Bulletin of the American Physical Society
APS March Meeting 2023
Volume 68, Number 3
Las Vegas, Nevada (March 5-10)
Virtual (March 20-22); Time Zone: Pacific Time
Session W04: Single-Molecule Characterization in Polymers and Soft Matter: Topology and Transport |
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Sponsoring Units: DPOLY Chair: Danielle Mai, Stanford University; Alexander Klotz Room: Room 127 |
Thursday, March 9, 2023 3:00PM - 3:12PM |
W04.00001: Polymer transport through a fractal metamaterial Robert Riehn Many natural environments, like the cell nucleus, feature polymer transport through a confined space that is characterized by multiple scales which follow a fractal scaling. One would expect that a polymer traversing such an environment must be capable of traveling using multiple qualitatively different transport and confinement regimes. However, the majority of prior experiments using single nanoconfined polymers have tested a single confinement regime, or the (possibly gradual) transition between two regimes. Here we test the transport of double-stranded DNA through nanochannel systems that form metamaterials with a dimensionality between one and two, and compare the observed configuations with hierarchical materials that follow the same design rules, but are of dimensionality two. |
Thursday, March 9, 2023 3:12PM - 3:24PM |
W04.00002: Diffusion of knots in nanochannel-confined DNA molecules Runfang Mao, Kevin D Dorfman Long polymers such as DNA can form knots in confinement. For linear DNA, these knots are destroyed by diffusion of the knot to the chain end. However, the diffusion mechanisms of knots in confined systems, especially the dynamic evolution of untying knots, remain open questions. To address this issue, we used Langevin dynamics simulations to probe the typical mechanisms governing the dynamic evolution and the spontaneous untying of trefoil knots in nanochannel-confined DNA molecules of different chain contour lengths in the extended de Gennes regime. Specifically, we investigate the unknotting process by quantifying how the structural properties, such as knot size, knot span, knot radius of gyration, vary with knot position along the chain. The knot untying follows an “opening up process”, wherein the knot continues growing in size and becomes increasingly looser as it moves to the end of DNA molecules. The calculated average size, span and radius of gyration of opened knots increase significantly with chain contour lengths. Additionally, the diffusion process of knots in nanochannel-confined DNA molecules is subdiffusive, albeit without hydrodynamic interactions between DNA and its environment. The unknotting time of knots as a function of chain contour lengths follows a power law, with a scaling exponent around 2.64. |
Thursday, March 9, 2023 3:24PM - 3:36PM |
W04.00003: On the settling dynamics of Brownian filaments in centrifuge systems and field-induced knot tightening Lucas Hildebrand Pires da Cunha, Sibani Lisa Biswal, Frederick C MacKintosh We investigate the settling dynamics of elastic Brownian filaments by analyzing a wide range of Peclet numbers. Using the Brownian Dynamics method, we make a statistical study on the dynamics of a single filament over a long period of time. We observe that the competition between gravitational and thermal effects can either increase or decrease the average settling velocity of the filaments. Also, the filament's flexibility plays a strong role in the diffusion of the filament perpendicular to gravity, resulting in supper diffusion-like behavior in some cases. At highly flexible regimes, we identify field-induced compaction of the filament, as well as the stabilization of knot structures at high Peclet numbers. |
Thursday, March 9, 2023 3:36PM - 3:48PM |
W04.00004: Mechanical Properties of Partially Degraded Kinetoplast DNA Henry S Sundland, Alexander R Klotz
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Thursday, March 9, 2023 3:48PM - 4:00PM |
W04.00005: Single-Molecule Studies of Confined Branched Polymers Louis Wang, Danielle J Mai Branched biopolymers such as lubricin and mucin play crucial roles in controlling biolubrication behavior. Biolubrication occurs at interfaces, which can be modeled as confined environments. Understanding the behavior of branched polymers at the single-molecule level is critical to understanding their behavior at the ensemble level. In this study, we investigate topologically complex polymers placed in confined environments by observing changes in the diffusivity and conformation of branched polymers in 1D slit-like confinement. We demonstrate the synthesis of branched DNA polymers by enzymatic replication of linear precursors and biochemical coupling of DNA branches onto DNA backbones. We fabricate nanofluidic devices with high-aspect-ratio nanochannels using wet etch nanolithography on borosilicate glass substrates and validate the channel dimensions using optical profilometry. We observe the single-molecule behavior of branched polymers inside nanochannels using fluorescence optical microscopy. Understanding of molecular-scale contributions to biolubrication will enable the design of novel materials to treat lubrication-deficient diseases. |
Thursday, March 9, 2023 4:00PM - 4:12PM |
W04.00006: Investigation of Bottlebrush Polymer Chain Conformations under Mechanical Deformation using Super-Resolution Optical Microscopy Ruiqi Xiao, Jonathan M Chan, Tyler R Heyl, Qifeng Wang, Kenneth R Shull, Muzhou Wang Understanding polymer behavior under mechanical deformation is a fundamentally important topic in polymer physics. Despite significant modeling, simulation, and experimental effort, studies at the molecular level are still challenging to perform, especially for real-time characterization of chain conformations. In this work, we directly visualized bottlebrush polymers in a thin film using super-resolution optical microscopy (SROM), as they were compressed under a spherical piezoelectric-controlled indenter. The film consists of poly(n-butyl acrylate) bottlebrushes where a small portion was labeled by a photoswitchable dye. Using SROM, we were able to observe and quantitatively describe the change in the orientation of the bottlebrush chains in the strain field during spherical indentation. We then solved the strain field by finite-element simulation and correlated the experimental and theoretical results. Our study provides a single-molecule description of polymer chain behavior within a solid material under deformation, which contributes to establishing the correlation between the unique macroscale mechanical properties of bottlebrush elastomers and microscale molecular motion. |
Thursday, March 9, 2023 4:12PM - 4:24PM |
W04.00007: Role of Topology on Properties of a Two-Dimensional Catenated DNA Network Indresh Yadav, Dana Al Sulaiman, Patrick S Doyle The topology of polymer molecules plays an important role in determining their physical properties. Tuning the topology of molecules is thus imperative in controlling the physiochemical properties tailored for desired applications. We studied herein the role of topology on the static and dynamic properties of a two-dimensional (2D) catenated network of DNA rings called a kinetoplast. A kinetoplast is a catenated DNA network of thousands (~ 5000) of rings and presents a robust model system to study the physical properties of 2D polymers and Olympic gels. The heterogeneity in base pair sequencing of different classes of rings within the kinetoplast network and the precise action of restriction enzymes have been harnessed to tune the topology of the kinetoplast network. We find that irrespective of topology the spatial extension of the network remains invariant, however, it significantly affects the shape fluctuations of the network. Irrespective of details of the molecular topology, the relationship between the time constant of thermal relaxation and variance of shape anisotropy shows a universal scaling. Our results provide a route to selectively tune the elastic properties of 2D catenated DNA networks by modifying the underlying topology. |
Thursday, March 9, 2023 4:24PM - 4:36PM |
W04.00008: Enhanced detection of single molecule and stochastic interactions under nanoconfinement Santosh Khatri, Jin He Individual molecular behavior influences biochemical processes and the properties of individual cells, ultimately involving the complex behavior of living beings. Many techniques have emerged to understand the single molecule. The single-molecule detection technique, namely the nanopore sensing method is being developed as a powerful tool to probe detailed investigation of single molecules because of its applications to diverse fields of nanoscience like drug discovery, early detection of diseases, and medical diagnostics. Nanopipette, as a sub-type of solid-state nanopores, has long been used to detect and identify proteins and DNAs for several years. However, an effective method for the detection of molecules with 1-2 nm size was currently lacking through nanopipette due to nanopipette size variation and fast translocation speed of biomolecules. In this talk, I will show our new method to employ the nanoconfinement effect of the nanopipette tip to detect small molecules, including nucleotides and short peptides, with high event rates and high signal-to-noise ratio. We have also successfully probed the intermolecular interactions between small biomolecules. |
Thursday, March 9, 2023 4:36PM - 4:48PM |
W04.00009: Unique Stretching Dynamics of Single Ring Polymers in 3-Dimensional Flows Hung V Nguyen, Charles M Schroeder Ring polymers are a unique class of macromolecules that lack free ends and exhibit unique flow properties due to their closed chain topology. Despite recent progress, we lack a complete understanding of the nonequilibrium behavior of ring polymers in flow. Prior work in single polymer dynamics has nearly exclusively focused on studying polymer motion in two-dimensional (2D) flows generated in planar microfluidic geometries. In this work, we report the direct observation of ring DNA dynamics in 3D flow fields using single molecule techniques. We study the transient and steady-state stretching dynamics of single DNA ring polymers in both uniaxial and biaxial extensional flows using a 3D-printed microfluidic device coupled with simultaneous dual orthogonal-plane imaging and fluorescence microscopy. Our results show clear differences in the conformational stretching dynamics and coil-stretch transition of ring polymers in 3D extensional flows relative to planar extensional flow. In all cases, results for ring polymer dynamics in 3D flows are directly compared to linear chain counterparts. Overall, our results provide a new understanding of the nonequilibrium dynamics of ring polymers in 3D flows. |
Thursday, March 9, 2023 4:48PM - 5:00PM |
W04.00010: Entropic force of cone-tethered polymers interacting with a planar surface James M Polson, Roland G MacLennan Computer simulations are used to characterize the entropic force of one or more polymers tethered to the tip of a hard conical object that interact with a nearby hard flat surface. Pruned-enriched-Rosenbluth-method (PERM) Monte Carlo simulations are used to calculate the variation of the conformational free energy, F, of a hard-sphere polymer with respect to cone-tip-to-surface distance, h, from which the variation of the entropic force, f ≡ |dF/dh|, with h is determined. We consider the following cases: (1) a single freely-jointed tethered chain, (2) a single semiflexible tethered chain, and (3) several freely-jointed chains of equal length each tethered to the cone tip. The simulation results are used to test the validity of a prediction by Maghrebi et al. (EPL, 96, 66002(2011); Phys. Rev. E 86, 061801 (2012)) that f ∝ (γ∞ - γ0) h-1, where γ0 and γ∞ are universal scaling exponents for the partition function of the tethered polymer for h=0 and ∞, respectively. The measured functions f(h) are generally consistent with the predictions, with small quantitative discrepancies arising from the approximations employed in the theory. In the case of multiple tethered polymers, the entropic force per polymer is roughly constant, which is qualitatively inconsistent with the predictions. |
Thursday, March 9, 2023 5:00PM - 5:12PM |
W04.00011: Molecular Mechanism of Chain Expulsion from a Diblock Copolymer Micelle Sarah C Seeger, Timothy P Lodge, Kevin D Dorfman The self-assembly of diblock copolymers in solution results in micelles with tunable properties relevant for numerous applications, including oil-based lubrication and drug delivery. Recent experiments studying single chain exchange, the relaxation mechanism governing the dynamics of micelles in solution around equilibrium, have resulted in controversy surrounding the molecular mechanism of this process. We will present results of coarse-grained dissipative particle dynamics simulations that characterize the trajectory of chain expulsion and furnish insights into the core-block conformations during expulsion from a micelle. Using umbrella sampling, we computed the free energy trajectory for the expulsion of a single chain of varying core block length from an isolated micelle. We find that the chain undergoing expulsion adopts a 'hyperstretched' configuration as it nears the transition state, allowing some monomers to remain in the micelle core until the chain is fully expelled. We will provide a simple model to describe this proposed mechanism of chain expulsion, which captures the scaling behavior of our simulations and is consistent with previous experimental results. |
Thursday, March 9, 2023 5:12PM - 5:24PM |
W04.00012: Scattering model to analyze non-Gaussian deformations of dilute polymers solutions in high shear flows Anukta Datta, Katie M Weigandt, Xiaoyan Wang, Ryan P Murphy, Patrick T Underhill, Matthew E Helgeson Applications of high molecular weight dilute polymer solutions typically involve extreme shear rates that cause nonlinear deformations and chain scission. Although various microscopy methods have been successful for resolving single-molecule deformations for specific biopolymer systems (e.g. DNA), these methods are inaccessible to conventional, synthetic polymers. Recent in situ measurement capabilities using a capillary device allow us to extract microstructural information from SANS measurements about flow-induced deformation at extreme shear rates (~106 s-1) and holds excellent potential for single-molecule studies. However, previously developed analyses for anisotropic scattering of polymers in flow are limited to Gaussian chains, and thus are inadequate for nonlinear strains and strain rates. We introduce a new modeling framework that resolves non-Gaussian deformations of polymers in high shear flows through moments of the chain conformation distribution. The method is then validated using synthetic datasets from parameter-matched Brownian dynamics simulations, and applied to capillary rheo-SANS measurements on a series of architecturally well-defined polymers at high shear flows in order to test the influence of chain topology on non-Gaussian polymer deformations. We anticipate that this new analysis method will inform the rational design of topologically-defined polymers to optimize their performance and lifetime in their applications as rheological modifiers. |
Thursday, March 9, 2023 5:24PM - 5:36PM |
W04.00013: Nanopore tomography for quantitative assessment of geometrical parameters of filamentous fd bacteriophage Arjav Shah, Kun Li, Slaven Garaj, Patrick S Doyle An understanding of the morphology of viruses is critical to understanding their function in a physiological environment as well as for modern, bio-inspired applications. Several imaging techniques including TEM and AFM have been used to characterize single particles. However, there is a need for a rapid and high-throughput method. Nanopore tomography (NT) is an emerging single-particle technique with the ability to measure the geometrical features of individual viruses. |
Thursday, March 9, 2023 5:36PM - 5:48PM |
W04.00014: Electrokinetic Brownian dynamics of current blockade of a dsDNA through a nanopore Swarnadeep Seth, Aniket Bhattacharya Brownian Dynamics (BD) simulation has been shown to be effective for understanding and providing physical insights into the complex processes of long dsDNA translocation through nanopores [1-3]. We expand our BD study by considering the movement of the co-ions and counter-ions along with a short-chain dsDNA decorated with oligo-flap markers through a nanopore. The inclusion of the ions and counterions enables us to calculate the current blockade (CB) directly from the electrokinetic Brownian dynamics (EKBD) simulation and compare it to a simpler but computationally efficient model of CB that uses the volumetric occupancy of the species in the nanopore. By comparing both CB data sets, we finally tune the adjustable parameters of the volumetric CB model, which enables us to construct the CB data for a very long dsDNA strand (~Mbp) with high accuracy but at a much lower computational cost. We further compare the Peclet number of both the simulation and experiments to validate our findings. Moreover, we investigate the effect of mono-and divalent ion concentration on the noise levels in the current blockade and the translocation speed, which we believe to be helpful for improving the signal-to-noise ratio of the nanopore current blockade data. |
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