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Tiwari C, Singh SP. Collective dynamics of active dumbbells near a circular obstacle. SOFT MATTER 2024; 20:4816-4826. [PMID: 38855922 DOI: 10.1039/d4sm00044g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
In this article, we present the collective dynamics of active dumbbells in the presence of a static circular obstacle using Brownian dynamics simulation. The active dumbbells aggregate on the surface of a circular obstacle beyond a critical radius. The aggregation is non-uniform along the circumference, and the aggregate size increases with the activity (Pe) and the curvature radius (Ro). The dense aggregate of active dumbbells displays persistent rotational motion with a certain angular speed, which linearly increases with activity. Furthermore, we show a strong polar ordering of the active dumbbells within the aggregate. The polar ordering exhibits long-range correlation, with the correlation length corresponding to the aggregate size. Additionally, we show that the residence time of an active dumbbell on the obstacle surface increases rapidly with area fraction due to many-body interactions that lead to a slowdown of the rotational diffusion. This article further considers the dynamical behavior of a tracer particle in the solution of active dumbbells. Interestingly, the speed of the passive tracer particle displays a crossover from monotonically decreasing to increasing with the size of the tracer particle upon increasing the dumbbells' speed. Furthermore, the effective diffusion of the tracer particle displays non-monotonic behavior with the area fraction; the initial increase in diffusivity is followed by a decrease for a larger area fraction.
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Affiliation(s)
- Chandranshu Tiwari
- Department of Physics, Indian Institute of Science Education and Research, Bhopal 462 066, Madhya Pradesh, India.
| | - Sunil P Singh
- Department of Physics, Indian Institute of Science Education and Research, Bhopal 462 066, Madhya Pradesh, India.
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2
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Black ME, Fei C, Alert R, Wingreen NS, Shaevitz JW. Capillary interactions drive the self-organization of bacterial colonies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596252. [PMID: 38853967 PMCID: PMC11160631 DOI: 10.1101/2024.05.28.596252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Many bacteria inhabit thin layers of water on solid surfaces both naturally in soils or on hosts or textiles and in the lab on agar hydrogels. In these environments, cells experience capillary forces, yet an understanding of how these forces shape bacterial collective behaviors remains elusive. Here, we show that the water menisci formed around bacteria lead to capillary attraction between cells while still allowing them to slide past one another. We develop an experimental apparatus that allows us to control bacterial collective behaviors by varying the strength and range of capillary forces. Combining 3D imaging and cell tracking with agent-based modeling, we demonstrate that capillary attraction organizes rod-shaped bacteria into densely packed, nematic groups, and profoundly influences their collective dynamics and morphologies. Our results suggest that capillary forces may be a ubiquitous physical ingredient in shaping microbial communities in partially hydrated environments.
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3
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Yadav RS, Sharma S, Metzler R, Chakrabarti R. A passive star polymer in a dense active bath: insights from computer simulations. SOFT MATTER 2024; 20:3910-3922. [PMID: 38700098 DOI: 10.1039/d4sm00144c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Using computer simulations in two dimensions (2D), we explore the structure and dynamics of a star polymer with three arms made of passive monomers immersed in a bath of active Brownian particles (ABPs). We analyze the conformational and dynamical changes of the polymer as a function of activity and packing fraction. We also study the process of motility induced phase separation (MIPS) in the presence of a star polymer, which acts as a mobile nucleation center. The presence of the polymer increases the growth rate of the clusters in comparison to a bath without the polymer. In particular, for low packing fraction, both nucleation and cluster growth are affected by the inclusion of the star polymer. Clusters grow in the vicinity of the star polymer, resulting in the star polymer experiencing a caged motion similar to a tagged ABP in the dense phase. Due to the topological constraints of the star polymers and clustering nearby, the conformational changes of the star polymer lead to interesting observations. Inter alia, we observe the shrinking of the arm with increasing activity along with a short-lived hairpin structure of one arm formed. We also see the transient pairing of two arms of the star polymer, while the third is largely separated at high activity. We hope our findings will help in understanding the behavior of active-passive mixtures, including biopolymers of complex topology in dense active suspensions.
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Affiliation(s)
- Ramanand Singh Yadav
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Sanaa Sharma
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Ralf Metzler
- Institute of Physics and Astronomy, University of Potsdam, Germany.
- Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
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4
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Wu-Zhang B, Fedosov DA, Gompper G. Collective behavior of squirmers in thin films. SOFT MATTER 2024. [PMID: 38639062 DOI: 10.1039/d4sm00075g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Bacteria in biofilms form complex structures and can collectively migrate within mobile aggregates, which is referred to as swarming. This behavior is influenced by a combination of various factors, including morphological characteristics and propulsive forces of swimmers, their volume fraction within a confined environment, and hydrodynamic and steric interactions between them. In our study, we employ the squirmer model for microswimmers and the dissipative particle dynamics method for fluid modeling to investigate the collective motion of swimmers in thin films. The film thickness permits a free orientation of non-spherical squirmers, but constraints them to form a two-layered structure at maximum. Structural and dynamic properties of squirmer suspensions confined within the slit are analyzed for different volume fractions of swimmers, motility types (e.g., pusher, neutral squirmer, puller), and the presence of a rotlet dipolar flow field, which mimics the counter-rotating flow generated by flagellated bacteria. Different states are characterized, including a gas-like phase, swarming, and motility-induced phase separation, as a function of increasing volume fraction. Our study highlights the importance of an anisotropic swimmer shape, hydrodynamic interactions between squirmers, and their interaction with the walls for the emergence of different collective behaviors. Interestingly, the formation of collective structures may not be symmetric with respect to the two walls. Furthermore, the presence of a rotlet dipole significantly mitigates differences in the collective behavior between various swimmer types. These results contribute to a better understanding of the formation of bacterial biofilms and the emergence of collective states in confined active matter.
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Affiliation(s)
- Bohan Wu-Zhang
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany.
| | - Dmitry A Fedosov
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany.
| | - Gerhard Gompper
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany.
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5
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Silvano N, Barci DG. Emergent gauge symmetry in active Brownian matter. Phys Rev E 2024; 109:044605. [PMID: 38755850 DOI: 10.1103/physreve.109.044605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/04/2024] [Indexed: 05/18/2024]
Abstract
We investigate a two-dimensional system of interacting active Brownian particles. Using the Martin-Siggia-Rose-Janssen-de Dominicis formalism, we built up the generating functional for correlation functions. We study in detail the hydrodynamic regime with a constant density stationary state. Our findings reveal that, within a small density fluctuations regime, an emergent U(1) gauge symmetry arises, originated from the conservation of fluid vorticity. Consequently, the interaction between the orientational order parameter and density fluctuations can be cast into a gauge theory, where the concept of "electric charge density" aligns with the local vorticity of the original fluid. We study in detail the case of a microscopic local two-body interaction. We show that, upon integrating out the gauge fields, the stationary states of the rotational degrees of freedom satisfy a nonlocal Frank free energy for a nematic fluid. We give explicit expressions for the splay and bend elastic constants as a function of the Péclet number (Pe) and the diffusion interaction constant (k_{d}).
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Affiliation(s)
- Nathan Silvano
- Center for Advanced Systems Understanding, Untermarkt 20, 02826 Görlitz, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
- Departamento de Física Teórica, 20270-004 Universidade do Estado do Rio de Janeiro, Rua São Francisco Xavier 524, 20550-013, Rio de Janeiro, RJ, Brazil
| | - Daniel G Barci
- Departamento de Física Teórica, 20270-004 Universidade do Estado do Rio de Janeiro, Rua São Francisco Xavier 524, 20550-013, Rio de Janeiro, RJ, Brazil
- Sorbonne Université, Laboratoire de Physique Théorique et Hautes Energies, CNRS UMR 7589, 4 Place Jussieu, 75252 Paris Cedex 05, France
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6
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Bickmann J, Bröker S, Te Vrugt M, Wittkowski R. Active Brownian particles in external force fields: Field-theoretical models, generalized barometric law, and programmable density patterns. Phys Rev E 2023; 108:044601. [PMID: 37978644 DOI: 10.1103/physreve.108.044601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 08/24/2023] [Indexed: 11/19/2023]
Abstract
We investigate the influence of external forces on the collective dynamics of interacting active Brownian particles in two as well as three spatial dimensions. Via explicit coarse graining, we derive predictive models, i.e., models that give a direct relation between the models' coefficients and the bare parameters of the system, that are applicable for space- and time-dependent external force fields. We study these models for the cases of gravity and harmonic traps. In particular, we derive a generalized barometric formula for interacting active Brownian particles under gravity that is valid for low to high concentrations and activities of the particles. Furthermore, we show that one can use an external harmonic trap to induce motility-induced phase separation in systems that, without external fields, remain in a homogeneous state. This finding makes it possible to realize programmable density patterns in systems of active Brownian particles. Our analytic predictions are found to be in very good agreement with Brownian dynamics simulations.
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Affiliation(s)
- Jens Bickmann
- Institut für Theoretische Physik, Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Stephan Bröker
- Institut für Theoretische Physik, Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Michael Te Vrugt
- Institut für Theoretische Physik, Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Raphael Wittkowski
- Institut für Theoretische Physik, Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
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7
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Martínez-Calvo A, Wingreen NS, Datta SS. Pattern formation by bacteria-phage interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558479. [PMID: 37786699 PMCID: PMC10541591 DOI: 10.1101/2023.09.19.558479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
The interactions between bacteria and phages-viruses that infect bacteria-play critical roles in agriculture, ecology, and medicine; however, how these interactions influence the spatial organization of both bacteria and phages remain largely unexplored. Here, we address this gap in knowledge by developing a theoretical model of motile, proliferating bacteria that aggregate via motility-induced phase separation (MIPS) and encounter phage that infect and lyse the cells. We find that the non-reciprocal predator-prey interactions between phage and bacteria strongly alter spatial organization, in some cases giving rise to a rich array of finite-scale stationary and dynamic patterns in which bacteria and phage coexist. We establish principles describing the onset and characteristics of these diverse behaviors, thereby helping to provide a biophysical basis for understanding pattern formation in bacteria-phage systems, as well as in a broader range of active and living systems with similar predator-prey or other non-reciprocal interactions.
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8
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Zhao H, Košmrlj A, Datta SS. Chemotactic Motility-Induced Phase Separation. PHYSICAL REVIEW LETTERS 2023; 131:118301. [PMID: 37774273 DOI: 10.1103/physrevlett.131.118301] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 06/08/2023] [Accepted: 08/16/2023] [Indexed: 10/01/2023]
Abstract
Collectives of actively moving particles can spontaneously separate into dilute and dense phases-a fascinating phenomenon known as motility-induced phase separation (MIPS). MIPS is well-studied for randomly moving particles with no directional bias. However, many forms of active matter exhibit collective chemotaxis, directed motion along a chemical gradient that the constituent particles can generate themselves. Here, using theory and simulations, we demonstrate that collective chemotaxis strongly competes with MIPS-in some cases, arresting or completely suppressing phase separation, or in other cases, generating fundamentally new dynamic instabilities. We establish principles describing this competition, thereby helping to reveal and clarify the rich physics underlying active matter systems that perform chemotaxis, ranging from cells to robots.
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Affiliation(s)
- Hongbo Zhao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Andrej Košmrlj
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, USA
- Princeton Materials Institute, Princeton University, Princeton, New Jersey 08544, USA
| | - Sujit S Datta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
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9
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Asp ME, Thanh MTH, Dutta S, Comstock JA, Welch RD, Patteson AE. Mechanobiology as a tool for addressing the genotype-to-phenotype problem in microbiology. BIOPHYSICS REVIEWS 2023; 4:021304. [PMID: 38504926 PMCID: PMC10903382 DOI: 10.1063/5.0142121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/03/2023] [Indexed: 03/21/2024]
Abstract
The central hypothesis of the genotype-phenotype relationship is that the phenotype of a developing organism (i.e., its set of observable attributes) depends on its genome and the environment. However, as we learn more about the genetics and biochemistry of living systems, our understanding does not fully extend to the complex multiscale nature of how cells move, interact, and organize; this gap in understanding is referred to as the genotype-to-phenotype problem. The physics of soft matter sets the background on which living organisms evolved, and the cell environment is a strong determinant of cell phenotype. This inevitably leads to challenges as the full function of many genes, and the diversity of cellular behaviors cannot be assessed without wide screens of environmental conditions. Cellular mechanobiology is an emerging field that provides methodologies to understand how cells integrate chemical and physical environmental stress and signals, and how they are transduced to control cell function. Biofilm forming bacteria represent an attractive model because they are fast growing, genetically malleable and can display sophisticated self-organizing developmental behaviors similar to those found in higher organisms. Here, we propose mechanobiology as a new area of study in prokaryotic systems and describe its potential for unveiling new links between an organism's genome and phenome.
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10
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Pfreundt U, Słomka J, Schneider G, Sengupta A, Carrara F, Fernandez V, Ackermann M, Stocker R. Controlled motility in the cyanobacterium Trichodesmium regulates aggregate architecture. Science 2023; 380:830-835. [PMID: 37228200 DOI: 10.1126/science.adf2753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
The ocean's nitrogen is largely fixed by cyanobacteria, including Trichodesmium, which forms aggregates comprising hundreds of filaments arranged in organized architectures. Aggregates often form upon exposure to stress and have ecological and biophysical characteristics that differ from those of single filaments. Here, we report that Trichodesmium aggregates can rapidly modulate their shape, responding within minutes to changes in environmental conditions. Combining video microscopy and mathematical modeling, we discovered that this reorganization is mediated by "smart reversals" wherein gliding filaments reverse when their overlap with other filaments diminishes. By regulating smart reversals, filaments control aggregate architecture without central coordination. We propose that the modulation of gliding motility at the single-filament level is a determinant of Trichodesmium's aggregation behavior and ultimately of its biogeochemical role in the ocean.
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Affiliation(s)
- Ulrike Pfreundt
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zürich, Switzerland
| | - Jonasz Słomka
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zürich, Switzerland
| | - Giulia Schneider
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zürich, Switzerland
| | - Anupam Sengupta
- Physics of Living Matter, Department of Physics and Materials Science, University of Luxembourg, Luxembourg City, Grand Duchy of Luxembourg
| | - Francesco Carrara
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zürich, Switzerland
| | - Vicente Fernandez
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zürich, Switzerland
| | - Martin Ackermann
- Department of Environmental Systems Sciences, Microbial Systems Ecology Group, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zürich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Sciences, Dübendorf, Switzerland
| | - Roman Stocker
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zürich, Switzerland
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11
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Black ME, Shaevitz JW. Rheological Dynamics of Active Myxococcus xanthus Populations during Development. PHYSICAL REVIEW LETTERS 2023; 130:218402. [PMID: 37295076 DOI: 10.1103/physrevlett.130.218402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/21/2023] [Indexed: 06/12/2023]
Abstract
The bacterium Myxococcus xanthus produces multicellular droplets called fruiting bodies when starved. These structures form initially through the active dewetting of a vegetative biofilm into surface-associated droplets. This motility-driven aggregation is succeeded by a primitive developmental process in which cells in the droplets mature into nonmotile spores. Here, we use atomic force microscopy to probe the mechanics of these droplets throughout their formation. Using a combination of time- and frequency-domain rheological experiments, we characterize and develop a simple model of the linear viscoelasticity of these aggregates. We then use this model to quantify how cellular behaviors predominant at different developmental times-motility during the dewetting phase and cellular sporulation during later development-manifest as decreased droplet viscosity and increased elasticity, respectively.
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Affiliation(s)
- Matthew E Black
- Joseph Henry Laboratories of Physics and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Joshua W Shaevitz
- Joseph Henry Laboratories of Physics and the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
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12
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Besse M, Fausti G, Cates ME, Delamotte B, Nardini C. Interface Roughening in Nonequilibrium Phase-Separated Systems. PHYSICAL REVIEW LETTERS 2023; 130:187102. [PMID: 37204903 DOI: 10.1103/physrevlett.130.187102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 04/10/2023] [Indexed: 05/21/2023]
Abstract
Interfaces of phase-separated systems roughen in time due to capillary waves. Because of fluxes in the bulk, their dynamics is nonlocal in real space and is not described by the Edwards-Wilkinson or Kardar-Parisi-Zhang (KPZ) equations, nor their conserved counterparts. We show that, in the absence of detailed balance, the phase-separated interface is described by a new universality class that we term |q|KPZ. We compute the associated scaling exponents via one-loop renormalization group and corroborate the results by numerical integration of the |q|KPZ equation. Deriving the effective interface dynamics from a minimal field theory of active phase separation, we finally argue that the |q|KPZ universality class generically describes liquid-vapor interfaces in two- and three-dimensional active systems.
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Affiliation(s)
- M Besse
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- CNRS, Laboratoire de Physique Théorique de la Matière Condensée, Sorbonne Université, 75005 Paris, France
| | - G Fausti
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- Max Planck Institute for Dynamics and Self-Organization, 37077 Göttingen, Germany
| | - M E Cates
- DAMTP, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
| | - B Delamotte
- CNRS, Laboratoire de Physique Théorique de la Matière Condensée, Sorbonne Université, 75005 Paris, France
| | - C Nardini
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- CNRS, Laboratoire de Physique Théorique de la Matière Condensée, Sorbonne Université, 75005 Paris, France
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13
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Bera A, Binder K, Egorov SA, Das SK. Phase behavior and dynamics in a colloid-polymer mixture under spherical confinement. SOFT MATTER 2023; 19:3386-3397. [PMID: 37128824 DOI: 10.1039/d3sm00362k] [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
From studies via molecular dynamics simulations, we report results on structure and dynamics in mixtures of active colloids and passive polymers that are confined inside a spherical container with a repulsive boundary. All interactions in the fully passive limit are chosen in such a way that in equilibrium coexistence between colloid-rich and polymer-rich phases occurs. For most part of the studies the chosen compositions give rise to Janus-like structure: nearly one side of the sphere is occupied by the colloids and the rest by the polymers. This partially wet situation mimics approximately a neutral wall in the fully passive scenario. Following the introduction of a velocity-aligning activity to the colloids, the shape of the polymer-rich domain changes to that of an ellipsoid, around the long axis of which the colloid-rich domain attains a macroscopic angular momentum. In the steady state, the orientation of this axis evolves via diffusion, magnitude of which depends upon the strength of activity, but only weakly.
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Affiliation(s)
- Arabinda Bera
- Theoretical Sciences Unit and School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, India.
| | - Kurt Binder
- Institut für Physik, Johannes Gutenberg-Universität, D-55099 Mainz, Staudinger Weg 7, Germany
| | - Sergei A Egorov
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, USA
| | - Subir K Das
- Theoretical Sciences Unit and School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, India.
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14
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Benvegnen B, Chaté H, Krapivsky PL, Tailleur J, Solon A. Flocking in one dimension: Asters and reversals. Phys Rev E 2022; 106:054608. [PMID: 36559354 DOI: 10.1103/physreve.106.054608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/23/2022] [Indexed: 06/17/2023]
Abstract
We study the one-dimensional active Ising model in which aligning particles undergo diffusion biased by the signs of their spins. The phase diagram obtained varying the density of particles, their hopping rate, and the temperature controlling the alignment shows a homogeneous disordered phase but no homogeneous ordered one, as well as two phases with localized dense structures. In the flocking phase, large ordered aggregates move ballistically and stochastically reverse their direction of motion. In what we termed the "aster" phase, dense immobile aggregates of opposite magnetization face each other, exchanging particles, without any net motion of the aggregates. Using a combination of numerical simulations and mean-field theory, we study the evolution of the shapes of the flocks, the statistics of their reversal times, and their coarsening dynamics. Solving exactly for the zero-temperature dynamics of an aster allows us to understand their coarsening, which shows extremal dynamics, while mean-field equations account for their shape.
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Affiliation(s)
- Brieuc Benvegnen
- 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
| | - Pavel L Krapivsky
- Department of Physics, Boston University, Boston, Massachusetts 02215, USA
- Santa Fe Institute, Santa Fe, New Mexico 87501, USA
| | - Julien Tailleur
- Université Paris Cité, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, F-75205 Paris, France
| | - Alexandre Solon
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, 75005 Paris, France
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15
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Pereira RG. Steady states and coarsening in one-dimensional driven Allen-Cahn system. Phys Rev E 2022; 106:014150. [PMID: 35974652 DOI: 10.1103/physreve.106.014150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
We study the steady states and the coarsening dynamics in a one-dimensional driven nonconserved system modeled by the so-called driven Allen-Cahn equation, which is the standard Allen-Cahn equation with an additional driving force. In particular, we derive equations of motion for the phase boundaries in a phase ordering system obeying this equation using a nearest-neighbor interaction approach. Using the equations of motion we explore kink binary and ternary interactions and analyze how the average domain size scale with respect to time. Further, we employ numerical techniques to perform a bifurcation analysis of the one-period stationary solutions of the equation. We then investigate the linear stability of the two-period solutions and thereby identify and study various coarsening modes.
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Affiliation(s)
- Rajiv G Pereira
- School of Physics, IISER Thiruvananthapuram, Vithura, Kerala 695551, India
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16
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Worlitzer VM, Jose A, Grinberg I, Bär M, Heidenreich S, Eldar A, Ariel G, Be’er A. Biophysical aspects underlying the swarm to biofilm transition. SCIENCE ADVANCES 2022; 8:eabn8152. [PMID: 35704575 PMCID: PMC9200279 DOI: 10.1126/sciadv.abn8152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Bacteria organize in a variety of collective states, from swarming-rapid surface exploration, to biofilms-highly dense immobile communities attributed to stress resistance. It has been suggested that biofilm and swarming are oppositely controlled, making this transition particularly interesting for understanding the ability of bacterial colonies to adapt to challenging environments. Here, the swarm to biofilm transition is studied in Bacillus subtilis by analyzing the bacterial dynamics both on the individual and collective scales. We show that both biological and physical processes facilitate the transition. A few individual cells that initiate the biofilm program cause nucleation of large, approximately scale-free, stationary aggregates of trapped swarm cells. Around aggregates, cells continue swarming almost unobstructed, while inside, trapped cells are added to the biofilm. While our experimental findings rule out previously suggested purely physical effects as a trigger for biofilm formation, they show how physical processes, such as clustering and jamming, accelerate biofilm formation.
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Affiliation(s)
- Vasco M. Worlitzer
- Department of Mathematical Modelling and Data Analysis, Physikalisch-Technische Bundesanstalt Braunschweig und Berlin, Abbestrasse 2-12, D-10587 Berlin, Germany
- Department of Mathematics, Bar-Ilan University, 52900 Ramat Gan, Israel
| | - Ajesh Jose
- 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
| | - Ilana Grinberg
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Markus Bär
- Department of Mathematical Modelling and Data Analysis, Physikalisch-Technische Bundesanstalt Braunschweig und Berlin, Abbestrasse 2-12, D-10587 Berlin, Germany
| | - Sebastian Heidenreich
- Department of Mathematical Modelling and Data Analysis, Physikalisch-Technische Bundesanstalt Braunschweig und Berlin, Abbestrasse 2-12, D-10587 Berlin, Germany
| | - Avigdor Eldar
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Gil Ariel
- Department of Mathematics, Bar-Ilan University, 52900 Ramat Gan, Israel
- Corresponding author. (G.A.); (A.B.)
| | - Avraham Be’er
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990 Midreshet Ben-Gurion, Israel
- Department of Physics, Ben-Gurion University of the Negev, 84105 Beer Sheva, Israel
- Corresponding author. (G.A.); (A.B.)
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17
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Spatial patterns in ecological systems: from microbial colonies to landscapes. Emerg Top Life Sci 2022; 6:245-258. [PMID: 35678374 DOI: 10.1042/etls20210282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 11/17/2022]
Abstract
Self-organized spatial patterns are ubiquitous in ecological systems and allow populations to adopt non-trivial spatial distributions starting from disordered configurations. These patterns form due to diverse nonlinear interactions among organisms and between organisms and their environment, and lead to the emergence of new (eco)system-level properties unique to self-organized systems. Such pattern consequences include higher resilience and resistance to environmental changes, abrupt ecosystem collapse, hysteresis loops, and reversal of competitive exclusion. Here, we review ecological systems exhibiting self-organized patterns. We establish two broad pattern categories depending on whether the self-organizing process is primarily driven by nonlinear density-dependent demographic rates or by nonlinear density-dependent movement. Using this organization, we examine a wide range of observational scales, from microbial colonies to whole ecosystems, and discuss the mechanisms hypothesized to underlie observed patterns and their system-level consequences. For each example, we review both the empirical evidence and the existing theoretical frameworks developed to identify the causes and consequences of patterning. Finally, we trace qualitative similarities across systems and propose possible ways of developing a more quantitative understanding of how self-organization operates across systems and observational scales in ecology.
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18
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Bickmann J, Bröker S, Jeggle J, Wittkowski R. Analytical approach to chiral active systems: suppressed phase separation of interacting Brownian circle swimmers. J Chem Phys 2022; 156:194904. [DOI: 10.1063/5.0085122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We consider chirality in active systems by exemplarily studying the phase behavior of planar systems of interacting Brownian circle swimmers with a spherical shape. For this purpose, we derive a predictive field theory that is able to describe the collective dynamics of circle swimmers. The theory yields a mapping between circle swimmers and noncircling active Brownian particles and predicts that the angular propulsion of the particles leads to a suppression of their motility-induced phase separation, being in line with recent simulation results. In addition, the theory provides analytical expressions for the spinodal corresponding to the onset of motility-induced phase separation and the associated critical point as well as for their dependence on the angular propulsion of the circle swimmers. We confirm our findings by Brownian dynamics simulations. The agreement between results from theory and simulations is found to be good.
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Affiliation(s)
- Jens Bickmann
- Westfälische Wilhelms-Universität Münster Fachbereich 11 Physik, Germany
| | - Stephan Bröker
- Westfälische Wilhelms-Universität Münster Fachbereich 11 Physik, Germany
| | - Julian Jeggle
- Westfälische Wilhelms-Universität Münster Fachbereich 11 Physik, Germany
| | - Raphael Wittkowski
- Institut für Theoretische Physik, Westfälische Wilhelms-Universität Münster Fachbereich 11 Physik, Germany
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19
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Asp ME, Ho Thanh MT, Germann DA, Carroll RJ, Franceski A, Welch RD, Gopinath A, Patteson AE. Spreading rates of bacterial colonies depend on substrate stiffness and permeability. PNAS NEXUS 2022; 1:pgac025. [PMID: 36712798 PMCID: PMC9802340 DOI: 10.1093/pnasnexus/pgac025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/25/2022] [Accepted: 03/09/2022] [Indexed: 02/01/2023]
Abstract
The ability of bacteria to colonize and grow on different surfaces is an essential process for biofilm development. Here, we report the use of synthetic hydrogels with tunable stiffness and porosity to assess physical effects of the substrate on biofilm development. Using time-lapse microscopy to track the growth of expanding Serratia marcescens colonies, we find that biofilm colony growth can increase with increasing substrate stiffness, unlike what is found on traditional agar substrates. Using traction force microscopy-based techniques, we find that biofilms exert transient stresses correlated over length scales much larger than a single bacterium, and that the magnitude of these forces also increases with increasing substrate stiffness. Our results are consistent with a model of biofilm development in which the interplay between osmotic pressure arising from the biofilm and the poroelastic response of the underlying substrate controls biofilm growth and morphology.
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Affiliation(s)
- Merrill E Asp
- Physics Department, Syracuse University, Syracuse, NY 13244, USA,BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Minh-Tri Ho Thanh
- Physics Department, Syracuse University, Syracuse, NY 13244, USA,BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Danielle A Germann
- Physics Department, Syracuse University, Syracuse, NY 13244, USA,BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Robert J Carroll
- Physics Department, Syracuse University, Syracuse, NY 13244, USA,BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Alana Franceski
- BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA,Biology Department, Syracuse University, Syracuse, NY 13244, USA
| | - Roy D Welch
- BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA,Biology Department, Syracuse University, Syracuse, NY 13244, USA
| | - Arvind Gopinath
- Department of Bioengineering, University of California, Merced, Merced, CA 95343, USA,Health Sciences Research Institute, University of California, Merced, Merced, CA 95343, USA
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20
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Microscopic Swarms: From Active Matter Physics to Biomedical and Environmental Applications. MICROMACHINES 2022; 13:mi13020295. [PMID: 35208419 PMCID: PMC8876490 DOI: 10.3390/mi13020295] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023]
Abstract
Microscopic swarms consisting of, e.g., active colloidal particles or microorganisms, display emergent behaviors not seen in equilibrium systems. They represent an emerging field of research that generates both fundamental scientific interest and practical technological value. This review seeks to unite the perspective of fundamental active matter physics and the perspective of practical applications of microscopic swarms. We first summarize experimental and theoretical results related to a few key aspects unique to active matter systems: the existence of long-range order, the prediction and observation of giant number fluctuations and motility-induced phase separation, and the exploration of the relations between information and order in the self-organizing patterns. Then we discuss microscopic swarms, particularly microrobotic swarms, from the perspective of applications. We introduce common methods to control and manipulate microrobotic swarms and summarize their potential applications in fields such as targeted delivery, in vivo imaging, biofilm removal, and wastewater treatment. We aim at bridging the gap between the community of active matter physics and the community of micromachines or microrobotics, and in doing so, we seek to inspire fruitful collaborations between the two communities.
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21
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Yang Y, Turci F, Kague E, Hammond CL, Russo J, Royall CP. Dominating lengthscales of zebrafish collective behaviour. PLoS Comput Biol 2022; 18:e1009394. [PMID: 35025883 PMCID: PMC8797201 DOI: 10.1371/journal.pcbi.1009394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 01/28/2022] [Accepted: 12/09/2021] [Indexed: 11/19/2022] Open
Abstract
Collective behaviour in living systems is observed across many scales, from bacteria to insects, to fish shoals. Zebrafish have emerged as a model system amenable to laboratory study. Here we report a three-dimensional study of the collective dynamics of fifty zebrafish. We observed the emergence of collective behaviour changing between ordered to randomised, upon adaptation to new environmental conditions. We quantify the spatial and temporal correlation functions of the fish and identify two length scales, the persistence length and the nearest neighbour distance, that capture the essence of the behavioural changes. The ratio of the two length scales correlates robustly with the polarisation of collective motion that we explain with a reductionist model of self-propelled particles with alignment interactions.
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Affiliation(s)
- Yushi Yang
- Bristol Centre for Functional Nanomaterials, University of Bristol, Bristol, United Kingdom
- H.H. Wills Physics Laboratory, University of Bristol, Bristol, United Kingdom
- * E-mail:
| | - Francesco Turci
- H.H. Wills Physics Laboratory, University of Bristol, Bristol, United Kingdom
| | - Erika Kague
- Department of Physiology, Pharmacology, and Neuroscience, Medical Sciences, University of Bristol, Bristol, United Kingdom
| | - Chrissy L. Hammond
- Department of Physiology, Pharmacology, and Neuroscience, Medical Sciences, University of Bristol, Bristol, United Kingdom
| | - John Russo
- Department of Physics, Sapienza Università di Roma, Rome, Italy
| | - C. Patrick Royall
- H.H. Wills Physics Laboratory, University of Bristol, Bristol, United Kingdom
- Gulliver UMR CNRS 7083, ESPCI Paris, Università PSL, Paris, France
- School of Chemistry, University of Bristol, Bristol, United Kingdom
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22
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Almeida RAL, Takeuchi KA. Phase-ordering kinetics in the Allen-Cahn (Model A) class: Universal aspects elucidated by electrically induced transition in liquid crystals. Phys Rev E 2021; 104:054103. [PMID: 34942720 DOI: 10.1103/physreve.104.054103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/27/2021] [Indexed: 11/07/2022]
Abstract
The two-dimensional (2D) Ising model is the statistical physics textbook example for phase transitions and their kinetics. Quenched through the Curie point with Glauber rates, the late-time description of the ferromagnetic domain coarsening finds its place at the scalar sector of the Allen-Cahn (or Model A) class, which encompasses phase-ordering kinetics endowed with a nonconserved order parameter. Resisting exact results sought for theoreticians since Lifshitz's first account in 1962, the central quantities of 2D Model A-most scaling exponents and correlation functions-remain known up to approximate theories whose disparate outcomes urge experimental assessment. Here we perform such assessment based on a comprehensive study of the coarsening of 2D twisted nematic liquid crystals whose kinetics is induced by a superfast electrical switching from a spatiotemporally chaotic (disordered) state to a two-phase concurrent, equilibrium one. Tracking the dynamics via optical microscopy, we first show the sharp evidence of well-established Model A aspects, such as the dynamic exponent z=2 and the dynamic scaling hypothesis, to then move forward. We confirm the Bray-Humayun theory for Porod's regime describing intradomain length scales of the two-point spatial correlators and show that their nontrivial decay beyond the Porod's scale can be captured in a free-from-parameter fashion by Gaussian theories, namely the Ohta-Jasnow-Kawasaki (OJK) and Mazenko theories. Regarding time-related statistics, we corroborate the aging hypothesis in Model A systems, which includes the collapse of two-time correlators into a master curve whose format is, actually, best accounted for by a solution of the local scaling invariance theory: the same solution that fits the 2D nonconserved Ising model correlator along with the Fisher-Huse conjecture. We also suggest the true value for the local persistence exponent in Model A class, in disfavor of the exact outcome for the diffusion and OJK equations. Finally, we observe a fractal morphology for persistence clusters and extract their universal dimension. Given its accuracy and possibilities, this experimental setup may work as a prototype to address further universality issues in the realm of nonequilibrium systems.
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Affiliation(s)
- Renan A L Almeida
- Department of Physics, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan.,Departmento de Física, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil.,Department of Physics, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazumasa A Takeuchi
- Department of Physics, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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23
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Santra I, Basu U, Sabhapandit S. Direction reversing active Brownian particle in a harmonic potential. SOFT MATTER 2021; 17:10108-10119. [PMID: 34726222 DOI: 10.1039/d1sm01118a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We study the two-dimensional motion of an active Brownian particle of speed v0, with intermittent directional reversals in the presence of a harmonic trap of strength μ. The presence of the trap ensures that the position of the particle eventually reaches a steady state where it is bounded within a circular region of radius v0/μ, centered at the minimum of the trap. Due to the interplay between the rotational diffusion constant DR, reversal rate γ, and the trap strength μ, the steady state distribution shows four different types of shapes, which we refer to as active-I & II, and passive-I & II phases. In the active-I phase, the weight of the distribution is concentrated along an annular region close to the circular boundary, whereas in active-II, an additional central diverging peak appears giving rise to a Mexican hat-like shape of the distribution. The passive-I is marked by a single Boltzmann-like centrally peaked distribution in the large DR limit. On the other hand, while the passive-II phase also shows a single central peak, it is distinguished from passive-I by a non-Boltzmann like divergence near the origin. We characterize these phases by calculating the exact analytical forms of the distributions in various limiting cases. In particular, we show that for DR ≪ γ, the shape transition of the two-dimensional position distribution from active-II to passive-II occurs at μ = γ. We compliment these analytical results with numerical simulations beyond the limiting cases and obtain a qualitative phase diagram in the (DR, γ, μ-1) space.
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Affiliation(s)
- Ion Santra
- Raman Research Institute, Bengaluru 560080, India
| | - Urna Basu
- Raman Research Institute, Bengaluru 560080, India
- S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
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24
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Ramos CH, Rodríguez-Sánchez E, Del Angel JAA, Arzola AV, Benítez M, Escalante AE, Franci A, Volpe G, Rivera-Yoshida N. The environment topography alters the way to multicellularity in Myxococcus xanthus. SCIENCE ADVANCES 2021; 7:7/35/eabh2278. [PMID: 34433567 PMCID: PMC8386931 DOI: 10.1126/sciadv.abh2278] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/02/2021] [Indexed: 05/10/2023]
Abstract
The social soil-dwelling bacterium Myxococcus xanthus can form multicellular structures, known as fruiting bodies. Experiments in homogeneous environments have shown that this process is affected by the physicochemical properties of the substrate, but they have largely neglected the role of complex topographies. We experimentally demonstrate that the topography alters single-cell motility and multicellular organization in M. xanthus In topographies realized by randomly placing silica particles over agar plates, we observe that the cells' interaction with particles drastically modifies the dynamics of cellular aggregation, leading to changes in the number, size, and shape of the fruiting bodies and even to arresting their formation in certain conditions. We further explore this type of cell-particle interaction in a computational model. These results provide fundamental insights into how the environment topography influences the emergence of complex multicellular structures from single cells, which is a fundamental problem of biological, ecological, and medical relevance.
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Affiliation(s)
- Corina H Ramos
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. de México, C.P. 4510, Mexico
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Edna Rodríguez-Sánchez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Juan Antonio Arias Del Angel
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Alejandro V Arzola
- Instituto de Física, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, México
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Ana E Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Alessio Franci
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. de México, C.P. 4510, Mexico
| | - Giovanni Volpe
- Department of Physics, University of Gothenburg, Gothenburg, Sweden
| | - Natsuko Rivera-Yoshida
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. de México, C.P. 4510, Mexico.
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
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25
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Santra I, Basu U, Sabhapandit S. Active Brownian motion with directional reversals. Phys Rev E 2021; 104:L012601. [PMID: 34412243 DOI: 10.1103/physreve.104.l012601] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Active Brownian motion with intermittent direction reversals is common in bacteria like Myxococcus xanthus and Pseudomonas putida. We show that, for such a motion in two dimensions, the presence of the two timescales set by the rotational diffusion constant D_{R} and the reversal rate γ gives rise to four distinct dynamical regimes: (I) t≪min(γ^{-1},D_{R}^{-1}), (II) γ^{-1}≪t≪D_{R}^{-1}, (III) D_{R}^{-1}≪t≪γ^{-1}, and (IV) t≫max(γ^{-1}, D_{R}^{-1}), showing distinct behaviors. We characterize these behaviors by analytically computing the position distribution and persistence exponents. The position distribution shows a crossover from a strongly nondiffusive and anisotropic behavior at short times to a diffusive isotropic behavior via an intermediate regime, II or III. In regime II, we show that, the position distribution along the direction orthogonal to the initial orientation is a function of the scaled variable z∝x_{⊥}/t with a nontrivial scaling function, f(z)=(2π^{3})^{-1/2}Γ(1/4+iz)Γ(1/4-iz). Furthermore, by computing the exact first-passage time distribution, we show that a persistence exponent α=1 emerges due to the direction reversal in this regime.
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Affiliation(s)
- Ion Santra
- Raman Research Institute, Bengaluru 560080, India
| | - Urna Basu
- Raman Research Institute, Bengaluru 560080, India
- S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
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26
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Wong GCL, Antani JD, Lele PP, Chen J, Nan B, Kühn MJ, Persat A, Bru JL, Høyland-Kroghsbo NM, Siryaporn A, Conrad JC, Carrara F, Yawata Y, Stocker R, V Brun Y, Whitfield GB, Lee CK, de Anda J, Schmidt WC, Golestanian R, O'Toole GA, Floyd KA, Yildiz FH, Yang S, Jin F, Toyofuku M, Eberl L, Nomura N, Zacharoff LA, El-Naggar MY, Yalcin SE, Malvankar NS, Rojas-Andrade MD, Hochbaum AI, Yan J, Stone HA, Wingreen NS, Bassler BL, Wu Y, Xu H, Drescher K, Dunkel J. Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation. Phys Biol 2021; 18. [PMID: 33462162 PMCID: PMC8506656 DOI: 10.1088/1478-3975/abdc0e] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/14/2021] [Indexed: 11/29/2022]
Abstract
Bacterial biofilms are communities of bacteria that exist as aggregates that can adhere to surfaces or be free-standing. This complex, social mode of cellular organization is fundamental to the physiology of microbes and often exhibits surprising behavior. Bacterial biofilms are more than the sum of their parts: single-cell behavior has a complex relation to collective community behavior, in a manner perhaps cognate to the complex relation between atomic physics and condensed matter physics. Biofilm microbiology is a relatively young field by biology standards, but it has already attracted intense attention from physicists. Sometimes, this attention takes the form of seeing biofilms as inspiration for new physics. In this roadmap, we highlight the work of those who have taken the opposite strategy: we highlight the work of physicists and physical scientists who use physics to engage fundamental concepts in bacterial biofilm microbiology, including adhesion, sensing, motility, signaling, memory, energy flow, community formation and cooperativity. These contributions are juxtaposed with microbiologists who have made recent important discoveries on bacterial biofilms using state-of-the-art physical methods. The contributions to this roadmap exemplify how well physics and biology can be combined to achieve a new synthesis, rather than just a division of labor.
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Affiliation(s)
- Gerard C L Wong
- Department of Bioengineering, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,California NanoSystems Institute, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America
| | - Jyot D Antani
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States of America
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States of America
| | - Jing Chen
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA24061, United States of America
| | - Beiyan Nan
- Department of Biology, Texas A&M University, College Station, Texas, TX 77845, United States of America
| | - Marco J Kühn
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexandre Persat
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jean-Louis Bru
- Department of Molecular Biology & Biochemistry, University of California-Irvine, California, CA 92697, United States of America
| | | | - Albert Siryaporn
- Department of Molecular Biology & Biochemistry, University of California-Irvine, California, CA 92697, United States of America.,Department of Physics & Astronomy, University of California-Irvine, California, CA 92697, United States of America
| | - Jacinta C Conrad
- William A Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, TX 77204, United States of America
| | - Francesco Carrara
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Yutaka Yawata
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, 305-8572 Tsukuba, Japan
| | - Roman Stocker
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, 8093 Zurich, Switzerland
| | - Yves V Brun
- University of Montreal, Faculty of Medicine, Montreal, Quebec, H3C 3J7, Canada
| | - Gregory B Whitfield
- University of Montreal, Faculty of Medicine, Montreal, Quebec, H3C 3J7, Canada
| | - Calvin K Lee
- Department of Bioengineering, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,California NanoSystems Institute, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America
| | - Jaime de Anda
- Department of Bioengineering, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,California NanoSystems Institute, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America
| | - William C Schmidt
- Department of Bioengineering, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America.,California NanoSystems Institute, University of California-Los Angeles, Los Angeles, California, CA 90095, United States of America
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), D-37077 Göttingen, Germany.,Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, United States of America
| | - Kyle A Floyd
- Department of Microbiology and Environmental Toxicology, University of California-Santa Cruz, Santa Cruz, California, CA 95060, United States of America
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California-Santa Cruz, Santa Cruz, California, CA 95060, United States of America
| | - Shuai Yang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Fan Jin
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Masanori Toyofuku
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, 305-8572 Tsukuba, Japan
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zürich, 8008 Zürich, Switzerland
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, 305-8572 Tsukuba, Japan
| | - Lori A Zacharoff
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, CA 90089, United States of America.,Department of Chemistry, University of Southern California, Los Angeles, California, CA 90089, United States of America
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, CA 90089, United States of America.,Department of Chemistry, University of Southern California, Los Angeles, California, CA 90089, United States of America.,Department of Biological Sciences, University of Southern California, Los Angeles, California, CA 90089, United States of America
| | - Sibel Ebru Yalcin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, CT 06516, United States of America.,Microbial Sciences Institute, Yale University, New Haven, Connecticut, CT 06516, United States of America
| | - Nikhil S Malvankar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, CT 06516, United States of America.,Microbial Sciences Institute, Yale University, New Haven, Connecticut, CT 06516, United States of America
| | - Mauricio D Rojas-Andrade
- Department of Materials Science and Engineering, University of California-Irvine, Irvine, California CA 92697, United States of America
| | - Allon I Hochbaum
- Department of Molecular Biology & Biochemistry, University of California-Irvine, California, CA 92697, United States of America.,Department of Materials Science and Engineering, University of California-Irvine, Irvine, California CA 92697, United States of America.,Department of Chemistry, University of California-Irvine, Irvine, California, CA 92697, United States of America.,Department of Chemical and Biomolecular Engineering, University of California-Irvine, Irvine, California, CA 92697, United States of America
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, CT 06511, United States of America
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey, NJ 08544, United States of America
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, NJ 08544, United States of America.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, NJ 08544, United States of America
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, NJ 08544, United States of America.,The Howard Hughes Medical Institute, Chevy Chase, Maryland MD 20815, United States of America
| | - Yilin Wu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, People's Republic of China
| | - Haoran Xu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, People's Republic of China
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.,Department of Physics, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, MA 02139-4307, United States of America
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27
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Devereux HL, Twomey CR, Turner MS, Thutupalli S. Whirligig beetles as corralled active Brownian particles. J R Soc Interface 2021; 18:20210114. [PMID: 33849331 DOI: 10.1098/rsif.2021.0114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We study the collective dynamics of groups of whirligig beetles Dineutus discolor (Coleoptera: Gyrinidae) swimming freely on the surface of water. We extract individual trajectories for each beetle, including positions and orientations, and use this to discover (i) a density-dependent speed scaling like v ∼ ρ-ν with ν ≈ 0.4 over two orders of magnitude in density (ii) an inertial delay for velocity alignment of approximately 13 ms and (iii) coexisting high and low-density phases, consistent with motility-induced phase separation (MIPS). We modify a standard active Brownian particle (ABP) model to a corralled ABP (CABP) model that functions in open space by incorporating a density-dependent reorientation of the beetles, towards the cluster. We use our new model to test our hypothesis that an motility-induced phase separation (MIPS) (or a MIPS like effect) can explain the co-occurrence of high- and low-density phases we see in our data. The fitted model then successfully recovers a MIPS-like condensed phase for N = 200 and the absence of such a phase for smaller group sizes N = 50, 100.
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Affiliation(s)
- Harvey L Devereux
- Department of Mathematics, University of Warwick, Coventry CV4 7AL, UK.,Simons Center for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore 560065, India
| | - Colin R Twomey
- Department of Biology, and Mind Center for Outreach, Research and Education, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew S Turner
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK.,Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, UK.,Department of Chemical Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Shashi Thutupalli
- Simons Center for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore 560065, India.,International Centre for Theoretical Sciences, Tata Institute for Fundamental Research, Bangalore 560089, India
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28
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Maggi C, Paoluzzi M, Crisanti A, Zaccarelli E, Gnan N. Universality class of the motility-induced critical point in large scale off-lattice simulations of active particles. SOFT MATTER 2021; 17:3807-3812. [PMID: 33645615 DOI: 10.1039/d0sm02162h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We perform large-scale computer simulations of an off-lattice two-dimensional model of active particles undergoing a motility-induced phase separation (MIPS) to investigate the system's critical behaviour close to the critical point of the MIPS curve. By sampling steady-state configurations for large system sizes and performing finite size scaling analysis we provide exhaustive evidence that the critical behaviour of this active system belongs to the Ising universality class. In addition to the scaling observables that are also typical of passive systems, we study the critical behaviour of the kinetic temperature difference between the two active phases. This quantity, which is always zero in equilibrium, displays instead a critical behavior in the active system which is well described by the same exponent of the order parameter in agreement with mean-field theory.
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Affiliation(s)
- Claudio Maggi
- NANOTEC-CNR, Institute of Nanotechnology, Soft and Living Matter Laboratory -Piazzale A. Moro 2, I-00185, Roma, Italy. and Dipartimento di Fisica, Università di Roma "Sapienza", I-00185, Roma, Italy
| | - Matteo Paoluzzi
- Departamento de Fìsica de la Matèria Condensada, Universitat de Barcelona, C. MartìFranquès 1, 08028 Barcelona, Spain
| | - Andrea Crisanti
- Dipartimento di Fisica, Università di Roma "Sapienza", I-00185, Roma, Italy and CNR-ISC, Institute of Complex Systems, Roma, Italy.
| | - Emanuela Zaccarelli
- Dipartimento di Fisica, Università di Roma "Sapienza", I-00185, Roma, Italy and CNR-ISC, Institute of Complex Systems, Roma, Italy.
| | - Nicoletta Gnan
- Dipartimento di Fisica, Università di Roma "Sapienza", I-00185, Roma, Italy and CNR-ISC, Institute of Complex Systems, Roma, Italy.
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29
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Martin D, Chaté H, Nardini C, Solon A, Tailleur J, Van Wijland F. Fluctuation-Induced Phase Separation in Metric and Topological Models of Collective Motion. PHYSICAL REVIEW LETTERS 2021; 126:148001. [PMID: 33891435 DOI: 10.1103/physrevlett.126.148001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
We study the role of noise on the nature of the transition to collective motion in dry active matter. Starting from field theories that predict a continuous transition at the deterministic level, we show that fluctuations induce a density-dependent shift of the onset of order, which in turn changes the nature of the transition into a phase-separation scenario. Our results apply to a range of systems, including models in which particles interact with their "topological" neighbors that have been believed so far to exhibit a continuous onset of order. Our analytical predictions are confirmed by numerical simulations of fluctuating hydrodynamics and microscopic models.
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Affiliation(s)
- David Martin
- Université de Paris, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, F-75205 Paris, France
| | - Hugues Chaté
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- Computational Science Research Center, Beijing 100193, China
| | - Cesare Nardini
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
| | - Alexandre Solon
- Sorbonne Université, CNRS, Laboratoire Physique Théorique de la Matière Condensée, 75005 Paris, France
| | - Julien Tailleur
- Université de Paris, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, F-75205 Paris, France
| | - Frédéric Van Wijland
- Université de Paris, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, F-75205 Paris, France
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30
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Grobas I, Polin M, Asally M. Swarming bacteria undergo localized dynamic phase transition to form stress-induced biofilms. eLife 2021; 10:62632. [PMID: 33722344 PMCID: PMC7963483 DOI: 10.7554/elife.62632] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/26/2021] [Indexed: 12/23/2022] Open
Abstract
Self-organized multicellular behaviors enable cells to adapt and tolerate stressors to a greater degree than isolated cells. However, whether and how cellular communities alter their collective behaviors adaptively upon exposure to stress is largely unclear. Here, we investigate this question using Bacillus subtilis, a model system for bacterial multicellularity. We discover that, upon exposure to a spatial gradient of kanamycin, swarming bacteria activate matrix genes and transit to biofilms. The initial stage of this transition is underpinned by a stress-induced multilayer formation, emerging from a biophysical mechanism reminiscent of motility-induced phase separation (MIPS). The physical nature of the process suggests that stressors which suppress the expansion of swarms would induce biofilm formation. Indeed, a simple physical barrier also induces a swarm-to-biofilm transition. Based on the gained insight, we propose a strategy of antibiotic treatment to inhibit the transition from swarms to biofilms by targeting the localized phase transition.
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Affiliation(s)
- Iago Grobas
- Warwick Medical School, Universityof Warwick, Coventry, United Kingdom
| | - Marco Polin
- Warwick Medical School, Universityof Warwick, Coventry, United Kingdom.,Centre for Mechanochemical Cell Biology, University of Warwick, Coventry, United Kingdom.,Physics Department, University of Warwick, Coventry, United Kingdom.,Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), C/ Miquel Marqués, Balearic Islands, Spain
| | - Munehiro Asally
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry, United Kingdom.,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom.,School of Life Sciences, University of Warwick, Coventry, United Kingdom
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31
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Brauns F, Weyer H, Halatek J, Yoon J, Frey E. Wavelength Selection by Interrupted Coarsening in Reaction-Diffusion Systems. PHYSICAL REVIEW LETTERS 2021; 126:104101. [PMID: 33784126 DOI: 10.1103/physrevlett.126.104101] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 10/19/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Wavelength selection in reaction-diffusion systems can be understood as a coarsening process that is interrupted by counteracting processes at certain wavelengths. We first show that coarsening in mass-conserving systems is driven by self-amplifying mass transport between neighboring high-density domains. We derive a general coarsening criterion and show that coarsening is generically uninterrupted in two-component systems that conserve mass. The theory is then generalized to study interrupted coarsening and anticoarsening due to weakly broken mass conservation, providing a general path to analyze wavelength selection in pattern formation far from equilibrium.
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Affiliation(s)
- Fridtjof Brauns
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 München, Germany
| | - Henrik Weyer
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 München, Germany
| | - Jacob Halatek
- Biological Computation Group, Microsoft Research, Cambridge CB1 2FB, United Kingdom
| | - Junghoon Yoon
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 München, Germany
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 München, Germany
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32
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Martin D, O'Byrne J, Cates ME, Fodor É, Nardini C, Tailleur J, van Wijland F. Statistical mechanics of active Ornstein-Uhlenbeck particles. Phys Rev E 2021; 103:032607. [PMID: 33862678 DOI: 10.1103/physreve.103.032607] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
We study the statistical properties of active Ornstein-Uhlenbeck particles (AOUPs). In this simplest of models, the Gaussian white noise of overdamped Brownian colloids is replaced by a Gaussian colored noise. This suffices to grant this system the hallmark properties of active matter, while still allowing for analytical progress. We study in detail the steady-state distribution of AOUPs in the small persistence time limit and for spatially varying activity. At the collective level, we show AOUPs to experience motility-induced phase separation both in the presence of pairwise forces or due to quorum-sensing interactions. We characterize both the instability mechanism leading to phase separation and the resulting phase coexistence. We probe how, in the stationary state, AOUPs depart from their thermal equilibrium limit by investigating the emergence of ratchet currents and entropy production. In the small persistence time limit, we show how fluctuation-dissipation relations are recovered. Finally, we discuss how the emerging properties of AOUPs can be characterized from the dynamics of their collective modes.
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Affiliation(s)
- David Martin
- Université de Paris, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS,F-75205 Paris, France
| | - Jérémy O'Byrne
- Université de Paris, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS,F-75205 Paris, France
| | - Michael E Cates
- DAMTP, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
| | - Étienne Fodor
- DAMTP, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg
| | - Cesare Nardini
- DAMTP, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
- Service de Physique de l'État Condensé, CNRS UMR 3680, CEA-Saclay, 91191 Gif-sur-Yvette, France
| | - Julien Tailleur
- Université de Paris, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS,F-75205 Paris, France
| | - Frédéric van Wijland
- Université de Paris, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS,F-75205 Paris, France
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33
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Ro S, Kafri Y, Kardar M, Tailleur J. Disorder-Induced Long-Ranged Correlations in Scalar Active Matter. PHYSICAL REVIEW LETTERS 2021; 126:048003. [PMID: 33576681 DOI: 10.1103/physrevlett.126.048003] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/05/2021] [Indexed: 06/12/2023]
Abstract
We study the impact of quenched random potentials and torques on scalar active matter. Microscopic simulations reveal that motility-induced phase separation is replaced in two dimensions by an asymptotically homogeneous phase with anomalous long-ranged correlations and nonvanishing steady-state currents. Using a combination of phenomenological models and a field-theoretical treatment, we show the existence of a lower-critical dimension d_{c}=4, below which phase separation is only observed for systems smaller than an Imry-Ma length scale. We identify a weak-disorder regime in which the structure factor scales as S(q)∼1/q^{2}, which accounts for our numerics. In d=2, we predict that, at larger scales, the behavior should cross over to a strong-disorder regime. In d>2, these two regimes exist separately, depending on the strength of the potential.
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Affiliation(s)
- Sunghan Ro
- Department of Physics, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Yariv Kafri
- Department of Physics, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Mehran Kardar
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Julien Tailleur
- Université de Paris, laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, 75205 Paris, France
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34
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Dinet C, Michelot A, Herrou J, Mignot T. Linking single-cell decisions to collective behaviours in social bacteria. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190755. [PMID: 33487114 DOI: 10.1098/rstb.2019.0755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Social bacteria display complex behaviours whereby thousands of cells collectively and dramatically change their form and function in response to nutrient availability and changing environmental conditions. In this review, we focus on Myxococcus xanthus motility, which supports spectacular transitions based on prey availability across its life cycle. A large body of work suggests that these behaviours require sensory capacity implemented at the single-cell level. Focusing on recent genetic work on a core cellular pathway required for single-cell directional decisions, we argue that signal integration, multi-modal sensing and memory are at the root of decision making leading to multicellular behaviours. Hence, Myxococcus may be a powerful biological system to elucidate how cellular building blocks cooperate to form sensory multicellular assemblages, a possible origin of cognitive mechanisms in biological systems. This article is part of the theme issue 'Basal cognition: conceptual tools and the view from the single cell'.
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Affiliation(s)
- Céline Dinet
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille University, 31 Chemin Joseph Aiguier, 13009 Marseille, France.,Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Alphée Michelot
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Julien Herrou
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille University, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Tâm Mignot
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille University, 31 Chemin Joseph Aiguier, 13009 Marseille, France
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35
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Turci F, Wilding NB. Phase Separation and Multibody Effects in Three-Dimensional Active Brownian Particles. PHYSICAL REVIEW LETTERS 2021; 126:038002. [PMID: 33543975 DOI: 10.1103/physrevlett.126.038002] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
Simulation studies of the phase diagram of repulsive active Brownian particles in three dimensions reveal that the region of motility-induced phase separation between a high and low density phase is enclosed by a region of gas-crystal phase separation. Near-critical loci and structural crossovers can additionally be identified in analogy with simple fluids. Motivated by the striking similarity to the behavior of equilibrium fluids with short-ranged pairwise attractions, we show that a direct mapping to pair potentials in the dilute limit implies interactions that are insufficiently attractive to engender phase separation. Instead, this is driven by the emergence of multibody effects associated with particle caging that occurs at sufficiently high number density. We quantify these effects via information-theoretical measures of n-body effective interactions extracted from the configurational structure.
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Affiliation(s)
- Francesco Turci
- H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, United Kingdom
| | - Nigel B Wilding
- H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, United Kingdom
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36
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Shi XQ, Fausti G, Chaté H, Nardini C, Solon A. Self-Organized Critical Coexistence Phase in Repulsive Active Particles. PHYSICAL REVIEW LETTERS 2020; 125:168001. [PMID: 33124871 DOI: 10.1103/physrevlett.125.168001] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
We revisit motility-induced phase separation in two models of active particles interacting by pairwise repulsion and uncover new qualitative features: the resulting dense phase contains gas bubbles distributed algebraically up to a typically extremely large cutoff scale. At large enough system size and/or global density, all the gas may be contained inside the bubbles, at which point the system is microphase separated with a finite cutoff bubble scale. We further observe that the ordering is clearly anomalous, with different dynamics for the coarsening of the dense phase and of the gas bubbles. This self-organized critical phenomenology is reproduced by a "reduced bubble model" that implements the basic idea of reverse Ostwald ripening put forward in Tjhung et al. [Phys. Rev. X 8, 031080 (2018)PRXHAE2160-330810.1103/PhysRevX.8.031080].
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Affiliation(s)
- Xia-Qing Shi
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
| | - Giordano Fausti
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
| | - Hugues Chaté
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- Computational Science Research Center, Beijing 100193, China
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, 75005 Paris, France
| | - Cesare Nardini
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, 75005 Paris, France
| | - Alexandre Solon
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, 75005 Paris, France
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37
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Arias Del Angel JA, Nanjundiah V, Benítez M, Newman SA. Interplay of mesoscale physics and agent-like behaviors in the parallel evolution of aggregative multicellularity. EvoDevo 2020; 11:21. [PMID: 33062243 PMCID: PMC7549232 DOI: 10.1186/s13227-020-00165-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
Myxobacteria and dictyostelids are prokaryotic and eukaryotic multicellular lineages, respectively, that after nutrient depletion aggregate and develop into structures called fruiting bodies. The developmental processes and resulting morphological outcomes resemble one another to a remarkable extent despite their independent origins, the evolutionary distance between them and the lack of traceable homology in molecular mechanisms. We hypothesize that the morphological parallelism between the two lineages arises as the consequence of the interplay within multicellular aggregates between generic processes, physical and physicochemical processes operating similarly in living and non-living matter at the mesoscale (~10-3-10-1 m) and agent-like behaviors, unique to living systems and characteristic of the constituent cells, considered as autonomous entities acting according to internal rules in a shared environment. Here, we analyze the contributions of generic and agent-like determinants in myxobacteria and dictyostelid development and their roles in the generation of their common traits. Consequent to aggregation, collective cell-cell contacts mediate the emergence of liquid-like properties, making nascent multicellular masses subject to novel patterning and morphogenetic processes. In both lineages, this leads to behaviors such as streaming, rippling, and rounding-up, as seen in non-living fluids. Later the aggregates solidify, leading them to exhibit additional generic properties and motifs. Computational models suggest that the morphological phenotypes of the multicellular masses deviate from the predictions of generic physics due to the contribution of agent-like behaviors of cells such as directed migration, quiescence, and oscillatory signal transduction mediated by responses to external cues. These employ signaling mechanisms that reflect the evolutionary histories of the respective organisms. We propose that the similar developmental trajectories of myxobacteria and dictyostelids are more due to shared generic physical processes in coordination with analogous agent-type behaviors than to convergent evolution under parallel selection regimes. Insights from the biology of these aggregative forms may enable a unified understanding of developmental evolution, including that of animals and plants.
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Affiliation(s)
- Juan A Arias Del Angel
- Laboratorio Nacional de Ciencias de La Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Centro de Ciencias de La Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY 10595 USA.,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Mariana Benítez
- Laboratorio Nacional de Ciencias de La Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Centro de Ciencias de La Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Stuart A Newman
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY 10595 USA
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38
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Das S, Ghosh S, Chelakkot R. Aggregate morphology of active Brownian particles on porous, circular walls. Phys Rev E 2020; 102:032619. [PMID: 33075888 DOI: 10.1103/physreve.102.032619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 09/10/2020] [Indexed: 06/11/2023]
Abstract
We study the motility-induced aggregation of active Brownian particles (ABPs) on a porous, circular wall. We observe that the morphology of aggregated dense-phase on a static wall depends on the wall porosity, particle motility, and the radius of the circular wall. Our analysis reveals two morphologically distinct, dense aggregates; a connected dense cluster that spreads uniformly on the circular wall and a localized cluster that breaks the rotational symmetry of the system. These distinct morphological states are similar to the macroscopic structures observed in aggregates on planar, porous walls. We systematically analyze the parameter regimes where the different morphological states are observed. We further extend our analysis to motile circular rings. We show that the motile ring propels almost ballistically due to the force applied by the active particles when they form a localized cluster, whereas it moves diffusively when the active particles form a continuous cluster. This property demonstrates the possibility of extracting useful work from a system of ABPs, even without artificially breaking the rotational symmetry.
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Affiliation(s)
- Suchismita Das
- Department of Physics, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sounok Ghosh
- Department of Physics, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Raghunath Chelakkot
- Department of Physics, Indian Institute of Technology Bombay, Mumbai 400076, India
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39
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Das S, Chelakkot R. Morphological transitions of active Brownian particle aggregates on porous walls. SOFT MATTER 2020; 16:7250-7255. [PMID: 32744272 DOI: 10.1039/d0sm00797h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Motility-induced wall aggregation of Active Brownian Particles (ABPs) is a well-studied phenomenon. Here, we study the aggregation of ABPs on porous walls, which allows the particles to penetrate through at large motility. We show that the active aggregates undergo a morphological transition from a connected dense-phase to disconnected droplets with an increase in wall porosity and the particle self-motility, similar to wetting-dewetting transitions in equilibrium fluids. We show that both morphologically distinct states are stable, and independent of initial conditions at least in some parameter regions. Our analysis reveals that changes in wall porosity affect the intrinsic properties of the aggregates and changes the effective wall-aggregate interfacial tension, consistent with the appearance of the morphological transition. Accordingly, a close analysis of the density, as well as orientational distribution, indicates that the underlying reason for such morphological transitions is not necessarily specific to the systems with porous walls, and it can be possible to observe in a larger class of confined, active systems by tuning the properties of confining walls.
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Affiliation(s)
- Suchismita Das
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, India.
| | - Raghunath Chelakkot
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, India.
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Bickmann J, Wittkowski R. Predictive local field theory for interacting active Brownian spheres in two spatial dimensions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:214001. [PMID: 31791019 DOI: 10.1088/1361-648x/ab5e0e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We present a predictive local field theory for the nonequilibrium dynamics of interacting active Brownian particles with a spherical shape in two spatial dimensions. The theory is derived by a rigorous coarse-graining starting from the Langevin equations that describe the trajectories of the individual particles. For high accuracy and generality of the theory, it includes configurational order parameters and derivatives up to infinite order. In addition, we discuss possible approximations of the theory and present reduced models that are easier to apply. We show that our theory contains popular models such as Active Model B+ as special cases and that it provides explicit expressions for the coefficients occurring in these and other, often phenomenological, models. As a further outcome, the theory yields an analytical expression for the density-dependent mean swimming speed of the particles. To demonstrate an application of the new theory, we analyze a simple reduced model of the lowest nontrivial order in derivatives, which is able to predict the onset of motility-induced phase separation of the particles. By a linear stability analysis, an analytical expression for the spinodal corresponding to motility-induced phase separation is obtained. This expression is evaluated for the case of particles interacting repulsively by a Weeks-Chandler-Andersen potential. The analytical predictions for the spinodal associated with these particles are found to be in very good agreement with the results of Brownian dynamics simulations that are based on the same Langevin equations as our theory. Furthermore, the critical point predicted by our analytical results agrees excellently with recent computational results from the literature.
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Affiliation(s)
- Jens Bickmann
- Institut für Theoretische Physik, Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany
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Abstract
The diffusion in two dimensions of noninteracting active particles that follow an arbitrary motility pattern is considered for analysis. A Fokker-Planck-like equation is generalized to take into account an arbitrary distribution of scattered angles of the swimming direction, which encompasses the pattern of active motion of particles that move at constant speed. An exact analytical expression for the marginal probability density of finding a particle on a given position at a given instant, independently of its direction of motion, is provided, and a connection with a generalized diffusion equation is unveiled. Exact analytical expressions for the time dependence of the mean-square displacement and of the kurtosis of the distribution of the particle positions are presented. The analysis is focused in the intermediate-time regime, where the effects of the specific pattern of active motion are conspicuous. For this, it is shown that only the expectation value of the first two harmonics of the scattering angle of the direction of motion are needed. The effects of persistence and of circular motion are discussed for different families of distributions of the scattered direction of motion.
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Affiliation(s)
- Francisco J Sevilla
- Instituto de Física, Universidad Nacional Autónoma de México, Apdo. Postal 20-364, 01000, Ciudad de México, México
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Mechanomicrobiology: how bacteria sense and respond to forces. Nat Rev Microbiol 2020; 18:227-240. [DOI: 10.1038/s41579-019-0314-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2019] [Indexed: 12/26/2022]
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van der Linden MN, Alexander LC, Aarts DGAL, Dauchot O. Interrupted Motility Induced Phase Separation in Aligning Active Colloids. PHYSICAL REVIEW LETTERS 2019; 123:098001. [PMID: 31524482 DOI: 10.1103/physrevlett.123.098001] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/19/2019] [Indexed: 06/10/2023]
Abstract
Switching on high activity in a relatively dense system of active Janus colloids, we observe fast clustering, followed by cluster aggregation towards full phase separation. The phase separation process is however interrupted when large enough clusters start breaking apart. Following the cluster size distribution as a function of time, we identify three successive dynamical regimes. Tracking both the particle positions and orientations, we characterize the structural ordering and alignment in the growing clusters and thereby unveil the mechanisms at play in these regimes. In particular, we identify how alignment between the neighboring particles is responsible for the interruption of the full phase separation. Our large scale quantification of the phase separation kinetics in active colloids points towards the new physics observed when both alignment and short-range repulsions are present.
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Affiliation(s)
- Marjolein N van der Linden
- Gulliver UMR CNRS 7083, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry-University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Lachlan C Alexander
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry-University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Dirk G A L Aarts
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry-University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Olivier Dauchot
- Gulliver UMR CNRS 7083, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
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