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....

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 👇

Our cell model looks massive on the big screen!! Thanks for capturing @aschahl.bsky.social 🙌

🔬 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

Registration deadline June 15 approaching ....

Get inside a bacterial cell with this cool combination of @cg-martini.bsky.social and @viamd.bsky.social

Also check out our recent webinars on each:

🎬 Whole cell simulation with Martini ▶️ youtu.be/fvFaPgSoM90

🎬 Visual analysis of #moleculardynamics with VIAMD ▶️ youtu.be/wVENzcx0XmQ

🚨 #LLPS: New trick for an old membrane protein!

Homo- and hetero- biomolecular condensates of a native membrane protein in E. coli tagged with PopTag 🔬🦠

LacY-PopTag is functional and localizes at cell poles or mobile foci in a curvature-dependent manner

🔗 doi.org/10.21203/rs.3.rs-6571918/v1

Martini workshop registration now open !!!!
See cgmartini.nl for details and how to apply.
Looking forward to seeing you in Groningen, Aug 11-15th.

Pre-announcement: MARTINI tutorial workshop, August 11-15th 2025 in Groningen, The Netherlands !!
Learn basic and advanced Martini from the cocktail masters themselves. Registration will open soon.

Very happy that our latest publication "Statistical mechanics of multiplectoneme phases in DNA" doi.org/10.1103/Phys... was selected as Editors' Suggestion. These suggestions list "a small number of papers that the editors and referees find of particular interest, importance, or clarity". (1/4)

New preprint: TS2CG version 2, building and simulating membranes with any shape and lateral organisation. We got Martini Globe, Martini Möbius strip and again mitochondrion.
www.biorxiv.org/content/10.1...
@cg-martini.bsky.social @janstevens.bsky.social @fabianschuhmann.bsky.social

MartiniGlass: a Tool for Enabling Visualization of Coarse-Grained Martini Topologies As molecular modeling gains ever more prominence in understanding cellular processes, high quality visualization of models and dynamics has never been more important. Naturally, much molecular visualization software is written to enable the visualization of atomic level details in structures. While necessary, this means that visualization of increasingly popular coarse-grained (CG) models remains a challenge. Here, we present a Python package, MartiniGlass, that facilitates the visualization of systems simulated with the widely used CG Martini force field using the popular visualization package VMD. MartiniGlass rapidly processes molecular topologies and accounts for important topological features at CG resolution, such as secondary structure restraints, preparing them for easy visualization of simulated trajectories.

#compchem Good read: MartiniGlass: a Tool for Enabling Visualization of Coarse-Grained Martini Topologies #compchemsky #biosky pubs.acs.org/doi/10.1021/...

CGsmiles: A Versatile Line Notation for Molecular Representations Across Multiple Resolutions

Authors: Fabian Grünewald, Leif Seute, Riccardo Alessandri, Melanie König, Peter Kroon
DOI: 10.26434/chemrxiv-2025-vhbnq

Impact of Ligand-Induced Oligomer Dissociation on Enzyme Diffusion, Directly Observed at the Single-Molecule Level The existence of the phenomenon of enhanced enzyme diffusion (EED) has been a topic of debate in recent literature. One proposed mechanism to explain the origin of EED is oligomeric enzyme dissociation. We used mass photometry (MP), a label-free single-molecule technique, to investigate the dependence of the oligomeric states of several enzymes on their ligands. The studied enzymes of interest are catalase, aldolase, alkaline phosphatase, and vanillyl-alcohol oxidase (VAO). We compared the ratios of oligomeric states in the presence and absence of the substrate as well as different substrate and inhibitor concentrations. Catalase and aldolase were found to dissociate into smaller oligomers in the presence of their substrates, independently of inhibition, while for alkaline phosphatase and VAO, different behaviors were observed. Thus, we have identified a possible mechanism which explains the previously observed diffusion enhancement in vitro. This enhancement may occur due to the dissociation of oligomers through ligand binding.

Proud to announce Yulia's paper in Nano Letters. We were planning to measure enzyme diffusion rates under different conditions using label-free single-molecule methods, and accidentally uncovered an interesting effect: pubs.acs.org/doi/10.1021/... 🧪

FIB-SEM dataset visualized with Microscopy Nodes, data from Mocaer et al 2023

Microscopy Nodes is now up on bioRxiv! 🚀

This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev).

High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬

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

G-Protein-Coupled Receptor Surface Creates a Favorable Pathway for Membrane Permeation of Drug Molecules G-protein-coupled receptors (GPCRs) play a crucial role in modulating physiological responses and serve as the main drug target. Specifically, salmeterol and salbutamol, which are used for the treatme...

G-Protein-Coupled Receptor Surface Creates a Favorable Pathway for Membrane Permeation of Drug Molecules | The Journal of Physical Chemistry Letters pubs.acs.org/doi/10.1021/...

Unlocking the potential of LOV domains!

Thrilled to share our latest publication on the Engineering of LOV-domains for their use as protein tags!

Many thanks to my supervisor Prof. Marco Fraaije and our collaborator Andrej Hovan.
doi.org/10.1016/j.ab...