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.