From bugs to bubbles

A quick introduction

My name is François Peaudecerf, I am a post-doctoral researcher at the Institute for Environmental Engineering of the ETH Zürich in the group of Prof. Roman Stocker.

Before joining ETH, I obtained my PhD at the Department of Applied Maths and Theoretical Physics (DAMTP) at the University of Cambridge (UK) in the group of Prof. Ray Goldstein.

My main research interests include microbial interactions, microswimmers and soft matter physics, in particular air-water interfaces. I investigate these topics by combining experiments with mathematical modelling.

News

Paper out in PNAS

1st August 2022

Our work on the predation of bacteria by amoeba, led by Frédéric de Schaetzen and Mingzhen Fan, is fresh out in PNAS! Chemotaxis assays, clever bacterial tracking, and scaling arguments of encounters enabled us to shed light on the bacterial capture process. Check it out there!

Talk at GRS Marine Microbes

29th May 2022

Another great opportunity to present my work on the microlayer, first as a talk at the Gordon Research Seminar Marine Microbes, and thereafter as a poster for the associated Gordon Research Conference. It was very interesting to get insight on the life in the microlayer from a more biological point of view.

Talk at MOB 6.0

25th May 2022

I got the chance to give a talk on my work on the behavior of bacteria in the microlayer in response to aerosol deposition at the 6th Microscale Ocean Biophysics conference in Port de Sollers (Mallorca). Great conference, great interactions and feedback, looking forward to the next one.

Microbial impact on marine snow paper

29th March 2022

I contributed to a modelling paper now out in Nature Communications, led by Dr. Trang Nguyen (in the group of Prof. Naomi Levine) which gives insight into the coupled dynamics of microbes and the marine snow particles they thrive on. Check the paper here! Illustration from Nguyen et al. 2022, CC BY 4.0

Book chapter in Marine Microbiomes

1 January 2022

I contributed to a book chapter in the second edition of "The Marine Microbiomes", describing how the microscale physics in the ocean create the complex landscape of resources marine bacteria have to navigate. It's a pleasure to see it published.

Thrombosis on a chip paper

27 October 2021

Jess Berry, from the University of Cambridge, led this study aiming to design and test a microfluidic chip enabling quantitative and accurate testing of drugs preventing blood clotting. I contributed to the development of the chip, and am very happy to this work published in Lab on a Chip! Check the paper here!

Marine snow paper is out!

23 September 2021

Our paper on the coupling between marine snow sinking speed and microbial degradation is just published in Nature Geosciences. I developped a mathematical model to extend the experimental results of my colleagues Uria Alcolombri to realistic marine snow distributions. Our work made it to the ETH news. Check the paper here, and the code behind the model here.

Art by Dr. Jen Nguyen

Workshop at Scientifica 2021!

4/5 September 2021

With my colleagues Dr. Jeanette Wheeler, Dr. Clara Martines-Pérez and Juanita Lara-Gutierrez, we organised a workshop for teenagers during the outreach event Scientifica 2021 happening all over ETH and UHZ. Taylor's robots, play-dough plankton sinking in glycerol and microscopy of daphnia were part of the fun!

Chemokinesis on cover of EPJE!

27 May 2021

The figure designed by lead author Theresa Jakuszeit for our paper on chemokinesis was chosen to be on cover of the March Issue of EPJE.

Algal-bacterial mutualism paper is out!

21 May 2021

I had the chance to contribute to a freshly published paper on microbial mutualisms. Led by Hannah Laeverenz Schlogelhofer under the supervision of Otti Croze, with further collaborators in Sweden and UK, the study combine mathematical modelling with nano-SIMS to reveal the hidden dynamics of mutualistic nutrient exchanges. Very pleased to see the paper in PLoS ONE, here.

Open lecture on tracking principles!

25 February 2021

With Margit Peaudecerf, we assembled and released a Jupyter notebook presenting some of the concepts behind the use of single particle tracking for probing the biophysical properties of the cell cytosol. Lots of interactive simulations! Download the whole repository from GitHub or open the notebook in Binder to start simulations directly in your browser! Binder DOI

New paper in Frontiers in Public Health

16 February 2021

We just published our paper on building an online platform linking hospital needs with academic resources during the COVID pandemic in Frontiers in Public Health, as a support for similar initiatives across the globe. I contributed to the early development and staffing of the initiative. News items at EPFL and on Frontiers blog, and full paper here.

Our letter on UV inactivation of SARS-CoV-2 published in JID

9 February 2021

The Journal of Infectious Diseases has just published our letter (free access) suggesting UVB on their own might not entirely explain the observed inactivation of SARS-CoV-2 in sunlight. This letter was motivated by the publication in the same journal of experimental results on inactivation rates of SARS-CoV-2 in sunlight, showing rates differing strongly from established theories including UVB only. Check also our related preprint.

Egan et al. 2021 CC BY NC ND

Turbulent flows over SHS in our latest published paper!

6 January 2021

In their recently published paper in the Journal of Computational Physics, to which I contributed, Raphael Egan and colleagues present a new parallel solver for incompressible flows, and demonstrate its performance by computing fully developped turbulent flows over a gratting-based super-hydrophobic surface (SHS). Check out the paper free of charge for 50 days here!

COVID-19 Seed Grant

3 May 2020

I have been awarded together with Prof. Paolo Luzzatto-Fegiz, Prof. Julie A. McMurry, and Prof. Julien R. Landel a VRC COVID-19 Seed Grant of 25k$ from UC Santa Barbara for our project on the role of UVA in inactivating SARS-CoV2 and its potential use in air-purifying respirators. You can find here our related preprint.

Contribution to Academic Resources for COVID platform (ARC)

20 March 2020

As ETH went into lockdown with the first wave of COVID-19 pandemic, I contributed with several colleagues from ETH to the development and staffing of a web platform to link needs of diagnostic labs and hospitals for equipment and consumables with resources available in academic labs. This development was extremely fast to serve the rapid increase in needs, which I moderated with others for several months. In parallel in the summer a second version of the platform was finalized (in an effort led by EPFL), available here.

Our latest SHSs paper is online!

25 November 2019

Our work on the modelling of super hydrophobic surfaces (SHSs) contaminated by surfactants, and their associated reduced drag reduction properties, has just been published in Journal of Fluid Mechanics!

Successful ETH Seed Grant application!

27 June 2019

I have been awarded together with Dr. Jeanette Wheeler an ETH Career Seed Grant of 30kCHF for our joint-project investigating bacterial chemotaxis response to aerosol deposition in the microlayer - the thin layer at the top of the water column. We will start working on it in September for one year!

More news here

Publications

  • F. Temprano- Coleto, S. M. Smith, F. J. Peaudecerf, J. R. Landel, F. Gibou, P. Luzzatto-Fegiz, "A single parameter can predict surfactant impairment of superhydrophobic drag reduction" in revision PNAS, (2022) linkpreprint
  • F. de Schaetzen, M. Fan, U. Alcolombri, F. J. Peaudecerf, M. Schuppler, R. Stocker and M. Loessner, "Random encounters and predator locomotion drive the predation of Listeria monocytogenes by Acanthamoeba castellanii" PNAS, 119:e2122659119 (2022) link
  • T. Nguyen, E. J. Zakem, A. Ebrahimi, J. Schwartzman, T. Calgar, U. Alcolombri, F. J. Peaudecerf, T. Hwa, R. Stocker, O. X. Cordero and N. M. Levine, "Microbes contribute to setting the ocean carbon flux by altering the fate of sinking particulates" Nature Communications, 13:1657 (2022) link download pdf Creative Commons License
  • U. Alcolombri, F. J. Peaudecerf, V. I. Fernandez, L. Behrendt, K. Soo Lee and R. Stocker, "Sinking accelerates the degradation of organic particles by marine bacteria" Nature Geosciences, 14:775-780 (2021) link
  • J. Berry, F. J. Peaudecerf, N. A. Masters, K. B. Neeves, R. E. Goldstein and M. T. Harper, "Development of a novel “arterial thrombosis-on-a-chip” microfluidic device." Lab on a Chip, 21:4104 (2021) download pdf link
  • H. Laeverenz Schlogelhofer, F. J. Peaudecerf, F. Bunbury, M. J. Whitehouse, R. A. Foster, A. G. Smith, O. A. Croze, "Combining SIMS and mechanistic modelling to reveal nutrient kinetics in an algal-bacterial mutualism" PLoS ONE, 16(5): e0251643 (2021) download pdf link
  • P. Luzzatto-Fegiz, F. Temprano-Coleto, F. J. Peaudecerf, J. R. Landel, Y. Zhu, and J. A. McMurry, "UVB radiation alone may not explain sunlight inactivation of SARS-CoV-2" Journal of Infectious Diseases, jiab070 (2021) link (free access)
  • J.-D. Courcol, C. F. Invernizzi, Z. C. Landry, M. Minisini, D. A. Baumgartner, S. Bonhoefer, B. Chabriw, E. E. Clerc, M. Daniels, P. Getta, M. Girod, K. Kazala, H. Markram, A. Pasqualini, C. Martínez-Pérez, F. J. Peaudecerf, M. S. Peaudecerf, U. Pfreundt, B. R.K. Roller, J. Słomka, M. Vasse, J. D. Wheeler, C. M. J. A. Metzger, R. Stocker and F. Schürmann, "ARC: An open web-platform for request/supply matching for a prioritized and controlled COVID-19 response" Frontiers in Public Health, 9:607677 (2021) link
  • T. Jakuszeit, J. Lindsey-Jones, F. J. Peaudecerf, O.A. Croze, "Migration and accumulation of bacteria with chemotaxis and chemokinesis" EPJE, 44:32 (2021) download pdf link
    Associated news releases: EurekaAlert! and EPJE News page
  • R. Egan, A. Guittet, F. Temprano-Coleto, T. Isaac, F. J. Peaudecerf, J. R. Landel, P. Luzzatto-Fegiz, C. Burstedde, F. Gibou, "Direct Numerical Simulation of Incompressible Flows on Parallel Octree Grids" Journal of Computational Physics, 428:110084 (2021) JCP versionPublished version
    Accepted manuscriptAccepted manuscript Creative Commons License
  • J. Landel, F. J. Peaudecerf, F. Temprano-Coleto, F. Gibou, R.E. Goldstein, P. Luzzatto-Fegiz, "A theory of the slip and drag of superhydrophobic surfaces with surfactant" Journal of Fluid Mechanics, 883:A18 (2020) arXiv link
  • F. J. Peaudecerf, J. R. Landel, R. E. Goldstein, and P. Luzzatto-Fegiz, "Impact of surfactant on the drag reduction potential of superhydrophobic surfaces" Proceedings of the 5th European Conference on Microfluidics – μFlu18 / 3rd European Conference on Non-Equilibrium Gas Flows – NEGF18, 387-389 (2018) download pdf
  • F. Temprano-Coleto, F. J. Peaudecerf, J. R. Landel, F. Gibou, and P. Luzzatto-Fegiz, "Soap opera in the maze: geometry matters in Marangoni flows" Physical Review Fluids, 3:100507 (2018) download pdf link
  • F. J. Peaudecerf, F. Bunbury, V. Bhardwaj, M. A. Bees, A. G. Smith, R. E. Goldstein, O. A. Croze, "Microbial mutualism at a distance: the role of geometry in diffusive exchanges", Physical Review E, 97:022411 (2018) download pdf link
  • F. Temprano-Coleto, F. Peaudecerf, J. Landel, F. Gibou, and P. Luzzatto-Fegiz, "Soap opera in the maze: geometry matters in Marangoni flows" Gallery of Fluid Motion, American Physical Society, Division of Fluid Dynamics, (2017) link
  • F. Peaudecerf, J. R. Landel, R. E. Goldstein, and P. Luzzatto-Fegiz, "Traces of surfactants can severely limit the drag reduction of superhydrophobic surfaces", PNAS, 114:7254-7259 (2017) download pdf link
  • S. Widder et al., "Challenges in microbial ecology: building predictive understanding of community function and dynamics.", The ISME Journal, 10:2557–2568 (2016) download pdf link
  • F. Peaudecerf and R. Goldstein, "Feeding ducks, bacterial chemotaxis and the Gini index", Physical Review E, 92:022701 (2015) download pdf link
  • K. Alim, G. Amselem, F. Peaudecerf, M. Brenner, and A. Pringle, "Random network peristalsis in Physarum polycephalum organizes fluid flows across an individual", PNAS, 110:13306-13311 (2013) link
  • W. Kim, F. Peaudecerf, M. W. Baldwin, and J. W. M. Bush, "The hummingbird’s tongue: a self-assembling capillary syphon", Proceedings of the Royal Society B, 279:4990 (2012) link
  • J. W. M. Bush, F. Peaudecerf, M. Prakash, and D. Quéré, "On a tweezer for droplets", Advances in Colloid and Interface Science, 161:10--14 (2010) link

Outreach and teaching

I have supervised in Mathematical Biology at the Department of Applied Mathematics and Theoretical Physics, University of Cambridge.

With Margit Peaudecerf, we assembled and released a Jupyter notebook presenting some of the concepts behind the use of single particle tracking for probing the biophysical properties of the cell cytosol. This material was used for the Block Course at the Institute for Biochemistry (ETH Zurich) and targets biology students. It contains several interactive simulations aiming at demonstrating Brownian motion in a cell. The whole repository can be downloaded from GitHub. ALternatively, the notebook can be launched in an executable environment in Binder to start simulations directly in the web browser with no required local installation. DOI Binder

I have developed several projects for reaching out to non-specialist audiences and share the excitement of science. A list of these project is available on this dedicated page.

Funding

EU emblem2017-2020: I have received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 798411.

ETH_logo2019-2020: I have received funding from an ETH Zurich Career Seed Grant.

Contact Information

    ETH Zürich
    Department of Civil, Environmental and Geomatic Engineering
    Institute for Environmental Engineering
    Stefano Franscini Platz 5
    8063 Zürich
    Switzerland

    +41 446324136

    peaudecerf[a]ifu.baug.ethz.ch

    ORCID iD iconhttps://orcid.org/0000-0003-0295-4556