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Ruiz-Garcia M, Barriuso G CM, Alexander LC, Aarts DGAL, Ghiringhelli LM, Valeriani C. Discovering dynamic laws from observations: The case of self-propelled, interacting colloids. Phys Rev E 2024; 109:064611. [PMID: 39020989 DOI: 10.1103/physreve.109.064611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 06/05/2024] [Indexed: 07/20/2024]
Abstract
Active matter spans a wide range of time and length scales, from groups of cells and synthetic self-propelled colloids to schools of fish and flocks of birds. The theoretical framework describing these systems has shown tremendous success in finding universal phenomenology. However, further progress is often burdened by the difficulty of determining forces controlling the dynamics of individual elements within each system. Accessing this local information is pivotal for the understanding of the physics governing an ensemble of active particles and for the creation of numerical models capable of explaining the observed collective phenomena. In this work, we present ActiveNet, a machine-learning tool consisting of a graph neural network that uses the collective motion of particles to learn active and two-body forces controlling their individual dynamics. We verify our approach using numerical simulations of active Brownian particles, active particles undergoing underdamped Langevin dynamics, and chiral active Brownian particles considering different interaction potentials and values of activity. Interestingly, ActiveNet can equally learn conservative or nonconservative forces as well as torques. Moreover, ActiveNet has proven to be a useful tool to learn the stochastic contribution to the forces, enabling the estimation of the diffusion coefficients. Therefore, all coefficients of the equation of motion of Active Brownian Particles are captured. Finally, we apply ActiveNet to experiments of electrophoretic Janus particles, extracting the active and two-body forces controlling colloids' dynamics. On the one side, we have learned that the active force depends on the electric field and area fraction. On the other side, we have also discovered a dependence of the two-body interaction with the electric field that leads us to propose that the dominant force between active colloids is a screened electrostatic interaction with a constant length scale. We believe that the proposed methodological tool, ActiveNet, might open a new avenue for the study and modeling of experimental suspensions of active particles.
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Affiliation(s)
- Miguel Ruiz-Garcia
- Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Department of Mathematics, Universidad Carlos III de Madrid, Avenida de la Universidad 30, 28911 Leganés, Spain
- Grupo Interdisciplinar Sistemas Complejos, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | | | | | | | - Luca M Ghiringhelli
- Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, Zum Großen Windkanal 6, 12489 Berlin, Germany
- Department of Materials Science, Friedrich-Alexander Universität Erlangen-Nürnberg, Martensstrasse 5-7, 91058 Erlangen, Germany
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Tah I, Haertter D, Crawford JM, Kiehart DP, Schmidt CF, Liu AJ. Minimal vertex model explains how the amnioserosa avoids fluidization during Drosophila dorsal closure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572544. [PMID: 38187730 PMCID: PMC10769242 DOI: 10.1101/2023.12.20.572544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Dorsal closure is a process that occurs during embryogenesis of Drosophila melanogaster . During dorsal closure, the amnioserosa (AS), a one-cell thick epithelial tissue that fills the dorsal opening, shrinks as the lateral epidermis sheets converge and eventually merge. During this process, the aspect ratio of amnioserosa cells increases markedly. The standard 2-dimensional vertex model, which successfully describes tissue sheet mechanics in multiple contexts, would in this case predict that the tissue should fluidize via cell neighbor changes. Surprisingly, however, the amnioserosa remains an elastic solid with no such events. We here present a minimal extension to the vertex model that explains how the amnioserosa can achieve this unexpected behavior. We show that continuous shrinkage of the preferred cell perimeter and cell perimeter polydispersity lead to the retention of the solid state of the amnioserosa. Our model accurately captures measured cell shape and orientation changes and predicts non-monotonic junction tension that we confirm with laser ablation experiments. Significance Statement During embryogenesis, cells in tissues can undergo significant shape changes. Many epithelial tissues fluidize, i.e. cells exchange neighbors, when the average cell aspect ratio increases above a threshold value, consistent with the standard vertex model. During dorsal closure in Drosophila melanogaster , however, the amnioserosa tissue remains solid even as the average cell aspect ratio increases well above threshold. We introduce perimeter polydispersity and allow the preferred cell perimeters, usually held fixed in vertex models, to decrease linearly with time as seen experimentally. With these extensions to the standard vertex model, we capture experimental observations quantitatively. Our results demonstrate that vertex models can describe the behavior of the amnioserosa in dorsal closure by allowing normally fixed parameters to vary with time.
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Tah I, Ridout SA, Liu AJ. Fragility in glassy liquids: A structural approach based on machine learning. J Chem Phys 2022; 157:124501. [PMID: 36182409 DOI: 10.1063/5.0099071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The rapid rise of viscosity or relaxation time upon supercooling is a universal hallmark of glassy liquids. The temperature dependence of viscosity, however, is quite nonuniversal for glassy liquids and is characterized by the system's "fragility," with liquids with nearly Arrhenius temperature-dependent relaxation times referred to as strong liquids and those with super-Arrhenius behavior referred to as fragile liquids. What makes some liquids strong and others fragile is still not well understood. Here, we explore this question in a family of harmonic spheres that range from extremely strong to extremely fragile, using "softness," a structural order parameter identified by machine learning to be highly correlated with dynamical rearrangements. We use a support vector machine to identify softness as the same linear combination of structural quantities across the entire family of liquids studied. We then use softness to identify the factors controlling fragility.
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Affiliation(s)
- Indrajit Tah
- Department of Physics and Astronomy, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, USA
| | - Sean A Ridout
- Department of Physics and Astronomy, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, USA
| | - Andrea J Liu
- Department of Physics and Astronomy, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, USA
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Tong S, Singh NK, Sknepnek R, Košmrlj A. Linear viscoelastic properties of the vertex model for epithelial tissues. PLoS Comput Biol 2022; 18:e1010135. [PMID: 35587514 PMCID: PMC9159552 DOI: 10.1371/journal.pcbi.1010135] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/01/2022] [Accepted: 04/25/2022] [Indexed: 12/13/2022] Open
Abstract
Epithelial tissues act as barriers and, therefore, must repair themselves, respond to environmental changes and grow without compromising their integrity. Consequently, they exhibit complex viscoelastic rheological behavior where constituent cells actively tune their mechanical properties to change the overall response of the tissue, e.g., from solid-like to fluid-like. Mesoscopic mechanical properties of epithelia are commonly modeled with the vertex model. While previous studies have predominantly focused on the rheological properties of the vertex model at long time scales, we systematically studied the full dynamic range by applying small oscillatory shear and bulk deformations in both solid-like and fluid-like phases for regular hexagonal and disordered cell configurations. We found that the shear and bulk responses in the fluid and solid phases can be described by standard spring-dashpot viscoelastic models. Furthermore, the solid-fluid transition can be tuned by applying pre-deformation to the system. Our study provides insights into the mechanisms by which epithelia can regulate their rich rheological behavior.
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Affiliation(s)
- Sijie Tong
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Navreeta K. Singh
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Rastko Sknepnek
- School of Science and Engineering, University of Dundee, Dundee, United Kingdom
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Andrej Košmrlj
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey, United States of America
- Princeton Institute of Materials, Princeton University, Princeton, New Jersey, United States of America
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Ridout SA, Rocks JW, Liu AJ. Correlation of plastic events with local structure in jammed packings across spatial dimensions. Proc Natl Acad Sci U S A 2022; 119:e2119006119. [PMID: 35412897 PMCID: PMC9169794 DOI: 10.1073/pnas.2119006119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/10/2022] [Indexed: 11/18/2022] Open
Abstract
In frictionless jammed packings, existing evidence suggests a picture in which localized physics dominates in low spatial dimensions, d = 2, 3, but quickly loses relevance as d rises, replaced by spatially extended mean-field behavior. For example, quasilocalized low-energy vibrational modes and low-coordination particles associated with deviation from mean-field behavior (rattlers and bucklers) all vanish rapidly with increasing d. These results suggest that localized rearrangements, which are associated with low-energy vibrational modes, correlated with local structure, and dominant in low dimensions, should give way in higher d to extended rearrangements uncorrelated with local structure. Here, we use machine learning to analyze simulations of jammed packings under athermal, quasistatic shear, identifying a local structural variable, softness, that correlates with rearrangements in dimensions d = 2 to d = 5. We find that softness—and even just the local coordination number Z—is essentially equally predictive of rearrangements in all d studied. This result provides direct evidence that local structure plays an important role in higher d, suggesting a modified picture for the dimensional cross-over to mean-field theory.
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Affiliation(s)
- Sean A. Ridout
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104
| | - Jason W. Rocks
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104
| | - Andrea J. Liu
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104
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Giannini JA, Stanifer EM, Manning ML. Searching for structural predictors of plasticity in dense active packings. SOFT MATTER 2022; 18:1540-1553. [PMID: 35107478 DOI: 10.1039/d1sm01675j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In amorphous solids subject to shear or thermal excitation, so-called structural indicators have been developed that predict locations of future plasticity or particle rearrangements. An open question is whether similar tools can be used in dense active materials, but a challenge is that under most circumstances, active systems do not possess well-defined solid reference configurations. We develop a computational model for a dense active crowd attracted to a point of interest, which does permit a mechanically stable reference state in the limit of infinitely persistent motion. Previous work on a similar system suggested that the collective motion of crowds could be predicted by inverting a matrix of time-averaged two-particle correlation functions. Seeking a first-principles understanding of this result, we demonstrate that this active matter system maps directly onto a granular packing in the presence of an external potential, and extend an existing structural indicator based on linear response to predict plasticity in the presence of noisy dynamics. We find that the strong pressure gradient necessitated by the directed activity, as well as a self-generated free boundary, strongly impact the linear response of the system. In low-pressure regions the linear-response-based indicator is predictive, but it does not work well in the high-pressure interior of our active packings. Our findings motivate and inform future work that could better formulate structure-dynamics predictions in systems with strong pressure gradients.
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Affiliation(s)
- Julia A Giannini
- Department of Physics, Syracuse University, Syracuse, New York 13244, USA.
- BioInspired Institute, Syracuse University, Syracuse, New York 13244, USA
| | - Ethan M Stanifer
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - M Lisa Manning
- Department of Physics, Syracuse University, Syracuse, New York 13244, USA.
- BioInspired Institute, Syracuse University, Syracuse, New York 13244, USA
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Tah I, Mutneja A, Karmakar S. Understanding Slow and Heterogeneous Dynamics in Model Supercooled Glass-Forming Liquids. ACS OMEGA 2021; 6:7229-7239. [PMID: 33778237 PMCID: PMC7992088 DOI: 10.1021/acsomega.0c04831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/24/2021] [Indexed: 05/07/2023]
Abstract
Glasses are ubiquitous in nature. Many common items such as ketchups, cosmetic products, toothpaste, etc. and metallic glasses are examples of such glassy materials whose dynamical and rheological properties matter in our daily life. The dynamics of these glass-forming systems are known to be very sluggish and heterogeneous, but a detailed understanding of the origin of such slowing down is still lacking. Slow heterogeneous dynamics occur in a wide variety of systems at scales ranging from microscopic to macroscopic. Polymeric liquids, granular material, such as powder and sand, gels, and foams and also metallic alloys show such complex glassy dynamics at appropriate conditions. Recently, the existence of dynamical heterogeneity has also been found in biological systems starting from collective cell migration in a monolayer of cells to embryonic morphogenesis, cancer invasion, and wound healing. Extensive research in the past decade or so lead to the understanding that there are growing dynamic and static correlation lengths associated with the observed dynamical heterogeneity and rapid rise in viscosity. In this review, we have highlighted the recent developments on measuring these correlation lengths in glass-forming liquids and their possible implications in the physics of the glass transition.
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Affiliation(s)
- Indrajit Tah
- Department
of Physics and Astronomy, University of
Pennsylvania, 209 South
33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Anoop Mutneja
- Tata
Institute of Fundamental Research, 36/P, Gopanpally Village, Serilingampally
Mandal, Ranga Reddy District, Hyderabad 500107, India
| | - Smarajit Karmakar
- Tata
Institute of Fundamental Research, 36/P, Gopanpally Village, Serilingampally
Mandal, Ranga Reddy District, Hyderabad 500107, India
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