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Mandal R, Jaramillo SS, Sollich P. Robustness of traveling states in generic nonreciprocal mixtures. Phys Rev E 2024; 109:L062602. [PMID: 39020950 DOI: 10.1103/physreve.109.l062602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/26/2024] [Indexed: 07/20/2024]
Abstract
Emergent nonreciprocal interactions violating Newton's third law are widespread in out-of-equilibrium systems. Phase separating mixtures with such interactions exhibit traveling states with no equilibrium counterpart. Using extensive Brownian dynamics simulations, we investigate the existence and stability of such traveling states in a generic nonreciprocal particle system. By varying a broad range of parameters including aggregate state of mixture components, diffusivity, degree of nonreciprocity, effective spatial dimension and density, we determine that traveling states do exist below the predator-prey regime, but nonetheless are only found in a narrow region of the parameter space. Our work also sheds light on the physical mechanisms for the disappearance of traveling states when relevant parameters are being varied, and has implications for a range of nonequilibrium systems including nonreciprocal phase separating mixtures, nonequilibrium pattern formation and predator-prey models.
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Hardoüin J, Laurent J, Lopez-Leon T, Ignés-Mullol J, Sagués F. Active microfluidic transport in two-dimensional handlebodies. SOFT MATTER 2020; 16:9230-9241. [PMID: 32926045 DOI: 10.1039/d0sm00610f] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Unlike traditional nematic liquid crystals, which adopt ordered equilibrium configurations compatible with the topological constraints imposed by the boundaries, active nematics are intrinsically disordered because of their self-sustained internal flows. Controlling the flow patterns of active nematics remains a limiting step towards their use as functional materials. Here we show that confining a tubulin-kinesin active nematic to a network of connected annular microfluidic channels enables controlled directional flows and autonomous transport. In single annular channels, for narrow widths, the typically chaotic streams transform into well-defined circulating flows, whose direction or handedness can be controlled by introducing asymmetric corrugations on the channel walls. The dynamics is altered when two or three annular channels are interconnected. These more complex topologies lead to scenarios of synchronization, anti-correlation, and frustration of the active flows, and to the stabilisation of high topological singularities in both the flow field and the orientational field of the material. Controlling textures and flows in these microfluidic platforms opens unexplored perspectives towards their application in biotechnology and materials science.
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Affiliation(s)
- Jérôme Hardoüin
- Departament de Ciència de Materials i Química Física, Universitat de Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain. and Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Barcelona, Spain
| | - Justine Laurent
- Laboratoire de Physique et Mécanique des Milieux hétérogènes (PMMH), CNRS, ESPCI Paris, PSL Research University, Paris, France and Laboratoire Gulliver, UMR CNRS 7083, ESPCI Paris, PSL Research University, Paris, France
| | - Teresa Lopez-Leon
- Laboratoire de Physique et Mécanique des Milieux hétérogènes (PMMH), CNRS, ESPCI Paris, PSL Research University, Paris, France and Laboratoire Gulliver, UMR CNRS 7083, ESPCI Paris, PSL Research University, Paris, France
| | - Jordi Ignés-Mullol
- Departament de Ciència de Materials i Química Física, Universitat de Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain. and Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Barcelona, Spain
| | - Francesc Sagués
- Departament de Ciència de Materials i Química Física, Universitat de Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain. and Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Barcelona, Spain
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Sone K, Ashida Y. Anomalous Topological Active Matter. PHYSICAL REVIEW LETTERS 2019; 123:205502. [PMID: 31809111 DOI: 10.1103/physrevlett.123.205502] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Indexed: 06/10/2023]
Abstract
Active systems exhibit spontaneous flows induced by self-propulsion of microscopic constituents and can reach a nonequilibrium steady state without an external drive. Constructing the analogy between the quantum anomalous Hall insulators and active matter with spontaneous flows, we show that topologically protected sound modes can arise in a steady-state active system in continuum space. We point out that the net vorticity of the steady-state flow, which acts as a counterpart of the gauge field in condensed-matter settings, must vanish under realistic conditions for active systems. The quantum anomalous Hall effect thus provides design principles for realizing topological metamaterials. We propose and analyze the concrete minimal model and numerically calculate its band structure and eigenvectors, demonstrating the emergence of nonzero bulk topological invariants with the corresponding edge sound modes. This new type of topological active systems can potentially expand possibilities for their experimental realizations and may have broad applications to practical active metamaterials. Possible realization of non-Hermitian topological phenomena in active systems is also discussed.
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Affiliation(s)
- Kazuki Sone
- Department of Applied Physics, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yuto Ashida
- Department of Applied Physics, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Physics, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Woodhouse FG, Dunkel J. Active matter logic for autonomous microfluidics. Nat Commun 2017; 8:15169. [PMID: 28440273 PMCID: PMC5414041 DOI: 10.1038/ncomms15169] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/06/2017] [Indexed: 01/24/2023] Open
Abstract
Chemically or optically powered active matter plays an increasingly important role in materials design, but its computational potential has yet to be explored systematically. The competition between energy consumption and dissipation imposes stringent physical constraints on the information transport in active flow networks, facilitating global optimization strategies that are not well understood. Here, we combine insights from recent microbial experiments with concepts from lattice-field theory and non-equilibrium statistical mechanics to introduce a generic theoretical framework for active matter logic. Highlighting conceptual differences with classical and quantum computation, we demonstrate how the inherent non-locality of incompressible active flow networks can be utilized to construct universal logical operations, Fredkin gates and memory storage in set-reset latches through the synchronized self-organization of many individual network components. Our work lays the conceptual foundation for developing autonomous microfluidic transport devices driven by bacterial fluids, active liquid crystals or chemically engineered motile colloids.
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Affiliation(s)
- Francis G. Woodhouse
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, USA
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Romenskyy M, Herbert-Read JE, Ward AJW, Sumpter DJT. Body size affects the strength of social interactions and spatial organization of a schooling fish ( Pseudomugil signifer). ROYAL SOCIETY OPEN SCIENCE 2017; 4:161056. [PMID: 28484622 PMCID: PMC5414259 DOI: 10.1098/rsos.161056] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/20/2017] [Indexed: 05/11/2023]
Abstract
While a rich variety of self-propelled particle models propose to explain the collective motion of fish and other animals, rigorous statistical comparison between models and data remains a challenge. Plausible models should be flexible enough to capture changes in the collective behaviour of animal groups at their different developmental stages and group sizes. Here, we analyse the statistical properties of schooling fish (Pseudomugil signifer) through a combination of experiments and simulations. We make novel use of a Boltzmann inversion method, usually applied in molecular dynamics, to identify the effective potential of the mean force of fish interactions. Specifically, we show that larger fish have a larger repulsion zone, but stronger attraction, resulting in greater alignment in their collective motion. We model the collective dynamics of schools using a self-propelled particle model, modified to include varying particle speed and a local repulsion rule. We demonstrate that the statistical properties of the fish schools are reproduced by our model, thereby capturing a number of features of the behaviour and development of schooling fish.
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Affiliation(s)
- Maksym Romenskyy
- Department of Mathematics, Uppsala University, PO Box 480, Uppsala 75106, Sweden
- e-mail:
| | - James E. Herbert-Read
- Department of Mathematics, Uppsala University, PO Box 480, Uppsala 75106, Sweden
- Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Ashley J. W. Ward
- School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - David J. T. Sumpter
- Department of Mathematics, Uppsala University, PO Box 480, Uppsala 75106, Sweden
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Strobl MAR, Barker D. On simulated annealing phase transitions in phylogeny reconstruction. Mol Phylogenet Evol 2016; 101:46-55. [PMID: 27150349 PMCID: PMC4912009 DOI: 10.1016/j.ympev.2016.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 04/29/2016] [Accepted: 05/01/2016] [Indexed: 11/24/2022]
Abstract
Phylogeny reconstruction with global criteria is NP-complete or NP-hard, hence in general requires a heuristic search. We investigate the powerful, physically inspired, general-purpose heuristic simulated annealing, applied to phylogeny reconstruction. Simulated annealing mimics the physical process of annealing, where a liquid is gently cooled to form a crystal. During the search, periods of elevated specific heat occur, analogous to physical phase transitions. These simulated annealing phase transitions play a crucial role in the outcome of the search. Nevertheless, they have received comparably little attention, for phylogeny or other optimisation problems. We analyse simulated annealing phase transitions during searches for the optimal phylogenetic tree for 34 real-world multiple alignments. In the same way in which melting temperatures differ between materials, we observe distinct specific heat profiles for each input file. We propose this reflects differences in the search landscape and can serve as a measure for problem difficulty and for suitability of the algorithm's parameters. We discuss application in algorithmic optimisation and as a diagnostic to assess parameterisation before computationally costly, large phylogeny reconstructions are launched. Whilst the focus here lies on phylogeny reconstruction under maximum parsimony, it is plausible that our results are more widely applicable to optimisation procedures in science and industry.
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Affiliation(s)
- Maximilian A R Strobl
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH, UK; School of Mathematics and Statistics, Mathematical Institute, North Haugh, St Andrews, Fife KY16 9SS, UK
| | - Daniel Barker
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH, UK.
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Abstract
Active biological flow networks pervade nature and span a wide range of scales, from arterial blood vessels and bronchial mucus transport in humans to bacterial flow through porous media or plasmodial shuttle streaming in slime molds. Despite their ubiquity, little is known about the self-organization principles that govern flow statistics in such nonequilibrium networks. Here we connect concepts from lattice field theory, graph theory, and transition rate theory to understand how topology controls dynamics in a generic model for actively driven flow on a network. Our combined theoretical and numerical analysis identifies symmetry-based rules that make it possible to classify and predict the selection statistics of complex flow cycles from the network topology. The conceptual framework developed here is applicable to a broad class of biological and nonbiological far-from-equilibrium networks, including actively controlled information flows, and establishes a correspondence between active flow networks and generalized ice-type models.
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