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Padhan NB, Kiran KV, Pandit R. Novel turbulence and coarsening arrest in active-scalar fluids. SOFT MATTER 2024; 20:3620-3627. [PMID: 38619449 DOI: 10.1039/d4sm00163j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
We uncover a new type of turbulence - activity-induced homogeneous and isotropic turbulence - in a model that has been employed to investigate motility-induced phase separation (MIPS) in a system of microswimmers. The active Cahn-Hilliard-Navier-Stokes (CHNS) equations, also called active model H, provide a natural theoretical framework for our study. In this CHNS model, a single scalar order parameter ϕ, positive (negative) in regions of high (low) microswimmer density, is coupled with the velocity field u. The activity of the microswimmers is governed by an activity parameter ζ that is positive for extensile swimmers and negative for contractile swimmers. With extensile swimmers, this system undergoes complete phase separation, which is similar to that in binary-fluid mixtures. By carrying out pseudospectral direct numerical simulations (DNSs), we show, for the first time, that (a) this model develops an emergent nonequilibrium, but statistically steady, state (NESS) of active turbulence, for the case of contractile swimmers, if ζ is sufficiently large and negative, and (b) this turbulence arrests the phase separation. We quantify this suppression by showing how the coarsening-arrest length scale does not grow indefinitely, with time t, but saturates at a finite value at large times. We characterise the statistical properties of this active-scalar turbulence by employing energy spectra and fluxes and the spectrum of ϕ. For sufficiently high Reynolds numbers, the energy spectrum (k) displays an inertial range, with a power-law dependence on the wavenumber k. We demonstrate that, in this range, the flux Π(k) assumes a nearly constant, negative value, which indicates that the system shows an inverse cascade of energy, even though energy injection occurs over a wide range of wavenumbers in our active-CHNS model.
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Affiliation(s)
- Nadia Bihari Padhan
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, 560012, India.
| | - Kolluru Venkata Kiran
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, 560012, India.
| | - Rahul Pandit
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, 560012, India.
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2
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Partovifard A, Grawitter J, Stark H. Controlling active turbulence by activity patterns. SOFT MATTER 2024; 20:1800-1814. [PMID: 38305449 DOI: 10.1039/d3sm01050c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
By patterning activity in space, one can control active turbulence. To show this, we use Doi's hydrodynamic equations of a semidilute solution of active rods. A linear stability analysis reveals the resting isotropic fluid to be unstable above an absolute pusher activity. The emergent activity-induced paranematic state displays active turbulence, which we characterize by different quantities including the energy spectrum, which shows the typical power-law decay with exponent -4. Then, we control the active turbulence by a square lattice of circular spots where activity is switched off. In the parameter space lattice constant versus surface-to-surface distance of the spots, we identify different flow states. Most interestingly, for lattice constants below the vorticity correlation length and for spot distances smaller than the nematic coherence length, we observe a multi-lane flow state, where flow lanes with alternating flow directions are separated by a street of vortices. The flow pattern displays pronounced multistability and also appears transiently at the transition to the isotropic active-turbulence state. At larger lattice constants a trapped vortex state is identified with a non-Gaussian vorticity distribution due to the low flow vorticity at the spots. It transitions to conventional active turbulence for increasing spot distance.
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Affiliation(s)
- Arghavan Partovifard
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
| | - Josua Grawitter
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
| | - Holger Stark
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
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3
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Rana N, Chatterjee R, Ro S, Levine D, Ramaswamy S, Perlekar P. Defect turbulence in a dense suspension of polar, active swimmers. Phys Rev E 2024; 109:024603. [PMID: 38491596 DOI: 10.1103/physreve.109.024603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 01/19/2024] [Indexed: 03/18/2024]
Abstract
We study the effects of inertia in dense suspensions of polar swimmers. The hydrodynamic velocity field and the polar order parameter field describe the dynamics of the suspension. We show that a dimensionless parameter R (ratio of the swimmer self-advection speed to the active stress invasion speed [Phys. Rev. X 11, 031063 (2021)2160-330810.1103/PhysRevX.11.031063]) controls the stability of an ordered swimmer suspension. For R smaller than a threshold R_{1}, perturbations grow at a rate proportional to their wave number q. Beyond R_{1} we show that the growth rate is O(q^{2}) until a second threshold R=R_{2} is reached. The suspension is stable for R>R_{2}. We perform direct numerical simulations to characterize the steady-state properties and observe defect turbulence for R
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Affiliation(s)
- Navdeep Rana
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), D-37077 Göttingen, Germany
| | - Rayan Chatterjee
- Stanford Medicine, Stanford University, Stanford, California 94305, USA
| | - Sunghan Ro
- Department of Physics, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Dov Levine
- Department of Physics, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Sriram Ramaswamy
- Department of Physics, Indian Institute of Science, Bengaluru 560 012, India
| | - Prasad Perlekar
- Tata Institute of Fundamental Research, Hyderabad 500046, India
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4
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Rønning J, Renaud J, Doostmohammadi A, Angheluta L. Spontaneous flows and dynamics of full-integer topological defects in polar active matter. SOFT MATTER 2023; 19:7513-7527. [PMID: 37493084 DOI: 10.1039/d3sm00316g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Polar active matter of self-propelled particles sustain spontaneous flows through the full-integer topological defects. We study theoretically the incompressible flow profiles around ±1 defects induced by polar and dipolar active forces. We show that dipolar forces induce vortical flows around the +1 defect, while the flow around the -1 defect has an 8-fold rotational symmetry. The vortical flow changes its chirality near the +1 defect core in the absence of the friction with a substrate. We show analytically that the flow induced by polar active forces is vortical near the +1 defect and is 4-fold symmetric near the -1 defect, while it becomes uniform in the far-field. For a pair of oppositely charged defects, this polar flow contributes to a mutual interaction force that depends only on the orientation of the defect pair relative to the background polarization, and that enhances defect pair annihilation. This is in contradiction with the effect of dipolar active forces which decay inversely proportional with the defect separation distance. As such, our analyses reveals a long-ranged mechanism for the pairwise interaction between topological defects in polar active matter.
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Affiliation(s)
- Jonas Rønning
- Department of Physics, Njord Centre, University of Oslo, P.O. Box 1048, 0316 Oslo, Norway.
| | - Julian Renaud
- École Normale Supérieure, PSL Research University, 45 rue d'Ulm, 75005 Paris, France
- Institute of Science and Technology Austria, Am Campus 1, A-3400 Klosterneuburg, Austria
| | - Amin Doostmohammadi
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, Copenhagen, Denmark.
| | - Luiza Angheluta
- Department of Physics, Njord Centre, University of Oslo, P.O. Box 1048, 0316 Oslo, Norway.
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5
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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: 0] [Impact Index Per Article: 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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6
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Self-mixing in microtubule-kinesin active fluid from nonuniform to uniform distribution of activity. Nat Commun 2022; 13:6573. [PMID: 36323696 PMCID: PMC9630547 DOI: 10.1038/s41467-022-34396-1] [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: 05/22/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Active fluids have applications in micromixing, but little is known about the mixing kinematics of systems with spatiotemporally-varying activity. To investigate, UV-activated caged ATP is used to activate controlled regions of microtubule-kinesin active fluid and the mixing process is observed with fluorescent tracers and molecular dyes. At low Péclet numbers (diffusive transport), the active-inactive interface progresses toward the inactive area in a diffusion-like manner that is described by a simple model combining diffusion with Michaelis-Menten kinetics. At high Péclet numbers (convective transport), the active-inactive interface progresses in a superdiffusion-like manner that is qualitatively captured by an active-fluid hydrodynamic model coupled to ATP transport. Results show that active fluid mixing involves complex coupling between distribution of active stress and active transport of ATP and reduces mixing time for suspended components with decreased impact of initial component distribution. This work will inform application of active fluids to promote micromixing in microfluidic devices.
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7
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Kumar S, Mishra S. Active nematic gel with quenched disorder. Phys Rev E 2022; 106:044603. [PMID: 36397569 DOI: 10.1103/physreve.106.044603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
With quenched disorder, we introduce two-dimensional active nematics suspended in an incompressible fluid. We write the coarse-grained hydrodynamic equations of motion for slow variables, viz. density, orientation, and flow fields. The quenched disorder is introduced such that it interacts with the local orientation at every point with some strength. Disorder strength is tuned from zero to large values. We numerically study the defect dynamics and system kinetics and find that the finite disorder slows the ordering. The presence of fluid induces large fluctuation in the orientation field, further disturbing the ordering. The large fluctuation in the orientation field due to the fluid is so dominant that it reduces the effect of the quenched disorder. We have also found that the disorder effect is almost the same for both the contractile and extensile nature of active stresses in the system. This study can help to understand the impact of quenched disorder on the ordering kinetics of active gels with nematic interaction among the constituent objects.
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Affiliation(s)
- Sameer Kumar
- Department of Physics, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh 221005, India
| | - Shradha Mishra
- Department of Physics, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh 221005, India
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8
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Pismen LM. Vector formalism for active nematic liquid crystals in two dimensions. Phys Rev E 2022; 106:034701. [PMID: 36266876 DOI: 10.1103/physreve.106.034701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Specific features of two-dimensional nematodynamics give rise to shortfalls of the tensor representation of the nematic order parameter commonly used in computations, especially in theory of active matter. The alternative representation in terms of the vector order parameter follows with small adjustments the classical director-based theory, but is applicable to 2D problems where both nematic alignment and deviation from the isotropic state are variable. Stability analysis of nematic alignment and flow is used as a testing ground. A director-based analysis demonstrates a shortfall of the standard theory, which does not ensure relaxation to equilibrium in a passive system. It also demonstrates the inadequacy of the director-based description, which misses a stabilizing effect of perturbations of the modulus ensuring stability of a passive system on scales far exceeding the healing length.
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Affiliation(s)
- L M Pismen
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
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9
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Kozhukhov T, Shendruk TN. Mesoscopic simulations of active nematics. SCIENCE ADVANCES 2022; 8:eabo5788. [PMID: 36001669 PMCID: PMC9401632 DOI: 10.1126/sciadv.abo5788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Coarse-grained, mesoscale simulations are invaluable for studying soft condensed matter because of their ability to model systems in which a background solvent plays a substantial role but is not the primary interest. Such methods generally model passive solvents; however, far-from-equilibrium systems may also be composed of complex solutes suspended in an active fluid. Yet, few coarse-grained simulation methods exist to model an active medium. We introduce an algorithm to simulate active nematics, which builds on multiparticle collision dynamics (MPCD) for passive fluctuating nematohydrodynamics by introducing dipolar activity in the local collision operator. Active nematic MPCD (AN-MPCD) simulations not only exhibit the key characteristics of active nematic turbulence but, as a particle-based algorithm, also reproduce crucial attributes of active particle models. Thus, mesoscopic AN-MPCD is an approach that bridges microscopic and continuum descriptions, allowing simulations of composite active-passive systems.
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10
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Kumar N, Zhang R, Redford SA, de Pablo JJ, Gardel ML. Catapulting of topological defects through elasticity bands in active nematics. SOFT MATTER 2022; 18:5271-5281. [PMID: 35789364 DOI: 10.1039/d2sm00414c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Active materials are those in which individual, uncoordinated local stresses drive the material out of equilibrium on a global scale. Examples of such assemblies can be seen across scales from schools of fish to the cellular cytoskeleton and underpin many important biological processes. Synthetic experiments that recapitulate the essential features of such active systems have been the object of study for decades as their simple rules allow us to elucidate the physical underpinnings of collective motion. One system of particular interest has been active nematic liquid crystals (LCs). Because of their well understood passive physics, LCs provide a rich platform to interrogate the effects of active stress. The flows and steady state structures that emerge in an active LCs have been understood to result from a competition between nematic elasticity and the local activity. However most investigations of such phenomena consider only the magnitude of the elastic resistance and not its peculiarities. Here we investigate a nematic liquid crystal and selectively change the ratio of the material's splay and bend elasticities. We show that increases in the nematic's bend elasticity specifically drives the material into an exotic steady state where elongated regions of acute bend distortion or "elasticity bands" dominate the structure and dynamics. We show that these bands strongly influence defect dynamics, including the rapid motion or "catapulting" along the disintegration of one of these bands thus converting bend distortion into defect transport. Thus, we report a novel dynamical state resultant from the competition between nematic elasticity and active stress.
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Affiliation(s)
- Nitin Kumar
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.
- Department of Physics, The University of Chicago, Chicago, Illinois 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, India
| | - Rui Zhang
- Department of Physics, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
| | - Steven A Redford
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, Illinois 60637, USA
| | - Juan J de Pablo
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
- Institute for Molecular Engineering, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Margaret L Gardel
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.
- Department of Physics, The University of Chicago, Chicago, Illinois 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
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11
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Keogh RR, Chandragiri S, Loewe B, Ala-Nissila T, Thampi SP, Shendruk TN. Helical flow states in active nematics. Phys Rev E 2022; 106:L012602. [PMID: 35974522 DOI: 10.1103/physreve.106.l012602] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
We show that confining extensile nematics in three-dimensional (3D) channels leads to the emergence of two self-organized flow states with nonzero helicity. The first is a pair of braided antiparallel streams-this double helix occurs when the activity is moderate, anchoring negligible, and reduced temperature high. The second consists of axially aligned counter-rotating vortices-this grinder train arises between spontaneous axial streaming and the vortex lattice. These two unanticipated helical flow states illustrate the potential of active fluids to break symmetries and form complex but organized spatiotemporal structures in 3D fluidic devices.
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Affiliation(s)
- Ryan R Keogh
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Santhan Chandragiri
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai 600036, India
| | - Benjamin Loewe
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Tapio Ala-Nissila
- MSP Group, QTF Centre of Excellence, Department of Applied Physics, Aalto University, P.O. Box 11000, FI-00076 Aalto, Espoo, Finland
- Interdisciplinary Centre for Mathematical Modelling, Department of Mathematical Sciences, Loughborough University, Loughborough LE11 3TU, United Kingdom
| | - Sumesh P Thampi
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai 600036, India
| | - Tyler N Shendruk
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
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Aranson IS. Bacterial active matter. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022; 85:076601. [PMID: 35605446 DOI: 10.1088/1361-6633/ac723d] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Bacteria are among the oldest and most abundant species on Earth. Bacteria successfully colonize diverse habitats and play a significant role in the oxygen, carbon, and nitrogen cycles. They also form human and animal microbiota and may become sources of pathogens and a cause of many infectious diseases. Suspensions of motile bacteria constitute one of the most studied examples of active matter: a broad class of non-equilibrium systems converting energy from the environment (e.g., chemical energy of the nutrient) into mechanical motion. Concentrated bacterial suspensions, often termed active fluids, exhibit complex collective behavior, such as large-scale turbulent-like motion (so-called bacterial turbulence) and swarming. The activity of bacteria also affects the effective viscosity and diffusivity of the suspension. This work reports on the progress in bacterial active matter from the physics viewpoint. It covers the key experimental results, provides a critical assessment of major theoretical approaches, and addresses the effects of visco-elasticity, liquid crystallinity, and external confinement on collective behavior in bacterial suspensions.
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Affiliation(s)
- Igor S Aranson
- Departments of Biomedical Engineering, Chemistry, and Mathematics, Pennsylvania State University, University Park, PA 16802, United States of America
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Zhang DQ, Li ZY, Li B. Self-rotation regulates interface evolution in biphasic active matter through taming defect dynamics. Phys Rev E 2022; 105:064607. [PMID: 35854599 DOI: 10.1103/physreve.105.064607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Chirality can endow nonequilibrium active matter with unique features and functions. Here, we explore the chiral dynamics in biphasic active nematics composed of self-rotating units that continuously inject energy and angular momentum at the microscale. We show that the self-rotation of units can regularize the boundaries between two phases, rendering sinusoidal-like interfaces, which allow lateral wave propagation and are characterized by chains of ordered antiferromagnetic cross-interface flow vortices. Through the spontaneous coordination of counter-rotating units across the interfaces, topological defects excited by activity are sorted spatiotemporally, where positive defects are locally trapped at the interfaces but, unexpectedly, are transported laterally in a unidirectional rather than wavy mode, whereas inertial negative defects remain spinning in the bulks. Our findings reveal that individual chirality could be harnessed to modulate interfacial morphodynamics in active systems and suggest a potential approach toward controlling topological defects for programmable microfluidics and logic operations.
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Affiliation(s)
- De-Qing Zhang
- Institute of Biomechanics and Medical Engineering, Applied Mechanics Laboratory, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China
| | - Zhong-Yi Li
- Institute of Biomechanics and Medical Engineering, Applied Mechanics Laboratory, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China
| | - Bo Li
- Institute of Biomechanics and Medical Engineering, Applied Mechanics Laboratory, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China
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14
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Filopodia rotate and coil by actively generating twist in their actin shaft. Nat Commun 2022; 13:1636. [PMID: 35347113 PMCID: PMC8960877 DOI: 10.1038/s41467-022-28961-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 02/10/2022] [Indexed: 12/19/2022] Open
Abstract
Filopodia are actin-rich structures, present on the surface of eukaryotic cells. These structures play a pivotal role by allowing cells to explore their environment, generate mechanical forces or perform chemical signaling. Their complex dynamics includes buckling, pulling, length and shape changes. We show that filopodia additionally explore their 3D extracellular space by combining growth and shrinking with axial twisting and buckling. Importantly, the actin core inside filopodia performs a twisting or spinning motion which is observed for a range of cell types spanning from earliest development to highly differentiated tissue cells. Non-equilibrium physical modeling of actin and myosin confirm that twist is an emergent phenomenon of active filaments confined in a narrow channel which is supported by measured traction forces and helical buckles that can be ascribed to accumulation of sufficient twist. These results lead us to conclude that activity induced twisting of the actin shaft is a general mechanism underlying fundamental functions of filopodia. The authors show how tubular surface structures in all cell types, have the ability to twist and perform rotary sweeping motion to explore the extracellular environment. This has implications for migration, sensing and cell communication.
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15
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Digregorio P, Levis D, Cugliandolo LF, Gonnella G, Pagonabarraga I. Unified analysis of topological defects in 2D systems of active and passive disks. SOFT MATTER 2022; 18:566-591. [PMID: 34928290 DOI: 10.1039/d1sm01411k] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We provide a comprehensive quantitative analysis of localized and extended topological defects in the steady state of 2D passive and active repulsive Brownian disk systems. We show that, both in and out-of-equilibrium, the passage from the solid to the hexatic is driven by the unbinding of dislocations, in quantitative agreement with the KTHNY singularity. Instead, extended clusters of defects largely dominate below the solid-hexatic critical line. The latter percolate in the liquid phase very close to the hexatic-liquid transition, both for continuous and discontinuous transitions, in the homogeneous liquid regime. At critical percolation the clusters of defects are fractal with statistical and geometric properties that are independent of the activity and compatible with the universality class of uncorrelated critical percolation. We also characterize the spatial organization of point-like defects and we show that the disclinations are not free, but rather always very near more complex defect structures. At high activity, the bulk of the dense phase generated by Motility-Induced Phase Separation is characterized by a density of point-like defects, and statistics and morphology of defect clusters, set by the amount of activity and not the packing fraction. Hexatic domains within the dense phase are separated by grain-boundaries along which a finite network of topological defects resides, interrupted by gas bubbles in cavitation. This structure is dynamic in the sense that the defect network allows for an unzipping mechanism that leaves free space for gas bubbles to appear, close, and even be released into the dilute phase.
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Affiliation(s)
- Pasquale Digregorio
- Centre Européen de Calcul Atomique et Moléculaire (CECAM), Ecole Polytechnique Fédérale de Lausanne (EPFL), Batochimie, Avenue Forel 2, 1015 Lausanne, Switzerland
| | - Demian Levis
- Departament de Fisica de la Materia Condensada, Universitat de Barcelona, Marti i Franques 1, 08028 Barcelona, Spain
- UBICS University of Barcelona Institute of Complex Systems, Martí i Franquès 1, E08028 Barcelona, Spain
| | - Leticia F Cugliandolo
- Laboratoire de Physique Théorique et Hautes Energies, Sorbonne Université, CNRS UMR 7589, 4 Place Jussieu, 75252 Paris Cedex 05, France
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris Cedex 05, France
| | - Giuseppe Gonnella
- Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, I-70126, Italy
| | - Ignacio Pagonabarraga
- Centre Européen de Calcul Atomique et Moléculaire (CECAM), Ecole Polytechnique Fédérale de Lausanne (EPFL), Batochimie, Avenue Forel 2, 1015 Lausanne, Switzerland
- Departament de Fisica de la Materia Condensada, Universitat de Barcelona, Marti i Franques 1, 08028 Barcelona, Spain
- UBICS University of Barcelona Institute of Complex Systems, Martí i Franquès 1, E08028 Barcelona, Spain
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16
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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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17
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Samui A, Yeomans JM, Thampi SP. Flow transitions and length scales of a channel-confined active nematic. SOFT MATTER 2021; 17:10640-10648. [PMID: 34788355 DOI: 10.1039/d1sm01434j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We perform lattice Boltzmann simulations of an active nematic fluid confined in a two-dimensional channel to study the range of flow states that are stabilised by the confinement: unidirectional flow, oscillatory flow, the dancing state, localised active turbulence and fully-developed active turbulence. We analyse the flows in Fourier space, and measure a range of different length scales which describe the flows. We argue that the different states occur as a result of flow instabilities inherent to the system. As a consequence the characteristic length scale for oscillatory flow, the dancing state and localised active turbulence is set by the channel width. Fully-developed active turbulence occurs only when the channel width is larger than the intrinsic, active length scale of the bulk fluid. The results clarify why the activity number is a control parameter for the flow transitions.
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Affiliation(s)
- Abhik Samui
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India.
| | - Julia M Yeomans
- The Rudolf Peierls Centre for Theoretical Physics, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK.
| | - Sumesh P Thampi
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai 600036, India.
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18
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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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19
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Nourhani A, Saintillan D. Spontaneous directional flow of active magnetic particles. Phys Rev E 2021; 103:L040601. [PMID: 34006000 DOI: 10.1103/physreve.103.l040601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/17/2021] [Indexed: 11/07/2022]
Abstract
We predict the emergence of large-scale polar order and spontaneous directional flows in a class of self-propelled autonomous particles that interact via passive repulsion between off-center sites. The coupling of active motion with the passive torque acting about the particle centers results in hybrid active-passive interactions responsible for a macroscopic phase transition from an isotropic state to a polar-aligned state in systems of particles with front interaction sites. We employ a continuum kinetic theory to explain that the emergence of long-ranged orientational order, which occurs in unbounded domains at finite densities, can be externally activated independently of the self-propulsion mechanism and drives a macroscopic particle flow in a direction selected by symmetry breaking.
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Affiliation(s)
- Amir Nourhani
- Department of Mechanical Engineering, University of Akron, Akron, Ohio 44325, USA.,Department of Biology, University of Akron, Akron, Ohio 44325, USA.,Department of Mathematics, University of Akron, Akron, Ohio 44325, USA.,Department of Chemical, Biomolecular, and Corrosion Engineering, University of Akron, Akron, Ohio 44325, USA.,Biomimicry Research and Innovation Center, University of Akron, Akron, Ohio 44325, USA
| | - David Saintillan
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California 92093, USA
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20
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Arora P, Sood AK, Ganapathy R. Emergent stereoselective interactions and self-recognition in polar chiral active ellipsoids. SCIENCE ADVANCES 2021; 7:7/9/eabd0331. [PMID: 33637525 PMCID: PMC7909878 DOI: 10.1126/sciadv.abd0331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
In many active matter systems, particle trajectories have a well-defined handedness or chirality. Whether such chiral activity can introduce stereoselective interactions between particles is not known. Here, we developed a strategy to tune the nature of chiral activity of three-dimensionally printed granular ellipsoids without altering their shape or size. In vertically agitated monolayers of these particles, we observed two types of dimers form depending on the chirality of the pairing monomers. Heterochiral dimers moved collectively as a single achiral active unit, while homochiral ones formed a translationally immobile spinner. In active racemic mixtures, the former was more abundant than the latter, indicating that interactions were stereoselective. Through dimer lifetime measurements, we further provide evidence for chiral self-recognition in mixtures of particles with different chiral activities. We lastly show that, at fixed particle number density, changing the net chirality of a dense active liquid fundamentally alters the nature of collective relaxation.
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Affiliation(s)
- Pragya Arora
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India.
| | - A K Sood
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
- International Centre for Materials Science, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Rajesh Ganapathy
- International Centre for Materials Science, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India.
- School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
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21
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Chandrakar P, Varghese M, Aghvami SA, Baskaran A, Dogic Z, Duclos G. Confinement Controls the Bend Instability of Three-Dimensional Active Liquid Crystals. PHYSICAL REVIEW LETTERS 2020; 125:257801. [PMID: 33416339 DOI: 10.1103/physrevlett.125.257801] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/15/2020] [Accepted: 11/11/2020] [Indexed: 06/12/2023]
Abstract
Spontaneous growth of long-wavelength deformations is a defining feature of active liquid crystals. We investigate the effect of confinement on the instability of 3D active liquid crystals in the isotropic phase composed of extensile microtubule bundles and kinesin molecular motors. When shear aligned, such fluids exhibit finite-wavelength self-amplifying bend deformations. By systematically changing the channel size we elucidate how the instability wavelength and its growth rate depend on the channel dimensions. Experimental findings are qualitatively consistent with a minimal hydrodynamic model, where the fastest growing deformation is set by a balance of active driving and elastic relaxation. Our results demonstrate that confinement determines the structure and dynamics of active fluids on all experimentally accessible length scales.
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Affiliation(s)
- Pooja Chandrakar
- 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
| | - S Ali Aghvami
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Aparna Baskaran
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Zvonimir Dogic
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Guillaume Duclos
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
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22
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Thijssen K, Nejad MR, Yeomans JM. Role of Friction in Multidefect Ordering. PHYSICAL REVIEW LETTERS 2020; 125:218004. [PMID: 33275020 DOI: 10.1103/physrevlett.125.218004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/30/2020] [Accepted: 10/22/2020] [Indexed: 06/12/2023]
Abstract
We use continuum simulations to study the impact of friction on the ordering of defects in an active nematic. Even in a frictionless system, +1/2 defects tend to align side by side and orient antiparallel reflecting their propensity to form, and circulate with, flow vortices. Increasing friction enhances the effectiveness of the defect-defect interactions, and defects form dynamically evolving, large-scale, positionally, and orientationally ordered structures, which can be explained as a competition between hexagonal packing, preferred by the -1/2 defects, and rectangular packing, preferred by the +1/2 defects.
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Affiliation(s)
- Kristian Thijssen
- The Rudolf Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Mehrana R Nejad
- The Rudolf Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Julia M Yeomans
- The Rudolf Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
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23
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Zhao L, Yao L, Golovaty D, Ignés-Mullol J, Sagués F, Carme Calderer M. Stability analysis of flow of active extensile fibers in confined domains. CHAOS (WOODBURY, N.Y.) 2020; 30:113105. [PMID: 33261333 DOI: 10.1063/5.0023924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/06/2020] [Indexed: 06/12/2023]
Abstract
In this article, we study shear flow of active extensile filaments confined in a narrow channel. They behave as nematic liquid crystals that we assumed are governed by the Ericksen-Leslie equations of balance of linear and angular momentum. The addition of an activity source term in the Leslie stress captures the role of the biofuel prompting the dynamics. The dimensionless form of the governing system includes the Ericksen, activity, and Reynolds numbers together with the aspect ratio of the channel as the main driving parameters affecting the stability of the system. The active system that guides our analysis is composed of microtubules concentrated in bundles, hundreds of microns long, placed in a narrow channel domain, of aspect ratios in the range between 10-2 and 10-3 dimensionless units, which are able to align due to the combination of adenosine triphosphate-supplied energy and confinement effects. Specifically, this work aims at studying the role of confinement on the behavior of active matter. It is experimentally observed that, at an appropriately low activity and channel width, the active flow is laminar, with the linear velocity profile and the angle of alignment analogous to those in passive shear, developing defects and becoming chaotic, at a large activity and a channel aspect ratio. The present work addresses the laminar regime, where defect formation does not play a role. We perform a normal mode stability analysis of the base shear flow. A comprehensive description of the stability properties is obtained in terms of the driving parameters of the system. Our main finding, in addition to the geometry and magnitude of the flow profiles, and also consistent with the experimental observations, is that the transition to instability of the uniformly aligned shear flow occurs at a threshold value of the activity parameter, with the transition also being affected by the channel aspect ratio. The role of the parameters on the vorticity and angular profiles of the perturbing flow is also analyzed and found to agree with the experimentally observed transition to turbulent regimes. A spectral method based on Chebyshev polynomials is used to solve the generalized eigenvalue problems arising in the stability analysis.
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Affiliation(s)
- Longhua Zhao
- Department of Mathematics, Applied Mathematics and Statistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Lingxing Yao
- Department of Mathematics, University of Akron, Akron, Ohio 44325, USA
| | - Dmitry Golovaty
- Department of Mathematics, University of Akron, Akron, Ohio 44325, USA
| | - Jordi Ignés-Mullol
- Department of Materials Science and Physical Chemistry, and Institute of Nanoscience and Nanotechnology, University of Barcelona, Barcelona 08028, Spain and Institute of Nanoscience and Nanotechnology, Barcelona 08028, Spain
| | - Francesc Sagués
- Department of Materials Science and Physical Chemistry, and Institute of Nanoscience and Nanotechnology, University of Barcelona, Barcelona 08028, Spain and Institute of Nanoscience and Nanotechnology, Barcelona 08028, Spain
| | - M Carme Calderer
- School of Mathematics, University of Minnesota, Minneapolis, Minnesota 55455, USA
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24
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Norton MM, Grover P, Hagan MF, Fraden S. Optimal Control of Active Nematics. PHYSICAL REVIEW LETTERS 2020; 125:178005. [PMID: 33156653 DOI: 10.1103/physrevlett.125.178005] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
In this work we present the first systematic framework to sculpt active nematic systems, using optimal control theory and a hydrodynamic model of active nematics. We demonstrate the use of two different control fields, (i) applied vorticity and (ii) activity strength, to shape the dynamics of an extensile active nematic that is confined to a disk. In the absence of control inputs, the system exhibits two attractors, clockwise and counterclockwise circulating states characterized by two co-rotating topological +1/2 defects. We specifically seek spatiotemporal inputs that switch the system from one attractor to the other; we also examine phase-shifting perturbations. We identify control inputs by optimizing a penalty functional with three contributions: total control effort, spatial gradients in the control, and deviations from the desired trajectory. This work demonstrates that optimal control theory can be used to calculate nontrivial inputs capable of restructuring active nematics in a manner that is economical, smooth, and rapid, and therefore will serve as a guide to experimental efforts to control active matter.
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Affiliation(s)
- Michael M Norton
- Center for Neural Engineering, Department of Engineering Science and Materials, Pennsylvania State University, University Park, Pennsylvania 16801, USA and Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Piyush Grover
- Mechanical and Materials Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Michael F Hagan
- Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Seth Fraden
- Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
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25
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Hughes R, Yeomans JM. Collective chemotaxis of active nematic droplets. Phys Rev E 2020; 102:020601. [PMID: 32942458 DOI: 10.1103/physreve.102.020601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/12/2020] [Indexed: 11/07/2022]
Abstract
Collective chemotaxis plays a key role in the navigation of cell clusters in, e.g., embryogenesis and cancer metastasis. Using the active nematic continuum equations, coupled to a chemical field that regulates activity, we demonstrate and explain a physical mechanism that results in collective chemotaxis. The activity naturally leads to cell polarization at the cluster interface which induces outward flows. The chemical gradient then breaks the symmetry of the flow field, leading to a net motion. The velocity is independent of the cluster size, in agreement with experiment.
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Affiliation(s)
- Rian Hughes
- 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
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26
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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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27
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Krajnik Ž, Kos Ž, Ravnik M. Spectral energy analysis of bulk three-dimensional active nematic turbulence. SOFT MATTER 2020; 16:9059-9068. [PMID: 32901629 DOI: 10.1039/c9sm02492a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We perform energy spectrum analysis of the active turbulence in a 3D bulk active nematic using continuum numerical modelling. Specifically, we calculate the spectra of the two main energy contributions - kinetic energy and nematic elastic energy - and combine this with the geometrical analysis of the nematic order and flow fields, based on direct defect tracking and calculation of autocorrelations. We show that the active nematic elastic energy is concentrated at scales corresponding to the effective defect-to-defect separation, scaling with activity as ∼ζ0.5, whereas the kinetic energy is largest at somewhat larger scales of typically several 100 nematic correlation lengths. Nematic biaxiality is shown to have no role in active turbulence at most length scales, but can affect the nematic elastic energy by an order of magnitude at scales of the active defect core size. The effect of an external aligning field on the 3D active turbulence is explored, showing a transition from an effective active turbulent to an aligned regime. The work is aimed at providing a contribution towards understanding active turbulence in general three-dimensions, from the perspective of main energy-relevant mechanisms at different length scales of the system.
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Affiliation(s)
- Žiga Krajnik
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia.
| | - Žiga Kos
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia.
| | - Miha Ravnik
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia. and JoŽef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
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28
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Zhang YH, Deserno M, Tu ZC. Dynamics of active nematic defects on the surface of a sphere. Phys Rev E 2020; 102:012607. [PMID: 32795046 DOI: 10.1103/physreve.102.012607] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022]
Abstract
A nematic liquid crystal confined to the surface of a sphere exhibits topological defects of total charge +2 due to the topological constraint. In equilibrium, the nematic field forms four +1/2 defects, located at the corners of a regular tetrahedron inscribed within the sphere, since this minimizes the Frank elastic energy. If additionally the individual nematogens exhibit self-driven directional motion, the resulting active system creates large-scale flow that drives it out of equilibrium. In particular, the defects now follow complex dynamic trajectories which, depending on the strength of the active forcing, can be periodic (for weak forcing) or chaotic (for strong forcing). In this paper we derive an effective particle theory for this system, in which the topological defects are the degrees of freedom, whose exact equations of motion we subsequently determine. Numerical solutions of these equations confirm previously observed characteristics of their dynamics and clarify the role played by the time dependence of their global rotation. We also show that Onsager's variational principle offers an exceptionally transparent way to derive these dynamical equations, and we explain the defect mobility at the hydrodynamics level.
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Affiliation(s)
- Yi-Heng Zhang
- Department of Physics, Beijing Normal University, Beijing 100875, China
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, USA
| | - Zhan-Chun Tu
- Department of Physics, Beijing Normal University, Beijing 100875, China
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29
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Vliegenthart GA, Ravichandran A, Ripoll M, Auth T, Gompper G. Filamentous active matter: Band formation, bending, buckling, and defects. SCIENCE ADVANCES 2020; 6:eaaw9975. [PMID: 32832652 PMCID: PMC7439626 DOI: 10.1126/sciadv.aaw9975] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/05/2020] [Indexed: 06/01/2023]
Abstract
Motor proteins drive persistent motion and self-organization of cytoskeletal filaments. However, state-of-the-art microscopy techniques and continuum modeling approaches focus on large length and time scales. Here, we perform component-based computer simulations of polar filaments and molecular motors linking microscopic interactions and activity to self-organization and dynamics from the filament level up to the mesoscopic domain level. Dynamic filament cross-linking and sliding and excluded-volume interactions promote formation of bundles at small densities and of active polar nematics at high densities. A buckling-type instability sets the size of polar domains and the density of topological defects. We predict a universal scaling of the active diffusion coefficient and the domain size with activity, and its dependence on parameters like motor concentration and filament persistence length. Our results provide a microscopic understanding of cytoplasmic streaming in cells and help to develop design strategies for novel engineered active materials.
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30
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Binysh J, Kos Ž, Čopar S, Ravnik M, Alexander GP. Three-Dimensional Active Defect Loops. PHYSICAL REVIEW LETTERS 2020; 124:088001. [PMID: 32167362 DOI: 10.1103/physrevlett.124.088001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
We describe the flows and morphological dynamics of topological defect lines and loops in three-dimensional active nematics and show, using theory and numerical modeling, that they are governed by the local profile of the orientational order surrounding the defects. Analyzing a continuous span of defect loop profiles, ranging from radial and tangential twist to wedge ±1/2 profiles, we show that the distinct geometries can drive material flow perpendicular or along the local defect loop segment, whose variation around a closed loop can lead to net loop motion, elongation, or compression of shape, or buckling of the loops. We demonstrate a correlation between local curvature and the local orientational profile of the defect loop, indicating dynamic coupling between geometry and topology. To address the general formation of defect loops in three dimensions, we show their creation via bend instability from different initial elastic distortions.
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Affiliation(s)
- Jack Binysh
- Mathematics Institute, Zeeman Building, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Žiga Kos
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia
| | - Simon Čopar
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia
| | - Miha Ravnik
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia
- Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Gareth P Alexander
- Department of Physics and Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, United Kingdom
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31
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Fischer A, Schmid F, Speck T. Quorum-sensing active particles with discontinuous motility. Phys Rev E 2020; 101:012601. [PMID: 32069622 DOI: 10.1103/physreve.101.012601] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Indexed: 06/10/2023]
Abstract
We develop a dynamic mean-field theory for polar active particles that interact through a self-generated field, in particular one generated through emitting a chemical signal. While being a form of chemotactic response, it is different from conventional chemotaxis in that particles discontinuously change their motility when the local concentration surpasses a threshold. The resulting coupled equations for density and polarization are linear and can be solved analytically for simple geometries, yielding inhomogeneous density profiles. Specifically, here we consider a planar and circular interface. Our theory thus explains the observed coexistence of dense aggregates with an active gas. There are, however, differences from the more conventional picture of liquid-gas coexistence based on a free energy, most notably the absence of a critical point. We corroborate our analytical predictions by numerical simulations of active particles under confinement and interacting through volume exclusion. Excellent quantitative agreement is reached through an effective translational diffusion coefficient. We finally show that an additional response to the chemical gradient direction is sufficient to induce vortex clusters. Our results pave the way to engineer motility responses in order to achieve aggregation and collective behavior even at unfavorable conditions.
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Affiliation(s)
- Andreas Fischer
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
| | - Friederike Schmid
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
| | - Thomas Speck
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
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32
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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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33
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Kempf F, Mueller R, Frey E, Yeomans JM, Doostmohammadi A. Active matter invasion. SOFT MATTER 2019; 15:7538-7546. [PMID: 31451816 DOI: 10.1039/c9sm01210a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biologically active materials such as bacterial biofilms and eukaryotic cells thrive in confined micro-spaces. Here, we show through numerical simulations that confinement can serve as a mechanical guidance to achieve distinct modes of collective invasion when combined with growth dynamics and the intrinsic activity of biological materials. We assess the dynamics of the growing interface and classify these collective modes of invasion based on the activity of the constituent particles of the growing matter. While at small and moderate activities the active material grows as a coherent unit, we find that blobs of active material collectively detach from the cohort above a well-defined activity threshold. We further characterise the mechanical mechanisms underlying the crossovers between different modes of invasion and quantify their impact on the overall invasion speed.
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Affiliation(s)
- Felix Kempf
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München - Theresienstr. 37, D-80333 Munich, Germany
| | - Romain Mueller
- The Rudolf Peierls Centre for Theoretical Physics - Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK.
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München - Theresienstr. 37, D-80333 Munich, Germany
| | - Julia M Yeomans
- The Rudolf Peierls Centre for Theoretical Physics - Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK.
| | - Amin Doostmohammadi
- The Rudolf Peierls Centre for Theoretical Physics - Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK.
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34
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Bayati P, Popescu MN, Uspal WE, Dietrich S, Najafi A. Dynamics near planar walls for various model self-phoretic particles. SOFT MATTER 2019; 15:5644-5672. [PMID: 31245803 DOI: 10.1039/c9sm00488b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
For chemically active particles suspended in a liquid solution and moving by self-phoresis, the dynamics near chemically inert, planar walls is studied theoretically by employing various choices for the activity function, i.e., the spatial distribution of the sites where various chemical reactions take place. We focus on the case of solutions composed of electrically neutral species. This analysis extends previous studies of the case that the chemical activity can be modeled effectively as the release of a "product" molecular species from parts of the surface of the particle by accounting for annihilation of the product molecules by chemical reactions, either on the rest of the surface of the particle or in the volume of the surrounding solution. We show that, for the models considered here, the emergence of "sliding" and "hovering" wall-bound states is a generic, robust feature. However, the details of these states, such as the range of parameters within which they occur, depend on the specific model for the activity function. Additionally, in certain cases there is a reversal of the direction of the motion compared to the one observed if the particle is far away from the wall. We have also studied the changes of the dynamics induced by a direct interaction between the particle and the wall by including a short-ranged repulsive component to the interaction in addition to the steric one (a procedure often employed in numerical simulations of active colloids). Upon increasing the strength of this additional component, while keeping its range fixed, significant qualitative changes occur in the phase portraits of the dynamics near the wall: for sufficiently strong short-ranged repulsion, the sliding steady states of the dynamics are transformed into hovering states. Furthermore, our studies provide evidence for an additional "oscillatory" wall-bound steady state of motion for chemically active particles due to a strong, short-ranged, and direct repulsion. This kind of particle translates along the wall at a distance from it which oscillates between a minimum and a maximum.
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Affiliation(s)
- Parvin Bayati
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran.
| | - Mihail N Popescu
- Max-Planck-Institut für Intelligente Systeme, Heisenbergstr. 3, D-70569 Stuttgart, Germany and IV. Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - William E Uspal
- Max-Planck-Institut für Intelligente Systeme, Heisenbergstr. 3, D-70569 Stuttgart, Germany and IV. Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany and Department of Mechanical Engineering, University of Hawai'i at Manoa, 2540 Dole Street, Holmes 302, Honolulu, HI 96822, USA
| | - S Dietrich
- Max-Planck-Institut für Intelligente Systeme, Heisenbergstr. 3, D-70569 Stuttgart, Germany and IV. Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Ali Najafi
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran. and Research Center for Basic Sciences & Modern Technologies (RBST), Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
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35
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Carenza LN, Gonnella G, Lamura A, Negro G, Tiribocchi A. Lattice Boltzmann methods and active fluids. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:81. [PMID: 31250142 DOI: 10.1140/epje/i2019-11843-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/24/2019] [Indexed: 05/24/2023]
Abstract
We review the state of the art of active fluids with particular attention to hydrodynamic continuous models and to the use of Lattice Boltzmann Methods (LBM) in this field. We present the thermodynamics of active fluids, in terms of liquid crystals modelling adapted to describe large-scale organization of active systems, as well as other effective phenomenological models. We discuss how LBM can be implemented to solve the hydrodynamics of active matter, starting from the case of a simple fluid, for which we explicitly recover the continuous equations by means of Chapman-Enskog expansion. Going beyond this simple case, we summarize how LBM can be used to treat complex and active fluids. We then review recent developments concerning some relevant topics in active matter that have been studied by means of LBM: spontaneous flow, self-propelled droplets, active emulsions, rheology, active turbulence, and active colloids.
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Affiliation(s)
- Livio Nicola Carenza
- Dipartimento di Fisica, Università degli Studi di Bari, and INFN Sezione di Bari, Via Amendola 173, 70126, Bari, Italy
| | - Giuseppe Gonnella
- Dipartimento di Fisica, Università degli Studi di Bari, and INFN Sezione di Bari, Via Amendola 173, 70126, Bari, Italy.
| | - Antonio Lamura
- Istituto Applicazioni Calcolo, CNR, Via Amendola 122/D, 70126, Bari, Italy
| | - Giuseppe Negro
- Dipartimento di Fisica, Università degli Studi di Bari, and INFN Sezione di Bari, Via Amendola 173, 70126, Bari, Italy
| | - Adriano Tiribocchi
- Center for Life Nano Science@La Sapienza, Istituto Italiano di Tecnologia, 00161, Roma, Italy
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36
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Rickman J, Nédélec F, Surrey T. Effects of spatial dimensionality and steric interactions on microtubule-motor self-organization. Phys Biol 2019; 16:046004. [PMID: 31013252 PMCID: PMC7655122 DOI: 10.1088/1478-3975/ab0fb1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Active networks composed of filaments and motor proteins can self-organize into a
variety of architectures. Computer simulations in two or three spatial
dimensions and including or omitting steric interactions between filaments can
be used to model active networks. Here we examine how these modelling choices
affect the state space of network self-organization. We compare the networks
generated by different models of a system of dynamic microtubules and
microtubule-crosslinking motors. We find that a thin 3D model that includes
steric interactions between filaments is the most versatile, capturing a variety
of network states observed in recent experiments. In contrast, 2D models either
with or without steric interactions which prohibit microtubule crossings can
produce some, but not all, observed network states. Our results provide
guidelines for the most appropriate choice of model for the study of different
network types and elucidate mechanisms of active network organization.
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Affiliation(s)
- Jamie Rickman
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom. Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London WC1 6BT, United Kingdom
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37
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Metselaar L, Doostmohammadi A, Yeomans JM. Topological states in chiral active matter: Dynamic blue phases and active half-skyrmions. J Chem Phys 2019; 150:064909. [DOI: 10.1063/1.5085282] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Luuk Metselaar
- The Rudolf Peierls Centre for Theoretical Physics, Clarendon Laboratory, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Amin Doostmohammadi
- The Rudolf Peierls Centre for Theoretical Physics, Clarendon Laboratory, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Julia M. Yeomans
- The Rudolf Peierls Centre for Theoretical Physics, Clarendon Laboratory, Parks Road, Oxford OX1 3PU, United Kingdom
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38
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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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39
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Saw TB, Xi W, Ladoux B, Lim CT. Biological Tissues as Active Nematic Liquid Crystals. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1802579. [PMID: 30156334 DOI: 10.1002/adma.201802579] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/11/2018] [Indexed: 05/27/2023]
Abstract
Live tissues can self-organize and be described as active materials composed of cells that generate active stresses through continuous injection of energy. In vitro reconstituted molecular networks, as well as single-cell cytoskeletons show that their filamentous structures can portray nematic liquid crystalline properties and can promote nonequilibrium processes induced by active processes at the microscale. The appearance of collective patterns, the formation of topological singularities, and spontaneous phase transition within the cell cytoskeleton are emergent properties that drive cellular functions. More integrated systems such as tissues have cells that can be seen as coarse-grained active nematic particles and their interaction can dictate many important tissue processes such as epithelial cell extrusion and migration as observed in vitro and in vivo. Here, a brief introduction to the concept of active nematics is provided, and the main focus is on the use of this framework in the systematic study of predominantly 2D tissue architectures and dynamics in vitro. In addition how the nematic state is important in tissue behavior, such as epithelial expansion, tissue homeostasis, and the atherosclerosis disease state, is discussed. Finally, how the nematic organization of cells can be controlled in vitro for tissue engineering purposes is briefly discussed.
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Affiliation(s)
- Thuan Beng Saw
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Engineering Block 4, #04-08, Singapore, 117583, Singapore
| | - Wang Xi
- Institut Jacques Monod (IJM), CNRS UMR 7592 and Université Paris Diderot, Paris, France
| | - Benoit Ladoux
- Institut Jacques Monod (IJM), CNRS UMR 7592 and Université Paris Diderot, Paris, France
- Mechanobiology Institute (MBI), National University of Singapore, Singapore, 117411, Singapore
| | - Chwee Teck Lim
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Engineering Block 4, #04-08, Singapore, 117583, Singapore
- Mechanobiology Institute (MBI), National University of Singapore, Singapore, 117411, Singapore
- Biomedical Institute for Global Health, Research and Technology (BIGHEART), National University of Singapore, MD6, 14 Medical Drive, #14-01, Singapore, 117599, Singapore
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40
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Kan A, Del Valle I, Rudge T, Federici F, Haseloff J. Intercellular adhesion promotes clonal mixing in growing bacterial populations. J R Soc Interface 2018; 15:rsif.2018.0406. [PMID: 30232243 PMCID: PMC6170782 DOI: 10.1098/rsif.2018.0406] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 08/28/2018] [Indexed: 12/22/2022] Open
Abstract
Dense bacterial communities, known as biofilms, can have functional spatial organization driven by self-organizing chemical and physical interactions between cells, and their environment. In this work, we investigated intercellular adhesion, a pervasive property of bacteria in biofilms, to identify effects on the internal structure of bacterial colonies. We expressed the self-recognizing ag43 adhesin protein in Escherichia coli to generate adhesion between cells, which caused aggregation in liquid culture and altered microcolony morphology on solid media. We combined the adhesive phenotype with an artificial colony patterning system based on plasmid segregation, which marked clonal lineage domains in colonies grown from single cells. Engineered E. coli were grown to colonies containing domains with varying adhesive properties, and investigated with microscopy, image processing and computational modelling techniques. We found that intercellular adhesion elongated the fractal-like boundary between cell lineages only when both domains within the colony were adhesive, by increasing the rotational motion during colony growth. Our work demonstrates that adhesive intercellular interactions can have significant effects on the spatial organization of bacterial populations, which can be exploited for biofilm engineering. Furthermore, our approach provides a robust platform to study the influence of intercellular interactions on spatial structure in bacterial populations.
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Affiliation(s)
- Anton Kan
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Ilenne Del Valle
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Tim Rudge
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile.,Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fernán Federici
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.,Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Systems and Synthetic Biology (MIISSB), Santiago, Chile
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
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41
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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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42
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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: 255] [Impact Index Per Article: 42.5] [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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43
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Shendruk TN, Thijssen K, Yeomans JM, Doostmohammadi A. Twist-induced crossover from two-dimensional to three-dimensional turbulence in active nematics. Phys Rev E 2018; 98:010601. [PMID: 30110824 DOI: 10.1103/physreve.98.010601] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Indexed: 12/27/2022]
Abstract
While studies of active nematics in two dimensions have shed light on various aspects of the flow regimes and topology of active matter, three-dimensional properties of topological defects and chaotic flows remain unexplored. By confining a film of active nematics between two parallel plates, we use continuum simulations and analytical arguments to demonstrate that the crossover from quasi-two-dimensional (quasi-2D) to three-dimensional (3D) chaotic flows is controlled by the morphology of the disclination lines. For small plate separations, the active nematic behaves as a quasi-2D material, with straight topological disclination lines spanning the height of the channel and exhibiting effectively 2D active turbulence. Upon increasing channel height, we find a crossover to 3D chaotic flows due to the contortion of disclinations above a critical activity. Above this critical activity highly contorted disclination lines and disclination loops are formed. We further show that these contortions are engendered by twist perturbations producing a sharp change in the curvature of disclinations.
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Affiliation(s)
- Tyler N Shendruk
- The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
| | - Kristian Thijssen
- 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
| | - Amin Doostmohammadi
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
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44
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Norton MM, Baskaran A, Opathalage A, Langeslay B, Fraden S, Baskaran A, Hagan MF. Insensitivity of active nematic liquid crystal dynamics to topological constraints. Phys Rev E 2018; 97:012702. [PMID: 29448352 DOI: 10.1103/physreve.97.012702] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Indexed: 11/07/2022]
Abstract
Confining a liquid crystal imposes topological constraints on the orientational order, allowing global control of equilibrium systems by manipulation of anchoring boundary conditions. In this article, we investigate whether a similar strategy allows control of active liquid crystals. We study a hydrodynamic model of an extensile active nematic confined in containers, with different anchoring conditions that impose different net topological charges on the nematic director. We show that the dynamics are controlled by a complex interplay between topological defects in the director and their induced vortical flows. We find three distinct states by varying confinement and the strength of the active stress: A topologically minimal state, a circulating defect state, and a turbulent state. In contrast to equilibrium systems, we find that anchoring conditions are screened by the active flow, preserving system behavior across different topological constraints. This observation identifies a fundamental difference between active and equilibrium materials.
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Affiliation(s)
- Michael M Norton
- Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Arvind Baskaran
- Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Achini Opathalage
- Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Blake Langeslay
- Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Seth Fraden
- Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Aparna Baskaran
- Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Michael F Hagan
- Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
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45
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Blanch-Mercader C, Yashunsky V, Garcia S, Duclos G, Giomi L, Silberzan P. Turbulent Dynamics of Epithelial Cell Cultures. PHYSICAL REVIEW LETTERS 2018; 120:208101. [PMID: 29864293 DOI: 10.1103/physrevlett.120.208101] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 02/12/2018] [Indexed: 05/23/2023]
Abstract
We investigate the large length and long time scales collective flows and structural rearrangements within in vitro human bronchial epithelial cell (HBEC) cultures. Activity-driven collective flows result in ensembles of vortices randomly positioned in space. By analyzing a large population of vortices, we show that their area follows an exponential law with a constant mean value and their rotational frequency is size independent, both being characteristic features of the chaotic dynamics of active nematic suspensions. Indeed, we find that HBECs self-organize in nematic domains of several cell lengths. Nematic defects are found at the interface between domains with a total number that remains constant due to the dynamical balance of nucleation and annihilation events. The mean velocity fields in the vicinity of defects are well described by a hydrodynamic theory of extensile active nematics.
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Affiliation(s)
- C Blanch-Mercader
- Laboratoire PhysicoChimie Curie, Institut Curie, PSL Research University-Sorbonne Université, UPMC-CNRS-Equipe labellisée Ligue Contre le Cancer, 75005 Paris, France
| | - V Yashunsky
- Laboratoire PhysicoChimie Curie, Institut Curie, PSL Research University-Sorbonne Université, UPMC-CNRS-Equipe labellisée Ligue Contre le Cancer, 75005 Paris, France
| | - S Garcia
- Laboratoire PhysicoChimie Curie, Institut Curie, PSL Research University-Sorbonne Université, UPMC-CNRS-Equipe labellisée Ligue Contre le Cancer, 75005 Paris, France
| | - G Duclos
- Laboratoire PhysicoChimie Curie, Institut Curie, PSL Research University-Sorbonne Université, UPMC-CNRS-Equipe labellisée Ligue Contre le Cancer, 75005 Paris, France
| | - L Giomi
- Instituut-Lorentz, Universiteit Leiden, P.O. Box 9506, 2300 RA Leiden, The Netherlands
| | - P Silberzan
- Laboratoire PhysicoChimie Curie, Institut Curie, PSL Research University-Sorbonne Université, UPMC-CNRS-Equipe labellisée Ligue Contre le Cancer, 75005 Paris, France
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46
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Shankar S, Ramaswamy S, Marchetti MC. Low-noise phase of a two-dimensional active nematic system. Phys Rev E 2018; 97:012707. [PMID: 29448420 DOI: 10.1103/physreve.97.012707] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Indexed: 06/08/2023]
Abstract
We consider a collection of self-driven apolar particles on a substrate that organize into an active nematic phase at sufficiently high density or low noise. Using the dynamical renormalization group, we systematically study the two-dimensional fluctuating ordered phase in a coarse-grained hydrodynamic description involving both the nematic director and the conserved density field. In the presence of noise, we show that the system always displays only quasi-long-ranged orientational order beyond a crossover scale. A careful analysis of the nonlinearities permitted by symmetry reveals that activity is dangerously irrelevant over the linearized description, allowing giant number fluctuations to persist although now with strong finite-size effects and a nonuniversal scaling exponent. Nonlinear effects from the active currents lead to power-law correlations in the density field, thereby preventing macroscopic phase separation in the thermodynamic limit.
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Affiliation(s)
- Suraj Shankar
- Physics Department and Syracuse Soft & 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
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - M Cristina Marchetti
- Physics Department and Syracuse Soft & Living Matter Program, Syracuse University, Syracuse, New York 13244, USA
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47
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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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48
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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: 82] [Impact Index Per Article: 11.7] [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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49
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Saw TB, Doostmohammadi A, Nier V, Kocgozlu L, Thampi S, Toyama Y, Marcq P, Lim CT, Yeomans JM, Ladoux B. Topological defects in epithelia govern cell death and extrusion. Nature 2017; 544:212-216. [PMID: 28406198 PMCID: PMC5439518 DOI: 10.1038/nature21718] [Citation(s) in RCA: 349] [Impact Index Per Article: 49.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 02/21/2017] [Indexed: 12/23/2022]
Abstract
Epithelial tissues (epithelia) remove excess cells through extrusion, preventing the accumulation of unnecessary or pathological cells. The extrusion process can be triggered by apoptotic signalling, oncogenic transformation and overcrowding of cells. Despite the important linkage of cell extrusion to developmental, homeostatic and pathological processes such as cancer metastasis, its underlying mechanism and connections to the intrinsic mechanics of the epithelium are largely unexplored. We approach this problem by modelling the epithelium as an active nematic liquid crystal (that has a long range directional order), and comparing numerical simulations to strain rate and stress measurements within monolayers of MDCK (Madin Darby canine kidney) cells. Here we show that apoptotic cell extrusion is provoked by singularities in cell alignments in the form of comet-shaped topological defects. We find a universal correlation between extrusion sites and positions of nematic defects in the cell orientation field in different epithelium types. The results confirm the active nematic nature of epithelia, and demonstrate that defect-induced isotropic stresses are the primary precursors of mechanotransductive responses in cells, including YAP (Yes-associated protein) transcription factor activity, caspase-3-mediated cell death, and extrusions. Importantly, the defect-driven extrusion mechanism depends on intercellular junctions, because the weakening of cell-cell interactions in an α-catenin knockdown monolayer reduces the defect size and increases both the number of defects and extrusion rates, as is also predicted by our model. We further demonstrate the ability to control extrusion hotspots by geometrically inducing defects through microcontact printing of patterned monolayers. On the basis of these results, we propose a mechanism for apoptotic cell extrusion: spontaneously formed topological defects in epithelia govern cell fate. This will be important in predicting extrusion hotspots and dynamics in vivo, with potential applications to tissue regeneration and the suppression of metastasis. Moreover, we anticipate that the analogy between the epithelium and active nematic liquid crystals will trigger further investigations of the link between cellular processes and the material properties of epithelia.
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Affiliation(s)
- Thuan Beng Saw
- Mechanobiology Institute, National University of Singapore, Singapore.,National University of Singapore Graduate School of Integrative Sciences and Engineering (NGS), National University of Singapore, Singapore
| | | | - Vincent Nier
- Sorbonne Universités, UPMC Université Paris 6, Institut Curie, CNRS, UMR 168, Laboratoire Physico-Chimie Curie, Paris, France
| | - Leyla Kocgozlu
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Sumesh Thampi
- The Rudolf Peierls Centre for Theoretical Physics, Oxford University, UK.,Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai, India
| | - Yusuke Toyama
- Mechanobiology Institute, National University of Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, and Temasek Life Sciences Laboratory, Singapore
| | - Philippe Marcq
- Sorbonne Universités, UPMC Université Paris 6, Institut Curie, CNRS, UMR 168, Laboratoire Physico-Chimie Curie, Paris, France
| | - Chwee Teck Lim
- Mechanobiology Institute, National University of Singapore, Singapore.,National University of Singapore Graduate School of Integrative Sciences and Engineering (NGS), National University of Singapore, Singapore
| | - Julia M Yeomans
- The Rudolf Peierls Centre for Theoretical Physics, Oxford University, UK
| | - Benoit Ladoux
- Mechanobiology Institute, National University of Singapore, Singapore.,Institut Jacques Monod (IJM), CNRS UMR 7592 & Université Paris Diderot, Paris, France
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50
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Wang L, Huang Y. Intrinsic flow structure and multifractality in two-dimensional bacterial turbulence. Phys Rev E 2017; 95:052215. [PMID: 28618644 DOI: 10.1103/physreve.95.052215] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Indexed: 11/07/2022]
Abstract
The active interaction between the bacteria and fluid generates turbulent structures even at zero Reynolds number. The velocity of such a flow obtained experimentally has been quantitatively investigated based on streamline segment analysis. There is a clear transition at about 16 times the organism body length separating two different scale regimes, which may be attributed to the different influence of the viscous effect. Surprisingly the scaling extracted from the streamline segment indicates the existence of scale similarity even at the zero Reynolds number limit. Moreover, the multifractal feature can be quantitatively described via a lognormal formula with the Hurst number H=0.76 and the intermittency parameter μ=0.20, which is coincidentally in agreement with the three-dimensional hydrodynamic turbulence result. The direction of cascade is measured via the filter-space technique. An inverse energy cascade is confirmed. For the enstrophy, a forward cascade is observed when r/R≤3, and an inverse one is observed when r/R>3, where r and R are the separation distance and the bacteria body size, respectively. Additionally, the lognormal statistics is verified for the coarse-grained energy dissipation and enstrophy, which supports the lognormal formula to fit the measured scaling exponent.
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Affiliation(s)
- Lipo Wang
- UM-SJTU Joint Institute, Shanghai JiaoTong University, Shanghai 200240, People's Republic of China
| | - Yongxiang Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China
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