1
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Ghosh S, Joshi C, Baskaran A, Hagan MF. Spatiotemporal control of structure and dynamics in a polar active fluid. SOFT MATTER 2024; 20:7059-7071. [PMID: 39188251 DOI: 10.1039/d4sm00547c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
We apply optimal control theory to a model of a polar active fluid (the Toner-Tu model), with the objective of driving the system into particular emergent dynamical behaviors or programming switching between states on demand. We use the effective self-propulsion speed as the control parameter (i.e. the means of external actuation). We identify control protocols that achieve outcomes such as relocating asters to targeted positions, forcing propagating solitary waves to reorient to a particular direction, and switching between stationary asters and propagating fronts. We analyze the solutions to identify generic principles for controlling polar active fluids. Our findings have implications for achieving spatiotemporal control of active polar systems in experiments, particularly in vitro cytoskeletal systems. Additionally, this research paves the way for leveraging optimal control methods to engineer the structure and dynamics of active fluids more broadly.
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Affiliation(s)
- Saptorshi Ghosh
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA.
| | - Chaitanya Joshi
- Department of Physics and Astronomy, Tufts University, Medford, Massachusetts 02155, USA
| | - Aparna Baskaran
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA.
| | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA.
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2
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Murphy P, Perepelitsa M, Timofeyev I, Lieber-Kotz M, Islas B, Igoshin OA. Breakdown of Boltzmann-type models for the alignment of self-propelled rods. Math Biosci 2024; 376:109266. [PMID: 39127094 DOI: 10.1016/j.mbs.2024.109266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 07/23/2024] [Accepted: 08/03/2024] [Indexed: 08/12/2024]
Abstract
Studies in the collective motility of organisms use a range of analytical approaches to formulate continuous kinetic models of collective dynamics from rules or equations describing agent interactions. However, the derivation of these kinetic models often relies on Boltzmann's "molecular chaos" hypothesis, which assumes that correlations between individuals are short-lived. While this assumption is often the simplest way to derive tractable models, it is often not valid in practice due to the high levels of cooperation and self-organization present in biological systems. In this work, we illustrated this point by considering a general Boltzmann-type kinetic model for the alignment of self-propelled rods where rod reorientation occurs upon binary collisions. We examine the accuracy of the kinetic model by comparing numerical solutions of the continuous equations to an agent-based model that implements the underlying rules governing microscopic alignment. Even for the simplest case considered, our comparison demonstrates that the kinetic model fails to replicate the discrete dynamics due to the formation of rod clusters that violate statistical independence. Additionally, we show that introducing noise to limit cluster formation helps improve the agreement between the analytical model and agent simulations but does not restore the agreement completely. These results highlight the need to both develop and disseminate improved moment-closure methods for modeling biological and active matter systems.
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Affiliation(s)
- Patrick Murphy
- Department of Mathematics and Statistics, San Jose State University, San Jose, CA 95192, United States of America.
| | - Misha Perepelitsa
- Department of Mathematics, University of Houston, TX 77204, United States of America
| | - Ilya Timofeyev
- Department of Mathematics, University of Houston, TX 77204, United States of America
| | - Matan Lieber-Kotz
- Department of Bioengineering, Rice University, Houston, TX 77005, United States of America
| | - Brandon Islas
- Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, United States of America
| | - Oleg A Igoshin
- Department of Bioengineering, Rice University, Houston, TX 77005, United States of America; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, United States of America; Department of Chemistry, Rice University, Houston, TX 77005, United States of America; Department of Biosciences, Rice University, Houston, TX 77005, United States of America
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3
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Saha NK, Salvia WS, Konkolewicz D, Hartley CS. Transient Covalent Polymers through Carbodiimide-Driven Assembly. Angew Chem Int Ed Engl 2024; 63:e202404933. [PMID: 38772695 DOI: 10.1002/anie.202404933] [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: 03/12/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 05/23/2024]
Abstract
Biochemical systems make use of out-of-equilibrium polymers generated under kinetic control. Inspired by these systems, many abiotic supramolecular polymers driven by chemical fuel reactions have been reported. Conversely, polymers based on transient covalent bonds have received little attention, even though they have the potential to complement supramolecular systems by generating transient structures based on stronger bonds and by offering a straightforward tuning of reaction kinetics. In this study, we show that simple aqueous dicarboxylic acids give poly(anhydrides) when treated with the carbodiimide EDC. Transient covalent polymers with molecular weights exceeding 15,000 are generated which then decompose over the course of hours to weeks. Disassembly kinetics can be controlled using simple substituent effects in the monomer design. The impact of solvent polarity, carbodiimide concentration, temperature, pyridine concentration, and monomer concentration on polymer properties and lifetimes has been investigated. The results reveal substantial control over polymer assembly and disassembly kinetics, highlighting the potential for fine-tuned kinetic control in nonequilibrium polymerization systems.
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Affiliation(s)
- Nirob K Saha
- Department of Chemistry and Biochemistry, Miami University, 651 E High St, Oxford, OH, 45056, United States
| | - William S Salvia
- Department of Chemistry and Biochemistry, Miami University, 651 E High St, Oxford, OH, 45056, United States
| | - Dominik Konkolewicz
- Department of Chemistry and Biochemistry, Miami University, 651 E High St, Oxford, OH, 45056, United States
| | - C Scott Hartley
- Department of Chemistry and Biochemistry, Miami University, 651 E High St, Oxford, OH, 45056, United States
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4
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Lemma B, Lemma LM, Ems-McClung SC, Walczak CE, Dogic Z, Needleman DJ. Structure and dynamics of motor-driven microtubule bundles. SOFT MATTER 2024; 20:5715-5723. [PMID: 38872426 PMCID: PMC11268426 DOI: 10.1039/d3sm01336g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 06/03/2024] [Indexed: 06/15/2024]
Abstract
Connecting the large-scale emergent behaviors of active cytoskeletal materials to the microscopic properties of their constituents is a challenge due to a lack of data on the multiscale dynamics and structure of such systems. We approach this problem by studying the impact of depletion attraction on bundles of microtubules and kinesin-14 molecular motors. For all depletant concentrations, kinesin-14 bundles generate comparable extensile dynamics. However, this invariable mesoscopic behavior masks the transition in the microscopic motion of microtubules. Specifically, with increasing attraction, we observe a transition from bi-directional sliding with extension to pure extension with no sliding. Small-angle X-ray scattering shows that the transition in microtubule dynamics is concurrent with a structural rearrangement of microtubules from an open hexagonal to a compressed rectangular lattice. These results demonstrate that bundles of microtubules and molecular motors can display the same mesoscopic extensile behaviors despite having different internal structures and microscopic dynamics. They provide essential information for developing multiscale models of active matter.
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Affiliation(s)
- Bezia Lemma
- Physics Department, Harvard University, Cambridge, MA 02138, USA
- Physics Department, Brandeis University, Waltham, MA 02453, USA.
- Physics Department, University of California, Santa Barbara, CA 93106, USA
| | - Linnea M Lemma
- Physics Department, Brandeis University, Waltham, MA 02453, USA.
- Physics Department, University of California, Santa Barbara, CA 93106, USA
| | | | - Claire E Walczak
- Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Zvonimir Dogic
- Physics Department, Brandeis University, Waltham, MA 02453, USA.
- Physics Department, University of California, Santa Barbara, CA 93106, USA
- Biomolecular Science & Engineering Department, University of California, Santa Barbara, CA 93106, USA
| | - Daniel J Needleman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
- Molecular & Cellular Biology Department, Harvard University, Cambridge, MA 02138, USA
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
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5
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Xu J, Brown NJS, Seol Y, Neuman KC. Heterogeneous distribution of kinesin-streptavidin complexes revealed by mass photometry. SOFT MATTER 2024; 20:5509-5515. [PMID: 38832814 PMCID: PMC11254546 DOI: 10.1039/d3sm01702h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Kinesin-streptavidin complexes are widely used in microtubule-based active-matter studies. The stoichiometry of the complexes is empirically tuned but experimentally challenging to determine. Here, mass photometry measurements reveal heterogenous distributions of kinesin-streptavidin complexes. Our binding model indicates that heterogeneity arises from both the kinesin-streptavidin mixing ratio and the kinesin-biotinylation efficiency.
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Affiliation(s)
- Jing Xu
- Department of Physics, University of California, Merced, CA 95343, USA.
| | - Nathaniel J S Brown
- Department of Quantitative and Systems Biology, University of California, Merced, CA 95343, USA
| | - Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
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6
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Kushwaha P, Maity S, Menon A, Chelakkot R, Chikkadi V. Percolation of nonequilibrium assemblies of colloidal particles in active chiral liquids. SOFT MATTER 2024; 20:4699-4706. [PMID: 38832669 DOI: 10.1039/d4sm00305e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
The growing interest in the non-equilibrium assembly of colloidal particles in active liquids is driven by the motivation to create novel structures endowed with tunable properties unattainable within the confines of equilibrium systems. Here, we present an experimental investigation of the structural features of colloidal assemblies in active liquids of chiral E. coli. The colloidal particles form dynamic clusters due to the effective interaction mediated by active media. The activity and chirality of the swimmers strongly influence the dynamics and local ordering of colloidal particles, resulting in clusters with persistent rotation, whose structure differs significantly from those in equilibrium systems with attractive interactions, such as colloid-polymer mixtures. Our colloid-bacteria mixture displays several hallmark features of a percolation transition at a critical density, where the clusters span the system size. A closer examination of the critical exponents associated with cluster size distribution, the average cluster size, and the correlation length in the vicinity of the critical density shows deviations from the prediction of the standard continuum percolation model. Therefore, our experiments reveal a richer phase behavior of colloidal assemblies in active liquids.
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Affiliation(s)
- Pragya Kushwaha
- Department of Physics, Indian Institute of Science Education and Research, Pune 411008, India.
| | - Sayan Maity
- Department of Physics, Indian Institute of Science Education and Research, Pune 411008, India.
| | - Anjaly Menon
- Department of Applied Physics, Aalto University School of Science, Konemiehentie 1, 02150 Espoo, Finland
| | - Raghunath Chelakkot
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Vijayakumar Chikkadi
- Department of Physics, Indian Institute of Science Education and Research, Pune 411008, India.
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7
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Zhu G, Gao L, Sun Y, Wei W, Yan LT. Non-equilibrium structural and dynamic behaviors of active polymers in complex and crowded environments. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2024; 87:054601. [PMID: 38608453 DOI: 10.1088/1361-6633/ad3e11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/12/2024] [Indexed: 04/14/2024]
Abstract
Active matter systems, which convert internal chemical energy or energy from the environment into directed motion, are ubiquitous in nature and exhibit a range of emerging non-equilibrium behaviors. However, most of the current works on active matter have been devoted to particles, and the study of active polymers has only recently come into the spotlight due to their prevalence within living organisms. The intricate interplay between activity and conformational degrees of freedom gives rise to novel structural and dynamical behaviors of active polymers. Research in active polymers remarkably broadens diverse concepts of polymer physics, such as molecular architecture, dynamics, scaling and so on, which is of significant importance for the development of new polymer materials with unique performance. Furthermore, active polymers are often found in strongly interacting and crowded systems and in complex environments, so that the understanding of this behavior is essential for future developments of novel polymer-based biomaterials. This review thereby focuses on the study of active polymers in complex and crowded environments, and aims to provide insights into the fundamental physics underlying the adaptive and collective behaviors far from equilibrium, as well as the open challenges that the field is currently facing.
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Affiliation(s)
- Guolong Zhu
- School of Physics and Electronics, Hunan University, Changsha 410082, People's Republic of China
| | - Lijuan Gao
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
| | - Yihang Sun
- School of Physics and Electronics, Hunan University, Changsha 410082, People's Republic of China
| | - Wenjie Wei
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
| | - Li-Tang Yan
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
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8
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Xu J, Brown NJS, Seol Y, Neuman KC. Heterogeneous distribution of kinesin-streptavidin complexes revealed by Mass Photometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.21.572878. [PMID: 38187562 PMCID: PMC10769409 DOI: 10.1101/2023.12.21.572878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Kinesin-streptavidin complexes are widely used in microtubule-based active-matter studies. The stoichiometry of the complexes is empirically tuned but experimentally challenging to determine. Here, mass photometry measurements reveal heterogenous distributions of kinesin-streptavidin complexes. Our binding model indicates that heterogeneity arises from both the kinesin-streptavidin mixing ratio and the kinesin-biotinylation efficiency.
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Affiliation(s)
- Jing Xu
- Department of Physics, University of California, Merced, CA 95343, USA
| | - Nathaniel J. S. Brown
- Department of Quantitative and Systems Biology, University of California, Merced, CA 95343, USA
| | - Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Keir C. Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
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9
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Rosfelter A, de Labbey G, Chenevert J, Dumollard R, Schaub S, Machaty Z, Besnardeau L, Gonzalez Suarez D, Hebras C, Turlier H, Burgess DR, McDougall A. Reduction of cortical pulling at mitotic entry facilitates aster centration. J Cell Sci 2024; 137:jcs262037. [PMID: 38469748 DOI: 10.1242/jcs.262037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 02/23/2024] [Indexed: 03/13/2024] Open
Abstract
Equal cell division relies upon astral microtubule-based centering mechanisms, yet how the interplay between mitotic entry, cortical force generation and long astral microtubules leads to symmetric cell division is not resolved. We report that a cortically located sperm aster displaying long astral microtubules that penetrate the whole zygote does not undergo centration until mitotic entry. At mitotic entry, we find that microtubule-based cortical pulling is lost. Quantitative measurements of cortical pulling and cytoplasmic pulling together with physical simulations suggested that a wavelike loss of cortical pulling at mitotic entry leads to aster centration based on cytoplasmic pulling. Cortical actin is lost from the cortex at mitotic entry coincident with a fall in cortical tension from ∼300pN/µm to ∼100pN/µm. Following the loss of cortical force generators at mitotic entry, long microtubule-based cytoplasmic pulling is sufficient to displace the aster towards the cell center. These data reveal how mitotic aster centration is coordinated with mitotic entry in chordate zygotes.
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Affiliation(s)
- Anne Rosfelter
- Laboratoire de Biologie du Developpement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-mer, France
| | - Ghislain de Labbey
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR7241 / INSERM U1050, Université PSL, 75002 Paris, France
| | - Janet Chenevert
- Laboratoire de Biologie du Developpement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-mer, France
| | - Rémi Dumollard
- Laboratoire de Biologie du Developpement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-mer, France
| | - Sebastien Schaub
- Laboratoire de Biologie du Developpement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-mer, France
| | - Zoltan Machaty
- Laboratoire de Biologie du Developpement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-mer, France
| | - Lydia Besnardeau
- Laboratoire de Biologie du Developpement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-mer, France
| | - Daniel Gonzalez Suarez
- Laboratoire de Biologie du Developpement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-mer, France
| | - Céline Hebras
- Laboratoire de Biologie du Developpement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-mer, France
| | - Hervé Turlier
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR7241 / INSERM U1050, Université PSL, 75002 Paris, France
| | - David R Burgess
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
| | - Alex McDougall
- Laboratoire de Biologie du Developpement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-mer, France
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10
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Peng Z, Kapral R. Self-organization of active colloids mediated by chemical interactions. SOFT MATTER 2024; 20:1100-1113. [PMID: 38221884 DOI: 10.1039/d3sm01272g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Self-propelled colloidal particles exhibit rich non-equilibrium phenomena and have promising applications in fields such as drug delivery and self-assembled active materials. Previous experimental and theoretical studies have shown that chemically active colloids that consume or produce a chemical can self-organize into clusters with diverse characteristics depending on the effective phoretic interactions. In this paper, we investigate self-organization in systems with multiple chemical species that undergo a network of reactions and multiple colloidal species that participate in different reactions. Active colloids propelled by complex chemical reactions with potentially nonlinear kinetics can be realized using enzymatic reactions that occur on the surface of enzyme-coated particles. To demonstrate how the self-organizing behavior depends on the chemical reactions active colloids catalyze and their chemical environment, we consider first a single type of colloid undergoing a simple catalytic reaction, and compare this often-studied case with self-organization in binary mixtures of colloids with sequential reactions, and binary mixtures with nonlinear autocatalytic reactions. Our results show that in general active colloids at low particle densities can form localized clusters in the presence of bulk chemical reactions and phoretic attractions. The characteristics of the clusters, however, depend on the reaction kinetics in the bulk and on the particles and phoretic coefficients. With one or two chemical species that only undergo surface reactions, the space for possible self-organizations are limited. By considering the additional system parameters that enter the chemical reaction network involving reactions on the colloids and in the fluid, the design space of colloidal self-organization can be enlarged, leading to a variety of non-equilibrium structures.
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Affiliation(s)
- Zhiwei Peng
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada.
| | - Raymond Kapral
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada.
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11
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Zaferani M, Song R, Petry S, Stone HA. Building on-chip cytoskeletal circuits via branched microtubule networks. Proc Natl Acad Sci U S A 2024; 121:e2315992121. [PMID: 38232292 PMCID: PMC10823238 DOI: 10.1073/pnas.2315992121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024] Open
Abstract
Controllable platforms to engineer robust cytoskeletal scaffolds have the potential to create novel on-chip nanotechnologies. Inspired by axons, we combined the branching microtubule (MT) nucleation pathway with microfabrication to develop "cytoskeletal circuits." This active matter platform allows control over the adaptive self-organization of uniformly polarized MT arrays via geometric features of microstructures designed within a microfluidic confinement. We build and characterize basic elements, including turns and divisions, as well as complex regulatory elements, such as biased division and MT diodes, to construct various MT architectures on a chip. Our platform could be used in diverse applications, ranging from efficient on-chip molecular transport to mechanical nano-actuators. Further, cytoskeletal circuits can serve as a tool to study how the physical environment contributes to MT architecture in living cells.
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Affiliation(s)
- Meisam Zaferani
- Department of Molecular Biology, Princeton University, Princeton, NJ08544
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ08544
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ08544
| | - Ryungeun Song
- Department of Molecular Biology, Princeton University, Princeton, NJ08544
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ08544
| | - Sabine Petry
- Department of Molecular Biology, Princeton University, Princeton, NJ08544
| | - Howard A. Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ08544
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12
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Shen YF, Hu HX, Luo MB. Adsorption of active polymers on attractive nanoparticles. SOFT MATTER 2024; 20:621-628. [PMID: 38131641 DOI: 10.1039/d3sm01380d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The adsorption of active polymers on an attractive nanoparticle (NP) is studied using Langevin dynamics simulations. The active polymers consist of an active Brownian particle (ABP) at the head and a subsequent passive polymer chain. The ABP experiences an active force of magnitude Fa. The interactions between the active polymer and NP are modeled as Lennard-Jones potential with a strength εpn. We find the critical adsorption point εpn* increases with increasing the active force Fa. The increment of εpn*, denoted as Δεpn*, due to Fa can be expressed approximately as Δεpn* ∝ Fa2.5 for the restricted rotating active polymer (RRAP) where the rotation of the head ABP is restricted and Δεpn* ∝ Fa1.7 for the freely rotating active polymer (FRAP) where the ABP rotates freely. Meanwhile, the conformation of the adsorbed polymer, such as adsorbed trains on NP and the tail near the ABP, are also dependent on Fa. When the tail near the ABP is short, the adsorption is significantly affected by the active force. However, when the tail is long, the whole polymer can be viewed as a long tail stretched by the active force and unperturbed adsorption monomers. Simulation results show that the active force has a direct and significant effect on εpn* and the structure of the adsorbed active polymers.
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Affiliation(s)
- Yi-Fan Shen
- School of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Han-Xian Hu
- School of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Meng-Bo Luo
- School of Physics, Zhejiang University, Hangzhou 310027, China.
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13
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Najma B, Wei WS, Baskaran A, Foster PJ, Duclos G. Microscopic interactions control a structural transition in active mixtures of microtubules and molecular motors. Proc Natl Acad Sci U S A 2024; 121:e2300174121. [PMID: 38175870 PMCID: PMC10786313 DOI: 10.1073/pnas.2300174121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 10/07/2023] [Indexed: 01/06/2024] Open
Abstract
Microtubules and molecular motors are essential components of the cellular cytoskeleton, driving fundamental processes in vivo, including chromosome segregation and cargo transport. When reconstituted in vitro, these cytoskeletal proteins serve as energy-consuming building blocks to study the self-organization of active matter. Cytoskeletal active gels display rich emergent dynamics, including extensile flows, locally contractile asters, and bulk contraction. However, it is unclear how the protein-protein interaction kinetics set their contractile or extensile nature. Here, we explore the origin of the transition from extensile bundles to contractile asters in a minimal reconstituted system composed of stabilized microtubules, depletant, adenosine 5'-triphosphate (ATP), and clusters of kinesin-1 motors. We show that the microtubule-binding and unbinding kinetics of highly processive motor clusters set their ability to end-accumulate, which can drive polarity sorting of the microtubules and aster formation. We further demonstrate that the microscopic time scale of end-accumulation sets the emergent time scale of aster formation. Finally, we show that biochemical regulation is insufficient to fully explain the transition as generic aligning interactions through depletion, cross-linking, or excluded volume interactions can drive bundle formation despite end-accumulating motors. The extensile-to-contractile transition is well captured by a simple self-assembly model where nematic and polar aligning interactions compete to form either bundles or asters. Starting from a five-dimensional organization phase space, we identify a single control parameter given by the ratio of the different component concentrations that dictates the material-scale organization. Overall, this work shows that the interplay of biochemical and mechanical tuning at the microscopic level controls the robust self-organization of active cytoskeletal materials.
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Affiliation(s)
- Bibi Najma
- Department of Physics, Brandeis University, Waltham, MA02453
| | - Wei-Shao Wei
- Department of Physics, Brandeis University, Waltham, MA02453
| | - Aparna Baskaran
- Department of Physics, Brandeis University, Waltham, MA02453
| | - Peter J. Foster
- Department of Physics, Brandeis University, Waltham, MA02453
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14
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Scrofani J, Ruhnow F, Chew WX, Normanno D, Nedelec F, Surrey T, Vernos I. Branched microtubule nucleation and dynein transport organize RanGTP asters in Xenopus laevis egg extract. Mol Biol Cell 2024; 35:ar12. [PMID: 37991893 PMCID: PMC10881172 DOI: 10.1091/mbc.e23-10-0407] [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: 10/24/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/24/2023] Open
Abstract
Chromosome segregation relies on the correct assembly of a bipolar spindle. Spindle pole self-organization requires dynein-dependent microtubule (MT) transport along other MTs. However, during M-phase RanGTP triggers MT nucleation and branching generating polarized arrays with nonastral organization in which MT minus ends are linked to the sides of other MTs. This raises the question of how branched-MT nucleation and dynein-mediated transport cooperate to organize the spindle poles. Here, we used RanGTP-dependent MT aster formation in Xenopus laevis (X. laevis) egg extract to study the interplay between these two seemingly conflicting organizing principles. Using temporally controlled perturbations of MT nucleation and dynein activity, we found that branched MTs are not static but instead dynamically redistribute over time as poles self-organize. Our experimental data together with computer simulations suggest a model where dynein together with dynactin and NuMA directly pulls and move branched MT minus ends toward other MT minus ends.
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Affiliation(s)
- Jacopo Scrofani
- Quantitative Cell Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Felix Ruhnow
- Quantitative Cell Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Wei-Xiang Chew
- Quantitative Cell Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Davide Normanno
- Quantitative Cell Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Francois Nedelec
- Sainsbury Laboratory, Cambridge University, Bateman street, CB2 1LR Cambridge, UK
| | - Thomas Surrey
- Quantitative Cell Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
- Institución Catalana de Investigación y Estudios Avanzados (ICREA), Pg. Lluis Companys 23, 08010 Barcelona, Spain
| | - Isabelle Vernos
- Quantitative Cell Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
- Institución Catalana de Investigación y Estudios Avanzados (ICREA), Pg. Lluis Companys 23, 08010 Barcelona, Spain
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15
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Dedenon M, Dessalles CA, Guillamat P, Roux A, Kruse K, Blanch-Mercader C. Density-Polarity Coupling in Confined Active Polar Films: Asters, Spirals, and Biphasic Orientational Phases. PHYSICAL REVIEW LETTERS 2023; 131:268301. [PMID: 38215373 DOI: 10.1103/physrevlett.131.268301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/06/2023] [Accepted: 11/27/2023] [Indexed: 01/14/2024]
Abstract
Topological defects in active polar fluids can organize spontaneous flows and influence macroscopic density patterns. Both of them play an important role during animal development. Yet the influence of density on active flows is poorly understood. Motivated by experiments on cell monolayers confined to disks, we study the coupling between density and polar order for a compressible active polar fluid in the presence of a +1 topological defect. As in the experiments, we find a density-controlled spiral-to-aster transition. In addition, biphasic orientational phases emerge as a generic outcome of such coupling. Our results highlight the importance of density gradients as a potential mechanism for controlling flow and orientational patterns in biological systems.
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Affiliation(s)
- Mathieu Dedenon
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
- Department of Theoretical Physics, University of Geneva, 1211 Geneva, Switzerland
| | - Claire A Dessalles
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Pau Guillamat
- Institute for Bioengineering of Catalonia, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - 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
| | - Carles Blanch-Mercader
- Laboratoire Physico-Chimie Curie, CNRS UMR168, Institut Curie, Université PSL, Sorbonne Université, 75005, Paris, France
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16
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Chen J, Wang H, Long F, Bai S, Wang Y. Dynamic supramolecular hydrogels mediated by chemical reactions. Chem Commun (Camb) 2023; 59:14236-14248. [PMID: 37964743 DOI: 10.1039/d3cc04353c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Supramolecular self-assembly in a biological system is usually dominated by sophisticated metabolic processes (chemical reactions) such as catalysis of enzymes and consumption of high energy chemicals, leading to groups of biomolecules with unique dynamics and functions in an aqueous environment. In recent years, increasing efforts have been made to couple chemical reactions to molecular self-assembly, with the aim of creating supramolecular materials with lifelike properties and functions. In this feature article, after summarising the work of chemical reaction mediated supramolecular hydrogels, we first focus on a typical example where dynamic self-assembly of molecular hydrogels is activated by in situ formation of a hydrazone bond in water. We discuss how the formation of the hydrazone-based supramolecular hydrogels can be controlled in time and space. After that, we describe transient assembly of supramolecular hydrogels powered by out-of-equilibrium chemical reaction networks regulated by chemical fuels, which show unique properties such as finite lifetime, dynamic structures, and regenerative capabilities. Finally, we provide a perspective on the future investigations that need to be done urgently, which range from fundamental research to real-life applications of dynamic supramolecular hydrogels.
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Affiliation(s)
- Jingjing Chen
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China.
| | - Hucheng Wang
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China.
| | - Feng Long
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China.
| | - Shengyu Bai
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China.
| | - Yiming Wang
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China.
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17
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Venkatareddy N, Mandal J, Maiti PK. Effect of confinement and topology: 2-TIPS vs. MIPS. SOFT MATTER 2023; 19:8561-8576. [PMID: 37905347 DOI: 10.1039/d3sm00796k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
2-TIPS (two temperature induced phase separation) refers to the phase separation phenomenon observed in mixtures of active and passive particles which are modelled using scalar activity. The active particles are connected to a thermostat at high temperature while the passive particles are connected to the thermostat at low temperature and the relative temperature difference between "hot" and "cold" particles is taken as the measure of the activity χ of the non-equilibrium system. The study of such binary mixtures of hot and cold particles under various kinds of confinement is an important problem in many physical and biological processes. The nature and extent of phase separation are heavily influenced by the geometry of confinement, activity, and density of the non-equilibrium binary mixture. Investigating such 3D binary mixtures confined by parallel walls, we observe that the active and passive particles phase separate, but the extent of phase separation is reduced compared to bulk phase separation at high densities and enhanced at low densities. However, when the binary mixture of active and passive particles is confined inside a spherical cavity, the phase separation is radial for small radii of the confining sphere and the extent of phase separation is higher compared to their bulk counterparts. Confinement leads to interesting properties in the passive (cold) region like enhanced layering and high compression in the direction parallel to the confining wall. In 2D, both the bulk and confined systems of the binary mixture show a significant decrement in the extent of phase separation at higher densities. This observation is attributed to the trapping of active particles inside the passive cluster, which increases with density. Thus the 2D systems show structures more akin to dense-dilute phase co-existence, which is observed in motility induced phase separation in 2D active systems. The binary mixture constrained on the spherical surface also shows similar phase co-existence. Our analyses reveal that the coexistent densities observed in 2-TIPS on the spherical surface agree with the findings of previous studies on MIPS in active systems on a sphere.
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Affiliation(s)
- Nayana Venkatareddy
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Jaydeep Mandal
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Prabal K Maiti
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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18
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Panda A, Winkler RG, Singh SP. Characteristic features of self-avoiding active Brownian polymers under linear shear flow. SOFT MATTER 2023; 19:8577-8586. [PMID: 37905462 DOI: 10.1039/d3sm01334k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
We present Brownian dynamics simulation results of a flexible linear polymer with excluded-volume interactions under shear flow in the presence of active noise. The active noise strongly affects the polymer's conformational and dynamical properties, such as the stretching in the flow direction and compression in the gradient direction, shear-induced alignment, and shear viscosity. In the asymptotic limit of large activities and shear rates, the power-law scaling exponents of these quantities differ significantly from those of passive polymers. The chain's shear-induced stretching at a given shear rate is reduced by active noise, and it displays a non-monotonic behavior, where an initial polymer compression is followed by its stretching with increasing active force. The compression of the polymer in the gradient direction follows the relation ∼WiPe-3/4 as a function of the activity-dependent Weissenberg number WiPe, which differs from the scaling observed in passive systems ∼WiPe-1/2. The flow-induced alignment at large Péclet numbers Pe ≫ 1, where Pe is the Péclet number, and large shear rates WiPe ≫ 1 displays the scaling behavior WiPe-1/2, with an exponent differing from the passive value -1/3. Furthermore, the polymer's zero-shear viscosity displays a non-monotonic behavior, decreasing in an intermediate activity regime due to excluded-volume interactions and increasing again for large Pe. Shear thinning appears with increasing Weissenberg number with the power-laws WiPe-1/2 and WiPe-3/4 for passive and active polymers, respectively. In addition, our simulation results are compared with the results of an analytical approach, which predicts quantitatively similar behaviors for the various aforementioned physical quantities.
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Affiliation(s)
- Arindam Panda
- Department of Physics, Indian Institute of Science Education and Research, Bhopal 462 066, Madhya Pradesh, India.
| | - Roland G Winkler
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, 52428 Jülich, Germany.
| | - Sunil P Singh
- Department of Physics, Indian Institute of Science Education and Research, Bhopal 462 066, Madhya Pradesh, India.
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19
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Lin G, Han Z, Shee A, Huepe C. Noise-Induced Quenched Disorder in Dense Active Systems. PHYSICAL REVIEW LETTERS 2023; 131:168301. [PMID: 37925685 DOI: 10.1103/physrevlett.131.168301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/15/2023] [Indexed: 11/07/2023]
Abstract
We report and characterize the emergence of a noise-induced state of quenched disorder in a generic model describing a dense sheet of active polar disks. In this state, self-propelled disks become jammed with random orientations, only displaying small fluctuations about their mean positions and headings. The quenched disorder phase appears at intermediate noise levels, between moving polar order and standard dynamic disorder. We show that it results from retrograde forces produced by angular fluctuations with Ornstein-Uhlenbeck dynamics, compute its critical noise, and argue that it could emerge in a variety of systems.
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Affiliation(s)
- Guozheng Lin
- School of Systems Science, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Zhangang Han
- School of Systems Science, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Amir Shee
- Northwestern Institute on Complex Systems and ESAM, Northwestern University, Evanston, Illinois 60208, USA
| | - Cristián Huepe
- School of Systems Science, Beijing Normal University, Beijing 100875, People's Republic of China
- Northwestern Institute on Complex Systems and ESAM, Northwestern University, Evanston, Illinois 60208, USA
- CHuepe Labs, 2713 West August Boulevard No. 1, Chicago, Illinois 60622, USA
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20
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Deblais A, Prathyusha KR, Sinaasappel R, Tuazon H, Tiwari I, Patil VP, Bhamla MS. Worm blobs as entangled living polymers: from topological active matter to flexible soft robot collectives. SOFT MATTER 2023; 19:7057-7069. [PMID: 37706563 PMCID: PMC10523214 DOI: 10.1039/d3sm00542a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023]
Abstract
Recently, the study of long, slender living worms has gained attention due to their unique ability to form highly entangled physical structures, exhibiting emergent behaviors. These organisms can assemble into an active three-dimensional soft entity referred to as the "blob", which exhibits both solid-like and liquid-like properties. This blob can respond to external stimuli such as light, to move or change shape. In this perspective article, we acknowledge the extensive and rich history of polymer physics, while illustrating how these living worms provide a fascinating experimental platform for investigating the physics of active, polymer-like entities. The combination of activity, long aspect ratio, and entanglement in these worms gives rise to a diverse range of emergent behaviors. By understanding the intricate dynamics of the worm blob, we could potentially stimulate further research into the behavior of entangled active polymers, and guide the advancement of synthetic topological active matter and bioinspired tangling soft robot collectives.
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Affiliation(s)
- Antoine Deblais
- van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - K R Prathyusha
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Rosa Sinaasappel
- van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - Harry Tuazon
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Ishant Tiwari
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Vishal P Patil
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - M Saad Bhamla
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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21
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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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22
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Singh JP, Mondal PS, Semwal V, Mishra S. Current reversal in polar flock at order-disorder interface. Phys Rev E 2023; 108:034608. [PMID: 37849122 DOI: 10.1103/physreve.108.034608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 09/07/2023] [Indexed: 10/19/2023]
Abstract
We studied a system of polar self-propelled particles (SPPs) on a thin rectangular channel designed into three regions of order-disorder-order. The division of the three regions is made on the basis of the noise SPPs experience in the respective regions. The noise in the two wide regions is chosen lower than the critical noise of order-disorder transition and noise in the middle region or interface is higher than the critical noise. This makes the geometry of the system analogous to the Josephson junction (JJ) in solid-state physics. Keeping all other parameters fixed, we study the properties of the moving SPPs in the bulk as well as along the interface for different widths of the junction. On increasing interface width, the system shows an order-to-disorder transition from coherent moving SPPs in the whole system to the interrupted current for large interface width. Surprisingly, inside the interface, we observed the current reversal for intermediate widths of the interface. Such current reversal is due to the strong randomness present inside the interface, which makes the wall of the interface reflecting. Hence, our study gives new interesting collective properties of SPPs at the interface which can be useful to design switching devices using active agents.
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Affiliation(s)
- Jay Prakash Singh
- Indian Institute of Technology (BHU), Varanasi 221005, India
- Israel Institute of Technology Technion, Haifa 3200003, Israel
| | | | - Vivek Semwal
- Indian Institute of Technology (BHU), Varanasi 221005, India
| | - Shradha Mishra
- Indian Institute of Technology (BHU), Varanasi 221005, India
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23
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Hembrow J, Deeks MJ, Richards DM. Automatic extraction of actin networks in plants. PLoS Comput Biol 2023; 19:e1011407. [PMID: 37647341 PMCID: PMC10497154 DOI: 10.1371/journal.pcbi.1011407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 09/12/2023] [Accepted: 08/01/2023] [Indexed: 09/01/2023] Open
Abstract
The actin cytoskeleton is essential in eukaryotes, not least in the plant kingdom where it plays key roles in cell expansion, cell division, environmental responses and pathogen defence. Yet, the precise structure-function relationships of properties of the actin network in plants are still to be unravelled, including details of how the network configuration depends upon cell type, tissue type and developmental stage. Part of the problem lies in the difficulty of extracting high-quality, quantitative measures of actin network features from microscopy data. To address this problem, we have developed DRAGoN, a novel image analysis algorithm that can automatically extract the actin network across a range of cell types, providing seventeen different quantitative measures that describe the network at a local level. Using this algorithm, we then studied a number of cases in Arabidopsis thaliana, including several different tissues, a variety of actin-affected mutants, and cells responding to powdery mildew. In many cases we found statistically-significant differences in actin network properties. In addition to these results, our algorithm is designed to be easily adaptable to other tissues, mutants and plants, and so will be a valuable asset for the study and future biological engineering of the actin cytoskeleton in globally-important crops.
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Affiliation(s)
- Jordan Hembrow
- Living Systems Institute and Department of Physics and Astronomy, University of Exeter, Exeter, United Kingdom
| | - Michael J. Deeks
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - David M. Richards
- Living Systems Institute and Department of Physics and Astronomy, University of Exeter, Exeter, United Kingdom
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24
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Vats A, Yadav PK, Banerjee V, Puri S. Symbiotic dynamics in living liquid crystals. Phys Rev E 2023; 108:024701. [PMID: 37723723 DOI: 10.1103/physreve.108.024701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/22/2023] [Indexed: 09/20/2023]
Abstract
An amalgam of nematic liquid crystals and active matter, referred to as living liquid crystals, is a promising self-healing material with futuristic applications for targeted delivery of information and microcargo. We provide a phenomenological model to study the symbiotic pattern dynamics in this contemporary system using the Toner-Tu model for active matter (AM), the Landau-de Gennes free energy for liquid crystals (LCs), and an experimentally motivated coupling term that favours coalignment of the active and nematic components. Our extensive theoretical studies unfold two novel steady states, chimeras and solitons, with sharp regions of distinct orientational order that sweep through the coupled system in synchrony. The induced dynamics in the passive nematic is unprecedented. We show that the symbiotic dynamics of the AM and LC components can be exploited to induce and manipulate order in an otherwise disordered system.
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Affiliation(s)
- Aditya Vats
- Department of Physics, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Pradeep Kumar Yadav
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - Varsha Banerjee
- Department of Physics, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Sanjay Puri
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi-110067, India
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25
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Sahu S, Chauhan P, Lumen E, Moody K, Peddireddy K, Mani N, Subramanian R, Robertson-Anderson R, Wolfe AJ, Ross JL. Interplay of self-organization of microtubule asters and crosslinking protein condensates. PNAS NEXUS 2023; 2:pgad231. [PMID: 37497046 PMCID: PMC10367440 DOI: 10.1093/pnasnexus/pgad231] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/28/2023]
Abstract
The cytoskeleton is a major focus of physical studies to understand organization inside cells given its primary role in cell motility, cell division, and cell mechanics. Recently, protein condensation has been shown to be another major intracellular organizational strategy. Here, we report that the microtubule crosslinking proteins, MAP65-1 and PRC1, can form phase separated condensates at physiological salt and temperature without additional crowding agents in vitro. The size of the droplets depends on the concentration of protein. MAP65 condensates are liquid at first and can gelate over time. We show that these condensates can nucleate and grow microtubule bundles that form asters, regardless of the viscoelasticity of the condensate. The droplet size directly controls the number of projections in the microtubule asters, demonstrating that the MAP65 concentration can control the organization of microtubules. When gel-like droplets nucleate and grow asters from a shell of tubulin at the surface, the microtubules are able to re-fluidize the MAP65 condensate, returning the MAP65 molecules to solution. This work implies that there is an interplay between condensate formation from microtubule-associated proteins, microtubule organization, and condensate dissolution that could be important for the dynamics of intracellular organization.
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Affiliation(s)
- Sumon Sahu
- Physics Department, Syracuse University, Syracuse, NY 13244, USA
- Department of Physics, New York University, New York, NY 10003, USA
| | - Prashali Chauhan
- Physics Department, Syracuse University, Syracuse, NY 13244, USA
- The Bioinspired Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Ellie Lumen
- Ichor Life Sciences, Inc., 2561 US Route 11, LaFayette, NY 13084, USA
| | - Kelsey Moody
- The Bioinspired Institute, Syracuse University, Syracuse, NY 13244, USA
- Ichor Life Sciences, Inc., 2561 US Route 11, LaFayette, NY 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | | | - Nandini Mani
- Massachusetts General Hospital, Boston, MA 02115, USA
| | | | | | - Aaron J Wolfe
- The Bioinspired Institute, Syracuse University, Syracuse, NY 13244, USA
- Ichor Life Sciences, Inc., 2561 US Route 11, LaFayette, NY 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Jennifer L Ross
- Physics Department, Syracuse University, Syracuse, NY 13244, USA
- The Bioinspired Institute, Syracuse University, Syracuse, NY 13244, USA
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26
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Stam S, Gardel ML, Weirich KL. Direct detection of deformation modes on varying length scales in active biopolymer networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.15.540780. [PMID: 37292666 PMCID: PMC10245561 DOI: 10.1101/2023.05.15.540780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Correlated flows and forces that emerge from active matter orchestrate complex processes such as shape regulation and deformations in biological cells and tissues. The active materials central to cellular mechanics are cytoskeletal networks, where molecular motor activity drives deformations and remodeling. Here, we investigate deformation modes in actin networks driven by the molecular motor myosin II through quantitative fluorescence microscopy. We examine the deformation anisotropy at different length scales in networks of entangled, cross-linked, and bundled actin. In sparsely cross-linked networks, we find myosin-dependent biaxial buckling modes across length scales. In cross-linked bundled networks, uniaxial contraction is predominate on long length scales, while the uniaxial or biaxial nature of the deformation depends on bundle microstructure at shorter length scales. The anisotropy of deformations may provide insight to regulation of collective behavior in a variety of active materials.
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Affiliation(s)
- Samantha Stam
- Biophysical Sciences Graduate Program, University of Chicago, Chicago, IL 60637
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112
| | - Margaret L Gardel
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637
- James Franck Institute, University of Chicago, Chicago, IL 60637
- Department of Physics, University of Chicago, Chicago, IL 60637
| | - Kimberly L Weirich
- James Franck Institute, University of Chicago, Chicago, IL 60637
- Department of Materials Science & Engineering, Clemson University, Clemson, SC 29634
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27
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Lemma LM, Varghese M, Ross TD, Thomson M, Baskaran A, Dogic Z. Spatio-temporal patterning of extensile active stresses in microtubule-based active fluids. PNAS NEXUS 2023; 2:pgad130. [PMID: 37168671 PMCID: PMC10165807 DOI: 10.1093/pnasnexus/pgad130] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 02/27/2023] [Accepted: 04/03/2023] [Indexed: 05/13/2023]
Abstract
Microtubule-based active fluids exhibit turbulent-like autonomous flows, which are driven by the molecular motor powered motion of filamentous constituents. Controlling active stresses in space and time is an essential prerequisite for controlling the intrinsically chaotic dynamics of extensile active fluids. We design single-headed kinesin molecular motors that exhibit optically enhanced clustering and thus enable precise and repeatable spatial and temporal control of extensile active stresses. Such motors enable rapid, reversible switching between flowing and quiescent states. In turn, spatio-temporal patterning of the active stress controls the evolution of the ubiquitous bend instability of extensile active fluids and determines its critical length dependence. Combining optically controlled clusters with conventional kinesin motors enables one-time switching from contractile to extensile active stresses. These results open a path towards real-time control of the autonomous flows generated by active fluids.
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Affiliation(s)
- Linnea M Lemma
- Department of Physics, Brandeis University, 415 South St., Waltham, 02453 MA, USA
- Department of Physics, University of California, Santa Barbara, 93106 CA, USA
| | - Minu Varghese
- Department of Physics, Brandeis University, 415 South St., Waltham, 02453 MA, USA
| | - Tyler D Ross
- Department of Computing and Mathematical Sciences, California Institute of Technology, 1200 E California Blvd. Pasadena, 91125 CA, USA
| | - Matt Thomson
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Blvd., Pasadena, 91125 CA, USA
| | - Aparna Baskaran
- Department of Physics, Brandeis University, 415 South St., Waltham, 02453 MA, USA
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28
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Savoie W, Tuazon H, Tiwari I, Bhamla MS, Goldman DI. Amorphous entangled active matter. SOFT MATTER 2023; 19:1952-1965. [PMID: 36809295 PMCID: PMC11164134 DOI: 10.1039/d2sm01573k] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The design of amorphous entangled systems, specifically from soft and active materials, has the potential to open exciting new classes of active, shape-shifting, and task-capable 'smart' materials. However, the global emergent mechanics that arise from the local interactions of individual particles are not well understood. In this study, we examine the emergent properties of amorphous entangled systems in an in silico collection of u-shaped particles ("smarticles") and in living entangled aggregate of worm blobs (L. variegatus). In simulations, we examine how material properties change for a collective composed of smarticles as they undergo different forcing protocols. We compare three methods of controlling entanglement in the collective: external oscillations of the ensemble, sudden shape-changes of all individuals, and sustained internal oscillations of all individuals. We find that large-amplitude changes of the particle's shape using the shape-change procedure produce the largest average number of entanglements, with respect to the aspect ratio (l/w), thus improving the tensile strength of the collective. We demonstrate applications of these simulations by showing how the individual worm activity in a blob can be controlled through the ambient dissolved oxygen in water, leading to complex emergent properties of the living entangled collective, such as solid-like entanglement and tumbling. Our work reveals principles by which future shape-modulating, potentially soft robotic systems may dynamically alter their material properties, advancing our understanding of living entangled materials, while inspiring new classes of synthetic emergent super-materials.
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Affiliation(s)
- William Savoie
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30318, USA
| | - Harry Tuazon
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30318, USA.
| | - Ishant Tiwari
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30318, USA.
| | - M Saad Bhamla
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30318, USA.
| | - Daniel I Goldman
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30318, USA
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29
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Peil A, Zhan P, Duan X, Krahne R, Garoli D, M Liz-Marzán L, Liu N. Transformable Plasmonic Helix with Swinging Gold Nanoparticles. Angew Chem Int Ed Engl 2023; 62:e202213992. [PMID: 36423337 DOI: 10.1002/anie.202213992] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/20/2022] [Accepted: 11/24/2022] [Indexed: 11/25/2022]
Abstract
Control over multiple optical elements that can be dynamically rearranged to yield substantial three-dimensional structural transformations is of great importance to realize reconfigurable plasmonic nanoarchitectures with sensitive and distinct optical feedback. In this work, we demonstrate a transformable plasmonic helix system, in which multiple gold nanoparticles (AuNPs) can be directly transported by DNA swingarms to target positions without undergoing consecutive stepwise movements. The swingarms allow for programmable AuNP translocations in large leaps within plasmonic nanoarchitectures, giving rise to tailored circular dichroism spectra. Our work provides an instructive bottom-up solution to building complex dynamic plasmonic systems, which can exhibit prominent optical responses through cooperative rearrangements of the constituent optical elements with high fidelity and programmability.
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Affiliation(s)
- Andreas Peil
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany.,Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569, Stuttgart, Germany
| | - Pengfei Zhan
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany.,Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569, Stuttgart, Germany
| | - Xiaoyang Duan
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany.,Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569, Stuttgart, Germany
| | - Roman Krahne
- Instituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Denis Garoli
- Instituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Luis M Liz-Marzán
- CIC BiomaGUNE, Paseo Miramón 182, 20014, Donostia/San Sebastián, Spain.,Biomedical Networking Center, Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Paseo Miramón 182, 20014, Donostia/San Sebastián, Spain.,Ikerbasque, Basque Foundation for Science, 43009, Bilbao, Spain
| | - Na Liu
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany.,Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569, Stuttgart, Germany
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30
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Gires PY, Thampi M, Krauss SW, Weiss M. Exploring generic principles of compartmentalization in a developmental in vitro model. Development 2023; 150:286676. [PMID: 36647820 DOI: 10.1242/dev.200851] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023]
Abstract
Self-organization of cells into higher-order structures is key for multicellular organisms, for example via repetitive replication of template-like founder cells or syncytial energids. Yet, very similar spatial arrangements of cell-like compartments ('protocells') are also seen in a minimal model system of Xenopus egg extracts in the absence of template structures and chromatin, with dynamic microtubule assemblies driving the self-organization process. Quantifying geometrical features over time, we show here that protocell patterns are highly organized with a spatial arrangement and coarsening dynamics similar to that of two-dimensional foams but without the long-range ordering expected for hexagonal patterns. These features remain invariant when enforcing smaller protocells by adding taxol, i.e. patterns are dominated by a single, microtubule-derived length scale. Comparing our data to generic models, we conclude that protocell patterns emerge by simultaneous formation of randomly assembling protocells that grow at a uniform rate towards a frustrated arrangement before fusion of adjacent protocells eventually drives coarsening. The similarity of protocell patterns to arrays of energids and cells in developing organisms, but also to epithelial monolayers, suggests generic mechanical cues to drive self-organized space compartmentalization.
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Affiliation(s)
- Pierre-Yves Gires
- Experimental Physics I, University of Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany
| | - Mithun Thampi
- Experimental Physics I, University of Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany
| | - Sebastian W Krauss
- Experimental Physics I, University of Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany
| | - Matthias Weiss
- Experimental Physics I, University of Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany
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31
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Abstract
The state of a classical point-particle system may often be specified by giving the position and momentum for each constituent particle. For non-pointlike particles, the center-of-mass position may be augmented by an additional coordinate that specifies the internal state of each particle. The internal state space is typically topologically simple, in the sense that the particle's internal coordinate belongs to a suitable symmetry group. In this paper, we explore the idea of giving internal complexity to the particles, by attributing to each particle an internal state space that is represented by a point on a strange (or otherwise) attracting set. It is, of course, very well known that strange attractors arise in a variety of nonlinear dynamical systems. However, rather than considering strange attractors as emerging from complex dynamics, we may employ strange attractors to drive such dynamics. In particular, by using an attractor (strange or otherwise) to model each particle's internal state space, we present a class of matter coined "attractor-driven matter." We outline the general formalism for attractor-driven matter and explore several specific examples, some of which are reminiscent of active matter. Beyond the examples studied in this paper, our formalism for attractor-driven dynamics may be applicable more broadly, to model complex dynamical and emergent behaviors in a variety of contexts.
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Affiliation(s)
- R N Valani
- School of Mathematical Sciences, University of Adelaide, South Australia 5005, Australia
| | - D M Paganin
- School of Physics and Astronomy, Monash University, Victoria 3800, Australia
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32
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Ji F, Wu Y, Pumera M, Zhang L. Collective Behaviors of Active Matter Learning from Natural Taxes Across Scales. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2203959. [PMID: 35986637 DOI: 10.1002/adma.202203959] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/23/2022] [Indexed: 06/15/2023]
Abstract
Taxis orientation is common in microorganisms, and it provides feasible strategies to operate active colloids as small-scale robots. Collective taxes involve numerous units that collectively perform taxis motion, whereby the collective cooperation between individuals enables the group to perform efficiently, adaptively, and robustly. Hence, analyzing and designing collectives is crucial for developing and advancing microswarm toward practical or clinical applications. In this review, natural taxis behaviors are categorized and synthetic microrobotic collectives are discussed as bio-inspired realizations, aiming at closing the gap between taxis strategies of living creatures and those of functional active microswarms. As collective behaviors emerge within a group, the global taxis to external stimuli guides the group to conduct overall tasks, whereas the local taxis between individuals induces synchronization and global patterns. By encoding the local orientations and programming the global stimuli, various paradigms can be introduced for coordinating and controlling such collective microrobots, from the viewpoints of fundamental science and practical applications. Therefore, by discussing the key points and difficulties associated with collective taxes of different paradigms, this review potentially offers insights into mimicking natural collective behaviors and constructing intelligent microrobotic systems for on-demand control and preassigned tasks.
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Affiliation(s)
- Fengtong Ji
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, 999077, China
| | - Yilin Wu
- Department of Physics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, 999077, China
| | - Martin Pumera
- Faculty of Electrical Engineering and Computer Science, VSB - Technical University of Ostrava, 17. listopadu 2172/15, Ostrava, 70800, Czech Republic
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Li Zhang
- Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, 999077, China
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33
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Chew WX, Henkin G, Nédélec F, Surrey T. Effects of microtubule length and crowding on active microtubule network organization. iScience 2023; 26:106063. [PMID: 36852161 PMCID: PMC9958361 DOI: 10.1016/j.isci.2023.106063] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/12/2022] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
Active filament networks can organize into various dynamic architectures driven by cross-linking motors. Densities and kinetic properties of motors and microtubules have been shown previously to determine active microtubule network self-organization, but the effects of other control parameters are less understood. Using computer simulations, we study here how microtubule lengths and crowding effects determine active network architecture and dynamics. We find that attractive interactions mimicking crowding effects or long microtubules both promote the formation of extensile nematic networks instead of asters. When microtubules are very long and the network is highly connected, a new isotropically motile network state resembling a "gliding mesh" is predicted. Using in vitro reconstitutions, we confirm the existence of this gliding mesh experimentally. These results provide a better understanding of how active microtubule network organization can be controlled, with implications for cell biology and active materials in general.
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Affiliation(s)
- Wei-Xiang Chew
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Gil Henkin
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain
| | - François Nédélec
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK,Corresponding author
| | - Thomas Surrey
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain,ICREA, Passeig de Lluis Companys 23, 08010 Barcelona, Spain,Corresponding author
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34
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Besse M, Chaté H, Solon A. Metastability of Constant-Density Flocks. PHYSICAL REVIEW LETTERS 2022; 129:268003. [PMID: 36608197 DOI: 10.1103/physrevlett.129.268003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
We study numerically the Toner-Tu field theory where the density field is maintained constant, a limit case of "Malthusian" flocks for which the asymptotic scaling of correlation functions in the ordered phase is known exactly. While we confirm these scaling laws, we also show that such constant-density flocks are metastable to the nucleation of a specific defect configuration, and are replaced by a globally disordered phase consisting of asters surrounded by shock lines that constantly evolves and remodels itself. We demonstrate that the main source of disorder lies along shock lines, rendering this active foam fundamentally different from the corresponding equilibrium system. We thus show that in the context of active matter also, a result obtained at all orders of perturbation theory can be superseded by nonperturbative effects, calling for a different approach.
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Affiliation(s)
- Marc Besse
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, 75005 Paris, France
| | - Hugues Chaté
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, 75005 Paris, France
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- Computational Science Research Center, Beijing 100094, China
| | - Alexandre Solon
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, 75005 Paris, France
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35
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Wu S, Li JX, Lei QL. Facilitated dynamics of an active polymer in 2D crowded environments with obstacles. SOFT MATTER 2022; 18:9263-9272. [PMID: 36441607 DOI: 10.1039/d2sm00974a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Understanding the behaviors of a single active chain in complex environments is not only an interesting topic in non-equilibrium physics but also has applicative implications in biological/medical engineering. In this work, by using molecular simulations, we systematically study the dynamical and conformational behaviors of an active polymer in crowded environments, i.e., a single active chain confined in 2D space with randomly arranged obstacles. We found that the competition between the chain's activity and rigidity in the presence of obstacles leads to many interesting dynamical and conformational states, such as the diffusive expanded state, the diffusive collapsed state, and the localized collapsed state. Importantly, we found a counter-intuitive phenomenon, i.e., crowded environments facilitate the diffusion of the active polymer within a large parameter space. As the crowdedness (packing fraction of obstacles) increases, the parameter space in which crowding-enhanced diffusion occurs still remains. This abnormal dynamics is attributed to a structural reason that the obstacles prevent active chains from collapsing. Our findings capture some generic features of active polymers in complex environments and provide insights into the design of novel drug delivery systems.
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Affiliation(s)
- Song Wu
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.
| | - Jia-Xiang Li
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.
| | - Qun-Li Lei
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.
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36
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Striebel M, Brauns F, Frey E. Length Regulation Drives Self-Organization in Filament-Motor Mixtures. PHYSICAL REVIEW LETTERS 2022; 129:238102. [PMID: 36563230 DOI: 10.1103/physrevlett.129.238102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/10/2022] [Indexed: 06/17/2023]
Abstract
Cytoskeletal networks form complex intracellular structures. Here we investigate a minimal model for filament-motor mixtures in which motors act as depolymerases and thereby regulate filament length. Combining agent-based simulations and hydrodynamic equations, we show that resource-limited length regulation drives the formation of filament clusters despite the absence of mechanical interactions between filaments. Even though the orientation of individual remains fixed, collective filament orientation emerges in the clusters, aligned orthogonal to their interfaces.
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Affiliation(s)
- Moritz Striebel
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstrasse 37, D-80333 Munich, Germany
| | - Fridtjof Brauns
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstrasse 37, D-80333 Munich, Germany
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstrasse 37, D-80333 Munich, Germany
- Max Planck School Matter to Life, Hofgartenstraße 8, D-80539 Munich, Germany
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37
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Yang X, Lu H, Wu B, Wang H. Triggered Self-Sorting of Peptides to Form Higher-Order Assemblies in a Living System. ACS NANO 2022; 16:18244-18252. [PMID: 36255266 DOI: 10.1021/acsnano.2c05825] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Biological components (protein, DNA, lipid rafts, etc.) self-sort to form higher-order structures with elegant modulation by endogenous stimuli for maintaining cellular functions in living cells. However, the challenge of producing self-sorted higher-order assemblies of peptides in living systems (cells and tissues) spatiotemporally has yet to be achieved. This work reports the using of a biocompatible strategy to construct self-sorted assemblies of peptides in living cells and tumor-bearing mice. The results show that the designed peptides self-sort to form distinct nanostructures in living cancer cells using an endogenous trigger, as evidenced by confocal laser scanning microscopy and Bio-EM. Wound-healing experiments indicate that the in situ generation of self-sorted nanostructures exhibits a synergistic effect that significantly decreases the migration of cancer cells. In vivo experiments demonstrate that the designed peptides could self-sort in tumor-bearing mice and improve the tumor penetrating ability of the impenetrable component in tumor tissue. We can further program the formation of self-sorted materials through orthogonal triggers by introducing an exogenous trigger (light) and an endogenous trigger independently. Thus, this work provides a strategy to control multiple self-assembling processes in the context of the living system and provides a general strategy to construct self-sorted structures for the emergent properties of materials science.
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Affiliation(s)
- Xuejiao Yang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Westlake University; Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Honglei Lu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Westlake University; Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Bihan Wu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Westlake University; Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Huaimin Wang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Westlake University; Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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38
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Bate TE, Varney ME, Taylor EH, Dickie JH, Chueh CC, Norton MM, Wu KT. Self-mixing in microtubule-kinesin active fluid from nonuniform to uniform distribution of activity. Nat Commun 2022; 13:6573. [PMID: 36323696 PMCID: PMC9630547 DOI: 10.1038/s41467-022-34396-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Active fluids have applications in micromixing, but little is known about the mixing kinematics of systems with spatiotemporally-varying activity. To investigate, UV-activated caged ATP is used to activate controlled regions of microtubule-kinesin active fluid and the mixing process is observed with fluorescent tracers and molecular dyes. At low Péclet numbers (diffusive transport), the active-inactive interface progresses toward the inactive area in a diffusion-like manner that is described by a simple model combining diffusion with Michaelis-Menten kinetics. At high Péclet numbers (convective transport), the active-inactive interface progresses in a superdiffusion-like manner that is qualitatively captured by an active-fluid hydrodynamic model coupled to ATP transport. Results show that active fluid mixing involves complex coupling between distribution of active stress and active transport of ATP and reduces mixing time for suspended components with decreased impact of initial component distribution. This work will inform application of active fluids to promote micromixing in microfluidic devices.
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Affiliation(s)
- Teagan E Bate
- Department of Physics, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Megan E Varney
- Department of Physics, New York University, New York, NY, 10003, USA
| | - Ezra H Taylor
- Department of Physics, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Joshua H Dickie
- Department of Physics, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Chih-Che Chueh
- Department of Aeronautics and Astronautics, National Cheng Kung University, Tainan, 701, Taiwan
| | - Michael M Norton
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Kun-Ta Wu
- Department of Physics, Worcester Polytechnic Institute, Worcester, MA, 01609, USA.
- Department of Mechanical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA.
- The Martin Fisher School of Physics, Brandeis University, Waltham, MA, 02454, USA.
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39
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Spukti FF, Schnauß J. Large and stable: actin aster networks formed via entropic forces. Front Chem 2022; 10:899478. [PMID: 36118308 PMCID: PMC9481034 DOI: 10.3389/fchem.2022.899478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/13/2022] [Indexed: 12/04/2022] Open
Abstract
Biopolymer networks play a major role as part of the cytoskeleton. They provide stable structures and act as a medium for signal transport. These features encourage the application of such networks as organic computation devices. While research on this topic is not advanced yet, previous results are very promising. The protein actin in particular appears advantageous. It can be arranged to various stable structures and transmit several signals. In this study aster shaped networks were self-assembled via entropic forces by the crowding agent methyl cellulose. These networks are characterised by a regular and uniquely thick bundle structure, but have so far only been accounted in droplets of 100 μm diameter. We report now regular asters in an area of a few mm2 that could be observed even after months. Such stability outside of an organism is striking and underlines the great potential actin aster networks display.
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Affiliation(s)
| | - Jörg Schnauß
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany.,Unconventional Computing Laboratory, Department of Computer Science, University of the West of England, Bristol, United Kingdom
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40
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Perepelitsa M, Timofeyev I, Murphy P, Igoshin OA. Mean-field model for nematic alignment of self-propelled rods. Phys Rev E 2022; 106:034613. [PMID: 36266908 DOI: 10.1103/physreve.106.034613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Self-propelled rods are a facet of the field of active matter relevant to many physical systems ranging in scale from shaken granular media and bacterial alignment to the flocking dynamics of animals. In this paper we develop a model for nematic alignment of self-propelled rods interacting through binary collisions. We avoid phenomenological descriptions of rod interaction in favor of rigorously using a set of microscopic-level rules. Under the assumption that each collision results in a small change to a rod's orientation, we derive the Fokker-Planck equation for the evolution of the kinetic density function. Using analytical and numerical methods, we study the emergence of the nematic order from a homogeneous, uniform steady state of the mean-field equation. We compare the level of orientational noise needed to destabilize this nematic order and compare our results to an existing phenomenological model that does not explicitly account for the physical collisions of rods. We show the presence of an additional geometric factor in our equations reflecting a reduced collision rate between nearly aligned rods that reduces the level of noise at which nematic order is destroyed, suggesting that alignment that depends on purely physical collisions is less robust.
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Affiliation(s)
| | - Ilya Timofeyev
- Department of Mathematics, University of Houston, Texas 77204, USA
| | - Patrick Murphy
- Department of Bioengineering, Rice University, Houston, Texas 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| | - Oleg A Igoshin
- Department of Bioengineering, Rice University, Houston, Texas 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
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41
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Henkin G, Chew WX, Nédélec F, Surrey T. Cross-linker design determines microtubule network organization by opposing motors. Proc Natl Acad Sci U S A 2022; 119:e2206398119. [PMID: 35960844 PMCID: PMC9388136 DOI: 10.1073/pnas.2206398119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/03/2022] [Indexed: 12/02/2022] Open
Abstract
During cell division, cross-linking motors determine the architecture of the spindle, a dynamic microtubule network that segregates the chromosomes in eukaryotes. It is unclear how motors with opposite directionality coordinate to drive both contractile and extensile behaviors in the spindle. Particularly, the impact of different cross-linker designs on network self-organization is not understood, limiting our understanding of self-organizing structures in cells but also our ability to engineer new active materials. Here, we use experiment and theory to examine active microtubule networks driven by mixtures of motors with opposite directionality and different cross-linker design. We find that although the kinesin-14 HSET causes network contraction when dominant, it can also assist the opposing kinesin-5 KIF11 to generate extensile networks. This bifunctionality results from HSET's asymmetric design, distinct from symmetric KIF11. These findings expand the set of rules underlying patterning of active microtubule assemblies and allow a better understanding of motor cooperation in the spindle.
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Affiliation(s)
- Gil Henkin
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Wei-Xiang Chew
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - François Nédélec
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Thomas Surrey
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010 Spain
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42
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Nakamoto M, Kitano S, Matsusaki M. Biomacromolecule-Fueled Transient Volume Phase Transition of a Hydrogel. Angew Chem Int Ed Engl 2022; 61:e202205125. [PMID: 35441476 DOI: 10.1002/anie.202205125] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Indexed: 12/15/2022]
Abstract
A metabolic cycle-inspired hydrogel which exhibits the biomacromolecule-fueled transient volume phase transition is reported. This hydrogel has the affinity and digestive capacity for a fuel α-poly-L-lysine by incorporating acrylic acid and trypsin. The hydrogel captured fuel and transiently shrank owing to the construction of electrostatic cross-linkages. This process was inherently connected with the digestion of these cross-linkages and the release of oligo-lysine as waste, which induced the reswelling of the hydrogel at equilibrium. The transient volume change of the hydrogel realized the fuel-stimulated transient release of a payload. This study provides a strategy for engineering materials with biomacromolecule-fueled dynamic functions under the out-of-equilibrium condition.
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Affiliation(s)
- Masahiko Nakamoto
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Shiro Kitano
- Joint Research Laboratory (TOPPAN) for Advanced Cell Regulatory Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Michiya Matsusaki
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan.,Joint Research Laboratory (TOPPAN) for Advanced Cell Regulatory Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
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43
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Abstract
Active cytoskeletal materials in vitro demonstrate self-organizing properties similar to those observed in their counterparts in cells. However, the search to emulate phenomena observed in living matter has fallen short of producing a cytoskeletal network that would be structurally stable yet possess adaptive plasticity. Here, we address this challenge by combining cytoskeletal polymers in a composite where self-assembling microtubules and actin filaments collectively self-organize due to the activity of microtubule-percolating molecular motors. We demonstrate that microtubules spatially organize actin filaments that in turn guide microtubules. The two networks align in an ordered fashion using this feedback loop. In this composite, actin filaments can act as structural memory and, depending on the concentration of the components, microtubules either write this memory or get guided by it. The system is sensitive to external stimuli, suggesting possible autoregulatory behavior in changing mechanochemical environments. We thus establish an artificial active actin-microtubule composite as a system demonstrating architectural stability and plasticity.
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44
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Xie S, Li J, Sun S, Chen W, Cheng H, Song Y, Li Y, Liu M, Zhu X, Liang X, Zhou J. TUBright: A Peptide Probe for Imaging Microtubules. Anal Chem 2022; 94:11168-11174. [PMID: 35917443 DOI: 10.1021/acs.analchem.2c01285] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In vitro assays using reconstituted microtubules have provided molecular insights into the principles of microtubule dynamics and the roles of microtubule-associated proteins. Emerging questions that further uncover the complexity in microtubule dynamics, especially those on tubulin isotypes and post-translational modifications, raise new technical challenges on how to visualize microtubules composed of tubulin purified from limited sources, primarily due to the low efficiency of the conventional tubulin labeling protocol. Here, we develop a peptide probe, termed TUBright, that labels in vitro reconstituted microtubules. TUBright, when coupled with different fluorescent dyes, provides flexible labeling of microtubules with a high signal-to-noise ratio. TUBright does not interfere with the dynamic behaviors of microtubules and microtubule-associated proteins. Therefore, TUBright is a useful tool for imaging microtubules, making it feasible to use tubulin from limited sources for answering many open questions on microtubule dynamics.
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Affiliation(s)
- Songbo Xie
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Jingrui Li
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Shuang Sun
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Wei Chen
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Center for Life Science, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haisu Cheng
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Center for Life Science, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yinlong Song
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Center for Life Science, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yuyang Li
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Min Liu
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Xueliang Zhu
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xin Liang
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Center for Life Science, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jun Zhou
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250014, China.,State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin 300071, China
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45
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Lemma B, Mitchell NP, Subramanian R, Needleman DJ, Dogic Z. Active Microphase Separation in Mixtures of Microtubules and Tip-Accumulating Molecular Motors. PHYSICAL REVIEW. X 2022; 12:031006. [PMID: 36643940 PMCID: PMC9835929 DOI: 10.1103/physrevx.12.031006] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Mixtures of filaments and molecular motors form active materials with diverse dynamical behaviors that vary based on their constituents' molecular properties. To develop a multiscale of these materials, we map the nonequilibrium phase diagram of microtubules and tip-accumulating kinesin-4 molecular motors. We find that kinesin-4 can drive either global contractions or turbulentlike extensile dynamics, depending on the concentrations of both microtubules and a bundling agent. We also observe a range of spatially heterogeneous nonequilibrium phases, including finite-sized radial asters, 1D wormlike chains, extended 2D bilayers, and system-spanning 3D active foams. Finally, we describe intricate kinetic pathways that yield microphase separated structures and arise from the inherent frustration between the orientational order of filamentous microtubules and the positional order of tip-accumulating molecular motors. Our work reveals a range of novel active states. It also shows that the form of active stresses is not solely dictated by the properties of individual motors and filaments, but is also contingent on the constituent concentrations and spatial arrangement of motors on the filaments.
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Affiliation(s)
- Bezia Lemma
- Physics Department, Harvard University, Cambridge, Massachusetts 02138, USA
- Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
- Physics Department, University of California, Santa Barbara, California 93106, USA
| | - Noah P. Mitchell
- Physics Department, University of California, Santa Barbara, California 93106, USA
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106, USA
| | - Radhika Subramanian
- Molecular Biology Department, Massachusetts General Hospital Boston, Massachusetts 02114, USA
- Genetics Department, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Daniel J. Needleman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
- Molecular and Cellular Biology Department, Harvard University, Cambridge, Massachusetts 02138, USA
- Center for Computational Biology, Flatiron Institute, New York, New York 10010, USA
| | - Zvonimir Dogic
- Physics Department, Brandeis University, Waltham, Massachusetts 02453, USA
- Physics Department, University of California, Santa Barbara, California 93106, USA
- Biomolecular Science and Engineering Department, University of California, Santa Barbara, California 93106, USA
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46
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Ansari S, Yan W, Lamson A, Shelley MJ, Glaser MA, Betterton MD. Active condensation of filaments under spatial confinement. FRONTIERS IN PHYSICS 2022; 10:897255. [PMID: 38116396 PMCID: PMC10730113 DOI: 10.3389/fphy.2022.897255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Living systems exhibit self-organization, a phenomenon that enables organisms to perform functions essential for life. The interior of living cells is a crowded environment in which the self-assembly of cytoskeletal networks is spatially constrained by membranes and organelles. Cytoskeletal filaments undergo active condensation in the presence of crosslinking motor proteins. In past studies, confinement has been shown to alter the morphology of active condensates. Here, we perform simulations to explore systems of filaments and crosslinking motors in a variety of confining geometries. We simulate spatial confinement imposed by hard spherical, cylindrical, and planar boundaries. These systems exhibit non-equilibrium condensation behavior where crosslinking motors condense a fraction of the overall filament population, leading to coexistence of vapor and condensed states. We find that the confinement lengthscale modifies the dynamics and condensate morphology. With end-pausing crosslinking motors, filaments self-organize into half asters and fully-symmetric asters under spherical confinement, polarity-sorted bilayers and bottle-brush-like states under cylindrical confinement, and flattened asters under planar confinement. The number of crosslinking motors controls the size and shape of condensates, with flattened asters becoming hollow and ring-like for larger motor number. End pausing plays a key role affecting condensate morphology: systems with end-pausing motors evolve into aster-like condensates while those with non-end-pausing crosslinking motor proteins evolve into disordered clusters and polarity-sorted bundles.
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Affiliation(s)
- Saad Ansari
- Department of Physics, University of Colorado Boulder, Colorado, USA
| | - Wen Yan
- Center for Computational Biology, Flatiron Institute, New York, USA
| | - Adam Lamson
- Center for Computational Biology, Flatiron Institute, New York, USA
| | - Michael J. Shelley
- Center for Computational Biology, Flatiron Institute, New York, USA
- Courant Institute, New York University, New York, USA
| | - Matthew A. Glaser
- Department of Physics, University of Colorado Boulder, Colorado, USA
- Center for Computational Biology, Flatiron Institute, New York, USA
| | - Meredith D. Betterton
- Department of Physics, University of Colorado Boulder, Colorado, USA
- Center for Computational Biology, Flatiron Institute, New York, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Colorado, USA
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47
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Jia H, Flommersfeld J, Heymann M, Vogel SK, Franquelim HG, Brückner DB, Eto H, Broedersz CP, Schwille P. 3D printed protein-based robotic structures actuated by molecular motor assemblies. NATURE MATERIALS 2022; 21:703-709. [PMID: 35618822 PMCID: PMC9156402 DOI: 10.1038/s41563-022-01258-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 04/13/2022] [Indexed: 06/10/2023]
Abstract
Upscaling motor protein activity to perform work in man-made devices has long been an ambitious goal in bionanotechnology. The use of hierarchical motor assemblies, as realized in sarcomeres, has so far been complicated by the challenges of arranging sufficiently high numbers of motor proteins with nanoscopic precision. Here, we describe an alternative approach based on actomyosin cortex-like force production, allowing low complexity motor arrangements in a contractile meshwork that can be coated onto soft objects and locally activated by ATP. The design is reminiscent of a motorized exoskeleton actuating protein-based robotic structures from the outside. It readily supports the connection and assembly of micro-three-dimensional printed modules into larger structures, thereby scaling up mechanical work. We provide an analytical model of force production in these systems and demonstrate the design flexibility by three-dimensional printed units performing complex mechanical tasks, such as microhands and microarms that can grasp and wave following light activation.
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Affiliation(s)
- Haiyang Jia
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Johannes Flommersfeld
- Arnold Sommerfeld Center for Theoretical Physics, Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Michael Heymann
- Max Planck Institute of Biochemistry, Martinsried, Germany
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Sven K Vogel
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - David B Brückner
- Arnold Sommerfeld Center for Theoretical Physics, Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hiromune Eto
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Chase P Broedersz
- Arnold Sommerfeld Center for Theoretical Physics, Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany.
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Martinsried, Germany.
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48
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Sarfati G, Maitra A, Voituriez R, Galas JC, Estevez-Torres A. Crosslinking and depletion determine spatial instabilities in cytoskeletal active matter. SOFT MATTER 2022; 18:3793-3800. [PMID: 35521993 DOI: 10.1039/d2sm00130f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Active gels made of cytoskeletal proteins are valuable materials with attractive non-equilibrium properties such as spatial self-organization and self-propulsion. At least four typical routes to spatial patterning have been reported to date in different types of cytoskeletal active gels: bending and buckling instabilities in extensile systems, and global and local contraction instabilities in contractile gels. Here we report the observation of these four instabilities in a single type of active gel and we show that they are controlled by two parameters: the concentrations of ATP and depletion agent. We demonstrate that as the ATP concentration decreases, the concentration of passive motors increases until the gel undergoes a gelation transition. At this point, buckling is selected against bending, while global contraction is favored over local ones. Our observations are coherent with a hydrodynamic model of a viscoelastic active gel where the filaments are crosslinked with a characteristic time that diverges as the ATP concentration decreases. Our work thus provides a unified view of spatial instabilities in cytoskeletal active matter.
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Affiliation(s)
- Guillaume Sarfati
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin, (LJP), F-75005 Paris, France.
| | - Ananyo Maitra
- Laboratoire de Physique Théorique et Modélisation, CNRS UMR 8089, CY Cergy Paris, Université, F-95302 Cergy-Pontoise Cedex, France
| | - Raphael Voituriez
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin, (LJP), F-75005 Paris, France.
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, (LPTMC), F-75005 Paris, France
| | - Jean-Christophe Galas
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin, (LJP), F-75005 Paris, France.
| | - André Estevez-Torres
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin, (LJP), F-75005 Paris, France.
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49
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Monderkamp PA, Wittmann R, Te Vrugt M, Voigt A, Wittkowski R, Löwen H. Topological fine structure of smectic grain boundaries and tetratic disclination lines within three-dimensional smectic liquid crystals. Phys Chem Chem Phys 2022; 24:15691-15704. [PMID: 35552573 DOI: 10.1039/d2cp00060a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Observing and characterizing the complex ordering phenomena of liquid crystals subjected to external constraints constitutes an ongoing challenge for chemists and physicists alike. To elucidate the delicate balance appearing when the intrinsic positional order of smectic liquid crystals comes into play, we perform Monte-Carlo simulations of rod-like particles in a range of cavities with a cylindrical symmetry. Based on recent insights into the topology of smectic orientational grain boundaries in two dimensions, we analyze the emerging three-dimensional defect structures from the perspective of tetratic symmetry. Using an appropriate three-dimensional tetratic order parameter constructed from the Steinhardt order parameters, we show that those grain boundaries can be interpreted as a pair of tetratic disclination lines that are located on the edges of the nematic domain boundary. Thereby, we shed light on the fine structure of grain boundaries in three-dimensional confined smectics.
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Affiliation(s)
- Paul A Monderkamp
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - René Wittmann
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Michael Te Vrugt
- Institut für Theoretische Physik, Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Axel Voigt
- Institut für Wissenschaftliches Rechnen, Technische Universität Dresden, 01062 Dresden, Germany
| | - Raphael Wittkowski
- Institut für Theoretische Physik, Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
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50
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Nakamoto M, Kitano S, Matsusaki M. Biomacromolecule‐Fueled Transient Volume Phase Transition of a Hydrogel. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Masahiko Nakamoto
- Division of Applied Chemistry Graduate School of Engineering Osaka University Suita Osaka 565-0871 Japan
| | - Shiro Kitano
- Joint Research Laboratory (TOPPAN) for Advanced Cell Regulatory Chemistry Graduate School of Engineering Osaka University Suita Osaka 565-0871 Japan
| | - Michiya Matsusaki
- Division of Applied Chemistry Graduate School of Engineering Osaka University Suita Osaka 565-0871 Japan
- Joint Research Laboratory (TOPPAN) for Advanced Cell Regulatory Chemistry Graduate School of Engineering Osaka University Suita Osaka 565-0871 Japan
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