Education

University of Illinois Urbana-Champaign

• Ph.D. in Computational Biophysics (Aug 2024 – Present)
• Advisor: Dr. Emad Tajkhorshid

University of Macau

• M.Phil. in Computational Pharmaceutics (Aug 2021 – Jul 2023)
• Advisor: Dr. Defang Ouyang

Chengdu University of Traditional Chinese Medicine

• B.S. in Pharmaceutics (Sep 2017 – Jun 2021)

Research Interests

Molecular Dynamics Simulation

• Elucidating the lipid-mediated mechanisms and conformational dynamics of macromolecular transmembrane transport, with a focus on ABC transporters.
• Employing advanced MD simulations to model and optimize drug delivery systems, including cyclodextrins and lipid nanoparticles (LNPs).

AI-Assisted Structural Biology

• Developing diffusion-based neural networks to integrate Cryo-EM density maps for precise protein and ligand pose prediction.

Cover

Front Cover Article

Microstructural Insights into Solid Dispersions

Our study on the molecular mechanism of the amorphous solid dispersion was featured as the Front Cover of Molecular Pharmaceutics (2026). This work utilizes coarse-grained MD simulation to reveal the critical role in solid dispersion.

→ Read the Full Article

Software & AI Tools

CryoDiffDock

• CryoDiffDock: A diffusion-based generative model designed for cryo-EM-guided molecular docking.

FormulationMM

• FormulationMM: An automated platform for predictive drug formulation modeling.

Publications

First- / Co-first-author Publications

• Gao, H., Zhang, Y. (Co-first author), Jiang, H., He, C., Ke, Y., Li, H., & Ouyang, D. (2026). Microstructural Insights into Solid Dispersions: A Combined Small Angle Neutron Scattering and Molecular Dynamics Approach. Molecular Pharmaceutics, 23, 4, 2350-2361.
• Yang, S., Zhang, Y. (Co-first author), Shi, Y., et al. & Sheng, X. (2026). Covalently targeting HSP90 with a natural small-molecule costunolide to inhibit necroptosis and ulcerative colitis. International Immunopharmacology, 174, 116348.
• Zhang, Y., Lin, C., Zhao, Z., et al. (2025). FormulationMM: A universal computer-driven drug formulation platform. Journal of Controlled Release, 114373.
• Wang, N., Zhang, Y. (Co-first author), Wang, W., et al. (2023). How can machine learning and multiscale modeling benefit ocular drug development? Advanced Drug Delivery Reviews, 114772.
• Han, R., Ye, Z., Zhang, Y. (Co-first author), et al. (2023). Predicting liposome formulations by the integrated machine learning and molecular modeling approaches. Asian Journal of Pharmaceutical Sciences, 100811.
• Liu, L., Zhang, Y. (Co-first author), Wang, L., et al. (2023). Scutellarein alleviates chronic obstructive pulmonary disease through inhibition of ferroptosis by chelating iron and interacting with arachidonate 15-lipoxygenase. Phytotherapy Research, 20, 37.
• Cai, Y., Ji, X., Zhang, Y. (Co-first author), et al. (2022). Near-infrared fluorophores with absolute aggregation-caused quenching and negligible fluorescence re-illumination for in vivo bioimaging of nanocarriers. Aggregate, e277.

Selected Co-author Publications

• Tang, Q., Sinclair, M., Bisignano, P., Zhang, Y., Tajkhorshid, E., & Mchaourab, H. S. (2025). Drug-bound outward-facing conformation of a heterodimeric ABC exporter suggests a putative mechanism of drug translocation. Nature Communications, 16,10403.
• Hu, Y., Schwab, S., Qiu, K., Zhang, Y., Baer, K., Reichle, H., ... & Alvarez, B. H. (2025). DNA wrapping by a tetrameric bacterial histone. Nature Communications. 16, 11108.

• → View full record on Google Scholar

Gallery

❮ ❯