Erik Thiede
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erikhthiede.bsky.social
Erik Thiede
@erikhthiede.bsky.social
Asst. Professor of Chemistry at Cornell University. Interests: Bio, Chem, ML, Statistical Estimation, Electron Microscopy, Good code.
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...
thiedelab.github.io
September 22, 2025 at 4:30 PM
Reposted by Erik Thiede
Faculty opening in Cornell Chemistry at the Assistant Professor level in the area of chemical biology, broadly defined! academicjobsonline.org/ajo/jobs/30338 #chemjobs
Cornell University, Chemistry and Chemical Biology
Job #AJO30338, WDR-00054776 Assistant Professor - Chemistry and Chemical Biology, Cornell University (Ithaca, NY), Chemistry and Chemical Biology, Cornell University, Ithaca, New York, US
academicjobsonline.org
August 25, 2025 at 8:30 PM
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!
August 26, 2025 at 7:06 PM
Excellent read for anyone trying to understand what is up with all the AI hype nowadays.
July 17, 2025 at 2:23 AM
July 16, 2025 at 10:35 PM
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...
Szkoła Doktorska Nauk Ścisłych i Przyrodniczych - Uniwersytet Jagielloński
science.phd.uj.edu.pl
May 29, 2025 at 3:04 PM
Happy to see our first collaboration with the Yang group come through!
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
Operando Heating and Cooling Electrochemical 4D-STEM Probing Nanoscale Dynamics at Solid–Liquid Interfaces
Operando/in situ methods have revolutionized our fundamental understanding of molecular and structural changes at solid–liquid interfaces and enabled the vision of “watching chemistry in action”. Operando transmission electron microscopy (TEM) emerges as a powerful tool to interrogate time-resolved nanoscale dynamics, which involve local electrical fields and charge transfer kinetics distinctly different from those of their bulk counterparts. Despite early reports on electrochemical or heating liquid-cell TEM, developing operando TEM with simultaneous electrochemical and thermal control remains a formidable challenge. Here, we developed operando heating and cooling electrochemical liquid-cell scanning TEM (EC-STEM). By integrating a three-electrode electrochemical circuit and an additional two-electrode thermal circuit, we can investigate heterogeneous electrochemical kinetics across a wide temperature range of −50 to 300 °C. We used Cu electrodeposition/stripping processes as a model system to demonstrate quantitative electrochemistry from −40 to 95 °C in both transient and steady states in aqueous and organic solutions, which paves the way for investigating energy materials operating in extreme climates. Machine learning-assisted quantitative 4D-STEM structural analysis in cold liquids (−40 °C) reveals a distinct two-stage growth of nanometer-scale mossy Cu nanoislands with random orientations followed by μm-scale Cu dendrites with preferential orientations. This work benchmarked electrochemistry in the three-electrode EC-STEM and systematically investigated the temperature and pH dependence of the Pt pseudoreference electrode (RE). At room temperature, the Pt pseudo-RE shows a reliable potential of 0.8 ± 0.1 V vs the standard hydrogen electrode and remains pH-independent on the reversible hydrogen electrode scale. We anticipate that operando heating/cooling EC-STEM will become invaluable for understanding fundamental temperature-controlled nanoscale electrochemistry and advancing renewable energy technologies (e.g., catalysts and batteries) in realistic climates.
pubs.acs.org
May 26, 2025 at 2:50 PM
Reposted by Erik Thiede
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
May 20, 2025 at 5:26 PM
Reposted by Erik Thiede
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
May 14, 2025 at 8:52 PM
Reposted by Erik Thiede
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
May 7, 2025 at 11:56 AM
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"
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.
April 16, 2025 at 1:05 PM
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).
April 1, 2025 at 3:55 PM
Wishing all the trans scientists out there who are continuing to do amazing work in adverse conditions a good trans day of visibility!
March 31, 2025 at 11:22 PM
Reposted by Erik Thiede
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
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.
Nervous about Trump, international tourists scrap their U.S. travel plans
International tourists are canceling plans to visit the United States, with Canadians leading the way.
www.washingtonpost.com
March 16, 2025 at 5:34 PM
Our (SMBP + SMBP alumns) man doing us proud.
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!
March 17, 2025 at 12:30 AM
How I've been generating nice equations in google slides:
January 11, 2025 at 7:33 PM
On Hanukkah, Jews participate in many ancient rituals such as helping their parents transfer files between computers.
December 29, 2024 at 4:32 PM
Y'all better have been getting those finger exercises in because those dreidels ain't gonna spin themselves.
December 25, 2024 at 8:49 PM
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
December 20, 2024 at 4:39 PM
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".
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... 🧬🧶
December 18, 2024 at 3:55 AM
Reposted by Erik Thiede
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.
Modeling Bias Toward Binding Sites in PDB Structural Models https://www.biorxiv.org/content/10.1101/2024.12.14.628518v1
December 16, 2024 at 6:05 AM
Reposted by Erik Thiede
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
December 12, 2024 at 3:49 PM
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.
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"
December 12, 2024 at 2:26 PM
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.
December 10, 2024 at 3:53 PM