北京大学分子模拟课题组

代表性论文

1. Zhirong Liu*. Accelerating kinetics with time-reversal path sampling. Molecules 28 (24), 8147/1-12 (2023).
2. Xiaohui Wang, Bin Chong, Zhaoxi Sun, Hao Ruan, Yingguang Yang, Pengbo Song, and Zhirong Liu*. More is simpler: decomposition of ligand-binding affinity for proteins being disordered. Protein Sci. 31, e4375 (2022).
3. Bin Chong, Yingguang Yang, Zi-Le Wang, Han Xing, and Zhirong Liu*. Reinforcement learning to boost molecular docking upon protein conformational ensemble. Phys. Chem. Chem. Phys. 23, 6800 (2021).
4. Qiaojing Huang, Maodong Li, Luhua Lai*, and Zhirong Liu*. Allostery of multidomain proteins with disordered linkers. Curr. Opin. Struct. Biol. 62, 175 (2020).
5. Miao Yu, Yixin Chen, Zi-Le Wang, and Zhirong Liu*. Fluctuation correlations as major determinants of structure- and dynamics-driven allosteric effects. Phys. Chem. Chem. Phys. 21, 5200 (2019).
6. Zi-Le Wang, Zhi-Feng Huang*, and Zhirong Liu*. Elastic constants of stressed and unstressed materials in the phase field crystal model. Phys. Rev. B 97, 144112 (2018).
7. Ting Cheng, Haifeng Lang, Zhenzhu Li, Zhongfan Liu, and Zhirong Liu*. Anisotropic carrier mobility in two-dimensional materials with tilted Dirac cones: theory and application. Phys. Chem. Chem. Phys. 19, 23942 (2017).
8. Maodong Li and Zhirong Liu*. Dimensions, energetics and denaturant effects of protein unstructured state. Protein Sci. 25, 734 (2016).
9. Jinying Wang, Shibin Deng, Zhongfan Liu, and Zhirong Liu*. The rare two-dimensional materials with Dirac cones. Natl. Sci. Rev. 2 (1), 22-39 (2015).
10. Zhenzhu Li, Jinying Wang, and Zhirong Liu*. Intrinsic carrier mobility of Dirac cones: the limitations of deformation potential theory. J. Chem. Phys. 141 (14), 144107/1-9 (2014).
11. Fan Jin, Chen Yu, Luhua Lai*, and Zhirong Liu*. Ligand clouds around protein clouds: a scenario of ligand binding with intrinsically disordered proteins. PLoS Comput. Biol. 9 (10), e1003249/1-11 (2013).
12. Mingmei Yang, Lin Zhou, Jinying Wang, Zhongfan Liu*, and Zhirong Liu*. Evolutionary chlorination of graphene: from charge-transfer complex to covalent bonding and non-bonding. J. Phys. Chem. C 116 (1), 844-850 (2012).
13. Fangping Ouyang, Shenglin Peng, Zhongfan Liu*, and Zhirong Liu*. Bandgap opening in graphene antidot lattices: the missing half. ACS Nano 5 (5), 4023-4030 (2011).
14. Zhirong Liu, Lynn Zechiedrich, and Hue Sun Chan. Local site preference rationalizes disentangling by DNA topoisomerases. Phys. Rev. E. 81 (3), 031902/1-4 (2010).
15. Yongqi Huang and Zhirong Liu*. Kinetic advantage of intrinsically disordered proteins in coupled folding-binding process: a critical assessment of the "fly-casting" mechanism. J. Mol. Biol. 393 (5), 1143-1159 (2009).