How do you choose a CV for MD enhenced sampling methods ? Well, this question is not easy to answer. We tried to help the MD community by giving some clues about it in the following review : www.sciencedirect.com/science/arti... Feedbacks appreciated :)

Collective variable design for biomolecular conformational dynamics

Describing conformational changes in biomolecules using molecular dynamics simulations requires defining an appropriate low-dimensional mathematical d…

sciencedirect.com

Here's our latest model development effort, with a set of Martini 3 steroid hormones parameterized straight from structures in the PDB. A big shout out to Tâmela and the team for the impressive work! Preprint: chemrxiv.org/doi/full/10.... Repo: github.com/Martini-Forc... #compchem #compbiol

After nearly 6 years of work, I’m excited (and honestly relieved) to share our paper in PNAS: www.pnas.org/doi/10.1073/... D614G reshapes allosteric networks and opening mechanisms of SARS-CoV-2 spikes Very happy to finally see it out in the world!!

How does biomolecular condensation and #LLPS look for membrane proteins in bacteria?🔬 See our📜: doi.org/10.1038/s414... @linnikdmitrii.bsky.social et al. "Structural and functional implications of phase separation of membrane protein LacY in E. coli🦠" #NatComm

The KULeuven Department of Physics and Astronomy is recruiting a new faculty member as Research Professor in Experimental Biophysics. The candidate is expected to develop and apply innovative experimental techniques to study the structure and behavior of living systems from a physics perspective.

🧵 Our new paper is out today in molecularcell.bsky.social! After 7 years of a truly intriguing discovery journey, we can finally share what controls how molecules move inside living E. coli cells. Spoiler: it's not what the field thought. A thread 👇 📄 doi.org/10.1016/j.molcel.2026.03.018

Happy to share the review that @apoorvam.bsky.social, Vanessa and I wrote about recent trends in modeling and simulation of biological phenomena in crowded and cell-like environments! I really like this topic, for me this is the future of #compchem. arxiv.org/abs/2603.26974

Recent advances in modeling and simulation of biological phenomena in crowded and cellular environments

While experiments and computer simulations to study biological phenomena are usually performed in diluted in vitro conditions, such phenomena happen inside the cellular cytoplasm, an environment dense...

arxiv.org

The Quantitative Cell Biology institute (QCB) at UIUC is hosting a summer school on studying living cells, both computationally and experimentally. Participants choose a theme: whole-cell computational modeling (Martini + Lattice Microbes), MINFLUX, or AFM-IR. Registration is free!

How do we build realistic cellular environments for simulations? @cg-martini.bsky.social, @ma3ke.bsky.social, @janstevens.bsky.social answer this with Bentopy, an integration tool for proteomics, metabolomics, and structural data that rapidly assembles simulation-ready molecular models.

Kinetic models can now capture the full cell cycle with division, cool to see the progress in whole-cell modeling. Worth a read!

Cell - a Cell Press journal@cp-cell.bsky.social · 5mo ago

Now online! Bringing the genetically minimal cell to life on a computer in 4D

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.

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. ...

arxiv.org

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.

Lipid‐Facilitated Opening of the ADAM10 Sheddase Revealed by Enhanced Sampling Simulations

Phosphatidylserine acts as a lipid trigger to enhance activation of the sheddase ADAM10. By integrating fluorescence spectroscopy assays with enhanced sampling molecular dynamics simulations, this st...

advanced.onlinelibrary.wiley.com

Adrien Schahl@aschahl.bsky.social · 12mo ago

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...

I just uploaded a video walkthrough of the tutorial I recorded this morning. youtu.be/C4LYZokS_t4

Bentopy tutorial walkthrough

YouTube video by Marieke

youtu.be

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 👇

Marieke Westendorp@ma3ke.bsky.social · 6mo ago

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

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 👇

Siewert-Jan Marrink@cg-martini.bsky.social · 7mo ago

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

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

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 !!

Carl Zimmer@carlzimmer.com · 8mo ago

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....

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 🎉

Pavol Harar@paloha.bsky.social · 8mo ago

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.

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...

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

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...

biorxiv.org

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