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researcher

Zak Hughes

Lecturer Theoretical/Computational Chem

Faculty/Dept/School School of Chemistry and Bioscience
(Faculty of Life Sciences)
Emailz.hughes@bradford.ac.uk
Telephone +441274 232217

Biography

My research primarily focuses on the molecular simulation of interfacial (e.g. membranes, interfacial interactions) and soft matter systems (e.g. biomolecules, liquid crystals) to help improve our understanding of the physical and chemical behaviour of these systems. The bulk of my research makes use of classical molecular dynamics (MD) simulations at the atomistic level, but I have used a wide range of computational chemistry techniques in my research, including coarse-grained MD, Monte Carlo simulations, density functional theory calculations, ab initio MD.


Professional History
  • 2018 – Present: Lecturer in Computational and Theoretical Chemistry at University of Bradford, UK
  • 2017 – 2018: Research Associate at the University of Manchester, UK
  • 2013 – 2017: Research Fellow at Deakin University, Waurn Ponds, Australia
  • 2008 – 2012: Research Fellow at Curtin University, Perth, Australia
  • 2006 – 2007: Post-doctoral Fellow at the University of Western Ontario, London, Canada

Research

My research primarily focuses on the molecular simulation of interfacial (e.g. membranes, interfacial interactions) and soft matter systems (e.g. biomolecules, liquid crystals) to help improve our understanding of the physical and chemical behaviour of these systems. The bulk of my research makes use of classical molecular dynamics (MD) simulations at the atomistic level, but I have used a wide range of computational chemistry techniques in my research, including coarse-grained MD, Monte Carlo simulations, density functional theory calculations, ab initio MD.

Professional activities

  • 01-JAN-18: University of Bradford - Lecturer in Computational and Theoretical Chemistry 
  • 01-JAN-17: University of Manchester, UK - Research Associate
  • 01-JAN-13: Deakin University, Waurn Ponds, Australia -  Research Fellow
  • 01-JAN-08: Curtin University, Perth, Australia -  Research Fellow
  • 01-JAN-06: University of Western Ontario, London, Canada - Post-doctoral Fellow
  • 01-JAN-07:  Durham University, UK - PhD
  • 01-JAN-03:  Durham University, UK - MChem

Publications

Peer Reviewed Journal
TitleDescription of Potential Energy Surfaces of Molecules Using FFLUX Machine Learning Models (2019)
AuthorsHughes Z.;Thacker J.;Wilson A.;Popelier P.
JournalJournal of Chemical Theory and Computation
DOI10.1021/acs.jctc.8b00806
 
TitleEffect of calcium ions on peptide adsorption at the aqueous rutile titania (110) interface (2018)
AuthorsSultan, A.M.; Hughes, Zak E.; Walsh, T.R.
 
TitleTowards the simulation of biomolecules: optimisation of peptide-capped glycine using FFLUX (2018)
AuthorsThacker, J.C.R.; Wilson, A.L.; Hughes, Zak E.; Burn, M.J.; Maxwell, P.I.; Popelier, P.L.A.
 
TitlePeptide-mediated growth and dispersion of Au nanoparticles in water via sequence engineering (2018)
AuthorsNguyen, M.A.; Hughes, Zak E.; Liu, Y.; Li, Y.; Swihart, M.T.; Knecht, M.R.; Walsh, T.R.
 
TitleDistinct differences in peptide adsorption on palladium and gold: introducing a polarizable model for Pd(111) (2018)
AuthorsHughes, Zak E.; Walsh, T.R.
 
TitleProbing nano-patterned peptide self-organisation at the aqueous graphene interface (2018)
AuthorsHughes, Zak E.; Walsh, T.R.
 
TitleOptical control of nanoparticle catalysis influenced by photoswitch positioning in hybrid peptide capping ligands (2018)
AuthorsLawrence, R.L.; Hughes, Zak E.; Cendan, V.J.; Liu, Y.; Lim, C.K.; Prasad, P.N.; Swihart, M.T.; Walsh, T.R.; Knecht, M.R.
 
TitleAdsorption of DNA Fragments at Aqueous Graphite and Au(111) via Integration of Experiment and Simulation (2017)
AuthorsHughes, Zak E.; Gang, W.; Drew, K.L.M.; Ciacchi, L.C.; Walsh, T.R.
 
TitleFacet-specific adsorption of tripeptides at aqueous au interfaces: open questions in reconciling experiment and simulation (2017)
AuthorsHughes, Zak E.; Kochandra, R.; Walsh, T.R.
 
TitleHalo-substituted azobenzenes adsorbed at Ag(111) and Au(111) interfaces: Structures and optical properties (2017)
AuthorsHughes, Zak E.; Baev, A.; Prasad, P.N.; Walsh, T.R.
 
TitleStructural Disruption of an Adenosine-Binding DNA Aptamer on Graphene: Implications for Aptasensor Design (2017)
AuthorsHughes, Zak E.; Walsh, T.R.
 
TitleSequence-dependent structure/function relationships of catalytic peptide-enabled gold nanoparticles generated under ambient synthetic conditions (2016)
AuthorsBedford, N.M.; Hughes, Zak E.; Tang, Z.; Li, Y.; Briggs, B.D.; Ren, Y.; Swihart, M.T.; Petkov, V.G.; Naik, R.R.; Knecht, M.R.; Walsh, T.R.
 
TitleNon-covalent adsorption of amino acid analogues on noble-metal nanoparticles: influence of edges and vertices (2016)
AuthorsHughes, Zak E.; Walsh, T.R.
 
TitleElucidating the mechanisms of nanodiamond-promoted structural disruption of crystallised lipid (2016)
AuthorsHughes, Zak E.; Walsh, T.R.
 
TitleOptical actuation of inorganic/organic interfaces: comparing peptide-azobenzene ligand reconfiguration on gold and silver nanoparticles (2016)
AuthorsPalafox-Hernandez, J.P.; Lim, C-K.; Tang, Z.; Drew, K.L.M.; Hughes, Zak E.; Li, Y.; Swihart, M.T.; Prasad, P.N.; Knecht, M.R.; Walsh, T.R.
 
TitleAqueous peptide-TiO2 interfaces: isoenergetic binding via either entropically or enthalpically driven mechanisms (2016)
AuthorsSultan, A.M.; Westcott, Z.C.; Hughes, Zak E.; Palafox-Hernandez, J.P.; Giesa, T.; Puddu, V.; Buehler, M.J.; Perry, C.C.; Walsh, T.R.
 
TitlePeptide sequence effects control the single pot reduction, nucleation, and growth of Au nanoparticles (2016)
AuthorsMunro, C.J.; Hughes, Zak E.; Walsh, T.R.; Knecht, M.R.
 
TitleElucidating the influence of materials-binding peptide sequence on Au surface interactions and colloidal stability of Au nanoparticles (2016)
AuthorsHughes, Zak E.; Nguyen, M.A.; Li, Y.; Swihart, M.T.; Walsh, T.R.; Knecht, M.R.
 
TitlePeptide-directed PdAu nanoscale surface segregation: Toward controlled bimetallic architecture for catalytic materials (2016)
AuthorsBedford, N.M.; Showalter, A.R.; Woehl, T.J.; Hughes, Zak E.; Lee, S.; Reinhart, B.; Ertem, S.P.; Coughlin, E.B.; Ren, Y.; Walsh, T.R.; Bunker, B.A.
 
TitleWhat makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces (2015)
AuthorsHughes, Zak E.; Walsh, T.R.
 
TitleTristearin bilayers: structure of the aqueous interface and stability in the presence of surfactants (2015)
AuthorsHughes, Zak E.; Walsh, T.R.
 
TitleImproving the description of interactions between Ca2+ and protein carboxylate groups, including γ–carboxyglutamic acid: revised CHARMM22* parameters (2015)
AuthorsChurch, A.T.; Hughes, Zak E.; Walsh, T.R.
 
TitleComputational chemistry for graphene-based energy applications: progress and challenges (2015)
AuthorsHughes, Zak E.; Walsh, T.R.
 
TitleMolecular mechanism of the synergistic effects of vitrification solutions on the stability of phospholipid bilayers. (2014)
AuthorsHughes ZE;Mancera RL;
JournalBiophysical Journal
DOI10.1016/j.bpj.2014.05.012
 
TitleBinding affinities of amino acid analogues at the charged aqueous titania interface: implications for titania-binding peptides. (2014)
AuthorsSultan AM;Hughes ZE;Walsh TR;
JournalLangmuir
DOI10.1021/la503312d
 
TitleEfficient simulations of the aqueous bio-interface of graphitic nanostructures with a polarisable model. (2014)
AuthorsHughes ZE;Tomásio SM;Walsh TR;
JournalNanoscale
DOI10.1039/c4nr00468j
 
TitleComparative study of materials-binding peptide interactions with gold and silver surfaces and nanostructures: A thermodynamic basis for biological selectivity of inorganic materials (2014)
AuthorsPalafox-Hernandez J.;Tang Z.;Hughes Z.;Li Y.;Swihart M.;Prasad P.;Walsh T.;Knecht M.
JournalChemistry of Materials
DOI10.1021/cm501529u
 
TitleStructure of the electrical double layer at aqueous gold and silver interfaces for saline solutions. (2014)
AuthorsHughes ZE;Walsh TR;
JournalJournal of Colloid and Interface Science
DOI10.1016/j.jcis.2014.08.045
 
TitleBiomolecular recognition principles for bionanocombinatorics: an integrated approach to elucidate enthalpic and entropic factors. (2013)
AuthorsTang Z;Palafox-Hernandez JP;Law WC;Hughes ZE;Swihart MT;Prasad PN;Knecht MR;Walsh TR;
JournalACS Nano
DOI10.1021/nn404427y
 
TitleThe effects of cryosolvents on DOPC-β-sitosterol bilayers determined from molecular dynamics simulations. (2013)
AuthorsHughes ZE;Malajczuk CJ;Mancera RL;
JournalJournal of Physical Chemistry B
DOI10.1021/jp400975y
 
TitleBiomolecular adsorption at aqueous silver interfaces: first-principles calculations, polarizable force-field simulations, and comparisons with gold. (2013)
AuthorsHughes ZE;Wright LB;Walsh TR;
JournalLangmuir
DOI10.1021/la402839q
 
TitleMolecular dynamics simulations of the interactions of DMSO, mono- and polyhydroxylated cryosolvents with a hydrated phospholipid bilayer (2013)
AuthorsMalajczuk C.;Hughes Z.;Mancera R.
JournalBiochimica et Biophysica Acta - Biomembranes
DOI10.1016/j.bbamem.2013.05.010
 
TitleMolecular dynamics simulations of mixed DOPC-β-sitosterol bilayers and their interactions with DMSO (2013)
AuthorsHughes Z.;Mancera R.
JournalSoft Matter
DOI10.1039/c3sm27805k
 
TitleMolecular dynamics simulations of the interactions of potential foulant molecules and a reverse osmosis membrane (2012)
AuthorsHughes Z.;Gale J.
JournalJournal of Materials Chemistry
DOI10.1039/c1jm13230j
 
TitleSimulation of water transport through functionalized single-walled carbon nanotubes (SWCNTs) (2012)
AuthorsHughes Z.;Shearer C.;Shapter J.;Gale J.
JournalJournal of Physical Chemistry C
DOI10.1021/jp307679h
 
TitleMolecular dynamics simulations of the interactions of DMSO with DPPC and DOPC phospholipid membranes. (2012)
AuthorsHughes ZE;Mark AE;Mancera RL;
JournalJournal of Physical Chemistry B
DOI10.1021/jp3035538
 
TitleA computational investigation into the suitability of purely siliceous zeolites as reverse osmosis membranes (2011)
AuthorsHughes Z.;Carrington L.;Raiteri P.;Gale J.
JournalJournal of Physical Chemistry C
DOI10.1021/jp109591f
 
TitleA computational investigation of the properties of a reverse osmosis membrane (2010)
AuthorsHughes Z.;Gale J.
JournalJournal of Materials Chemistry
DOI10.1039/c0jm01545h
 
TitleEvidence for electronic gap-driven metal-semiconductor transition in phase-change materials. (2009)
AuthorsShakhvorostov D;Nistor RA;Krusin-Elbaum L;Martyna GJ;Newns DM;Elmegreen BG;Liu XH;Hughes ZE;Paul S;Cabral C;Raoux S;Shrekenhamer DB;Basov DN;Song Y;Müser MH;
JournalProceedings of the National Academy of Sciences of the United States of America
DOI10.1073/pnas.0812942106
 
TitleAn investigation of soft-core potentials for the simulation of mesogenic molecules and molecules composed of rigid and flexible segments (2008)
AuthorsHughes Z.;Stimson L.;Slim H.;Lintuvuori J.;Ilnytskyi J.;Wilson M.
JournalComputer Physics Communications
DOI10.1016/j.cpc.2008.01.047
 
TitleCoarse-grained simulation studies of a liquid crystal dendrimer: Towards computational predictions of nanoscale structure through microphase separation (2005)
AuthorsHughes Z.;Wilson M.;Stimson L.
JournalSoft Matter
DOI10.1039/b511082c