Yu, Haibo

Overview

Dr Haibo Yu completed his undergraduate study at the University of Science and Technology of China under the supervision of Professor Yunyu Shi and his Ph.D. at the ETH Zürich under the supervision of Professor Wilfred F. van Gunsteren. He then conducted postdoctoral training at the University of Wisconsin-Madison with Professor Qiang Cui and the University of Chicago with Professor Benoît Roux in the United States. He joined the School of Chemistry and Molecular Bioscience at the University of Wollongong in July 2010. Currently, he is also a Senior Research Fellow at IHMRI.

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

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.

Available as Research Supervisor

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
2020	Ab initio study on physical and chemical interactions at borates and iron oxide interface at high temperature Published In Chemical Physics Volume 529 Pages 110548-1 - 110548-9 ISSN 0301-0104 Altmetric
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 Volume 4 Pages 12385 - 12392 Altmetric
2019	Comparative studies of catalytic pathways for Streptococcus pneumoniae sialidases NanA, NanB and NanC Published In Scientific Reports Volume 9 Pages 2157-1 - 2157-13 ISSN 2045-2322 Altmetric
2019	Divergent Pd-catalyzed cross-coupling of allenyloxazolidinones to give chiral 1,3-dienes and vinyloxazolidinones Published In Chemical Science Volume 10 Pages 9051 - 9056 ISSN 2041-6520 Altmetric
2019	Electrocatalytically inactive SnS2 promotes water adsorption/dissociation on molybdenum dichalcogenides for accelerated alkaline hydrogen evolution Published In Nano Energy Volume 64 Pages 1 - 6 ISSN 2211-3282 Altmetric
2019	Heteroatom-doped MoSe2 Nanosheets with Enhanced Hydrogen Evolution Kinetics for Alkaline Water Splitting Published In Chemistry: An Asian Journal Volume 14 Pages 301 - 306 ISSN 1861-471X Altmetric
2019	Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols Published In Journal of Computational Chemistry Volume Online First Pages 1 - 12 ISSN 0192-8651 Altmetric
2019	Theoretical Investigation on The Single Transition-Metal Atom-Decorated Defective MoS2 for Electrocatalytic Ammonia Synthesis Published In ACS Applied Materials and Interfaces Volume 11 Pages 36506 - 36514 ISSN 1944-8244 Altmetric
2019	Theoretical Screening of Single Transition Metal Atoms Embedded in MXene Defects as Superior Electrocatalyst of Nitrogen Reduction Reaction Published In Small Methods Volume Online First Pages 1900337-1 - 1900337-7 Altmetric
2019	Towards an Accurate Prediction of Nitrogen Chemical Shifts by Density Functional Theory and Gauge-Including Atomic Orbital Published In Advanced Theory and Simulations Volume 2 Pages 1800148-1 - 1800148-8 Altmetric
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 Volume 39 Pages 2067 - 2078 ISSN 0192-8651 Altmetric
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 Volume 122 Pages 635 - 647 ISSN 1932-7447 Altmetric
2018	Computer‐aided design of human sialyltransferase inhibitors of hST8Sia III Published In Journal of Molecular Recognition Volume 31 Pages e2684-1 - e2684-11 ISSN 0952-3499 Altmetric
2018	Depolymerization of sodium polyphosphates on an iron oxide surface at high temperature Published In Physical Chemistry Chemical Physics Volume 20 Pages 7819 - 7835 ISSN 1463-9076 Altmetric
2018	Differential-Mobility Spectrometry of 1-Deoxysphingosine Isomers: New Insights into the Gas Phase Structures of Ionized Lipids Published In Analytical Chemistry Volume 90 Pages 5343 - 5351 ISSN 0003-2700 Altmetric
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 Volume 122 Pages 2454 - 2460 ISSN 1932-7447 Altmetric
2018	Molecular docking studies to explore potential binding pockets and inhibitors for chikungunya virus envelope glycoproteins Published In Interdisciplinary Sciences: Computational Life Sciences Volume 10 Pages 515 - 524 Altmetric
2018	Remodeling the endoplasmic reticulum proteostasis network restores proteostasis of pathogenic GABA A receptors Published In PLoS One Volume 13 Pages e0207948-1 - e0207948-23 ISSN 1932-6203 Altmetric
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 Volume 24 Pages 319-1 - 319-9 ISSN 0948-5023 Altmetric
2017	Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design Published In Advances in Protein Chemistry and Structural Biology Volume 109 Pages 25 - 76 Altmetric
2017	Theoretical pKa prediction of the α-phosphate moiety of uridine 5′-diphosphate-GlcNAc Published In Chemical Physics Letters Volume 667 Pages 220 - 225 ISSN 0009-2614 Altmetric
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 Volume 7 Pages 14428-1 - 14428-11 ISSN 2045-2322 Altmetric
2016	Ammonium aminodiboranate: A long-sought isomer of diammoniate of diborane and ammonia borane dimer Published In Chemistry: A European Journal Volume 22 Pages 7727 - 7729 ISSN 1521-3765 Altmetric
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 Volume 29 Pages 210 - 222 ISSN 0952-3499 Altmetric
2016	Rationalising pKa shifts in Bacillus circulans xylanase with computational studies Published In Physical Chemistry Chemical Physics Volume 18 Pages 30305 - 30312 ISSN 1463-9076 Altmetric
2016	Selective binding modes and allosteric inhibitory effects of lupane triterpenes on protein tyrosine phosphatase 1B Published In Scientific Reports Volume 6 Pages 20766-1 - 20766-14 ISSN 2045-2322 Altmetric
2015	Identification of chikungunya virus nsP2 protease inhibitors using structure-base approaches Published In Journal of Molecular Graphics and Modelling Volume 57 Pages 1 - 8 ISSN 1093-3263 Altmetric
2014	Discovery of in silico hits targeting the nsP3 macro domain of chikungunya virus Published In Journal of Molecular Modeling Volume 20 Pages 2216-1 - 2216-12 ISSN 0948-5023 Altmetric
2014	In silico enzyme modelling Published In Australian Biochemist Volume 45 Pages 12 - 15
2014	Oxygen binding sites in obelin: a computational study into the formation of active photoproteins Published In Luminescence: journal of biological and chemical luminescence Volume 29 Pages 21 - 21 ISSN 0884-3996 Altmetric
2014	PKa cycling of the general acid/base in glycoside hydrolase families 33 and 34 Published In Physical Chemistry Chemical Physics Volume 16 Pages 5785 - 5792 ISSN 1463-9076 Altmetric
2013	Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations Published In Topics in Current Chemistry Volume 337 Pages 139 - 164 ISSN 0340-1022 Altmetric
2013	Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field Published In Faraday Discussions Volume 160 Pages 135 - 149 ISSN 1359-6640 Altmetric
2012	Molecular mechanisms of K+ selectivity in Na/K pump Published In Australian Journal of Chemistry: an international journal for chemical science Volume 65 Pages 448 - 456 ISSN 0004-9425 Altmetric
2011	Ion selectivity in channels and transporters Published In Journal of General Physiology Volume 137 Pages 415 - 426 ISSN 0022-1295 Altmetric
2011	Protonation of key acidic residues is critical for the K+-selectivity of the Na/K pump Published In Nature Structural and Molecular Biology Volume 18 Pages 1159 - 1163 ISSN 1545-9993 Altmetric
2010	A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide Published In Journal of the American Chemical Society Volume 132 Pages 10847 - 10856 ISSN 0002-7863 Altmetric
2010	Assessing the accuracy of approximate treatments of ion hydration based on primitive quasichemical theory Published In Journal of Chemical Physics Volume 132 Pages 234101-1 - 234101-13 ISSN 0021-9606 Altmetric
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 Volume 107 Pages 18718 - 18723 ISSN 0027-8424 Altmetric
2010	Simulating monovalent and divalent ions in aqueous solution using a drude polarizable force field Published In Journal of Chemical Theory and Computation Volume 6 Pages 774 - 786 ISSN 1549-9618 Altmetric
2010	Two mechanisms of ion selectivity in protein binding sites Published In Proceedings of the National Academy of Sciences of USA Volume 107 Pages 20329 - 20334 ISSN 0027-8424 Altmetric
2009	Hydration number, topological control, and ion selectivity Published In The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter Volume 113 Pages 8725 - 8730 ISSN 1520-6106 Altmetric
2009	On the utilization of energy minimization to the study of ion selectivity Published In Biophysical Journal Volume 97 Pages L15 - L17 ISSN 0006-3495 Altmetric
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 Volume 105 Pages 19672 - 19677 ISSN 0027-8424 Altmetric
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 Volume 4 Pages 2067 - 2084 ISSN 1549-9618 Altmetric
2008	Extensive conformational transitions are required to turn on ATP hydrolysis in myosin Published In Journal of Molecular Biology Volume 381 Pages 1407 - 1420 ISSN 0022-2836 Altmetric
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 Volume 452 Pages 78 - 83 ISSN 0009-2614 Altmetric
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 Volume 111 Pages 10861 - 10873 ISSN 1520-5215 Altmetric
2007	Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations Published In PLoS Computational Biology Volume 3 Pages 0199 - 0213 ISSN 1553-734X Altmetric
2007	Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues Published In PLoS Computational Biology Volume 3 Pages 0214 - 0230 ISSN 1553-734X Altmetric
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 Volume 33 Pages 1143 - 1154 ISSN 0892-7022 Altmetric
2007	The vibrational spectra of protonated water clusters: a benchmark for self-consistent-charge density-functional tight binding Published In Journal of Chemical Physics Volume 127 Pages 234504-1 - 234504-8 ISSN 0021-9606 Altmetric

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: CRC Press Pages 23 - 46 ISBN 9781420087031

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 Pages 122 - 122
2012	Catalysis in silico Published In Proceedings of the Australian Physiological Society Pages 176 - 176

Investigator On

Year	Title
2018 - 2020	Anti-sporulation strategies for Clostridium difficile infections Awarded by: National Health and Medical Research Council (NHMRC) Funding Scheme: Project Grant
2017	Liquid-phase hydrogen carriers for energy storage and delivery Awarded by: Australian Research Council (ARC) Funding Scheme: Discovery Projects
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)

Available as Research Supervisor

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	Computational Vibrational Spectroscopic Studies of Biolomolecular systems	Inakollu, Venkatasaisandeep
Doctor of Philosophy	Drug Design and Development Targetting Viruses	Metwaly, Mohamed
Doctor of Philosophy	Quantum modelling of lubricant at interface in metal forming at high temperatures	Ta, Thi Thuy Huong
Doctor of Philosophy	Medicinal Chemistry Studies into 6-Substituted Amiloride Analogues as Inhibitors of the Human and Murine Urokinase Plasminogen Activators	Elsalamouny, Nehad
Doctor of Philosophy	Development of Glycosyltransferase Inhibitors as a Novel Antimetastatic Strategy for Cancer Treatment	Dobie, Chris
Doctor of Philosophy	Computer-aided Hydrogen Storage Materials Design: Accurate Predictions of NMR Chemical Shifts and MD Simulation of Nitrogen and Boron Containing Compounds	Gao, Peng
Doctor of Philosophy	Understanding the Molecular Mechanisms of Single-strand Annealing Homologous DNA Recombination in Bacteriophages, by cryo-EM	Mantri, Bhanu

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 -
The National Computational Merit Allocation Committee Member 2018 - 2021
Scientific Reports Editorial Board Member 2014 - 2018

Education And Training

Ph.D., ETH Zurich, 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 18 Room G26

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

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
2020	Ab initio study on physical and chemical interactions at borates and iron oxide interface at high temperature Published In Chemical Physics Volume 529 Pages 110548-1 - 110548-9 ISSN 0301-0104 Altmetric
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 Volume 4 Pages 12385 - 12392 Altmetric
2019	Comparative studies of catalytic pathways for Streptococcus pneumoniae sialidases NanA, NanB and NanC Published In Scientific Reports Volume 9 Pages 2157-1 - 2157-13 ISSN 2045-2322 Altmetric
2019	Divergent Pd-catalyzed cross-coupling of allenyloxazolidinones to give chiral 1,3-dienes and vinyloxazolidinones Published In Chemical Science Volume 10 Pages 9051 - 9056 ISSN 2041-6520 Altmetric
2019	Electrocatalytically inactive SnS2 promotes water adsorption/dissociation on molybdenum dichalcogenides for accelerated alkaline hydrogen evolution Published In Nano Energy Volume 64 Pages 1 - 6 ISSN 2211-3282 Altmetric
2019	Heteroatom-doped MoSe2 Nanosheets with Enhanced Hydrogen Evolution Kinetics for Alkaline Water Splitting Published In Chemistry: An Asian Journal Volume 14 Pages 301 - 306 ISSN 1861-471X Altmetric
2019	Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols Published In Journal of Computational Chemistry Volume Online First Pages 1 - 12 ISSN 0192-8651 Altmetric
2019	Theoretical Investigation on The Single Transition-Metal Atom-Decorated Defective MoS2 for Electrocatalytic Ammonia Synthesis Published In ACS Applied Materials and Interfaces Volume 11 Pages 36506 - 36514 ISSN 1944-8244 Altmetric
2019	Theoretical Screening of Single Transition Metal Atoms Embedded in MXene Defects as Superior Electrocatalyst of Nitrogen Reduction Reaction Published In Small Methods Volume Online First Pages 1900337-1 - 1900337-7 Altmetric
2019	Towards an Accurate Prediction of Nitrogen Chemical Shifts by Density Functional Theory and Gauge-Including Atomic Orbital Published In Advanced Theory and Simulations Volume 2 Pages 1800148-1 - 1800148-8 Altmetric
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 Volume 39 Pages 2067 - 2078 ISSN 0192-8651 Altmetric
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 Volume 122 Pages 635 - 647 ISSN 1932-7447 Altmetric
2018	Computer‐aided design of human sialyltransferase inhibitors of hST8Sia III Published In Journal of Molecular Recognition Volume 31 Pages e2684-1 - e2684-11 ISSN 0952-3499 Altmetric
2018	Depolymerization of sodium polyphosphates on an iron oxide surface at high temperature Published In Physical Chemistry Chemical Physics Volume 20 Pages 7819 - 7835 ISSN 1463-9076 Altmetric
2018	Differential-Mobility Spectrometry of 1-Deoxysphingosine Isomers: New Insights into the Gas Phase Structures of Ionized Lipids Published In Analytical Chemistry Volume 90 Pages 5343 - 5351 ISSN 0003-2700 Altmetric
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 Volume 122 Pages 2454 - 2460 ISSN 1932-7447 Altmetric
2018	Molecular docking studies to explore potential binding pockets and inhibitors for chikungunya virus envelope glycoproteins Published In Interdisciplinary Sciences: Computational Life Sciences Volume 10 Pages 515 - 524 Altmetric
2018	Remodeling the endoplasmic reticulum proteostasis network restores proteostasis of pathogenic GABA A receptors Published In PLoS One Volume 13 Pages e0207948-1 - e0207948-23 ISSN 1932-6203 Altmetric
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 Volume 24 Pages 319-1 - 319-9 ISSN 0948-5023 Altmetric
2017	Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design Published In Advances in Protein Chemistry and Structural Biology Volume 109 Pages 25 - 76 Altmetric
2017	Theoretical pKa prediction of the α-phosphate moiety of uridine 5′-diphosphate-GlcNAc Published In Chemical Physics Letters Volume 667 Pages 220 - 225 ISSN 0009-2614 Altmetric
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 Volume 7 Pages 14428-1 - 14428-11 ISSN 2045-2322 Altmetric
2016	Ammonium aminodiboranate: A long-sought isomer of diammoniate of diborane and ammonia borane dimer Published In Chemistry: A European Journal Volume 22 Pages 7727 - 7729 ISSN 1521-3765 Altmetric
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 Volume 29 Pages 210 - 222 ISSN 0952-3499 Altmetric
2016	Rationalising pKa shifts in Bacillus circulans xylanase with computational studies Published In Physical Chemistry Chemical Physics Volume 18 Pages 30305 - 30312 ISSN 1463-9076 Altmetric
2016	Selective binding modes and allosteric inhibitory effects of lupane triterpenes on protein tyrosine phosphatase 1B Published In Scientific Reports Volume 6 Pages 20766-1 - 20766-14 ISSN 2045-2322 Altmetric
2015	Identification of chikungunya virus nsP2 protease inhibitors using structure-base approaches Published In Journal of Molecular Graphics and Modelling Volume 57 Pages 1 - 8 ISSN 1093-3263 Altmetric
2014	Discovery of in silico hits targeting the nsP3 macro domain of chikungunya virus Published In Journal of Molecular Modeling Volume 20 Pages 2216-1 - 2216-12 ISSN 0948-5023 Altmetric
2014	In silico enzyme modelling Published In Australian Biochemist Volume 45 Pages 12 - 15
2014	Oxygen binding sites in obelin: a computational study into the formation of active photoproteins Published In Luminescence: journal of biological and chemical luminescence Volume 29 Pages 21 - 21 ISSN 0884-3996 Altmetric
2014	PKa cycling of the general acid/base in glycoside hydrolase families 33 and 34 Published In Physical Chemistry Chemical Physics Volume 16 Pages 5785 - 5792 ISSN 1463-9076 Altmetric
2013	Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations Published In Topics in Current Chemistry Volume 337 Pages 139 - 164 ISSN 0340-1022 Altmetric
2013	Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field Published In Faraday Discussions Volume 160 Pages 135 - 149 ISSN 1359-6640 Altmetric
2012	Molecular mechanisms of K+ selectivity in Na/K pump Published In Australian Journal of Chemistry: an international journal for chemical science Volume 65 Pages 448 - 456 ISSN 0004-9425 Altmetric
2011	Ion selectivity in channels and transporters Published In Journal of General Physiology Volume 137 Pages 415 - 426 ISSN 0022-1295 Altmetric
2011	Protonation of key acidic residues is critical for the K+-selectivity of the Na/K pump Published In Nature Structural and Molecular Biology Volume 18 Pages 1159 - 1163 ISSN 1545-9993 Altmetric
2010	A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide Published In Journal of the American Chemical Society Volume 132 Pages 10847 - 10856 ISSN 0002-7863 Altmetric
2010	Assessing the accuracy of approximate treatments of ion hydration based on primitive quasichemical theory Published In Journal of Chemical Physics Volume 132 Pages 234101-1 - 234101-13 ISSN 0021-9606 Altmetric
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 Volume 107 Pages 18718 - 18723 ISSN 0027-8424 Altmetric
2010	Simulating monovalent and divalent ions in aqueous solution using a drude polarizable force field Published In Journal of Chemical Theory and Computation Volume 6 Pages 774 - 786 ISSN 1549-9618 Altmetric
2010	Two mechanisms of ion selectivity in protein binding sites Published In Proceedings of the National Academy of Sciences of USA Volume 107 Pages 20329 - 20334 ISSN 0027-8424 Altmetric
2009	Hydration number, topological control, and ion selectivity Published In The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter Volume 113 Pages 8725 - 8730 ISSN 1520-6106 Altmetric
2009	On the utilization of energy minimization to the study of ion selectivity Published In Biophysical Journal Volume 97 Pages L15 - L17 ISSN 0006-3495 Altmetric
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 Volume 105 Pages 19672 - 19677 ISSN 0027-8424 Altmetric
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 Volume 4 Pages 2067 - 2084 ISSN 1549-9618 Altmetric
2008	Extensive conformational transitions are required to turn on ATP hydrolysis in myosin Published In Journal of Molecular Biology Volume 381 Pages 1407 - 1420 ISSN 0022-2836 Altmetric
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 Volume 452 Pages 78 - 83 ISSN 0009-2614 Altmetric
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 Volume 111 Pages 10861 - 10873 ISSN 1520-5215 Altmetric
2007	Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations Published In PLoS Computational Biology Volume 3 Pages 0199 - 0213 ISSN 1553-734X Altmetric
2007	Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues Published In PLoS Computational Biology Volume 3 Pages 0214 - 0230 ISSN 1553-734X Altmetric
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 Volume 33 Pages 1143 - 1154 ISSN 0892-7022 Altmetric
2007	The vibrational spectra of protonated water clusters: a benchmark for self-consistent-charge density-functional tight binding Published In Journal of Chemical Physics Volume 127 Pages 234504-1 - 234504-8 ISSN 0021-9606 Altmetric

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: CRC Press Pages 23 - 46 ISBN 9781420087031

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 Pages 122 - 122
2012	Catalysis in silico Published In Proceedings of the Australian Physiological Society Pages 176 - 176

Investigator On

Year	Title
2018 - 2020	Anti-sporulation strategies for Clostridium difficile infections Awarded by: National Health and Medical Research Council (NHMRC) Funding Scheme: Project Grant
2017	Liquid-phase hydrogen carriers for energy storage and delivery Awarded by: Australian Research Council (ARC) Funding Scheme: Discovery Projects
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)

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	Computational Vibrational Spectroscopic Studies of Biolomolecular systems	Inakollu, Venkatasaisandeep
Doctor of Philosophy	Drug Design and Development Targetting Viruses	Metwaly, Mohamed
Doctor of Philosophy	Quantum modelling of lubricant at interface in metal forming at high temperatures	Ta, Thi Thuy Huong
Doctor of Philosophy	Medicinal Chemistry Studies into 6-Substituted Amiloride Analogues as Inhibitors of the Human and Murine Urokinase Plasminogen Activators	Elsalamouny, Nehad
Doctor of Philosophy	Development of Glycosyltransferase Inhibitors as a Novel Antimetastatic Strategy for Cancer Treatment	Dobie, Chris
Doctor of Philosophy	Computer-aided Hydrogen Storage Materials Design: Accurate Predictions of NMR Chemical Shifts and MD Simulation of Nitrogen and Boron Containing Compounds	Gao, Peng
Doctor of Philosophy	Understanding the Molecular Mechanisms of Single-strand Annealing Homologous DNA Recombination in Bacteriophages, by cryo-EM	Mantri, Bhanu

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 -
The National Computational Merit Allocation Committee Member 2018 - 2021
Scientific Reports Editorial Board Member 2014 - 2018

Education And Training

Ph.D., ETH Zurich, 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 18 Room G26

Orcid Id

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

Web Of Science Researcher Id

B-9750-2008

Overview

Overview

Top Publications

Research Areas

Research Overview

Available as Research Supervisor

Affiliation

Member Of

Publications

Selected Publications

Journal Article

Chapter

Conference Paper

Funding

Investigator On

Supervision

Available as Research Supervisor

Potential Supervision Topics

Advisees

Graduate Advising Relationship

Service

Organizer Of Event

Professional Service Activities

Background

Education And Training

Awards And Honors

Keywords

Contact

Full Name

Mailing Address

Located In Facility

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