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Vafa F, Nelson DR, Doostmohammadi A. Periodic orbits, pair nucleation, and unbinding of active nematic defects on cones. Phys Rev E 2024; 109:064606. [PMID: 39020887 DOI: 10.1103/physreve.109.064606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/06/2024] [Indexed: 07/20/2024]
Abstract
Geometric confinement and topological constraints present promising means of controlling active materials. By combining analytical arguments derived from the Born-Oppenheimer approximation with numerical simulations, we investigate the simultaneous impact of confinement together with curvature singularity by characterizing the dynamics of an active nematic on a cone. Here, the Born-Oppenheimer approximation means that textures can follow defect positions rapidly on the timescales of interest. Upon imposing strong anchoring boundary conditions at the base of a cone, we find a rich phase diagram of multidefect dynamics, including exotic periodic orbits of one or two +1/2 flank defects, depending on activity and nonquantized geometric charge at the cone apex. By characterizing the transitions between these ordered dynamical states, we present detailed understanding of (i) defect unbinding, (ii) defect absorption, and (iii) defect pair nucleation at the apex. Numerical simulations confirm theoretical predictions of not only the nature of the circular orbits but also defect unbinding from the apex.
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Barakat JM, Modica KJ, Lu L, Anujarerat S, Choi KH, Takatori SC. Surface Topography Induces and Orients Nematic Swarms of Active Filaments: Considerations for Lab-On-A-Chip Devices. ACS APPLIED NANO MATERIALS 2024; 7:12142-12152. [PMID: 38808306 PMCID: PMC11129142 DOI: 10.1021/acsanm.4c02020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/30/2024]
Abstract
Surface-bound molecular motors can drive the collective motion of cytoskeletal filaments in the form of nematic bands and polar flocks in reconstituted gliding assays. Although these "swarming transitions" are an emergent property of active filament collisions, they can be controlled and guided by tuning the surface chemistry or topography of the substrate. To date, the impact of surface topography on collective motion in active nematics is only partially understood, with most experimental studies focusing on the escape of a single filament from etched channels. Since the late 1990s, significant progress has been made to utilize the nonequilibrium properties of active filaments and create a range of functional nanodevices relevant to biosensing and parallel computation; however, the complexity of these swarming transitions presents a challenge when attempting to increase filament surface concentrations. In this work, we etch shallow, linear trenches into glass substrates to induce the formation of swarming nematic bands and investigate the mechanisms by which surface topography regulates the two-dimensional (2D) collective motion of driven filamentous actin (F-actin). We demonstrate that nematic swarms only appear at intermediate trench spacings and vanish if the trenches are made too narrow, wide, or tortuous. To rationalize these results, we simulate the F-actin as self-propelled, semiflexible chains subject to a soft, spatially modulated potential that encodes the energetic cost of bending a filament along the edge of a trench. In our model, we hypothesize that an individual filament experiences a penalty when its projected end-to-end distance is smaller than the trench spacing ("bending and turning"). However, chains that span the channel width glide above the trenches in a force- and torque-free manner ("crowd-surfing"). Our simulations demonstrate that collections of filaments form nematic bands only at intermediate trench spacings, consistent with our experimental findings.
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Affiliation(s)
| | | | - Le Lu
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Stephanie Anujarerat
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Kyu Hwan Choi
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Sho C. Takatori
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
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Shankar S, Scharrer LVD, Bowick MJ, Marchetti MC. Design rules for controlling active topological defects. Proc Natl Acad Sci U S A 2024; 121:e2400933121. [PMID: 38748571 PMCID: PMC11127047 DOI: 10.1073/pnas.2400933121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/12/2024] [Indexed: 05/27/2024] Open
Abstract
Topological defects play a central role in the physics of many materials, including magnets, superconductors, and liquid crystals. In active fluids, defects become autonomous particles that spontaneously propel from internal active stresses and drive chaotic flows stirring the fluid. The intimate connection between defect textures and active flow suggests that properties of active materials can be engineered by controlling defects, but design principles for their spatiotemporal control remain elusive. Here, we propose a symmetry-based additive strategy for using elementary activity patterns, as active topological tweezers, to create, move, and braid such defects. By combining theory and simulations, we demonstrate how, at the collective level, spatial activity gradients act like electric fields which, when strong enough, induce an inverted topological polarization of defects, akin to a negative susceptibility dielectric. We harness this feature in a dynamic setting to collectively pattern and transport interacting active defects. Our work establishes an additive framework to sculpt flows and manipulate active defects in both space and time, paving the way to design programmable active and living materials for transport, memory, and logic.
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Affiliation(s)
- Suraj Shankar
- Department of Physics, Harvard University, Cambridge, MA02138
- Department of Physics, University of Michigan, Ann Arbor, MI48109
| | - Luca V. D. Scharrer
- Department of Physics, University of California, Santa Barbara, CA93106
- Department of Physics, The University of Chicago, Chicago, IL60637
| | - Mark J. Bowick
- Department of Physics, University of California, Santa Barbara, CA93106
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA93106
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Vélez-Cerón I, Guillamat P, Sagués F, Ignés-Mullol J. Probing active nematics with in situ microfabricated elastic inclusions. Proc Natl Acad Sci U S A 2024; 121:e2312494121. [PMID: 38451942 PMCID: PMC10945829 DOI: 10.1073/pnas.2312494121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/27/2024] [Indexed: 03/09/2024] Open
Abstract
In this work, we report a direct measurement of the forces exerted by a tubulin/kinesin active nematic gel as well as its complete rheological characterization, including the quantification of its shear viscosity, η, and its activity parameter, α. For this, we develop a method that allows us to rapidly photo-polymerize compliant elastic inclusions in the continuously remodeling active system. Moreover, we quantitatively settle long-standing theoretical predictions, such as a postulated relationship encoding the intrinsic time scale of the active nematic in terms of η and α. In parallel, we infer a value for the nematic elasticity constant, K, by combining our measurements with the theorized scaling of the active length scale. On top of the microrheology capabilities, we demonstrate strategies for defect encapsulation, quantification of defect mechanics, and defect interactions, enabled by the versatility of the microfabrication strategy that allows to combine elastic motifs of different shapes and stiffnesses that are fabricated in situ.
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Affiliation(s)
- Ignasi Vélez-Cerón
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Barcelona08028, Spain
- Institute of Nanoscience and Nanotechnology, IN2UB, Universitat de Barcelona, Barcelona08028, Spain
| | - Pau Guillamat
- Institute for Bioengineering of Catalonia, The Barcelona Institute for Science and Technology, Barcelona08028, Spain
| | - Francesc Sagués
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Barcelona08028, Spain
- Institute of Nanoscience and Nanotechnology, IN2UB, Universitat de Barcelona, Barcelona08028, Spain
| | - Jordi Ignés-Mullol
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Barcelona08028, Spain
- Institute of Nanoscience and Nanotechnology, IN2UB, Universitat de Barcelona, Barcelona08028, Spain
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Canavello D, Damascena RH, Cabral LRE, de Souza Silva CC. Polar order, shear banding, and clustering in confined active matter. SOFT MATTER 2024; 20:2310-2320. [PMID: 38363303 DOI: 10.1039/d3sm01721d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
We investigate the collective behavior of sterically interacting self-propelled particles confined in a harmonic potential. Our theoretical and numerical study unveils the emergence of distinctive collective polar organizations, revealing how different levels of interparticle torques and noise influence the system. The observed phases include the shear-banded vortex, where the system self organizes in two concentric bands rotating in opposite directions around the potential center; the uniform vortex, where the two bands merge into a close packed configuration rotating uniformly as a quasi-rigid body; and the orbiting polar state, characterized by parallel orientation vectors and the cluster revolving around the potential center, without rotation, as a rigid body. Intriguingly, at lower filling fractions, the vortex and polar phases merge into a single phase where the trapped cluster breaks into smaller polarized clusters, each one orbiting the potential center as a rigid body.
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Affiliation(s)
- Daniel Canavello
- Departamento de Física, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Recife, PE, 50670-901, Brazil.
| | - Rubens H Damascena
- Departamento de Física, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Recife, PE, 50670-901, Brazil.
| | - Leonardo R E Cabral
- Departamento de Física, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Recife, PE, 50670-901, Brazil.
| | - Clécio C de Souza Silva
- Departamento de Física, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Recife, PE, 50670-901, Brazil.
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Li Y, Zarei Z, Tran PN, Wang Y, Baskaran A, Fraden S, Hagan MF, Hong P. A machine learning approach to robustly determine director fields and analyze defects in active nematics. SOFT MATTER 2024; 20:1869-1883. [PMID: 38318759 DOI: 10.1039/d3sm01253k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Active nematics are dense systems of rodlike particles that consume energy to drive motion at the level of the individual particles. They exist in natural systems like biological tissues and artificial materials such as suspensions of self-propelled colloidal particles or synthetic microswimmers. Active nematics have attracted significant attention in recent years due to their spectacular nonequilibrium collective spatiotemporal dynamics, which may enable applications in fields such as robotics, drug delivery, and materials science. The director field, which measures the direction and degree of alignment of the local nematic orientation, is a crucial characteristic of active nematics and is essential for studying topological defects. However, determining the director field is a significant challenge in many experimental systems. Although director fields can be derived from images of active nematics using traditional imaging processing methods, the accuracy of such methods is highly sensitive to the settings of the algorithms. These settings must be tuned from image to image due to experimental noise, intrinsic noise of the imaging technology, and perturbations caused by changes in experimental conditions. This sensitivity currently limits automatic analysis of active nematics. To address this, we developed a machine learning model for extracting reliable director fields from raw experimental images, which enables accurate analysis of topological defects. Application of the algorithm to experimental data demonstrates that the approach is robust and highly generalizable to experimental settings that are different from those in the training data. It could be a promising tool for investigating active nematics and may be generalized to other active matter systems.
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Affiliation(s)
- Yunrui Li
- Computer Science Department, Brandeis University, USA.
| | - Zahra Zarei
- Physics Department, Brandeis University, USA
| | - Phu N Tran
- Physics Department, Brandeis University, USA
| | - Yifei Wang
- Computer Science Department, Brandeis University, USA.
| | | | - Seth Fraden
- Physics Department, Brandeis University, USA
| | | | - Pengyu Hong
- Computer Science Department, Brandeis University, USA.
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Mitchell KA, Sabbir MMH, Geumhan K, Smith SA, Klein B, Beller DA. Maximally mixing active nematics. Phys Rev E 2024; 109:014606. [PMID: 38366395 DOI: 10.1103/physreve.109.014606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/30/2023] [Indexed: 02/18/2024]
Abstract
Active nematics are an important new paradigm in soft condensed matter systems. They consist of rodlike components with an internal driving force pushing them out of equilibrium. The resulting fluid motion exhibits chaotic advection, in which a small patch of fluid is stretched exponentially in length. Using simulation, this paper shows that this system can exhibit stable periodic motion when confined to a sufficiently small square with periodic boundary conditions. Moreover, employing tools from braid theory, we show that this motion is maximally mixing, in that it optimizes the (dimensionless) "topological entropy"-the exponential stretching rate of a material line advected by the fluid. That is, this periodic motion of the defects, counterintuitively, produces more chaotic mixing than chaotic motion of the defects. We also explore the stability of the periodic state. Importantly, we show how to stabilize this orbit into a larger periodic tiling, a critical necessity for it to be seen in future experiments.
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Affiliation(s)
- Kevin A Mitchell
- Physics Department, University of California, Merced, California 95344, USA
| | | | - Kevin Geumhan
- Physics Department, University of California, Merced, California 95344, USA
| | - Spencer A Smith
- Physics Department, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
| | - Brandon Klein
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Daniel A Beller
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, USA
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Mori F, Bhattacharyya S, Yeomans JM, Thampi SP. Viscoelastic confinement induces periodic flow reversals in active nematics. Phys Rev E 2023; 108:064611. [PMID: 38243430 DOI: 10.1103/physreve.108.064611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/22/2023] [Indexed: 01/21/2024]
Abstract
We use linear stability analysis and hybrid lattice Boltzmann simulations to study the dynamical behavior of an active nematic confined in a channel made of viscoelastic material. We find that the quiescent, ordered active nematic is unstable above a critical activity. The transition is to a steady flow state for high elasticity of the channel surroundings. However, below a threshold elastic modulus, the system produces spontaneous oscillations with periodic flow reversals. We provide a phase diagram that highlights the region where time-periodic oscillations are observed and explain how they are produced by the interplay of activity and viscoelasticity. Our results suggest experiments to study the role of viscoelastic confinement in the spatiotemporal organization and control of active matter.
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Affiliation(s)
- Francesco Mori
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - Saraswat Bhattacharyya
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - Julia M Yeomans
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - Sumesh P Thampi
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai-36, India
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Ray S, Zhang J, Dogic Z. Rectified Rotational Dynamics of Mobile Inclusions in Two-Dimensional Active Nematics. PHYSICAL REVIEW LETTERS 2023; 130:238301. [PMID: 37354394 DOI: 10.1103/physrevlett.130.238301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/14/2023] [Indexed: 06/26/2023]
Abstract
We investigate the dynamics of mobile inclusions embedded in 2D active nematics. The interplay between the inclusion shape, boundary-induced nematic order, and autonomous flows powers the inclusion motion. Disks and achiral gears exhibit unbiased rotational motion, but with distinct dynamics. In comparison, chiral gear-shaped inclusions exhibit long-term rectified rotation, which is correlated with dynamics and polarization of nearby +1/2 topological defects. The chirality of defect polarities and the active nematic texture around the inclusion correlate with the inclusion's instantaneous rotation rate. Inclusions provide a promising tool for probing the rheological properties of active nematics and extracting ordered motion from their inherently chaotic motion.
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Affiliation(s)
- Sattvic Ray
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Jie Zhang
- Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China (USTC), 230026 Hefei, China
- Department of Polymer Science and Engineering, CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China (USTC), 230026 Hefei, China
| | - Zvonimir Dogic
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
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de Oliveira E, Mirantsev L, Lyra M, de Oliveira I. Orientational ordering of active nematics confined to a 2D nanoscopic ring-shaped cavity. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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