Jan Stevens

MesoMem: A mesoscale membrane model based on an additive potential Bridging the gap between atomistic detail and continuum mechanics is a central challenge in modeling biological membranes, particularly for mesoscopic phenomena spanning large length and time scales. ...

New preprint from our group: MesoMem: A mesoscale membrane model based on an additive potential on arxiv.org/abs/2602.24123. Using an additive potential combining positional and orientational terms, we get a stable and robust membrane model. Great work of PhD student Pietro Sillano.

Ligand Binding Free Energy Landscapes at the Tubulin Colchicine Site from Coarse-Grained Metadynamics https://www.biorxiv.org/content/10.64898/2026.02.24.707696v1

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

YouTube video by Marieke Bentopy tutorial walkthrough

I just uploaded a video walkthrough of the tutorial I recorded this morning.

youtu.be/C4LYZokS_t4

Big thanks to all the coauthors, especially @ma3ke.bsky.social for driving this paper forward. Really nice to have this work finally out there, and especially cool that it's part of the special issue honoring the work of David Goodsell. A huge inspiration for whole-cell modeling!

Bentopy: from simple packing to building cellular models – Martini Force Field Initiative

Beyond the minimal cell, we also packed the multi-compartment architecture of a mitochondrion and built an all-atom SARS-CoV-2 virion in a respiratory aerosol (based on work from the Amaro lab). Want to try it yourself? We wrote a tutorial on the Martini website, give it a go!

Building realistic models of cells means fitting proteins, RNA, and metabolites at experimental concentrations inside complex cellular architectures. Here's a movie showing how we pack the cytoplasmic space of the JCVI-Syn3A cell:

Cutaway and close-up views of a Martini coarse-grained whole-cell model of JCVI-syn3A, showing the densely packed cytoplasm with proteins, RNA, metabolites, and chromosome inside a lipid membrane with embedded membrane proteins

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👇

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 👇

Model of mitochondrial compartments. The assembly of the mitochondrial model based on an experimentally informed membrane structure (white), from an empty structure (left) into a mask representation of the IMS (yellow) and matrix (pink) compartments represented by 3 nm voxels. Structures are packed into their assigned compartments based on the mask. In the last section and the magnified inset, structures are colored by kind: Proteins (green), RNA (dark blue), metabolites (pale blue).

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

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 👇

Unlocking High-Throughput Investigation of Transport Tunnels in Enzymes Using Coarse-Grained Simulation Methods Transport tunnels in enzymes with buried active sites are critical gatekeepers of enzymatic function, controlling substrate access, product release, and catalytic efficiency. Despite their importance,...

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

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....

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...

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....

Congrats Pavol! That poster looks incredible, amazing design 🎉

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...

Beautiful picture looking out of the chemistry building at the University of Freiburg in Freiburg Germany. The old cathedral can be seen in the distance with a backdrop of a blue sky with clouds and distant foothills of the black forrest with fall colors showing through in the trees

picture of the Münster at dawn in the Altstadt of Freiburg, Germany, with a still dark sky in the background and moon over the Münster, in the foreground a well-lit flowers stand can be seen preparing for the daily morning market

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

Inferring DNA kinkability from biased MD simulations https://www.biorxiv.org/content/10.1101/2025.09.08.674847v1

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

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...

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...

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

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 ...

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....

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 😊

Classification of containment hierarchy for point clouds in periodic space https://www.biorxiv.org/content/10.1101/2025.08.06.668936v1

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.

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

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)

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

A stylized image of the molecular model of a mitochondrial crista, with proteins and lipids shown

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 👇