Lightnews — Scholar-powered news

Xuhui Huang @xuhuihuangchem.bsky.social · 13d

Big congratulations to Frank on receiving this year’s Hirschfelder Prize! Excited to welcome Frank and Cecilia to Madison in late Oct!

Frank Noe @franknoe.bsky.social · 15d

Thank you UW–Madison for this great honor! In 2016 I changed my group to AI4Science and went all-in on deep learning solutions for the molecular sciences. Best decision of my career in hindsight. Amazing what's become of that field - now AI for Science is a @msftresearch.bsky.social lab.

Microsoft Research @msftresearch.bsky.social · 15d

Congratulations to Frank Noé, Partner Research Manager at Microsoft Research AI for Science, who received the 2025–2026 Joseph O. Hirschfelder Prize in Theoretical Chemistry for pioneering contributions at the interface of AI and chemistry. msft.it/6015sqq4R

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Reposted by Xuhui Huang

Jeff Martell @jeffmartell.bsky.social · Aug 28

We teamed up with @xuhuihuangchem.bsky.social to perform structural modeling and substrate docking to gain insights into the beneficial mutations.

7/n

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Reposted by Xuhui Huang

Jeff Martell @jeffmartell.bsky.social · Aug 28

Congrats to Ashley Ogorek and @shubha-pani.bsky.social‬, who co-led this study, as well as the entire team: Eli, Jelena, Yichong, Fernando, Rachel, @xuhuihuangchem.bsky.social‬. This was a really fun collaboration with ‪@chembiobryan.bsky.social‬ - stay tuned for more to come!

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Xuhui Huang @xuhuihuangchem.bsky.social · Aug 25

Check out our new Python package, EPIPY!

It streamlines 3DRISM calculations—great for studying RNA/DNA solvation, predicting dewetting, and placing water molecules, etc.

Github: github.com/EPISOLreleas...
Preprint for a tutorial: chemrxiv.org/engage/chemr...

Congs to Peter and Siqin!

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Xuhui Huang @xuhuihuangchem.bsky.social · Aug 12

This study led by Sasha’s group
@nyumedpostdocs.bsky.social reveals the mechanisms of de-capping Np4N, a noncanonical initiating nucleotide for RNAP. It binds substrates in two orientations, so target-mimic drugs might fail if one still works! Glad we contributed to this work! Congs to team!

Nature Chemical Biology @natchembio.nature.com · Aug 11

A new paper reports how E. coli ApaH hydrolyzes enigmatic Np4N alarmones and decaps Np4-capped RNA, thereby impacting their lifetimes

www.nature.com/articles/s41...

ApaH decaps Np4N-capped RNAs in two alternative orientations - Nature Chemical Biology

This study shows how Escherichia coli ApaH hydrolyzes enigmatic Np4N alarmones and decaps Np4-capped RNAs, thereby impacting their lifetimes. Key features enable ApaH to bind RNA substrates in two ori...

www.nature.com

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Xuhui Huang @xuhuihuangchem.bsky.social · Jul 19

Thanks, Vince! It was great hanging out during the workshop!

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Xuhui Huang @xuhuihuangchem.bsky.social · Jul 19

Super excited 3 days at the CECAM workshop co-organized with @drgregbowman.bsky.social @bettinagkeller.bsky.social! Protein dynamics is definitely shaping up to be the next big topic in AI for Science! Huge thanks to @cecamevents.bsky.social, @uwdsi.bsky.social, TCI, Chem, Emma and the DSI staff!

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Xuhui Huang @xuhuihuangchem.bsky.social · Jul 14

Squeaks, brats, and Spotted Cows! Warmed up for the CECAM Flagship Workshop “Biomolecular Dynamics in the Age of Machine Learning” starting tomorrow — the first CECAM workshop in Wisconsin! @bettinagkeller.bsky.social @drgregbowman.bsky.social @cecamevents.bsky.social

www.cecam.org/workshop-det...

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Xuhui Huang @xuhuihuangchem.bsky.social · Jun 13

Congratulations to Mingyi on an outstanding PhD defense—our lab’s 19th PhD! Wishing you all the best as you begin your next chapter in the Bay Area biotech industry! @uwmadisonchem.bsky.social

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Xuhui Huang @xuhuihuangchem.bsky.social · Jun 10

MEMnets reliably identifies the slow CVs governing WW-domain folding and shows robust numerical stability in modeling the complex conformational changes of tRNA polymerase. These results highlight the power of integrating new analytical stat-mech theory with deep learning!

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Xuhui Huang @xuhuihuangchem.bsky.social · Jun 10

Capturing slow collective variables (CVs) is critical for understanding protein dynamics. When projecting high-dimensional dynamics onto reduced CVs, the memory effects will emerge. We analytically derives an upper bound of the time-integrated memory kernel of CVs using the IGME theory.

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Xuhui Huang @xuhuihuangchem.bsky.social · Jun 10

Excited to share our latest paper on @natcomputsci.nature.com‬! We present MEMnets, a deep learning framework for coarse-graining protein dynamics, driven by an analytical statistical mechanics theory to minimize memory kernels. Congratulations to all the authors! @uwmadisonchem.bsky.social

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Xuhui Huang @xuhuihuangchem.bsky.social · Jun 6

Congratulations to Jordan Boysen on winning the 2025 ACS Division of Physical Chemistry Undergraduate Award!

Jordan has been with our group since Jan 2023 and is an exceptionally talented student. Best wishes as he begins grad school at U. Chicago Chem.

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Xuhui Huang @xuhuihuangchem.bsky.social · Jun 6

Big congratulations to Bojun Lin from our group on winning the APL Computational Physics Best Poster Award at 55th Midwest Theoretical Chemistry Conference (MWTCC55)! Great job, Bojun! @uwmadisonchem.bsky.social @waynestatechem.bsky.social

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Xuhui Huang @xuhuihuangchem.bsky.social · May 31

Thank you and the other organizers for putting together this wonderful workshop!

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Xuhui Huang @xuhuihuangchem.bsky.social · May 23

Happy Birthday to Peter!

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Xuhui Huang @xuhuihuangchem.bsky.social · Apr 30

We observed that 8OG, initially in the anti-conformation, can partially backtrack, switch to the syn-conformation, and reload into the active site - leading to the mis-incorporation of ATP.

Xuhui Huang @xuhuihuangchem.bsky.social · Apr 30

Dong Wang @ucsdpharmacy.bsky.social and our group @uwmadscience.bsky.social used time-resolved X-ray and metadynamics simulations to uncover how 8-oxoguanine (8OG) flips conformation to help RNA Pol II bypass oxidative DNA damage. @jacs.acspublications.org

pubs.acs.org/doi/full/10....

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Xuhui Huang @xuhuihuangchem.bsky.social · Apr 26

The semester is wrapping up! I gave my final Chem361 lecture last Thur. Looking forward to next week's final project presentations - every student who passes will receive a custom 3D-printed keychain I designed as a souvenir for the inaugural ML in Chemistry class!

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Xuhui Huang @xuhuihuangchem.bsky.social · Apr 21

Excited to share that our AMUSET-TICA, a tensor-based approach for identifying CVs, is now published in JCTC’s MSM special issue (guest-edited by @drgregbowman.bsky.social, @cecclementi.bsky.social, and me)! Big congrats to all the authors!

pubs.acs.org/doi/full/10....

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Xuhui Huang @xuhuihuangchem.bsky.social · Apr 16

We developed an unsupervised ML model @pnas.org to relate structure of supercooled liquid to its long-term dynamics. It uncovers a a surprising role of medium- & long-range structure on long-time behavior. First collab with Arun, led by @yunruiqiu.bsky.social!
www.pnas.org/doi/10.1073/...

https://www.pnas.org/doi/10.1073/pnas.2427246122

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Xuhui Huang @xuhuihuangchem.bsky.social · Apr 16

Thanks for contributing to F@H! Our PP2A mutant simulations are ongoing, and it may still take some time for us to collect enough data for analysis.

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Xuhui Huang @xuhuihuangchem.bsky.social · Mar 26

Just one week left! Please consider submitting an abstract to our Pacifichem 2025 @pacifichem.bsky.social symposium on machine learning for biomolecular dynamics. Deadline: April 2!

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Xuhui Huang @xuhuihuangchem.bsky.social · Mar 26

It seems that I missed a great party:)

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Xuhui Huang @xuhuihuangchem.bsky.social · Mar 23

Hello San Diego! I’m giving two talks #ACSSpring2025: one this afternoon on transition states in protein conformational changes in enhanced sampling symposium @barakhirshberg.bsky.social and another tomorrow on memory kernels in the reaction coordinate symposium. Stop by if you're interested!

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