Erik Thiede
@erikhthiede.bsky.social
Asst. Professor of Chemistry at Cornell University. Interests: Bio, Chem, ML, Statistical Estimation, Electron Microscopy, Good code.
(Jokes aside: package looks great! Thanks for putting this together.)
October 29, 2025 at 3:39 AM
(Jokes aside: package looks great! Thanks for putting this together.)
Request: I think with a little bit of effort, we could further improve dimensional efficiency and make py1Dmol. I've attached a quick proof of concept in the image. Happy to submit a PR if you want to follow up.
October 29, 2025 at 3:38 AM
Request: I think with a little bit of effort, we could further improve dimensional efficiency and make py1Dmol. I've attached a quick proof of concept in the image. Happy to submit a PR if you want to follow up.
I almost think it's inherent in the field. I think we are a "wastebasket taxon" for all the things that didn't fit in Biology and Physics 😅.
September 25, 2025 at 4:18 PM
I almost think it's inherent in the field. I think we are a "wastebasket taxon" for all the things that didn't fit in Biology and Physics 😅.
And here I thought it was if you try *non*-symplectic integrators you don't go back.... to the same energy value.
June 8, 2025 at 11:34 AM
And here I thought it was if you try *non*-symplectic integrators you don't go back.... to the same energy value.
Yes, Bogdan is a smart guy who does great work: we met briefly at a conference two (?) years ago, and I've been following his work since.
May 8, 2025 at 12:39 PM
Yes, Bogdan is a smart guy who does great work: we met briefly at a conference two (?) years ago, and I've been following his work since.
No worries, I'll start by reading that code.
We are working on some techniques for cryo-EM that look mathematically similar to Lucy-Richardson, so I'm on the lookout for new tricks :)
We are working on some techniques for cryo-EM that look mathematically similar to Lucy-Richardson, so I'm on the lookout for new tricks :)
May 8, 2025 at 12:53 AM
No worries, I'll start by reading that code.
We are working on some techniques for cryo-EM that look mathematically similar to Lucy-Richardson, so I'm on the lookout for new tricks :)
We are working on some techniques for cryo-EM that look mathematically similar to Lucy-Richardson, so I'm on the lookout for new tricks :)
Can we get a reference for the algorithm? (I saw your bioRxiv preprint from last week, but am not 100% if that is the right paper to refer to.)
May 7, 2025 at 6:00 PM
Can we get a reference for the algorithm? (I saw your bioRxiv preprint from last week, but am not 100% if that is the right paper to refer to.)
Welcome to upstate NY: it's great up here!
April 14, 2025 at 3:09 PM
Welcome to upstate NY: it's great up here!
Our work also solves generalizability. As we know from a plethora of JCP, JPC, and JCTC articles, if something works on the alanine dipeptide it basically works on everything.
April 1, 2025 at 4:05 PM
Our work also solves generalizability. As we know from a plethora of JCP, JPC, and JCTC articles, if something works on the alanine dipeptide it basically works on everything.
This makes the latent encoding immediately interpretable. (Although paradoxically, as anyone who has taught free energy in an undergrad p-chem class knows, this doesn't mean it is explainable).
April 1, 2025 at 4:02 PM
This makes the latent encoding immediately interpretable. (Although paradoxically, as anyone who has taught free energy in an undergrad p-chem class knows, this doesn't mean it is explainable).
The variational alanine encoder takes arbitrary data and transforms it into a latent random variable whose negative log-probability is given by the free energy surface for the alanine dipeptide in vacuum.
April 1, 2025 at 3:59 PM
The variational alanine encoder takes arbitrary data and transforms it into a latent random variable whose negative log-probability is given by the free energy surface for the alanine dipeptide in vacuum.