1
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Schimming CD, Reichhardt CJO, Reichhardt C. Active nematic ratchet in asymmetric obstacle arrays. Phys Rev E 2024; 109:064602. [PMID: 39021011 DOI: 10.1103/physreve.109.064602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/03/2024] [Indexed: 07/20/2024]
Abstract
We numerically investigate the effect of an asymmetric periodic obstacle array in a two-dimensional active nematic. We find that activity in conjunction with the asymmetry leads to a ratchet effect or unidirectional flow of the fluid along the asymmetry direction. The directional flow is still present even in the active turbulent phase when the gap between obstacles is sufficiently small. We demonstrate that the dynamics of the topological defects transition from flow mirroring to smectic-like as the gap between obstacles is made smaller, and explain this transition in terms of the pinning of negative winding number defects between obstacles. This also leads to a nonmonotonic ratchet effect magnitude as a function of obstacle size, so that there is an optimal obstacle size for ratcheting at fixed activity.
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2
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Barakat JM, Modica KJ, Lu L, Anujarerat S, Choi KH, Takatori SC. Surface Topography Induces and Orients Nematic Swarms of Active Filaments: Considerations for Lab-On-A-Chip Devices. ACS APPLIED NANO MATERIALS 2024; 7:12142-12152. [PMID: 38808306 PMCID: PMC11129142 DOI: 10.1021/acsanm.4c02020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/30/2024]
Abstract
Surface-bound molecular motors can drive the collective motion of cytoskeletal filaments in the form of nematic bands and polar flocks in reconstituted gliding assays. Although these "swarming transitions" are an emergent property of active filament collisions, they can be controlled and guided by tuning the surface chemistry or topography of the substrate. To date, the impact of surface topography on collective motion in active nematics is only partially understood, with most experimental studies focusing on the escape of a single filament from etched channels. Since the late 1990s, significant progress has been made to utilize the nonequilibrium properties of active filaments and create a range of functional nanodevices relevant to biosensing and parallel computation; however, the complexity of these swarming transitions presents a challenge when attempting to increase filament surface concentrations. In this work, we etch shallow, linear trenches into glass substrates to induce the formation of swarming nematic bands and investigate the mechanisms by which surface topography regulates the two-dimensional (2D) collective motion of driven filamentous actin (F-actin). We demonstrate that nematic swarms only appear at intermediate trench spacings and vanish if the trenches are made too narrow, wide, or tortuous. To rationalize these results, we simulate the F-actin as self-propelled, semiflexible chains subject to a soft, spatially modulated potential that encodes the energetic cost of bending a filament along the edge of a trench. In our model, we hypothesize that an individual filament experiences a penalty when its projected end-to-end distance is smaller than the trench spacing ("bending and turning"). However, chains that span the channel width glide above the trenches in a force- and torque-free manner ("crowd-surfing"). Our simulations demonstrate that collections of filaments form nematic bands only at intermediate trench spacings, consistent with our experimental findings.
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Affiliation(s)
| | | | - Le Lu
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Stephanie Anujarerat
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Kyu Hwan Choi
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Sho C. Takatori
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
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3
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Shankar S, Scharrer LVD, Bowick MJ, Marchetti MC. Design rules for controlling active topological defects. Proc Natl Acad Sci U S A 2024; 121:e2400933121. [PMID: 38748571 PMCID: PMC11127047 DOI: 10.1073/pnas.2400933121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/12/2024] [Indexed: 05/27/2024] Open
Abstract
Topological defects play a central role in the physics of many materials, including magnets, superconductors, and liquid crystals. In active fluids, defects become autonomous particles that spontaneously propel from internal active stresses and drive chaotic flows stirring the fluid. The intimate connection between defect textures and active flow suggests that properties of active materials can be engineered by controlling defects, but design principles for their spatiotemporal control remain elusive. Here, we propose a symmetry-based additive strategy for using elementary activity patterns, as active topological tweezers, to create, move, and braid such defects. By combining theory and simulations, we demonstrate how, at the collective level, spatial activity gradients act like electric fields which, when strong enough, induce an inverted topological polarization of defects, akin to a negative susceptibility dielectric. We harness this feature in a dynamic setting to collectively pattern and transport interacting active defects. Our work establishes an additive framework to sculpt flows and manipulate active defects in both space and time, paving the way to design programmable active and living materials for transport, memory, and logic.
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Affiliation(s)
- Suraj Shankar
- Department of Physics, Harvard University, Cambridge, MA02138
- Department of Physics, University of Michigan, Ann Arbor, MI48109
| | - Luca V. D. Scharrer
- Department of Physics, University of California, Santa Barbara, CA93106
- Department of Physics, The University of Chicago, Chicago, IL60637
| | - Mark J. Bowick
- Department of Physics, University of California, Santa Barbara, CA93106
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA93106
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4
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Keogh RR, Kozhukhov T, Thijssen K, Shendruk TN. Active Darcy's Law. PHYSICAL REVIEW LETTERS 2024; 132:188301. [PMID: 38759204 DOI: 10.1103/physrevlett.132.188301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 03/11/2024] [Indexed: 05/19/2024]
Abstract
While bacterial swarms can exhibit active turbulence in vacant spaces, they naturally inhabit crowded environments. We numerically show that driving disorderly active fluids through porous media enhances Darcy's law. While purely active flows average to zero flux, hybrid active/driven flows display greater drift than purely pressure-driven flows. This enhancement is nonmonotonic with activity, leading to an optimal activity to maximize flow rate. We incorporate the active contribution into an active Darcy's law, which may serve to help understand anomalous transport of swarming in porous media.
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Affiliation(s)
- Ryan R Keogh
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, United Kingdom
| | - Timofey Kozhukhov
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, United Kingdom
| | - Kristian Thijssen
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, Copenhagen, Denmark
| | - Tyler N Shendruk
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, United Kingdom
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5
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Langeslay B, Fahy W, Juarez G. Stress and alignment response to curved obstacles in growing bacterial monolayers. Phys Rev E 2024; 109:054608. [PMID: 38907398 DOI: 10.1103/physreve.109.054608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/09/2024] [Indexed: 06/24/2024]
Abstract
Monolayers of growing bacteria, confined within channel geometries, exhibit self-organization into a highly aligned laminar state along the axis of the channel. Although this phenomenon has been observed in experiments and simulations under various boundary conditions, the underlying physical mechanism driving this alignment remains unclear. In this study, we conduct simulations of growing bacteria in two-dimensional channel geometries perturbed by fixed obstacles, either circular or arc shaped, placed at the channel's center. Our findings reveal that even sizable obstacles cause only short-ranged disruptions to the baseline laminar state. These disruptions arise from a competition between local planar anchoring and bulk laminar alignment. At smaller obstacle sizes, bulk alignment fully dominates, while at larger sizes planar anchoring induces increasing local disruptions. Furthermore, our analysis indicates that the resulting configurations of the bacterial system display a striking resemblance to the arrangement of hard-rod smectic liquid crystals around circular obstacles. This suggests that modeling hard-rod bacterial monolayers as smectic, rather than nematic, liquid crystals may yield successful outcomes. The insights gained from our study contribute to the expanding body of research on bacterial growth in channels. Our work provides perspectives on the stability of the laminar state and extends our understanding to encompass more intricate confinement schemes.
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Vélez-Cerón I, Guillamat P, Sagués F, Ignés-Mullol J. Probing active nematics with in situ microfabricated elastic inclusions. Proc Natl Acad Sci U S A 2024; 121:e2312494121. [PMID: 38451942 PMCID: PMC10945829 DOI: 10.1073/pnas.2312494121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/27/2024] [Indexed: 03/09/2024] Open
Abstract
In this work, we report a direct measurement of the forces exerted by a tubulin/kinesin active nematic gel as well as its complete rheological characterization, including the quantification of its shear viscosity, η, and its activity parameter, α. For this, we develop a method that allows us to rapidly photo-polymerize compliant elastic inclusions in the continuously remodeling active system. Moreover, we quantitatively settle long-standing theoretical predictions, such as a postulated relationship encoding the intrinsic time scale of the active nematic in terms of η and α. In parallel, we infer a value for the nematic elasticity constant, K, by combining our measurements with the theorized scaling of the active length scale. On top of the microrheology capabilities, we demonstrate strategies for defect encapsulation, quantification of defect mechanics, and defect interactions, enabled by the versatility of the microfabrication strategy that allows to combine elastic motifs of different shapes and stiffnesses that are fabricated in situ.
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Affiliation(s)
- Ignasi Vélez-Cerón
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Barcelona08028, Spain
- Institute of Nanoscience and Nanotechnology, IN2UB, Universitat de Barcelona, Barcelona08028, Spain
| | - Pau Guillamat
- Institute for Bioengineering of Catalonia, The Barcelona Institute for Science and Technology, Barcelona08028, Spain
| | - Francesc Sagués
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Barcelona08028, Spain
- Institute of Nanoscience and Nanotechnology, IN2UB, Universitat de Barcelona, Barcelona08028, Spain
| | - Jordi Ignés-Mullol
- Department of Materials Science and Physical Chemistry, Universitat de Barcelona, Barcelona08028, Spain
- Institute of Nanoscience and Nanotechnology, IN2UB, Universitat de Barcelona, Barcelona08028, Spain
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7
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Ye H, Ouyang Z, Lin J. On particle motion in a confined square domain filled with active fluids. SOFT MATTER 2024; 20:1786-1799. [PMID: 38305105 DOI: 10.1039/d3sm01321a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
The motion of passive particles in a confined square domain filled with active fluids has been numerically simulated using a direct-fictitious domain method. The ratio of particle diameter to the side length of the square domain (dp/L) is adopted to classify the degree of confinement (i.e., strong or weak confinement). The translational mean-squared displacement (MSDT) of weakly-confined particles scales well with the reported theoretical and experimental results in a short time and eventually reaches a plateau because of the confined environment. Additionally, the radial probability densities of the particle positions gradually increase with increasing distance from the center of the square domain at relatively high activity levels, displaying an apparent rise near the boundary and maximize near the corner. Conversely, the strongly confined particles migrate toward the center of the square domain or approach the corner with continuous rotation. In addition, the localized minima of the angular velocity of the particles show a periodic behavior, with the vortices periodically becoming more organized. Moreover, with increasing activity, two distinct linearly correlated regimes emerge in the relationship between the particle's rotational velocity and the activity. A comprehensive analysis of the collective dynamics reveals that the cutoff length is Rc ≈ 0.19(2.375dp), pointing to the distance at which the velocities of two particles are uncorrelated. Moreover, the spatial correlation function (Ip) shows a small peak at Rr ≈ 0.12(1.5dp), suggesting a relatively strong correlation between a given particle and another particle located at a distance Rr from it. Interestingly, both Rc and Rr are smaller than those observed in an unbounded flow, which indicates that boundary confinement significantly influences the ability of the particles to form coherent structures.
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Affiliation(s)
- Hao Ye
- Department of Mechanics, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310027 Hangzhou, China.
| | - Zhenyu Ouyang
- Zhejiang Provincial Engineering Research Center for the Safety of Pressure Vessel and Pipeline, 315210 Ningbo, China.
| | - Jianzhong Lin
- Department of Mechanics, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310027 Hangzhou, China.
- Zhejiang Provincial Engineering Research Center for the Safety of Pressure Vessel and Pipeline, 315210 Ningbo, China.
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8
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Li Y, Zarei Z, Tran PN, Wang Y, Baskaran A, Fraden S, Hagan MF, Hong P. A machine learning approach to robustly determine director fields and analyze defects in active nematics. SOFT MATTER 2024; 20:1869-1883. [PMID: 38318759 DOI: 10.1039/d3sm01253k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Active nematics are dense systems of rodlike particles that consume energy to drive motion at the level of the individual particles. They exist in natural systems like biological tissues and artificial materials such as suspensions of self-propelled colloidal particles or synthetic microswimmers. Active nematics have attracted significant attention in recent years due to their spectacular nonequilibrium collective spatiotemporal dynamics, which may enable applications in fields such as robotics, drug delivery, and materials science. The director field, which measures the direction and degree of alignment of the local nematic orientation, is a crucial characteristic of active nematics and is essential for studying topological defects. However, determining the director field is a significant challenge in many experimental systems. Although director fields can be derived from images of active nematics using traditional imaging processing methods, the accuracy of such methods is highly sensitive to the settings of the algorithms. These settings must be tuned from image to image due to experimental noise, intrinsic noise of the imaging technology, and perturbations caused by changes in experimental conditions. This sensitivity currently limits automatic analysis of active nematics. To address this, we developed a machine learning model for extracting reliable director fields from raw experimental images, which enables accurate analysis of topological defects. Application of the algorithm to experimental data demonstrates that the approach is robust and highly generalizable to experimental settings that are different from those in the training data. It could be a promising tool for investigating active nematics and may be generalized to other active matter systems.
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Affiliation(s)
- Yunrui Li
- Computer Science Department, Brandeis University, USA.
| | - Zahra Zarei
- Physics Department, Brandeis University, USA
| | - Phu N Tran
- Physics Department, Brandeis University, USA
| | - Yifei Wang
- Computer Science Department, Brandeis University, USA.
| | | | - Seth Fraden
- Physics Department, Brandeis University, USA
| | | | - Pengyu Hong
- Computer Science Department, Brandeis University, USA.
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9
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Schimming CD, Reichhardt CJO, Reichhardt C. Vortex Lattices in Active Nematics with Periodic Obstacle Arrays. PHYSICAL REVIEW LETTERS 2024; 132:018301. [PMID: 38242662 DOI: 10.1103/physrevlett.132.018301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/16/2023] [Indexed: 01/21/2024]
Abstract
We numerically model a two-dimensional active nematic confined by a periodic array of fixed obstacles. Even in the passive nematic, the appearance of topological defects is unavoidable due to planar anchoring by the obstacle surfaces. We show that a vortex lattice state emerges as activity is increased, and that this lattice may be tuned from "ferromagnetic" to "antiferromagnetic" by varying the gap size between obstacles. We map the rich variety of states exhibited by the system as a function of distance between obstacles and activity, including a pinned defect state, motile defects, the vortex lattice, and active turbulence. We demonstrate that the flows in the active turbulent phase can be tuned by the presence of obstacles, and explore the effects of a frustrated lattice geometry on the vortex lattice phase.
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Affiliation(s)
- Cody D Schimming
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - C J O Reichhardt
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - C Reichhardt
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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10
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Caballero F, You Z, Marchetti MC. Vorticity phase separation and defect lattices in the isotropic phase of active liquid crystals. SOFT MATTER 2023; 19:7828-7835. [PMID: 37796173 DOI: 10.1039/d3sm00744h] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
We use numerical simulations and linear stability analysis to study the dynamics of an active liquid crystal film on a substrate in the regime where the passive system would be isotropic. Extensile activity builds up local orientational order and destabilizes the quiescent isotropic state above a critical activity, eventually resulting in spatiotemporal chaotic dynamics akin to the one observed ubiquitously in the nematic state. Here we show that tuning substrate friction yields a variety of emergent structures at intermediate activity, including lattices of flow vortices with associated regular arrangements of topological defects and a new state where flow vortices trap pairs of +1/2 defect that chase each other's tail. These chiral units spontaneously pick the sense of rotation and organize in a hexagonal lattice, surrounded by a diffuse flow of opposite rotation to maintain zero net vorticity. The length scale of these emergent structures is set by the screening length of the flow, controlled by the shear viscosity η and the substrate friction Γ, and can be captured by simple mode selection of the vortical flows. We demonstrate that the emergence of coherent structures can be interpreted as a phase separation of vorticity, where friction plays a role akin to that of birth/death processes in breaking conservation of the phase separating species and selecting a characteristic scale for the patterns. Our work shows that friction provides an experimentally accessible tuning parameter for designing controlled active flows.
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Affiliation(s)
- Fernando Caballero
- Department of Physics, University of California Santa Barbara, Santa Barbara, CA 93106, USA.
| | - Zhihong You
- Fujian Provincial Key Laboratory for Soft Functional Materials Research, Research Institute for Biomimetics and Soft Matter, Department of Physics, Xiamen University, Xiamen, Fujian 361005, China
| | - M Cristina Marchetti
- Department of Physics, University of California Santa Barbara, Santa Barbara, CA 93106, USA.
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11
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Zarei Z, Berezney J, Hensley A, Lemma L, Senbil N, Dogic Z, Fraden S. Light-activated microtubule-based two-dimensional active nematic. SOFT MATTER 2023; 19:6691-6699. [PMID: 37609884 DOI: 10.1039/d3sm00270e] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
We assess the ability of two light responsive kinesin motor clusters to drive dynamics of microtubule-based active nematics: opto-K401, a processive motor, and opto-K365, a non-processive motor. Measurements reveal an order of magnitude improvement in the contrast of nematic flow speeds between maximally- and minimally-illuminated states for opto-K365 motors when compared to opto-K401 construct. For opto-K365 nematics, we characterize both the steady-state flow and defect density as a function of applied light. We also examine the transient behavior as the system switches between steady-states upon changes in light intensities. Although nematic flows reach a steady state within tens of seconds, the defect density exhibits transient behavior for up to 10 minutes, showing a separation between small-scale active flows and system-scale structural states. Our work establishes an experimental platform that can exploit spatiotemporally-heterogeneous patterns of activity to generate targeted dynamical states.
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Affiliation(s)
- Zahra Zarei
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
| | - John Berezney
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
| | - Alexander Hensley
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
| | - Linnea Lemma
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
- The Department of Chemical and Biological Engineering, Princeton, NJ 08544, USA
- Department of Physics, University of California, Santa Barbara, California 93106, USA
| | - Nesrin Senbil
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
| | - Zvonimir Dogic
- Department of Physics, University of California, Santa Barbara, California 93106, USA
- Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106, USA
| | - Seth Fraden
- The Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.
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12
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McGorty RJ, Currie CJ, Michel J, Sasanpour M, Gunter C, Lindsay KA, Rust MJ, Katira P, Das M, Ross JL, Robertson-Anderson RM. Kinesin and myosin motors compete to drive rich multiphase dynamics in programmable cytoskeletal composites. PNAS NEXUS 2023; 2:pgad245. [PMID: 37575673 PMCID: PMC10416814 DOI: 10.1093/pnasnexus/pgad245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/07/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023]
Abstract
The cellular cytoskeleton relies on diverse populations of motors, filaments, and binding proteins acting in concert to enable nonequilibrium processes ranging from mitosis to chemotaxis. The cytoskeleton's versatile reconfigurability, programmed by interactions between its constituents, makes it a foundational active matter platform. However, current active matter endeavors are limited largely to single force-generating components acting on a single substrate-far from the composite cytoskeleton in cells. Here, we engineer actin-microtubule (MT) composites, driven by kinesin and myosin motors and tuned by crosslinkers, to ballistically restructure and flow with speeds that span three orders of magnitude depending on the composite formulation and time relative to the onset of motor activity. Differential dynamic microscopy analyses reveal that kinesin and myosin compete to delay the onset of acceleration and suppress discrete restructuring events, while passive crosslinking of either actin or MTs has an opposite effect. Our minimal advection-diffusion model and spatial correlation analyses correlate these dynamics to structure, with motor antagonism suppressing reconfiguration and demixing, while crosslinking enhances clustering. Despite the rich formulation space and emergent formulation-dependent structures, the nonequilibrium dynamics across all composites and timescales can be organized into three classes-slow isotropic reorientation, fast directional flow, and multimode restructuring. Moreover, our mathematical model demonstrates that diverse structural motifs can arise simply from the interplay between motor-driven advection and frictional drag. These general features of our platform facilitate applicability to other active matter systems and shed light on diverse ways that cytoskeletal components can cooperate or compete to enable wide-ranging cellular processes.
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Affiliation(s)
- Ryan J McGorty
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92110, USA
| | - Christopher J Currie
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92110, USA
| | - Jonathan Michel
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Mehrzad Sasanpour
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92110, USA
| | - Christopher Gunter
- Department of Mechanical Engineering, San Diego State University, San Diego, CA 92182, USA
| | - K Alice Lindsay
- Department of Physics, Syracuse University, Syracuse, NY 13244, USA
| | - Michael J Rust
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Parag Katira
- Department of Mechanical Engineering, San Diego State University, San Diego, CA 92182, USA
| | - Moumita Das
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Jennifer L Ross
- Department of Physics, Syracuse University, Syracuse, NY 13244, USA
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13
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Schimming CD, Reichhardt CJO, Reichhardt C. Friction-mediated phase transition in confined active nematics. Phys Rev E 2023; 108:L012602. [PMID: 37583137 DOI: 10.1103/physreve.108.l012602] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/28/2023] [Indexed: 08/17/2023]
Abstract
Using a minimal continuum model, we investigate the interplay between circular confinement and substrate friction in active nematics. Upon increasing the friction from low to high, we observe a dynamical phase transition from a circulating flow phase to an anisotropic flow phase in which the flow tends to align perpendicular to the nematic director at the boundary. We demonstrate that both the flow structure and dynamic correlations in the latter phase differ from those of an unconfined, active turbulent system and may be controlled by the prescribed nematic boundary conditions. Our results show that substrate friction and geometric confinement act as valuable control parameters in active nematics.
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Affiliation(s)
- Cody D Schimming
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - C J O Reichhardt
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - C Reichhardt
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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14
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Shen Z, Lintuvuori JS. Collective Flows Drive Cavitation in Spinner Monolayers. PHYSICAL REVIEW LETTERS 2023; 130:188202. [PMID: 37204910 DOI: 10.1103/physrevlett.130.188202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 04/14/2023] [Indexed: 05/21/2023]
Abstract
Hydrodynamic interactions can give rise to a collective motion of rotating particles. This, in turn, can lead to coherent fluid flows. Using large scale hydrodynamic simulations, we study the coupling between these two in spinner monolayers at weakly inertial regime. We observe an instability, where the initially uniform particle layer separates into particle void and particle rich areas. The particle void region corresponds to a fluid vortex, and it is driven by a surrounding spinner edge current. We show that the instability originates from a hydrodynamic lift force between the particle and fluid flows. The cavitation can be tuned by the strength of the collective flows. It is suppressed when the spinners are confined by a no-slip surface, and multiple cavity and oscillating cavity states are observed when the particle concentration is reduced.
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Affiliation(s)
- Zaiyi Shen
- Université de Bordeaux, CNRS, LOMA, UMR 5798, F-33400 Talence, France
- State Key Laboratory for Turbulence and Complex Systems, Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing 100871, China
| | - Juho S Lintuvuori
- Université de Bordeaux, CNRS, LOMA, UMR 5798, F-33400 Talence, France
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15
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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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16
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Rønning J, Marchetti MC, Angheluta L. Defect self-propulsion in active nematic films with spatially varying activity. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221229. [PMID: 36816847 PMCID: PMC9929493 DOI: 10.1098/rsos.221229] [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: 09/21/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
We study the dynamics of topological defects in active nematic films with spatially varying activity and consider two set-ups: (i) a constant activity gradient and (ii) a sharp jump in activity. A constant gradient of extensile (contractile) activity endows the comet-like +1/2 defect with a finite vorticity that drives the defect to align its nose in the direction of decreasing (increasing) gradient. A constant gradient does not, however, affect the known self-propulsion of the +1/2 defect and has no effect on the -1/2 that remains a non-motile particle. A sharp jump in activity acts like a wall that traps the defects, affecting the translational and rotational motion of both charges. The +1/2 defect slows down as it approaches the interface and the net vorticity tends to reorient the defect polarization so that it becomes perpendicular to the interface. The -1/2 defect acquires a self-propulsion towards the activity interface, while the vorticity-induced active torque tends to align the defect to a preferred orientation. This effective attraction of the negative defects to the wall is consistent with the observation of an accumulation of negative topological charge at both active/passive interfaces and physical boundaries.
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Affiliation(s)
- Jonas Rønning
- Njord Centre, Department of Physics, University of Oslo, PO Box 1048, Oslo 0316, Norway
| | - M. Cristina Marchetti
- Department of Physics and Biomolecular Science and Engineering Program, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Luiza Angheluta
- Njord Centre, Department of Physics, University of Oslo, PO Box 1048, Oslo 0316, Norway
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17
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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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18
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Assante R, Corbett D, Marenduzzo D, Morozov A. Active turbulence and spontaneous phase separation in inhomogeneous extensile active gels. SOFT MATTER 2023; 19:189-198. [PMID: 36503973 DOI: 10.1039/d2sm01188c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We report numerical results for the hydrodynamics of inhomogeneous lyotropic and extensile active nematic gels. By simulating the coupled Cahn-Hilliard, Navier-Stokes, and Beris-Edwards equation for the evolution of the composition, flow and orientational order of an active nematic, we ask whether composition variations are important to determine its emergent physics. As in active gels of uniform composition, we find that increasing either activity or nematic tendency (e.g., overall active matter concentration) triggers a transition between an isotropic passive phase and an active nematic one. We show that composition inhomogeneities are important in the latter phase, where we find three types of possible dynamical regimes. First, we observe regular patterns with defects and vortices: these exist close to the passive-active transition. Second, for larger activity, or deeper in the nematic phase, we find active turbulence, as in active gels of uniform composition, but with exceedingly large composition variation. In the third regime, which is uniquely associated with inhomogeneity and occurs for large nematic tendency and low activity, we observe spontaneous microphase separation into active and passive domains. The microphase separated regime is notable in view of the absence of an explicit demixing term in the underlying free energy which we use, and we provide a theoretical analysis based on the common tangent construction which explains its existence. We hope this regime can be probed experimentally in the future.
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Affiliation(s)
- Renato Assante
- SUPA, School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Dom Corbett
- SUPA, School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Alexander Morozov
- SUPA, School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
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19
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Joshi C, Ray S, Lemma LM, Varghese M, Sharp G, Dogic Z, Baskaran A, Hagan MF. Data-Driven Discovery of Active Nematic Hydrodynamics. PHYSICAL REVIEW LETTERS 2022; 129:258001. [PMID: 36608242 DOI: 10.1103/physrevlett.129.258001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Active nematics can be modeled using phenomenological continuum theories that account for the dynamics of the nematic director and fluid velocity through partial differential equations (PDEs). While these models provide a statistical description of the experiments, the relevant terms in the PDEs and their parameters are usually identified indirectly. We adapt a recently developed method to automatically identify optimal continuum models for active nematics directly from spatiotemporal data, via sparse regression of the coarse-grained fields onto generic low order PDEs. After extensive benchmarking, we apply the method to experiments with microtubule-based active nematics, finding a surprisingly minimal description of the system. Our approach can be generalized to gain insights into active gels, microswimmers, and diverse other experimental active matter systems.
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Affiliation(s)
- Chaitanya Joshi
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
- Department of Physics and Astronomy, Tufts University, Medford, Massachusetts 02155, USA
| | - Sattvic Ray
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Linnea M Lemma
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Minu Varghese
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109 USA
| | - Graham Sharp
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Zvonimir Dogic
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
| | - Aparna Baskaran
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Michael F Hagan
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
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20
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Kučera O, Gaillard J, Guérin C, Utzschneider C, Théry M, Blanchoin L. Actin Architecture Steers Microtubules in Active Cytoskeletal Composite. NANO LETTERS 2022; 22:8584-8591. [PMID: 36279243 DOI: 10.1021/acs.nanolett.2c03117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Motility assays use surface-immobilized molecular motors to propel cytoskeletal filaments. They have been widely used to characterize motor properties and their impact on cytoskeletal self-organization. Moreover, the motility assays are a promising class of bioinspired active tools for nanotechnological applications. While these assays involve controlling the filament direction and speed, either as a sensory readout or a functional feature, designing a subtle control embedded in the assay is an ongoing challenge. Here, we investigate the interaction between gliding microtubules and networks of actin filaments. We demonstrate that the microtubule's behavior depends on the actin architecture. Both unbranched and branched actin decelerate microtubule gliding; however, an unbranched actin network provides additional guidance and effectively steers the microtubules. This effect, which resembles the recognition of cortical actin by microtubules, is a conceptually new means of controlling the filament gliding with potential application in the design of active materials and cytoskeletal nanodevices.
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Affiliation(s)
- Ondřej Kučera
- CytoMorpho Lab, Laboratoire de Physiologie Cellulaire et Végétale, Interdisciplinary Research Institute of Grenoble, CEA/CNRS/Université Grenoble Alpes, 17 Avenue des Martyrs, Grenoble38 054, France
| | - Jérémie Gaillard
- CytoMorpho Lab, Laboratoire de Physiologie Cellulaire et Végétale, Interdisciplinary Research Institute of Grenoble, CEA/CNRS/Université Grenoble Alpes, 17 Avenue des Martyrs, Grenoble38 054, France
| | - Christophe Guérin
- CytoMorpho Lab, Laboratoire de Physiologie Cellulaire et Végétale, Interdisciplinary Research Institute of Grenoble, CEA/CNRS/Université Grenoble Alpes, 17 Avenue des Martyrs, Grenoble38 054, France
| | - Clothilde Utzschneider
- CytoMorpho Lab, Laboratoire de Physiologie Cellulaire et Végétale, Interdisciplinary Research Institute of Grenoble, CEA/CNRS/Université Grenoble Alpes, 17 Avenue des Martyrs, Grenoble38 054, France
| | - Manuel Théry
- CytoMorpho Lab, Laboratoire de Physiologie Cellulaire et Végétale, Interdisciplinary Research Institute of Grenoble, CEA/CNRS/Université Grenoble Alpes, 17 Avenue des Martyrs, Grenoble38 054, France
- CytoMorpho Lab, Unité de Thérapie Cellulaire, Hôpital Saint Louis/CNRS/CEA, 1 Avenue Claude Vellefaux, Paris75 010, France
| | - Laurent Blanchoin
- CytoMorpho Lab, Laboratoire de Physiologie Cellulaire et Végétale, Interdisciplinary Research Institute of Grenoble, CEA/CNRS/Université Grenoble Alpes, 17 Avenue des Martyrs, Grenoble38 054, France
- CytoMorpho Lab, Unité de Thérapie Cellulaire, Hôpital Saint Louis/CNRS/CEA, 1 Avenue Claude Vellefaux, Paris75 010, France
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21
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Active boundary layers in confined active nematics. Nat Commun 2022; 13:6675. [PMID: 36335213 PMCID: PMC9637202 DOI: 10.1038/s41467-022-34336-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 10/21/2022] [Indexed: 11/08/2022] Open
Abstract
The role of boundary layers in conventional liquid crystals is commonly related to the mesogen anchoring on confining walls. In the classical view, anchoring enslaves the orientational field of the passive material under equilibrium conditions. In this work, we show that an active nematic can develop active boundary layers that topologically polarize the confining walls. We find that negatively-charged defects accumulate in the boundary layer, regardless of the wall curvature, and they influence the overall dynamics of the system to the point of fully controlling the behavior of the active nematic in situations of strong confinement. Further, we show that wall defects exhibit behaviors that are essentially different from those of their bulk counterparts, such as high motility or the ability to recombine with another defect of like-sign topological charge. These exotic behaviors result from a change of symmetry induced by the wall in the director field around the defect. Finally, we suggest that the collective dynamics of wall defects might be described in terms of a model equation for one-dimensional spatio-temporal chaos.
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22
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Coelho RCV, Araújo NAM, Telo da Gama MM. Dispersion of activity at an active-passive nematic interface. SOFT MATTER 2022; 18:7642-7653. [PMID: 36169262 DOI: 10.1039/d2sm00988a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Efficient nutrient mixing is crucial for the survival of bacterial colonies and other living systems known as active nematics. However, the dynamics of this mixing is non-trivial as there is a coupling between nutrients concentration and velocity field. To address this question, we solve the hydrodynamic equation for active nematics to model the bacterial swarms coupled to an advection-diffusion equation for the activity field, which is proportional to the concentration of nutrients. At the interface between active and passive nematics the activity field is transported by the interfacial flows and in turn it modifies them through the generation of active stresses. We find that the dispersion of this conserved activity field is subdiffusive due to the emergence of a barrier of negative defects at the active-passive interface, which hinders the propagation of the motile positive defects.
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Affiliation(s)
- Rodrigo C V Coelho
- Centro de Física Teórica e Computacional, Faculdade de Ciências, Universidade de Lisboa, P-1749-016 Lisboa, Portugal.
- Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, P-1749-016 Lisboa, Portugal
| | - Nuno A M Araújo
- Centro de Física Teórica e Computacional, Faculdade de Ciências, Universidade de Lisboa, P-1749-016 Lisboa, Portugal.
- Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, P-1749-016 Lisboa, Portugal
| | - Margarida M Telo da Gama
- Centro de Física Teórica e Computacional, Faculdade de Ciências, Universidade de Lisboa, P-1749-016 Lisboa, Portugal.
- Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, P-1749-016 Lisboa, Portugal
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23
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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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24
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Kozhukhov T, Shendruk TN. Mesoscopic simulations of active nematics. SCIENCE ADVANCES 2022; 8:eabo5788. [PMID: 36001669 PMCID: PMC9401632 DOI: 10.1126/sciadv.abo5788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Coarse-grained, mesoscale simulations are invaluable for studying soft condensed matter because of their ability to model systems in which a background solvent plays a substantial role but is not the primary interest. Such methods generally model passive solvents; however, far-from-equilibrium systems may also be composed of complex solutes suspended in an active fluid. Yet, few coarse-grained simulation methods exist to model an active medium. We introduce an algorithm to simulate active nematics, which builds on multiparticle collision dynamics (MPCD) for passive fluctuating nematohydrodynamics by introducing dipolar activity in the local collision operator. Active nematic MPCD (AN-MPCD) simulations not only exhibit the key characteristics of active nematic turbulence but, as a particle-based algorithm, also reproduce crucial attributes of active particle models. Thus, mesoscopic AN-MPCD is an approach that bridges microscopic and continuum descriptions, allowing simulations of composite active-passive systems.
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25
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Sasanpour M, Achiriloaie DH, Lee G, Leech G, Hendija M, Lindsay KA, Ross JL, McGorty RJ, Robertson-Anderson RM. Reconstituting and Characterizing Actin-Microtubule Composites with Tunable Motor-Driven Dynamics and Mechanics. J Vis Exp 2022:10.3791/64228. [PMID: 36094259 PMCID: PMC10290881 DOI: 10.3791/64228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023] Open
Abstract
The composite cytoskeleton, comprising interacting networks of semiflexible actin filaments and rigid microtubules, restructures and generates forces using motor proteins such as myosin II and kinesin to drive key processes such as migration, cytokinesis, adhesion, and mechanosensing. While actin-microtubule interactions are key to the cytoskeleton's versatility and adaptability, an understanding of their interplay with myosin and kinesin activity is still nascent. This work describes how to engineer tunable three-dimensional composite networks of co-entangled actin filaments and microtubules that undergo active restructuring and ballistic motion, driven by myosin II and kinesin motors, and are tuned by the relative concentrations of actin, microtubules, motor proteins, and passive crosslinkers. Protocols for fluorescence labeling of the microtubules and actin filaments to most effectively visualize composite restructuring and motion using multi-spectral confocal imaging are also detailed. Finally, the results of data analysis methods that can be used to quantitatively characterize non-equilibrium structure, dynamics, and mechanics are presented. Recreating and investigating this tunable biomimetic platform provides valuable insight into how coupled motor activity, composite mechanics, and filament dynamics can lead to myriad cellular processes from mitosis to polarization to mechano-sensation.
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Affiliation(s)
| | - Daisy H Achiriloaie
- Department of Physics and Biophysics, University of San Diego; W. M. Keck Science Department, Scripps College, Pitzer College, and Claremont McKenna College
| | - Gloria Lee
- Department of Physics and Biophysics, University of San Diego
| | - Gregor Leech
- Department of Physics and Biophysics, University of San Diego
| | - Maya Hendija
- Department of Physics and Biophysics, University of San Diego
| | | | | | - Ryan J McGorty
- Department of Physics and Biophysics, University of San Diego
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26
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Keogh RR, Chandragiri S, Loewe B, Ala-Nissila T, Thampi SP, Shendruk TN. Helical flow states in active nematics. Phys Rev E 2022; 106:L012602. [PMID: 35974522 DOI: 10.1103/physreve.106.l012602] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
We show that confining extensile nematics in three-dimensional (3D) channels leads to the emergence of two self-organized flow states with nonzero helicity. The first is a pair of braided antiparallel streams-this double helix occurs when the activity is moderate, anchoring negligible, and reduced temperature high. The second consists of axially aligned counter-rotating vortices-this grinder train arises between spontaneous axial streaming and the vortex lattice. These two unanticipated helical flow states illustrate the potential of active fluids to break symmetries and form complex but organized spatiotemporal structures in 3D fluidic devices.
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Affiliation(s)
- Ryan R Keogh
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Santhan Chandragiri
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai 600036, India
| | - Benjamin Loewe
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Tapio Ala-Nissila
- MSP Group, QTF Centre of Excellence, Department of Applied Physics, Aalto University, P.O. Box 11000, FI-00076 Aalto, Espoo, Finland
- Interdisciplinary Centre for Mathematical Modelling, Department of Mathematical Sciences, Loughborough University, Loughborough LE11 3TU, United Kingdom
| | - Sumesh P Thampi
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai 600036, India
| | - Tyler N Shendruk
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
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27
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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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28
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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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29
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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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