Erik Thiede

#BPS2026 The T&C subgroup is hosting a fun event on Saturday evening, Feb 21st 🎉 Open bar for 2 hours + food! Tickets are selling fast, so sign up soon: www.biophysics.org/2026meeting/...

CryoJAX: a cryo-electron microscopy image-simulation library in JAX The authors have developed cryoJAX, a cryo-EM image-simulation library for developing data-analysis techniques across cryo-EM modalities. CryoJAX is built on JAX, an emerging scientific computing framework in Python well suited for cryo-EM data analysis.

M​ichael J. O'Brien et al.: CryoJAX: a cryo-electron microscopy image-simulation library in JAX #CryoEM #ImageSimulation #AutomaticDifferentiation @harvard@unewhaven@Cornell...#IUCr https://journals.iucr.org/paper?S2059798326000550

(Just looked at the comments and saw that @liweichang.bsky.social beat me to it)

That's unfair! Sometimes it's a fast-folding protein without solvent :p.

To be pedantic it just "calls a tool that returns info". That tool *could* be a web search, but it could be something else. For instance, if your LLM is focused on sports, you could have it consult a database of baseball scores directly -- you don't need to pass through a web search.

RAG queries an external tool (e.g. the raw data from a search), compress its content into a numeric representation, and incorporate that alongside your prompt.

Another closely related technique is CAG (cache-augment generation). CAG works on fixed data sources, but is typically much faster.

Good question. There are two options here. The first (naive) option is you keep retraining the model. Obviously this is slow, expensive.

The other option is do basically what you described. The keyword to look up here is "RAG": Retrieval Augmented Generation.

Postdoc opportunity with Michel Goedert and myself to work on #cryoEM/#cryoET structures of #amyloids. Feel free to email me with any questions you might have.

mrc.tal.net/vx/mobile-0/...

Really interesting work. Is there a github somewhere we can play around with?

Using some matrix perturbation theory, we can build heuristics for which MSM states are sensitive to error: we find that states at transition states or in metastable regions on pathways can lead to large errors.

When I started working on MSMs I was told never to trust rate estimates from MSMs -- the errors were just too big. Now, almost a decade later (jeez I'm old) I think we have some ideas around where this error comes from.

Error Breakdown and Sensitivity Analysis of Dynamical Quantities in Markov State Models Markov state models (MSMs) are widely employed to analyze the kinetics of complex systems. But despite their effectiveness in many applications, MSMs are prone to systematic or statistical errors, oft...

Bit belated, but our article on error analysis for MSMs is in JCTC!

pubs.acs.org/doi/abs/10.1...

I'm giving a talk at One World Cryo EM (cryoem.world) tomorrow at 11:00am EST. Topic is 'Deconstructing Algorithms for “Discrete” Heterogeneity in Cryo-EM'. Sign up for their mailing list to tune in!

It leaves me feeling conflicted when we mention him as senior scientists, so I thought I'd say something. But if others feel differently about him and interpret his character differently, that's entirely their prerogative :).

The reason I commented is that when we tell the next generation to turn to Feynman for inspiration we are also teaching them how to "be" in science. As such it is also worth discussing the bad with the good.

I absolutely do not want to take away from anything that gave anyone inspiration to pursue science. On a personal level I have considerable respect for your work, and I am glad this inspiration occurred.

And you do see it in this interview as well: like when he talks about social science.

I think it's that while Feynman's attitudes towards women were quite problematic, I think it's part of a broader pattern that underlies some of his stories: other people are there for Feynman to use.

Right, there's a good question on why I'm not just posting by myself about Feynman's attitudes towards women (I'd certainly not be the first to do so!) And certainly one thing I would never want to take away from the inspiration we find as young scientists.

He then is curious if it works with a "nice, ordinary, Southern girl" so he tries it "with the sister of a grad student." And he says it works, and he sleeps with her.

But presumably he realizes this is all somewhat distateful, so he decides to stop doing it because "he didn't enjoy it."

He learns to pick up girls by, "adopting the
attitude that those bar girls are all bitches, that they aren't worth anything, and all they're in there for is to get you to buy them a drink, and they're not going to give you a goddamn thing; I'm not going to be a gentleman to such worthless bitches"

He's really an amazing storyteller and they're all charmingly told. You really start rooting for this rebellious underdog who comes in with his simple questions that upset the scientific apple cart.

But halfway through you get to the part where he starts talking about going to bars.

My own experience really starts with having read "Surely your Joking" Mr. Feynman, a set of interviews that serve his memoirs, which I was asked to read as part of an undergrad chemistry class.

I wish I could feel the same way. He's an amazing storyteller, but the more you read between the lines, you see how often he is using his stories to whitewash his own sexual harassment or condescend to the people around him.

www.thecrimson.com/article/2025...

...and what's more, absolutely none of this happens in a vacuum. There's much I love about academia, but one thing I absolutely hate is the way it permits professors to abuse the power they have over their mentees. We have systemic issues we need to face.

(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.

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 😅.

We are hiring for a postdoc to work on the intersection of molecular simulation, machine learning, and cryo-EM! Please find the job posting here.

thiedelab.github.io/docs/postdoc...