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Zhu G, Gao L, Sun Y, Wei W, Yan LT. Non-equilibrium structural and dynamic behaviors of active polymers in complex and crowded environments. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2024; 87:054601. [PMID: 38608453 DOI: 10.1088/1361-6633/ad3e11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/12/2024] [Indexed: 04/14/2024]
Abstract
Active matter systems, which convert internal chemical energy or energy from the environment into directed motion, are ubiquitous in nature and exhibit a range of emerging non-equilibrium behaviors. However, most of the current works on active matter have been devoted to particles, and the study of active polymers has only recently come into the spotlight due to their prevalence within living organisms. The intricate interplay between activity and conformational degrees of freedom gives rise to novel structural and dynamical behaviors of active polymers. Research in active polymers remarkably broadens diverse concepts of polymer physics, such as molecular architecture, dynamics, scaling and so on, which is of significant importance for the development of new polymer materials with unique performance. Furthermore, active polymers are often found in strongly interacting and crowded systems and in complex environments, so that the understanding of this behavior is essential for future developments of novel polymer-based biomaterials. This review thereby focuses on the study of active polymers in complex and crowded environments, and aims to provide insights into the fundamental physics underlying the adaptive and collective behaviors far from equilibrium, as well as the open challenges that the field is currently facing.
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Affiliation(s)
- Guolong Zhu
- School of Physics and Electronics, Hunan University, Changsha 410082, People's Republic of China
| | - Lijuan Gao
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
| | - Yihang Sun
- School of Physics and Electronics, Hunan University, Changsha 410082, People's Republic of China
| | - Wenjie Wei
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
| | - Li-Tang Yan
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
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2
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Shin S, Shi G, Cho HW, Thirumalai D. Transcription-induced active forces suppress chromatin motion. Proc Natl Acad Sci U S A 2024; 121:e2307309121. [PMID: 38489381 PMCID: PMC10963020 DOI: 10.1073/pnas.2307309121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 02/06/2024] [Indexed: 03/17/2024] Open
Abstract
The organization of interphase chromosomes in a number of species is starting to emerge thanks to advances in a variety of experimental techniques. However, much less is known about the dynamics, especially in the functional states of chromatin. Some experiments have shown that the motility of individual loci in human interphase chromosome decreases during transcription and increases upon inhibiting transcription. This is a counterintuitive finding because it is thought that the active mechanical force (F) on the order of ten piconewtons, generated by RNA polymerase II (RNAPII) that is presumably transmitted to the gene-rich region of the chromatin, would render it more open, thus enhancing the mobility. We developed a minimal active copolymer model for interphase chromosomes to investigate how F affects the dynamical properties of chromatin. The movements of the loci in the gene-rich region are suppressed in an intermediate range of F and are enhanced at small F values, which has also been observed in experiments. In the intermediate F, the bond length between consecutive loci increases, becoming commensurate with the distance at the minimum of the attractive interaction between nonbonded loci. This results in a transient disorder-to-order transition, leading to a decreased mobility during transcription. Strikingly, the F-dependent change in the locus dynamics preserves the organization of the chromosome at [Formula: see text]. Transient ordering of the loci, which is not found in the polymers with random epigenetic profiles, in the gene-rich region might be a plausible mechanism for nucleating a dynamic network involving transcription factors, RNAPII, and chromatin.
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Affiliation(s)
- Sucheol Shin
- Department of Chemistry, The University of Texas at Austin, Austin, TX78712
| | - Guang Shi
- Department of Chemistry, The University of Texas at Austin, Austin, TX78712
- Department of Materials Science, University of Illinois, Urbana, IL61801
| | - Hyun Woo Cho
- Department of Fine Chemistry and Center for Functional Biomaterials, Seoul National University of Science and Technology, Seoul01811, Republic of Korea
| | - D. Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, TX78712
- Department of Physics, The University of Texas at Austin, Austin, TX78712
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3
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Casert C, Tamblyn I, Whitelam S. Learning stochastic dynamics and predicting emergent behavior using transformers. Nat Commun 2024; 15:1875. [PMID: 38424071 PMCID: PMC10904374 DOI: 10.1038/s41467-024-45629-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
We show that a neural network originally designed for language processing can learn the dynamical rules of a stochastic system by observation of a single dynamical trajectory of the system, and can accurately predict its emergent behavior under conditions not observed during training. We consider a lattice model of active matter undergoing continuous-time Monte Carlo dynamics, simulated at a density at which its steady state comprises small, dispersed clusters. We train a neural network called a transformer on a single trajectory of the model. The transformer, which we show has the capacity to represent dynamical rules that are numerous and nonlocal, learns that the dynamics of this model consists of a small number of processes. Forward-propagated trajectories of the trained transformer, at densities not encountered during training, exhibit motility-induced phase separation and so predict the existence of a nonequilibrium phase transition. Transformers have the flexibility to learn dynamical rules from observation without explicit enumeration of rates or coarse-graining of configuration space, and so the procedure used here can be applied to a wide range of physical systems, including those with large and complex dynamical generators.
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Affiliation(s)
- Corneel Casert
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- Department of Physics and Astronomy, Ghent University, 9000, Ghent, Belgium.
| | - Isaac Tamblyn
- Cash App, Block, Toronto, ON, M5A 1J7, Canada.
- Vector Institute for Artificial Intelligence, Toronto, ON, M5G 1M1, Canada.
- Department of Physics, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
| | - Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
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4
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Turci F, Jack RL, Wilding NB. Partial and complete wetting of droplets of active Brownian particles. SOFT MATTER 2024; 20:2060-2074. [PMID: 38345308 DOI: 10.1039/d3sm01493b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
We study wetting droplets formed of active Brownian particles in contact with a repulsive potential barrier, in a wedge geometry. Our numerical results demonstrate a transition between partially wet and completely wet states, as a function of the barrier height, analogous to the corresponding surface phase transition in passive fluids. We analyse partially wet configurations characterised by a nonzero contact angle θ between the droplet surface and the barrier including the average density profile and its fluctuations. These findings are compared with two equilibrium systems: a Lennard-Jones fluid and a simple contour model for a liquid-vapour interface. We locate the wetting transition where cos(θ) = 1, and the neutral state where cos(θ) = 0. We discuss the implications of these results for possible definitions of surface tensions in active fluids.
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Affiliation(s)
- Francesco Turci
- H. H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, UK.
| | - Robert L Jack
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Nigel B Wilding
- H. H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, UK.
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5
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Spera G, Duclut C, Durand M, Tailleur J. Nematic Torques in Scalar Active Matter: When Fluctuations Favor Polar Order and Persistence. PHYSICAL REVIEW LETTERS 2024; 132:078301. [PMID: 38427854 DOI: 10.1103/physrevlett.132.078301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 07/12/2023] [Accepted: 01/08/2024] [Indexed: 03/03/2024]
Abstract
We study the impact of nematic alignment on scalar active matter in the disordered phase. We show that nematic torques control the emergent physics of particles interacting via pairwise forces and can either induce or prevent phase separation. The underlying mechanism is a fluctuation-induced renormalization of the mass of the polar field that generically arises from nematic torques. The correlations between the fluctuations of the polar and nematic fields indeed conspire to increase the particle persistence length, contrary to what phenomenological computations predict. This effect is generic and our theory also quantitatively accounts for how nematic torques enhance particle accumulation along confining boundaries and opposes demixing in mixtures of active and passive particles.
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Affiliation(s)
- Gianmarco Spera
- Université Paris Cité, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, F-75205 Paris, France
| | - Charlie Duclut
- Université Paris Cité, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, F-75205 Paris, France
- Laboratoire Physique des Cellules et Cancer (PCC), CNRS UMR 168, Institut Curie, Université PSL, Sorbonne Université, 75005 Paris, France
| | - Marc Durand
- Université Paris Cité, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, F-75205 Paris, France
| | - Julien Tailleur
- Université Paris Cité, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, F-75205 Paris, France
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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6
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Hermann S, Schmidt M. Active crystallization from power functional theory. Phys Rev E 2024; 109:L022601. [PMID: 38491681 DOI: 10.1103/physreve.109.l022601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 02/06/2024] [Indexed: 03/18/2024]
Abstract
We address the gas, liquid, and crystal phase behaviors of active Brownian particles in three dimensions. The nonequilibrium force balance at coexistence leads to equality of state functions for which we use power functional approximations. Motility-induced phase separation starts at a critical point and quickly becomes metastable against active freezing for Péclet numbers above a nonequilibrium triple point. The mean swim speed acts as a state variable, similar to the density of depletion agents in colloidal demixing. We obtain agreement with recent simulation results and correctly predict the strength of particle number fluctuations in active fluids.
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Affiliation(s)
- Sophie Hermann
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95447 Bayreuth, Germany
| | - Matthias Schmidt
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95447 Bayreuth, Germany
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7
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Yu H, Jack RL. Competition between lanes and transient jammed clusters in driven binary mixtures. Phys Rev E 2024; 109:024123. [PMID: 38491710 DOI: 10.1103/physreve.109.024123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 01/23/2024] [Indexed: 03/18/2024]
Abstract
We consider mixtures of oppositely driven particles, showing that their nonequilibrium steady states form lanes parallel to the drive, which coexist with transient jammed clusters where particles are temporarily immobilized. We analyze the interplay between these two types of nonequilibrium pattern formation, including their implications for macroscopic demixing perpendicular to the drive. Finite-size scaling analysis indicates that there is no critical driving force associated with demixing, which appears as a crossover in finite systems. We attribute this effect to the disruption of long-ranged order by the transient jammed clusters.
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Affiliation(s)
- Honghao Yu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Robert L Jack
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
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8
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Caporusso CB, Negro G, Suma A, Digregorio P, Carenza LN, Gonnella G, Cugliandolo LF. Phase behaviour and dynamics of three-dimensional active dumbbell systems. SOFT MATTER 2024; 20:923-939. [PMID: 38189452 DOI: 10.1039/d3sm01030a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
We present a comprehensive numerical study of the phase behavior and dynamics of a three-dimensional active dumbbell system with attractive interactions. We demonstrate that attraction is essential for the system to exhibit nontrivial phases. We construct a detailed phase diagram by exploring the effects of the system's activity, density, and attraction strength. We identify several distinct phases, including a disordered, a gel, and a completely phase-separated phase. Additionally, we discover a novel dynamical phase, that we name percolating network, which is characterized by the presence of a spanning network of connected dumbbells. In the phase-separated phase we characterize numerically and describe analytically the helical motion of the dense cluster.
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Affiliation(s)
- C B Caporusso
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, I-70126, Italy.
| | - G Negro
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, I-70126, Italy.
| | - A Suma
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, I-70126, Italy.
| | - P Digregorio
- Departement de Fisica de la Materia Condensada, Facultat de Fisica, Universitat de Barcelona, Martí i Franquès 1, E08028 Barcelona, Spain
- UBICS University of Barcelona Institute of Complex Systems, Martí i Franquès 1, E08028 Barcelona, Spain
| | - L N Carenza
- Instituut-Lorentz, Universiteit Leiden, P.O. Box 9506, 2300 RA Leiden, The Netherlands
- Department of Physics, Koç University, Rumelifeneri Yolu, 34450 Saryer, Istanbul, Turkey
| | - G Gonnella
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, I-70126, Italy.
| | - L F Cugliandolo
- CNRS, Laboratoire de Physique Théorique et Hautes Energies, LPTHE, Sorbonne Université, F-75005 Paris, France
- Institut Universitaire de France, 1 rue Descartes, 75231 Paris Cedex 05, France
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9
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Schiltz-Rouse E, Row H, Mallory SA. Kinetic temperature and pressure of an active Tonks gas. Phys Rev E 2023; 108:064601. [PMID: 38243499 DOI: 10.1103/physreve.108.064601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/06/2023] [Indexed: 01/21/2024]
Abstract
Using computer simulation and analytical theory, we study an active analog of the well-known Tonks gas, where active Brownian particles are confined to a periodic one-dimensional (1D) channel. By introducing the notion of a kinetic temperature, we derive an accurate analytical expression for the pressure and clarify the paradoxical behavior where active Brownian particles confined to 1D exhibit anomalous clustering but no motility-induced phase transition. More generally, this work provides a deeper understanding of pressure in active systems as we uncover a unique link between the kinetic temperature and swim pressure valid for active Brownian particles in higher dimensions.
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Affiliation(s)
- Elijah Schiltz-Rouse
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Hyeongjoo Row
- Department of Chemical and Biomolecular Engineering, UC Berkeley, Berkeley, California 94720, USA
| | - Stewart A Mallory
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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10
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Wiese R, Kroy K, Levis D. Fluid-Glass-Jamming Rheology of Soft Active Brownian Particles. PHYSICAL REVIEW LETTERS 2023; 131:178302. [PMID: 37955492 DOI: 10.1103/physrevlett.131.178302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/13/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023]
Abstract
We numerically study the shear rheology of a binary mixture of soft active Brownian particles, from the fluid to the disordered solid regime. At low shear rates, we find a Newtonian regime, where a Green-Kubo relation with an effective temperature provides the linear viscosity. It is followed by a shear-thinning regime at high shear rates. At high densities, solidification is signaled by the emergence of a finite yield stress. We construct a "fluid-glass-jamming" phase diagram with activity replacing temperature. While both parameters gauge fluctuations, activity also changes the exponent characterizing the decay of the diffusivity close to the glass transition and the shape of the yield stress surface. The dense disordered active solid appears to be mostly dominated by athermal jamming rather than glass rheology.
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Affiliation(s)
- Roland Wiese
- Institute for Theoretical Physics, Leipzig University, 04103 Leipzig, Germany
| | - Klaus Kroy
- Institute for Theoretical Physics, Leipzig University, 04103 Leipzig, Germany
| | - Demian Levis
- Departement de Física de la Materia Condensada, Facultat de Física, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- University of Barcelona Institute of Complex Systems (UBICS), Facultat de Física, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
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11
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Caprini L, Marini Bettolo Marconi U, Löwen H. Entropy production and collective excitations of crystals out of equilibrium: The concept of entropons. Phys Rev E 2023; 108:044603. [PMID: 37978682 DOI: 10.1103/physreve.108.044603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/21/2023] [Indexed: 11/19/2023]
Abstract
We study the collective vibrational excitations of crystals under out-of-equilibrium steady conditions that give rise to entropy production. Their excitation spectrum comprises equilibriumlike phonons of thermal origin and additional collective excitations called entropons because each of them represents a mode of spectral entropy production. Entropons coexist with phonons and dominate them when the system is far from equilibrium while they are negligible in near-equilibrium regimes. The concept of entropons has been recently introduced and verified in a special case of crystals formed by self-propelled particles. Here we show that entropons exist in a broader class of active crystals that are intrinsically out of equilibrium and characterized by the lack of detailed balance. After a general derivation, several explicit examples are discussed, including crystals consisting of particles with alignment interactions and frictional contact forces.
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Affiliation(s)
- L Caprini
- Heinrich-Heine-Universität Düsseldorf, Institut für Theoretische Physik II: Weiche Materie, Universitätsstrasse, 40225 Düsseldorf, Germany
| | - U Marini Bettolo Marconi
- Physics Department, Scuola di Scienze e Tecnologie, Università di Camerino - via Madonna delle Carceri, 62032 Camerino, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - H Löwen
- Heinrich-Heine-Universität Düsseldorf, Institut für Theoretische Physik II: Weiche Materie, Universitätsstrasse, 40225 Düsseldorf, Germany
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12
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Caprini L, Marini Bettolo Marconi U, Puglisi A, Löwen H. Entropons as collective excitations in active solids. J Chem Phys 2023; 159:041102. [PMID: 37486049 DOI: 10.1063/5.0156312] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/05/2023] [Indexed: 07/25/2023] Open
Abstract
The vibrational dynamics of solids is described by phonons constituting basic collective excitations in equilibrium crystals. Here, we consider a non-equilibrium active solid, formed by self-propelled particles, which bring the system into a non-equilibrium steady-state. We identify novel vibrational collective excitations of non-equilibrium (active) origin, which coexist with phonons and dominate over them when the system is far from equilibrium. These vibrational excitations are interpreted in the framework of non-equilibrium physics, in particular, stochastic thermodynamics. We call them "entropons" because they are the modes of spectral entropy production (at a given frequency and wave vector). The existence of entropons could be verified in future experiments on dense self-propelled colloidal Janus particles and granular active matter, as well as in living systems, such as dense cell monolayers.
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Affiliation(s)
- Lorenzo Caprini
- Heinrich-Heine-Universität Düsseldorf, Institut für Theoretische Physik II-Weiche Materie, D-40225 Düsseldorf, Germany
| | - Umberto Marini Bettolo Marconi
- Scuola di Scienze e Tecnologie, Università di Camerino, via Madonna delle Carceri, 62032 Camerino, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Perugia, Via A. Pascoli, I-06123 Perugia, Italy
| | - Andrea Puglisi
- Istituto dei Sistemi Complessi-CNR and Università di Roma Sapienza, P.le Aldo Moro 2, 00185 Rome, Italy
- INFN, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Hartmut Löwen
- Heinrich-Heine-Universität Düsseldorf, Institut für Theoretische Physik II-Weiche Materie, D-40225 Düsseldorf, Germany
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13
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Omar AK, Row H, Mallory SA, Brady JF. Mechanical theory of nonequilibrium coexistence and motility-induced phase separation. Proc Natl Acad Sci U S A 2023; 120:e2219900120. [PMID: 37094152 PMCID: PMC10160997 DOI: 10.1073/pnas.2219900120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/24/2023] [Indexed: 04/26/2023] Open
Abstract
Nonequilibrium phase transitions are routinely observed in both natural and synthetic systems. The ubiquity of these transitions highlights the conspicuous absence of a general theory of phase coexistence that is broadly applicable to both nonequilibrium and equilibrium systems. Here, we present a general mechanical theory for phase separation rooted in ideas explored nearly a half-century ago in the study of inhomogeneous fluids. The core idea is that the mechanical forces within the interface separating two coexisting phases uniquely determine coexistence criteria, regardless of whether a system is in equilibrium or not. We demonstrate the power and utility of this theory by applying it to active Brownian particles, predicting a quantitative phase diagram for motility-induced phase separation in both two and three dimensions. This formulation additionally allows for the prediction of novel interfacial phenomena, such as an increasing interface width while moving deeper into the two-phase region, a uniquely nonequilibrium effect confirmed by computer simulations. The self-consistent determination of bulk phase behavior and interfacial phenomena offered by this mechanical perspective provide a concrete path forward toward a general theory for nonequilibrium phase transitions.
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Affiliation(s)
- Ahmad K. Omar
- Department of Materials Science and Engineering, University of California, Berkeley, CA94720
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Hyeongjoo Row
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
| | - Stewart A. Mallory
- Department of Chemistry, The Pennsylvania State University, University Park, PA16802
| | - John F. Brady
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA91125
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14
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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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15
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Bouvard J, Moisy F, Auradou H. Ostwald-like ripening in the two-dimensional clustering of passive particles induced by swimming bacteria. Phys Rev E 2023; 107:044607. [PMID: 37198759 DOI: 10.1103/physreve.107.044607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 03/28/2023] [Indexed: 05/19/2023]
Abstract
Clustering passive particles by active agents is a promising route for fabrication of colloidal structures. Here, we report the dynamic clustering of micrometric beads in a suspension of motile bacteria. We characterize the coarsening dynamics for various bead sizes, surface fractions, and bacterial concentrations. We show that the time scale τ for the onset of clustering is governed by the time of first encounter of diffusing beads. At large time (t≫τ), we observe a robust cluster growth as t^{1/3}, similar to the Ostwald ripening mechanism. From bead tracking measurements, we extract the short-range bacteria-induced attractive force at the origin of this clustering.
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Affiliation(s)
- J Bouvard
- Université Paris-Saclay, CNRS, FAST, 91405 Orsay, France
| | - F Moisy
- Université Paris-Saclay, CNRS, FAST, 91405 Orsay, France
| | - H Auradou
- Université Paris-Saclay, CNRS, FAST, 91405 Orsay, France
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16
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Kryuchkov NP, Nasyrov AD, Gursky KD, Yurchenko SO. Inertia changes evolution of motility-induced phase separation in active matter across particle activity. Phys Rev E 2023; 107:044601. [PMID: 37198785 DOI: 10.1103/physreve.107.044601] [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: 03/14/2023] [Indexed: 05/19/2023]
Abstract
The effects of inertia in active matter and motility-induced phase separation (MIPS) have attracted growing interest but still remain poorly studied. We studied MIPS behavior in the Langevin dynamics across a broad range of particle activity and damping rate values with molecular dynamic simulations. Here we show that the MIPS stability region across particle activity values consists of several domains separated by discontinuous or sharp changes in susceptibility of mean kinetic energy. These domain boundaries have fingerprints in the system's kinetic energy fluctuations and characteristics of gas, liquid, and solid subphases, such as the number of particles, densities, or the power of energy release due to activity. The observed domain cascade is most stable at intermediate damping rates but loses its distinctness in the Brownian limit or vanishes along with phase separation at lower damping values.
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Affiliation(s)
- Nikita P Kryuchkov
- Bauman Moscow State Technical University, 2nd Baumanskaya Street 5, 105005 Moscow, Russia
| | - Artur D Nasyrov
- Bauman Moscow State Technical University, 2nd Baumanskaya Street 5, 105005 Moscow, Russia
| | - Konstantin D Gursky
- Bauman Moscow State Technical University, 2nd Baumanskaya Street 5, 105005 Moscow, Russia
| | - Stanislav O Yurchenko
- Bauman Moscow State Technical University, 2nd Baumanskaya Street 5, 105005 Moscow, Russia
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17
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Moore F, Russo J, Liverpool TB, Royall CP. Active Brownian particles in random and porous environments. J Chem Phys 2023; 158:104907. [PMID: 36922118 DOI: 10.1063/5.0131340] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
The transport of active particles may occur in complex environments, in which it emerges from the interplay between the mobility of the active components and the quenched disorder of the environment. Here, we explore the structural and dynamical properties of active Brownian particles (ABPs) in random environments composed of fixed obstacles in three dimensions. We consider different arrangements of the obstacles. In particular, we consider two particular situations corresponding to experimentally realizable settings. First, we model pinning particles in (non-overlapping) random positions and, second, in a percolating gel structure and provide an extensive characterization of the structure and dynamics of ABPs in these complex environments. We find that the confinement increases the heterogeneity of the dynamics, with new populations of absorbed and localized particles appearing close to the obstacles. This heterogeneity has a profound impact on the motility induced phase separation exhibited by the particles at high activity, ranging from nucleation and growth in random disorder to a complex phase separation in porous environments.
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Affiliation(s)
- Fergus Moore
- Bristol Centre for Functional Nanomaterials, University of Bristol, Bristol BS8 1FD, United Kingdom
| | - John Russo
- Department of Physics, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | | | - C Patrick Royall
- H. H. Wills Physics Laboratory, Tyndall Ave., Bristol BS8 1TL, United Kingdom
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18
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Omar AK, Klymko K, GrandPre T, Geissler PL, Brady JF. Tuning nonequilibrium phase transitions with inertia. J Chem Phys 2023; 158:074904. [PMID: 36813709 DOI: 10.1063/5.0138256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In striking contrast to equilibrium systems, inertia can profoundly alter the structure of active systems. Here, we demonstrate that driven systems can exhibit effective equilibrium-like states with increasing particle inertia, despite rigorously violating the fluctuation-dissipation theorem. Increasing inertia progressively eliminates motility-induced phase separation and restores equilibrium crystallization for active Brownian spheres. This effect appears to be general for a wide class of active systems, including those driven by deterministic time-dependent external fields, whose nonequilibrium patterns ultimately disappear with increasing inertia. The path to this effective equilibrium limit can be complex, with finite inertia sometimes acting to accentuate nonequilibrium transitions. The restoration of near equilibrium statistics can be understood through the conversion of active momentum sources to passive-like stresses. Unlike truly equilibrium systems, the effective temperature is now density dependent, the only remnant of the nonequilibrium dynamics. This density-dependent temperature can in principle introduce departures from equilibrium expectations, particularly in response to strong gradients. Our results provide additional insight into the effective temperature ansatz while revealing a mechanism to tune nonequilibrium phase transitions.
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Affiliation(s)
- Ahmad K Omar
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720, USA
| | - Katherine Klymko
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Trevor GrandPre
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - Phillip L Geissler
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - John F Brady
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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19
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Feng M, Hou Z. Mode-coupling theory for the dynamics of dense underdamped active Brownian particle system. J Chem Phys 2023; 158:024102. [PMID: 36641396 DOI: 10.1063/5.0131080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We present a theory to study the inertial effect on glassy dynamics of the underdamped active Brownian particle (UABP) system. Using the assumption of the nonequilibrium steady-state, we obtain an effective Fokker-Planck equation for the probability distribution function (PDF) as a function of positions and momentums. With this equation, we achieve the evolution equation of the intermediate scattering function through the Zwanzig-Mori projection operator method and the mode-coupling theory (MCT). Theoretical analysis shows that the inertia of the particle affects the memory function and corresponding glass transition by influencing the structure factor and a velocity correlation function. The theory provides theoretical support and guidance for subsequent simulation work.
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Affiliation(s)
- Mengkai Feng
- Hefei National Research Center for Physical Sciences at the Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhonghuai Hou
- Hefei National Research Center for Physical Sciences at the Microscale and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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20
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Keta YE, Jack RL, Berthier L. Disordered Collective Motion in Dense Assemblies of Persistent Particles. PHYSICAL REVIEW LETTERS 2022; 129:048002. [PMID: 35939008 DOI: 10.1103/physrevlett.129.048002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/19/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
We explore the emergence of nonequilibrium collective motion in disordered nonthermal active matter when persistent motion and crowding effects compete, using simulations of a two-dimensional model of size polydisperse self-propelled particles. In stark contrast with monodisperse systems, we find that polydispersity stabilizes a homogeneous active liquid at arbitrary large persistence times, characterized by remarkable velocity correlations and irregular turbulent flows. For all persistence values, the active fluid undergoes a nonequilibrium glass transition at large density. This is accompanied by collective motion, whose nature evolves from near-equilibrium spatially heterogeneous dynamics at small persistence, to a qualitatively different intermittent dynamics when persistence is large. This latter regime involves a complex time evolution of the correlated displacement field.
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Affiliation(s)
- Yann-Edwin Keta
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS, 34095 Montpellier, France
| | - Robert L Jack
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
| | - Ludovic Berthier
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS, 34095 Montpellier, France
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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21
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Abstract
Active crystals are highly ordered structures that emerge from the self-organization of motile objects, and have been widely studied in synthetic1,2 and bacterial3,4 active matter. Whether persistent crystalline order can emerge in groups of autonomously developing multicellular organisms is currently unknown. Here we show that swimming starfish embryos spontaneously assemble into chiral crystals that span thousands of spinning organisms and persist for tens of hours. Combining experiments, theory and simulations, we demonstrate that the formation, dynamics and dissolution of these living crystals are controlled by the hydrodynamic properties and the natural development of embryos. Remarkably, living chiral crystals exhibit self-sustained chiral oscillations as well as various unconventional deformation response behaviours recently predicted for odd elastic materials5,6. Our results provide direct experimental evidence for how non-reciprocal interactions between autonomous multicellular components may facilitate non-equilibrium phases of chiral active matter.
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22
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Yang J, Ni R, Ciamarra MP. Interplay between jamming and motility-induced phase separation in persistent self-propelling particles. Phys Rev E 2022; 106:L012601. [PMID: 35974520 DOI: 10.1103/physreve.106.l012601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
In living and engineered systems of active particles, self-propulsion induces an unjamming transition from a solid to a fluid phase and phase separation between a gas and a liquidlike phase. We demonstrate an interplay between these two nonequilibrium transitions in systems of persistent active particles. The coexistence and jamming lines in the activity-density plane meet at the jamming transition point in the limit of hard particles or zero activity. This interplay induces an anomalous dynamic in the liquid phase and hysteresis at the active jamming transition.
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Affiliation(s)
- Jing Yang
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Ran Ni
- Chemical Engineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459
| | - Massimo Pica Ciamarra
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
- CNRS@CREATE LTD, 1 Create Way, 08-01 CREATE Tower, Singapore 138602
- CNR-SPIN, Dipartimento di Scienze Fisiche, Università di Napoli Federico II, I-80126 Napoli, Italy
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23
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Boymelgreen A, Schiffbauer J, Khusid B, Yossifon G. Synthetic electrically driven colloids: a platform for understanding collective behavior in soft matter. Curr Opin Colloid Interface Sci 2022. [DOI: 10.1016/j.cocis.2022.101603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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Speck T. Critical behavior of active Brownian particles: Connection to field theories. Phys Rev E 2022; 105:064601. [PMID: 35854575 DOI: 10.1103/physreve.105.064601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
We explore the relation between active Brownian particles, a minimal particle-based model for active matter, and scalar field theories. Both show a liquid-gas-like phase transition toward stable coexistence of a dense liquid with a dilute active gas that terminates in a critical point. However, a comprehensive mapping between the particle-based model parameters and the effective coefficients governing the field theories has not been established yet. We discuss conflicting recent numerical results for the critical exponents of active Brownian particles in two dimensions. Starting from the intermediate effective hydrodynamic equations, we then present a construction for a scalar order parameter for active Brownian particles that yields the active model B+. We argue that a crucial ingredient is the coupling between density and polarization in the particle current. The renormalization flow close to two dimensions exhibits a pair of perturbative fixed points that limit the attractive basin of the Wilson-Fisher fixed point, with the perspective that the critical behavior of active Brownian particles in two dimensions is governed by a strong-coupling fixed point different from Wilson-Fisher and not necessarily corresponding to Ising universality.
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Affiliation(s)
- Thomas Speck
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
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25
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Lei T, Yan R, Zhao N. Biased-angle effect on diffusion dynamics and phase separation in anisotropic active particle system. J Chem Phys 2022; 156:204901. [DOI: 10.1063/5.0090427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A deep understanding for collective behavior in an active matter system with complex interactions has far-reaching impact in biology. In the present work, we adopt Langevin dynamics simulations to investigate diffusion dynamics and phase separation in an anisotropic active particle system with a tunable biased angle α defined as the deviation between the active force direction and anisotropic orientation. Our results demonstrate that the biased angle can induce super-rotational diffusion dynamics characterized by a power-law relationship between the mean square angle displacement (MSAD) and the time interval Δ t in the form of MSAD ∼ Δ t β with β > 1 and also result in non-trivial phase separation kinetics. As activity is dominant, nucleation time shows a non-monotonic dependence on the biased angle. Moreover, there arises a distinct transition of phase separation, from spinodal decomposition without apparent nucleation time to binodal decomposition with prominent nucleation delay. A significant inhibition effect occurs at right and obtuse angles, where the remarkable super-rotational diffusion prevents particle aggregation, leading to a slow nucleation process. As active force is competitive to anisotropic interactions, the system is almost homogeneous, while, intriguingly, we observe a re-entrant phase separation as a small acute angle is introduced. The prominent super-rotational diffusion under small angles provides an optimum condition for particle adsorption and cluster growth and, thus, accounts for the re-entrance of phase separation. A consistent scenario for the physical mechanism of our observations is achieved by properly considering the modulation of the biased angle on the interplay between activity and anisotropic interactions.
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Affiliation(s)
- Ting Lei
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Ran Yan
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610064, China
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26
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Martin Roca J, Martinez R, martinez pedrero F, Ramirez J, Valeriani C. Dynamical anomalies and structural features of Active Brownian Particles characterised by two repulsive length scales. J Chem Phys 2022; 156:164502. [DOI: 10.1063/5.0087601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In this work we study a two-dimensional system composed by Active Brownian Particles (ABPs) interacting via a repulsive potential with two-length-scales, a soft shell and a hard-core. Depending on the ratio between the strength of the soft shell barrier and the activity, we find two regimes: If this ratio is much larger or smaller than 1, the observed behavior is comparable with ABPs interacting via a single length-scale potential. If this ratio is similar to 1, the two length-scales are relevant for both structure and dynamical properties. On the structural side, when the system exhibits a motility induced phase separation, the dense phase is characterised by new and more complex structures compared with the hexatic phase observed in single length-scale systems.On the dynamical side, as far as we are aware, this is the first representation of an anomalous dynamics in active particles.
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Affiliation(s)
| | | | | | - Jorge Ramirez
- Chemical Engineering, Universidad Politécnica de Madrid Escuela Técnica Superior de Ingenieros Industriales, Spain
| | - Chantal Valeriani
- Estructura de la Materia, Fisica Termica y Electronica, Universidad Complutense de Madrid, Spain
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27
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Das A, Kuznets-Speck B, Limmer DT. Direct Evaluation of Rare Events in Active Matter from Variational Path Sampling. PHYSICAL REVIEW LETTERS 2022; 128:028005. [PMID: 35089729 DOI: 10.1103/physrevlett.128.028005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Active matter represents a broad class of systems that evolve far from equilibrium due to the local injection of energy. Like their passive analogs, transformations between distinct metastable states in active matter proceed through rare fluctuations; however, their detailed balance violating dynamics renders these events difficult to study. Here, we present a simulation method for evaluating the rate and mechanism of rare events in generic nonequilibrium systems and apply it to study the conformational changes of a passive solute in an active fluid. The method employs a variational optimization of a control force that renders the rare event a typical one, supplying an exact estimate of its rate as a ratio of path partition functions. Using this method we find that increasing activity in the active bath can enhance the rate of conformational switching of the passive solute in a manner consistent with recent bounds from stochastic thermodynamics.
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Affiliation(s)
- Avishek Das
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - David T Limmer
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawerence Berkeley National Laboratory, Berkeley, California 94720, USA
- Material Sciences Division, Lawerence Berkeley National Laboratory, Berkeley, California 94720, USA
- Kavli Energy NanoSciences Institute, University of California, Berkeley, California 94720, USA
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28
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Turci F, Wilding NB. Wetting Transition of Active Brownian Particles on a Thin Membrane. PHYSICAL REVIEW LETTERS 2021; 127:238002. [PMID: 34936774 DOI: 10.1103/physrevlett.127.238002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/14/2021] [Accepted: 11/01/2021] [Indexed: 06/14/2023]
Abstract
We study nonequilibrium analogues of surface phase transitions in a minimal model of active particles in contact with a purely repulsive potential barrier that mimics a thin porous membrane. Under conditions of bulk motility-induced phase separation, the interaction strength ϵ_{w} of the barrier controls the affinity of the dense phase for the barrier region. We uncover clear signatures of a wetting phase transition as ϵ_{w} is varied. In common with its equilibrium counterpart, the character of this transition depends on the system dimensionality: a continuous transition with large density fluctuations and gas bubbles is uncovered in 2D while 3D systems exhibit a sharp transition absent of large correlations.
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Affiliation(s)
- Francesco Turci
- H.H.Wills Physics Laboratory, Royal Fort, Bristol BS8 1TL, United Kingdom
| | - Nigel B Wilding
- H.H.Wills Physics Laboratory, Royal Fort, Bristol BS8 1TL, United Kingdom
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29
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Mallory SA, Omar AK, Brady JF. Dynamic overlap concentration scale of active colloids. Phys Rev E 2021; 104:044612. [PMID: 34781543 DOI: 10.1103/physreve.104.044612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 10/06/2021] [Indexed: 11/07/2022]
Abstract
By introducing the notion of a dynamic overlap concentration scale, we identify additional universal features of the mechanical properties of active colloids. We codify these features by recognizing that the characteristic length scale of an active particle's trajectory, the run length, introduces a concentration scale ϕ^{*}. Large-scale simulations of repulsive active Brownian particles (ABPs) confirm that this run-length dependent concentration, the trajectory-space analog of the overlap concentration in polymer solutions, delineates distinct concentration regimes in which interparticle collisions alter particle trajectories. Using ϕ^{*} and concentration scales associated with colloidal jamming, the mechanical equation of state for ABPs collapses onto a set of principal curves that contain several overlooked features. The inclusion of these features qualitatively alters previous predictions of the behavior for active colloids, as we demonstrate by computing the spinodal for a suspension of purely repulsive ABPs. Our findings suggest that dynamic overlap concentration scales should help unravel the behavior of active and driven systems.
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Affiliation(s)
- Stewart A Mallory
- Department of Chemistry, The Pennsylvania State University, University Park, Pennyslvania 16802, USA
| | - Ahmad K Omar
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720, USA
| | - John F Brady
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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30
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Wang D, Treado JD, Boromand A, Norwick B, Murrell MP, Shattuck MD, O'Hern CS. The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions. SOFT MATTER 2021; 17:9901-9915. [PMID: 34697616 PMCID: PMC9118367 DOI: 10.1039/d1sm01228b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We investigate the structural, vibrational, and mechanical properties of jammed packings of deformable particles with shape degrees of freedom in three dimensions (3D). Each 3D deformable particle is modeled as a surface-triangulated polyhedron, with spherical vertices whose positions are determined by a shape-energy function with terms that constrain the particle surface area, volume, and curvature, and prevent interparticle overlap. We show that jammed packings of deformable particles without bending energy possess low-frequency, quartic vibrational modes, whose number decreases with increasing asphericity and matches the number of missing contacts relative to the isostatic value. In contrast, jammed packings of deformable particles with non-zero bending energy are isostatic in 3D, with no quartic modes. We find that the contributions to the eigenmodes of the dynamical matrix from the shape degrees of freedom are significant over the full range of frequency and shape parameters for particles with zero bending energy. We further show that the ensemble-averaged shear modulus 〈G〉 scales with pressure P as 〈G〉 ∼ Pβ, with β ≈ 0.75 for jammed packings of deformable particles with zero bending energy. In contrast, β ≈ 0.5 for packings of deformable particles with non-zero bending energy, which matches the value for jammed packings of soft, spherical particles with fixed shape. These studies underscore the importance of incorporating particle deformability and shape change when modeling the properties of jammed soft materials.
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Affiliation(s)
- Dong Wang
- Department of Mechanical Engineering & Materials Science, Yale University, New Haven, Connecticut 06520, USA.
| | - John D Treado
- Department of Mechanical Engineering & Materials Science, Yale University, New Haven, Connecticut 06520, USA.
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Arman Boromand
- Department of Mechanical Engineering & Materials Science, Yale University, New Haven, Connecticut 06520, USA.
| | - Blake Norwick
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Michael P Murrell
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA
- Systems Biology Institute, Yale University, West Haven, Connecticut, 06516, USA
| | - Mark D Shattuck
- Benjamin Levich Institute and Physics Department, The City College of New York, New York, New York 10031, USA
| | - Corey S O'Hern
- Department of Mechanical Engineering & Materials Science, Yale University, New Haven, Connecticut 06520, USA.
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
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31
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Abstract
A framework for performant Brownian Dynamics (BD) many-body simulations with adaptive timestepping is presented. Contrary to the Euler-Maruyama scheme in common non-adaptive BD, we employ an embedded Heun-Euler integrator for the propagation of the overdamped coupled Langevin equations of motion. This enables the derivation of a local error estimate and the formulation of criteria for the acceptance or rejection of trial steps and for the control of optimal stepsize. Introducing erroneous bias in the random forces is avoided by rejection sampling with memory due to Rackauckas and Nie, which makes use of the Brownian bridge theorem and guarantees the correct generation of a specified random process even when rejecting trial steps. For test cases of Lennard-Jones fluids in bulk and in confinement, it is shown that adaptive BD solves performance and stability issues of conventional BD, already outperforming the latter even in standard situations. We expect this novel computational approach to BD to be especially helpful in long-time simulations of complex systems, e.g., in non-equilibrium, where concurrent slow and fast processes occur.
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Affiliation(s)
- Florian Sammüller
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95447 Bayreuth, Germany
| | - Matthias Schmidt
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95447 Bayreuth, Germany
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