1
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Sadhukhan S, Nandi MK, Pandey S, Paoluzzi M, Dasgupta C, Gov NS, Nandi SK. Motility driven glassy dynamics in confluent epithelial monolayers. SOFT MATTER 2024; 20:6160-6175. [PMID: 39044639 DOI: 10.1039/d4sm00352g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
As wounds heal, embryos develop, cancer spreads, or asthma progresses, the cellular monolayer undergoes a glass transition between solid-like jammed and fluid-like flowing states. During some of these processes, the cells undergo an epithelial-to-mesenchymal transition (EMT): they acquire in-plane polarity and become motile. Thus, how motility drives the glassy dynamics in epithelial systems is critical for the EMT process. However, no analytical framework that is indispensable for deeper insights exists. Here, we develop such a theory inspired by a well-known glass theory. One crucial result of this work is that the confluency affects the effective persistence time-scale of active force, described by its rotational diffusivity, Deffr. Deffr differs from the bare rotational diffusivity, Dr, of the motile force due to cell shape dynamics, which acts to rectify the force dynamics: Deffr is equal to Dr when Dr is small and saturates when Dr is large. We test the theoretical prediction of Deffr and how it affects the relaxation dynamics in our simulations of the active Vertex model. This novel effect of Deffr is crucial to understanding the new and previously published simulation data of active glassy dynamics in epithelial monolayers.
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Affiliation(s)
- Souvik Sadhukhan
- Tata Institute of Fundamental Research, 36/P Gopanpally Village, Hyderabad-500046, India.
| | - Manoj Kumar Nandi
- Institut National de la Santé et de la Recherche Médicale, Stem Cell and Brain Research Institute, Université Claude Bernard Lyon 1, Bron 69500, France
| | - Satyam Pandey
- Tata Institute of Fundamental Research, 36/P Gopanpally Village, Hyderabad-500046, India.
| | - Matteo Paoluzzi
- Istituto per le Applicazioni del Calcolo del Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Chandan Dasgupta
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
- International Centre for Theoretical Sciences, TIFR, Bangalore 560089, India
| | - Nir S Gov
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Saroj Kumar Nandi
- Tata Institute of Fundamental Research, 36/P Gopanpally Village, Hyderabad-500046, India.
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2
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Szamel G, Flenner E. Extremely persistent dense active fluids. SOFT MATTER 2024; 20:5237-5244. [PMID: 38904184 DOI: 10.1039/d4sm00338a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
We study the dynamics of dense three-dimensional systems of active particles for large persistence times τp at constant average self-propulsion force f. These systems are fluid counterparts of previously investigated extremely persistent systems, which in the large persistence time limit relax only on the time scale of τp. We find that many dynamic properties of the systems we study, such as the mean-squared velocity, the self-intermediate scattering function, and the shear-stress correlation function, become τp-independent in the large persistence time limit. In addition, the large τp limits of many dynamic properties, such as the mean-square velocity and the relaxation times of the scattering function, and the shear-stress correlation function, depend on f as power laws with non-trivial exponents. We conjecture that these systems constitute a new class of extremely persistent active systems.
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Affiliation(s)
- Grzegorz Szamel
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
| | - Elijah Flenner
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
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3
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Mo R, Xu D, Xu N. Thinning by cluster breaking: Active matter and shear flows share thinning mechanisms. Proc Natl Acad Sci U S A 2024; 121:e2318917121. [PMID: 38843185 PMCID: PMC11181082 DOI: 10.1073/pnas.2318917121] [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: 10/29/2023] [Accepted: 05/04/2024] [Indexed: 06/19/2024] Open
Abstract
Among many unexpected phenomena of active matter is the recently observed superfluid-like thinning (viscosity drop) behavior of bacteria suspensions. Understanding this peculiar self-propelled thinning by active matter is of theoretical and practical importance. Here, we find that, although distinct in driving mechanisms, active matter and shear flows exhibit similar thinning behaviors upon the increase of self-propulsion and shear forces, respectively. Our structural characterizations reveal that they actually share the same cluster-breaking mechanism of thinning. How fast and how shattered the cluster is broken determines the (dis)continuity of the thinning. This explains why adding active particles to Newtonian fluids can cause thinning, in which rotation of active particles play a key role in breaking clusters. Our work proposes a mechanism of self-propelled thinning and further establishes the underlying connections between active matter and shear flows.
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Affiliation(s)
- Ruoyang Mo
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei230026, People’s Republic of China
- Chinese Academy of Sciences Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei230026, People’s Republic of China
- Department of Physics, University of Science and Technology of China, Hefei230026, People’s Republic of China
| | - Ding Xu
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei230026, People’s Republic of China
- Chinese Academy of Sciences Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei230026, People’s Republic of China
- Department of Physics, University of Science and Technology of China, Hefei230026, People’s Republic of China
| | - Ning Xu
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei230026, People’s Republic of China
- Chinese Academy of Sciences Key Laboratory of Microscale Magnetic Resonance, University of Science and Technology of China, Hefei230026, People’s Republic of China
- Department of Physics, University of Science and Technology of China, Hefei230026, People’s Republic of China
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4
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Ai BQ, Guo RX, Zeng CH, He YF. Rotational inertia-induced glassy transition in chiral particle systems. Phys Rev E 2024; 109:064902. [PMID: 39020947 DOI: 10.1103/physreve.109.064902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 05/12/2024] [Indexed: 07/20/2024]
Abstract
The dense active matter exhibits characteristics reminiscent of traditional glassy phenomena, yet the role of rotational inertia in glass dynamics remains elusive. In this study, we investigate the glass dynamics of chiral active particles influenced by rotational inertia. Rotational inertia endows exponential memory to particle orientation, restricting its alteration and amplifying the effective persistence time. At lower spinning frequencies, the diffusion coefficient exhibits a peak function relative to rotational inertia for shorter persistence times, while it steadily increases with rotational inertia for longer persistence times. In the realm of high-frequency spinning, the impact of rotational inertia on diffusion behavior becomes more pronounced, resulting in a nonmonotonic and intricate relationship between the diffusion coefficient and rotational inertia. Consequently, the introduction of rotational inertia significantly alters the glassy dynamics of chiral active particles, allowing for the control over transitions between fluid and glassy states by modulating rotational inertia. Moreover, our findings indicate that at a specific spinning temperature, there exists an optimal spinning frequency at which the diffusion coefficient attains its maximum value.
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Affiliation(s)
- Bao-Quan Ai
- Key Laboratory of Atomic and Subatomic Structure and Quantum Control (Ministry of Education), and School of Physics, South China Normal University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, and Guangdong-Hong Kong Joint Laboratory of Quantum Matter, South China Normal University, Guangzhou 510006, China
| | - Rui-Xue Guo
- Key Laboratory of Atomic and Subatomic Structure and Quantum Control (Ministry of Education), and School of Physics, South China Normal University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, and Guangdong-Hong Kong Joint Laboratory of Quantum Matter, South China Normal University, Guangzhou 510006, China
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5
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Keta YE, Klamser JU, Jack RL, Berthier L. Emerging Mesoscale Flows and Chaotic Advection in Dense Active Matter. PHYSICAL REVIEW LETTERS 2024; 132:218301. [PMID: 38856251 DOI: 10.1103/physrevlett.132.218301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/23/2023] [Accepted: 04/17/2024] [Indexed: 06/11/2024]
Abstract
We study two models of overdamped self-propelled disks in two dimensions, with and without aligning interactions. Both models support active mesoscale flows, leading to chaotic advection and transport over large length scales in their homogeneous dense fluid states, away from dynamical arrest. They form streams and vortices reminiscent of multiscale flow patterns in turbulence. We show that the characteristics of these flows do not depend on the specific details of the active fluids, and result from the competition between crowding effects and persistent propulsions. This observation suggests that dense active suspensions of self-propelled particles present a type of "active turbulence" distinct from collective flows reported in other types of active systems.
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Affiliation(s)
- Yann-Edwin Keta
- Laboratoire Charles Coulomb (L2C), Université de Montpellier and CNRS (UMR 5221), 34095 Montpellier, France
| | - Juliane U Klamser
- Laboratoire Charles Coulomb (L2C), Université de Montpellier and CNRS (UMR 5221), 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 and CNRS (UMR 5221), 34095 Montpellier, France
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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6
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Villarroel C, Düring G. Avalanche properties at the yielding transition: from externally deformed glasses to active systems. SOFT MATTER 2024; 20:3520-3528. [PMID: 38600803 DOI: 10.1039/d3sm01354e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
We investigated the yielding phenomenon in the quasistatic limit using numerical simulations of soft particles. Two different deformation scenarios, simple shear (passive) and self-random force (active), and two interaction potentials were used. Our approach reveals that the exponents describing the avalanche distribution are universal within the margin of error, showing consistency between the passive and active systems. This indicates that any differences observed in the flow curves may have resulted from a dynamic effect on the avalanche propagation mechanism. The evolution time required to reach a steady state differs significantly between active and passive scenarios under similar conditions. However, we demonstrated that plastic avalanches under athermal quasistatic simulation dynamics display a similar scaling relationship between avalanche size and relaxation time, which cannot explain the different flow curves.
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Affiliation(s)
- Carlos Villarroel
- Instituto de Física, Pontificia Universidad Católica de Chile, Casilla 306, Santiago, Chile.
| | - Gustavo Düring
- Instituto de Física, Pontificia Universidad Católica de Chile, Casilla 306, Santiago, Chile.
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7
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Chakraborty T, Pradhan P. Time-dependent properties of run-and-tumble particles. II. Current fluctuations. Phys Rev E 2024; 109:044135. [PMID: 38755901 DOI: 10.1103/physreve.109.044135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 03/19/2024] [Indexed: 05/18/2024]
Abstract
We investigate steady-state current fluctuations in two models of hardcore run-and-tumble particles (RTPs) on a periodic one-dimensional lattice of L sites, for arbitrary tumbling rate γ=τ_{p}^{-1} and density ρ; model I consists of standard hardcore RTPs, while model II is an analytically tractable variant of model I, called a long-ranged lattice gas (LLG). We show that, in the limit of L large, the fluctuation of cumulative current Q_{i}(T,L) across the ith bond in a time interval T≫1/D grows first subdiffusively and then diffusively (linearly) with T: 〈Q_{i}^{2}〉∼T^{α} with α=1/2 for 1/D≪T≪L^{2}/D and α=1 for T≫L^{2}/D, where D(ρ,γ) is the collective- or bulk-diffusion coefficient; at small times T≪1/D, exponent α depends on the details. Remarkably, regardless of the model details, the scaled bond-current fluctuations D〈Q_{i}^{2}(T,L)〉/2χL≡W(y) as a function of scaled variable y=DT/L^{2} collapse onto a universal scaling curve W(y), where χ(ρ,γ) is the collective particle mobility. In the limit of small density and tumbling rate, ρ,γ→0, with ψ=ρ/γ fixed, there exists a scaling law: The scaled mobility γ^{a}χ(ρ,γ)/χ^{(0)}≡H(ψ) as a function of ψ collapses onto a scaling curve H(ψ), where a=1 and 2 in models I and II, respectively, and χ^{(0)} is the mobility in the limiting case of a symmetric simple exclusion process; notably, the scaling function H(ψ) is model dependent. For model II (LLG), we calculate exactly, within a truncation scheme, both the scaling functions, W(y) and H(ψ). We also calculate spatial correlation functions for the current and compare our theory with simulation results of model I; for both models, the correlation functions decay exponentially, with correlation length ξ∼τ_{p}^{1/2} diverging with persistence time τ_{p}≫1. Overall, our theory is in excellent agreement with simulations and complements the prior findings [T. Chakraborty and P. Pradhan, Phys. Rev. E 109, 024124 (2024)1539-375510.1103/PhysRevE.109.024124].
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Affiliation(s)
- Tanmoy Chakraborty
- Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Punyabrata Pradhan
- Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
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8
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McCarthy E, Manna RK, Damavandi O, Manning ML. Demixing in Binary Mixtures with Differential Diffusivity at High Density. PHYSICAL REVIEW LETTERS 2024; 132:098301. [PMID: 38489657 DOI: 10.1103/physrevlett.132.098301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/15/2023] [Accepted: 01/30/2024] [Indexed: 03/17/2024]
Abstract
Spontaneous phase separation, or demixing, is important in biological phenomena such as cell sorting. In particle-based models, an open question is whether differences in diffusivity can drive such demixing. While differential-diffusivity-induced phase separation occurs in mixtures with a packing fraction up to 0.7 [S. N. Weber et al. Binary mixtures of particles with different diffusivities demix, Phys. Rev. Lett. 116, 058301 (2016)PRLTAO0031-900710.1103/PhysRevLett.116.058301], here we investigate whether demixing persists at even higher densities relevant for cells. For particle packing fractions between 0.7 and 1.0 the system demixes, but at packing fractions above unity the system remains mixed, exposing re-entrant behavior in the phase diagram that occurs when phase separation can no longer drive a change in entropy production at high densities. We also find that a confluent Voronoi model for tissues does not phase separate, consistent with particle-based simulations.
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Affiliation(s)
- Erin McCarthy
- Department of Physics and BioInspired Institute, Syracuse University, Syracuse, New York 13244, USA
| | - Raj Kumar Manna
- Department of Physics and BioInspired Institute, Syracuse University, Syracuse, New York 13244, USA
| | - Ojan Damavandi
- Department of Physics and BioInspired Institute, Syracuse University, Syracuse, New York 13244, USA
| | - M Lisa Manning
- Department of Physics and BioInspired Institute, Syracuse University, Syracuse, New York 13244, USA
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9
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Xu H, Wu Y. Self-enhanced mobility enables vortex pattern formation in living matter. Nature 2024; 627:553-558. [PMID: 38480895 DOI: 10.1038/s41586-024-07114-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 01/24/2024] [Indexed: 03/22/2024]
Abstract
Ranging from subcellular organelle biogenesis to embryo development, the formation of self-organized structures is a hallmark of living systems. Whereas the emergence of ordered spatial patterns in biology is often driven by intricate chemical signalling that coordinates cellular behaviour and differentiation1-4, purely physical interactions can drive the formation of regular biological patterns such as crystalline vortex arrays in suspensions of spermatozoa5 and bacteria6. Here we discovered a new route to self-organized pattern formation driven by physical interactions, which creates large-scale regular spatial structures with multiscale ordering. Specifically we found that dense bacterial living matter spontaneously developed a lattice of mesoscale, fast-spinning vortices; these vortices each consisted of around 104-105 motile bacterial cells and were arranged in space at greater than centimetre scale and with apparent hexagonal order, whereas individual cells in the vortices moved in coordinated directions with strong polar and vortical order. Single-cell tracking and numerical simulations suggest that the phenomenon is enabled by self-enhanced mobility in the system-that is, the speed of individual cells increasing with cell-generated collective stresses at a given cell density. Stress-induced mobility enhancement and fluidization is prevalent in dense living matter at various scales of length7-9. Our findings demonstrate that self-enhanced mobility offers a simple physical mechanism for pattern formation in living systems and, more generally, in other active matter systems10 near the boundary of fluid- and solid-like behaviours11-17.
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Affiliation(s)
- Haoran Xu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P.R. China
| | - Yilin Wu
- Department of Physics and Shenzhen Research Institute, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P.R. China.
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10
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Chakraborty T, Pradhan P. Time-dependent properties of run-and-tumble particles: Density relaxation. Phys Rev E 2024; 109:024124. [PMID: 38491605 DOI: 10.1103/physreve.109.024124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/03/2024] [Indexed: 03/18/2024]
Abstract
We characterize collective diffusion of hardcore run-and-tumble particles (RTPs) by explicitly calculating the bulk-diffusion coefficient D(ρ,γ) for arbitrary density ρ and tumbling rate γ, in systems on a d-dimensional periodic lattice. We study two minimal models of RTPs: Model I is the standard version of hardcore RTPs introduced in [Phys. Rev. E 89, 012706 (2014)10.1103/PhysRevE.89.012706], whereas model II is a long-ranged lattice gas (LLG) with hardcore exclusion, an analytically tractable variant of model I. We calculate the bulk-diffusion coefficient analytically for model II and numerically for model I through an efficient Monte Carlo algorithm; notably, both models have qualitatively similar features. In the strong-persistence limit γ→0 (i.e., dimensionless ratio r_{0}γ/v→0), with v and r_{0} being the self-propulsion speed and particle diameter, respectively, the fascinating interplay between persistence and interaction is quantified in terms of two length scales: (i) persistence length l_{p}=v/γ and (ii) a "mean free path," being a measure of the average empty stretch or gap size in the hopping direction. We find that the bulk-diffusion coefficient varies as a power law in a wide range of density: D∝ρ^{-α}, with exponent α gradually crossing over from α=2 at high densities to α=0 at low densities. As a result, the density relaxation is governed by a nonlinear diffusion equation with anomalous spatiotemporal scaling. In the thermodynamic limit, we show that the bulk-diffusion coefficient-for ρ,γ→0 with ρ/γ fixed-has a scaling form D(ρ,γ)=D^{(0)}F(ρav/γ), where a∼r_{0}^{d-1} is particle cross section and D^{(0)} is proportional to the diffusion coefficient of noninteracting particles; the scaling function F(ψ) is calculated analytically for model II (LLG) and numerically for model I. Our arguments are independent of dimensions and microscopic details.
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Affiliation(s)
- Tanmoy Chakraborty
- Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Punyabrata Pradhan
- Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
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11
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McDermott D, Reichhardt C, Reichhardt CJO. Characterizing different motility-induced regimes in active matter with machine learning and noise. Phys Rev E 2023; 108:064613. [PMID: 38243443 DOI: 10.1103/physreve.108.064613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/29/2023] [Indexed: 01/21/2024]
Abstract
We examine motility-induced phase separation (MIPS) in two-dimensional run-and-tumble disk systems using both machine learning and noise fluctuation analysis. Our measures suggest that within the MIPS state there are several distinct regimes as a function of density and run time, so that systems with MIPS transitions exhibit an active fluid, an active crystal, and a critical regime. The different regimes can be detected by combining an order parameter extracted from principal component analysis with a cluster stability measurement. The principal component-derived order parameter is maximized in the critical regime, remains low in the active fluid, and has an intermediate value in the active crystal regime. We demonstrate that machine learning can better capture dynamical properties of the MIPS regimes compared to more standard structural measures such as the maximum cluster size. The different regimes can also be characterized via changes in the noise power of the fluctuations in the average speed. In the critical regime, the noise power passes through a maximum and has a broad spectrum with a 1/f^{1.6} signature, similar to the noise observed near depinning transitions or for solids undergoing plastic deformation.
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Affiliation(s)
- D McDermott
- X-Theoretical Design Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - C Reichhardt
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - C J O Reichhardt
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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12
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Umeda K, Nishizawa K, Nagao W, Inokuchi S, Sugino Y, Ebata H, Mizuno D. Activity-dependent glassy cell mechanics II: Nonthermal fluctuations under metabolic activity. Biophys J 2023; 122:4395-4413. [PMID: 37865819 PMCID: PMC10698330 DOI: 10.1016/j.bpj.2023.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/28/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023] Open
Abstract
The glassy cytoplasm, crowded with bio-macromolecules, is fluidized in living cells by mechanical energy derived from metabolism. Characterizing the living cytoplasm as a nonequilibrium system is crucial in elucidating the intricate mechanism that relates cell mechanics to metabolic activities. In this study, we conducted active and passive microrheology in eukaryotic cells, and quantified nonthermal fluctuations by examining the violation of the fluctuation-dissipation theorem. The power spectral density of active force generation was estimated following the Langevin theory extended to nonequilibrium systems. However, experiments performed while regulating cellular metabolic activity showed that the nonthermal displacement fluctuation, rather than the active nonthermal force, is linked to metabolism. We discuss that mechano-enzymes in living cells do not act as microscopic objects. Instead, they generate meso-scale collective fluctuations with displacements controlled by enzymatic activity. The activity induces structural relaxations in glassy cytoplasm. Even though the autocorrelation of nonthermal fluctuations is lost at long timescales due to the structural relaxations, the nonthermal displacement fluctuation remains regulated by metabolic reactions. Our results therefore demonstrate that nonthermal fluctuations serve as a valuable indicator of a cell's metabolic activities, regardless of the presence or absence of structural relaxations.
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Affiliation(s)
| | | | - Wataru Nagao
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Shono Inokuchi
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Yujiro Sugino
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Ebata
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Daisuke Mizuno
- Department of Physics, Kyushu University, Fukuoka, Japan.
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13
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Chakraborty S, Krishnan VV, Ramola K, Karmakar S. Enhanced vibrational stability in glass droplets. PNAS NEXUS 2023; 2:pgad289. [PMID: 37746327 PMCID: PMC10516527 DOI: 10.1093/pnasnexus/pgad289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/28/2023] [Indexed: 09/26/2023]
Abstract
We show through simulations of amorphous solids prepared in open-boundary conditions that they possess significantly fewer low-frequency vibrational modes compared to their periodic boundary counterparts. Specifically, using measurements of the vibrational density of states, we find that the D ( ω ) ∼ ω 4 law changes to D ( ω ) ∼ ω δ with δ ≈ 5 in two dimensions and δ ≈ 4.5 in three dimensions. Crucially, this enhanced stability is achieved when utilizing slow annealing protocols to generate solid configurations. We perform an anharmonic analysis of the minima corresponding to the lowest frequency modes in such open-boundary systems and discuss their correlation with the density of states. A study of various system sizes further reveals that small systems display a higher degree of localization in vibrations. Lastly, we confine open-boundary solids in order to introduce macroscopic stresses in the system, which are absent in the unconfined system and find that the D ( ω ) ∼ ω 4 behavior is recovered.
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Affiliation(s)
| | - Vishnu V Krishnan
- Tata Institute of Fundamental Research, Hyderabad, 500046 Telangana, India
| | - Kabir Ramola
- Tata Institute of Fundamental Research, Hyderabad, 500046 Telangana, India
| | - Smarajit Karmakar
- Tata Institute of Fundamental Research, Hyderabad, 500046 Telangana, India
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14
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Paul K, Mutneja A, Nandi SK, Karmakar S. Dynamical heterogeneity in active glasses is inherently different from its equilibrium behavior. Proc Natl Acad Sci U S A 2023; 120:e2217073120. [PMID: 37585467 PMCID: PMC10450852 DOI: 10.1073/pnas.2217073120] [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: 10/06/2022] [Accepted: 07/12/2023] [Indexed: 08/18/2023] Open
Abstract
Activity-driven glassy dynamics, while ubiquitous in collective cell migration, intracellular transport, dynamics in bacterial and ant colonies, etc., also extends the scope and extent of the as-yet mysterious physics of glass transition. Active glasses are hitherto assumed to be qualitatively similar to their equilibrium counterparts at an effective temperature, [Formula: see text]. Here, we combine large-scale simulations and an analytical mode-coupling theory (MCT) for such systems and show that, in fact, an active glass is inherently different from an equilibrium glass. Although the relaxation dynamics can be equilibrium-like at a [Formula: see text], effects of activity on the dynamic heterogeneity (DH), which is a hallmark of glassy dynamics, are quite nontrivial and complex. With no preexisting data, we employ four distinct methods for reliable estimates of the DH length scales. Our work shows that active glasses exhibit dramatic growth of DH and systems with similar relaxation times, and thus, [Formula: see text] can have widely varying DH. To theoretically study DH, we extend active MCT and find good qualitative agreement between the theory and simulation results. Our results pave avenues for understanding the role of DH in glassy dynamics and can have fundamental significance even in equilibrium.
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Affiliation(s)
- Kallol Paul
- Tata Institute of Fundamental Research Center for Interdisciplinary Science, Hyderabad500046, Telangana, India
| | - Anoop Mutneja
- Tata Institute of Fundamental Research Center for Interdisciplinary Science, Hyderabad500046, Telangana, India
| | - Saroj Kumar Nandi
- Tata Institute of Fundamental Research Center for Interdisciplinary Science, Hyderabad500046, Telangana, India
| | - Smarajit Karmakar
- Tata Institute of Fundamental Research Center for Interdisciplinary Science, Hyderabad500046, Telangana, India
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15
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Teboul V. Dynamic phase transition induced by active molecules in a supercooled liquid. Phys Rev E 2023; 108:024605. [PMID: 37723732 DOI: 10.1103/physreve.108.024605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/21/2023] [Indexed: 09/20/2023]
Abstract
The purpose of this work is to use active particles to investigate the effect of facilitation on supercooled liquids. To this end we examine the behavior of a model supercooled liquid that is doped with a mixture of active particles and slowed particles. To simulate the facilitation mechanism, the activated particles are subjected to a force that follows the mobility of their most mobile neighboring molecule, while the slowed particles experience a friction force. Upon activation, we observe a fluidization of the entire medium along with a significant increase in dynamic heterogeneity. This effect is reminiscent of the fluidization observed experimentally when introducing molecular motors into soft materials. Interestingly, when the characteristic time τ_{μ}, used to define the mobility in the facilitation mechanism, matches the physical time t^{*} that characterizes the spontaneous cooperativity of the material, we observe a phase transition accompanied by structural aggregation of the active molecules. This transition is characterized by a sharp increase in fluidization and dynamic heterogeneity.
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Affiliation(s)
- Victor Teboul
- Laboratoire de Photonique d'Angers EA 4464, Université d'Angers, Physics Department, 2 Bd Lavoisier, 49045 Angers, France
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16
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Ebata H, Umeda K, Nishizawa K, Nagao W, Inokuchi S, Sugino Y, Miyamoto T, Mizuno D. Activity-dependent glassy cell mechanics Ⅰ: Mechanical properties measured with active microrheology. Biophys J 2023; 122:1781-1793. [PMID: 37050875 PMCID: PMC10209042 DOI: 10.1016/j.bpj.2023.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 01/27/2023] [Accepted: 04/07/2023] [Indexed: 04/14/2023] Open
Abstract
Active microrheology was conducted in living cells by applying an optical-trapping force to vigorously fluctuating tracer beads with feedback-tracking technology. The complex shear modulus G(ω)=G'(ω)-iG″(ω) was measured in HeLa cells in an epithelial-like confluent monolayer. We found that G(ω)∝(-iω)1/2 over a wide range of frequencies (1 Hz < ω/2π < 10 kHz). Actin disruption and cell-cycle progression from G1 to S and G2 phases only had a limited effect on G(ω) in living cells. On the other hand, G(ω) was found to be dependent on cell metabolism; ATP-depleted cells showed an increased elastic modulus G'(ω) at low frequencies, giving rise to a constant plateau such that G(ω)=G0+A(-iω)1/2. Both the plateau and the additional frequency dependency ∝(-iω)1/2 of ATP-depleted cells are consistent with a rheological response typical of colloidal jamming. On the other hand, the plateau G0 disappeared in ordinary metabolically active cells, implying that living cells fluidize their internal states such that they approach the critical jamming point.
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Affiliation(s)
- Hiroyuki Ebata
- Department of Physics, Kyushu University, Fukuoka, Japan
| | | | - Kenji Nishizawa
- Institute of Developmental Biology of Marseille, Marseille, France
| | - Wataru Nagao
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Shono Inokuchi
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Yujiro Sugino
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Takafumi Miyamoto
- Department of Endocrinology and Metabolism, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan; Transborder Medical Research Center, University of Tsukuba, Ibaraki, Japan
| | - Daisuke Mizuno
- Department of Physics, Kyushu University, Fukuoka, Japan.
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17
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Chatterjee AK, Hayakawa H. Counterflow-induced clustering: Exact results. Phys Rev E 2023; 107:054905. [PMID: 37329055 DOI: 10.1103/physreve.107.054905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 04/27/2023] [Indexed: 06/18/2023]
Abstract
We analyze the cluster formation in a nonergodic stochastic system as a result of counterflow, with the aid of an exactly solvable model. To illustrate the clustering, a two species asymmetric simple exclusion process with impurities on a periodic lattice is considered, where the impurity can activate flips between the two nonconserved species. Exact analytical results, supported by Monte Carlo simulations, show two distinct phases, free-flowing phase and clustering phase. The clustering phase is characterized by constant density and vanishing current of the nonconserved species, whereas the free-flowing phase is identified with nonmonotonic density and nonmonotonic finite current of the same. The n-point spatial correlation between n consecutive vacancies grows with increasing n in the clustering phase, indicating the formation of two macroscopic clusters in this phase, one of the vacancies and the other consisting of all the particles. We define a rearrangement parameter that permutes the ordering of particles in the initial configuration, keeping all the input parameters fixed. This rearrangement parameter reveals the significant effect of nonergodicity on the onset of clustering. For a special choice of the microscopic dynamics, we connect the present model to a system of run-and-tumble particles used to model active matter, where the two species having opposite net bias manifest the two possible run directions of the run-and-tumble particles, and the impurities act as tumbling reagents that enable the tumbling process.
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Affiliation(s)
- Amit Kumar Chatterjee
- Yukawa Institute for Theoretical Physics, Kyoto University, Kitashirakawa Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hisao Hayakawa
- Yukawa Institute for Theoretical Physics, Kyoto University, Kitashirakawa Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- Center for Gravitational Physics and Quantum Information, Yukawa Institute for Theoretical Physics, Kyoto University, Kitashirakawa Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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18
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Kroo LA, Bull MS, Prakash M. Active foam: the adaptive mechanics of 2D air-liquid foam under cyclic inflation. SOFT MATTER 2023; 19:2539-2553. [PMID: 36942719 DOI: 10.1039/d3sm00019b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Foam is a canonical example of disordered soft matter where local force balance leads to the competition of many metastable configurations. We present an experimental and theoretical framework for "active foam" where an individual voxel inflates and deflates periodically. Local periodic activity leads to irreversible and reversible T1 transitions throughout the foam, eventually reaching a reversible limit cycle. Individual vertices displace outwards and subsequently return back to their approximate original radial position; this radial displacement follows an inverse law. Surprisingly, each return trajectory does not retrace its outbound path but encloses a finite area, with a clockwise (CW) or counterclockwise (CCW) direction, which we define as a local swirl. These swirls form coherent patterns spanning the scale of the material. Using a dynamical model, we demonstrate that swirl arises from disorder in the local micro-structure. We demonstrate that disorder and strain-rate control a crossover between cooperation and competition between swirls in adjacent vertices. Over 5-10 cycles, the region around the active voxel structurally adapts from a higher-energy metastable state to a lower-energy state, locally ordering and stiffening the structure. The coherent domains of CW/CCW swirl become smaller as the system stabilizes, indicative of a process similar to the Hall-Petch effect. Finally, we introduce a statistical model that evolves edge lengths with a set of rules to explore how this class of materials adapts as a function of initial structure. Adding activity to foam couples structural disorder and adaptive dynamics to encourage the development of a new class of abiotic, cellularized active matter.
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Affiliation(s)
- L A Kroo
- Department of Mechanical Engineering, Stanford University, USA
| | | | - Manu Prakash
- Department of Bioengineering, Stanford University, USA.
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19
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Manning ML. Essay: Collections of Deformable Particles Present Exciting Challenges for Soft Matter and Biological Physics. PHYSICAL REVIEW LETTERS 2023; 130:130002. [PMID: 37067323 DOI: 10.1103/physrevlett.130.130002] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Indexed: 05/11/2023]
Abstract
The field of soft matter physics has expanded rapidly over the past several decades, as physicists realize that a broad set of materials and systems are amenable to a physical understanding based on the interplay of entropy, elasticity, and geometry. The fields of biological physics and the physics of living systems have similarly emerged as bona fide independent areas of physics in part because tools from molecular and cell biology and optical physics allow scientists to make new quantitative measurements to test physical principles in living systems. This Essay will highlight two exciting future challenges I see at the intersection of these two fields: characterizing emergent behavior and harnessing actuation in highly deformable active objects. I will attempt to show how this topic is a natural extension of older and more recent discoveries and why I think it is likely to unfurl into a wide range of projects that can transform both fields. Progress in this area will enable new platforms for creating adaptive smart materials that can execute large-scale changes in shape in response to stimuli and improve our understanding of biological function, potentially allowing us to identify new targets for fighting disease. Part of a series of Essays which concisely present author visions for the future of their field.
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Affiliation(s)
- M Lisa Manning
- Syracuse University, Department of Physics and BioInspired Institute, Syracuse, New York 13244, USA
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20
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Baggio R, Salman OU, Truskinovsky L. Inelastic rotations and pseudoturbulent plastic avalanches in crystals. Phys Rev E 2023; 107:025004. [PMID: 36932476 DOI: 10.1103/physreve.107.025004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Plastic deformations in crystals produce microstructures with randomly oriented patches of unstressed lattice forming complex textures. We use a mesoscopic Landau-type tensorial model of crystal plasticity to show that in such textures rotations can originate from crystallographically exact microslips which self organize in the form of laminates of a pseudotwin type. The formation of such laminates can be viewed as an effective internal "wrinkling" of the crystal lattice. While such "wrinkling" disguises itself as an elastically neutral rotation, behind it is inherently dissipative, dislocation-mediated process. Our numerical experiments reveal pseudoturbulent effective rotations with power-law distributed spatial correlations which suggests that the process of dislocational self-organization is inherently unstable and points toward the necessity of a probabilistic description of crystal plasticity.
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Affiliation(s)
- R Baggio
- LSPM, CNRS UPR3407, Paris Nord Sorbonne Université, 93400 Villateneuse, France
- PMMH, CNRS UMR 7636 ESPCI ParisTech, 10 Rue Vauquelin,75005 Paris, France
- UMR SPE 6134, Université de Corse, CNRS, Campus Grimaldi, 20250 Corte, France
| | - O U Salman
- LSPM, CNRS UPR3407, Paris Nord Sorbonne Université, 93400 Villateneuse, France
| | - L Truskinovsky
- PMMH, CNRS UMR 7636 ESPCI ParisTech, 10 Rue Vauquelin,75005 Paris, France
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21
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Saw S, Costigliola L, Dyre JC. Configurational temperature in active matter. I. Lines of invariant physics in the phase diagram of the Ornstein-Uhlenbeck model. Phys Rev E 2023; 107:024609. [PMID: 36932558 DOI: 10.1103/physreve.107.024609] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
This paper shows that the configurational temperature of liquid-state theory, T_{conf}, defines an energy scale, which can be used for adjusting model parameters of active Ornstein-Uhlenbeck particle (AOUP) models in order to achieve approximately invariant structure and dynamics upon a density change. The required parameter changes are calculated from the variation of a single configuration's T_{conf} for a uniform scaling of all particle coordinates. The resulting equations are justified theoretically for models involving a potential-energy function with hidden scale invariance. The validity of the procedure is illustrated by computer simulations of the Kob-Andersen binary Lennard-Jones AOUP model, showing the existence of lines of approximate invariance of the reduced-unit radial distribution function and time-dependent mean-square displacement.
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Affiliation(s)
- Shibu Saw
- Glass and Time, IMFUFA, Department of Science and Environment, Roskilde University, P.O. Box 260, DK-4000 Roskilde, Denmark
| | - Lorenzo Costigliola
- Glass and Time, IMFUFA, Department of Science and Environment, Roskilde University, P.O. Box 260, DK-4000 Roskilde, Denmark
| | - Jeppe C Dyre
- Glass and Time, IMFUFA, Department of Science and Environment, Roskilde University, P.O. Box 260, DK-4000 Roskilde, Denmark
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22
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Chloroplasts in plant cells show active glassy behavior under low-light conditions. Proc Natl Acad Sci U S A 2023; 120:e2216497120. [PMID: 36638210 PMCID: PMC9934296 DOI: 10.1073/pnas.2216497120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Plants have developed intricate mechanisms to adapt to changing light conditions. Besides phototropism and heliotropism (differential growth toward light and diurnal motion with respect to sunlight, respectively), chloroplast motion acts as a fast mechanism to change the intracellular structure of leaf cells. While chloroplasts move toward the sides of the plant cell to avoid strong light, they accumulate and spread out into a layer on the bottom of the cell at low light to increase the light absorption efficiency. Although the motion of chloroplasts has been studied for over a century, the collective organelle motion leading to light-adapting self-organized structures remains elusive. Here, we study the active motion of chloroplasts under dim-light conditions, leading to an accumulation in a densely packed quasi-2D layer. We observe burst-like rearrangements and show that these dynamics resemble systems close to the glass transition by tracking individual chloroplasts. Furthermore, we provide a minimal mathematical model to uncover relevant system parameters controlling the stability of the dense configuration of chloroplasts. Our study suggests that the meta-stable caging close to the glass transition in the chloroplast monolayer serves a physiological relevance: Chloroplasts remain in a spread-out configuration to increase the light uptake but can easily fluidize when the activity is increased to efficiently rearrange the structure toward an avoidance state. Our research opens questions about the role that dynamical phase transitions could play in self-organized intracellular responses of plant cells toward environmental cues.
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23
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Dey S, Mutneja A, Karmakar S. Enhanced short time peak in four-point dynamic susceptibility in dense active glass-forming liquids. SOFT MATTER 2022; 18:7309-7316. [PMID: 36111612 DOI: 10.1039/d2sm00727d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Active glassy systems are simple model systems that imitate complex biological processes. Sometimes, it becomes crucial to estimate the amount of activity present in such biological systems, such as predicting the progression rate of the cancer cells or the healing time of the wound, etc. In this work, we study a model active glassy system to quantify the degree of activity from the collective, long-wavelength fluctuations in the system. These long-wavelength fluctuations present themselves as an additional peak in the four-point dynamic susceptibility (χ4(t)) apart from the usual peak at structural relaxation time. We then show how the degree of the activity at such a small timescale can be obtained by measuring the variation in χ4(t) due to changing activity. A Detailed finite size analysis of the peak height of χ4(t) suggests the existence of an intrinsic dynamic length scale that grows with increasing activity. Finally, we show that this peak height is a unique function of effective activity across all system sizes, serving as a possible parameter for characterizing the degree of activity in a system.
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Affiliation(s)
- Subhodeep Dey
- Tata Institute of Fundamental Research, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, 500046, Telangana, India.
| | - Anoop Mutneja
- Tata Institute of Fundamental Research, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, 500046, Telangana, India.
| | - Smarajit Karmakar
- Tata Institute of Fundamental Research, 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, 500046, Telangana, India.
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24
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Negro G, Caporusso CB, Digregorio P, Gonnella G, Lamura A, Suma A. Hydrodynamic effects on the liquid-hexatic transition of active colloids. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2022; 45:75. [PMID: 36098879 PMCID: PMC9470657 DOI: 10.1140/epje/s10189-022-00230-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 08/25/2022] [Indexed: 05/06/2023]
Abstract
We study numerically the role of hydrodynamics in the liquid-hexatic transition of active colloids at intermediate activity, where motility induced phase separation (MIPS) does not occur. We show that in the case of active Brownian particles (ABP), the critical density of the transition decreases upon increasing the particle's mass, enhancing ordering, while self-propulsion has the opposite effect in the activity regime considered. Active hydrodynamic particles (AHP), instead, undergo the liquid-hexatic transition at higher values of packing fraction [Formula: see text] than the corresponding ABP, suggesting that hydrodynamics have the net effect of disordering the system. At increasing densities, close to the hexatic-liquid transition, we found in the case of AHP the appearance of self-sustained organized motion with clusters of particles moving coherently.
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Affiliation(s)
- G Negro
- Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, 70126, Italy
| | - C B Caporusso
- Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, 70126, Italy.
| | - P Digregorio
- Centre Européen de Calcul Atomique et Moléculaire (CECAM), Ecole Polytechnique Fédérale de Lausanne (EPFL), Batochimie, Avenue Forel 2, 1015, Lausanne, Switzerland
| | - G Gonnella
- Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, 70126, Italy
| | - A Lamura
- Istituto Applicazioni Calcolo, CNR, Via Amendola 122/D, 70126, Bari, Italy
| | - A Suma
- Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, 70126, Italy
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25
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Banerjee JP, Mandal R, Banerjee DS, Thutupalli S, Rao M. Unjamming and emergent nonreciprocity in active ploughing through a compressible viscoelastic fluid. Nat Commun 2022; 13:4533. [PMID: 35927258 PMCID: PMC9352703 DOI: 10.1038/s41467-022-31984-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 07/08/2022] [Indexed: 11/09/2022] Open
Abstract
A dilute suspension of active Brownian particles in a dense compressible viscoelastic fluid, forms a natural setting to study the emergence of nonreciprocity during a dynamical phase transition. At these densities, the transport of active particles is strongly influenced by the passive medium and shows a dynamical jamming transition as a function of activity and medium density. In the process, the compressible medium is actively churned up - for low activity, the active particle gets self-trapped in a cavity of its own making, while for large activity, the active particle ploughs through the medium, either accompanied by a moving anisotropic wake, or leaving a porous trail. A hydrodynamic approach makes it evident that the active particle generates a long-range density wake which breaks fore-aft symmetry, consistent with the simulations. Accounting for the back-reaction of the compressible medium leads to (i) dynamical jamming of the active particle, and (ii) a dynamical non-reciprocal attraction between two active particles moving along the same direction, with the trailing particle catching up with the leading one in finite time. We emphasize that these nonreciprocal effects appear only when the active particles are moving and so manifest in the vicinity of the jamming-unjamming transition.
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Affiliation(s)
- Jyoti Prasad Banerjee
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences (TIFR), Bangalore, India
| | - Rituparno Mandal
- Institute for Theoretical Physics, Georg-August-Universität Göttingen, 37077, Göttingen, Germany
| | | | - Shashi Thutupalli
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences (TIFR), Bangalore, India. .,International Centre for Theoretical Sciences (TIFR), Bangalore, India.
| | - Madan Rao
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences (TIFR), Bangalore, India.
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26
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Robust prediction of force chains in jammed solids using graph neural networks. Nat Commun 2022; 13:4424. [PMID: 35908018 PMCID: PMC9338954 DOI: 10.1038/s41467-022-31732-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 06/29/2022] [Indexed: 11/08/2022] Open
Abstract
Force chains are quasi-linear self-organised structures carrying large stresses and are ubiquitous in jammed amorphous materials like granular materials, foams or even cell assemblies. Predicting where they will form upon deformation is crucial to describe the properties of such materials, but remains an open question. Here we demonstrate that graph neural networks (GNN) can accurately predict the location of force chains in both frictionless and frictional materials from the undeformed structure, without any additional information. The GNN prediction accuracy also proves to be robust to changes in packing fraction, mixture composition, amount of deformation, friction coefficient, system size, and the form of the interaction potential. By analysing the structure of the force chains, we identify the key features that affect prediction accuracy. Our results and methodology will be of interest for granular matter and disordered systems, e.g. in cases where direct force chain visualisation or force measurements are impossible.
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27
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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: 15] [Impact Index Per Article: 7.5] [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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28
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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: 3] [Impact Index Per Article: 1.5] [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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29
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Arora P, Sood AK, Ganapathy R. Motile Topological Defects Hinder Dynamical Arrest in Dense Liquids of Active Ellipsoids. PHYSICAL REVIEW LETTERS 2022; 128:178002. [PMID: 35570456 DOI: 10.1103/physrevlett.128.178002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/22/2022] [Indexed: 06/15/2023]
Abstract
Recent numerical studies have identified the persistence time of active motion as a critical parameter governing glassy dynamics in dense active matter. Here we studied dynamics in liquids of granular active ellipsoids with tunable persistence and velocity. We show that increasing the persistence time at moderate supercooling is equivalent to increasing the strength of attraction in equilibrium liquids and results in reentrant dynamics not just in the translational degrees of freedom, as anticipated, but also in the orientational ones. However, at high densities, motile topological defects, unique to active liquids of elongated particles, hindered dynamical arrest. Most remarkably, for the highest activity, we observed intermittent dynamics due to the jamming-unjamming of these defects for the first time.
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Affiliation(s)
- Pragya Arora
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore - 560064, India
| | - A K Sood
- Department of Physics, Indian Institute of Science, Bangalore- 560012, India
- International Centre for Materials Science, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore - 560064, India
| | - Rajesh Ganapathy
- International Centre for Materials Science, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore - 560064, India
- School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore - 560064, India
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30
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Klongvessa N, Ybert C, Cottin-Bizonne C, Kawasaki T, Leocmach M. Aging or DEAD: Origin of the non-monotonic response to weak self-propulsion in active glasses. J Chem Phys 2022; 156:154509. [PMID: 35459302 DOI: 10.1063/5.0087578] [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
Among amorphous states, glass is defined by relaxation times longer than the observation time. This nonergodic nature makes the understanding of glassy systems an involved topic, with complex aging effects or responses to further out-of-equilibrium external drivings. In this respect, active glasses made of self-propelled particles have recently emerged as a stimulating systems, which broadens and challenges our current understanding of glasses by considering novel internal out-of-equilibrium degrees of freedom. In previous experimental studies we have shown that in the ergodicity broken phase, the dynamics of dense passive particles first slows down as particles are made slightly active, before speeding up at larger activity. Here, we show that this nonmonotonic behavior also emerges in simulations of soft active Brownian particles and explore its cause. We refute that the deadlock by emergence of active directionality model we proposed earlier describes our data. However, we demonstrate that the nonmonotonic response is due to activity enhanced aging and thus confirm the link with ergodicity breaking. Beyond self-propelled systems, our results suggest that aging in active glasses is not fully understood.
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Affiliation(s)
- Natsuda Klongvessa
- School of Physics, Center of Excellence in Advanced Functional Materials, Institute of Science, Suranaree University of Technology, 3000 Nakhon Ratchasima, Thailand
| | - Christophe Ybert
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - Cécile Cottin-Bizonne
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - Takeshi Kawasaki
- Department of Physics, Nagoya University, 464-8602 Nagoya, Japan
| | - Mathieu Leocmach
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
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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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Giannini JA, Stanifer EM, Manning ML. Searching for structural predictors of plasticity in dense active packings. SOFT MATTER 2022; 18:1540-1553. [PMID: 35107478 DOI: 10.1039/d1sm01675j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In amorphous solids subject to shear or thermal excitation, so-called structural indicators have been developed that predict locations of future plasticity or particle rearrangements. An open question is whether similar tools can be used in dense active materials, but a challenge is that under most circumstances, active systems do not possess well-defined solid reference configurations. We develop a computational model for a dense active crowd attracted to a point of interest, which does permit a mechanically stable reference state in the limit of infinitely persistent motion. Previous work on a similar system suggested that the collective motion of crowds could be predicted by inverting a matrix of time-averaged two-particle correlation functions. Seeking a first-principles understanding of this result, we demonstrate that this active matter system maps directly onto a granular packing in the presence of an external potential, and extend an existing structural indicator based on linear response to predict plasticity in the presence of noisy dynamics. We find that the strong pressure gradient necessitated by the directed activity, as well as a self-generated free boundary, strongly impact the linear response of the system. In low-pressure regions the linear-response-based indicator is predictive, but it does not work well in the high-pressure interior of our active packings. Our findings motivate and inform future work that could better formulate structure-dynamics predictions in systems with strong pressure gradients.
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Affiliation(s)
- Julia A Giannini
- Department of Physics, Syracuse University, Syracuse, New York 13244, USA.
- BioInspired Institute, Syracuse University, Syracuse, New York 13244, USA
| | - Ethan M Stanifer
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - M Lisa Manning
- Department of Physics, Syracuse University, Syracuse, New York 13244, USA.
- BioInspired Institute, Syracuse University, Syracuse, New York 13244, USA
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Natesan R, Gowrishankar K, Kuttippurathu L, Kumar PBS, Rao M. Active Remodeling of Chromatin and Implications for In Vivo Folding. J Phys Chem B 2021; 126:100-109. [DOI: 10.1021/acs.jpcb.1c08655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ramakrishnan Natesan
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Lakshmi Kuttippurathu
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - P. B. Sunil Kumar
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
- Department of Physics, Indian Institute of Technology Palakkad, Palakkad 668557, Kerala, India
| | - Madan Rao
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences (TIFR), Bengaluru 560065, India
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34
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Casiulis M, Hexner D, Levine D. Self-propulsion and self-navigation: Activity is a precursor to jamming. Phys Rev E 2021; 104:064614. [PMID: 35030902 DOI: 10.1103/physreve.104.064614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
Traffic jams are an everyday hindrance to transport and typically arise when many vehicles have the same or a similar destination. We show, however, that even when uniformly distributed in space and uncorrelated, targets have a crucial effect on transport. At modest densities an instability arises leading to jams with emergent correlations between the targets. By considering limiting cases of the dynamics which map onto active Brownian particles, we argue that motility induced phase separation is the precursor to jams. That is, jams are MIPS seeds that undergo an extra instability due to target accumulation. This provides a quantitative prediction of the onset density for jamming, and suggests how jamming might be delayed or prevented. We study the transition between jammed and flowing phase, and find that transport is most efficient on the cusp of jamming.
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Affiliation(s)
| | - Daniel Hexner
- Department of Mechanical Engineering, Technion-IIT, 32000 Haifa, Israel
| | - Dov Levine
- Department of Physics, Technion-IIT, 32000 Haifa, Israel
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35
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Villarroel C, Düring G. Critical yielding rheology: from externally deformed glasses to active systems. SOFT MATTER 2021; 17:9944-9949. [PMID: 34693958 DOI: 10.1039/d1sm00948f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We use extensive computer simulations to study the yielding transition under two different loading schemes: standard simple shear dynamics and self-propelled dense active systems. In the active systems, a yielding transition toward an out-of-equilibrium flowing state known as the liquid phase is observed when self-propulsion is increased. The range of self-propulsions in which this pure liquid regime exists appears to vanish upon approaching the so-called 'jamming point' at which the solidity of soft-sphere packings is lost. Such an 'active yielding' transition shares similarities with the generic yielding transition for shear flows. A Herschel-Bulkley law is observed along the liquid regime in both loading scenarios, with a clear difference in the critical scaling exponents between the two, suggesting the existence of different universality classes for the yielding transition under different driving conditions. In addition, we present the direct measurements of growing length and time scales for both driving scenarios. A comparison with theoretical predictions from the recent literature reveals poor agreement with our numerical results.
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Affiliation(s)
- Carlos Villarroel
- Instituto de Física, Pontificia Universidad Católica de Chile, Casilla 306, Santiago, Chile.
| | - Gustavo Düring
- Instituto de Física, Pontificia Universidad Católica de Chile, Casilla 306, Santiago, Chile.
- ANID - Millenium Nucleus of Soft Smart Mechanical Metamaterials, Santiago, Chile
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36
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Klamser JU, Dauchot O, Tailleur J. Kinetic Monte Carlo Algorithms for Active Matter Systems. PHYSICAL REVIEW LETTERS 2021; 127:150602. [PMID: 34678030 DOI: 10.1103/physrevlett.127.150602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/07/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
We study kinetic Monte Carlo (KMC) descriptions of active particles. We show that, when they rely on purely persistent, active steps, their continuous-time limit is ill-defined, leading to the vanishing of trademark behaviors of active matter such as the motility-induced phase separation, ratchet effects, as well as to a diverging mechanical pressure. We then show how, under an appropriate scaling, mixing passive steps with active ones leads to a well-defined continuous-time limit that however differs from standard active dynamics. Finally, we propose new KMC algorithms whose continuous-time limits lead to the dynamics of active Ornstein-Uhlenbeck, active Brownian, and run-and-tumble particles.
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Affiliation(s)
- Juliane U Klamser
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
| | - Olivier Dauchot
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005 Paris, France
| | - Julien Tailleur
- Laboratoire Matière et Systèmes Complexes (MSC),UMR 7057 CNRS, Université de Paris, 75205 Paris, France
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37
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Mandal R, Sollich P. Shear-induced orientational ordering in an active glass former. Proc Natl Acad Sci U S A 2021; 118:e2101964118. [PMID: 34551973 PMCID: PMC8488658 DOI: 10.1073/pnas.2101964118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2021] [Indexed: 11/18/2022] Open
Abstract
Dense assemblies of self-propelled particles that can form solid-like states also known as active or living glasses are abundant around us, covering a broad range of length scales and timescales: from the cytoplasm to tissues, from bacterial biofilms to vehicular traffic jams, and from Janus colloids to animal herds. Being structurally disordered as well as strongly out of equilibrium, these systems show fascinating dynamical and mechanical properties. Using extensive molecular dynamics simulation and a number of distinct dynamical and mechanical order parameters, we differentiate three dynamical steady states in a sheared model active glassy system: 1) a disordered state, 2) a propulsion-induced ordered state, and 3) a shear-induced ordered state. We supplement these observations with an analytical theory based on an effective single-particle Fokker-Planck description to rationalize the existence of the shear-induced orientational ordering behavior in an active glassy system without explicit aligning interactions of, for example, Vicsek type. This ordering phenomenon occurs in the large persistence time limit and is made possible only by the applied steady shear. Using a Fokker-Planck description with parameters that can be measured independently, we make testable predictions for the joint distribution of single-particle position and orientation. These predictions match well with the joint distribution measured from direct numerical simulation. Our results are of relevance for experiments exploring the rheological response of dense active colloids and jammed active granular matter systems.
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Affiliation(s)
- Rituparno Mandal
- Institute for Theoretical Physics, Georg-August-Universität Göttingen, 37 077 Göttingen, Germany;
| | - Peter Sollich
- Institute for Theoretical Physics, Georg-August-Universität Göttingen, 37 077 Göttingen, Germany
- Department of Mathematics, King's College London, London WC2R 2LS, United Kingdom
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38
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Bag S, Mandal R. Interaction from structure using machine learning: in and out of equilibrium. SOFT MATTER 2021; 17:8322-8330. [PMID: 34018535 DOI: 10.1039/d1sm00358e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Prediction of pair potential given a typical configuration of an interacting classical system is a difficult inverse problem. There exists no exact result that can predict the potential given the structural information. We demonstrate that using machine learning (ML) one can get a quick but accurate answer to the question: "which pair potential lead to the given structure (represented by pair correlation function)?" We use artificial neural network (NN) to address this question and show that this ML technique is capable of providing very accurate prediction of pair potential irrespective of whether the system is in a crystalline, liquid or gas phase. We show that the trained network works well for sample system configurations taken from both equilibrium and out of equilibrium simulations (active matter systems) when the later is mapped to an effective equilibrium system with a modified potential. We show that the ML prediction about the effective interaction for the active system is not only useful to make prediction about the MIPS (motility induced phase separation) phase but also identifies the transition towards this state.
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Affiliation(s)
- Saientan Bag
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Karlsruhe, Germany.
| | - Rituparno Mandal
- Institute for Theoretical Physics, Georg-August-Universität Göttingen, 37077, Göttingen, Germany.
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39
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Kryuchkov NP, Yurchenko SO. Collective excitations in active fluids: Microflows and breakdown in spectral equipartition of kinetic energy. J Chem Phys 2021; 155:024902. [PMID: 34266286 DOI: 10.1063/5.0054854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The effect of particle activity on collective excitations in active fluids of microflyers is studied. With an in silico study, we observed an oscillating breakdown of equipartition (uniform spectral distribution) of kinetic energy in reciprocal space. The phenomenon is related to short-range velocity-velocity correlations that were realized without forming of long-lived mesoscale vortices in the system. This stands in contrast to well-known mesoscale turbulence operating in active nematic systems (bacterial or artificial) and reveals the features of collective dynamics in active fluids, which should be important for structural transitions and glassy dynamics in active matter.
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Affiliation(s)
- Nikita P Kryuchkov
- Bauman Moscow State Technical University, 2nd Baumanskaya str. 5, 105005 Moscow, Russia
| | - Stanislav O Yurchenko
- Bauman Moscow State Technical University, 2nd Baumanskaya str. 5, 105005 Moscow, Russia
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40
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Das D, Acharya P, Ramola K. Long-range correlations in pinned athermal networks. Phys Rev E 2021; 104:014503. [PMID: 34412209 DOI: 10.1103/physreve.104.014503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
We derive exact results for displacement fields that develop as a response to external pinning forces in two-dimensional athermal networks. For a triangular lattice arrangement of particles interacting through soft potentials, we develop a Green's function formalism which we use to derive exact results for displacement fields produced by localized external forces. We show that in the continuum limit the displacement fields decay as 1/r at large distances r away from a force dipole. Finally, we extend our formulation to study correlations in the displacement fields produced by the external pinning forces. We show that uncorrelated pinned forces at each vertex give rise to long-range correlations in displacements in athermal systems, with a nontrivial system size dependence. We verify our predictions with numerical simulations of athermal networks in two dimensions.
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Affiliation(s)
- Debankur Das
- Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Pappu Acharya
- Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Kabir Ramola
- Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500107, India
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41
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Abstract
The similarity in mechanical properties of dense active matter and sheared amorphous solids has been noted in recent years without a rigorous examination of the underlying mechanism. We develop a mean-field model that predicts that their critical behavior-as measured by their avalanche statistics-should be equivalent in infinite dimensions up to a rescaling factor that depends on the correlation length of the applied field. We test these predictions in two dimensions using a numerical protocol, termed "athermal quasistatic random displacement," and find that these mean-field predictions are surprisingly accurate in low dimensions. We identify a general class of perturbations that smoothly interpolates between the uncorrelated localized forces that occur in the high-persistence limit of dense active matter and system-spanning correlated displacements that occur under applied shear. These results suggest a universal framework for predicting flow, deformation, and failure in active and sheared disordered materials.
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42
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Mandal R, Sollich P. How to study a persistent active glassy system. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:184001. [PMID: 33730708 DOI: 10.1088/1361-648x/abef9b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
We explore glassy dynamics of dense assemblies of soft particles that are self-propelled by active forces. These forces have a fixed amplitude and a propulsion direction that varies on a timescaleτp, the persistence timescale. Numerical simulations of such active glasses are computationally challenging when the dynamics is governed by large persistence times. We describe in detail a recently proposed scheme that allows one to study directly the dynamics in the large persistence time limit, on timescales around and well above the persistence time. We discuss the idea behind the proposed scheme, which we call 'activity-driven dynamics', as well as its numerical implementation. We establish that our prescription faithfully reproduces all dynamical quantities in the appropriate limitτp→ ∞. We deploy the approach to explore in detail the statistics of Eshelby-like plastic events in the steady state dynamics of a dense and intermittent active glass.
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Affiliation(s)
- Rituparno Mandal
- Institute for Theoretical Physics, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Peter Sollich
- Institute for Theoretical Physics, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Department of Mathematics, King's College London, Strand, London WC2R 2LS, United Kingdom
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43
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Tiwari I, Upadhye S, Akella VS, Parmananda P. Revealing the deterministic components in active avalanche-like dynamics. SOFT MATTER 2021; 17:2865-2871. [PMID: 33586749 DOI: 10.1039/d0sm01999b] [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
Avalanche dynamics in an ensemble of self-propelled camphor boats are studied. The self-propelled agents are camphor infused circular paper disks moving on the surface of water. The ensemble exhibits bursts of activity in the autonomous state triggered by stochastic fluctuations. This type of dynamics has been previously reported in a slightly different system (J. Phys. Soc. Jpn., 2015, 84, 034802). Fourier analysis of the autonomous ensemble's average speed reveals a unimodal spectrum, indicating the presence of a preferred time scale in the dynamics. We therefor, entrain such an ensemble by external forcing by using periodic air perturbations on the surface of the water. This forcing is able to replace the stochastic fluctuations which trigger a burst in the autonomous ensemble, thus entraining the system. Upon varying the periodic forcing frequency, an optimal frequency is revealed at which the quality of entrainment of the ensemble by the forcing is augmented. This optimal frequency is found to be in the vicinity of the Fourier spectrum peak of the autonomous ensemble's average speed. This indicates the existence of an underlying deterministic component in the apparent aperiodic bursts of motion of the autonomous ensemble of active particles. A qualitative reasoning for the observed phenomenon is presented.
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Affiliation(s)
- Ishant Tiwari
- Department of Physics, Indian Institute of Technology-Bombay, Mumbai, Maharashtra-400076, India.
| | - Swanith Upadhye
- Department of Physics, Indian Institute of Technology-Bombay, Mumbai, Maharashtra-400076, India.
| | - V S Akella
- Department of Physics, Indian Institute of Technology, Jammu, Jagti Campus, Jammu & Kashmir, 181221, India.
| | - P Parmananda
- Department of Physics, Indian Institute of Technology-Bombay, Mumbai, Maharashtra-400076, India.
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44
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de Castro P, Diles S, Soto R, Sollich P. Active mixtures in a narrow channel: motility diversity changes cluster sizes. SOFT MATTER 2021; 17:2050-2061. [PMID: 33475129 DOI: 10.1039/d0sm02052d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The persistent motion of bacteria produces clusters with a stationary cluster size distribution (CSD). Here we develop a minimal model for bacteria in a narrow channel to assess the relative importance of motility diversity (i.e. polydispersity in motility parameters) and confinement. A mixture of run-and-tumble particles with a distribution of tumbling rates (denoted generically by α) is considered on a 1D lattice. Particles facing each other cross at constant rate, rendering the lattice quasi-1D. To isolate the role of diversity, the global average α stays fixed. For a binary mixture with no particle crossing, the average cluster size (Lc) increases with the diversity as lower-α particles trap higher-α ones for longer. At finite crossing rate, particles escape from the clusters sooner, making Lc smaller and the diversity less important, even though crossing can enhance demixing of particle types between the cluster and gas phases. If the crossing rate is increased further, the clusters become controlled by particle crossing. We also consider an experiment-based continuous distribution of tumbling rates, revealing similar physics. Using parameters fitted from experiments with Escherichia coli bacteria, we predict that the error in estimating Lc without accounting for polydispersity is around 60%. We discuss how to find a binary system with the same CSD as the fully polydisperse mixture. An effective theory is developed and shown to give accurate expressions for the CSD, the effective α, and the average fraction of mobile particles. We give reasons why our qualitative results are expected to be valid for other active matter models and discuss the changes that would result from polydispersity in the active speed rather than in the tumbling rate.
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Affiliation(s)
- Pablo de Castro
- Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Avenida Blanco Encalada 2008, Santiago, Chile.
| | - Saulo Diles
- Faculdade de Física, Universidade Federal do Pará, Campus Salinópolis, Rua Raimundo Santana Cruz S/N, 68721-000, Salinópolis, Pará, Brazil
| | - Rodrigo Soto
- Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Avenida Blanco Encalada 2008, Santiago, Chile.
| | - Peter Sollich
- Disordered Systems Group, Department of Mathematics, King's College London, London, UK and Institut für Theoretische Physik, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
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45
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Mandal R, Sollich P. Multiple Types of Aging in Active Glasses. PHYSICAL REVIEW LETTERS 2020; 125:218001. [PMID: 33274976 DOI: 10.1103/physrevlett.125.218001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 10/20/2020] [Indexed: 06/12/2023]
Abstract
Recent experiments and simulations have revealed glassy features in, e.g., cytoplasm, living tissues and dense assemblies of self-propelled colloids. This leads to a fundamental question: how do these nonequilibrium (active) amorphous materials differ from conventional passive glasses, created by lowering temperature or increasing density? To address this we investigate the aging after a quench to an almost arrested state of a model active glass former, a Kob-Andersen glass in two dimensions. Each constituent particle is driven by a constant propulsion force whose direction diffuses over time. Using extensive molecular dynamics simulations we reveal rich aging behavior of this dense active matter system: short persistence times of the active forcing give effective thermal aging; in the opposite limit we find a two-step aging process with active athermal aging at short times and activity-driven aging at late times. We develop a dedicated simulation method that gives access to this longtime scaling regime for highly persistent active forces.
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Affiliation(s)
- Rituparno Mandal
- Institute for Theoretical Physics, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Peter Sollich
- Institute for Theoretical Physics, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Department of Mathematics, King's College London, London WC2R 2LS, United Kingdom
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46
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Caprini L, Marini Bettolo Marconi U. Active matter at high density: Velocity distribution and kinetic temperature. J Chem Phys 2020; 153:184901. [DOI: 10.1063/5.0029710] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Lorenzo Caprini
- Dipartimento di Fisica, Universitá di Camerino, Via Madonna delle Carceri, I-62032 Camerino, Italy
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47
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Chaki S, Chakrabarti R. Escape of a passive particle from an activity-induced energy landscape: emergence of slow and fast effective diffusion. SOFT MATTER 2020; 16:7103-7115. [PMID: 32657294 DOI: 10.1039/d0sm00711k] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Spontaneous persistent motions driven by active processes play a central role in maintaining living cells far from equilibrium. In the majority of research studies, the steady state dynamics of an active system has been described in terms of an effective temperature. By contrast, we have examined a prototype model for diffusion in an activity-induced rugged energy landscape to describe the slow dynamics of a tagged particle in a dense active environment. The expression for the mean escape time from the activity-induced rugged energy landscape holds only in the limit of low activity and the mean escape time from the rugged energy landscape increases with activity. The precise form of the active correlation will determine whether the mean escape time will depend on the persistence time or not. The activity-induced rugged energy landscape approach also allows an estimate of the non-equilibrium effective diffusivity characterizing the slow diffusive motion of the tagged particle due to activity. On the other hand, in a dilute environment, high activity augments the diffusion of the tagged particle. The enhanced diffusion can be attributed to an effective temperature higher than the ambient temperature and this is used to calculate the Kramers' mean escape time, which decreases with activity. Our results have direct relevance to recent experiments on tagged particle diffusion in condensed phases.
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Affiliation(s)
- Subhasish Chaki
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Powai 400076, India.
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48
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Henkes S, Kostanjevec K, Collinson JM, Sknepnek R, Bertin E. Dense active matter model of motion patterns in confluent cell monolayers. Nat Commun 2020; 11:1405. [PMID: 32179745 PMCID: PMC7075903 DOI: 10.1038/s41467-020-15164-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 02/07/2020] [Indexed: 11/09/2022] Open
Abstract
Epithelial cell monolayers show remarkable displacement and velocity correlations over distances of ten or more cell sizes that are reminiscent of supercooled liquids and active nematics. We show that many observed features can be described within the framework of dense active matter, and argue that persistent uncoordinated cell motility coupled to the collective elastic modes of the cell sheet is sufficient to produce swirl-like correlations. We obtain this result using both continuum active linear elasticity and a normal modes formalism, and validate analytical predictions with numerical simulations of two agent-based cell models, soft elastic particles and the self-propelled Voronoi model together with in-vitro experiments of confluent corneal epithelial cell sheets. Simulations and normal mode analysis perfectly match when tissue-level reorganisation occurs on times longer than the persistence time of cell motility. Our analytical model quantitatively matches measured velocity correlation functions over more than a decade with a single fitting parameter.
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Affiliation(s)
- Silke Henkes
- School of Mathematics, University of Bristol, Bristol, BS8 1TW, United Kingdom.
- Institute of Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, AB24 3UE, United Kingdom.
| | - Kaja Kostanjevec
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, United Kingdom
| | - J Martin Collinson
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, United Kingdom
| | - Rastko Sknepnek
- School of Science and Engineering, University of Dundee, Dundee, DD1 4HN, United Kingdom.
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom.
| | - Eric Bertin
- Université Grenoble Alpes and CNRS, LIPHY, F-38000, Grenoble, France.
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Caprini L, Hernández-García E, López C, Marini Bettolo Marconi U. A comparative study between two models of active cluster crystals. Sci Rep 2019; 9:16687. [PMID: 31723160 PMCID: PMC6853940 DOI: 10.1038/s41598-019-52420-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/19/2019] [Indexed: 12/28/2022] Open
Abstract
We study a system of active particles with soft repulsive interactions that lead to an active cluster-crystal phase in two dimensions. We use two different modelizations of the active force - Active Brownian particles (ABP) and Ornstein-Uhlenbeck particles (AOUP) - and focus on analogies and differences between them. We study the different phases appearing in the system, in particular, the formation of ordered patterns drifting in space without being altered. We develop an effective description which captures some properties of the stable clusters for both ABP and AOUP. As an additional point, we confine such a system in a large channel, in order to study the interplay between the cluster crystal phase and the well-known accumulation near the walls, a phenomenology typical of active particles. For small activities, we find clusters attached to the walls and deformed, while for large values of the active force they collapse in stripes parallel to the walls.
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Affiliation(s)
- Lorenzo Caprini
- Gran Sasso Science Institute (GSSI), Via. F. Crispi 7, 67100, L'Aquila, Italy.
| | - Emilio Hernández-García
- IFISC (CSIC-UIB), Instituto de Física Interdisciplinar y Sistemas Complejos, Campus Universitat de les Illes Balears, E-07122, Palma de Mallorca, Spain
| | - Cristóbal López
- IFISC (CSIC-UIB), Instituto de Física Interdisciplinar y Sistemas Complejos, Campus Universitat de les Illes Balears, E-07122, Palma de Mallorca, Spain
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