个人简介
Honors and Awards
2016 Pople Medal (Asia-Pacific Association of Theoretical & Computational Chemists)
2015 Young scientific and technological innovation leader (Ministry of Science and Technology of China)
2014 Promising Scientist Prize of CMOA
2014 Keynote lecture Award, Chemical Society of Japan
2012 Leader of Innovative Research Team in University (Ministry of Education of China)
2011 NSFC Outstanding Young Investigator Award
2008 Cheung Kong Professor (Ministry of Education of China)
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
Employment
2001-2002 Postdoctoral Research Fellow, California Institute of Technology
2002-2004 Postdoctoral Research Fellow, Harvard University
2005-2010 Assistant Professor, Department of Chemistry, Texas A&M University
2010-present Cheung Kong Professor, College of Chemistry and Molecular Engineering, Peking University
2013-present Principal Investigator, BIOPIC, Peking University
2015-2019 Dean, College of Chemistry and Molecular Engineering, Peking University
2019-present Principal Investigator, Shenzhen Bay Laboratory
研究领域
Our lab is doing research in the fields of theoretical/computational chemistry and biophysical chemistry. We are developing efficient computational methods and statistical mechanics tools to study the conformations of biological molecules in aqueous solutions, mechanisms of enzymatic reactions, and the solvation effects in chemical reactions. We are also interested in understanding the chromosome folding principle and gene expression regulatory mechansim. The lab is working on the simulation/theoretical studies of the following systems: (1) thermodynamics, dynamics and kinetics of electrolytes solutions (2) dynamics and spectra calculations for aqueous solutions (3) chemical/enzymatic reactions in solutions/at interfaces (4) the modeling of chromatin spatial structures and studying the relations between structures and important genome features (5) multiscale gene regulation mechansim in cell.
近期论文
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Zhang Z, Xie WJ, Yang YI, Sun G, & Gao YQ (2017) Simulation Studies of the Self-Assembly of Halogen-Bonded Sierpinski Triangle Fractals. Acta Phys-Chim Sin 33(3):539.
Zhang Q, et al. (2017) The opposite effects of sodium and potassium cations on water dynamics. Chem Sci 8(2):1429-1435.
Zhang L, et al. (2017) DNA Methylation Landscape Reflects the Spatial Organization of Chromatin in Different Cells. Biophysical Journal 113(7):1395-1404.
Zhang J, et al. (2017) Rich Dynamics Underlying Solution Reactions Revealed by Sampling and Data Mining of Reactive Trajectories. Acs Central Sci 3(5):407-414.
Xie WJ, et al. (2017) Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle. Sci Rep 7(1):2818.
Kan ZG, et al. (2017) Polarization Effects on the Cellulose Dissolution in Ionic Liquids: Molecular Dynamics Simulations with Polarization Model and Integrated Tempering Enhanced Sampling Method. J Phys Chem B 121(17):4319.
Hou GL, et al. (2017) Emergence of Solvent-Separated Na+-Cl- Ion Pair in Salt Water: Photoelectron Spectroscopy and Theoretical Calculations. Journal of Physical Chemistry Letters 8(1):13-20.
Che X, et al. (2017) Single Mutations Reshape the Structural Correlation Network of the DMXAA-Human STING Complex. J Phys Chem B 121(9):2073-2082.
Zhu CX, et al. (2016) Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair. P Natl Acad Sci USA 113(28):7792-7797.
Yang YI, Zhang J, Che X, Yang LJ, & Gao YQ (2016) Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling. J Chem Phys 144(9).
Yang LJ & Gao YQ (2016) Molecular Dynamic Simulations of the Effects of Trimethylamine-N-oxide/Urea Mixture on the Hydration of Single-Walled Carbon Nanotube Interiors. Acta Phys-Chim Sin 32(1):313-320.
Yang L, Zhang J, Che X, & Gao YQ (2016) Simulation Studies of Protein and Small Molecule Interactions and Reaction. Method Enzymol 578:169-212.
Xie WJ, Zhang Z, & Gao YQ (2016) Ion Pairing in Alkali Nitrate Electrolyte Solutions. J Phys Chem B 120(9):2343-2351.
Wang HB, Yang LJ, & Niu XG (2016) Conformation switching of AIM2 PYD domain revealed by NMR relaxation and MD simulation. Biochemical and Biophysical Research Communications 473(2):636-641.
Li X, et al. (2016) Direct Oxidation of Aliphatic C-H Bonds in Amino P-Containing Molecules under Transition-Metal-Free Conditions. Org Lett 18(6):1234-1237.
Li RZ, et al. (2016) Hydration of potassium iodide dimer studied by photoelectron spectroscopy and ab initio calculations. J Chem Phys 145(18).
Li RZ, et al. (2016) Initial hydration behavior of sodium iodide dimer: photoelectron spectroscopy and ab initio calculations. Phys Chem Chem Phys 18(1):557-565.
Jin JS, et al. (2016) The effects of cytosine methylation on general transcription factors. Sci Rep-Uk 6.
He ZY, et al. (2016) Tuning ice nucleation with counterions on polyelectrolyte brush surfaces. Science Advances 2(6).
Fu J, et al. (2016) Structural Characteristics of Homogeneous Hydrophobic Ionic Liquid-HNO3-H2O Ternary System: Experimental Studies and Molecular Dynamics Simulations. J Phys Chem B 120(23):5194-5202.
Che X, et al. (2016) Structural Flexibility and Conformation Features of Cyclic Dinucleotides in Aqueous Solutions. J Phys Chem B 120(10):2670-2680.
Zhang J, Yang YI, Yang L, & Gao YQ (2015) Dynamics and Kinetics Study of "In-Water" Chemical Reactions by Enhanced Sampling of Reactive Trajectories. J Phys Chem B 119(45):14505-14514.
Zhang J, Yang YI, Yang L, & Gao YQ (2015) Conformational Preadjustment in Aqueous Claisen Rearrangement Revealed by SITS-QM/MM MD Simulations. J Phys Chem B 119(17):5518-5530.
Yang YI & Gao YQ (2015) Computer Simulation Studies of A beta(37-42) Aggregation Thermodynamics and Kinetics in Water and Salt Solution. J Phys Chem B 119(3):662-670.
Yang L, Liu C-W, Shao Q, Zhang J, & Gao YQ (2015) From Thermodynamics to Kinetics: Enhanced Sampling of Rare Events. Accounts Chem Res 48(4):947-955.
Xie WJ, Yang YI, & Gao YQ (2015) Dual reorientation relaxation routes of water molecules in oxyanion's hydration shell: A molecular geometry perspective. J Chem Phys 143(22).
Wang P, Yang L, Gao YQ, & Zhao XS (2015) Accurate placement of substrate RNA by Gar1 in H/ACA RNA-guided pseudouridylation. Nucleic Acids Res 43(15):7207-7216.
Liu C-W & Gao YQ (2015) Understanding the Microsolvation of Salts in Molecular Clusters. International Journal of Quantum Chemistry 115(9):541-544.
Guo F, et al. (2015) The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells. Cell 161(6):1437-1452.
Gu C, et al. (2015) DNA Structural Correlation in Short and Long Ranges. J Phys Chem B 119(44):13980-13990.
Zhao X, et al. (2014) Progress in Biophysical Chemistry 77(7):699-702.
Zhang Q, et al. (2014) Pairing preferences of the model mono-valence mono-atomic ions investigated by molecular simulation. J Chem Phys 140(18).
Yin Y, et al. (2014) Dynamics of spontaneous flipping of a mismatched base in DNA duplex. P Natl Acad Sci USA 111(22):8043-8048.
Yang M, Yang L, Gao Y, & Hu H (2014) Combine umbrella sampling with integrated tempering method for efficient and accurate calculation of free energy changes of complex energy surface. J Chem Phys 141(4).
Xie W, Liu C, Yang L, & Gao Y (2014) On the molecular mechanism of ion specific Hofmeister series. Science China-Chemistry 57(1):36-47.
Wu T, Zhang R, Li H, Yang L, & Zhuang W (2014) Discriminating trpzip2 and trpzip4 peptides' folding landscape using the two-dimensional infrared spectroscopy: A simulation study. J Chem Phys 140(5).
Markiewicz BN, Yang L, Culik RM, Gao YQ, & Gai F (2014) How Quickly Can a beta-Hairpin Fold from Its Transition State? J Phys Chem B 118(12):3317-3325.
Liu C-W, et al. (2014) Stable Salt-Water Cluster Structures Reflect the Delicate Competition between Ion-Water and Water-Water Interactions. J Phys Chem B 118(3):743-751.
Liu C-W, Hou G-L, Zheng W-J, & Gao YQ (2014) Adsorption of water molecules on sodium chloride trimer. Theoretical Chemistry Accounts 133(10).
Bezrukavnikov S, et al. (2014) Trehalose facilitates DNA melting: a single-molecule optical tweezers study. Soft Matter 10(37):7269-7277.
Zhao P, Yang LJ, Gao YQ, & Lu Z-Y (2013) Facile implementation of integrated tempering sampling method to enhance the sampling over a broad range of temperatures. Chemical Physics 415:98-105.
Zhang Q, et al. (2013) Microscopic Origin of the Deviation from Stokes-Einstein Behavior Observed in Dynamics of the KSCN Aqueous Solutions: A MD Simulation Study. J Phys Chem B 117(10):2992-3004.
Xu X, et al. (2013) Modeling Spatial Correlation of DNA Deformation: DNA Allostery in Protein Binding. J Phys Chem B 117(42):13378-13387.
Xie WJ & Gao YQ (2013) A Simple Theory for the Hofmeister Series. Journal of Physical Chemistry Letters 4(24):4247-4252.
Xie WJ & Gao YQ (2013) Ion cooperativity and the effect of salts on polypeptide structure - a molecular dynamics study of BBA5 in salt solutions. Faraday Discussions 160:191-206.
Wang P, Yang L, Liu P, Gao YQ, & Zhao XS (2013) Single-Molecule Detection Reveals Knot Sliding in TrmD Denaturation. Chemistry-a European Journal 19(19):5909-5916.
Li R-Z, et al. (2013) Microsolvation of LiI and CsI in Water: Anion Photoelectron Spectroscopy and ab initio Calculations. Journal of the American Chemical Society 135(13):5190-5199.
Kim S, et al. (2013) Probing Allostery Through DNA. Science 339(6121):816-819.
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