relaxation time, we observe that knot untying near the coil-stretch transition can result in dramatic changes in the molecule's conformation. For example, a knotted molecule at a given strain rate can experience a stretch-coil transition, followed by a coil-stretch transition, after the knot partially or fully unties.

Topology-Sensitive Microfluidic Filter for Polymers of Varying Stiffness

The separation of polymers based on their size, rigidity, and topology is an essential but also highly challenging task for nanoscience and engineering. Using hybrid molecular dynamics simulations that correctly take into account hydrodynamics, we have designed microfluidic channels for separating linear from ring polymers in dilute solutions. We establish that the transport velocity of the polymers is independent of their topology and rigidity when the channel walls are smooth and repulsive. However, when the walls are decorated with attractive spots arranged on lines parallel to the flow, ring polymers exhibit an order of magnitude higher transport velocity compared to linear chains. The spots induce a homeotropic-like reorientation of ring polymers close to walls leading to a tank treading motion along them, whereas linear chains are immobilized upon adsorption. This mechanism becomes more enhanced with increasing polymer rigidity. The presented technique holds thus promise for reliably separating nanoparticles based on their topology.

Steady-State and Transient Behavior of Knotted Chains in Extensional Fields

Recently, there has been a push to understand how molecular topology alters the nonequilibrium dynamics of polymer systems. In this paper, we probe how knotted polymers evolve in planar extensional fields using Brownian dynamics simulations and single-molecule experiments. In the first part of the study, we quantify the extension versus strain-rate curves of polymers and find that knots shift these curves to larger strain-rates. These trends can be quantitatively explained by Rouse-like scaling theories. In the second half of the study, we examine the consequences of knot untying on the time-dependent conformations of polymers in these external fields. We find that knot untying creates significant, transient changes in chain extension. If the topology is complex, the chain undergoes a wide range of time-dependent conformations since knot untying proceeds through many different stages. We provide examples of such untying trajectories over time.

Unfolding Kinetics of a Wormlike Chain under Elongational Flow

A simple theory of the unfolding kinetics of a semi-flexible polymer chain is presented in terms of a Kramers type picture for the energy of elongation. The hydrodynamic interactions are discussed in terms of slender body theory. It turns out that the elongation of the chain is basically linear in time and independent of the viscosity. The former prediction agrees with experiments on the stretching dynamics of DNA under planar elongational flow. Nevertheless, the theory overestimates the experimental rate by a significant amount for reasons that are unclear.

Stagnation point flows in analytical chemistry and life sciences

Isolated microfluidic stagnation points – formed within microfluidic interfaces – have come a long way as a tool for characterizing materials, manipulating micro particles, and generating confined flows and localized chemistries.

Molecular Processes Leading to "Necking" in Extensional Flow of Polymer Solutions: Using Microfluidics and Single DNA Imaging

We study the necking and pinch-off dynamics of liquid droplets that contain a semidilute polymer solution of polyacrylamide close to overlap concentration by combining microfluidics and single DNA observation. Polymeric droplets are stretched by passing them through the stagnation point of a T-shaped microfluidic junction. In contrast with the sudden breakup of Newtonian droplets, a stable neck is formed between the separating ends of the droplet which delays the breakup process. Initially, polymeric filaments experience exponential thinning by forming a stable neck with extensional flow within the filament. Later, thin polymeric filaments develop a structure resembling a series of beads-on-a-string along their length and finally rupture during the final stages of the thinning process. To unravel the molecular picture behind these phenomena, we integrate a T-shaped microfluidic device with advanced fluorescence microscopy to visualize stained DNA molecules at the stagnation point within the necking region. We find that the individual polymer molecules suddenly stretch from their coiled conformation at the onset of necking. The extensional flow inside the neck is strong enough to deform and stretch polymer chains; however, the distribution of polymer conformations is broad, and it remains stationary in time during necking. Furthermore, we study the dynamics of single molecules during formation of beads-on-a-string structure. We observe that polymer chains gradually recoil inside beads while polymer chains between beads remain stretched to keep the connection between beads. The present work effectively extends single molecule experiments to free surface flows, which provides a unique opportunity for molecular-scale observation within the polymeric filament during necking and rupture.

DNA as a Model for Probing Polymer Entanglements: Circular Polymers and Non-Classical Dynamics

Double-stranded DNA offers a robust platform for investigating fundamental questions regarding the dynamics of entangled polymer solutions. The exceptional monodispersity and multiple naturally occurring topologies of DNA, as well as a wide range of tunable lengths and concentrations that encompass the entanglement regime, enable direct testing of molecular-level entanglement theories and corresponding scaling laws. DNA is also amenable to a wide range of techniques from passive to nonlinear measurements and from single-molecule to bulk macroscopic experiments. Over the past two decades, researchers have developed methods to directly visualize and manipulate single entangled DNA molecules in steady-state and stressed conditions using fluorescence microscopy, particle tracking and optical tweezers. Developments in microfluidics, microrheology and bulk rheology have also enabled characterization of the viscoelastic response of entangled DNA from molecular levels to macroscopic scales and over timescales that span from linear to nonlinear regimes. Experiments using DNA have uniquely elucidated the debated entanglement properties of circular polymers and blends of linear and circular polymers. Experiments have also revealed important lengthscale and timescale dependent entanglement dynamics not predicted by classical tube models, both validating and refuting new proposed extensions and alternatives to tube theory and motivating further theoretical work to describe the rich dynamics exhibited in entangled polymer systems.

Flow of DNA in micro/nanofluidics: From fundamentals to applications

Thanks to direct observation and manipulation of DNA in micro/nanofluidic devices, we are now able to elucidate the relationship between the polymer microstructure and its rheological properties, as well as to design new single-molecule platforms for biophysics and biomedicine. This allows exploration of many new mechanisms and phenomena, which were previously unachievable with conventional methods such as bulk rheometry tests. For instance, the field of polymer rheology is at a turning point to relate the complex molecular conformations to the nonlinear viscoelasticity of polymeric fluids (such as coil-stretch transition, shear thinning, and stress overshoot in startup shear). In addition, nanofluidic devices provided a starting point for manipulating single DNA molecules by applying basic principles of polymer physics, which is highly relevant to numerous processes in biosciences. In this article, we review recent progress regarding the flow and deformation of DNA in micro/nanofluidic systems from both fundamental and application perspectives. We particularly focus on advances in the understanding of polymer rheology and identify the emerging research trends and challenges, especially with respect to future applications of nanofluidics in the biomedical field.