Publications

Preprints : Journal : Chapters : Conferences : Theses : Downloads

Preprints

  1. Awoonor-Williams, E.; Isley, W.; Dale, S.; Johnson, E.; Yu, H.; Becke, A.; Roux Benoı̂t; Rowley, C. Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols, 2019.

Peer Reviewed Journal Articles

  1. Chen, Y.; Wang, X.; Lao, M.; Rui, K.; Zheng, X.; Yu, H.; Ma, J.; Dou, S. X.; Sun, W. Electrocatalytically Inactive SnS2 Promotes Water Adsorption/Dissociation on Molybdenum Dichalcogenides for Accelerated Alkaline Hydrogen Evolution. Nano Energy 2019, in press.
  2. Zhao, G.; Wang, X.; Wang, S.; Rui, K.; Chen, Y.; Yu, H.; Ma, J.; Dou, S. X.; Sun, W. Heteroatom-Doped MoSe2 Nanosheets with Enhanced Hydrogen Evolution Kinetics for Alkaline Water Splitting. Chemistry - An Asian Journal 2019, 14, 301–306.
  3. Gao, P.; Wang, X.; Huang, Z.; Yu, H. 11B NMR Chemical Shift Predictions via Density Functional Theory and Gauge-Including Atomic Orbital Approach: Applications to Structural Elucidations of Boron-Containing Molecules. ACS Omega 2019, accepted.
  4. Li, L.; Wang, X.; Guo, H.; Yao, G.; Yu, H.; Tian, Z.; Li, B.; Chen, L. Theoretical Screening of Single Transition Metal Atoms Embedded in MXene Defects as Superior Electrocatalyst of Nitrogen Reduction Reaction. Small Methods 2019, 1900337.
  5. Xiao, K.; Wang, X.; Yu, H. Comparative Studies of Catalytic Pathways for Streptococcus Pneumoniae Sialidases NanA, NanB and NanC. Scientific Reports 2019, 9, 2157.
  6. Gao, P.; Wang, X.; Yu, H. Towards an Accurate Prediction of Nitrogen Chemical Shifts by Density Functional Theory and Gauge-Including Atomic Orbital. Advanced Theory and Simulations 2019, 2, 1800148.
  7. Wang, X.; Yu, L.; Inakollu, V. S. S.; Pan, X.; Ma, J.; Yu, H. Molecular Quantum-Dot Cellular Automata Based on Diboryl Radical Anions. Journal of Physical Chemistry C 2018, 122, 2454–2460.
  8. Nguyen, P. T. V.; Yu, H.; Keller, P. A. Molecular Docking Studies to Explore Potential Binding Pockets and Inhibitors for Chikungunya Virus Envelope Glycoproteins. Interdisciplinary Sciences: Computational Life Sciences 2018, 515–524.
  9. Dobie, C.; Montgomery, A. P.; Szabo, R.; Skropeta, D.; Yu, H. Computer-Aided Design of Human Sialyltransferase Inhibitors of hST8Sia III. Journal of Molecular Recognition 2018, 31 (2), e2684.
  10. Wang, X.; Yu, H. The Effect of DNA Backbone on the Triplet Mechanism of UV-Induced Thymine-Thymine (6–4) Dimer Formation. Journal of Molecular Modeling 2018, 24, 319.
  11. Le, M. H.; Tieu, K.; Zhu, H.; Ta, D. T.; Yu, H.; Ta, T. T. H.; Tran, N. V.; Wan, S. Depolymerization of Sodium Polyphosphates on Iron Oxide Surface at High Temperature. Physical Chemistry Chemial Physics 2018, 20, 7819–7835.
  12. Fu, Y.; Han, D.; Wang, Y.; Di, X.; Yu, H.; Mu, T. Remodeling the Endoplasmic Reticulum Proteostasis Network Restores Proteostasis of Pathogenic GABAA Receptors. PLoS One 2018, 13, e0207948.
  13. Inakollu, V. S. S.; Yu, H. A Systematic Benchmarking of Computational Vibrational Spectroscopy with DFTB3: Normal Mode Analysis and Fast Fourier Transform Dipole Autocorrelation Function. Journal of Computational Chemistry 2018, 39, 2067–2078.
  14. Poad, B. L. J.; Maccarone, A. T.; Yu, H.; Mitchell, T. W.; Saied, E. M.; Arenz, C.; Hornemann, T.; Bull, J. N.; Bieske, E. J.; Blanksby, S. J. Differential-Mobility Spectrometry of 1-Deoxysphingosine Isomers: New Insights into the Gas Phase Structures of Ionized Lipids. Analytical Chemistry 2018, 90, 5343–5351.
  15. Huong, T. T. T.; Tieu, K.; Zhu, H.; Yu, H.; Ta, T. D.; Wan, S.; Tran, N. V.; Le, M. H. Chemical Origin of Sodium Phosphate Interactions on Iron and Iron Oxide Surfaces by First Principle Calculations. Journal of Physical Chemistry C 2018, 122, 635–647.
  16. Montgomery, A. P.; Xiao, K.; Wang, X.; Skropeta, D.; Yu, H. Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design. Advances in Protein Chemistry and Structural Biology 2017, 109, 25–76.
  17. Montgomery, A. P.; Skropeta, D.; Yu, H. Transition State-Based ST6Gal I Inhibitors: Mimicking the Phosphodiester Linkage with a Triazole or Carbamate through an Enthalpy-Entropy Compensation. Scientific Reports 2017, 7, 14428.
  18. Vipperla, B.; Griffiths, T. M.; Wang, X.; Yu, H. Theoretical PKa Prediction of the Alpha-Phosphate Moiety of Uridine 5’-Diphosphate-GlcNAc. Chemical Physics Letters 2017, 667, 220–225.
  19. Xiao, K.; Yu, H. Rationalising PKa Shifts in Bacillus Circulans Xylanase with Computational Studies. Physical Chemistry Chemial Physics 2016, 18, 30305–30312.
  20. Jin, T.; Yu, H.; Huang, X.-F. Selective Binding Modes and Allosteric Inhibitory Effects of Lupane Triterpenes on Protein Tyrosine Phosphatase 1B. Scientific Reports 2016, 6, 20766.
  21. Montgomery, A.; Szabo, R.; Skropeta, D.; Yu, H. Computational Characterisation of the Interactions between Human ST6Gal I and Transition-State Analogue Inhibitors: Insights for Inhibitor Design. Journal of Molecular Recognition 2016, 29 (5), 210–222.
  22. Chen, W.; Yu, H.; Wu, G.; He, T.; Li, Z.; Guo, Z.; Liu, H.; Huang, Z.; Chen, P. Ammonium Aminodiboranate: A Long-Sought Isomer of Diammoniate of Diborane and Ammonia Borane Dimer. Chemistry - A European Journal 2016, 22 (23), 7727–7729.
  23. Nguyen, P. T. V.; Yu, H.; Keller, P. A. Identification of Chikungunya Virus nsP2 Protease Inhibitors Using Structure-Base Approaches. Journal of Molecular Graphics and Modelling 2015, 57, 1–8.
  24. Yu, H.; Griffiths, T. M. PKa Cycling of the General Acid/Base in Glycoside Hydrolase Families 33 and 34. Physical Chemistry Chemial Physics 2014, 16 (12), 5785–5792.
  25. Nguyen, P. T. V.; Yu, H.; Keller, P. A. Discovery of in Silico Hits Targeting the nsP3 Macro Domain of Chikungunya Virus. Journal of Molecular Modeling 2014, 20 (5), 1–12.
  26. Zhu, X.; Yang, Y.; Yu, H. In Silico Enzyme Modelling. Australian Biochemist 2014, 45, 12–15.
  27. Daily, M.; Yu, H.; Phillips, J., George N.; Cui, Q. Allosteric Activation Transitions in Enzymes and Biomolecular Motors: Insights from Atomistic and Coarse-Grained Simulations. Topics in Current Chemistry 2013, 2013, 1–26.
  28. Luo, Y.; Jiang, W.; Yu, H.; MacKerell, A. D.; Roux, B. Simulation Study of Ion Pairing in Concentrated Aqueous Salt Solutions with a Polarizable Force Field. Faraday Discussions 2013, 160, 135–149.
  29. Yu, H.; Ratheal, I. M.; Artigas, P.; Roux, B. Molecular Mechanisms of K Selectivity in Na/K Pump. Australian Journal of Chemistry 2012, 65, 448–456.
  30. Roux, B.; Berneche, S.; Egwolf, B.; Lev, B.; Noskov, S. Y.; Rowley, C. N.; Yu, H. Ion Selectivity in Channels and Transporters. Journal of General Physiology 2011, 137, 415–426.
  31. Yu, H.; Ratheal, I. M.; Artigas, P.; Roux, B. Protonation of Key Acidic Residues Is Critical for the K Selectivity of the Na/K Pump. Nature Structural and Molecular Biology 2010, 18, 1159–1163.
  32. Yu, H.; Whitfield, T. W.; Harder, E.; Lamoureux, G.; Vorobyov, I.; Anisimov, V. M.; MacKerell, A. D.; Roux, B. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. Journal of Chemical Theory and Computation 2010, 6, 774–786.
  33. Roux, B.; Yu, H. Assessing the Accuracy of Approximate Treatments of Ion Hydration Based on Primitive Quasichemical Theory. Journal of Chemical Physics 2010, 132, 234101.
  34. Yu, H.; Mazzanti, C. L.; Whitfield, T. W.; Koeppe, R. E.; Andersen, O. S.; Roux, B. A Combined Experimental and Theoretical Study of Ion Solvation in Liquid N-Methylacetamide. Journal of the American Chemical Society 2010, 132, 10847–10856.
  35. Ratheal, I. M.; Virgin, G. K.; Yu, H.; Roux, B.; Gatto, C.; Artigas, P. Selectivity of Externally Facing Ion-Binding Sites in the Na/K Pump to Alkali Metals and Organic Cations. Proceedings of the National Academy of Sciences of the United States of America 2010, 107, 18718–18723.
  36. Yu, H.; Noskov, S. Y.; Roux, B. Two Mechanisms of Ion Selectivity in Protein Binding Sites. Proceedings of the National Academy of Sciences of the United States of America 2010, 107, 20329–20334.
  37. Yu, H.; Roux, B. On the Utilization of Energy Minimization to the Study of Ion Selectivity. Biophysical Journal 2009, 97, L15–L17.
  38. Yu, H.; Noskov, S. Y.; Roux, B. Hydration Number, Topological Control, and Ion Selectivity. Journal of Physical Chemistry B 2009, 113, 8725–8730.
  39. Yang, Y.; Yu, H.; York, D.; Elstner, M.; Cui, Q. Description of Phosphate Hydrolysis Reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) Theory. 1. Parameterization. Journal of Chemical Theory and Computation 2008, 4, 2067–2084.
  40. Yang, Y.; Yu, H.; Cui, Q. Extensive Conformational Transitions Are Required to Turn on ATP Hydrolysis in Myosin. Journal of Molecular Biology 2008, 381, 1407–1420.
  41. Li, Z. Y.; Yu, H.; Zhuang, W.; Mukamel, S. Geometry and Excitation Energy Fluctuations of NMA in Aqueous Solution with CHARMM, AMBER, OPLS, and GROMOS Force Fields: Implications for Protein Ultraviolet Spectra Simulation. Chemical Physics Letters 2008, 452, 78–83.
  42. Phatak, P.; Ghosh, N.; Yu, H.; Cui, Q.; Elstner, M. Amino Acids with an Intermolecular Proton Bond as Proton Storage Site in Bacteriorhodopsin. Proceedings of the National Academy of Sciences of the United States of America 2008, 105, 19672–19677.
  43. Yu, H.; Ma, L.; Yang, Y.; Cui, Q. Mechanochemical Coupling in the Myosin Motor Domain. I. Insights from Equilibrium Active-Site Simulations. PLoS Computational Biology 2007, 3, 199–213.
  44. Yu, H.; Cui, Q. The Vibrational Spectra of Protonated Water Clusters: A Benchmark for Self-Consistent-Charge Density-Functional Tight Binding. Journal of Chemical Physics 2007, 127, 234504.
  45. Yang, Y.; Yu, H.; York, D.; Cui, Q.; Elstner, M. Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method: Third-Order Expansion of the Density Functional Theory Total Energy and Introduction of a Modified Effective Coulomb Interaction. Journal of Physical Chemistry A 2007, 111, 10861–10873.
  46. Winger, M.; Yu, H.; Redfield, C.; van Gunsteren, W. F. Molecular Dynamics Simulation of Human Interleukin-4: Comparison with NMR Data and Effect of PH, Counterions and Force Field on Tertiary Structure Stability. Molecular Simulation 2007, 33, 1143–1154.
  47. Yu, H.; Ma, L.; Yang, Y.; Cui, Q. Mechanochemical Coupling in the Myosin Motor Domain. II. Analysis of Critical Residues. PLoS Computational Biology 2007, 3, 214–230.
  48. Yu, H.; Kohl, A.; Binz, H. K.; Pluckthun, A.; Grutter, M. G.; van Gunsteren, W. F. Molecular Dynamics Study of the Stabilities of Consensus Designed Ankyrin Repeat Proteins. Proteins-Structure Function and Bioinformatics 2006, 65, 285–295.
  49. Yu, H.; Geerke, D. P.; Liu, H.; van Gunsteren, W. Molecular Dynamics Simulations of Liquid Methanol and Methanol-Water Mixtures with Polarizable Models. Journal of Computational Chemistry 2006, 27, 1494–1504.
  50. Riccardi, D.; Schaefer, P.; Yang, Y.; Yu, H.; Ghosh, N.; Prat-Resina, X.; Konig, P.; Li, G.; Xu, D.; Guo, H.; Elstner, M.; Cui, Q. Development of Effective Quantum Mechanical/Molecular Mechanical (QM/MM) Methods for Complex Biological Processes. Journal of Physical Chemistry B 2006, 110, 6458–6469.
  51. van Gunsteren, W.; Bakowies, D.; Baron, R.; Chandrasekhar, I.; Christen, M.; Daura, X.; Gee, P.; Geerke, D. P.; Glattli, A.; Hunenberger, P. H.; Kastenholz, M. A.; Ostenbrink, C.; Schenk, M.; Trzesniak, D.; Vegt, N. F. A. van der; Yu, H. Biomolecular Modeling: Goals, Problems, Perspectives. Angewandte Chemie-International Edition 2006, 45, 4064–4092.
  52. Riccardi, D.; Konig, P.; Prat-Resina, X.; Yu, H.; Elstner, M.; Frauenheim, T.; Cui, Q. "Proton Holes" in Long-Range Proton Transfer Reactions in Solution and Enzymes: A Theoretical Analysis. Journal of the American Chemical Society 2006, 128, 16302–16311.
  53. Yu, H.; van Gunsteren, W. Accounting for Polarization in Molecular Simulation. Computer Physics Communications 2005, 172, 69–85.
  54. Yu, H.; Amann, M.; Hansson, T.; Kohler, J.; Wich, G.; van Gunsteren, W. Effect of Methylation on the Stability and Solvation Free Energy of Amylose and Cellulose Fragments: a Molecular Dynamics Study. Carbohydrate Research 2004, 339, 1697–1709.
  55. Glattli, A.; Oostenbrink, C.; Daura, X.; Geerke, D. P.; Yu, H.; van Gunsteren, W. On the Transferability of the SPCAL Water Model to Biomolecular Simulation. Brazilian Journal of Physics 2004, 34, 116–125.
  56. Yu, H.; Daura, X.; van Gunsteren, W. Molecular Dynamics Simulations of Peptides Containing an Unnatural Amino Acid: Dimerization, Folding, and Protein Binding. Proteins-Structure Function and Genetics 2004, 54, 116–127.
  57. Yu, H.; van Gunsteren, W. Charge-on-Spring Polarizable Water Models Revisited: From Water Clusters to Liquid Water to Ice. Journal of Chemical Physics 2004, 121, 9549–9564.
  58. Yu, H.; Ramseier, M.; Burgi, R.; van Gunsteren, W. Comparison of Properties of Aib-Rich Peptides in Crystal and Solution: A Molecular Dynamics Study. ChemPhysChem 2004, 5, 633–641.
  59. Yu, H.; Hansson, T.; van Gunsteren, W. Development of a Simple, Self-Consistent Polarizable Model for Liquid Water. Journal of Chemical Physics 2003, 118, 221–234.
  60. van Gunsteren, W.; Bakowies, D.; Burgi, R.; Chandrasekhar, I.; Christen, M.; Daura, X.; Gee, P.; Glattli, A.; Hansson, T.; Oostenbrink, C.; Peter, C.; Pitera, J.; Schuler, L.; Soares, T.; Yu, H. Molecular Dynamics Simulation of Biomolecular Systems. CHIMIA 2001, 55, 856–860.
  61. Zhu, J.; Yu, H.; Fan, H.; Liu, H.; Shi, Y. Design of New Selective Inhibitors of Cyclooxygenase-2 by Dynamic Assembly of Molecular Building Blocks. Journal of Computer-Aided Molecular Design 2001, 15, 447–463.

Book Chapters

  1. Yu, H.; Yang, Y.; Ma, L.; Cui, Q. Mechanochemical Coupling in Molecular Motors: Insights from Molecular Simulations of the Myosin Motor Domain. In Proteins: Energy, Heat and Signal Flow; Leitner, D. M., Straub, J. E., Eds.; CRC Press, 2010; pp 23–46.

Conference Abstracts

  1. Wang, X.; Inakollu, V. S. S.; Yu, H. Molecular Quantum-Dot Cellular Automata Based on Diboryl Monoradical Anions. In Abstracts of Papers of The American Chemical Society; Amer Chem Soc, 2018; Vol. 256.
  2. Griffith, T. M.; Yu, H. Oxygen Binding Sites in Obelin: A Computational Study into the Formation of Active Photoproteins. In Luminescence; 2014; Vol. 29, p 21.
  3. Yu, H. Catalysis in Silico. In Proceeding of Australian Physiological Society; 2012; Vol. 43, p 176.
  4. Cordero-Morales, J. F.; Jogini, V.; Vasquez, V.; Bourdeau, R. W.; Yu, H.; Roux, B.; Tristani-Firouzi, M.; Perozo, E. Engineering the hERG1 Selectivity Filter into the NaK Pore Domain. In Biophysical Journal; 2011; Vol. 100, p 584a.
  5. Yu, H.; Artigas, P.; Roux, B. Microscopic Mechanism of Ion Selectivity in the Nak Pump. In Biophysical Journal; 2010; Vol. 98, p 330a.
  6. Yu, H.; Noskov, S. Y.; Roux, B. The Role of Architectural and Structural Forces in Ion Selectivity. In Biophysical Journal; 2010; Vol. 98, p 330a.
  7. Virgin, G.; Ratheal, I.; Yaragatupalli, S.; Yu, H.; Roux, B.; Gatto, C.; Artigas, P. Ion-Selectivity of Externally Facing Na+-Exclusive and Na+/K+-Shared Sites in the Na/K-Pump. In Biophysical Journal; 2010; Vol. 98, p 168a.
  8. Yu, H.; Whitfield, T. W.; Noskov, S. Y.; Mazzanti, C. L.; II, R. E. K.; Andersen, O. S.; Roux, B. Development of a Drude Polarizable Force Field for Ion-Water and Ion-NMA Interactions and Application to Selectivity in Ion Channels. In Biophysical Journal; 2009; Vol. 96, p 660a.

Theses

  1. Montgomery, A. Rational Design of Inhibitors Targeting Human Sialyltransferases. PhD thesis, UOW, 2019.
  2. Xiao, K. Understanding the Catalytic Mechanisms of Selected Glycoside Hydrolases. PhD thesis, UOW, 2018.
  3. Griffiths, T. Atomistic Insights into Photoprotein Formation: Computational Prediction of the Properties of Coelenterazine and Oxygen Binding in Obelin. PhD thesis, UOW, 2018.
  4. Jin, T. Investigation of Lupane Triterpene as a Novel PTP1B Allosteric Inhibitor for the Improvement of Neurite Outgrowth and Synaptogenesis. PhD thesis, UOW, 2017.
  5. Dobie, C. Rational Design of Selective Inhibitors Targeting Human Sialyltransferases. BSc Hons thesis, UOW, 2016.
  6. Nguyen, P. T. V. In Silico Drug Discovery Targeting Chikungunya Virus. PhD thesis, UOW, 2015.
  7. Montgomery, A. Rational Design of Selective Inhibitors Targeting Human Sialyltransferases. BSc Hons thesis, UOW, 2014.
  8. Wright, B. Development of a Polarisable Force Field for Nafion. BSc Hons thesis, UOW, 2011.
  9. Yu, H. Biomolecular Simulation: Inclusion of Polarizability, Prediction of Conformational Stability, and Analysis of Peptide Folding and Association. PhD thesis, ETH Zurich, 2004.
  10. Yu, H. Molecular Dynamics Simulation of MoPrP (121-231) Unfolding at Low PH. BSc thesis, USTC, 2000.

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