Marieke Westendorp
@ma3ke.bsky.social
I like making cool models and I create tools that help me and others to do that.
PhD student at the Marrink lab, University of Groningen.
Very interested in CG MD and system construction.
git.sr.ht/~ma3ke
github.com/ma3ke
she/they—🏳️🌈🏳️⚧️🌷🚲⛵161
PhD student at the Marrink lab, University of Groningen.
Very interested in CG MD and system construction.
git.sr.ht/~ma3ke
github.com/ma3ke
she/they—🏳️🌈🏳️⚧️🌷🚲⛵161
Reposted by Marieke Westendorp
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:
February 13, 2026 at 3:37 PM
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:
Reposted by Marieke Westendorp
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👇
February 13, 2026 at 3:37 PM
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
Bentopy makes assembling large-scale MD models accessible and fast.
doi.org/10.1002/pro....
@janstevens.bsky.social, @cg-martini.bsky.social
February 13, 2026 at 3:07 PM
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
Bentopy makes assembling large-scale MD models accessible and fast.
doi.org/10.1002/pro....
@janstevens.bsky.social, @cg-martini.bsky.social
Reposted by Marieke Westendorp
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....
Built using bentopy, based on David Naranjo's idea.
The input file can be found here: gist.github.com/ma3ke/723f9c....
December 24, 2025 at 4:35 PM
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....
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
December 25, 2024 at 10:31 PM
I wish everybody a very cozy computation
Almost put ‘I make computers do things fast’ in my bio but bluesky wouldn’t let me.
December 18, 2024 at 8:52 AM
Almost put ‘I make computers do things fast’ in my bio but bluesky wouldn’t let me.
My spiritual home is over at the fediverse but I will take this opportunity to repost only my best material here.
December 18, 2024 at 8:33 AM
My spiritual home is over at the fediverse but I will take this opportunity to repost only my best material here.