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!

i literally do this sometimes and nobody can stop me

did my open source gardening for today and it was very pleasant this is important because last month i was having a bit of a hard time with it all and it is great to see the joy returning in something i love

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.

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

I bet this would feel so good if I was a cell.

Jan Stevens@janstevens.bsky.social · 6mo ago

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:

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:

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👇

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

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....

I wish everybody a very cozy computation

Almost put ‘I make computers do things fast’ in my bio but bluesky wouldn’t let me.

I love VMD 🥹

My spiritual home is over at the fediverse but I will take this opportunity to repost only my best material here.