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Department PIV

Physics and Engineering of Living Systems

Leader: Kheya Sengupta

Introduction

We are a department of physics of biological systems, and engineering for biology, health and the environment.

We build bridges between physical and biological sciences, and study the interaction of biological objects with their physical environment, building new tools to do so.

An overarching motivation is to find out how small variations at a local scale impact macroscopic properties and function at the level of assemblies. We ask this question both in the context of soft-matter systems and living organisms, our activities covering both fundamental and applied research.

Our questions often revolve around the working of single animal cells, covering sub-cellular to tissular scales.

Examples include membrane organization, its active dynamics and interactions; mechanics and rheology of biofluids, nuclei, single cells and mammalian tissues; largescale self-assembly in active matter, etc. Recently, we have started exploring other diverse directions – including genetic pathologies, host-pathogen interactions etc.

These activities are complemented by applied research where we aim to build novel tools to probe biological systems.

A typical example is our current effort to mimic various aspects of cells (surface nano-bio patterning, including of soft elastomers) or tissues (splenic slits) using micro/nano-fabrication techniques. We innovate imaging techniques as well as image and data analysis tools. Another major focus is on diverse innovative sensors: x-ray nanosensors for simultaneous topography and chemical mapping, lipid based FET sensors for ultra-sensitive detection of ions and biomolecules, and fast photo-thermal sensors for single molecule detection of biochemical reactions.

Techniques and Methods developed in the Department

Experimental techniques

  • Microfluidic techniques coupled with optical video-microscopy, force application, interfacial rheology
  • Nano/microfabrication techniques (functionalization, structuring, patterning of surfaces by organic molecules)
  • Techniques for in-vitro reconstitution of biological objects and processes and minimal systems (biological membranes...)
  • Techniques for manipulation, application and detection of forces at the nano-micro scale (optical tweezers, force application at the micron and submicron scale...)
  • Advanced optical microscopy techniques
  • Coupling of near-field spectroscopy and X-ray spectroscopy.

Theoretical and numerical methods and approaches

  • Theoretical approaches based on statistical physics, stochastic processes, non-linear phenomena, soft matter and active matter physics
  • Numerical simulation of deformable particles and biomaterials
  • Data analysis and interpretation (e.g. images, particle velocities (PIV), trajectories), stochastic model inference

Publications

2025

Dynamics of diazotroph particle colonization in the Arctic Ocean

Arthur Coët, Cécile Carpaneto Bastos, Mathias Lechelon, Ruth Hawley, Oliver Flanagan, Maeve C Lohan, Pierre Ronceray, Joanne E Hopkins, Claire Mahaffey, Mar Benavides

The International Society of Microbiologial Ecology Journal (2025)10.1093/ismejo/wraf098

Reply to Kaestner et al.: Activation of PIEZO1 is not significant for the passage of red blood cells through biomimetic splenic slits

Alexis Moreau, François Yaya, Huijie Lu, Anagha Surendranath, Anne Charrier, Benoit Dehapiot, Emmanuèle Helfer, Annie Viallat, Zhangli Peng

Proceedings of the National Academy of Sciences of the United States of America 122 (2025)10.1073/pnas.2411469121

A novel red blood cell deformability biomarker is associated with hemolysis and vaso-occlusive crises in sickle cell disease

Maxime Sahun, Emmanuelle Bernit, Scott Atwell, Alexander Hornung, Anne M Charrier, Imane Agouti, Nathalie Bonello-Palot, Mathieu Cerino, Emmanuèle Helfer, Catherine Badens, Annie Viallat

Scientific Reports 15:15864 (2025)10.1038/s41598-025-00152-w

Characterization of a high lateral resolution and high sensitivity dosimeter for proton beams using inorganic scintillator detector

Gaël Simonin, Sree Bash Chandra Debnath, Kévin Lalanne, Didier Tonneau, Sébastien Lavandier, Marc Rousseau, David Brasse, Julien Darreon, Carole Fauquet

IEEE Sensors Journal 25:4563-4569 (2025)10.1109/JSEN.2024.3502906

2024

Inferring geometrical dynamics of cell nucleus translocation

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

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

Margination of artificially stiffened red blood cells

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

Physical Review Fluids 9:L091101 (2024)10.1103/physrevfluids.9.l091101

Cerenkov free micro-dosimetry in small-field radiation therapy technique

Sree Bash Chandra Debnath, Didier Tonneau, Carole Fauquet, Agnes Tallet, Julien Darréon

Physics in Medicine and Biology 69:125018 (2024)10.1088/1361-6560/ad51c6

Geometrical Characterization of an Inorganic Scintillator Detector for Proton Therapy using a Micrometer Scale Ion Beam

Kevin Lalanne, Sree Bash Chandra Debnath, Gaël Simonin, D. Tonneau, François Vianna-Legros, Marc Rousseau, David Brasse, J. Darréon, Carole Fauquet

IEEE Sensors Journal 24:20587-20594 (2024)10.1109/JSEN.2024.3401630

Substrate stiffness alters layer architecture and biophysics of human induced pluripotent stem cells to modulate their differentiation potential

Jack Llewellyn, Anne Charrier, Rossana Cuciniello, Emmanuèle Helfer, Rosanna Dono

iScience 27:110557 (2024)10.1016/j.isci.2024.110557

Dans les bronches, cils et mucus collaborent pour protéger nos voies aériennes

Étienne Loiseau, Annie Viallat

Reflets de la Physique 14-17 (2024)10.1051/refdp/202479014

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

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

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

Morphodynamics of T-lymphocytes: Scanning to spreading

Kheya Sengupta, Pierre Dillard, Laurent Limozin

Biophysical Journal 123:2224-2233 (2024)10.1016/j.bpj.2024.02.023

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

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

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

2023

Transit Time Theory for a Droplet Passing through a Slit in Pressure-Driven Low Reynolds Number Flows

Spencer W Borbas, Kevin Shen, Catherine Ji, Annie Viallat, Emmanuèle Helfer, Zhangli Peng

Micromachines 14:2040 (2023)10.3390/mi14112040

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

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

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

Breakups of Chitosan microcapsules in extensional flow

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

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

Classification of red cell dynamics with convolutional and recurrent neural networks: a sickle cell disease case study

Maxime Darrin, Ashwin Samudre, Maxime Sahun, Scott Atwell, Catherine Badens, Anne Charrier, Emmanuèle Helfer, Annie Viallat, Vincent Cohen-Addad, Sophie Giffard-Roisin

Scientific Reports 13:745 (2023)10.1038/s41598-023-27718-w

Curvature gradient drives polarized tissue flow in the Drosophila embryo

Emily W Gehrels, Bandan Chakrabortty, Marc-Eric Perrin, Matthias Merkel, Thomas Lecuit

Proceedings of the National Academy of Sciences of the United States of America 120 (2023)10.1073/pnas.2214205120

Enhanced cell viscosity: a new phenotype associated with lamin A/C alterations

Cécile Jebane, Alice-Anaïs Varlet, Marc Karnat, Lucero Hernandez- Cedillo, Amélie Lecchi, Frédéric Bedu, Camille Desgrouas, Corinne Vigouroux, Marie-Christine Vantyghem, Annie Viallat, Jean-François Rupprecht, Emmanuèle Helfer, Catherine Badens

iScience 26:107714 (2023)10.1016/j.isci.2023.107714

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

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

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

Probing mechanical interaction of immune receptors and cytoskeleton by membrane nanotube extraction

Fabio Manca, Gautier Eich, Omar N’dao, Lucie Normand, Kheya Sengupta, Laurent Limozin, Pierre-Henri Puech

Scientific Reports 13:15652 (2023)10.1101/2022.09.15.508080

Physical mechanisms of red blood cell splenic filtration

Alexis Moreau, François Yaya, Huije Lu, Anagha Surendranath, Anne Charrier, Benoit Dehapiot, Emmanuèle Helfer, Annie Viallat, Zhangli Peng

Proceedings of the National Academy of Sciences of the United States of America (2023)10.1101/2023.01.10.523245

Talin and kindlin cooperate to control the density of integrin clusters

Julien Pernier, Marcelina Cardoso Dos Santos, Mariem Souissi, Adrien Joly, Hemalatha Narassimprakash, Olivier Rossier, Grégory Giannone, Emmanuèle Helfer, Kheya Sengupta, Christophe Le Clainche

Journal of Cell Science 136:jcs260746 (2023)10.1242/jcs.260746

Two steps forward – and one step back?

Pierre Ronceray

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

Analytical theory for a droplet squeezing through a circular pore in creeping flows under constant pressures

Zhengxin Tang, François Yaya, Ethan Sun, Lubna Shah, Jie Xu, Annie Viallat, Emmanuèle Helfer, Zhangli Peng

Physics of Fluids 35:082016 (2023)10.1063/5.0156349

Mechanical characterization of core-shell microcapsules

Kaili Xie, Marc Leonetti

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

Local response and emerging nonlinear elastic length scale in biopolymer matrices

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

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

2022

Protocol for measuring weak cellular traction forces using well-controlled ultra-soft polyacrylamide gels

Farah Mustapha, Kheya Sengupta, Pierre-Henri Puech

STAR Protocols 3:101133 (2022)10.3389/fimmu.2022.898558

A Rare Mutation in LMNB2 Associated with Lipodystrophy Drives Premature Cell Senescence

Alice-Anaïs Varlet, Camille Desgrouas, Cécile Jebane, Nathalie Bonello-Palot, Patrice Bourgeois, Nicolas Levy, Emmanuèle Helfer, Noémie Dubois, René Valero, Catherine Badens, Sophie Beliard

Cells 11:50 (2022)10.3390/cells11010050

Financement

 Physique et nano-micro Ingénierie pour le Vivant 1 Sources et sondes ponctuelles 2

2023-2025

  • ANR PRC: MultiPhysC2M - Multiphysics of confined cell migration (2025-2028)
  • ANR JCJC: N-EDEV - Non-equilibrium fluctuations as drivers of tissue fluidization during embryonic development (2025-28)
  • ANR PRC: AMPLI - Amplification du potentiel de surface par la réorientation du moment dipolaire moléculaire induit à longue distance
  • ANR PRC: SOCA - Suspensions de capsules souples
  • ANR PRCI France/Germany: ActFun - Rôle des fluctuations actives des membranes dans la régulation de fonctions biologiques
  • ERC: SuperStoc - Super-resolved stochastic inference: learning the dynamics of soft biological matter (2023-2028)
  • ANR PRCE with Rheonova company: BronchoClogDrain - Natural and assisted airways drainage in COPD (2023-27)
  • ANR PRC: DNAnonobodies - DNA-nanobody agents to interrogate and manipulate immune cell interfaces (2023-27)
  • ANR PRCI France/U.S.A: RedEnuc - Mechanisms of terminal erythroide nucleation (2023-26)
  • Contrat industriel Idylle:Tech transfer: Nanofilter - Système microfluidique qui mime la filtration mécanique des globules rouges par la rate (2023-24)
  • Chaire d'excellence AMIDEX: Mechano-technologies for Organoids (2023-26)

2017-2022

  • Immunobiomechanics IRP INP-CNRS:  Mechanobiology: collaboration France (CINaM/LAI) & Mexico (UNAM) (2022-27)
  • PI startup package CENTURI: Measuring and modeling soft living matter (2022-26)
  • AMIDEX transfert; Aide à la création de startup : FitRed - Marqueur de l'aptitude des globules rouges à la microcirculation (2022-2024)
  • ANR: SPLEENMARK - Markers of Spleen Function for Patient Management (2020-24)
  • A*Midex International 'dvanced Photon Source pour la détection des Ondes Stationnaires de Surface sous radiation X' (2019-2021)
  • ANR ‘RECAMECA’ (2019-2022)
  • NANOPTIX (2019 -2022)
  • ANR MicroCJ (2019-2021)
  • Prématuration AMIDEX (2019)
  • ECO (Academy of Excellence, A*MIDEX) (2018-2021)
  • AMIDEX ”NORMAL PCW”  (2018-2021)
  • AMIDEX ”Macbio”  (2018-2021)
  • ANR: “Ultra-high throughput sequencing by synchronized synthesis” (2018-2021)
  • A*Midex Interdisciplinarité ‘MecaLam’ (2018-2021)
  • X-R2P2 (DOC2AMU PhD grant, Cofunded by Europe, PACA District Council, In Excellence A*MIDEX)
  • Prématuration CNRS (2017-2019)
  • Région PACA Projet exploratoire ‘BioMimWASH’ (2017-2018)
  • ANR TMOL “SENSEI” (2017-2020)

Equipment and Facilities

Physique et nano-micro Ingénierie pour le Vivant 2

  • Photo luminescense : excitation with cw He-Cd laser (10 mW, Gaussian TEM00 mode). Spectro resolution of 21 nm/mm of slit aperture
  • Micro-XRF analysis: Rh target X-ray source, lateral resolution 20 µm, total X-ray photon flux within the spot area of 2.109 photons/s, EDX SDD detector from Brücker (X-flash)
  • AFM
  • Electrical measurement platform
  • Confocal microscope
  • TIRF and RICM microscopy
  • Langmuir Film Balance
  • Microfluidics combined with high-speed videomicroscopy
  • Optical microscopes equipped with temperature and CO2 control
  • Optical microscope (bright field, phase contrast, epifluorescence) combined with Atomic Force Microscopy (AFM) and optical tweezers (in construction)

Collaborations

International

  • Zhangli Peng (University of Illinois at Chicago, USA)
  • Peng Ji (Northwestern University, Chicago, USA)
  • Ali Passian & Rubye Farahi (Oak Ridge National Laboratory, USA)
  • Yutaka Wakayama (NIMS, Japan)
  • Ana Smith (University of Erlangen, Germany)
  • Mostefa Ghamnia (LSMC laboratory, University Oran 1, Ben Bella, Algeria)
  • Saw Hla & Volker Rose (Argonne National Laboratory, Center for Nanoscale Materials and Advanced Photon Source, USA)

National

  • Rachele Allena, Laboratoire Jean Alexandre Dieudonné (LJAD), Université Côte d'Azur, Nice
  • Slimane Ait-Si-Ali, Epigénétique et Destin Cellulaire (EDC), CNRS-Université Paris Cité, Paris
  • Jean-Baptiste Manneville et Sylvie Hénon, Matière et Systèmes Complexes (MSC), CNRS-Université Paris Cité, Paris
  • Catherine Henry de Villeneuve (LPMC, Palaiseau)
  • Anthony Goncalves (CRCM, Marseille)
  • Agnès Tallet & Julien Darreon (Paoli-Calmettes Institute, Marseille)
  • Thierry Grosjean (FEMTO-ST, Besançon)
  • Guillaume  Baffou (Institut Fresnel, Marseille)
  • Aude Lereu (Institut Fresnel, Marseille)
  • Catherine Badens (APHM, Marseille)
  • Julien Favier (M2P2, Marseille)
  • Laurent Limozin (LAI, Marseille)
  • Pierre-Henri Puech (LAI, Marseille)
  • Pascal Chanez et Delphine Gras (CV2M, Marseille)
  • Vincent Gressier, François Vianna-Legris, Christelle Adam-Guillermin (LMDN lab from IRSN)

Inter departmental (intra-CINaM)

Past Collaborators

  • Christophe Le Clainche (I2BC, Paris)
  • Gregory Gianonne (IINS, Bordeaux)

Patents

  • Nano−scale stimulating substrates

Inventeurs: K. Sengupta, E. Benard, I. Ozrov, F. Bedu, H. Dallaporta, N° of deposition/publication: FR1853414 (2018), WO/2019/202260 (2019).

 

  • Method and device for determining red blood cells deformability

Inventeurs: A. Viallat, S. Atwell, E. Helfer, A. Charrier, C. Badens. Application N°EP18305914.6, 10 juillet 2018.

 

  • Amphiphilic molecules layers

Inventeurs: A. Charrier, J.M Raimundo, A. Kenaan, S. Lavandier. N° of publication: PCT/EP2016/074569

 

  • Transistor à effet de champ pouvant notamment être utilisé comme détecteur et procédé de fabrication de ce détecteur

Inventeurs: A. Charrier, Tuyen Nguyen Duc, Hervé Dallaporta. N° of publication: WO/2013/083490; EP 2 788 747 B1

 

  • Device to detect the fixation of a target object on a probe object immobilized on a solid substrate and detection process

Inventeurs: A. Charrier, F. Thibaudau. (FR2873818, WO/2006/021716). N° of deposition/publication: 0451747. Publication date: 02.03.2006.

jobs and internships

PhD, Post-doc and internship opportunity for all topics: contact relevant researcher.

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