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Shee A, Henkes S, Huepe C. Emergent mesoscale correlations in active solids with noisy chiral dynamics. SOFT MATTER 2024; 20:7865-7879. [PMID: 39315646 DOI: 10.1039/d4sm00958d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
We present the linear response theory for an elastic solid composed of active Brownian particles with intrinsic individual chirality, deriving both a normal mode formulation and a continuum elastic formulation. Using this theory, we compute analytically the velocity correlations and energy spectra under different conditions, showing an excellent agreement with simulations. We generate the corresponding phase diagram, identifying chiral and achiral disordered regimes (for high chirality or noise levels), as well as chiral and achiral states with mesoscopic-range order (for low chirality and noise). The chiral ordered states display mesoscopic spatial correlations and oscillating time correlations, but no wave propagation. In the high chirality regime, we find a peak in the elastic energy spectrum that leads to a non-monotonic behavior with increasing noise strength that is consistent with the emergence of the 'hammering state' recently identified in chiral glasses. Finally, we show numerically that our theory, despite its linear response nature, can be applied beyond the idealized homogeneous solid assumed in our derivations. Indeed, by increasing the level of activity, we show that it remains a good approximation of the system dynamics until just below the melting transition. In addition, we show that there is still an excellent agreement between our analytical results and simulations when we extend our results to heterogeneous solids composed of mixtures of active particles with different intrinsic chirality and noise levels. The derived linear response theory is therefore robust and applicable to a broad range of real-world active systems. Our work provides a thorough analytical and numerical description of the emergent states in a densely packed system of chiral self-propelled Brownian disks, thus allowing a detailed understanding of the phases and dynamics identified in a minimal chiral active system.
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Affiliation(s)
- Amir Shee
- Northwestern Institute on Complex Systems and ESAM, Northwestern University, Evanston, IL 60208, USA
| | - Silke Henkes
- Lorentz Institute for Theoretical Physics, LION, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands.
| | - Cristián Huepe
- Northwestern Institute on Complex Systems and ESAM, Northwestern University, Evanston, IL 60208, USA
- School of Systems Science, Beijing Normal University, Beijing, People's Republic of China
- CHuepe Labs, 2713 West August Blvd #1, Chicago, IL 60622, USA.
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2
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Khalilian H, Peruani F, Sarabadani J. Structural dynamics and optimal transport of an active polymer. SOFT MATTER 2024; 20:7592-7600. [PMID: 39279682 DOI: 10.1039/d4sm00504j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Abstract
We study the spontaneous configuration transitions of an active semi-flexible polymer between spiral and non-spiral states, and show that the configuration dynamics is fully described by a subcritical pitchfork bifurcation. Exploiting the fact that an active polymer barely moves in spiral states and exhibits net displacements in non-spiral states, we theoretically prove that the motion of the active polymer is consistent with a run-and-tumble-like dynamics. Moreover, we find that there exists an optimal self-propelling force that maximizes the diffusion coefficient.
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Affiliation(s)
- Hamidreza Khalilian
- School of Nano sciences, Institute for Research in Fundamental Sciences (IPM), 19395-5531, Tehran, Iran.
| | - Fernando Peruani
- Laboratoire de Physique Théorique et Modélisation, UMR 8089, CY Cergy Paris Université, 95302 Cergy-Pontoise, France.
| | - Jalal Sarabadani
- School of Nano sciences, Institute for Research in Fundamental Sciences (IPM), 19395-5531, Tehran, Iran.
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3
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Murphy P, Perepelitsa M, Timofeyev I, Lieber-Kotz M, Islas B, Igoshin OA. Breakdown of Boltzmann-type models for the alignment of self-propelled rods. Math Biosci 2024; 376:109266. [PMID: 39127094 DOI: 10.1016/j.mbs.2024.109266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 07/23/2024] [Accepted: 08/03/2024] [Indexed: 08/12/2024]
Abstract
Studies in the collective motility of organisms use a range of analytical approaches to formulate continuous kinetic models of collective dynamics from rules or equations describing agent interactions. However, the derivation of these kinetic models often relies on Boltzmann's "molecular chaos" hypothesis, which assumes that correlations between individuals are short-lived. While this assumption is often the simplest way to derive tractable models, it is often not valid in practice due to the high levels of cooperation and self-organization present in biological systems. In this work, we illustrated this point by considering a general Boltzmann-type kinetic model for the alignment of self-propelled rods where rod reorientation occurs upon binary collisions. We examine the accuracy of the kinetic model by comparing numerical solutions of the continuous equations to an agent-based model that implements the underlying rules governing microscopic alignment. Even for the simplest case considered, our comparison demonstrates that the kinetic model fails to replicate the discrete dynamics due to the formation of rod clusters that violate statistical independence. Additionally, we show that introducing noise to limit cluster formation helps improve the agreement between the analytical model and agent simulations but does not restore the agreement completely. These results highlight the need to both develop and disseminate improved moment-closure methods for modeling biological and active matter systems.
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Affiliation(s)
- Patrick Murphy
- Department of Mathematics and Statistics, San Jose State University, San Jose, CA 95192, United States of America.
| | - Misha Perepelitsa
- Department of Mathematics, University of Houston, TX 77204, United States of America
| | - Ilya Timofeyev
- Department of Mathematics, University of Houston, TX 77204, United States of America
| | - Matan Lieber-Kotz
- Department of Bioengineering, Rice University, Houston, TX 77005, United States of America
| | - Brandon Islas
- Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, United States of America
| | - Oleg A Igoshin
- Department of Bioengineering, Rice University, Houston, TX 77005, United States of America; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, United States of America; Department of Chemistry, Rice University, Houston, TX 77005, United States of America; Department of Biosciences, Rice University, Houston, TX 77005, United States of America
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4
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Cavallini C, Olivi E, Tassinari R, Ventura C. Mechanotransduction, cellular biophotonic activity, and signaling patterns for tissue regeneration. J Biol Chem 2024:107847. [PMID: 39357824 DOI: 10.1016/j.jbc.2024.107847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/23/2024] [Accepted: 09/20/2024] [Indexed: 10/04/2024] Open
Abstract
Signaling molecules exhibit mechanical oscillations, entailing precise vibrational directionalities. These steering signatures have profound functional implications, and are intimately connected with the onset of molecular electric oscillations and biophoton emission. We discuss biophotonic activity as a form of endogenous photobiomodulation, orchestrating the mechano-sensing/-transduction in signaling players. We focus on exogenous photobiomodulation in the form of pulsed wave modulation of selected light wavelengths to direct endogenous biophotonic activity and molecular cellular dynamics. We highlight the relevance of this strategy to target and reprogram the developmental potential of tissue resident stem cells in damaged tissues, affording a precision regenerative medicine without the needs for cell or tissue transplantation.
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Affiliation(s)
| | - Elena Olivi
- ELDOR LAB, via Corticella 183, 40128, Bologna, Italy
| | | | - Carlo Ventura
- ELDOR LAB, via Corticella 183, 40128, Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Italy.
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Khatri D, Yadav SA, Athale CA. KnotResolver: tracking self-intersecting filaments in microscopy using directed graphs. BIOINFORMATICS (OXFORD, ENGLAND) 2024; 40:btae538. [PMID: 39226176 DOI: 10.1093/bioinformatics/btae538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 08/05/2024] [Accepted: 08/30/2024] [Indexed: 09/05/2024]
Abstract
MOTIVATION Quantification of microscopy time series of in vitro reconstituted motor-driven microtubule transport in "gliding assays" is typically performed using computational object tracking tools. However, these are limited to non-intersecting and rod-like filaments. RESULTS Here, we describe a novel computational image-analysis pipeline, KnotResolver, to track image time series of highly curved self-intersecting looped filaments (knots) by resolving cross-overs. The code integrates filament segmentation and cross-over or "knot" identification based on directed graph representation, where nodes represent cross-overs and edges represent the path connecting them. The graphs are mapped back to contours and the distance to a reference minimized. The accuracy of contour detection is sub-pixel with a robustness to noise. We demonstrate the utility of KnotResolver by automatically quantifying "flagella-like" curvature dynamics and wave-like oscillations of clamped microtubules in a "gliding assay." AVAILABILITY AND IMPLEMENTATION The MATLAB-based source code is released as OpenSource and is available at https://github.com/CyCelsLab/MTKnotResolver.
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Affiliation(s)
- Dhruv Khatri
- Division of Biology, Indian Institute of Science Education and Research Pune (IISER Pune), Pashan, Pune, Maharashtra 411008, India
| | - Shivani A Yadav
- Division of Biology, Indian Institute of Science Education and Research Pune (IISER Pune), Pashan, Pune, Maharashtra 411008, India
| | - Chaitanya A Athale
- Division of Biology, Indian Institute of Science Education and Research Pune (IISER Pune), Pashan, Pune, Maharashtra 411008, India
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Janzen G, Matoz-Fernandez DA. Density and inertia effects on two-dimensional active semiflexible filament suspensions. SOFT MATTER 2024; 20:6618-6626. [PMID: 39108173 DOI: 10.1039/d4sm00572d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
We examine the influence of density on the transition between chain and spiral structures in planar assemblies of active semiflexible filaments, utilizing detailed numerical simulations. We focus on how increased density, and higher Péclet numbers, affect the activity-induced transition spiral state in a semiflexible, self-avoiding active chain. Our findings show that increasing the density causes the spiral state to break up, reverting to a motile chain-like shape. This results in a density-dependent reentrant phase transition from spirals back to open chains. We attribute this phenomenon to an inertial effect observed at the single polymer level, where increased persistence length due to inertia has been shown in recent three-dimensional studies to cause polymers to open up. Our two-dimensional simulations further reveal that a reduction in the damping coefficient leads to partial unwinding of the spirals, forming longer arms. In suspension, interactions among these extended arms can trigger a complete unwinding of the spirals, driven by the combined effects of density and inertia.
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Affiliation(s)
- Giulia Janzen
- Department of Theoretical Physics, Complutense University of Madrid, 28040 Madrid, Spain.
| | - D A Matoz-Fernandez
- Department of Theoretical Physics, Complutense University of Madrid, 28040 Madrid, Spain.
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7
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Xu TL, Qin CR, Tang B, Gao JC, Zhou J, Chen K, Zhang TH, Tian WD. Constrained motion of self-propelling eccentric disks linked by a spring. J Chem Phys 2024; 161:064905. [PMID: 39140446 DOI: 10.1063/5.0217158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/10/2024] [Indexed: 08/15/2024] Open
Abstract
It has been supposed that the interplay of elasticity and activity plays a key role in triggering the non-equilibrium behaviors in biological systems. However, the experimental model system is missing to investigate the spatiotemporally dynamical phenomena. Here, a model system of an active chain, where active eccentric-disks are linked by a spring, is designed to study the interplay of activity, elasticity, and friction. Individual active chain exhibits longitudinal and transverse motions; however, it starts to self-rotate when pinning one end and self-beat when clamping one end. In addition, our eccentric-disk model can qualitatively reproduce such behaviors and explain the unusual self-rotation of the first disk around its geometric center. Furthermore, the structure and dynamics of long chains were studied via simulations without steric interactions. It was found that a hairpin conformation emerges in free motion, while in the constrained motions, the rotational and beating frequencies scale with the flexure number (the ratio of self-propelling force to bending rigidity), χ, as ∼(χ)4/3. Scaling analysis suggests that it results from the balance between activity and energy dissipation. Our findings show that topological constraints play a vital role in non-equilibrium synergy behaviors.
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Affiliation(s)
- Tian-Liang Xu
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | - Chao-Ran Qin
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | - Bin Tang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | - Jin-Cheng Gao
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | - Jiankang Zhou
- School of Optoelectronic Science and Engineering, Soochow University, Suzhou 215006, China
| | - Kang Chen
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | - Tian Hui Zhang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | - Wen-de Tian
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
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8
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Packard CR, Unnikrishnan S, Phuyal S, Cheong SH, Manning ML, Tung CK, Sussman DM. Self-organized vortex phases and hydrodynamic interactions in Bos taurus sperm cells. Phys Rev E 2024; 110:014407. [PMID: 39160914 PMCID: PMC11338586 DOI: 10.1103/physreve.110.014407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 07/01/2024] [Indexed: 08/21/2024]
Abstract
Flocking behavior is observed in biological systems from the cellular to superorganismal length scales, and the mechanisms and purposes of this behavior are objects of intense interest. In this paper, we study the collective dynamics of bovine sperm cells in a viscoelastic fluid. These cells appear not to spontaneously flock, but transition into a long-lived flocking phase after being exposed to a transient ordering pulse of fluid flow. Surprisingly, this induced flocking phase has many qualitative similarities with the spontaneous polar flocking phases predicted by Toner-Tu theory, such as anisotropic giant number fluctuations and nontrivial transverse density correlations, despite the induced nature of the phase and the clearly important role of momentum conservation between the swimmers and the surrounding fluid in these experiments. We also find a self-organized global vortex state of the sperm cells, and map out an experimental phase diagram of states of collective motion as a function of cell density and motility statistics. We compare our experiments with a parameter-matched computational model of persistently turning active particles and find that the experimental order-disorder phase boundary as a function of cell density and persistence time can be approximately predicted from measures of single-cell properties. Our results may have implications for the evaluation of sample fertility by studying the collective phase behavior of dense groups of swimming sperm.
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Affiliation(s)
| | | | - Shiva Phuyal
- Department of Physics, North Carolina A&T State University, Greensboro, NC, USA
| | - Soon Hon Cheong
- Department of Clinical Sciences, Cornell University, Ithaca, NY, USA
| | - M. Lisa Manning
- Department of Physics, Syracuse University, Syracuse, NY, USA and BioInspired Institute, Syracuse University, Syracuse, NY, USA
| | - Chih-Kuan Tung
- Department of Physics, North Carolina A&T State University, Greensboro, NC, USA
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9
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Li Z, Ye H, Lin J, Ouyang Z. Analysis of the number of topological defects in active nematic fluids under applied shear flow. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2024; 47:43. [PMID: 38900310 DOI: 10.1140/epje/s10189-024-00437-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024]
Abstract
The number of topological defects in the shear flow of active nematic fluids is numerically investigated in this study. The evolution of the flow state of extensile active nematic fluids is explored by increasing the activity of active nematic fluids. Evidently, medium-activity active nematic fluids exhibit a highly ordered vortex lattice fluid state. However, high-activity active nematic fluids exhibit a meso-scale turbulent flow accompanied by topological defects. The number of topological defects (Ndef) increases with increasing shear Reynolds number (Res). Fluid viscosity strongly influences Ndef, while the influence of fluid density is relatively weak. Ndef decreases with increasing activity length scale (lζ) value. A small Res value strongly influences Ndef, whereas a large lζ value only weakly influences Ndef. As the activity increases, Ndef in contractile active nematic fluids becomes larger than that of extensile active nematic fluids.
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Affiliation(s)
- Zhenna Li
- State Key Laboratory of Fluid Power Transmission and Control, Zhejiang University, Hangzhou, 310027, China
| | - Hao Ye
- State Key Laboratory of Fluid Power Transmission and Control, Zhejiang University, Hangzhou, 310027, China
| | - Jianzhong Lin
- State Key Laboratory of Fluid Power Transmission and Control, Zhejiang University, Hangzhou, 310027, China.
- Zhejiang Provincial Engineering Research Center for the Safety of Pressure Vessel and Pipeline, Ningbo University, Ningbo, 315201, China.
| | - Zhenyu Ouyang
- Zhejiang Provincial Engineering Research Center for the Safety of Pressure Vessel and Pipeline, Ningbo University, Ningbo, 315201, China
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10
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Bandyopadhyay S, Chatterjee S, Dutta AK, Karmakar M, Rieger H, Paul R. Ordering kinetics in the active Ising model. Phys Rev E 2024; 109:064143. [PMID: 39020881 DOI: 10.1103/physreve.109.064143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 06/06/2024] [Indexed: 07/20/2024]
Abstract
We undertake a numerical study of the ordering kinetics in the two-dimensional (2D) active Ising model (AIM), a discrete flocking model with a conserved density field coupled to a nonconserved magnetization field. We find that for a quench into the liquid-gas coexistence region and in the ordered liquid region, the characteristic length scale of both the density and magnetization domains follows the Lifshitz-Cahn-Allen growth law, R(t)∼t^{1/2}, consistent with the growth law of passive systems with scalar order parameter and nonconserved dynamics. The system morphology is analyzed with the two-point correlation function and its Fourier transform, the structure factor, which conforms to the well-known Porod's law, a manifestation of the coarsening of compact domains with smooth boundaries. We also find the domain growth exponent unaffected by different noise strengths and self-propulsion velocities of the active particles. However, transverse diffusion is found to play the most significant role in the growth kinetics of the AIM. We extract the same growth exponent by solving the hydrodynamic equations of the AIM.
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11
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Yadav RS, Sharma S, Metzler R, Chakrabarti R. A passive star polymer in a dense active bath: insights from computer simulations. SOFT MATTER 2024; 20:3910-3922. [PMID: 38700098 DOI: 10.1039/d4sm00144c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Using computer simulations in two dimensions (2D), we explore the structure and dynamics of a star polymer with three arms made of passive monomers immersed in a bath of active Brownian particles (ABPs). We analyze the conformational and dynamical changes of the polymer as a function of activity and packing fraction. We also study the process of motility induced phase separation (MIPS) in the presence of a star polymer, which acts as a mobile nucleation center. The presence of the polymer increases the growth rate of the clusters in comparison to a bath without the polymer. In particular, for low packing fraction, both nucleation and cluster growth are affected by the inclusion of the star polymer. Clusters grow in the vicinity of the star polymer, resulting in the star polymer experiencing a caged motion similar to a tagged ABP in the dense phase. Due to the topological constraints of the star polymers and clustering nearby, the conformational changes of the star polymer lead to interesting observations. Inter alia, we observe the shrinking of the arm with increasing activity along with a short-lived hairpin structure of one arm formed. We also see the transient pairing of two arms of the star polymer, while the third is largely separated at high activity. We hope our findings will help in understanding the behavior of active-passive mixtures, including biopolymers of complex topology in dense active suspensions.
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Affiliation(s)
- Ramanand Singh Yadav
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Sanaa Sharma
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Ralf Metzler
- Institute of Physics and Astronomy, University of Potsdam, Germany.
- Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
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12
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Wang Y, Chen H, Xie L, Liu J, Zhang L, Yu J. Swarm Autonomy: From Agent Functionalization to Machine Intelligence. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2312956. [PMID: 38653192 DOI: 10.1002/adma.202312956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/17/2024] [Indexed: 04/25/2024]
Abstract
Swarm behaviors are common in nature, where individual organisms collaborate via perception, communication, and adaptation. Emulating these dynamics, large groups of active agents can self-organize through localized interactions, giving rise to complex swarm behaviors, which exhibit potential for applications across various domains. This review presents a comprehensive summary and perspective of synthetic swarms, to bridge the gap between the microscale individual agents and potential applications of synthetic swarms. It is begun by examining active agents, the fundamental units of synthetic swarms, to understand the origins of their motility and functionality in the presence of external stimuli. Then inter-agent communications and agent-environment communications that contribute to the swarm generation are summarized. Furthermore, the swarm behaviors reported to date and the emergence of machine intelligence within these behaviors are reviewed. Eventually, the applications enabled by distinct synthetic swarms are summarized. By discussing the emergent machine intelligence in swarm behaviors, insights are offered into the design and deployment of autonomous synthetic swarms for real-world applications.
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Affiliation(s)
- Yibin Wang
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, 518172, China
- Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen, 518172, China
| | - Hui Chen
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, 518172, China
- Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen, 518172, China
| | - Leiming Xie
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, 518172, China
- Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen, 518172, China
| | - Jinbo Liu
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, 518172, China
- Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen, 518172, China
| | - Li Zhang
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Jiangfan Yu
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, 518172, China
- Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen, 518172, China
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13
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Zhu G, Gao L, Sun Y, Wei W, Yan LT. Non-equilibrium structural and dynamic behaviors of active polymers in complex and crowded environments. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2024; 87:054601. [PMID: 38608453 DOI: 10.1088/1361-6633/ad3e11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/12/2024] [Indexed: 04/14/2024]
Abstract
Active matter systems, which convert internal chemical energy or energy from the environment into directed motion, are ubiquitous in nature and exhibit a range of emerging non-equilibrium behaviors. However, most of the current works on active matter have been devoted to particles, and the study of active polymers has only recently come into the spotlight due to their prevalence within living organisms. The intricate interplay between activity and conformational degrees of freedom gives rise to novel structural and dynamical behaviors of active polymers. Research in active polymers remarkably broadens diverse concepts of polymer physics, such as molecular architecture, dynamics, scaling and so on, which is of significant importance for the development of new polymer materials with unique performance. Furthermore, active polymers are often found in strongly interacting and crowded systems and in complex environments, so that the understanding of this behavior is essential for future developments of novel polymer-based biomaterials. This review thereby focuses on the study of active polymers in complex and crowded environments, and aims to provide insights into the fundamental physics underlying the adaptive and collective behaviors far from equilibrium, as well as the open challenges that the field is currently facing.
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Affiliation(s)
- Guolong Zhu
- School of Physics and Electronics, Hunan University, Changsha 410082, People's Republic of China
| | - Lijuan Gao
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
| | - Yihang Sun
- School of Physics and Electronics, Hunan University, Changsha 410082, People's Republic of China
| | - Wenjie Wei
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
| | - Li-Tang Yan
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
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14
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Lång E, Lång A, Blicher P, Rognes T, Dommersnes PG, Bøe SO. Topology-guided polar ordering of collective cell migration. SCIENCE ADVANCES 2024; 10:eadk4825. [PMID: 38630812 PMCID: PMC11023523 DOI: 10.1126/sciadv.adk4825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024]
Abstract
The ability of epithelial monolayers to self-organize into a dynamic polarized state, where cells migrate in a uniform direction, is essential for tissue regeneration, development, and tumor progression. However, the mechanisms governing long-range polar ordering of motility direction in biological tissues remain unclear. Here, we investigate the self-organizing behavior of quiescent epithelial monolayers that transit to a dynamic state with long-range polar order upon growth factor exposure. We demonstrate that the heightened self-propelled activity of monolayer cells leads to formation of vortex-antivortex pairs that undergo sequential annihilation, ultimately driving the spread of long-range polar order throughout the system. A computational model, which treats the monolayer as an active elastic solid, accurately replicates this behavior, and weakening of cell-to-cell interactions impedes vortex-antivortex annihilation and polar ordering. Our findings uncover a mechanism in epithelia, where elastic solid material characteristics, activated self-propulsion, and topology-mediated guidance converge to fuel a highly efficient polar self-ordering activity.
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Affiliation(s)
- Emma Lång
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Anna Lång
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Pernille Blicher
- Department of Medical Biochemistry, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Torbjørn Rognes
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Paul Gunnar Dommersnes
- Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Stig Ove Bøe
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
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15
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Yadav A, J K, Chandrasekar VK, Zou W, Kurths J, Senthilkumar DV. Exotic swarming dynamics of high-dimensional swarmalators. Phys Rev E 2024; 109:044212. [PMID: 38755849 DOI: 10.1103/physreve.109.044212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/28/2024] [Indexed: 05/18/2024]
Abstract
Swarmalators are oscillators that can swarm as well as sync via a dynamic balance between their spatial proximity and phase similarity. Swarmalator models employed so far in the literature comprise only one-dimensional phase variables to represent the intrinsic dynamics of the natural collectives. Nevertheless, the latter can indeed be represented more realistically by high-dimensional phase variables. For instance, the alignment of velocity vectors in a school of fish or a flock of birds can be more realistically set up in three-dimensional space, while the alignment of opinion formation in population dynamics could be multidimensional, in general. We present a generalized D-dimensional swarmalator model, which more accurately captures self-organizing behaviors of a plethora of real-world collectives by self-adaptation of high-dimensional spatial and phase variables. For a more sensible visualization and interpretation of the results, we restrict our simulations to three-dimensional spatial and phase variables. Our model provides a framework for modeling complicated processes such as flocking, schooling of fish, cell sorting during embryonic development, residential segregation, and opinion dynamics in social groups. We demonstrate its versatility by capturing the maneuvers of a school of fish, qualitatively and quantitatively, by a suitable extension of the original model to incorporate appropriate features besides a gallery of its intrinsic self-organizations for various interactions. We expect the proposed high-dimensional swarmalator model to be potentially useful in describing swarming systems and programmable and reconfigurable collectives in a wide range of disciplines, including the physics of active matter, developmental biology, sociology, and engineering.
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Affiliation(s)
- Akash Yadav
- School of Physics, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695551, India
| | - Krishnanand J
- School of Physics, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695551, India
| | - V K Chandrasekar
- Center for Nonlinear Science and Engineering, SASTRA Deemed University, Thanjavur, Tamil Nadu 613401, India
| | - Wei Zou
- School of Mathematical Sciences, South China Normal University, Guangzhou 510631, China
| | - Jürgen Kurths
- Potsdam Institute for Climate Impact Research, Telegraphenberg, D-14415 Potsdam, Germany
- Institute of Physics, Humboldt University Berlin, D-12489 Berlin, Germany
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai 200433, China
| | - D V Senthilkumar
- School of Physics, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695551, India
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16
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Wang B, Lu Y. Collective Molecular Machines: Multidimensionality and Reconfigurability. NANO-MICRO LETTERS 2024; 16:155. [PMID: 38499833 PMCID: PMC10948734 DOI: 10.1007/s40820-024-01379-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/17/2024] [Indexed: 03/20/2024]
Abstract
Molecular machines are key to cellular activity where they are involved in converting chemical and light energy into efficient mechanical work. During the last 60 years, designing molecular structures capable of generating unidirectional mechanical motion at the nanoscale has been the topic of intense research. Effective progress has been made, attributed to advances in various fields such as supramolecular chemistry, biology and nanotechnology, and informatics. However, individual molecular machines are only capable of producing nanometer work and generally have only a single functionality. In order to address these problems, collective behaviors realized by integrating several or more of these individual mechanical units in space and time have become a new paradigm. In this review, we comprehensively discuss recent developments in the collective behaviors of molecular machines. In particular, collective behavior is divided into two paradigms. One is the appropriate integration of molecular machines to efficiently amplify molecular motions and deformations to construct novel functional materials. The other is the construction of swarming modes at the supramolecular level to perform nanoscale or microscale operations. We discuss design strategies for both modes and focus on the modulation of features and properties. Subsequently, in order to address existing challenges, the idea of transferring experience gained in the field of micro/nano robotics is presented, offering prospects for future developments in the collective behavior of molecular machines.
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Affiliation(s)
- Bin Wang
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, People's Republic of China.
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17
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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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18
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Cao J, Wu J, Hou Z. Quorum sensing-induced transition from colloidal waves to Turing-like patterns in chemorepulsive active colloids. Phys Chem Chem Phys 2024; 26:7783-7793. [PMID: 38375586 DOI: 10.1039/d3cp04910h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
The study of active systems, especially in the presence of a chemical background field, is garnering significant attention. Traditionally, the self-propelled velocity of active colloids was assumed to be constant, independent of the local density of colloids. In this work, we introduce a chemotactic active system that features quorum sensing (QS), wherein particles act as chemorepellents. Interestingly, these particles lose their activity in regions of high local particle density. Our findings reveal that QS leads to a transition from an oscillatory colloidal wave to a Turing-like pattern, with the observation of an intermediate state. With the variation of the sensing threshold, both the mean oscillation frequency of the system and the number of clusters exhibit non-monotonic dependence. Furthermore, the QS-induced pattern differs markedly from systems without QS, primarily due to the competitive interplay between diffusion and chemotaxis. The dynamics of this phenomenon are explained using a coarse-grained mean field model.
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Affiliation(s)
- Jiaqi Cao
- Department of Chemical Physics & Hefei National Laboratory for Physical Sciences at Microscales, ichEM, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Jiaxin Wu
- Department of Chemical Physics & Hefei National Laboratory for Physical Sciences at Microscales, ichEM, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Zhonghuai Hou
- Department of Chemical Physics & Hefei National Laboratory for Physical Sciences at Microscales, ichEM, University of Science and Technology of China, Hefei, Anhui 230026, China.
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19
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Vatin M, Kundu S, Locatelli E. Conformation and dynamics of partially active linear polymers. SOFT MATTER 2024; 20:1892-1904. [PMID: 38323323 DOI: 10.1039/d3sm01162c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
We perform numerical simulations of isolated, partially active polymers, driven out-of-equilibrium by a fraction of their monomers. We show that, if the active beads are all gathered in a contiguous block, the position of the section along the chain determines the conformational and dynamical properties of the system. Notably, one can modulate the diffusion coefficient of the polymer from active-like to passive-like just by changing the position of the active block. Further, we show that a slight modification of the self-propulsion rule may give rise to an enhancement of diffusion under certain conditions, despite a decrease of the overall polymer activity. Our findings may help in the modelisation of active biophysical systems, such as filamentous bacteria or worms.
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Affiliation(s)
- Marin Vatin
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy.
- INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - Sumanta Kundu
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy.
- INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
- International School for Advanced Studies (SISSA), 34136, Trieste, Italy
| | - Emanuele Locatelli
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy.
- INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
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20
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Spera G, Duclut C, Durand M, Tailleur J. Nematic Torques in Scalar Active Matter: When Fluctuations Favor Polar Order and Persistence. PHYSICAL REVIEW LETTERS 2024; 132:078301. [PMID: 38427854 DOI: 10.1103/physrevlett.132.078301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 07/12/2023] [Accepted: 01/08/2024] [Indexed: 03/03/2024]
Abstract
We study the impact of nematic alignment on scalar active matter in the disordered phase. We show that nematic torques control the emergent physics of particles interacting via pairwise forces and can either induce or prevent phase separation. The underlying mechanism is a fluctuation-induced renormalization of the mass of the polar field that generically arises from nematic torques. The correlations between the fluctuations of the polar and nematic fields indeed conspire to increase the particle persistence length, contrary to what phenomenological computations predict. This effect is generic and our theory also quantitatively accounts for how nematic torques enhance particle accumulation along confining boundaries and opposes demixing in mixtures of active and passive particles.
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Affiliation(s)
- Gianmarco Spera
- Université Paris Cité, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, F-75205 Paris, France
| | - Charlie Duclut
- Université Paris Cité, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, F-75205 Paris, France
- Laboratoire Physique des Cellules et Cancer (PCC), CNRS UMR 168, Institut Curie, Université PSL, Sorbonne Université, 75005 Paris, France
| | - Marc Durand
- Université Paris Cité, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, F-75205 Paris, France
| | - Julien Tailleur
- Université Paris Cité, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, F-75205 Paris, France
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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21
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Chen Z, Ding H, Kollipara PS, Li J, Zheng Y. Synchronous and Fully Steerable Active Particle Systems for Enhanced Mimicking of Collective Motion in Nature. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2304759. [PMID: 37572374 PMCID: PMC10859548 DOI: 10.1002/adma.202304759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/20/2023] [Indexed: 08/14/2023]
Abstract
The collective motion observed in living active matter, such as fish schools and bird flocks, is characterized by its dynamic and complex nature, involving various moving states and transitions. By tailoring physical interactions or incorporating information exchange capabilities, inanimate active particles can exhibit similar behavior. However, the lack of synchronous and arbitrary control over individual particles hinders their use as a test system for the study of more intricate collective motions in living species. Herein, a novel optical feedback control system that enables the mimicry of collective motion observed in living objects using active particles is proposed. This system allows for the experimental investigation of the velocity alignment, a seminal model of collective motion (known as the Vicsek model), in a microscale perturbed environment with controllable and realistic conditions. The spontaneous formation of different moving states and dynamic transitions between these states is observed. Additionally, the high robustness of the active-particle group at the critical density under the influence of different perturbations is quantitatively validated. These findings support the effectiveness of velocity alignment in real perturbed environments, thereby providing a versatile platform for fundamental studies on collective motion and the development of innovative swarm microrobotics.
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Affiliation(s)
- Zhihan Chen
- Materials Science and Engineering Program and Texas Materials Institute, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Hongru Ding
- Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | | | - Jingang Li
- Materials Science and Engineering Program and Texas Materials Institute, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Yuebing Zheng
- Materials Science and Engineering Program and Texas Materials Institute, The University of Texas at Austin, Austin, TX, 78712, USA
- Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
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22
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张 德, 张 豪, 李 博. [The Dynamic Model of the Active-Inactive Cell Interface]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2024; 55:39-46. [PMID: 38322532 PMCID: PMC10839493 DOI: 10.12182/20240160508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Indexed: 02/08/2024]
Abstract
Objective To explore the morphodynamics of the active-inactive cell monolayer interfaces by using the active liquid crystal model. Methods A continuum mechanical model was established based on the active liquid crystal theory and the active-inactive cell monolayer interfaces were established by setting the activity difference of cell monolayers. The theoretical equations were solved numerically by the finite difference and the lattice Boltzmann method. Results The active-inactive cell interfaces displayed three typical morphologies, namely, flat interface, wavy interface, and finger-like interface. On the flat interfaces, the cells were oriented perpendicular to the interface, the -1/2 topological defects were clustered in the interfaces, and the interfaces were negatively charged. On the wavy interfaces, cells showed no obvious preference for orientation at the interfaces and the interfaces were neutrally charged. On the finger-like interfaces, cells were tangentially oriented at the interfaces, the +1/2 topological defects were collected at the interfaces, driving the growth of the finger-like structures, and the interfaces were positively charged. Conclusion The orientation of the cell alignment at the interface can significantly affect the morphologies of the active-inactive cell monolayer interfaces, which is closely associated with the dynamics of topological defects at the interfaces.
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Affiliation(s)
- 德清 张
- 清华大学工程力学系 生物力学与医学工程研究所 (北京 100084)Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China
| | - 豪舜 张
- 清华大学工程力学系 生物力学与医学工程研究所 (北京 100084)Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China
| | - 博 李
- 清华大学工程力学系 生物力学与医学工程研究所 (北京 100084)Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China
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23
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Vilfan M, Lampret B, Gregorin Ž, Cmok L, Vilfan A, Klepp J, Kohlbrecher J, Hribar Boštjančič P, Lisjak D, Mertelj A. Spontaneous Chiral Symmetry Breaking and Lane Formation in Ferromagnetic Ferrofluids. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2304387. [PMID: 37643398 DOI: 10.1002/smll.202304387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/04/2023] [Indexed: 08/31/2023]
Abstract
Ferromagnetic ferrofluids are synthetic materials consisting of magnetic nanoplatelets dispersed in an isotropic fluid. Their main characteristics are the formation of stable magnetic domains and the presence of macroscopic magnetization even in the absence of a magnetic field. Here, the authors report on the experimental observation of spontaneous stripe formation in a ferromagnetic ferrofluid in the presence of an oscillating external magnetic field. The striped structure is identified as elongated magnetic domains, which exhibit reorientation upon reversal of the magnetic field. The stripes are oriented perpendicular to the magnetic field and are separated by alternating flow lanes. The velocity profile is measured using a space-time correlation technique that follows the motion of the thermally excited fluctuations in the sample. The highest velocities are found in the depleted regions between individual domains and reach values up to several µm s-1 . The fluid in adjacent lanes moves in the opposite directions despite the applied magnetic field being uniform. The formation of bidirectional flow lanes can be explained by alternating rotation of magnetic nanoparticles in neighboring stripes, which indicates spontaneous breaking of the chiral symmetry in the sample.
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Affiliation(s)
- Mojca Vilfan
- J. Stefan Institute, Ljubljana, 1000, Slovenia
- Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, 1000, Slovenia
| | | | | | - Luka Cmok
- J. Stefan Institute, Ljubljana, 1000, Slovenia
| | - Andrej Vilfan
- J. Stefan Institute, Ljubljana, 1000, Slovenia
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), 37077, Göttingen, Germany
| | - Jürgen Klepp
- Faculty of Physics, University of Vienna, Vienna, 1090, Austria
| | - Joachim Kohlbrecher
- Laboratory for Neutron Scattering and Imaging, PSI, Villigen, 5303, Switzerland
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24
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Bao Z, Guo Y, Deng Y, Zang J, Zhang J, Deng Y, Ouyang B, Qu X, Bürstenbinder K, Wang P. Microtubule-associated protein SlMAP70 interacts with IQ67-domain protein SlIQD21a to regulate fruit shape in tomato. THE PLANT CELL 2023; 35:4266-4283. [PMID: 37668409 PMCID: PMC10689142 DOI: 10.1093/plcell/koad231] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/01/2023] [Accepted: 08/06/2023] [Indexed: 09/06/2023]
Abstract
Tomato (Solanum lycopersicum) fruit shape is related to microtubule organization and the activity of microtubule-associated proteins (MAPs). However, insights into the mechanism of fruit shape formation from a cell biology perspective remain limited. Analysis of the tissue expression profiles of different microtubule regulators revealed that functionally distinct classes of MAPs, including members of the plant-specific MICROTUBULE-ASSOCIATED PROTEIN 70 (MAP70) and IQ67 DOMAIN (IQD, also named SUN in tomato) families, are differentially expressed during fruit development. SlMAP70-1-3 and SlIQD21a are highly expressed during fruit initiation, which relates to the dramatic microtubule pattern rearrangements throughout this developmental stage of tomato fruits. Transgenic tomato lines overexpressing SlMAP70-1 or SlIQD21a produced elongated fruits with reduced cell circularity and microtubule anisotropy, while their loss-of-function mutants showed the opposite phenotype, harboring flatter fruits. Fruits were further elongated in plants coexpressing both SlMAP70-1 and SlIQD21a. We demonstrated that SlMAP70s and SlIQD21a physically interact and that the elongated fruit phenotype is likely due to microtubule stabilization induced by the SlMAP70-SlIQD21a interaction. Together, our results identify SlMAP70 proteins and SlIQD21a as important regulators of fruit elongation and demonstrate that manipulating microtubule function during early fruit development provides an effective approach to alter fruit shape.
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Affiliation(s)
- Zhiru Bao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Ye Guo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yaling Deng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jingze Zang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Junhong Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingtian Deng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Bo Ouyang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaolu Qu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Katharina Bürstenbinder
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale) 06120, Germany
| | - Pengwei Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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25
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Krüger T, Maryshev I, Frey E. Hierarchical defect-induced condensation in active nematics. SOFT MATTER 2023; 19:8954-8964. [PMID: 37971530 DOI: 10.1039/d3sm00895a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Topological defects play a central role in the formation and organization of various biological systems. Historically, such nonequilibrium defects have been mainly studied in the context of homogeneous active nematics. Phase-separated systems, in turn, are known to form dense and dynamic nematic bands, but typically lack topological defects. In this paper, we use agent-based simulations of weakly aligning, self-propelled polymers and demonstrate that contrary to the existing paradigm phase-separated active nematics form -1/2 defects. Moreover, these defects, emerging due to interactions among dense nematic bands, constitute a novel second-order collective state. We investigate the morphology of defects in detail and find that their cores correspond to a strong increase in density, associated with a condensation of nematic fluxes. Unlike their analogs in homogeneous systems, such condensed defects form and decay in a different way and do not involve positively charged partners. We additionally observe and characterize lateral arc-like structures that separate from a band's bulk and move in transverse direction. We show that the key control parameters defining the route from stable bands to the coexistence of dynamic lanes and defects are the total density of particles and their path persistence length. We introduce a hydrodynamic theory that qualitatively recapitulates all the main features of the agent-based model, and use it to show that the emergence of both defects and arcs can be attributed to the same anisotropic active fluxes. Finally, we present a way to artificially engineer and position defects, and speculate about experimental verification of the provided model.
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Affiliation(s)
- Timo Krüger
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, Theresienstrasse 37, 80333 Munich, Germany.
| | - Ivan Maryshev
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, Theresienstrasse 37, 80333 Munich, Germany.
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität München, Theresienstrasse 37, 80333 Munich, Germany.
- Max Planck School Matter to Life, Hofgartenstraße 8, 80539 Munich, Germany
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Dinelli A, O'Byrne J, Curatolo A, Zhao Y, Sollich P, Tailleur J. Non-reciprocity across scales in active mixtures. Nat Commun 2023; 14:7035. [PMID: 37923724 PMCID: PMC10624904 DOI: 10.1038/s41467-023-42713-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
In active matter, particles typically experience mediated interactions, which are not constrained by Newton's third law and are therefore generically non-reciprocal. Non-reciprocity leads to a rich set of emerging behaviors that are hard to account for starting from the microscopic scale, due to the absence of a generic theoretical framework out of equilibrium. Here we consider bacterial mixtures that interact via mediated, non-reciprocal interactions (NRI) like quorum-sensing and chemotaxis. By explicitly relating microscopic and macroscopic dynamics, we show that, under conditions that we derive explicitly, non-reciprocity may fade upon coarse-graining, leading to large-scale equilibrium descriptions. In turn, this allows us to account quantitatively, and without fitting parameters, for the rich behaviors observed in microscopic simulations including phase separation, demixing, and multi-phase coexistence. We also derive the condition under which non-reciprocity survives coarse-graining, leading to a wealth of dynamical patterns. Again, our analytical approach allows us to predict the phase diagram of the system starting from its microscopic description. All in all, our work demonstrates that the fate of non-reciprocity across scales is a subtle and important question.
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Affiliation(s)
- Alberto Dinelli
- Université Paris Cité, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, F-75205, Paris, France
| | - Jérémy O'Byrne
- Université Paris Cité, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, F-75205, Paris, France
- Department of Applied Maths and Theoretical Physics, University of Cambridge, Centre for Mathematical Sciences, Wilberforce Rd, Cambridge, CB3 0WA, UK
| | - Agnese Curatolo
- John A. Paulson School of Engineering and Applied Sciences and Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, MA, 02138, USA
| | - Yongfeng Zhao
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, 215006, Suzhou, China
| | - Peter Sollich
- Institute for Theoretical Physics, Georg-August-Universität Göttingen, 37 077, Göttingen, Germany
- Department of Mathematics, King's College London, London, WC2R 2LS, UK
| | - Julien Tailleur
- Université Paris Cité, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, F-75205, Paris, France.
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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27
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Feng K, Chen L, Zhang X, Gong J, Qu J, Niu R. Collective Behaviors of Isotropic Micromotors: From Assembly to Reconstruction and Motion Control under External Fields. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2900. [PMID: 37947744 PMCID: PMC10650937 DOI: 10.3390/nano13212900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
Swarms of self-propelled micromotors can mimic the processes of natural systems and construct artificial intelligent materials to perform complex collective behaviors. Compared to self-propelled Janus micromotors, the isotropic colloid motors, also called micromotors or microswimmers, have advantages in self-assembly to form micromotor swarms, which are efficient in resistance to external disturbance and the delivery of large quantity of cargos. In this minireview, we summarize the fundamental principles and interactions for the assembly of isotropic active particles to generate micromotor swarms. Recent discoveries based on either catalytic or external physical field-stimulated micromotor swarms are also presented. Then, the strategy for the reconstruction and motion control of micromotor swarms in complex environments, including narrow channels, maze, raised obstacles, and high steps/low gaps, is summarized. Finally, we outline the future directions of micromotor swarms and the remaining challenges and opportunities.
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Affiliation(s)
- Kai Feng
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Semiconductor Chemistry Center, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Ministry of Education, Wuhan 430074, China; (K.F.); (L.C.); (X.Z.); (J.Q.)
| | - Ling Chen
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Semiconductor Chemistry Center, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Ministry of Education, Wuhan 430074, China; (K.F.); (L.C.); (X.Z.); (J.Q.)
| | - Xinle Zhang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Semiconductor Chemistry Center, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Ministry of Education, Wuhan 430074, China; (K.F.); (L.C.); (X.Z.); (J.Q.)
| | - Jiang Gong
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Semiconductor Chemistry Center, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Ministry of Education, Wuhan 430074, China; (K.F.); (L.C.); (X.Z.); (J.Q.)
| | - Jinping Qu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Semiconductor Chemistry Center, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Ministry of Education, Wuhan 430074, China; (K.F.); (L.C.); (X.Z.); (J.Q.)
- Key Laboratory of Polymer Processing Engineering, Ministry of Education, Guangdong Provincial Key Laboratory of Technique and Equipment for Macromolecular Advanced Manufacturing, National Engineering Research Center of Novel Equipment for Polymer Processing, School of Mechanical and Automotive Engineering, South China University of Technology, Ministry of Education, Guangzhou 510641, China
| | - Ran Niu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Semiconductor Chemistry Center, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Ministry of Education, Wuhan 430074, China; (K.F.); (L.C.); (X.Z.); (J.Q.)
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28
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Zhang B, Glatz A, Aranson IS, Snezhko A. Spontaneous shock waves in pulse-stimulated flocks of Quincke rollers. Nat Commun 2023; 14:7050. [PMID: 37923744 PMCID: PMC10624688 DOI: 10.1038/s41467-023-42633-4] [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: 06/01/2023] [Accepted: 10/16/2023] [Indexed: 11/06/2023] Open
Abstract
Active matter demonstrates complex spatiotemporal self-organization not accessible at equilibrium and the emergence of collective behavior. Fluids comprised of microscopic Quincke rollers represent a popular realization of synthetic active matter. Temporal activity modulations, realized by modulated external electric fields, represent an effective tool to expand the variety of accessible dynamic states in active ensembles. Here, we report on the emergence of shockwave patterns composed of coherently moving particles energized by a pulsed electric field. The shockwaves emerge spontaneously and move faster than the average particle speed. Combining experiments, theory, and simulations, we demonstrate that the shockwaves originate from intermittent spontaneous vortex cores due to a vortex meandering instability. They occur when the rollers' translational and rotational decoherence times, regulated by the electric pulse durations, become comparable. The phenomenon does not rely on the presence of confinement, and multiple shock waves continuously arise and vanish in the system.
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Affiliation(s)
- Bo Zhang
- Materials Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA.
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, and Department of Physics, Nanjing University, Nanjing, 210093, China.
| | - Andreas Glatz
- Materials Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
- Department of Physics, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Igor S Aranson
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Mathematics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Alexey Snezhko
- Materials Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA.
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29
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Faluweki MK, Cammann J, Mazza MG, Goehring L. Active Spaghetti: Collective Organization in Cyanobacteria. PHYSICAL REVIEW LETTERS 2023; 131:158303. [PMID: 37897773 DOI: 10.1103/physrevlett.131.158303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 08/30/2023] [Indexed: 10/30/2023]
Abstract
Filamentous cyanobacteria can show fascinating examples of nonequilibrium self-organization, which, however, are not well understood from a physical perspective. We investigate the motility and collective organization of colonies of these simple multicellular lifeforms. As their area density increases, linear chains of cells gliding on a substrate show a transition from an isotropic distribution to bundles of filaments arranged in a reticulate pattern. Based on our experimental observations of individual behavior and pairwise interactions, we introduce a nonreciprocal model accounting for the filaments' large aspect ratio, fluctuations in curvature, motility, and nematic interactions. This minimal model of active filaments recapitulates the observations, and rationalizes the appearance of a characteristic length scale in the system, based on the Péclet number of the cyanobacteria filaments.
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Affiliation(s)
- Mixon K Faluweki
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, United Kingdom
- Malawi Institute of Technology, Malawi University of Science and Technology, S150 Road, Thyolo 310105, Malawi
| | - Jan Cammann
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom
| | - Marco G Mazza
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Am Faßberg 17, 37077 Göttingen, Germany
| | - Lucas Goehring
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, United Kingdom
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30
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Jia B, Jian Y. Stability of a liquid film on inclined flexible substrates: Effect of the spontaneous odd viscosity. Phys Rev E 2023; 108:045104. [PMID: 37978679 DOI: 10.1103/physreve.108.045104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 09/08/2023] [Indexed: 11/19/2023]
Abstract
We report the stability of a falling incompressible odd viscosity fluid on flexible substrates when the time-reversal symmetry is broken. The flexible wall equation incorporates the contribution of odd viscosity, where the stress at an interface is determined by the viscosities of the adjacent fluids. The Orr-Sommerfeld (OS) equation is derived using the modified linear flexible wall equation taking the inertia, flexural rigidity, and spring stiffness effects of the elastic plate into account. Here, we solve the above eigenvalue problem using Chebyshev collocation methods to obtain the neutral curve in the k-Re plane and the temporal growth rate under varying values of odd viscosity. There is an interesting finding that, for moderate Reynolds numbers, the presence of odd viscosity leads to an increase in instability when the stiffness coefficient A_{K} is small. However, as the value of the stiffness coefficient A_{K} rises, the effect of odd viscosity changes to suppress the onset of instability. Additionally, at higher Reynolds numbers and extremely small inclination angles, both shear and wall modes of falling film are observed. The results demonstrate that the unstable domain for the wall mode increases as the odd viscosity coefficient value rises, while an opposite trend occurs in the shear mode.
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Affiliation(s)
- Beinan Jia
- School of Mathematical Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, People's Republic of China
| | - Yongjun Jian
- School of Mathematical Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, People's Republic of China
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31
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Xue D, Zhang R, Liu Q, Ding Z. Instability of Liquid Film with Odd Viscosity over a Non-Uniformly Heated and Corrugated Substrate. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2660. [PMID: 37836301 PMCID: PMC10574128 DOI: 10.3390/nano13192660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023]
Abstract
The effect of odd viscosity on the instability of liquid film along a wavy inclined bottom with linear temperature variation is investigated. By utilizing the long-wave approximation, the non-linear evolution equation of the free surface is derived. By applying the normal mode method, the linear instability of thin film flow is investigated. With the help of multi-scale analysis methods, the weakly non-linear instability of thin film flow is also investigated. The results reveal that the Marangoni effect caused by non-uniform temperature distribution promotes the instability of the liquid film, while the odd viscosity has a stabilizing effect. In addition, for a positive local inclination angle θ, an increase in bottom steepness ζ inhibits the instability of the liquid film flow. In contrast, with a negative local inclination angle θ, increased bottom steepness ζ promotes the instability of the liquid film flow. The results of the temporal linear instability analysis and the weakly non-linear instability analysis have been substantiated through numerical simulations of the non-linear evolution equations.
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Affiliation(s)
| | | | - Quansheng Liu
- School of Mathematical Science, Inner Mongolia University, Hohhot 010021, China
| | - Zhaodong Ding
- School of Mathematical Science, Inner Mongolia University, Hohhot 010021, China
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32
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Deblais A, Prathyusha KR, Sinaasappel R, Tuazon H, Tiwari I, Patil VP, Bhamla MS. Worm blobs as entangled living polymers: from topological active matter to flexible soft robot collectives. SOFT MATTER 2023; 19:7057-7069. [PMID: 37706563 PMCID: PMC10523214 DOI: 10.1039/d3sm00542a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023]
Abstract
Recently, the study of long, slender living worms has gained attention due to their unique ability to form highly entangled physical structures, exhibiting emergent behaviors. These organisms can assemble into an active three-dimensional soft entity referred to as the "blob", which exhibits both solid-like and liquid-like properties. This blob can respond to external stimuli such as light, to move or change shape. In this perspective article, we acknowledge the extensive and rich history of polymer physics, while illustrating how these living worms provide a fascinating experimental platform for investigating the physics of active, polymer-like entities. The combination of activity, long aspect ratio, and entanglement in these worms gives rise to a diverse range of emergent behaviors. By understanding the intricate dynamics of the worm blob, we could potentially stimulate further research into the behavior of entangled active polymers, and guide the advancement of synthetic topological active matter and bioinspired tangling soft robot collectives.
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Affiliation(s)
- Antoine Deblais
- van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - K R Prathyusha
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Rosa Sinaasappel
- van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - Harry Tuazon
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Ishant Tiwari
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Vishal P Patil
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - M Saad Bhamla
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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33
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Shi XQ, Cheng F, Chaté H. Extreme Spontaneous Deformations of Active Crystals. PHYSICAL REVIEW LETTERS 2023; 131:108301. [PMID: 37739375 DOI: 10.1103/physrevlett.131.108301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/16/2023] [Indexed: 09/24/2023]
Abstract
We demonstrate that two-dimensional crystals made of active particles can experience extremely large spontaneous deformations without melting. Using particles mostly interacting via pairwise repulsive forces, we show that such active crystals maintain long-range bond order and algebraically decaying positional order, but with an exponent η not limited by the 1/3 bound given by the (equilibrium) KTHNY theory. We rationalize our findings using linear elastic theory and show the existence of two well-defined effective temperatures quantifying respectively large-scale deformations and bond-order fluctuations. The root of these phenomena lies in the sole time-persistence of the intrinsic axes of particles, and they should thus be observed in many different situations.
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Affiliation(s)
- Xia-Qing Shi
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | - Fu Cheng
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | - Hugues Chaté
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- Computational Science Research Center, Beijing 100094, China
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34
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Tiribocchi A, Durve M, Lauricella M, Montessori A, Succi S. Spontaneous motion of a passive fluid droplet in an active microchannel. SOFT MATTER 2023; 19:6556-6568. [PMID: 37599649 PMCID: PMC10467333 DOI: 10.1039/d3sm00561e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/08/2023] [Indexed: 08/22/2023]
Abstract
We numerically study the dynamics of a passive fluid droplet confined within a microchannel whose walls are covered with a thin layer of active gel. The latter represents a fluid of extensile material modelling, for example, a suspension of cytoskeletal filaments and molecular motors. Our results show that the layer is capable of producing a spontaneous flow triggering a rectilinear motion of the passive droplet. For a hybrid design (a single wall covered by the active layer), at the steady state the droplet attains an elliptical shape, resulting from an asymmetric saw-toothed structure of the velocity field. In contrast, if the active gel covers both walls, the velocity field exhibits a fully symmetric pattern considerably mitigating morphological deformations. We further show that the structure of the spontaneous flow in the microchannel can be controlled by the anchoring conditions of the active gel at the wall. These findings are also confirmed by selected 3D simulations. Our results may stimulate further research addressed to design novel microfludic devices whose functioning relies on the collective properties of active gels.
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Affiliation(s)
- Adriano Tiribocchi
- Istituto per le Applicazioni del Calcolo CNR, via dei Taurini 19, 00185 Rome, Italy.
| | - Mihir Durve
- Center for Life Nano Science@La Sapienza, Istituto Italiano di Tecnologia, 00161, Roma, Italy
| | - Marco Lauricella
- Istituto per le Applicazioni del Calcolo CNR, via dei Taurini 19, 00185 Rome, Italy.
| | - Andrea Montessori
- Dipartimento di Ingegneria Civile, Informatica e delle Tecnologie Aeronautiche (DICITA), Università degli studi Roma Tre, Via Vito Volterra 62, 00146 Rome, Italy
| | - Sauro Succi
- Istituto per le Applicazioni del Calcolo CNR, via dei Taurini 19, 00185 Rome, Italy.
- Center for Life Nano Science@La Sapienza, Istituto Italiano di Tecnologia, 00161, Roma, Italy
- Department of Physics, Harvard University, Cambridge, MA, 02138, USA
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35
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Sahoo R, Chakrabarti R. Structure and dynamics of an active polymer chain inside a nanochannel grafted with polymers. SOFT MATTER 2023; 19:5978-5988. [PMID: 37497754 DOI: 10.1039/d3sm00618b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
We use computer simulations to investigate the complex dynamics of a polymer, made of active Brownian particles, inside a channel grafted internally with passive polymer chains. Our simulations reveal that this probe-polymer, if passive, exhibits a compact structure when its interaction is repulsive with the grafted chains as it tends to stay within the hollow space created along the axis of the channel. On increasing the attractive interaction, the passive probe-polymer is pulled towards the grafted polymeric region and adopts an extended structure. By contrast, switching on the activity helps the probe-polymer to escape from the local traps caused by the sticky grafted chains. The interplay between the activity of the probe-polymer and its sticky interaction with the grafted chains results in shrinking, followed by swelling as the activity is increased. To elucidate the dynamics we compute the mean square displacement (MSD) of the center of mass of the probe-polymer, which increases monotonically with activity and displays superdiffusive behavior at an intermediate time and enhanced diffusion at a long time period. In addition, compared with the attractive interaction, the active probe-polymer shows faster dynamics when the interaction is repulsive to the grafted polymers. We believe that our current study will provide insights into the structural changes and dynamics of active polymers in heterogeneous media and will be useful in designing polymer-based drug delivery vehicles.
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Affiliation(s)
- Rajiblochan Sahoo
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
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36
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Vats A, Yadav PK, Banerjee V, Puri S. Symbiotic dynamics in living liquid crystals. Phys Rev E 2023; 108:024701. [PMID: 37723723 DOI: 10.1103/physreve.108.024701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/22/2023] [Indexed: 09/20/2023]
Abstract
An amalgam of nematic liquid crystals and active matter, referred to as living liquid crystals, is a promising self-healing material with futuristic applications for targeted delivery of information and microcargo. We provide a phenomenological model to study the symbiotic pattern dynamics in this contemporary system using the Toner-Tu model for active matter (AM), the Landau-de Gennes free energy for liquid crystals (LCs), and an experimentally motivated coupling term that favours coalignment of the active and nematic components. Our extensive theoretical studies unfold two novel steady states, chimeras and solitons, with sharp regions of distinct orientational order that sweep through the coupled system in synchrony. The induced dynamics in the passive nematic is unprecedented. We show that the symbiotic dynamics of the AM and LC components can be exploited to induce and manipulate order in an otherwise disordered system.
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Affiliation(s)
- Aditya Vats
- Department of Physics, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Pradeep Kumar Yadav
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - Varsha Banerjee
- Department of Physics, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Sanjay Puri
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi-110067, India
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37
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Karmakar M, Chatterjee S, Mangeat M, Rieger H, Paul R. Jamming and flocking in the restricted active Potts model. Phys Rev E 2023; 108:014604. [PMID: 37583144 DOI: 10.1103/physreve.108.014604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 06/21/2023] [Indexed: 08/17/2023]
Abstract
We study the active Potts model with either site occupancy restriction or on-site repulsion to explore jamming and kinetic arrest in a flocking model. The incorporation of such volume exclusion features leads to a surprisingly rich variety of self-organized spatial patterns. While bands and lanes of moving particles commonly occur without or under weak volume exclusion, strong volume exclusion along with low temperature, high activity, and large particle density facilitates jams due to motility-induced phase separation. Through several phase diagrams, we identify the phase boundaries separating the jammed and free-flowing phases and study the transition between these phases which provide us with both qualitative and quantitative predictions of how jamming might be delayed or dissolved. We further formulate and analyze a hydrodynamic theory for the restricted APM which predicts various features of the microscopic model.
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Affiliation(s)
- Mintu Karmakar
- School of Mathematical & Computational Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Swarnajit Chatterjee
- Center for Biophysics & Department for Theoretical Physics, Saarland University, D-66123 Saarbrücken, Germany
| | - Matthieu Mangeat
- Center for Biophysics & Department for Theoretical Physics, Saarland University, D-66123 Saarbrücken, Germany
| | - Heiko Rieger
- Center for Biophysics & Department for Theoretical Physics, Saarland University, D-66123 Saarbrücken, Germany
- INM-Leibniz Institute for New Materials, Campus D2 2, D-66123 Saarbrücken, Germany
| | - Raja Paul
- School of Mathematical & Computational Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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38
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Montana F, Camporeale C, Porporato A, Rondoni L. Inertial and geometrical effects of self-propelled elliptical Brownian particles. Phys Rev E 2023; 107:054607. [PMID: 37328983 DOI: 10.1103/physreve.107.054607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/11/2023] [Indexed: 06/18/2023]
Abstract
Active particles that self-propel by transforming energy into mechanical motion represent a growing area of research in mathematics, physics, and chemistry. Here we investigate the dynamics of nonspherical inertial active particles moving in a harmonic potential, introducing geometric parameters which take into account the role of eccentricity for nonspherical particles. A comparison between the overdamped and underdamped models for elliptical particles is performed. The model of overdamped active Brownian motion has been used to describe most of the basic aspects of micrometer-sized particles moving in a liquid ("microswimmers"). We consider active particles by extending the active Brownian motion model to incorporate translation and rotation inertia and account for the role of eccentricity. We show how the overdamped and the underdamped models behave in the same way for small values of activity (Brownian case) if eccentricity is equal to zero, but increasing eccentricity leads the two dynamics to substantially depart from each other-in particular, the action of a torque induced by external forces, induced a marked difference close to the walls of the domain if eccentricity is high. Effects induced by inertia include an inertial delay time of the self-propulsion direction from the particle velocity, and the differences between the overdamped and underdamped systems are particularly evident in the first and second moments of the particle velocities. Comparison with the experimental results of vibrated granular particles shows good agreement and corroborates the notion that self-propelling massive particles moving in gaseous media are dominated by inertial effects.
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Affiliation(s)
- Federica Montana
- Department of Mathematical Sciences, Politecnico di Torino, Turin, Italy and INFN, Sezione di Torino, Turin, Italy
| | - Carlo Camporeale
- Department of Environmental, Land and Infrastructure Engineering, Politecnico di Torino, Turin, Italy
| | - Amilcare Porporato
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey, USA and High Meadows Environmental Institute, Princeton University, Princeton, New Jersey, USA
| | - Lamberto Rondoni
- Department of Mathematical Sciences, Politecnico di Torino, Turin, Italy and INFN, Sezione di Torino, Turin, Italy
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39
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Lan Y, Xu M, Xie J, Yang Y, Jiang H. Spontaneous symmetry-breaking of the active cluster drives the directed movement and self-sustained oscillation of symmetric rod-like passive particles. SOFT MATTER 2023; 19:3222-3227. [PMID: 37083022 DOI: 10.1039/d2sm01243j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Active particles without detailed balance can rectify their random motions to drive the directed movement or rotation of asymmetric passive obstacles. However, whether they can drive the directed movement of symmetric passive obstacles is still unclear. Here, we show that a rod-like passive particle which is fixed to move along the x-axis in an active bath can keep long-lived directed movement at nearly constant speed due to the spontaneous symmetry breaking of the neighboring active particle cluster. If the passive particle is further confined by a harmonic potential, it may undergo self-sustained periodic oscillation for an appropriate length of the passive particle and self-propelled velocity of active particles. The restoring force from the harmonic potential will trigger the velocity jump-off and thus lead to self-sustained periodic oscillation. Remarkably, the relationship between the velocity of the passive particle and the external force shows that the effective viscosity of the active bath may become negative in some regime. Finally, we develop a minimum 1D theoretical model to further probe the mechanism underlying the directed movement and self-sustained oscillation of the passive particle. Our findings reveal the effect of the moving boundary on the active bath and demonstrate a novel method to extract practical mechanical work from the active bath to propel microdevices.
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Affiliation(s)
- Ying Lan
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Man Xu
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Jinjiang Xie
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Yuehua Yang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Hongyuan Jiang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei, Anhui 230026, China.
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40
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Feng GQ, Tian WD. Desorption of a Flexible Polymer with Activity from a Homogeneous Attractive Surface. Macromolecules 2023. [DOI: 10.1021/acs.macromol.2c01907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Affiliation(s)
- Guo-qiang Feng
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu 215006, China
| | - Wen-de Tian
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu 215006, China
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41
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Karan C, Chaudhuri D. Cooperation and competition in the collective drive by motor proteins: mean active force, fluctuations, and self-load. SOFT MATTER 2023; 19:1834-1843. [PMID: 36789956 DOI: 10.1039/d2sm01183b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We consider the dynamics of a bio-filament under the collective drive of motor proteins. They are attached irreversibly to a substrate and undergo stochastic attachment-detachment with the filament to produce a directed force on it. We establish the dependence of the mean directed force and force correlations on the parameters describing the individual motor proteins using analytical theory and direct numerical simulations. The effective Langevin description for the filament motion gives mean-squared displacement, asymptotic diffusion constant, and mobility leading to an effective temperature. Finally, we show how competition between motor protein extensions generates a self-load, describable in terms of the effective temperature, affecting the filament motion.
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Affiliation(s)
- Chitrak Karan
- Institute of Physics, Sachivalaya Marg, Sainik School, Bhubaneswar, 751005, India.
- Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Debasish Chaudhuri
- Institute of Physics, Sachivalaya Marg, Sainik School, Bhubaneswar, 751005, India.
- Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
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42
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The crucial role of adhesion in the transmigration of active droplets through interstitial orifices. Nat Commun 2023; 14:1096. [PMID: 36841803 PMCID: PMC9968312 DOI: 10.1038/s41467-023-36656-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 02/09/2023] [Indexed: 02/26/2023] Open
Abstract
Active fluid droplets are a class of soft materials exhibiting autonomous motion sustained by an energy supply. Such systems have been shown to capture motility regimes typical of biological cells and are ideal candidates as building-block for the fabrication of soft biomimetic materials of interest in pharmacology, tissue engineering and lab on chip devices. While their behavior is well established in unconstrained environments, much less is known about their dynamics under strong confinement. Here, we numerically study the physics of a droplet of active polar fluid migrating within a microchannel hosting a constriction with adhesive properties, and report evidence of a striking variety of dynamic regimes and morphological features, whose properties crucially depend upon droplet speed and elasticity, degree of confinement within the constriction and adhesiveness to the pore. Our results suggest that non-uniform adhesion forces are instrumental in enabling the crossing through narrow orifices, in contrast to larger gaps where a careful balance between speed and elasticity is sufficient to guarantee the transition. These observations may be useful for improving the design of artificial micro-swimmers, of interest in material science and pharmaceutics, and potentially for cell sorting in microfluidic devices.
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43
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Ceron S, O’Keeffe K, Petersen K. Diverse behaviors in non-uniform chiral and non-chiral swarmalators. Nat Commun 2023; 14:940. [PMID: 36806287 PMCID: PMC9941214 DOI: 10.1038/s41467-023-36563-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 02/06/2023] [Indexed: 02/22/2023] Open
Abstract
We study the emergent behaviors of a population of swarming coupled oscillators, dubbed swarmalators. Previous work considered the simplest, idealized case: identical swarmalators with global coupling. Here we expand this work by adding more realistic features: local coupling, non-identical natural frequencies, and chirality. This more realistic model generates a variety of new behaviors including lattices of vortices, beating clusters, and interacting phase waves. Similar behaviors are found across natural and artificial micro-scale collective systems, including social slime mold, spermatozoa vortex arrays, and Quincke rollers. Our results indicate a wide range of future use cases, both to aid characterization and understanding of natural swarms, and to design complex interactions in collective systems from soft and active matter to micro-robotics.
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Affiliation(s)
- Steven Ceron
- grid.5386.8000000041936877XSibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14853 USA ,grid.116068.80000 0001 2341 2786Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Kevin O’Keeffe
- grid.116068.80000 0001 2341 2786Senseable City Lab, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Kirstin Petersen
- Electrical and Computer Engineering, Cornell University, 136 Hoy Road, Ithaca, NY, 14853, USA.
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44
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Yadav RS, Das C, Chakrabarti R. Dynamics of a spherical self-propelled tracer in a polymeric medium: interplay of self-propulsion, stickiness, and crowding. SOFT MATTER 2023; 19:689-700. [PMID: 36598025 DOI: 10.1039/d2sm01626e] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We employ computer simulations to study the dynamics of a self-propelled spherical tracer particle in a viscoelastic medium, made of a long polymer chain. Here, the interplay between viscoelasticity, stickiness, and activity (self-propulsion) brings additional complexity to the tracer dynamics. Our simulations show that on increasing the stickiness of the tracer particle to the polymer beads, the dynamics of the tracer particle slows down as it gets stuck to the polymer chain and moves along with it. But with increasing self-propulsion velocity, the dynamics gets enhanced. In the case of increasing stickiness as well as activity, the non-Gaussian parameter (NGP) exhibits non-monotonic behavior, which also shows up in the re-scaled self part of the van-Hove function. Non-Gaussianity results owing to the enhanced binding events and the sticky motion of the tracer along with the chain with increasing stickiness. On the other hand, with increasing activity, initially non-Gaussianity increases as the tracer moves through the heterogeneous polymeric environment but for higher activity, the tracer escapes resulting in a negative NGP. For higher values of stickiness, the trapping time distributions of the passive tracer particle broaden and have long tails. On the other hand, for a given stickiness with increasing self-propulsion force, the trapping time distributions become narrower and have short tails. We believe that our current simulation study will be helpful in elucidating the complex motion of activity-driven probes in viscoelastic media.
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Affiliation(s)
- Ramanand Singh Yadav
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Chintu Das
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
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45
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Zhang YH, Yao Z. Alignment rule and geometric confinement lead to stability of a vortex in active flow. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:4. [PMID: 36682015 DOI: 10.1140/epje/s10189-023-00260-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Vortices are hallmarks of a wide range of nonequilibrium phenomena in fluids at multiple length scales. In this work, we numerically study the whirling motion of self-propelled soft point particles confined in circular domain, and aim at addressing the stability issue of the coherent vortex structure. By the combination of dynamical and statistical analysis at the individual particle level, we reveal the persistence of the whirling motion resulting from the subtle competition of activity and geometric confinement. In the stable whirling motion, the scenario of the coexistence of the irregular microscopic motions of individual particles and the regular global whirling motion is fundamentally different from the motion of a vortex in passive fluid. Possible orientational order coexisting with the whirling are further explored. This work shows the stability mechanism of vortical dynamics in active media under the alignment rule in confined space and may have implications in creating and harnessing macroscale coherent dynamical states by tuning the confining geometry.
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Affiliation(s)
- Yi-Heng Zhang
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Zhenwei Yao
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
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46
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Kumar P, Chakrabarti R. Dynamics of self-propelled tracer particles inside a polymer network. Phys Chem Chem Phys 2023; 25:1937-1946. [PMID: 36541408 DOI: 10.1039/d2cp04253c] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The transport of tracer particles through mesh-like environments such as biological hydrogels and polymer matrices is ubiquitous in nature. These tracers can be passive, such as colloids, or active (self-propelled), for example, synthetic nanomotors or bacteria. Computer simulations in principle could be extremely useful in exploring the mechanism of the active transport of tracer particles through mesh-like environments. Therefore, we construct a polymer network on a diamond lattice and use computer simulations to investigate the dynamics of spherical self-propelled particles inside the network. Our main objective is to elucidate the effect of the self-propulsion on the tracer particle dynamics as a function of the tracer size and the stiffness of the polymer network. We compute the time-averaged mean-squared displacement (MSD) and the van-Hove correlations of the tracer. On the one hand, in the case of a bigger sticky particle, the caging caused by the network particles wins over the escape assisted by the self-propulsion. This results an intermediate-time subdiffusion. On the other hand, smaller tracers or tracers with high self-propulsion velocities can easily escape from the cages and show intermediate-time superdiffusion. The stiffer the network, the slower the dynamics of the tracer, and bigger tracers exhibit longer lived intermediate time superdiffusion, since the persistence time scales as ∼σ3, where σ is the diameter of the tracer. At the intermediate time, non-Gaussianity is more pronounced for active tracers. At the long time, the dynamics of the tracer, if passive or weakly active, becomes Gaussian and diffusive, but remains flat for tracers with high self-propulsion, accounting for their seemingly unrestricted motion inside the network.
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Affiliation(s)
- Praveen Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
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47
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Hiraiwa T, Akiyama R, Inoue D, Kabir AMR, Kakugo A. Collision-induced torque mediates the transition of chiral dynamic patterns formed by active particles. Phys Chem Chem Phys 2022; 24:28782-28787. [PMID: 36382471 DOI: 10.1039/d2cp03879j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Controlling the patterns formed by self-propelled particles through dynamic self-organization is a challenging task. Although varieties of patterns associated with chiral self-propelled particles have been reported, essential factors that determine the morphology of the patterns have remained unclear. Here, we explore theoretically how torque formed upon collision of the particles affects the dynamic self-organization of the particles and determine the patterns. Based on a particle-based model with collision-induced torque and torque associated with self-propulsion, we find that introducing collision-induced torque turns the homogeneous bi-directionally aligned particles into rotating mono-polar flocks, which helps resolve a discrepancy in the earlier observations in microfilament gliding assays.
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Affiliation(s)
- Tetsuya Hiraiwa
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore. .,Universal Biology Institute, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Ryo Akiyama
- Department of Chemistry, Kyushu University, Fukuoka 819-0395, Japan
| | - Daisuke Inoue
- Faculty of Design, Kyushu University, Fukuoka 815-8540, Japan
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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48
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Nasirimarekani V, Subramani S, Herzog S, Vilfan A, Guido I. Active Bending of Disordered Microtubule Bundles by Kinesin Motors. ACS OMEGA 2022; 7:43820-43828. [PMID: 36506136 PMCID: PMC9730755 DOI: 10.1021/acsomega.2c04958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
Active networks of biopolymers and motor proteins in vitro self-organize and exhibit dynamic structures on length scales much larger than the interacting individual components of which they consist. How the dynamics is related across the range of length scales is still an open question. Here, we experimentally characterize and quantify the dynamic behavior of isolated microtubule bundles that bend due to the activity of motor proteins. At the motor level, we track and describe the motion features of kinesin-1 clusters stepping within the bending bundles. We find that there is a separation of length scales by at least 1 order of magnitude. At a run length of <1 μm, kinesin-1 activity leads to a bundle curvature in the range of tens of micrometers. We propose that the distribution of microtubule polarity plays a crucial role in the bending dynamics that we observe at both the bundle and motor levels. Our results contribute to the understanding of fundamental principles of vital intracellular processes by disentangling the multiscale dynamics in out-of-equilibrium active networks composed of cytoskeletal elements.
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Affiliation(s)
- Vahid Nasirimarekani
- Max
Planck Institute for Dynamics and Self-Organization (MPIDS), Am Fassberg 17, 37077Göttingen, Germany
| | - Smrithika Subramani
- Max
Planck Institute for Dynamics and Self-Organization (MPIDS), Am Fassberg 17, 37077Göttingen, Germany
- Department
of Physics, University of Wisconsin-Milwaukee, 3135 N Maryland Avenue, Milwaukee, Wisconsin53211, United States
| | - Sebastian Herzog
- Max
Planck Institute for Dynamics and Self-Organization (MPIDS), Am Fassberg 17, 37077Göttingen, Germany
- Department
for Computational Neuroscience, Third Institute of Physics −
Biophysics, University of Göttingen, Friedrich-Hund-Platz 1, 37077Göttingen, Germany
| | - Andrej Vilfan
- Max
Planck Institute for Dynamics and Self-Organization (MPIDS), Am Fassberg 17, 37077Göttingen, Germany
- Jožef
Stefan Institute, Jamova
39, 1000Ljubljana, Slovenia
| | - Isabella Guido
- Max
Planck Institute for Dynamics and Self-Organization (MPIDS), Am Fassberg 17, 37077Göttingen, Germany
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49
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Benvegnen B, Chaté H, Krapivsky PL, Tailleur J, Solon A. Flocking in one dimension: Asters and reversals. Phys Rev E 2022; 106:054608. [PMID: 36559354 DOI: 10.1103/physreve.106.054608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/23/2022] [Indexed: 06/17/2023]
Abstract
We study the one-dimensional active Ising model in which aligning particles undergo diffusion biased by the signs of their spins. The phase diagram obtained varying the density of particles, their hopping rate, and the temperature controlling the alignment shows a homogeneous disordered phase but no homogeneous ordered one, as well as two phases with localized dense structures. In the flocking phase, large ordered aggregates move ballistically and stochastically reverse their direction of motion. In what we termed the "aster" phase, dense immobile aggregates of opposite magnetization face each other, exchanging particles, without any net motion of the aggregates. Using a combination of numerical simulations and mean-field theory, we study the evolution of the shapes of the flocks, the statistics of their reversal times, and their coarsening dynamics. Solving exactly for the zero-temperature dynamics of an aster allows us to understand their coarsening, which shows extremal dynamics, while mean-field equations account for their shape.
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Affiliation(s)
- Brieuc Benvegnen
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, 75005 Paris, France
| | - Hugues Chaté
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, 75005 Paris, France
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- Computational Science Research Center, Beijing 100094, China
| | - Pavel L Krapivsky
- Department of Physics, Boston University, Boston, Massachusetts 02215, USA
- Santa Fe Institute, Santa Fe, New Mexico 87501, USA
| | - Julien Tailleur
- Université Paris Cité, Laboratoire Matière et Systèmes Complexes (MSC), UMR 7057 CNRS, F-75205 Paris, France
| | - Alexandre Solon
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, 75005 Paris, France
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50
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Li ZY, Zhang DQ, Lin SZ, Góźdź WT, Li B. Spontaneous organization and phase separation of skyrmions in chiral active matter. SOFT MATTER 2022; 18:7348-7359. [PMID: 36124977 DOI: 10.1039/d2sm00819j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Skyrmions are topologically protected vortex-like excitations that hold promise for applications such as information processing and electron manipulation. Here we combine theoretical analysis and numerical simulations to show that skyrmions can spontaneously emerge in chiral active matter without external confinements or regulation. Strikingly, these activity-driven skyrmions can either self-organize into a periodic, stable square lattice consisting of half Néel skyrmions and antiskyrmions, where the in-plane flows display an antiferromagnetic vortex array, or undergo phase separation between skyrmions with different topological numbers. We identify that the emerging skyrmion dynamics stems from the competition between the chiral and polar coherence length scales dictated by the interplay of intrinsic chirality, polarity, and elasticity in the system. Our results reveal unanticipated topological excitations, self-organization, and phase separation in non-equilibrium systems and also suggest a potential way towards engineering complicated bespoke skyrmionic structures through manipulating active matter.
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Affiliation(s)
- Zhong-Yi Li
- Institute of Biomechanics and Medical Engineering, Applied Mechanics Laboratory, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China.
| | - De-Qing Zhang
- Institute of Biomechanics and Medical Engineering, Applied Mechanics Laboratory, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China.
| | - Shao-Zhen Lin
- Aix Marseille Université, CNRS, Centre de Physique Théorique, Turing Center for Living Systems, 13009 Marseille, France
| | - Wojciech T Góźdź
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Bo Li
- Institute of Biomechanics and Medical Engineering, Applied Mechanics Laboratory, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China.
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