Jakub Rydzewski @jkrd.bsky.social

Now available in Journal of Chemical Information and Modeling! pubs.acs.org/doi/10.1021/ac…

Nowe zasady open access w NCN: większa elastyczność – ta sama idea. ❗️Z dniem dzisiejszym odchodzimy od wymogu publikowania wyłącznie w otwartym dostępie, jednak nadal rekomendujemy otwarte udostępnianie wyników badań. ncn.gov.pl/aktualnosci/20…

Together with my students, we have implemented a PyTorch Lightning package for dimensionality reduction with a parametric version of tSNE. More methods soon! Paper: arxiv.org/abs/2505.16476 Code: github.com/NeuralTSNE

A modern overview of spatial techniques for machine learning of slow collective variables and enhanced sampling in molecular dynamics simulations. @tugceegokdemir @JakubRydzewski Learn more 👇 aippub.org/3XsQxEQ

For those seeking postdoc opportunities in Poland -- NAWA has opened the Ulam program. If you are interested in applying for a scholarship in our group, please contact me! nawa.gov.pl/en/programy-na…

Very happy to announce that our featured review on thermodynamics-informed learning of slow CVs has finally been published in Chemical Physics Reviews as part of the Special Collection on AI and Machine Learning in Chemical and Materials Science! doi.org/10.1063/5.0245…

Our review on ML, CVs, and enhanced sampling has been accepted in Chem. Phys. Rev. Congratulations to @tugceegokdemir on her 1st first-author paper! arxiv.org/abs/2412.20868 Many thanks to Haochuan Chen, @lukeevanshandle, @LuigiBonati, and @OmarValsson for their great feedback!

For anyone interested in spectral maps. I made a typo in one equation in the original paper published in JCPL. This has now been fixed; see the accompanying correction note. pubs.acs.org/doi/full/10.10…

Interested in doing MD simulations of protein-ligand dissociation? Check out our PLUMED tutorial on the new version of maze: plumed-tutorials.org/lessons/24/008… Implementation: github.com/jakryd/plumed2… More details about PLUMED Tutorials in our collaborative work: arxiv.org/abs/2412.03595

📢 New #preprint describing our community effort to share #plumed tutorials arxiv.org/abs/2412.03595 ! Explore the tutorials at plumed-tutorials.org

To PhD students -- if you are interested in molecular dynamics and machine learning, you can now apply for a one-month visit to our group! Mail or DM me for more information. fizyka.umk.pl/en/prom-eng/

BREAKING NEWS The Royal Swedish Academy of Sciences has decided to award the 2024 #NobelPrize in Physics to John J. Hopfield and Geoffrey E. Hinton “for foundational discoveries and inventions that enable machine learning with artificial neural networks.”

If you are curious about how #JCTC got started and how #JCIM got its name, check this out. @ACSPublications @JCIM_JCTC pubs.acs.org/doi/full/10.10…

Congratulations to Prof. Michele Perrinello for being included in the list of Citation Laureates 2024! @GroupParrinello usi.ch/en/feeds/29831

Glad to have had the opportunity to present as an invited speaker at the @RoySocChem Theoretical Chemistry Group's Graduate Student Meeting at the University of Warwick. It was a rewarding experience, and thanks to the organizers for a well-organized event.

Happy to share my latest work on spectral maps 🌈 Out now in @JCIM_JCTC special issue "Machine Learning and Statistical Mechanics: Shared Synergies for Next Generation of Chemical Theory and Computation" pubs.acs.org/doi/10.1021/ac…

能勢熱浴40周年記念国際ワークショップ(11/2,慶應大・日吉)の参加登録が始まっています。 sites.google.com/view/nose40/

Phys. Rev. Lett. 131, 158001 (2023) - Mechanistic Insights into Water Autoionization through Metadynamics Simulation Enhanced by Machine Learning journals.aps.org/prl/abstract/1…

Very excited to present our work at @CCP5UK Summer School. Many thanks to the organizers for this opportunity.

Dynamical Reweighting for Biased Rare Event Simulations | Annual Reviews - go.shr.lc/3ROY26c