Publications

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Preprints

    Peer Reviewed Journal Articles

    1. Ta HTT, et al. (2020) Ab Initio Study on Physical and Chemical Interactions at Borates and Iron Oxide Interface at High Temperature. Chemical Physics 529:110548.
    2. Chen Y, et al. (2019) Electrocatalytically Inactive SnS2 Promotes Water Adsorption/Dissociation on Molybdenum Dichalcogenides for Accelerated Alkaline Hydrogen Evolution. Nano Energy 64:103918.
    3. Gao P, Wang X, Huang Z, Yu H (2019) 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 4:12385−12392.
    4. Gao P, Wang X, Yu H (2019) Towards an Accurate Prediction of Nitrogen Chemical Shifts by Density Functional Theory and Gauge‐Including Atomic Orbital. Advanced Theory and Simulations 2(2):1800148.
    5. Griffiths TM, Oakley AJ, Yu H (2019) Atomistic Insights into Photoprotein Formation: Computational Prediction of the Properties of Coelenterazine and Oxygen Binding in Obelin. Journal of Computational Chemistry. doi:10.1002/jcc.26125.
    6. Guo H, et al. (2019) Theoretical Investigation on The Single Transition Metal Atom Decorated Defective MoS2 for Electrocatalytic Ammonia Synthesis. ACS Applied Materials & Interfaces 11:36506−36514.
    7. Brown R, et al. (2019) Divergent Pd-Catalyzed Cross-Coupling of Allenyloxazolidinones to Give Chiral 1,3-Dienes and Vinyloxazolidinones. Chemical Science 10:9051–9056.
    8. Inakollu VSS, Geerke DP, Rowley CN, Yu H (2019) Polarisable Force Fields: What Do They Add in Biomolecular Simulations? Current Opinion in Structural Biology accepted on 19/12/2019. Available at: http://arxiv.org/abs/1910.14237.
    9. Li L, et al. (2019) Theoretical Screening of Single Transition Metal Atoms Embedded in MXene Defects as Superior Electrocatalyst of Nitrogen Reduction Reaction. Small Methods:1900337.
    10. Luna-Ramirez K, et al. (2019) Structural Basis of the Potency and Selectivity of Urotoxin, a Potent Kv1 Blocker from Scorpion Venom. Biochemical Pharmacology:113782.
    11. Ta HTT, et al. (2019) Mechanisms of Pressure-Induced Structural Transformation in Confined Sodium Borate Glasses. The Journal of Physical Chemistry B. doi:10.1021/acs.jpcb.9b09676.
    12. Xiao K, Wang X, Yu H (2019) Comparative Studies of Catalytic Pathways for Streptococcus Pneumoniae Sialidases NanA, NanB and NanC. Scientific Reports 9(9):2157.
    13. Awoonor‐Williams E, et al. (2019) Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols. Journal of Computational Chemistry. doi:10.1002/jcc.26064.
    14. Zhao G, et al. (2019) Heteroatom-Doped MoSe2 Nanosheets with Enhanced Hydrogen Evolution Kinetics for Alkaline Water Splitting. Chemistry – An Asian Journal 14(2):301–306.
    15. Dobie C, Montgomery AP, Szabo R, Skropeta D, Yu H (2018) Computer-aided design of human sialyltransferase inhibitors of hST8Sia III. Journal of Molecular Recognition 31(2):e2684.
    16. Fu Y, et al. (2018) Remodeling the endoplasmic reticulum proteostasis network restores proteostasis of pathogenic GABAA receptors. PLoS One 13:e0207948.
    17. Inakollu VSS, Yu H (2018) A systematic benchmarking of computational vibrational spectroscopy with DFTB3: Normal mode analysis and fast Fourier transform dipole autocorrelation function. Journal of Computational Chemistry 39:2067–2078.
    18. Poad BLJ, et al. (2018) Differential-mobility spectrometry of 1-deoxysphingosine isomers: new insights into the gas phase structures of ionized lipids. Analytical Chemistry 90:5343–5351.
    19. Wang X, et al. (2018) Molecular Quantum-Dot Cellular Automata Based on Diboryl Radical Anions. Journal of Physical Chemistry C 122:2454–2460.
    20. Huong TTT, et al. (2018) Chemical Origin of Sodium Phosphate Interactions on Iron and Iron Oxide Surfaces by First Principle Calculations. Journal of Physical Chemistry C 122:635–647.
    21. Nguyen PTV, Yu H, Keller PA (2018) Molecular Docking Studies to Explore Potential Binding Pockets and Inhibitors for Chikungunya Virus Envelope Glycoproteins. Interdisciplinary Sciences: Computational Life Sciences:515–524.
    22. Wang X, Yu H (2018) The effect of DNA backbone on the triplet mechanism of UV-induced thymine-thymine (6–4) dimer formation. Journal of Molecular Modeling 24:319.
    23. Le MH, et al. (2018) Depolymerization of sodium polyphosphates on iron oxide surface at high temperature. Physical Chemistry Chemial Physics 20:7819–7835.
    24. Montgomery AP, Skropeta D, Yu H (2017) Transition state-based ST6Gal I inhibitors: Mimicking the phosphodiester linkage with a triazole or carbamate through an enthalpy-entropy compensation. Scientific Reports 7:14428.
    25. Montgomery AP, Xiao K, Wang X, Skropeta D, Yu H (2017) Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design. Advances in Protein Chemistry and Structural Biology 109:25–76.
    26. Vipperla B, Griffiths TM, Wang X, Yu H (2017) Theoretical pKa prediction of the alpha-phosphate moiety of uridine 5’-diphosphate-GlcNAc. Chemical Physics Letters 667:220–225.
    27. Montgomery A, Szabo R, Skropeta D, Yu H (2016) Computational characterisation of the interactions between human ST6Gal I and transition-state analogue inhibitors: insights for inhibitor design. Journal of Molecular Recognition 29(5):210–222.
    28. Xiao K, Yu H (2016) Rationalising pKa shifts in Bacillus circulans xylanase with computational studies. Physical Chemistry Chemial Physics 18:30305–30312.
    29. Chen W, et al. (2016) Ammonium Aminodiboranate: A Long-Sought Isomer of Diammoniate of Diborane and Ammonia Borane Dimer. Chemistry - A European Journal 22(23):7727–7729.
    30. Jin T, Yu H, Huang X-F (2016) Selective binding modes and allosteric inhibitory effects of lupane triterpenes on protein tyrosine phosphatase 1B. Scientific Reports 6:20766.
    31. Nguyen PTV, Yu H, Keller PA (2015) Identification of chikungunya virus nsP2 protease inhibitors using structure-base approaches. Journal of Molecular Graphics and Modelling 57:1–8.
    32. Nguyen PTV, Yu H, Keller PA (2014) Discovery of in silico hits targeting the nsP3 macro domain of chikungunya virus. Journal of Molecular Modeling 20(5):1–12.
    33. Zhu X, Yang Y, Yu H (2014) In Silico Enzyme Modelling. Australian Biochemist 45:12–15.
    34. Yu H, Griffiths TM (2014) pKa cycling of the general acid/base in glycoside hydrolase families 33 and 34. Physical Chemistry Chemial Physics 16(12):5785–5792.
    35. Luo Y, Jiang W, Yu H, MacKerell AD, Roux B (2013) Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field. Faraday Discussions 160:135–149.
    36. Daily M, Yu H, Phillips J George N., Cui Q (2013) Allosteric Activation Transitions in Enzymes and Biomolecular Motors: Insights from Atomistic and Coarse-Grained Simulations. Topics in Current Chemistry 2013:1–26.
    37. Yu H, Ratheal IM, Artigas P, Roux B (2012) Molecular Mechanisms of K Selectivity in Na/K Pump. Australian Journal of Chemistry 65:448–456.
    38. Roux B, et al. (2011) Ion selectivity in channels and transporters. Journal of General Physiology 137:415–426.
    39. Roux B, Yu H (2010) Assessing the accuracy of approximate treatments of ion hydration based on primitive quasichemical theory. Journal of Chemical Physics 132:234101.
    40. Yu H, Noskov SY, Roux B (2010) Two mechanisms of ion selectivity in protein binding sites. Proceedings of the National Academy of Sciences of the United States of America 107:20329–20334.
    41. Yu H, et al. (2010) Simulating monovalent and divalent ions in aqueous solution using a Drude polarizable force field. Journal of Chemical Theory and Computation 6:774–786.
    42. Yu H, et al. (2010) A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide. Journal of the American Chemical Society 132:10847–10856.
    43. Ratheal IM, et al. (2010) 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 107:18718–18723.
    44. Yu H, Ratheal IM, Artigas P, Roux B (2010) Protonation of key acidic residues is critical for the K selectivity of the Na/K pump. Nature Structural and Molecular Biology 18:1159–1163.
    45. Yu H, Noskov SY, Roux B (2009) Hydration number, topological control, and ion selectivity. Journal of Physical Chemistry B 113:8725–8730.
    46. Yu H, Roux B (2009) On the utilization of energy minimization to the study of ion selectivity. Biophysical Journal 97:L15–L17.
    47. Li ZY, Yu H, Zhuang W, Mukamel S (2008) 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 452:78–83.
    48. Phatak P, Ghosh N, Yu H, Cui Q, Elstner M (2008) 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 105:19672–19677.
    49. Yang Y, Yu H, York D, Elstner M, Cui Q (2008) 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 4:2067–2084.
    50. Yang Y, Yu H, Cui Q (2008) Extensive conformational transitions are required to turn on ATP hydrolysis in myosin. Journal of Molecular Biology 381:1407–1420.
    51. Winger M, Yu H, Redfield C, Gunsteren WF van (2007) 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 33:1143–1154.
    52. Yu H, Cui Q (2007) The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding. Journal of Chemical Physics 127:234504.
    53. Yang Y, Yu H, York D, Cui Q, Elstner M (2007) 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 111:10861–10873.
    54. Yu H, Ma L, Yang Y, Cui Q (2007) Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations. PLoS Computational Biology 3:199–213.
    55. Yu H, Ma L, Yang Y, Cui Q (2007) Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues. PLoS Computational Biology 3:214–230.
    56. Riccardi D, et al. (2006) Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. Journal of Physical Chemistry B 110:6458–6469.
    57. Yu H, Geerke DP, Liu H, Gunsteren W van (2006) Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models. Journal of Computational Chemistry 27:1494–1504.
    58. Yu H, et al. (2006) Molecular dynamics study of the stabilities of consensus designed ankyrin repeat proteins. Proteins-Structure Function and Bioinformatics 65:285–295.
    59. Riccardi D, et al. (2006) "Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis. Journal of the American Chemical Society 128:16302–16311.
    60. Gunsteren W van, et al. (2006) Biomolecular modeling: Goals, problems, perspectives. Angewandte Chemie-International Edition 45:4064–4092.
    61. Yu H, Gunsteren W van (2005) Accounting for polarization in molecular simulation. Computer Physics Communications 172:69–85.
    62. Yu H, Gunsteren W van (2004) Charge-on-spring polarizable water models revisited: From water clusters to liquid water to ice. Journal of Chemical Physics 121:9549–9564.
    63. Glattli A, et al. (2004) On the transferability of the SPCAL water model to biomolecular simulation. Brazilian Journal of Physics 34:116–125.
    64. Yu H, Ramseier M, Burgi R, Gunsteren W van (2004) Comparison of properties of aib-rich peptides in crystal and solution: A molecular dynamics study. ChemPhysChem 5:633–641.
    65. Yu H, et al. (2004) Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study. Carbohydrate Research 339:1697–1709.
    66. Yu H, Daura X, Gunsteren W van (2004) Molecular dynamics simulations of peptides containing an unnatural amino acid: Dimerization, folding, and protein binding. Proteins-Structure Function and Genetics 54:116–127.
    67. Yu H, Hansson T, Gunsteren W van (2003) Development of a simple, self-consistent polarizable model for liquid water. Journal of Chemical Physics 118:221–234.
    68. Zhu J, Yu H, Fan H, Liu H, Shi Y (2001) Design of new selective inhibitors of cyclooxygenase-2 by dynamic assembly of molecular building blocks. Journal of Computer-Aided Molecular Design 15:447–463.
    69. Gunsteren W van, et al. (2001) Molecular dynamics simulation of biomolecular systems. CHIMIA 55:856–860.

    Book Chapters

    1. Yu H, Yang Y, Ma L, Cui Q (2010) Mechanochemical coupling in molecular motors: insights from molecular simulations of the myosin motor domain. Proteins: Energy, Heat and Signal Flow, eds Leitner DM, Straub JE (CRC Press), pp 23–46.

    Conference Abstracts

    1. Wang X, Inakollu VSS, Yu H (2018) Molecular quantum-dot cellular automata based on diboryl monoradical anions. Abstracts of Papers of The American Chemical Society (Amer Chem Soc).
    2. Griffith TM, Yu H (2014) Oxygen Binding Sites in Obelin: A Computational Study into the Formation of Active Photoproteins. Luminescence, p 21.
    3. Yu H (2012) Catalysis in silico. Proceeding of Australian Physiological Society, p 176.
    4. Cordero-Morales JF, et al. (2011) Engineering the hERG1 Selectivity Filter into the NaK Pore Domain. Biophysical Journal, p 584a.
    5. Yu H, Artigas P, Roux B (2010) Microscopic Mechanism of Ion Selectivity in the Nak Pump. Biophysical Journal, p 330a.
    6. Yu H, Noskov SY, Roux B (2010) The Role of Architectural and Structural Forces in Ion Selectivity. Biophysical Journal, p 330a.
    7. Virgin G, et al. (2010) Ion-Selectivity of Externally Facing Na+-Exclusive and Na+/K+-Shared Sites in the Na/K-Pump. Biophysical Journal, p 168a.
    8. Yu H, et al. (2009) Development of a Drude Polarizable Force Field for Ion-water and Ion-NMA Interactions and Application to Selectivity in Ion Channels. Biophysical Journal, p 660a.

    Theses

    1. Montgomery A (2019) Rational Design of Inhibitors Targeting Human Sialyltransferases. PhD thesis (UOW).
    2. Xiao K (2018) Understanding the Catalytic Mechanisms of Selected Glycoside Hydrolases. PhD thesis (UOW).
    3. Griffiths T (2018) Atomistic insights into photoprotein formation: computational prediction of the properties of coelenterazine and oxygen binding in Obelin. PhD thesis (UOW).
    4. Dyer T (2018) Mathematical Modelling for Graphitic Nanostructures. PhD thesis (UOW).
    5. Jin T (2017) Investigation of lupane triterpene as a novel PTP1B allosteric inhibitor for the improvement of neurite outgrowth and synaptogenesis. PhD thesis (UOW).
    6. Birrento M (2017) Characterisation of the selectivity and binding interactions of berberine derivatives with G-quadruplex DNA and a DNA/RNA hybrid. PhD thesis (UOW).
    7. Dobie C (2016) Rational Design of Selective Inhibitors Targeting Human Sialyltransferases. BSc Hons thesis (UOW).
    8. Nguyen PTV (2015) In silico drug discovery targeting Chikungunya virus. PhD thesis (UOW).
    9. Montgomery A (2014) Rational Design of Selective Inhibitors Targeting Human Sialyltransferases. BSc Hons thesis (UOW).
    10. Wright B (2011) Development of a Polarisable Force Field for Nafion. BSc Hons thesis (UOW).
    11. Yu H (2004) Biomolecular simulation: inclusion of polarizability, prediction of conformational stability, and analysis of peptide folding and association. PhD thesis (ETH Zurich).
    12. Yu H (2000) Molecular dynamics simulation of MoPrP (121-231) unfolding at low pH. BSc thesis (USTC).

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