Jules Marien
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marienj.bsky.social
Jules Marien
@marienj.bsky.social
50 followers 130 following 13 posts
PhD student in biophysics/biochemistry working on the interaction between the phosphorylated Tau protein and microtubules. Molecular dynamist. Tamer of IDRs and IDPs since 2022
(They/Them)

https://scholar.google.com/citations?user=4S1QUPgAAAAJ&hl=fr
Posts Replies Media Videos
Reposted by Jules Marien
ca-fait-science.bsky.social
Voici notre 6ème épisode de Qrieux, la série:
ADN sous tension : condition essentielle à sa réparation
Avec Chantal Prévost, Afra Sabei et Mara Prentiss (IBPC), Paris, France.
Qrieuz, la série met en valeur les recherches des scientifiques de @pslqlife.bsky.social.
#scicomm

ouvaton.link/Azp8fQ
Qrieux, la série - Episode 6 - ADN sous tension : condition essentielle à sa réparation
Enjoy the videos and music you love, upload original content, and share it all with friends, family, and the world on YouTube.
ouvaton.link
November 12, 2025 at 9:30 PM
Reposted by Jules Marien
justinlemkulvt.bsky.social
Excited to share a new update to the Drude polarizable force field - phosphorylated amino acids! A long-term project that took quite a bit of effort. Great work with PhD student Laura Gil Pineda, former undergrad Candace Miller, and @alexmackerell.bsky.social

authors.elsevier.com/a/1m2md1SPTB...
November 6, 2025 at 1:27 PM
marienj.bsky.social
Soon ! 😬😊
November 10, 2025 at 1:59 PM
Reposted by Jules Marien
sacquin-mo.bsky.social
En 2026, au concours de la nouvelle section 08 du CNRS "Physique de la matière complexe et du vivant", il y a un poste de CRCN colorié pour aller dans un labo de CNRS Chimie.
Si vous portez un projet de modélisation des biomolécules ça peut vous intéresser... #JDCJDR
section8.cnrs.fr/concours/
Concours - Section 08 du Comité National
08/01 : 6 directeur·rices de recherche de deuxième classe.
section8.cnrs.fr
November 9, 2025 at 5:16 PM
Reposted by Jules Marien
sacquin-mo.bsky.social
My colleagues Afra Sabei and Chantal Prévost were interviewed by @ca-fait-science.bsky.social to present their work on DNA repair (in french)
youtu.be/Xc8XE-UQMPc?...
Qrieux, la série - Episode 6 - ADN sous tension : condition essentielle à sa réparation
YouTube video by Ça Fait Science
youtu.be
November 7, 2025 at 8:06 AM
Reposted by Jules Marien
sacquin-mo.bsky.social
Congratulations Laetitia for winning the best oral presentation award ! 🎉👏🏅
modsim.bsky.social ModSim DCP 🇲🇫👩🏻‍💻⚗️ @modsim.bsky.social · 11d
Describing large systems with DFT accuracy without increasing computational cost? That's the work of Laetitia Kantin at LBT @upcite.bsky.social,supervised by @elisedd.bsky.social #JTMS2025
November 6, 2025 at 8:27 AM
Reposted by Jules Marien
biorxiv-biochem.bsky.social
Elevated Na+/K+ Ratio in Alzheimers Disease: A Potential Biomarker for Braak Stage https://www.biorxiv.org/content/10.1101/2025.11.04.686539v1
November 5, 2025 at 8:45 PM
Reposted by Jules Marien
modsim.bsky.social
Describing large systems with DFT accuracy without increasing computational cost? That's the work of Laetitia Kantin at LBT @upcite.bsky.social,supervised by @elisedd.bsky.social #JTMS2025
November 5, 2025 at 2:16 PM
Reposted by Jules Marien
adapalmer.bsky.social
One of the major fruits of research is delight. Think of how often you’ve read about a discovery and really enjoyed it. Often the most pleasurable kind of news. Public delight isn’t discussed enough as one of the major outputs of funding research.
ela-bambust.bsky.social Ela Bambust 🏳️‍⚧️ (Not very scary) @ela-bambust.bsky.social · 15d
I strongly recommend everyone do research sometimes 𝘫𝘶𝘴𝘵 𝘧𝘰𝘳 𝘧𝘶𝘯.

Look something up on Wikipedia. Go to the little citation. Follow it. Read the article it's referencing. Follow links to the original interview. Read the paper written by the interviewee

It genuinely makes you appreciate journalism
November 2, 2025 at 3:06 AM
Reposted by Jules Marien
biorxiv-biophys.bsky.social
Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16 https://www.biorxiv.org/content/10.1101/2025.11.03.685595v1
November 4, 2025 at 2:48 AM
Reposted by Jules Marien
baam93.bsky.social
Want to know exactly how many proteins fit in an E. coli cell or how fast a ribosome works? BioNumbers serves up thousands of curated biological constants—perfect for models, experiments, or trivia night. 🚀🔬
Read more → https://idees.moleculair.es/bionumbers
#bionumbers #biology #datascience
October 30, 2025 at 9:36 AM
Reposted by Jules Marien
m-correa-m.bsky.social
Hot off the press! Our paper, “Global comparative structural analysis of responses to protein phosphorylation”, is now out in Nature Communications!

www.nature.com/articles/s41...
Global comparative structural analysis of responses to protein phosphorylation - Nature Communications
Phosphorylation is central to protein regulation, yet its structural mechanisms remain poorly understood. Here, the authors conduct a global, systematic analysis of phosphorylated versus non-phosphory...
www.nature.com
October 27, 2025 at 10:29 AM
Reposted by Jules Marien
maksimkalutskii.bsky.social
📜 New preprint! We developed PoGö, an algorithm to optimize the essential dynamics of GöMartini proteins based on all-atom simulations: www.biorxiv.org/content/10.1...
October 27, 2025 at 7:54 AM
Reposted by Jules Marien
elisafadda.bsky.social
Polarizable FF news!! 🧪⤵️

www.cell.com/biophysj/abs...
Drude Polarizable Force Field for Phosphorylated Polypeptides and Proteins
Phosphorylation is a ubiquitous post-translational modification used across all domains of life to regulate protein stability, folding, subcellular localization, function, and activity. The most commo...
www.cell.com
October 24, 2025 at 9:22 PM
Reposted by Jules Marien
anton-bushuiev.bsky.social
We train machine learning models on millions of proteins. But when it comes to making predictions, do we need them to understand all proteins at once? Often, we need an accurate model for the specific protein we are studying or designing. We address this with ProteinTTT arxiv.org/abs/2411.02109 1/🧵
October 23, 2025 at 1:08 PM
Reposted by Jules Marien
biorxivpreprint.bsky.social
Molecular Grammar of Microtubule-WettingCondensates https://www.biorxiv.org/content/10.1101/2025.10.20.683522v1
October 21, 2025 at 8:48 PM
Reposted by Jules Marien
stephanieaw.bsky.social
Structural biology techniques capture an enormous amount of conformational heterogeneity, which is often lost during the transition from experimental data to deposited models, including how we encode this heterogeneity. @diffuseproject.bsky.social
October 21, 2025 at 4:30 PM
Reposted by Jules Marien
lindorfflarsen.bsky.social
We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale

See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs

📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...
Figure showing the AF-CALVADOS restraining and simulation protocol based on AF2 structure, PAE and pLDDT
October 20, 2025 at 11:26 AM
Reposted by Jules Marien
biorxiv-biophys.bsky.social
AF-CALVADOS: AlphaFold-guided simulations of multi-domain proteins at the proteome level https://www.biorxiv.org/content/10.1101/2025.10.19.683306v1
October 20, 2025 at 1:47 AM
Reposted by Jules Marien
biorxivpreprint.bsky.social
Advancing Protein Ensemble Predictions Across the Order-Disorder Continuum https://www.biorxiv.org/content/10.1101/2025.10.18.680935v1
October 19, 2025 at 2:48 AM
Reposted by Jules Marien
betterwithchem.bsky.social
New preprint by @lavagnae.bsky.social from Barducci lab (@cbsmontpellier.bsky.social): we show how energy-consuming enzymatic reactions, like phosphorylation, regulate biomolecular condensates with complex effects on condensate stability and reactive interfaces. Any feedback welcome!
biorxiv-biophys.bsky.social bioRxiv Biophysics @biorxiv-biophys.bsky.social · Oct 14
Uncovering the thermodynamic principles of enzymaticregulation in biomolecular condensates with reactivesimulations https://www.biorxiv.org/content/10.1101/2025.10.13.682073v1
October 15, 2025 at 6:12 AM
Reposted by Jules Marien
biorxiv-biophys.bsky.social
Dynamical buffering of reconfiguration dynamics in intrinsically disordered proteins https://www.biorxiv.org/content/10.1101/2025.10.12.681911v1
October 13, 2025 at 2:48 AM
Reposted by Jules Marien
paulrobustelli.bsky.social
Our work developing a maximum entropy reweighting method to refine all-atom ensembles of IDPs with extensive NMR and SAXS datasets is now out in @natcomms.nature.com:

rdcu.be/eKlK7

Led by @dartmouthchem.bsky.social graduate student Kaushilk Borthakur in collaboration with @bonomimax.bsky.social
Determining accurate conformational ensembles of intrinsically disordered proteins at atomic resolution
Nature Communications - This study demonstrates how to combine molecular dynamics computer simulations with experimental biophysical data to determine accurate atomic-resolution ensembles of...
rdcu.be
October 10, 2025 at 3:33 PM
Reposted by Jules Marien
daviddesancho.bsky.social
Check out our latest, where we investigate the molecular origin of differences between Lys and Arg and their roles in biomolecular #condensates

@dipcehu.bsky.social

www.biorxiv.org/content/10.1...
October 3, 2025 at 5:21 AM
Reposted by Jules Marien
lindorfflarsen.bsky.social
Integrative modelling of biomolecular dynamics

Time-dependent and -resolved experiments combined with computation provide a view on molecular dynamics beyond that available from static, ensemble-averaged experiments

Review w @dariagusew.bsky.social & Carl G Henning Hansen
doi.org/10.48550/arX...
Figure 1 from the review. Caption: Comparison of a schematic example showing static, time-dependent, and time-resolved experiments illustrated by a protein folding process. (a) A static experiment measuring the observable O$_{\text{exp}}$ is shown, which can be modelled as a distribution of simulated values, O$_{\text{calc}}$, representing a conformational ensemble of folded and unfolded states. (b) Shows a time-dependent experiment, where the equilibrium dynamics of reversible folding gives rise to measured transition times $\tau_1$ and $\tau_2$. These can be modelled as equilibrium dynamics, illustrated by a free energy (FE) surface along a chosen degree of freedom (D.O.F.) (c) A time-resolved experiment probes a non-equilibrium process, where the system begins at $t_{0}$ in the folded state. During the observation time $t$ the protein unfolds until $t_{\text{max}}$. At each time point, a distinct ensemble average, O$_{\text{exp}}$, can be observed, reflecting the proteins changing structure. This evolution can be modelled as distributions of O$_{\text{calc}}$ at each time point. These are shown together with a FE surface.
October 2, 2025 at 7:54 AM