Juergen Koefinger
@jkoefinger.bsky.social
Theory and computation of soft and condensed matter, dead or alive. Currently project leader at MPI of Biophysics in Frankfurt/Germany.
Reposted by Juergen Koefinger
**Job Alert** Exciting postdoc position available: theoretical and experimental cryo-EM studies of flexible biomolecules. Competitive salary, collaborative environment at NYSBC and Flatiron Institute. Please share!! and contact: [email protected]
October 22, 2025 at 2:55 PM
**Job Alert** Exciting postdoc position available: theoretical and experimental cryo-EM studies of flexible biomolecules. Competitive salary, collaborative environment at NYSBC and Flatiron Institute. Please share!! and contact: [email protected]
Reposted by Juergen Koefinger
"For our scientists" 🧪
By ellecordova on Instagram
By ellecordova on Instagram
September 6, 2025 at 12:36 PM
"For our scientists" 🧪
By ellecordova on Instagram
By ellecordova on Instagram
Reposted by Juergen Koefinger
📢 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
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...
arxiv.org
July 14, 2025 at 6:50 AM
📢 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
If you draw from a distribution, but you don’t like the outcome, then it’s a hallucination.
June 27, 2025 at 12:03 PM
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.
June 25, 2025 at 9:47 AM
Authors of scientific articles are far too often utilizing things, when they are actually just using them.
Reposted by Juergen Koefinger
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
February 14, 2025 at 5:50 AM
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
Reposted by Juergen Koefinger
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
Congrats to all co-authors, especially to the project leads:
@maximemaria.bsky.social and @matthieumontes.bsky.social
#compchem #compchemsky #biosky #hpc
February 4, 2025 at 6:12 AM
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
Congrats to all co-authors, especially to the project leads:
@maximemaria.bsky.social and @matthieumontes.bsky.social
#compchem #compchemsky #biosky #hpc
Reposted by Juergen Koefinger
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 [email protected].
Repost appreciated.
Repost appreciated.
January 9, 2025 at 2:58 AM
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 [email protected].
Repost appreciated.
Repost appreciated.
Reposted by Juergen Koefinger
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.
December 19, 2024 at 7:36 AM
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.
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!
December 19, 2024 at 12:02 PM
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!
Reposted by Juergen Koefinger
@plumed.org is finally on BlueSky 🦋!!
December 10, 2024 at 8:52 AM
@plumed.org is finally on BlueSky 🦋!!
Reposted by Juergen Koefinger
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
One PhD thesis in integrative structural biology | Research - Institut Pasteur
research.pasteur.fr
December 6, 2024 at 8:31 AM
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
Reposted by Juergen Koefinger
The most diverse group of organisms on the planet are in trouble and the consequences could be dire.
www.reuters.com/graphics/GLO...
www.reuters.com/graphics/GLO...
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.
www.reuters.com
November 30, 2024 at 4:18 AM
The most diverse group of organisms on the planet are in trouble and the consequences could be dire.
www.reuters.com/graphics/GLO...
www.reuters.com/graphics/GLO...
Reposted by Juergen Koefinger
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.
1/15
The fold of a protein is critical to its function. Yet no one really knows specifically how protein folding happens.
1/15
June 27, 2024 at 3:49 PM
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.
1/15
The fold of a protein is critical to its function. Yet no one really knows specifically how protein folding happens.
1/15
Reposted by Juergen Koefinger
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...
🧪 🧬 🧶
💧Biomolecular condensates: From fundamental principles to applications in health and biotech 💧
Lots of amazing speakers and great venue 🍻
events.au.dk/biomolecular...
🧪 🧬 🧶
June 14, 2024 at 8:23 PM
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...
🧪 🧬 🧶
💧Biomolecular condensates: From fundamental principles to applications in health and biotech 💧
Lots of amazing speakers and great venue 🍻
events.au.dk/biomolecular...
🧪 🧬 🧶
Reposted by Juergen Koefinger
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...
AlphaFold3 Transparency and Reproducibility
Link for endorsement signatures: https://forms.gle/d47w29eGHeL1ejXw9
zenodo.org
May 11, 2024 at 10:53 PM
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.
March 27, 2024 at 12:04 PM
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
March 27, 2024 at 9:44 AM
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...
March 27, 2024 at 9:20 AM
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!
February 27, 2024 at 7:52 AM
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!
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.
Encoding prior knowledge in ensemble refinement
The proper balancing of information from experiment and theory is a long-standing problem in the analysis of noisy and incomplete data. Viewed as a Pareto optimization problem, improved agreement with...
www.doi.org
December 1, 2023 at 1:53 PM
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.
November 7, 2023 at 1:00 PM
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.
After work pumpkin carving - Max Planck style
October 27, 2023 at 8:16 AM
After work pumpkin carving - Max Planck style
My biggest beef with LateX and bibtex are non-sensical error messages.
October 9, 2023 at 11:48 AM
My biggest beef with LateX and bibtex are non-sensical error messages.
Thanks @chhdellago.bsky.social for the invite! Bluesky looks quite cozy. I guess chances are better than ever that ALL of my (two!) followers will like a post from me.
October 4, 2023 at 7:52 AM
Thanks @chhdellago.bsky.social for the invite! Bluesky looks quite cozy. I guess chances are better than ever that ALL of my (two!) followers will like a post from me.