Cilia-powered 3D flow patterns

Host laboratory and collaborators



Julien FAVIER (M2P2) /


The purpose of this PhD project is to generate an experimental and theoretical framework to study cilia-driven fluid flow in vivo. The project brings together biology, physics and numerical simulation of fluid mechanics to understand how flows powered by beating cilia are organized to clean the surface of the amphibian Xenopus embryo. This animal model has generated extensive knowledge on fundamental parameters of ciliated epithelium biology, such as ciliated cell determination, cilia synthesis, and polarized beating. The PhD student will adapt light-sheet microscopy to image beating cilia in all cells of the mature embryo, so as to derive a global map of ciliated cell location and orientation (Teams 1 and 2). Special focus will be set on regions of complex topology (head, branchial arches, anal cavity), which deviate from the typical and simpler 2D organization studied so far. These experimental parameters will be used to feed Lattice Boltzmann-based simulation, with the aim of generating numerical paradigms to explain the emergence of metachronal ciliary beat waves and spatial flow patterns (Team 3). This work will help to understand how ciliated epithelium organization is modulated to fulfill its physiological role in a complex 3D organism.


Mucociliary epithelium, cilia, cell and tissue polarity, live imaging, image processing, metachronal waves, flow patterns, collective motion, active matter, Lattice Boltzmann simulations


The global aim of this PhD project is to link quantitative experimental analysis to numerical simulation to build a global 3D model of ciliated epithelium organization and activity. The ambition is to generate a multi-parametric model able to explain the emergence of cilia-driven fluid flows at the level of an entire organism. To this aim quantitative live imaging of cilia will be implemented on the 3D embryo, which has never been done before. Numerical models will be challenged in silico and through experiments to test their predictive capacity.

Proposed approach (experimental / theoretical / computational)

Live imaging (teams 1 and 2): The PhD student will adapt light-sheet microscopy to film fluorescent beating cilia in all MCCs of the Xenopus embryo at various developmental stages. Transgenic animals with fluorescent cilia are available in team 1.
Image processing (teams 1 and 2): Methods developed in team 2 will be applied to extract quantitative information regarding cilia beating frequency and orientation, so as to build a global map of the embryo.
Numerical simulation (team 3): The quantitative experimental parameters thus acquired will be used to feed Lattice Boltzmann-based simulations, with the aim of generating numerical paradigms to explain the emergence of metachronal ciliary beat waves and 3D flow patterns.
Validation (teams 1, 2 and 3): In silico challenges (changes in ciliated cell density or orientation) will be introduced to predict outcomes on flow patterns, which will be verified through our experimental pipeline.


We propose an interdisciplinary collaboration between three CenTuri groups already involved in the analysis of cilia-driven fluid flows, who have already engaged multiple collaborations and co-authored several publications. The biologists at IBDM (team 1) have developed multiple axes of research and methods to decipher the molecular mechanisms of multiciliated cell differentiation, spatial distribution and polarity in the Xenopus embryonic skin. The experimental biophysicists at CINaM (team 2) are experts in bioactive matter, having a long-lasting collaboration with lung specialists in Marseille. They have been exploring the relationship between self-organization of ciliary activity and mucus transport for several years. The numericists at M2P2 (team 3) have developed a pioneering approach, which allowed to tackle numerically the fluid-structure interaction mechanisms governing the dynamics of ciliated cells, both at the cell level and collectively. The project draws its originality from a mixed experimental and numerical approach on a topic whose state-of-the-art mainly presents disciplinary studies.

Expected profile

The selected PhD student must have a keen interest in interdisciplinary and quantitative approaches to study biological problems. The selected candidate is expected to be able to adapt light-sheet microscopy (commercial or custom systems) to the constraints of the Xenopus embryo. The ideal candidate should therefore have a strong taste for imaging and engineering, as well as for image processing. Candidates with a strong interest in modeling will be favorably considered.

Is this project the continuation of an existing project or an entirely new one? In the case of an existing project, please explain the links between the two projects

This project is the continuation of a successful ongoing project carried out by Athullya BABY (3rd year Centuri PhD) entitled "Quantitative analysis and simulation of fluid flows powered by cilia in vivo". In her work, Athullya has been able to measure cilia-powered fluid flow on Xenopus epidermal explants in 2D. She could as well identify both experimentally and numerically key parameters of the system, such as the optimal distribution of ciliated cells as a factor of their density in the explant. This new project now aims at expanding this analysis at the scale of the whole embryo, which will be technically more challenging and will allow us to uncover new optimal solutions of the system in more complex parts of the body.

2 to 5 references related to the project

  • Boutin, C. and Kodjabachian, L. 2019. Biology of multiciliated cells. Curr. Opin. Genet. Dev. 56, 1-7.
  • Gsell, S., D’Ortona, & Favier, J. 2020. Multigrid dual-time stepping Lattice-Boltzmann method. Physical Review E, Vol. 101, 0233099.

3 main publications from each PI over the last 5 years

Laurent Kodjabachian:

Nommick, A., Boutin, C., Rosnet, O., Schirmer, C., Bazellieres, E., Thome, V., Loiseau, E., Viallat, A. and Kodjabachian, L. Lrrcc1 and Ccdc61 are conserved effectors of multiciliated cell function. Under favourable revision at JOURNAL OF CELL SCIENCE.

Chuyen, A., Rulquin, C., Daian, F., Thome, V., Clement, R., Kodjabachian, L*$. and Pasini, A*. 2021. The Scf/Kit pathway implements self-organized epithelial patterning. DEVELOPMENTAL CELL. 56:795-810. *Corresponding authors, $Lead contact.

Revinski, DR†., Zaragosi, L-E†., Boutin, C†., Ruiz Garcia, S., Deprez, M., Rosnet, O., Thomé, V., Mercey, O., Paquet, A., Pons, N., Marcet, B*., Kodjabachian, L*. and Barbry, P*. 2018. CDC20B is required for deuterosome-mediated centriole production in multiciliated cells. equal contribution†, corresponding authors*. NATURE COMMUNICATIONS. 9:4668.

Annie Viallat:
J. Dupire, P.-H. Puech, E. Helfer, and A. Viallat. 2020. Mechanical Adaptation of Monocytes in Model Lung Capillary Networks, PNAS. 117, 14798.

C. Iss, D. Midou, A. Moreau, D. Held, A. Charrier, S. Mendez, A. Viallat, and E. Helfer. 2019. Self-Organization of Red Blood Cell Suspensions under Confined 2D Flows, SOFT MATTER 15, 2971.

M.-K. Khelloufi, E. Loiseau, M. Jaeger, N. Molinari, P. Chanez, D. Gras, and A. Viallat. 2018. Spatiotemporal Organization of Cilia Drives Multiscale Mucus Swirls in Model Human Bronchial Epithelium, SCIENTIFIC REPORTS, 8.

Julien Favier:
Gsell, S., Loiseau, E., D’Ortona, U. Viallat, A. & Favier, J. 2020. Hydrodynamic model of directional ciliary-beat organization in human airways. SCIENTIFIC REPORTS, 10, 8405.

Loiseau, E., Gsell, S., Nommick, A., Jomard, C., Gras, D., Cha- nez, P., D’Ortona, U., Kodjabachian, L., Favier, J. & Viallat, A. 2020. Active mucus-cilia hydrodynamic coupling drives the self-organisation of human bronchial epithelium. NATURE PHYSICS, 16, 1158–1164.

Chateau, S., D’Ortona, U., Poncet, S. & Favier, J. 2018. Transport and mixing induced by beating cilia in human airways. FRONTIERS IN PHYSIOLOGY, Vol. 9, 161, pp. 1-16.