Jean-François Rupprecht

Welcome to my personal webpage

I am a CNRS researcher at the Centre Physique Théorique (Université Aix-Marseille, Luminy campus)
and CENTURI (Turing Center for Living Systems) Group Leader.
Please click here for the Out-of-equilibrium Mechanics (OM) team webpage.

Opportunities

Join the OM team! We have a doctoral opening with Thomas Lecuit on a modeling project related to Drosophila embryogenesis, as well as
potential post-doctoral openings on:

• ANR PRC IMPERIS (Inducing Mechanical Perturbations on the Immune Synapse) with P. Pierobon, E. Donnadieu, J. Fattacioli,
  
• ANR PRCi CODAC (CO-Dynamics of cell Adhesion and Contraction) with P.-F. Lenne, Ed. Munroe, P. Recouvreux.
  
• ANR PRC DENDROMORPH (Dendrite Morphology) with T. Lecuit and Claire Bertet.

Please contact me by email for more info. Informal inquiries are welcome.
In addition to joining a dynamic team composed of highly motivated people, please have in mind that the Luminy campus is arguably one the most beautiful campus in the world (see some images here).

Research highlight: Cell motility and Tissue Mechanics

We aim at understanding how flows emerge in living matter. Recent projects were supported by the ANR JCJC COVFEFE (COVariant Fluctuating theory of Epithelial Flows): see French/English summaries.

Flows in active nematics over curved geometries

- [Bell 2023] We extend the active nematics framework for curved surfaces with an up-down asymmetry; we find thresholdless active flows, discontinuous transitions and hysteresis between flowing steady states. See also the CNRS press release (in French).
- [Prasad 2023] We use a curved active nematics framework to understand how oil-eating bacteria maximize their food intake by pulling tubes out of oil droplets Here for the link to our publication + There for the cool YouTube video by Science Magazine.

Flows in vertex models

- [Lin 2021]: Vertex models were first used to described for passive foams made of pressurized bubbles. In epithelial tissues, the bulk of cells can also exert anisotropic stresses on top of pressure. How do you reconcile that with vertex models? (link to paper pdf)
- [Lin 2023]: In vitro epithelial tissues often display chaotic flows. These generically appear in active nematic theories; yet, as these are coarse-grained descriptions, they may miss important aspects that are specific to a cellular material. Here we simulate the onset of flows in an active cellular material with extensile stresses. We find a previously unreported rhombile cell shape motif. Lowering the cell-cell tension, we find that the cell shape undergoes a first order transition with a vanishing low extensile activity. Overall, our work challenges established views on the solid-fluid transitions in cellular materials. (link to preprint)
- [Sonam 2022]: We use our vertex model to test models of epithelial tissue fracture and how topological defects can underpin extreme events in mechanical tension. See also the CNRS press release (in French).
- [Lou 2022] During the Drosophila embryogenesis, the epithelial cellular arrangement can differ between the apical and basal side of the embryo. Our numerical description of tissues (3D vertex model) explains how such shapes can appear [see preprint 27 and publication 11]
See also: MBI science feature.

Flows during dendritic arborization

- [Palavalli 2019] For a summary, see M.-E. Perrin PhD thesis. We received a local press coverage in La Marseillaise journal.

Less recent research

MODCOV-19 initiative

• Group Testing: We proposed a model and estimates of the risks and benefits of group testing techniques, with application to the surveillance of epidemic outbreaks in closed communities (e.g. nursing homes, universities).
  See related our publication [21] and the related CNRS global press release.

Tissue mechanics

• Mechanical pattern formation - Fish slices show a V-pattern, why?
  Active stresses, differential tissue-friction and tissue plasticity shapes the zebrafish myotome [see publication Tlili 2019] See also: MBI science feature.

Cell motility

• Universal law of cell migration
  fast cells take more time to change direction than slow cells [see publication 5].
  Our random walk model relies on a chemical inertia mechanism whereby the distribution of polarity markers is controlled by the speed of the actin retrograde flow.
  See also: Le Monde feature.
• Magnetotactic bacteria
  We propose a new run-and-tumble walk model that predicts a new type of phase transition to collective flow [see publication 6].
• Fluctuating active gel theory
  We show that cortical stress fluctuations affect the position distribution of the cell nucleus and cell polarity [see publications 12-13].
  See also: MBI science feature.

Molecular processes

• Molecular ratchet - We proposed a new model on force generation by molecular motor assemblies [see publication 14].
  Cells sense the rigidity of their environment through local pinching – just as you would do with your fingers when you want to test if something is soft or rough;
  cells rely on myosin II motor assemblies – which contract over bundles of polymers called actin – to pinch their environment.
  Our model explains the challenging observations drawn from highly resolved experiments on these myosin assemblies.
  See also Nature Physics News and View feature, Curie Institute review and MBI summary.
• Super-resolution imaging - I developped algorithms optimizing image acquisition by stochastic optical microscopy [see publication 10].
• Theory of reactivity - We identify search strategies minimizing the average time of first encounter between a reactant and a fixed catalytic site.
  See also: A popular science overview of my PhD work (in French)
  
  

Publication list

See Google Scholar profile.

• Membrane tilt drives phase separation of adhesion receptors
  S.-Z. Lin, R. Changede, A. J. Farrugia, A. D. Bershadsky, M. P. Sheetz, J. Prost, J.-F. Rupprecht
  Physical Review Letters, accepted (2024)
• Inferring the location and orientation of cell divisions on time-lapse image sequences
  M. Karnat, R. Karpinski*, M. Saadaoui, S. Tlili, J.-F. Rupprecht*
  [bioRxiv version]
• E-cadherin-dependent phosphorylation of EGFR governs a homeostatic feedback loop controlling intercellular junction viscosity and collective migration modes
  C. Fu(1), F. Dilasser(1), S.-Z. Lin(1), M. Karnat(1), A. Arora, H. Rajendiran, H. T. Ong, N. M. Hoon Brenda, S. W. Phow, T. Hirashima, M. P. Sheetz, J.-F. Rupprecht*, S. Tlili*, V. Viasnoff*
  [bioRxiv version]
• Curvature-induced clustering of cell adhesion proteins
  S.-Z. Lin, J. Prost, J.-F. Rupprecht
  to be published in Physical Review E (2023)
• Alcanivorax borkumensis Biofilms Enhance Oil Degradation By Interfacial Tubulation
  M. Prasad, N. Obana, S.-Z. Lin, K. Sakai, C. Blanch-Mercader, J. Prost, N. Nomura, J.-F. Rupprecht, J. Fattaccioli, A. S. Utada
  Science (2023) -- [bioRxiv version]
• Soft Matter Roadmap
  Jean-Louis Barrat et al 2023
  J. Phys. Mater. in press (2023)
• Enhanced cell viscosity as a marker of premature senescence induced by lamin A/C alterations
  C. Jebane(1), A.-A. Varlet(1), M. Karnat(1),...,J.-F. Rupprecht, E. Helfer, and C. Badens
  IScience (2023) -- [bioRxiv version]
• Two-point optical manipulation reveals mechanosensitive remodeling of cell-cell contacts in vivo
  K. Nishizawa, S.-Z. Lin, C. Chardes, J.-F. Rupprecht, P.-F. Lenne
  PNAS (2023)
• Curvature-induced cell rearrangements in biological tissues
  Y. Lou, S. Theis, J.-F. Rupprecht, T. Hiraiwa, T. E. Saunders
  Physical Review Letters (2023) -- [bioRxiv version]
• Structure and Rheology in Vertex Models under Cell-Shape-Dependent Active Stresses
  S.-Z. Lin, M. Merkel, J.-F. Rupprecht
  Physical Review Letters (2023) -- [arxiv - HAL]
• Active nematic flows on curved surfaces
  S. Bell (1), S.-Z. Lin(1), J.-F. Rupprecht, J. Prost
  Physical Review Letters (2022) -- [HAL version]
• Mechanical stress driven by rigidity sensing governs epithelial stability
  S. Sonam(1), L. Balasubramaniam(1), S.-Z. Lin(1), ..., J.-F. Rupprecht, B. Ladoux
  Nature Physics (2022) -- [bioRxiv - HAL] . Featured in Nature Physics News and Views
• Implementation of cellular bulk stresses in vertex models of biological tissues
  S.-Z. Lin, M. Merkel, J.-F. Rupprecht,
  EPJE (2021) [author pdf]
• Screening for SARS-CoV-2 by RT-PCR: Saliva or Nasopharyngeal Swab? Rapid Review and Meta-Analysis
  N. Ibrahimi, A. Delaunay-Moisan, C. Hill, G. Le Teuff, J.-F. Rupprecht, J.-Y. Thuret, D. Chaltiel, M.-C. Potier
  PLOS One (2021)
• Group testing as a strategy for COVID-19 epidemiological monitoring and community surveillance
  V. Brault, B. Mallein, J.-F. Rupprecht
  PLOS Computational Biology (2021) + see CNRS press release and interviews in The Academic Times , News Medical, and Biologiste Infos
• Cell junction mechanics beyond the bounds of adhesion and tension
  P.F. Lenne, J.-F. Rupprecht, V. Viasnoff
  Developmental Cell (2021) [HAL version]
• Deterministic and stochastic rules of branching govern dendritic morphogenesis of sensory neurons
  A. Palavalli, N. Tizón-Escamilla, J.-F. Rupprecht, T. Lecuit
  Current Biology (2020) [HAL version]
  See also our press coverage in La Marseillaise journal.
• Adhesion-mediated heterogeneous actin organization governs apoptotic cell extrusion
  A. P. Le, J.-F. Rupprecht, R.-M. Mège, Y. Toyama, C. T. Lim, B. Ladoux
  Nature Communications (2020) [HAL version]
• Embryonic geometry underlies phenotypic variation in decanalized conditions
  A. Huang, J.-F. Rupprecht, and T. E. Saunders
  eLife, 9, e47380 (2020)
• Microtubule plus-end dynamics link wound repair to the innate immune response
  C. Taffoni, S. Omi, C. Huber, S. Mailfert, M. Fallet, J.-F. Rupprecht, J. J. Ewbank, N. Pujol,
  eLife (2020)
• Shaping the zebrafish myotome by intertissue friction and active stress
  S. Tlili, J. Yin, J.-F. Rupprecht, M. A. Mendieta-Serranoa, G. Weissbart, N. Verma, X. Teng, Y. Toyama, J. Prost, T. E. Saunders
  PNAS 116, 25430 (2019) [HAL version]
• Myosin filaments reversibly generate large forces in cells
  J. Lohner (1), J.-F. Rupprecht (1), J. Hu, N. Mandriota, M. Saxena, J. Hone, D. Pitta de Araujo, O. Sahin, J. Prost, M. P. Sheetz
  Nature Physics, 15, 689–695 (2019)
• Maximal fluctuations of confined actomyosin gels: dynamics of the cell nucleus
  J.-F. Rupprecht, A. Singh, G. V. Shivashankar, M. Rao, J. Prost
  Physical Review Letters, 120, 098001 (2018) Arxiv version.
  
• Soft inclusion in a confined fluctuating active fluid
  A. Singh, J.-F. Rupprecht, G. V. Shivashankar, J. Prost, M. Rao
  Physical Review E, 97, 032602 (2018) Arxiv version.
• Geometric constraints alter cell arrangements within curved epithelial tissues
  J.-F. Rupprecht, K. H. Ong, J. Yin, A. Huang, A. P Singh, S. Zhang, W. Yu, T. E Saunders
  Molecular Biology of the Cell, mbc. E17-01-0060 (2017).
  
• Trade-offs between structural integrity and acquisition time in stochastic super-resolution microscopy techniques
  J.-F. Rupprecht, A. Martinez-Marrades, Z. Zhang, R. Changede, P. Kanchanawong, G. Tessier
  Optics Express, 25, Issue 19, 23146 (2017).
• The escape problem for mortal walkers
  D. Grebenkov, J.-F. Rupprecht
  The Journal of Chemical Physics, 146, 084106 (2017) -- Arxiv version.
• Perspective: A fresh eye on nonequilibrium systems
  J.-F. Rupprecht, J. Prost
  Science, 352, Issue 6285, p. 514 (2016) , [HAL] .
• Optimal search by run-and-tumble particles
  J.-F. Rupprecht, O. Bénichou, R. Voituriez,
  Physical Review E, 94, 012117 (2016) -- Arxiv version.
• Velocity condensation of magnetotactic bacteria
  J.-F. Rupprecht, N. Waisbord, C. Ybert, C. Cottin-Bizonne and L. Bocquet
  Physical Review Letter 116, 168101 (2016) --- Arxiv version.
• Actin flows mediate a universal coupling between cell speed and persistence
  P. Maiuri (1), J.-F. Rupprecht (1), S. Wieser (1),
  V. Ruprecht, N. Carpi, M. Coppey, S. De Beco, O. Bénichou, N. Gov, C.P. Heisenberg, C. Large-Crespo, F. Lautenschlaeger,
  M. Le Berre, A. M. Lennon-Dumenil, M. Raab, H.R. Thiam, M. Piel, M. Sixt, R. Voituriez,
  Cell, 161, 2, pp 374 (2015).
  
• Exit time distribution in spherically symmetric two dimensional domains
  J.-F. Rupprecht, O. Bénichou, D. S. Grebenkov, R. Voituriez
  Journal of Statistical Physics 158, 1, pp 192 (2015) --- Arxiv version.
• Stochastic 3D field mapping using Brownian scatterers
  A. Martinez-Marrades, J.-F. Rupprecht, M. Gross, G. Tessier
  Optics Express, Vol. 22, 23, pp. 29191-29203 (2014)
• Kinetics of Active Surface-Mediated Diffusion in Spherically Symmetric Domains
  J.-F. Rupprecht, O. Bénichou, D. S. Grebenkov, R. Voituriez
  Journal of Statistical Physics 147, pp 891 (2012) --- Arxiv version.
• Exact Mean Time for surface-mediated diffusion
  J.-F. Rupprecht, O. Bénichou, D. S. Grebenkov, R. Voituriez
  Physical Review E 86, pp 041135 (2012) --- Arxiv version.

Short CV

• 01/2019 onwards - CNRS researcher at the Centre Physique Théorique (Université Aix-Marseille, Luminy campus).
• 2015-2019 - Research fellow with J. Prost (Mechanobiology Institute, National University of Singapore).
• 2014-2015 - Post-doctoral research with L. Bocquet (LPS, Ecole Normale Supérieure, Paris).
• 2012-2014 - Graduate student with R. Voituriez and O. Bénichou (LPTMC, Université Pierre-et-Marie-Curie, Paris).

Administrative duties

2021/2024 - Member of the CoNRS section 02 and 51.

Contact

Email: jean-francois.RUPPRECHT@univ-amu.fr
Address: Centre de Physique Théorique, Université Aix-Marseille, Campus de Luminy, 163 Avenue de Luminy, 13009 Marseille
Office: 5th floor, office 514
Phone: number in my email signature.