June 2025
Congratulations to Bojun, Siqin, Jordan, and Mingyi on publishing MEMnets in Nature Computational Science! MEMnets is a deep learning framework for coarse-graining protein dynamics, driven by a new statistical mechanics theory to minimize memory kernels. …
May 2025
Congratulations to Jordan Boysen on winning the 2025 ACS Division of Physical Chemistry Undergraduate Award!
May 2025
Congratulations to Bojun Liu from our group on winning the APL Computational Physics Best Poster Award at the 55th Midwest Theoretical Chemistry Conference (MWTCC55)!
April 2025
Our group has been awarded a new NSF grant from Division of Chemistry to develop a polarizable 3DRISM implicit solvent model for AMOEBA solutes to enable efficient and accurate RNA simulations!
Jan 2025
Congratulations to Bojun, Jordan, and Ilona on publishing the TS-DAR method in Nature Communications! Many thanks as well to our collaborators, Prof. Sharon Li and Xuefeng. The TS-DAR method simultaneously identifies transition states across multiple …
Nov 2024
We’re excited to welcome 3 new graduate students: Chengwei Dong (Chemistry, B.S. from Peking U.), Peter Swanson (Chemistry, B.S. from UNE, jointly supervised with Arun Yethiraj), and Andres Lira (Biophysics, B.S. from UC Davis, jointly …
June 2024
Our lab (PI) receive a Research Forward award for funding our development of a chemical feature-based Transformer platform to predict molecular glues! Excited to collaborate with Prof. Sharon Li (UW-Madison, CS) and Weiping Tang (UW-Madison, Pharmacy)!
March 2024
Our tutorial on building non-Markovian models (qMSMs, IGME) from MD simulations for protein dynamics was published as a featured and cover article at JCP. Please try it out on GitHub: https://github.com/xuhuihuang/GME_tutorials!
Feb 2024
Our 2nd collaborative NIH R01 grant with Prof. Jiaoyang Jiang (PI, UW-Madison Pharmacy) and Prof. Lingjun Li (co-I) was funded. We’ll study the enzyme removing O-GlcNAc post-translational modifications.
Dec 2023
We welcome three new group members: Yichong Lao (1st year graduate student from Biophysics Program), Longbang Liu (1st year graduate student from Chemistry), and Kazuya Okita (a visiting student from Osaka University, Japan)!
Oct 2023
Our IGME paper is selected as a Featured Article by JCP! It efficiently models biomolecular dynamics by employing time integrations of memory kernels and avoiding numerical instability in time-dependent memory kernels.
Sept 2023
Our GraphVAMPnets provides an efficient way to find CVs for self-assembly. Graph embeddings ensure structures invariant to permutations and rotations, and the VAMP theory (no detailed-balance requirement) handles insufficient sampling of dissociation transitions. This article …
Sept 2023
Our Latent space Path Clustering (LPC) method can efficiently group parallel kinetic pathways into distinct metastable path channels. It utilizes the variational autoencoder (VAE) to learn the spatial distributions of kinetic pathways and perform path …
Sept 2023
Our collaborative research with Prof. Jiaoyang Jiang and Prof. Lingjun Li in School of Pharmacy at UW-Madison has been funded by a new $1.65 million NIH R01 grant (PI: Jiang)! Congratulations! We look forward to …
Sept 2023
Our collaborative research with Prof. Yongna Xing in the Oncology Department at UW-Madison has been funded by a new $1.45 million NIH R01 grant (PI: Xing)! Congratulations! We look forward to exciting collaborations on allostery …
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