::: Preprints ::: Journal ::: Chapters ::: Theses ::: Downloads


    Peer Reviewed Journal Articles

    1. Ta HTT, Tieu AK, Zhu H, Yu H, Tran NV, Tran BH, Wan S, Ta TD (2020) Ab Initio Study on Physical and Chemical Interactions at Borates and Iron Oxide Interface at High Temperature. Chemical Physics 529:110548.
    2. Fan H-N, Wang X-Y, Yu H-B, Gu Q-F, Chen S-L, Liu Z, Chen X-H, Luo W-B, Liu H-K (2020) Enhanced Potassium Ion Battery by Inducing Interlayer Anionic Ligands in MoS 1.5Se0.5 Nanosheets with Exploration of the Mechanism. Adv Energy Mater 10(21):1904162.
    3. Gao P, Huang Z, Yu H (2020) Exploration of the Dehydrogenation Pathways of Ammonia Diborane and Diammoniate of Diborane by Molecular Dynamics Simulations Using Reactive Force Fields. J Phys Chem A 124(9):1698–1704.
    4. Gaston JJ, McCosker PM, Yu H, Keller PA (2020) Predicting Phosphirane Air Stability Using Density Functional Theory. Journal of Physical Organic Chemistry (n/a):e4110.
    5. Griffiths TM, Oakley AJ, Yu H (2020) Atomistic Insights into Photoprotein Formation: Computational Prediction of the Properties of Coelenterazine and Oxygen Binding in Obelin. J Comput Chem 41(6):587–603.
    6. Inakollu VSS, Geerke DP, Rowley CN, Yu H (2020) Polarisable Force Fields: What Do They Add in Biomolecular Simulations? Current Opinion in Structural Biology 61:182–190.
    7. Le MH, Tieu AK, Zhu H, Ta DT, Yu H, T. H. Ta T, Tran VN (2020) Surface Transformation and Interactions of Iron Oxide in Glassy Lubricant: An Ab Initio Study. Chemical Physics:110919.
    8. Luna-Ramirez K, Csoti A, McArthur JR, Chin YKY, Anangi R, Najera Rdel C, Possani LD, King GF, Panyi G, Yu H, Adams DJ, Finol-Urdaneta RK (2020) Structural Basis of the Potency and Selectivity of Urotoxin, a Potent Kv1 Blocker from Scorpion Venom. Biochemical Pharmacology 174:113782.
    9. Montgomery AP, Dobie C, Szabo R, Hallam L, Ranson M, Yu H, Skropeta D (2020) Design, Synthesis and Evaluation of Carbamate-Linked Uridyl-Based Inhibitors of Human ST6Gal I. Bioorganic & Medicinal Chemistry 28(14):115561.
    10. Awoonor-Williams E, Isley WC, Dale SG, Johnson ER, Yu H, Becke AD, Roux B, Rowley CN (2020) Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols. J Comput Chem 41(5):427–438.
    11. Pham SQT, Assadawi N, Wells J, Sophocleous R, Davis KJ, Yu H, Sluyter R, Dillon CT, Kelso C, Beck J, Willis A, Richardson C, Ralph S (2020) A New Class of Quadruplex DNA-Binding Nickel Schiff Base Complexes. Dalton Trans 48(15):4843–4860.
    12. Ta HTT, Tieu AK, Zhu H, Yu H, Tran NV, Le HM, Ta TD (2020) Structural Response of Alkali Metal Borates at Fe2O3 Sliding Interface: The Effect of Alkali Cations. Computational Materials Science 184:109930.
    13. Ta HTT, Tieu AK, Zhu H, Yu H, Tran NV, Ta TD (2020) Mechanisms of Pressure-Induced Structural Transformation in Confined Sodium Borate Glasses. J Phys Chem B 124(1):277–287.
    14. Guo H, Li L, Wang X, Yao G, Yu H, Tian Z, Li B, Chen L (2019) Theoretical Investigation on the Single Transition-Metal Atom-Decorated Defective MoS \textsubscript2 for Electrocatalytic Ammonia Synthesis. ACS Appl Mater Interfaces 11(40):36506–36514.
    15. Xiao K, Wang X, Yu H (2019) Comparative Studies of Catalytic Pathways for Streptococcus Pneumoniae Sialidases NanA, NanB and NanC. Scientific Reports 9(1):2157.
    16. Li L, Wang X, Guo H, Yao G, Yu H, Tian Z, Li B, Chen L (2019) Theoretical Screening of Single Transition Metal Atoms Embedded in MXene Defects as Superior Electrocatalyst of Nitrogen Reduction Reaction. Small Methods 3(11):1900337.
    17. Brown R, Zamani F, Gardiner M, Yu H, Pyne SG, Hyland CJT (2019) Divergent Pd-Catalyzed Cross-Coupling of Allenyloxazolidinones to Give Chiral 1,3-Dienes and Vinyloxazolidinones. Chemical Science 10:9051.
    18. Chen Y, Wang X, Lao M, Rui K, Zheng X, Yu H, Ma J, Dou SX, Sun W (2019) Electrocatalytically Inactive SnS2 Promotes Water Adsorption/Dissociation on Molybdenum Dichalcogenides for Accelerated Alkaline Hydrogen Evolution. Nano Energy 64:103918.
    19. 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.
    20. 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.
    21. Zhao G, Wang X, Wang S, Rui K, Chen Y, Yu H, Ma J, Dou SX, Sun W (2019) Heteroatom-Doped MoSe2 Nanosheets with Enhanced Hydrogen Evolution Kinetics for Alkaline Water Splitting. Chemistry – An Asian Journal 14(2):301–306.
    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(11):319.
    23. 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.
    24. 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(25):2067–2078.
    25. Le MH, Tieu AK, Zhu H, Ta DT, Yu H, Ta TTH, Tran VN, Wan S (2018) Depolymerization of Sodium Polyphosphates on an Iron Oxide Surface at High Temperature. Physical Chemistry Chemical Physics 20(11):7819–7835.
    26. Ta HTT, Tieu AK, Zhu H, Yu H, Ta TD, Wan S, Tran NV, Le HM (2018) Chemical Origin of Sodium Phosphate Interactions on Iron and Iron Oxide Surfaces by First Principle Calculations. The Journal of Physical Chemistry C 122(1):635–647.
    27. Fu Y-L, Han D-Y, Wang Y-J, Di X-J, Yu H-B, Mu T-W (2018) Remodeling the Endoplasmic Reticulum Proteostasis Network Restores Proteostasis of Pathogenic GABAA Receptors. PLOS ONE 13(11):e0207948.
    28. 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 10(3):515–524.
    29. Wang X, Yu L, Inakollu VSS, Pan X, Ma J, Yu H (2018) Molecular Quantum Dot Cellular Automata Based on Diboryl Monoradical Anions. The Journal of Physical Chemistry C 122(4):2454–2460.
    30. Poad BLJ, Maccarone AT, Yu H, Mitchell TW, Saied EM, Arenz C, Hornemann T, Bull JN, Bieske EJ, Blanksby SJ (2018) Differential-Mobility Spectrometry of 1-Deoxysphingosine Isomers: New Insights into the Gas Phase Structures of Ionized Lipids. Analytical Chemistry 90(8):5343–5351.
    31. 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(1):14428.
    32. Vipperla B, Griffiths TM, Wang X, Yu H (2017) Theoretical p Ka Prediction of the α-Phosphate Moiety of Uridine 5’-Diphosphate-GlcNAc. Chemical Physics Letters 667:220–225.
    33. Xiao K, Yu H (2016) Rationalising pK \textsubscripta Shifts in Bacillus Circulans Xylanase with Computational Studies. Physical Chemistry Chemical Physics 18(44):30305–30312.
    34. 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: Molecular Modelling of Human ST6Gal I-Inhibitor Complexes. Journal of Molecular Recognition 29(5):210–222.
    35. Chen W, Yu H, Wu G, He T, Li Z, Guo Z, Liu H, Huang Z, Chen P (2016) Ammonium Aminodiboranate: A Long-Sought Isomer of Diammoniate of Diborane and Ammonia Borane Dimer. Chemistry - A European Journal 22(23):7727–7729.
    36. 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(1):20766.
    37. 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.
    38. 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.
    39. Zhu X, Yang Y, Yu H (2014) In Silico Enzyme Modelling. Australian Biochemist 45(2):4.
    40. Yu H, Griffiths TM (2014) pKa Cycling of the General Acid/Base in Glycoside Hydrolase Families 33 and 34. Physical Chemistry Chemical Physics 16(12):5785.
    41. 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 Discuss 160:135–149.
    42. Yu H, Ratheal I, Artigas P, Roux B (2012) Molecular Mechanisms of K+ Selectivity in Na/K Pump. Australian Journal of Chemistry 65(5):448.
    43. Roux B, Bernèche S, Egwolf B, Lev B, Noskov SY, Rowley CN, Yu H (2011) Ion Selectivity in Channels and Transporters. The Journal of General Physiology 137(5):415–426.
    44. Yu H, Ratheal IM, Artigas P, Roux B (2011) Protonation of Key Acidic Residues Is Critical for the K+-Selectivity of the Na/K Pump. Nature Structural & Molecular Biology 18(10):1159–1163.
    45. Roux B, Yu H (2010) Assessing the Accuracy of Approximate Treatments of Ion Hydration Based on Primitive Quasichemical Theory. The Journal of Chemical Physics 132(23):234101.
    46. Yu H, Whitfield TW, Harder E, Lamoureux G, Vorobyov I, Anisimov VM, MacKerell AD, Roux B (2010) Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. Journal of Chemical Theory and Computation 6(3):774–786.
    47. Yu H, Mazzanti CL, Whitfield TW, Koeppe RE, Andersen OS, Roux B (2010) A Combined Experimental and Theoretical Study of Ion Solvation in Liquid \emphN -Methylacetamide. Journal of the American Chemical Society 132(31):10847–10856.
    48. Ratheal IM, Virgin GK, Yu H, Roux B, Gatto C, Artigas P (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 107(43):18718–18723.
    49. Yu H, Noskov SY, Roux B (2010) Two Mechanisms of Ion Selectivity in Protein Binding Sites. Proceedings of the National Academy of Sciences 107(47):20329–20334.
    50. Yu H, Roux B (2009) On the Utilization of Energy Minimization to the Study of Ion Selectivity. Biophysical Journal 97(8):L15–L17.
    51. Yu H, Noskov SY, Roux B (2009) Hydration Number, Topological Control, and Ion Selectivity. The Journal of Physical Chemistry B 113(25):8725–8730.
    52. 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 105(50):19672–19677.
    53. Li Z, 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(1-3):78–83.
    54. 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(12):2067–2084.
    55. Yang Y, Yu H, Cui Q (2008) Extensive Conformational Transitions Are Required to Turn On ATP Hydrolysis in Myosin. Journal of Molecular Biology 381(5):1407–1420.
    56. Yang, 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. The Journal of Physical Chemistry A 111(42):10861–10873.
    57. Yu H, Cui Q (2007) The Vibrational Spectra of Protonated Water Clusters: A Benchmark for Self-Consistent-Charge Density-Functional Tight Binding. The Journal of Chemical Physics 127(23):234504.
    58. 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(2):15.
    59. 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(2):17.
    60. Winger M, Yu H, Redfield C, van Gunsteren WF (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(14):1143–1154.
    61. van Gunsteren WF, Bakowies D, Baron R, Chandrasekhar I, Christen M, Daura X, Gee P, Geerke DP, Glättli A, Hünenberger PH, Kastenholz MA, Oostenbrink C, Schenk M, Trzesniak D, van der Vegt NFA, Yu HB (2006) Biomolecular Modeling: Goals, Problems, Perspectives. Angewandte Chemie International Edition 45(25):4064–4092.
    62. Riccardi D, Schaefer P, Yang, Yu H, Ghosh N, Prat-Resina X, König P, Li G, Xu D, Guo H, Elstner M, Cui Q (2006) Development of Effective Quantum Mechanical/Molecular Mechanical (QM/MM) Methods for Complex Biological Processes. The Journal of Physical Chemistry B 110(13):6458–6469.
    63. Riccardi D, König P, Prat-Resina X, Yu H, Elstner M, Frauenheim T, Cui Q (2006) “Proton Holes” in Long-Range Proton Transfer Reactions in Solution and Enzymes: A Theoretical Analysis. Journal of the American Chemical Society 128(50):16302–16311.
    64. Yu H, Geerke DP, Liu H, van Gunsteren WF (2006) Molecular Dynamics Simulations of Liquid Methanol and Methanol–Water Mixtures with Polarizable Models. Journal of Computational Chemistry 27(13):1494–1504.
    65. Yu H, Kohl A, Binz HK, Plückthun A, Grütter MG, van Gunsteren WF (2006) Molecular Dynamics Study of the Stabilities of Consensus Designed Ankyrin Repeat Proteins. Proteins: Structure, Function, and Bioinformatics 65(2):285–295.
    66. Yu H, van Gunsteren WF (2005) Accounting for Polarization in Molecular Simulation. Computer Physics Communications 172(2):69–85.
    67. Yu H, van Gunsteren WF (2004) Charge-on-Spring Polarizable Water Models Revisited: From Water Clusters to Liquid Water to Ice. The Journal of Chemical Physics 121(19):9549–9564.
    68. Yu H, Ramseier M, Bürgi R, van Gunsteren WF (2004) Comparison of Properties of Aib-Rich Peptides in Crystal and Solution: A Molecular Dynamics Study. ChemPhysChem 5(5):633–641.
    69. Yu H, Amann M, Hansson T, Köhler J, Wich G, van Gunsteren WF (2004) Effect of Methylation on the Stability and Solvation Free Energy of Amylose and Cellulose Fragments: A Molecular Dynamics Study. Carbohydrate Research 339(10):1697–1709.
    70. Glättli A, Oostenbrink C, Daura X, Geerke DP, Yu H, van Gunsteren WF (2004) On the Transferability of the SPC/L Water Model to Biomolecular Simulation. Brazilian Journal of Physics 34(1):116–125.
    71. Yu H, Hansson T, van Gunsteren WF (2003) Development of a Simple, Self-Consistent Polarizable Model for Liquid Water. The Journal of Chemical Physics 118(1):221–234.
    72. Yu H, Daura X, van Gunsteren WF (2003) Molecular Dynamics Simulations of Peptides Containing an Unnatural Amino Acid: Dimerization, Folding, and Protein Binding. Proteins: Structure, Function, and Bioinformatics 54(1):116–127.
    73. van Gunsteren WF, Bakowies D, Bürgi R, Chandrasekhar I, Christen M, Daura X, Gee P, Glättli A, Hansson T, Oostenbrink C, Peter C, Pitera J, Schuler L, Soares T, Yu H (2001) Molecular Dynamics Simulation of Biomolecular Systems. CHIMIA International Journal for Chemistry 55(10):856–860.
    74. 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. J Comput Aided Mol Des 15(5):447–463.

    Book Chapters

    1. 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 (Elsevier), pp 25–76.
    2. Daily MD, Yu H, Phillips GN, Cui Q (2013) Allosteric Activation Transitions in Enzymes and Biomolecular Motors: Insights from Atomistic and Coarse-Grained Simulations. Dynamics in Enzyme Catalysis, eds Klinman J, Hammes- Schiffer S, pp 139–164.
    3. Yu H, Yang Y, Ma L, Qiang C (2010) Mechanochemical Coupling in Molecular Motors: Insights from Molecular Simulations of the Myosin Motor Domain. Proteins: Energy Heata Nd Signal Flow (CRC Press, Boca Raton, FL), p 24. 1st Ed.


    1. Gao P (2020) Computer-Aided Hydrogen Storage Materials Design: Accurate Predictions of NMR Chemical Shifts and MD Simulation of Nitrogen and Boron Containing Compounds. PhD thesis (UOW).
    2. Montgomery A (2019) Rational Design of Inhibitors Targeting Human Sialyltransferases. PhD thesis (UOW).
    3. Griffiths TM (2019) Atomistic Insights into Photoprotein Formation: Computational Prediction of the Properties of Coelenterazine and Oxygen Binding in Obelin. PhD thesis (UOW).
    4. Xiao K (2018) Understanding the Catalytic Mechanisms of Selected Glycoside Hydrolases. PhD thesis (UOW).
    5. 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).
    6. Jin T (2017) Investigation of Lupane Triterpene as a Novel PTP1B Allosteric Inhibitor for the Improvement of Neurite Outgrowth and Synaptogenesis. 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).