1
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Li Y, Zarei Z, Tran PN, Wang Y, Baskaran A, Fraden S, Hagan MF, Hong P. A machine learning approach to robustly determine director fields and analyze defects in active nematics. SOFT MATTER 2024; 20:1869-1883. [PMID: 38318759 DOI: 10.1039/d3sm01253k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Active nematics are dense systems of rodlike particles that consume energy to drive motion at the level of the individual particles. They exist in natural systems like biological tissues and artificial materials such as suspensions of self-propelled colloidal particles or synthetic microswimmers. Active nematics have attracted significant attention in recent years due to their spectacular nonequilibrium collective spatiotemporal dynamics, which may enable applications in fields such as robotics, drug delivery, and materials science. The director field, which measures the direction and degree of alignment of the local nematic orientation, is a crucial characteristic of active nematics and is essential for studying topological defects. However, determining the director field is a significant challenge in many experimental systems. Although director fields can be derived from images of active nematics using traditional imaging processing methods, the accuracy of such methods is highly sensitive to the settings of the algorithms. These settings must be tuned from image to image due to experimental noise, intrinsic noise of the imaging technology, and perturbations caused by changes in experimental conditions. This sensitivity currently limits automatic analysis of active nematics. To address this, we developed a machine learning model for extracting reliable director fields from raw experimental images, which enables accurate analysis of topological defects. Application of the algorithm to experimental data demonstrates that the approach is robust and highly generalizable to experimental settings that are different from those in the training data. It could be a promising tool for investigating active nematics and may be generalized to other active matter systems.
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Affiliation(s)
- Yunrui Li
- Computer Science Department, Brandeis University, USA.
| | - Zahra Zarei
- Physics Department, Brandeis University, USA
| | - Phu N Tran
- Physics Department, Brandeis University, USA
| | - Yifei Wang
- Computer Science Department, Brandeis University, USA.
| | | | - Seth Fraden
- Physics Department, Brandeis University, USA
| | | | - Pengyu Hong
- Computer Science Department, Brandeis University, USA.
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2
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Wang W, Ren H, Zhang R. Symmetry Breaking of Self-Propelled Topological Defects in Thin-Film Active Chiral Nematics. PHYSICAL REVIEW LETTERS 2024; 132:038301. [PMID: 38307071 DOI: 10.1103/physrevlett.132.038301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/09/2023] [Accepted: 11/28/2023] [Indexed: 02/04/2024]
Abstract
Active nematics represent a range of dense active matter systems which can engender spontaneous flows and self-propelled topological defects. Two-dimensional (2D) active nematic theory and simulation have been successful in explaining many quasi-2D experiments in which self-propelled +1/2 defects are observed to move along their symmetry axis. However, many active liquid crystals are essentially chiral nematic, but their twist mode becomes irrelevant under the 2D assumption. Here, we use theory and simulation to examine a three-dimensional active chiral nematic confined to a thin film, thus forming a quasi-2D system. We predict that the self-propelled +1/2 disclination in a curved thin film can break its mirror symmetry by moving circularly. Our prediction is confirmed by hydrodynamic simulations of thin spherical-shell and thin cylindrical-shell systems. In the spherical-shell confinement, the four emerged +1/2 disclinations exhibit rich dynamics as a function of activity and chirality. As such, we have proposed a new symmetry-breaking scenario in which self-propelled defects in quasi-2D active nematics can acquire an active angular velocity, greatly enriching their dynamics for finer control and emerging applications.
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Affiliation(s)
- Weiqiang Wang
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR
| | - Haijie Ren
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR
| | - Rui Zhang
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR
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3
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Ray S, Zhang J, Dogic Z. Rectified Rotational Dynamics of Mobile Inclusions in Two-Dimensional Active Nematics. PHYSICAL REVIEW LETTERS 2023; 130:238301. [PMID: 37354394 DOI: 10.1103/physrevlett.130.238301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/14/2023] [Indexed: 06/26/2023]
Abstract
We investigate the dynamics of mobile inclusions embedded in 2D active nematics. The interplay between the inclusion shape, boundary-induced nematic order, and autonomous flows powers the inclusion motion. Disks and achiral gears exhibit unbiased rotational motion, but with distinct dynamics. In comparison, chiral gear-shaped inclusions exhibit long-term rectified rotation, which is correlated with dynamics and polarization of nearby +1/2 topological defects. The chirality of defect polarities and the active nematic texture around the inclusion correlate with the inclusion's instantaneous rotation rate. Inclusions provide a promising tool for probing the rheological properties of active nematics and extracting ordered motion from their inherently chaotic motion.
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Affiliation(s)
- Sattvic Ray
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Jie Zhang
- Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China (USTC), 230026 Hefei, China
- Department of Polymer Science and Engineering, CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China (USTC), 230026 Hefei, China
| | - Zvonimir Dogic
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
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4
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Kozhukhov T, Shendruk TN. Mesoscopic simulations of active nematics. SCIENCE ADVANCES 2022; 8:eabo5788. [PMID: 36001669 PMCID: PMC9401632 DOI: 10.1126/sciadv.abo5788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Coarse-grained, mesoscale simulations are invaluable for studying soft condensed matter because of their ability to model systems in which a background solvent plays a substantial role but is not the primary interest. Such methods generally model passive solvents; however, far-from-equilibrium systems may also be composed of complex solutes suspended in an active fluid. Yet, few coarse-grained simulation methods exist to model an active medium. We introduce an algorithm to simulate active nematics, which builds on multiparticle collision dynamics (MPCD) for passive fluctuating nematohydrodynamics by introducing dipolar activity in the local collision operator. Active nematic MPCD (AN-MPCD) simulations not only exhibit the key characteristics of active nematic turbulence but, as a particle-based algorithm, also reproduce crucial attributes of active particle models. Thus, mesoscopic AN-MPCD is an approach that bridges microscopic and continuum descriptions, allowing simulations of composite active-passive systems.
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Arora P, Sood AK, Ganapathy R. Motile Topological Defects Hinder Dynamical Arrest in Dense Liquids of Active Ellipsoids. PHYSICAL REVIEW LETTERS 2022; 128:178002. [PMID: 35570456 DOI: 10.1103/physrevlett.128.178002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/22/2022] [Indexed: 06/15/2023]
Abstract
Recent numerical studies have identified the persistence time of active motion as a critical parameter governing glassy dynamics in dense active matter. Here we studied dynamics in liquids of granular active ellipsoids with tunable persistence and velocity. We show that increasing the persistence time at moderate supercooling is equivalent to increasing the strength of attraction in equilibrium liquids and results in reentrant dynamics not just in the translational degrees of freedom, as anticipated, but also in the orientational ones. However, at high densities, motile topological defects, unique to active liquids of elongated particles, hindered dynamical arrest. Most remarkably, for the highest activity, we observed intermittent dynamics due to the jamming-unjamming of these defects for the first time.
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Affiliation(s)
- Pragya Arora
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore - 560064, India
| | - A K Sood
- Department of Physics, Indian Institute of Science, Bangalore- 560012, India
- International Centre for Materials Science, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore - 560064, India
| | - Rajesh Ganapathy
- International Centre for Materials Science, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore - 560064, India
- School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore - 560064, India
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6
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Wu JC, Lin FJ, Ai BQ. Absolute negative mobility of active polymer chains in steady laminar flows. SOFT MATTER 2022; 18:1194-1200. [PMID: 35037681 DOI: 10.1039/d1sm01664d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We investigate the transport of active polymer chains in steady laminar flows in the presence of thermal noise and an external constant force. In the model, the polymer chain is worm-like and is propelled by active forces along its tangent vectors. Compared with inertial Brownian particles, active polymer chains in steady laminar flows exhibit richer movement patterns due to their specific spatial structures. The simulation results show that the velocity-force relation is strongly dependent on the system parameters such as the chain length, bending rigidity, active force and so on. The polymer chain may move in some preferential movement directions and exhibits absolute negative mobility within appropriate parameter regimes, i.e., the polymer chain can move in a direction opposite to the external constant force. In particular, we can observe giant negative mobility in a broad range of parameter regimes.
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Affiliation(s)
- Jian-Chun Wu
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, South China Normal University, Guangzhou 510006, China.
- School of Physics and Electronic Information, Shangrao Normal University, Shangrao 334001, China
| | - Fu-Jun Lin
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, South China Normal University, Guangzhou 510006, China.
| | - Bao-Quan Ai
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, South China Normal University, Guangzhou 510006, China.
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7
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Palmer B, Chen S, Govan P, Yan W, Gao T. Understanding topological defects in fluidized dry active nematics. SOFT MATTER 2022; 18:1013-1018. [PMID: 35018951 DOI: 10.1039/d1sm01405f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Dense assemblies of self-propelling rods (SPRs) may exhibit fascinating collective behaviors and anomalous physical properties that are far away from equilibrium. Using large-scale Brownian dynamics simulations, we investigate the dynamics of disclination defects in 2D fluidized swarming motions of dense dry SPRs (i.e., without hydrodynamic effects) that form notable local positional topological structures that are reminiscent of smectic order. We find the deformations of smectic-like rod layers can create unique polar structures that lead to slow translations and rotations of ±1/2-order defects, which are fundamentally different from the fast streaming defect motions observed in wet active matter. We measure and characterize the statistical properties of topological defects and reveal their connections with the coherent structures. Furthermore, we construct a bottom-up active-liquid-crystal model to analyze the instability of polar lanes, which effectively leads to defect formation between interlocked polar lanes and serves as the origin of the large-scale swarming motions.
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Affiliation(s)
- Bryce Palmer
- Department of Mechanical Engineering, Michigan State University, East Lansing, MI 48864, USA.
| | - Sheng Chen
- Department of Mechanical Engineering, Michigan State University, East Lansing, MI 48864, USA.
- Department of Biomedical Engineering, Yale University, West Haven, CT 06516, USA
| | - Patrick Govan
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48864, USA
| | - Wen Yan
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Tong Gao
- Department of Mechanical Engineering, Michigan State University, East Lansing, MI 48864, USA.
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48864, USA
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8
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Monderkamp PA, Wittmann R, Cortes LBG, Aarts DGAL, Smallenburg F, Löwen H. Topology of Orientational Defects in Confined Smectic Liquid Crystals. PHYSICAL REVIEW LETTERS 2021; 127:198001. [PMID: 34797147 DOI: 10.1103/physrevlett.127.198001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/28/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
We propose a general formalism to characterize orientational frustration of smectic liquid crystals in confinement by interpreting the emerging networks of grain boundaries as objects with a topological charge. In a formal idealization, this charge is distributed in pointlike units of quarter-integer magnitude, which we identify with tetratic disclinations located at the end points and nodes. This coexisting nematic and tetratic order is analyzed with the help of extensive Monte Carlo simulations for a broad range of two-dimensional confining geometries as well as colloidal experiments, showing how the observed defect networks can be universally reconstructed from simple building blocks. We further find that the curvature of the confining wall determines the anchoring behavior of grain boundaries, such that the number of nodes in the emerging networks and the location of their end points can be tuned by changing the number and smoothness of corners, respectively.
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Affiliation(s)
- Paul A Monderkamp
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - René Wittmann
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Louis B G Cortes
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Dirk G A L Aarts
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Frank Smallenburg
- Laboratoire de Physique des Solides, CNRS, Université Paris-Saclay, 91405 Orsay, France
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
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9
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Ni SD, Chen YL, Chen YQ, Zhou K, Ding HM. Molecular Simulation Studies on the Interactions of Bilirubin at Different States with a Lipid Bilayer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11707-11715. [PMID: 34570511 DOI: 10.1021/acs.langmuir.1c01613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The unconjugated bilirubin (BR) may penetrate through the cell membrane and cause a severe cytotoxicity. However, the molecular mechanism underlying the penetration of BR into the cell membrane is still largely unknown. In this work, we systematically investigate the interaction of BR and a lipid bilayer under different conditions by using all-atom molecular dynamics simulations. It is found that BR at the Z,Z conformation can easily enter into the interior of the lipid bilayer due to its hydrophobicity. However, when BR transforms from the Z,Z conformation to the E,E conformation (after the blue-light emission), its penetration ability is greatly reduced (especially at its ionized state). This study may offer useful physical insights into the effect of phototherapy on the penetration behavior and the cytotoxicity of the unconjugated BR.
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Affiliation(s)
- Song-Di Ni
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Ya-Li Chen
- Rugao Guangci Hospital, Nantong 226500, China
| | - Yuan-Qiang Chen
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Kun Zhou
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Hong-Ming Ding
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
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10
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Lemma LM, Norton MM, Tayar AM, DeCamp SJ, Aghvami SA, Fraden S, Hagan MF, Dogic Z. Multiscale Microtubule Dynamics in Active Nematics. PHYSICAL REVIEW LETTERS 2021; 127:148001. [PMID: 34652175 DOI: 10.1103/physrevlett.127.148001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 06/14/2021] [Accepted: 08/12/2021] [Indexed: 05/12/2023]
Abstract
In microtubule-based active nematics, motor-driven extensile motion of microtubule bundles powers chaotic large-scale dynamics. We quantify the interfilament sliding motion both in isolated bundles and in a dense active nematic. The extension speed of an isolated microtubule pair is comparable to the molecular motor stepping speed. In contrast, the net extension in dense 2D active nematics is significantly slower; the interfilament sliding speeds are widely distributed about the average and the filaments exhibit both contractile and extensile relative motion. These measurements highlight the challenge of connecting the extension rate of isolated bundles to the multimotor and multifilament interactions present in a dense 2D active nematic. They also provide quantitative data that is essential for building multiscale models.
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Affiliation(s)
- Linnea M Lemma
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Michael M Norton
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Alexandra M Tayar
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Stephen J DeCamp
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - S Ali Aghvami
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Seth Fraden
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Michael F Hagan
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Zvonimir Dogic
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
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11
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Qian BS, Tian WD, Chen K. Absorption of self-propelled particles into a dense porous medium. Phys Chem Chem Phys 2021; 23:20388-20397. [PMID: 34491254 DOI: 10.1039/d1cp01234g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We study the absorption of self-propelled particles into a finite-size dense porous medium, which is mimicked by an obstacle array. We find that, depending on the competition of the propelling strength versus the repulsive barrier formed by obstacles and the contrast between the characteristic time scales of permeation and propelling persistence, the absorption process exhibits three distinct types of behavior. In Type I and II behavior, the propelling strength is not large enough to surmount the barrier, and hence particles transport in the medium by barrier-hopping dynamics. The initial permeation of particles toward the medium center is phenomenologically similar to a normal slow diffusion process. But, surprisingly, after the initial permeation process, a concentrated nucleus of particle aggregates forms and grows at the medium center in Type I, due to the long propelling persistence. Such an abnormal "nucleation" phenomenon does not appear in Type II, in which the propelling persistence is low. When the propelling strength is very high (Type III), particles transport smoothly in the medium, hence the initial slow diffusion process disappears and small particle clusters form and merge randomly in the medium. Our results provide a foundation for applications of active objects in a complex environment and also suggest the possible usage of a porous medium, for example, in the selection or sorting of active matter.
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Affiliation(s)
- Bing-Shuang Qian
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China.
| | - Wen-de Tian
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China.
| | - Kang Chen
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China. .,School of Physics and Information Engineering, Shanxi Normal University, Linfen 041004, China
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12
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Abstract
Cytoskeletal active nematics exhibit striking nonequilibrium dynamics that are powered by energy-consuming molecular motors. To gain insight into the structure and mechanics of these materials, we design programmable clusters in which kinesin motors are linked by a double-stranded DNA linker. The efficiency by which DNA-based clusters power active nematics depends on both the stepping dynamics of the kinesin motors and the chemical structure of the polymeric linker. Fluorescence anisotropy measurements reveal that the motor clusters, like filamentous microtubules, exhibit local nematic order. The properties of the DNA linker enable the design of force-sensing clusters. When the load across the linker exceeds a critical threshold, the clusters fall apart, ceasing to generate active stresses and slowing the system dynamics. Fluorescence readout reveals the fraction of bound clusters that generate interfilament sliding. In turn, this yields the average load experienced by the kinesin motors as they step along the microtubules. DNA-motor clusters provide a foundation for understanding the molecular mechanism by which nanoscale molecular motors collectively generate mesoscopic active stresses, which in turn power macroscale nonequilibrium dynamics of active nematics.
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13
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Lei QL, Hu H, Ni R. Barrier-controlled nonequilibrium criticality in reactive particle systems. Phys Rev E 2021; 103:052607. [PMID: 34134288 DOI: 10.1103/physreve.103.052607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/03/2021] [Indexed: 11/07/2022]
Abstract
Nonequilibrium critical phenomena generally exist in many dynamic systems, like chemical reactions and some driven-dissipative reactive particle systems. Here, by using computer simulation and theoretical analysis, we demonstrate the crucial role of the activation barrier on the criticality of dynamic phase transitions in a minimal reactive hard-sphere model. We find that at zero thermal noise, with increasing the activation barrier, the type of transition changes from a continuous conserved directed percolation into a discontinuous dynamic transition by crossing a tricritical point. A mean-field theory combined with field simulation is proposed to explain this phenomenon. The possibility of Ising-type criticality in the nonequilibrium system at finite thermal noise is also discussed.
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Affiliation(s)
- Qun-Li Lei
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459, Singapore
| | - Hao Hu
- School of Physics and Materials Science, Anhui University, Hefei 230601, China
| | - Ran Ni
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459, Singapore
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14
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Tang X, Selinger JV. Alignment of a topological defect by an activity gradient. Phys Rev E 2021; 103:022703. [PMID: 33736015 DOI: 10.1103/physreve.103.022703] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 01/21/2021] [Indexed: 01/10/2023]
Abstract
As a method for controlling active materials, researchers have suggested designing patterns of activity on a substrate, which should guide the motion of topological defects. To investigate this concept, we model the behavior of a single defect of topological charge +1/2, moving in an activity gradient. This modeling uses three methods: (1) approximate analytic solution of hydrodynamic equations, (2) macroscopic, symmetry-based theory of the defect as an effective oriented particle, and (3) numerical simulation. All three methods show that an activity gradient aligns the defect orientation, and hence should be useful to control defect motion.
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Affiliation(s)
- Xingzhou Tang
- Department of Physics, Advanced Materials and Liquid Crystal Institute, Kent State University, Kent, Ohio 44242, USA
| | - Jonathan V Selinger
- Department of Physics, Advanced Materials and Liquid Crystal Institute, Kent State University, Kent, Ohio 44242, USA
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15
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Nejad MR, Doostmohammadi A, Yeomans JM. Memory effects, arches and polar defect ordering at the cross-over from wet to dry active nematics. SOFT MATTER 2021; 17:2500-2511. [PMID: 33503081 DOI: 10.1039/d0sm01794a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We use analytic arguments and numerical solutions of the continuum, active nematohydrodynamic equations to study how friction alters the behaviour of active nematics. Concentrating on the case where there is nematic ordering in the passive limit, we show that, as the friction is increased, memory effects become more prominent and +1/2 topological defects leave increasingly persistent trails in the director field as they pass. The trails are preferential sites for defect formation and they tend to impose polar order on any new +1/2 defects. In the absence of noise and for high friction, it becomes very difficult to create defects, but trails formed by any defects present at the beginning of the simulations persist and organise into parallel arch-like patterns in the director field. We show aligned arches of equal width are approximate steady state solutions of the equations of motion which co-exist with the nematic state. We compare our results to other models in the literature, in particular dry systems with no hydrodynamics, where trails, arches and polar defect ordering have also been observed.
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Affiliation(s)
- Mehrana R Nejad
- The Rudolf Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK.
| | | | - Julia M Yeomans
- The Rudolf Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK.
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16
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Xu XB, Tang T, Wang ZH, Xu XN, Fang GY, Gu M. Nonequilibrium pattern formation in circularly confined two-dimensional systems with competing interactions. Phys Rev E 2021; 103:012604. [PMID: 33601588 DOI: 10.1103/physreve.103.012604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/19/2020] [Indexed: 11/07/2022]
Abstract
We numerically investigate the nonequilibrium behaviors of classic particles with competing interactions confined in a two-dimensional logarithmic trap. We reveal a quench-induced surprising dynamics exhibiting rich dynamic patterns depending upon confinement strength and trap size, which is attributed to the time-dependent competition between interparticle repulsions and attractions under a circular confinement. Moreover, in the collectively diffusive motions of the particles, we find that the emergence of dynamic structure transformation coincides with a diffusive mode transition from superdiffusion to subdiffusion. These findings are likely useful in understanding the pattern selection and evolution in various chemical and biological systems in addition to modulated systems, and add a new route to tailoring the morphology of pattern-forming systems.
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Affiliation(s)
- X B Xu
- Collaborative Innovation Center of Advanced Microstructures, School of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - T Tang
- Collaborative Innovation Center of Advanced Microstructures, School of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - Z H Wang
- Collaborative Innovation Center of Advanced Microstructures, School of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - X N Xu
- Collaborative Innovation Center of Advanced Microstructures, School of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - G Y Fang
- Collaborative Innovation Center of Advanced Microstructures, School of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - M Gu
- Collaborative Innovation Center of Advanced Microstructures, School of Physics, Nanjing University, Nanjing 210093, People's Republic of China
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17
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Zhou Z, Joshi C, Liu R, Norton MM, Lemma L, Dogic Z, Hagan MF, Fraden S, Hong P. Machine learning forecasting of active nematics. SOFT MATTER 2021; 17:738-747. [PMID: 33220675 DOI: 10.1039/d0sm01316a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Active nematics are a class of far-from-equilibrium materials characterized by local orientational order of force-generating, anisotropic constitutes. Traditional methods for predicting the dynamics of active nematics rely on hydrodynamic models, which accurately describe idealized flows and many of the steady-state properties, but do not capture certain detailed dynamics of experimental active nematics. We have developed a deep learning approach that uses a Convolutional Long-Short-Term-Memory (ConvLSTM) algorithm to automatically learn and forecast the dynamics of active nematics. We demonstrate our purely data-driven approach on experiments of 2D unconfined active nematics of extensile microtubule bundles, as well as on data from numerical simulations of active nematics.
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18
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Wang Z, Chu KC, Tsao HK, Sheng YJ. Preferred penetration of active nano-rods into narrow channels and their clustering. Phys Chem Chem Phys 2021; 23:16234-16241. [PMID: 34308947 DOI: 10.1039/d1cp01065d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In a channel connected to a reservoir, passive particles prefer staying in the reservoir than the channel due to the entropic effect, as the size of the particles is comparable to that of the channel. Self-propelled rods can exhibit out-of-equilibrium phenomena, and their partition behavior may differ from that of passive rods due to their persistent swimming ability. In this work, the distribution of active nano-rods between the nanoscale channel and reservoir is explored using dissipative particle dynamics. The ratio of the nano-rod concentration in the slit to that in the reservoir, defined as the partition ratio Ψ, is a function of active force, channel width, and rod length. Although passive nano-rods prefer staying in bulk (Ψ < 1), active rods can overcome the entropic barrier and show favorable partition toward narrow channels (Ψ > 1). As the slit width decreases to about the rod's width, active rods entering the slit behave like a quasi-two-dimensional system dynamically. At sufficiently high concentrations and Peclet numbers, nano-rods tend to align and move together in the same direction for a certain time. The distribution (PM) of the cluster size (M) follows a power law, PM ∝ M-2, for small clusters.
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Affiliation(s)
- Zhengjia Wang
- Condensed Matter Science and Technology Institute, School of Instrumentation Science and Engineering, Harbin Institute of Technology, Harbin 150080, People's Republic of China
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19
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Kumar S, Mishra S. Active nematics with quenched disorder. Phys Rev E 2020; 102:052609. [PMID: 33327090 DOI: 10.1103/physreve.102.052609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 11/02/2020] [Indexed: 11/07/2022]
Abstract
We introduce a two-dimensional active nematic with quenched disorder. We write the coarse-grained hydrodynamic equations of motion for slow variables, viz. density and orientation. Disorder strength is tuned from zero to large values. Results from the numerical solution of equations of motion as well as the calculation of two-point orientation correlation function using linear approximation shows that the ordered steady state follows a disorder dependent crossover from quasi-long-range order to short-range order. Such crossover is due to the pinning of ±1/2 topological defects in the presence of finite disorder, which breaks the system in uncorrelated domains. Finite disorder slows the dynamics of +1/2 defect, and it leads to slower growth dynamics. The two-point correlation functions for the density and orientation fields show good dynamic scaling but no static scaling for the different disorder strengths. Our findings can motivate experimentalists to verify the results and find applications in living and artificial apolar systems in the presence of a quenched disorder.
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Affiliation(s)
- Sameer Kumar
- Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh 221005, India
| | - Shradha Mishra
- Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh 221005, India
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20
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Yu YS, Tan RR, Ding HM. Controlling ion transport in a C 2N-based nanochannel with tunable interlayer spacing. Phys Chem Chem Phys 2020; 22:16855-16861. [PMID: 32666963 DOI: 10.1039/d0cp02993a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Selective ion transport through a nanochannel formed by stacked two-dimensional materials plays a key role in water desalination, nanofiltration, and ion separation. Although there have been many functional nanomaterials used in these applications, how to well control ion transport in a laminar structure so as to obtain the desired selectivity still remains a challenging problem. In the present work, the transport of ions through a C2N-based nanochannel is investigated by using all-atom molecular dynamics simulation. It is found that C2N-based nanochannels with different interlayer spacing posses diverse ion selectivity, which is mainly attributed to the distinct loading capability among ions and the different velocity of ions inside the nanochannel. Moreover, we also find that the ion selectivity is dependent on the electric field, but nearly independent of the salt concentration. The present study may provide some physical insights into the experimental design of C2N-based nanodevices in nanofiltration.
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Affiliation(s)
- You-Sheng Yu
- School of Science, East China University of Technology, Nanchang 330013, China
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21
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Shi SJ, Li HS, Feng GQ, Tian WD, Chen K. Transport of self-propelled particles across a porous medium: trapping, clogging, and the Matthew effect. Phys Chem Chem Phys 2020; 22:14052-14060. [PMID: 32568323 DOI: 10.1039/d0cp01923b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We study the transport of self-propelled particles from one free chamber to another across two stripe-like areas of dense porous medium. The medium is mimicked by arrays of obstacles. We find that active motion could greatly speed up the transport of particles. However, more and more particles become trapped in the obstacle arrays with the enhancement of activity. At high persistence (low rotational diffusion rate) and moderate particle concentration, we observe the Matthew effect in the aggregation of particles in the two obstacle arrays. This effect is weakened by introduction of randomness or deformability into the obstacle arrays. Moreover, the dependence on deformability shows the characteristics of first-order phase transition. In rare situations, the system could be stuck in a dynamic unstable state, e.g. the particles alternatively gather more in one of the two obstacle arrays, exhibiting oscillation of particle number between the arrays. Our results reveal new features in the transport of active objects in a complex medium and have implications for manipulating their collective assembly.
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Affiliation(s)
- Shen-Jia Shi
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China.
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22
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Collective Dynamics of Model Pili-Based Twitcher-Mode Bacilliforms. Sci Rep 2020; 10:10747. [PMID: 32612117 PMCID: PMC7330051 DOI: 10.1038/s41598-020-67212-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 05/27/2020] [Indexed: 11/29/2022] Open
Abstract
Pseudomonas aeruginosa, like many bacilliforms, are not limited only to swimming motility but rather possess many motility strategies. In particular, twitching-mode motility employs hair-like pili to transverse moist surfaces with a jittery irregular crawl. Twitching motility plays a critical role in redistributing cells on surfaces prior to and during colony formation. We combine molecular dynamics and rule-based simulations to study twitching-mode motility of model bacilliforms and show that there is a critical surface coverage fraction at which collective effects arise. Our simulations demonstrate dynamic clustering of twitcher-type bacteria with polydomains of local alignment that exhibit spontaneous correlated motions, similar to rafts in many bacterial communities.
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23
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Vliegenthart GA, Ravichandran A, Ripoll M, Auth T, Gompper G. Filamentous active matter: Band formation, bending, buckling, and defects. SCIENCE ADVANCES 2020; 6:eaaw9975. [PMID: 32832652 PMCID: PMC7439626 DOI: 10.1126/sciadv.aaw9975] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/05/2020] [Indexed: 06/01/2023]
Abstract
Motor proteins drive persistent motion and self-organization of cytoskeletal filaments. However, state-of-the-art microscopy techniques and continuum modeling approaches focus on large length and time scales. Here, we perform component-based computer simulations of polar filaments and molecular motors linking microscopic interactions and activity to self-organization and dynamics from the filament level up to the mesoscopic domain level. Dynamic filament cross-linking and sliding and excluded-volume interactions promote formation of bundles at small densities and of active polar nematics at high densities. A buckling-type instability sets the size of polar domains and the density of topological defects. We predict a universal scaling of the active diffusion coefficient and the domain size with activity, and its dependence on parameters like motor concentration and filament persistence length. Our results provide a microscopic understanding of cytoplasmic streaming in cells and help to develop design strategies for novel engineered active materials.
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24
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Pan JX, Wei H, Qi MJ, Wang HF, Zhang JJ, Tian WD, Chen K. Vortex formation of spherical self-propelled particles around a circular obstacle. SOFT MATTER 2020; 16:5545-5551. [PMID: 32510067 DOI: 10.1039/d0sm00277a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A vortex is a common ratchet phenomenon in active systems. The spatial symmetry is usually broken by introducing asymmetric shapes or spontaneously by collective motion in the presence of hydrodynamic interactions or other alignment effects. Unexpectedly, we observe, by simulations, the formation of a vortex in the simplest model of a circular obstacle immersed in a bath of spherical self-propelled particles. No symmetry-breaking factors mentioned above are included in this model. The vortex forms only when the particle activity is high, i.e. large persistence. The obstacle size is also a key factor and the vortex only forms in a limited range of obstacle sizes. The sustainment of the vortex originates from the bias of the rotating particle cluster around the obstacle in accepting the incoming particles based on their propelling directions. Our results provide new understanding of and insights into the spontaneous symmetry-breaking and ratchet phenomena in active matter.
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Affiliation(s)
- Jun-Xing Pan
- School of Physics and Information Engineering, Shanxi Normal University, Linfen 041004, China.
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25
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Duclos G, Adkins R, Banerjee D, Peterson MSE, Varghese M, Kolvin I, Baskaran A, Pelcovits RA, Powers TR, Baskaran A, Toschi F, Hagan MF, Streichan SJ, Vitelli V, Beller DA, Dogic Z. Topological structure and dynamics of three-dimensional active nematics. Science 2020; 367:1120-1124. [PMID: 32139540 DOI: 10.1126/science.aaz4547] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/07/2020] [Indexed: 12/30/2022]
Abstract
Topological structures are effective descriptors of the nonequilibrium dynamics of diverse many-body systems. For example, motile, point-like topological defects capture the salient features of two-dimensional active liquid crystals composed of energy-consuming anisotropic units. We dispersed force-generating microtubule bundles in a passive colloidal liquid crystal to form a three-dimensional active nematic. Light-sheet microscopy revealed the temporal evolution of the millimeter-scale structure of these active nematics with single-bundle resolution. The primary topological excitations are extended, charge-neutral disclination loops that undergo complex dynamics and recombination events. Our work suggests a framework for analyzing the nonequilibrium dynamics of bulk anisotropic systems as diverse as driven complex fluids, active metamaterials, biological tissues, and collections of robots or organisms.
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Affiliation(s)
- Guillaume Duclos
- Department of Physics, Brandeis University, Waltham, MA 02453, USA
| | - Raymond Adkins
- Department of Physics, University of California, Santa Barbara, CA 93111, USA
| | - Debarghya Banerjee
- Max Planck Institute for Dynamics and Self-Organization, 37077 Göttingen, Germany.,Instituut-Lorentz, Universiteit Leiden, 2300 RA Leiden, Netherlands
| | | | - Minu Varghese
- Department of Physics, Brandeis University, Waltham, MA 02453, USA
| | - Itamar Kolvin
- Department of Physics, University of California, Santa Barbara, CA 93111, USA
| | - Arvind Baskaran
- Department of Physics, Brandeis University, Waltham, MA 02453, USA
| | | | - Thomas R Powers
- School of Engineering, Brown University, Providence, RI 02912, USA.,Department of Physics, Brown University, Providence, RI 02912, USA
| | - Aparna Baskaran
- Department of Physics, Brandeis University, Waltham, MA 02453, USA
| | - Federico Toschi
- Department of Applied Physics, Eindhoven University of Technology, 5600 MB Eindhoven, Netherlands.,Instituto per le Applicazioni del Calcolo CNR, 00185 Rome, Italy
| | - Michael F Hagan
- Department of Physics, Brandeis University, Waltham, MA 02453, USA
| | | | - Vincenzo Vitelli
- James Frank Institute and Department of Physics, The University of Chicago, Chicago, IL 60637, USA
| | - Daniel A Beller
- Department of Physics, University of California, Merced, CA 95343, USA.
| | - Zvonimir Dogic
- Department of Physics, Brandeis University, Waltham, MA 02453, USA. .,Department of Physics, University of California, Santa Barbara, CA 93111, USA
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26
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Patelli A, Djafer-Cherif I, Aranson IS, Bertin E, Chaté H. Understanding Dense Active Nematics from Microscopic Models. PHYSICAL REVIEW LETTERS 2019; 123:258001. [PMID: 31922774 DOI: 10.1103/physrevlett.123.258001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/13/2019] [Indexed: 06/10/2023]
Abstract
We study dry, dense active nematics at both particle and continuous levels. Specifically, extending the Boltzmann-Ginzburg-Landau approach, we derive well-behaved hydrodynamic equations from a Vicsek-style model with nematic alignment and pairwise repulsion. An extensive study of the phase diagram shows qualitative agreement between the two levels of description. We find in particular that the dynamics of topological defects strongly depends on parameters and can lead to "arch" solutions forming a globally polar, smecticlike arrangement of Néel walls. We show how these configurations are at the origin of the defect ordered states reported previously. This work offers a detailed understanding of the theoretical description of dense active nematics directly rooted in their microscopic dynamics.
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Affiliation(s)
- Aurelio Patelli
- Service de Physique de l'Etat Condensé, CEA, CNRS, Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
| | - Ilyas Djafer-Cherif
- Service de Physique de l'Etat Condensé, CEA, CNRS, Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- School of Mathematics, University of Bristol, Bristol BS8 1TW, United Kingdom
| | - Igor S Aranson
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Eric Bertin
- Univ. Grenoble Alpes, CNRS, LIPhy, 38000 Grenoble, France
| | - Hugues Chaté
- Service de Physique de l'Etat Condensé, CEA, CNRS, Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- Computational Science Research Center, Beijing 100094, China
- LPTMC, Sorbonne Université, CNRS, 75005 Paris, France
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27
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Wang Z, Si T, Hao J, Guan Y, Qin F, Yang B, Cao W. Defect dynamics in clusters of self-propelled rods in circular confinement. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:150. [PMID: 31773335 DOI: 10.1140/epje/i2019-11911-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/22/2019] [Indexed: 06/10/2023]
Abstract
Rod-shaped active micro/nano-particles, such as bacterial and bipolar metallic micro/nano-motors, demonstrate novel collective phenomena far from the equilibrium state compared to passive particles. We apply a simulation approach --dissipative particle dynamics (DPD)-- to explore the collectively ordered states of self-propelled rods (SPRs). The SPRs are confined in a finite circular zone and repel each other when two rods touch each other. It is found that for a long enough rods system, the global vortex patterns, dynamic pattern oscillation between hedgehog pattern and vortex pattern, and hedgehog patterns are observed successively with increasing active force Fa. For the vortex pattern, the total interaction energy between the rods U is linear with active force Fa, i.e., U ∼ Fa . While the relation U ∼ Fa2 is obtained for the hedgehog structure. It is observed that a new hedgehog pattern with one defect core is created by two ejections of polar cluster in opposite directions from the original hedgehog pattern, and then merges into one through the diffusion of the two aggregates, i.e., the creation and annihilation of topological charges.
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Affiliation(s)
- Zhengjia Wang
- Condensed Matter Science and Technology Institute, School of Instrumentation Science and Engineering, Harbin Institute of Technology, 150080, Harbin, P.R. China
| | - Tieyan Si
- School of Physics, Harbin Institute of Technology, 150080, Harbin, P.R. China
| | - Junhua Hao
- Department of Physics, Tianjin University Renai College, 301636, Tianjin, P.R. China.
| | - Yu Guan
- Amur State University, 675004, Blagoveshchensk, Russia
| | - Feng Qin
- Condensed Matter Science and Technology Institute, School of Instrumentation Science and Engineering, Harbin Institute of Technology, 150080, Harbin, P.R. China
| | - Bin Yang
- Condensed Matter Science and Technology Institute, School of Instrumentation Science and Engineering, Harbin Institute of Technology, 150080, Harbin, P.R. China
| | - Wenwu Cao
- Condensed Matter Science and Technology Institute, School of Instrumentation Science and Engineering, Harbin Institute of Technology, 150080, Harbin, P.R. China
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28
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Zhao J, Gulan U, Horie T, Ohmura N, Han J, Yang C, Kong J, Wang S, Xu BB. Advances in Biological Liquid Crystals. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900019. [PMID: 30892830 DOI: 10.1002/smll.201900019] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/17/2019] [Indexed: 06/09/2023]
Abstract
Biological liquid crystals, a rich set of soft materials with rod-like structures widely existing in nature, possess typical lyotropic liquid crystalline phase properties both in vitro (e.g., cellulose, peptides, and protein assemblies) and in vivo (e.g., cellular lipid membrane, packed DNA in bacteria, and aligned fibroblasts). Given the ability to undergo phase transition in response to various stimuli, numerous practices are exercised to spatially arrange biological liquid crystals. Here, a fundamental understanding of interactions between rod-shaped biological building blocks and their orientational ordering across multiple length scales is addressed. Discussions are made with regard to the dependence of physical properties of nonmotile objects on the first-order phase transition and the coexistence of multi-phases in passive liquid crystalline systems. This work also focuses on how the applied physical stimuli drives the reorganization of constituent passive particles for a new steady-state alignment. A number of recent progresses in the dynamics behaviors of active liquid crystals are presented, and particular attention is given to those self-propelled animate elements, like the formation of motile topological defects, active turbulence, correlation of orientational ordering, and cellular functions. Finally, future implications and potential applications of the biological liquid crystalline materials are discussed.
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Affiliation(s)
- Jianguo Zhao
- Quanzhou Institute of Equipment Manufacturing, Haixi Institutes, Chinese Academy of Sciences, Quanzhou, 362200, China
- Third Institute of Physics-Biophysics, University of Göttingen, 37077, Göttingen, Germany
| | - Utku Gulan
- Institute of Environmental Engineering, ETH Zurich, 8093, Zurich, Switzerland
| | - Takafumi Horie
- Department of Chemical Science and Engineering, Kobe University, Kobe, 657-8501, Japan
| | - Naoto Ohmura
- Department of Chemical Science and Engineering, Kobe University, Kobe, 657-8501, Japan
| | - Jun Han
- Quanzhou Institute of Equipment Manufacturing, Haixi Institutes, Chinese Academy of Sciences, Quanzhou, 362200, China
| | - Chao Yang
- CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jie Kong
- Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Science, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Steven Wang
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Ben Bin Xu
- Mechanical and Construction Engineering, Faculty of Engineering and Environment, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
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29
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Xia YQ, Shen ZL, Tian WD, Chen K. Unfolding of a diblock chain and its anomalous diffusion induced by active particles. J Chem Phys 2019; 150:154903. [PMID: 31005072 DOI: 10.1063/1.5095850] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We study the structural and dynamical behavior of an A-B diblock chain in the bath of active Brownian particles (ABPs) by Brownian dynamics simulations in two dimensions. We are interested in the situation that the effective interaction between the A segments is attractive, while that between the B segments is repulsive. Therefore, in thermal (nonactive) equilibrium, the A block "folds" into a compact globule, while the B block is in the expanded coil state. Interestingly, we find that the A block could "unfold" sequentially like unknitting a sweater, driven by the surrounding ABPs when the propelling strength on them is beyond a certain value. This threshold value decreases and then levels off as the length of the B block increases. We also find a simple power-law relation between the unfolding time of the A block and the self-propelling strength and an exponential relation between the unfolding time and the length of the B block. Finally, we probe the translational and rotational diffusion of the chain and find that both of them show "super-diffusivity" in a large time window, especially when the self-propelling strength is small and the A block is in the folded state. Such super-diffusivity is due to the strong asymmetric distribution of ABPs around the chain. Our work provides new insights into the behavior of a polymer chain in the environment of active objects.
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Affiliation(s)
- Yi-Qi Xia
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Zhuang-Lin Shen
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Wen-de Tian
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Kang Chen
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
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30
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Lemma LM, DeCamp SJ, You Z, Giomi L, Dogic Z. Statistical properties of autonomous flows in 2D active nematics. SOFT MATTER 2019; 15:3264-3272. [PMID: 30920553 PMCID: PMC6924514 DOI: 10.1039/c8sm01877d] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We study the dynamics of a tunable 2D active nematic liquid crystal composed of microtubules and kinesin motors confined to an oil-water interface. Kinesin motors continuously inject mechanical energy into the system through ATP hydrolysis, powering the relative microscopic sliding of adjacent microtubules, which in turn generates macroscale autonomous flows and chaotic dynamics. We use particle image velocimetry to quantify two-dimensional flows of active nematics and extract their statistical properties. In agreement with the hydrodynamic theory, we find that the vortex areas comprising the chaotic flows are exponentially distributed, which allows us to extract the characteristic system length scale. We probe the dependence of this length scale on the ATP concentration, which is the experimental knob that tunes the magnitude of the active stress. Our data suggest a possible mapping between the ATP concentration and the active stress that is based on the Michaelis-Menten kinetics that governs the motion of individual kinesin motors.
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Affiliation(s)
- Linnea M Lemma
- Department of Physics, Brandeis University, Waltham, MA 02454, USA
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31
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Abstract
Active matter comprises individual units that convert energy into mechanical motion. In many examples, such as bacterial systems and biofilament assays, constituent units are elongated and can give rise to local nematic orientational order. Such "active nematics" systems have attracted much attention from both theorists and experimentalists. However, despite intense research efforts, data-driven quantitative modeling has not been achieved, a situation mainly due to the lack of systematic experimental data and to the large number of parameters of current models. Here, we introduce an active nematics system made of swarming filamentous bacteria. We simultaneously measure orientation and velocity fields and show that the complex spatiotemporal dynamics of our system can be quantitatively reproduced by a type of microscopic model for active suspensions whose important parameters are all estimated from comprehensive experimental data. This provides unprecedented access to key effective parameters and mechanisms governing active nematics. Our approach is applicable to different types of dense suspensions and shows a path toward more quantitative active matter research.
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32
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Joshi A, Putzig E, Baskaran A, Hagan MF. The interplay between activity and filament flexibility determines the emergent properties of active nematics. SOFT MATTER 2018; 15:94-101. [PMID: 30520495 DOI: 10.1039/c8sm02202j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Active nematics are microscopically driven liquid crystals that exhibit dynamical steady states characterized by the creation and annihilation of topological defects. Motivated by differences between previous simulations of active nematics based on rigid rods and experimental realizations based on semiflexible biopolymer filaments, we describe a large-scale simulation study of a particle-based computational model that explicitly incorporates filament semiflexibility. We find that energy injected into the system at the particle scale preferentially excites bend deformations, reducing the apparent filament bend modulus. The emergent characteristics of the active nematic depend on activity and flexibility only through this activity-renormalized bend 'modulus', demonstrating that apparent values of material parameters, such as the Frank 'constants', depend on activity. Thus, phenomenological parameters within continuum hydrodynamic descriptions of active nematics must account for this dependence. Further, we present a systematic way to estimate these parameters from observations of deformation fields and defect shapes in experimental or simulation data.
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Affiliation(s)
- Abhijeet Joshi
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02453, USA.
| | - Elias Putzig
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02453, USA.
| | - Aparna Baskaran
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02453, USA.
| | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02453, USA.
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33
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Shankar S, Ramaswamy S, Marchetti MC, Bowick MJ. Defect Unbinding in Active Nematics. PHYSICAL REVIEW LETTERS 2018; 121:108002. [PMID: 30240234 DOI: 10.1103/physrevlett.121.108002] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/18/2018] [Indexed: 06/08/2023]
Abstract
We formulate the statistical dynamics of topological defects in the active nematic phase, formed in two dimensions by a collection of self-driven particles on a substrate. An important consequence of the nonequilibrium drive is the spontaneous motility of strength +1/2 disclinations. Starting from the hydrodynamic equations of active nematics, we derive an interacting particle description of defects that includes active torques. We show that activity, within perturbation theory, lowers the defect-unbinding transition temperature, determining a critical line in the temperature-activity plane that separates the quasi-long-range ordered (nematic) and disordered (isotropic) phases. Below a critical activity, defects remain bound as rotational noise decorrelates the directed dynamics of +1/2 defects, stabilizing the quasi-long-range ordered nematic state. This activity threshold vanishes at low temperature, leading to a reentrant transition. At large enough activity, active forces always exceed thermal ones and the perturbative result fails, suggesting that in this regime activity will always disorder the system. Crucially, rotational diffusion being a two-dimensional phenomenon, defect unbinding cannot be described by a simplified one-dimensional model.
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Affiliation(s)
- Suraj Shankar
- Physics Department and Syracuse Soft and Living Matter Program, Syracuse University, Syracuse, New York 13244, USA
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106, USA
| | - Sriram Ramaswamy
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106, USA
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560 012, India
| | - M Cristina Marchetti
- Physics Department and Syracuse Soft and Living Matter Program, Syracuse University, Syracuse, New York 13244, USA
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106, USA
| | - Mark J Bowick
- Physics Department and Syracuse Soft and Living Matter Program, Syracuse University, Syracuse, New York 13244, USA
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106, USA
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Doostmohammadi A, Ignés-Mullol J, Yeomans JM, Sagués F. Active nematics. Nat Commun 2018; 9:3246. [PMID: 30131558 PMCID: PMC6104062 DOI: 10.1038/s41467-018-05666-8] [Citation(s) in RCA: 255] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 06/28/2018] [Accepted: 07/19/2018] [Indexed: 11/09/2022] Open
Abstract
Active matter extracts energy from its surroundings at the single particle level and transforms it into mechanical work. Examples include cytoskeleton biopolymers and bacterial suspensions. Here, we review experimental, theoretical and numerical studies of active nematics - a type of active system that is characterised by self-driven units with elongated shape. We focus primarily on microtubule-kinesin mixtures and the hydrodynamic theories that describe their properties. An important theme is active turbulence and the associated motile topological defects. We discuss ways in which active turbulence may be controlled, a pre-requisite to harvesting energy from active materials, and we consider the appearance, and possible implications, of active nematics and topological defects to cellular systems and biological processes.
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Affiliation(s)
- Amin Doostmohammadi
- The Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Clarendon Laboratory, Parks Rd., Oxford, OX1 3PU, UK.
| | - Jordi Ignés-Mullol
- Departament de Ciència de Materials i Química Física and Institute of Nanoscience and Nanotechnology, Universitat de Barcelona, Martí I Franquès 1, 08028, Barcelona, Catalonia, Spain
| | - Julia M Yeomans
- The Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Clarendon Laboratory, Parks Rd., Oxford, OX1 3PU, UK
| | - Francesc Sagués
- Departament de Ciència de Materials i Química Física and Institute of Nanoscience and Nanotechnology, Universitat de Barcelona, Martí I Franquès 1, 08028, Barcelona, Catalonia, Spain
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35
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Cortese D, Eggers J, Liverpool TB. Pair creation, motion, and annihilation of topological defects in two-dimensional nematic liquid crystals. Phys Rev E 2018; 97:022704. [PMID: 29548179 DOI: 10.1103/physreve.97.022704] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Indexed: 11/07/2022]
Abstract
We present a framework for the study of disclinations in two-dimensional active nematic liquid crystals and topological defects in general. The order tensor formalism is used to calculate exact multiparticle solutions of the linearized static equations inside a planar uniformly aligned state so that the total charge has to vanish. Topological charge conservation then requires that there is always an equal number of q=1/2 and q=-1/2 charges. Starting from a set of hydrodynamic equations, we derive a low-dimensional dynamical system for the parameters of the static solutions, which describes the motion of a half-disclination pair or of several pairs. Within this formalism, we model defect production and annihilation, as observed in experiments. Our dynamics also provide an estimate for the critical density at which production and annihilation rates are balanced.
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Affiliation(s)
- Dario Cortese
- School of Mathematics, University of Bristol, Bristol BS8 1TW, United Kingdom
| | - Jens Eggers
- School of Mathematics, University of Bristol, Bristol BS8 1TW, United Kingdom
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36
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37
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Henkes S, Marchetti MC, Sknepnek R. Dynamical patterns in nematic active matter on a sphere. Phys Rev E 2018; 97:042605. [PMID: 29758687 DOI: 10.1103/physreve.97.042605] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Indexed: 01/24/2023]
Abstract
Using simulations of self-propelled agents with short-range repulsion and nematic alignment, we explore the dynamical phases of a dense active nematic confined to the surface of a sphere. We map the nonequilibrium phase diagram as a function of curvature, alignment strength, and activity. Our model reproduces several phases seen in recent experiments on active microtubule bundles confined the surfaces of vesicles. At low driving, we recover the equilibrium nematic ground state with four +1/2 defects. As the driving is increased, geodesic forces drive the transition to a polar band wrapping around an equator, with large empty spherical caps corresponding to two +1 defects at the poles. Upon further increasing activity, the bands fold onto themselves, and the system eventually transitions to a turbulent state marked by the proliferation of pairs of topological defects. We highlight the key role of the nematic persistence length in controlling pattern formation in these confined systems with positive Gaussian curvature.
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Affiliation(s)
- Silke Henkes
- Institute for Complex Systems and Mathematical Biology, Department of Physics, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
| | - M Cristina Marchetti
- Department of Physics and Soft Matter Program, Syracuse University, Syracuse, New York 13244, USA
| | - Rastko Sknepnek
- School of Sciences and Engineering and School of Life Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom
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38
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Prathyusha KR, Henkes S, Sknepnek R. Dynamically generated patterns in dense suspensions of active filaments. Phys Rev E 2018; 97:022606. [PMID: 29548173 DOI: 10.1103/physreve.97.022606] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Indexed: 06/08/2023]
Abstract
We use Langevin dynamics simulations to study dynamical behavior of a dense planar layer of active semiflexible filaments. Using the strength of active force and the thermal persistence length as parameters, we map a detailed phase diagram and identify several nonequilibrium phases in this system. In addition to a slowly flowing melt phase, we observe that, for sufficiently high activity, collective flow accompanied by signatures of local polar and nematic order appears in the system. This state is also characterized by strong density fluctuations. Furthermore, we identify an activity-driven crossover from this state of coherently flowing bundles of filaments to a phase with no global flow, formed by individual filaments coiled into rotating spirals. This suggests a mechanism where the system responds to activity by changing the shape of active agents, an effect with no analog in systems of active particles without internal degrees of freedom.
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Affiliation(s)
- K R Prathyusha
- School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom
| | - Silke Henkes
- Institute of Complex Systems and Mathematical Biology, Department of Physics, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
| | - Rastko Sknepnek
- School of Science and Engineering, University of Dundee, Dundee DD1 4HN, United Kingdom
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
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39
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Guillamat P, Hardoüin J, Prat BM, Ignés-Mullol J, Sagués F. Control of active turbulence through addressable soft interfaces. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:504003. [PMID: 29125475 DOI: 10.1088/1361-648x/aa99c8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present an experimental study of a kinesin/tubulin active nematic formed at different oil interfaces. By tuning the interfacial rheology of the contacting oil, we have been able to condition and control the seemingly chaotic motion that characterizes the self-sustained active flows in our preparations. The active nematic is inherently unstable and spontaneously develops defects from an initial homogeneous state. We show that the steady state and, in particular, the density and dynamics of the defects strongly depends on the rheology of the contacting oil. Using a smectic-A thermotropic liquid crystal as the oil phase, we pattern the interface thanks to the anisotropy of the shear viscosity in this material. The geometry of the active nematic adapts to the boundary conditions at the interface by changing from the so-called active turbulent regime to laminar flows along the easy flow directions. The latter can be either a lattice of self-assembled circular paths or reconfigurable homogeneous orientations that can be addressed by means of an external magnetic field. We show that, under all confinement conditions, the spatiotemporal modes exhibited by the active liquid are consistent with a single intrinsic length scale, which can be tuned by the material parameters, and obey basic topological requirements imposed on the defects that drive the active flows. Future control strategies, including a tunable depleting agent, are discussed.
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Affiliation(s)
- P Guillamat
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Barcelona, Catalonia. Institute of Nanoscience and Nanotechnology, IN2UB, Universitat de Barcelona, Barcelona, Catalonia
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40
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Guillamat P, Ignés-Mullol J, Sagués F. Taming active turbulence with patterned soft interfaces. Nat Commun 2017; 8:564. [PMID: 28916801 PMCID: PMC5601458 DOI: 10.1038/s41467-017-00617-1] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/13/2017] [Indexed: 11/30/2022] Open
Abstract
Active matter embraces systems that self-organize at different length and time scales, often exhibiting turbulent flows apparently deprived of spatiotemporal coherence. Here, we use a layer of a tubulin-based active gel to demonstrate that the geometry of active flows is determined by a single length scale, which we reveal in the exponential distribution of vortex sizes of active turbulence. Our experiments demonstrate that the same length scale reemerges as a cutoff for a scale-free power law distribution of swirling laminar flows when the material evolves in contact with a lattice of circular domains. The observed prevalence of this active length scale can be understood by considering the role of the topological defects that form during the spontaneous folding of microtubule bundles. These results demonstrate an unexpected strategy for active systems to adapt to external stimuli, and provide with a handle to probe the existence of intrinsic length and time scales. Active nematics consist of self-driven components that develop orientational order and turbulent flow. Here Guillamat et al. investigate an active nematic constrained in a quasi-2D geometrical setup and show that there exists an intrinsic length scale that determines the geometry in all forcing regimes.
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Affiliation(s)
- P Guillamat
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Barcelona, 08028 Catalonia, Spain.,Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Barcelona, 08028 Catalonia, Spain
| | - J Ignés-Mullol
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Barcelona, 08028 Catalonia, Spain.,Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Barcelona, 08028 Catalonia, Spain
| | - F Sagués
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Barcelona, 08028 Catalonia, Spain. .,Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Barcelona, 08028 Catalonia, Spain.
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Abstract
Long-range alignment ordering of fibroblasts have been observed in the vicinity of cancerous tumors and can be recapitulated with in vitro experiments. However, the mechanisms driving their ordering are not understood. Here, we show that local collision-driven nematic alignment interactions among fibroblasts are insufficient to explain observed long-range alignment. One possibility is that there exists another orientation field coevolving with the cells and reinforcing their alignment. We propose that this field reflects the mechanical cross-talk between the fibroblasts and the underlying fibrous material on which they move. We show that this long-range interaction can give rise to high nematic order and to the observed patterning of the cancer microenvironment.
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Das R, Kumar M, Mishra S. Order-disorder transition in active nematic: A lattice model study. Sci Rep 2017; 7:7080. [PMID: 28765553 PMCID: PMC5539249 DOI: 10.1038/s41598-017-07301-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 06/27/2017] [Indexed: 11/26/2022] Open
Abstract
We introduce a lattice model for active nematic composed of self-propelled apolar particles, study its different ordering states in the density-temperature parameter space, and compare with the corresponding equilibrium model. The active particles interact with their neighbours within the framework of the Lebwohl-Lasher model, and move anisotropically along their orientation to an unoccupied nearest neighbour lattice site. An interplay of the activity, thermal fluctuations and density gives rise distinct states in the system. For a fixed temperature, the active nematic shows a disordered isotropic state, a locally ordered inhomogeneous mixed state, and bistability between the inhomogeneous mixed and a homogeneous globally ordered state in different density regime. In the low temperature regime, the isotropic to the inhomogeneous mixed state transition occurs with a jump in the order parameter at a density less than the corresponding equilibrium disorder-order transition density. Our analytical calculations justify the shift in the transition density and the jump in the order parameter. We construct the phase diagram of the active nematic in the density-temperature plane.
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Affiliation(s)
- Rakesh Das
- S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata, 700106, India.
| | - Manoranjan Kumar
- S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata, 700106, India.
| | - Shradha Mishra
- S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata, 700106, India.
- Department of Physics, Indian Institute of Technology (BHU), Varanasi, 221005, India.
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43
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Kawaguchi K, Kageyama R, Sano M. Topological defects control collective dynamics in neural progenitor cell cultures. Nature 2017; 545:327-331. [PMID: 28403137 DOI: 10.1038/nature22321] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 03/30/2017] [Indexed: 12/12/2022]
Abstract
Cultured stem cells have become a standard platform not only for regenerative medicine and developmental biology but also for biophysical studies. Yet, the characterization of cultured stem cells at the level of morphology and of the macroscopic patterns resulting from cell-to-cell interactions remains largely qualitative. Here we report on the collective dynamics of cultured murine neural progenitor cells (NPCs), which are multipotent stem cells that give rise to cells in the central nervous system. At low densities, NPCs moved randomly in an amoeba-like fashion. However, NPCs at high density elongated and aligned their shapes with one another, gliding at relatively high velocities. Although the direction of motion of individual cells reversed stochastically along the axes of alignment, the cells were capable of forming an aligned pattern up to length scales similar to that of the migratory stream observed in the adult brain. The two-dimensional order of alignment within the culture showed a liquid-crystalline pattern containing interspersed topological defects with winding numbers of +1/2 and -1/2 (half-integer due to the nematic feature that arises from the head-tail symmetry of cell-to-cell interaction). We identified rapid cell accumulation at +1/2 defects and the formation of three-dimensional mounds. Imaging at the single-cell level around the defects allowed us to quantify the velocity field and the evolving cell density; cells not only concentrate at +1/2 defects, but also escape from -1/2 defects. We propose a generic mechanism for the instability in cell density around the defects that arises from the interplay between the anisotropic friction and the active force field.
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Affiliation(s)
- Kyogo Kawaguchi
- Department of Physics, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Universal Biology Institute, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryoichiro Kageyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Masaki Sano
- Department of Physics, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Universal Biology Institute, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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44
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Guillamat P, Ignés-Mullol J, Shankar S, Marchetti MC, Sagués F. Probing the shear viscosity of an active nematic film. Phys Rev E 2016; 94:060602. [PMID: 28085294 DOI: 10.1103/physreve.94.060602] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Indexed: 12/12/2022]
Abstract
In vitro reconstituted active systems, such as the adenosine triphosphate (ATP)-driven microtubule bundle suspension developed by the Dogic group [T. Sanchez, D. T. Chen, S. J. DeCamp, M. Heymann, and Z. Dogic, Nature (London) 491, 431 (2012)10.1038/nature11591], provide a fertile testing ground for elucidating the phenomenology of active liquid crystalline states. Controlling such novel phases of matter crucially depends on our knowledge of their material and physical properties. In this Rapid Communication, we show that the shear viscosity of an active nematic film can be probed by varying its hydrodynamic coupling to a bounding oil layer. Using the motion of disclinations as intrinsic tracers of the flow field and a hydrodynamic model, we obtain an estimate for the shear viscosity of the nematic film. Knowing this now provides us with an additional handle for robust and precision tunable control of the emergent dynamics of active fluids.
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Affiliation(s)
- Pau Guillamat
- Departament de Química Física and Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Catalonia, Spain
| | - Jordi Ignés-Mullol
- Departament de Química Física and Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Catalonia, Spain
| | - Suraj Shankar
- Physics Department and Syracuse Soft Matter Program, Syracuse University, Syracuse, New York 13244, USA
| | - M Cristina Marchetti
- Physics Department and Syracuse Soft Matter Program, Syracuse University, Syracuse, New York 13244, USA
| | - Francesc Sagués
- Departament de Química Física and Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Catalonia, Spain
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45
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Großmann R, Peruani F, Bär M. Mesoscale pattern formation of self-propelled rods with velocity reversal. Phys Rev E 2016; 94:050602. [PMID: 27967147 DOI: 10.1103/physreve.94.050602] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Indexed: 11/07/2022]
Abstract
We study self-propelled particles with velocity reversal interacting by uniaxial (nematic) alignment within a coarse-grained hydrodynamic theory. Combining analytical and numerical continuation techniques, we show that the physics of this active system is essentially controlled by the reversal frequency. In particular, we find that elongated, high-density, ordered patterns, called bands, emerge via subcritical bifurcations from spatially homogeneous states. Our analysis reveals further that the interaction of bands is weakly attractive and, consequently, bands fuse upon collision in analogy with nonequilibrium nucleation processes. Moreover, we demonstrate that a renormalized positive line tension can be assigned to stable bands below a critical reversal rate, beyond which they are transversally unstable. In addition, we discuss the kinetic roughening of bands as well as their nonlinear dynamics close to the threshold of transversal instability. Altogether, the reduction of the multiparticle system onto the dynamics of bands provides a unified framework to understand the emergence and stability of nonequilibrium patterns in this self-propelled particle system. In this regard, our results constitute a proof of principle in favor of the hypothesis in microbiology that velocity reversal of gliding rod-shaped bacteria regulates the transitions between various self-organized patterns observed during the bacterial life cycle.
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Affiliation(s)
- Robert Großmann
- Physikalisch-Technische Bundesanstalt, Abbestraße 2-12, D-10587 Berlin, Germany.,Laboratoire J. A. Dieudonné, Université de Nice Sophia Antipolis, UMR 7351 CNRS, Parc Valrose, F-06108 Nice Cedex 02, France
| | - Fernando Peruani
- Laboratoire J. A. Dieudonné, Université de Nice Sophia Antipolis, UMR 7351 CNRS, Parc Valrose, F-06108 Nice Cedex 02, France
| | - Markus Bär
- Physikalisch-Technische Bundesanstalt, Abbestraße 2-12, D-10587 Berlin, Germany
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Oza AU, Heidenreich S, Dunkel J. Generalized Swift-Hohenberg models for dense active suspensions. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2016; 39:97. [PMID: 27815788 DOI: 10.1140/epje/i2016-16097-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 09/20/2016] [Indexed: 06/06/2023]
Abstract
In describing the physics of living organisms, a mathematical theory that captures the generic ordering principles of intracellular and multicellular dynamics is essential for distinguishing between universal and system-specific features. Here, we compare two recently proposed nonlinear high-order continuum models for active polar and nematic suspensions, which aim to describe collective migration in dense cell assemblies and the ordering processes in ATP-driven microtubule-kinesin networks, respectively. We discuss the phase diagrams of the two models and relate their predictions to recent experiments. The satisfactory agreement with existing experimental data lends support to the hypothesis that non-equilibrium pattern formation phenomena in a wide range of active systems can be described within the same class of higher-order partial differential equations.
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Affiliation(s)
- Anand U Oza
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, 10012, New York, NY, USA.
| | - Sebastian Heidenreich
- Physikalisch-Technische Bundesanstalt Braunschweig und Berlin, Abbestr. 2-12, 10587, Berlin, Germany
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 02139-4307, Cambridge, MA, USA
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Abstract
We investigate the dynamics of an active particle in two-dimensional spherical crystals, which provide an ideal environment to illustrate the interplay between active particles and crystallographic defects. A moving active particle is observed to be surrounded by localized topological defects, becoming a dressed active particle. Such a physical picture characterizes both the lattice distortion around the moving particle and the healing of the distorted lattice in its trajectory. We find that the dynamical behaviors of an active particle in both random and ballistic motions uniformly conform to this featured scenario, whether the particle is initially a defect or not. We further observe that the defect pattern around a dressed ballistic active particle randomly oscillates between two well-defined wing-like defect motifs regardless of its speed. The established physical picture of dressed active particles in this work partially deciphers the complexity of the intriguing nonequilibrium behaviors in active crystals, and opens the promising possibility of introducing the activity to engineer defects, which has strong connections with the design of materials.
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Affiliation(s)
- Zhenwei Yao
- Department of Physics and Astronomy, and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.
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48
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Putzig E, Redner GS, Baskaran A, Baskaran A. Instabilities, defects, and defect ordering in an overdamped active nematic. SOFT MATTER 2016; 12:3854-9. [PMID: 26983376 PMCID: PMC5166704 DOI: 10.1039/c6sm00268d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We consider a phenomenological continuum theory for an extensile, overdamped active nematic liquid crystal, applicable in the dense regime. Constructed from general principles, the theory is universal, with parameters independent of any particular microscopic realization. We show that it exhibits two distinct instabilities, one of which arises due to shear forces, and the other due to active torques. Both lead to the proliferation of defects. We focus on the active torque bend instability and find three distinct nonequilibrium steady states including a defect-ordered nematic in which +½ disclinations develop polar ordering. We characterize the phenomenology of these phases and identify the relationship of this theoretical description to experimental realizations and other theoretical models of active nematics.
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Affiliation(s)
- Elias Putzig
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02453, USA.
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Abstract
Living cells sense the mechanical features of their environment and adapt to it by actively remodeling their peripheral network of filamentary proteins, known as cortical cytoskeleton. By mimicking this principle, we demonstrate an effective control strategy for a microtubule-based active nematic in contact with a hydrophobic thermotropic liquid crystal. By using well-established protocols for the orientation of liquid crystals with a uniform magnetic field, and through the mediation of anisotropic shear stresses, the active nematic reversibly self-assembles with aligned flows and textures that feature orientational order at the millimeter scale. The turbulent flow, characteristic of active nematics, is in this way regularized into a laminar flow with periodic velocity oscillations. Once patterned, the microtubule assembly reveals its intrinsic length and time scales, which we correlate with the activity of motor proteins, as predicted by existing theories of active nematics. The demonstrated commanding strategy should be compatible with other viable active biomaterials at interfaces, and we envision its use to probe the mechanics of the intracellular matrix.
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50
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Pešek J, Baerts P, Smeets B, Maes C, Ramon H. Mathematical model suitable for efficient simulation of thin semi-flexible polymers in complex environments. SOFT MATTER 2016; 12:3360-3387. [PMID: 26957013 DOI: 10.1039/c5sm03106k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We present an alternative approach to simulations of semi-flexible polymers. In contrast with the usual bead-rod compromise between bead-spring and rigid rod models, we use deformable cylindrical segments as basic units of the polymer. The length of each segment is not preserved with end points diffusing under constraints keeping the polymer chain nature intact. The model allows the simulation of tension transport and elasticity properties. In particular we describe a new cooperative regime in the relaxation of the polymer from its fully elongated configuration.
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Affiliation(s)
- Jiří Pešek
- KU Leuven, BIOSYST-MeBioS, Kasteelpark Arenberg 30, B-3001 Leuven, Belgium.
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