Dr. Jules Marien

Characterizing the Conformational Dynamics of the Ribose Transporter B Protein in Escherichia coli: Enhanced Sampling via Multiple Force Fields We present a molecular dynamics simulation study of the E. coli ribose transporter protein B (RbsB), a conformationally labile protein found in the periplasm of the bacterium. The ribose transporter e...

Our latest paper in which we use multiple force fields to recover various conformations of the ribose transporter from E. coli. The work of DPhil student Nikolai Juraschko and postdoc Florencia Klein Rocha

pubs.acs.org/doi/full/10....

Role of desolvation on biomolecular liquid-liquid phase separation https://www.biorxiv.org/content/10.64898/2026.03.09.710469v1

The Martini 3 Metabolome https://www.biorxiv.org/content/10.64898/2026.03.06.710121v1

🚀 New Preprint Alert!
We’re excited to share our latest work on a community-driven framework for determining conformational ensembles of intrinsically disordered proteins (IDPs) — now available as a preprint on arXiv!

📄 Read the full preprint here: [ arxiv.org/abs/2504.03590 ]

Community perspective:

Toward a unified framework for determining conformational ensembles of disordered proteins 🍝

with framework for experimental data acquisition, computational ensemble generation & validation

Led by @hamidrgh.bsky.social, Silvio Tosatto & Alex Monzon

doi.org/10.1038/s415...

Tubulin C-terminal tails are pH sensors that regulate microtubule function https://www.biorxiv.org/content/10.64898/2026.03.06.710195v1

Interplay between Local Diffusion, Concentration, and Inter-Protein Alignment Promotes Cross-β-Sheet Transitions at Condensate Interfaces https://www.biorxiv.org/content/10.64898/2026.03.05.709844v1

Minimal Amino Acid Alphabet for Protein Design https://www.biorxiv.org/content/10.64898/2026.03.06.710107v1

I put together a #ChimeraX plugin to display circos-like contact maps between proteins/DNA. I'm using it all the time now (after doing this manually for years) so I hope someone else may find it useful!

https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxcircoscontacts […]

These brain cells clear proteins that contribute to Alzheimer’s When specialized cells called tanycytes stop working, disease-causing tau proteins build up in the brain.

When specialized cells called tanycytes stop working, disease-causing tau proteins build up in the brain.

go.nature.com/4ldhrez

Confidence Without Verification: Screening pLDDT Unreliability in AlphaFold2 Fold-Switching Predictions https://www.biorxiv.org/content/10.64898/2026.02.19.706878v1

A molecular grammar for programmable multiphase protein-RNA vesicles https://www.biorxiv.org/content/10.64898/2026.03.04.709570v1

L'évènement #ReCombinaisons est de retour à @pasteur.fr en 2026 avec un programme alléchant !
(On y retrouvera notamment @jeanneadebats.bsky.social et @audreypleynet.bsky.social !)

Progressive Backmapping of Highly Coarse-Grained Protein Models https://www.biorxiv.org/content/10.64898/2026.03.02.709104v1

I'm grateful to the Biophysical Society of Canada
‪@biophyscanada.bsky.social‬ for this recognition of our lab's research, and I'm very much looking forward to giving a lecture at this year's annual meeting in Winnipeg!

The Biophysical Society of Canada is pleased to announce that Dr. Sarah Rauscher @sarahrauscher.bsky.social is the recipient of the 2026 Early Career Investigator Award. Congratulations!!

Wee thread 🧵⬇️ on our new #glycotime with @siglecdude.bsky.social John Klassen and @glycocode.bsky.social 🥳 where we show Siglecs as molecular precision tools, able to recognise sialylated glycans with surgical precision in their natural environment, not bad for a lectin! 😎

doi.org/10.1038/s420...

Large-scale simulations reveal evolutionary constraints on intrinsically disordered regions imposed by full-length protein architecture https://www.biorxiv.org/content/10.64898/2026.02.27.708199v1

New (well, very old, but 100% updated) preprint:

Rational design of disordered proteins for systematic sequence-to-function investigation

Work done in collaboration with @shaharsu.bsky.social lab - check out the three (3) threads from the folks who did the work!

How do DNA sequence and histone composition modulate nucleosome plasticity? We investigated this by comparing the behaviour of 40 chemically different nucleosomes. Check our preprint below.

Our recent work showing that tau phosphorylation alters cooperative binding and organelle transport in neurons is now posted at @elife.bsky.social. A big thanks to the reviewers and editors for their thoughtful assessment.

doi.org/10.7554/eLif...

Conformational ensembles of flexible multidomain proteins: How close are we to accurate and reliable predictions? https://www.biorxiv.org/content/10.64898/2026.02.24.707687v1

Check out our new review on Graph #NeuralNetworks in #MolecularDynamics!
We show how #AI is used for #ForceField development, free-energy, and analysis - including our attention-based GNN workflow - and how you can integrate your favorite AI into #compchem!
www.sciencedirect.com/science/arti...

Now published in JCTC pubs.acs.org/doi/10.1021/... Works also for ENM!

📣 Excited to co-organize this @embo.org Lecture Course - #AI driven approaches in structural biology 📅 26 April - 2 May 2026 in Bengalore (India). More info and registration below @pasteur.fr @cnrsbiologie.bsky.social meetings.embo.org/event/26-ai-...

Our Story about ADAM10 modulation by PS lipids found its home in Advanced Science !
Many thanks to all co-authors for an amazing collaboration.

Partition Coefficients Reveal Changes in Properties of Low-Contrast Biomolecular Condensates https://www.biorxiv.org/content/10.64898/2026.02.20.707107v1

Des p’tits trous partout : les perforines, poinçonneuses de la cellule Dans le vivant, la membrane lipidique est la première garante de l’intégrité des cellules, ce qui en fait également une cible de choix pour les pathogènes. Elle peut notamment être visée par …

J'avais dit qu'en 2026, #TOTProts serait au repos, mais en fait non. Et donc aujourd'hui on va parler de perforines (la vérité, regardez-moi la beauté de ces assemblages !)
#Vulgarisation #FunScience
topoftheprots.com/2026/02/23/d...

A theoretical framework for random acceleration molecular dynamics simulations The dissociation of a ligand bound to a receptor is a rare event occurring on a timescale that is far longer than can be afforded by standard simulation methodo

We developed a simple theory and showed that Random Acceleration Molecular Dynamics (RAMD) is consistent with a Smoluchowski equation with an effective temperature and diffusion coefficient that depend quadratically on the magnitude of the random force.
pubs.aip.org/aip/jcp/arti...

Excited to share our latest preprint: 𝗟𝗲𝗮𝗿𝗻𝗶𝗻𝗴 𝗛𝗮𝗺𝗶𝗹𝘁𝗼𝗻𝗶𝗮𝗻 𝗙𝗹𝗼𝘄 𝗠𝗮𝗽𝘀: 𝗠𝗲𝗮𝗻 𝗙𝗹𝗼𝘄 𝗖𝗼𝗻𝘀𝗶𝘀𝘁𝗲𝗻𝗰𝘆 𝗳𝗼𝗿 𝗟𝗮𝗿𝗴𝗲-𝗧𝗶𝗺𝗲𝘀𝘁𝗲𝗽 𝗠𝗼𝗹𝗲𝗰𝘂𝗹𝗮𝗿 𝗗𝘆𝗻𝗮𝗺𝗶𝗰𝘀 🎉