Erik Thiede
@erikhthiede.bsky.social
240 followers 220 following 82 posts
Asst. Professor of Chemistry at Cornell University. Interests: Bio, Chem, ML, Statistical Estimation, Electron Microscopy, Good code.
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erikhthiede.bsky.social
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 😅.
erikhthiede.bsky.social
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
erikhthiede.bsky.social
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!
erikhthiede.bsky.social
Excellent read for anyone trying to understand what is up with all the AI hype nowadays.
erikhthiede.bsky.social
And here I thought it was if you try *non*-symplectic integrators you don't go back.... to the same energy value.
erikhthiede.bsky.social
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
erikhthiede.bsky.social
Happy to see our first collaboration with the Yang group come through!
yaoyang-cornell.bsky.social
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
Reposted by Erik Thiede
fraserlab.com
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
Reposted by Erik Thiede
samblau.bsky.social
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
erikhthiede.bsky.social
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.
erikhthiede.bsky.social
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 :)
erikhthiede.bsky.social
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.)
Reposted by Erik Thiede
weedenkim.bsky.social
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
erikhthiede.bsky.social
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"
bobkopp.net
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.
erikhthiede.bsky.social
Welcome to upstate NY: it's great up here!
erikhthiede.bsky.social
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.
erikhthiede.bsky.social
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).
erikhthiede.bsky.social
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.
erikhthiede.bsky.social
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).
erikhthiede.bsky.social
Wishing all the trans scientists out there who are continuing to do amazing work in adverse conditions a good trans day of visibility!
erikhthiede.bsky.social
Ugh god yes. Drives me insane, and it actively stands in the way of scientific progress. I really wish I could go through arXiv and find/replaced every use of "AI" or "Machine Learning" with "A complicated statistical model".
erikhthiede.bsky.social
On top of that, I really wish they had discussed WHY drug repurposing is so hot: if you are a pharma company and can find a new disease that your drug treats, you can keep the patent active, stop the drug from becoming generic, and continue charging crazy amounts of money *for its original use*.