2
|
Goswami K, Cherstvy AG, Godec A, Metzler R. Anomalous diffusion of active Brownian particles in responsive elastic gels: Nonergodicity, non-Gaussianity, and distributions of trapping times. Phys Rev E 2024; 110:044609. [PMID: 39562954 DOI: 10.1103/physreve.110.044609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Accepted: 09/24/2024] [Indexed: 11/21/2024]
Abstract
Understanding actual transport mechanisms of self-propelled particles (SPPs) in complex elastic gels-such as in the cell cytoplasm, in in vitro networks of chromatin or of F-actin fibers, or in mucus gels-has far-reaching consequences. Implications beyond biology/biophysics are in engineering and medicine, with a particular focus on microrheology and on targeted drug delivery. Here, we examine via extensive computer simulations the dynamics of SPPs in deformable gellike structures responsive to thermal fluctuations. We treat tracer particles comparable to and larger than the mesh size of the gel. We observe distinct trapping events of active tracers at relatively short times, leading to subdiffusion; it is followed by an escape from meshwork-induced traps due to the flexibility of the network, resulting in superdiffusion. We thus find crossovers between different transport regimes. We also find pronounced nonergodicity in the dynamics of SPPs and non-Gaussianity at intermediate times. The distributions of trapping times of the tracers escaping from "cages" in our quasiperiodic gel often reveal the existence of two distinct timescales in the dynamics. At high activity of the tracers these timescales become comparable. Furthermore, we find that the mean waiting time exhibits a power-law dependence on the activity of SPPs (in terms of their Péclet number). Our results additionally showcase both exponential and nonexponential trapping events at high activities. Extensions of this setup are possible, with the factors such as anisotropy of the particles, different topologies of the gel network, and various interactions between the particles (also of a nonlocal nature) to be considered.
Collapse
|
3
|
Divoux T, Agoritsas E, Aime S, Barentin C, Barrat JL, Benzi R, Berthier L, Bi D, Biroli G, Bonn D, Bourrianne P, Bouzid M, Del Gado E, Delanoë-Ayari H, Farain K, Fielding S, Fuchs M, van der Gucht J, Henkes S, Jalaal M, Joshi YM, Lemaître A, Leheny RL, Manneville S, Martens K, Poon WCK, Popović M, Procaccia I, Ramos L, Richards JA, Rogers S, Rossi S, Sbragaglia M, Tarjus G, Toschi F, Trappe V, Vermant J, Wyart M, Zamponi F, Zare D. Ductile-to-brittle transition and yielding in soft amorphous materials: perspectives and open questions. SOFT MATTER 2024; 20:6868-6888. [PMID: 39028363 DOI: 10.1039/d3sm01740k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Soft amorphous materials are viscoelastic solids ubiquitously found around us, from clays and cementitious pastes to emulsions and physical gels encountered in food or biomedical engineering. Under an external deformation, these materials undergo a noteworthy transition from a solid to a liquid state that reshapes the material microstructure. This yielding transition was the main theme of a workshop held from January 9 to 13, 2023 at the Lorentz Center in Leiden. The manuscript presented here offers a critical perspective on the subject, synthesizing insights from the various brainstorming sessions and informal discussions that unfolded during this week of vibrant exchange of ideas. The result of these exchanges takes the form of a series of open questions that represent outstanding experimental, numerical, and theoretical challenges to be tackled in the near future.
Collapse
Affiliation(s)
- Thibaut Divoux
- ENSL, CNRS, Laboratoire de physique, F-69342 Lyon, France.
| | - Elisabeth Agoritsas
- Department of Quantum Matter Physics (DQMP), University of Geneva, Quai Ernest-Ansermet 24, CH-1211 Geneva, Switzerland
| | - Stefano Aime
- Molecular, Macromolecular Chemistry, and Materials, ESPCI Paris, Paris, France
| | - Catherine Barentin
- Univ. de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - Jean-Louis Barrat
- Laboratoire de Physique de l'Ecole Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France
| | - Roberto Benzi
- Department of Physics & INFN, Tor Vergata University of Rome, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Ludovic Berthier
- Laboratoire Charles Coulomb (L2C), Université Montpellier, CNRS, Montpellier, France
| | - Dapeng Bi
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Giulio Biroli
- Laboratoire de Physique de l'Ecole Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France
| | - Daniel Bonn
- Soft Matter Group, van der Waals-Zeeman Institute, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Philippe Bourrianne
- PMMH, CNRS, ESPCI Paris, Université PSL, Sorbonne Université, Université Paris Cité, Paris, France
| | - Mehdi Bouzid
- Univ. Grenoble Alpes, CNRS, Grenoble INP, 3SR, F-38000 Grenoble, France
| | - Emanuela Del Gado
- Georgetown University, Department of Physics, Institute for Soft Matter Synthesis and Metrology, Washington, DC, USA
| | - Hélène Delanoë-Ayari
- Univ. de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - Kasra Farain
- Soft Matter Group, van der Waals-Zeeman Institute, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Suzanne Fielding
- Department of Physics, Durham University, South Road, Durham DH1 3LE, UK
| | - Matthias Fuchs
- Fachbereich Physik, Universität Konstanz, 78457 Konstanz, Germany
| | - Jasper van der Gucht
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Silke Henkes
- Lorentz Institute, Leiden University, 2300 RA Leiden, The Netherlands
| | - Maziyar Jalaal
- Institute of Physics, University of Amsterdam, Science Park 904, Amsterdam, The Netherlands
| | - Yogesh M Joshi
- Department of Chemical Engineering, Indian Institute of Technology, Kanpur 208016, Uttar Pradesh, India
| | - Anaël Lemaître
- Navier, École des Ponts, Univ Gustave Eiffel, CNRS, Marne-la-Vallée, France
| | - Robert L Leheny
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | | | | | - Wilson C K Poon
- SUPA and the School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Marko Popović
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str.38, 01187 Dresden, Germany
| | - Itamar Procaccia
- Dept. of Chemical Physics, The Weizmann Institute of Science, Rehovot 76100, Israel
- Sino-Europe Complex Science Center, School of Mathematics, North University of China, Shanxi, Taiyuan 030051, China
| | - Laurence Ramos
- Laboratoire Charles Coulomb (L2C), Université Montpellier, CNRS, Montpellier, France
| | - James A Richards
- SUPA and the School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Simon Rogers
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Saverio Rossi
- LPTMC, CNRS-UMR 7600, Sorbonne Université, 4 Pl. Jussieu, F-75005 Paris, France
| | - Mauro Sbragaglia
- Department of Physics & INFN, Tor Vergata University of Rome, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Gilles Tarjus
- LPTMC, CNRS-UMR 7600, Sorbonne Université, 4 Pl. Jussieu, F-75005 Paris, France
| | - Federico Toschi
- Department of Applied Physics and Science Education, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- CNR-IAC, Via dei Taurini 19, 00185 Rome, Italy
| | - Véronique Trappe
- Department of Physics, University of Fribourg, Chemin du Musée 3, Fribourg 1700, Switzerland
| | - Jan Vermant
- Department of Materials, ETH Zürich, Vladimir Prelog Weg 5, 8032 Zürich, Switzerland
| | - Matthieu Wyart
- Department of Quantum Matter Physics (DQMP), University of Geneva, Quai Ernest-Ansermet 24, CH-1211 Geneva, Switzerland
| | - Francesco Zamponi
- Laboratoire de Physique de l'Ecole Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Davoud Zare
- Fonterra Research and Development Centre, Dairy Farm Road, Fitzherbert, Palmerston North 4442, New Zealand
- Nestlé Institute of Food Sciences, Nestlé Research, Vers Chez les Blancs, Lausanne, Switzerland
| |
Collapse
|
4
|
Rajput SS, Singh SB, Subramanyam D, Patil S. Soft glassy rheology of single cells with pathogenic protein aggregates. SOFT MATTER 2024; 20:6266-6274. [PMID: 39054893 DOI: 10.1039/d4sm00595c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
A correlation between the mechanical properties of cells and various diseases has been emerging in recent years. Atomic force microscopy (AFM) has been widely used to measure a single cell's apparent Young's modulus by treating it as a fully elastic object. More recently, quantitative characterization of the complete viscoelasticity of single cells has become possible. We performed AFM-based nano-indentation experiments on hemocytes isolated from third instar larvae to determine their viscoelasticity and found that live hemocytes, like many other cells, follow a scale-free power-law rheology (PLR) akin to soft glasses. Further, we examined the changes in the rheological response of hemocytes in the presence of pathogenic protein aggregates known to cause neurodegenerative diseases such as Huntington's disorder and amyotrophic lateral sclerosis. Our results show that cells lose their fluidity and appear more solid-like in the presence of certain aggregates, in a manner correlated to actin reorganization. More solid-like cells also display reduced intracellular transport through clathrin-mediated endocytosis (CME). However, the cell's rheology remains largely unaffected and is similar to that of wild-type (WT) hemocytes, if aggregates do not perturb the actin organization and CME. Moreover, the fluid-like nature was significantly recovered when actin organization was rescued by overexpressing specific actin interacting proteins or chaperones. Our study, for the first time, underscores a direct correlation between parameters governing glassy dynamics, actin organization and CME.
Collapse
Affiliation(s)
- Shatruhan Singh Rajput
- Department of Physics, Indian Institute of Science Education and Research, Pune 411008, India
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Surya Bansi Singh
- National Centre for Cell Science, SP Pune University Campus, Pune 411007, India.
- SP Pune University, Pune 411007, India
| | - Deepa Subramanyam
- National Centre for Cell Science, SP Pune University Campus, Pune 411007, India.
| | - Shivprasad Patil
- Department of Physics, Indian Institute of Science Education and Research, Pune 411008, India.
| |
Collapse
|
5
|
Zhou G, Li T, Du J, Wu M, Lin D, Pu W, Zhang J, Gu Z. Harnessing HetHydrogel: A Universal Platform to Dropletize Single-Cell Multiomics. SMALL METHODS 2024; 8:e2301631. [PMID: 38419597 DOI: 10.1002/smtd.202301631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 01/12/2024] [Indexed: 03/02/2024]
Abstract
A universal platform is developed for dropletizing single cell plate-based multiomic assays, consisting of three main pillars: a miniaturized open Heterogeneous Hydrogel reactor (abbreviated HetHydrogel) for multi-step biochemistry, its tunable permeability that allows Tn5 tagmentation, and single cell droplet barcoding. Through optimizing the HetHydrogel manufacturing procedure, the chemical composition, and cell permeation conditions, simultaneous high-throughput mitochondrial DNA genotyping and chromatin profiling at the single-cell level are demonstrated using a mixed-species experiment. This platform offers a powerful way to investigate the genotype-phenotype relationships of various mtDNA mutations in biological processes. The HetHydrogel platform is believed to have the potential to democratize droplet technologies, upgrading a whole range of plate-based single cell assays to high throughput format.
Collapse
Affiliation(s)
- Guoqiang Zhou
- Center for Mitochondrial Genetics and Health, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
| | - Ting Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Jingjing Du
- Center for Mitochondrial Genetics and Health, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
| | - Mengying Wu
- Center for Mitochondrial Genetics and Health, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
| | - Deng Lin
- Center for Mitochondrial Genetics and Health, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
| | - Weilin Pu
- Center for Mitochondrial Genetics and Health, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
| | - Jingwei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, 200438, China
- Zhejiang Lab, Hangzhou, 310000, China
| | - Zhenglong Gu
- Center for Mitochondrial Genetics and Health, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
| |
Collapse
|
6
|
Kurilovich AA, Mantsevich VN, Chechkin AV, Palyulin VV. Negative diffusion of excitons in quasi-two-dimensional systems. Phys Chem Chem Phys 2024; 26:922-935. [PMID: 38088027 DOI: 10.1039/d3cp03521b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
We show how two different mobile-immobile type models explain the observation of negative diffusion of excitons reported in experimental studies in quasi-two-dimensional semiconductor systems. The main reason for the effect is the initial trapping and a delayed release of free excitons in the area close to the original excitation spot. The density of trapped excitons is not registered experimentally. Hence, the signal from the free excitons alone includes the delayed release of not diffusing trapped particles. This is seen as the narrowing of the exciton density profile or decrease of mean-squared displacement which is then interpreted as a negative diffusion. The effect is enhanced with the increase of recombination intensity as well as the rate of the exciton-exciton binary interactions.
Collapse
Affiliation(s)
- Aleksandr A Kurilovich
- Center for Energy Science and Technology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205, Moscow, Russia
| | - Vladimir N Mantsevich
- Chair of Semiconductors and Cryoelectronics, Physics department, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Aleksei V Chechkin
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wroclaw University of Science and Technology, Wyspianskiego 27, 50-370 Wroclaw, Poland
- Institute for Physics & Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany
- Akhiezer Institute for Theoretical Physics National Science Center "Kharkov Institute of Physics and Technology", 61108, Kharkov, Ukraine
| | - Vladimir V Palyulin
- Applied AI centre, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Moscow, 121205, Russia.
| |
Collapse
|
7
|
Defaveri L, Dos Santos MAF, Kessler DA, Barkai E, Anteneodo C. Non-normalizable quasiequilibrium states under fractional dynamics. Phys Rev E 2023; 108:024133. [PMID: 37723721 DOI: 10.1103/physreve.108.024133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/31/2023] [Indexed: 09/20/2023]
Abstract
Particles anomalously diffusing in contact with a thermal bath are initially released from an asymptotically flat potential well. For temperatures that are sufficiently low compared to the potential depth, the dynamical and thermodynamical observables of the system remain almost constant for long times. We show how these stagnated states are characterized as non-normalizable quasiequilibrium (NNQE) states. We use the fractional-time Fokker-Planck equation (FTFPE) and continuous-time random walk approaches to calculate ensemble averages. We obtain analytical estimates of the durations of NNQE states, depending on the fractional order, from approximate theoretical solutions of the FTFPE. We study and compare two types of observables, the mean square displacement typically used to characterize diffusion, and the thermodynamic energy. We show that the typical timescales for transient stagnation depend exponentially on the value of the depth of the potential well, in units of temperature, multiplied by a function of the fractional exponent.
Collapse
Affiliation(s)
| | - Maike A F Dos Santos
- Department of Physics, PUC-Rio, Rua Marquês de São Vicente 225, 22451-900 Gávea, Rio de Janeiro, Brazil
| | - David A Kessler
- Department of Physics, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Eli Barkai
- Department of Physics, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Celia Anteneodo
- Department of Physics, PUC-Rio, Rua Marquês de São Vicente 225, 22451-900 Gávea, Rio de Janeiro, Brazil
- National Institute of Science and Technology for Complex Systems, 22290-180 Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|