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Published and accepted papers are shown newest first with monotonically decreasing numbering, while the earliest paper remains number 1. * indicates equal contribution.
Published and Accepted Papers
- Meysam Mohammadi-Zerankeshi, Dylan J. Charland, Keira A. Donnelly, Geoffrey T. Nash, Jiale Shi, ..., Qiang Cui, Keith P. Johnston, Daniel A. Estabrook, Alexander E. Marras. Storage Buffer Composition Impacts Internal Structure, Freeze-Thaw Stability, and Transfection Efficiency of mRNA-Lipid Nanoparticles. ACS Nano Published online June 12, 2026. [Publisher]
- Jiale Shi, Zhongyi Wan, Renjie Zhu, Qiang Cui. Measuring Differences in Protein Allosteric Graphs Constructed via Molecular Dynamics Simulations. J. Chem. Theory Comput. Published online June 4, 2026. [Publisher] [Preprint] [PDF]
- Jiale Shi, Runzhong Wang, Nathan J. Rebello, Jiarui Lu, Debra J. Audus, Bradley D. Olsen. MacroSimGNN: Efficient and Accurate Calculation of Macromolecule Pairwise Similarity via Graph Neural Network. Macromolecules 2026, 59, 4, 1885-1900. [Publisher] [Preprint] [PDF] [Code]
- Joren Van Herck, ..., Jiale Shi, ..., Jonathan K. Whitmer, ..., Berend Smit. Assessment of Fine-Tuned Large Language Models for Real-World Chemistry and Material Science Applications. Chemical Science 2025, 16, 670-684. [Publisher]
- Qianxiang Ai, Fanwang Meng, Jiale Shi, Brenden Pelkie, Connor W. Coley. Extracting Structured Data from Organic Synthesis Procedures Using a Fine-Tuned Large Language Model. Digital Discovery 2024, 3, 1822-1831. [Publisher]
- Nathan J. Rebello, Akash Arora, Hidenobu Mochigase, Tzyy-Shyang Lin, Jiale Shi, Debra J. Audus, Eric S. Muckley, Bradley D. Olsen. BCDB: The Block Copolymer Phase Behavior Database. Journal of Chemical Information and Modeling 2024, 64, 16, 6464-6476. [Publisher]
- Jiale Shi, Dylan Walsh, Nathan J. Rebello, Weizhong Zou, Michael E. Deagen, Katharina A. Fransen, Xian Gao, Bradley D. Olsen, Debra J. Audus. Calculating Pairwise Similarity of Polymer Ensemble via Earth Mover's Distance. ACS Polymers Au. 2024, 4, 1, 66-76. [Publisher] [PDF] [Code]
- Kevin Maik Jablonka, ..., Jiale Shi, ... 14 Examples of How LLMs Can Transform Materials Science and Chemistry: A Reflection on a Large Language Model Hackathon. Digital Discovery 2023, 2, 1233-1250. [Publisher]
- Jiale Shi, Nathan J. Rebello, Dylan Walsh, Weizhong Zou, Michael Deagen, Bruno Salomao Leao, Debra J. Audus, Bradley D. Olsen. Quantifying Pairwise Similarity for Complex Polymers. Macromolecules. 2023, 56, 18, 7344-7357. [Publisher] [PDF] [Code]
- Jiale Shi, Fahed Albreiki, Yamil J. Colon, Samanvaya Srivastava, Jonathan K. Whitmer. Using Transfer Learning to Leverage Prior Knowledge in the Prediction of Adhesive Free Energies between Polymers and Surfaces. J. Chem. Theory Comput. 2023, 19, 14, 4631-4640. [Publisher] [PDF] [Code]
- Jiale Shi, Michael J. Quevillon, Pedro H. Amorim Valenca, Jonathan K. Whitmer. Predicting Adhesion Free Energies of Polymer-Surface Interactions with Machine Learning. ACS Appl. Mater. Interfaces 2022, 14, 32, 37161-37169. [Publisher] [PDF] [Code]
- Jiale Shi, Shanghui Huang, Francois Gygi, Jonathan K. Whitmer. Free-Energy Landscape and Isomerization Rates of Au4 Clusters at Finite Temperatures. J. Phys. Chem. A 2022, 126, 21, 3392-3400. [Publisher] [PDF] [Code]
- Jiale Shi*, Hythem Sidky*, Jonathan K. Whitmer. Automated determination of n-cyanobiphenyl and n-cyanobiphenyl binary mixtures elastic constants in the nematic phase from molecular simulation. Mol. Syst. Des. Eng. 2020, 5, 1131-1136. [Publisher] [PDF] [Code]
- Jiale Shi, Hythem Sidky, Jonathan K. Whitmer. Novel elastic response in twist-bend nematic models. Soft Matter 2019, 15(41), 8219-8226. [Publisher] [PDF]