Matthieu Chavent
@matthchavent.bsky.social
Multiscale molecular dynamics, biological membranes, TB, host-pathogen interactions, CNRS researcher, group leader at @cbitoulouse.bsky.social
Recent review: "Adapting Architecture: Lipid Membrane Remodeling in Mycobacteria" www.annualreviews.org/content/jour...
Adapting Architecture: Lipid Membrane Remodeling in Mycobacteria
The mycobacterial cell envelope is a formidable barrier, regarded as one of the most chemically and structurally elaborate architectures in the Bacteria kingdom. Membrane remodeling, defined as change...
annualreviews.org
⚡ Time is running out! ⚡ The deadline for the @biophysicalsoc.bsky.social Theory & Computation Awards is Sept 15! 🧬💻 Recognizing outstanding research across: 🎓 Postdocs 🌱 Early Career 🚀 Mid-Career Nominate a student or colleague! 🧪✨ 👇 Details: www.biophysics.org/Awards-Fundi...
Subgroup Awards - The Biophysical Society
biophysics.org
Latest preprint where we pooled our sim experiences to create "MDArena" for AI agents trying to automate MD simulation and analysis. Great work led by Nithishwer Mouroug Anand and @weitse-hsu.bsky.social and thanks to all lab members! @oxfordbiochemistry.bsky.social arxiv.org/abs/2608.02642
MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows
Accelerating scientific discovery is among the most consequential applications of AI, and computational biomolecular simulation stands out as a particularly promising target within this broader effort...
arxiv.org
Excited to share our latest work with Wonpil Im lab about the modeling of mycobacterial inner membrane using atomistic simulations, published in the @pubs.acs.org the Journal of Chemical Information and Modeling! Congratulations Hwayoung and Nate! More details here: pubs.acs.org/jcisd8/artic...
New paper on SLC10 (bile acid) transporters. Based on a 9-TM prokaryotic protein, ASBT_LB (same topology as mammalian ASBT) we show standard alternating access outward facing and inward conformations with a curious proteo-lipidic binding site for bile acids authors.elsevier.com/sd/article/S...
From fuzzy to ridig We are pleased to share a new paper entitled “Intrinsic flexibility of the Type VII secretion central pore is required for substrate translocation”, published now in www.biorxiv.org/content/10.6... Great thanks to all contributing authors for their outstanding work.
PhD position in Heidelberg: generating amorphous molecular thin films with diffusion models rather than waiting for MD to equilibrate them — free energies from the same model. With U. Köthe. 3 years, funded. Physics degree required. tristanbereau.com/positions/ge...
Generative machine learning for molecular thin films – Tristan Bereau
tristanbereau.com
Basement membrane turnover controls cell shape www.cell.com/cell/fulltex...
Basement membrane turnover controls cell shape
Basement membranes are scaffolds of proteins, like collagen, that give organs shape. During development, basement membranes must adapt to the growing organ. We infer how fast the basement membrane ada...
cell.com
New OA Article: "Membrane remodelling mediates lipopeptide-induced immunity in Arabidopsis" rdcu.be/feoNF Lipid-driven mechanism for immune activation by a bacterial lipopeptide. Perception at the cell membrane leads to deformation, mechanosensing and early signalling. #PlantScience
Lipids build the membranes of all cells, but identifying their precise functions is extremely challenging. Here’s our attempt to change that: How to find and understand lipid-protein interactions, by Katelyn Cook & company. www.biorxiv.org/content/10.6...
"FAIR + COPE (Comparable, Organized, Predictive, Engaged) takes FAIR data and makes it Comparable, rapidly Organized (applying / updating standards) for Predictive models, which can be validated and improved by an Engaged community."
Advancing FAIR data towards comparable, organized, predictive AI-ready data for community validation
Communications Biology - This Perspective explores how updating static, FAIR data/databases can lead to COPE: Comparable, Organized (AI-ready) data that supports novel Predictions of biological...
nature.com
Very happy to have this work finally published! How do embryos sculpt their shape? We map the contractile & adhesive forces shaping early C. elegans embryos. With K. Yamamoto @ittoku04.bsky.social G. Charras' lab @gcharras.bsky.social & my team @turlierlab.bsky.social shorturl.at/xv7G5 1/6
Fantastic opportunity at @pasteur.fr in Spyros’ brand new lab, especially if you like protein design 🎉
Antigen Evolution & Design Lab@antigenevo.bsky.social · 3w ago🚨 JOB ALERT🚨 We are very excited to be hiring the lab's ✨very first postdoc✨! Work on new AI technologies for decoding antigen protein evolution in a fresh research environment, at the heart of Paris 🇫🇷 Details & link to apply: research.pasteur.fr/en/job/postd... Deadline: Sep 1st
🎉 Finally out!! Our paper, "DynaPIN: A tool for characterizing dynamic protein interfaces" is accepted in JMB! @ezgikaraca.bsky.social (in collaboration with @sacquin-mo.eurosky.social & co.) DynaPIN is an open-source pipeline for analyzing dynamic protein interfaces. 🧵👇 📄 doi.org/10.1016/j.jm...
Great collaboration with @weiss-lab.bsky.social lab! Happy that the team participate to this wonderful project!
Gregor Weiss@weiss-lab.bsky.social · last mo.Some bacteria do not live as individuals. They build multicellular filaments and connect neighboring cells through tiny cell-cell junctions. Cyanobacteria are among the most beautiful examples 😍 In our new paper, we reveal first molecuar insights on the cyanobacterial septal junction architecture 🧵
Happy that our team - aka @aschahl.bsky.social 😆 - helped a little on this really cool project! Congratulations @romet-jegou-lab.bsky.social team!
Journal of Cell Biology@jcb.org · last mo.Xiao et al. @romet-jegou-lab.bsky.social show that #actin branch junctions whose Arp2/3 complex contains inorganic phosphate are mechanically more stable & protected from GMF-induced destabilization, but are not stabilized further by cortactin. rupress.org/jcb/article/... #Cytoskeleton #Biophysics
Good news everyone! 🎉 The new version 3.0 of graph-tool is just out with major improvements! See below. graph-tool.skewed.de graph-tool is a comprehensive and efficient Python library to work with networks, including structural, dynamical, and statistical algorithms, as well as visualization. 1/N
Glover, Wilkinson, @ianofbristol.bsky.social et al. show that cells subject to mitochondrial protein import failure induce Intercellular Mitochondrial Transfer via tunnelling nanotubes. rupress.org/jcb/article/... #Organelles #Biochemistry #Mitochondria
Read about the cover art for the newly released issue of Biophysical Journal on the BPS Blog: www.biophysics.org/blog/bacteri...
Bacterial Lipids on the Move in Molecular Dynamics Simulations
In our research, we used molecular dynamics simulations that act as a computational microscope to visualize how membrane proteins perform their physiological functions and interact with surrounding li...
biophysics.org
🚨 New in @natmicrobiol.nature.com! We reveal how the antibiotic target PBP1b fortifies the E.coli division site against osmotic rupture. Proud this was completed in our independent labs @dmf-unil.bsky.social, with @avettiger.bsky.social. Congratulations to all authors! 🦠❄️🔬 #teamtomo bit.ly/3SCbOg1 👇
The penicillin-binding protein PBP1b fortifies the Escherichia coli division site against osmotic rupture - Nature Microbiology
A specific isoform of PBP1b functions independently of the activator protein, LpoB, to drive generation of a wedge-like peptidoglycan structure that strengthens the division site in Escherichia coli.
doi.org
Out Now! Identification of chemical features for improved outer membrane permeation in mycobacteria using machine learning #MicroSky
Identification of chemical features for improved outer membrane permeation in mycobacteria using machine learning
Nature Microbiology, Published online: 30 June 2026; doi:10.1038/s41564-026-02412-5Screening 1,572 compounds for mycomembrane permeation plus cheminformatic and machine learning analyses reveals features associated with improved permeation in the pathogen Mycobacterium tuberculosis and model organism M. smegmatis.
go.nature.com
New paper in collaboration with @proftracypalmer.bsky.social, @lislowe.bsky.social and many more. We show that mycobacteria produce Type VII secreted anti-bacterial protein toxins. Excited to explore this new area of mycobacterial biology. www.nature.com/articles/s41...
A Type VII-secreted toxin enables inter-mycobacterial competition - Nature Communications
Mycobacteria have not yet been reported to engage in interbacterial competition via secretion of proteinaceous toxins. Here, Benedict et al. show that some mycobacteria can use their type-VII secretio...
nature.com
Cryo-ET is often framed as a tool for in situ protein structure. But what if the real revolution is contextualization? I explore how #teamtomo is redefining what "local" means in organelle biology, revealing membrane states rather than just protein structures. tinyurl.com/localmembrane
Think globally, act locally: Redefining organellar membrane environments through cryo-electron tomography
Early enthusiasm for the “cellular revolution” in cryo-electron tomography (cryo-ET) was largely driven by the promise of resolving protein structures…
sciencedirect.com
This amazing work by @danialv.bsky.social and Bodan Hu is now out in peer-reviewed form at @cp-cell.bsky.social with a lot of new simulations! Check it out if interested in lipid transport!
Vanni Lab at UNIFR, Switzerland@labvanni.bsky.social · 7mo agoHappy to finally share the amazing results of our long-term collaboration with Karin Reinisch’s lab on how bridge lipid-transfer proteins (BLTPs) cooperate with partner proteins to orchestrate lipid delivery. A quick thread (1/7) www.biorxiv.org/content/10.6...
I'm incredibly proud to share our paper on the preclinical evaluation of the BNT164 mRNA tuberculosis vaccine candidates. Now online in the final version at Nature Immunology. www.nature.com/articles/s41...
mRNA-based tuberculosis vaccines BNT164a1 and BNT164b1 are immunogenic, well tolerated and efficacious in rodent models - Nature Immunology
Here the authors characterize mRNA-based tuberculosis vaccine candidates BNT164a1 and BNT164b1 and show that they are immunogenic, well tolerated and efficacious in preclinical animal models.
nature.com
A Perspective discusses challenges in macromolecular ensemble prediction and the methodological advances that are needed. @stephanieaw.bsky.social www.nature.com/articles/s41...
From possibility to precision in macromolecular ensemble prediction - Nature Methods
This Perspective discusses current challenges in macromolecular ensemble prediction and the infrastructure and methodological advances needed to overcome these barriers.
nature.com
What would happen if Darwin, Russell Wallace and Koch walked into a bar? We present our new way to study mycobacteria, employing a macroevolution framework (species not strains). Possibilities are endless!! Thanks to Fernanda Subtil for pushing this. elifesciences.org/articles/101...
A macroevolution-inspired approach to reveal novel antibiotic resistance mechanisms
Using macroevolution, species not strains, uncovered important diversity in how mycobacteria respond to and resist antibiotics, revealing novel resistance determinants.
elifesciences.org
🚀 Sponsorship opportunities still available 📍 Lyon, France | 14–16 October 2026 Registration opening soon. Stay tuned for further announcements! #CGML2026 #MachineLearning #MolecularModeling #CoarseGrained #DrugDiscovery #Formulations #MaterialsScience
