Yu, Haibo Associate Professor

Member Of

• Molecular Horizons Member 2019 -
• School of Chemistry and Molecular Bioscience Academic Staff 2010 -
• Illawarra Health and Medical Research Institute Honorary Research Fellow 2016 - 2019

Selected Publications

• Journal Article

  Year	Title
  2022	Direct SN2 or SN2X Manifold-Mechanistic Study of Ion-Pair-Catalyzed Carbon(sp3)-Carbon(sp3) Bond Formation Published In Journal of Organic Chemistry
  2022	Disruption of Water Networks is the Cause of Human/Mouse Species Selectivity in Urokinase Plasminogen Activator (uPA) Inhibitors Derived from Hexamethylene Amiloride (HMA) Published In Journal of Medicinal Chemistry
  2022	Urokinase plasminogen activator as an anti-metastasis target: inhibitor design principles, recent amiloride derivatives, and issues with human/mouse species selectivity Published In Biophysical Reviews
  2021	1,6;2,3-Bis-BN Cyclohexane: Synthesis, Structure, and Hydrogen Release Published In Journal of the American Chemical Society
  2021	A first-principles study of impurity-enhanced adhesion and lubricity of graphene on iron oxide surface Published In Journal of Physical Chemistry C
  2021	An Amine¿Borane System Featuring Room-Temperature Dehydrogenation and Regeneration Published In Angewandte Chemie - International Edition
  2021	An Amine¿Borane System Featuring Room-Temperature Dehydrogenation and Regeneration Published In Angewandte Chemie
  2021	Comparative studies of IR spectra of deprotonated serine with classical and thermostated ring polymer molecular dynamics simulations Published In Structural Dynamics
  2021	Computational Tribochemistry: A Review from Classical and Quantum Mechanics Studies Published In Journal of Physical Chemistry C
  2021	Postsynthetic Modification of Half-Sandwich Ruthenium Complexes by Mechanochemical Synthesis Published In Inorganic Chemistry
  2021	Sialyltransferase Inhibitors as Potential Anti-Cancer Agents Published In Australian Journal of Chemistry
  2021	Synthesis and biological evaluation of selective phosphonate-bearing 1,2,3-triazole-linked sialyltransferase inhibitors Published In RSC Medicinal Chemistry
  2021	The Detosylation of Chiral 1,2-Bis(tosylamides) Published In Journal of Organic Chemistry
  2020	11B NMR Chemical Shift Predictions via Density Functional Theory and Gauge-Including Atomic Orbital Approach: Applications to Structural Elucidations of Boron-Containing Molecules Published In ACS Omega
  2020	Atomistic Insights into Photoprotein Formation: Computational Prediction of the Properties of Coelenterazine and Oxygen Binding in Obelin Published In Journal of Computational Chemistry
  2020	Comparative studies of catalytic pathways for Streptococcus pneumoniae sialidases NanA, NanB and NanC Published In Scientific Reports
  2020	Divergent Pd-catalyzed cross-coupling of allenyloxazolidinones to give chiral 1,3-dienes and vinyloxazolidinones Published In Chemical Science
  2020	Electrocatalytically inactive SnS2 promotes water adsorption/dissociation on molybdenum dichalcogenides for accelerated alkaline hydrogen evolution Published In Nano Energy
  2020	Heteroatom-doped MoSe2 Nanosheets with Enhanced Hydrogen Evolution Kinetics for Alkaline Water Splitting Published In Chemistry: An Asian Journal
  2020	Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols Published In Journal of Computational Chemistry
  2020	Theoretical Investigation on The Single Transition-Metal Atom-Decorated Defective MoS2 for Electrocatalytic Ammonia Synthesis Published In ACS Applied Materials and Interfaces
  2020	Theoretical Screening of Single Transition Metal Atoms Embedded in MXene Defects as Superior Electrocatalyst of Nitrogen Reduction Reaction Published In Small Methods
  2020	Towards an Accurate Prediction of Nitrogen Chemical Shifts by Density Functional Theory and Gauge-Including Atomic Orbital Published In Advanced Theory and Simulations
  2020	A new class of quadruplex DNA-binding nickel Schiff base complexes Published In Dalton Transactions
  2020	Ab initio study on physical and chemical interactions at borates and iron oxide interface at high temperature Published In Chemical Physics
  2020	Design, synthesis and evaluation of carbamate-linked uridyl-based inhibitors of human ST6Gal I Published In Bioorganic and Medicinal Chemistry
  2020	Enhanced Potassium Ion Battery by Inducing Interlayer Anionic Ligands in MoS1.5Se0.5 Nanosheets with Exploration of the Mechanism Published In Advanced Energy Materials
  2020	Exploration of the Dehydrogenation Pathways of Ammonia Diborane and Diammoniate of Diborane by Molecular Dynamics Simulations Using Reactive Force Fields Published In The Journal of Physical Chemistry A: Isolated Molecules, Clusters, Radicals, and Ions; Environmental Chemistry, Geochemistry, and Astrochemistry; Theory
  2020	Mechanisms of Pressure-Induced Structural Transformation in Confined Sodium Borate Glasses Published In Journal of Physical Chemistry B
  2020	Polarisable force fields: what do they add in biomolecular simulations? Published In Current Opinion in Structural Biology
  2020	Predicting phosphirane air stability using density functional theory Published In Journal of Physical Organic Chemistry
  2020	Structural basis of the potency and selectivity of Urotoxin, a potent Kv1 blocker from scorpion venom Published In Biochemical Pharmacology
  2020	Structural basis of the potency and selectivity of Urotoxin, a potent Kv1 blocker from scorpion venom Published In Biochemical Pharmacology
  2020	Structural response of alkali metal borates at Fe2O3 sliding interface: The effect of alkali cations Published In Computational Materials Science
  2020	Surface transformation and interactions of iron oxide in glassy lubricant: An ab initio study Published In Chemical Physics
  2019	11B NMR Chemical Shift Predictions via Density Functional Theory and Gauge-Including Atomic Orbital Approach: Applications to Structural Elucidations of Boron-Containing Molecules Published In ACS Omega
  2019	Atomistic Insights into Photoprotein Formation: Computational Prediction of the Properties of Coelenterazine and Oxygen Binding in Obelin Published In Journal of Computational Chemistry
  2019	Comparative studies of catalytic pathways for Streptococcus pneumoniae sialidases NanA, NanB and NanC Published In Scientific Reports
  2019	Divergent Pd-catalyzed cross-coupling of allenyloxazolidinones to give chiral 1,3-dienes and vinyloxazolidinones Published In Chemical Science
  2019	Electrocatalytically inactive SnS2 promotes water adsorption/dissociation on molybdenum dichalcogenides for accelerated alkaline hydrogen evolution Published In Nano Energy
  2019	Heteroatom-doped MoSe2 Nanosheets with Enhanced Hydrogen Evolution Kinetics for Alkaline Water Splitting Published In Chemistry: An Asian Journal
  2019	Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols Published In Journal of Computational Chemistry
  2019	Theoretical Investigation on The Single Transition-Metal Atom-Decorated Defective MoS2 for Electrocatalytic Ammonia Synthesis Published In ACS Applied Materials and Interfaces
  2019	Theoretical Screening of Single Transition Metal Atoms Embedded in MXene Defects as Superior Electrocatalyst of Nitrogen Reduction Reaction Published In Small Methods
  2019	Towards an Accurate Prediction of Nitrogen Chemical Shifts by Density Functional Theory and Gauge-Including Atomic Orbital Published In Advanced Theory and Simulations
  2018	A systematic benchmarking of computational vibrational spectroscopy with DFTB3: Normal mode analysis and fast Fourier transform dipole autocorrelation function Published In Journal of Computational Chemistry
  2018	Chemical Origin of Sodium Phosphate Interactions on Iron and Iron Oxide Surfaces by First Principle Calculations Published In The Journal of Physical Chemistry C: Energy Conversion and Storage, Optical and Electronic Devices, Interfaces, Nanomaterials, and Hard Matter
  2018	Computer‐aided design of human sialyltransferase inhibitors of hST8Sia III Published In Journal of Molecular Recognition
  2018	Depolymerization of sodium polyphosphates on an iron oxide surface at high temperature Published In Physical Chemistry Chemical Physics
  2018	Differential-Mobility Spectrometry of 1-Deoxysphingosine Isomers: New Insights into the Gas Phase Structures of Ionized Lipids Published In Analytical Chemistry
  2018	Molecular Quantum Dot Cellular Automata Based on Diboryl Monoradical Anions Published In The Journal of Physical Chemistry C: Energy Conversion and Storage, Optical and Electronic Devices, Interfaces, Nanomaterials, and Hard Matter
  2018	Molecular docking studies to explore potential binding pockets and inhibitors for chikungunya virus envelope glycoproteins Published In Interdisciplinary Sciences: Computational Life Sciences
  2018	Remodeling the endoplasmic reticulum proteostasis network restores proteostasis of pathogenic GABA A receptors Published In PLoS One
  2018	The effect of DNA backbone on the triplet mechanism of UV-induced thymine-thymine (6–4) dimer formation Published In Journal of Molecular Modeling
  2017	Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design Published In Advances in Protein Chemistry and Structural Biology
  2017	Theoretical pKa prediction of the α-phosphate moiety of uridine 5′-diphosphate-GlcNAc Published In Chemical Physics Letters
  2017	Transition state-based ST6Gal I inhibitors: Mimicking the phosphodiester linkage with a triazole or carbamate through an enthalpy-entropy compensation Published In Scientific Reports
  2016	Ammonium aminodiboranate: A long-sought isomer of diammoniate of diborane and ammonia borane dimer Published In Chemistry: A European Journal
  2016	ChemInform Abstract: Ammonium Aminodiboranate: A Long¿Sought Isomer of Diammoniate of Diborane and Ammonia Borane Dimer. Published In ChemInform
  2016	Computational characterisation of the interactions between human ST6Gal I and transition-state analogue inhibitors: insights for inhibitor design Published In Journal of Molecular Recognition
  2016	Rationalising pKa shifts in Bacillus circulans xylanase with computational studies Published In Physical Chemistry Chemical Physics
  2016	Selective binding modes and allosteric inhibitory effects of lupane triterpenes on protein tyrosine phosphatase 1B Published In Scientific Reports
  2015	Identification of chikungunya virus nsP2 protease inhibitors using structure-base approaches Published In Journal of Molecular Graphics and Modelling
  2014	Discovery of in silico hits targeting the nsP3 macro domain of chikungunya virus Published In Journal of Molecular Modeling
  2014	In silico enzyme modelling Published In Australian Biochemist
  2014	Oxygen binding sites in obelin: a computational study into the formation of active photoproteins Published In Luminescence: journal of biological and chemical luminescence
  2014	PKa cycling of the general acid/base in glycoside hydrolase families 33 and 34 Published In Physical Chemistry Chemical Physics
  2013	Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations Published In Topics in Current Chemistry
  2013	Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field Published In Faraday Discussions
  2012	Molecular mechanisms of K+ selectivity in Na/K pump Published In Australian Journal of Chemistry: an international journal for chemical science
  2011	Ion selectivity in channels and transporters Published In Journal of General Physiology
  2011	Protonation of key acidic residues is critical for the K+-selectivity of the Na/K pump Published In Nature Structural and Molecular Biology
  2010	A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide Published In Journal of the American Chemical Society
  2010	Assessing the accuracy of approximate treatments of ion hydration based on primitive quasichemical theory Published In Journal of Chemical Physics
  2010	Microscopic Mechanism of Ion Selectivity in the Nak Pump Published In Biophysical Journal
  2010	Selectivity of externally facing ion-binding sites in the Na/K pump to alkali metals and organic cations Published In Proceedings of the National Academy of Sciences of USA
  2010	Simulating monovalent and divalent ions in aqueous solution using a drude polarizable force field Published In Journal of Chemical Theory and Computation
  2010	The Role of Architectural and Structural Forces in Ion Selectivity Published In Biophysical Journal
  2010	Two mechanisms of ion selectivity in protein binding sites Published In Proceedings of the National Academy of Sciences of USA
  2009	Hydration number, topological control, and ion selectivity Published In The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter
  2009	On the utilization of energy minimization to the study of ion selectivity Published In Biophysical Journal
  2008	Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin Published In Proceedings of the National Academy of Sciences of USA
  2008	Description of phosphate hydrolysis reactions with the self-consistent-charge density-functional-tight-binding (SCC-DFTB) theory: 1. Parameterization Published In Journal of Chemical Theory and Computation
  2008	Extensive conformational transitions are required to turn on ATP hydrolysis in myosin Published In Journal of Molecular Biology
  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 Published In Chemical Physics Letters
  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 Published In The Journal of Physical Chemistry A: Isolated Molecules, Clusters, Radicals, and Ions; Environmental Chemistry, Geochemistry, and Astrochemistry; Theory
  2007	Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations Published In PLoS Computational Biology
  2007	Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues Published In PLoS Computational Biology
  2007	Molecular dynamics simulation of human interleukin-4: comparison with NMR data and effect of pH, counterions and force field on tertiary structure stability Published In Molecular Simulation
  2007	The vibrational spectra of protonated water clusters: a benchmark for self-consistent-charge density-functional tight binding Published In Journal of Chemical Physics
  2006	Biomolekulare Modellierung: Ziele, Probleme, Perspektiven Published In Angewandte Chemie

• Chapter

  Year	Title
  2010	Mechanochemical coupling in molecular motors: insights from molecular simulations of the myosin motor domain Published In Proteins: Energy, Heat and Signal Flow Publisher Boca Raton, FL

• Conference Paper

  Year	Title
  2013	Virtual screening identifies lupeol as an allosteric inhibitor of PTP1B Published In 33rd Meeting of the Australian Neuroscience Society: Program, Abstracts & List of Registrants
  2012	Catalysis in silico Published In Proceedings of the Australian Physiological Society
  2011	Engineering the hERG1 Selectivity Filter into the NaK Pore Domain Published In BIOPHYSICAL JOURNAL
  2010	Ion-Selectivity of Externally Facing Na+-Exclusive and Na+/K+-Shared Sites in the Na/K-Pump Published In BIOPHYSICAL JOURNAL
  2010	Microscopic Mechanism of Ion Selectivity in the Nak Pump Published In BIOPHYSICAL JOURNAL
  2010	The Role of Architectural and Structural Forces in Ion Selectivity Published In BIOPHYSICAL JOURNAL
  2009	Development of a Drude Polarizable Force Field for Ion-water and Ion-NMA Interactions and Application to Selectivity in Ion Channels Published In BIOPHYSICAL JOURNAL

Investigator On

Year	Title
2022	Novel hydrogen-rich liquids for transporting hydrogen at scale Awarded by: Australian Research Council (ARC) Funding Scheme: Discovery Projects
2021 - 2022	Australiasian Computational and Simulation Commons (ACSC) Awarded by: Australian Research Data Commons (ARDC) Funding Scheme: Australian Data Partnerships
2018 - 2021	Anti-sporulation strategies for Clostridium difficile infections Awarded by: National Health and Medical Research Council (NHMRC) Funding Scheme: Project Grant
2012 - 2016	Computational enzymology: exploring the free energy landscape of enzymatic catalysis Awarded by: Australian Research Council (ARC) Funding Scheme: Future Fellowships
2014	Renewing Intersect's share of the National Computational Infrastructure's peak facility Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage Infrastructure Equipment & Facilities (LIEF)
	Liquid-phase hydrogen carriers for energy storage and delivery Awarded by: Australian Research Council (ARC) Funding Scheme: Discovery Projects

Impact Story

Potential Supervision Topics

• • Develop computational and theoretical models to study biomolecular and nanoscale systems
  • Computer-aided drug design
  • Computational enzymology (combined QM/MM simulations)
  • Computer-aided materials design

Advisees

• Graduate Advising Relationship

  Degree	Research Title	Advisee
  Doctor of Philosophy	Molecular Modelling Studies into Amiloride Analogues as Inhibitors of Human Urokinase Plasminogen Activator and Sodium Hydrogen Exchanger 1
  Doctor of Philosophy	Understanding the Molecular Mechanisms of Single-strand Annealing Homologous DNA Recombination in Bacteriophages, by cryo-EM	Mantri, Bhanu
  Doctor of Philosophy	Computational Techniques for Determining Radical Reaction Pathways	Turner, Jack
  Doctor of Philosophy	Structure based design of inhibitors targeting galectins	Siddiqui, Muhammad Zahir
  Doctor of Philosophy	Improving Cancer Radiotherapy with Therapeutic Agents Targeting Cell Surface Sugars	Steele, Harrison

Organizer Of Event

• MM2015 - the annual conference of the Association of Molecular Modellers of Australasia 2015

Professional Service Activities

• PeerJ Physical Chemistry Editorial Board Member 2019 -
• The Association of Molecular Modellers of Australasia (AMMA) Committee member 2018 -
• Journal of Molecular Modeling Associate Editor 2012 -
• Scientific Reports Editorial Board Member 2014 - 2018

Education And Training

• Ph.D., ETH Zürich, Department of Chemistry and Applied Biosciences 2000 - 2004
• B.Sc., University of Science and Technology of China, School of Life Sciences 1995 - 2000
• University of Chicago, USA, Department of Biochemistry and Molecular Biology 2007 - 2010
• University of Wisconsin - Madison, USA, Department of Chemistry 2005 - 2007

Awards And Honors

• Future Fellowship, conferred by Australian Research Council (ARC), 2012 - 2016

Keywords

• Biomolecular simulations, free energy calculations, combined QM/MM simulations, computational biophysics, computer-aided drug design, computer-aided materials design

Full Name

• Haibo Yu

Mailing Address

• School of Chemistry and Molecular Bioscience

  University of Wollongong

  Wollongong

  NSW

  2500

  Australia

Located In Facility

• Building 42 
• Room 112 

Orcid Id

• http://orcid.org/0000-0002-1099-2803 (confirmed)

Web Of Science Researcher Id

• B-9750-2008

Top Publications

Year	Title
2017	Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design Published in   Advances in Protein Chemistry and Structural Biology
2016	Ammonium aminodiboranate: A long-sought isomer of diammoniate of diborane and ammonia borane dimer Published in   Chemistry: A European Journal
2014	PKa cycling of the general acid/base in glycoside hydrolase families 33 and 34 Published in   Physical Chemistry Chemical Physics
2011	Protonation of key acidic residues is critical for the K+-selectivity of the Na/K pump Published in   Nature Structural and Molecular Biology
2010	A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide Published in   Journal of the American Chemical Society

Research Areas

• 0304 - MEDICINAL AND BIOMOLECULAR CHEMISTRY
• 0307 - THEORETICAL AND COMPUTATIONAL CHEMISTRY
• 0601 - BIOCHEMISTRY AND CELL BIOLOGY

Research Overview

• The research program in the Yu Research Group covers a broad range of topics in the area of theoretical/computational chemistry and biophysics. The common goal underlying these research directions is to develop effective theoretical and computational models for complex molecular processes in order to gain new physical insights into the mechanism at a quantitative level.

Member Of

• Molecular Horizons Member 2019 -
• School of Chemistry and Molecular Bioscience Academic Staff 2010 -
• Illawarra Health and Medical Research Institute Honorary Research Fellow 2016 - 2019

Selected Publications

• Journal Article

  Year	Title
  2022	Direct SN2 or SN2X Manifold-Mechanistic Study of Ion-Pair-Catalyzed Carbon(sp3)-Carbon(sp3) Bond Formation Published In Journal of Organic Chemistry
  2022	Disruption of Water Networks is the Cause of Human/Mouse Species Selectivity in Urokinase Plasminogen Activator (uPA) Inhibitors Derived from Hexamethylene Amiloride (HMA) Published In Journal of Medicinal Chemistry
  2022	Urokinase plasminogen activator as an anti-metastasis target: inhibitor design principles, recent amiloride derivatives, and issues with human/mouse species selectivity Published In Biophysical Reviews
  2021	1,6;2,3-Bis-BN Cyclohexane: Synthesis, Structure, and Hydrogen Release Published In Journal of the American Chemical Society
  2021	A first-principles study of impurity-enhanced adhesion and lubricity of graphene on iron oxide surface Published In Journal of Physical Chemistry C
  2021	An Amine¿Borane System Featuring Room-Temperature Dehydrogenation and Regeneration Published In Angewandte Chemie - International Edition
  2021	An Amine¿Borane System Featuring Room-Temperature Dehydrogenation and Regeneration Published In Angewandte Chemie
  2021	Comparative studies of IR spectra of deprotonated serine with classical and thermostated ring polymer molecular dynamics simulations Published In Structural Dynamics
  2021	Computational Tribochemistry: A Review from Classical and Quantum Mechanics Studies Published In Journal of Physical Chemistry C
  2021	Postsynthetic Modification of Half-Sandwich Ruthenium Complexes by Mechanochemical Synthesis Published In Inorganic Chemistry
  2021	Sialyltransferase Inhibitors as Potential Anti-Cancer Agents Published In Australian Journal of Chemistry
  2021	Synthesis and biological evaluation of selective phosphonate-bearing 1,2,3-triazole-linked sialyltransferase inhibitors Published In RSC Medicinal Chemistry
  2021	The Detosylation of Chiral 1,2-Bis(tosylamides) Published In Journal of Organic Chemistry
  2020	11B NMR Chemical Shift Predictions via Density Functional Theory and Gauge-Including Atomic Orbital Approach: Applications to Structural Elucidations of Boron-Containing Molecules Published In ACS Omega
  2020	Atomistic Insights into Photoprotein Formation: Computational Prediction of the Properties of Coelenterazine and Oxygen Binding in Obelin Published In Journal of Computational Chemistry
  2020	Comparative studies of catalytic pathways for Streptococcus pneumoniae sialidases NanA, NanB and NanC Published In Scientific Reports
  2020	Divergent Pd-catalyzed cross-coupling of allenyloxazolidinones to give chiral 1,3-dienes and vinyloxazolidinones Published In Chemical Science
  2020	Electrocatalytically inactive SnS2 promotes water adsorption/dissociation on molybdenum dichalcogenides for accelerated alkaline hydrogen evolution Published In Nano Energy
  2020	Heteroatom-doped MoSe2 Nanosheets with Enhanced Hydrogen Evolution Kinetics for Alkaline Water Splitting Published In Chemistry: An Asian Journal
  2020	Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols Published In Journal of Computational Chemistry
  2020	Theoretical Investigation on The Single Transition-Metal Atom-Decorated Defective MoS2 for Electrocatalytic Ammonia Synthesis Published In ACS Applied Materials and Interfaces
  2020	Theoretical Screening of Single Transition Metal Atoms Embedded in MXene Defects as Superior Electrocatalyst of Nitrogen Reduction Reaction Published In Small Methods
  2020	Towards an Accurate Prediction of Nitrogen Chemical Shifts by Density Functional Theory and Gauge-Including Atomic Orbital Published In Advanced Theory and Simulations
  2020	A new class of quadruplex DNA-binding nickel Schiff base complexes Published In Dalton Transactions
  2020	Ab initio study on physical and chemical interactions at borates and iron oxide interface at high temperature Published In Chemical Physics
  2020	Design, synthesis and evaluation of carbamate-linked uridyl-based inhibitors of human ST6Gal I Published In Bioorganic and Medicinal Chemistry
  2020	Enhanced Potassium Ion Battery by Inducing Interlayer Anionic Ligands in MoS1.5Se0.5 Nanosheets with Exploration of the Mechanism Published In Advanced Energy Materials
  2020	Exploration of the Dehydrogenation Pathways of Ammonia Diborane and Diammoniate of Diborane by Molecular Dynamics Simulations Using Reactive Force Fields Published In The Journal of Physical Chemistry A: Isolated Molecules, Clusters, Radicals, and Ions; Environmental Chemistry, Geochemistry, and Astrochemistry; Theory
  2020	Mechanisms of Pressure-Induced Structural Transformation in Confined Sodium Borate Glasses Published In Journal of Physical Chemistry B
  2020	Polarisable force fields: what do they add in biomolecular simulations? Published In Current Opinion in Structural Biology
  2020	Predicting phosphirane air stability using density functional theory Published In Journal of Physical Organic Chemistry
  2020	Structural basis of the potency and selectivity of Urotoxin, a potent Kv1 blocker from scorpion venom Published In Biochemical Pharmacology
  2020	Structural basis of the potency and selectivity of Urotoxin, a potent Kv1 blocker from scorpion venom Published In Biochemical Pharmacology
  2020	Structural response of alkali metal borates at Fe2O3 sliding interface: The effect of alkali cations Published In Computational Materials Science
  2020	Surface transformation and interactions of iron oxide in glassy lubricant: An ab initio study Published In Chemical Physics
  2019	11B NMR Chemical Shift Predictions via Density Functional Theory and Gauge-Including Atomic Orbital Approach: Applications to Structural Elucidations of Boron-Containing Molecules Published In ACS Omega
  2019	Atomistic Insights into Photoprotein Formation: Computational Prediction of the Properties of Coelenterazine and Oxygen Binding in Obelin Published In Journal of Computational Chemistry
  2019	Comparative studies of catalytic pathways for Streptococcus pneumoniae sialidases NanA, NanB and NanC Published In Scientific Reports
  2019	Divergent Pd-catalyzed cross-coupling of allenyloxazolidinones to give chiral 1,3-dienes and vinyloxazolidinones Published In Chemical Science
  2019	Electrocatalytically inactive SnS2 promotes water adsorption/dissociation on molybdenum dichalcogenides for accelerated alkaline hydrogen evolution Published In Nano Energy
  2019	Heteroatom-doped MoSe2 Nanosheets with Enhanced Hydrogen Evolution Kinetics for Alkaline Water Splitting Published In Chemistry: An Asian Journal
  2019	Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols Published In Journal of Computational Chemistry
  2019	Theoretical Investigation on The Single Transition-Metal Atom-Decorated Defective MoS2 for Electrocatalytic Ammonia Synthesis Published In ACS Applied Materials and Interfaces
  2019	Theoretical Screening of Single Transition Metal Atoms Embedded in MXene Defects as Superior Electrocatalyst of Nitrogen Reduction Reaction Published In Small Methods
  2019	Towards an Accurate Prediction of Nitrogen Chemical Shifts by Density Functional Theory and Gauge-Including Atomic Orbital Published In Advanced Theory and Simulations
  2018	A systematic benchmarking of computational vibrational spectroscopy with DFTB3: Normal mode analysis and fast Fourier transform dipole autocorrelation function Published In Journal of Computational Chemistry
  2018	Chemical Origin of Sodium Phosphate Interactions on Iron and Iron Oxide Surfaces by First Principle Calculations Published In The Journal of Physical Chemistry C: Energy Conversion and Storage, Optical and Electronic Devices, Interfaces, Nanomaterials, and Hard Matter
  2018	Computer‐aided design of human sialyltransferase inhibitors of hST8Sia III Published In Journal of Molecular Recognition
  2018	Depolymerization of sodium polyphosphates on an iron oxide surface at high temperature Published In Physical Chemistry Chemical Physics
  2018	Differential-Mobility Spectrometry of 1-Deoxysphingosine Isomers: New Insights into the Gas Phase Structures of Ionized Lipids Published In Analytical Chemistry
  2018	Molecular Quantum Dot Cellular Automata Based on Diboryl Monoradical Anions Published In The Journal of Physical Chemistry C: Energy Conversion and Storage, Optical and Electronic Devices, Interfaces, Nanomaterials, and Hard Matter
  2018	Molecular docking studies to explore potential binding pockets and inhibitors for chikungunya virus envelope glycoproteins Published In Interdisciplinary Sciences: Computational Life Sciences
  2018	Remodeling the endoplasmic reticulum proteostasis network restores proteostasis of pathogenic GABA A receptors Published In PLoS One
  2018	The effect of DNA backbone on the triplet mechanism of UV-induced thymine-thymine (6–4) dimer formation Published In Journal of Molecular Modeling
  2017	Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design Published In Advances in Protein Chemistry and Structural Biology
  2017	Theoretical pKa prediction of the α-phosphate moiety of uridine 5′-diphosphate-GlcNAc Published In Chemical Physics Letters
  2017	Transition state-based ST6Gal I inhibitors: Mimicking the phosphodiester linkage with a triazole or carbamate through an enthalpy-entropy compensation Published In Scientific Reports
  2016	Ammonium aminodiboranate: A long-sought isomer of diammoniate of diborane and ammonia borane dimer Published In Chemistry: A European Journal
  2016	ChemInform Abstract: Ammonium Aminodiboranate: A Long¿Sought Isomer of Diammoniate of Diborane and Ammonia Borane Dimer. Published In ChemInform
  2016	Computational characterisation of the interactions between human ST6Gal I and transition-state analogue inhibitors: insights for inhibitor design Published In Journal of Molecular Recognition
  2016	Rationalising pKa shifts in Bacillus circulans xylanase with computational studies Published In Physical Chemistry Chemical Physics
  2016	Selective binding modes and allosteric inhibitory effects of lupane triterpenes on protein tyrosine phosphatase 1B Published In Scientific Reports
  2015	Identification of chikungunya virus nsP2 protease inhibitors using structure-base approaches Published In Journal of Molecular Graphics and Modelling
  2014	Discovery of in silico hits targeting the nsP3 macro domain of chikungunya virus Published In Journal of Molecular Modeling
  2014	In silico enzyme modelling Published In Australian Biochemist
  2014	Oxygen binding sites in obelin: a computational study into the formation of active photoproteins Published In Luminescence: journal of biological and chemical luminescence
  2014	PKa cycling of the general acid/base in glycoside hydrolase families 33 and 34 Published In Physical Chemistry Chemical Physics
  2013	Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations Published In Topics in Current Chemistry
  2013	Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field Published In Faraday Discussions
  2012	Molecular mechanisms of K+ selectivity in Na/K pump Published In Australian Journal of Chemistry: an international journal for chemical science
  2011	Ion selectivity in channels and transporters Published In Journal of General Physiology
  2011	Protonation of key acidic residues is critical for the K+-selectivity of the Na/K pump Published In Nature Structural and Molecular Biology
  2010	A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide Published In Journal of the American Chemical Society
  2010	Assessing the accuracy of approximate treatments of ion hydration based on primitive quasichemical theory Published In Journal of Chemical Physics
  2010	Microscopic Mechanism of Ion Selectivity in the Nak Pump Published In Biophysical Journal
  2010	Selectivity of externally facing ion-binding sites in the Na/K pump to alkali metals and organic cations Published In Proceedings of the National Academy of Sciences of USA
  2010	Simulating monovalent and divalent ions in aqueous solution using a drude polarizable force field Published In Journal of Chemical Theory and Computation
  2010	The Role of Architectural and Structural Forces in Ion Selectivity Published In Biophysical Journal
  2010	Two mechanisms of ion selectivity in protein binding sites Published In Proceedings of the National Academy of Sciences of USA
  2009	Hydration number, topological control, and ion selectivity Published In The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter
  2009	On the utilization of energy minimization to the study of ion selectivity Published In Biophysical Journal
  2008	Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin Published In Proceedings of the National Academy of Sciences of USA
  2008	Description of phosphate hydrolysis reactions with the self-consistent-charge density-functional-tight-binding (SCC-DFTB) theory: 1. Parameterization Published In Journal of Chemical Theory and Computation
  2008	Extensive conformational transitions are required to turn on ATP hydrolysis in myosin Published In Journal of Molecular Biology
  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 Published In Chemical Physics Letters
  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 Published In The Journal of Physical Chemistry A: Isolated Molecules, Clusters, Radicals, and Ions; Environmental Chemistry, Geochemistry, and Astrochemistry; Theory
  2007	Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations Published In PLoS Computational Biology
  2007	Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues Published In PLoS Computational Biology
  2007	Molecular dynamics simulation of human interleukin-4: comparison with NMR data and effect of pH, counterions and force field on tertiary structure stability Published In Molecular Simulation
  2007	The vibrational spectra of protonated water clusters: a benchmark for self-consistent-charge density-functional tight binding Published In Journal of Chemical Physics
  2006	Biomolekulare Modellierung: Ziele, Probleme, Perspektiven Published In Angewandte Chemie

• Chapter

  Year	Title
  2010	Mechanochemical coupling in molecular motors: insights from molecular simulations of the myosin motor domain Published In Proteins: Energy, Heat and Signal Flow Publisher Boca Raton, FL

• Conference Paper

  Year	Title
  2013	Virtual screening identifies lupeol as an allosteric inhibitor of PTP1B Published In 33rd Meeting of the Australian Neuroscience Society: Program, Abstracts & List of Registrants
  2012	Catalysis in silico Published In Proceedings of the Australian Physiological Society
  2011	Engineering the hERG1 Selectivity Filter into the NaK Pore Domain Published In BIOPHYSICAL JOURNAL
  2010	Ion-Selectivity of Externally Facing Na+-Exclusive and Na+/K+-Shared Sites in the Na/K-Pump Published In BIOPHYSICAL JOURNAL
  2010	Microscopic Mechanism of Ion Selectivity in the Nak Pump Published In BIOPHYSICAL JOURNAL
  2010	The Role of Architectural and Structural Forces in Ion Selectivity Published In BIOPHYSICAL JOURNAL
  2009	Development of a Drude Polarizable Force Field for Ion-water and Ion-NMA Interactions and Application to Selectivity in Ion Channels Published In BIOPHYSICAL JOURNAL

Investigator On

Year	Title
2022	Novel hydrogen-rich liquids for transporting hydrogen at scale Awarded by: Australian Research Council (ARC) Funding Scheme: Discovery Projects
2021 - 2022	Australiasian Computational and Simulation Commons (ACSC) Awarded by: Australian Research Data Commons (ARDC) Funding Scheme: Australian Data Partnerships
2018 - 2021	Anti-sporulation strategies for Clostridium difficile infections Awarded by: National Health and Medical Research Council (NHMRC) Funding Scheme: Project Grant
2012 - 2016	Computational enzymology: exploring the free energy landscape of enzymatic catalysis Awarded by: Australian Research Council (ARC) Funding Scheme: Future Fellowships
2014	Renewing Intersect's share of the National Computational Infrastructure's peak facility Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage Infrastructure Equipment & Facilities (LIEF)
	Liquid-phase hydrogen carriers for energy storage and delivery Awarded by: Australian Research Council (ARC) Funding Scheme: Discovery Projects

Impact Story

Potential Supervision Topics

• • Develop computational and theoretical models to study biomolecular and nanoscale systems
  • Computer-aided drug design
  • Computational enzymology (combined QM/MM simulations)
  • Computer-aided materials design

Advisees

• Graduate Advising Relationship

  Degree	Research Title	Advisee
  Doctor of Philosophy	Molecular Modelling Studies into Amiloride Analogues as Inhibitors of Human Urokinase Plasminogen Activator and Sodium Hydrogen Exchanger 1
  Doctor of Philosophy	Understanding the Molecular Mechanisms of Single-strand Annealing Homologous DNA Recombination in Bacteriophages, by cryo-EM	Mantri, Bhanu
  Doctor of Philosophy	Computational Techniques for Determining Radical Reaction Pathways	Turner, Jack
  Doctor of Philosophy	Structure based design of inhibitors targeting galectins	Siddiqui, Muhammad Zahir
  Doctor of Philosophy	Improving Cancer Radiotherapy with Therapeutic Agents Targeting Cell Surface Sugars	Steele, Harrison

Organizer Of Event

• MM2015 - the annual conference of the Association of Molecular Modellers of Australasia 2015

Professional Service Activities

• PeerJ Physical Chemistry Editorial Board Member 2019 -
• The Association of Molecular Modellers of Australasia (AMMA) Committee member 2018 -
• Journal of Molecular Modeling Associate Editor 2012 -
• Scientific Reports Editorial Board Member 2014 - 2018

Education And Training

• Ph.D., ETH Zürich, Department of Chemistry and Applied Biosciences 2000 - 2004
• B.Sc., University of Science and Technology of China, School of Life Sciences 1995 - 2000
• University of Chicago, USA, Department of Biochemistry and Molecular Biology 2007 - 2010
• University of Wisconsin - Madison, USA, Department of Chemistry 2005 - 2007

Awards And Honors

• Future Fellowship, conferred by Australian Research Council (ARC), 2012 - 2016

Keywords

• Biomolecular simulations, free energy calculations, combined QM/MM simulations, computational biophysics, computer-aided drug design, computer-aided materials design

Full Name

• Haibo Yu

Mailing Address

• School of Chemistry and Molecular Bioscience

  University of Wollongong

  Wollongong

  NSW

  2500

  Australia

Located In Facility

• Building 42 
• Room 112 

Orcid Id

• http://orcid.org/0000-0002-1099-2803 (confirmed)

Web Of Science Researcher Id

• B-9750-2008