主要用分子动力学模拟来研究跨膜转运蛋白催化ATP水解机理及转运机理，光解酶催化受损DNA修复的机理。

1 Zhou Y, Pu J. Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations. J. Chem. Theory Comput., 2014,10(8):3038-3054.

2 Zhou Y, Ojeda-May P, Pu J. H-loop histidine catalyzes ATP hydrolysis in the E. coli ABC-transporter HlyB. Phys. Chem. Chem. Phys., 2013,15(38):15811-15815.

3 Liu D, Zhou Y, Pu J, et al. Expanding the Horizon of the Thymine Isostere Biochemistry: Unique Cyclobutane Dimers Formed by Photoreaction between a Thymine and a Toluene Residue in the Dinucleotide Framework. Chem. Eur. J., 2012,18(25):7823-7833.