Office:Rm. C318, College of Chemistry and Molecular Engineering
Mailing Address:College of Chemistry and Molecular Engineering, Peking University, Yiheyuan Rd., No. 5, Haidian District, Beijing, 100871

Lab Web:

Yiqin Gao
Cheung Kong Professor (PI)

2019-Present, Beijing Advanced Innovation Center for Genomics, Principal Investigator

2013-Present, BIOPIC, Peking University, Principal Investigator

2010-Present, College of Chemistry and Molecular Engineering, Peking UniversityCheung Kong Professor

2005-2010, Department of Chemistry, Texas A&M UniversityAssistant Professor

2002-2004, Harvard University, Postdoctoral Research Fellow

2001-2002, California Institute of Technology, Postdoctoral Research Fellow

2001Ph.D in Chemistry, California Institute of Technology

1996M.S. in Chemistry, Institute of Chemistry, Chinese Academy of Science

1993B.S. in Chemistry, Sichuan University, China

Research Interests

Gao and his lab focus on systematic basic theory research. We develop efficient computational methods and statistical mechanics tools to study the biological molecule conformations in aqueous solutions, enzymatic reaction mechanisms, and the solvation effects in chemical reactions. We are also interested in understanding the chromosome folding principle and gene expression regulatory mechanism. The lab is working on the simulation/theoretical studies of the following systems: (1) the solvation effects in chemical reactions. By establishing theoretical models, developing enhanced sampling methods combined with machine learning techniques, we conduct comprehensive thermodynamic and dynamic analyses of chemical reactions, and focus on the roles of solution environment in chemical reactions from the microscopic scale. (2) Based on high-throughput sequencing and high-precision imaging data, we conduct computational biology analyses to understand biological processes from a perspective of physical chemistry. By modeling 3D chromatin structure and integrating multi-omic data, including genome, transcriptome, and epigenome, we aim to understand multi-scale chromatin assembly mechanism and structure-based epigenetic and transcriptional regulation in essential biological processes, including development, differentiation, aging, and pathology, and provide novel perspectives for scientific and medical researches.

Awards and Honors

2016 Pople Medal, Asia-Pacific Association of Theoretical and Computational Chemists

2014 Promising Scientist Prize of CMOA

2014 Distinguished Lectureship Award, The Chemical Society of Japan

2012 Innovation Research Team, Ministry of Education

2011 NSFC Outstanding Young Investigator Award

2008 Cheung Kong Professor

2006 Searle Scholar

2004 Camille and Henry Dreyfus New Faculty Award

2001 Milton and Francis Clauser Prize for the Best Doctoral Thesis, Caltech

2001 Herbert Newby McCoy Award

Selected Publication
  1. Manas Mondal, Lijiang Yang, Zhicheng Cai, Piya Patra, Yi Qin Gao*,A Perspective on the Molecular Simulation of DNA from Structural and Functional Aspects,Chem.sci, 2021, 12: 5390-5409.
  2. Quan, H.; Yang, Y.; Liu, S. R.; Tian, H.; Xue, Y.; Gao, Y. Q., Chromatin structure changes during various processes from a DNA sequence view. Current Opinion in Structural Biology 2020, 62, 1-8.
  3.  Wang, J. P.; Gao, H.; Yang, L. J.; Gao, Y. Q., Role of Engineered Iron-haem Enzyme in Reactivity and Stereoselectivity of Intermolecular Benzylic C-H Bond Amination. Acs Catal 2020, 10 (9), 5318-5327.
  4. Zhang, J.; Lei, Y. K.; Yang, Y. I.; Gao, Y. Q., Deep learning for variational multiscale molecular modeling. J Chem Phys 2020, 153 (17).
  5. Zhou, R.; Gao, Y. Q., Polymer models for the mechanisms of chromatin 3D folding: review and perspective. Phys Chem Chem Phys 2020, 22 (36), 20189-20201.
  6. Lei, Y. K.; Zhang, J.; Zhang, Z.; Gao, Y. Q., Dynamic Electric Field Complicates Chemical Reactions in Solutions. Journal of Physical Chemistry Letters 2019, 10 (11), 2991-2997.
  7. Mondal, M.; Bhattacharyya, D.; Gao, Y. Q., Structural properties and influence of solvent on the stability of telomeric four-stranded i-motif DNA. Phys Chem Chem Phys 2019, 21 (38), 21549-21560.
  8. Qiao, Z. R.; Zhao, Y. H.; Gao, Y. Q., Ice Nucleation of Confined Monolayer Water Conforms to Classical Nucleation Theory. Journal of Physical Chemistry Letters 2019, 10 (11), 3115-3121.
  9. Zeng, H.; Mondal, M.; Song, R. Y.; Zhang, J.; Xia, B.; Liu, M. H.; Zhu, C. X.; He, B.; Gao, Y. Q.; Yi, C. Q., Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry. Angew Chem Int Edit 2019, 58 (1), 130-133.
  10. Zhang, J.; Lei, Y. K.; Che, X.; Zhang, Z.; Yang, Y. I.; Gao, Y. Q., Deep Representation Learning for Complex Free-Energy Landscapes. Journal of Physical Chemistry Letters 2019, 10 (18), 5571-5576.
  11. Ding, B.; Yang, L. J.; Mukherjee, D.; Chen, J. X.; Gao, Y. Q.; Gai, F., Microscopic Insight into the Protein Denaturation Action of Urea and Its Methyl Derivatives. Journal of Physical Chemistry Letters 2018, 9 (11), 2933-2940.
  12. Liu, S.; Zhang, L.; Quan, H.; Tian, H.; Meng, L.; Yang, L.; Feng, H.; Gao, Y. Q., From 1D sequence to 3D chromatin dynamics and cellular functions: a phase separation perspective. Nucleic Acids Res 2018, 46 (18), 9367-9383.
  13. Mondal, M.; Yang, Y.; Yang, L.; Yang, W.; Gao, Y. Q., Role of Conformational Fluctuations of Protein toward Methylation in DNA by Cytosine-5-methyltransferase. J Chem Theory Comput 2018.
  14. Peng, J. B.; Cao, D. Y.; He, Z. L.; Guo, J.; Hapala, P.; Ma, R. Z.; Cheng, B. W.; Chen, J.; Xie, W. J.; Li, X. Z.; Jelinek, P.; Xu, L. M.; Gao, Y. Q.; Wang, E. G.; Jiang, Y., The effect of hydration number on the interfacial transport of sodium ions. Nature 2018, 557 (7707), 701-705.
  15. Che, X.; Zhang, J.; Quan, H.; Yang, L. J.; Gao, Y. Q., CDNs-STING Interaction Mechanism Investigations and Instructions on Design of CDN-Derivatives. J Phys Chem B 2018, 122 (6), 1862-1868.
  16. Che, X.; Du, X. X.; Cai, X. X.; Zhang, J.; Xie, W. J.; Long, Z. R.; Ye, Z. Y.; Zhang, H.; Yang, L. J.; Su, X. D.; Gao, Y. Q., Single Mutations Reshape the Structural Correlation Network of the DMXAA-Human STING Complex. J Phys Chem B 2017, 121 (9), 2073-2082.
  17. Xie, W. J.; Meng, L.; Liu, S.; Zhang, L.; Cai, X.; Gao, Y. Q., Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle. Sci Rep 2017, 7 (1), 2818.
  18. Zhang, J.; Zhang, Z.; Yang, Y. I.; Liu, S. R.; Yang, L. J.; Gao, Y. Q., Rich Dynamics Underlying Solution Reactions Revealed by Sampling and Data Mining of Reactive Trajectories. Acs Central Sci 2017, 3 (5), 407-414.
  19. Zhang, L.; Gu, C.; Yang, L. J.; Tang, F. C.; Gao, Y. Q., The sequence preference of DNA methylation variation in mammalians. Plos One 2017, 12 (10).
  20. Zhang, L.; Xie, W. J.; Liu, S. R.; Meng, L. M.; Gu, C.; Gao, Y. Q., DNA Methylation Landscape Reflects the Spatial Organization of Chromatin in Different Cells. Biophysical Journal 2017, 113 (7), 1395-1404.
  21. Zhang, Q.; Chen, H. L.; Wu, T. M.; Jin, T.; Pan, Z. J.; Zheng, J. R.; Gao, Y. Q.; Zhuang, W., The opposite effects of sodium and potassium cations on water dynamics. Chem Sci 2017, 8 (2), 1429-1435.
  22. Che, X.; Zhang, J.; Zhu, Y. Y.; Yang, L. J.; Quan, H.; Gao, Y. Q., Structural Flexibility and Conformation Features of Cyclic Dinucleotides in Aqueous Solutions. J Phys Chem B 2016, 120 (10), 2670-2680.
  23. He, Z. Y.; Xie, W. J.; Liu, Z. Q.; Liu, G. M.; Wang, Z. W.; Gao, Y. Q.; Wang, J. J., Tuning ice nucleation with counterions on polyelectrolyte brush surfaces. Science Advances 2016, 2 (6), e1600345-7.
  24.  Jin, J. S.; Lian, T. F.; Gu, C.; Yu, K.; Gao, Y. Q.; Su, X. D., The effects of cytosine methylation on general transcription factors. Sci Rep-Uk 2016, 6, 29119.
  25. Zhu, C. X.; Lu, L. M.; Zhang, J.; Yue, Z. W.; Song, J. H.; Zong, S.; Liu, M. H.; Stovicek, O.; Gao, Y. Q.; Yi, C. Q., Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair. P Natl Acad Sci USA 2016, 113 (28), 7792-7797.
  26. Wang, P.; Yang, L.; Gao, Y. Q.; Zhao, X. S., Accurate placement of substrate RNA by Gar1 in H/ACA RNA-guided pseudouridylation. Nucleic Acids Res 2015, 43 (15), 7207-7216.
  27. Yang, L.; Liu, C.-W.; Shao, Q.; Zhang, J.; Gao, Y. Q., From Thermodynamics to Kinetics: Enhanced Sampling of Rare Events. Accounts Chem Res 2015, 48 (4), 947-955.
  28. Xie, W.; Liu, C.; Yang, L.; Gao, Y., On the molecular mechanism of ion specific Hofmeister series. Science China-Chemistry 2014, 57 (1), 36-47.
  29. Yin, Y.; Yang, L.; Zheng, G.; Gu, C.; Yi, C.; He, C.; Gao, Y. Q.; Zhao, X. S., Dynamics of spontaneous flipping of a mismatched base in DNA duplex. P Natl Acad Sci USA 2014, 111 (22), 8043-8048.
  30. Xie, W. J.; Gao, Y. Q., A Simple Theory for the Hofmeister Series. Journal of Physical Chemistry Letters 2013, 4 (24), 4247-4252.
  31. Kim, S.; Brostroemer, E.; Xing, D.; Jin, J.; Chong, S.; Ge, H.; Wang, S.; Gu, C.; Yang, L.; Gao, Y. Q.; Su, X.-d.; Sun, Y.; Xie, X. S., Probing Allostery Through DNA. Science 2013, 339 (6121), 816-819.
  32. Li, R.-Z.; Liu, C.-W.; Gao, Y. Q.; Jiang, H.; Xu, H.-G.; Zheng, W.-J., Microsolvation of LiI and CsI in Water: Anion Photoelectron Spectroscopy and ab initio Calculations. Journal of the American Chemical Society 2013, 135 (13), 5190-5199.
  33. Yang, L.; Gao, Y. Q., Effects of Cosolvents on the Hydration of Carbon Nanotubes. Journal of the American Chemical Society 2010, 132 (2), 842-848.
  34. Lund, L.; Fan, Y.; Shao, Q.; Gao, Y. Q.; Raushel, F. M., Carbamate Transport in Carbamoyl Phosphate Synthetase: A Theoretical and Experimental Investigation. Journal of the American Chemical Society 2010, 132 (11), 3870-3878.
  35. Fan, Y.; Lund, L.; Shao, Q.; Gao, Y.-Q.; Raushel, F. M., A Combined Theoretical and Experimental Study of the Ammonia Tunnel in Carbamoyl Phosphate Synthetase. Journal of the American Chemical Society 2009, 131 (29), 10211-10219.
  36. Gao, Y. Q.; Yang, L.; Fan, Y.; Shao, Q., Thermodynamics and kinetics simulations of multi-time-scale processes for complex systems. International Reviews in Physical Chemistry 2008, 27 (2), 201-227.
  37. Fan, Y.; Gao, Y. Q., A DFT study on the mechanism of phosphodiester cleavage mediated by monozinc complexes. Journal of the American Chemical Society 2007, 129 (4), 905-913.
  38. Shao, Q.; Gao, Y. Q., On the hand-over-hand mechanism of kinesin. P Natl Acad Sci USA 2006, 103 (21), 8072-8077.
  39. Gao, Y. Q.; Yang, W.; Karplus, M., A structure-based model for the synthesis and hydrolysis of ATP by F-1-ATPase. Cell 2005, 123 (2), 195-205.
  40. Gao, Y. Q.; Yang, W.; Marcus, R. A.; Karplus, M., A model for the cooperative free energy transduction and kinetics of ATP hydrolysis by F-1-ATPase. P Natl Acad Sci USA 2003, 100 (20), 11339-11344.
  41. Gao, Y. Q.; Marcus, R. A., Strange and unconventional isotope effects in ozone formation. Science 2001, 293 (5528), 259-263.