Publications

Preprints / In Review (“†” Equal contribution, “*” corresponding author, “_” advised student.)

• S.M. Elgengehi, D.P. Karothu*, W. He, R. Paul, S. Kirmizialtin*, and P. Naumov*. Accurate Prediction of Young’s Moduli of Organic Crystals. Submitted to Nature Communications, 2025.

Selected Publications (“†” Equal contribution, “*” corresponding author, “_” advised student.)

RNA Modifications and Photocontrol

1. J. Li†, J. Du†, W. He†, I. Adelakun, M. Zhong, S. Boyer, Y.Y. Zheng, Q. Lin, S. Kirmizialtin*, J. Sheng*, and T. Wang*. Designing reversible photoswitching azobenzene modified nucleotide for controlling biological function. Journal of the American Chemical Society, 2025, Accepted. ChemRxiv

RNA & DNA Biophysics and Computational Methods

2. W. He†, Y. Chen†, L. Pollack*, and S. Kirmizialtin*. The Structural Plasticity of Nucleic Acid Duplexes Revealed by WAXS and MD. Science Advances, 2021, 7, 17. Link
3. Y. Chen†, W. He†, L. Pollack*, and S. Kirmizialtin*. Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations. Cell Reports Physical Science, 2022, 3, 100971. Cover article Link Media
4. T. Wang†, W. He†, S.A. Pabit, L. Pollack*, and S. Kirmizialtin*. Sequence-dependent conformational preferences of disordered single-stranded RNA. Cell Reports Physical Science, 2024, 5, 102264. Link
5. W. He†, A. Henning-Knechtel†, and S. Kirmizialtin*. Visualizing RNA Structures by SAXS-driven MD Simulations. Frontiers in Bioinformatics, 2022, 2. Link

SARS-CoV-2 RNA in COVID-19

6. W. He†, J.S. Emeterio†, M. Woodside, S. Kirmizialtin*, and L. Pollack*. Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics. Nucleic Acids Research, 2023, 51, 11332. Link Media

RNA Force Field Optimization and Development Methods

7. W. He, N. Naleem, D. Kleiman, and S. Kirmizialtin*. Refining RNA force field with Small-Angle X-ray Scattering of Helix-Junction-Helix RNA. Journal of Physical Chemistry Letters, 2022, 13, 3400. Link Code

DNA Assembly and Disassembly

8. W. He, and S. Kirmizialtin*. Mechanism of Cationic Lipid-Induced DNA Condensation: Lipid-DNA coordination and divalent cation charge fluctuations. ACS Biomacromolecules, 2024, 25, 4819. Link
9. W. He, X. Qiu*, and S. Kirmizialtin*. Sequence-dependent orientational coupling and electrostatic attraction in cation-mediated DNA-DNA interactions. Journal of Chemical Theory and Computation, 2023, 19, 6827. Cover article Link

Early Work and Book Chapters

10. W. He, and S. Kirmizialtin*. Exploring Cation Mediated DNA Interactions Using Computer Simulations. International Conference on Bio and Nanomaterials, Springer, Cham, 2020. Link
11. J. Lin, F. Wang, X. Dong, W. He, Y. Yuan, S. Chen, and X. Liu*. Catalytic Asymmetric Radical Aminoperfluoroalkylation and Aminodifluoromethylation of Alkenes with Fluoroalkylsulfonyl Chlorides. Nature Communications, 2017, 8, 14841. Link
12. M. Wu, W. He, X. Liu*, and B. Tan*. Asymmetric Construction of Spirooxindoles via Organocatalytic Multicomponent Reactions of Diazooxindoles. Angewandte Chemie International Edition, 2015, 54, 9409. Link