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Yi Qin Gao, Ph.D. - Publications

Affiliations: 
1989-1993 Chemistry Sichuan University, Chengdu Shi, Sichuan Sheng, China 
 1993-1996 Institute of Chemistry Chinese Academy of Sciences, Beijing, China 
 1996-2001 Chemistry & Chemical Engineering California Institute of Technology, Pasadena, CA 
 2001-2002 Chemistry & Chemical Engineering California Institute of Technology, Pasadena, CA 
 2002-2004 Chemistry & Chemical Biology Harvard University, Cambridge, MA, United States 
 2004-2010 Chemistry Texas A & M University, College Station, TX, United States 
 2010- Chemistry & Molecular Engineering Peking University, Beijing, Beijing Shi, China 
Area:
Theoretical/Computational Chemistry and Biophysical Chemistry
Website:
http://www.chem.pku.edu.cn/index.php?id=382
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79 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Zhang J, Liu S, Chen M, Chu H, Wang M, Wang Z, Yu J, Ni N, Yu F, Chen D, Yang YI, Xue B, Yang L, Liu Y, Gao YQ. Unsupervisedly Prompting AlphaFold2 for Accurate Few-Shot Protein Structure Prediction. Journal of Chemical Theory and Computation. PMID 37947474 DOI: 10.1021/acs.jctc.3c00528  0.439
2023 Zhang J, Chen D, Xia Y, Huang YP, Lin X, Han X, Ni N, Wang Z, Yu F, Yang L, Yang YI, Gao YQ. Artificial Intelligence Enhanced Molecular Simulations. Journal of Chemical Theory and Computation. PMID 37358079 DOI: 10.1021/acs.jctc.3c00214  0.455
2022 Lei YK, Zhang Z, Han X, Yang YI, Zhang J, Gao YQ. Locating Transition Zone in Phase Space. Journal of Chemical Theory and Computation. PMID 36135927 DOI: 10.1021/acs.jctc.2c00385  0.465
2022 Li M, Zhang J, Niu H, Lei YK, Han X, Yang L, Ye Z, Yang YI, Gao YQ. Phase Transition between Crystalline Variants of Ordinary Ice. The Journal of Physical Chemistry Letters. 13: 8601-8606. PMID 36073968 DOI: 10.1021/acs.jpclett.2c02176  0.475
2022 Han X, Zhang J, Yang YI, Zhang Z, Yang L, Gao YQ. Enhanced Sampling Simulation Reveals How Solvent Influences Chirogenesis of the Intra-Molecular Diels-Alder Reaction. Journal of Chemical Theory and Computation. PMID 35666128 DOI: 10.1021/acs.jctc.2c00233  0.514
2021 Zhang J, Lei YK, Zhang Z, Han X, Li M, Yang L, Yang YI, Gao YQ. Deep reinforcement learning of transition states. Physical Chemistry Chemical Physics : Pccp. PMID 33729229 DOI: 10.1039/d0cp06184k  0.47
2020 Zhang J, Lei YK, Yang YI, Gao YQ. Deep learning for variational multiscale molecular modeling. The Journal of Chemical Physics. 153: 174115. PMID 33167648 DOI: 10.1063/5.0026836  0.466
2020 Zhang J, Lei YK, Zhang Z, Chang J, Li M, Han X, Yang L, Yang YI, Gao YQ. A Perspective on Deep Learning for Molecular Modeling and Simulations. The Journal of Physical Chemistry. A. PMID 32786668 DOI: 10.1021/acs.jpca.0c04473  0.438
2020 Zhang J, Lei YK, Zhang Z, Chang J, Li M, Han X, Yang L, Yang YI, Gao YQ. A Perspective on Deep Learning for Molecular Modeling and Simulations. The Journal of Physical Chemistry. B. PMID 32663004 DOI: 10.1021/acs.jpcb.0c04473  0.438
2020 Su QP, Zhao ZW, Meng L, Ding M, Zhang W, Li Y, Liu M, Li R, Gao YQ, Xie XS, Sun Y. Superresolution imaging reveals spatiotemporal propagation of human replication foci mediated by CTCF-organized chromatin structures. Proceedings of the National Academy of Sciences of the United States of America. PMID 32541019 DOI: 10.1073/pnas.2001521117  0.533
2019 Zhang J, Lei YK, Che X, Zhang Z, Yang YI, Gao YQ. Deep Representation Learning for Complex Free-Energy Landscapes. The Journal of Physical Chemistry Letters. 5571-5576. PMID 31476868 DOI: 10.1021/acs.jpclett.9b02012  0.448
2019 Yang YI, Shao Q, Zhang J, Yang L, Gao YQ. Enhanced sampling in molecular dynamics. The Journal of Chemical Physics. 151: 070902. PMID 31438687 DOI: 10.1063/1.5109531  0.596
2019 Qiao Z, Zhao Y, Gao YQ. Ice Nucleation of Confined Monolayer Water Conforms to Classical Nucleation Theory. The Journal of Physical Chemistry Letters. 3115-3121. PMID 31117689 DOI: 10.1021/Acs.Jpclett.9B01169  0.568
2019 Cai X, Xie WJ, Yang Y, Long Z, Zhang J, Qiao Z, Yang L, Gao YQ. Structure of water confined between two parallel graphene plates. The Journal of Chemical Physics. 150: 124703. PMID 30927866 DOI: 10.1063/1.5080788  0.561
2019 Qiao Z, Xie WJ, Cai X, Gao YQ. Interlayer hopping dynamics of bilayer water confined between graphene sheets Chemical Physics Letters. 722: 153-159. DOI: 10.1016/J.Cplett.2019.02.046  0.563
2018 Liu S, Zhang L, Quan H, Tian H, Meng L, Yang L, Feng H, Gao YQ. From 1D sequence to 3D chromatin dynamics and cellular functions: a phase separation perspective. Nucleic Acids Research. PMID 30053116 DOI: 10.1093/nar/gky633  0.531
2018 He Z, Feng G, Yang B, Yang L, Liu CW, Xu HG, Xu XL, Zheng WJ, Gao YQ. Molecular dynamics simulation, ab initio calculation, and size-selected anion photoelectron spectroscopy study of initial hydration processes of calcium chloride. The Journal of Chemical Physics. 148: 222839. PMID 29907039 DOI: 10.1063/1.5024279  0.46
2017 Zhang L, Xie WJ, Liu S, Meng L, Gu C, Gao YQ. DNA Methylation Landscape Reflects the Spatial Organization of Chromatin in Different Cells. Biophysical Journal. 113: 1395-1404. PMID 28978434 DOI: 10.1016/j.bpj.2017.08.019  0.513
2017 Xie WJ, Meng L, Liu S, Zhang L, Cai X, Gao YQ. Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle. Scientific Reports. 7: 2818. PMID 28588240 DOI: 10.1038/s41598-017-02923-6  0.517
2017 Zhang J, Zhang Z, Yang YI, Liu S, Yang L, Gao YQ. Rich Dynamics Underlying Solution Reactions Revealed by Sampling and Data Mining of Reactive Trajectories. Acs Central Science. 3: 407-414. PMID 28573202 DOI: 10.1021/acscentsci.7b00037  0.504
2016 Hou GL, Liu CW, Li RZ, Xu HG, Gao YQ, Zheng WJ. Emergence of Solvent-Separated Na(+)-Cl(-) Ion Pair in Salt Water: Photoelectron Spectroscopy and Theoretical Calculations. The Journal of Physical Chemistry Letters. 13-20. PMID 27935718 DOI: 10.1021/Acs.Jpclett.6B02670  0.434
2016 Fu J, Yang YI, Zhang J, Chen Q, Shen X, Gao YQ. Structural Characteristics of Homogeneous Hydrophobic Ionic Liquid-HNO3-H2O Ternary System: Experimental Studies and Molecular Dynamics Simulations. The Journal of Physical Chemistry. B. PMID 27196811 DOI: 10.1021/acs.jpcb.6b01214  0.488
2016 Yang YI, Zhang J, Che X, Yang L, Gao YQ. Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling. The Journal of Chemical Physics. 144: 094105. PMID 26957155 DOI: 10.1063/1.4943004  0.49
2016 Li X, Che X, Chen GH, Zhang J, Yan JL, Zhang YF, Zhang LS, Hsu CP, Gao YQ, Shi ZJ. Direct Oxidation of Aliphatic C-H Bonds in Amino-Containing Molecules under Transition-Metal-Free Conditions. Organic Letters. PMID 26949833 DOI: 10.1021/Acs.Orglett.5B03690  0.571
2016 Gao Y, Wu G, Ma F, Liu C, Jiang F, Wang Y, Wang A. Modified seeding method for preparing hierarchical nanocrystalline ZSM-5 catalysts for methanol aromatisation Microporous and Mesoporous Materials. 226: 251-259. DOI: 10.1016/j.micromeso.2015.11.066  0.329
2016 Gao Y, Hu Y, Ren P, Zhou D, Qiu J. Effect of Li+ ions on the enhancement upconversion and stokes emission of NaYF4:Tb, Yb co-doped in glass-ceramics Journal of Alloys and Compounds. 667: 297-301. DOI: 10.1016/j.jallcom.2016.01.200  0.356
2015 Xie WJ, Yang YI, Gao YQ. Dual reorientation relaxation routes of water molecules in oxyanion's hydration shell: A molecular geometry perspective. The Journal of Chemical Physics. 143: 224504. PMID 26671387 DOI: 10.1063/1.4937361  0.463
2015 Li RZ, Hou GL, Liu CW, Xu HG, Zhao X, Gao YQ, Zheng WJ. Initial hydration behavior of sodium iodide dimer: photoelectron spectroscopy and ab initio calculations. Physical Chemistry Chemical Physics : Pccp. PMID 26618327 DOI: 10.1039/C5Cp05550D  0.418
2015 Zhang J, Yang YI, Yang L, Gao YQ. Dynamics and Kinetics Study of "In-Water" Chemical Reactions by Enhanced Sampling of Reactive Trajectories. The Journal of Physical Chemistry. B. PMID 26485567 DOI: 10.1021/acs.jpcb.5b08690  0.517
2015 Gu C, Zhang J, Yang YI, Chen X, Ge H, Sun Y, Su X, Yang L, Xie XS, Gao YQ. DNA Structural Correlation in Short and Long Ranges. The Journal of Physical Chemistry. B. PMID 26439165 DOI: 10.1021/Acs.Jpcb.5B06217  0.454
2015 Zhang J, Yang YI, Yang L, Gao YQ. Conformational Preadjustment in Aqueous Claisen Rearrangement Revealed by SITS-QM/MM MD Simulations. The Journal of Physical Chemistry. B. 119: 5518-30. PMID 25849201 DOI: 10.1021/jp511057f  0.527
2015 Yang L, Liu CW, Shao Q, Zhang J, Gao YQ. From thermodynamics to kinetics: enhanced sampling of rare events. Accounts of Chemical Research. 48: 947-55. PMID 25781363 DOI: 10.1021/Ar500267N  0.612
2015 Zeng Z, Liu CW, Hou GL, Feng G, Xu HG, Gao YQ, Zheng WJ. Photoelectron spectroscopy and ab initio calculations of Li(H₂O)n(-) and Cs(H₂O)n(-) (n = 1-6) clusters. The Journal of Physical Chemistry. A. 119: 2845-56. PMID 25723570 DOI: 10.1021/Jp512177J  0.427
2015 Yang YI, Gao YQ. Computer simulation studies of Aβ37-42 aggregation thermodynamics and kinetics in water and salt solution. The Journal of Physical Chemistry. B. 119: 662-70. PMID 24861904 DOI: 10.1021/jp502169b  0.44
2015 Xiao H, Tang B, Liu C, Gao Y, Yu S, Jiang S. Dynamic precipitation in a Mg-Gd-Y-Zr alloy during hot compression Materials Science and Engineering A. 645: 241-247. DOI: 10.1016/j.msea.2015.08.022  0.344
2015 Liu CW, Gao YQ. Understanding the microsolvation of salts in molecular clusters International Journal of Quantum Chemistry. 115: 541-544. DOI: 10.1002/Qua.24827  0.439
2014 Liu CW, Wang F, Yang L, Li XZ, Zheng WJ, Gao YQ. Stable salt-water cluster structures reflect the delicate competition between ion-water and water-water interactions. The Journal of Physical Chemistry. B. 118: 743-51. PMID 24387307 DOI: 10.1021/Jp408439J  0.435
2014 Liu CW, Hou GL, Zheng WJ, Gao YQ. Adsorption of water molecules on sodium chloride trimer Theoretical Chemistry Accounts. 133. DOI: 10.1007/S00214-014-1550-1  0.442
2013 Li RZ, Liu CW, Gao YQ, Jiang H, Xu HG, Zheng WJ. Microsolvation of LiI and CsI in water: anion photoelectron spectroscopy and ab initio calculations. Journal of the American Chemical Society. 135: 5190-9. PMID 23432353 DOI: 10.1021/Ja4006942  0.41
2013 Zhang Q, Xie W, Bian H, Gao YQ, Zheng J, Zhuang W. Microscopic origin of the deviation from Stokes-Einstein behavior observed in dynamics of the KSCN aqueous solutions: a MD simulation study. The Journal of Physical Chemistry. B. 117: 2992-3004. PMID 23414456 DOI: 10.1021/Jp400441E  0.549
2012 Shao Q, Fan Y, Yang L, Gao YQ. Counterion Effects on the Denaturing Activity of Guanidinium Cation to Protein. Journal of Chemical Theory and Computation. 8: 4364-4373. PMID 26605599 DOI: 10.1021/Ct3002267  0.452
2012 Shao Q, Zhu W, Gao YQ. Robustness in protein folding revealed by thermodynamics calculations. The Journal of Physical Chemistry. B. 116: 13848-56. PMID 23130913 DOI: 10.1021/Jp307684H  0.446
2012 Shao Q, Gao YQ. Water plays an important role in osmolyte-induced hairpin structure change: a molecular dynamics simulation study. The Journal of Chemical Physics. 137: 145101. PMID 23061865 DOI: 10.1063/1.4757419  0.478
2012 Lyu ZX, Shao Q, Gao YQ, Zhao XS. Direct observation of the uptake of outer membrane proteins by the periplasmic chaperone Skp. Plos One. 7: e46068. PMID 23049938 DOI: 10.1371/Journal.Pone.0046068  0.473
2012 Shao Q, Fan Y, Yang L, Gao YQ. From protein denaturant to protectant: comparative molecular dynamics study of alcohol/protein interactions. The Journal of Chemical Physics. 136: 115101. PMID 22443795 DOI: 10.1063/1.3692801  0.454
2012 Cao Q, Wang XJ, Liu CW, Liu DF, Li LF, Gao YQ, Su XD. Inhibitory mechanism of caspase-6 phosphorylation revealed by crystal structures, molecular dynamics simulations, and biochemical assays. The Journal of Biological Chemistry. 287: 15371-9. PMID 22433863 DOI: 10.1074/Jbc.M112.351213  0.394
2012 Yang L, Shao Q, Gao Y. Enhanced sampling method in molecular simulations Progress in Chemistry. 24: 1199-1213.  0.441
2011 Shao Q, Yang L, Gao YQ. Structure change of β-hairpin induced by turn optimization: an enhanced sampling molecular dynamics simulation study. The Journal of Chemical Physics. 135: 235104. PMID 22191904 DOI: 10.1063/1.3668288  0.472
2011 Shao Q, Gao YQ. The relative helix and hydrogen bond stability in the B domain of protein A as revealed by integrated tempering sampling molecular dynamics simulation. The Journal of Chemical Physics. 135: 135102. PMID 21992340 DOI: 10.1063/1.3630127  0.494
2011 Hwang S, Shao Q, Williams H, Hilty C, Gao YQ. Methanol strengthens hydrogen bonds and weakens hydrophobic interactions in proteins--a combined molecular dynamics and NMR study. The Journal of Physical Chemistry. B. 115: 6653-60. PMID 21534580 DOI: 10.1021/Jp111448A  0.497
2011 Chen L, Shao Q, Gao YQ, Russell DH. Molecular dynamics and ion mobility spectrometry study of model β-hairpin peptide, trpzip1. The Journal of Physical Chemistry. A. 115: 4427-35. PMID 21476523 DOI: 10.1021/Jp110014J  0.454
2010 Shao Q, Wei H, Gao YQ. Effects of turn stability and side-chain hydrophobicity on the folding of β-structures. Journal of Molecular Biology. 402: 595-609. PMID 20804769 DOI: 10.1016/J.Jmb.2010.08.037  0.464
2010 Wei H, Shao Q, Gao YQ. The effects of side chain hydrophobicity on the denaturation of simple beta-hairpins. Physical Chemistry Chemical Physics : Pccp. 12: 9292-9. PMID 20571679 DOI: 10.1039/B924593F  0.443
2010 Lund L, Fan Y, Shao Q, Gao YQ, Raushel FM. Carbamate transport in carbamoyl phosphate synthetase: a theoretical and experimental investigation. Journal of the American Chemical Society. 132: 3870-8. PMID 20187643 DOI: 10.1021/Ja910441V  0.48
2010 Shao Q, Gao YQ. Temperature dependence of hydrogen-bond stability in β-hairpin structures Journal of Chemical Theory and Computation. 6: 3750-3760. DOI: 10.1021/Ct100436R  0.426
2009 Fan Y, Lund L, Shao Q, Gao YQ, Raushel FM. A combined theoretical and experimental study of the ammonia tunnel in carbamoyl phosphate synthetase. Journal of the American Chemical Society. 131: 10211-9. PMID 19569682 DOI: 10.1021/Ja902557R  0.489
2009 Shao Q, Yang L, Gao YQ. A test of implicit solvent models on the folding simulation of the GB1 peptide. The Journal of Chemical Physics. 130: 195104. PMID 19466868 DOI: 10.1063/1.3132850  0.462
2009 Yang L, Shao Q, Gao YQ. Comparison between integrated and parallel tempering methods in enhanced sampling simulations. The Journal of Chemical Physics. 130: 124111. PMID 19334812 DOI: 10.1063/1.3097129  0.454
2009 Yang L, Shao Q, Gao YQ. Thermodynamics and folding pathways of trpzip2: an accelerated molecular dynamics simulation study. The Journal of Physical Chemistry. B. 113: 803-8. PMID 19113829 DOI: 10.1021/Jp803160F  0.501
2008 Gao YQ, Yang L, Fan Y, Shao Q. Thermodynamics and kinetics simulations of multi-time-scale processes for complex systems International Reviews in Physical Chemistry. 27: 201-227. DOI: 10.1080/01442350801920334  0.454
2007 Gao YQ, Marcus RA. An approximate theory of the ozone isotopic effects: rate constant ratios and pressure dependence. The Journal of Chemical Physics. 127: 244316. PMID 18163684 DOI: 10.1063/1.2806189  0.559
2007 Shao Q, Gao YQ. Asymmetry in kinesin walking. Biochemistry. 46: 9098-106. PMID 17630771 DOI: 10.1021/Bi602382W  0.425
2007 Wu Y, Gao YQ, Karplus M. A kinetic model of coordinated myosin V. Biochemistry. 46: 6318-30. PMID 17487986 DOI: 10.1021/Bi700526R  0.347
2006 Shao Q, Gao YQ. On the hand-over-hand mechanism of kinesin. Proceedings of the National Academy of Sciences of the United States of America. 103: 8072-7. PMID 16698919 DOI: 10.1073/Pnas.0602828103  0.418
2006 Gao YQ, Yang W, Karplus M. Thermodynamics and kinetic analysis of F0F1-ATPase Modern Methods For Theoretical Physical Chemistry of Biopolymers. 249-263. DOI: 10.1016/B978-044452220-7/50077-0  0.346
2005 Gao YQ, Yang W, Karplus M. A structure-based model for the synthesis and hydrolysis of ATP by F1-ATPase. Cell. 123: 195-205. PMID 16239139 DOI: 10.1016/J.Cell.2005.10.001  0.339
2005 Karplus M, Gao YQ, Ma J, van der Vaart A, Yang W. Protein structural transitions and their functional role. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 363: 331-55; discussion 3. PMID 15664887 DOI: 10.1098/Rsta.2004.1496  0.603
2004 Karplus M, Gao YQ. Biomolecular motors: the F1-ATPase paradigm. Current Opinion in Structural Biology. 14: 250-9. PMID 15093841 DOI: 10.1016/J.Sbi.2004.03.012  0.327
2003 Gao YQ, Yang W, Marcus RA, Karplus M. A model for the cooperative free energy transduction and kinetics of ATP hydrolysis by F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America. 100: 11339-44. PMID 14500780 DOI: 10.1073/Pnas.1334188100  0.619
2003 Yang W, Gao YQ, Cui Q, Ma J, Karplus M. The missing link between thermodynamics and structure in F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America. 100: 874-9. PMID 12552084 DOI: 10.1073/Pnas.0337432100  0.486
2002 Gao YQ, Chen WC, Marcus RA. A theoretical study of ozone isotopic effects using a modified ab initio potential energy surface Journal of Chemical Physics. 117: 1536-1543. DOI: 10.1063/1.1488577  0.576
2002 Gao YQ, Marcus RA. Erratum: “On the theory of the strange and unconventional isotopic effects in ozone formation” [J. Chem. Phys. 116, 137 (2002)] The Journal of Chemical Physics. 116: 5913-5913. DOI: 10.1063/1.1458540  0.523
2002 Gao YQ, Marcus RA. On the theory of the strange and unconventional isotopic effects in ozone formation Journal of Chemical Physics. 116: 137-154. DOI: 10.1063/1.1415448  0.579
2002 Gao YQ, Marcus RA. Theoretical investigation of the directional electron transfer in 4-aminonaphthalimide compounds Journal of Physical Chemistry A. 106: 1956-1960. DOI: 10.1021/Jp011980S  0.535
2001 Gao YQ, Marcus RA. Strange and unconventional isotope effects in ozone formation. Science (New York, N.Y.). 293: 259-63. PMID 11387441 DOI: 10.1126/Science.1058528  0.569
2001 Gao YQ, Marcus RA. Application of the z-transform to composite materials Journal of Chemical Physics. 115: 9929-9934. DOI: 10.1063/1.1416127  0.537
2001 Marcus RA, Gao YQ. Pressure effects on bimolecular recombination and unimolecular dissociation reactions Journal of Chemical Physics. 114: 9807-9812. DOI: 10.1063/1.1370552  0.562
2000 Gao YQ, Georgievskii Y, Marcus RA. On the theory of electron transfer reactions at semiconductor electrode/liquid interfaces Journal of Chemical Physics. 112: 3358-3369. DOI: 10.1063/1.480918  0.568
2000 Gao YQ, Marcus RA. On the theory of electron transfer reactions at semiconductor/liquid interfaces. II. A free electron model Journal of Chemical Physics. 113: 6351-6360. DOI: 10.1063/1.1309528  0.55
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