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    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:
    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.


    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).