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
Applications are open for graduate students and postdocs. Housing, some meals, and course materials are included.
A snapshot from a whole-cell Lattice Microbes simulation of the JCVI-syn3A minimal. Credit: Thornburg et al., Cell (2026)
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!
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 www.biorxiv.org/content/10.64898/2026.02...
Our Story about ADAM10 modulation by PS lipids found its home in Advanced Science !
Many thanks to all co-authors for an amazing collaboration.
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!
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 👇
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 www.biorxiv.org/content/10.1101/2025.09....
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...
