Dr Zak Hughes
Assistant Professor
| Faculty/Dept/School |
School of Chemistry and Bioscience (Faculty of Life Sciences) |
|---|---|
| z.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-07: Durham University, UK - PhD
- 01-JAN-03: Durham University, UK - MChem
- 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
Publications
| Title | Description of Potential Energy Surfaces of Molecules Using FFLUX Machine Learning Models (2019) |
|---|---|
| Authors | Hughes Z.;Thacker J.;Wilson A.;Popelier P. |
| Journal | Journal of Chemical Theory and Computation |
| DOI | 10.1021/acs.jctc.8b00806 |
| Title | Effect of calcium ions on peptide adsorption at the aqueous rutile titania (110) interface (2018) |
| Authors | Sultan, A.M.; Hughes, Zak E.; Walsh, T.R. |
| Title | Distinct differences in peptide adsorption on palladium and gold: introducing a polarizable model for Pd(111) (2018) |
| Authors | Hughes, Zak E.; Walsh, T.R. |
| Title | Peptide-mediated growth and dispersion of Au nanoparticles in water via sequence engineering (2018) |
| Authors | Nguyen, M.A.; Hughes, Zak E.; Liu, Y.; Li, Y.; Swihart, M.T.; Knecht, M.R.; Walsh, T.R. |
| Title | Optical control of nanoparticle catalysis influenced by photoswitch positioning in hybrid peptide capping ligands (2018) |
| Authors | 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. |
| Title | Towards the simulation of biomolecules: optimisation of peptide-capped glycine using FFLUX (2018) |
| Authors | Thacker, J.C.R.; Wilson, A.L.; Hughes, Zak E.; Burn, M.J.; Maxwell, P.I.; Popelier, P.L.A. |
| Title | Probing nano-patterned peptide self-organisation at the aqueous graphene interface (2018) |
| Authors | Hughes, Zak E.; Walsh, T.R. |
| Title | Structural Disruption of an Adenosine-Binding DNA Aptamer on Graphene: Implications for Aptasensor Design (2017) |
| Authors | Hughes, Zak E.; Walsh, T.R. |
| Title | Facet-specific adsorption of tripeptides at aqueous au interfaces: open questions in reconciling experiment and simulation (2017) |
| Authors | Hughes, Zak E.; Kochandra, R.; Walsh, T.R. |
| Title | Halo-substituted azobenzenes adsorbed at Ag(111) and Au(111) interfaces: Structures and optical properties (2017) |
| Authors | Hughes, Zak E.; Baev, A.; Prasad, P.N.; Walsh, T.R. |
| Title | Adsorption of DNA Fragments at Aqueous Graphite and Au(111) via Integration of Experiment and Simulation (2017) |
| Authors | Hughes, Zak E.; Gang, W.; Drew, K.L.M.; Ciacchi, L.C.; Walsh, T.R. |
| Title | Peptide-directed PdAu nanoscale surface segregation: Toward controlled bimetallic architecture for catalytic materials (2016) |
| Authors | 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. |
| Title | Elucidating the influence of materials-binding peptide sequence on Au surface interactions and colloidal stability of Au nanoparticles (2016) |
| Authors | Hughes, Zak E.; Nguyen, M.A.; Li, Y.; Swihart, M.T.; Walsh, T.R.; Knecht, M.R. |
| Title | Sequence-dependent structure/function relationships of catalytic peptide-enabled gold nanoparticles generated under ambient synthetic conditions (2016) |
| Authors | 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. |
| Title | Peptide sequence effects control the single pot reduction, nucleation, and growth of Au nanoparticles (2016) |
| Authors | Munro, C.J.; Hughes, Zak E.; Walsh, T.R.; Knecht, M.R. |
| Title | Aqueous peptide-TiO2 interfaces: isoenergetic binding via either entropically or enthalpically driven mechanisms (2016) |
| Authors | 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. |
| Title | Optical actuation of inorganic/organic interfaces: comparing peptide-azobenzene ligand reconfiguration on gold and silver nanoparticles (2016) |
| Authors | 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. |
| Title | Elucidating the mechanisms of nanodiamond-promoted structural disruption of crystallised lipid (2016) |
| Authors | Hughes, Zak E.; Walsh, T.R. |
| Title | Non-covalent adsorption of amino acid analogues on noble-metal nanoparticles: influence of edges and vertices (2016) |
| Authors | Hughes, Zak E.; Walsh, T.R. |
| Title | Tristearin bilayers: structure of the aqueous interface and stability in the presence of surfactants (2015) |
| Authors | Hughes, Zak E.; Walsh, T.R. |
| Title | Computational chemistry for graphene-based energy applications: progress and challenges (2015) |
| Authors | Hughes, Zak E.; Walsh, T.R. |
| Title | What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces (2015) |
| Authors | Hughes, Zak E.; Walsh, T.R. |
| Title | Improving the description of interactions between Ca2+ and protein carboxylate groups, including γ–carboxyglutamic acid: revised CHARMM22* parameters (2015) |
| Authors | Church, A.T.; Hughes, Zak E.; Walsh, T.R. |
| Title | Comparative study of materials-binding peptide interactions with gold and silver surfaces and nanostructures: A thermodynamic basis for biological selectivity of inorganic materials (2014) |
| Authors | Palafox-Hernandez J.;Tang Z.;Hughes Z.;Li Y.;Swihart M.;Prasad P.;Walsh T.;Knecht M. |
| Journal | Chemistry of Materials |
| DOI | 10.1021/cm501529u |
| Title | Structure of the electrical double layer at aqueous gold and silver interfaces for saline solutions. (2014) |
| Authors | Hughes ZE;Walsh TR; |
| Journal | Journal of Colloid and Interface Science |
| DOI | 10.1016/j.jcis.2014.08.045 |
| Title | Molecular mechanism of the synergistic effects of vitrification solutions on the stability of phospholipid bilayers. (2014) |
| Authors | Hughes ZE;Mancera RL; |
| Journal | Biophysical Journal |
| DOI | 10.1016/j.bpj.2014.05.012 |
| Title | Molecular dynamics simulations of mixed DOPC-β-sitosterol bilayers and their interactions with DMSO (2013) |
| Authors | Hughes Z.;Mancera R. |
| Journal | Soft Matter |
| DOI | 10.1039/c3sm27805k |
| Title | Biomolecular recognition principles for bionanocombinatorics: an integrated approach to elucidate enthalpic and entropic factors. (2013) |
| Authors | Tang Z;Palafox-Hernandez JP;Law WC;Hughes ZE;Swihart MT;Prasad PN;Knecht MR;Walsh TR; |
| Journal | ACS Nano |
| DOI | 10.1021/nn404427y |
| Title | Biomolecular adsorption at aqueous silver interfaces: first-principles calculations, polarizable force-field simulations, and comparisons with gold. (2013) |
| Authors | Hughes ZE;Wright LB;Walsh TR; |
| Journal | Langmuir |
| DOI | 10.1021/la402839q |
| Title | The effects of cryosolvents on DOPC-β-sitosterol bilayers determined from molecular dynamics simulations. (2013) |
| Authors | Hughes ZE;Malajczuk CJ;Mancera RL; |
| Journal | Journal of Physical Chemistry B |
| DOI | 10.1021/jp400975y |
| Title | Molecular dynamics simulations of the interactions of DMSO, mono- and polyhydroxylated cryosolvents with a hydrated phospholipid bilayer (2013) |
| Authors | Malajczuk C.;Hughes Z.;Mancera R. |
| Journal | Biochimica et Biophysica Acta - Biomembranes |
| DOI | 10.1016/j.bbamem.2013.05.010 |
| Title | Simulation of water transport through functionalized single-walled carbon nanotubes (SWCNTs) (2012) |
| Authors | Hughes Z.;Shearer C.;Shapter J.;Gale J. |
| Journal | Journal of Physical Chemistry C |
| DOI | 10.1021/jp307679h |
| Title | Molecular dynamics simulations of the interactions of potential foulant molecules and a reverse osmosis membrane (2012) |
| Authors | Hughes Z.;Gale J. |
| Journal | Journal of Materials Chemistry |
| DOI | 10.1039/c1jm13230j |
| Title | Molecular dynamics simulations of the interactions of DMSO with DPPC and DOPC phospholipid membranes. (2012) |
| Authors | Hughes ZE;Mark AE;Mancera RL; |
| Journal | Journal of Physical Chemistry B |
| DOI | 10.1021/jp3035538 |
| Title | A computational investigation into the suitability of purely siliceous zeolites as reverse osmosis membranes (2011) |
| Authors | Hughes Z.;Carrington L.;Raiteri P.;Gale J. |
| Journal | Journal of Physical Chemistry C |
| DOI | 10.1021/jp109591f |
| Title | A computational investigation of the properties of a reverse osmosis membrane (2010) |
| Authors | Hughes Z.;Gale J. |
| Journal | Journal of Materials Chemistry |
| DOI | 10.1039/c0jm01545h |
| Title | Evidence for electronic gap-driven metal-semiconductor transition in phase-change materials. (2009) |
| Authors | 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; |
| Journal | Proceedings of the National Academy of Sciences of the United States of America |
| DOI | 10.1073/pnas.0812942106 |
| Title | An investigation of soft-core potentials for the simulation of mesogenic molecules and molecules composed of rigid and flexible segments (2008) |
| Authors | Hughes Z.;Stimson L.;Slim H.;Lintuvuori J.;Ilnytskyi J.;Wilson M. |
| Journal | Computer Physics Communications |
| DOI | 10.1016/j.cpc.2008.01.047 |
| Title | Coarse-grained simulation studies of a liquid crystal dendrimer: Towards computational predictions of nanoscale structure through microphase separation (2005) |
| Authors | Hughes Z.;Wilson M.;Stimson L. |
| Journal | Soft Matter |
| DOI | 10.1039/b511082c |