Theory of soft and living matter

Leader: M. Leonetti, P. Ronceray, N. Levernier

Introduction

Nonlinear mechanics of biopolymer networks.

Principal investigator: P. Ronceray
PhD Student: Andonis Gerardos, Arthur Coët
Postdoc: Yuri Zhang

Networks of stiff, entangled biopolymers play a central role in the mechanical properties of biological matter, from the cell cytoskeleton to the extracellular matrix. Such networks contribute to the mechanical integrity of living matter, and permit force transmission from the motor protein to the tissue scale. Importantly, at the stress levels relevant to biology, the mechanical properties of these disordered assemblies of fibrous, quasi-one-dimensional objects are very different from usual elastic materials. Indeed, they tend to respond nonlinearly to stresses, due both to single filament properties and to emergent, collective deformation modes controlled by the connectivity and disorder of the network. Through simulations and collaborations with experimentalists, we study the fundamental nonlinear mechanical properties of biopolymer networks and their interplay with cell behavior. We aim to address the following question: When probing their complex environment, what do cells actually “feel”?

 

Inferring the dynamics of living matter.

Principal investigator: P. Ronceray
PhD Student: Andonis Gerardos, Arthur Coët
Postdoc: Yuri Zhang

Networks of stiff, entangled biopolymers play a central role in the mechanical properties of biological matter, from the cell cytoskeleton to the extracellular matrix. Such networks contribute to the mechanical integrity of living matter, and permit force transmission from the motor protein to the tissue scale. Importantly, at the stress levels relevant to biology, the mechanical properties of these disordered assemblies of fibrous, quasi-one-dimensional objects are very different from usual elastic materials. Indeed, they tend to respond nonlinearly to stresses, due both to single filament properties and to emergent, collective deformation modes controlled by the connectivity and disorder of the network. Through simulations and collaborations with experimentalists, we study the fundamental nonlinear mechanical properties of biopolymer networks and their interplay with cell behavior. We aim to address the following question: When probing their complex environment, what do cells actually “feel”?

 

Encapsulation

Principal investigateur: M. Leonetti

A - dynamics, shape, wrinkling and rupture of an elastic capsule

Doctorant: P. Regazzi

Funding: CNES

Encapsulation is a simple way of protecting, transporting and delivering internalized principles, but also of structuring space. This concerns very diverse fields such as food, cosmetics, new materials for construction or medicine. The capsules studied are droplets bounded by a thin polymer film (shell) and immersed in a liquid. The structural and mechanical properties of such objects are still poorly known: behaviour laws, elastic and viscous moduli, rupture, dynamics, etc. Indeed, there are few experimental results. The behavior of this closed elastic system is governed by the coupling at the interface between the viscous stress jump and the elastic response of the shell (also called skin or membrane depending on the domain).

We are interested in the rupture of capsules as a function of the nature of its membrane, the winkling/folding instabilities and the spatiotemporal dynamics of the shape by a multiscale analysis.

B – Interactions between capsules, collective behaviors

The strong deformation of capsules in flow induces more complex hydrodynamic interactions than between rigid particles. To this, it is necessary to add colloidal interactions as well as friction, key ingredients for the understanding of the rheology of rigid particle suspensions. We propose to study the implication of all these contributions to the case of binary interactions and more broadly in suspension.

 

 

Forme et dynamique de vésicules sous écoulement : théorie et simulation

Principal investigateur: M. Leonetti

Collaboration : P. G. Chen, M. Jaeger (M2P2, Marseille)

Souvent, l'objectif principal de la recherche sur l'adhésion cellulaire est d'identifier les protéines d'adhésion et les voies de signalisation pertinentes. Cependant, pour une description complète, il est essentiel de comprendre également la physique et la physico-chimie des processus qui régissent l'adhésion – ce qui n’est pas facile dans le contexte des complexités associées à une cellule vivante. Une façon de résoudre ce problème est d’utiliser des membranes modèles fonctionnalisées pour imiter la membrane cellulaire. Une percée importante a été l'intégration réussie de l’intégrine, protéine transmembranaire d’adhésion, dans des membranes lipidiques synthétiques. Nous sommes en train d'explorer de nouveaux protocoles pour fabriquer des vésicules dérivées de cellules qui contiennent les protéines d'adhésion transmembranaires endogènes.

Publications

2024

Inferring geometrical dynamics of cell nucleus translocation

Sirine Amiri, Yirui Zhang, Andonis Gerardos, Cécile Sykes, Pierre Ronceray

Physical Review Research 6:043030 (2024)10.1103/physrevresearch.6.043030

Margination of artificially stiffened red blood cells

Revaz Chachanidze, Othmane Aouane, Jens Harting, Christian Wagner, Marc Leonetti

Physical Review Fluids 9:L091101 (2024)10.1103/PhysRevFluids.9.L091101

Assessment of coupled bilayer-cytoskeleton modelling strategy for red blood cell dynamics in flow

V Puthumana, Paul G. Chen, M Leonetti, R Lasserre, M Jaeger

Journal of Fluid Mechanics 979:A44 (2024)10.1017/jfm.2023.1092

Drop deformation in a planar elongational flow: impact of surfactant dynamics

Julian Wailliez, Paul Regazzi, Anniina Salonen, Paul G Chen, Marc Jaeger, Marc Leonetti, Emmanuelle Rio

Soft Matter 20:8793-8803 (2024)10.1039/D4SM00642A

2023

CNT effective interfacial energy and pre-exponential kinetic factor from measured NaCl crystal nucleation time distributions in contracting microdroplets

Ruel Cedeno, Romain Grossier, Nadine Candoni, Nicolas Levernier, Adrian Flood, Stéphane Veesler

The Journal of Chemical Physics 158:194705 (2023)10.1063/5.0143704

Breakups of Chitosan microcapsules in extensional flow

Revaz Chachanidze, Kaili Xie, Jinming Lyu, Marc Jaeger, Marc Leonetti

Journal of Colloid and Interface Science 629:445-454 (2023)10.1016/j.jcis.2022.08.169

Swirling of vesicles: Shapes and dynamics in Poiseuille flow as a model of RBC microcirculation

Jinming Lyu, Paul G. Chen, Alexander Farutin, Marc Jaeger, Chaouqi Misbah, Marc Leonetti

Physical Review Fluids 8:L021602 (2023)10.1103/PhysRevFluids.8.L021602

Two steps forward – and one step back?

Pierre Ronceray

Journal Club for Condensed Matter Physics (2023)10.36471/jccm_July_2023_02

Mechanical characterization of core-shell microcapsules

Kaili Xie, Marc Leonetti

Comptes Rendus. Mécanique 351:1-20 (2023)10.5802/crmeca.148

Local response and emerging nonlinear elastic length scale in biopolymer matrices

Haiqian Yang, Estelle Berthier, Chenghai Li, Pierre Ronceray, Yu Long Han, Chase Broedersz, Shengqiang Cai, Ming Guo

Proceedings of the National Academy of Sciences of the United States of America 120 (2023)10.1073/pnas.2304666120

2022

Nonlinear mechanosensation in fiber networks

Estelle Berthier, Haiqian Yang, Ming Guo, Pierre Ronceray, Chase Broedersz

Physical Review Research 6:013327 (2022)10.1103/PhysRevResearch.6.013327

Twenty-five years of nanoscale thermodynamics

Chase Broedersz, Pierre Ronceray

Nature 604:46-47 (2022)10.1038/d41586-022-00869-y

Structural characterization of the interfacial self-assembly of chitosan with oppositely charged surfactant

Revaz Chachanidze, Kaili Xie, Hanna Massaad, Denis C.D. Roux, Marc Léonetti, Clément de Loubens

Journal of Colloid and Interface Science 616:911-920 (2022)10.1016/j.jcis.2022.01.143

Liquid demixing in elastic networks: Cavitation, permeation, or size selection?

Pierre Ronceray, Sheng Mao, Andrej Košmrlj, Mikko Haataja

EPL - Europhysics Letters 137:67001 (2022)10.1209/0295-5075/ac56ac

Stoichiometry Controls the Dynamics of Liquid Condensates of Associative Proteins

Pierre Ronceray, Yaojun Zhang, Xichong Liu, Ned Wingreen

Physical Review Letters 128:038102 (2022)10.1103/PhysRevLett.128.038102

2021

Effect of pulse width on the dynamics of a deflated vesicle in unipolar and bipolar pulsed electric fields

Sudip Das, Marc Jaeger, Marc Leonetti, Rochish M. Thaokar, Paul G. Chen

Physics of Fluids 33:081905 (2021)10.1063/5.0057168

Pinching the cortex of live cells reveals thickness instabilities caused by myosin II motors

Valentin Laplaud, Nicolas Levernier, Judith Pineau, Mabel San, Lucie Barbier, Pablo J Sáez, Ana-Maria Lennon-Duménil, Pablo Vargas, Karsten Kruse, Olivia Du Roure, Matthieu Piel, Julien Heuvingh

Science Advances (2021)

An integrative model of plant gravitropism linking statoliths position and auxin transport

Nicolas Levernier, Olivier Pouliquen, Yoel Forterre

Frontiers in Plant Science (2021)10.3389/fpls.2021.651928

Reply to “Comment on ‘Inverse Square Lévy Walks are not Optimal Search Strategies for d ≥ 2 ”’

Nicolas Levernier, Johannes Textor, Olivier Bénichou, Raphaël Voituriez

Physical Review Letters 126 (2021)10.1103/PhysRevLett.126.048902

Dynamics of pearling instability in polymersomes: the role of shear membrane viscosity and spontaneous curvature

J Lyu, K Xie, R Chachanidze, A Kahli, Gwenn Boedec, Marc Leonetti

Physics of Fluids 33:122016 (2021)10.1063/5.0075266

An isogeometric boundary element method for soft particles flowing in microfluidic channels

Jinming Lyu, Paul G. Chen, G. Boedec, M. Leonetti, Marc Jaeger

Computers and Fluids 214:104786 (2021)10.1016/j.compfluid.2020.104786

Membrane emulsification for the production of suspensions of uniform microcapsules with tunable mechanical properties

Mehdi Maleki, Clément de Loubens, Kaili Xie, Emeline Talansier, Hugues Bodiguel, Marc Léonetti

Chemical Engineering Science 237 (2021)10.1016/j.ces.2021.116567

The Open State Selectivity of the Bean Seed VDAC Depends on Stigmasterol and Ion Concentration

Hayet Saidani, Marc Léonetti, Hanna Kmita, Fabrice Homblé

International Journal of Molecular Sciences 22:3034 (2021)10.3390/ijms22063034

Self-organization and shape change by active polarization in nematic droplets

Fabian Jan Schwarzendahl, Pierre Ronceray, Kimberly Weirich, Kinjal Dasbiswas

Physical Review Research 3:043061 (2021)10.1103/PhysRevResearch.3.043061

Nucleation landscape of biomolecular condensates

Shunsuke Shimobayashi, Pierre Ronceray, David Sanders, Mikko Haataja, Clifford Brangwynne

Nature 599:503-506 (2021)10.1038/s41586-021-03905-5

Physical bioenergetics: Energy fluxes, budgets, and constraints in cells

Xingbo Yang, Matthias Heinemann, Jonathon Howard, Greg Huber, Srividya Iyer-Biswas, Guillaume Le Treut, Michael Lynch, Kristi L Montooth, Daniel J Needleman, Simone Pigolotti, Jonathan Rodenfels, Pierre Ronceray, Sadasivan Shankar, Iman Tavassoly, Shashi Thutupalli, Denis V Titov, Jin Wang, Peter J Foster

Proceedings of the National Academy of Sciences of the United States of America 118:e2026786118 (2021)10.1073/pnas.2026786118

2020

Shape transition and hydrodynamics of vesicles in tube flow

Paul G. Chen, J M Lyu, M Jaeger, M. Leonetti

Physical Review Fluids 5:043602 (2020)10.1103/PhysRevFluids.5.043602

Inverse Square Lévy Walks are not Optimal Search Strategies for d ≥ 2

Nicolas Levernier, Johannes Textor, Olivier Bénichou, Raphaël Voituriez

Physical Review Letters 124 (2020)10.1103/PhysRevLett.124.080601

2019

Glutaraldehyde – A Subtle Tool in the Investigation of Healthy and Pathologic Red Blood Cells

Asena Abay, Greta Simionato, Revaz Chachanidze, Anna Bogdanova, Laura Hertz, Paola Bianchi, Emile van den Akker, Marieke von Lindern, Marc Léonetti, Giampaolo Minetti, Christian Wagner, Lars Kaestner

Frontiers in Physiology 10 (2019)10.3389/fphys.2019.00514

Financement

• PI startup package CENTURI , 2021-26 Measuring and modeling soft living matter
• CENTURI 2023-2025, Understanding margination, from vessels to vascular networks