Juergen Koefinger

It might be. But even the very wise cannot see all ends.

RNA Dynamics and Interactions Revealed through Atomistic Simulations RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in di...

📢 New #preprint alert! Our review "RNA Dynamics and Interactions Revealed through Atomistic Simulations" is now available on arxiv.org/abs/2507.08474 ! Written by @bussigio.bsky.social and @ollyfutur.bsky.social

Delving into LLM-assisted writing in biomedical publications through excess vocabulary Excess words track LLM usage in biomedical publications.

As it turns out, "utilizing" and "leveraging" are both among a list of 291 "rare excess style words" which show a jump-like increase in frequency correlating with the emergence of LLMs as AI assistants like ChatGPT: doi.org/10.1126/scia...

If you draw from a distribution, but you don’t like the outcome, then it’s a hallucination.

Authors of scientific articles are far too often utilizing things, when they are actually just using them.

If you are interested in postdoctoral research on ligand-gated ion channels and the synapse, or simulation/AI methods for structural biology - drop me a line if you'll be around at Biophysical Society in LA! #bps2025 #bps #biophysics

New preprint: VTX: Real-time high-performance molecular structure and dynamics visualization software

Congrats to all co-authors, especially to the project leads:
@maximemaria.bsky.social and @matthieumontes.bsky.social

#compchem #compchemsky #biosky #hpc

@zotero.org dramatically improved my reading. Highly recommended! The browser plugin to add a paper to your library with only one click makes a huge difference.

PhDs in biochemistry, structural biology, pharmacology, or similar, located in the US and with strong publication track records and a high motivation to solve Parkinson's, please send CV directly to me at jimhurley@berkeley.edu.
Repost appreciated.

By the way, I love this picture. It emphasizes the power of combining theory and computation. What could Boltzmann have achieved if he had powerful computers available? Of course, it could be that he’s just checking his banking account. We will never know.

I’ve been wondering for a long time if Bernhard had a reason to make Boltzmann left-handed.

During my PhD I experienced severe anxiety and depression, along with suicide ideation. Thankfully I got help and I'm still here. As a student I went to find a book mental illness and how to cope during a PhD and didn't find one. That's how "Managing Your Mental Health During Your PhD" came to be.

The Signal and the Noise - Wikipedia

In the end, their posterior probability of a terror attack increased from 1% after the first plane crash to 99% after the second plane crash. I believe these numbers roughly reflect the experience of many of us. en.wikipedia.org/wiki/The_Sig...

For warm-up, the students first solved a Fermi problem. They guesstimated within a factor 5 the money thrown into Trevi Fountain in Rome each year. Much better than their initial guesses. It eased them into guesstimating probabilities.

What was a good moment for you in 2024? Here is mine: I had spontaneously decided before the lecture to illustrate Bayes theorem with Nate Silver’s example about the tragic events of 9/11. I did not have the book with me, but the students did a terrific job and the example worked beautifully!

@plumed.org is finally on BlueSky 🦋!!

Do you want to work at the interface of molecular simulations, structural biology experiments and #AI? Come to Paris for a PhD at @pasteur.fr 1 PhD position is available in our lab funded by ERC_Research. Please repost!! #compchem #compbio Info 👇 research.pasteur.fr/b/15Hr

Insect populations are declining at an unprecedented rate The most diverse group of organisms on the planet are in trouble and the consequences could be dire.

The most diverse group of organisms on the planet are in trouble and the consequences could be dire.

www.reuters.com/graphics/GLO...

Proteins do it all. Hemoglobin ferries oxygen around the body. Keratin structures hair, nails and skin. Insulin helps glucose convert into energy.

The fold of a protein is critical to its function. Yet no one really knows specifically how protein folding happens.

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Flyer for the meeting including a list of speakers

Join us in Copenhagen 🇩🇰 for a meeting on May 13–15 2025 ☀️ on

💧Biomolecular condensates: From fundamental principles to applications in health and biotech 💧

Lots of amazing speakers and great venue 🍻

events.au.dk/biomolecular...
🧪 🧬 🧶

It appears to be as @agrossfield.bsky.social was saying. Surely, not everything that impacts science is suited for a research (!) article. AlphaFold 3 doesn't need Nature for success. I doubt that Nature has done itself a service. At least they have confirmed some opinions about them. 😉

We were incredibly disappointed with the lack of code or executable accompanying the publication of AF3 in @Nature . This contradicts scientific principles of the ability to evaluate, use, and build upon existing work. zenodo.org/records/1117.... Sign to endorse: docs.google.com/forms/d/e/1F...

To all Austrians supporting dual-citizinship for Austrian expatriates: Please check out www.beibehaltung.at and consider signing the petition.

Why "back calculation" for the calculation of experimental observables from a "forward model", e.g., molecular model. Why not "forward calculation"? Why not "back-calculate" non-observable parameters from experiments? Is there a reference? @lindorfflarsen.bsky.social @carlocamilloni.bsky.social

Back then when I did my PhD, a fellow student told me that any typo I find in his printed poster, I can cut out and keep! I guess the same applies to "Encoding prior knowledge in ensemble refinement", which is out now. doi.org/10.1063/5.01...

We suggest to use the energy uncertainty in the force field to encode prior knowledge in ensemble refinement of MD. It is determined in the coarse space of observables. See updated doi.org/10.26434/che.... Thanks @carlocamilloni.bsky.social for your feedback!

One reason why proofreading is so hard

Have you ever wondered how to properly balance information from theory and experiment? If so, check out our preprint. If not, check out our preprint. In any case, please share.

I felt so confident that the number of draws is n and not k that I've actually corrected the Wikipedia page en.wikipedia.org/wiki/Hyperge.... Not that I have made the world a better place. But it still feels nice.

To stay up-to-date in my field, I like to check who is citing some seminal papers. I also like to check who cites some popular papers which I think are wrong or just bad.