1
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Sinha A, Chaudhuri D. Activity-induced phase transition and coarsening dynamics in dry apolar active nematics. SOFT MATTER 2024. [PMID: 39355944 DOI: 10.1039/d4sm00775a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Abstract
Using the Lebwohl-Lasher interaction for reciprocal local alignment, we present a comprehensive phase diagram for a dry, apolar, active nematic system using its stochastic off-lattice dynamics. The nematic-isotropic transition in this system is first-order and occurs alongside a fluctuation-dominated phase separation. Our phase diagram identifies three distinct regions based on activity and orientational noise relative to alignment strength: a homogeneous isotropic phase, a nematic phase with giant density fluctuations, and a coexistence region. Using mean-field analysis and hydrodynamic theory, we demonstrate that reciprocal interactions lead to a density fluctuation-induced first-order transition and derive a phase boundary consistent with numerical results. Quenching from the isotropic to nematic phase reveals coarsening dynamics where nematic ordering precedes particle clustering. Both the nematic and density fields exhibit similar scaling behaviors, exhibiting dynamic exponents zS ≈ 2.5 and zρ ≈ 2.34, consistently falling within the range of 2 and 3.
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Affiliation(s)
- Arpan Sinha
- Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Debasish Chaudhuri
- Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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2
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Adar RM, Joanny JF. Environment-Stored Memory in Active Nematics and Extra-Cellular Matrix Remodeling. PHYSICAL REVIEW LETTERS 2024; 133:118402. [PMID: 39331992 DOI: 10.1103/physrevlett.133.118402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 08/12/2024] [Indexed: 09/29/2024]
Abstract
Many active systems display nematic order, while interacting with their environment. In this Letter, we show theoretically how environment-stored memory acts an effective external field that aligns active nematics. The coupling to the environment leads to substantial modifications of the known phase diagram and dynamics of active nematics, including nematic order at arbitrarily low densities and arrested domain coarsening. We are motivated mainly by cells that remodel fibers in their extra-cellular matrix (ECM), while being directed by the fibers during migration. Our predictions indicate that remodeling promotes cellular and ECM alignment, and possibly limits the range of ordered ECM domains, in accordance with recent experiments.
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Affiliation(s)
| | - Jean-François Joanny
- Collège de France, 11 Place Marcelin Berthelot, 75005 Paris, France
- Laboratoire Physico-Chimie Curie, Institut Curie, Centre de Recherche, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, 75005 Paris, France
- Université Pierre et Marie Curie, Sorbonne Universités, 75248 Paris, France
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3
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Suzaka M, Ito H, Kitahata H. Aspect-ratio-dependent void formation in active rhomboidal and elliptical particle systems. Phys Rev E 2024; 110:024609. [PMID: 39294987 DOI: 10.1103/physreve.110.024609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/01/2024] [Indexed: 09/21/2024]
Abstract
We execute a numerical simulation of active nematics with particles interacting by an excluded-volume effect. Systems with rhomboidal particles and with elliptical particles are considered in order to investigate the effect of the direct contact of particles. In our simulation, the void regions, where the local number density is almost zero, appear in both systems when the aspect ratio of the particles is high. We focus on the relationship between the void regions and the particle orientation of the bulk. The particle number density, particle orientation, topological defects, and void regions are analyzed for different aspect ratios in both systems. The systems with rhomboidal particles have characteristic void sizes, which increase with an increase in the aspect ratio. In contrast, the distribution of the void-region size in the systems with elliptical particles is broad. The present results suggest that the void size in the systems with rhomboidal particles is determined by the correlation length of the particle orientational field around the void regions, while the void size might be determined by the system size in the systems with elliptical particles.
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4
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Leech V, Kenny FN, Marcotti S, Shaw TJ, Stramer BM, Manhart A. Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment. PLoS Comput Biol 2024; 20:e1011879. [PMID: 39074138 PMCID: PMC11309491 DOI: 10.1371/journal.pcbi.1011879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 08/08/2024] [Accepted: 07/13/2024] [Indexed: 07/31/2024] Open
Abstract
Collective alignment of cell populations is a commonly observed phenomena in biology. An important example are aligning fibroblasts in healthy or scar tissue. In this work we derive and simulate a mechanistic agent-based model of the collective behaviour of actively moving and interacting cells, with a focus on understanding collective alignment. The derivation strategy is based on energy minimisation. The model ingredients are motivated by data on the behaviour of different populations of aligning fibroblasts and include: Self-propulsion, overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces. We find that there is an optimal ratio of self-propulsion speed and overlap avoidance that maximises collective alignment. Further we find that deformability aids alignment, and that cell-cell junctions by themselves hinder alignment. However, if cytoskeletal forces are transmitted via cell-cell junctions we observe strong collective alignment over large spatial scales.
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Affiliation(s)
- Vivienne Leech
- Department of Mathematics, University College London, London, United Kingdom
| | - Fiona N. Kenny
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | - Stefania Marcotti
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | - Tanya J. Shaw
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | - Brian M. Stramer
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | - Angelika Manhart
- Department of Mathematics, University College London, London, United Kingdom
- Faculty of Mathematics, University of Vienna, Vienna, Austria
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5
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Krüger T, Maryshev I, Frey E. Hierarchical defect-induced condensation in active nematics. SOFT MATTER 2023; 19:8954-8964. [PMID: 37971530 DOI: 10.1039/d3sm00895a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Topological defects play a central role in the formation and organization of various biological systems. Historically, such nonequilibrium defects have been mainly studied in the context of homogeneous active nematics. Phase-separated systems, in turn, are known to form dense and dynamic nematic bands, but typically lack topological defects. In this paper, we use agent-based simulations of weakly aligning, self-propelled polymers and demonstrate that contrary to the existing paradigm phase-separated active nematics form -1/2 defects. Moreover, these defects, emerging due to interactions among dense nematic bands, constitute a novel second-order collective state. We investigate the morphology of defects in detail and find that their cores correspond to a strong increase in density, associated with a condensation of nematic fluxes. Unlike their analogs in homogeneous systems, such condensed defects form and decay in a different way and do not involve positively charged partners. We additionally observe and characterize lateral arc-like structures that separate from a band's bulk and move in transverse direction. We show that the key control parameters defining the route from stable bands to the coexistence of dynamic lanes and defects are the total density of particles and their path persistence length. We introduce a hydrodynamic theory that qualitatively recapitulates all the main features of the agent-based model, and use it to show that the emergence of both defects and arcs can be attributed to the same anisotropic active fluxes. Finally, we present a way to artificially engineer and position defects, and speculate about experimental verification of the provided model.
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Affiliation(s)
- Timo Krüger
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, Theresienstrasse 37, 80333 Munich, Germany.
| | - Ivan Maryshev
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, Theresienstrasse 37, 80333 Munich, Germany.
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, Theresienstrasse 37, 80333 Munich, Germany.
- Max Planck School Matter to Life, Hofgartenstraße 8, 80539 Munich, Germany
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6
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Sultan SA, R Nejad M, Doostmohammadi A. Quadrupolar active stress induces exotic patterns of defect motion in compressible active nematics. SOFT MATTER 2022; 18:4118-4126. [PMID: 35579323 DOI: 10.1039/d1sm01683k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A wide range of living and artificial active matter exists in close contact with substrates and under strong confinement, where in addition to dipolar active stresses, quadrupolar active stresses can become important. Here, we numerically investigate the impact of quadrupolar non-equilibrium stresses on the emergent patterns of self-organisation in non-momentum conserving active nematics. Our results reveal that beyond having stabilising effects, the quadrupolar active forces can induce various modes of topological defect motion in active nematics. In particular, we find the emergence of both polar and nematic ordering of the defects, as well as new patterns of self-organisation that comprise topological defect chains and transient topological defect asters. The results contribute to further understanding of emergent patterns of collective motion and non-equilibrium self-organisation in active matter.
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Affiliation(s)
- Salik A Sultan
- The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Mehrana R Nejad
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, UK
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7
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Ventejou B, Chaté H, Montagne R, Shi XQ. Susceptibility of Orientationally Ordered Active Matter to Chirality Disorder. PHYSICAL REVIEW LETTERS 2021; 127:238001. [PMID: 34936788 DOI: 10.1103/physrevlett.127.238001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/27/2021] [Indexed: 06/14/2023]
Abstract
We investigate the susceptibility of long-range ordered phases of two-dimensional dry aligning active matter to population disorder, taken in the form of a distribution of intrinsic individual chiralities. Using a combination of particle-level models and hydrodynamic theories derived from them, we show that while in finite systems all ordered phases resist a finite amount of such chirality disorder, the homogeneous ones (polar flocks and active nematics) are unstable to any amount of disorder in the infinite-size limit. On the other hand, we find that the inhomogeneous solutions of the coexistence phase (bands) may resist a finite amount of chirality disorder even asymptotically.
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Affiliation(s)
- Bruno Ventejou
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, 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 100193, China
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, 75005 Paris, France
| | - Raul Montagne
- Departamento de Fisica, Universidade Federal Rural de Pernambuco (UFRPE), 52171-900 Recife, Pernambuco, Brazil
| | - Xia-Qing Shi
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
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8
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Abstract
The emergence of macroscopic order and patterns is a central paradigm in systems of (self-)propelled agents and a key component in the structuring of many biological systems. The relationships between the ordering process and the underlying microscopic interactions have been extensively explored both experimentally and theoretically. While emerging patterns often show one specific symmetry (e.g., nematic lane patterns or polarized traveling flocks), depending on the symmetry of the alignment interactions patterns with different symmetries can apparently coexist. Indeed, recent experiments with an actomysin motility assay suggest that polar and nematic patterns of actin filaments can interact and dynamically transform into each other. However, theoretical understanding of the mechanism responsible remains elusive. Here, we present a kinetic approach complemented by a hydrodynamic theory for agents with mixed alignment symmetries, which captures the experimentally observed phenomenology and provides a theoretical explanation for the coexistence and interaction of patterns with different symmetries. We show that local, pattern-induced symmetry breaking can account for dynamically coexisting patterns with different symmetries. Specifically, in a regime with moderate densities and a weak polar bias in the alignment interaction, nematic bands show a local symmetry-breaking instability within their high-density core region, which induces the formation of polar waves along the bands. These instabilities eventually result in a self-organized system of nematic bands and polar waves that dynamically transform into each other. Our study reveals a mutual feedback mechanism between pattern formation and local symmetry breaking in active matter that has interesting consequences for structure formation in biological systems.
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9
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A particle-field approach bridges phase separation and collective motion in active matter. Nat Commun 2020; 11:5365. [PMID: 33097711 PMCID: PMC7584633 DOI: 10.1038/s41467-020-18978-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/21/2020] [Indexed: 12/20/2022] Open
Abstract
Whereas self-propelled hard discs undergo motility-induced phase separation, self-propelled rods exhibit a variety of nonequilibrium phenomena, including clustering, collective motion, and spatio-temporal chaos. In this work, we present a theoretical framework representing active particles by continuum fields. This concept combines the simplicity of alignment-based models, enabling analytical studies, and realistic models that incorporate the shape of self-propelled objects explicitly. By varying particle shape from circular to ellipsoidal, we show how nonequilibrium stresses acting among self-propelled rods destabilize motility-induced phase separation and facilitate orientational ordering, thereby connecting the realms of scalar and vectorial active matter. Though the interaction potential is strictly apolar, both, polar and nematic order may emerge and even coexist. Accordingly, the symmetry of ordered states is a dynamical property in active matter. The presented framework may represent various systems including bacterial colonies, cytoskeletal extracts, or shaken granular media. Interacting self-propelled particles exhibit phase separation or collective motion depending on particle shape. A unified theory connecting these paradigms represents a major challenge in active matter, which the authors address here by modeling active particles as continuum fields.
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10
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Shellard A, Mayor R. Rules of collective migration: from the wildebeest to the neural crest. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190387. [PMID: 32713298 PMCID: PMC7423382 DOI: 10.1098/rstb.2019.0387] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Collective migration, the movement of groups in which individuals affect the behaviour of one another, occurs at practically every scale, from bacteria up to whole species' populations. Universal principles of collective movement can be applied at all levels. In this review, we will describe the rules governing collective motility, with a specific focus on the neural crest, an embryonic stem cell population that undergoes extensive collective migration during development. We will discuss how the underlying principles of individual cell behaviour, and those that emerge from a supracellular scale, can explain collective migration. This article is part of the theme issue 'Multi-scale analysis and modelling of collective migration in biological systems'.
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Affiliation(s)
- Adam Shellard
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Roberto Mayor
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
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11
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Nava-Sedeño JM, Voß-Böhme A, Hatzikirou H, Deutsch A, Peruani F. Modelling collective cell motion: are on- and off-lattice models equivalent? Philos Trans R Soc Lond B Biol Sci 2020; 375:20190378. [PMID: 32713300 DOI: 10.1098/rstb.2019.0378] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Biological processes, such as embryonic development, wound repair and cancer invasion, or bacterial swarming and fruiting body formation, involve collective motion of cells as a coordinated group. Collective cell motion of eukaryotic cells often includes interactions that result in polar alignment of cell velocities, while bacterial patterns typically show features of apolar velocity alignment. For analysing the population-scale effects of these different alignment mechanisms, various on- and off-lattice agent-based models have been introduced. However, discriminating model-specific artefacts from general features of collective cell motion is challenging. In this work, we focus on equivalence criteria at the population level to compare on- and off-lattice models. In particular, we define prototypic off- and on-lattice models of polar and apolar alignment, and show how to obtain an on-lattice from an off-lattice model of velocity alignment. By characterizing the behaviour and dynamical description of collective migration models at the macroscopic level, we suggest the type of phase transitions and possible patterns in the approximative macroscopic partial differential equation descriptions as informative equivalence criteria between on- and off-lattice models. This article is part of the theme issue 'Multi-scale analysis and modelling of collective migration in biological systems'.
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Affiliation(s)
- Josué Manik Nava-Sedeño
- Technische Universität Dresden, Center for Information Services and High Performance Computing, Nöthnitzer Straße 46, 01062 Dresden, Germany
| | - Anja Voß-Böhme
- Technische Universität Dresden, Center for Information Services and High Performance Computing, Nöthnitzer Straße 46, 01062 Dresden, Germany.,Fakultät Informatik/Mathematik, Hochschule für Technik und Wirtschaft, Dresden, Germany
| | - Haralampos Hatzikirou
- Department of Systems Immunology and Braunschweig Integrated Center of Systems Biology, Helmholtz Center for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Andreas Deutsch
- Technische Universität Dresden, Center for Information Services and High Performance Computing, Nöthnitzer Straße 46, 01062 Dresden, Germany
| | - Fernando Peruani
- Laboratoire J. A. Dieudonné, Université Côte d'Azur, UMR 7351 CNRS, Parc Valrose, 06108 Nice Cedex 02, France
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12
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Collective Dynamics of Model Pili-Based Twitcher-Mode Bacilliforms. Sci Rep 2020; 10:10747. [PMID: 32612117 PMCID: PMC7330051 DOI: 10.1038/s41598-020-67212-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 05/27/2020] [Indexed: 11/29/2022] Open
Abstract
Pseudomonas aeruginosa, like many bacilliforms, are not limited only to swimming motility but rather possess many motility strategies. In particular, twitching-mode motility employs hair-like pili to transverse moist surfaces with a jittery irregular crawl. Twitching motility plays a critical role in redistributing cells on surfaces prior to and during colony formation. We combine molecular dynamics and rule-based simulations to study twitching-mode motility of model bacilliforms and show that there is a critical surface coverage fraction at which collective effects arise. Our simulations demonstrate dynamic clustering of twitcher-type bacteria with polydomains of local alignment that exhibit spontaneous correlated motions, similar to rafts in many bacterial communities.
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13
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Gompper G, Winkler RG, Speck T, Solon A, Nardini C, Peruani F, Löwen H, Golestanian R, Kaupp UB, Alvarez L, Kiørboe T, Lauga E, Poon WCK, DeSimone A, Muiños-Landin S, Fischer A, Söker NA, Cichos F, Kapral R, Gaspard P, Ripoll M, Sagues F, Doostmohammadi A, Yeomans JM, Aranson IS, Bechinger C, Stark H, Hemelrijk CK, Nedelec FJ, Sarkar T, Aryaksama T, Lacroix M, Duclos G, Yashunsky V, Silberzan P, Arroyo M, Kale S. The 2020 motile active matter roadmap. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:193001. [PMID: 32058979 DOI: 10.1088/1361-648x/ab6348] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Activity and autonomous motion are fundamental in living and engineering systems. This has stimulated the new field of 'active matter' in recent years, which focuses on the physical aspects of propulsion mechanisms, and on motility-induced emergent collective behavior of a larger number of identical agents. The scale of agents ranges from nanomotors and microswimmers, to cells, fish, birds, and people. Inspired by biological microswimmers, various designs of autonomous synthetic nano- and micromachines have been proposed. Such machines provide the basis for multifunctional, highly responsive, intelligent (artificial) active materials, which exhibit emergent behavior and the ability to perform tasks in response to external stimuli. A major challenge for understanding and designing active matter is their inherent nonequilibrium nature due to persistent energy consumption, which invalidates equilibrium concepts such as free energy, detailed balance, and time-reversal symmetry. Unraveling, predicting, and controlling the behavior of active matter is a truly interdisciplinary endeavor at the interface of biology, chemistry, ecology, engineering, mathematics, and physics. The vast complexity of phenomena and mechanisms involved in the self-organization and dynamics of motile active matter comprises a major challenge. Hence, to advance, and eventually reach a comprehensive understanding, this important research area requires a concerted, synergetic approach of the various disciplines. The 2020 motile active matter roadmap of Journal of Physics: Condensed Matter addresses the current state of the art of the field and provides guidance for both students as well as established scientists in their efforts to advance this fascinating area.
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Affiliation(s)
- Gerhard Gompper
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany
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14
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Park D, Wershof E, Boeing S, Labernadie A, Jenkins RP, George S, Trepat X, Bates PA, Sahai E. Extracellular matrix anisotropy is determined by TFAP2C-dependent regulation of cell collisions. NATURE MATERIALS 2020; 19:227-238. [PMID: 31659294 PMCID: PMC6989216 DOI: 10.1038/s41563-019-0504-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 09/10/2019] [Indexed: 05/12/2023]
Abstract
The isotropic or anisotropic organization of biological extracellular matrices has important consequences for tissue function. We study emergent anisotropy using fibroblasts that generate varying degrees of matrix alignment from uniform starting conditions. This reveals that the early migratory paths of fibroblasts are correlated with subsequent matrix organization. Combined experimentation and adaptation of Vicsek modelling demonstrates that the reorientation of cells relative to each other following collision plays a role in generating matrix anisotropy. We term this behaviour 'cell collision guidance'. The transcription factor TFAP2C regulates cell collision guidance in part by controlling the expression of RND3. RND3 localizes to cell-cell collision zones where it downregulates actomyosin activity. Cell collision guidance fails without this mechanism in place, leading to isotropic matrix generation. The cross-referencing of alignment and TFAP2C gene expression signatures against existing datasets enables the identification and validation of several classes of pharmacological agents that disrupt matrix anisotropy.
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Affiliation(s)
- Danielle Park
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
| | - Esther Wershof
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
| | - Stefan Boeing
- Bioinformatics Laboratory, The Francis Crick Institute, London, UK
| | - Anna Labernadie
- Institute for Bioengineering of Catalonia, The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Robert P Jenkins
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
| | - Samantha George
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
| | - Xavier Trepat
- Institute for Bioengineering of Catalonia, The Barcelona Institute for Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina, University of Barcelona, Barcelona, Spain
| | - Paul A Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
| | - Erik Sahai
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK.
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15
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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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16
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Maryshev I, Goryachev AB, Marenduzzo D, Morozov A. Dry active turbulence in a model for microtubule-motor mixtures. SOFT MATTER 2019; 15:6038-6043. [PMID: 31298679 DOI: 10.1039/c9sm00558g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We study the dynamics and phase behaviour of a dry suspension of microtubules and molecular motors. We obtain a set of continuum equations by rigorously coarse graining a microscopic model where motor-induced interactions lead to parallel or antiparallel ordering. Through numerical simulations, we show that this model generically creates either stable stripes, or a never-settling pattern where stripes periodically form, rotate and then split up. We derive a minimal model which displays the same instability as the full model, and clarifies the underlying physical mechanism. The necessary ingredients are an extensile flux arising from microtubule sliding and an interfacial torque favouring ordering along density gradients. We argue that our minimal model unifies various previous observations of chaotic behaviour in dry active matter into a general universality class.
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Affiliation(s)
- Ivan Maryshev
- Centre for Synthetic and Systems Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK.
| | - Andrew B Goryachev
- Centre for Synthetic and Systems Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK.
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Alexander Morozov
- SUPA, School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
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17
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Liu G, Patch A, Bahar F, Yllanes D, Welch RD, Marchetti MC, Thutupalli S, Shaevitz JW. Self-Driven Phase Transitions Drive Myxococcus xanthus Fruiting Body Formation. PHYSICAL REVIEW LETTERS 2019; 122:248102. [PMID: 31322369 DOI: 10.1103/physrevlett.122.248102] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Indexed: 06/10/2023]
Abstract
Combining high-resolution single cell tracking experiments with numerical simulations, we show that starvation-induced fruiting body formation in Myxococcus xanthus is a phase separation driven by cells that tune their motility over time. The phase separation can be understood in terms of cell density and a dimensionless Péclet number that captures cell motility through speed and reversal frequency. Our work suggests that M. xanthus takes advantage of a self-driven nonequilibrium phase transition that can be controlled at the single cell level.
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Affiliation(s)
- Guannan Liu
- Joseph Henry Laboratories of Physics and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Adam Patch
- Department of Physics and Soft and Living Matter Program, Syracuse University, Syracuse, New York 13244, USA
| | - Fatmagül Bahar
- Department of Biology, Syracuse University, Syracuse, New York 13244, USA
| | - David Yllanes
- Department of Physics and Soft and Living Matter Program, Syracuse University, Syracuse, New York 13244, USA
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), 50009 Zaragoza, Spain
| | - Roy D Welch
- Department of Biology, Syracuse University, Syracuse, New York 13244, USA
| | - M Cristina Marchetti
- Department of Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Shashi Thutupalli
- Simons Center for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore 560065, India
| | - Joshua W Shaevitz
- Joseph Henry Laboratories of Physics and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
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18
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Ding SS, Schumacher LJ, Javer AE, Endres RG, Brown AEX. Shared behavioral mechanisms underlie C. elegans aggregation and swarming. eLife 2019; 8:e43318. [PMID: 31021320 PMCID: PMC6522220 DOI: 10.7554/elife.43318] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 04/19/2019] [Indexed: 11/13/2022] Open
Abstract
In complex biological systems, simple individual-level behavioral rules can give rise to emergent group-level behavior. While collective behavior has been well studied in cells and larger organisms, the mesoscopic scale is less understood, as it is unclear which sensory inputs and physical processes matter a priori. Here, we investigate collective feeding in the roundworm C. elegans at this intermediate scale, using quantitative phenotyping and agent-based modeling to identify behavioral rules underlying both aggregation and swarming-a dynamic phenotype only observed at longer timescales. Using fluorescence multi-worm tracking, we quantify aggregation in terms of individual dynamics and population-level statistics. Then we use agent-based simulations and approximate Bayesian inference to identify three key behavioral rules for aggregation: cluster-edge reversals, a density-dependent switch between crawling speeds, and taxis towards neighboring worms. Our simulations suggest that swarming is simply driven by local food depletion but otherwise employs the same behavioral mechanisms as the initial aggregation.
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Affiliation(s)
- Siyu Serena Ding
- Instititue of Clinical SciencesImperial College LondonLondonUnited Kingdom
- MRC London Institute of Medical SciencesLondonUnited Kingdom
| | - Linus J Schumacher
- Department of Life SciencesImperial College LondonLondonUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Avelino E Javer
- Instititue of Clinical SciencesImperial College LondonLondonUnited Kingdom
- MRC London Institute of Medical SciencesLondonUnited Kingdom
| | - Robert G Endres
- Department of Life SciencesImperial College LondonLondonUnited Kingdom
| | - André EX Brown
- Instititue of Clinical SciencesImperial College LondonLondonUnited Kingdom
- MRC London Institute of Medical SciencesLondonUnited Kingdom
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19
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Yan W, Zhang H, Shelley MJ. Computing collision stress in assemblies of active spherocylinders: Applications of a fast and generic geometric method. J Chem Phys 2019; 150:064109. [DOI: 10.1063/1.5080433] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Wen Yan
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York 10010, USA
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
| | - Huan Zhang
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
- Zhiyuan College and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Michael J. Shelley
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York 10010, USA
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
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20
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Be’er A, Ariel G. A statistical physics view of swarming bacteria. MOVEMENT ECOLOGY 2019; 7:9. [PMID: 30923619 PMCID: PMC6419441 DOI: 10.1186/s40462-019-0153-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/18/2019] [Indexed: 05/18/2023]
Abstract
Bacterial swarming is a collective mode of motion in which cells migrate rapidly over surfaces, forming dynamic patterns of whirls and jets. This review presents a physical point of view of swarming bacteria, with an emphasis on the statistical properties of the swarm dynamics as observed in experiments. The basic physical principles underlying the swarm and their relation to contemporary theories of collective motion and active matter are reviewed and discussed in the context of the biological properties of swarming cells. We suggest a paradigm according to which bacteria have optimized some of their physical properties as a strategy for rapid surface translocation. In other words, cells take advantage of favorable physics, enabling efficient expansion that enhances survival under harsh conditions.
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Affiliation(s)
- Avraham Be’er
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990 Midreshet Ben-Gurion, Israel
- Department of Physics, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel
| | - Gil Ariel
- Department of Mathematics, Bar-Ilan University, 52000 Ramat Gan, Israel
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21
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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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22
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Doostmohammadi A, Ignés-Mullol J, Yeomans JM, Sagués F. Active nematics. Nat Commun 2018; 9:3246. [PMID: 30131558 PMCID: PMC6104062 DOI: 10.1038/s41467-018-05666-8] [Citation(s) in RCA: 268] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 06/28/2018] [Accepted: 07/19/2018] [Indexed: 11/09/2022] Open
Abstract
Active matter extracts energy from its surroundings at the single particle level and transforms it into mechanical work. Examples include cytoskeleton biopolymers and bacterial suspensions. Here, we review experimental, theoretical and numerical studies of active nematics - a type of active system that is characterised by self-driven units with elongated shape. We focus primarily on microtubule-kinesin mixtures and the hydrodynamic theories that describe their properties. An important theme is active turbulence and the associated motile topological defects. We discuss ways in which active turbulence may be controlled, a pre-requisite to harvesting energy from active materials, and we consider the appearance, and possible implications, of active nematics and topological defects to cellular systems and biological processes.
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Affiliation(s)
- Amin Doostmohammadi
- The Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Clarendon Laboratory, Parks Rd., Oxford, OX1 3PU, UK.
| | - Jordi Ignés-Mullol
- Departament de Ciència de Materials i Química Física and Institute of Nanoscience and Nanotechnology, Universitat de Barcelona, Martí I Franquès 1, 08028, Barcelona, Catalonia, Spain
| | - Julia M Yeomans
- The Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Clarendon Laboratory, Parks Rd., Oxford, OX1 3PU, UK
| | - Francesc Sagués
- Departament de Ciència de Materials i Química Física and Institute of Nanoscience and Nanotechnology, Universitat de Barcelona, Martí I Franquès 1, 08028, Barcelona, Catalonia, Spain
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23
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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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24
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Mahault B, Jiang XC, Bertin E, Ma YQ, Patelli A, Shi XQ, Chaté H. Self-Propelled Particles with Velocity Reversals and Ferromagnetic Alignment: Active Matter Class with Second-Order Transition to Quasi-Long-Range Polar Order. PHYSICAL REVIEW LETTERS 2018; 120:258002. [PMID: 29979075 DOI: 10.1103/physrevlett.120.258002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Indexed: 06/08/2023]
Abstract
We introduce and study in two dimensions a new class of dry, aligning active matter that exhibits a direct transition to orientational order, without the phase-separation phenomenology usually observed in this context. Characterized by self-propelled particles with velocity reversals and a ferromagnetic alignment of polarities, systems in this class display quasi-long-range polar order with continuously varying scaling exponents, yet a numerical study of the transition leads to conclude that it does not belong to the Berezinskii-Kosterlitz-Thouless universality class but is best described as a standard critical point with an algebraic divergence of correlations. We rationalize these findings by showing that the interplay between order and density changes the role of defects.
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Affiliation(s)
- B Mahault
- Service de Physique de l'Etat Condensé, CEA, CNRS, Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
| | - X-C Jiang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | - E Bertin
- LIPHY, Université Grenoble Alpes and CNRS, F-38000 Grenoble, France
| | - Y-Q Ma
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China
| | - A Patelli
- Service de Physique de l'Etat Condensé, CEA, CNRS, Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
| | - X-Q Shi
- Service de Physique de l'Etat Condensé, CEA, CNRS, Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | - H Chaté
- Service de Physique de l'Etat Condensé, CEA, CNRS, Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- Beijing Computational Science Research Center, Beijing 100094, China
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, 75005 Paris, France
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25
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Kürsten R, Sushkov V, Ihle T. Giant Kovacs-Like Memory Effect for Active Particles. PHYSICAL REVIEW LETTERS 2017; 119:188001. [PMID: 29219569 DOI: 10.1103/physrevlett.119.188001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Indexed: 06/07/2023]
Abstract
Dynamical properties of self-propelled particles obeying a bounded confidence rule are investigated by means of kinetic theory and agent-based simulations. While memory effects are observed in disordered systems, we show that they also occur in active matter systems. In particular, we find that the system exhibits a giant Kovacs-like memory effect that is much larger than predicted by a generic linear theory. Based on a separation of time scales we develop a nonlinear theory to explain this effect. We apply this theory to driven granular gases and propose further applications to spin glasses.
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Affiliation(s)
- Rüdiger Kürsten
- Institut für Physik, Universität Greifswald, Felix-Hausdorff-Str. 6, 17489 Greifswald, Germany
| | - Vladimir Sushkov
- Hochschule für angewandte Wissenschaften München, Fakultät für angewandte Naturwissenschaften und Mechatronik, Lothstr. 34, 80335 München, Germany
| | - Thomas Ihle
- Institut für Physik, Universität Greifswald, Felix-Hausdorff-Str. 6, 17489 Greifswald, Germany
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26
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Abstract
Long-range alignment ordering of fibroblasts have been observed in the vicinity of cancerous tumors and can be recapitulated with in vitro experiments. However, the mechanisms driving their ordering are not understood. Here, we show that local collision-driven nematic alignment interactions among fibroblasts are insufficient to explain observed long-range alignment. One possibility is that there exists another orientation field coevolving with the cells and reinforcing their alignment. We propose that this field reflects the mechanical cross-talk between the fibroblasts and the underlying fibrous material on which they move. We show that this long-range interaction can give rise to high nematic order and to the observed patterning of the cancer microenvironment.
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