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Tran PN, Ray S, Lemma L, Li Y, Sweeney R, Baskaran A, Dogic Z, Hong P, Hagan MF. Deep-learning optical flow for measuring velocity fields from experimental data. SOFT MATTER 2024; 20:7246-7257. [PMID: 39225732 DOI: 10.1039/d4sm00483c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Deep learning-based optical flow (DLOF) extracts features in adjacent video frames with deep convolutional neural networks. It uses those features to estimate the inter-frame motions of objects. We evaluate the ability of optical flow to quantify the spontaneous flows of microtubule (MT)-based active nematics under different labeling conditions, and compare its performance to particle image velocimetry (PIV). We obtain flow velocity ground truths either by performing semi-automated particle tracking on samples with sparsely labeled filaments, or from passive tracer beads. DLOF produces more accurate velocity fields than PIV for densely labeled samples. PIV cannot reliably distinguish contrast variations at high densities, particularly along the nematic director. DLOF overcomes this limitation. For sparsely labeled samples, DLOF and PIV produce comparable results, but DLOF gives higher-resolution fields. Our work establishes DLOF as a versatile tool for measuring fluid flows in a broad class of active, soft, and biophysical systems.
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Affiliation(s)
- Phu N Tran
- Department of Physics, Brandeis University, Waltham, MA 02453, USA.
| | - Sattvic Ray
- Department of Physics, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
| | - Linnea Lemma
- Department of Physics, Brandeis University, Waltham, MA 02453, USA.
- Department of Physics, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
| | - Yunrui Li
- Department of Computer Science, Brandeis University, Waltham, MA 02453, USA.
| | - Reef Sweeney
- Department of Physics, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
| | - Aparna Baskaran
- Department of Physics, Brandeis University, Waltham, MA 02453, USA.
| | - Zvonimir Dogic
- Department of Physics, Brandeis University, Waltham, MA 02453, USA.
- Department of Physics, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
- Biomolecular and Engineering Science, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
| | - Pengyu Hong
- Department of Computer Science, Brandeis University, Waltham, MA 02453, USA.
| | - Michael F Hagan
- Department of Physics, Brandeis University, Waltham, MA 02453, USA.
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2
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Schimming CD, Reichhardt CJO, Reichhardt C. Active nematic ratchet in asymmetric obstacle arrays. Phys Rev E 2024; 109:064602. [PMID: 39021011 DOI: 10.1103/physreve.109.064602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/03/2024] [Indexed: 07/20/2024]
Abstract
We numerically investigate the effect of an asymmetric periodic obstacle array in a two-dimensional active nematic. We find that activity in conjunction with the asymmetry leads to a ratchet effect or unidirectional flow of the fluid along the asymmetry direction. The directional flow is still present even in the active turbulent phase when the gap between obstacles is sufficiently small. We demonstrate that the dynamics of the topological defects transition from flow mirroring to smectic-like as the gap between obstacles is made smaller, and explain this transition in terms of the pinning of negative winding number defects between obstacles. This also leads to a nonmonotonic ratchet effect magnitude as a function of obstacle size, so that there is an optimal obstacle size for ratcheting at fixed activity.
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3
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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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4
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Schimming CD, Reichhardt CJO, Reichhardt C. Vortex Lattices in Active Nematics with Periodic Obstacle Arrays. PHYSICAL REVIEW LETTERS 2024; 132:018301. [PMID: 38242662 DOI: 10.1103/physrevlett.132.018301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/16/2023] [Indexed: 01/21/2024]
Abstract
We numerically model a two-dimensional active nematic confined by a periodic array of fixed obstacles. Even in the passive nematic, the appearance of topological defects is unavoidable due to planar anchoring by the obstacle surfaces. We show that a vortex lattice state emerges as activity is increased, and that this lattice may be tuned from "ferromagnetic" to "antiferromagnetic" by varying the gap size between obstacles. We map the rich variety of states exhibited by the system as a function of distance between obstacles and activity, including a pinned defect state, motile defects, the vortex lattice, and active turbulence. We demonstrate that the flows in the active turbulent phase can be tuned by the presence of obstacles, and explore the effects of a frustrated lattice geometry on the vortex lattice phase.
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Affiliation(s)
- Cody D Schimming
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - C J O Reichhardt
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - C Reichhardt
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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5
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Caballero F, You Z, Marchetti MC. Vorticity phase separation and defect lattices in the isotropic phase of active liquid crystals. SOFT MATTER 2023; 19:7828-7835. [PMID: 37796173 DOI: 10.1039/d3sm00744h] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
We use numerical simulations and linear stability analysis to study the dynamics of an active liquid crystal film on a substrate in the regime where the passive system would be isotropic. Extensile activity builds up local orientational order and destabilizes the quiescent isotropic state above a critical activity, eventually resulting in spatiotemporal chaotic dynamics akin to the one observed ubiquitously in the nematic state. Here we show that tuning substrate friction yields a variety of emergent structures at intermediate activity, including lattices of flow vortices with associated regular arrangements of topological defects and a new state where flow vortices trap pairs of +1/2 defect that chase each other's tail. These chiral units spontaneously pick the sense of rotation and organize in a hexagonal lattice, surrounded by a diffuse flow of opposite rotation to maintain zero net vorticity. The length scale of these emergent structures is set by the screening length of the flow, controlled by the shear viscosity η and the substrate friction Γ, and can be captured by simple mode selection of the vortical flows. We demonstrate that the emergence of coherent structures can be interpreted as a phase separation of vorticity, where friction plays a role akin to that of birth/death processes in breaking conservation of the phase separating species and selecting a characteristic scale for the patterns. Our work shows that friction provides an experimentally accessible tuning parameter for designing controlled active flows.
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Affiliation(s)
- Fernando Caballero
- Department of Physics, University of California Santa Barbara, Santa Barbara, CA 93106, USA.
| | - Zhihong You
- Fujian Provincial Key Laboratory for Soft Functional Materials Research, Research Institute for Biomimetics and Soft Matter, Department of Physics, Xiamen University, Xiamen, Fujian 361005, China
| | - M Cristina Marchetti
- Department of Physics, University of California Santa Barbara, Santa Barbara, CA 93106, USA.
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6
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Zarei Z, Berezney J, Hensley A, Lemma L, Senbil N, Dogic Z, Fraden S. Light-activated microtubule-based two-dimensional active nematic. SOFT MATTER 2023; 19:6691-6699. [PMID: 37609884 DOI: 10.1039/d3sm00270e] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
We assess the ability of two light responsive kinesin motor clusters to drive dynamics of microtubule-based active nematics: opto-K401, a processive motor, and opto-K365, a non-processive motor. Measurements reveal an order of magnitude improvement in the contrast of nematic flow speeds between maximally- and minimally-illuminated states for opto-K365 motors when compared to opto-K401 construct. For opto-K365 nematics, we characterize both the steady-state flow and defect density as a function of applied light. We also examine the transient behavior as the system switches between steady-states upon changes in light intensities. Although nematic flows reach a steady state within tens of seconds, the defect density exhibits transient behavior for up to 10 minutes, showing a separation between small-scale active flows and system-scale structural states. Our work establishes an experimental platform that can exploit spatiotemporally-heterogeneous patterns of activity to generate targeted dynamical states.
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Affiliation(s)
- Zahra Zarei
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
| | - John Berezney
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
| | - Alexander Hensley
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
| | - Linnea Lemma
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
- The Department of Chemical and Biological Engineering, Princeton, NJ 08544, USA
- Department of Physics, University of California, Santa Barbara, California 93106, USA
| | - Nesrin Senbil
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
| | - Zvonimir Dogic
- Department of Physics, University of California, Santa Barbara, California 93106, USA
- Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106, USA
| | - Seth Fraden
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
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7
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Schimming CD, Reichhardt CJO, Reichhardt C. Friction-mediated phase transition in confined active nematics. Phys Rev E 2023; 108:L012602. [PMID: 37583137 DOI: 10.1103/physreve.108.l012602] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/28/2023] [Indexed: 08/17/2023]
Abstract
Using a minimal continuum model, we investigate the interplay between circular confinement and substrate friction in active nematics. Upon increasing the friction from low to high, we observe a dynamical phase transition from a circulating flow phase to an anisotropic flow phase in which the flow tends to align perpendicular to the nematic director at the boundary. We demonstrate that both the flow structure and dynamic correlations in the latter phase differ from those of an unconfined, active turbulent system and may be controlled by the prescribed nematic boundary conditions. Our results show that substrate friction and geometric confinement act as valuable control parameters in active nematics.
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Affiliation(s)
- Cody D Schimming
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - C J O Reichhardt
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - C Reichhardt
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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8
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Kinoshita Y, Uchida N. Flow patterns and defect dynamics of active nematic liquid crystals under an electric field. Phys Rev E 2023; 108:014605. [PMID: 37583184 DOI: 10.1103/physreve.108.014605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/19/2023] [Indexed: 08/17/2023]
Abstract
The effects of an electric field on the flow patterns and defect dynamics of two-dimensional active nematic liquid crystals are numerically investigated. We found that field-induced director reorientation causes anisotropic active turbulence characterized by enhanced flow perpendicular to the electric field. The average flow speed and its anisotropy are maximized at an intermediate field strength. Topological defects in the anisotropic active turbulence are localized and show characteristic dynamics with simultaneous creation of two pairs of defects. A laning state characterized by stripe domains with alternating flow directions is found at a larger field strength near the transition to the uniformly aligned state. We obtained periodic oscillations between the laning state and active turbulence, which resembles an experimental observation of active nematics subject to anisotropic friction.
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Affiliation(s)
- Yutaka Kinoshita
- Department of Physics, Tohoku University, Sendai 980-8578, Japan
| | - Nariya Uchida
- Department of Physics, Tohoku University, Sendai 980-8578, Japan
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9
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Joshi C, Ray S, Lemma LM, Varghese M, Sharp G, Dogic Z, Baskaran A, Hagan MF. Data-Driven Discovery of Active Nematic Hydrodynamics. PHYSICAL REVIEW LETTERS 2022; 129:258001. [PMID: 36608242 DOI: 10.1103/physrevlett.129.258001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Active nematics can be modeled using phenomenological continuum theories that account for the dynamics of the nematic director and fluid velocity through partial differential equations (PDEs). While these models provide a statistical description of the experiments, the relevant terms in the PDEs and their parameters are usually identified indirectly. We adapt a recently developed method to automatically identify optimal continuum models for active nematics directly from spatiotemporal data, via sparse regression of the coarse-grained fields onto generic low order PDEs. After extensive benchmarking, we apply the method to experiments with microtubule-based active nematics, finding a surprisingly minimal description of the system. Our approach can be generalized to gain insights into active gels, microswimmers, and diverse other experimental active matter systems.
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Affiliation(s)
- Chaitanya Joshi
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
- Department of Physics and Astronomy, Tufts University, Medford, Massachusetts 02155, USA
| | - Sattvic Ray
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Linnea M Lemma
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Minu Varghese
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109 USA
| | - Graham Sharp
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Zvonimir Dogic
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Aparna Baskaran
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Michael F Hagan
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
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10
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Active boundary layers in confined active nematics. Nat Commun 2022; 13:6675. [PMID: 36335213 PMCID: PMC9637202 DOI: 10.1038/s41467-022-34336-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 10/21/2022] [Indexed: 11/08/2022] Open
Abstract
The role of boundary layers in conventional liquid crystals is commonly related to the mesogen anchoring on confining walls. In the classical view, anchoring enslaves the orientational field of the passive material under equilibrium conditions. In this work, we show that an active nematic can develop active boundary layers that topologically polarize the confining walls. We find that negatively-charged defects accumulate in the boundary layer, regardless of the wall curvature, and they influence the overall dynamics of the system to the point of fully controlling the behavior of the active nematic in situations of strong confinement. Further, we show that wall defects exhibit behaviors that are essentially different from those of their bulk counterparts, such as high motility or the ability to recombine with another defect of like-sign topological charge. These exotic behaviors result from a change of symmetry induced by the wall in the director field around the defect. Finally, we suggest that the collective dynamics of wall defects might be described in terms of a model equation for one-dimensional spatio-temporal chaos.
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11
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Rønning J, Marchetti CM, Bowick MJ, Angheluta L. Flow around topological defects in active nematic films. Proc Math Phys Eng Sci 2022; 478:20210879. [PMID: 35153617 PMCID: PMC8791053 DOI: 10.1098/rspa.2021.0879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/22/2021] [Indexed: 11/14/2022] Open
Abstract
We study the active flow around isolated defects and the self-propulsion velocity of +1/2 defects in an active nematic film with both viscous dissipation (with viscosity η) and frictional damping Γ with a substrate. The interplay between these two dissipation mechanisms is controlled by the hydrodynamic dissipation length ℓd=η/Γ that screens the flows. For an isolated defect, in the absence of screening from other defects, the size of the shear vorticity around the defect is controlled by the system size R. In the presence of friction that leads to a finite value of ℓd, the vorticity field decays to zero on the lengthscales larger than ℓd. We show that the self-propulsion velocity of +1/2 defects grows with R in small systems where R<ℓd, while in the infinite system limit or when R≫ℓd, it approaches a constant value determined by ℓd.
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Affiliation(s)
- Jonas Rønning
- Njord Centre, Department of Physics, University of Oslo, PO Box 1048, Oslo 0316, Norway
| | - Cristina M Marchetti
- Department of Physics, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Mark J Bowick
- Kavli Institute for Theoretical Physics, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Luiza Angheluta
- Njord Centre, Department of Physics, University of Oslo, PO Box 1048, Oslo 0316, Norway
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12
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Koch CM, Wilczek M. Role of Advective Inertia in Active Nematic Turbulence. PHYSICAL REVIEW LETTERS 2021; 127:268005. [PMID: 35029495 DOI: 10.1103/physrevlett.127.268005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 10/22/2021] [Indexed: 06/14/2023]
Abstract
Suspensions of active agents with nematic interactions exhibit complex spatiotemporal dynamics such as mesoscale turbulence. Since the Reynolds number of microscopic flows is very small on the scale of individual agents, inertial effects are typically excluded in continuum theories of active nematic turbulence. Whether active stresses can collectively excite inertial flows is currently unclear. To address this question, we investigate a two-dimensional continuum theory for active nematic turbulence. In particular, we compare mesoscale turbulence with and without the effects of advective inertia. We find that inertial effects can influence the flow already close to the onset of the turbulent state and, moreover, give rise to large-scale fluid motion for strong active driving. A detailed analysis of the kinetic energy budget reveals an energy transfer to large scales mediated by inertial advection. While this transfer is small in comparison to energy injection and dissipation, its effects accumulate over time. The inclusion of friction, which is typically present in experiments, can compensate for this effect. The findings suggest that the inclusion of inertia and friction may be necessary for dynamically consistent theories of active nematic turbulence.
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Affiliation(s)
- Colin-Marius Koch
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany and Faculty of Physics, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Michael Wilczek
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany and Faculty of Physics, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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13
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Pearce DJG, Nambisan J, Ellis PW, Fernandez-Nieves A, Giomi L. Orientational Correlations in Active and Passive Nematic Defects. PHYSICAL REVIEW LETTERS 2021; 127:197801. [PMID: 34797140 DOI: 10.1103/physrevlett.127.197801] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
We investigate the emergence of orientational order among +1/2 disclinations in active nematic liquid crystals. Using a combination of theoretical and experimental methods, we show that +1/2 disclinations have short-range antiferromagnetic alignment, as a consequence of the elastic torques originating from their polar structure. The presence of intermediate -1/2 disclinations, however, turns this interaction from antialigning to aligning at scales that are smaller than the typical distance between like-sign defects. No long-range orientational order is observed. Strikingly, these effects are insensitive to material properties and qualitatively similar to what is found for defects in passive nematic liquid crystals.
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Affiliation(s)
- D J G Pearce
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
- Departments of Biochemistry and Theoretical Physics, Université de Genéve, 1205 Genéve, Switzerland
| | - J Nambisan
- Department of Condensed Matter Physics, University of Barcelona, 08028 Barcelona, Spain
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - P W Ellis
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - A Fernandez-Nieves
- Department of Condensed Matter Physics, University of Barcelona, 08028 Barcelona, Spain
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- ICREA-Institucio Catalana de Recerca i Estudis Avancats, 08010 Barcelona, Spain
| | - L Giomi
- Instituut-Lorentz, Universiteit Leiden, P.O. Box 9506, 2300 RA Leiden, Netherlands
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14
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Submersed micropatterned structures control active nematic flow, topology, and concentration. Proc Natl Acad Sci U S A 2021; 118:2106038118. [PMID: 34535551 DOI: 10.1073/pnas.2106038118] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2021] [Indexed: 01/10/2023] Open
Abstract
Coupling between flows and material properties imbues rheological matter with its wide-ranging applicability, hence the excitement for harnessing the rheology of active fluids for which internal structure and continuous energy injection lead to spontaneous flows and complex, out-of-equilibrium dynamics. We propose and demonstrate a convenient, highly tunable method for controlling flow, topology, and composition within active films. Our approach establishes rheological coupling via the indirect presence of fully submersed micropatterned structures within a thin, underlying oil layer. Simulations reveal that micropatterned structures produce effective virtual boundaries within the superjacent active nematic film due to differences in viscous dissipation as a function of depth. This accessible method of applying position-dependent, effective dissipation to the active films presents a nonintrusive pathway for engineering active microfluidic systems.
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15
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Chen YC, Jolicoeur B, Chueh CC, Wu KT. Flow coupling between active and passive fluids across water-oil interfaces. Sci Rep 2021; 11:13965. [PMID: 34234195 PMCID: PMC8263611 DOI: 10.1038/s41598-021-93310-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 06/23/2021] [Indexed: 01/17/2023] Open
Abstract
Active fluid droplets surrounded by oil can spontaneously develop circulatory flows. However, the dynamics of the surrounding oil and their influence on the active fluid remain poorly understood. To investigate interactions between the active fluid and the passive oil across their interface, kinesin-driven microtubule-based active fluid droplets were immersed in oil and compressed into a cylinder-like shape. The droplet geometry supported intradroplet circulatory flows, but the circulation was suppressed when the thickness of the oil layer surrounding the droplet decreased. Experiments with tracers and network structure analyses and continuum models based on the dynamics of self-elongating rods demonstrated that the flow transition resulted from flow coupling across the interface between active fluid and oil, with a millimeter-scale coupling length. In addition, two novel millifluidic devices were developed that could trigger and suppress intradroplet circulatory flows in real time: one by changing the thickness of the surrounding oil layer and the other by locally deforming the droplet. This work highlights the role of interfacial dynamics in the active fluid droplet system and shows that circulatory flows within droplets can be affected by millimeter-scale flow coupling across the interface between the active fluid and the oil.
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Affiliation(s)
- Yen-Chen Chen
- Department of Mechanical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Brock Jolicoeur
- Department of Physics, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Chih-Che Chueh
- Department of Aeronautics and Astronautics, National Cheng Kung University, Tainan, 701, Taiwan
| | - Kun-Ta Wu
- Department of Mechanical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA.
- Department of Physics, Worcester Polytechnic Institute, Worcester, MA, 01609, USA.
- The Martin Fisher School of Physics, Brandeis University, Waltham, MA, 02454, USA.
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16
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Abstract
Pattern formation processes in active systems give rise to a plethora of collective structures. Predicting how the emergent structures depend on the microscopic interactions between the moving agents remains a challenge. By introducing a high-density actin gliding assay on a fluid membrane, we demonstrate the emergence of polar structures in a regime of nematic binary interactions dominated by steric repulsion. The transition from a microscopic nematic symmetry to a macroscopic polar structure is linked to microscopic polarity sorting mechanisms, including accumulation in wedge-like topological defects. Our results should be instrumental for a better understanding of pattern formation and polarity sorting processes in active matter. Collective motion of active matter is ubiquitously observed, ranging from propelled colloids to flocks of bird, and often features the formation of complex structures composed of agents moving coherently. However, it remains extremely challenging to predict emergent patterns from the binary interaction between agents, especially as only a limited number of interaction regimes have been experimentally observed so far. Here, we introduce an actin gliding assay coupled to a supported lipid bilayer, whose fluidity forces the interaction between self-propelled filaments to be dominated by steric repulsion. This results in filaments stopping upon binary collisions and eventually aligning nematically. Such a binary interaction rule results at high densities in the emergence of dynamic collectively moving structures including clusters, vortices, and streams of filaments. Despite the microscopic interaction having a nematic symmetry, the emergent structures are found to be polar, with filaments collectively moving in the same direction. This is due to polar biases introduced by the stopping upon collision, both on the individual filaments scale as well as on the scale of collective structures. In this context, positive half-charged topological defects turn out to be a most efficient trapping and polarity sorting conformation.
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17
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Blanch-Mercader C, Guillamat P, Roux A, Kruse K. Integer topological defects of cell monolayers: Mechanics and flows. Phys Rev E 2021; 103:012405. [PMID: 33601623 DOI: 10.1103/physreve.103.012405] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/10/2020] [Indexed: 12/13/2022]
Abstract
Monolayers of anisotropic cells exhibit long-ranged orientational order and topological defects. During the development of organisms, orientational order often influences morphogenetic events. However, the linkage between the mechanics of cell monolayers and topological defects remains largely unexplored. This holds specifically at the timescales relevant for tissue morphogenesis. Here, we build on the physics of liquid crystals to determine material parameters of cell monolayers. In particular, we use a hydrodynamical description of an active polar fluid to study the steady-state mechanical patterns at integer topological defects. Our description includes three distinct sources of activity: traction forces accounting for cell-substrate interactions as well as anisotropic and isotropic active nematic stresses accounting for cell-cell interactions. We apply our approach to C2C12 cell monolayers in small circular confinements, which form isolated aster or spiral topological defects. By analyzing the velocity and orientational order fields in spirals as well as the forces and cell number density fields in asters, we determine mechanical parameters of C2C12 cell monolayers. Our work shows how topological defects can be used to fully characterize the mechanical properties of biological active matter.
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Affiliation(s)
- Carles Blanch-Mercader
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
- Department of Theoretical Physics, University of Geneva, 1211 Geneva, Switzerland
| | - Pau Guillamat
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Karsten Kruse
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
- Department of Theoretical Physics, University of Geneva, 1211 Geneva, Switzerland
- NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
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18
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Rivas DP, Shendruk TN, Henry RR, Reich DH, Leheny RL. Driven topological transitions in active nematic films. SOFT MATTER 2020; 16:9331-9338. [PMID: 32935705 DOI: 10.1039/d0sm00693a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The topological properties of many materials are central to their behavior. In intrinsically out-of-equilibrium active materials, the dynamics of topological defects can be particularly important. In this paper, local manipulation of the order, dynamics, and topological properties of microtubule-based active nematic films is demonstrated in a joint experimental and simulation study. Hydrodynamic stresses created by magnetically actuated rotation of disk-shaped colloids in proximity to the films compete with internal stresses in the active nematic, influencing the local motion of +1/2 charge topological defects that are intrinsic to the nematic order in the spontaneously turbulent active films. Sufficiently large applied stresses drive the formation of +1 charge topological vortices through the merger of two +1/2 defects. The directed motion of the defects is accompanied by ordering of the vorticity and velocity of the active flows within the film that is qualitatively unlike the response of passive viscous films. Many features of the film's response to the stress are captured by lattice Boltzmann simulations, providing insight into the anomalous viscoelastic nature of the active nematic. The topological vortex formation is accompanied by a rheological instability in the film that leads to significant increase in the flow velocities. Comparison of the velocity profile in vicinity of the vortex with fluid-dynamics calculations provides an estimate of the film viscosity.
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Affiliation(s)
- David P Rivas
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Tyler N Shendruk
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough, UKLE11 3TU and School of Physics and Astronomy, The University of Edinburgh, Edinburgh, UKEH9 3FD
| | - Robert R Henry
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Daniel H Reich
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Robert L Leheny
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218, USA.
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19
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Hardoüin J, Laurent J, Lopez-Leon T, Ignés-Mullol J, Sagués F. Active microfluidic transport in two-dimensional handlebodies. SOFT MATTER 2020; 16:9230-9241. [PMID: 32926045 DOI: 10.1039/d0sm00610f] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Unlike traditional nematic liquid crystals, which adopt ordered equilibrium configurations compatible with the topological constraints imposed by the boundaries, active nematics are intrinsically disordered because of their self-sustained internal flows. Controlling the flow patterns of active nematics remains a limiting step towards their use as functional materials. Here we show that confining a tubulin-kinesin active nematic to a network of connected annular microfluidic channels enables controlled directional flows and autonomous transport. In single annular channels, for narrow widths, the typically chaotic streams transform into well-defined circulating flows, whose direction or handedness can be controlled by introducing asymmetric corrugations on the channel walls. The dynamics is altered when two or three annular channels are interconnected. These more complex topologies lead to scenarios of synchronization, anti-correlation, and frustration of the active flows, and to the stabilisation of high topological singularities in both the flow field and the orientational field of the material. Controlling textures and flows in these microfluidic platforms opens unexplored perspectives towards their application in biotechnology and materials science.
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Affiliation(s)
- Jérôme Hardoüin
- Departament de Ciència de Materials i Química Física, Universitat de Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain. and Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Barcelona, Spain
| | - Justine Laurent
- Laboratoire de Physique et Mécanique des Milieux hétérogènes (PMMH), CNRS, ESPCI Paris, PSL Research University, Paris, France and Laboratoire Gulliver, UMR CNRS 7083, ESPCI Paris, PSL Research University, Paris, France
| | - Teresa Lopez-Leon
- Laboratoire de Physique et Mécanique des Milieux hétérogènes (PMMH), CNRS, ESPCI Paris, PSL Research University, Paris, France and Laboratoire Gulliver, UMR CNRS 7083, ESPCI Paris, PSL Research University, Paris, France
| | - Jordi Ignés-Mullol
- Departament de Ciència de Materials i Química Física, Universitat de Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain. and Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Barcelona, Spain
| | - Francesc Sagués
- Departament de Ciència de Materials i Química Física, Universitat de Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain. and Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Barcelona, Spain
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20
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Strübing T, Khosravanizadeh A, Vilfan A, Bodenschatz E, Golestanian R, Guido I. Wrinkling Instability in 3D Active Nematics. NANO LETTERS 2020; 20:6281-6288. [PMID: 32786934 PMCID: PMC7496740 DOI: 10.1021/acs.nanolett.0c01546] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/04/2020] [Indexed: 05/13/2023]
Abstract
In nature, interactions between biopolymers and motor proteins give rise to biologically essential emergent behaviors. Besides cytoskeleton mechanics, active nematics arise from such interactions. Here we present a study on 3D active nematics made of microtubules, kinesin motors, and depleting agent. It shows a rich behavior evolving from a nematically ordered space-filling distribution of microtubule bundles toward a flattened and contracted 2D ribbon that undergoes a wrinkling instability and subsequently transitions into a 3D active turbulent state. The wrinkle wavelength is independent of the ATP concentration and our theoretical model describes its relation with the appearance time. We compare the experimental results with a numerical simulation that confirms the key role of kinesin motors in cross-linking and sliding the microtubules. Our results on the active contraction of the network and the independence of wrinkle wavelength on ATP concentration are important steps forward for the understanding of these 3D systems.
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Affiliation(s)
- Tobias Strübing
- Max
Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen, Germany
| | - Amir Khosravanizadeh
- Max
Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen, Germany
- Department
of Physics, Institute for Advanced Studies
in Basic Sciences, Zanjan 45137-66731, Iran
| | - Andrej Vilfan
- Max
Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen, Germany
- Jožef
Stefan Institute, 1000 Ljubljana, Slovenia
| | - Eberhard Bodenschatz
- Max
Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen, Germany
- Institute
for Dynamics of Complex Systems, Georg-August-University
Göttingen, 37073 Göttingen, Germany
- Laboratory
of Atomic and Solid-State Physics, Cornell
University, Ithaca, New York 14853, United
States
| | - Ramin Golestanian
- Max
Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen, Germany
- Rudolf
Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - Isabella Guido
- Max
Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen, Germany
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21
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Brown AT. A theoretical phase diagram for an active nematic on a spherical surface. SOFT MATTER 2020; 16:4682-4691. [PMID: 32391540 DOI: 10.1039/d0sm00166j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Systems combining rod-shaped objects with self-generated motion such as suspensions of microtubules or growing bacterial colonies are commonly modeled as active nematics - nematic liquid crystals with an additional active stress term. Confining a 2D active nematic to the surface of a sphere generates novel behaviour as the four +1/2 nematic defects which are produced by the spherical geometry move round each other in an intricate dance. Here, these defects are modeled as point particles experiencing elastic forces from defect position and orientation, and self-propulsion due to activity. This model exhibits four qualitatively distinct types of trajectory state: two which are consistent with previous experimental and simulated trajectories; and two others, which are apparently novel and in regions of parameter space that may not yet have been explored. This work also explains a discrepancy between some previous point-particle models and the trajectories seen in experiments and simulations: this was due to a failure to fully account for the spherical geometry in the point-particle models.
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Affiliation(s)
- Aidan T Brown
- SUPA, School of Physics & Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, UK.
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22
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Epstein JM, Mandadapu KK. Time-reversal symmetry breaking in two-dimensional nonequilibrium viscous fluids. Phys Rev E 2020; 101:052614. [PMID: 32575182 DOI: 10.1103/physreve.101.052614] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
We study the rheological signatures of departure from equilibrium in two-dimensional viscous fluids with and without internal spin. Under the assumption of isotropy, we provide the most general linear constitutive relations for stress and couple stress in terms of the velocity and spin fields. Invoking Onsager's regression hypothesis for fluctuations about steady states, we derive the Green-Kubo formulas relating the transport coefficients to time-correlation functions of the fluctuating stress. In doing so, we show that one of the nonequilibrium transport coefficients, the odd viscosity, requires time-reversal symmetry breaking in the case of systems without internal spin. However, the Green-Kubo relations for systems with internal spin also show that there is a possibility for nonvanishing odd viscosity even when time-reversal symmetry is preserved. Furthermore, we find that breakdown of equipartition in nonequilibrium steady states results in the decoupling of the two rotational viscosities relating the vorticity and the internal spin.
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Affiliation(s)
- Jeffrey M Epstein
- Department of Physics, University of California, Berkeley, California, USA
| | - Kranthi K Mandadapu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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23
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Patelli A, Djafer-Cherif I, Aranson IS, Bertin E, Chaté H. Understanding Dense Active Nematics from Microscopic Models. PHYSICAL REVIEW LETTERS 2019; 123:258001. [PMID: 31922774 DOI: 10.1103/physrevlett.123.258001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/13/2019] [Indexed: 06/10/2023]
Abstract
We study dry, dense active nematics at both particle and continuous levels. Specifically, extending the Boltzmann-Ginzburg-Landau approach, we derive well-behaved hydrodynamic equations from a Vicsek-style model with nematic alignment and pairwise repulsion. An extensive study of the phase diagram shows qualitative agreement between the two levels of description. We find in particular that the dynamics of topological defects strongly depends on parameters and can lead to "arch" solutions forming a globally polar, smecticlike arrangement of Néel walls. We show how these configurations are at the origin of the defect ordered states reported previously. This work offers a detailed understanding of the theoretical description of dense active nematics directly rooted in their microscopic dynamics.
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Affiliation(s)
- Aurelio Patelli
- Service de Physique de l'Etat Condensé, CEA, CNRS, Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
| | - Ilyas Djafer-Cherif
- Service de Physique de l'Etat Condensé, CEA, CNRS, Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- School of Mathematics, University of Bristol, Bristol BS8 1TW, United Kingdom
| | - Igor S Aranson
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Eric Bertin
- Univ. Grenoble Alpes, CNRS, LIPhy, 38000 Grenoble, France
| | - Hugues Chaté
- Service de Physique de l'Etat Condensé, CEA, CNRS, Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- Computational Science Research Center, Beijing 100094, China
- LPTMC, Sorbonne Université, CNRS, 75005 Paris, France
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24
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Emergence of active nematics in chaining bacterial biofilms. Nat Commun 2019; 10:2285. [PMID: 31123251 PMCID: PMC6533293 DOI: 10.1038/s41467-019-10311-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/01/2019] [Indexed: 01/06/2023] Open
Abstract
Growing tissue and bacterial colonies are active matter systems where cell divisions and cellular motion generate active stress. Although they operate in the non-equilibrium regime, these biological systems can form large-scale ordered structures. How mechanical instabilities drive the dynamics of active matter systems and form ordered structures are not well understood. Here, we use chaining Bacillus subtilis, also known as a biofilm, to study the relation between mechanical instabilities and nematic ordering. We find that bacterial biofilms have intrinsic length scales above which a series of mechanical instabilities occur. Localized stress and friction drive buckling and edge instabilities which further create nematically aligned structures and topological defects. We also observe that topological defects control stress distribution and initiate the formation of sporulation sites by creating three-dimensional structures. In this study we propose an alternative active matter platform to study the essential roles of mechanics in growing biological tissue.
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25
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Epstein JM, Klymko K, Mandadapu KK. Statistical mechanics of transport processes in active fluids. II. Equations of hydrodynamics for active Brownian particles. J Chem Phys 2019; 150:164111. [DOI: 10.1063/1.5054912] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Jeffrey M. Epstein
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - Katherine Klymko
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 USA
| | - Kranthi K. Mandadapu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 USA
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26
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Cai LB, Chaté H, Ma YQ, Shi XQ. Dynamical subclasses of dry active nematics. Phys Rev E 2019; 99:010601. [PMID: 30780307 DOI: 10.1103/physreve.99.010601] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Indexed: 06/09/2023]
Abstract
We show that the dominant mode of alignment plays an important role in dry active nematics, leading to two dynamical subclasses defined by the nature of the instability of the nematic bands that characterize, in these systems, the coexistence phase separating the isotropic and fluctuating nematic states. In addition to the well-known instability inducing long undulations along the band, another stronger instability leading to the breakup of the band in many transversal segments may arise. We elucidate the origin of this strong instability for a realistic model of self-propelled rods and determine the high-order nonlinear terms responsible for it at the hydrodynamic level.
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Affiliation(s)
- Li-Bing Cai
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Hugues Chaté
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, China
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- Computational Science Research Center, Beijing 100094, China
| | - Yu-Qiang Ma
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Xia-Qing Shi
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou 215006, China
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
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27
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Abstract
Active matter comprises individual units that convert energy into mechanical motion. In many examples, such as bacterial systems and biofilament assays, constituent units are elongated and can give rise to local nematic orientational order. Such "active nematics" systems have attracted much attention from both theorists and experimentalists. However, despite intense research efforts, data-driven quantitative modeling has not been achieved, a situation mainly due to the lack of systematic experimental data and to the large number of parameters of current models. Here, we introduce an active nematics system made of swarming filamentous bacteria. We simultaneously measure orientation and velocity fields and show that the complex spatiotemporal dynamics of our system can be quantitatively reproduced by a type of microscopic model for active suspensions whose important parameters are all estimated from comprehensive experimental data. This provides unprecedented access to key effective parameters and mechanisms governing active nematics. Our approach is applicable to different types of dense suspensions and shows a path toward more quantitative active matter research.
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28
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Kumar N, Zhang R, de Pablo JJ, Gardel ML. Tunable structure and dynamics of active liquid crystals. SCIENCE ADVANCES 2018; 4:eaat7779. [PMID: 30333990 PMCID: PMC6184751 DOI: 10.1126/sciadv.aat7779] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/31/2018] [Indexed: 05/21/2023]
Abstract
Active materials are capable of converting free energy into directional motion, giving rise to notable dynamical phenomena. Developing a general understanding of their structure in relation to the underlying nonequilibrium physics would provide a route toward control of their dynamic behavior and pave the way for potential applications. The active system considered here consists of a quasi-two-dimensional sheet of short (≈1 μm) actin filaments driven by myosin II motors. By adopting a concerted theoretical and experimental strategy, new insights are gained into the nonequilibrium properties of active nematics over a wide range of internal activity levels. In particular, it is shown that topological defect interactions can be led to transition from attractive to repulsive as a function of initial defect separation and relative orientation. Furthermore, by examining the +1/2 defect morphology as a function of activity, we found that the apparent elastic properties of the system (the ratio of bend-to-splay elastic moduli) are altered considerably by increased activity, leading to an effectively lower bend elasticity. At high levels of activity, the topological defects that decorate the material exhibit a liquid-like structure and adopt preferred orientations depending on their topological charge. Together, these results suggest that it should be possible to tune internal stresses in active nematic systems with the goal of designing out-of-equilibrium structures with engineered dynamic responses.
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Affiliation(s)
- Nitin Kumar
- James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
- Department of Physics, The University of Chicago, Chicago, IL 60637, USA
| | - Rui Zhang
- Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
| | - Juan J. de Pablo
- Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
- Institute for Molecular Engineering, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Margaret L. Gardel
- James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
- Department of Physics, The University of Chicago, Chicago, IL 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
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29
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Shankar S, Ramaswamy S, Marchetti MC, Bowick MJ. Defect Unbinding in Active Nematics. PHYSICAL REVIEW LETTERS 2018; 121:108002. [PMID: 30240234 DOI: 10.1103/physrevlett.121.108002] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/18/2018] [Indexed: 06/08/2023]
Abstract
We formulate the statistical dynamics of topological defects in the active nematic phase, formed in two dimensions by a collection of self-driven particles on a substrate. An important consequence of the nonequilibrium drive is the spontaneous motility of strength +1/2 disclinations. Starting from the hydrodynamic equations of active nematics, we derive an interacting particle description of defects that includes active torques. We show that activity, within perturbation theory, lowers the defect-unbinding transition temperature, determining a critical line in the temperature-activity plane that separates the quasi-long-range ordered (nematic) and disordered (isotropic) phases. Below a critical activity, defects remain bound as rotational noise decorrelates the directed dynamics of +1/2 defects, stabilizing the quasi-long-range ordered nematic state. This activity threshold vanishes at low temperature, leading to a reentrant transition. At large enough activity, active forces always exceed thermal ones and the perturbative result fails, suggesting that in this regime activity will always disorder the system. Crucially, rotational diffusion being a two-dimensional phenomenon, defect unbinding cannot be described by a simplified one-dimensional model.
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Affiliation(s)
- Suraj Shankar
- Physics Department and Syracuse Soft and Living Matter Program, Syracuse University, Syracuse, New York 13244, USA
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106, USA
| | - Sriram Ramaswamy
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106, USA
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560 012, India
| | - M Cristina Marchetti
- Physics Department and Syracuse Soft and Living Matter Program, Syracuse University, Syracuse, New York 13244, USA
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106, USA
| | - Mark J Bowick
- Physics Department and Syracuse Soft and Living Matter Program, Syracuse University, Syracuse, New York 13244, USA
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106, USA
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30
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Doostmohammadi A, Ignés-Mullol J, Yeomans JM, Sagués F. Active nematics. Nat Commun 2018; 9:3246. [PMID: 30131558 PMCID: PMC6104062 DOI: 10.1038/s41467-018-05666-8] [Citation(s) in RCA: 268] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 06/28/2018] [Accepted: 07/19/2018] [Indexed: 11/09/2022] Open
Abstract
Active matter extracts energy from its surroundings at the single particle level and transforms it into mechanical work. Examples include cytoskeleton biopolymers and bacterial suspensions. Here, we review experimental, theoretical and numerical studies of active nematics - a type of active system that is characterised by self-driven units with elongated shape. We focus primarily on microtubule-kinesin mixtures and the hydrodynamic theories that describe their properties. An important theme is active turbulence and the associated motile topological defects. We discuss ways in which active turbulence may be controlled, a pre-requisite to harvesting energy from active materials, and we consider the appearance, and possible implications, of active nematics and topological defects to cellular systems and biological processes.
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Affiliation(s)
- Amin Doostmohammadi
- The Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Clarendon Laboratory, Parks Rd., Oxford, OX1 3PU, UK.
| | - Jordi Ignés-Mullol
- Departament de Ciència de Materials i Química Física and Institute of Nanoscience and Nanotechnology, Universitat de Barcelona, Martí I Franquès 1, 08028, Barcelona, Catalonia, Spain
| | - Julia M Yeomans
- The Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Clarendon Laboratory, Parks Rd., Oxford, OX1 3PU, UK
| | - Francesc Sagués
- Departament de Ciència de Materials i Química Física and Institute of Nanoscience and Nanotechnology, Universitat de Barcelona, Martí I Franquès 1, 08028, Barcelona, Catalonia, Spain
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31
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Henkes S, Marchetti MC, Sknepnek R. Dynamical patterns in nematic active matter on a sphere. Phys Rev E 2018; 97:042605. [PMID: 29758687 DOI: 10.1103/physreve.97.042605] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Indexed: 01/24/2023]
Abstract
Using simulations of self-propelled agents with short-range repulsion and nematic alignment, we explore the dynamical phases of a dense active nematic confined to the surface of a sphere. We map the nonequilibrium phase diagram as a function of curvature, alignment strength, and activity. Our model reproduces several phases seen in recent experiments on active microtubule bundles confined the surfaces of vesicles. At low driving, we recover the equilibrium nematic ground state with four +1/2 defects. As the driving is increased, geodesic forces drive the transition to a polar band wrapping around an equator, with large empty spherical caps corresponding to two +1 defects at the poles. Upon further increasing activity, the bands fold onto themselves, and the system eventually transitions to a turbulent state marked by the proliferation of pairs of topological defects. We highlight the key role of the nematic persistence length in controlling pattern formation in these confined systems with positive Gaussian curvature.
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Affiliation(s)
- Silke Henkes
- Institute for Complex Systems and Mathematical Biology, Department of Physics, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
| | - M Cristina Marchetti
- Department of Physics and Soft Matter Program, Syracuse University, Syracuse, New York 13244, USA
| | - Rastko Sknepnek
- School of Sciences and Engineering and School of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom
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32
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Guillamat P, Hardoüin J, Prat BM, Ignés-Mullol J, Sagués F. Control of active turbulence through addressable soft interfaces. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:504003. [PMID: 29125475 DOI: 10.1088/1361-648x/aa99c8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present an experimental study of a kinesin/tubulin active nematic formed at different oil interfaces. By tuning the interfacial rheology of the contacting oil, we have been able to condition and control the seemingly chaotic motion that characterizes the self-sustained active flows in our preparations. The active nematic is inherently unstable and spontaneously develops defects from an initial homogeneous state. We show that the steady state and, in particular, the density and dynamics of the defects strongly depends on the rheology of the contacting oil. Using a smectic-A thermotropic liquid crystal as the oil phase, we pattern the interface thanks to the anisotropy of the shear viscosity in this material. The geometry of the active nematic adapts to the boundary conditions at the interface by changing from the so-called active turbulent regime to laminar flows along the easy flow directions. The latter can be either a lattice of self-assembled circular paths or reconfigurable homogeneous orientations that can be addressed by means of an external magnetic field. We show that, under all confinement conditions, the spatiotemporal modes exhibited by the active liquid are consistent with a single intrinsic length scale, which can be tuned by the material parameters, and obey basic topological requirements imposed on the defects that drive the active flows. Future control strategies, including a tunable depleting agent, are discussed.
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Affiliation(s)
- P Guillamat
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Barcelona, Catalonia. Institute of Nanoscience and Nanotechnology, IN2UB, Universitat de Barcelona, Barcelona, Catalonia
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Pismen LM, Sagués F. Viscous dissipation and dynamics of defects in an active nematic interface ⋆. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2017; 40:92. [PMID: 29063989 DOI: 10.1140/epje/i2017-11582-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/11/2017] [Indexed: 06/07/2023]
Abstract
We consider active flow and dynamics of topological defects in an active nematic interfacial layer confined between immissible viscous fluid layers. The velocity of defects is determined by asymptotic matching of solutions in the defect core and the far field. Self-propulsion of positive defects along the direction of their "comet tails" is identified as the principal deterministic component of defect dynamics, while topological and hydrodynamic interactions among mobile defects is responsible for quasi-random jitter.
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Affiliation(s)
- Len M Pismen
- Department of Chemical Engineering, Technion - Israel Institute of Technology, 32000, Haifa, Israel.
| | - Francesc Sagués
- Departament of Materials Science and Physical Chemistry, Institut de Nanociència i Nanotecnologia, Universitat de Barcelona, Martí Franquès 1, 08028, Barcelona, Spain
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Guillamat P, Ignés-Mullol J, Sagués F. Taming active turbulence with patterned soft interfaces. Nat Commun 2017; 8:564. [PMID: 28916801 PMCID: PMC5601458 DOI: 10.1038/s41467-017-00617-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/13/2017] [Indexed: 11/30/2022] Open
Abstract
Active matter embraces systems that self-organize at different length and time scales, often exhibiting turbulent flows apparently deprived of spatiotemporal coherence. Here, we use a layer of a tubulin-based active gel to demonstrate that the geometry of active flows is determined by a single length scale, which we reveal in the exponential distribution of vortex sizes of active turbulence. Our experiments demonstrate that the same length scale reemerges as a cutoff for a scale-free power law distribution of swirling laminar flows when the material evolves in contact with a lattice of circular domains. The observed prevalence of this active length scale can be understood by considering the role of the topological defects that form during the spontaneous folding of microtubule bundles. These results demonstrate an unexpected strategy for active systems to adapt to external stimuli, and provide with a handle to probe the existence of intrinsic length and time scales. Active nematics consist of self-driven components that develop orientational order and turbulent flow. Here Guillamat et al. investigate an active nematic constrained in a quasi-2D geometrical setup and show that there exists an intrinsic length scale that determines the geometry in all forcing regimes.
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Affiliation(s)
- P Guillamat
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Barcelona, 08028 Catalonia, Spain.,Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Barcelona, 08028 Catalonia, Spain
| | - J Ignés-Mullol
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Barcelona, 08028 Catalonia, Spain.,Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Barcelona, 08028 Catalonia, Spain
| | - F Sagués
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Barcelona, 08028 Catalonia, Spain. .,Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Barcelona, 08028 Catalonia, Spain.
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