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

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

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

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

Synthesis and Investigation of Pure and Cu-Doped NiO Nanofilms for Future Applications in Wastewater Treatment Rejected by Textile Industry

Malika Allali, Mohamed Amine Dahamni, Mostefa Ghamnia, Abdelwahab Boukhachem, Djamel Boukrédimi, Didier Tonneau, Carole Fauquet

Catalysts 12:931 (2022)10.3390/catal12090931

Characterization of Some Physical and Photocatalytic Properties of CuO Nanofilms Synthesized by a Gentle Chemical Technique

Soumia Aroussi, Mohamed Amine Dahamni, Mostefa Ghamnia, Didier Tonneau, Carole Fauquet

Condensed Matter 7:37 (2022)10.3390/condmat7020037

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

Twenty-five years of nanoscale thermodynamics

Chase Broedersz, Pierre Ronceray

Nature 604:46-47 (2022)10.1038/d41586-022-00869-y

Structural characterization of the interfacial self-assembly of chitosan with oppositely charged surfactant

Revaz Chachanidzea, Kaili Xie, Hanna Massaad, Denis C.D. Roux, Marc Léonetti, Clément de Loubens

Journal of Colloid and Interface Science 616:911-920 (2022)10.1016/j.jcis.2022.01.143

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

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

Liquid demixing in elastic networks: Cavitation, permeation, or size selection?

Pierre Ronceray, Sheng Mao, Andrej Košmrlj, Mikko Haataja

EPL - Europhysics Letters 137:67001 (2022)10.1209/0295-5075/ac56ac

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

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

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

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

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.