1
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Yashunsky V, Pearce DJG, Ariel G, Be'er A. Topological defects in multi-layered swarming bacteria. SOFT MATTER 2024; 20:4237-4245. [PMID: 38747575 PMCID: PMC11135144 DOI: 10.1039/d4sm00038b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/06/2024] [Indexed: 05/30/2024]
Abstract
Topological defects, which are singular points in a director field, play a major role in shaping active systems. Here, we experimentally study topological defects and the flow patterns around them, that are formed during the highly rapid dynamics of swarming bacteria. The results are compared to the predictions of two-dimensional active nematics. We show that, even though some of the assumptions underlying the theory do not hold, the swarm dynamics is in agreement with two-dimensional nematic theory. In particular, we look into the multi-layered structure of the swarm, which is an important feature of real, natural colonies, and find a strong coupling between layers. Our results suggest that the defect-charge density is hyperuniform, i.e., that long range density-fluctuations are suppressed.
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Affiliation(s)
- Victor Yashunsky
- The Swiss Institute for Dryland Environmental and Energy Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990 Midreshet Ben-Gurion, Israel.
| | - Daniel J G Pearce
- Department of Theoretical Physics, University of Geneva, 1211 Geneva, Switzerland
| | - Gil Ariel
- Department of Mathematics, Bar-Ilan University, 52900 Ramat-Gan, Israel.
| | - Avraham Be'er
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990 Midreshet Ben-Gurion, Israel
- The Department of Physics, Ben-Gurion University of the Negev, 84105 Beer-Sheva, Israel.
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2
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Shankar S, Scharrer LVD, Bowick MJ, Marchetti MC. Design rules for controlling active topological defects. Proc Natl Acad Sci U S A 2024; 121:e2400933121. [PMID: 38748571 PMCID: PMC11127047 DOI: 10.1073/pnas.2400933121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/12/2024] [Indexed: 05/27/2024] Open
Abstract
Topological defects play a central role in the physics of many materials, including magnets, superconductors, and liquid crystals. In active fluids, defects become autonomous particles that spontaneously propel from internal active stresses and drive chaotic flows stirring the fluid. The intimate connection between defect textures and active flow suggests that properties of active materials can be engineered by controlling defects, but design principles for their spatiotemporal control remain elusive. Here, we propose a symmetry-based additive strategy for using elementary activity patterns, as active topological tweezers, to create, move, and braid such defects. By combining theory and simulations, we demonstrate how, at the collective level, spatial activity gradients act like electric fields which, when strong enough, induce an inverted topological polarization of defects, akin to a negative susceptibility dielectric. We harness this feature in a dynamic setting to collectively pattern and transport interacting active defects. Our work establishes an additive framework to sculpt flows and manipulate active defects in both space and time, paving the way to design programmable active and living materials for transport, memory, and logic.
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Affiliation(s)
- Suraj Shankar
- Department of Physics, Harvard University, Cambridge, MA02138
- Department of Physics, University of Michigan, Ann Arbor, MI48109
| | - Luca V. D. Scharrer
- Department of Physics, University of California, Santa Barbara, CA93106
- Department of Physics, The University of Chicago, Chicago, IL60637
| | - Mark J. Bowick
- Department of Physics, University of California, Santa Barbara, CA93106
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA93106
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3
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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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4
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Killeen A, Bertrand T, Lee CF. Machine learning topological defects in confluent tissues. BIOPHYSICAL REPORTS 2024; 4:100142. [PMID: 38313863 PMCID: PMC10837480 DOI: 10.1016/j.bpr.2024.100142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 01/04/2024] [Indexed: 02/06/2024]
Abstract
Active nematics is an emerging paradigm for characterizing biological systems. One aspect of particularly intense focus is the role active nematic defects play in these systems, as they have been found to mediate a growing number of biological processes. Accurately detecting and classifying these defects in biological systems is, therefore, of vital importance to improving our understanding of such processes. While robust methods for defect detection exist for systems of elongated constituents, other systems, such as epithelial layers, are not well suited to such methods. Here, we address this problem by developing a convolutional neural network to detect and classify nematic defects in confluent cell layers. Crucially, our method is readily implementable on experimental images of cell layers and is specifically designed to be suitable for cells that are not rod shaped, which we demonstrate by detecting defects on experimental data using the trained model. We show that our machine learning model outperforms current defect detection techniques and that this manifests itself in our method as requiring less data to accurately capture defect properties. This could drastically improve the accuracy of experimental data interpretation while also reducing costs, advancing the study of nematic defects in biological systems.
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Affiliation(s)
- Andrew Killeen
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Thibault Bertrand
- Department of Mathematics, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Chiu Fan Lee
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, United Kingdom
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5
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Vélez-Cerón I, Guillamat P, Sagués F, Ignés-Mullol J. Probing active nematics with in situ microfabricated elastic inclusions. Proc Natl Acad Sci U S A 2024; 121:e2312494121. [PMID: 38451942 PMCID: PMC10945829 DOI: 10.1073/pnas.2312494121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/27/2024] [Indexed: 03/09/2024] Open
Abstract
In this work, we report a direct measurement of the forces exerted by a tubulin/kinesin active nematic gel as well as its complete rheological characterization, including the quantification of its shear viscosity, η, and its activity parameter, α. For this, we develop a method that allows us to rapidly photo-polymerize compliant elastic inclusions in the continuously remodeling active system. Moreover, we quantitatively settle long-standing theoretical predictions, such as a postulated relationship encoding the intrinsic time scale of the active nematic in terms of η and α. In parallel, we infer a value for the nematic elasticity constant, K, by combining our measurements with the theorized scaling of the active length scale. On top of the microrheology capabilities, we demonstrate strategies for defect encapsulation, quantification of defect mechanics, and defect interactions, enabled by the versatility of the microfabrication strategy that allows to combine elastic motifs of different shapes and stiffnesses that are fabricated in situ.
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Affiliation(s)
- Ignasi Vélez-Cerón
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Barcelona08028, Spain
- Institute of Nanoscience and Nanotechnology, IN2UB, Universitat de Barcelona, Barcelona08028, Spain
| | - Pau Guillamat
- Institute for Bioengineering of Catalonia, The Barcelona Institute for Science and Technology, Barcelona08028, Spain
| | - Francesc Sagués
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Barcelona08028, Spain
- Institute of Nanoscience and Nanotechnology, IN2UB, Universitat de Barcelona, Barcelona08028, Spain
| | - Jordi Ignés-Mullol
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Barcelona08028, Spain
- Institute of Nanoscience and Nanotechnology, IN2UB, Universitat de Barcelona, Barcelona08028, Spain
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6
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Zheng Z, Xu C, Fan J, Liu M, Chen X. Order parameter dynamics in complex systems: From models to data. CHAOS (WOODBURY, N.Y.) 2024; 34:022101. [PMID: 38341762 DOI: 10.1063/5.0180340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/14/2023] [Indexed: 02/13/2024]
Abstract
Collective ordering behaviors are typical macroscopic manifestations embedded in complex systems and can be ubiquitously observed across various physical backgrounds. Elements in complex systems may self-organize via mutual or external couplings to achieve diverse spatiotemporal coordinations. The order parameter, as a powerful quantity in describing the transition to collective states, may emerge spontaneously from large numbers of degrees of freedom through competitions. In this minireview, we extensively discussed the collective dynamics of complex systems from the viewpoint of order-parameter dynamics. A synergetic theory is adopted as the foundation of order-parameter dynamics, and it focuses on the self-organization and collective behaviors of complex systems. At the onset of macroscopic transitions, slow modes are distinguished from fast modes and act as order parameters, whose evolution can be established in terms of the slaving principle. We explore order-parameter dynamics in both model-based and data-based scenarios. For situations where microscopic dynamics modeling is available, as prototype examples, synchronization of coupled phase oscillators, chimera states, and neuron network dynamics are analytically studied, and the order-parameter dynamics is constructed in terms of reduction procedures such as the Ott-Antonsen ansatz, the Lorentz ansatz, and so on. For complicated systems highly challenging to be well modeled, we proposed the eigen-microstate approach (EMP) to reconstruct the macroscopic order-parameter dynamics, where the spatiotemporal evolution brought by big data can be well decomposed into eigenmodes, and the macroscopic collective behavior can be traced by Bose-Einstein condensation-like transitions and the emergence of dominant eigenmodes. The EMP is successfully applied to some typical examples, such as phase transitions in the Ising model, climate dynamics in earth systems, fluctuation patterns in stock markets, and collective motion in living systems.
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Affiliation(s)
- Zhigang Zheng
- Institute of Systems Science, Huaqiao University, Xiamen 361021, China and College of Information Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Can Xu
- Institute of Systems Science, Huaqiao University, Xiamen 361021, China and College of Information Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Jingfang Fan
- School of Systems Science, Beijing Normal University, Beijing 100875, China and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing 100875, China
| | - Maoxin Liu
- School of Systems Science, Beijing Normal University, Beijing 100875, China and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing 100875, China
| | - Xiaosong Chen
- School of Systems Science, Beijing Normal University, Beijing 100875, China and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing 100875, China
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7
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Wang W, Ren H, Zhang R. Symmetry Breaking of Self-Propelled Topological Defects in Thin-Film Active Chiral Nematics. PHYSICAL REVIEW LETTERS 2024; 132:038301. [PMID: 38307071 DOI: 10.1103/physrevlett.132.038301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/09/2023] [Accepted: 11/28/2023] [Indexed: 02/04/2024]
Abstract
Active nematics represent a range of dense active matter systems which can engender spontaneous flows and self-propelled topological defects. Two-dimensional (2D) active nematic theory and simulation have been successful in explaining many quasi-2D experiments in which self-propelled +1/2 defects are observed to move along their symmetry axis. However, many active liquid crystals are essentially chiral nematic, but their twist mode becomes irrelevant under the 2D assumption. Here, we use theory and simulation to examine a three-dimensional active chiral nematic confined to a thin film, thus forming a quasi-2D system. We predict that the self-propelled +1/2 disclination in a curved thin film can break its mirror symmetry by moving circularly. Our prediction is confirmed by hydrodynamic simulations of thin spherical-shell and thin cylindrical-shell systems. In the spherical-shell confinement, the four emerged +1/2 disclinations exhibit rich dynamics as a function of activity and chirality. As such, we have proposed a new symmetry-breaking scenario in which self-propelled defects in quasi-2D active nematics can acquire an active angular velocity, greatly enriching their dynamics for finer control and emerging applications.
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Affiliation(s)
- Weiqiang Wang
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR
| | - Haijie Ren
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR
| | - Rui Zhang
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR
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8
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Panda A, Winkler RG, Singh SP. Characteristic features of self-avoiding active Brownian polymers under linear shear flow. SOFT MATTER 2023; 19:8577-8586. [PMID: 37905462 DOI: 10.1039/d3sm01334k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
We present Brownian dynamics simulation results of a flexible linear polymer with excluded-volume interactions under shear flow in the presence of active noise. The active noise strongly affects the polymer's conformational and dynamical properties, such as the stretching in the flow direction and compression in the gradient direction, shear-induced alignment, and shear viscosity. In the asymptotic limit of large activities and shear rates, the power-law scaling exponents of these quantities differ significantly from those of passive polymers. The chain's shear-induced stretching at a given shear rate is reduced by active noise, and it displays a non-monotonic behavior, where an initial polymer compression is followed by its stretching with increasing active force. The compression of the polymer in the gradient direction follows the relation ∼WiPe-3/4 as a function of the activity-dependent Weissenberg number WiPe, which differs from the scaling observed in passive systems ∼WiPe-1/2. The flow-induced alignment at large Péclet numbers Pe ≫ 1, where Pe is the Péclet number, and large shear rates WiPe ≫ 1 displays the scaling behavior WiPe-1/2, with an exponent differing from the passive value -1/3. Furthermore, the polymer's zero-shear viscosity displays a non-monotonic behavior, decreasing in an intermediate activity regime due to excluded-volume interactions and increasing again for large Pe. Shear thinning appears with increasing Weissenberg number with the power-laws WiPe-1/2 and WiPe-3/4 for passive and active polymers, respectively. In addition, our simulation results are compared with the results of an analytical approach, which predicts quantitatively similar behaviors for the various aforementioned physical quantities.
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Affiliation(s)
- Arindam Panda
- Department of Physics, Indian Institute of Science Education and Research, Bhopal 462 066, Madhya Pradesh, India.
| | - Roland G Winkler
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, 52428 Jülich, Germany.
| | - Sunil P Singh
- Department of Physics, Indian Institute of Science Education and Research, Bhopal 462 066, Madhya Pradesh, India.
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9
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Macías-Durán J, Duarte-Alaniz V, Híjar H. Active nematic liquid crystals simulated by particle-based mesoscopic methods. SOFT MATTER 2023; 19:8052-8069. [PMID: 37700612 DOI: 10.1039/d3sm00481c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Two Multi-particle collision dynamics algorithms that simulate nematic liquid crystals are generalised to reproduce active behaviour. One of the algorithms is due to Shendruk and Yeomans and is based on particles that carry an orientation vector ordered by a mean-field energy [T. N. Shendruk and J. M. Yeomans, Soft Matter, 2015, 11, 5101]. In the other algorithm, due to Mandal and Mazza, particles possess an order parameter tensor which evolves according to the Qian-Sheng model of nematohydrodynamics [S. Mandal and M. G. Mazza, Phys. Rev. E, 2019, 99, 063319]. For both methods activity is incorporated through a force proportional to the divergence of the local average order parameter tensor. Both implementations produce disclination curves in the nematic fluid that undergo nucleation and self-annihilation dynamics. Topological defects are found to be consistent with those observed in recent experiments of three-dimensional active nematics. Results permit to compare the length-scales over which the different nematic Multi-particle collision dynamics methods operate. The structure and dynamics of the orientation and flow fields agree with those obtained recently in numerical studies of continuum three-dimensional active nematics. Overall, our results open the opportunity to use mesoscopic particle-based approaches to study active liquid crystals in situations such as nonequilibrium states driven by flow or colloidal particles in active anisotropic solvents.
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Affiliation(s)
- Jesús Macías-Durán
- La Salle University Mexico, Benjamin Franklin 45, 06140, Mexico City, Mexico.
| | | | - Humberto Híjar
- La Salle University Mexico, Benjamin Franklin 45, 06140, Mexico City, Mexico.
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10
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Han E, Fei C, Alert R, Copenhagen K, Koch MD, Wingreen NS, Shaevitz JW. Local polar order controls mechanical stress and triggers layer formation in developing Myxococcus xanthus colonies. ARXIV 2023:arXiv:2308.00368v1. [PMID: 37576128 PMCID: PMC10418523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Colonies of the social bacterium Myxococcus xanthus go through a morphological transition from a thin colony of cells to three-dimensional droplet-like fruiting bodies as a strategy to survive starvation. The biological pathways that control the decision to form a fruiting body have been studied extensively. However, the mechanical events that trigger the creation of multiple cell layers and give rise to droplet formation remain poorly understood. By measuring cell orientation, velocity, polarity, and force with cell-scale resolution, we reveal a stochastic local polar order in addition to the more obvious nematic order. Average cell velocity and active force at topological defects agree with predictions from active nematic theory, but their fluctuations are anomalously large due to polar active forces generated by the self-propelled rod-shaped cells. We find that M. xanthus cells adjust their reversal frequency to tune the magnitude of this local polar order, which in turn controls the mechanical stresses and triggers layer formation in the colonies.
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Affiliation(s)
- Endao Han
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
| | - Chenyi Fei
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ricard Alert
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzerstraße 38, 01187 Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstraße 108, 01307 Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, 01062, Dresden, Germany
| | - Katherine Copenhagen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Matthias D. Koch
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ned S. Wingreen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Joshua W. Shaevitz
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
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11
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Golden M, Grigoriev RO, Nambisan J, Fernandez-Nieves A. Physically informed data-driven modeling of active nematics. SCIENCE ADVANCES 2023; 9:eabq6120. [PMID: 37406118 PMCID: PMC10321743 DOI: 10.1126/sciadv.abq6120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/31/2023] [Indexed: 07/07/2023]
Abstract
A continuum description is essential for understanding a variety of collective phenomena in active matter. However, building quantitative continuum models of active matter from first principles can be extremely challenging due to both the gaps in our knowledge and the complicated structure of nonlinear interactions. Here, we use a physically informed data-driven approach to construct a complete mathematical model of an active nematic from experimental data describing kinesin-driven microtubule bundles confined to an oil-water interface. We find that the structure of the model is similar to the Leslie-Ericksen and Beris-Edwards models, but there are appreciable and important differences. Rather unexpectedly, elastic effects are found to play no role in the experiments considered, with the dynamics controlled entirely by the balance between active stresses and friction stresses.
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Affiliation(s)
- Matthew Golden
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Roman O. Grigoriev
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jyothishraj Nambisan
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Condensed Matter Physics, University of Barcelona, Barcelona 08028, Spain
- Institute of Complex Systems (UBICS), University of Barcelona, Barcelona 08028, Spain
| | - Alberto Fernandez-Nieves
- Department of Condensed Matter Physics, University of Barcelona, Barcelona 08028, Spain
- Institute of Complex Systems (UBICS), University of Barcelona, Barcelona 08028, Spain
- ICREA-Institució Catalanade Recerca i Estudis Avançats, Barcelona 08010, Spain
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12
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Ray S, Zhang J, Dogic Z. Rectified Rotational Dynamics of Mobile Inclusions in Two-Dimensional Active Nematics. PHYSICAL REVIEW LETTERS 2023; 130:238301. [PMID: 37354394 DOI: 10.1103/physrevlett.130.238301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/14/2023] [Indexed: 06/26/2023]
Abstract
We investigate the dynamics of mobile inclusions embedded in 2D active nematics. The interplay between the inclusion shape, boundary-induced nematic order, and autonomous flows powers the inclusion motion. Disks and achiral gears exhibit unbiased rotational motion, but with distinct dynamics. In comparison, chiral gear-shaped inclusions exhibit long-term rectified rotation, which is correlated with dynamics and polarization of nearby +1/2 topological defects. The chirality of defect polarities and the active nematic texture around the inclusion correlate with the inclusion's instantaneous rotation rate. Inclusions provide a promising tool for probing the rheological properties of active nematics and extracting ordered motion from their inherently chaotic motion.
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Affiliation(s)
- Sattvic Ray
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Jie Zhang
- Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China (USTC), 230026 Hefei, China
- Department of Polymer Science and Engineering, CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China (USTC), 230026 Hefei, China
| | - Zvonimir Dogic
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
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13
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Lan Y, Xu M, Xie J, Yang Y, Jiang H. Spontaneous symmetry-breaking of the active cluster drives the directed movement and self-sustained oscillation of symmetric rod-like passive particles. SOFT MATTER 2023; 19:3222-3227. [PMID: 37083022 DOI: 10.1039/d2sm01243j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Active particles without detailed balance can rectify their random motions to drive the directed movement or rotation of asymmetric passive obstacles. However, whether they can drive the directed movement of symmetric passive obstacles is still unclear. Here, we show that a rod-like passive particle which is fixed to move along the x-axis in an active bath can keep long-lived directed movement at nearly constant speed due to the spontaneous symmetry breaking of the neighboring active particle cluster. If the passive particle is further confined by a harmonic potential, it may undergo self-sustained periodic oscillation for an appropriate length of the passive particle and self-propelled velocity of active particles. The restoring force from the harmonic potential will trigger the velocity jump-off and thus lead to self-sustained periodic oscillation. Remarkably, the relationship between the velocity of the passive particle and the external force shows that the effective viscosity of the active bath may become negative in some regime. Finally, we develop a minimum 1D theoretical model to further probe the mechanism underlying the directed movement and self-sustained oscillation of the passive particle. Our findings reveal the effect of the moving boundary on the active bath and demonstrate a novel method to extract practical mechanical work from the active bath to propel microdevices.
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Affiliation(s)
- Ying Lan
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Man Xu
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Jinjiang Xie
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Yuehua Yang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Hongyuan Jiang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei, Anhui 230026, China.
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14
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Supekar R, Song B, Hastewell A, Choi GPT, Mietke A, Dunkel J. Learning hydrodynamic equations for active matter from particle simulations and experiments. Proc Natl Acad Sci U S A 2023; 120:e2206994120. [PMID: 36763535 PMCID: PMC9963139 DOI: 10.1073/pnas.2206994120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 01/12/2023] [Indexed: 02/11/2023] Open
Abstract
Recent advances in high-resolution imaging techniques and particle-based simulation methods have enabled the precise microscopic characterization of collective dynamics in various biological and engineered active matter systems. In parallel, data-driven algorithms for learning interpretable continuum models have shown promising potential for the recovery of underlying partial differential equations (PDEs) from continuum simulation data. By contrast, learning macroscopic hydrodynamic equations for active matter directly from experiments or particle simulations remains a major challenge, especially when continuum models are not known a priori or analytic coarse graining fails, as often is the case for nondilute and heterogeneous systems. Here, we present a framework that leverages spectral basis representations and sparse regression algorithms to discover PDE models from microscopic simulation and experimental data, while incorporating the relevant physical symmetries. We illustrate the practical potential through a range of applications, from a chiral active particle model mimicking nonidentical swimming cells to recent microroller experiments and schooling fish. In all these cases, our scheme learns hydrodynamic equations that reproduce the self-organized collective dynamics observed in the simulations and experiments. This inference framework makes it possible to measure a large number of hydrodynamic parameters in parallel and directly from video data.
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Affiliation(s)
- Rohit Supekar
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Boya Song
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Alasdair Hastewell
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Gary P. T. Choi
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Alexander Mietke
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA02139
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15
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Joshi C, Ray S, Lemma LM, Varghese M, Sharp G, Dogic Z, Baskaran A, Hagan MF. Data-Driven Discovery of Active Nematic Hydrodynamics. PHYSICAL REVIEW LETTERS 2022; 129:258001. [PMID: 36608242 DOI: 10.1103/physrevlett.129.258001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Active nematics can be modeled using phenomenological continuum theories that account for the dynamics of the nematic director and fluid velocity through partial differential equations (PDEs). While these models provide a statistical description of the experiments, the relevant terms in the PDEs and their parameters are usually identified indirectly. We adapt a recently developed method to automatically identify optimal continuum models for active nematics directly from spatiotemporal data, via sparse regression of the coarse-grained fields onto generic low order PDEs. After extensive benchmarking, we apply the method to experiments with microtubule-based active nematics, finding a surprisingly minimal description of the system. Our approach can be generalized to gain insights into active gels, microswimmers, and diverse other experimental active matter systems.
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Affiliation(s)
- Chaitanya Joshi
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
- Department of Physics and Astronomy, Tufts University, Medford, Massachusetts 02155, USA
| | - Sattvic Ray
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Linnea M Lemma
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Minu Varghese
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109 USA
| | - Graham Sharp
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Zvonimir Dogic
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Aparna Baskaran
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Michael F Hagan
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
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16
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Topological defect-mediated morphodynamics of active-active interfaces. Proc Natl Acad Sci U S A 2022; 119:e2122494119. [PMID: 36469777 PMCID: PMC9897450 DOI: 10.1073/pnas.2122494119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
Physical interfaces widely exist in nature and engineering. Although the formation of passive interfaces is well elucidated, the physical principles governing active interfaces remain largely unknown. Here, we combine simulation, theory, and cell-based experiment to investigate the evolution of an active-active interface. We adopt a biphasic framework of active nematic liquid crystals. We find that long-lived topological defects mechanically energized by activity display unanticipated dynamics nearby the interface, where defects perform "U-turns" to keep away from the interface, push the interface to develop local fingers, or penetrate the interface to enter the opposite phase, driving interfacial morphogenesis and cross-interface defect transport. We identify that the emergent interfacial morphodynamics stems from the instability of the interface and is further driven by the activity-dependent defect-interface interactions. Experiments of interacting multicellular monolayers with extensile and contractile differences in cell activity have confirmed our predictions. These findings reveal a crucial role of topological defects in active-active interfaces during, for example, boundary formation and tissue competition that underlie organogenesis and clinically relevant disorders.
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17
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Yin Y, Yu HT, Tan H, Cai H, Chen HY, Lo CJ, Guo S. Escaping speed of bacteria from confinement. Biophys J 2022; 121:4656-4665. [PMID: 36271621 PMCID: PMC9748248 DOI: 10.1016/j.bpj.2022.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/07/2022] [Accepted: 10/17/2022] [Indexed: 12/15/2022] Open
Abstract
Microswimmers such as bacteria exhibit large speed fluctuation when exploring their living environment. Here, we show that the bacterium Escherichia coli with a wide range of length speeds up beyond its free-swimming speed when passing through narrow and short confinement. The speedup is observed in two modes: for short bacteria with L <20 μm, the maximum speed occurs when the cell body leaves the confinement, but a flagellar bundle is still confined. For longer bacteria (L ≥ 20 μm), the maximum speed occurs when the middle of the cell, where the maximum number of flagellar bundles locate, is confined. The two speed-up modes are explained by a vanishing body drag and an increased flagella drag-a universal property of an "ideal swimmer." The spatial variance of speed can be quantitatively explained by a simple model based on the resistance matrix of a partially confined bacterium. The speed change depends on the distribution of motors, and the latter is confirmed by fluorescent imaging of flagellar hooks. By measuring the duration of slowdown and speedup, we find that the effective chemotaxis is biased in filamentous bacteria, which might benefit their survival. The experimental setup can be useful to study the motion of microswimmers near surfaces with different surface chemistry.
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Affiliation(s)
- Yuanfeng Yin
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Hsin-Tzu Yu
- Department of Physics and Center for Complex Systems, National Central University, Jhongli, Taoyuan City, Taiwan
| | - Hong Tan
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Hong Cai
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Hsuan-Yi Chen
- Department of Physics and Center for Complex Systems, National Central University, Jhongli, Taoyuan City, Taiwan; Institute of Physics, Academia Sinica, Taipei, Taiwan; Physics Division, National Center for Theoretical Sciences, Taipei, Taiwan
| | - Chien-Jung Lo
- Department of Physics and Center for Complex Systems, National Central University, Jhongli, Taoyuan City, Taiwan
| | - Shuo Guo
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China.
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18
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Coelho RCV, Araújo NAM, Telo da Gama MM. Dispersion of activity at an active-passive nematic interface. SOFT MATTER 2022; 18:7642-7653. [PMID: 36169262 DOI: 10.1039/d2sm00988a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Efficient nutrient mixing is crucial for the survival of bacterial colonies and other living systems known as active nematics. However, the dynamics of this mixing is non-trivial as there is a coupling between nutrients concentration and velocity field. To address this question, we solve the hydrodynamic equation for active nematics to model the bacterial swarms coupled to an advection-diffusion equation for the activity field, which is proportional to the concentration of nutrients. At the interface between active and passive nematics the activity field is transported by the interfacial flows and in turn it modifies them through the generation of active stresses. We find that the dispersion of this conserved activity field is subdiffusive due to the emergence of a barrier of negative defects at the active-passive interface, which hinders the propagation of the motile positive defects.
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Affiliation(s)
- Rodrigo C V Coelho
- Centro de Física Teórica e Computacional, Faculdade de Ciências, Universidade de Lisboa, P-1749-016 Lisboa, Portugal.
- Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, P-1749-016 Lisboa, Portugal
| | - Nuno A M Araújo
- Centro de Física Teórica e Computacional, Faculdade de Ciências, Universidade de Lisboa, P-1749-016 Lisboa, Portugal.
- Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, P-1749-016 Lisboa, Portugal
| | - Margarida M Telo da Gama
- Centro de Física Teórica e Computacional, Faculdade de Ciências, Universidade de Lisboa, P-1749-016 Lisboa, Portugal.
- Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, P-1749-016 Lisboa, Portugal
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19
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Wang H, Zou B, Su J, Wang D, Xu X. Variational methods and deep Ritz method for active elastic solids. SOFT MATTER 2022; 18:6015-6031. [PMID: 35920447 DOI: 10.1039/d2sm00404f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Variational methods have been widely used in soft matter physics for both static and dynamic problems. These methods are mostly based on two variational principles: the variational principle of minimum free energy (MFEVP) and Onsager's variational principle (OVP). Our interests lie in the applications of these variational methods to active matter physics. In our former work [H. Wang, T. Qian and X. Xu, Soft Matter, 2021, 17, 3634-3653], we have explored the applications of OVP-based variational methods for the modeling of active matter dynamics. In the present work, we explore variational (or energy) methods that are based on MFEVP for static problems in active elastic solids. We show that MFEVP can be used not only to derive equilibrium equations, but also to develop approximate solution methods, such as the Ritz method, for active solid statics. Moreover, the power of the Ritz-type method can be further enhanced using deep learning methods if we use deep neural networks to construct the trial functions of the variational problems. We then apply these variational methods and the deep Ritz method to study the spontaneous bending and contraction of a thin active circular plate that is induced by internal asymmetric active contraction. The circular plate is found to be bent towards its contracting side. The study of such a simple toy system gives implications for understanding the morphogenesis of solid-like confluent cell monolayers. In addition, we introduce a so-called activogravity length to characterize the importance of gravitational forces relative to internal active contraction in driving the bending of the active plate. When the lateral plate dimension is larger than the activogravity length (about 100 micron), gravitational forces become important. Such gravitaxis behaviors at multicellular scales may play significant roles in the morphogenesis and in the up-down symmetry broken during tissue development.
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Affiliation(s)
- Haiqin Wang
- Physics Program, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, China.
- Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Boyi Zou
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China
| | - Jian Su
- Physics Program, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, China.
| | - Dong Wang
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China
- Shenzhen International Center for Industrial and Applied Mathematics, Shenzhen Research Institute of Big Data, Shenzhen, Guangdong, 518172, China
| | - Xinpeng Xu
- Physics Program, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, China.
- Technion - Israel Institute of Technology, Haifa, 32000, Israel
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20
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Giomi L, Toner J, Sarkar N. Hydrodynamic theory of p-atic liquid crystals. Phys Rev E 2022; 106:024701. [PMID: 36109977 DOI: 10.1103/physreve.106.024701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
We formulate a comprehensive hydrodynamic theory of two-dimensional liquid crystals with generic p-fold rotational symmetry, also known as p-atics, of which nematics (p=2) and hexatics (p=6) are the two best known examples. Previous hydrodynamic theories of p-atics are characterized by continuous O(2) rotational symmetry, which is higher than the discrete rotational symmetry of p-atic phases. By contrast, here we demonstrate that the discrete rotational symmetry allows the inclusion of additional terms in the hydrodynamic equations, which, in turn, lead to novel phenomena, such as the possibility of flow alignment at high shear rates, even for p>2. Furthermore, we show that any finite imposed shear will induce long-ranged orientational order in any p-atic liquid crystal, in contrast to the quasi-long-ranged order that occurs in the absence of shear. The induced order parameter scales like a nonuniversal power of the applied shear rate at small shear rates.
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Affiliation(s)
- Luca Giomi
- Instituut-Lorentz, Universiteit Leiden, P.O. Box 9506, 2300 RA Leiden, The Netherlands
| | - John Toner
- Department of Physics and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, USA
| | - Niladri Sarkar
- Instituut-Lorentz, Universiteit Leiden, P.O. Box 9506, 2300 RA Leiden, The Netherlands
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21
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Li W, Li L, Shi Q, Yang M, Zheng N. Spontaneous population oscillation of confined active granular particles. SOFT MATTER 2022; 18:5459-5464. [PMID: 35822840 DOI: 10.1039/d2sm00134a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Spontaneous collective oscillation may emerge from seemingly irregular active matter systems. Here, we experimentally demonstrate a spontaneous population oscillation of active granular particles confined in two chambers connected by a narrow channel, and verify the intriguing behavior predicted in simulation [M. Paoluzzi, R. Di Leonardo and L. Angelani, Self-sustained density oscillations of swimming bacteria confined in microchambers, Phys. Rev. Lett., 2015, 115(18), 188303]. During the oscillation, the two chambers are alternately (nearly) filled up and emptied by the self-propelled particles in a periodic manner. We show that the stable unidirectional flow induced due to the confined channel and its periodic reversal triggered by the particle concentration difference between two chambers jointly give rise to the oscillatory collective behavior. Furthermore, we propose a minimal theoretical model that properly reproduces the experimental results without free parameters. This self-sustained collective oscillation could serve as a robust active granular clock, capable of providing rhythmic signals.
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Affiliation(s)
- Wenjian Li
- School of Physics, Beijing Institute of Technology, Beijing 100081, China.
| | - Longfei Li
- School of Physics, Beijing Institute of Technology, Beijing 100081, China.
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Qingfan Shi
- School of Physics, Beijing Institute of Technology, Beijing 100081, China.
| | - Mingcheng Yang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China.
| | - Ning Zheng
- School of Physics, Beijing Institute of Technology, Beijing 100081, China.
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22
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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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23
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Li L, Liu P, Chen K, Zheng N, Yang M. Active depletion torque between two passive rods. SOFT MATTER 2022; 18:4265-4272. [PMID: 35609282 DOI: 10.1039/d2sm00469k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The active depletion torque experienced by two anisotropic objects in an active bath is a conceptional generalization of the equilibrium entropic torque. Using Brownian dynamics simulations, we compute the active depletion torque suffered by two passive rods immersed in an ensemble of active Brownian particles. Our results demonstrate that the active depletion torque is qualitatively different from its passive counterpart. Interestingly, we find that the active depletion torque can be greatly affected by the external constraint applied on the rotational degree of freedom of the rods, and even the direction may be changed with the orientational constraint, which is in contrast to the equilibrium depletion torque. The main reason for the remarkable features of the active depletion torque is that the active particles can significantly accumulate in the vicinity of the rods due to persistent self-propulsion, which is sensitively dependent on the constraint strength and the rod configurations. Our findings could be relevant for understanding the self-assembly and dynamics of anisotropic macromolecules in living environments.
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Affiliation(s)
- Longfei Li
- School of Physics, Beijing Institute of Technology, Beijing 100081, China.
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Peng Liu
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Ke Chen
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Ning Zheng
- School of Physics, Beijing Institute of Technology, Beijing 100081, China.
| | - Mingcheng Yang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
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24
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Solon A, Chaté H, Toner J, Tailleur J. Susceptibility of Polar Flocks to Spatial Anisotropy. PHYSICAL REVIEW LETTERS 2022; 128:208004. [PMID: 35657869 DOI: 10.1103/physrevlett.128.208004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
We study the effect of spatial anisotropy on polar flocks by investigating active q-state clock models in two dimensions. In contrast to the equilibrium case, we find that any amount of anisotropy is asymptotically relevant, drastically altering the phenomenology from that of the rotationally invariant case. All of the well-known physics of the Vicsek model, from giant density fluctuations to microphase separation, is replaced by that of the active Ising model, with short-range correlations and complete phase separation. These changes appear beyond a length scale that diverges in the q→∞ limit, so that the Vicsek-model phenomenology is observed in finite systems for weak enough anisotropy, i.e., sufficiently high q. We provide a scaling argument which explains why anisotropy has such different effects in the passive and active cases.
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Affiliation(s)
- Alexandre Solon
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, 75005 Paris, France
| | - Hugues Chaté
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, 75005 Paris, France
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- Computational Science Research Center, Beijing 100094, China
| | - John Toner
- Department of Physics and Institute for Fundamental Science, University of Oregon, Eugene, Oregon 97403, USA
| | - Julien Tailleur
- Université de Paris, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, 75205 Paris, France
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25
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Chen J, Ren Y, Huang WL, Zhang L, Li J. Multilevel Mesoscale Complexities in Mesoregimes: Challenges in Chemical and Biochemical Engineering. Annu Rev Chem Biomol Eng 2022; 13:431-455. [PMID: 35378042 DOI: 10.1146/annurev-chembioeng-092220-115031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review discusses the complex behaviors in diverse chemical and biochemical systems to elucidate their commonalities and thus help develop a mesoscience methodology to address the complexities in even broader topics. This could possibly build a new scientific paradigm for different disciplines and could meanwhile provide effective tools to tackle the big challenges in various fields, thus paving a path toward combining the paradigm shift in science with the breakthrough in technique developments. Starting with our relatively fruitful understanding of chemical systems, the discussion focuses on the relatively pristine but very intriguing biochemical systems. It is recognized that diverse complexities are multilevel in nature, with each level being multiscale and the complexity emerging always at mesoscales in mesoregimes. Relevant advances in theoretical understandings and mathematical tools are summarized as well based on case studies, and the convergence between physics and mathematics is highlighted. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Jianhua Chen
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, People's Republic of China;
| | - Ying Ren
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, People's Republic of China;
| | - Wen Lai Huang
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, People's Republic of China;
| | - Lin Zhang
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, People's Republic of China;
| | - Jinghai Li
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, People's Republic of China;
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26
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Zhang R, Mozaffari A, de Pablo JJ. Logic operations with active topological defects. SCIENCE ADVANCES 2022; 8:eabg9060. [PMID: 35196084 PMCID: PMC8865799 DOI: 10.1126/sciadv.abg9060] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 12/30/2021] [Indexed: 05/31/2023]
Abstract
Logic operations performed by semiconductor-based transistors are the basis of modern computing. There is considerable interest in creating autonomous materials systems endowed with the capability to make decisions. In this work, we introduce the concept of using topological defects in active matter to perform logic operations. When an extensile active stress in a nematic liquid crystal is turned on, +1/2 defects can self-propel, in analogy to electron transport under a voltage gradient. By relying on hydrodynamic simulations of active nematics, we demonstrate that patterns of activity, when combined with surfaces imparting certain orientations, can be used to control the formation and transport of +1/2 defects. We further show that asymmetric high- and low-activity patterns can be used to create effective defect gates, tunnels, and amplifiers. The proposed active systems offer the potential to perform computations and transmit information in active soft materials, including actin-, tubulin-, and cell-based systems.
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Affiliation(s)
- Rui Zhang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
- Department of Physics, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR
| | - Ali Mozaffari
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
- OpenEye Scientific Software, Inc., 9 Bisbee Court Suite D, Santa Fe, New Mexico 87508, USA
| | - Juan J. de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
- Materials Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
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27
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Palmer B, Chen S, Govan P, Yan W, Gao T. Understanding topological defects in fluidized dry active nematics. SOFT MATTER 2022; 18:1013-1018. [PMID: 35018951 DOI: 10.1039/d1sm01405f] [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
Dense assemblies of self-propelling rods (SPRs) may exhibit fascinating collective behaviors and anomalous physical properties that are far away from equilibrium. Using large-scale Brownian dynamics simulations, we investigate the dynamics of disclination defects in 2D fluidized swarming motions of dense dry SPRs (i.e., without hydrodynamic effects) that form notable local positional topological structures that are reminiscent of smectic order. We find the deformations of smectic-like rod layers can create unique polar structures that lead to slow translations and rotations of ±1/2-order defects, which are fundamentally different from the fast streaming defect motions observed in wet active matter. We measure and characterize the statistical properties of topological defects and reveal their connections with the coherent structures. Furthermore, we construct a bottom-up active-liquid-crystal model to analyze the instability of polar lanes, which effectively leads to defect formation between interlocked polar lanes and serves as the origin of the large-scale swarming motions.
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Affiliation(s)
- Bryce Palmer
- Department of Mechanical Engineering, Michigan State University, East Lansing, MI 48864, USA.
| | - Sheng Chen
- Department of Mechanical Engineering, Michigan State University, East Lansing, MI 48864, USA.
- Department of Biomedical Engineering, Yale University, West Haven, CT 06516, USA
| | - Patrick Govan
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48864, USA
| | - Wen Yan
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Tong Gao
- Department of Mechanical Engineering, Michigan State University, East Lansing, MI 48864, USA.
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48864, USA
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28
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Liu ZT, Shi Y, Zhao Y, Chaté H, Shi XQ, Zhang TH. Activity waves and freestanding vortices in populations of subcritical Quincke rollers. Proc Natl Acad Sci U S A 2021; 118:e2104724118. [PMID: 34588304 PMCID: PMC8501844 DOI: 10.1073/pnas.2104724118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2021] [Indexed: 11/18/2022] Open
Abstract
Virtually all of the many active matter systems studied so far are made of units (biofilaments, cells, colloidal particles, robots, animals, etc.) that move even when they are alone or isolated. Their collective properties continue to fascinate, and we now understand better how they are unique to the bulk transduction of energy into work. Here we demonstrate that systems in which isolated but potentially active particles do not move can exhibit specific and remarkable collective properties. Combining experiments, theory, and numerical simulations, we show that such subcritical active matter can be realized with Quincke rollers, that is, dielectric colloidal particles immersed in a conducting fluid subjected to a vertical DC electric field. Working below the threshold field value marking the onset of motion for a single colloid, we find fast activity waves, reminiscent of excitable systems, and stable, arbitrarily large self-standing vortices made of thousands of particles moving at the same speed. Our theoretical model accounts for these phenomena and shows how they can arise in the absence of confining boundaries and individual chirality. We argue that our findings imply that a faithful description of the collective properties of Quincke rollers need to consider the fluid surrounding particles.
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Affiliation(s)
- Zeng Tao Liu
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
- School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Yan Shi
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
- School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Yongfeng Zhao
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
- School of Physical Science and Technology, Soochow University, Suzhou 215006, China
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hugues Chaté
- Service de Physique de l'Etat Condensé, Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France;
- Computational Science Research Center, Beijing 100193, China
| | - Xia-Qing Shi
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China;
- School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Tian Hui Zhang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China;
- School of Physical Science and Technology, Soochow University, Suzhou 215006, China
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29
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Edge current and pairing order transition in chiral bacterial vortices. Proc Natl Acad Sci U S A 2021; 118:2107461118. [PMID: 34561308 DOI: 10.1073/pnas.2107461118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 12/21/2022] Open
Abstract
Bacterial suspensions show turbulence-like spatiotemporal dynamics and vortices moving irregularly inside the suspensions. Understanding these ordered vortices is an ongoing challenge in active matter physics, and their application to the control of autonomous material transport will provide significant development in microfluidics. Despite the extensive studies, one of the key aspects of bacterial propulsion has remained elusive: The motion of bacteria is chiral, i.e., it breaks mirror symmetry. Therefore, the mechanism of control of macroscopic active turbulence by microscopic chirality is still poorly understood. Here, we report the selective stabilization of chiral rotational direction of bacterial vortices in achiral circular microwells sealed by an oil/water interface. The intrinsic chirality of bacterial swimming near the top and bottom interfaces generates chiral collective motions of bacteria at the lateral boundary of the microwell that are opposite in directions. These edge currents grow stronger as bacterial density increases, and, within different top and bottom interfaces, their competition leads to a global rotation of the bacterial suspension in a favored direction, breaking the mirror symmetry of the system. We further demonstrate that chiral edge current favors corotational configurations of interacting vortices, enhancing their ordering. The intrinsic chirality of bacteria is a key feature of the pairing order transition from active turbulence, and the geometric rule of pairing order transition may shed light on the strategy for designing chiral active matter.
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30
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Submersed micropatterned structures control active nematic flow, topology, and concentration. Proc Natl Acad Sci U S A 2021; 118:2106038118. [PMID: 34535551 DOI: 10.1073/pnas.2106038118] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2021] [Indexed: 01/10/2023] Open
Abstract
Coupling between flows and material properties imbues rheological matter with its wide-ranging applicability, hence the excitement for harnessing the rheology of active fluids for which internal structure and continuous energy injection lead to spontaneous flows and complex, out-of-equilibrium dynamics. We propose and demonstrate a convenient, highly tunable method for controlling flow, topology, and composition within active films. Our approach establishes rheological coupling via the indirect presence of fully submersed micropatterned structures within a thin, underlying oil layer. Simulations reveal that micropatterned structures produce effective virtual boundaries within the superjacent active nematic film due to differences in viscous dissipation as a function of depth. This accessible method of applying position-dependent, effective dissipation to the active films presents a nonintrusive pathway for engineering active microfluidic systems.
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31
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Sampat PB, Mishra S. Polar swimmers induce several phases in active nematics. Phys Rev E 2021; 104:024130. [PMID: 34525577 DOI: 10.1103/physreve.104.024130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/16/2021] [Indexed: 01/04/2023]
Abstract
Swimming bacteria in passive nematics in the form of lyotropic liquid crystals are defined as a new class of active matter known as living liquid crystals in recent studies. It has also been shown that liquid crystal solutions are promising candidates for trapping and detecting bacteria. We ask the question, can a similar class of matter be designed for background nematics which are also active? Hence, we developed a minimal model for the mixture of polar particles in active nematics. It is found that the active nematics in such a mixture are highly sensitive to the presence of polar particles and show the formation of large scale higher order structures for a relatively low polar particle density. Upon increasing the density of polar particles, different phases of active nematics are found and it is observed that the system shows two phase transitions. The first phase transition is a first order transition from quasi-long-ranged ordered active nematics to disordered active nematics with larger scale structures. On further increasing density of polar particles, the system transitions to a third phase, where polar particles form large, mutually aligned clusters. These clusters sweep the whole system and enforce local order in the nematics. The current study can be helpful for detecting the presence of very low densities of polar swimmers in active nematics and can be used to design and control different structures in active nematics.
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Affiliation(s)
- Pranay Bimal Sampat
- Department of Physics, Indian Institute of Technology (BHU), Varanasi, U.P. - 221005 India
| | - Shradha Mishra
- Department of Physics, Indian Institute of Technology (BHU), Varanasi, U.P. - 221005 India
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32
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Rouzaire Y, Levis D. Defect Superdiffusion and Unbinding in a 2D XY Model of Self-Driven Rotors. PHYSICAL REVIEW LETTERS 2021; 127:088004. [PMID: 34477446 DOI: 10.1103/physrevlett.127.088004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
We consider a nonequilibrium extension of the 2D XY model, equivalent to the noisy Kuramoto model of synchronization with short-range coupling, where rotors sitting on a square lattice are self-driven by random intrinsic frequencies. We study the static and dynamic properties of topological defects (vortices) and establish how self-spinning affects the Berezenskii-Kosterlitz-Thouless phase transition scenario. The nonequilibrium drive breaks the quasi-long-range ordered phase of the 2D XY model into a mosaic of ordered domains of controllable size and results in self-propelled vortices that generically unbind at any temperature, featuring superdiffusion ⟨r^{2}(t)⟩∼t^{3/2} with a Gaussian distribution of displacements. Our work provides a simple framework to investigate topological defects in nonequilibrium matter and sheds new light on the problem of synchronization of locally coupled oscillators.
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Affiliation(s)
- Ylann Rouzaire
- Institute of Physics, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Departament de Física de la Materia Condensada, Universitat de Barcelona, Martí i Franquès 1, E08028 Barcelona, Spain
| | - Demian Levis
- Departament de Física de la Materia Condensada, Universitat de Barcelona, Martí i Franquès 1, E08028 Barcelona, Spain
- UBICS University of Barcelona Institute of Complex Systems, Martí i Franquès 1, E08028 Barcelona, Spain
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33
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Mahault B, Chaté H. Long-Range Nematic Order in Two-Dimensional Active Matter. PHYSICAL REVIEW LETTERS 2021; 127:048003. [PMID: 34355959 DOI: 10.1103/physrevlett.127.048003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Working in two space dimensions, we show that the orientational order emerging from self-propelled polar particles aligning nematically is quasi-long-ranged beyond ℓ_{r}, the scale associated to induced velocity reversals, which is typically extremely large and often cannot even be measured. Below ℓ_{r}, nematic order is long-range. We construct and study a hydrodynamic theory for this de facto phase and show that its structure and symmetries differ from conventional descriptions of active nematics. We check numerically our theoretical predictions, in particular the presence of π-symmetric propagative sound modes, and provide estimates of all scaling exponents governing long-range space-time correlations.
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Affiliation(s)
- Benoît Mahault
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen, Germany
| | - Hugues Chaté
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- Computational Science Research Center, Beijing 100193, China
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34
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Mitchell KA, Tan AJ, Arteaga J, Hirst LS. Fractal generation in a two-dimensional active-nematic fluid. CHAOS (WOODBURY, N.Y.) 2021; 31:073125. [PMID: 34340333 DOI: 10.1063/5.0050795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/18/2021] [Indexed: 06/13/2023]
Abstract
Active fluids, composed of individual self-propelled agents, can generate complex large-scale coherent flows. A particularly important laboratory realization of such an active fluid is a system composed of microtubules, aligned in a quasi-two-dimensional (2D) nematic phase and driven by adenosine-triphosphate-fueled kinesin motor proteins. This system exhibits robust chaotic advection and gives rise to a pronounced fractal structure in the nematic contours. We characterize such experimentally derived fractals using the power spectrum and discover that the power spectrum decays as k-β for large wavenumbers k. The parameter β is measured for several experimental realizations. Though β is effectively constant in time, it does vary with experimental parameters, indicating differences in the scale-free behavior of the microtubule-based active nematic. Though the fractal patterns generated in this active system are reminiscent of passively advected dye in 2D chaotic flows, the underlying mechanism for fractal generation is more subtle. We provide a simple, physically inspired mathematical model of fractal generation in this system that relies on the material being locally compressible, though the total area of the material is conserved globally. The model also requires that large-scale density variations are injected into the material periodically. The model reproduces the power-spectrum decay k-β seen in experiments. Linearizing the model of fractal generation about the equilibrium density, we derive an analytic relationship between β and a single dimensionless quantity r, which characterizes the compressibility.
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Affiliation(s)
- Kevin A Mitchell
- Physics Department, University of California, Merced, Merced, California 95344, USA
| | - Amanda J Tan
- Physics Department, University of California, Merced, Merced, California 95344, USA
| | - Jorge Arteaga
- Physics Department, University of California, Merced, Merced, California 95344, USA
| | - Linda S Hirst
- Physics Department, University of California, Merced, Merced, California 95344, USA
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35
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Unraveling hidden interactions in complex systems with deep learning. Sci Rep 2021; 11:12804. [PMID: 34140551 PMCID: PMC8211832 DOI: 10.1038/s41598-021-91878-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/26/2021] [Indexed: 11/08/2022] Open
Abstract
Rich phenomena from complex systems have long intrigued researchers, and yet modeling system micro-dynamics and inferring the forms of interaction remain challenging for conventional data-driven approaches, being generally established by scientists with human ingenuity. In this study, we propose AgentNet, a model-free data-driven framework consisting of deep neural networks to reveal and analyze the hidden interactions in complex systems from observed data alone. AgentNet utilizes a graph attention network with novel variable-wise attention to model the interaction between individual agents, and employs various encoders and decoders that can be selectively applied to any desired system. Our model successfully captured a wide variety of simulated complex systems, namely cellular automata (discrete), the Vicsek model (continuous), and active Ornstein-Uhlenbeck particles (non-Markovian) in which, notably, AgentNet's visualized attention values coincided with the true variable-wise interaction strengths and exhibited collective behavior that was absent in the training data. A demonstration with empirical data from a flock of birds showed that AgentNet could identify hidden interaction ranges exhibited by real birds, which cannot be detected by conventional velocity correlation analysis. We expect our framework to open a novel path to investigating complex systems and to provide insight into general process-driven modeling.
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36
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Mozaffari A, Zhang R, Atzin N, de Pablo JJ. Defect Spirograph: Dynamical Behavior of Defects in Spatially Patterned Active Nematics. PHYSICAL REVIEW LETTERS 2021; 126:227801. [PMID: 34152186 DOI: 10.1103/physrevlett.126.227801] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 01/06/2021] [Accepted: 05/03/2021] [Indexed: 06/13/2023]
Abstract
Topological defects in active liquid crystals can be confined by introducing gradients of activity. Here, we examine the dynamical behavior of two defects confined by a sharp gradient of activity that separates an active circular region and a surrounding passive nematic material. Continuum simulations are used to explain how the interplay among energy injection into the system, hydrodynamic interactions, and frictional forces governs the dynamics of topologically required self-propelling +1/2 defects. Our findings are rationalized in terms of a phase diagram for the dynamical response of defects in terms of activity and frictional damping strength. Different regions of the underlying phase diagram correspond to distinct dynamical modes, namely immobile defects, steady rotation of defects, bouncing defects, bouncing-cruising defects, dancing defects, and multiple defects with irregular dynamics. These dynamic states raise the prospect of generating synchronized defect arrays for microfluidic applications.
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Affiliation(s)
- Ali Mozaffari
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
| | - Rui Zhang
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
- Department of Physics, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Noe Atzin
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
| | - Juan J de Pablo
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
- Center for Molecular Engineering, Argonne National Laboratory, Lemont, Illinois 60439, USA
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37
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Zhang R, Redford SA, Ruijgrok PV, Kumar N, Mozaffari A, Zemsky S, Dinner AR, Vitelli V, Bryant Z, Gardel ML, de Pablo JJ. Spatiotemporal control of liquid crystal structure and dynamics through activity patterning. NATURE MATERIALS 2021; 20:875-882. [PMID: 33603187 PMCID: PMC8404743 DOI: 10.1038/s41563-020-00901-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 12/03/2020] [Indexed: 05/26/2023]
Abstract
Active materials are capable of converting free energy into mechanical work to produce autonomous motion, and exhibit striking collective dynamics that biology relies on for essential functions. Controlling those dynamics and transport in synthetic systems has been particularly challenging. Here, we introduce the concept of spatially structured activity as a means of controlling and manipulating transport in active nematic liquid crystals consisting of actin filaments and light-sensitive myosin motors. Simulations and experiments are used to demonstrate that topological defects can be generated at will and then constrained to move along specified trajectories by inducing local stresses in an otherwise passive material. These results provide a foundation for the design of autonomous and reconfigurable microfluidic systems where transport is controlled by modulating activity with light.
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Affiliation(s)
- Rui Zhang
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
- Department of Physics, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Steven A Redford
- The Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- James Franck Institute, The University of Chicago, Chicago, IL, USA
| | - Paul V Ruijgrok
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Nitin Kumar
- James Franck Institute, The University of Chicago, Chicago, IL, USA
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, India
| | - Ali Mozaffari
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
| | - Sasha Zemsky
- Program in Biophysics, Stanford University, Stanford, CA, USA
| | - Aaron R Dinner
- James Franck Institute, The University of Chicago, Chicago, IL, USA
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Vincenzo Vitelli
- James Franck Institute, The University of Chicago, Chicago, IL, USA
- Department of Physics, The University of Chicago, Chicago, IL, USA
| | - Zev Bryant
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University Medical Center, Stanford, CA, USA
| | - Margaret L Gardel
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA.
- James Franck Institute, The University of Chicago, Chicago, IL, USA.
- Department of Physics, The University of Chicago, Chicago, IL, USA.
| | - Juan J de Pablo
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA.
- Center for Molecular Engineering, Argonne National Laboratory, Lemont, IL, USA.
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38
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Wang H, Qian T, Xu X. Onsager's variational principle in active soft matter. SOFT MATTER 2021; 17:3634-3653. [PMID: 33480912 DOI: 10.1039/d0sm02076a] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Onsagers variational principle (OVP) was originally proposed by Lars Onsager in 1931 [L. Onsager, Phys. Rev., 1931, 37, 405]. This fundamental principle provides a very powerful tool for formulating thermodynamically consistent models. It can also be employed to find approximate solutions, especially in the study of soft matter dynamics. In this work, OVP is extended and applied to the dynamic modeling of active soft matter such as suspensions of bacteria and aggregates of animal cells. We first extend the general formulation of OVP to active matter dynamics where active forces are included as external non-conservative forces. We then use OVP to analyze the directional motion of individual active units: a molecular motor walking on a stiff biofilament and a toy two-sphere microswimmer. Next we use OVP to formulate a diffuse-interface model for an active polar droplet on a solid substrate. In addition to the generalized hydrodynamic equations for active polar fluids in the bulk region, we have also derived thermodynamically consistent boundary conditions. Finally, we consider the dynamics of a thin active polar droplet under the lubrication approximation. We use OVP to derive a generalized thin film equation and then employ OVP as an approximation tool to find the spreading laws for the thin active polar droplet. By incorporating the activity of biological systems into OVP, we develop a general approach to construct thermodynamically consistent models for better understanding the emergent behaviors of individual animal cells and cell aggregates or tissues.
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Affiliation(s)
- Haiqin Wang
- Technion - Israel Institute of Technology, Haifa, 32000, Israel
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39
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Peng Y, Liu Z, Cheng X. Imaging the emergence of bacterial turbulence: Phase diagram and transition kinetics. SCIENCE ADVANCES 2021; 7:eabd1240. [PMID: 33893094 PMCID: PMC8064640 DOI: 10.1126/sciadv.abd1240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 03/05/2021] [Indexed: 05/12/2023]
Abstract
We experimentally study the emergence of collective bacterial swimming, a phenomenon often referred to as bacterial turbulence. A phase diagram of the flow of 3D Escherichia coli suspensions spanned by bacterial concentration, the swimming speed of bacteria, and the number fraction of active swimmers is systematically mapped, which shows quantitative agreement with kinetic theories and demonstrates the dominant role of hydrodynamic interactions in bacterial collective swimming. We trigger bacterial turbulence by suddenly increasing the swimming speed of light-powered bacteria and image the transition to the turbulence in real time. Our experiments identify two unusual kinetic pathways, i.e., the one-step transition with long incubation periods near the phase boundary and the two-step transition driven by long-wavelength instabilities deep inside the turbulent phase. Our study provides not only a quantitative verification of existing theories but also insights into interparticle interactions and transition kinetics of bacterial turbulence.
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Affiliation(s)
- Yi Peng
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhengyang Liu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Xiang Cheng
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA.
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40
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Clusella P, Pastor-Satorras R. Phase transitions on a class of generalized Vicsek-like models of collective motion. CHAOS (WOODBURY, N.Y.) 2021; 31:043116. [PMID: 34251260 DOI: 10.1063/5.0046926] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/18/2021] [Indexed: 06/13/2023]
Abstract
Systems composed of interacting self-propelled particles (SPPs) display different forms of order-disorder phase transitions relevant to collective motion. In this paper, we propose a generalization of the Vicsek model characterized by an angular noise term following an arbitrary probability density function, which might depend on the state of the system and thus have a multiplicative character. We show that the well established vectorial Vicsek model can be expressed in this general formalism by deriving the corresponding angular probability density function, as well as we propose two new multiplicative models consisting of bivariate Gaussian and wrapped Gaussian distributions. With the proposed formalism, the mean-field system can be solved using the mean resultant length of the angular stochastic term. Accordingly, when the SPPs interact globally, the character of the phase transition depends on the choice of the noise distribution, being first order with a hybrid scaling for the vectorial and wrapped Gaussian distributions, and second order for the bivariate Gaussian distribution. Numerical simulations reveal that this scenario also holds when the interactions among SPPs are given by a static complex network. On the other hand, using spatial short-range interactions displays, in all the considered instances, a discontinuous transition with a coexistence region, consistent with the original formulation of the Vicsek model.
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Affiliation(s)
- Pau Clusella
- Departament de Física, Universitat Politècnica de Catalunya, Campus Nord B4, 08034 Barcelona, Spain
| | - Romualdo Pastor-Satorras
- Departament de Física, Universitat Politècnica de Catalunya, Campus Nord B4, 08034 Barcelona, Spain
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41
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Learning active nematics one step at a time. Proc Natl Acad Sci U S A 2021; 118:2102169118. [PMID: 33707217 DOI: 10.1073/pnas.2102169118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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42
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Colen J, Han M, Zhang R, Redford SA, Lemma LM, Morgan L, Ruijgrok PV, Adkins R, Bryant Z, Dogic Z, Gardel ML, de Pablo JJ, Vitelli V. Machine learning active-nematic hydrodynamics. Proc Natl Acad Sci U S A 2021; 118:e2016708118. [PMID: 33653956 PMCID: PMC7958379 DOI: 10.1073/pnas.2016708118] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrodynamic theories effectively describe many-body systems out of equilibrium in terms of a few macroscopic parameters. However, such parameters are difficult to determine from microscopic information. Seldom is this challenge more apparent than in active matter, where the hydrodynamic parameters are in fact fields that encode the distribution of energy-injecting microscopic components. Here, we use active nematics to demonstrate that neural networks can map out the spatiotemporal variation of multiple hydrodynamic parameters and forecast the chaotic dynamics of these systems. We analyze biofilament/molecular-motor experiments with microtubule/kinesin and actin/myosin complexes as computer vision problems. Our algorithms can determine how activity and elastic moduli change as a function of space and time, as well as adenosine triphosphate (ATP) or motor concentration. The only input needed is the orientation of the biofilaments and not the coupled velocity field which is harder to access in experiments. We can also forecast the evolution of these chaotic many-body systems solely from image sequences of their past using a combination of autoencoders and recurrent neural networks with residual architecture. In realistic experimental setups for which the initial conditions are not perfectly known, our physics-inspired machine-learning algorithms can surpass deterministic simulations. Our study paves the way for artificial-intelligence characterization and control of coupled chaotic fields in diverse physical and biological systems, even in the absence of knowledge of the underlying dynamics.
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Affiliation(s)
- Jonathan Colen
- Department of Physics, University of Chicago, Chicago, IL 60637
- James Franck Institute, University of Chicago, Chicago, IL 60637
| | - Ming Han
- James Franck Institute, University of Chicago, Chicago, IL 60637
- Pritzer School of Molecular Engineering, University of Chicago, Chicago, IL 60637
| | - Rui Zhang
- Pritzer School of Molecular Engineering, University of Chicago, Chicago, IL 60637
- Department of Physics, Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, People's Republic of China
| | - Steven A Redford
- James Franck Institute, University of Chicago, Chicago, IL 60637
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637
| | - Linnea M Lemma
- Department of Physics, Brandeis University, Waltham, MA 02454
- Department of Physics, University of California, Santa Barbara, CA 92111
| | - Link Morgan
- Department of Physics, University of California, Santa Barbara, CA 92111
| | - Paul V Ruijgrok
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Raymond Adkins
- Department of Physics, University of California, Santa Barbara, CA 92111
| | - Zev Bryant
- Department of Bioengineering, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University Medical Center, Stanford, CA 94305
| | - Zvonimir Dogic
- Department of Physics, University of California, Santa Barbara, CA 92111
| | - Margaret L Gardel
- Department of Physics, University of Chicago, Chicago, IL 60637
- James Franck Institute, University of Chicago, Chicago, IL 60637
| | - Juan J de Pablo
- Pritzer School of Molecular Engineering, University of Chicago, Chicago, IL 60637;
- Center for Molecular Engineering, Argonne National Laboratory, Lemont, IL 60439
| | - Vincenzo Vitelli
- Department of Physics, University of Chicago, Chicago, IL 60637;
- James Franck Institute, University of Chicago, Chicago, IL 60637
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43
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Yang S, Huang M, Zhao Y, Zhang HP. Controlling Cell Motion and Microscale Flow with Polarized Light Fields. PHYSICAL REVIEW LETTERS 2021; 126:058001. [PMID: 33605769 DOI: 10.1103/physrevlett.126.058001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/26/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
We investigate how light polarization affects the motion of photoresponsive algae, Euglena gracilis. In a uniformly polarized field, cells swim approximately perpendicular to the polarization direction and form a nematic state with zero mean velocity. When light polarization varies spatially, cell motion is modulated by local polarization. In such light fields, cells exhibit complex spatial distribution and motion patterns which are controlled by topological properties of the underlying fields; we further show that ordered cell swimming can generate directed transporting fluid flow. Experimental results are quantitatively reproduced by an active Brownian particle model in which particle motion direction is nematically coupled to local light polarization.
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Affiliation(s)
- Siyuan Yang
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingji Huang
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yongfeng Zhao
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - H P Zhang
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, China
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44
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Kumar S, Mishra S. Active nematics with quenched disorder. Phys Rev E 2020; 102:052609. [PMID: 33327090 DOI: 10.1103/physreve.102.052609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 11/02/2020] [Indexed: 11/07/2022]
Abstract
We introduce a two-dimensional active nematic with quenched disorder. We write the coarse-grained hydrodynamic equations of motion for slow variables, viz. density and orientation. Disorder strength is tuned from zero to large values. Results from the numerical solution of equations of motion as well as the calculation of two-point orientation correlation function using linear approximation shows that the ordered steady state follows a disorder dependent crossover from quasi-long-range order to short-range order. Such crossover is due to the pinning of ±1/2 topological defects in the presence of finite disorder, which breaks the system in uncorrelated domains. Finite disorder slows the dynamics of +1/2 defect, and it leads to slower growth dynamics. The two-point correlation functions for the density and orientation fields show good dynamic scaling but no static scaling for the different disorder strengths. Our findings can motivate experimentalists to verify the results and find applications in living and artificial apolar systems in the presence of a quenched disorder.
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Affiliation(s)
- Sameer Kumar
- Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh 221005, India
| | - Shradha Mishra
- Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh 221005, India
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Clopés J, Gompper G, Winkler RG. Hydrodynamic interactions in squirmer dumbbells: active stress-induced alignment and locomotion. SOFT MATTER 2020; 16:10676-10687. [PMID: 33089276 DOI: 10.1039/d0sm01569e] [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
Hydrodynamic interactions are fundamental for the dynamics of swimming self-propelled particles. Specifically, bonds between microswimmers enforce permanent spatial proximity and, thus, enhance emergent correlations by microswimmer-specific flow fields. We employ the squirmer model to study the swimming behavior of microswimmer dumbbells by mesoscale hydrodynamic simulations, where the squirmers' rotational motion is geometrically unrestricted. An important aspect of the applied particle-based simulation approach-the multiparticle collision dynamics method-is the intrinsic account for thermal fluctuations. We find a strong effect of active stress on the motility of dumbbells. In particular, pairs of strong pullers exhibit orders of magnitude smaller swimming efficiency than pairs of pushers. This is a consequence of the inherent thermal fluctuations in combination with the strong coupling of the squirmers' rotational motion, which implies non-exponentially decaying auto- and cross-correlation functions of the propulsion directions, and active stress-dependent characteristic decay times. As a consequence, specific stationary-state relative alignments of the squirmer propulsion directions emerge, where pullers are preferentially aligned in an antiparallel manner along the bond vector, whereas pushers are preferentially aligned normal to the bond vector with a relative angle of approximately 60° at weak active stress, and one of the propulsion directions is aligned with the bond at strong active stress. The distinct differences between dumbbells comprised of pusher or pullers suggest means to control microswimmer assemblies for future microbot applications.
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Affiliation(s)
- Judit Clopés
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich and JARA, D-52425 Jülich, Germany.
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Thijssen K, Nejad MR, Yeomans JM. Role of Friction in Multidefect Ordering. PHYSICAL REVIEW LETTERS 2020; 125:218004. [PMID: 33275020 DOI: 10.1103/physrevlett.125.218004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/30/2020] [Accepted: 10/22/2020] [Indexed: 06/12/2023]
Abstract
We use continuum simulations to study the impact of friction on the ordering of defects in an active nematic. Even in a frictionless system, +1/2 defects tend to align side by side and orient antiparallel reflecting their propensity to form, and circulate with, flow vortices. Increasing friction enhances the effectiveness of the defect-defect interactions, and defects form dynamically evolving, large-scale, positionally, and orientationally ordered structures, which can be explained as a competition between hexagonal packing, preferred by the -1/2 defects, and rectangular packing, preferred by the +1/2 defects.
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Affiliation(s)
- Kristian Thijssen
- The Rudolf Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Mehrana R Nejad
- The Rudolf Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Julia M Yeomans
- The Rudolf Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
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Affiliation(s)
- Roland G. Winkler
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Gerhard Gompper
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
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48
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Abstract
We introduce and shortly summarize a variety of more recent aspects of lyotropic liquid crystals (LLCs), which have drawn the attention of the liquid crystal and soft matter community and have recently led to an increasing number of groups studying this fascinating class of materials, alongside their normal activities in thermotopic LCs. The diversity of topics ranges from amphiphilic to inorganic liquid crystals, clays and biological liquid crystals, such as viruses, cellulose or DNA, to strongly anisotropic materials such as nanotubes, nanowires or graphene oxide dispersed in isotropic solvents. We conclude our admittedly somewhat subjective overview with materials exhibiting some fascinating properties, such as chromonics, ferroelectric lyotropics and active liquid crystals and living lyotropics, before we point out some possible and emerging applications of a class of materials that has long been standing in the shadow of the well-known applications of thermotropic liquid crystals, namely displays and electro-optic devices.
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49
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Liu P, Ye S, Ye F, Chen K, Yang M. Constraint Dependence of Active Depletion Forces on Passive Particles. PHYSICAL REVIEW LETTERS 2020; 124:158001. [PMID: 32357018 DOI: 10.1103/physrevlett.124.158001] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/22/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Using simulations and experiments, we demonstrate that the effective interaction between passive particles in an active bath substantially depends on an external constraint suffered by the passive particles. Particularly, the effective interaction between two free passive particles, which is directly measured in simulation, is qualitatively different from the one between two fixed particles. Moreover, we find that the friction experienced by the passive particles-a kinematic constraint-similarly influences the effective interaction. These remarkable features are in significant contrast to the equilibrium cases, and mainly arise from the accumulation of the active particles near the concave gap formed by the passive spheres. This constraint dependence not only deepens our understanding of the "active depletion force," but also provides an additional tool to tune the effective interactions in an active bath.
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Affiliation(s)
- Peng Liu
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Simin Ye
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangfu Ye
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Ke Chen
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Mingcheng Yang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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50
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Duclos G, Adkins R, Banerjee D, Peterson MSE, Varghese M, Kolvin I, Baskaran A, Pelcovits RA, Powers TR, Baskaran A, Toschi F, Hagan MF, Streichan SJ, Vitelli V, Beller DA, Dogic Z. Topological structure and dynamics of three-dimensional active nematics. Science 2020; 367:1120-1124. [PMID: 32139540 DOI: 10.1126/science.aaz4547] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/07/2020] [Indexed: 12/30/2022]
Abstract
Topological structures are effective descriptors of the nonequilibrium dynamics of diverse many-body systems. For example, motile, point-like topological defects capture the salient features of two-dimensional active liquid crystals composed of energy-consuming anisotropic units. We dispersed force-generating microtubule bundles in a passive colloidal liquid crystal to form a three-dimensional active nematic. Light-sheet microscopy revealed the temporal evolution of the millimeter-scale structure of these active nematics with single-bundle resolution. The primary topological excitations are extended, charge-neutral disclination loops that undergo complex dynamics and recombination events. Our work suggests a framework for analyzing the nonequilibrium dynamics of bulk anisotropic systems as diverse as driven complex fluids, active metamaterials, biological tissues, and collections of robots or organisms.
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Affiliation(s)
- Guillaume Duclos
- Department of Physics, Brandeis University, Waltham, MA 02453, USA
| | - Raymond Adkins
- Department of Physics, University of California, Santa Barbara, CA 93111, USA
| | - Debarghya Banerjee
- Max Planck Institute for Dynamics and Self-Organization, 37077 Göttingen, Germany.,Instituut-Lorentz, Universiteit Leiden, 2300 RA Leiden, Netherlands
| | | | - Minu Varghese
- Department of Physics, Brandeis University, Waltham, MA 02453, USA
| | - Itamar Kolvin
- Department of Physics, University of California, Santa Barbara, CA 93111, USA
| | - Arvind Baskaran
- Department of Physics, Brandeis University, Waltham, MA 02453, USA
| | | | - Thomas R Powers
- School of Engineering, Brown University, Providence, RI 02912, USA.,Department of Physics, Brown University, Providence, RI 02912, USA
| | - Aparna Baskaran
- Department of Physics, Brandeis University, Waltham, MA 02453, USA
| | - Federico Toschi
- Department of Applied Physics, Eindhoven University of Technology, 5600 MB Eindhoven, Netherlands.,Instituto per le Applicazioni del Calcolo CNR, 00185 Rome, Italy
| | - Michael F Hagan
- Department of Physics, Brandeis University, Waltham, MA 02453, USA
| | | | - Vincenzo Vitelli
- James Frank Institute and Department of Physics, The University of Chicago, Chicago, IL 60637, USA
| | - Daniel A Beller
- Department of Physics, University of California, Merced, CA 95343, USA.
| | - Zvonimir Dogic
- Department of Physics, Brandeis University, Waltham, MA 02453, USA. .,Department of Physics, University of California, Santa Barbara, CA 93111, USA
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