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Kanazawa T, Furukawa A. Microrheology of active suspensions. SOFT MATTER 2024; 20:5527-5537. [PMID: 38920265 DOI: 10.1039/d4sm00408f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
We study the microrheology of active suspensions through direct hydrodynamic simulations using model pusher-like microswimmers. We demonstrate that the friction coefficient of a probe particle is notably reduced by hydrodynamic interactions (HIs) among a moving probe and the swimmers. When a swimmer approaches a probe from the rear (front) side, the repulsive HIs between them are weakened (intensified), which results in a slight front-rear asymmetry in swimmer orientation distribution around the probe, creating a significant additional net driving force acting on the probe from the rear side. The present drag-reduction mechanism qualitatively differs from that of the viscosity-reduction observed in sheared bulk systems and depends on probing details. This study provides insights into our fundamental knowledge of hydrodynamic effects in active suspensions and serves as a practical example illuminating distinctions between micro- and macrorheology measurements.
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Affiliation(s)
- Takahiro Kanazawa
- Department of Physics, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akira Furukawa
- Institute of Industrial Science, University of Tokyo, Meguro-ku, Tokyo 153-8505, Japan.
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2
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Keogh RR, Kozhukhov T, Thijssen K, Shendruk TN. Active Darcy's Law. PHYSICAL REVIEW LETTERS 2024; 132:188301. [PMID: 38759204 DOI: 10.1103/physrevlett.132.188301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 03/11/2024] [Indexed: 05/19/2024]
Abstract
While bacterial swarms can exhibit active turbulence in vacant spaces, they naturally inhabit crowded environments. We numerically show that driving disorderly active fluids through porous media enhances Darcy's law. While purely active flows average to zero flux, hybrid active/driven flows display greater drift than purely pressure-driven flows. This enhancement is nonmonotonic with activity, leading to an optimal activity to maximize flow rate. We incorporate the active contribution into an active Darcy's law, which may serve to help understand anomalous transport of swarming in porous media.
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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
| | - Timofey Kozhukhov
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, United Kingdom
| | - Kristian Thijssen
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, Copenhagen, Denmark
| | - 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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3
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Luo W, Baskaran A, Pelcovits RA, Powers TR. Flow states of two dimensional active gels driven by external shear. SOFT MATTER 2024; 20:738-753. [PMID: 38168972 DOI: 10.1039/d3sm00919j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Using a minimal hydrodynamic model, we theoretically and computationally study the Couette flow of active gels in straight and annular two-dimensional channels subject to an externally imposed shear. The gels are isotropic in the absence of externally- or activity-driven shear, but have nematic order that increases with shear rate. Using the finite element method, we determine the possible flow states for a range of activities and shear rates. Linear stability analysis of an unconfined gel in a straight channel shows that an externally imposed shear flow can stabilize an extensile fluid that would be unstable to spontaneous flow in the absence of the shear flow, and destabilize a contractile fluid that would be stable against spontaneous flow in the absence of shear flow. These results are in rough agreement with the stability boundaries between the base shear flow state and the nonlinear flow states that we find numerically for a confined active gel. For extensile fluids, we find three kinds of nonlinear flow states in the range of parameters we study: unidirectional flows, oscillatory flows, and dancing flows. To highlight the activity-driven spontaneous component of the nonlinear flows, we characterize these states by the average volumetric flow rate and the wall stress. For contractile fluids, we only find the linear shear flow and a nonlinear unidirectional flow in the range of parameters that we studied. For large magnitudes of the activity, the unidirectional contractile flow develops a boundary layer. Our analysis of annular channels shows how curvature of the streamlines in the base flow affects the transitions among flow states.
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Affiliation(s)
- Wan Luo
- School of Engineering, Brown University, Providence, RI 02912, USA.
- Center for Fluid Mechanics, Brown University, Providence, RI 02912, USA
| | - Aparna Baskaran
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02453, USA
| | - Robert A Pelcovits
- Department of Physics, Brown University, Providence, RI 02912, USA
- Brown Theoretical Physics Center, Brown University, Providence, RI 02912, USA
| | - Thomas R Powers
- School of Engineering, Brown University, Providence, RI 02912, USA.
- Center for Fluid Mechanics, Brown University, Providence, RI 02912, USA
- Department of Physics, Brown University, Providence, RI 02912, USA
- Brown Theoretical Physics Center, Brown University, Providence, RI 02912, USA
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4
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Bayram AG, Schwarzendahl FJ, Löwen H, Biancofiore L. Motility-induced shear thickening in dense colloidal suspensions. SOFT MATTER 2023. [PMID: 37309209 DOI: 10.1039/d3sm00035d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Phase transitions and collective dynamics of active colloidal suspensions are fascinating topics in soft matter physics, particularly for out-of-equilibrium systems, which can lead to rich rheological behaviours in the presence of steady shear flow. Here the role of self-propulsion in the rheological response of a dense colloidal suspension is investigated by using particle-resolved Brownian dynamics simulations. First, the combined effect of activity and shear in the solid on the disordering transition of the suspension is analyzed. While both self-propulsion and shear destroy order and melt the system if critical values are exceeded, self-propulsion largely lowers the stress barrier needed to be overcome during the transition. We further explore the rheological response of the active sheared system once a steady state is reached. While passive suspensions show a solid-like behaviour, turning on particle motility fluidises the system. At low self-propulsion, the active suspension behaves in the steady state as a shear-thinning fluid. Increasing the self-propulsion changes the behaviour of the liquid from shear-thinning to shear-thickening. We attribute this to clustering in the sheared suspensions induced by motility. This new phenomenon of motility-induced shear thickening (MIST) can be used to tailor the rheological response of colloidal suspensions.
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Affiliation(s)
- A Gülce Bayram
- FluidFrame Lab, Department of Mechanical Engineering, Bilkent University, Çankaya, 06800 Ankara, Turkey.
| | - Fabian Jan Schwarzendahl
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Luca Biancofiore
- FluidFrame Lab, Department of Mechanical Engineering, Bilkent University, Çankaya, 06800 Ankara, Turkey.
- Department of Mechanical Engineering, Imperial College London, SW7 2AZ, UK
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5
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Rorai C, Toschi F, Pagonabarraga I. Coexistence of Active and Hydrodynamic Turbulence in Two-Dimensional Active Nematics. PHYSICAL REVIEW LETTERS 2022; 129:218001. [PMID: 36461968 DOI: 10.1103/physrevlett.129.218001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/29/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
In active nematic liquid crystals, activity is able to drive chaotic spatiotemporal flows referred to as active turbulence. Active turbulence has been characterized through theoretical and experimental work as a low Reynolds number phenomenon. We show that, in two dimensions, the active forcing alone is able to trigger hydrodynamic turbulence leading to the coexistence of active and inertial turbulence. This type of flow develops for sufficiently active and extensile flow-aligning nematics. We observe that the combined effect of an extensile nematic and large values of the flow-aligning parameter leads to a broadening of the elastic energy spectrum that promotes a growth of kinetic energy able to trigger an inverse energy cascade.
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Affiliation(s)
- C Rorai
- CECAM, Centre Européen de Calcul Atomique et Moléculaire, École Polytechnique Fédérale de Lausanne (EPFL), Batochime, Avenue Forel 2, 1015 Lausanne, Switzerland
| | - F Toschi
- Department of Applied Physics, Eindhoven University of Technology, Den Dolech 2, 5600 MB Eindhoven, Netherlands
- CNR-IAC, I-00185 Rome, Italy
| | - I Pagonabarraga
- CECAM, Centre Européen de Calcul Atomique et Moléculaire, École Polytechnique Fédérale de Lausanne (EPFL), Batochime, Avenue Forel 2, 1015 Lausanne, Switzerland
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, C. Martí i Franquès 1, 08028 Barcelona, Spain
- University of Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, 08028 Barcelona, Spain
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6
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Vafa F. Defect dynamics in active polar fluids vs. active nematics. SOFT MATTER 2022; 18:8087-8097. [PMID: 36239265 DOI: 10.1039/d2sm00830k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Topological defects play a key role in two-dimensional active nematics, and a transient role in two-dimensional active polar fluids. Using a variational method, we study both the transient and long-time behavior of defects in two-dimensional active polar fluids in the limit of strong order and overdamped, compressible flow, and compare the defect dynamics with the corresponding active nematics model studied recently. One result is non-central interactions between defect pairs for active polar fluids, and by extending our analysis to allow orientation dynamics of defects, we find that the orientation of +1 defects, unlike that of ±1/2 defects in active nematics, is not locked to defect positions and relaxes to asters. Moreover, using a scaling argument, we explain the transient feature of active polar defects and show that in the steady state, active polar fluids are either devoid of defects or consist of a single aster. We argue that for contractile (extensile) active nematic systems, +1 vortices (asters) should emerge as bound states of a pair of +1/2 defects, which has been recently observed. Moreover, unlike the polar case, we show that for active nematics, a linear chain of equally spaced bound states of pairs of +1/2 defects can screen the activity term. A common feature in both models is the appearance of +1 defects (elementary in polar and composite in nematic) in the steady state.
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Affiliation(s)
- Farzan Vafa
- Center of Mathematical Sciences and Applications, Harvard University, Cambridge, MA 02138, USA.
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7
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Pokawanvit S, Chen Z, You Z, Angheluta L, Marchetti MC, Bowick MJ. Active nematic defects in compressible and incompressible flows. Phys Rev E 2022; 106:054610. [PMID: 36559507 DOI: 10.1103/physreve.106.054610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
We study the dynamics of active nematic films on a substrate driven by active flows with or without the incompressible constraint. Through simulations and theoretical analysis, we show that arch patterns are stable in the compressible case, while they become unstable under the incompressibility constraint. For compressible flows at high enough activity, stable arches organize themselves into a smecticlike pattern, which induce an associated global polar ordering of +1/2 nematic defects. By contrast, divergence-free flows give rise to a local nematic order of the +1/2 defects, consisting of antialigned pairs of neighboring defects, as established in previous studies.
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Affiliation(s)
- Supavit Pokawanvit
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
| | - Zhitao Chen
- Department of Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Zhihong You
- Fujian Provincial Key Laboratory for Soft Functional Materials Research, Research Institute for Biomimetics and Soft Matter, Department of Physics, Xiamen University, Xiamen, Fujian 361005, China
| | - Luiza Angheluta
- Department of Physics, University of Oslo, P.O. Box 1048, 0316 Oslo, Norway
| | - M Cristina Marchetti
- Department of Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Mark J Bowick
- Kavli Institute for Theoretical Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
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8
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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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9
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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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Mandal R, Sollich P. Shear-induced orientational ordering in an active glass former. Proc Natl Acad Sci U S A 2021; 118:e2101964118. [PMID: 34551973 PMCID: PMC8488658 DOI: 10.1073/pnas.2101964118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2021] [Indexed: 11/18/2022] Open
Abstract
Dense assemblies of self-propelled particles that can form solid-like states also known as active or living glasses are abundant around us, covering a broad range of length scales and timescales: from the cytoplasm to tissues, from bacterial biofilms to vehicular traffic jams, and from Janus colloids to animal herds. Being structurally disordered as well as strongly out of equilibrium, these systems show fascinating dynamical and mechanical properties. Using extensive molecular dynamics simulation and a number of distinct dynamical and mechanical order parameters, we differentiate three dynamical steady states in a sheared model active glassy system: 1) a disordered state, 2) a propulsion-induced ordered state, and 3) a shear-induced ordered state. We supplement these observations with an analytical theory based on an effective single-particle Fokker-Planck description to rationalize the existence of the shear-induced orientational ordering behavior in an active glassy system without explicit aligning interactions of, for example, Vicsek type. This ordering phenomenon occurs in the large persistence time limit and is made possible only by the applied steady shear. Using a Fokker-Planck description with parameters that can be measured independently, we make testable predictions for the joint distribution of single-particle position and orientation. These predictions match well with the joint distribution measured from direct numerical simulation. Our results are of relevance for experiments exploring the rheological response of dense active colloids and jammed active granular matter systems.
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Affiliation(s)
- Rituparno Mandal
- Institute for Theoretical Physics, Georg-August-Universität Göttingen, 37 077 Göttingen, Germany;
| | - Peter Sollich
- Institute for Theoretical Physics, Georg-August-Universität Göttingen, 37 077 Göttingen, Germany
- Department of Mathematics, King's College London, London WC2R 2LS, United Kingdom
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11
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Kumar S, Singh JP, Giri D, Mishra S. Effect of polydispersity on the dynamics of active Brownian particles. Phys Rev E 2021; 104:024601. [PMID: 34525623 DOI: 10.1103/physreve.104.024601] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/09/2021] [Indexed: 11/07/2022]
Abstract
We numerically study the dynamics and the phases of self-propelled disk-shaped particles of different sizes with soft repulsive potential in two dimensions. Size diversity is introduced by the polydispersity index (PDI) ε, which is the width of the uniform distribution of the particle's radius. The self-propulsion speed of the particles controls the activity v. We observe enhanced dynamics for large size diversity among the particles. We calculate the effective diffusion coefficient D_{eff} in the steady state. The system exhibits four distinct phases, jammed phase with small D_{eff} for small activity and liquid phase with enhanced D_{eff} for large activity. The number fluctuation is larger and smaller than the equilibrium limit in the liquid and jammed phases, respectively. Further, the jammed phase is of two types: solid jammed and liquid jammed for small and large PDI. Whereas the liquid phase is called motility induced phase separation (MIPS) liquid for small PDI and for large PDI, we find enhanced diffusivity and call it the pure liquid phase. The system is studied for three packing densities ϕ, and the response of the system for polydispersity is the same for all ϕ's. Our study can help understand the behavior of cells of various sizes in a tissue, artificial self-driven granular particles, or living organisms of different sizes in a dense environment.
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Affiliation(s)
- Sameer Kumar
- Department of Physics, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh 221005, India
| | - Jay Prakash Singh
- Department of Physics, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh 221005, India
| | - Debaprasad Giri
- 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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12
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Chui JYY, Douarche C, Auradou H, Juanes R. Rheology of bacterial superfluids in viscous environments. SOFT MATTER 2021; 17:7004-7013. [PMID: 34240724 DOI: 10.1039/d1sm00243k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Viscous environments are ubiquitous in nature and in engineering applications, from mucus in lungs to oil recovery strategies in the earth's subsurface - and in all these environments, bacteria also thrive. The behavior of bacteria in viscous environments has been investigated for a single bacterium, but not for active suspensions. Dense populations of pusher-type bacteria are known to create superfluidic regimes where the effective viscosity of the entire suspension is reduced through collective motion, and the main purpose of this study is to investigate how a viscous environment will affect this behavior. Using a Couette rheometer, we measure shear stress as a function of the applied shear rate to define the effective viscosity of suspensions of Escherichia coli (E. coli), while varying both the bacterial density within the suspension and the viscosity of the suspending fluid. We document the remarkable observation that E. coli decreases the effective suspension viscosity to near-zero (superfluidic regime) for all solvent viscosities tested (1-17 mPa s). Specifically, we observe that the bacterial density needed to trigger this superfluidic regime and the maximum shear rate under which this regime can be sustained both decrease with increasing solvent viscosity. We find that the resulting rheograms can be well approximated by the Carreau-Yasuda law. Using this, we propose a constitutive model as a function of the solvent viscosity and the bacterial concentration only. This model captures the onset of the superfluidic regime and offers promising avenues for the modelling of flow of bacterial suspensions in viscous environments.
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Affiliation(s)
- Jane Y Y Chui
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | | | - Harold Auradou
- Université Paris-Saclay, CNRS, FAST, 91405, Orsay, France.
| | - Ruben Juanes
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. and Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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13
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Vafa F, Bowick MJ, Shraiman BI, Marchetti MC. Fluctuations can induce local nematic order and extensile stress in monolayers of motile cells. SOFT MATTER 2021; 17:3068-3073. [PMID: 33596291 DOI: 10.1039/d0sm02027c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recent experiments in various cell types have shown that two-dimensional tissues often display local nematic order, with evidence of extensile stresses manifest in the dynamics of topological defects. Using a mesoscopic model where tissue flow is generated by fluctuating traction forces coupled to the nematic order parameter, we show that the resulting tissue dynamics can spontaneously produce local nematic order and an extensile internal stress. A key element of the model is the assumption that in the presence of local nematic alignment, cells preferentially crawl along the nematic axis, resulting in anisotropy of fluctuations. Our work shows that activity can drive either extensile or contractile stresses in tissue, depending on the relative strength of the contractility of the cortical cytoskeleton and tractions by cells on the extracellular matrix.
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Affiliation(s)
- Farzan Vafa
- Department of Physics, University of California Santa Barbara, Santa Barbara, CA 93106, USA.
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14
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Lenne PF, Rupprecht JF, Viasnoff V. Cell Junction Mechanics beyond the Bounds of Adhesion and Tension. Dev Cell 2021; 56:202-212. [PMID: 33453154 DOI: 10.1016/j.devcel.2020.12.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/06/2020] [Accepted: 12/21/2020] [Indexed: 12/22/2022]
Abstract
Cell-cell junctions, in particular adherens junctions, are major determinants of tissue mechanics during morphogenesis and homeostasis. In attempts to link junctional mechanics to tissue mechanics, many have utilized explicitly or implicitly equilibrium approaches based on adhesion energy, surface energy, and contractility to determine the mechanical equilibrium at junctions. However, it is increasingly clear that they have significant limitations, such as that it remains challenging to link the dynamics of the molecular components to the resulting physical properties of the junction, to its remodeling ability, and to its adhesion strength. In this perspective, we discuss recent attempts to consider the aspect of energy dissipation at junctions to draw contact points with soft matter physics where energy loss plays a critical role in adhesion theories. We set the grounds for a theoretical framework of the junction mechanics that bridges the dynamics at the molecular scale to the mechanics at the tissue scale.
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Affiliation(s)
- Pierre-François Lenne
- Aix Marseille Université, CNRS, IBDM, Turing Centre for Living Systems, 13288 Marseille, France.
| | - Jean-François Rupprecht
- Aix Marseille Université, CNRS, CPT, Turing Centre for Living Systems, 13288 Marseille, France.
| | - Virgile Viasnoff
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; CNRS Biomechanics of Cell Contacts, Singapore 117411, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117411, Singapore.
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15
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Ishikawa T, Omori T, Kikuchi K. Bacterial biomechanics-From individual behaviors to biofilm and the gut flora. APL Bioeng 2020; 4:041504. [PMID: 33163845 PMCID: PMC7595747 DOI: 10.1063/5.0026953] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Bacteria inhabit a variety of locations and play important roles in the environment and health. Our understanding of bacterial biomechanics has improved markedly in the last decade and has revealed that biomechanics play a significant role in microbial biology. The obtained knowledge has enabled investigation of complex phenomena, such as biofilm formation and the dynamics of the gut flora. A bottom-up strategy, i.e., from the cellular to the macroscale, facilitates understanding of macroscopic bacterial phenomena. In this Review, we first cover the biomechanics of individual bacteria in the bulk liquid and on surfaces as the base of complex phenomena. The collective behaviors of bacteria in simple environments are next introduced. We then introduce recent advances in biofilm biomechanics, in which adhesion force and the flow environment play crucial roles. We also review transport phenomena in the intestine and the dynamics of the gut flora, focusing on that in zebrafish. Finally, we provide an overview of the future prospects for the field.
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Affiliation(s)
| | - Toshihiro Omori
- Department Finemechanics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
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16
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Walton J, McKay G, Grinfeld M, Mottram NJ. Pressure-driven changes to spontaneous flow in active nematic liquid crystals. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2020; 43:51. [PMID: 32743686 DOI: 10.1140/epje/i2020-11973-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/07/2020] [Indexed: 06/11/2023]
Abstract
We consider the effects of a pressure gradient on the spontaneous flow of an active nematic liquid crystal in a channel, subject to planar anchoring and no-slip conditions on the boundaries of the channel. We employ a model based on the Ericksen-Leslie theory of nematics, with an additional active stress accounting for the activity of the fluid. By directly solving the flow equation, we consider an asymptotic solution for the director angle equation for large activity parameter values and predict the possible values of the director angle in the bulk of the channel. Through a numerical solution of the full nonlinear equations, we examine the effects of pressure on the branches of stable and unstable equilibria, some of which are disconnected from the no-flow state. In the absence of a pressure gradient, solutions are either symmetric or antisymmetric about the channel midpoint; these symmetries are changed by the pressure gradient. Considering the activity-pressure state space allows us to predict qualitatively the extent of each solution type and to show, for large enough pressure gradients, that a branch of non-trivial director angle solutions exists for all activity values.
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Affiliation(s)
- Joshua Walton
- Department of Mathematics and Statistics, University of Strathclyde, 26 Richmond Street, G1 1XH, Glasgow, UK
| | - Geoffrey McKay
- Department of Mathematics and Statistics, University of Strathclyde, 26 Richmond Street, G1 1XH, Glasgow, UK.
| | - Michael Grinfeld
- Department of Mathematics and Statistics, University of Strathclyde, 26 Richmond Street, G1 1XH, Glasgow, UK
| | - Nigel J Mottram
- School of Mathematics and Statistics, University of Glasgow, University Place, G12 8SU, Glasgow, UK
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17
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Wang C, Jiang H. The inhibition of concentrated active baths. J Chem Phys 2020; 152:184907. [PMID: 32414266 DOI: 10.1063/5.0005313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Passive tracers in the active bath express fascinating behaviors. However, most studies are restricted to dilute active baths. Here, we use 2D simulation of suspensions consisting of active Brownian particles and a passive disk-shaped tracer to investigate tracers' diffusive behaviors in a wide range of volume fractions. Due to the competition between the thermal noise and collisions with active particles, tracers express a first transition from the normal diffusion to the superdiffusion at a short time scale and recur to normal diffusion at a long time scale. At a low volume fraction, infrequent active collisions retard the first transition of smaller tracers. At a high volume fraction, active particles with high activity aggregating around tracers induce a bimodal probability distribution function of tracer displacements during superdiffusion. Considering the enhancement of diffusion, the non-dimensional enhanced diffusivity increases asymptotically with the Peclet number. The asymptotic line gives an upper limit of non-dimensional enhanced diffusivity of tracers. Cases with lower enhanced diffusion have a high volume fraction and a low active velocity that indicates the inhibition of concentrated active baths. With the high negentropic work of these cases, the inhibition is explained as the change of the configuration of active baths for introducing tracers.
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Affiliation(s)
- Chen Wang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Hefei National Laboratory for Physical Science at the Microscale, CAS Center for Excellence in Complex System Mechanics, Department of Modern Mechanics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Hongyuan Jiang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Hefei National Laboratory for Physical Science at the Microscale, CAS Center for Excellence in Complex System Mechanics, Department of Modern Mechanics, University of Science and Technology of China, Hefei, Anhui 230026, China
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18
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Wang C, Jiang H. Different-shaped micro-objects driven by active particle aggregations. SOFT MATTER 2020; 16:4422-4430. [PMID: 32364209 DOI: 10.1039/d0sm00160k] [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
The dynamics of passive micro-objects in an active bath has been receiving much attention. However, the influence of the shapes of micro-objects remains unclear. Here, we use 2D simulation to investigate the interaction between active Brownian particles and different-shaped passive micro-objects. We show that active particles accumulate around micro-objects and self-assemble into living aggregations at a high active velocity and high volume fraction. The shapes of micro-objects affect the distributions of the aggregations. In turn, the different distribution of aggregations influences the motion of micro-objects and induces abnormal diffusive behaviors. We further demonstrate that polar distributed aggregations at a high active velocity and the inhibition of the active bath at a low active velocity induce the counterintuitive anisotropic enhanced diffusion of rods, and the steric interaction between active particles induces the reverse translation-rotation coupled diffusion of chevrons.
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Affiliation(s)
- Chen Wang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Hefei National Laboratory for Physical Science at the Microscale, CAS Center for Excellence in Complex System Mechanics, Department of Modern Mechanics, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Hongyuan Jiang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Hefei National Laboratory for Physical Science at the Microscale, CAS Center for Excellence in Complex System Mechanics, Department of Modern Mechanics, University of Science and Technology of China, Hefei, Anhui 230026, China.
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19
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Mackay F, Toner J, Morozov A, Marenduzzo D. Darcy's Law without Friction in Active Nematic Rheology. PHYSICAL REVIEW LETTERS 2020; 124:187801. [PMID: 32441954 DOI: 10.1103/physrevlett.124.187801] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/19/2020] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
We study the dynamics of a contractile active nematic fluid subjected to a Poiseuille flow. In a quasi-1D geometry, we find that the linear rheology of this material is reminiscent of Darcy's law in complex fluids, with a pluglike flow decaying to zero over a well-defined "permeation" length. As a result, the viscosity increases with size, but never diverges, thereby evading the yield stress predicted by previous theories. We find strong shear thinning controlled by an active Ericksen number quantifying the ratio between external pressure difference and internal active stresses. In 2D, the increase of linear regime viscosity with size only persists up to a critical length beyond which we observe active turbulent patterns, with very low apparent viscosity. The ratio between the critical and permeation length determining the stability of the Darcy regime can be made indefinitely large by varying the flow aligning parameter or magnitude of nematic order.
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Affiliation(s)
- Fraser Mackay
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - John Toner
- Institute for Fundamental Science and Department of Physics, University of Oregon, Eugene, Oregon 97403, USA
| | - Alexander Morozov
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
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20
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Deblais A, Woutersen S, Bonn D. Rheology of Entangled Active Polymer-Like T. Tubifex Worms. PHYSICAL REVIEW LETTERS 2020; 124:188002. [PMID: 32441969 DOI: 10.1103/physrevlett.124.188002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/18/2020] [Accepted: 04/13/2020] [Indexed: 06/11/2023]
Abstract
We experimentally study the rheology of long, slender, and entangled living worms (Tubifex Tubifex). Their level of activity can be controlled by changing the temperature or by adding small amounts of alcohol to make the worms temporarily inactive. Performing classical rheology experiments on this entangled polymer-like system, we find that the rheology is qualitatively similar to that of usual polymers, but, quantitatively, (i) shear thinning is reduced by activity, (ii) the characteristic shear rate for the onset of shear-thinning is given by the time scale of the activity, and (iii) the low shear viscosity as a function of concentration shows a very different scaling from that of regular polymers. Our study paves the way towards a new experimental research field of active "polymer-like worms."
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Affiliation(s)
- A Deblais
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098XH Amsterdam, The Netherlands
| | - S Woutersen
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - D Bonn
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098XH Amsterdam, The Netherlands
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21
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Kobayashi F, Sasaki Y, Fujii S, Orihara H, Nagaya T. Negative viscosity of liquid crystals in the presence of turbulence: Conductivity dependence, phase diagram, and self-oscillation. Phys Rev E 2020; 101:022702. [PMID: 32168609 DOI: 10.1103/physreve.101.022702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 01/15/2020] [Indexed: 11/07/2022]
Abstract
Recently, we reported the discovery of enormous negative viscosity of a nematic liquid crystal in the presence of turbulence induced by ac electric fields, which enabled us to observe unique phenomena related to the negative viscosity, such as spontaneous shear flow, hysteresis in flow curves, and self-oscillation [Orihara et al., Phys. Rev. E 99, 012701 (2019)10.1103/PhysRevE.99.012701]. In the present paper, we report the rheological properties of another nematic liquid crystal, which is a homologue of the previous one. The properties of the present liquid crystal are strongly dependent on electrical conductivity. Three samples with different conductivities were prepared by changing the amount of an ionic dopant. It was found that the lowest-conductivity sample without dopant shows no negative viscosity whereas the other ion-doped samples exhibit negative viscosity with strong dependence on the frequency of the ac electric field, consistent with microscopic observations. Phase diagrams of the negative- and positive-viscosity states in the amplitude and frequency plane are constructed to show the conductivity effect. Furthermore, we propose a model to reproduce another type of self-oscillation found in the present study.
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Affiliation(s)
- Fumiaki Kobayashi
- Division of Applied Physics, Hokkaido University, Sapporo 060-8628, Japan
| | - Yuji Sasaki
- Division of Applied Physics, Hokkaido University, Sapporo 060-8628, Japan
| | - Shuji Fujii
- Division of Applied Physics, Hokkaido University, Sapporo 060-8628, Japan
| | - Hiroshi Orihara
- Division of Applied Physics, Hokkaido University, Sapporo 060-8628, Japan
| | - Tomoyuki Nagaya
- Division of Natural Sciences, Oita University, Oita 870-1192, Japan
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22
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Maitra A, Srivastava P, Marchetti MC, Ramaswamy S, Lenz M. Swimmer Suspensions on Substrates: Anomalous Stability and Long-Range Order. PHYSICAL REVIEW LETTERS 2020; 124:028002. [PMID: 32004049 DOI: 10.1103/physrevlett.124.028002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 09/08/2019] [Indexed: 06/10/2023]
Abstract
We present a comprehensive theory of the dynamics and fluctuations of a two-dimensional suspension of polar active particles in an incompressible fluid confined to a substrate. We show that, depending on the sign of a single parameter, a state with polar orientational order is anomalously stable (or anomalously unstable), with a nonzero relaxation (or growth) rate for angular fluctuations, not parallel to the ordering direction, at zero wave number. This screening of the broken-symmetry mode in the stable state does lead to conventional rather than giant number fluctuations as argued by Bricard et al., Nature 503, 95 (2013), but their bend instability in a splay-stable flock does not exist and the polar phase has long-range order in two dimensions. Our theory also describes confined three-dimensional thin-film suspensions of active polar particles as well as dense compressible active polar rods, and predicts a flocking transition without a banding instability.
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Affiliation(s)
- Ananyo Maitra
- Sorbonne Université and CNRS, Laboratoire Jean Perrin, F-75005, Paris, France
- LPTMS, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Pragya Srivastava
- The Francis Crick Institute, Lincoln's Inn Fields Laboratory, 44 Lincoln's Inn Fields WC2A 3LY, London
- School of Engineering & Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - M Cristina Marchetti
- Department of Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Sriram Ramaswamy
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560 012, India
- Tata Institute of Fundamental Research, Centre for Interdisciplinary Sciences, Hyderabad 500 107, India
| | - Martin Lenz
- LPTMS, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
- PMMH, CNRS, ESPCI Paris, PSL University, Sorbonne Université, Université de Paris, F-75005, Paris, France
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23
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Negro G, Carenza LN, Lamura A, Tiribocchi A, Gonnella G. Rheology of active polar emulsions: from linear to unidirectional and inviscid flow, and intermittent viscosity. SOFT MATTER 2019; 15:8251-8265. [PMID: 31553342 DOI: 10.1039/c9sm01288e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The rheological behaviour of an emulsion made of an active polar component and an isotropic passive fluid is studied by lattice Boltzmann methods. Different flow regimes are found by varying the values of the shear rate and extensile activity (occurring, e.g., in microtubule-motor suspensions). By increasing the activity, a first transition occurs from the linear flow regime to spontaneous persistent unidirectional macro-scale flow, followed by another transition either to a (low shear) intermittent flow regime with the coexistence of states with positive, negative, and vanishing apparent viscosity, or to a (high shear) symmetric shear thinning regime. The different behaviours can be explained in terms of the dynamics of the polarization field close to the walls. A maximum entropy production principle selects the most likely states in the intermittent regime.
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Affiliation(s)
- G Negro
- Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, I-70126, Italy.
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24
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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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25
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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: 37] [Impact Index Per Article: 7.4] [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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26
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Linkmann M, Boffetta G, Marchetti MC, Eckhardt B. Phase Transition to Large Scale Coherent Structures in Two-Dimensional Active Matter Turbulence. PHYSICAL REVIEW LETTERS 2019; 122:214503. [PMID: 31283308 DOI: 10.1103/physrevlett.122.214503] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Indexed: 06/09/2023]
Abstract
The collective motion of microswimmers in suspensions induce patterns of vortices on scales that are much larger than the characteristic size of a microswimmer, attaining a state called bacterial turbulence. Hydrodynamic turbulence acts on even larger scales and is dominated by inertial transport of energy. Using an established modification of the Navier-Stokes equation that accounts for the small-scale forcing of hydrodynamic flow by microswimmers, we study the properties of a dense suspension of microswimmers in two dimensions, where the conservation of enstrophy can drive an inverse cascade through which energy is accumulated on the largest scales. We find that the dynamical and statistical properties of the flow show a sharp transition to the formation of vortices at the largest length scale. The results show that 2D bacterial and hydrodynamic turbulence are separated by a subcritical phase transition.
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Affiliation(s)
- Moritz Linkmann
- Fachbereich Physik, Philipps-Universität of Marburg, D-35032 Marburg, Germany
| | - Guido Boffetta
- Dipartimento di Fisica and INFN, Università di Torino, via P. Giuria 1, 10125 Torino, Italy
| | - M Cristina Marchetti
- Department of Physics, University of California, Santa Barbara, California 93106, USA
| | - Bruno Eckhardt
- Fachbereich Physik, Philipps-Universität of Marburg, D-35032 Marburg, Germany
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27
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Loisy A, Thompson AP, Eggers J, Liverpool TB. Exact results for sheared polar active suspensions with variable liquid crystalline order. J Chem Phys 2019; 150:104902. [PMID: 30876347 DOI: 10.1063/1.5080343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We consider a confined sheared active polar liquid crystal with a uniform orientation and study the effect of variations in the magnitude of polarization. Restricting our analysis to one-dimensional geometries, we demonstrate that with asymmetric boundary conditions, this system is characterized, macroscopically, by a linear shear stress vs. shear strain relationship that does not pass through the origin: At a zero strain rate, the fluid sustains a non-zero stress. Analytic solutions for the polarization, density, and velocity fields are derived for asymptotically large or small systems and are shown by comparison with precise numerical solutions to be good approximations for finite-size systems.
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Affiliation(s)
- Aurore Loisy
- School of Mathematics, University of Bristol, Bristol BS8 1TW, United Kingdom
| | - Anthony P Thompson
- School of Mathematics, University of Bristol, Bristol BS8 1TW, United Kingdom
| | - Jens Eggers
- School of Mathematics, University of Bristol, Bristol BS8 1TW, United Kingdom
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28
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Markovich T, Tjhung E, Cates ME. Shear-Induced First-Order Transition in Polar Liquid Crystals. PHYSICAL REVIEW LETTERS 2019; 122:088004. [PMID: 30932571 DOI: 10.1103/physrevlett.122.088004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Indexed: 06/09/2023]
Abstract
The hydrodynamic theory of polar liquid crystals is widely used to describe biological active fluids as well as passive molecular materials. Depending on the "shear-alignment parameter", in passive or weakly active polar fluids under external shear, the polar order parameter p is either inclined to the flow at a fixed (Leslie) angle, or rotates continuously. Here, we study the role of an additional "shear-elongation parameter" that has been neglected in the recent literature and causes |p| to change under flow. We show that this effect can give rise to a shear-induced first-order phase transition from isotropic to polar, and significantly change the rheological properties of both active and passive polar fluids.
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Affiliation(s)
- Tomer Markovich
- DAMTP, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77030, USA
| | - Elsen Tjhung
- DAMTP, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
| | - Michael E Cates
- DAMTP, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
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29
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Orihara H, Harada Y, Kobayashi F, Sasaki Y, Fujii S, Satou Y, Goto Y, Nagaya T. Negative viscosity of a liquid crystal in the presence of turbulence. Phys Rev E 2019; 99:012701. [PMID: 30780349 DOI: 10.1103/physreve.99.012701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Indexed: 06/09/2023]
Abstract
We report on the discovery of enormous negative viscosity in a nematic liquid crystal in the presence of turbulence induced by electric fields. As the negative viscosity in this system is so large, we are able to observe several phenomena originating from it. For example, we observe a spontaneous shear flow that rotates the upper disk of a rheometer, as well as the reversal of the rotational direction upon applying an external torque in the opposite direction. Hysteresis loops are also observed in the shear-stress-shear-rate curves, which is reminiscent of those seen for ferromagnetic and ferroelectric materials. The similarities between the phenomena observed for our system and ferroic materials are comprehensively demonstrated, although the two systems are fundamentally different in that the former is out of equilibrium. We elucidate the origin of the negative viscosity and propose a simple model that reproduces the phenomena observed in this active fluid.
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Affiliation(s)
- Hiroshi Orihara
- Division of Applied Physics, Hokkaido University, Sapporo 060-8628, Japan
| | - Yuko Harada
- Division of Applied Physics, Hokkaido University, Sapporo 060-8628, Japan
| | - Fumiaki Kobayashi
- Division of Applied Physics, Hokkaido University, Sapporo 060-8628, Japan
| | - Yuji Sasaki
- Division of Applied Physics, Hokkaido University, Sapporo 060-8628, Japan
| | - Shuji Fujii
- Division of Applied Physics, Hokkaido University, Sapporo 060-8628, Japan
| | - Yuki Satou
- Division of Electrical and Electronic Engineering, Oita University, Oita 870-1192, Japan
| | - Yoshitomo Goto
- Beppu University Junior College, Beppu 874-8501, Japan
- Division of Materials Science and Production Engineering, Oita University, Oita 870-1192, Japan
| | - Tomoyuki Nagaya
- Division of Electrical and Electronic Engineering, Oita University, Oita 870-1192, Japan
- Division of Materials Science and Production Engineering, Oita University, Oita 870-1192, Japan
- Division of Natural Sciences, Oita University, Oita 870-1192, Japan
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30
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Soni H, Pelcovits RA, Powers TR. Enhancement of Microorganism Swimming Speed in Active Matter. PHYSICAL REVIEW LETTERS 2018; 121:178002. [PMID: 30411941 DOI: 10.1103/physrevlett.121.178002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Indexed: 06/08/2023]
Abstract
We study a swimming undulating sheet in the isotropic phase of an active nematic liquid crystal. Activity changes the effective shear viscosity, reducing it to zero at a critical value of activity. Expanding in the sheet amplitude, we find that the correction to the swimming speed due to activity is inversely proportional to the effective shear viscosity. Our perturbative calculation becomes invalid near the critical value of activity; using numerical methods to probe this regime, we find that activity enhances the swimming speed by an order of magnitude compared to the passive case.
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Affiliation(s)
- Harsh Soni
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA
| | - Robert A Pelcovits
- Department of Physics, Brown University, Providence, Rhode Island 02012, USA
| | - Thomas R Powers
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA
- Department of Physics, Brown University, Providence, Rhode Island 02012, USA
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31
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Nandi SK, Gov NS. Effective temperature of active fluids and sheared soft glassy materials. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:117. [PMID: 30302578 DOI: 10.1140/epje/i2018-11731-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 09/12/2018] [Indexed: 06/08/2023]
Abstract
The dynamics within active fluids, driven by internal activity of the self-propelled particles, is a subject of intense study in non-equilibrium physics. These systems have been explored using simulations, where the motion of a passive tracer particle is followed. Similar studies have been carried out for a soft glassy material that is driven by shearing its boundaries. In both types of systems the non-equilibrium motion have been quantified by defining a set of "effective temperatures", using both the tracer particle kinetic energy and the fluctuation-dissipation relation. We demonstrate that these effective temperatures extracted from the many-body simulations fit analytical expressions that are obtained for a single active particle inside a visco-elastic fluid. This result provides testable predictions and suggests a unified description for the dynamics inside active systems.
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Affiliation(s)
- Saroj Kumar Nandi
- Department of Chemical and Biological Physics, The Weizmann Institute of Science, 76100, Rehovot, Israel
| | - N S Gov
- Department of Chemical and Biological Physics, The Weizmann Institute of Science, 76100, Rehovot, Israel.
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32
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Maryshev I, Marenduzzo D, Goryachev AB, Morozov A. Kinetic theory of pattern formation in mixtures of microtubules and molecular motors. Phys Rev E 2018; 97:022412. [PMID: 29548141 DOI: 10.1103/physreve.97.022412] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Indexed: 11/07/2022]
Abstract
In this study we formulate a theoretical approach, based on a Boltzmann-like kinetic equation, to describe pattern formation in two-dimensional mixtures of microtubular filaments and molecular motors. Following the previous work by Aranson and Tsimring [Phys. Rev. E 74, 031915 (2006)PLEEE81539-375510.1103/PhysRevE.74.031915] we model the motor-induced reorientation of microtubules as collision rules, and devise a semianalytical method to calculate the corresponding interaction integrals. This procedure yields an infinite hierarchy of kinetic equations that we terminate by employing a well-established closure strategy, developed in the pattern-formation community and based on a power-counting argument. We thus arrive at a closed set of coupled equations for slowly varying local density and orientation of the microtubules, and study its behavior by performing a linear stability analysis and direct numerical simulations. By comparing our method with the work of Aranson and Tsimring, we assess the validity of the assumptions required to derive their and our theories. We demonstrate that our approximation-free evaluation of the interaction integrals and our choice of a systematic closure strategy result in a rather different dynamical behavior than was previously reported. Based on our theory, we discuss the ensuing phase diagram and the patterns observed.
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Affiliation(s)
- Ivan Maryshev
- Centre for Synthetic and Systems Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, United Kingdom
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Andrew B Goryachev
- Centre for Synthetic and Systems Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, United Kingdom
| | - Alexander Morozov
- SUPA, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
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Loisy A, Eggers J, Liverpool TB. Active Suspensions have Nonmonotonic Flow Curves and Multiple Mechanical Equilibria. PHYSICAL REVIEW LETTERS 2018; 121:018001. [PMID: 30028150 DOI: 10.1103/physrevlett.121.018001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/16/2018] [Indexed: 06/08/2023]
Abstract
We point out unconventional mechanical properties of confined active fluids, such as bacterial suspensions, under shear. Using a minimal model of an active liquid crystal with no free parameters, we predict the existence of a window of bacteria concentration for which a suspension of E. Coli effectively behaves, at steady-state, as a negative viscosity fluid and reach a quantitative agreement with experimental measurements. Our theoretical analysis further shows that a negative apparent viscosity is due to a nonmonotonic local velocity profile, and it is associated with a nonmonotonic stress versus strain rate flow curve. This implies that fixed stress and fixed strain rate ensembles are not equivalent for active fluids.
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Affiliation(s)
- Aurore Loisy
- School of Mathematics, University of Bristol-Bristol BS8 1 TW, United Kingdom
| | - Jens Eggers
- School of Mathematics, University of Bristol-Bristol BS8 1 TW, United Kingdom
| | - Tanniemola B Liverpool
- School of Mathematics, University of Bristol-Bristol BS8 1 TW, United Kingdom
- BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
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Symmetric shear banding and swarming vortices in bacterial superfluids. Proc Natl Acad Sci U S A 2018; 115:7212-7217. [PMID: 29941551 DOI: 10.1073/pnas.1722505115] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial suspensions-a premier example of active fluids-show an unusual response to shear stresses. Instead of increasing the viscosity of the suspending fluid, the emergent collective motions of swimming bacteria can turn a suspension into a superfluid with zero apparent viscosity. Although the existence of active superfluids has been demonstrated in bulk rheological measurements, the microscopic origin and dynamics of such an exotic phase have not been experimentally probed. Here, using high-speed confocal rheometry, we study the dynamics of concentrated bacterial suspensions under simple planar shear. We find that bacterial superfluids under shear exhibit unusual symmetric shear bands, defying the conventional wisdom on shear banding of complex fluids, where the formation of steady shear bands necessarily breaks the symmetry of unsheared samples. We propose a simple hydrodynamic model based on the local stress balance and the ergodic sampling of nonequilibrium shear configurations, which quantitatively describes the observed symmetric shear-banding structure. The model also successfully predicts various interesting features of swarming vortices in stationary bacterial suspensions. Our study provides insights into the physical properties of collective swarming in active fluids and illustrates their profound influences on transport processes.
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Oriola D, Alert R, Casademunt J. Fluidization and Active Thinning by Molecular Kinetics in Active Gels. PHYSICAL REVIEW LETTERS 2017; 118:088002. [PMID: 28282157 DOI: 10.1103/physrevlett.118.088002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Indexed: 05/13/2023]
Abstract
We derive the constitutive equations of an active polar gel from a model for the dynamics of elastic molecules that link polar elements. Molecular binding kinetics induces the fluidization of the material, giving rise to Maxwell viscoelasticity and, provided that detailed balance is broken, to the generation of active stresses. We give explicit expressions for the transport coefficients of active gels in terms of molecular properties, including nonlinear contributions on the departure from equilibrium. In particular, when activity favors linker unbinding, we predict a decrease of viscosity with activity-active thinning-of kinetic origin, which could explain some experimental results on the cell cortex. By bridging the molecular and hydrodynamic scales, our results could help understand the interplay between molecular perturbations and the mechanics of cells and tissues.
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Affiliation(s)
- David Oriola
- Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Avinguda Diagonal 647 and Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Ricard Alert
- Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Avinguda Diagonal 647 and Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Jaume Casademunt
- Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Avinguda Diagonal 647 and Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
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36
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Guillamat P, Ignés-Mullol J, Shankar S, Marchetti MC, Sagués F. Probing the shear viscosity of an active nematic film. Phys Rev E 2016; 94:060602. [PMID: 28085294 DOI: 10.1103/physreve.94.060602] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Indexed: 12/12/2022]
Abstract
In vitro reconstituted active systems, such as the adenosine triphosphate (ATP)-driven microtubule bundle suspension developed by the Dogic group [T. Sanchez, D. T. Chen, S. J. DeCamp, M. Heymann, and Z. Dogic, Nature (London) 491, 431 (2012)10.1038/nature11591], provide a fertile testing ground for elucidating the phenomenology of active liquid crystalline states. Controlling such novel phases of matter crucially depends on our knowledge of their material and physical properties. In this Rapid Communication, we show that the shear viscosity of an active nematic film can be probed by varying its hydrodynamic coupling to a bounding oil layer. Using the motion of disclinations as intrinsic tracers of the flow field and a hydrodynamic model, we obtain an estimate for the shear viscosity of the nematic film. Knowing this now provides us with an additional handle for robust and precision tunable control of the emergent dynamics of active fluids.
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Affiliation(s)
- Pau Guillamat
- Departament de Química Física and Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Catalonia, Spain
| | - Jordi Ignés-Mullol
- Departament de Química Física and Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Catalonia, Spain
| | - Suraj Shankar
- Physics Department and Syracuse Soft Matter Program, Syracuse University, Syracuse, New York 13244, USA
| | - M Cristina Marchetti
- Physics Department and Syracuse Soft Matter Program, Syracuse University, Syracuse, New York 13244, USA
| | - Francesc Sagués
- Departament de Química Física and Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Catalonia, Spain
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Yang O, Peng Y, Liu Z, Tang C, Xu X, Cheng X. Dynamics of ellipsoidal tracers in swimming algal suspensions. Phys Rev E 2016; 94:042601. [PMID: 27841492 DOI: 10.1103/physreve.94.042601] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Indexed: 11/07/2022]
Abstract
Enhanced diffusion of passive tracers immersed in active fluids is a universal feature of active fluids and has been extensively studied in recent years. Similar to microrheology for equilibrium complex fluids, the unusual enhanced particle dynamics reveal intrinsic properties of active fluids. Nevertheless, previous studies have shown that the translational dynamics of spherical tracers are qualitatively similar, independent of whether active particles are pushers or pullers-the two fundamental classes of active fluids. Is it possible to distinguish pushers from pullers by simply imaging the dynamics of passive tracers? Here, we investigated the diffusion of isolated ellipsoids in algal C. reinhardtii suspensions-a model for puller-type active fluids. In combination with our previous results on pusher-type E. coli suspensions [Peng et al., Phys. Rev. Lett. 116, 068303 (2016)PRLTAO0031-900710.1103/PhysRevLett.116.068303], we showed that the dynamics of asymmetric tracers show a profound difference in pushers and pullers due to their rotational degree of freedom. Although the laboratory-frame translation and rotation of ellipsoids are enhanced in both pushers and pullers, similar to spherical tracers, the anisotropic diffusion in the body frame of ellipsoids shows opposite trends in the two classes of active fluids. An ellipsoid diffuses fastest along its major axis when immersed in pullers, whereas it diffuses slowest along the major axis in pushers. This striking difference can be qualitatively explained using a simple hydrodynamic model. In addition, our study on algal suspensions reveals that the influence of the near-field advection of algal swimming flows on the translation and rotation of ellipsoids shows different ranges and strengths. Our work provides not only new insights into universal organizing principles of active fluids, but also a convenient tool for detecting the class of active particles.
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Affiliation(s)
- Ou Yang
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Yi Peng
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Zhengyang Liu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Chao Tang
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Xinliang Xu
- Beijing Computational Science Research Center, Beijing 100193, China
| | - Xiang Cheng
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Srivastava P, Mishra P, Marchetti MC. Negative stiffness and modulated states in active nematics. SOFT MATTER 2016; 12:8214-8225. [PMID: 27714318 DOI: 10.1039/c6sm01493c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We examine the dynamics of an active nematic liquid crystal on a frictional substrate. When frictional damping dominates over viscous dissipation, we eliminate flow in favor of active stresses to obtain a minimal dynamical model for the nematic order parameter, with elastic constants renormalized by activity. The renormalized elastic constants can become negative at large activity, leading to the selection of spatially inhomogeneous patterns via a mechanism analogous to that responsible for modulated phases arising at an equilibrium Lifshitz point. Tuning activity and the degree of nematic order in the passive system, we obtain a linear stability phase diagram that exhibits a nonequilibrium tricritical point where ordered, modulated and disordered phases meet. Numerical solution of the nonlinear equations yields a succession of spatial structures of increasing complexity with increasing activity, including kink walls and active turbulence, as observed in experiments on microtubule bundles confined at an oil-water interface. Our work provides a minimal model for an overdamped active nematic that reproduces all the nonequilibrium structures seen in simulations of the full active nematic hydrodynamics and provides a framework for understanding some of the mechanisms for selection of the nonequilibrium patterns in the language of equilibrium critical phenomena.
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Affiliation(s)
- Pragya Srivastava
- Physics Department and Syracuse Soft Matter Program, Syracuse University, Syracuse, NY 13244, USA
| | - Prashant Mishra
- Physics Department and Syracuse Soft Matter Program, Syracuse University, Syracuse, NY 13244, USA
| | - M Cristina Marchetti
- Physics Department and Syracuse Soft Matter Program, Syracuse University, Syracuse, NY 13244, USA
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39
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Hagan MF, Baskaran A. Emergent self-organization in active materials. Curr Opin Cell Biol 2016; 38:74-80. [PMID: 26971116 DOI: 10.1016/j.ceb.2016.02.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 02/04/2016] [Accepted: 02/25/2016] [Indexed: 11/20/2022]
Abstract
Biological systems exhibit large-scale self-organized dynamics and structures which enable organisms to perform the functions of life. The field of active matter strives to develop and understand microscopically driven nonequilibrium materials, with emergent properties comparable to those of living systems. This review will describe two recently developed classes of active matter systems, in which simple building blocks-self-propelled colloidal particles or extensile rod-like particles-self-organize to form macroscopic structures with features not possible in equilibrium systems. We summarize the recent experimental and theoretical progress on each of these systems, and we present simple descriptions of the physics underlying their emergent behaviors.
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Affiliation(s)
- Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02453, USA.
| | - Aparna Baskaran
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02453, USA.
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40
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Chen Q, Ai BQ. Sorting of chiral active particles driven by rotary obstacles. J Chem Phys 2015; 143:104113. [DOI: 10.1063/1.4930282] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Qun Chen
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, School of Physics and Telecommunication Engineering, South China Normal University, 510006 Guangzhou, China
| | - Bao-quan Ai
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, School of Physics and Telecommunication Engineering, South China Normal University, 510006 Guangzhou, China
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López HM, Gachelin J, Douarche C, Auradou H, Clément E. Turning Bacteria Suspensions into Superfluids. PHYSICAL REVIEW LETTERS 2015; 115:028301. [PMID: 26207507 DOI: 10.1103/physrevlett.115.028301] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Indexed: 05/26/2023]
Abstract
The rheological response under simple shear of an active suspension of Escherichia coli is determined in a large range of shear rates and concentrations. The effective viscosity and the time scales characterizing the bacterial organization under shear are obtained. In the dilute regime, we bring evidence for a low-shear Newtonian plateau characterized by a shear viscosity decreasing with concentration. In the semidilute regime, for particularly active bacteria, the suspension displays a "superfluidlike" transition where the viscous resistance to shear vanishes, thus showing that, macroscopically, the activity of pusher swimmers organized by shear is able to fully overcome the dissipative effects due to viscous loss.
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Affiliation(s)
- Héctor Matías López
- Université Paris-Sud, CNRS, F-91405, Lab FAST, Bâtiment 502, Campus Univ, Orsay F-91405, France
| | - Jérémie Gachelin
- Physique et Mécanique des Milieux Hétérogenes (UMR 7636 ESPCI/CNRS/Université P.M. Curie/Université Paris-Diderot), 10 rue Vauquelin, 75005 Paris, France
| | - Carine Douarche
- Laboratoire de Physique des Solides, Université Paris-Sud, CNRS UMR 8502, F-91405 Orsay, France
| | - Harold Auradou
- Université Paris-Sud, CNRS, F-91405, Lab FAST, Bâtiment 502, Campus Univ, Orsay F-91405, France
| | - Eric Clément
- Physique et Mécanique des Milieux Hétérogenes (UMR 7636 ESPCI/CNRS/Université P.M. Curie/Université Paris-Diderot), 10 rue Vauquelin, 75005 Paris, France
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Elgeti J, Winkler RG, Gompper G. Physics of microswimmers--single particle motion and collective behavior: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:056601. [PMID: 25919479 DOI: 10.1088/0034-4885/78/5/056601] [Citation(s) in RCA: 647] [Impact Index Per Article: 71.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Locomotion and transport of microorganisms in fluids is an essential aspect of life. Search for food, orientation toward light, spreading of off-spring, and the formation of colonies are only possible due to locomotion. Swimming at the microscale occurs at low Reynolds numbers, where fluid friction and viscosity dominates over inertia. Here, evolution achieved propulsion mechanisms, which overcome and even exploit drag. Prominent propulsion mechanisms are rotating helical flagella, exploited by many bacteria, and snake-like or whip-like motion of eukaryotic flagella, utilized by sperm and algae. For artificial microswimmers, alternative concepts to convert chemical energy or heat into directed motion can be employed, which are potentially more efficient. The dynamics of microswimmers comprises many facets, which are all required to achieve locomotion. In this article, we review the physics of locomotion of biological and synthetic microswimmers, and the collective behavior of their assemblies. Starting from individual microswimmers, we describe the various propulsion mechanism of biological and synthetic systems and address the hydrodynamic aspects of swimming. This comprises synchronization and the concerted beating of flagella and cilia. In addition, the swimming behavior next to surfaces is examined. Finally, collective and cooperate phenomena of various types of isotropic and anisotropic swimmers with and without hydrodynamic interactions are discussed.
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Affiliation(s)
- J Elgeti
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
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44
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Córdoba A, Schieber JD, Indei T. The role of filament length, finite-extensibility and motor force dispersity in stress relaxation and buckling mechanisms in non-sarcomeric active gels. SOFT MATTER 2015; 11:38-57. [PMID: 25375087 DOI: 10.1039/c4sm01944j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
After relaxing some assumptions we apply a single-chain mean-field mathematical model recently introduced [RSC Adv. (2014)] to describe the role of molecular motors in the mechanical properties of active gels. The model allows physics that are not available in models postulated on coarser levels of description. Moreover it proposes a level of description that allows the prediction of observables at time scales too difficult to achieve in multi-chain simulations for realistic filament lengths and densities. We model the semiflexible filaments that compose the active gel as bead-spring chains; molecular motors are accounted for by using a mean-field approach, in which filaments undergo transitions of one motor attachment state depending on the state of the probe filament. The level of description includes the end-to-end distance and attachment state of the filaments, and the motor-generated forces, as stochastic state variables which evolve according to a proposed differential Chapman-Kolmogorov equation. The motor-generated forces are drawn from a stationary distribution of motor stall forces. We consider bead-spring chains with multiple beads, explore the effect of finite-extensibility of the strands and incorporate into the model motor force distributions that have been measured experimentally. The model can no longer be solved analytically but is amenable to numerical simulation. This version of the model allows a more quantitative description of buckling dynamics [Lenz et. al. PRL, 2012, 108, 238107] and the dynamic modulus of active gels. The effect of finite extensibility of the filament strands on the dynamic modulus was also found to be in agreement with the microrheology experiments of Mizuno et. al., [Science, 2007, 315, 370-373].
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Affiliation(s)
- Andrés Córdoba
- Department of Chemical and Biological Engineering and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, 3440 S. Dearborn St, Chicago, Illinois 60616, USA.
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45
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Saintillan D, Shelley MJ. Theory of Active Suspensions. COMPLEX FLUIDS IN BIOLOGICAL SYSTEMS 2015. [DOI: 10.1007/978-1-4939-2065-5_9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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46
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Giomi L, Bowick MJ, Mishra P, Sknepnek R, Cristina Marchetti M. Defect dynamics in active nematics. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2014; 372:20130365. [PMID: 25332389 PMCID: PMC4223672 DOI: 10.1098/rsta.2013.0365] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Topological defects are distinctive signatures of liquid crystals. They profoundly affect the viscoelastic behaviour of the fluid by constraining the orientational structure in a way that inevitably requires global changes not achievable with any set of local deformations. In active nematic liquid crystals, topological defects not only dictate the global structure of the director, but also act as local sources of motion, behaving as self-propelled particles. In this article, we present a detailed analytical and numerical study of the mechanics of topological defects in active nematic liquid crystals.
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Affiliation(s)
- Luca Giomi
- SISSA, International School for Advanced Studies, Via Bonomea 265, 34136 Trieste, Italy Instituut-Lorentz, Universiteit Leiden, PO Box 9506, 2300 RA Leiden, The Netherlands
| | - Mark J Bowick
- Physics Department and Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Prashant Mishra
- Physics Department, Syracuse University, Syracuse, NY 13244, USA
| | - Rastko Sknepnek
- School of Engineering, Physics, and Mathematics, University of Dundee, Dundee DD1 4HN, UK
| | - M Cristina Marchetti
- Physics Department and Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY 13244, USA
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47
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De Magistris G, Tiribocchi A, Whitfield CA, Hawkins RJ, Cates ME, Marenduzzo D. Spontaneous motility of passive emulsion droplets in polar active gels. SOFT MATTER 2014; 10:7826-7837. [PMID: 25156695 DOI: 10.1039/c4sm00937a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We study by computer simulations the dynamics of a droplet of passive, isotropic fluid, embedded in a polar active gel. The latter represents a fluid of active force dipoles, which exert either contractile or extensile stresses on their surroundings, modelling for instance a suspension of cytoskeletal filaments and molecular motors. When the polarisation of the active gel is anchored normal to the droplet at its surface, the nematic elasticity of the active gel drives the formation of a hedgehog defect; this defect then drives an active flow which propels the droplet forward. In an extensile gel, motility can occur even with tangential anchoring, which is compatible with a defect-free polarisation pattern. In this case, upon increasing activity the droplet first rotates uniformly, and then undergoes a discontinuous nonequilibrium transition into a translationally motile state, powered by bending deformations in the surrounding active medium.
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Affiliation(s)
- G De Magistris
- SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, UK.
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48
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Yang X, Wang Q. Capillary instability of axisymmetric, active liquid crystal jets. SOFT MATTER 2014; 10:6758-6776. [PMID: 25074458 DOI: 10.1039/c4sm00511b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We study linear stability of an infinitely long, axisymmetric, cylindrical active liquid crystal (ALC) jet in a passive isotropic fluid matrix using a polar active liquid crystal (ALC) model. We identify three possible unstable modes (or mechanisms) as the result of the interaction between the flow and the active (or self-propelled) molecular motion. The first unstable mode is related to the polarity vector instability when coupled to the flow field in the presence of the molecular activity. It can be traced back to the inherent polarity vector instability in a bulk active liquid crystal flow. However, it can be grossly amplified in the ALC jet to encompass up to infinitely many unstable growth rates when the long range distortional elastic interaction is weak in certain parameter regimes; it can also be suppressed in other parameter regimes completely. The second unstable mode is related to the classical capillary or Rayleigh instability, which exists in a finite wave interval [0, k(cutoff)]. The new feature for this instability lies in the dependence of the cutoff wave number (k(cutoff)) on the activity of the active matter system. For ALC jets with sufficiently strong contractile activity, the instability can be completely suppressed though. The third unstable mode is due to the active viscous stress. This unstable mode can emerge in the intermediate wave number regime at a sufficiently strong active viscosity and even expand all the way to the zero wave number limit when the Rayleigh unstable mode is absent. It can also be suppressed in the regime of weak active viscous stress. At any given values of the model parameters, the three types of instabilities can show up either individually or in a certain combination, or be completely suppressed altogether. In this paper, we discuss the positive growth rates associated with the instabilities, windows of instability and their dependence on model parameters through extensive numerical computations aided by asymptotic analyses.
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Affiliation(s)
- Xiaogang Yang
- School of Mathematical Sciences, Nankai University, Tianjin, China 300071.
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49
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Head DA, Briels WJ, Gompper G. Nonequilibrium structure and dynamics in a microscopic model of thin-film active gels. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:032705. [PMID: 24730872 DOI: 10.1103/physreve.89.032705] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Indexed: 06/03/2023]
Abstract
In the presence of adenosine triphosphate, molecular motors generate active force dipoles that drive suspensions of protein filaments far from thermodynamic equilibrium, leading to exotic dynamics and pattern formation. Microscopic modeling can help to quantify the relationship between individual motors plus filaments to organization and dynamics on molecular and supramolecular length scales. Here, we present results of extensive numerical simulations of active gels where the motors and filaments are confined between two infinite parallel plates. Thermal fluctuations and excluded-volume interactions between filaments are included. A systematic variation of rates for motor motion, attachment, and detachment, including a differential detachment rate from filament ends, reveals a range of nonequilibrium behavior. Strong motor binding produces structured filament aggregates that we refer to as asters, bundles, or layers, whose stability depends on motor speed and differential end detachment. The gross features of the dependence of the observed structures on the motor rate and the filament concentration can be captured by a simple one-filament model. Loosely bound aggregates exhibit superdiffusive mass transport, where filament translocation scales with lag time with nonunique exponents that depend on motor kinetics. An empirical data collapse of filament speed as a function of motor speed and end detachment is found, suggesting a dimensional reduction of the relevant parameter space. We conclude by discussing the perspectives of microscopic modeling in the field of active gels.
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Affiliation(s)
- D A Head
- School of Computing, Leeds University, Leeds LS2 9JT, United Kingdom
| | - W J Briels
- Computational Biophysics, University of Twente, 7500 AE Enschede, The Netherlands
| | - 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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50
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Córdoba A, Schieber JD, Indei T. A single-chain model for active gels I: active dumbbell model. RSC Adv 2014. [DOI: 10.1039/c4ra02262a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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