Dr. Zak Hughes
Information about Dr. Zak Hughes at the University of Bradford.
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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
Information about education, employment and areas of particular interest for Dr. Zak Hughes is as follows:
Employment
- University of Bradford - Lecturer in Computational and Theoretical Chemistry in the year 2018 (specified as 01/01/2018)
- University of Manchester, UK - Research Associate in the year 2017 (specified as 01/01/2017)
- Deakin University, Waurn Ponds, Australia - Research Fellow in the year 2013 (specified as 01/01/2013)
- Curtin University, Perth, Australia - Research Fellow in the year 2008 (specified as 01/01/2008)
- University of Western Ontario, London, Canada - Post-doctoral Fellow in the year 2006 (specified as 01/01/2006)
Education
- Durham University, UK - PhD
- Durham University, UK - MChem
Publications
There are 39 publications involving or that are attributed to Dr. Zak Hughes.
Peer Reviewed Journal
| Title | Year | Publication name | Journal | Volume | Pages | Authors | Editors | ISSN | Publisher | DOI | Location |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Peptide-mediated growth and dispersion of Au nanoparticles in water via sequence engineering | 2018 | Nguyen, M.A.; Hughes, Zak E.; Liu, Y.; Li, Y.; Swihart, M.T.; Knecht, M.R.; Walsh, T.R. | |||||||||
| Improving the description of interactions between Ca2+ and protein carboxylate groups, including γ–carboxyglutamic acid: revised CHARMM22* parameters | 2015 | Church, A.T.; Hughes, Zak E.; Walsh, T.R. | |||||||||
| Tristearin bilayers: structure of the aqueous interface and stability in the presence of surfactants | 2015 | Hughes, Zak E.; Walsh, T.R. | |||||||||
| What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces | 2015 | Hughes, Zak E.; Walsh, T.R. | |||||||||
| Computational chemistry for graphene-based energy applications: progress and challenges | 2015 | Hughes, Zak E.; Walsh, T.R. | |||||||||
| Probing nano-patterned peptide self-organisation at the aqueous graphene interface | 2018 | Hughes, Zak E.; Walsh, T.R. | |||||||||
| Towards the simulation of biomolecules: optimisation of peptide-capped glycine using FFLUX | 2018 | Thacker, J.C.R.; Wilson, A.L.; Hughes, Zak E.; Burn, M.J.; Maxwell, P.I.; Popelier, P.L.A. | |||||||||
| Structural Disruption of an Adenosine-Binding DNA Aptamer on Graphene: Implications for Aptasensor Design | 2017 | Hughes, Zak E.; Walsh, T.R. | |||||||||
| Adsorption of DNA Fragments at Aqueous Graphite and Au(111) via Integration of Experiment and Simulation | 2017 | Hughes, Zak E.; Gang, W.; Drew, K.L.M.; Ciacchi, L.C.; Walsh, T.R. | |||||||||
| Halo-substituted azobenzenes adsorbed at Ag(111) and Au(111) interfaces: Structures and optical properties | 2017 | Hughes, Zak E.; Baev, A.; Prasad, P.N.; Walsh, T.R. | |||||||||
| Facet-specific adsorption of tripeptides at aqueous au interfaces: open questions in reconciling experiment and simulation | 2017 | Hughes, Zak E.; Kochandra, R.; Walsh, T.R. | |||||||||
| Elucidating the influence of materials-binding peptide sequence on Au surface interactions and colloidal stability of Au nanoparticles | 2016 | Hughes, Zak E.; Nguyen, M.A.; Li, Y.; Swihart, M.T.; Walsh, T.R.; Knecht, M.R. | |||||||||
| Peptide-directed PdAu nanoscale surface segregation: Toward controlled bimetallic architecture for catalytic materials | 2016 | 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. | |||||||||
| Peptide sequence effects control the single pot reduction, nucleation, and growth of Au nanoparticles | 2016 | Munro, C.J.; Hughes, Zak E.; Walsh, T.R.; Knecht, M.R. | |||||||||
| Aqueous peptide-TiO2 interfaces: isoenergetic binding via either entropically or enthalpically driven mechanisms | 2016 | 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. | |||||||||
| Optical actuation of inorganic/organic interfaces: comparing peptide-azobenzene ligand reconfiguration on gold and silver nanoparticles | 2016 | 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. | |||||||||
| Sequence-dependent structure/function relationships of catalytic peptide-enabled gold nanoparticles generated under ambient synthetic conditions | 2016 | 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. | |||||||||
| Non-covalent adsorption of amino acid analogues on noble-metal nanoparticles: influence of edges and vertices | 2016 | Hughes, Zak E.; Walsh, T.R. | |||||||||
| Elucidating the mechanisms of nanodiamond-promoted structural disruption of crystallised lipid | 2016 | Hughes, Zak E.; Walsh, T.R. | |||||||||
| Optical control of nanoparticle catalysis influenced by photoswitch positioning in hybrid peptide capping ligands | 2018 | 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. | |||||||||
| Distinct differences in peptide adsorption on palladium and gold: introducing a polarizable model for Pd(111) | 2018 | Hughes, Zak E.; Walsh, T.R. | |||||||||
| Effect of calcium ions on peptide adsorption at the aqueous rutile titania (110) interface | 2018 | Sultan, A.M.; Hughes, Zak E.; Walsh, T.R. | |||||||||
| Structure of the electrical double layer at aqueous gold and silver interfaces for saline solutions. | 2014 | Journal of Colloid and Interface Science | 436 | Hughes ZE;Walsh TR; | 1095-7103 | 10.1016/j.jcis.2014.08.045 | |||||
| Comparative study of materials-binding peptide interactions with gold and silver surfaces and nanostructures: A thermodynamic basis for biological selectivity of inorganic materials | 2014 | Chemistry of Materials | 26 | 4960 - 4969 | Palafox-Hernandez J.;Tang Z.;Hughes Z.;Li Y.;Swihart M.;Prasad P.;Walsh T.;Knecht M. | 0897-4756 | 10.1021/cm501529u | ||||
| Description of Potential Energy Surfaces of Molecules Using FFLUX Machine Learning Models | 2019 | Journal of Chemical Theory and Computation | 15 | 116 - 126 | Hughes Z.;Thacker J.;Wilson A.;Popelier P. | 1549-9618 | 10.1021/acs.jctc.8b00806 | ||||
| Molecular mechanism of the synergistic effects of vitrification solutions on the stability of phospholipid bilayers. | 2014 | Biophysical Journal | 106 | Hughes ZE;Mancera RL; | 1542-0086 | 10.1016/j.bpj.2014.05.012 | |||||
| Biomolecular recognition principles for bionanocombinatorics: an integrated approach to elucidate enthalpic and entropic factors. | 2013 | ACS Nano | 7 | Tang Z;Palafox-Hernandez JP;Law WC;Hughes ZE;Swihart MT;Prasad PN;Knecht MR;Walsh TR; | 1936-086X | 10.1021/nn404427y | |||||
| Biomolecular adsorption at aqueous silver interfaces: first-principles calculations, polarizable force-field simulations, and comparisons with gold. | 2013 | Langmuir | 29 | Hughes ZE;Wright LB;Walsh TR; | 1520-5827 | 10.1021/la402839q | |||||
| Molecular dynamics simulations of the interactions of DMSO, mono- and polyhydroxylated cryosolvents with a hydrated phospholipid bilayer | 2013 | Biochimica et Biophysica Acta - Biomembranes | 1828 | 2041 - 2055 | Malajczuk C.;Hughes Z.;Mancera R. | 0005-2736 | 10.1016/j.bbamem.2013.05.010 | ||||
| The effects of cryosolvents on DOPC-β-sitosterol bilayers determined from molecular dynamics simulations. | 2013 | Journal of Physical Chemistry B | 117 | Hughes ZE;Malajczuk CJ;Mancera RL; | 1520-5207 | 10.1021/jp400975y | |||||
| Molecular dynamics simulations of mixed DOPC-β-sitosterol bilayers and their interactions with DMSO | 2013 | Soft Matter | 9 | 2920 - 2935 | Hughes Z.;Mancera R. | 1744-683X | 10.1039/c3sm27805k | ||||
| Simulation of water transport through functionalized single-walled carbon nanotubes (SWCNTs) | 2012 | Journal of Physical Chemistry C | 116 | 24943 - 24953 | Hughes Z.;Shearer C.;Shapter J.;Gale J. | 1932-7447 | 10.1021/jp307679h | ||||
| Molecular dynamics simulations of the interactions of DMSO with DPPC and DOPC phospholipid membranes. | 2012 | Journal of Physical Chemistry B | 116 | Hughes ZE;Mark AE;Mancera RL; | 1520-5207 | 10.1021/jp3035538 | |||||
| Molecular dynamics simulations of the interactions of potential foulant molecules and a reverse osmosis membrane | 2012 | Journal of Materials Chemistry | 22 | 175 - 184 | Hughes Z.;Gale J. | 0959-9428 | 10.1039/c1jm13230j | ||||
| A computational investigation into the suitability of purely siliceous zeolites as reverse osmosis membranes | 2011 | Journal of Physical Chemistry C | 115 | 4063 - 4075 | Hughes Z.;Carrington L.;Raiteri P.;Gale J. | 1932-7447 | 10.1021/jp109591f | ||||
| A computational investigation of the properties of a reverse osmosis membrane | 2010 | Journal of Materials Chemistry | 20 | 7788 - 7799 | Hughes Z.;Gale J. | 0959-9428 | 10.1039/c0jm01545h | ||||
| Evidence for electronic gap-driven metal-semiconductor transition in phase-change materials. | 2009 | Proceedings of the National Academy of Sciences of the United States of America | 106 | 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; | 1091-6490 | 10.1073/pnas.0812942106 | |||||
| An investigation of soft-core potentials for the simulation of mesogenic molecules and molecules composed of rigid and flexible segments | 2008 | Computer Physics Communications | 178 | 724 - 731 | Hughes Z.;Stimson L.;Slim H.;Lintuvuori J.;Ilnytskyi J.;Wilson M. | 0010-4655 | 10.1016/j.cpc.2008.01.047 | ||||
| Coarse-grained simulation studies of a liquid crystal dendrimer: Towards computational predictions of nanoscale structure through microphase separation | 2005 | Soft Matter | 1 | 436 - 443 | Hughes Z.;Wilson M.;Stimson L. | 1744-683X | 10.1039/b511082c |