Laboratoire Interdisciplinaire de Physique
140 rue de la physique 38400 Saint Martin d’Hères

aurelie.dupont(a)univ-grenoble-alpes.fr

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Motivated students welcome!

We offer several internship projects from L3 to M2 students about fish schools and hydrodynamics, with a numerical approach or an experimental one. An exciting new topic is also available about the mechanics of honeybee clusters tackled with rheology experiments and continuum mechanics modeling. Don't hesitate to contact me to know more and if you are interested in joining the group!

The central question of my research activity concerns the interactions between the living matter and its physical environment along two axes: FRET microscopy and active cognitive matter. On the one hand, I am developing a method allowing the absolute measurement of the FRET phenomenon (energy transfer between fluorophores) on a standard epifluorescence microscope. The objectives of this part are: (i) to improve the accessibility and robustness of the existing method to better disseminate it; (ii) to extend the framework to allow the reliable measurement of inter-molecular biosensors and the measurement of stoichiometry in living cells. On the other hand, I propose original experimental models to improve the understanding of collective phenomena in complex environments and the role of cognition in macroscopic active matter. The model is based on small fish swimming in a school that we subject to controlled environments (obstacles and flows). The objectives of this part are: (i) to propose a complete model including hydrodynamic and social interactions; (ii) to improve the understanding of collective behaviour and collective intelligence.

Keywords: Collective movements, active matter, Fluorescence microscopy, FRET

Collective movements

In a join work with Philippe Peyla (LIPhy), we are interested in the spontaneous emergence of an ordered movement in a system composed of a large number of individuals. This intriguing and almost universal phenomenon can be found in bacteria on a sub-millimetre scale, in schools of fish stretching for kilometres, in human crowds or in flocks of birds. These collective movements result from local interactions between individuals from which large-scale patterns emerge. We approach this topic in an original way by seeking to understand the effect of a complex physical environment (flows, obstacles) on the collective swimming behaviour of small aquarium fish (Blue Neon, Zebrafish). In particular, we aim to investigate the coupling between their social interactions and their hydrodynamic interactions, which have so far mainly been studied separately. To this end, we combine an experimental approach in a controlled environment providing quantitative measurements with a numerical approach coupling the direct resolution of the 3D hydrodynamics with a cognitive model in collaboration with Thibaut Métivet (INRIA).

Quantitative FRET microscopy

Being able to measure the biochemical activity of a target protein in a living cell in a spatially and temporally resolved manner is quite a challenge. This is not possible with classical molecular biology methods, however, new tools have recently emerged, namely fluorescent biosensors. Most of them are based on the principle of "Förster Resonance Energy Transfer" (FRET), i.e. the transfer of energy between two fluorophores allowing to probe distances of the order of a few nanometers and thus changes in protein conformation. These biosensors have enormous potential but their development is hampered on the one hand by the difficulty to develop them and on the other hand by the difficulty of measuring FRET reliably in living cells. To unblock this last point,we developed a new method for measuring and quantitatively analysing FRET during Alexis Coullomb’s thesis, in collaboration with the teams of Don Lamb (LMU Munich) and Corinne Albigès-Rizo (IAB Grenoble). Starting again from the physical equations of fluorescence signal acquisition, we have refreshed the theoretical framework and proposed a new calibration method that allows the measurement of absolute FRET values and thus opening the way to new experiments. In addition, this method gives access to the relative stoichiometry between donor and acceptor molecules and hence allows the quantitative measurement of inter-molecular FRET biosensors (where the stoichiometry is not fixed).

Collaborations

• Philippe Peyla, LIPhy, Grenoble
• Carine Douarche, FAST, Orsay
• Aurore Avarguès-Weber, CRCA, Toulouse
• Christian Graff, LPNC, Grenoble
• Thibaut Métivet, INRIA, Grenoble
• Henda Djeridi, LEGI, Grenoble
• Eric Bertin, LIPhy, Grenoble
• Uwe Schlattner, LBFA, Grenoble
• Nora Dempsey et Thibaut Devillers, Institut Néel, Grenoble
• Corinne Albigès-Rizo et Olivier Destaing, IAB, Grenoble
• Martial Balland, Thomas Boudou, LIPhy, Grenoble
• Alice Nicolas, LTM, Grenoble
• Don C Lamb, LMU, Munich

Current group

• Boris Kossovsky, PhD candidate
• Jeremiah Sutherland, master student from the Soft Nano graduate school
• Adrien Saumureau, software engineer
• Bruno Ventéjou, Postdoc researcher, supervised with Philippe Peyla, team MOVE, LIPhy

Alumni

• Océane Terral, PhD candidate 2021-2024, supervised with Cécile Delacour, Institut Néel
• Renaud Larrieu, PhD candidate 2020-2023
• Julien Leblanc, research engineer, 2020-2021, currently engineer in Genscale team in Rennes
• Alain Lombard: PhD candidate 2017-2020, now teacher
• Alexis Coullomb: PhD candidate 2015-2018, now postdoc in Toulouse
• Cécile Bidan: postdoc 2014-2017, now junior group leader MPI Potsdam, Germany
• Sadequa Sultana: postdoc 2017, now biomedical research engineer
• and every year students for short-term internships

Publications

Selected publications, the complete list is on google scholar

• "Live-cell quantitative FRET imaging made simple by autocalibration in QuanTI-FRET" J. Leblanc, A.H. Lombard, A. Saumureau, S. Costrel, J. Revilloud A. Dupont European Physical Journal E 48:74 (2025)
  In this work, we demonstrate that it is possible to diretly calibrate a FRET experiment from the images of interest, FRET biosensors in our case. Cherry on the cake, we produced an open-source software to deal with the QuanTI-FRET calibration directly from Napari or through an independent GUI. See the QuanTI-FRET section!

• "Universal Scaling Laws for a Generic Swimmer Model." B. Ventéjou, T. Métivet, A. Dupont, P. Peyla Physical Review Letters 134 (13) (2025)
  Progressing in our work to unravel the roles of social and hydrodynamic forces on the collective behavior of fish. Here, we propose a toy model that will allow us to simulate large fish schools with hydrodynamic interactions. We also propose a new adimensional number, the Thrust number, allowing to give universal scaling laws between forces (Thrust number) and velocity (Reynolds number) of swimmers.

• "Graphene Field‐Effect Transistors for Sensing Ion‐Channel Coupled Receptors: Toward Biohybrid Nanoelectronics for Chemical Detection." O Terral, G Audic, A Claudel, J Magnat, A Dupont, CJ Moreau, C Delacour Advanced Electronic Materials 10 (10) (2024)
  This a joint work with C. Delacour at Institut Néel as part of our efforts to couple advanced micro-electronics and functional fluorescence microscopy. O. Terral, during her PhD work, has been hardly working at measuring at the same time electric membrane potential of neurons and local concentrations of Calcium ions with fluorescent biosensors. This article is the result of a fruitful collaboration with C. Moreau at IBS and a proof of concept of the power of G-FET for sensing ion flows.

• "Behavioral transition of a fish school in a crowded environment.” B Ventéjou, I Magniez--Papillon, E Bertin, P Peyla, A Dupont, Physical Review E (2024)
  We perturbed the social behavior of a small group of zebrafish by introducing obstacles in the aquarium. Whe increasing the obstacles density, we observe a behavioral transition from an aligned group of fish to scattered fish aligned with the obstacles lattice. The transition from natural to artificial orientation happens when the pillars inter-distance is comparable to the social distance of the fish. We developed a stochastic model of the relative orientation between fish pairs which captures the behavioral transition. Check out our video clip summarizing this paper for the general audience.

• "Fish evacuate smoothly respecting a social bubble.” R Larrieu, P Moreau, C Graff, P Peyla et A Dupont, Scientific Reports (2023)
  We propose an original model experiment that allows us to compare the evacuation behaviour of fish with that of other species when crossing a bottleneck. Whereas most species behave like granular material with clogging events slowing down the evacuation, fish evacuate smoothly without any clogging. They seem to strictly follow social rules and social distances, and can be described like deformable bubbles. With a press release from the Nature group, Université Grenoble Alpes and the CNRS, we got a couple of interviews from the general audience media (Le Parisien, Le Dauphiné Libéré, La Recherche web, Pour la Science, BBC Science Focus, Mediapart,...). Check out our video clip summarizing this paper for the general audience.

• "Collective orientation of an immobile fish school and effect on rheotaxis." R Larrieu, C Quilliet, A Dupont et P Peyla Physical Review E 103 (2), 022137 (2021)
  Here we modeled the polarization of a school of fish in presence of a flow. Each fish experience a social torque to align with his neighbors and a rheotactic torque to aligh against the flow. We show that with the social interactions the school of fish improves its ability to detect the orientaion of the flow in presence of noise.

• "QuanTI-FRET: a framework for quantitative FRET measurements in living cells." A Coullomb, CM Bidan, C Qian, F Wehnekamp, C Oddou, C Albiges-Rizo, DC Lamb et A Dupont. Scientific Reports 10 (1), 1-11 (2020)
  We have developed a method that allows for the first time to measure absolutely the energy transfer between two fluorophores (FRET) in living cells on a simple epifluorescence microscope. We have demonstrated its robustness and efficiency even on noisy or limited data. This method allows the direct comparison of FRET values between different experimental conditions and even between different labs.

• "Synthetic energy sensor AMPfret deciphers adenylate-dependent AMPK activation mechanism" M Pelosse, C Cottet-Rousselle, CM Bidan, A Dupont, K Gupta, I Berger, U Schlattner Nature communications 10 (1), 1-13 (2019)
  Our collaborators developped a FRET-based biosensor that allows the spatiotemporal analysis of energy state and allosteric AMPK activation, in living cells.

• "Magneto-active substrates for local mechanical stimulation of living cells" CM Bidan, M Fratzl, A Coullomb, P Moreau, AH Lombard, I Wang, M Balland, T Boudou, NM Dempsey, T Devillers et A Dupont Scientific reports 8 (1), 1-13 (2018)
  We have created magneto-active substrates to mechanically stimulate cells in a dynamic and spatially resolved manner that is compatible with force measurement and fluorescence microscopy. This type of stimulation was not possible with continuous substrates and thus does not bias the mechanical adhesions of the cell and its force distribution.

• Optical nanotopography of fluorescent surfaces by axial position modulation.” I Kim, J Leblanc, P Moreau, K Kyhm, A Dupont, I Wang. Optics Express 30 (4), 6425-6439 (2022)
  By vertically oscillating a focused laser beam, the topography of any fluorescent surface (even inside cells) can be determined with nanometer resolution.

Short CV

Scientific track

Education

Teaching and supervision