From Soft Matter to Biophysics 2023

A workshop in honour of Jean-François Joanny Ecole de Physique des Houches, France

Table of Contents

Acknowledgements ………………………………………………………………………………………… page 2

Biography of Jean-François Joanny …………………………………………………………………. page 3

Schedule ……………….……………………………………………………………………………………. pages 4-7

List of posters ………………………………………………………………..................................... page 8

List of abstracts ………………………………………………………………………………………………. page 9

Abstracts ………………………………………………………………………………………………… pages 10-48

List of participants ………………………………………………………………………………….. pages 49-50

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From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Acknowledgements

Anyone who has organized a conference knows that such a project may only be realized thanks to crucial help from many sides. On the financial side, this workshop would not have been possible without the generous support from our sponsors, listed below. We would like to thank them all warmly Furthermore, the scientific program has obtained its final shape through the valuable help from our Scientific Advisory Board. For this, we are indebted to F. Brochard-Wyart, E. Charlaix, B. Goud, F. Jülicher, P. Pincus, and C. Marchetti. No scientific conference can be organized without professional andefficientadministrativesupport.Inthis respect, weare particularly grateful toMrs. Claudine LeVaou and Mrs. Karoline Kolodziej from the Laboratoire de Physique Théorique et Modèles Statistiques (LPTMS, Paris), to Mrs. Melissa Delwulf from the Labex Cell(n)Scale (Institut Curie, Paris), and to Mrs. Elsa Glasson, the Administrative Manager of the École de Physique des Houches, as well as to the Secretariat of the École de Physique.

Finally, we are infinitely grateful to Jean-François Joanny for the scientific inspiration and benevolence that he transmitted to all of us and we hope that this workshop in honour of his career will live up to his expectations.

The organizing committee

Jörg Baschnagel, University of Strasbourg & CNRS Institut Charles Sadron, France

Jens Elgeti, Forschungszentrum Jülich, Germany Martin Lenz, Université Paris-Saclay & CNRS LPTMS, France

Hervé Turlier, Collège de France & CNRS CIRB, France

Sponsors

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Biography of Jean-François Joanny

Jean-FrançoisJoannyis atheoretical physicist with a broad interest in diverse aspects of soft matter and biological systems.

After studying physics at the École Normale Supérieure de Paris, Jean-François obtained a Thèse de 3e cycle in 1978 on polymer demixing and a Thèse d’Etat in 1985 on wetting phenomena, both under the supervision ofPierre-Gilles de Gennes.After a year (1978-1979) of post-doctoral research at the University of California Los Angeles with Philip Pincus, Jean-François began his career at the CNRS, where he held a researcher position, first in the Condensed Matter Physics Laboratory of the Collège de France in Paris, and then from 1985 to 1989 in Lyon. In 1989, he was appointed Professor of Physics at Louis-Pasteur University in Strasbourg and carried out his research in the field of soft matter at the Institut Charles Sadron.

In 2001, he moved from Strasbourg to the Institut Curie in Paris to become Professor at the Pierre-etMarie-Curie University (UPMC) and, in 2003, the Director of the Physical Chemistry Laboratory at the Institut Curie, a position he held until 2012. His research activities have since focused on cell biophysics and fundamental cell processes, mechanics and tissue growth, and the physics of cancer by describing these biological phenomena through the concept of active materials.

From 2014 to 2018, he was Director General of the prestigious School of Industrial Physics and Chemistry of the City of Paris (ESPCI), where he also taught.

Since January 2019, he is Professor at Collège de France, where he holds the chair of soft matter and biophysics.

Jean-François Joanny received several distinctions, involving the bronze and silver medals from the CNRS, the Gentner Kastler Prize, the Ampère Prize from the Académie des sciences and the “Grand Prix Cino Del Duca” together with Jacques Prost. He was also a junior and a senior member of the Institut Universitaire de France (IUF).

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Schedule

Monday, Jan 30

08:50 – 09:00 Opening remarks

Session 1 Chair : Frank Jülicher

09:00 – 09:25 Sriram Ramaswamy : Surprises in the hydrodynamics of aligned active suspensions

09:25 – 09:50 Purnima Jain : Effect of concentration fluctuations in active polar fluids

09:50 – 10:15 Elisabeth Charlaix : Wall slip of complex fluids: from slip length to Navier's friction coefficient

10:15 – 11:00 Coffee break

11:00 – 11:25 Alexander Grosberg : Nuclear chromodynamics (active hydrodynamics of chromatin)

11:25 – 11:50 Ignasi Vélez Ceron : Photosensitive active nematics

11:50 – 12:15 Joël Lemière : Control of nuclear size by osmotic forces in Schizosaccharomyces pombe

12:15 – 12:40 Time for discussion

12:45 – 14:00 Lunch

14:00 – 17:00 Time for discussion

Session 2 Chair : Pierre Sens

17:00 – 17:25 Jacques Prost : Having fun with epitheliums

17:25 – 17:50 Carles Blanch-Mercader : Morphogenesis of anisotropic cell monolayers by integer topological defects

17:50 – 18:15 Edouard Hannezo, EMBO young investigator lecture : Mechanochemical instabilities of epithelial sheets

18:15 – 18:40 Romain Rollin : Physical principles at the root of the cell size scaling laws

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From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

18:40 – 19:30 Time for discussion

19:30 – 20:30 Dinner

20:30 – 21:30 Outreach talk by Vincent Rivasseau : Science without Borders, the Pledge for Africa

Tuesday, Jan 31

Session 3 Chair : Jaume Casademunt

09:00 – 09:25 Jean-Louis Barrat : Can we compute the heat conductivity of solids?

09:25 – 09:50 Vincent Debets : Competing length and time scales in active glassy matter

09:50 – 10:15 Catherine Barentin : Wetting of yield-stress fluid

10:15 – 11:00 Coffee break

11:00 – 11:25 Günter Reiter : Non-equilibrium properties of thin polymer films

11:25 – 11:50 Etienne Fodor : Pulsating active matter

11:50 – 12:15 Patrick Kékicheff : Relationships between chemical and physical alterations of oil-based pictorial paintings: craquelures and metal ion-migration

12:15 – 12:40 Time for discussion

12:45 – 14:00 Lunch

14:00 – 17:00 Time for discussion

17:00 – 18:40 Poster session

18:40 – 19:30 Time for discussion

19:30 – 20:30 Dinner

20:30 – 21:30 Outreach talk by Aurélien Peilloux : From science to art, a transition under a benevolent and curious eye

Wednesday, Feb 1

Session 4 Chair : Carlos Marques

09:00 – 09:25 Françoise Brochard-Wyart : Pipette aspiration : from gas vesicles to granules

09:25 – 09:50 Maria Tatulea-Codrean : Physical modelling of cell adhesion on fluid substrates

09:50 – 10:15 David Andelman : One hundred years of electrified interfaces: what's new with the theories of Debye and Onsager?

10:15 – 11:00 Coffee break

11:00 – 11:25 Cristina Marchetti : Active interfaces

11:25 – 11:50 Livio Nicola Carenza : Defect-mediated morphogenesis

11:50 – 12:15 Patricia Bassereau : Interplay between membrane mechanics and membrane proteins' diffusion, clustering and function

12:15 – 12:40 Billie Meadowcroft : Mechanochemical rules shape-shifting filaments that reshape membranes

12:45 – 14:00 Lunch

14:00 – 19:30 Time for discussion

19:30 – 20:30 Dinner

20:30 – 21:30 After-Dinner talk by Jean-François Joanny

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From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Thursday, Feb 2

Session 5 Chair : Pascal Silberzan

09:00 – 09:25 Karsten Kruse : Cortical actin dynamics

09:25 – 09:50 Charlotte Aumeier : Motor usage imprints microtubule stability in the shaft

09:50 – 10:15 Roland Winkler : The physics of active polymers and filaments

10:15 – 11:00 Coffee break

11:00 – 11:25 Timo Betz : Inferring detailed broken balance and active energies from purely passive observation of active systems

11:25 – 11:50 Ricard Alert : Active Turbulence

11:50 – 12:15 Albert Johner : Star Polymers: "critical" versus stretched

12:15 – 12:40 Time for discussion

12:45 – 14:00 Lunch

14:00 – 17:00 Time for discussion

Session 6 Chair : Ralf Everaers

17:00 – 17:25 Kurt Kremer : Topological constraints matter

17:25 – 17:50 Tzer Han Tan : Odd dynamics of living chiral systems

17:50 – 18:15 Stephan Grill : Activating active matter

18:15 – 18:40 Pierre Ronceray : What can we learn from the stochastic trajectories of biological systems?

18:40 – 19:30 Time for discussion

19:30 – 20:30 Dinner

20:30 – 21:30 Outreach talk by François Piuzzi : L'approche frugale pour la conception et la fabrication de l'instrumentation scientifique

Friday, Feb 3

Session 7 Chair : David Lacoste

09:00 – 09:25 Antonio Stocco : Dynamics of active and driven colloids interacting with soft membranes

09:25 – 09:50 Susanne Liese : Chemically active wetting

09:50 – 10:15 Cécile Sykes : Phase diagrams in biophysics

10:15 – 11:00 Coffee break

11:00 – 11:25 Claire Dessalles : Interplay between topological defects and curvature in developing tissues

11:25 – 11:50 Mulugeta Bekele Ogato : A sparcely confined water molecules undergoing finite-time cyclic process: A case study in extracting equilibrium information from non-equilibrium processes

11:50 – 12:15 Matthias Merkel : What can stabilize oriented tissue deformation ?

12:15 – 12:40 Time for discussion

12:45 – 14:00 Lunch & departure

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From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

List of posters

1. Andrew Callan-Jones – Flow localization on curved, active ordered surfaces

2. Giovanni Cappello – Extracellular matrix-dependent mechanosensing : role in proliferation, migration and contractility

3. Luis Dinis – Pareto-optimal trade-off: gambling in horse races and growing bacteria

4. David Lacoste – Emergence of homochirality in large molecular systems

5. Martin Lenz – Slimming down through frustration

6. Ananyo Maitra – Chiral, active liquid crystals

7. Pascal Martin – Flagella-like beating of actin bundles driven by self-organized myosin waves

8. Jonas Ranft – Biophysical aspects of postsynaptic domain formation and maintenance

9. Romain Rollin – Nuclear size scaling and breakdown

10. Valério Sorichetti – Transverse fluctuations control the assembly of semiflexible filaments

11. Yergou Tatek – Star-shaped polymer translocation into a nanochannel: Langevin dynamics simulations

12. Maria Tatulea-Codrean – Cell-o-Tape: Physical modelling of cell adhesion to membranes

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List of abstracts

ALERT, Ricard – p.10

ANDELMAN, David – p.11

AUMEIER, Charlotte – p.12

BARENTIN, Catherine – p.13

BARRAT, Jean-Louis – p.14

BASSERAU, Patricia – p.15

BEKELE, Mulugeta – p.16

BETZ, Timo – p.17

BLANCH-MERCADER, Carles – p.18

BROCHARD-WYART, Françoise – p.19

CARENZA, Livio N. – p.20

CHARLAIX, Elisabeth – p.21

DEBETS, Vincent E. – p.22

DESSALLES, Claire – p.23

FODOR, Etienne – p.24

GRILL, Stephan – p.25

GROSBERG, Alexander Y. – p.26

HANNEZO, Edouard – p.27

JAIN, Purnima – p.28

JOHNER, Albert – p.29

KÉKICHEFF, Patrick – p.30

KREMER, Kurt – p.31

KRUSE, Karsten – p.32

LEMIÈRE, Joël – p.33

LIESE, Susanne – p.34

MARCHETTI, Cristina – p.35

MEADOWCROFT, Billie – p.36

MERKEL, Matthias – p.37

PROST, Jacques – p.38

RAMASWAMY, Sriram – p.39

REITER, Günter – p.40

ROLLIN, Romain – p.41

RONCERAY, Pierre – p.42

STOCCO, Antonio – p.43

SYKES, Cécile – p.44

TAN, Tzer Han – p.45

TATULEA-CODREAN, Maria – p.46

VÉLEZ-CERON, Ignasi – p.47

WINKLER, Roland G. – p.48

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Active Turbulence

Ricard Alert1*, Jean-François Joanny2, Jaume Casademunt3

1 Max Planck Institute for the Physics of Complex Systems & Center for Systems Biology Dresden, Germany

2 Collège de France & Institut Curie, Paris, France

3 University of Barcelona & Institute of Complex Systems, Barcelona, Spain

*PRESENTER

A milestone in the transition from soft matter to biophysics was the development of active matter physics – a field of which Jean-François is one of the founding fathers. Together with collaborators, they established the hydrodynamic equations foractiveliquid crystals,and theyshowed thatthese active fluids canflow spontaneously, powered by their microscopic components. At high activity, these spontaneous flows become chaotic and exhibit complex spatiotemporal dynamics, which are commonly observed in several systems, from bacterial suspensions to cytoskeletal mixtures and cell layers. Despite occurring in a non-inertial regime (low Reynolds), chaotic active flows are reminiscent of inertial turbulence, and hence they are known as active turbulence [Alert 2022]. I will presentourwork with Jean-François and others tounderstand the fundamentalsimilarities and differences between active and inertialturbulence [Alert 2020]. Iwill show that,unlike inclassic turbulence, active nematic turbulence does not feature an energy cascade. As in classic turbulence, however, the statistical properties of these active flows are described by scaling laws with universal exponents. I will close by outlining how we verified these scaling laws in experiments (Fig. 1) [Martínez-Prat 2021].

References:

- [Alert 2022] R. Alert, J. Casademunt, and J-F. Joanny. Active Turbulence. Annu. Rev. Condens. Matter Phys. 13, 143 (2022).

- [Alert 2020] R. Alert, J-F. Joanny, and J. Casademunt. Universal scaling of active nematic turbulence. Nat. Phys. 16, 682 (2020).

- [Martínez-Prat 2021] B. Martínez-Prat*, R. Alert*, F. Meng, J. Ignés-Mullol, J-F. Joanny, J. Casademunt, R. Golestanian, and F. Sagués. Scaling Regimes of Active Turbulence with External Dissipation. Phys. Rev. X 11, 031065 (2021).

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From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Figure 1: Active turbulence in a nematic suspension of microtubule bundles and kinesin motors. The panels show an image of the fluorescent microtubules (left), the vorticity field (center), and the kinetic energy spectrum (right). From Ref. [Alert 2022]

One Hundred Years of Modeling Conductivity of Electrolytes: What’s New with the Theories of Debye and Onsager?

Yael Avni1, Ram M. Adar2, Henri Orland3 , David Andelman1*

1 School of Physics, Tel Aviv University, Ramat Aviv 69978 Tel Aviv, Israel

2 Collège de France, 11 place Marcelin Berthelot, 75005 Paris, France

3Institut de Physique Théorique, Université de Paris-Saclay, CEA, CNRS, F-91191 Gif-sur-Yvette Cedex, France

*PRESENTER

The Poisson-Boltzmann theory stems from the pioneering works of Debye and Onsager and is considered even today as the benchmark ofionic solutions and electrified interfaces. Ithas been instrumentalduring the lastcentury in predicting charge distributions and interactions between charged surfaces, membranes, electrodes, macromolecules,and colloids.Afterabriefreview ofthe Poisson-Boltzmann theory, Iwilldiscuss theconductivity of ionic solutions, which is arguably their most important trait, being widely used inelectrochemical,biochemical, and environmental applications. The Debye-Hückel-Onsager theory successfully predicts the conductivity at very low ionic concentrations of up to a few millimolars, but there is no well-established theory applicable at higher concentrations. Iwillpresentourrecentstudy [Avni2022]of the conductivityusing a stochastic density functional theory, paired with a modified Coulomb interaction that accounts for the hard-core repulsion between the ions. The modified potential suppresses unphysical, short-range electrostatic interactions, which are present in the Debye-Hückel-Onsagertheory. Ourresults for the conductivity show very goodagreementwith experimentaldata up to 3 molars, without any fit parameters. We provide a compact expression for the conductivity, accompanied by a simple analytical approximation.

Figure 1: The conductivity, κ, of NaCl, T =25 °C, normalized by κ0 (the conductivity in the infinite dilution limit), as a function of the salt concentration n. Black dots experimental data; full blue line numerical result, dotted-dashed purple line analytical approximation; dashed red line the DHO theory.

References:

Y. Avni, R. M. Adar, D. Andelman, H. Orland (2022) Conductivity of Concentrated Electrolytes, Phys. Rev. Lett. 128, 098002.

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Motor usage imprints microtubule stability in the shaft

Mireia Andreu-Carbó1, Simon Fernandes1, Marie-Claire Velluz1 , Karsten Kruse1,2,3 , Charlotte Aumeier1,2,*

1Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland

2National Center for Competence in Research Chemical Biology, University of Geneva, 1211 Geneva Switzerland

3 Department of Theoretical Physics, University of Geneva, 1211 Geneva Switzerland *PRESENTER

Tubulindimers assemble intodynamic microtubules which are used by molecularmotors as tracks forintracellular transport. Dynamics of the microtubule network is commonly thought to be regulated at the polymer ends, but recent results show that exchange of dimers along the microtubule shaft also impacts microtubule dynamics. Here we show that molecular motors running on microtubules cause exchange of dimers along the shaft. These sites of dimer exchange act as rescue sites where de-polymerizing microtubules stop shrinking and start re-growing. Consequently, the average length of microtubules increases depending on how frequently they are used as motor tracks. We found that beyond a threshold of motor usage, microtubule length transitions from a steady state to an unlimited growth regime. We therefore demonstrate that running motors control the microtubule length and life time and regulate the polymer mass in the network through shaft dynamics in vitro and in cells. Our data show that an increase of motor activity densifies the cellular microtubule network and enhances cell polarity. Running motors leave marks in the shaft that serve as traces of microtubule usage to organize the polarity landscape of the cell.

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Wetting of yield-stress fluids

B. Géraud1, L. Jorgensen2, G. Martouzet1 , C. Barentin1*

1 Institut Lumière Matière, Université Claude Bernard Lyon 1, Villeurbanne, France 2 SIMM, ESPCI Paris, France

*PRESENTER

Yield-stress fluids such as emulsions, gels or foams exhibit interesting mechanical properties depending on the applied stress. Below a critical stress called “yield stress”, they behave like an elastic. As the stress increases, they deform plastically and finally flow like a liquid. This intermediate visco-elasto-plastic behavior makes them particularly interesting for applications (food industry, cosmetics, building industry), but fundamentally difficult to describe.

In many applications (coating, printing, imbibition), interfaces between solid surfaces and yield-stress fluids are encountered so that the understanding of their wetting properties is relevant and raises interesting fundamental questions.

During my talk, I will discuss three wetting situations: a)the capillary rise [Géraud 2014], b) the adhesion between surfaces due to a capillary bridge [Jorgensen 2015] and c) the spontaneous spreading of a drop made by a yieldstress fluid [Martouzet 2021]. In the case of simple Newtonian fluids, such experiments are classical and the wetting laws (Jurin's law or Young’s law) are well known. Here I will study the influence of the yield stress on the final capillary rise or on the final contact angle. I will also show the strong impact of the dynamic history and of the boundary conditions. More importantly, I will show that exploring the competition between surface tension, which is an equilibrium property, and yield stress effects that often keep the system out of thermodynamic equilibrium due to a dynamic arrest is possible as soon as force balance is performed.

Figure: a) Capillary rises of simple and yield-stress fluids, b) Capillary bridge of yield-stress fluid, c) Spreading on a solid surface of a drop made by a yield-stress fluid.

References:

- B. Géraud, L. Jorgensen, L. Petit, H. Delanoë-Ayari, P. Jop, C. Barentin. (2014). Capillary rise of yieldstress fluids. European Physical Letters.

- L. Jorgensen, M. Le Merrer H. Delanoë-Ayari, C. Barentin. (2015). Soft Matter.

- G. Martouzet, A.-L. Biance, C. Barentin. (2021). Dynamic arrest during the spreading of a yield stress fluid drop. Physical Review Fluids

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From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Can we compute the heat conductivity of solids?

Jean-Louis

Barrat1,*

1 Laboratoire Interdisciplinaire de Physique, Université Grenoble-Alpes

*PRESENTER

Heat transport in a crystalline, insulating solid, described by Fourier’s law, is probably the simplest conceivable nonequilibriumtransportphenomenon. Still,its understanding and prediction are ofconsiderable importance, with many recent efforts to design efficient thermoelectric materials with low heat conductivity by combining bulk and interfacialeffects. However, there exists no exactnumericalframework tocompute this transportcoefficient, even for very simple solids. One major difficulty one has to face is the fact that, even at high temperature, quantum effects are important, while quantum dynamics is numerically intractable.

In this talk, Iwill describe efforts to address this difficulty by using the PathintegralMonte-Carloapproach, which in principle gives access to time dependent correlation functions in quantum systems by simulating an equivalent classical system analogous to a system of ring polymers. While straightforward in principle, the method faces the difficult problem of inverting an ill posed problem to obtain the real time correlations from their imaginary time continuations. I will discuss how this can be achieved for correlation functions relevant to heat transport, with the hope that the method may eventually be used to obtain an exact calculation of the heat conductivity.

References:

- O.N. Bedoya-Martinez, JL Barrat, D. Rodney (2014) Computation of the thermal conductivity using methods based on classical and quantum molecular dynamics, Phys. Rev. B 89, 014303

- H. Mizuno, S. Mossa, JL Barrat (2015), Beating the amorphous limit in thermal conductivity by superlattices design, Scientific reports, 5, 14116

- V. Efremkin, J-L. Barrat, S. Mossa, M. Holzmann (2022) Time correlation functions for quantum systems: Validating Bayesian approaches for harmonic oscillators and beyond. J. Chem. Phys. 155, 134108.

Interplay between Membrane Mechanics and Membrane Proteins' Diffusion and Function

1 Physico-Chimie Curie, Institut Curie, Paris 5e, France *PRESENTER

Cell membranes are highly deformable and have to be strongly curved, for instance during trafficking when small buds form and eventually detach from cell membranes. Membrane-shaping processes always require proteins, for instance proteins with an intrinsically-curved shape. In vitro membrane systems with controlled curvature, combined to theoretical models, have been instrumental for understanding the rich interplay between membrane shape, protein concentration, activity and lateral diffusion. I will summarize some results we have obtained with in vitro membrane systems and reconstituted trans-membrane proteins. Trans-membrane proteins with a conical shape (the K+ channel KvAP) are enriched in curved membranes (membrane nanotubes) (Fig. 1A) due to their coupling to membrane curvature, while cylindrical proteins (Aquaporin 0) are not [Aimon 2014]. In addition, using smallliposomes with various diameters and single molecule FRET (Fig. 1B), we have shown thatmembrane curvature affects the conformation distribution of the ABC transporter BmrA, and thus its transport activity [In preparation]. Moreover, deviation to inclusion mobility described by Saffman-Delbrück is observed for conical trans-membrane proteins (KvAP), due to the local membrane deformation they produce(Fig. 1C) [Quemeneur 2014]. When proteins such as BmrA switch between 2 conformations using ATP hydrolysis, which confers different shapes on them, they have a bimodal mobility that is not intermediate between the 2 states of the cycle, alternating confinement and fast diffusion, which still requires to be modeled.

Figure 1: Various model membrane systems used to probe the effect of membrane curvature on protein distribution (A), protein conformation (B), or the effect of protein conformation on its own diffusion (C). A: membrane nanotube. B: small liposomes tethered to a solid surface. C: Single protein tracking at the bottom of a Giant Unilamellar Vesicle.

References:

- Aimon S., Callan-Jones A., Berthaud A., Pinot M., Toombes G.E., Bassereau P. (2014) Membrane shape modulates trans-membrane protein distribution, Dev. Cell, 28, 212-218

- Quemeneur F., Sigurdsson J.K., Renner M., Atzberger P.J., Bassereau P., Lacoste D. (2014) Shape matters in protein mobility within membranes, Proc. Natl Acad. Sci. USA, 111 5083-5087

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

A. Damm1, R. Regmi1 , S.J. Paik1, M. Dahan1 , D. Lévy1 , P. Bassereau1,*

Yigermal Bassie1, Mohammed Mahmud1 , Mulugeta

Bekele

1 Department of Physics, Wolkite University, Wolkite, Ethiopia

2Department of Physics, Addis Ababa University, Addis Ababa, Ethiopia

*PRESENTER

2*

A large number of water molecules are each placed on a lattice far apart so that they are very weakly interacting with each other and in contact with a heat bath at temperature T. A strong static electric field, E0, is applied to these molecules along a Z axis causing three level split energy values. A weak AC electric field that acts for a finite-time τ applied in the xy-plane induces transitions between the three levels. This weak AC field acts as a protocolζ, thatis switched on att=0 and switched off att=τ.Thesame cyclic process is repeated fora large number of times. The data available for this finite-time non-equilibrium process allowed us to extract equilibrium thermodynamic quantities like free energy, which is what we call Jarzynski equality and its relation to the second law of thermodynamics. The work distributions of the three-level system in the optimum condition is obtained. Besides, the averagework ofthe systemas a function ofωand time, t,around the optimumfrequency are evaluated where ω is the frequency of the AC electric field.

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

A sparcely confined water molecules undergoing finite-time cyclic process: A case study in extracting equilibrium information from non-equilibrium process

Inferring detailed broken balance and active energies from purely passive observation of active systems

Till Muenker1, Gabriel Knotz2, Matthias Krüger2 , Timo Betz1*

1 Third Institute of Physics, Georg-August University Göttingen

2 Institute of Theoretical Physics, Georg-August University Göttingen

*PRESENTER

Understanding life is arguably among the most complex scientific problems faced in modern research. From a physics perspective, living systems are complex dynamic entities that operate far from thermodynamic equilibrium. This active, non-equilibrium behavior, with its constant hunger for energy, allows life to overcome the dispersing forces of entropy and hence drives cellular organization and dynamics at the micrometer scale. Unfortunately, most analysis methods provided by the powerful toolbox of statistical mechanics cannot be used in such non-equilibrium situations, forcing researchers to use sophisticated and often invasive approaches to study the mechanistic processes inside living organisms. Inspired by Onsager's regression hypothesis, we introduce here a Mean Back Relaxation (MBR) observable, which detects active motion in purely passive measurements of particle fluctuations [Muenker 2021]. The MBR, which is based on three-point probabilities, is theoretically and experimentally shown to exhibit markers of non-equilibrium, i.e., of detailed balance-breaking dynamics. We furthermore observe an astonishing relation between the MBR and the effective non-equilibrium energy in living cellular systems. This is used to successfully predict the viscoelastic response function and the complex shear modulus from a purely passive approach, hence opening the door for rapid and simple passive mechanics measurements even in active systems.

Figure 1: The mean back relaxation (MBR) quantifies a correlation at three different times. a) Schematic of a particle in a harmonic potential. When the particle has moved from the equilibrium position to an excited state in time τ, it will on average go back to the equilibrium position. Contrary, when it moved from an excited state to equilibrium, it will on average stay there in the future. b) The MBR relies on particle trajectories that fulfill the condition of a displacement d in the history τ. This can be visualized by shifting the original trajectory (red) by these parameters (gray). The crosspoints mark the trajectories that obey both conditions. c) The average (black) of many (here 10 000, red) such reconditioned trajectories defines the MBR. In blue is the example trajectory from panel a.

References: Muenker, T. M.; Knotz, G.; Krüger, M.; Betz, T. “Onsager Regression Characterizes Living Systems in Passive Measurements” bioRxiv 2022. https://doi.org/10.1101/2022.05.15.491928.

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Morphogenesis of anisotropic cell monolayers by integer topological defects

C. Blanch-Mercader1,2,4,*, P. Guillamat1, A. Roux1,3, K. Kruse1,2,3

1 Department of Biochemistry, Université de Genève, CH-1211 Genève, Switzerland

2 Department of Theoretical Physics, Université de Genève, CH-1211 Genève, Switzerland

3 NCCR for Chemical Biology, Université de Genève, CH-1211 Genève, Switzerland

4Current affiliation: Institut Curie, Université PSL, Sorbonne Université, CNRS, UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France.

*PRESENTER

Tissues made of anisotropic cells can exhibit features of liquid crystals, such as long-ranged orientational order and topological defects. During the development of organisms, such features often influence shape formation. However, the linkage between geometry, topological defects and tissue mechanics remains largely unexplored. First, I will show how can we build on the physics of liquid crystals to determine material parameters of cell monolayers. In particular, we use a hydrodynamical description of a 2d active liquid crystal to study the steadystate mechanical patterns around integer topological defects and apply our approach to spindle-shaped myoblast cellmonolayers insmallcircularconfinements, whichspontaneouslyformasterorspiraltopologicaldefects.Next, I will discuss how these findings can help one interpreting with mechanics a secondary transition from 2d cell monolayers to 3d multicellular structures, such as mounds or protrusions. Finally, I will discuss some preliminary results on the effects of curvature-order couplings on the formation of shapes by integer defects.

P. Guillamat and the presenter contributed equally to this work.

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From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Compressibility and porosity modulate the mechanical properties of giant gas vesicles

Gregory Beaune 1 and Françoise Brochard-Wyart 2,*

1Aalto university School of Science , Finland

2Institut Curie, Sorbonne Université France

*PRESENTER

Gas vesicles, used as contrastagents for noninvasive ultrasound imaging must be formulated to be stable, and their mechanical properties must be assessed. We report here the formation of perfluoro-n -butane microbubbles coated with hydrophobinsurface-active proteins thatare produced by filamentous fungi(HFBI fromTrichoderma reesei). Using pendant drop and pipette aspiration techniques, we show that these giant gas vesicles behave like glassy polymersomes, and we discover novel gas extraction regimes. We develop a model to analyze the micropipette aspiration of these compressible gas vesicles and compare them to incompressible liquid-filled vesicles. We introduce a sealing parameter to characterize the leakage of gas under aspiration through the pores of the protein coating. Utilizing this model, we can determine the elastic dilatation modulus, surface viscosity, and porosity of the membrane. These results demonstrate the engineering potential of protein-coated bubbles for echogenic and therapeutic applications and extend the use ofthe pipette aspiration technique tocompressible and porous systems.

Figure 1: Aspiration of a giant gas vesicle (A–C) in a liquid-like regime and (D–F) in a glassy regime.

References:

- A.Bar-Zion, M. G. Shapiro (2021) Acoustically triggered mechanotherapy using genetically encoded gas vesicles Nature Nanotechnology

- E. Evans, D. Needham (1987) Physical properties of surfactant bilayer membranes: Thermal transitions,J. Phys. Chem. 91

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Defect-mediated morphogenesis

1 Instituut-Lorentz, Universiteit Leiden, P.O. Box 9506, 2300 RA, Leiden, Netherlands.

2 Physics of Life Processes, Leiden Institute of Physics, Universiteit Leiden, P.O. Box 9506, 2300 RA, Leiden, Netherlands.

*PRESENTER

It has been a long-standing mystery how complex biological structures emerge during embryonic development from such seemingly uncoordinated building blocks as cells and tissues without guidance. Recent experiments have suggested that misalignment in the collective structure of tissues –the so called topological defects– could play a fundamental guiding role in morphogenesis.

Inspired by tentacle development in the Hydra and using a combination of linear stability analysis and computational fluid dynamics we demonstrate that active layers, such as cell monolayers, are unstable to the formation of protrusions in the presence of disclinations. To this aim, we considered a thin layer of active polar gel [Marchetti 2013] confined at the interface between two passive and isotropic fluids in a cylindrical geometry to stabilize a +1 topological defect. Under the effect of the active stress, the system generates in-plane vortical flows, consistently with a classic result by Kruse et al. [Kruse 2004]. Importantly, this active flow yet plays a crucial role in driving the active membrane out of its flat configuration and buckle out of plane. Indeed, the buckling instability, analytically predicted here, originates from the interplay between the focusing of the elastic forces, mediated by defects, and the renormalization of the system’s surface tension due to the active vortical flow [Hoffmann 2022a].

Finally, to make progress beyond analytical predictions, we support our findings with 3D numerical simulations. First, we recover the predicted instabilities, then we focus on the post-transitional scenario and we find a plethora of complex morphodynamical processes, such as oscillatory deformations, droplet nucleation (see Figure 1), and active turbulence. Analogous instabilities also appear in spherical topologies [Hoffmann 2022b].

Figure 1: Simulation snapshots at different times during the process of droplet nucleation. First the active membrane buckles out of plane in correspondence of the topological defect, then stresses driven by surface tension and elastic effects lead to the breaking of the interface and the consequent nucleation of a droplet.

References:

- M. C. Marchetti, J. F. Joanny, S. Ramaswamy, T. B. Liverpool, J. Prost, Madan Rao, and R. Aditi Simha. (2013) Hydrodynamics of soft active matter. Rev. Mod. Phys. 85, 1143.

- K. Kruse, J. F. Joanny, F. Jülicher, J. Prost, and K. Sekimoto. (2004) Asters, Vortices, and Rotating Spirals in Active Gels of Polar Filaments. Phys. Rev. Lett. 92, 078101.

- L. Hoffmann, L. N. Carenza, J. Eckert and L. Giomi. (2022a) Sci. Adv. 8, eabk2712.

- L. Hoffmann, L. N. Carenza and L. Giomi. (2022b) arXiv preprint. arXiv:2205.06805.

Livio N. Carenza1*, Ludwig A. Hoffmann2 , Julia Eckert2 , Luca Giomi1

Wall slip of complex fluids: from slip length to Navier's friction coefficient

B. Cross 1, C. Barraud1 , F. Restagno2, L. Léger2 , E. Charlaix 1,*

1 LiPHy, Université Grenoble Alpes, Grenoble, France

2 Laboratoire de Physique des Solides, Université Paris Sud, F-91405 Orsay, France

*PRESENTER

Flow of complex liquids are familiar and useful. Unlike Newtonian fluids, they display complex bulk rheological behaviors, and have also a different way to flow on solid surfaces. This is of practical importance in micro and nano-fluidics systems, bio-medical applications, oil engineering, and many industrial applications. A generic question with the boundary flow of complex liquid is to understand how it relates to the interfacial structure, boundary interactions, and adsorption. In this talk I will address the case of viscoelastic polyelectrolytes exhibiting large slippage at wall. The slippage is usually attributed to a depletion layer at interface whose origin, properties and interactions with the flow are poorly understood. I will show that the measurement of equilibrium and dynamic surface forces allows to bridge comprehensively the interfacial structure, interactions, and flow properties. An important result is that the usual notion of slip length is it not appropriate for complex liquids, and that the original Navier’s condition should be used to describe their boundary flow.

References:

- C. Barraud, B. Cross, C. Picard, L. Leger, F. Restagno, E. Charlaix (2018) Wall slip of complex fluids: interfacial friction versus slip length, Physical Review Fluids

- C. Barraud, B. Cross, F. Restagno, L. Leger, E. Charlaix (2019) Large slippage and depletion layer at the polyelectrolyte /solid interface , Soft Matter

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Glassy Dynamics in Chiral Fluids

V.E. Debets1*, H. Löwen2, L.M.C. Janssen1

1 Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands 2 Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, D-40225 Düsseldorf, Germany

*PRESENTER

Chiral active matter is enjoying a rapid increase of interest, spurred by the rich variety of asymmetries that can be attained in e.g., the shape or self-propulsion mechanism of active particles [Bowick, 2022]. For a collection of these chiral particles, that is, a chiral active fluid, this has already led to the experimental and theoretical observation ofawealthofdistinctand intriguing featuressuchashyperuniformity, odd viscosity,and theformation of spontaneously rotating crystals. An exploration of chiral liquids into the glassy regime is, however, still fundamentally lacking. We will discuss how the inclusion of chirality (circle swimming) in active glassy matter can give rise to unexpected and new dynamical phenomena, especially compared to a standard linear active glassy fluid. Despite the added complexity, we present a full rationalization for all identified dynamical regimes of our chiral glassy fluid [Debets, 2022]. Most notably, we introduce a new 'hammering' mechanism, unique to rapidly spinning particles in high-density conditions, that can fluidize a chiral active solid (see Fig. 1).

Figure 1: (a-c) Schematic depiction of the 'hammering' effect. (a-b) For large enough persistence and spinning frequency, particles undergo back-and-forth motion inside their cage and systematically collide with the same particle whose motion is slightly altered by the collision. (c) After repeated collisions the cage of a particle is sufficiently remodeled such that the particle can break out and migrate through the material.

References: - M.J. Bowick et al. (2022) Symmetry, Thermodynamics, and Topology in Active Matter, Phys. Rev. X. - V.E. Debets, H. Löwen, L.M.C. Janssen. (2022) Glassy Dynamics in Chiral Fluids, arXiv:2210.03196 (Accepted for publication in Phys. Rev. Lett.).

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From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Topology and geometry organize the morphogenesis of active nematic surfaces

Dessalles1*, Mathieu Dedenon1, Karsten Kruse1, Aurélien Roux1

1 Department of Biochemistry, University of Geneva, CH-1211 Geneva, Switzerland

*PRESENTER

Morphogenesis, the process by which tissues acquire their shape, hinges on a finely orchestrated collective motion of cells autonomously choreographing themselves to a well-defined final position. Accumulating evidence shows that many biological tissues behave as active nematics, both in vitro and in vivo. The collective motion of cells is controlled by the nematic order, and topological defects - regions where the order is lost - have been proposed as morphogenic organizers through their role in organizing active stresses [Guillamat 2022]. For instance, in Hydra, the nematic organization of actin fibers across endoderm cells is correlated with morphogenetic events such as the subsequent formation of the mouth and the foot. However, the generation and control of tissue-scale forces involved in morphogenesis remain poorly understood, in particular within 3D surfaces.

The goal of my project is to understand how geometry and topology controls the spontaneous organization of cells that drives morphogenesis, i.e. the growth from a 3D surface to tissues with complex shapes. To investigate this phenomenon, I grow cells on the surface of deformable capsules [Trushko 2020] and monitor the nematic field, cellular flows, and tissue growth. Capsule shape can be altered, to control the local gaussian curvature and its anisotropy. Shell rigidity can be tuned, and forces inferred from the elastic deformations of the shell.

The nematic field is shown to depend on confinement and curvature. Confinement on a surface of finite area constrains the number of defects, while the topology of a surface dictates the totalnematic charge, +2 in the case of our spherical capsules. Indeed, four equidistant +1/2 defects are observed in the actin network of a monolayer of C2C12 on a spherical capsule. Furthermore, the contribution of the anisotropy of curvature pushes defects from regions of high anisotropy towards the poles, as seen on the surface of ellipsoidal capsules.

Subsequent growth of the monolayer shows the formation of multilayers with orthogonal orientation. The high long-range contractile stresses due to the nematic ordering leads to anisotropic folding of the capsule or the formation of an oscillating aggregate, depending on the level of surface adhesion. The oscillations correspond to alternating phases of wetting-dewetting influenced by topology changes. In future work, by quantifying cell motion, collective alignment, and stress fields as a response to topology and geometry, I aim uncover the coupling terms between nematic order and stress fields that shape tissues.

References:

- Trushko, …, Roux. (2020) Buckling of an Epithelium Growing under Spherical Confinement, Developmental Cell.

- Guillamat, …, Roux. (2022) Integer topological defects organize stresses driving tissue morphogenesis, Nature materials.

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Claire

Figure 1: Mercator projection of the actin network of C2C12 cells on a spherical capsule showing four +1/2 topological defects.

Pulsating active matter

Yiwei Zhang and Étienne Fodor*

Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg

*PRESENTER

Cells in tissues consume fuel to sustain periodic mechanical deformation [Zehnder 2015]. The combination of individual deformation and local interactions yields contraction waves, propagating throughout tissues with only negligible cell displacement [Serra-Picamal 2012]. We consider a model of dense repulsive particles whose activity drives periodic change in size of each individual [Zhang 2022]. It reveals that, in dense environments, pulsation of synchronised particles is a generic route to contraction waves.The competition between repulsion and synchronisation triggers an instability which promotes a wealth of dynamical patterns, ranging from spiral waves to defect turbulence. We identify the mechanisms underlying the emergence of patterns, and characterize the corresponding transitions. We derive the hydrodynamics of our model, and propose an analogy with that of reaction-diffusion systems.

Figure 1: Repulsive particles with pulsating size yield contraction waves: (a) planar, (b) spiral, (c) circular, and (d) turbulent. Waves propagation (black arrows) stabilizes dynamical patterns reminiscent of reaction-diffusion systems

References:

- S. Zehnder, M. Suaris, M. Bellaire, and T. Angelini. (2015) Cell volume fluctuations in MDCK monolayers, Biophys. J.

- X. Serra-Picamal, V. Conte, R. Vincent, E. Anon, D. T. Tambe, E. Bazellieres, J. P. Butler, J. J. Fredberg, and X. Trepat. (2012) Mechanical waves during tissue expansion, Nat. Phys.

- Y. Zhang and É. Fodor. (2022) Pulsating active matter, arXiv:2208.06831.

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Activating Active Matter

Stephan Grill1*

1 MPI-CBG, Pfotenhauer Str. 108, 01307 Dresden, Germany

*PRESENTER

One of the most remarkable examples of self-organized structure formation is the development of a complex organism from a single fertilized egg. With the identification of many molecules that participate in this process of morphogenesis, attention has now turned to capturing the physical principles that govern the emergence of biological form. What are the physical laws that govern the dynamics and the formation of structure in living matter? Much of the force generation that drives morphogenesis stems from the actomyosin cortical layer inside cells, which endows the surface of the cell with the ability to generate active forces and stresses that can drive reshaping. We combine theory and experiment and investigate how the actomyosin cell cortex self-contracts, reshapes and deforms, and how these physical activities couple to regulatory biochemical pathways to give rise to the emergenceofshape inlivingsystems. Aparticularfocuswillbe the investigation ofhowan actomyosincortical layer is formed for the first time at the oocyte to embryo transition in the nematode worm.

Nuclear Chromodynamics

Alexander Y. Grosberg1*

1 Department of Physics and Center for Soft Matter Research, New York University, New York, NY 10003, USA

*PRESENTER

In this talk, I will review the results of the recent works [Eshghi 2022, Eshghi 2023] performed together with Iraj Eshghi and Alexandra Zidovska. We develop a theoretical explanation of the observed micron and second scale coherent motions in chromatin based on hydrodynamic description of active two-fluid system - polymeric genome soaked by nucleoplasm. We discoverthatalthough active proteins incellnucleus are too dilute tointeractdirectly, they can nevertheless cooperate toproduce large scale coherentchromatin motions. Cooperation becomes possible if each motor couples chromatin polymer with surrounding nucleoplasmic fluid, exerting on them equal and opposite forces (the model illustrated in Fig. A). These motors can generate flows of solvent past polymer, and these flows can feedback on motors orientation. Thus, the active polar (“ferromagnetic”) phase can spontaneously form if the drive is strong enough. Depending on the force and concentration of motors, polar order arises through a phase transition, accompanied by critical slowing down. Depending on boundary conditions, either transverse flows (Fig. B) or sustained longitudinal oscillations (Fig. C) or waves are possible. Predicted time and length scales are consistent with experiments.

Figure 1: Sketch of our model and the two types of solutions. A: Example of a region of disordered polymer and attached force dipoles, with a zoomed-in section where the variables describing the microscopic features of the motors are shown. B: Sketch of the transverse solution in a spherical domain, showing the polar alignment of the sources and the sustained solvent flow being pumped in the opposite direction of their orientation. C: Sketch of the longitudinal, oscillatory solution to the equations of motion. Dashed arrows show the relaxational (osmotic) flow of polymer in the absence of active forces, which seeks to even out density fluctuations. Solid arrows show the active polymer flow induced by the sources. Time goes from the upper panel to the lower one.

References:

- Iraj Eshghi, Alexandra Zidovska, Alexander Y. Grosberg (2022) Symmetry-Based Classification of Forces Driving Chromatin Dynamics, Soft Matter, 18, 8134 - 8146.

- Iraj Eshghi, Alexandra Zidovska, Alexander Y. Grosberg (2023) Chromatin as a Polar Active Fluid, in preparation.

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From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Mechanochemical instabilities of epithelial sheets

Edouard Hannezo1,*

1 IST Austria, Am Campus 1, 3400 Klosterneuburg, Austria

*PRESENTER

There is increasing evidence that both mechanical and biochemical signals play important roles in morphogenesis and collective cell migration. The development of complex organisms, in particular, has been proposed to rely on the feedback between mechanical and biochemical patterning events. However, integrating the two in a theoretical framework capable of making meaningful and quantitative predictions has remained challenging. Here, I will discuss two examples of our current efforts towards this. I will first present work on intestinal organoid morphogenesis, which relies on an interplay between cellularfate, tissue geometry and osmotic/cytoskeletalforces [Yang*, Xue* et al, 2021, Xue*, Yang* et al, in prep]. I will then talk about how mechanochemical waves in 1D and 2D vertex models, and how cells use them for optimal long-ranged polarization in wound healing [Boocock*, Hino* et al, 2020, Boocock et al, in prep].

References: - D. Boocock*, N. Hino* et al, (2020) Theory of mechano-chemical patterning and optimal migration in cell monolayers. Nat Phys - Q. Yang*, S.-L. Xue* et al, (2021) Cell fate coordinates mechano-osmotic forces in intestinal crypt formation Nat Cell Biol

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Concentration-driven instability in polar active suspensions

Purnima Jain1*, Navdeep Rana2, Sriram Ramaswamy3, and Prasad Perlekar1

1 Tata Institute of Fundamental Research, Hyderabad, India 2 Max Planck Institute for Dynamics and Self-Organization, Göttingen, German 3 Indian Institute of Science, Bangalore, India

*PRESENTER

Active Polar Fluids consist of head-tail asymmetric self-propelled particles (SPPs) suspended in a fluid medium. Theyshowspectacularcollectivebehavioracrossa broadrangeoflength scales, forexample, bacterialsuspensions at the microscopic level to fish schools in an ocean. In the Stokesian regime, where viscosity dominates over inertia, the flocking state is unstable to small perturbations [Simha 2002]. This instability leads to complex spatiotemporal flows also known as Active Turbulence. Recent works have shown that inertia can stabilize the ordered state and drives a flocking transition from defect turbulence to noisy but aligned states [Chatterjee 2021]. However, these results are limited to the regime where concentration relaxes quickly and is not considered a hydrodynamic variable of the system. We show that when concentration fluctuations are taken into account, a hitherto unseen instability of the ordered state arises. This instability occurs from the interplay of inertia, the selfpropulsion speed of SPPs, and concentration fluctuations. Using high-resolution direct numerical simulations we show that it leads to new kinds of non-equilibrium steady states which are absent in the concentration-free limit. We call these states as Motility-Induced Wave Turbulence.

References:

- Simha, R. Aditi, and Sriram Ramaswamy. "Hydrodynamic fluctuations and instabilities in ordered suspensions of self-propelled particles." Physical Review Letters 89.5 (2002): 058101.

- Chatterjee, Rayan, et al. "Inertia drives a flocking phase transition in viscous active fluids." Physical Review X 11.3 (2021): 031063.

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Figure 1: Concentration waves due to new instability. Lower Concentration (Blue) and higher concentration (yellow).

Star Polymers: critical vs. stretched

Albert Johner1*

1 Institut Charles Sadron, Strasbourg University, C.N.R.S., Strasbourg, France.

*PRESENTER

Starpolymers are composedoflong polymeric arms radiating froma centralcore. Wesolvea seemingly unnoticed contradiction between two theories of star homopolymers both well established for decades. Asymptotically exact renormalization group results for large stars at the θ-point in three dimensions qualitatively strongly disagree with mean-field results. This is unexpected because the mean field should be marginally correct in three dimensions (the uppercriticaldimension foreffective three-body interactions). We show thatthe two theories actually describe different physical situations: unstretched stars with (very) large arms and (relatively) low functionality and crowded stretched stars. The available RG results apply to very large, not so crowded stars where the arms are essentially unstretched. Explicitly, the arm size has to be exponentially large in the functionality squared. Stars with a reasonable number of arms, say ten or more, do typically not belong to this regime, while the four-arm stars relevant to standard contact probabilities do. To a lesser extent a similar conflict between theories did exist for thin molten layers of linear polymers. From a formal point of view the reason is the following: In 2d the noncrossing constraint is relevant to the polymer statistics (in 3d it is only relevant to the polymer dynamics). Thin layers can be seen as 2d layers with crossings.

Relationships between chemical and physical alterations of historical oil-based pictorial

paintings: craquelures and metal ion-migration

P. Kékicheff1,2*, T. Roland1, A. Egele1, D. Favier1, L. Tranchant2, S. Schoeder2 , F. C. Izzo3, L. Fuster-López4, C. K. Andersen5, M. F. Mecklenburg6

*PRESENTER

1 Institut Charles Sadron, Strasbourg University, C.N.R.S., Strasbourg, France; 2 Synchrotron SOLEIL, Saint Aubin, France; 3 Ca’ Foscari Venezia, Mestre Venezia, Italy; 4 Univ. Politècnica de València, Spain; 5 The Royal Danish Academy of Fine Arts, Copengagen, Denmark; 6 Museum Conserv. Instit., Smithsonian Institution, Maryland, USA

Oil paintings are subject to slow deterioration processes that affect their appearance and structural integrity. Ongoing reaction between metal ions (from metal-containing pigments) and free fatty acids (from hydrolyzed triglycerides of the oil binding medium and additives) leads to the formation of metal carboxylates (soaps). These complexes of metal ions (usually lead and zinc) and long-chain saturated fatty acids can induce craquelures, form large crystalline aggregates that may protrude through the paint surface, lead to spalling, cracking, brittleness, delamination, and the development of pimpled surfaces on artworks.1-3 Despite progress in the understanding of metal soap formation, many issues are still unresolved. One concerns the connections between chemical (hydrolysis, metal soap formation, oxidation state) and physical alterations of the multilayered structure leading to the formation of craquelure patterns. Another one is related to the diffusion of metal ions through the paint layers matrix: they may likely migrate in their hydrated form assisted by the diffusion of water via interconnected channels and pores of various sizes, ultimately forming soaps,2,3 or through an ion hopping mechanism in the glassy or rubbery polymeric matrix. However, the exact mechanism of metal ion diffusion remains difficult to quantify, especially since no direct measurement of the coefficient of diffusion, D, of metal ions has so far been reported for paint layers that have naturally aged.

Several examples will illustrate the relationships between the chemical nature of metal ions and aging craquelure formation:4-6 At SOLEIL synchrotron, France, using specimens from historical easel paintings (XVIXIX century oil on wood and canvas panels) we combine microtomography, 2D micrometric maps of X-ray fluorescence for speciation (µ-XRF; 10x10 µm step size), and XANES, to determine the correlation functions.

The metal ion-migration issue is addressed, also at SOLEIL, using specimens from samples in well controlled 2-layers paints.6 This collection of oil films belongs to the Mecklenburg’s Paint Reference Collection at the Smithsonian MuseumConservation Institute, USA, and is unique inthe world. A 100 µm thick white lead pigment in cold pressed linseed oil was applied on polyester film in 1990 and allowed to dry in controlled environmental conditions during a 15–25 years period. Then, a second 100 µm ochre-orange colored paint film (Fe-based pigment) was applied on top. The Fe concentration profile across the interface separating the ochre layer with the pure Pb-white layer is measured by µ-XRF; in addition, µ-XANES spectroscopy and µ-XRD confirm the presence ofFe ions thathave migrated intothe pure Pb-white layeroverthe ~20 years period. Fromthe concentration profile a coefficient of diffusion can be inferred: D ~ 5x10-17 m2/s (i.e. ~ 1600 µm2/year). The analysis uses numerical simulations of the diffusion mechanism by comparing the classical Fick’s law with non-Fickian behaviors within a framework of finite elements to describe accurately the complex morphometry of the 2-layers paint sample (geometry, interface curvature, inhomogeneities, small air bubbles and voids, etc.).6 To our knowledge, this is the first time that a coefficient of diffusion of metal ions migrating in a pictorial paint panel is reported.

References:

1. Mecklenburg, M.F.; Tumosa, C.S.; Erhardt, D.; Structural response of painted wood surfaces to changes in ambient relative humidity, In: V. Dorge & F.C. Howlett (Eds.), Painted Wood: History and Conservation, The Getty Conservation Institute, 464-483 (1998).

2. Chen-Wiegart, Y.K.; Catalano, J.; Williams, G.J.; Murphy, A.; Yao, Y.; Zumbulyadis, N.; Centeno, S.A.; Dybowski, C.; Thieme, J.; Elemental and molecular segregation in oil paintings due to lead soap degradation, Sci. Rep. 7, 11656, 1-9 (2017).

3. Eumelen, G.J.A.M.; Bosco, E.; Suiker, A.S.J.; van Loon, A.; Iedema, P.D.; A computational model for chemo-mechanical degradation of historical oil paintings due to metal soap formation. J. Mech. Phys. Solid. 132, 1-21 (2019).

4. Bratasz, Ł.; Akoglu, K.G.; Kékicheff, P.; Fracture saturation in paintings makes them less vulnerable to environmental variations in museums, Heritage Science 8, 11, 1-12 (2020).

5. Janas, A.; Mecklenburg, M.F.; Fuster-López, L.; Kozłowski, R.; Kékicheff, P.; Favier, D.; Andersen, C.K.; Scharff, M.; Bratasz, Ł.; Shrinkage and mechanical properties of drying oil paints, Heritage Science 10, 181, 1-10 (2022).

6. Kékicheff, P. et al.; to be submitted (2023).

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From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

29

Topological Constraints Do Matter

Jan Smrek2 , Kurt Kremer1*

1 Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany

2 Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria

*PRESENTER

Mixtures of two kind of particles, where the only difference is stemming from the coupling of the particles to two thermostats at different temperatures can phase segregate into regions of predominantly ‘hot’ and ‘cold’ particles, if the ratio of temperatures is high enough. For single particles the required hot/cold temperature ratio is too high for any experimental realization. For polymers, however, just as in classical polymer mixture phase separation, this ratio becomes chain length dependent and decreases dramatically with chain length. For a melt of nonconcatenated rings, where one part of the ring is a ‘hot’ and one a ‘cold’ block, this leads to dramatic conformation changes and eventually to an activity stabilized topological glass.

Figure 1: The mean radius of gyration obtained as an average over all rings at a given time t after the onset of activity. Insets: snapshots of two rings in equilibrium (left) and two at late times (right). The hot segment on the active rings is shown in orange (on the equilibrium rings the orange segment is highlighted for comparison only and has the same temperature as the rest of the system). From Smrek et al. Nat. Comm. 2020

References:

- Halverson, J. D., Smrek, J., Kremer, K. & Grosberg, A. Y. From a melt of rings to chromosome territories: the role of topological constraints in genome folding. Rep. Prog. Phys. 77, 022601 (2014).

- Grosberg, A. Y. & Joanny, J.-F. Nonequilibrium statistical mechanics of mixtures of particles in contact with different thermostats. Phys. Rev. E 92, 032118 (2015)

- Smrek, J. & Kremer, K. Small activity differences drive phase separation in active-passive polymer mixtures. Phys. Rev. Lett. 118, 098002 (2017).

- Smrek, J., Chubak, I., Likos, C. N., Kremer, K., Active topological glass, Nat. Commun. 11, 26 (2020)

➔ Table of contents

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Localized states in active fluids

Luca Barberi1 , Karsten Kruse1,*

1 Depts. of Biochemistry and Theoretical Physics, University of Geneva, 30, Quai Ernest-Ansermet, 1211 Geneva, Switzerland

*PRESENTER

Biologicalactive matteris typically tightlycoupled to chemicalreaction networks affecting its assembly and stress generation. We show that localized states can emerge spontaneously if assembly of active matter is regulated by chemical species that are advected with flows resulting from gradients in the active stress. The localized patterns form at a subcritical instability and for parameter values for which patterns do not existin absence of the advective coupling. They come in a large variety and also comprise localized oscillatory and chaotic states. Our work identifies a generic mechanism underlying localized cellular patterns.

Figure 1: Spontaneous localization in the actomyosin cortex. a) Pictorial representation of a localized state. b) Biochemical processes included in our theory: 1) spontaneous disassembly of actomyosin, 2) nucleator-mediated assembly of actomyosin, 3) spontaneous activation of nucleators, 4) cooperative activation of nucleators, 5) actomyosin-mediated deactivation of nucleators.

References: - L. Barberi, K. Kruse. (2022) Localized states in active fluids, arXiv:2209.02581.

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

1

Control of nuclear size by osmotic forces in Schizosaccharomyces pombe

Joël Lemière1*, Zhidong Tan1, Paula Real Calderon1,2, Liam J Holt3, Thomas G Fai4, Fred Chang1

Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, United States

2 Centro Andaluz de Biología del Desarrollo, Sevilla, Spain

3 Institute for Systems Genetics, New York University Langone Health, New York, United States

4 Department of Mathematics and Volen Center for Complex Systems, Brandeis University, Waltham, United States

*PRESENTER

The size of the nucleus scales robustly with cell size so that the nuclear-to-cell volume ratio (N/C ratio) is maintained during cell growth in many cell types [Conklin 1912, Gregory 2005, Neumann 2007, Willis 2016] The mechanism responsible for this scaling remains mysterious. Previous studies have established that the N/C ratio is not determined by DNA amount but is instead influenced by factors such as nuclear envelope mechanics and nuclear transport [Cantwell 2019, Finan 2009]. Here, we developed a quantitative model for nuclear size control based upon colloid osmotic pressure and tested key predictions in the fission yeast Schizosaccharomyces pombe. This model posits that the N/C ratio is determined by the numbers of macromolecules in the nucleoplasm and cytoplasm. Osmotic shift experiments showed that the fission yeast nucleus behaves as an ideal osmometer whose volume is primarily dictated by osmotic forces. Inhibition of nuclear export caused accumulation of macromolecules in the nucleoplasm, leading to nuclear swelling. We further demonstrated that the N/C ratio is maintained by a homeostasis mechanism based upon synthesis of macromolecules during growth. These studies demonstrate the functions of colloid osmotic pressure in intracellular organization and size control.

Figure 1: (A) Schematic of the model of the nucleus and the cell as “a vesicle within a vesicle”, osmotically challenged, and parameters used in the mathematical model: membrane tension σ, non-osmotic volume b, number of macromolecules that cannot freely cross either the cell or nuclear membranes (N), concentration of the buffer Cout . (B) Predictions of osmotic shifts on the N/C ratio for various nuclear membrane tensions (σN), keeping cell tension (σC) constant.

References:

- E. G. Conklin. (1912) Cell size and nuclear size, J. Exp. Zool.

- T. R. Gregory, B. K. Mable. (2005) Polyploidy in Animals, The Evolution of the Genome

- F. R. Neumann and P. Nurse. (2007) Nuclear size control in fission yeast, J. Cell Biol.

- Willis L, Refahi Y, Wightman R, Landrein B, Teles J, Huang KC, Meyerowitz EM, Jönsson H. (2016) Cell size and growth regulation in the Arabidopsis thaliana apical stem cell niche, PNAS

- Cantwell H, Nurse P. (2019) A systematic genetic screen identifies essential factors involved in nuclear size control, PLOS Genetics

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From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Chemically Active Wetting

1 University of Augsburg, Germany

2 Max-Planck Institute for Complex Systems, Germany *PRESENTER

In living cells, wetting of condensed phases on membrane surfaces provides a mechanism for positioning biomolecules. Biomolecules are also able to bind to such membrane surfaces. In living cells, this binding is often chemically active as it is kept out of equilibrium by the supply of energy and matter. Here, we investigate how active binding on membranes affects the wetting of condensates. To this, we derive the non-equilibrium thermodynamic theory of active wetting. We find that active binding significantly alters the wetting behavior leading to non-equilibrium steady states with condensate shapes reminiscent of a fried egg or a mushroom. We further show that such condensate shapes are determined by the strength of active binding in the dense and dilute phases, respectively. Strikingly, such condensate shapes can be explained by an electrostatic analogy where binding sinks and sources correspond to electrostatic dipoles along the triple line. Through this analogy, we can understand how fluxes at the triple line control the three-dimensional shape of condensates.

- Finan JD, Chalut KJ, Wax A, Guilak F. (2009) Nonlinear osmotic properties of the cell nucleus, Annals of Biomedical Engineering

Susanne Liese1*, Xueping Zhao2 , Frank Jülicher2, Christoph Weber1

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From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Active fluid interfaces

M. Cristina Marchetti1,*

Department of Physics

UC Santa Barbara Santa Barbara, CA, 93108, USA

*PRESENTER

There are many situations where active fluids coexist with passive ones. In bacterial swarms internal boundaries form separating cells of different type or separating live and dead cells. In cell biology the evidence for the formation of membraneless organelles has fueled interest in the role of active processes in liquid-liquid phase separation. Inspired by recentexperiments by the group of ZvonimirDogic, we have used numericaland analytical methods to explore how activity can both arrest and suppress phase separation in an immiscible fluid mixture that phase separates when passive. Active stresses and associated flows additionally modify the properties of the soft fluid interfaces. Experiments and theory have revealed a wealth of intriguing phenomena, including giant interfacial fluctuation, traveling interfacial waves, activity suppressed phase separation, and activity controlled wetting transitions.

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Mechanochemical Rules for Shape-Shifting Filaments that Remodel Membranes

Billie Meadowcroft1,2*, Ivan Palaia2 , Anna-Katharina Pfitzner3, Aurélien Roux3, Buzz Baum4 , Anđela Šarić2

1University College London, London WC1E 6BT, United Kingdom 2Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria 3Biochemistry Department, University of Geneva, CH-1211 Geneva, Switzerland

4MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge CB2 1TN, United Kingdom

*PRESENTER

Membrane reshaping proteins are important for a number of physiological cellular processes such as vesicle and viral budding, cell division and membrane repair. The sequential exchange of filament composition to increase filament curvature was proposed as a mechanism for how ESCRT-III polymers deform and cut membranes. The relationship between the filament composition and its mechanical effect is lacking. Here, I will speak about our kinetic model for the assembly of composite filaments that includes protein membrane adhesion, filament mechanics and membrane mechanics. We identify the physical conditions for such a membrane remodeling and show this mechanism is efficient because sequential polymer assembly lowers the energetic barrier for membrane deformation.

Figure 1: The geometry of a membrane-bound filament has been proposed to change together with its composition, driving membrane remodeling for cargo transport.

References: - Billie Meadowcroft, Ivan Palaia, Anna Katerina-Pfitzner, Aurelién Roux, Buzz Baum, Anđela Šarić (2022) Mechanochemical rules for Shape-Shifting Filaments that Remodel Membranes, Physical Review Letters.

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From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

What can stabilize oriented tissue deformation?

Muhamet Ibrahimi1 , Matthias Merkel1*

1 Turing Center for Living Systems, CNRS, Centre de Physique Théorique ( CPT, UMR 7332), Aix Marseille Université, Marseille, France *PRESENTER

Oriented tissue deformation is a fundamental process omnipresent during animal development. However, how exactly cells coordinate to achieve robust oriented deformation on the tissue scale remains elusive. From a physics perspective, deforming tissues can be described as oriented active materials. However, it is known that oriented active materials can inherently exhibit instabilities such as the Simha-Ramaswamy instability. This instability destroys the homogeneously deforming state of active materials. We want to understand: How is this instability prevented during animal development? In particular, we ask whether the presence of a chemicalsignaling gradient (e.g. a morphogen gradient) can help stabilize oriented tissue deformation. Using a combination of vertex and hydrodynamic models, we find that stability depends on whether the signaling gradient acts to extend or contract the tissue along the gradient direction. In particular, gradient-extensile coupling can be stable, while gradientcontractile coupling is generally unstable. Intriguingly, developing tissues seem to exclusively use the gradientextensile and not the unstable gradient-contractile coupling, suggesting that the instability discussed here might act as an evolutionary selection criterion. Our work thus points to a potential developmental principle that is directly rooted in active matter physics.

Figure 1: Vertex model simulations. (a) Active polar tissues display the well-known Simha-Ramaswamy instability. (b,c) Active scalar tissues are stable in the gradient-extensile case (b), but display an instability in the gradientcontractile case (c), where the color indicates the local value of the scalar field.

References: - M. Ibrahimi, M. Merkel (2022) Deforming polar active matter in a scalar field gradient, arXiv: https://arxiv.org/abs/2206.12850

Broken living layers:

F.

Dislocations in

active smectic liquid crystals

Jülicher

1 , J. Prost2* , J.

Toner

3

1 Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany, and Cluster of Excellence, Physics of Life, TU Dresden, 01307 Dresden, Germany

2 Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France

3 Department of Physics and Institute for Fundamental Science, University of Oregon, Eugene, Oregon 97403, USA

*PRESENTER

Two dimensional smectic layering can be observed in biological systems such as the acto-myosin network in lamellipodia (1) and also monolayer tissues. Such systems are often not mono-crystalline and display dislocations densities, dynamical behaviour etc. This raises the question of the description of active smectics in the presence of dislocation densities. After discussing the existence or non-existence of a steady state depending on boundary conditions, and giving one simple example of non-equilibrium behavior, I will address the question of long range order or quasi-long range order in the presence or absence of an external field.

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From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Surprises in the hydrodynamics of aligned active suspensions

Lokrshi Prawar Dadhichi1,2 , Sriram Ramaswamy3*

1Tata Institute of Fundamental Research, Gopanpally, Hyderabad 500 046, India

2Institute for Theoretical Physics, Leipzig University, 04103 Leipzig, Germany

3Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560 012 India

*PRESENTER

We study the fluctuating hydrodynamics of suspensions of swimmers at zero Reynolds number, in a fluid with a permanent uniaxial anisotropy. We show that the homogeneous phase of this system lies in a new dynamic universality class, with collective diffusivity diverging as a power of system size. For large enough activity we find that the uniform state is unstable to the growth of concentration fluctuations in selected directions, implying a purely active hydrodynamic mechanism for condensation. The condensation mechanism operates in bulk 3D suspensions as well under planar confinement, whereas the superdiffusion arises only in the unconfined case. We discuss possible experimental realisations in which to test our predictions.

References:

- LP Dadhichi, TIFR PhD thesis 2021

- LP Dadhichi and S Ramaswamy, preprint

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From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Non-equilibrium Properties of Thin Polymer Films

Günter Reiter1*, Sivasurender Chandran2

1 Physikalisches Institut, Albert-Ludwigs Universität Freiburg, Germany

2 Department of Physics, Indian Institute of Technology Kanpur, India

*PRESENTER

Rapid industrial processes often freeze polymers in non-equilibrium conformations, which, in turn, cause material properties that are significantly different from the predictions of equilibrium theories [1]. Thus, by choosing appropriate processing pathways, we potentially can control macroscopic properties and performance of polymers [2]. However, due to our current lack of fundamental understanding of the behavior of non-equilibrated polymers, we have to rely on empirical knowledge, imposing trial-and-error approaches for achieving desired properties.

Considering these aspects, we discuss recent studies on polymer films revealing that quantitative relations exist between properties and processing pathways, suggesting possible relations for processing-induced deviations in chainconformations.These relationsproposethatlong-living and long-ranged correlations betweenpolymers have been induced by processing, as indicated by the observation of relaxation times much longer than known for equilibrated polymers.

We present an example [3,4] where control of processing conditions for thin films allowed to translate the molecular relaxations during equilibration into a predictable lifting of macroscopic loads.

Figure 1: Richness of non-equilibrium conformations. Schematic illustration of a test chain adopting different conformations, in blue for equilibrium and in red for non-equilibrium, which may result in significant deviations in macroscopic material properties.

References:

1. Sivasurender Chandran, Günter Reiter (2022) Non-equilibrium Properties of Thin Polymer Films, In Matyjaszewski et al. (Eds.): Macromolecular Engineering: From Precise Synthesis to Macroscopic Materials and Applications, 4 Volumes, 2nd ed. Edition, Wiley-VCH. DOI: 10.1002/9783527815562.mme0058.

2. S. Chandran, J. Baschnagel, D. Cangialosi, K. Fukao, E. Glynos, L. M. C. Janssen, M. Müller, M. Muthukumar, U. Steiner, J. Xu, S. Napolitano, G. Reiter. (2019) Processing Pathways Decide Polymer Properties at the Molecular Level Macromolecules 52, 7146-7156.

3. Farzad Ramezani, Jörg Baschnagel, Günter Reiter. (2020) Translating molecular relaxations in nonequilibrated polymer melts into lifting macroscopic loads, Phys. Rev. Materials 4, 082601.

4. Günter Reiter, Farzad Ramezani, Jörg Baschnagel. (2022) The memory of thin polymer films generated by spin coating, EPJE 45, 51.

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From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Density homeostasis and breakdown in growing cells

Rollin1*, Jean-François Joanny1,2 , Pierre Sens1

1 Institut Curie 2 Collège de France

*PRESENTER

While the principles regulating cell size are now well established, the precise relationships between cell size and other fundamental biological quantities such as nucleus size or cellular dry mass remain unclear. Accumulating experimentalevidence have shown thatduring mostofthe cellcycle, nucleus size and dry mass are linearlyrelated to cell volume both in yeasts, bacteria, and mammalian cells. Such ubiquitous proportional relationships are often referred to as “cellular scaling laws” by biologists. Despite being observed for more than a century, a theoretical understanding of these scaling laws and their breakdown in diseases is lacking. In this talk, I will focus on the linear relationship between dry mass and cell volume, which implies that cell density is maintained during growth. Based on three simple yet generic physical constraints defining altogether the Pump-Leak model, and a precise estimation of the model coarse-grained parameters, I will show that cell volume is mostly fixed by the contribution to the osmotic pressure of small osmolytes, mainly amino-acids and ions, while the cellular dry mass is dominated by proteins. The homeostasis of cell density during growth is then due to a linear scaling relation between protein and small osmolyte numbers. Combining simplified models of gene transcription and translation and of amino-acid biosynthesis to the PumpLeak model, I will show that this scaling relation is naturally achieved in the exponential growth regime of cells by virtue of the enzymatic control of amino-acid production. On the other hand, our theory predicts this scaling to naturally fail, both at senescence when DNA and RNAs are saturated by RNA polymerases and ribosomes respectively, and at mitotic entry due to the counterion release following histone tail modifications. I will finally end this talk by testing these theoretical predictions on experimental data.

References: - Rollin, Joanny, Sens. (2022) “Cell size scaling laws: a unified theory”, BioRxiv.

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Romain

What can we learn from the stochastic trajectories of biological systems?

Pierre Ronceray1,*

1Aix Marseille Univ, CNRS, CINAM, Turing Center for Living Systems, Marseille, France

*PRESENTER

Stochastic differential equations are often used to model the dynamics of living systems, from Brownian motion at the molecular scale to the dynamics of cells and animals. How does one learn such models from experimental data? This task faces multiple challenges, from information-theoretical limitations to practical considerations. I will present a recent and ongoing effort to develop new methods to reconstruct such stochastic dynamical models from experimental data, with a focus on robustness and data efficiency. This provides a generic means to quantify complex behavior and unfold the underlying mechanisms of an apparently erratic trajectory.

Figure 1: An active flock trajectory (green), and a simulation of the model inferred from this dataset (red).

References:

[1] Frishman, A. & Ronceray, P. Learning Force Fields from Stochastic Trajectories. Phys. Rev. X 10, 021009 (2020).

[2] Brückner, D. B., Ronceray, P. & Broedersz, C. P. Inferring the Dynamics of Underdamped Stochastic Systems. Phys. Rev. Lett. 125, 058103 (2020).

[3] Brückner, D. B., Arlt, N., Fink, A., Ronceray, P., Rädler, J. O. & Broedersz, C. P. Learning the dynamics of cell–cell interactions in confined cell migration. PNAS 118 (2021).

Dynamics of Active and Driven Colloids interacting with Soft Membranes

1 Institut Charles Sadron, UPR22 CNRS, Strasbourg, France

*PRESENTER

When a colloid is close to a lipid giant vesicle, the interaction between the Brownian particle and the fluctuating soft membrane affects not only the particle motion but also the membrane properties. The membrane may change its shape to accommodate the particle and partial or complete particle wrapping by the membrane may occur as a function of the energy of adhesion, membrane tension and bending. Furthermore, the interaction between a hard particle and a soft membrane may lead to complex dynamics when the system is driven out of equilibrium.

Here, we report our efforts with self-propelled Janus colloids and with bare colloids under optical trapping to mimic complex dynamics such as transport of vesicles by active particles, the orbital motion of active colloids around vesicles, or the physics of particle wrapping by a membrane. In a wide range of experimental conditions, we have observed that a self-propelled Janus colloid is able to perform orbital motion around a giant vesicle remaining in a non-wrapped state [1]. Still, the active particle is able to impart a force of the order of 0.01 pN on the vesicle, which is however too small to trigger membrane wrapping. By applying external forces in the 1-100 pN range, we were able to observe membrane wrapping of bare and Janus colloids by a giant vesicle, see Figure 1 [2]. Finally, recent optical tweezers experiments on particle penetration inside giant vesicles will be presented and discussed in the limit of a vanishing adhesion energy [3].

Figure 1: Active transport of a self-propelled Janus colloid partially wrapped by a giant vesicle membrane

References:

- [1] V Sharma, E Azar, AP Schroder, CM Marques, A Stocco. (2021) Active colloids orbiting giant vesicles, Soft Matter.

- [2] V Sharma, CM Marques, A Stocco. (2022) Driven Engulfment of Janus Particles by Giant Vesicles in and out of thermal equilibrium, Nanomaterials.

- [3] F. Fessler, V Sharma, P Muller, A Stocco. (2023) Entry of Microparticles into Giant Lipid Vesicles by Optical Tweezers, https://arxiv.org/abs/2301.02504

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Vaibhav Sharma1, Florent Fessler1, Carlos M Marques1 , Antonio Stocco1*

Phase diagrams in biophysics

Cécile Sykes

1*

1 “Active Cell Matter” team, Laboratoire de Physique de l’Ecole Normale Supérieure, 24 rue Lhomond, 75005 Paris, FRANCE

*PRESENTER

Cell functions such as motility and division can be described by soft matter physics with the use of stripped-down experimental systems that reproduce cellular behaviours in simplified and controlled conditions. As an example, cytoskeleton dynamics are reproduced on liposome membranes , (Figure 1) and soft matter variables, such as membrane tension and the structural details of the cytoskeletonarchitecture can be tuned. Experimental results are gathered in phase diagrams using subtle mathematical tricks that Jean-François Joanny masters. I will present a few examples including inward or outward membrane deformations generated by actin dynamics , and buckling/wrinkling ofliposomes underosmotic deflation . Iwill also presentsome preliminary results on nu-cleuscytoskeleton organisation during squeezed cell motility that we infer using a Langevin equation analysis.

Figure 1:

References:

i C. Simon, V. Caorsi, C. Campillo, C. Sykes, "Interplay between membrane tension and the actin cytoskeleton determines shape changes", Physical Biology, 5(6):065004, doi: 10.1088/1478-3975/aad1ab. (2018)

ii A. Allard, M. Bouzid, T. Betz, C. Simon, M. Abou-Ghali, J. Lemière, F. Valentino, J. Manzi, F. Brochard-Wyart, K. Guevorkian, J. Plastino, M. Lenz, C. Campillo*, C. Sykes*, "Actin modulates shape and mechanics of tubular membranes” Science advances, 6 : eaaz3050 (2020)

iii C. Simon, R. Kusters, V. Caorsi, A. Allard, M. Abou-Ghali, J. Manzi, A. Di Cicco, D. Lévy, M. Lenz, J.-F. Joanny, C. Campillo, J. Plastino, P. Sens, C. Sykes " Actin dynamics drive cell-like membrane deformation " Nature Physics, https://doi.org/10.1038/s41567-019-0464-1 (2019)

iv R. Kusters, C. Simon, R. Lopes Dos Santos, V. Caorsi, Sangsong Wu, J.-F. Joanny, P. Sens, C. Sykes, “Actin shells control buckling and wrinkling of biomembranes” Soft Matter, 15, 9647 – 9653 doi: 10.1039/c9sm01902b (2019)

➔ Table of contents

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

The dynamic actin cytoskeleton (marked by the presence of capping proteins, Alexa Fluor 488 C5-maleimide, green) is able to deform the membrane (TexasRed-DHPE, red) inward (spikes towards the liposome center) and outward (tubes emanating from the liposome membrane). Scale bar: 5μm

Odd dynamics of living chiral crystals

Tzer Han Tan1,2*, Alexander Mietke3, Junang Li2, Yuchao Chen2, Hugh Higinbotham2, Peter J. Foster2, Shreyas Gokhale2, Jörn Dunkel3

1 MPI-PKS, MPI-CBG, CSBD, Dresden, Germany

2 MIT Department of Physics, Cambridge, USA

3 MIT Department of Mathematics, Cambridge, USA

*PRESENTER

Active crystals are highly ordered structures that emerge from the self-organization of motile objects, and have been widely studied in synthetic and bacterial active matter. Whether persistent crystalline order can emerge in groups of autonomously developing multicellular organisms is currently unknown. Here we show that swimming starfish embryos spontaneouslyassemble intochiralcrystals thatspan thousands ofspinning organisms and persist for tens of hours. Combining experiments, theory and simulations, we demonstrate that the formation, dynamics and dissolution of these living crystals are controlled by the hydrodynamic properties and the natural development of embryos. Remarkably, living chiral crystals exhibit self-sustained chiral oscillations as well as various unconventional deformation response behaviours recently predicted for odd elastic materials. Our results provide direct experimental evidence for how non-reciprocal interactions between autonomous multicellular components may facilitate non-equilibrium phases of chiral active matter.

Figure 1: (a) Embryos assembled in a crystal perform a global collective rotation. (b) Spinning embryos (yellow arrows) in the crystal form a hexagonal lattice, containing fivefold (purple) and sevenfold (orange) defects. (c) Schematic of embryo dynamics and fluid flows from side view (left) and top view (right).

References: - Tan TH*, Mietke A*, Li J, Chen Y, Higinbotham H, Gokhale S, Foster PJ, Dunkel J, Fakhri N. (2022), Odd dynamics of living chiral crystals, Nature, 607(7918), 287-293

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

& Nikta Fakhri2

Bacterial Olympics: Multiflagellarity allows bacteria to maintain constant motility across cell size

S. Kamdar1, D. Ghosh1, W. Lee2 , M. Tătulea-Codrean3*, Y. Kim4, S. Ghosh1, Y. Kim1, T. Cheepuru1, E. Lauga3, S. Lim5, X. Cheng1

1 Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, USA

3

2 National Institute for Mathematical Sciences, Daejeon 34047, Republic of Korea

Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, United Kingdom

4 Department of Mathematics, Chung-Ang University, Seoul 06974, Republic of Korea

5 Department of Mathematical Sciences, University of Cincinnati, Cincinnati, Ohio 45221, USA *PRESENTER

In Olympic swimming, size typically matters: podiums are occupied by the tallest swimmers who use their long limbs to push the fluid and move faster. In contrast to Olympic athletes who swim at high Reynolds numbers of ���� ∼106, bacteria swimat ���� ∼10 5, where viscous drag dominates the hydrodynamics and suggests a decrease in the swimming speed of bacteria of large sizes due to the elevated drag on their bodies. Here, we measure the swimming speed of E. coli, a model multiflagellar bacteria, and we find that the population-averaged swimming speed of bacteria is constant over a three-fold increase in their body length. We show how bacteria utilize the increasing number of flagella to regulate flagellar motor load, which results in higher rotational speeds as well as a constant swimming speed for large cell sizes. We perform simulations that reveal the role of interflagellar interactions in controlling the increase of rotational speeds. Our mechanism predicts that the swimming speed of uniflagellar species decreases with increasing cell size, which we verify directly through experiments on several strains of uniflagellar bacteria. Until now, it is believed that the presence of additional flagella does not confer strong benefits for swimming speed. The stark difference between the uniflagellar and multiflagellar swimming demonstrated in our study provides new insight into the crucial role of multiflagellarity in maintaining optimum motility for navigation and survival of bacteria in their native habitats.

➔ Table of contents

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Photosensitive active nematics

Ignasi Vélez-Ceron1,2*, Jordi Ignés-Mullol1,2, Francesc Sagués1,2

1 Departament de Ciència dels Materials i Química Física, Universitat de Barcelona, Barcelona, Spain

2 Institute of Nanoscience and Nanotechnology, Universitat de Barcelona, Barcelona, Spain

*PRESENTER

Cytoskeletal active nematics are one of the most fascinating active matter systems [Sanchez 2012]. Tubulinkinesin gels have been shown to organize as an ordered active material when condensed at a soft and flat interface. This active layer, known as active nematic, adopts a characteristic long-range orientational order, continuously permeated by large-scale flows and locally interrupted by regions void ofmicrotubules thatconfigure semi-integer defects. The chaotic dynamics of this active layer with continuous defect creation and annihilation corresponds to a state of active nematic turbulence [Martínez-Prat 2019].

Active nematic dynamics can be influenced by means of rheology [Guillamat 2016], magnetic fields [Guilamat 2016] and confinement [Hardoüin 2019]. Nevertheless, these experimental systems lack spatiotemporal control. Taking advantage of novel bioengineering, kinesin motors have been fused to optically dimerizable iLID proteins [Guntas 2014], offering the opportunity to include light control in the active nematic. Unlike the strategies mentioned above, the new protocol offers a control ability that is intrinsic to the material. In the modified system, light activates reversible linking between kinesins (Figure 1), allowing the formation and spontaneous motion of the active nematic filaments, while, turning off the light, motor clusters are disengaged thus decreasing active nematic movement. Employing light patterns with arbitrary spatial and temporal characteristics we intend to couple external and intrinsic length and time scales, and unveil new scenarios of spatio-temporal dynamics in active nematics.

References:

- Sanchez, T., Chen, D., DeCamp, S., Heymann, M. and Dogic, Z. (2012) Spontaneous motion in hierarchically assembled active matter, Nature, 491, 431-434.

- Martínez-Prat, B., Ignés-Mullol, J., Casademunt, J. and Sagués, F. (2019) Selection mechanism at the onset of active turbulence. Nat. Phys., 15, 362–366.

- Guillamat, P., Ignés-Mullol, J., Shankar, S., Marchetti,. C. and Sagués, F. (2016) Probing the shear viscosity of an active nematic film, Phys. Rev. E, 94, 060602.

- Guillamat, P., Ignés-Mullol, J. and Sagués, F. (2016) Control of active liquid crystals with a magnetic field, Proc. Natl. Acad. Sci. U. S. A., 113, 5498-5502.

- Hardoüin, J., Hughes, R., Doostmohammadi, A., Laurent, J., Lopez-Leon, T., Yeomans, J., IgnésMullol, J. and Sagués, F. (2019) Reconfigurable flows and defect landscape of confined active nematics. Commun Phys, 2, 121.

- Guntas, G., Hallett, R. A., Zimmerman, S. P., Williams, T., Yumerefendi, H., Bear, J. E. and Kulhman, B. (2014) Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins, Proc. Natl. Acad. Sci. U. S. A., 112, 112-117.

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From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Figure 1: Employing novel kinesin motors, active nematic formation can be controlled using light patterns. A half dark (left) and half bright (right) pattern is used. Scale bar, 200 µm.

The physics of active polymers and filaments

Christian A. Philipps1, Gerhard Gompper1 , Roland G. Winkler1*

1 Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, 52428 Jülich, Germany *PRESENTER

Active soft matter composed of filaments or polymers is a promising new class of materials. The tight coupling between their nonequilibrium dynamics and the polymer conformations gives rise of new functional properties. There are various realizations of active polymers. ATP-dependent enzymatic activity-induced mechanical fluctuations drive molecular motion in the cytoplasm of bacteria and eukaryotic cells and affect the properties of DNA/RNA molecules. Linear polymers, such as filamentous actin or microtubules of the cell cytoskeleton are propelled by tread-milling and motor proteins [1,2]. In addition, the dynamics of passive colloidal particles and polymers is enhanced ina bathofpropelled filaments [2]. We analyze theconformationaland dynamicalproperties of self-propelled ring and linear polymers by analytical theory and computer simulations. Two models for active driving are considered, polymers with active sites represented by active Brownian particles (ABPs) (active Brownian polymers, ABPOs)[2-5]and polymers driven by tangentialforces (active polarlinearpolymers, APLPs) [2,6,7]. In case of ABPOs, activity leads to a swelling of flexible and, at intermediate activities, shrinkage of semiflexible polymers followed by a reswelling at large activities [3-5]. In contrast, the conformations of tangentially driven phantom polymers are independent of activity [6,7]. In general, activity drastically enhances both, the center-of-mass and the intramolecular dynamics. Interestingly, hydrodynamic interactions in ABPOs leads to shrinkage of even flexible polymers at intermediate activities [5]. A comparison between ABPOs and APLPs shows distinct differences in their diffusive behavior, in particular the relevance of the intramolecular dynamics and the dependence on the activity [7]. The various aspects will be addressed in the presentation.

Figure 1: Subsequent temporal conformations of a discrete flexible active polar linear polymer. To illustrate the clockwise tank-treading motion, half of the monomers are colored blue and red, respectively.

References:

[1] J. Prost, F. Jülicher, J.-F. Joanny, Nat. Phys. 11, 111 (2015).

[2] R. G. Winkler, G. Gompper, J. Chem. Phys. 153, 040901 (2020).

[3] T. Eisenstecken, G. Gompper, R. G. Winkler, J. Chem. Phys. 146, 154903 (2017).

[4] S. M. Mousavi, G. Gompper, R. G. Winkler, J. Chem. Phys. 150, 064913 (2019).

[5] A. Martín-Gómez, T. Eisenstecken, G. Gompper, R. G. Winkler, Soft Matter 15, 3957 (2019).

[6] C. A. Philipps, G. Gompper, R. G. Winkler, Phys. Rev. E 105, L062501 (2022).

[7] C. A. Philipps, G. Gompper, R. G. Winkler, J. Chem. Phys. 157, 194904 (2022).

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

List of participants

Ram Adar Collège de France

ram.adar@college-de-france.fr

Ricard Alert Max Planck Institute for the Physics of Complex Systems ralert@pks.mpg.de

David Andelman Tel Aviv University andelman@post.tau.ac.il

Charlotte Aumeier University of Geneva, Biochemistry Department charlotte.aumeier@unige.ch

Catherine Barentin University of Lyon 1 catherine.barentin@univ-lyon1.fr

Jean-Louis Barrat Université Grenoble-Alpes jean-louis.barrat@univ-grenoble-alpes.fr

Jorg Baschnagel University of Strasbourg, Institut Charles Sadron, jorg.baschnagel@ics-cnrs.unistra.fr

Patricia Bassereau Institut Curie patricia.bassereau@curie.fr

Timo Betz University of Göttingen timo.betz@phys.uni-goettingen.de

Carles Blanch-Mercader Institut Curie carles.blanch-mercader@curie.fr

Françoise Brochard-Wyart Institut Curie francoise.brochard@curie.fr

Andrew Callan-Jones Laboratoire Matière et Systèmes Complexes acallanjones@gmail.com

Giovanni Cappello CNRS - Laboratoire Interdisciplinaire de Physique Giovanni.Cappello@univ-grenoble-alpes.fr

Livio Nicola Carenza Leiden University carenza@lorentz.leidenuniv.nl

Jaume Casademunt University of Barcelona jaume.casademunt@ub.edu

Elisabeth Charlaix Université Grenoble Alpes elisabeth.charlaix@univ-grenoble-alpes.fr

Vincent Debets Eindhoven University of Technology v.e.debets@tue.nl

Filippo De Luca Ludwig-Maximilians-Universtität München delucafilippo@ymail.com

Claire Dessalles Université de Genève claire.dessalles@unige.ch

Luis Dinis Universidad Complutense de Madrid ldinis@ucm.es

Jens Elgeti Forschungszentrum Juelich j.elgeti@fz-juelich.de

Ralf Everaers Ecole Normale Supérieure de Lyon ralf.everaers@ens-lyon.fr

Etienne Fodor University of Luxembourg etienne.fodor@uni.lu

Bruno Goud Institut Curie bruno.goud@curie.fr

Stephan Grill MPI-CBG grill@mpi-cbg.de

Alexander Grosberg New York University ayg1@nyu.edu

Edouard Hannezo Institute of Science and Technology Austria edouard.hannezo@ist.ac.at

Purnima Jain Tata Institute of Fundamental Research, Hyderabad purnimajain@tifrh.res.in

Jean-François Joanny Collège de France jean-francois.joanny@college-de-france.fr

Albert Johner Institut Charles Sadron albert.johner@ics-cnrs.unistra.fr

Frank Jülicher

Max Planck Institute for the Physics of Complex Systems julicher@pks.mpg.de

Patrick Kékicheff Institut Charles Sadron, C.N.R.S. patrick.kekicheff@ics-cnrs.unistra.fr

Kurt Kremer

Max Planck Institute for Polymer Research kremer@mpip-mainz.mpg.de

Karsten Kruse Université de Genève karsten.kruse@unige.ch

David Lacoste

ESPCI Paris PSL david.lacoste@gmail.com

Ludwik Leibler ESPCI Paris PSL ludwik.leibler@espci.fr

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

Joël Lemière University of California San Francisco lemiere.joel@gmail.com

Martin Lenz CNRS, U. Paris-Saclay, ESPCI martin.lenz@universite-paris-saclay.fr

Susanne Liese Universität Augsburg susanne.liese@physik.uni-augsburg.de

Ananyo Maitra LPTM, CY Cergy Paris Universite nyomaitra07@gmail.com

Cristina Marchetti University of California Santa Barbara cmarchetti@ucsb.edu

Carlos Marques Ecole Normale Supérieure de Lyon carlos.marques@ens-lyon.fr

Pascal Martin Institut Curie pascal.martin@curie.fr

Billie Meadowcroft Institute of Science and Technology Austria billie.meadowcroft@ist.ac.at

Matthias Merkel Aix-Marseille Université / CNRS matthias.merkel@univ-amu.fr

Mulugeta Bekele Ogato Addis Ababa University mulugetabekele1@gmail.com

Andrea Parmeggiani Laboratory Charles CoulombCNRS-University of Montpellier andrea.parmeggiani@umontpellier.fr

Aurélien Peilloux Learning Planet Institute, SACRe aurelien.peilloux@gmail.com

Francois Piuzzi Société Française de Physique et Société Française d'Optique piuzzifr@gmail.com

Jacques Prost Institut Curie jacques.prost@curie.fr

Sriram Ramaswamy Indian Institute of Science sriram@iisc.ac.in

Jonas Ranft Institut de Biologie de l'ENS, Ecole Normale Supérieure & CNRS jonas.ranft@ens.psl.eu

Pierre Recho CNRS, Université Grenoble Alpes pierre.recho@univ-grenoble-alpes.fr

Günter Reiter University of Freiburg guenter.reiter@physik.uni-freiburg.de

Vincent Rivasseau Université Paris-Saclay vincent.rivasseau@gmail.com

Romain Rollin Institut Curie romain.rollin@curie.fr

Pierre Ronceray Aix-Marseille Université / CNRS pierre.ronceray@univ-amu.fr

Aurelien Roux University of Geneva aurelien.roux@unige.ch

Pablo Saez Universitat Politecnica de Catalunya pablo.saez@upc.edu

Pierre Sens CNRS - Institut Curie pierre.sens@curie.fr

Pascal Silberzan Institut Curie pascal.silberzan@curie.fr

Valerio Sorichetti Institute of Science and Technology Austria valeriosorichetti@gmail.com

Antonio Stocco Institut Charles Sadron, C.N.R.S. stocco@unistra.fr

Cécile Sykes CNRS-ENS Paris-Sorbonne Université-Université Paris Cité cecile.sykes@phys.ens.fr

Tzer Han Tan Max Planck Institute for the Physics of Complex Systems ttan@mpi-cbg.de

Yergou Tatek Addis Ababa University ytatek@gmail.com

Maria Tatulea-Codrean DAMTP, University of Cambridge m.tatulea-codrean@damtp.cam.ac.uk

Lev Truskinovsky ESPCI truskino@gmail.com

Hervé Turlier Collège de France, CNRS herve.turlier@college-de-france.fr

Ignasi Vélez Ceron Universitat de Barcelona nacho.ivc@gmail.com

Roland Winkler Forschungszentrum Jülich r.winkler@fz-juelich.de

➔ Table of contents

From soft matter to biophysics – Ecole des Houches – January 29th-February 3rd 2023

From soft matter to biophysics

Ecole de Physique des Houches, France

January 29th – February 3rd 2023