Dr. Zak Hughes

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
Education (2)
- Durham University, UK - PhD
- Durham University, UK - MChem
Employment (5)
- University of Bradford - Lecturer in Computational and Theoretical Chemistry (1 January 2018)
- University of Manchester, UK - Research Associate (1 January 2017)
- Deakin University, Waurn Ponds, Australia - Research Fellow (1 January 2013)
- Curtin University, Perth, Australia - Research Fellow (1 January 2008)
- University of Western Ontario, London, Canada - Post-doctoral Fellow (1 January 2006)
Publications
Peer reviewed journal (39)
Description of Potential Energy Surfaces of Molecules Using FFLUX Machine Learning Models
Hughes Z.;Thacker J.;Wilson A.;Popelier P. (2019) Journal of Chemical Theory and Computation. 15, 116-126.
Probing nano-patterned peptide self-organisation at the aqueous graphene interface
Hughes, Zak E.; Walsh, T.R. (2018)
Distinct differences in peptide adsorption on palladium and gold: introducing a polarizable model for Pd(111)
Hughes, Zak E.; Walsh, T.R. (2018)
Optical control of nanoparticle catalysis influenced by photoswitch positioning in hybrid peptide capping ligands
Lawrence, 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. (2018)
Towards the simulation of biomolecules: optimisation of peptide-capped glycine using FFLUX
Thacker, J.C.R.; Wilson, A.L.; Hughes, Zak E.; Burn, M.J.; Maxwell, P.I.; Popelier, P.L.A. (2018)
Peptide-mediated growth and dispersion of Au nanoparticles in water via sequence engineering
Nguyen, M.A.; Hughes, Zak E.; Liu, Y.; Li, Y.; Swihart, M.T.; Knecht, M.R.; Walsh, T.R. (2018)
Effect of calcium ions on peptide adsorption at the aqueous rutile titania (110) interface
Sultan, A.M.; Hughes, Zak E.; Walsh, T.R. (2018)
Halo-substituted azobenzenes adsorbed at Ag(111) and Au(111) interfaces: Structures and optical properties
Hughes, Zak E.; Baev, A.; Prasad, P.N.; Walsh, T.R. (2017)
Structural Disruption of an Adenosine-Binding DNA Aptamer on Graphene: Implications for Aptasensor Design
Hughes, Zak E.; Walsh, T.R. (2017)
Facet-specific adsorption of tripeptides at aqueous au interfaces: open questions in reconciling experiment and simulation
Hughes, Zak E.; Kochandra, R.; Walsh, T.R. (2017)
Adsorption of DNA Fragments at Aqueous Graphite and Au(111) via Integration of Experiment and Simulation
Hughes, Zak E.; Gang, W.; Drew, K.L.M.; Ciacchi, L.C.; Walsh, T.R. (2017)
Elucidating the influence of materials-binding peptide sequence on Au surface interactions and colloidal stability of Au nanoparticles
Hughes, Zak E.; Nguyen, M.A.; Li, Y.; Swihart, M.T.; Walsh, T.R.; Knecht, M.R. (2016)
Peptide-directed PdAu nanoscale surface segregation: Toward controlled bimetallic architecture for catalytic materials
Bedford, 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. (2016)
Elucidating the mechanisms of nanodiamond-promoted structural disruption of crystallised lipid
Hughes, Zak E.; Walsh, T.R. (2016)
Sequence-dependent structure/function relationships of catalytic peptide-enabled gold nanoparticles generated under ambient synthetic conditions
Bedford, 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. (2016)
Non-covalent adsorption of amino acid analogues on noble-metal nanoparticles: influence of edges and vertices
Hughes, Zak E.; Walsh, T.R. (2016)
Optical actuation of inorganic/organic interfaces: comparing peptide-azobenzene ligand reconfiguration on gold and silver nanoparticles
Palafox-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. (2016)
Aqueous peptide-TiO2 interfaces: isoenergetic binding via either entropically or enthalpically driven mechanisms
Sultan, 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. (2016)
Peptide sequence effects control the single pot reduction, nucleation, and growth of Au nanoparticles
Munro, C.J.; Hughes, Zak E.; Walsh, T.R.; Knecht, M.R. (2016)
Computational chemistry for graphene-based energy applications: progress and challenges
Hughes, Zak E.; Walsh, T.R. (2015)
What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces
Hughes, Zak E.; Walsh, T.R. (2015)
Tristearin bilayers: structure of the aqueous interface and stability in the presence of surfactants
Hughes, Zak E.; Walsh, T.R. (2015)
Improving the description of interactions between Ca2+ and protein carboxylate groups, including γ–carboxyglutamic acid: revised CHARMM22* parameters
Church, A.T.; Hughes, Zak E.; Walsh, T.R. (2015)
Structure of the electrical double layer at aqueous gold and silver interfaces for saline solutions.
Hughes ZE;Walsh TR; (2014) Journal of Colloid and Interface Science. 436
Comparative study of materials-binding peptide interactions with gold and silver surfaces and nanostructures: A thermodynamic basis for biological selectivity of inorganic materials
Palafox-Hernandez J.;Tang Z.;Hughes Z.;Li Y.;Swihart M.;Prasad P.;Walsh T.;Knecht M. (2014) Chemistry of Materials. 26, 4960-4969.
Molecular mechanism of the synergistic effects of vitrification solutions on the stability of phospholipid bilayers.
Hughes ZE;Mancera RL; (2014) Biophysical Journal. 106
The effects of cryosolvents on DOPC-β-sitosterol bilayers determined from molecular dynamics simulations.
Hughes ZE;Malajczuk CJ;Mancera RL; (2013) Journal of Physical Chemistry B. 117
Biomolecular adsorption at aqueous silver interfaces: first-principles calculations, polarizable force-field simulations, and comparisons with gold.
Hughes ZE;Wright LB;Walsh TR; (2013) Langmuir. 29
Biomolecular recognition principles for bionanocombinatorics: an integrated approach to elucidate enthalpic and entropic factors.
Tang Z;Palafox-Hernandez JP;Law WC;Hughes ZE;Swihart MT;Prasad PN;Knecht MR;Walsh TR; (2013) ACS Nano. 7
Molecular dynamics simulations of mixed DOPC-β-sitosterol bilayers and their interactions with DMSO
Hughes Z.;Mancera R. (2013) Soft Matter. 9, 2920-2935.
Molecular dynamics simulations of the interactions of DMSO, mono- and polyhydroxylated cryosolvents with a hydrated phospholipid bilayer
Malajczuk C.;Hughes Z.;Mancera R. (2013) Biochimica et Biophysica Acta - Biomembranes. 1828, 2041-2055.
Molecular dynamics simulations of the interactions of DMSO with DPPC and DOPC phospholipid membranes.
Hughes ZE;Mark AE;Mancera RL; (2012) Journal of Physical Chemistry B. 116
Simulation of water transport through functionalized single-walled carbon nanotubes (SWCNTs)
Hughes Z.;Shearer C.;Shapter J.;Gale J. (2012) Journal of Physical Chemistry C. 116, 24943-24953.
Molecular dynamics simulations of the interactions of potential foulant molecules and a reverse osmosis membrane
Hughes Z.;Gale J. (2012) Journal of Materials Chemistry. 22, 175-184.
A computational investigation into the suitability of purely siliceous zeolites as reverse osmosis membranes
Hughes Z.;Carrington L.;Raiteri P.;Gale J. (2011) Journal of Physical Chemistry C. 115, 4063-4075.
A computational investigation of the properties of a reverse osmosis membrane
Hughes Z.;Gale J. (2010) Journal of Materials Chemistry. 20, 7788-7799.
Evidence for electronic gap-driven metal-semiconductor transition in phase-change materials.
Shakhvorostov 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; (2009) Proceedings of the National Academy of Sciences of the United States of America. 106
An investigation of soft-core potentials for the simulation of mesogenic molecules and molecules composed of rigid and flexible segments
Hughes Z.;Stimson L.;Slim H.;Lintuvuori J.;Ilnytskyi J.;Wilson M. (2008) Computer Physics Communications. 178, 724-731.
Coarse-grained simulation studies of a liquid crystal dendrimer: Towards computational predictions of nanoscale structure through microphase separation
Hughes Z.;Wilson M.;Stimson L. (2005) Soft Matter. 1, 436-443.