03

publications

  • 119. 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.
  • 118. Zhang Q, et al. (2017) The opposite effects of sodium and potassium cations on water dynamics. Chem Sci 8(2):1429-1435.
  • 117. Zhang L, et al. (2017) DNA Methylation Landscape Reflects the Spatial Organization of Chromatin in Different Cells. Biophysical Journal 113(7):1395-1404.
  • 116. 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.
  • 115. Xie WJ, et al. (2017) Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle. Sci Rep 7(1):2818.
  • 114. 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.
  • 113. 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.
  • 112. 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.
  • 111. 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.
  • 110. 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).
  • 109. 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.
  • 108. Yang L, Zhang J, Che X, & Gao YQ (2016) Simulation Studies of Protein and Small Molecule Interactions and Reaction. Method Enzymol 578:169-212.
  • 107. Xie WJ, Zhang Z, & Gao YQ (2016) Ion Pairing in Alkali Nitrate Electrolyte Solutions. J Phys Chem B 120(9):2343-2351.
  • 106. 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.
  • 105. 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.
  • 104. Li RZ, et al. (2016) Hydration of potassium iodide dimer studied by photoelectron spectroscopy and ab initio calculations. J Chem Phys 145(18).
  • 103. 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.
  • 102. Jin JS, et al. (2016) The effects of cytosine methylation on general transcription factors. Sci Rep-Uk 6.
  • 101. He ZY, et al. (2016) Tuning ice nucleation with counterions on polyelectrolyte brush surfaces. Science Advances 2(6).
  • 100. 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.
  • 99. Che X, et al. (2016) Structural Flexibility and Conformation Features of Cyclic Dinucleotides in Aqueous Solutions. J Phys Chem B 120(10):2670-2680.
  • 98. 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.
  • 97. 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.
  • 96. 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.
  • 95. 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.
  • 94. 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).
  • 93. 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.
  • 92. Liu C-W & Gao YQ (2015) Understanding the Microsolvation of Salts in Molecular Clusters. International Journal of Quantum Chemistry 115(9):541-544.
  • 91. Guo F, et al. (2015) The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells. Cell 161(6):1437-1452.
  • 90. Gu C, et al. (2015) DNA Structural Correlation in Short and Long Ranges. J Phys Chem B 119(44):13980-13990.
  • 89. Zhao X, et al. (2014) Progress in Biophysical Chemistry 77(7):699-702.
  • 88. Zhang Q, et al. (2014) Pairing preferences of the model mono-valence mono-atomic ions investigated by molecular simulation. J Chem Phys 140(18).
  • 87. 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.
  • 86. 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).
  • 85. 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.
  • 84. 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).
  • 83. 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.
  • 82. 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.
  • 81. 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).
  • 80. Bezrukavnikov S, et al. (2014) Trehalose facilitates DNA melting: a single-molecule optical tweezers study. Soft Matter 10(37):7269-7277.
  • 79. 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.
  • 78. 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.
  • 77. Xu X, et al. (2013) Modeling Spatial Correlation of DNA Deformation: DNA Allostery in Protein Binding. J Phys Chem B 117(42):13378-13387.
  • 76. Xie WJ & Gao YQ (2013) A Simple Theory for the Hofmeister Series. Journal of Physical Chemistry Letters 4(24):4247-4252.
  • 75. 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.
  • 74. 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.
  • 73. 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.
  • 72. Kim S, et al. (2013) Probing Allostery Through DNA. Science 339(6121):816-819.
  • 71. Yang L, Shao Q, & Gao Y (2012) Enhanced Sampling Method in Molecular Simulations. Progress in Chemistry 24(6):1199-1213.
  • 70. Shao Q, Zhu W, & Gao YQ (2012) Robustness in Protein Folding Revealed by Thermodynamics Calculations. J Phys Chem B 116(47):13848-13856.
  • 69. Shao Q & Gao YQ (2012) Water plays an important role in osmolyte-induced hairpin structure change: A molecular dynamics simulation study. J Chem Phys 137(14).
  • 68. Shao Q, Fan Y, Yang L, & Gao YQ (2012) Counterion Effects on the Denaturing Activity of Guanidinium Cation to Protein. Journal of Chemical Theory and Computation 8(11):4364-4373.
  • 67. Shao Q, Fan Y, Yang L, & Gao YQ (2012) From protein denaturant to protectant: Comparative molecular dynamics study of alcohol/protein interactions. J Chem Phys 136(11).
  • 66. Shao Q, Fan Y, Yang L, & Gao YQ (2012) From protein denaturant to protectant: comparative molecular dynamics study of alcohol/protein interactions. The Journal of chemical physics 136(11):115101-115101.
  • 65. Lyu Z-X, Shao Q, Gao YQ, & Zhao XS (2012) Direct Observation of the Uptake of Outer Membrane Proteins by the Periplasmic Chaperone Skp. Plos One 7(9).
  • 64. Gao YQ (2012) Simple Theory for Salt Effects on the Solubility of Amide. J Phys Chem B 116(33):9934-9943.
  • 63. Chen L, Gao YQ, & Russell DH (2012) How Alkali Metal Ion Binding Alters the Conformation Preferences of Gramicidin A: A Molecular Dynamics and Ion Mobility Study. Journal of Physical Chemistry A 116(1):689-696.
  • 62. Cao Q, et al. (2012) Inhibitory Mechanism of Caspase-6 Phosphorylation Revealed by Crystal Structures, Molecular Dynamics Simulations, and Biochemical Assays. Journal of Biological Chemistry 287(19):15371-15379.
  • 61. Bian H, et al. (2012) Ion Segregation in Aqueous Solutions. J Phys Chem B 116(49):14426-14432.
  • 60. Yang L, Fan Y, & Gao YQ (2011) Differences of Cations and Anions: Their Hydration, Surface Adsorption, and Impact on Water Dynamics. J Phys Chem B 115(43):12456-12465.
  • 59. Shao Q, Yang L, & Gao YQ (2011) Structure change of beta-hairpin induced by turn optimization: An enhanced sampling molecular dynamics simulation study. J Chem Phys 135(23).
  • 58. Shao Q & Gao YQ (2011) The relative helix and hydrogen bond stability in the B domain of protein A as revealed by integrated tempering sampling molecular dynamics simulation. J Chem Phys 135(13).
  • 57. Hwang S, Shao Q, Williams H, Hilty C, & Gao YQ (2011) Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR study. J Phys Chem B 115(20):6653-6660.
  • 56. Gao YQ (2011) Simple Theoretical Model for Ion Cooperativity in Aqueous Solutions of Simple Inorganic Salts and Its Effect on Water Surface Tension. J Phys Chem B 115(43):12466-12472.
  • 55. Chen L, Shao Q, Gao Y-Q, & Russell DH (2011) Molecular Dynamics and Ion Mobility Spectrometry Study of Model beta-Hairpin Peptide, Trpzip1. Journal of Physical Chemistry A 115(17):4427-4435.
  • 54. Yang L & Gao YQ (2010) Effects of Cosolvents on the Hydration of Carbon Nanotubes. Journal of the American Chemical Society 132(2):842-848.
  • 53. Wei H, Yang L, & Gao YQ (2010) Mutation of Charged Residues to Neutral Ones Accelerates Urea Denaturation of HP-35. J Phys Chem B 114(36):11820-11826.
  • 52. Wei H, Shao Q, & Gao YQ (2010) The effects of side chain hydrophobicity on the denaturation of simple beta-hairpins. Phys Chem Chem Phys 12(32):9292-9299.
  • 51. Wei H, Fan Y, & Gao YQ (2010) Effects of Urea, Tetramethyl Urea, and Trimethylamine N-Oxide on Aqueous Solution Structure and Solvation of Protein Backbones: A Molecular Dynamics Simulation Study. J Phys Chem B 114(1):557-568.
  • 50. Tsai P-C, et al. (2010) Structural Determinants for the Stereoselective Hydrolysis of Chiral Substrates by Phosphotriesterase. Biochemistry 49(37):7988-7997.
  • 49. Shao Q, Wei H, & Gao YQ (2010) Effects of Turn Stability and Side-Chain Hydrophobicity on the Folding of beta-Structures. Journal of Molecular Biology 402(3):595-609.
  • 48. Shao Q & Gao YQ (2010) Temperature Dependence of Hydrogen-Bond Stability in beta-Hairpin Structures. Journal of Chemical Theory and Computation 6(12):3750-3760.
  • 47. Lund L, Fan Y, Shao Q, Gao YQ, & Raushel FM (2010) Carbamate Transport in Carbamoyl Phosphate Synthetase: A Theoretical and Experimental Investigation. Journal of the American Chemical Society 132(11):3870-3878.
  • 46. Fan Y-B & Gao Y-Q (2010) Coorperativity between Metals, Ligands and Solvent: a DFT Study on the Mechanism of a Dizinc Complex-Mediated Phosphodiester Cleavage. Acta Phys-Chim Sin 26(4):1034-1042.
  • 45. Fan Y & Gao YQ (2010) Long-Range Effects of Confinement on Water Structure. J Phys Chem B 114(12):4246-4251.
  • 44. Zegarra FC, Peralta GN, Coronado AM, & Gao YQ (2009) Free energies and forces in helix-coil transition of homopolypeptides under stretching. Phys Chem Chem Phys 11(20):4019-4024.
  • 43. Yang L, Shao Q, & Gao YQ (2009) Comparison between integrated and parallel tempering methods in enhanced sampling simulations. J Chem Phys 130(12).
  • 42. Yang L, Shao Q, & Gao YQ (2009) Thermodynamics and Folding Pathways of Trpzip2: An Accelerated Molecular Dynamics Simulation Study. J Phys Chem B 113(3):803-808.
  • 41. Yang L & Gao YQ (2009) A selective integrated tempering method. J Chem Phys 131(21).
  • 40. Shao Q, Yang L, & Gao YQ (2009) A test of implicit solvent models on the folding simulation of the GB1 peptide. J Chem Phys 130(19).
  • 39. Mu Y & Gao YQ (2009) Self-assembly of polypeptides into left-handedly twisted fibril-like structures. Physical Review E 80(4).
  • 38. Fernandez-Lima FA, Wei H, Gao YQ, & Russell DH (2009) On the Structure Elucidation Using Ion Mobility Spectrometry and Molecular Dynamics. Journal of Physical Chemistry A 113(29):8221-8234.
  • 37. Fan Y, Lund L, Shao Q, Gao Y-Q, & Raushel FM (2009) A Combined Theoretical and Experimental Study of the Ammonia Tunnel in Carbamoyl Phosphate Synthetase. Journal of the American Chemical Society 131(29):10211-10219.
  • 36. Fan Y, Chen X, Yang L, Cremer PS, & Gao YQ (2009) On the Structure of Water at the Aqueous/Air Interface. J Phys Chem B 113(34):11672-11679.
  • 35. Gao YQ, Yang L, Fan Y, & Shao Q (2008) Thermodynamics and kinetics simulations of multi-time-scale processes for complex systems. International Reviews in Physical Chemistry 27(2):201-227.
  • 34. Gao YQ (2008) Self-adaptive enhanced sampling in the energy and trajectory spaces: Accelerated thermodynamics and kinetic calculations. J Chem Phys 128(13).
  • 33. Gao YQ (2008) An integrate-over-temperature approach for enhanced sampling. J Chem Phys 128(6).
  • 32. Fan Y, Lund L, Yang L, Raushel FM, & Gao Y-Q (2008) Mechanism for the transport of ammonia within carbamoyl phosphate synthetase determined by molecular dynamics Simulations. Biochemistry 47(9):2935-2944.
  • 31. Yang L, Grubb MP, & Gao YQ (2007) Application of the accelerated molecular dynamics simulations to the folding of a small protein. J Chem Phys 126(12).
  • 30. Yang L & Gao YQ (2007) An approximate method in using molecular mechanics simulations to study slow protein conformational changes. J Phys Chem B 111(11):2969-2975.
  • 29. Wu Y, Gao YQ, & Karplus M (2007) A kinetic model of coordinated myosin V. Biochemistry 46(21):6318-6330.
  • 28. Shao Q & Gao YQ (2007) Asymmetry in kinesin walking. Biochemistry 46(31):9098-9106.
  • 27. Mu Y & Gao YQ (2007) Effects of hydrophobic and dipole-dipole interactions on the conformational transitions of a model polypeptide. J Chem Phys 127(10).
  • 26. Gao YQ & Marcus RA (2007) An approximate theory of the ozone isotopic effects: Rate constant ratios and pressure dependence. J Chem Phys 127(24).
  • 25. Fu X, Yang L, & Gao YQ (2007) Selective sampling of transition paths. J Chem Phys 127(15).
  • 24. Fan Y & Gao YQ (2007) A DFT study on the mechanism of phosphodiester cleavage mediated by monozinc complexes. Journal of the American Chemical Society 129(4):905-913.
  • 23. Shao Q & Gao YQ (2006) On the hand-over-hand mechanism of kinesin. P Natl Acad Sci USA 103(21):8072-8077.
  • 22. Gao YQ & Yang L (2006) On the enhanced sampling over energy barriers in molecular dynamics simulations. J Chem Phys 125(11).
  • 21. Gao YQ (2006) Simple theoretical model explains dynein's response to load. Biophysical Journal 90(3):811-821.
  • 20. Karplus M, Gao YQ, Ma JP, van der Vaart A, & Yang W (2005) Protein structural transitions and their functional role. Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences 363(1827):331-355.
  • 19. Gao YQ, Yang W, & Karplus M (2005) A structure-based model for the synthesis and hydrolysis of ATP by F-1-ATPase. Cell 123(2):195-205.
  • 18. Karplus M & Gao YQ (2004) Biomolecular motors: the F-1-ATPase paradigm. Current Opinion in Structural Biology 14(2):250-259.
  • 17. Yang W, Gao YQ, Cui Q, Ma J, & Karplus M (2003) The missing link between thermodynamics and structure in F1-ATPase. P Natl Acad Sci USA 100(3):874-879.
  • 16. Gao YQ, Yang W, Marcus RA, & Karplus M (2003) A model for the cooperative free energy transduction and kinetics of ATP hydrolysis by F-1-ATPase. P Natl Acad Sci USA 100(20):11339-11344.
  • 15. Gao YQ & Marcus RA (2002) Theoretical investigation of the directional electron transfer in 4-aminonaphthalimide compounds. Journal of Physical Chemistry A 106(10):1956-1960.
  • 14. Gao YQ & Marcus RA (2002) On the theory of the strange and unconventional isotopic effects in ozone formation. J Chem Phys 116(1):137-154.
  • 13. Gao YQ, Chen WC, & Marcus RA (2002) A theoretical study of ozone isotopic effects using a modified ab initio potential energy surface. J Chem Phys 117(4):1536-1543.
  • 12. Marcus RA & Gao YQ (2001) Pressure effects on bimolecular recombination and unimolecular dissociation reactions. J Chem Phys 114(22):9807-9812.
  • 11. Gosavi S, Gao YQ, & Marcus RA (2001) Temperature dependence of the electronic factor in the nonadiabatic electron transfer at metal and semiconductor electrodes. Journal of Electroanalytical Chemistry 500(1-2):71-77.
  • 10. Gao YQ & Marcus RA (2001) Application of the z-transform to composite materials. J Chem Phys 115(21):9929-9934.
  • 9. Gao YQ & Marcus RA (2001) Strange and unconventional isotope effects in ozone formation. Science 293(5528):259-263.
  • 8. Gao YQ & Marcus RA (2000) On the theory of electron transfer reactions at semiconductor/liquid interfaces. II. A free electron model. J Chem Phys 113(15):6351-6360.
  • 7. Gao YQ, Georgievskii Y, & Marcus RA (2000) On the theory of electron transfer reactions at semiconductor electrode/liquid interfaces. J Chem Phys 112(7):3358-3369.
  • 6. 吴国胜，等 (1997) 四氢呋喃的同步辐射光电离研究 物理化学学报 13(2):188-188.
  • 5. 陈文武，等 (1997) 噻吩和吡啶的同步辐射光电离解离 化学物理学报 10(5):385-385.
  • 4. Wang DX, et al. (1996) HeI photoelectron spectroscopic (PES) studies of the electronic structure for alkyl nitrites CH3(CH2)(n)ONO (n=0, 1, 2, 3). Journal of Electron Spectroscopy and Related Phenomena 82(1-2):19-22.
  • 3. Wang DX, et al. (1996) HeI photoelectron spectroscopic (PES) studies of the electronic structure of Al(CH3)(3), In(C2H5)(3) and Cd(CH3)(2) compounds. Chemical Physics Letters 260(1-2):95-98.
  • 2. Li S, et al. (1996) Het Photoelectron Spectroscopic Study of the Electronic Structure on B(OCH3)(3). Acta Phys-Chim Sin 12(7):641-643.
  • 1. 陈文武，等 (1996) 六氢吡啶团簇的研究 物理化学学报 12(12):1067-1067.

Selected Recent Publications