#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/...

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

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.

journals.iucr.org

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/...

Bit belated, but our article on error analysis for MSMs is in JCTC! pubs.acs.org/doi/abs/10.1...

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...

pubs.acs.org

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!

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.

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...

Faculty opening in Cornell Chemistry at the Assistant Professor level in the area of chemical biology, broadly defined! academicjobsonline.org/ajo/jobs/30338 #chemjobs

Back from our first group conference trip to ACS Fall. Was great to not only see new science, but also excellent watch the very excellent presentations from Josh (Rhodes), Diego, and Jeffrey, as well as the great reception Josh (Almonte)'s poster received!

Excellent read for anyone trying to understand what is up with all the AI hype nowadays.

Jonathan Jacobs@bioinformer.bsky.social · last yr.

LMFAO… 😂 “When I was a kid, calling something “AI” meant Commander Data from Star Trek, something that can do what humans do. Now, AI is, like, really good autocomplete. “ 💯 this www.rollingstone.com/culture/cult...

Martin Vögele@martinvoegele.bsky.social · last yr.

It's all just the harmonic oscillator. #Physics 🧪

Posting a job ad on behalf of Mat Sikora, who is doing some fascinating work on cryo-EM for glycans. He's looking both for PhDs and postdocs. science.phd.uj.edu.pl/join/biomedi...

Happy to see our first collaboration with the Yang group come through!

Yang Group @ Cornell@yaoyang-cornell.bsky.social · last yr.

Who wants to study chemistry like watching movies? Operando electrochemical STEM offers a new opportunity! In our group's first publication, we probe the evolution of energy materials in real time at extreme temperatures🌡️ pubs.acs.org/doi/10.1021/... @erikhthiede.bsky.social

We are looking to hire (yes, even in this economy!) a jr. specialist to train in protein prep/structural biology related to our AVOID-ome work as part of openadmet.org. A great position for someone who is looking to be a tech for a few years before grad or med school. aprecruit.ucsf.edu/JPF05424

Junior/Assistant/Associate/Full Specialist Positions Available

University of California, San Francisco is hiring. Apply now!

aprecruit.ucsf.edu

The Open Molecules 2025 dataset is out! With >100M gold-standard ωB97M-V/def2-TZVPD calcs of biomolecules, electrolytes, metal complexes, and small molecules, OMol is by far the largest, most diverse, and highest quality molecular DFT dataset for training MLIPs ever made 1/N

One of grants frozen at Cornell: $6.7M (4 yrs) to develop heart pumps for babies born w/ heart defects. It took decades of work to get to point of prepping device for in-human clinical trials. No private company could do this. The cruelty of the Trump administration is heartbreaking. So to speak.

Research at risk: Life-saving heart pumps for babies | Cornell Chronicle

After receiving a stop-work order from the federal government, the future of a device to help children with heart defects is uncertain.

news.cornell.edu

Agreed: Universities are far too quick to ignore the words of the actual people in power, e.g. J.D. Vance saying, "Professors are the enemy" and "[Orban's seizure of universities is] the closest that conservatives have ever gotten to successfully dealing with leftwing domination of universities"

Bob Kopp@bobkopp.net · last yr.

Clearer F&A explanations would be great. (I actually think Princeton does this pretty well, and it’d be great for all schools to do this: finance.princeton.edu/budgeting-fi...) But the point of the policy is to take down universities, not improve F&A. These aren’t people to take at the word.

It is with great pleasure that I announce that the Thiede lab has solved the problem of interpretability in AI for Chemistry with our new neural network architecture: the Variational Alanine Encoder (VAE).

Wishing all the trans scientists out there who are continuing to do amazing work in adverse conditions a good trans day of visibility!

I think it has more to do with you might get locked up for absolutely no reason at all and then flown to El Salvador to die in prison even though a judge said you should be released

The Washington Post@washingtonpost.com · last yr.

International travelers concerned about President Donald Trump’s trade policies and bellicose rhetoric have been canceling trips to the United States, depriving the U.S. tourism industry of billions of dollars at a time when the economy has started to appear wobbly.

Our (SMBP + SMBP alumns) man doing us proud.

Lander Lab@landerlab.bsky.social · last yr.

We’ve seen some good grids and some bad at the CSHL #CryoEM course, but I think we all agree that @miroastore.bsky.social should be awarded the 2025 “worst grid” award. But for someone who never held a pipette prior to this course he also deserves the “most improved” award - keep it up Miro!

How I've been generating nice equations in google slides:

On Hanukkah, Jews participate in many ancient rituals such as helping their parents transfer files between computers.

Y'all better have been getting those finger exercises in because those dreidels ain't gonna spin themselves.

First little piece of funding for our new project direction joint with the Yang group: characterizing electrochemical situations with ML + in-situ EM. Congratulations to Yao for the successful proposal! news.cornell.edu/stories/2024...

2030 Project Fast Grant awards support energy systems of the future | Cornell Chronicle

Researchers from five colleges have received awards to support work on sustainable energy systems.

news.cornell.edu

An excellent point, and something that we run afoul of in far too many of our algorithms that boil down to "generalization of PCA / CCA in some conformational space".

Kresten Lindorff-Larsen@lindorfflarsen.bsky.social · 2y ago

A periodic reminder that biologically meaningful conformational changes do not have to be large While textbooks may indicate that relevant motions are large, even the original paper on alternating access makes it clear that atoms just need to move a bit to have an effect. doi.org/10.1038/2119... 🧬🧶

It is obvious that the PDB is biased towards proteins that scientists are more interested in. Similarly, its structures appear to be biased towards more interesting regions of proteins. This preprint finds that ligand binding sites tend to be more carefully modeled than the rest of the structure.

bioRxiv Biophysics@biorxiv-biophys.bsky.social · 2y ago

Modeling Bias Toward Binding Sites in PDB Structural Models https://www.biorxiv.org/content/10.1101/2024.12.14.628518v1

Googles claim that their result "lends credence to the notion that quantum computation occurs in many parallel universes" is nonsense, because their results are perfectly well explained by quantum mechanics independent of how you interpret it. 4/5

ESM3 structure predictions for multimers seem to be broken: In our (preliminary) experiments, it seems to always predict chain breaks around one amino acid in length.

Josh Almonte@josh-almonte.bsky.social · 2y ago

ESM 3 chain break token may be broken. (1/4) Predicted structure of insulin (red). An NMR structure (PDB:1A7F, green). The chain break token distance is 3.4A while the experimentally determined distance is 18.9A. sequence prompt: "GIVEQCCTSICSLYQLENYCN|FVNQHLCGSHLVEALELVCGERGGFYTPK"

Spent the last day of class yesterday telling my students that orbitals don't actually exist and real electrons exist in indescribable many-electron wavefunctions. For my next trick I'm telling all my nephews and nieces that Santa isn't real.