1
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Suzaka M, Ito H, Kitahata H. Aspect-ratio-dependent void formation in active rhomboidal and elliptical particle systems. Phys Rev E 2024; 110:024609. [PMID: 39294987 DOI: 10.1103/physreve.110.024609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/01/2024] [Indexed: 09/21/2024]
Abstract
We execute a numerical simulation of active nematics with particles interacting by an excluded-volume effect. Systems with rhomboidal particles and with elliptical particles are considered in order to investigate the effect of the direct contact of particles. In our simulation, the void regions, where the local number density is almost zero, appear in both systems when the aspect ratio of the particles is high. We focus on the relationship between the void regions and the particle orientation of the bulk. The particle number density, particle orientation, topological defects, and void regions are analyzed for different aspect ratios in both systems. The systems with rhomboidal particles have characteristic void sizes, which increase with an increase in the aspect ratio. In contrast, the distribution of the void-region size in the systems with elliptical particles is broad. The present results suggest that the void size in the systems with rhomboidal particles is determined by the correlation length of the particle orientational field around the void regions, while the void size might be determined by the system size in the systems with elliptical particles.
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2
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Vafa F, Nelson DR, Doostmohammadi A. Periodic orbits, pair nucleation, and unbinding of active nematic defects on cones. Phys Rev E 2024; 109:064606. [PMID: 39020887 DOI: 10.1103/physreve.109.064606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/06/2024] [Indexed: 07/20/2024]
Abstract
Geometric confinement and topological constraints present promising means of controlling active materials. By combining analytical arguments derived from the Born-Oppenheimer approximation with numerical simulations, we investigate the simultaneous impact of confinement together with curvature singularity by characterizing the dynamics of an active nematic on a cone. Here, the Born-Oppenheimer approximation means that textures can follow defect positions rapidly on the timescales of interest. Upon imposing strong anchoring boundary conditions at the base of a cone, we find a rich phase diagram of multidefect dynamics, including exotic periodic orbits of one or two +1/2 flank defects, depending on activity and nonquantized geometric charge at the cone apex. By characterizing the transitions between these ordered dynamical states, we present detailed understanding of (i) defect unbinding, (ii) defect absorption, and (iii) defect pair nucleation at the apex. Numerical simulations confirm theoretical predictions of not only the nature of the circular orbits but also defect unbinding from the apex.
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3
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Hendley RS, Zhang L, Bevan MA. Multistate Dynamic Pathways for Anisotropic Colloidal Assembly and Reconfiguration. ACS NANO 2023; 17:20512-20524. [PMID: 37788439 DOI: 10.1021/acsnano.3c07202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
We report the controlled interfacial assembly and reconfiguration of rectangular prism colloidal particles between microstructures of varying positional and orientational order including stable, metastable, and transient states. Structurally diverse states are realized by programming time dependent electric fields that mediate dipolar interactions determining particle position, orientation, compression, and chaining. We identify an order parameter set that defines each state as a combination of the positional and orientational order. These metrics are employed as reaction coordinates to capture the microstructure evolution between initial and final states upon field changes. Assembly trajectory manifolds between states in the low-dimensional reaction coordinate space reveal a dynamic pathway map including information about pathway accessibility, reversibility, and kinetics. By navigating the dynamic pathway map, we demonstrate reconfiguration between states on minute time scales, which is practically useful for particle-based materials processing and device responses. Our findings demonstrate a conceptually general approach to discover dynamic pathways as a basis to control assembly and reconfiguration of self-organizing building blocks that respond to global external stimuli.
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Affiliation(s)
- Rachel S Hendley
- Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Lechuan Zhang
- Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Michael A Bevan
- Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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4
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Molaei M, Redford SA, Chou WH, Scheff D, de Pablo JJ, Oakes PW, Gardel ML. Measuring response functions of active materials from data. Proc Natl Acad Sci U S A 2023; 120:e2305283120. [PMID: 37819979 PMCID: PMC10589671 DOI: 10.1073/pnas.2305283120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/08/2023] [Indexed: 10/13/2023] Open
Abstract
From flocks of birds to biomolecular assemblies, systems in which many individual components independently consume energy to perform mechanical work exhibit a wide array of striking behaviors. Methods to quantify the dynamics of these so-called active systems generally aim to extract important length or time scales from experimental fields. Because such methods focus on extracting scalar values, they do not wring maximal information from experimental data. We introduce a method to overcome these limitations. We extend the framework of correlation functions by taking into account the internal headings of displacement fields. The functions we construct represent the material response to specific types of active perturbation within the system. Utilizing these response functions we query the material response of disparate active systems composed of actin filaments and myosin motors, from model fluids to living cells. We show we can extract critical length scales from the turbulent flows of an active nematic, anticipate contractility in an active gel, distinguish viscous from viscoelastic dissipation, and even differentiate modes of contractility in living cells. These examples underscore the vast utility of this method which measures response functions from experimental observations of complex active systems.
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Affiliation(s)
- Mehdi Molaei
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
- James Franck Institute, University of Chicago, Chicago, IL60637
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL60637
| | - Steven A. Redford
- James Franck Institute, University of Chicago, Chicago, IL60637
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL60637
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL60637
| | - Wen-Hung Chou
- James Franck Institute, University of Chicago, Chicago, IL60637
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL60637
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL60637
| | - Danielle Scheff
- James Franck Institute, University of Chicago, Chicago, IL60637
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL60637
- Department of Physics, University of Chicago, Chicago, IL60637
| | - Juan J. de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
| | - Patrick W. Oakes
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL60153
| | - Margaret L. Gardel
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
- James Franck Institute, University of Chicago, Chicago, IL60637
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL60637
- Department of Physics, University of Chicago, Chicago, IL60637
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5
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Abstract
Matter self-assembling into layers generates unique properties, including structures of stacked surfaces, directed transport, and compact area maximization that can be highly functionalized in biology and technology. Smectics represent the paradigm of such lamellar materials - they are a state between fluids and solids, characterized by both orientational and partial positional ordering in one layering direction, making them notoriously difficult to model, particularly in confining geometries. We propose a complex tensor order parameter to describe the local degree of lamellar ordering, layer displacement and orientation of the layers for simple, lamellar smectics. The theory accounts for both dislocations and disclinations, by regularizing singularities within defect cores and so remaining continuous everywhere. The ability to describe disclinations and dislocation allows this theory to simulate arrested configurations and inclusion-induced local ordering. This tensorial theory for simple smectics considerably simplifies numerics, facilitating studies on the mesoscopic structure of topologically complex systems.
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6
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Sciortino A, Neumann LJ, Krüger T, Maryshev I, Teshima TF, Wolfrum B, Frey E, Bausch AR. Polarity and chirality control of an active fluid by passive nematic defects. NATURE MATERIALS 2023; 22:260-268. [PMID: 36585435 PMCID: PMC9894751 DOI: 10.1038/s41563-022-01432-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Much like passive materials, active systems can be affected by the presence of imperfections in their microscopic order, called defects, that influence macroscopic properties. This suggests the possibility to steer collective patterns by introducing and controlling defects in an active system. Here we show that a self-assembled, passive nematic is ideally suited to control the pattern formation process of an active fluid. To this end, we force microtubules to glide inside a passive nematic material made from actin filaments. The actin nematic features self-assembled half-integer defects that steer the active microtubules and lead to the formation of macroscopic polar patterns. Moreover, by confining the nematic in circular geometries, chiral loops form. We find that the exact positioning of nematic defects in the passive material deterministically controls the formation and the polarity of the active flow, opening the possibility of efficiently shaping an active material using passive defects.
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Affiliation(s)
- Alfredo Sciortino
- Lehrstuhl für Zellbiophysik E27, Technische Universität München, Garching, Germany
- Center for Functional Protein Assemblies, Garching bei München, Germany
| | - Lukas J Neumann
- Lehrstuhl für Zellbiophysik E27, Technische Universität München, Garching, Germany
- Center for Functional Protein Assemblies, Garching bei München, Germany
| | - Timo Krüger
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität, München, Germany
| | - Ivan Maryshev
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität, München, Germany
| | - Tetsuhiko F Teshima
- Neuroelectronics, Department of Electrical Engineering, Technische Universität München, Garching, Germany
- Medical & Health Informatics Laboratories, NTT Research Incorporated, Sunnyvale, CA, USA
| | - Bernhard Wolfrum
- Neuroelectronics, Department of Electrical Engineering, Technische Universität München, Garching, Germany
- Medical & Health Informatics Laboratories, NTT Research Incorporated, Sunnyvale, CA, USA
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics (ASC) and Center for NanoScience (CeNS), Department of Physics, Ludwig-Maximilians-Universität, München, Germany
- Matter to Life Program, Max Planck School, München, Germany
| | - Andreas R Bausch
- Lehrstuhl für Zellbiophysik E27, Technische Universität München, Garching, Germany.
- Center for Functional Protein Assemblies, Garching bei München, Germany.
- Matter to Life Program, Max Planck School, München, Germany.
- Center for Organoid Systems and Tissue Engineering (COS), Technische Universität München, Garching, Germany.
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7
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Bonn L, Ardaševa A, Mueller R, Shendruk TN, Doostmohammadi A. Fluctuation-induced dynamics of nematic topological defects. Phys Rev E 2022; 106:044706. [PMID: 36397561 DOI: 10.1103/physreve.106.044706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Topological defects are increasingly being identified in various biological systems, where their characteristic flow fields and stress patterns are associated with continuous active stress generation by biological entities. Here, using numerical simulations of continuum fluctuating nematohydrodynamics, we show that even in the absence of any specific form of active stresses associated with self-propulsion, mesoscopic fluctuations in either orientational alignment or hydrodynamics can independently result in flow patterns around topological defects that resemble the ones observed in active systems. Our simulations further show the possibility of extensile- and contractile-like motion of fluctuation-induced positive half-integer topological defects. Remarkably, isotropic stress fields also reproduce the experimentally measured stress patterns around topological defects in epithelia. Our findings further reveal that extensile- or contractile-like flow and stress patterns around fluctuation-induced defects are governed by passive elastic stresses and flow-aligning behavior of the nematics.
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Affiliation(s)
- Lasse Bonn
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, Copenhagen 2100, Denmark
| | - Aleksandra Ardaševa
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, Copenhagen 2100, Denmark
| | - Romain Mueller
- The Rudolf Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Tyler N Shendruk
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Amin Doostmohammadi
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, Copenhagen 2100, Denmark
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8
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Kumar S, Mishra S. Active nematic gel with quenched disorder. Phys Rev E 2022; 106:044603. [PMID: 36397569 DOI: 10.1103/physreve.106.044603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
With quenched disorder, we introduce two-dimensional active nematics suspended in an incompressible fluid. We write the coarse-grained hydrodynamic equations of motion for slow variables, viz. density, orientation, and flow fields. The quenched disorder is introduced such that it interacts with the local orientation at every point with some strength. Disorder strength is tuned from zero to large values. We numerically study the defect dynamics and system kinetics and find that the finite disorder slows the ordering. The presence of fluid induces large fluctuation in the orientation field, further disturbing the ordering. The large fluctuation in the orientation field due to the fluid is so dominant that it reduces the effect of the quenched disorder. We have also found that the disorder effect is almost the same for both the contractile and extensile nature of active stresses in the system. This study can help to understand the impact of quenched disorder on the ordering kinetics of active gels with nematic interaction among the constituent objects.
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Affiliation(s)
- Sameer Kumar
- Department of Physics, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh 221005, India
| | - Shradha Mishra
- Department of Physics, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh 221005, India
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9
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Zheng K, Zhang Z, Cao B, Granick S. Biopolymer Filament Entanglement Softens Then Hardens with Shear. PHYSICAL REVIEW LETTERS 2022; 129:147801. [PMID: 36240408 DOI: 10.1103/physrevlett.129.147801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
It is unsatisfactory that regarding the problem of entangled macromolecules driven out of equilibrium, experimentally based understanding is usually inferred from the ensemble average of polydisperse samples. Here, confronting with single-molecule imaging this common but poorly understood situation, over a wide range of shear rate we use single-molecule fluorescence imaging to track alignment and stretching of entangled aqueous filamentous actin filaments in a homebuilt rheo-microscope. With increasing shear rate, tube "softening" is followed by "hardening." Physically, this means that dynamical localization first weakens from molecular alignment, then strengthens from filament stretching, even for semiflexible biopolymers shorter than their persistence length.
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Affiliation(s)
- Kaikai Zheng
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Korea
| | - Zitong Zhang
- School of Aerospace, Tsinghua University, Beijing 100084, People's Republic of China
| | - Bingyang Cao
- School of Aerospace, Tsinghua University, Beijing 100084, People's Republic of China
| | - Steve Granick
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Korea
- Departments of Chemistry and Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
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10
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Zhang DQ, Li ZY, Li B. Self-rotation regulates interface evolution in biphasic active matter through taming defect dynamics. Phys Rev E 2022; 105:064607. [PMID: 35854599 DOI: 10.1103/physreve.105.064607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Chirality can endow nonequilibrium active matter with unique features and functions. Here, we explore the chiral dynamics in biphasic active nematics composed of self-rotating units that continuously inject energy and angular momentum at the microscale. We show that the self-rotation of units can regularize the boundaries between two phases, rendering sinusoidal-like interfaces, which allow lateral wave propagation and are characterized by chains of ordered antiferromagnetic cross-interface flow vortices. Through the spontaneous coordination of counter-rotating units across the interfaces, topological defects excited by activity are sorted spatiotemporally, where positive defects are locally trapped at the interfaces but, unexpectedly, are transported laterally in a unidirectional rather than wavy mode, whereas inertial negative defects remain spinning in the bulks. Our findings reveal that individual chirality could be harnessed to modulate interfacial morphodynamics in active systems and suggest a potential approach toward controlling topological defects for programmable microfluidics and logic operations.
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Affiliation(s)
- De-Qing Zhang
- Institute of Biomechanics and Medical Engineering, Applied Mechanics Laboratory, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China
| | - Zhong-Yi Li
- Institute of Biomechanics and Medical Engineering, Applied Mechanics Laboratory, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China
| | - Bo Li
- Institute of Biomechanics and Medical Engineering, Applied Mechanics Laboratory, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China
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11
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Filopodia rotate and coil by actively generating twist in their actin shaft. Nat Commun 2022; 13:1636. [PMID: 35347113 PMCID: PMC8960877 DOI: 10.1038/s41467-022-28961-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 02/10/2022] [Indexed: 12/19/2022] Open
Abstract
Filopodia are actin-rich structures, present on the surface of eukaryotic cells. These structures play a pivotal role by allowing cells to explore their environment, generate mechanical forces or perform chemical signaling. Their complex dynamics includes buckling, pulling, length and shape changes. We show that filopodia additionally explore their 3D extracellular space by combining growth and shrinking with axial twisting and buckling. Importantly, the actin core inside filopodia performs a twisting or spinning motion which is observed for a range of cell types spanning from earliest development to highly differentiated tissue cells. Non-equilibrium physical modeling of actin and myosin confirm that twist is an emergent phenomenon of active filaments confined in a narrow channel which is supported by measured traction forces and helical buckles that can be ascribed to accumulation of sufficient twist. These results lead us to conclude that activity induced twisting of the actin shaft is a general mechanism underlying fundamental functions of filopodia. The authors show how tubular surface structures in all cell types, have the ability to twist and perform rotary sweeping motion to explore the extracellular environment. This has implications for migration, sensing and cell communication.
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12
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Zhang R, Mozaffari A, de Pablo JJ. Logic operations with active topological defects. SCIENCE ADVANCES 2022; 8:eabg9060. [PMID: 35196084 PMCID: PMC8865799 DOI: 10.1126/sciadv.abg9060] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 12/30/2021] [Indexed: 05/31/2023]
Abstract
Logic operations performed by semiconductor-based transistors are the basis of modern computing. There is considerable interest in creating autonomous materials systems endowed with the capability to make decisions. In this work, we introduce the concept of using topological defects in active matter to perform logic operations. When an extensile active stress in a nematic liquid crystal is turned on, +1/2 defects can self-propel, in analogy to electron transport under a voltage gradient. By relying on hydrodynamic simulations of active nematics, we demonstrate that patterns of activity, when combined with surfaces imparting certain orientations, can be used to control the formation and transport of +1/2 defects. We further show that asymmetric high- and low-activity patterns can be used to create effective defect gates, tunnels, and amplifiers. The proposed active systems offer the potential to perform computations and transmit information in active soft materials, including actin-, tubulin-, and cell-based systems.
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Affiliation(s)
- Rui Zhang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
- Department of Physics, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR
| | - Ali Mozaffari
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
- OpenEye Scientific Software, Inc., 9 Bisbee Court Suite D, Santa Fe, New Mexico 87508, USA
| | - Juan J. de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
- Materials Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
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13
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Esmaeili M, George K, Rezvan G, Taheri-Qazvini N, Zhang R, Sadati M. Capillary Flow Characterizations of Chiral Nematic Cellulose Nanocrystal Suspensions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:2192-2204. [PMID: 35133841 DOI: 10.1021/acs.langmuir.1c01881] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Studying the flow-induced alignment of anisotropic liquid crystalline materials is of major importance in the 3D printing of advanced architectures. However, in situ characterization and quantitative measurements of local orientations during the 3D printing process are challenging. Here, we report a microfluidic strategy integrated with polarized optical microscopy (POM) to perform the in situ characterization of the alignment of cellulose nanocrystals (CNCs) under the shear-flow condition of the 3D printer's nozzle in the direct ink writing process. To quantify the alignment, we exploited birefringence measurements under white and monochromatic light. We show that the flow-induced birefringence patterns are significantly influenced by the initial structure of the aqueous CNC suspensions. Depending on the CNC concentration and sonication treatment, various structures can form in the CNC suspensions, such as isotropic, chiral nematic (cholesteric), and nematic (gel-like) structures. In the chiral nematic phase, in particular, the shear flow in the microfluidic capillary has a distinct effect on the alignment of the CNC particles. Our experimental results, complemented by hydrodynamic simulations, reveal that at high flow rates (Er ≈ 1000), individual CNC particles align with the flow exhibiting a weak chiral structure. In contrast, at lower flow rates (Er ≈ 241), they display the double-twisted cylinder structure. Understanding the flow effect on the alignment of the chiral liquid crystal can pave the way to designing 3D printed architectures with internal chirality for advanced mechanical and smart photonic applications.
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Affiliation(s)
- Mohsen Esmaeili
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Kyle George
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Gelareh Rezvan
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Nader Taheri-Qazvini
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Rui Zhang
- Department of Physics, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Monirosadat Sadati
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
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14
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Nano/Micromotors in Active Matter. MICROMACHINES 2022; 13:mi13020307. [PMID: 35208431 PMCID: PMC8878230 DOI: 10.3390/mi13020307] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/12/2022] [Accepted: 02/15/2022] [Indexed: 02/04/2023]
Abstract
Nano/micromotors (NMMs) are tiny objects capable of converting energy into mechanical motion. Recently, a wealth of active matter including synthetic colloids, cytoskeletons, bacteria, and cells have been used to construct NMMs. The self-sustained motion of active matter drives NMMs out of equilibrium, giving rise to rich dynamics and patterns. Alongside the spontaneous dynamics, external stimuli such as geometric confinements, light, magnetic field, and chemical potential are also harnessed to control the movements of NMMs, yielding new application paradigms of active matter. Here, we review the recent advances, both experimental and theoretical, in exploring biological NMMs. The unique dynamical features of collective NMMs are focused on, along with some possible applications of these intriguing systems.
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15
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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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16
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Berezney J, Goode BL, Fraden S, Dogic Z. Extensile to contractile transition in active microtubule-actin composites generates layered asters with programmable lifetimes. Proc Natl Acad Sci U S A 2022; 119:e2115895119. [PMID: 35086931 PMCID: PMC8812548 DOI: 10.1073/pnas.2115895119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022] Open
Abstract
We study a reconstituted composite system consisting of an active microtubule network interdigitated with a passive network of entangled F-actin filaments. Increasing the concentration of filamentous actin controls the emergent dynamics, inducing a transition from turbulent-like flows to bulk contractions. At intermediate concentrations, where the active stresses change their symmetry from anisotropic extensile to isotropic contracting, the composite separates into layered asters that coexist with the background turbulent fluid. Contracted onion-like asters have a radially extending microtubule-rich cortex that envelops alternating layers of microtubules and F-actin. These self-regulating structures undergo internal reorganization, which appears to minimize the surface area and maintain the ordered layering, even when undergoing aster merging events. Finally, the layered asters are metastable structures. Their lifetime, which ranges from minutes to hours, is encoded in the material properties of the composite. These results challenge the current models of active matter. They demonstrate self-organized dynamical states and patterns evocative of those observed in the cytoskeleton do not require precise biochemical regulation, but can arise from purely mechanical interactions of actively driven filamentous materials.
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Affiliation(s)
- John Berezney
- Department of Physics, Brandeis University, Waltham, MA 02454
| | - Bruce L Goode
- Department of Biology, Brandeis University, Waltham, MA 02454
| | - Seth Fraden
- Department of Physics, Brandeis University, Waltham, MA 02454
| | - Zvonimir Dogic
- Department of Physics, Brandeis University, Waltham, MA 02454;
- Department of Physics, University of California, Santa Barbara, CA 93106
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106
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17
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Physics of liquid crystals in cell biology. Trends Cell Biol 2021; 32:140-150. [PMID: 34756501 DOI: 10.1016/j.tcb.2021.09.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 11/21/2022]
Abstract
The past decade has witnessed a rapid growth in understanding of the pivotal roles of mechanical stresses and physical forces in cell biology. As a result, an integrated view of cell biology is evolving, where genetic and molecular features are scrutinised hand in hand with physical and mechanical characteristics of cells. Physics of liquid crystals has emerged as a burgeoning new frontier in cell biology over the past few years, fuelled by an increasing identification of orientational order and topological defects in cell biology, spanning scales from subcellular filaments to individual cells and multicellular tissues. Here, we provide an account of the most recent findings and developments, together with future promises and challenges in this rapidly evolving interdisciplinary research direction.
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18
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Submersed micropatterned structures control active nematic flow, topology, and concentration. Proc Natl Acad Sci U S A 2021; 118:2106038118. [PMID: 34535551 DOI: 10.1073/pnas.2106038118] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2021] [Indexed: 01/10/2023] Open
Abstract
Coupling between flows and material properties imbues rheological matter with its wide-ranging applicability, hence the excitement for harnessing the rheology of active fluids for which internal structure and continuous energy injection lead to spontaneous flows and complex, out-of-equilibrium dynamics. We propose and demonstrate a convenient, highly tunable method for controlling flow, topology, and composition within active films. Our approach establishes rheological coupling via the indirect presence of fully submersed micropatterned structures within a thin, underlying oil layer. Simulations reveal that micropatterned structures produce effective virtual boundaries within the superjacent active nematic film due to differences in viscous dissipation as a function of depth. This accessible method of applying position-dependent, effective dissipation to the active films presents a nonintrusive pathway for engineering active microfluidic systems.
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19
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Structures and topological defects in pressure-driven lyotropic chromonic liquid crystals. Proc Natl Acad Sci U S A 2021; 118:2108361118. [PMID: 34446562 DOI: 10.1073/pnas.2108361118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lyotropic chromonic liquid crystals are water-based materials composed of self-assembled cylindrical aggregates. Their behavior under flow is poorly understood, and quantitatively resolving the optical retardance of the flowing liquid crystal has so far been limited by the imaging speed of current polarization-resolved imaging techniques. Here, we employ a single-shot quantitative polarization imaging method, termed polarized shearing interference microscopy, to quantify the spatial distribution and the dynamics of the structures emerging in nematic disodium cromoglycate solutions in a microfluidic channel. We show that pure-twist disclination loops nucleate in the bulk flow over a range of shear rates. These loops are elongated in the flow direction and exhibit a constant aspect ratio that is governed by the nonnegligible splay-bend anisotropy at the loop boundary. The size of the loops is set by the balance between nucleation forces and annihilation forces acting on the disclination. The fluctuations of the pure-twist disclination loops reflect the tumbling character of nematic disodium cromoglycate. Our study, including experiment, simulation, and scaling analysis, provides a comprehensive understanding of the structure and dynamics of pressure-driven lyotropic chromonic liquid crystals and might open new routes for using these materials to control assembly and flow of biological systems or particles in microfluidic devices.
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20
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Pearce DJG, Kruse K. Properties of twisted topological defects in 2D nematic liquid crystals. SOFT MATTER 2021; 17:7408-7417. [PMID: 34318862 PMCID: PMC8356798 DOI: 10.1039/d1sm00825k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/08/2021] [Indexed: 05/11/2023]
Abstract
Topological defects are one of the most conspicuous features of liquid crystals. In two dimensional nematics, they have been shown to behave effectively as particles with both charge and orientation, which dictate their interactions. Here, we study "twisted" defects that have a radially dependent orientation. We find that twist can be partially relaxed through the creation and annihilation of defect pairs. By solving the equations for defect motion and calculating the forces on defects, we identify four distinct elements that govern the relative relaxational motion of interacting topological defects, namely attraction, repulsion, co-rotation and co-translation. The interaction of these effects can lead to intricate defect trajectories, which can be controlled by setting relevant timescales.
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Affiliation(s)
- D J G Pearce
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland. and Department of Theoretical Physics, University of Geneva, 1211 Geneva, Switzerland and NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland and Dept. of Mathematics, Massachusetts Institute of Technology, Massachusetts, USA
| | - K Kruse
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland. and Department of Theoretical Physics, University of Geneva, 1211 Geneva, Switzerland and NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
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21
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Abstract
Pattern formation processes in active systems give rise to a plethora of collective structures. Predicting how the emergent structures depend on the microscopic interactions between the moving agents remains a challenge. By introducing a high-density actin gliding assay on a fluid membrane, we demonstrate the emergence of polar structures in a regime of nematic binary interactions dominated by steric repulsion. The transition from a microscopic nematic symmetry to a macroscopic polar structure is linked to microscopic polarity sorting mechanisms, including accumulation in wedge-like topological defects. Our results should be instrumental for a better understanding of pattern formation and polarity sorting processes in active matter. Collective motion of active matter is ubiquitously observed, ranging from propelled colloids to flocks of bird, and often features the formation of complex structures composed of agents moving coherently. However, it remains extremely challenging to predict emergent patterns from the binary interaction between agents, especially as only a limited number of interaction regimes have been experimentally observed so far. Here, we introduce an actin gliding assay coupled to a supported lipid bilayer, whose fluidity forces the interaction between self-propelled filaments to be dominated by steric repulsion. This results in filaments stopping upon binary collisions and eventually aligning nematically. Such a binary interaction rule results at high densities in the emergence of dynamic collectively moving structures including clusters, vortices, and streams of filaments. Despite the microscopic interaction having a nematic symmetry, the emergent structures are found to be polar, with filaments collectively moving in the same direction. This is due to polar biases introduced by the stopping upon collision, both on the individual filaments scale as well as on the scale of collective structures. In this context, positive half-charged topological defects turn out to be a most efficient trapping and polarity sorting conformation.
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22
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Mozaffari A, Zhang R, Atzin N, de Pablo JJ. Defect Spirograph: Dynamical Behavior of Defects in Spatially Patterned Active Nematics. PHYSICAL REVIEW LETTERS 2021; 126:227801. [PMID: 34152186 DOI: 10.1103/physrevlett.126.227801] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 01/06/2021] [Accepted: 05/03/2021] [Indexed: 06/13/2023]
Abstract
Topological defects in active liquid crystals can be confined by introducing gradients of activity. Here, we examine the dynamical behavior of two defects confined by a sharp gradient of activity that separates an active circular region and a surrounding passive nematic material. Continuum simulations are used to explain how the interplay among energy injection into the system, hydrodynamic interactions, and frictional forces governs the dynamics of topologically required self-propelling +1/2 defects. Our findings are rationalized in terms of a phase diagram for the dynamical response of defects in terms of activity and frictional damping strength. Different regions of the underlying phase diagram correspond to distinct dynamical modes, namely immobile defects, steady rotation of defects, bouncing defects, bouncing-cruising defects, dancing defects, and multiple defects with irregular dynamics. These dynamic states raise the prospect of generating synchronized defect arrays for microfluidic applications.
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Affiliation(s)
- Ali Mozaffari
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
| | - Rui Zhang
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
- Department of Physics, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Noe Atzin
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
| | - Juan J de Pablo
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
- Center for Molecular Engineering, Argonne National Laboratory, Lemont, Illinois 60439, USA
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23
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Senyuk B, Mozaffari A, Crust K, Zhang R, de Pablo JJ, Smalyukh II. Transformation between elastic dipoles, quadrupoles, octupoles, and hexadecapoles driven by surfactant self-assembly in nematic emulsion. SCIENCE ADVANCES 2021; 7:7/25/eabg0377. [PMID: 34144988 PMCID: PMC8213233 DOI: 10.1126/sciadv.abg0377] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Emulsions comprising isotropic fluid drops within a nematic host are of interest for applications ranging from biodetection to smart windows, which rely on changes of molecular alignment structures around the drops in response to chemical, thermal, electric, and other stimuli. We show that absorption or desorption of trace amounts of common surfactants can drive continuous transformations of elastic multipoles induced by the droplets within the uniformly aligned nematic host. Out-of-equilibrium dynamics of director structures emerge from a controlled self-assembly or desorption of different surfactants at the drop-nematic interfaces, with ensuing forward and reverse transformations between elastic dipoles, quadrupoles, octupoles, and hexadecapoles. We characterize intertransformations of droplet-induced surface and bulk defects, probe elastic pair interactions, and discuss emergent prospects for fundamental science and applications of the reconfigurable nematic emulsions.
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Affiliation(s)
- Bohdan Senyuk
- Department of Physics and Soft Materials Research Center, University of Colorado, Boulder, CO 80309, USA
| | - Ali Mozaffari
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
| | - Kevin Crust
- Department of Physics and Soft Materials Research Center, University of Colorado, Boulder, CO 80309, USA
| | - Rui Zhang
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR
| | - Juan J de Pablo
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
- Center for Molecular Engineering, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Ivan I Smalyukh
- Department of Physics and Soft Materials Research Center, University of Colorado, Boulder, CO 80309, USA.
- Department of Electrical, Computer, and Energy Engineering and Materials Science and Engineering Program, University of Colorado, Boulder, CO 80309, USA
- Renewable and Sustainable Energy Institute, National Renewable Energy Laboratory and University of Colorado, Boulder, CO 80309, USA
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24
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Zhang R, Redford SA, Ruijgrok PV, Kumar N, Mozaffari A, Zemsky S, Dinner AR, Vitelli V, Bryant Z, Gardel ML, de Pablo JJ. Spatiotemporal control of liquid crystal structure and dynamics through activity patterning. NATURE MATERIALS 2021; 20:875-882. [PMID: 33603187 PMCID: PMC8404743 DOI: 10.1038/s41563-020-00901-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 12/03/2020] [Indexed: 05/26/2023]
Abstract
Active materials are capable of converting free energy into mechanical work to produce autonomous motion, and exhibit striking collective dynamics that biology relies on for essential functions. Controlling those dynamics and transport in synthetic systems has been particularly challenging. Here, we introduce the concept of spatially structured activity as a means of controlling and manipulating transport in active nematic liquid crystals consisting of actin filaments and light-sensitive myosin motors. Simulations and experiments are used to demonstrate that topological defects can be generated at will and then constrained to move along specified trajectories by inducing local stresses in an otherwise passive material. These results provide a foundation for the design of autonomous and reconfigurable microfluidic systems where transport is controlled by modulating activity with light.
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Affiliation(s)
- Rui Zhang
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
- Department of Physics, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Steven A Redford
- The Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- James Franck Institute, The University of Chicago, Chicago, IL, USA
| | - Paul V Ruijgrok
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Nitin Kumar
- James Franck Institute, The University of Chicago, Chicago, IL, USA
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, India
| | - Ali Mozaffari
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
| | - Sasha Zemsky
- Program in Biophysics, Stanford University, Stanford, CA, USA
| | - Aaron R Dinner
- James Franck Institute, The University of Chicago, Chicago, IL, USA
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Vincenzo Vitelli
- James Franck Institute, The University of Chicago, Chicago, IL, USA
- Department of Physics, The University of Chicago, Chicago, IL, USA
| | - Zev Bryant
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University Medical Center, Stanford, CA, USA
| | - Margaret L Gardel
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA.
- James Franck Institute, The University of Chicago, Chicago, IL, USA.
- Department of Physics, The University of Chicago, Chicago, IL, USA.
| | - Juan J de Pablo
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA.
- Center for Molecular Engineering, Argonne National Laboratory, Lemont, IL, USA.
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25
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Lavrentovich OD. Design of nematic liquid crystals to control microscale dynamics. LIQUID CRYSTALS REVIEWS 2021; 8:59-129. [PMID: 34956738 PMCID: PMC8698256 DOI: 10.1080/21680396.2021.1919576] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/11/2021] [Indexed: 05/25/2023]
Abstract
The dynamics of small particles, both living such as swimming bacteria and inanimate, such as colloidal spheres, has fascinated scientists for centuries. If one could learn how to control and streamline their chaotic motion, that would open technological opportunities in the transformation of stored or environmental energy into systematic motion, with applications in micro-robotics, transport of matter, guided morphogenesis. This review presents an approach to command microscale dynamics by replacing an isotropic medium with a liquid crystal. Orientational order and associated properties, such as elasticity, surface anchoring, and bulk anisotropy, enable new dynamic effects, ranging from the appearance and propagation of particle-like solitary waves to self-locomotion of an active droplet. By using photoalignment, the liquid crystal can be patterned into predesigned structures. In the presence of the electric field, these patterns enable the transport of solid and fluid particles through nonlinear electrokinetics rooted in anisotropy of conductivity and permittivity. Director patterns command the dynamics of swimming bacteria, guiding their trajectories, polarity of swimming, and distribution in space. This guidance is of a higher level of complexity than a simple following of the director by rod-like microorganisms. Namely, the director gradients mediate hydrodynamic interactions of bacteria to produce an active force and collective polar modes of swimming. The patterned director could also be engraved in a liquid crystal elastomer. When an elastomer coating is activated by heat or light, these patterns produce a deterministic surface topography. The director gradients define an activation force that shapes the elastomer in a manner similar to the active stresses triggering flows in active nematics. The patterned elastomer substrates could be used to define the orientation of cells in living tissues. The liquid-crystal guidance holds a major promise in achieving the goal of commanding microscale active flows.
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Affiliation(s)
- Oleg D Lavrentovich
- Advanced Materials and Liquid Crystal Institute, Department of Physics, Materials Science Graduate Program, Kent State University, Kent, OH 44242, USA
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26
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Plan ELCVM, Yeomans JM, Doostmohammadi A. Activity pulses induce spontaneous flow reversals in viscoelastic environments. J R Soc Interface 2021; 18:20210100. [PMID: 33849330 PMCID: PMC8086915 DOI: 10.1098/rsif.2021.0100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Complex interactions between cellular systems and their surrounding extracellular matrices are emerging as important mechanical regulators of cell functions, such as proliferation, motility and cell death, and such cellular systems are often characterized by pulsating actomyosin activities. Here, using an active gel model, we numerically explore spontaneous flow generation by activity pulses in the presence of a viscoelastic medium. The results show that cross-talk between the activity-induced deformations of the viscoelastic surroundings and the time-dependent response of the active medium to these deformations can lead to the reversal of spontaneously generated active flows. We explain the mechanism behind this phenomenon based on the interaction between the active flow and the viscoelastic medium. We show the importance of relaxation time scales of both the polymers and the active particles and provide a phase space over which such spontaneous flow reversals can be observed. Our results suggest new experiments investigating the role of controlled pulses of activity in living systems ensnared in complex mircoenvironments.
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Affiliation(s)
- Emmanuel L C Vi M Plan
- Institute of Theoretical and Applied Research, Duy Tan University, Ha Noi 100 000, Viet Nam.,Faculty of Natural Science, Duy Tan University, Da Nang 550 000, Viet Nam
| | - Julia M Yeomans
- The Rudolf Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, Clarendon Laboratory, Oxford OX1 3PU, UK
| | - Amin Doostmohammadi
- The Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
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27
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Szuba A, Bano F, Castro-Linares G, Iv F, Mavrakis M, Richter RP, Bertin A, Koenderink GH. Membrane binding controls ordered self-assembly of animal septins. eLife 2021; 10:63349. [PMID: 33847563 PMCID: PMC8099429 DOI: 10.7554/elife.63349] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 04/12/2021] [Indexed: 12/23/2022] Open
Abstract
Septins are conserved cytoskeletal proteins that regulate cell cortex mechanics. The mechanisms of their interactions with the plasma membrane remain poorly understood. Here, we show by cell-free reconstitution that binding to flat lipid membranes requires electrostatic interactions of septins with anionic lipids and promotes the ordered self-assembly of fly septins into filamentous meshworks. Transmission electron microscopy reveals that both fly and mammalian septin hexamers form arrays of single and paired filaments. Atomic force microscopy and quartz crystal microbalance demonstrate that the fly filaments form mechanically rigid, 12- to 18-nm thick, double layers of septins. By contrast, C-terminally truncated septin mutants form 4-nm thin monolayers, indicating that stacking requires the C-terminal coiled coils on DSep2 and Pnut subunits. Our work shows that membrane binding is required for fly septins to form ordered arrays of single and paired filaments and provides new insights into the mechanisms by which septins may regulate cell surface mechanics.
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Affiliation(s)
- Agata Szuba
- AMOLF, Department of Living Matter, Biological Soft Matter group, Amsterdam, Netherlands
| | - Fouzia Bano
- School of Biomedical Sciences, Faculty of Biological Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds, United Kingdom.,Bragg Centre for Materials Research, University of Leeds, Leeds, United Kingdom
| | - Gerard Castro-Linares
- AMOLF, Department of Living Matter, Biological Soft Matter group, Amsterdam, Netherlands.,Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Francois Iv
- Institut Fresnel, CNRS, Aix-Marseille Univ, Centrale Marseille, Marseille, France
| | - Manos Mavrakis
- Institut Fresnel, CNRS, Aix-Marseille Univ, Centrale Marseille, Marseille, France
| | - Ralf P Richter
- School of Biomedical Sciences, Faculty of Biological Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds, United Kingdom.,Bragg Centre for Materials Research, University of Leeds, Leeds, United Kingdom
| | - Aurélie Bertin
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Paris, France.,Sorbonne Université, Paris, France
| | - Gijsje H Koenderink
- AMOLF, Department of Living Matter, Biological Soft Matter group, Amsterdam, Netherlands.,Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
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28
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Colen J, Han M, Zhang R, Redford SA, Lemma LM, Morgan L, Ruijgrok PV, Adkins R, Bryant Z, Dogic Z, Gardel ML, de Pablo JJ, Vitelli V. Machine learning active-nematic hydrodynamics. Proc Natl Acad Sci U S A 2021; 118:e2016708118. [PMID: 33653956 PMCID: PMC7958379 DOI: 10.1073/pnas.2016708118] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrodynamic theories effectively describe many-body systems out of equilibrium in terms of a few macroscopic parameters. However, such parameters are difficult to determine from microscopic information. Seldom is this challenge more apparent than in active matter, where the hydrodynamic parameters are in fact fields that encode the distribution of energy-injecting microscopic components. Here, we use active nematics to demonstrate that neural networks can map out the spatiotemporal variation of multiple hydrodynamic parameters and forecast the chaotic dynamics of these systems. We analyze biofilament/molecular-motor experiments with microtubule/kinesin and actin/myosin complexes as computer vision problems. Our algorithms can determine how activity and elastic moduli change as a function of space and time, as well as adenosine triphosphate (ATP) or motor concentration. The only input needed is the orientation of the biofilaments and not the coupled velocity field which is harder to access in experiments. We can also forecast the evolution of these chaotic many-body systems solely from image sequences of their past using a combination of autoencoders and recurrent neural networks with residual architecture. In realistic experimental setups for which the initial conditions are not perfectly known, our physics-inspired machine-learning algorithms can surpass deterministic simulations. Our study paves the way for artificial-intelligence characterization and control of coupled chaotic fields in diverse physical and biological systems, even in the absence of knowledge of the underlying dynamics.
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Affiliation(s)
- Jonathan Colen
- Department of Physics, University of Chicago, Chicago, IL 60637
- James Franck Institute, University of Chicago, Chicago, IL 60637
| | - Ming Han
- James Franck Institute, University of Chicago, Chicago, IL 60637
- Pritzer School of Molecular Engineering, University of Chicago, Chicago, IL 60637
| | - Rui Zhang
- Pritzer School of Molecular Engineering, University of Chicago, Chicago, IL 60637
- Department of Physics, Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, People's Republic of China
| | - Steven A Redford
- James Franck Institute, University of Chicago, Chicago, IL 60637
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637
| | - Linnea M Lemma
- Department of Physics, Brandeis University, Waltham, MA 02454
- Department of Physics, University of California, Santa Barbara, CA 92111
| | - Link Morgan
- Department of Physics, University of California, Santa Barbara, CA 92111
| | - Paul V Ruijgrok
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Raymond Adkins
- Department of Physics, University of California, Santa Barbara, CA 92111
| | - Zev Bryant
- Department of Bioengineering, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University Medical Center, Stanford, CA 94305
| | - Zvonimir Dogic
- Department of Physics, University of California, Santa Barbara, CA 92111
| | - Margaret L Gardel
- Department of Physics, University of Chicago, Chicago, IL 60637
- James Franck Institute, University of Chicago, Chicago, IL 60637
| | - Juan J de Pablo
- Pritzer School of Molecular Engineering, University of Chicago, Chicago, IL 60637;
- Center for Molecular Engineering, Argonne National Laboratory, Lemont, IL 60439
| | - Vincenzo Vitelli
- Department of Physics, University of Chicago, Chicago, IL 60637;
- James Franck Institute, University of Chicago, Chicago, IL 60637
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29
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Nikoubashman A. Ordering, phase behavior, and correlations of semiflexible polymers in confinement. J Chem Phys 2021; 154:090901. [DOI: 10.1063/5.0038052] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Arash Nikoubashman
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
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30
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Eom W, Lee E, Lee SH, Sung TH, Clancy AJ, Lee WJ, Han TH. Carbon nanotube-reduced graphene oxide fiber with high torsional strength from rheological hierarchy control. Nat Commun 2021; 12:396. [PMID: 33452251 PMCID: PMC7810860 DOI: 10.1038/s41467-020-20518-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 11/20/2020] [Indexed: 01/30/2023] Open
Abstract
High torsional strength fibers are of practical interest for applications such as artificial muscles, electric generators, and actuators. Herein, we maximize torsional strength by understanding, measuring, and overcoming rheological thresholds of nanocarbon (nanotube/graphene oxide) dopes. The formed fibers show enhanced structure across multiple length scales, modified hierarchy, and improved mechanical properties. In particular, the torsional properties were examined, with high shear strength (914 MPa) attributed to nanotubes but magnified by their structure, intercalating graphene sheets. This design approach has the potential to realize the hierarchical dimensional hybrids, and may also be useful to build the effective network structure of heterogeneous materials.
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Affiliation(s)
- Wonsik Eom
- Department of Organic and Nano Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Eunsong Lee
- Department of Organic and Nano Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Sang Hoon Lee
- Department of Organic and Nano Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Tae Hyun Sung
- Department of Electrical Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Adam J Clancy
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
| | - Won Jun Lee
- Department of Fiber System Engineering, Dankook University, Yongin-si, 16890, Republic of Korea.
| | - Tae Hee Han
- Department of Organic and Nano Engineering, Hanyang University, Seoul, 04763, Republic of Korea.
- Human-Tech Convergence Program, Hanyang University, Seoul, 04763, Republic of Korea.
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31
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Razbin M, Mashaghi A. Elasticity of connected semiflexible quadrilaterals. SOFT MATTER 2021; 17:102-112. [PMID: 33150925 DOI: 10.1039/d0sm01719a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Using the positional-orientational propagator of a semiflexible filament in the weakly bending regime, we analytically calculate the probability densities associated with the fluctuating tip and the corners of a grafted system of connected quadrilaterals. We calculate closed analytic expressions for the probability densities within the framework of the worm-like chain model, which are valid in the weakly bending regime. The probability densities give the physical quantities related to the elasticity of the system such as the force-extension relation in the fixed extension ensemble, the Poisson's ratio and the average of the force exerted to a confining stiff planar wall by the fluctuating tip of the system. Our analysis reveals that the force-extension relations depend on the contour length of the system (material content), the bending stiffness (chemical nature), the geometrical angle and the number of the quadrilaterals, while the Poisson's ratio depends only on the geometrical angle and the number of the quadrilaterals, and is thus a purely geometric property of the system.
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Affiliation(s)
- Mohammadhosein Razbin
- Department of Energy Engineering and Physics, Amirkabir University of Technology, 14588 Tehran, Iran.
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Blanch-Mercader C, Guillamat P, Roux A, Kruse K. Integer topological defects of cell monolayers: Mechanics and flows. Phys Rev E 2021; 103:012405. [PMID: 33601623 DOI: 10.1103/physreve.103.012405] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/10/2020] [Indexed: 12/13/2022]
Abstract
Monolayers of anisotropic cells exhibit long-ranged orientational order and topological defects. During the development of organisms, orientational order often influences morphogenetic events. However, the linkage between the mechanics of cell monolayers and topological defects remains largely unexplored. This holds specifically at the timescales relevant for tissue morphogenesis. Here, we build on the physics of liquid crystals to determine material parameters of cell monolayers. In particular, we use a hydrodynamical description of an active polar fluid to study the steady-state mechanical patterns at integer topological defects. Our description includes three distinct sources of activity: traction forces accounting for cell-substrate interactions as well as anisotropic and isotropic active nematic stresses accounting for cell-cell interactions. We apply our approach to C2C12 cell monolayers in small circular confinements, which form isolated aster or spiral topological defects. By analyzing the velocity and orientational order fields in spirals as well as the forces and cell number density fields in asters, we determine mechanical parameters of C2C12 cell monolayers. Our work shows how topological defects can be used to fully characterize the mechanical properties of biological active matter.
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Affiliation(s)
- Carles Blanch-Mercader
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
- Department of Theoretical Physics, University of Geneva, 1211 Geneva, Switzerland
| | - Pau Guillamat
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Karsten Kruse
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
- Department of Theoretical Physics, University of Geneva, 1211 Geneva, Switzerland
- NCCR Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
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Revignas D, Ferrarini A. Interplay of Particle Morphology and Director Distortions in Nematic Fluids. PHYSICAL REVIEW LETTERS 2020; 125:267802. [PMID: 33449752 DOI: 10.1103/physrevlett.125.267802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/16/2020] [Accepted: 10/26/2020] [Indexed: 06/12/2023]
Abstract
The existing microscopic theories for elasticity of nematics are challenged by recent findings on systems, whether bent molecules or semiflexible polymers, which do not comply with the model of rigid rodlike particles. Here, we propose an extension of Onsager-Straley second-virial theory, based on a model for the orientational distribution function that, through explicit account of the director profile along a particle, changes in the presence of deformations. The elastic constants reveal specific effects of particle morphology, which are not captured by the existing theories. This paves the way to microscopic modeling of the elastic properties of semiflexible liquid crystal polymers, which is a longstanding issue.
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Affiliation(s)
- Davide Revignas
- Università di Padova, Dipartimento di Scienze Chimiche, via Marzolo 1, 35131 Padova, Italy
| | - Alberta Ferrarini
- Università di Padova, Dipartimento di Scienze Chimiche, via Marzolo 1, 35131 Padova, Italy
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Tang X, Selinger JV. Annihilation trajectory of defects in smectic-C films. Phys Rev E 2020; 102:012702. [PMID: 32795041 DOI: 10.1103/physreve.102.012702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/07/2020] [Indexed: 12/21/2022]
Abstract
In a two-dimensional liquid crystal, each topological defect has a topological charge and a characteristic orientation and hence can be regarded as an oriented particle. Theories predict that the trajectories of annihilating defects depend on their relative orientation. Recently, these predictions have been tested in experiments on smectic-C films. Those experiments find curved trajectories that are similar to the predictions, but the detailed relationship between the defect orientations and the far-field director is different. To understand this difference, we extend the previous theories by adding the effects of elastic anisotropy and find that it significantly changes the curved trajectories.
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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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Zhang YH, Deserno M, Tu ZC. Dynamics of active nematic defects on the surface of a sphere. Phys Rev E 2020; 102:012607. [PMID: 32795046 DOI: 10.1103/physreve.102.012607] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022]
Abstract
A nematic liquid crystal confined to the surface of a sphere exhibits topological defects of total charge +2 due to the topological constraint. In equilibrium, the nematic field forms four +1/2 defects, located at the corners of a regular tetrahedron inscribed within the sphere, since this minimizes the Frank elastic energy. If additionally the individual nematogens exhibit self-driven directional motion, the resulting active system creates large-scale flow that drives it out of equilibrium. In particular, the defects now follow complex dynamic trajectories which, depending on the strength of the active forcing, can be periodic (for weak forcing) or chaotic (for strong forcing). In this paper we derive an effective particle theory for this system, in which the topological defects are the degrees of freedom, whose exact equations of motion we subsequently determine. Numerical solutions of these equations confirm previously observed characteristics of their dynamics and clarify the role played by the time dependence of their global rotation. We also show that Onsager's variational principle offers an exceptionally transparent way to derive these dynamical equations, and we explain the defect mobility at the hydrodynamics level.
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Affiliation(s)
- Yi-Heng Zhang
- Department of Physics, Beijing Normal University, Beijing 100875, China
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, USA
| | - Zhan-Chun Tu
- Department of Physics, Beijing Normal University, Beijing 100875, China
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Abstract
Moumita Das, Michael Murrell and Christoph Schmidt introduce the Soft Matter collection on active matter.
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Affiliation(s)
- Moumita Das
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, NY 14623, USA.
| | - Christoph F Schmidt
- Department of Physics and Soft Matter Center, Duke University, Durham, NC 27708, USA.
| | - Michael Murrell
- Physics & Biomedical Engineering Departments, Systems Biology Institute, Yale University, New Haven, CT 06520, USA.
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Abstract
We introduce and shortly summarize a variety of more recent aspects of lyotropic liquid crystals (LLCs), which have drawn the attention of the liquid crystal and soft matter community and have recently led to an increasing number of groups studying this fascinating class of materials, alongside their normal activities in thermotopic LCs. The diversity of topics ranges from amphiphilic to inorganic liquid crystals, clays and biological liquid crystals, such as viruses, cellulose or DNA, to strongly anisotropic materials such as nanotubes, nanowires or graphene oxide dispersed in isotropic solvents. We conclude our admittedly somewhat subjective overview with materials exhibiting some fascinating properties, such as chromonics, ferroelectric lyotropics and active liquid crystals and living lyotropics, before we point out some possible and emerging applications of a class of materials that has long been standing in the shadow of the well-known applications of thermotropic liquid crystals, namely displays and electro-optic devices.
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38
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Fang WZ, Ham S, Qiao R, Tao WQ. Magnetic Actuation of Surface Walkers: The Effects of Confinement and Inertia. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:7046-7055. [PMID: 32125866 DOI: 10.1021/acs.langmuir.9b03487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Driven by a magnetic field, the rotation of a particle near a wall can be rectified into a net translation. The particles thus actuated, or surface walkers, are a kind of active colloid that finds application in biology and microfluidics. Here, we investigate the motion of spherical surface walkers confined between two walls using simulations based on the immersed-boundary lattice Boltzmann method. The degree of confinement and the nature of the confining walls (slip vs no-slip) significantly affect a particle's translational speed and can even reverse its translational direction. When the rotational Reynolds number Reω is larger than 1, inertia effects reduce the critical frequency of the magnetic field, beyond which the sphere can no longer follow the external rotating field. The reduction of the critical frequency is especially pronounced when the sphere is confined near a no-slip wall. As Reω increases beyond 1, even when the sphere can still rotate in the synchronous regime, its translational Reynolds number ReT no longer increases linearly with Reω and even decreases when Reω exceeds ∼10.
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Affiliation(s)
- Wen-Zhen Fang
- Key Laboratory of Thermo-Fluid Science and Engineering, MOE, Xi'an Jiaotong University, Xi'an, China 710049
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Seokgyun Ham
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Rui Qiao
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Wen-Quan Tao
- Key Laboratory of Thermo-Fluid Science and Engineering, MOE, Xi'an Jiaotong University, Xi'an, China 710049
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Scheff DR, Weirich KL, Dasbiswas K, Patel A, Vaikuntanathan S, Gardel ML. Tuning shape and internal structure of protein droplets via biopolymer filaments. SOFT MATTER 2020; 16:5659-5668. [PMID: 32519715 DOI: 10.1039/c9sm02462j] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Macromolecules can phase separate to form liquid condensates, which are emerging as critical compartments in fields as diverse as intracellular organization and soft materials design. A myriad of macromolecules, including the protein FUS, form condensates which behave as isotropic liquids. Here, we investigate the influence of filament dopants on the material properties of protein liquids. We find that the short, biopolymer filaments of actin spontaneously partition into FUS droplets to form composite liquid droplets. As the concentration of the filament dopants increases, the coalescence time decreases, indicating that the dopants control viscosity relative to surface tension. The droplet shape is tunable and ranges from spherical to tactoid as the filament length or concentration is increased. We find that the tactoids are well described by a model of a quasi bipolar liquid crystal droplet, where nematic order from the anisotropic actin filaments competes with isotropic interfacial energy from the FUS, controlling droplet shape in a size-dependent manner. Our results demonstrate a versatile approach to construct tunable, anisotropic macromolecular liquids.
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Affiliation(s)
- Danielle R Scheff
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA. and Department of Physics, University of Chicago, Chicago, IL 60637, USA
| | - Kimberly L Weirich
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA. and HHMI HCIA Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA and Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Kinjal Dasbiswas
- Department of Physics, University of California, Merced, CA 95343, USA
| | - Avinash Patel
- HHMI HCIA Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA and Dewpoint Therapeutics GmbH, Pfotenhauer Strasse 108, Dresden 01307, USA
| | - Suriyanarayanan Vaikuntanathan
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA. and Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Margaret L Gardel
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA. and Department of Physics, University of Chicago, Chicago, IL 60637, USA and HHMI HCIA Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA and Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
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40
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Hoffmann LA, Schakenraad K, Merks RMH, Giomi L. Chiral stresses in nematic cell monolayers. SOFT MATTER 2020; 16:764-774. [PMID: 31830190 DOI: 10.1039/c9sm01851d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recent experiments on monolayers of spindle-like cells plated on adhesive stripe-shaped domains have provided a convincing demonstration that certain types of collective phenomena in epithelia are well described by active nematic hydrodynamics. While recovering some of the hallmark predictions of this framework, however, these experiments have also revealed a number of unexpected features that could be ascribed to the existence of chirality over length scales larger than the typical size of a cell. In this article we elaborate on the microscopic origin of chiral stresses in nematic cell monolayers and investigate how chirality affects the motion of topological defects, as well as the collective motion in stripe-shaped domains. We find that chirality introduces a characteristic asymmetry in the collective cellular flow, from which the ratio between chiral and non-chiral active stresses can be inferred by particle-image-velocimetry measurements. Furthermore, we find that chirality changes the nature of the spontaneous flow transition under confinement and that, for specific anchoring conditions, the latter has the structure of an imperfect pitchfork bifurcation.
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Affiliation(s)
- Ludwig A Hoffmann
- Instituut-Lorentz, Leiden University, P.O. Box 9506, 2300 RA Leiden, The Netherlands.
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41
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Adeli Koudehi M, Rutkowski DM, Vavylonis D. Organization of associating or crosslinked actin filaments in confinement. Cytoskeleton (Hoboken) 2019; 76:532-548. [PMID: 31525281 DOI: 10.1002/cm.21565] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 09/09/2019] [Accepted: 09/12/2019] [Indexed: 12/13/2022]
Abstract
A key factor of actin cytoskeleton organization in cells is the interplay between the dynamical properties of actin filaments and cell geometry, which restricts, confines and directs their orientation. Crosslinking interactions among actin filaments, together with geometrical cues and regulatory proteins can give rise to contractile rings in dividing cells and actin rings in neurons. Motivated by recent in vitro experiments, in this work we performed computer simulations to study basic aspects of the interplay between confinement and attractive interactions between actin filaments. We used a spring-bead model and Brownian dynamics to simulate semiflexible actin filaments that polymerize in a confining sphere with a rate proportional to the monomer concentration. We model crosslinking, or attraction through the depletion interaction, implicitly as an attractive short-range potential between filament beads. In confining geometries smaller than the persistence length of actin filaments, we show rings can form by curving of filaments of length comparable to, or longer than the confinement diameter. Rings form for optimal ranges of attractive interactions that exist in between open bundles, irregular loops, aggregated, and unbundled morphologies. The probability of ring formation is promoted by attraction to the confining sphere boundary and decreases for large radii and initial monomer concentrations, in agreement with prior experimental data. The model reproduces ring formation along the flat plane of oblate ellipsoids.
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42
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Wu D, Sinha N, Lee J, Sutherland BP, Halaszynski NI, Tian Y, Caplan J, Zhang HV, Saven JG, Kloxin CJ, Pochan DJ. Polymers with controlled assembly and rigidity made with click-functional peptide bundles. Nature 2019; 574:658-662. [PMID: 31666724 DOI: 10.1038/s41586-019-1683-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/14/2019] [Indexed: 01/20/2023]
Abstract
The engineering of biological molecules is a key concept in the design of highly functional, sophisticated soft materials. Biomolecules exhibit a wide range of functions and structures, including chemical recognition (of enzyme substrates or adhesive ligands1, for instance), exquisite nanostructures (composed of peptides2, proteins3 or nucleic acids4), and unusual mechanical properties (such as silk-like strength3, stiffness5, viscoelasticity6 and resiliency7). Here we combine the computational design of physical (noncovalent) interactions with pathway-dependent, hierarchical 'click' covalent assembly to produce hybrid synthetic peptide-based polymers. The nanometre-scale monomeric units of these polymers are homotetrameric, α-helical bundles of low-molecular-weight peptides. These bundled monomers, or 'bundlemers', can be designed to provide complete control of the stability, size and spatial display of chemical functionalities. The protein-like structure of the bundle allows precise positioning of covalent linkages between the ends of distinct bundlemers, resulting in polymers with interesting and controllable physical characteristics, such as rigid rods, semiflexible or kinked chains, and thermally responsive hydrogel networks. Chain stiffness can be controlled by varying only the linkage. Furthermore, by controlling the amino acid sequence along the bundlemer periphery, we use specific amino acid side chains, including non-natural 'click' chemistry functionalities, to conjugate moieties into a desired pattern, enabling the creation of a wide variety of hybrid nanomaterials.
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Affiliation(s)
- Dongdong Wu
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA
| | - Nairiti Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA
| | - Jeeyoung Lee
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA
| | - Bryan P Sutherland
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA
| | - Nicole I Halaszynski
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA
| | - Yu Tian
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA
| | - Jeffrey Caplan
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Huixi Violet Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.
| | - Christopher J Kloxin
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA. .,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA.
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43
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Bashirzadeh Y, Liu AP. Encapsulation of the cytoskeleton: towards mimicking the mechanics of a cell. SOFT MATTER 2019; 15:8425-8436. [PMID: 31621750 DOI: 10.1039/c9sm01669d] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The cytoskeleton of a cell controls all the aspects of cell shape changes and motility from its physiological functions for survival to reproduction to death. The structure and dynamics of the cytoskeletal components: actin, microtubules, intermediate filaments, and septins - recently regarded as the fourth member of the cytoskeleton family - are conserved during evolution. Such conserved and effective control over the mechanics of the cell makes the cytoskeletal components great candidates for in vitro reconstitution and bottom-up synthetic biology studies. Here, we review the recent efforts in reconstitution of the cytoskeleton in and on membrane-enclosed biomimetic systems and argue that co-reconstitution and synergistic interplay between cytoskeletal filaments might be indispensable for efficient mechanical functionality of active minimal cells. Further, mechanical equilibrium in adherent eukaryotic cells is achieved by the formation of integrin-based focal contacts with extracellular matrix (ECM) and the transmission of stresses generated by actomyosin contraction to ECM. Therefore, a minimal mimic of such balance of forces and quasi-static kinetics of the cell by bottom-up reconstitution requires a careful construction of contractile machineries and their link with adhesive contacts. In this review, in addition to cytoskeletal crosstalk, we provide a perspective on reconstruction of cell mechanical equilibrium by reconstitution of cortical actomyosin networks in lipid membrane vesicles adhered on compliant substrates and also discuss future perspectives of this active research area.
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Affiliation(s)
- Yashar Bashirzadeh
- Department of Mechanical Engineering, University of Michigan, 2350 Hayward Street, Ann Arbor, Michigan, USA.
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Andorfer R, Alper JD. From isolated structures to continuous networks: A categorization of cytoskeleton-based motile engineered biological microstructures. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 11:e1553. [PMID: 30740918 PMCID: PMC6881777 DOI: 10.1002/wnan.1553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/27/2018] [Accepted: 12/28/2018] [Indexed: 11/06/2022]
Abstract
As technology at the small scale is advancing, motile engineered microstructures are becoming useful in drug delivery, biomedicine, and lab-on-a-chip devices. However, traditional engineering methods and materials can be inefficient or functionally inadequate for small-scale applications. Increasingly, researchers are turning to the biology of the cytoskeleton, including microtubules, actin filaments, kinesins, dyneins, myosins, and associated proteins, for both inspiration and solutions. They are engineering structures with components that range from being entirely biological to being entirely synthetic mimics of biology and on scales that range from isotropic continuous networks to single isolated structures. Motile biological microstructures trace their origins from the development of assays used to study the cytoskeleton to the array of structures currently available today. We define 12 types of motile biological microstructures, based on four categories: entirely biological, modular, hybrid, and synthetic, and three scales: networks, clusters, and isolated structures. We highlight some key examples, the unique functionalities, and the potential applications of each microstructure type, and we summarize the quantitative models that enable engineering them. By categorizing the diversity of motile biological microstructures in this way, we aim to establish a framework to classify these structures, define the gaps in current research, and spur ideas to fill those gaps. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Nanotechnology Approaches to Biology > Cells at the Nanoscale Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Therapeutic Approaches and Drug Discovery > Emerging Technologies.
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Affiliation(s)
- Rachel Andorfer
- Department of Bioengineering, Clemson University, Clemson, South Carolina
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina
| | - Joshua D. Alper
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina
- Department of Biological Sciences, Clemson University, Clemson, South Carolina
- Eukaryotic Pathogen Innovations Center, Clemson University, Clemson, South Carolina
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45
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Edozie B, Sahu S, Pitta M, Englert A, do Rosario CF, Ross JL. Self-organization of spindle-like microtubule structures. SOFT MATTER 2019; 15:4797-4807. [PMID: 31123741 DOI: 10.1039/c8sm01835a] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Microtubule self-organization is an essential physical process underlying several essential cellular functions, including cell division. In cell division, the dominant arrangement is the mitotic spindle, a football-shaped microtubule-based machine responsible for separating the chromosomes. We are interested in the underlying fundamental principles behind the self-organization of the spindle shape. Prior biological works have hypothesized that motor proteins control the proper formation of the spindle. Many of these motor proteins are also microtubule-crosslinkers, so it is unclear if the critical aspect is the motor activity or the crosslinking. In this study, we seek to address this question by examining the self-organization of microtubules using crosslinkers alone. We use a minimal system composed of tubulin, an antiparallel microtubule-crosslinking protein, and a crowding agent to explore the phase space of organizations as a function of tubulin and crosslinker concentration. We find that the concentration of the antiparallel crosslinker, MAP65, has a significant effect on the organization and resulted in spindle-like arrangements at relatively low concentration without the need for motor activity. Surprisingly, the length of the microtubules only moderately affects the equilibrium phase. We characterize both the shape and dynamics of these spindle-like organizations. We find that they are birefringent homogeneous tactoids. The microtubules have slow mobility, but the crosslinkers have fast mobility within the tactoids. These structures represent a first step in the recapitulation of self-organized spindles of microtubules that can be used as initial structures for further biophysical and active matter studies relevant to the biological process of cell division.
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Affiliation(s)
- Bianca Edozie
- Department of Physics, University of Massachusetts, 666 N. Pleasant St., Amherst, MA 01003, USA.
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46
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Abstract
The cytoskeleton is a collection of protein assemblies that dynamically impose spatial structure in cells and coordinate processes such as cell division and mechanical regulation. Biopolymer filaments, cross-linking proteins, and enzymatically active motor proteins collectively self-organize into various precise cytoskeletal assemblies critical for specific biological functions. An outstanding question is how the precise spatial organization arises from the component macromolecules. We develop a system to investigate simple physical mechanisms of self-organization in biological assemblies. Using a minimal set of purified proteins, we create droplets of cross-linked biopolymer filaments. Through the addition of enzymatically active motor proteins, we construct composite assemblies, evocative of cellular structures such as spindles, where the inherent anisotropy drives motor self-organization, droplet deformation, and division into two droplets. These results suggest that simple physical principles underlie self-organization in complex biological assemblies and inform bioinspired materials design.
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47
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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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48
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Krishnamurthy KS, Kanakala MB, Yelamaggad CV, Madhusudana NV. Microscale Structures Arising from Nanoscale Inhomogeneities in Nematics Made of Bent-Shaped Molecules. J Phys Chem B 2019; 123:1423-1431. [PMID: 30668915 DOI: 10.1021/acs.jpcb.8b11481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nanoscale structures in fluid media normally require techniques such as freeze fracture electron microscopy and atomic force microscopy for their visualization. As demonstrated in the present study, the surface modification due to nanoscale clusters occurring intrinsically in nematics made of bent-shaped molecules with either rigid or flexible cores leads to microscale structures, which are visible in an optical microscope. The underlying physical mechanism proposed here involves a quasiperiodic change in anchoring conditions on untreated glass plates for the medium made of islands of clusters surrounded by unclustered molecules. The resulting pattern of stripes outlines the director-normal field around line defects in the well-known schlieren texture. The instability, which is seen over most of the nematic range, with increasing visibility under continued cooling of the sample, sets the nematics made of bent-shaped molecules apart from the classical nematics of rod-shaped molecules.
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Affiliation(s)
| | - Madhu B Kanakala
- Centre for Nano and Soft Matter Sciences , P.O. Box 1329, Jalahalli, Bangalore 560013 , India
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Tang X, Selinger JV. Theory of defect motion in 2D passive and active nematic liquid crystals. SOFT MATTER 2019; 15:587-601. [PMID: 30608104 DOI: 10.1039/c8sm01901k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The motion of topological defects is an important feature of the dynamics of all liquid crystals, and is especially conspicuous in active liquid crystals. Understanding defect motion is a challenging theoretical problem, because the dynamics of orientational order is coupled with backflow of the fluid, and because a liquid crystal has several distinct viscosity coefficients. Here, we suggest a coarse-grained, variational approach, which describes the motion of defects as effective "particles". For passive liquid crystals, the theory shows how the drag depends on defect orientation, and shows the coupling between translational and rotational motion. For active liquid crystals, the theory provides an alternative way to describe motion induced by the activity coefficient.
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Affiliation(s)
- Xingzhou Tang
- Department of Physics and Liquid Crystal Institute, Kent State University, Kent, OH 44242, USA.
| | - Jonathan V Selinger
- Department of Physics and Liquid Crystal Institute, Kent State University, Kent, OH 44242, USA.
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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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