Xuhui Huang
@xuhuihuangchem.bsky.social
Hirschfelder Chair, Professor of Chemistry, University of Wisconsin-Madison, Director, Theoretical Chemistry Institute, Theoretical chemistry and Biophysics, previously at HKUST, https://huang.chem.wisc.edu/
I received many requests to share materials from our undergraduate course “Machine Learning in Chemistry”
— here you go!
A preprint summarizing insights and lessons learned:
chemrxiv.org/engage/chemr...
A Jupyter Notebook Tutorial Gallery:
xuhuihuang.github.io/mlchem/html/...
— here you go!
A preprint summarizing insights and lessons learned:
chemrxiv.org/engage/chemr...
A Jupyter Notebook Tutorial Gallery:
xuhuihuang.github.io/mlchem/html/...
October 16, 2025 at 1:27 AM
I received many requests to share materials from our undergraduate course “Machine Learning in Chemistry”
— here you go!
A preprint summarizing insights and lessons learned:
chemrxiv.org/engage/chemr...
A Jupyter Notebook Tutorial Gallery:
xuhuihuang.github.io/mlchem/html/...
— here you go!
A preprint summarizing insights and lessons learned:
chemrxiv.org/engage/chemr...
A Jupyter Notebook Tutorial Gallery:
xuhuihuang.github.io/mlchem/html/...
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!
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!
August 25, 2025 at 10:53 PM
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!
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!
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!
July 19, 2025 at 5:05 PM
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!
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...
www.cecam.org/workshop-det...
July 14, 2025 at 4:11 AM
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...
www.cecam.org/workshop-det...
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
June 13, 2025 at 10:44 PM
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
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!
June 10, 2025 at 8:42 PM
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!
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
June 10, 2025 at 8:42 PM
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
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.
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.
June 6, 2025 at 4:53 AM
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.
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.
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
June 6, 2025 at 3:50 AM
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
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.
April 30, 2025 at 7:24 PM
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.
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....
pubs.acs.org/doi/full/10....
April 30, 2025 at 7:24 PM
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....
pubs.acs.org/doi/full/10....
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!
April 26, 2025 at 11:18 PM
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!
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/...
www.pnas.org/doi/10.1073/...
April 16, 2025 at 7:37 PM
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/...
www.pnas.org/doi/10.1073/...
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!
March 26, 2025 at 5:48 PM
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!
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!
March 23, 2025 at 5:34 PM
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!
A much-needed escape from a hectic semester—insightful scientific discussions, inspiration, and fun! Mesilla is a hidden gem in New Mexico. Thanks to the organizers Rui Sun & Greg Voth!
March 13, 2025 at 9:05 PM
A much-needed escape from a hectic semester—insightful scientific discussions, inspiration, and fun! Mesilla is a hidden gem in New Mexico. Thanks to the organizers Rui Sun & Greg Voth!
Tomorrow marks the first day of the Year of the Snake! Happy Lunar New Year! Wishing everyone endless good fortune - we’re going to need it!
January 29, 2025 at 5:51 AM
Tomorrow marks the first day of the Year of the Snake! Happy Lunar New Year! Wishing everyone endless good fortune - we’re going to need it!
My focus for Spring 2025: launching an undergraduate course developed from scratch - "Chem361: Machine Learning in Chemistry"! @UW-Madison Chemistry
Here's a glimpse of what we'll explore:
Here's a glimpse of what we'll explore:
January 11, 2025 at 10:31 PM
My focus for Spring 2025: launching an undergraduate course developed from scratch - "Chem361: Machine Learning in Chemistry"! @UW-Madison Chemistry
Here's a glimpse of what we'll explore:
Here's a glimpse of what we'll explore:
The @cecamevents.bsky.social Flagship Workshop is coming to Madison! Hosted at @datascience_uw(thanks!), organized by @drgregbowman.bsky.social, @bettinagkeller.bsky.social, and me (CECAM-US-CENTRAL).
We have slots for contributed talks - apply here (deadline: June 11): www.cecam.org/workshop-det...
We have slots for contributed talks - apply here (deadline: June 11): www.cecam.org/workshop-det...
January 4, 2025 at 7:00 PM
The @cecamevents.bsky.social Flagship Workshop is coming to Madison! Hosted at @datascience_uw(thanks!), organized by @drgregbowman.bsky.social, @bettinagkeller.bsky.social, and me (CECAM-US-CENTRAL).
We have slots for contributed talks - apply here (deadline: June 11): www.cecam.org/workshop-det...
We have slots for contributed talks - apply here (deadline: June 11): www.cecam.org/workshop-det...
Inspired by Trustworthy AI, TS-DAR detects transition states as Out-of-Distribution data in the hyperspherical latent space!
January 3, 2025 at 10:13 PM
Inspired by Trustworthy AI, TS-DAR detects transition states as Out-of-Distribution data in the hyperspherical latent space!
Exciting news! Our TS-DAR method is now published in @naturecomms.bsky.social! 🎉
TS-DAR identifies transition states across multiple free energy barriers in biomolecular dynamics—all at once!
Paper: www.nature.com/articles/s41...
Code: github.com/xuhuihuang/t...
TS-DAR identifies transition states across multiple free energy barriers in biomolecular dynamics—all at once!
Paper: www.nature.com/articles/s41...
Code: github.com/xuhuihuang/t...
January 3, 2025 at 10:13 PM
Exciting news! Our TS-DAR method is now published in @naturecomms.bsky.social! 🎉
TS-DAR identifies transition states across multiple free energy barriers in biomolecular dynamics—all at once!
Paper: www.nature.com/articles/s41...
Code: github.com/xuhuihuang/t...
TS-DAR identifies transition states across multiple free energy barriers in biomolecular dynamics—all at once!
Paper: www.nature.com/articles/s41...
Code: github.com/xuhuihuang/t...
Happy holidays! Best wishes for 2025!
December 25, 2024 at 1:00 AM
Happy holidays! Best wishes for 2025!
Yijing was my faculty mentor at HKUST - a brilliant mind in open system quantum dynamics and one of the most rigorous theoretical chemists I’ve ever met! Grateful to J Chem Phys @aip.bsky.social for this special issue in his honor - proud to be a guest editor. Please consider submitting your work!
December 12, 2024 at 3:31 AM
Yijing was my faculty mentor at HKUST - a brilliant mind in open system quantum dynamics and one of the most rigorous theoretical chemists I’ve ever met! Grateful to J Chem Phys @aip.bsky.social for this special issue in his honor - proud to be a guest editor. Please consider submitting your work!
Benoît Roux gave two fantastic lectures this week as part of our department's John Ferry Lectureship series in Macromolecular Science. I thoroughly enjoyed the exciting discussions on many topics in Stat Mech!
December 5, 2024 at 4:58 AM
Benoît Roux gave two fantastic lectures this week as part of our department's John Ferry Lectureship series in Macromolecular Science. I thoroughly enjoyed the exciting discussions on many topics in Stat Mech!
First-year grad students at UW-Madison Chemistry Dept have just completed their group selection process. We’re excited to welcome Chengwei Dong (B.S. from Peking U.) and Peter Swanson (B.S. from UNE, jointly supervised with Arun Yethiraj) to our group! Thrilled to have you both on board!
November 28, 2024 at 3:36 AM
First-year grad students at UW-Madison Chemistry Dept have just completed their group selection process. We’re excited to welcome Chengwei Dong (B.S. from Peking U.) and Peter Swanson (B.S. from UNE, jointly supervised with Arun Yethiraj) to our group! Thrilled to have you both on board!