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 Q09: Active Polymers: Organisation and DynamicsFocus
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Sponsoring Units: DSOFT DPOLY GSNP Chair: Antoine Deblais, University of Amsterdam; Saad Bhamla Room: Room 132 |
Wednesday, March 8, 2023 3:00PM - 3:36PM |
Q09.00001: Interplay between topology and confinement in active polymers Invited Speaker: Emanuele Locatelli Active systems, due to the local breaking of equilibrium, allow for phenomena that their equilibrium counterparts cannot attain. This correspondence between microscopic local equilibrium breaking and the meso/macroscopic structure formation is a general feature that have been observed in diverse systems including bacteria and synthetic swimmers. A similar behaviour can be observed also in the case of polar active polymers, i.e. polymers made of active monomers whose activity is directed as the local tangent to the polymer backbone. For example, a coil-to-globule-like transition takes place for isolated active chains in three dimension, highlighted by a marked change of the scaling exponent of the gyration radius[1]. Driven by the relevance of confinement and topology on the structural and dynamical properties of passive systems, we investigate the interplay between these latter and activity for tangentially active polymers. We explore the dynamics of active polymers in corrugated channels, highlighting the differences with respect to the passive case[2]. In the bulk, isolated rings display two different regimes at high enough activity: short rings tend to become "stiffer" and to assume a disk-like conformation, whereas long rings collapse, forming tight structures that show the hallmarks of dynamical arrest[3]. Finally, when placed under confinement, suspensions of short active rings assemble in ordered phases [4]. |
Wednesday, March 8, 2023 3:36PM - 3:48PM |
Q09.00002: Ultrafast reversible self-assembly of living tangled matter Vishal P Patil, Harry Tuazon, Emily Kaufman, Tuhin Chakrabortty, David Qin, Jorn Dunkel, Saad Bhamla Tangled active filaments are ubiquitous in nature, from chromosomal DNA and cilia carpets to root networks and worm blobs. How activity and elasticity facilitate collective topological transformations in living tangled matter is not well understood. Here, we report an experimental and theoretical study of California blackworms (Lumbriculus variegatus), which slowly form tangles over minutes but can untangle in milliseconds. Combining ultrasound imaging, theoretical analysis and simulations, we develop and validate a mechanistic model that explains how the kinematics of individual active filaments determines their emergent collective topological dynamics. The model reveals that resonantly alternating helical waves enable both tangle formation and ultrafast untangling. By identifying generic dynamical principles of topological self-transformations, our results can provide guidance for designing new classes of topologically tunable active materials. |
Wednesday, March 8, 2023 3:48PM - 4:00PM |
Q09.00003: Navigating disordered landscapes with touch: Lessons from blackworms Arshad Kudrolli, Animesh Biswas We will discuss the dynamics of {it Lumbriculus variegatus}, also known as the blackworm, as they navigate a series of chambers connected by narrow passages where steric interactions with confining walls lead to significant barriers for transport. By observing these long slender worms inside transparent hard-walled chambers, we visualize and track the entire shape of their body as they collide with the walls, locate passages, and repeatedly pass back and forth between the chambers. We show that the worm does not explore the chambers ergodically but remains close to the boundary as its head repeatedly collide with the wall, while its tail and center of mass stay away, as the worm follows the boundary. In a regime where the passage width is greater than the worm width, the frequency with which the worm's head locates the passage is found to increase rapidly before essentially becoming constant with increasing width. We discuss this crossover in terms of the time scale and distance over which the head loses contact with the boundary. We further show the impact of the body strokes on the penetration depth of the worm down the passage, and in successfully traversing the passage between the chambers. The implication of the measured traversal rates on the transport properties in a randomly connected set of chambers representing a quasi-2D porous medium will be discussed. |
Wednesday, March 8, 2023 4:00PM - 4:12PM |
Q09.00004: Tunable stiffness exhibited in entangled collectives of aquatic worms and biomimetic soft robots Ishant Tiwari, Harry Tuazon, Junghan Kwon, Robert J Wood, Justin Werfel, Saad Bhamla The California blackworm (Lumbriculus variegatus) is an aquatic worm that forms aggregate structures called worm blobs by twisting their slender bodies around other worms of its kind. These blobs provide a variety of advantages to the worm in its natural environment, ranging from protection from the elements, nourishment and better mobility than what is achievable in isolation. These entangled collectives have been found to tune their rigidity under varied stimuli. Here, we modulate the dissolved oxygen (DO) concentration inside the water to tune the worm blob's rigidity/entanglement. We measure the force applied by the blob under different DO concentrations, when subjected to external untangling forces. It is found that the blob applies a significantly larger force when in a high DO environment compared to when in a low DO one. We also find that their structural integrity is higher when present in high oxygen environments, showing typical solid like effects such as toppling over in the presence of unbalanced forces. The insights obtained from these biological aggregates have applications in development of soft robotic systems which can act as a "programmable glue" between substrates. |
Wednesday, March 8, 2023 4:12PM - 4:24PM |
Q09.00005: Aggregation of entangled active polymers Saad Bhamla, Prathyusha K R Nature provides various examples of active matter systems containing self-driven constituents capable of coordinated motion. When the individual objects are flexible, fascinating collective behavior is observed, and most studies were inspired by coherently moving bundles of flexible microtubules or clustering bacteria on two-dimensional surfaces. Recent experiments on Tubifex worms and California blackworms demonstrated that the active worms could entangle their bodies to form a worm bundle, and the structure greatly resembles an entangled passive polymer blob. However, it is largely unclear how the interplay between length, flexibility, and self-propulsion of the individual unit controls the behavior of such an entangled active polymer bundle. Using computer simulation that employs a three-dimensional model for entangled active polymer, we study the individual dynamics of the polymer and the aggregation mechanism. We consider the poly-disperse system of active polymers, and we vary the flexibility and activity of the polymer. We demonstrate that the individual activity of polymer has different effects on the collective properties of the system. We believe that our study will shed light not only on the self-organization of flexible invertebrates but also on the design principles of entangled soft robotic models. |
Wednesday, March 8, 2023 4:24PM - 4:36PM |
Q09.00006: Chromatographic Separation of Active Polymer-like Worm Mixtures by Contour Length and Activity Antoine Deblais, Tess Heeremans, Daniel Bonn, Sander Woutersen The convective transport rate of polymers through confined geometries depends on their size, allowing for size-based separation of polymer mixtures (chromatography). Here, we investigate if mixtures of active polymers can be separated in a similar manner based on their activity. We use thin living worms Tubifex tubifex as a model system for active polymers and study the transport of these worms by an imposed flow through a channel filled with a hexagonal-pillar array. The transport rate through the channel depends strongly on the degree of activity, an effect that we assign to the different distribution of conformations sampled by the worms depending on their activity. Our results demonstrate a unique way to sort mixtures of active polymers based on their activity and provide a versatile and convenient experimental system to investigate the hydrodynamics of active polymers. |
Wednesday, March 8, 2023 4:36PM - 4:48PM |
Q09.00007: Relating the steady states of 3D dry active nematics to microscopic parameters through particle-based simulations Yingyou Ma, Michael F Hagan, Aparna Baskaran, Chris Amey Active nematic liquid crystals exhibit a wide range of fascinating topological structures and dynamics, many of which are forbidden in equilibrium systems. Although it is well known that such systems form complex defect networks in 3D [1-4], the relationship between a system’s microscopic parameters and its coarse-grained macroscopic properties is unclear. In this work, we perform large-scale particle-based simulations of 3D dry active nematic filaments to understand the connection between microscopic simulation parameters, such as the bending stiffness and active force amplitude, and the emergent coarse-grained parameters. We find that the collective behaviors of this nonequilibrium system can be described by coarse-grained moduli analogous to an equilibrium system, but that activity significantly renormalizes the apparent material constants. The relative values of these effective moduli reflect the fact that the particle-scale energy injected by activity dissipates preferentially into certain modes. For example, the coarse-grained effective bending modulus can be understood to arise from a balance between the filaments’ intrinsic bending stiffness and activity-induced collisions. |
Wednesday, March 8, 2023 4:48PM - 5:00PM |
Q09.00008: Reorientation dynamics in simulated pair-interactions of flexible, penetrable, active filaments Nathan W Prouse, Madhuvanthi Athani, Julian Davis, Patrick Noerr, Niranjan Sarpangala, Ajay Gopinathan, Kinjal Dasbiswas, Daniel A Beller Recent gliding assay experiments on microtubules and actin show that long-range ordered (LRO) active nematic phases of self-propelled filaments can emerge through a combination of collision-induced alignment and crossover events. To gain understanding about how this LRO arises from microscopic interactions, we employ Brownian dynamics simulations of flexible, self-propelled bead-spring chains with a finite energetic penalty for overlap, which permits crossovers when the incident angle of collision is sufficiently large. The interactions in our model contain no aligning potentials; rather, we show how alignment emerges from isotropic interactions between the beads of neighboring active chains. Our results indicate that the reorientation of filament pairs is highly sensitive to their incident angle, their bending rigidity, and their penetrability. |
Wednesday, March 8, 2023 5:00PM - 5:12PM |
Q09.00009: Microtubules in Elastic Networks Isabel Ruffin, Zvonimir Dogic Microtubules and their associated motor proteins are a model system for understanding fundamental properties of active materials. Dynamic interactions of these proteins have predominantly been investigated using fluorescence microscopy and 2D gliding assays in which either the microtubules or the motors are immobilized on a glass surface. We study the motion of gliding microtubules in 3D networks. In addition, cooperative behavior of multiple kinesin motors is poorly understood even in 2D, though individual motor activity is well understood. A 3D motility assay coupled to an elastic medium has potential to provide a more complete picture into cooperative behavior of multiple interacting microtubules. The medium's response to activity provides a way to measure motor force and characterize motor cooperativity. |
Wednesday, March 8, 2023 5:12PM - 5:24PM |
Q09.00010: Conformational dynamics of a flexible polymer in a confined active fluid Scott Weady, David Stein, Michael J Shelley, Alexandra Zidovska Chromatin, the functional form of DNA inside cells, has a form of a complex biopolymer immersed in the nucleoplasmic fluid and confined in the cell nucleus. Recent in vivo experiments have shown that ATP-powered activity drives coherent motions of chromatin inside the nucleus, which persist for several seconds and extend over a few microns. Motivated by these observations, here we consider a long flexible polymeric chain immersed in a suspension of active force dipoles as a simplified model for a chromatin fiber in an active fluid, the nucleoplasm. Using multiscale continuum modeling and immersed boundary simulations, we study how the dynamics and conformations of these confined, densely packed chains are affected by active nucleoplasmic flows and by the details of their microstructure. Our simulations show that extensile activity can increase correlations of coherent motions in time, and these correlations are closely tied to alignment interactions between the chain and the suspension. This work demonstrates how interactions between active and passive structures can lead to large-scale organization in a general setting. |
Wednesday, March 8, 2023 5:24PM - 5:36PM |
Q09.00011: Asters, bilayers and foams in coarse-grained model of active filament interactions Filippo De Luca, Ivan Maryshev, Erwin Frey Microtubule-motor mixtures are a prime example of how living matter self-organizes into complex structures emerging from interactions between relatively simple constituents. Recently, experimental advances found a novel non-equilibrium phase of matter in these mixtures known as active foams [1], that consist of a network of bilayers experiencing continuous reconfiguration. We propose a microscopic model for motor-mediated filament-filament interactions and rigorously derive a continuum theory for the system. We discuss the phase diagram of our model, exhibiting asters, bilayers and active foams, and we inspect the mechanisms that drive the transition between these structures. Our work demonstrates the link between microscopic interactions and mesoscopic pattern formation in active filament systems and paves the way for higher-level theoretical studies on active foams. |
Wednesday, March 8, 2023 5:36PM - 5:48PM |
Q09.00012: Mesoscale Polymer Ribbon Arrays: Biofilm-Inspired, Flexible, Fibrillar Adhesives Demi E Moed, Alfred J Crosby Biofilm formation and surface fouling cause many problems in aqueous environments. Thin, filamentous pili are one of the many tools leveraged by bacteria to adhere to numerous surface topographies and chemistries. These micron-long, nanometer-wide organelles create multiple points of flexible, adhesive contact with nearby substrates. To create a synthetic analog of this system, we turn to high aspect-ratio mesoscale polymer ribbons. These nanometer-thick and millimeter-long structures exhibit geometrically driven, environmentally sensitive 3D conformations in aqueous environments. Although single-ribbon dynamics are well-explored, it is essential that we understand the impact of environmental factors on the conformation of multi-ribbon systems, as this will likely dictate interactions with nearby surfaces. Using flow coating, we deposit fluorescent poly(tert-butyl methacrylate) ribbon arrays onto glass substrates coated with a poly(sodium styrene sulfonate) sacrificial layer. We probe the morphology of the ribbon arrays released into acidic, basic, and pH neutral environments as a function of time with confocal microscopy and machine vision techniques. We correlate these relationships to the capillary-driven adhesion of ribbon arrays to perfluorodecalin droplets using cantilever deflection. This work elucidates the underlying design principles of flexible, fibrillar underwater adhesives, and informs the development of future systems. |
Wednesday, March 8, 2023 5:48PM - 6:00PM Author not Attending |
Q09.00013: Active foams Ivan Maryshev, Filippo De Luca, Erwin Frey Recent experimental evidence revealed a new state of active matter in biofilaments and molecular motors mixtures called active foam [1]. These disordered cellular solids are always out of equilibrium – the edges constituting the foam appear and disappear, changing the morphology and topology of the whole network. Here we introduce a classification of such structures based on the dominating orientational order. We focus on two particular classes – nematic and polar active foams. We develop the hydrodynamic model for each foam type and show how the corresponding continuum theories can be derived by coarse-graining the motor-induced microscopic interactions between the filaments. Moreover, we demonstrate that the imbalance between polar and antipolar interactions determines the eventual macroscopic patterns. We investigate the instabilities and the characteristic length scales associated with each model and pin down the mechanisms underlying the foam formation. We also describe the motors' inhomogeneity role in forming "bilayers" – essential building blocks constituting polar active foams. Finally, we discuss potentially related experimental systems where the active foams could be realized. |
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