Jan Stevens
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janstevens.bsky.social
Jan Stevens
@janstevens.bsky.social
PhD student @univgroningen | Computational biophysicist | CG Martini
Our paper on [Bentopy](doi.org/10.1002/pro....) is out in Protein Science! We developed Bentopy to make assembling large-scale MD models more accessible, building on what we learned from trying to simulate whole-cell models. Here's our updated Martini JCVI-syn3A cell model👇
February 13, 2026 at 3:37 PM
Reposted by Jan Stevens
So pleased this is finally out! Wonderful work by the incredibly talented @ma3ke.bsky.social and @janstevens.bsky.social to generate densely packed systems, even with complex topologies

Go to the paper for cool science, stay for the mesmerizing figures 🤩

Read more about it in this thread 👇
Our paper about Bentopy is now published in Protein Science!

Bentopy makes assembling large-scale MD models accessible and fast.

doi.org/10.1002/pro....

@janstevens.bsky.social, @cg-martini.bsky.social
February 13, 2026 at 3:22 PM
Reposted by Jan Stevens
Our paper about Bentopy is now published in Protein Science!

Bentopy makes assembling large-scale MD models accessible and fast.

doi.org/10.1002/pro....

@janstevens.bsky.social, @cg-martini.bsky.social
February 13, 2026 at 3:07 PM
Reposted by Jan Stevens
It was great to be a small part of this work with the incredibly talented PhD student Andrea!!

If you want to find out how you can save heaps of time while still maintaining accurate results with CG metadynamics, look no further!! Read the article here 👇
January 12, 2026 at 10:11 AM
Reposted by Jan Stevens
Instead of a tree, I can offer a snowman! ☃️

Built using bentopy, based on David Naranjo's idea.

The input file can be found here: gist.github.com/ma3ke/723f9c....
December 24, 2025 at 4:35 PM
Reposted by Jan Stevens
Opportunity: postdoctoral fellowships at the center for Quantitative Cell Biology (QCB), Univ. of Illinois, in close collaboration with our group. Your ticket to become an expert in whole-cell Martini simulations !
qcb.illinois.edu/postdoctoral...
December 22, 2025 at 10:27 AM
Reposted by Jan Stevens
My little outlook on how our lungs 🫁 are like the sea 🌊 is finally out in Central Science. Thanks to the support from incredible mentors @rommieamaro.bsky.social and @kprather.bsky.social !!
A new review explores one of the themes of my book Air-Borne: our lungs are like the ocean. Both send life into the atmosphere. pubs.acs.org/doi/full/10....
December 11, 2025 at 12:18 PM
Reposted by Jan Stevens
A new review explores one of the themes of my book Air-Borne: our lungs are like the ocean. Both send life into the atmosphere. pubs.acs.org/doi/full/10....
December 7, 2025 at 9:26 PM
Congrats Pavol! That poster looks incredible, amazing design 🎉
Our poster was awarded “Best Poster” at the Institute of Science and Technology Austria PhD Welcome Poster Session 🎉 Huge thanks to everyone who stopped by to look at our 2.5-dimensional dive into AI-Ready Cryo-Electron Tomography Simulations of the Whole Cell.
November 27, 2025 at 2:08 PM
Reposted by Jan Stevens
Are you a postdoc stuck in the US?! Is your research stalled or are you in any way affected by the whims of that unfettered madman? Interested in MD simulations of large biomolecules?!

Consider joining me at the University of Freiburg!

uni-freiburg.de/frias/call-f...
Call for Applications: Early Career Rescue Fellowship – Freiburg Institute for Advanced Studies
uni-freiburg.de
November 17, 2025 at 8:51 AM
Reposted by Jan Stevens
I have a PhD position available in my lab at the University of Freiburg!! If you, or someone you know, might be looking for a position using modeling and simulations to uncover secrets in (glyco-)protein structure/function relationships please take a look at our website!
www.kearnslab.org
October 17, 2025 at 8:21 PM
Reposted by Jan Stevens
Inferring DNA kinkability from biased MD simulations https://www.biorxiv.org/content/10.1101/2025.09.08.674847v1
September 12, 2025 at 9:47 PM
Reposted by Jan Stevens
4️⃣ Featuring the fourth of our showcase projects

Upgrading GROMACS to handle billion-atom systems and enhancing I/O performance and precision, making the first-ever whole-cell simulation possible ➡️ bioexcel.eu/uw67

#MolecularDynamics #GROMACS #ComputationalBiology
September 12, 2025 at 6:22 AM
Reposted by Jan Stevens
New preprint about my work done under the direction of @sciezgin.bsky.social, @delemottelab.bsky.social and Rebecca Howard.
We studied the opening process of ADAM10 enhanced sampling MD, MSM and Fluorescence microscopy!
Let us know what you think about it 😁

www.biorxiv.org/content/10.1...
Lipid-facilitated opening of the ADAM10 sheddase revealed by enhanced sampling simulations
ADAM10 is a crucial membrane-bound metalloprotease that regulates cellular physiology by cleaving and releasing membrane-anchored proteins, including adhesion molecules and growth factor precursors, t...
www.biorxiv.org
August 22, 2025 at 12:13 PM
Reposted by Jan Stevens
New preprint: www.biorxiv.org/content/10.1...
We used molecular dynamics simulations and solid-state NMR (@fmp-berlin.de) to look at calcium binding to the pore domain of the calcium-gated K+ channel MthK. @wojciechkopec.bsky.social @compbiophys.bsky.social
August 19, 2025 at 7:42 AM
Reposted by Jan Stevens
Cool simulations from my former PhD student Petteri Vainikka now published: "Molecular Dynamics Simulation of Fatty Acid Extraction Using a Type V Deep Eutectic Solvent with Tunable Hydrophobicity" | The Journal of Physical Chemistry B pubs.acs.org/doi/full/10....
Molecular Dynamics Simulation of Fatty Acid Extraction Using a Type V Deep Eutectic Solvent with Tunable Hydrophobicity
Deep eutectic solvents (DESs) are often promoted as a more environmentally friendly alternative for ionic liquids and other ionic solvents. Like ionic liquids, DESs can be designed for specific tasks ...
pubs.acs.org
August 20, 2025 at 9:39 AM
Reposted by Jan Stevens
Weird lipids, weird effects on membranes ! Happy to see this story out 😄
If you like MD simulations, NMR spectroscopy and membranes this story will interest you 😊
August 11, 2025 at 1:44 PM
Reposted by Jan Stevens
Classification of containment hierarchy for point clouds in periodic space https://www.biorxiv.org/content/10.1101/2025.08.06.668936v1
August 10, 2025 at 5:47 AM
Reposted by Jan Stevens
Our collaborative work "The #Martini3 #Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior" is now published in #ACSCentralScience! 🎉

📄 Read: pubs.acs.org/doi/10.1021/...

💾 GitHub: github.com/Martini-Forc...

#MolecularDynamics #Biophysics #Simulations #Lipids
The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior
Lipid membranes are central to cellular life. Complementing experiments, computational modeling has been essential in unraveling complex lipid-biomolecule interactions, crucial in both academia and industry. The Martini model, a coarse-grained force field for efficient molecular dynamics simulations, is widely used to study membrane phenomena but has faced limitations, particularly in capturing realistic lipid phase behavior. Here, we present refined Martini 3 lipid models with a mapping scheme that distinguishes lipid tails that differ by just two carbon atoms, enhancing the structural resolution and thermodynamic accuracy of model membrane systems including ternary mixtures. The expanded Martini lipid library includes thousands of models, enabling simulations of complex and biologically relevant systems. These advancements establish Martini as a robust platform for lipid-based simulations across diverse fields.
pubs.acs.org
August 1, 2025 at 1:49 PM
Reposted by Jan Stevens
Happy to share the latest work from the lab, led by @mudgal17.bsky.social‬, in collaboration with the Weis lab @ethzurich.bsky.social.
How do nuclear membranes fuse during NPC assembly? We answer this question in our latest work, where we identify a new mechanism for membrane fusion… (1/13)
July 23, 2025 at 11:40 AM
Reposted by Jan Stevens
1/6 One of the key features of functional proteins is their inherent structural flexibility. In our recent work at #ICML, we introduce flexibility to protein structure design! More in a thread below.

Code / Tutorial: github.com/graeter-grou...
Poster: W-109, Thu 17 Jul 11 a.m. PDT — 1:30 p.m. PDT
July 17, 2025 at 4:19 AM
Reposted by Jan Stevens
What better way to use my first proper post than to share my first big piece of post-doctoral work with @cg-martini.bsky.social!
Here, we used integrative modelling to build and simulate a mitochondrial cristae.
Find the paper here (rdcu.be/eujAC) or see below for a quick overview 👇
July 1, 2025 at 3:34 PM
Our cell model looks massive on the big screen!! Thanks for capturing @aschahl.bsky.social 🙌
@cg-martini.bsky.social presenting the work of his lab about CG modelling of whole cell, notably with publications from @janstevens.bsky.social #EBSA2025 🤩
July 4, 2025 at 11:35 AM
Reposted by Jan Stevens
🔬 Looking for a postdoc or scientist position in the Netherlands!
My passion: proteins, especially enzymes, antibodies, and protein engineering.
Hands-on experience in biochemistry & molecular biology.
Open to exciting opportunities! DMs open 📩

#JobSearch #ProteinEngineering #Postdoc #Biotech
June 23, 2025 at 4:34 PM