Yunrui Qiu
Assistant Professor
- Office
- 372 Nieuwland Science Hall
Notre Dame, IN 46556 - yqiu8@nd.edu
Research Areas
- Biochemistry
- Physical/Analytical Chemistry
Research Specialties
- Life Processes
- Theory
Prospective Graduate Students
Biography
| Year | Title |
|---|---|
| Fall 2026 | Assistant Professor, University of Notre Dame |
| 2024-2026 | IPST Postdoctoral Fellow, University of Maryland - College Park |
| 2024 | Ph.D. in Theoretical Chemistry, University of Wisconsin - Madison |
| 2020 | Honors B.S. in Chemical Physics, University of Science and Technology of China |
Selected Awards
2026 Wiley Computers in Chemistry Outstanding Postdoc Award
2025 Hirschfelder Prize Graduate Fellowship
2020 Hong Kong PhD Fellowship
2020 Outstanding USTC Graduate Scholarship
2020 Chinese National Scholarship
Research Interests
The Qiu research group works at the interface of computational biophysics, statistical mechanics, and artificial intelligence to understand the structural dynamics of complex biomolecular systems. Our research integrates physical theory, molecular simulations, and machine learning to investigate how biomolecules fluctuate, interact, and function across multiple spatial and temporal scales. By combining these different approaches, we aim to develop predictive and interpretable computational frameworks that accelerate the design of new therapeutics.
Our research focuses on the development of AI-enhanced molecular dynamics sampling strategies and dynamical modeling approaches. These tools are designed to efficiently generate reliable structural ensembles and predict long-timescale transitions in highly heterogeneous systems. In parallel, we are interested in how physical principles can help improve the interpretability and generalizability of modern AI models. A major application area of the group is the study of RNA structural dynamics and RNA-mediated biological processes. By combining generative AI, large language models, enhanced sampling, and experimental constraints, we aim to build predictive frameworks for RNA structural ensemble prediction, RNA-protein and RNA-ligand interaction modeling, and RNA drug discovery.
Selected Publications
- Qiu, Y. R.; John, R.; Herron, L. and Tiwary, P. "Latent Thermodynamic Flows: Unified Representation Learning and Generative Modeling of Temperature-Dependent Behaviors from Limited Data" 2026 Chemical Science, 17 (7), pp.3743–3757. DOI: 10.1039/d5sc06402c.
- Qiu, Y. R.; Liu, S. M.; Lin, X. C.; Unarta, I. C.; Huang, X. H. and Zhang, B. "Nucleosome Condensate and Linker DNA Alter Chromatin Folding Pathways and Rates" 2026 Biophysical Journal, 125 (1), pp.282–293. DOI: 10.1016/j.bpj.2025.11.2686.
- Qiu, Y. R.; Jang, I.; Huang, X. H. and Yethiraj, A. "Unsupervised Learning of Structural Relaxation in Supercooled Liquids from Short-Term Fluctuations" 2025 Proceedings of the National Academy of Sciences of the United States of America, 122 (15), e2427246122. DOI: 10.1073/pnas.2427246122.
- Qiu, Y. R.; Wiewiora, R. P.; Izaguirre, J. A.; Xu, H. F.; Sherman, W.; Tang, W. P. and Huang, X. H. "Non-Markovian Dynamic Models Identify Non-Canonical KRAS-VHL Encounter Complex Conformations for Novel PROTAC Design" 2024 JACS Au, 4 (10), pp.3857–3868. DOI: 10.1021/jacsau.4c00503.
- Wang, D. D.; Qiu, Y. R.; Beyerle, E. R.; Huang, X. H. and Tiwary, P. "Information Bottleneck Approach for Markov Model Construction" 2024 Journal of Chemical Theory and Computation, 20 (12), pp.5352–5367. DOI: 10.1021/acs.jctc.4c00449.
- Qiu, Y. R.; O'Connor, M. S.; Xue, M.; Liu, B. and Huang, X. "An Efficient Path Classification Algorithm Based on Variational Autoencoder to Identify Metastable Path Channels for Complex Conformational Changes" 2023 Journal of Chemical Theory and Computation, 19 (14), pp.4728-4742. DOI: 10.1021/acs.jctc.3c00318.