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!
wikipedia figure of a grey head with a flower inside with the caption 'aesthetic experience', an arrow pointing from that to a flower with the caption 'aesthetic object'. The caption above the arrow says 'aesthetic attitude'.
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.
I bet this would feel so good if I was a cell.
Depending on the kind of analysis you're doing, you may be interested in checking out molly. It's a very fast reader and writer for XTC files I created and maintain.
For example, molly can often skip reading solvent through clever buffering. And it has python bindings.
github.com/ma3ke/molly
I just uploaded a video walkthrough of the tutorial I recorded this morning.
youtu.be/C4LYZokS_t4
I love this video so much...
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👇
Here is a fun thread about how the Bentopy logo was created, by the way.
hachyderm.io/@ma3ke/11408...
We have an excellent tutorial that is available at cgmartini.nl/docs/tutoria....
In-depth information can also be found on the wiki for the Bentopy repository: github.com/marrink-lab/....
The bentopy logo, packed with proteins using bentopy!
Bentopy is open source software and can be installed directly through pip.
$ pip install bentopy
github.com/marrink-lab/...
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
A snowman made of beads with some snow (ions!) around it. It has a black round hat, eyes, a smile, red buttons, and of course a carrot nose.
And here is a still that does not suffer under the heavy burden of the video compression 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....
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....
Actual picture of a screen, shows a very early stage, rudimentary molecular structure viewer for plan 9
As is tradition, I’m reinventing computational biochemistry on an obscure operating system
plan9 on a monitor set up on a table with a jigsaw puzzle. In the background is a bookshelf and to the side a big pot of colored pencils
I wish everybody a very cozy computation
Wow these are excellent!!
My phone reflects on a window in the Linnaeusborg overlooking the RUG campus as the sun sets
Woah saw some too, yesterday
It is true though.
Almost put ‘I make computers do things fast’ in my bio but bluesky wouldn’t let me.
A colored pencil and black ink pen drawing of a SARS-CoV-2 virion.
I love VMD 🥹
My spiritual home is over at the fediverse but I will take this opportunity to repost only my best material here.
