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Departement PIV

Physics and Engineering of Living Systems

Leader: Annie Viallat

Introduction

We are a biophysics/bio-engineering department in a research unit mainly dedicated to physics and chemistry.

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

2023

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

2022

Dynamics of Individual Red Blood Cells Under Shear Flow: A Way to Discriminate Deformability Alterations

Scott Atwell, Catherine Badens, Anne Charrier, Emmanuèle Helfer, Annie Viallat

Frontiers in Physiology 12 (2022)10.3389/fphys.2021.775584

First-Principle Coarse-Graining Framework for Scale-Free Bell-Like Association and Dissociation Rates in Thermal and Active Systems

Josip Augustin Janeš, Cornelia Monzel, Daniel Schmidt, Rudolf Merkel, Udo Seifert, Kheya Sengupta, Ana-Sunčana Smith

Physical Review X 12:031030 (2022)10.1103/PhysRevX.12.031030

Physics of Organelle Membrane Bridging via Cytosolic Tethers is Distinct From Cell Adhesion

Mohammad Arif Kamal, Josip Augustin Janeš, Long Li, Franck Thibaudau, Ana-Sunčana Smith, Kheya Sengupta

Frontiers in Physics 9:1-12 (2022)10.3389/fphy.2021.750539

Longitudinal to Transverse Metachronal Wave Transitions in an In Vitro Model of Ciliated Bronchial Epithelium

Olivier Mesdjian, Chenglei Wang, Simon Gsell, Umberto D’ortona, Julien Favier, Annie Viallat, Etienne Loiseau

Physical Review Letters 129:038101 (2022)10.1103/PhysRevLett.129.038101

May the force be with your (immune) cells: an introduction to traction force microscopy in Immunology

Farah Mustapha, Kheya Sengupta, Pierre-Henri Puech

Frontiers in Physics 13:898558 (2022)10.3389/fimmu.2022.898558

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

Affinity driven ion exchange EG-OFET sensor for high selectivity and low limit of detection of Cesium in seawater

Tin Phan Nguy, Volkan Kilinc, Ryoma Hayakawa, Catherine Henry-De-Villeneuve, Jean-Manuel Raimundo, Yutaka Wakayama, Anne Charrier

Sensors and Actuators B: Chemical 351:130956 (2022)10.1016/j.snb.2021.130956

Lrrcc1 and Ccdc61 are conserved effectors of multiciliated cell function

Aude Nommick, Camille Boutin, Olivier Rosnet, Claire Schirmer, Elsa Bazellières, Virginie Thomé, Etienne Loiseau, Annie Viallat, Laurent Kodjabachian

Journal of Cell Science (2022)10.1242/jcs.258960

Stoichiometry Controls the Dynamics of Liquid Condensates of Associative Proteins

Pierre Ronceray, Yaojun Zhang, Xichong Liu, Ned Wingreen

Physical Review Letters 128:038102 (2022)10.1103/PhysRevLett.128.038102

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

2021

OC-0133 Dosimetric characterizations of a novel inorganic scintillating detector - HDR brachytherapy

S. B.C. Debnath, D. Tonneau, C. Fauquet, A. Tallet, A. Goncalves, M. Ferre, J. Darreon

Radiotherapy & Oncology 158:S99 (2021)10.1016/S0167-8140(21)06324-6

In situ plant materials hyperspectral imaging by multimodal scattering near-field optical microscopy

Anne Charrier, Aubin C Normand, Ali Passian, Philip Schaefer, Aude L. L. Lereu

Communications Materials 2:59 (2021)10.1038/s43246-021-00166-7

Spray Pyrolysis Synthesis of Pure and Mg-Doped Manganese Oxide Thin Films

Mohamed Amine Dahamni, Mostefa Ghamnia, Salah Eddine Naceri, Carole Fauquet, Didier Tonneau, Jean-Jacques Pireaux, Abed Bouadi

Coatings 11:598 (2021)10.3390/coatings11050598

Signal amplification of fiber integrated X-ray detector and energy independence

S.B.C. Debnath, J. Darreon, A. Tallet, A. Goncalves, D. Tonneau, C. Fauquet

IEEE Sensors Journal 1-1 (2021)10.1109/JSEN.2021.3091660

Dosimetric characterization of a small-scale (Zn,Cd)S:Ag inorganic scintillating detector to be used in radiotherapy

Sree Bash Chandra Debnath, Didier Tonneau, Carole Fauquet, Agnes Tallet, Anthony Goncalves, Julien Darreon

Physica Medica 84:15-23 (2021)10.1016/j.ejmp.2021.03.022

High resolution small‐scale inorganic scintillator detector: HDR brachytherapy application

Sree Bash Chandra Debnath, Marjorie Ferre, Didier Tonneau, Carole Fauquet, Agnes Tallet, Anthony Goncalves, Julien Darreon

Medical Physics (2021)10.1002/mp.14727

Signal Amplification of Fiber Integrated X-Ray Detector and Energy Independence

Sree Bash Chandra Debnath, Julien Darreon, Agnes Tallet, Anthony Goncalves, Didier Tonneau, Carole Fauquet

IEEE Sensors Journal 21:18793-18799 (2021)10.1109/JSEN.2021.3091660

Ligand Nanocluster Array Enables Artificial-Intelligence-Based Detection of Hidden Features in T-Cell Architecture

Aya Nassereddine, Ahmed Abdelrahman, Emmanuelle Benard, F. Bedu, Igor Ozerov, Laurent Limozin, Kheya Sengupta

Nano Letters 21:5606-5613 (2021)10.1021/acs.nanolett.1c01073

Influence of force volume indentation parameters and processing method in wood cell walls nanomechanical studies

Aubin C Normand, Anne Charrier, Olivier Arnould, Aude L. Lereu

Scientific Reports 11:5739 (2021)10.1038/s41598-021-84994-0

Self-organization and shape change by active polarization in nematic droplets

Fabian Jan Schwarzendahl, Pierre Ronceray, Kimberly Weirich, Kinjal Dasbiswas

Physical Review Research 3:043061 (2021)10.1103/PhysRevResearch.3.043061

Biomechanics as driver of aggregation of tethers in adherent membranes

Kheya Sengupta, Long Li, Mohammad Arif Kamal, Bernd Henning Stumpf, Franck Thibaudau, Ana-Sunčana Smith

Soft Matter 17:10101-10107 (2021)10.1039/D1SM00921D

Integrin-Functionalised Giant Unilamellar Vesicles via Gel-Assisted Formation: Good Practices and Pitfalls

Kheya Sengupta, Mariem Souissi, Julien Pernier, Olivier Rossier, Gregory Giannone, Christophe Le Clainche, Emmanuèle Helfer

International Journal of Molecular Sciences 22:6335 (2021)10.3390/ijms22126335

On the control of dispersion interactions between biological membranes and protein coated biointerfaces

Kheya Sengupta, Robert Blackwell, Arnaud Hemmerle, Andreas Baer, Matthias Späth, Wolfgang Peukert, Drew Parsons, Ana-Sunčana Smith

Journal of Colloid and Interface Science 598:464-473 (2021)10.1016/j.jcis.2021.02.078

Nucleation landscape of biomolecular condensates

Shunsuke Shimobayashi, Pierre Ronceray, David Sanders, Mikko Haataja, Clifford Brangwynne

Nature 599:503-506 (2021)10.1038/s41586-021-03905-5

An Interactive micromanipulation station combined to a confocal XRF instrument : proof of concept and volume resolution

D. Tonneau, D. Renahy, S. Douillet, H. Maradj, C. Fauquet, F. Marchi

IEEEXplore Digital Library (2021)10.1109/MARSS49294.2020.9307924

Signal amplification of fiber integrated X-ray detectors by metallization

D. Tonneau

IEEE Sensors Journal 21:18793 (2021)10.1109/JSEN.2021.3091660

Physical bioenergetics: Energy fluxes, budgets, and constraints in cells

Xingbo Yang, Matthias Heinemann, Jonathon Howard, Greg Huber, Srividya Iyer-Biswas, Guillaume Le Treut, Michael Lynch, Kristi L Montooth, Daniel J Needleman, Simone Pigolotti, Jonathan Rodenfels, Pierre Ronceray, Sadasivan Shankar, Iman Tavassoly, Shashi Thutupalli, Denis V Titov, Jin Wang, Peter J Foster

Proceedings of the National Academy of Sciences of the United States of America 118:e2026786118 (2021)10.1073/pnas.2026786118

Financement

 

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

2017-2022

  • 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

  • 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)

  • ANR ‘RECAMECA’ (2019-2022)

  • NANOPTIX (ANR, 01/01/2019 to 06/30/2022)

  • ANR MicroCJ (2019-2021)

  • Prématuration AMIDEX (2019)

2023-

  • ANR (SPLEENMARK) Natural and assisted airways drainage in COPD (2023-27)

  • ANR "DNANobodies" DNA-nanobody agents to interrogate and manipulate immune cell interfaces (2023-27)

  • ANR "RedEnuc" Mechanisms of terminal erythroid enucleation (2023-26)

  • Contrat industriel Idylle "Nanofilter" Tech transfer:  Système microfluidique qui mime la filtration mécanique des globules rouges par la rate (2023-24)

  • AMIDEX Chaire d'excellence Mechano-technologies for Organoids (2023-26)

  • CENTURI PI startup package: Measuring and modeling soft living matter (2022-2026)

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)
  • Saw Hla & Volker Rose (Argonne National Laboratory, Center for Nanoscale Materials and Advanced Photon Source, USA)

    National

  • Christophe Le Clainche (Paris)
  •  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)

    Inter departmental (intra-CINaM)

  • Ling Peng (IMMF)
  • Jean-Manuel Raimundo (IMMF)
  • Matthieu Petit (NM)

Patents

  • 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.

  • 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).

jobs and internships

internship opportunities available at Master level on the theme 'Mechanics of active biofluids'

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

© 2023 CINaM