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Matthieu Chavent

@matthchavent.bsky.social
663 followers 581 following 106 posts

Multiscale molecular dynamics, molecular visualization, biological membranes, TB, host-pathogen interactions, CNRS researcher, group leader at @cbitoulouse.bsky.social

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Reposted by Matthieu Chavent
Chrystal Starbird @drstarbird.bsky.social · 01/10/2026
And… I am SO excited to share the first research preprint from my group! In this paper we determined several cryoEM structures to visualize the entire cell-to-cell bridging complex formed by TAM receptor and ligand, bringing into 3D a common graphical depiction. www.biorxiv.org/content/10.6...
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Cell Biology J-Club @cellclub.bsky.social · 29/09/2026
Quantification of lipid sorting during clathrin-mediated endocytosis www.nature.com/articles/s41...
nature.com
Quantification of lipid sorting during clathrin-mediated endocytosis - Nature Cell Biology
Lennartz et al. evaluate lipid enrichment in clathrin-coated pits and observe that the differential lipid partitioning into clathrin-coated pits is largely driven by the lipid asymmetry of the plasma ...
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Matthieu Chavent @matthchavent.bsky.social · 28/09/2026
Je veux bien en être aussi! On peut monter un (micro)parti ? 😆
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Reposted by Matthieu Chavent
Emmanuel Margeat @emmanuelmargeat.bsky.social · 27/09/2026
As climate change and resource scarcity reshape our world, the carbon footprint of scientific computing cannot be ignored. Join this BPS webinar to discuss these questions with : Loic Lannelongue @loiclnlg.bsky.social Alexandre Bonvin @amjjbonvin.bsky.social Rommie Amaro @rommieamaro.bsky.social
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Reposted by Matthieu Chavent
Maksim Kalutskii @maksimkalutskii.bsky.social · 23/09/2026
Excited to share our new preprint! 📜 Here, we used CALVADOS and ultra-CG models to show how the kinetochore establishes a robust attachment to the dynamic microtubule end. Spoiler: IDRs 🧵 1/n www.biorxiv.org/content/10.6...
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 23/09/2026
What if any dataset, any size, any number of dimensions, opened in a browser tab from a link? 🔬🧪💻 Luxar is out today: write it in Python, share it as a link, explore it in any browser. Open source. 🧵 @biohub.org Preprint: doi.org/10.5281/zen... Code: github.com/royerlab/luxar
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Audrey Dussutour @docteur-drey.bsky.social · 23/09/2026
Notre labo le CBI - Centre for Integrative Biology of Toulouse ouvre ses portes en soirée, le vendredi 2 octobre de 18 à 23h. Hâte de vous y retrouver ! www.fetedelascience.fr/nuit-de-la-s...
fetedelascience.fr
Nuit de la Science au CBI
Le CBI organise une Nuit de la Science et accueille le public pour visiter les laboratoires et participer à différents ateliers pratiques proposés par les scientifiques du CBI.
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Matthieu Chavent @matthchavent.bsky.social · 18/09/2026
On change vraiment d'échelle, je pense qu'on peut créer des plugins "à façon" pour un grand nombre de programmes. Par contre, il faut savoir quoi demander (prompting) et avoir un minimum de connaissance pour être sûr de ce que l'on obtient.
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Matthieu Chavent @matthchavent.bsky.social · 18/09/2026
J'imagine qu'il pourrait y avoir des gains très rapides chez vous dans la sélection des jeux d'images, l'analyse, l'amélioration de la netteté... Je serai curieux de voir si vous avez un jeux d'image de mauvaise résolution et vous essayez d'obtenir des images améliorées ce que cela donne. for fun
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Matthieu Chavent @matthchavent.bsky.social · 18/09/2026
De mon côté, c'est d'abord pour faire du protyping rapide. Je pense que l'on rate encore l'ampleur de ce que l'on peut faire: j'ai recodé mon travail de thèse en computer graphics (2 ans de travail) en qq jours alors que le code me semble très avancé - calculs sur carte graphique...
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Matthieu Chavent @matthchavent.bsky.social · 18/09/2026
C ce que je fais depuis plusieurs mois...
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Reposted by Matthieu Chavent
Phil Biggin @philbiggin.bsky.social · 18/09/2026
Congratulations to @jchvh.bsky.social as his part II simulation work in @oxfordbiochemistry.bsky.social appears, Carl's simulations nicely revealed the dynamic connection between binding and biased signalling in GPR84. www.nature.com/articles/s41.... With Russell, Tikhonova, Zhang and Milligan labs
nature.com
Steric control of signaling bias in the immunometabolic receptor GPR84 - Nature Communications
This study reveals how subtle changes in ligand structure control signaling bias at the immunometabolic receptor GPR84, providing structural details for the rational design of drugs with tailored sign...
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Reposted by Matthieu Chavent
German National Research Data Infrastructure (NFDI) @nfdi.de · 11/09/2026
🏆️ PERLA by @fairmat.bsky.social transforms thousands of annual publications into structured data, combining AI & research data infrastructure to identify trends & fuel innovation. 🔗Preprint: arxiv.org/abs/2601.17807 🔗Docs: fairmat-nfdi.github.io/perla/ 🔗Database: nomad-lab.eu/prod/v1/stag...
NFDI Success Stories graphic highlighting FAIRmat’s PERLA (PERovskite Living Archive). The graphic explains that PERLA accelerates perovskite solar cell research by making knowledge immediately usable through AI-driven, continuously updated data. A stylised microscope icon and laboratory-themed background complement the design.
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Matthieu Chavent @matthchavent.bsky.social · 12/09/2026
Fun to decompose the Molecular Skin Surface in different patches while keeping the CPK coloring. Here shrinked Voronoï patches (green) and Hyperboloid prisms (pink)
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Matthieu Chavent @matthchavent.bsky.social · 12/09/2026
Almost 20 years ago, my first author article was about the Molecular Skin Surface under @brunolevy01.bsky.social supervision: www.sciencedirect.com/science/arti... Now, the Molecular Skin Surface is back in the webbrowser!
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chipotlab.bsky.social @chipotlab.bsky.social · 10/09/2026
No predefined reaction coordinate. No mechanistic guesswork. No massive sampling campaign. Gen-COMPAS reconstructs biomolecular transition pathways from endpoint structures alone. Protein folding, allostery, membrane transport. Now in Nature. @nature.com @springernature.com
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Science Magazine @science.org · 06/09/2026
Drawing the mind, one neuron at a time: A 2022 book walks readers through the life and work of Santiago Ramón y Cajal, the Spaniard whom many consider the founder of modern neuroscience. Check out the Science Books Review on #ReadABookDay: scim.ag/4rbS1kR
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Jim Hurley @jimhurley.bsky.social · 06/09/2026
The ULK1 complex triggers autophagy on membranes, but with no typical membrane binding domains, how does it get there? See the answer in a brilliant collective effort out now in Science Advances: www.science.org/doi/10.1126/....
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André Nadler @nadlerlab.bsky.social · 03/09/2026
This is a great, great paper.
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Chelsea Brown @chelseabrown.bsky.social · 01/09/2026
Delighted to share my first author paper on how the MIC10 protein complex generates curvature in mitochondrial crista out now in Science Advances!! 🥳🥳 www.science.org/doi/10.1126/... See below for a run through of why we were interested and what we found 👇
science.org
The molecular basis of mitochondrial crista formation by the MIC10 complex
Mitochondrial cristae are essential for respiration, yet the molecular basis of how the high curvature of these membrane folds is maintained remains unclear. Using structure prediction tools and multi...
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Matthieu Chavent @matthchavent.bsky.social · 01/09/2026
If not already done, I encourage you to follow @lumen-eu.bsky.social projects. Lots of synergies are possible!
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Matthieu Chavent @matthchavent.bsky.social · 28/08/2026
A roadmap to create FAIR collections of microbial strains @natmicrobiol.nature.com www.nature.com/articles/s41...
nature.com
A roadmap to create FAIR collections of microbial strains - Nature Microbiology
Here the authors propose guidance on the process of establishing a state-of-the-art collection of microorganisms, including project planning, strain deposition and the naming of new taxa.
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Reposted by Matthieu Chavent
bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 25/08/2026
Characterizing the interaction of a type VII-secreted antimycobacterial toxin with its small helical partner proteins www.biorxiv.org/content/10.64898/20…
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Sjors Scheres @sjorsscheres.bsky.social · 25/08/2026
This should be fun for the computer-minded among us who find joy in supporting science . 😍
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Kedrov Lab @ HHU @kedrov-lab.bsky.social · 23/08/2026
Preprint🚨: Exopolysaccharide export complex PelBC of Pseudomonas aeruginosa attenuates the dynamics of the surrounding outer membrane. Longer in preparation than in actual making. Blame summer time and perfectionism 🫠 A brief tour, to keep the feed alive over the wknd www.biorxiv.org/content/10.6...
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Tanmay Bharat @tbharat-lab.bsky.social · 23/08/2026
Molecular architecture of colossal surface layers from hyperthermophilic archaea Led by @idocaspy.bsky.social (Ido) In collaboration with @mkrupovic.bsky.social and @vikramalva.bsky.social labs doi.org/10.64898/202...
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LUMEN @lumen-eu.bsky.social · 20/08/2026
From the 14-18 of Sep 2026, the GRAPHIA and the LUMEN project come together in Brussels. Sessions taking place in the main room will be publicly live streamed. Sign up for the livestream here: docs.google.com/forms/d/e/1FAIpQLSe…
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Sergey Ovchinnikov @sokrypton.org · 15/08/2026
Try for your protein at py2dmol.solab.org (Style → Cartoon)
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Reichow Lab @reichowlab.bsky.social · 13/08/2026
Long-timescale simulations reveal multi-ion flux through wide pore gap junction channels -– and an unexpected transition involving loop–NT domain interactions that suggest a dynamic ensemble of micro-states define the “open” channel www.biorxiv.org/content/10.6...
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Kay Severin @kay-severin.bsky.social · 13/08/2026
Faculty position in our institute @EPFL: www.epfl.ch/about/workin...
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henrietteautzen.bsky.social @henrietteautzen.bsky.social · 12/08/2026
Happy to see our NHE6 story published today in @natcomms.nature.com! Led by @lukasfeilen.bsky.social we reveal the #cryoEM structure, ion selectivity and regulation of the endosomal Na+/H+ exchanger NHE6, providing a framework for understanding Christianson syndrome. www.nature.com/articles/s41...
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Matthieu Chavent @matthchavent.bsky.social · 09/08/2026
Recent review: "Adapting Architecture: Lipid Membrane Remodeling in Mycobacteria" www.annualreviews.org/content/jour...
annualreviews.org
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...
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Reposted by Matthieu Chavent
pilarcossio.bsky.social @pilarcossio.bsky.social · 07/08/2026
⚡ 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...
biophysics.org
Subgroup Awards - The Biophysical Society
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Matthieu Chavent @matthchavent.bsky.social · 06/08/2026
Soon new tools will be released so that one can setup membrane models with specific lipid composition - and also add membrane proteins - to study interesting biophysical phenomena such as synthesis of lipids, transport, etc ... 2/2
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Matthieu Chavent @matthchavent.bsky.social · 06/08/2026
Our goal here is to detail atomistic models of LAM/LM and prototype a model of inner mb in its full complexity. Modeling the turn over of lipids during the course of a simulation is challenging and was out of the scope of this work. 1/2
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Phil Biggin @philbiggin.bsky.social · 05/08/2026
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
arxiv.org
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...
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Matthieu Chavent @matthchavent.bsky.social · 05/08/2026
This new work completes our previous collaborative model of the inner membrane developed few years ago and spearheaded by @chelseabrown.bsky.social in Phil @pstansfeld.bsky.social lab! www.pnas.org/doi/10.1073/...
pnas.org
Supramolecular organization and dynamics of mannosylated phosphatidylinositol lipids in the mycobacterial plasma membrane | PNAS
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB), a disease that claims ~1.6 million lives annually. The current treatm...
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Matthieu Chavent @matthchavent.bsky.social · 05/08/2026
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...
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Robert Arkowitz @robertarkowitz.bsky.social · 04/08/2026
www.cell.com/trends/cell-...
cell.com
Cellular lipid imaging at the ultrastructural level
Lipids are fundamental organizers of biological membranes, yet visualizing lipid species within subcellular organelles has remained beyond experimental reach. Lennartz et al. introduce Lipid-correlati...
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Reposted by Matthieu Chavent
Oliver Beckstein [he/him] @orbeckst.bsky.social · 04/08/2026
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...
Cross section through the ASBT_LB transporter protein in a membrane in its outward facing conformation. The extracellular side is at the top and the substrate binding site is accessible from the extracellular side but not the intracellular side. A deoxycholate molecule (DCA) is bound and the binding site is also exposed to the lipid membrane, forming a proteo-lipidic site. The membrane is shown simplified as a density (in yellow). DCA is colored by its contacts with protein (green) and lipids (yellow), showing that its carboxylate group is anchored to a conserved Threonine residue while the bulky sterol rings are in contact with lipids.  The protein is shown as a translucent surface (green) that shows the two bound Na+ ions.
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Matthias Wilmanns @matthiaswilmanns.bsky.social · 02/08/2026
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.
In pathogenic mycobacteria up to five Type VII secretion systems serve as gates for substrate transport between the pathogen and the infected host. Recent high-resolution structures of these systems have revealed a complex architecture with separate sections facing the periplasm, crossing the inner cell wall membrane, and facing the cytosol. Substrate translocation occurs through a central pore that is formed by the inner transmembrane helices of the EccC subunits, 

Despite conservation of the overall structural scaffold, an unexpected level of diversity has been observed, including variable assemblies, symmetries and subunit compositions. These differences also affect the central pore, which appears to be fuzzy, in sharp contrast to rigid transmembrane helices from other subunits surrounding it. This diversity has provoked hypotheses about additional features for establishing functional Type VII secretion.

To address this question, we have probed a series of mutants of residues involved in pore formation in one of the Type VII secretion systems (ESX-5) using secretion assays. We found that most of them impair its function. By in addition solving the single particle cryo-EM structure of one of these mutants in which an invariant proline was mutated, we discovered an unexpected rigidification of the pore. In this ESX-5 variant, the pore is formed by stalagmite-like structures from the inner transmembrane helices of the mutated EccC subunit. 

Taken together, our data demonstrate that the pore’s intrinsic plasticity is essential to the system’s ability for substrate translocation. Our findings point to the importance of investigating both the structural and associated dynamic properties of functional Type VII machineries.
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Tristan Bereau @tbereau.bsky.social · 03/08/2026
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...
tristanbereau.com
Generative machine learning for molecular thin films – Tristan Bereau
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Matthieu Chavent @matthchavent.bsky.social · 03/08/2026
Basement membrane turnover controls cell shape www.cell.com/cell/fulltex...
cell.com
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...
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Reposted by Matthieu Chavent
Nature Plants @natplants.nature.com · 20/04/2026
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
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André Nadler @nadlerlab.bsky.social · 29/07/2026
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...
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RCSB Protein Data Bank @rcsbpdb.bsky.social · 28/07/2026
"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."
nature.com
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...
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Turlier lab @turlierlab.bsky.social · 24/07/2026
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
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Max Bonomi @bonomimax.bsky.social · 22/07/2026
Fantastic opportunity at @pasteur.fr in Spyros’ brand new lab, especially if you like protein design 🎉
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Ján Bíňovský @jbinovsky.bsky.social · 02/07/2026
🔥My first (co)first-author paper is out🔥 The surfaces of Gram+ and Gram- bacteria are markedly different from each other. How are phages equipped to breach the Gram+ envelope❓ 💡We report a baseplate structure uniquely adapted to infect Gram+ S. aureus. A 🧵⬇️ 1/8 #phagesky #cryoEM 🧪
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