Dr. Jules Marien
marienj.bsky.social
Dr. Jules Marien
@marienj.bsky.social
PhD 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
Reposted by Dr. Jules Marien
AlphaFlex: Ensembles of the human proteome representing disordered regions https://www.biorxiv.org/content/10.1101/2025.11.24.690279v1
November 26, 2025 at 2:45 AM
Reposted by Dr. Jules Marien
Our manuscript on using the knot theory descriptor writhe to build kinetic models of IDP dynamics is now out in JCTC

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

We think this approach establishes a new state-of-the-art for building markov state models of IDP dynamics.
November 23, 2025 at 4:56 PM
Reposted by Dr. Jules Marien
In case you're still looking for a gift idea for your PhD students, I made a tutorial on how to sew a tote bag in a fabric poster. It's in french but I'm sure you're all smart enough to get it.
C'est la saison des thèses et vous ne savez pas quoi offrir aux futur·e·s docteur·e·s de votre laboratoire ?
Sachez que vous pouvez recycler leurs posters (textiles) en tote bag et en plus je vous ai fait un tuto !
November 22, 2025 at 5:41 PM
Reposted by Dr. Jules Marien
Proud to share our manuscript:

"How small molecules stabilize oligomers of a phase-separating disordered protein"

www.biorxiv.org/content/10.1...

by Jiaqi Zhu and Tommy Sisk, in collaboration with @borjaml.bsky.social , Stase Bielskute-Garcia & @xsalvatella1.bsky.social
November 22, 2025 at 7:11 PM
Tutorial on how to make a postote-bag by my supervisor Sophie !

I'll cherish mine forever, it's such a cool post-defense gift 😊
C'est la saison des thèses et vous ne savez pas quoi offrir aux futur·e·s docteur·e·s de votre laboratoire ?
Sachez que vous pouvez recycler leurs posters (textiles) en tote bag et en plus je vous ai fait un tuto !
November 22, 2025 at 11:02 PM
Reposted by Dr. Jules Marien
C'est la saison des thèses et vous ne savez pas quoi offrir aux futur·e·s docteur·e·s de votre laboratoire ?
Sachez que vous pouvez recycler leurs posters (textiles) en tote bag et en plus je vous ai fait un tuto !
November 22, 2025 at 5:38 PM
PhDone ! 😊
November 22, 2025 at 12:33 PM
Reposted by Dr. Jules Marien
Congratulations Dr. @marienj.bsky.social for your brillant defense, and your amazing thesis! 🎉
November 21, 2025 at 4:02 PM
Thank you so much Sophie and Chantal for these incredible 3 years of PhD, I'm beyond proud and grateful for all of this journey, I couldn't have dreamt of better supervisors 😊
Congratulations Dr. @marienj.bsky.social for your brillant defense, and your amazing thesis! 🎉
November 22, 2025 at 12:29 PM
Reposted by Dr. Jules Marien
Today !
November 21, 2025 at 8:22 AM
Reposted by Dr. Jules Marien
Binding Paths: Describing Small Molecule Interactionswith Disordered Proteins via Markov State Models https://www.biorxiv.org/content/10.1101/2025.11.19.688850v1
November 19, 2025 at 4:48 PM
So proud of this work in which we managed to extract valuable information from the intra- and interdomain dynamics of the Tau protein, it indeed looks like there is valuable information to find in protein disorder, if one figures out how to retrieve it !
"Across (Conformational) Space and (Relaxation) Time", @marienj.bsky.social's latest work, is now out in J. Phys. Chem. B @pubs.acs.org. In this paper, we used coarse-grain simulations with the CALVADOS model to investigate the dynamics of a large IDP.
pubs.acs.org/doi/10.1021/...
Across (Conformational) Space and (Relaxation) Time: Using Coarse-Grain Simulations to Probe the Intra- and Interdomain Dynamics of the Tau Protein
The biological importance of intrinsically disordered proteins (IDPs) has been established for over two decades, yet these systems remain difficult to characterize, as they are better described by conformational ensembles instead of a single reference structure for their folded counterparts. Tau is a prominent member of the IDP family, which sees its cellular function regulated by multiple phosphorylation sites and whose hyperphosphorylation is involved in neurodegenerative diseases such as Alzheimer’s. We used coarse-grain MD simulations with the CALVADOS model to investigate the conformational landscape of tau without and with phosphorylations. Characterizing the local compactness of IDPs allows us to highlight how disorder comes in various flavors, as we can define different domains along the tau sequence. We define the IDP’s Statistical Tertiary Organization (STO) as the average spatial arrangements of domains, which constitute an extension of the tertiary structure of folded proteins. We also use IDP-specific metrics to characterize the local curvature and flexibility of tau. Comparing the local flexibilities with T2 relaxation times from NMR experiments, we show how this metric is related to the protein dynamics. A curvature and flexibility pattern in the repeat domains can also be connected to tau binding properties, without having to explicitly model the protein’s interaction partner. Finally, we rediscuss the original paperclip model that describes the spatial organization of tau and how phosphorylations impact it. The resulting changes in the protein intradomain and interdomain interaction pattern allow us to propose experimental setups to test our hypothesis.
pubs.acs.org
November 19, 2025 at 12:56 PM
Reposted by Dr. Jules Marien
🎉 New publication in JCIM at @pubs.acs.org!
We present eRMSF, a Python package for ensemble-based RMSF analysis of biomolecular systems, supporting MD, PDB, and ML ensembles.
Proud to collaborate with Rodrigo Ligabue-Braun and @conradopedebos.bsky.social

pubs.acs.org/doi/10.1021/...
eRMSF: A Python Package for Ensemble-Based RMSF Analysis of Biomolecular Systems
Understanding molecular flexibility and dynamics across different structural ensembles is essential for interpreting the behavior of complex biological systems. Here, we introduce eRMSF, a fast and user-friendly Python package built with MDAKit from MDAnalysis, designed to perform ensemble-based root mean square fluctuation (RMSF) analyses. Unlike traditional approaches limited to molecular dynamics trajectories, eRMSF extends flexibility analysis to ensembles generated by different methods, such as MD simulations, BioEmu (a deep learning tool for equilibrium ensemble prediction), subsampled AlphaFold2 (AlphaFold ensemble generation), and other computational or experimental sources. By enabling RMSF calculations across heterogeneous ensembles, eRMSF provides a unified framework to evaluate residue or atomic fluctuations in both simulated and predicted structures. Users can easily customize atom, residue, or region selections, tailoring analyses to specific research questions. This approach delivers high-resolution insights into localized motions, complements global stability assessments, and reveals dynamic regions often overlooked by single-method analyses. The repository for eRMSF is available at https://github.com/pablo-arantes/ermsfkit.
pubs.acs.org
November 19, 2025 at 11:08 AM
Reposted by Dr. Jules Marien
Excited to share our new preprint in collaboration with Ahmet Yildiz's lab. Check out how our team uncovers a novel binding footprint and motor regulation mechanism for MAP9 Congrats to Burak Cetin and @aryantaheri.bsky.social

www.biorxiv.org/content/10.1...
November 18, 2025 at 10:43 PM
Reposted by Dr. Jules Marien
Very excited to present OpenCGChromatin🔥🔥🔥

A new coarse-grained model that probes full chromatin condensates at near-atomistic resolution to reveal the molecular regulation of chromatin structure and phase separation

Brilliantly led by @kieran-russell.bsky.social, with the Rosen and Orozco groups
November 18, 2025 at 3:07 PM
Reposted by Dr. Jules Marien
Our preprint on a single-bead-per-nucleotide DNA model is live! This model reproduces both atomistic simulations and persistent length for a variety of sequences. It's compatible with openMM, allowing for highly efficient GPU simulations.
www.biorxiv.org/content/10.1....
NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations
DNA's physical properties play a central role in genome organization and regulation, but simulating its behavior across biologically relevant scales remains a major computational challenge. Coarse gra...
www.biorxiv.org
November 9, 2025 at 12:26 PM
Reposted by Dr. Jules Marien
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 Dr. Jules Marien
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
Soon ! 😬😊
November 10, 2025 at 1:59 PM
Reposted by Dr. Jules Marien
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 Dr. Jules Marien
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 Dr. Jules Marien
Congratulations Laetitia for winning the best oral presentation award ! 🎉👏🏅
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 Dr. Jules Marien
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 Dr. Jules Marien
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 Dr. Jules Marien
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.
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