iiinova — where your digital self keeps evolving

Reposted by Marieke Westendorp

Jan Stevens @handle.invalid · 31/03/2026

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!

A snapshot from a whole-cell Lattice Microbes simulation of the JCVI-syn3A minimal. Credit: Thornburg et al., Cell (2026)

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Marieke Westendorp @ma3ke.bsky.social · 14/03/2026

i literally do this sometimes and nobody can stop me

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'.

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Marieke Westendorp @ma3ke.bsky.social · 14/03/2026

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

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Reposted by Marieke Westendorp

Protein Society @proteinsociety.bsky.social · 13/03/2026

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.

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Reposted by Marieke Westendorp

Timon Idema @timonidema.bsky.social · 02/03/2026

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.

arxiv.org

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. ...

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Marieke Westendorp @ma3ke.bsky.social · 19/02/2026

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

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Marieke Westendorp @ma3ke.bsky.social · 15/02/2026

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

github.com

GitHub - ma3ke/molly: Read xtc files, fast.

Read xtc files, fast. Contribute to ma3ke/molly development by creating an account on GitHub.

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Marieke Westendorp @ma3ke.bsky.social · 13/02/2026

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

youtu.be

Bentopy tutorial walkthrough

YouTube video by Marieke

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Reposted by Marieke Westendorp

Jan Stevens @handle.invalid · 13/02/2026

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:

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Reposted by Marieke Westendorp

Jan Stevens @handle.invalid · 13/02/2026

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👇

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

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Marieke Westendorp @ma3ke.bsky.social · 13/02/2026

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/....

cgmartini.nl

Bentopy: from simple packing to building cellular models – Martini Force Field Initiative

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Marieke Westendorp @ma3ke.bsky.social · 13/02/2026

Bentopy is open source software and can be installed directly through pip. $ pip install bentopy github.com/marrink-lab/...

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Marieke Westendorp @ma3ke.bsky.social · 13/02/2026

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

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).

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Marieke Westendorp @ma3ke.bsky.social · 24/12/2025

And here is a still that does not suffer under the heavy burden of the video compression here.

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.

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Reposted by Marieke Westendorp

Marieke Westendorp @ma3ke.bsky.social · 24/12/2025

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....

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Marieke Westendorp @ma3ke.bsky.social · 24/12/2025

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....

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Marieke Westendorp @ma3ke.bsky.social · 25/12/2024

As is tradition, I’m reinventing computational biochemistry on an obscure operating system

Actual picture of a screen, shows a very early stage, rudimentary molecular structure viewer for plan 9

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Marieke Westendorp @ma3ke.bsky.social · 25/12/2024

I wish everybody a very cozy computation

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

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Marieke Westendorp @ma3ke.bsky.social · 18/12/2024

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

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Marieke Westendorp @ma3ke.bsky.social · 18/12/2024

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

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