Damien Thompson


researcher

Biography

2013-present: Lecturer in Physics, University of Limerick, Ireland

2005-2013:Scientist in the Theory Modelling and Design Center at Tyndall National Institute, University College Cork, Ireland

2003-2005: Postdoctoral fellow in Computational Biophysics at Ecole Polytechnique (Advisor: Prof Thomas Simonson)

1999-2003: PhD in Computational Chemistry at University of Limerick (Supervisor: Prof Kieran Hodnett)

Research Interests

  • Rational design ofmaterials for energy-efficient electronics, medical devices and clean energy
  • High-performance computing
  • Molecular dynamics simulations
  • Electronic structure calculations

Book Chapters

Year Publication
2014 'Frontiers of Cu Electrodeposition and Electroless Plating for On-chip Interconnects'
James F. Rohan and Damien Thompson (2014) 'Frontiers of Cu Electrodeposition and Electroless Plating for On-chip Interconnects' In: Copper Electrodeposition for Nanofabrication of Electronics Devices. New York: Springer. [DOI] [Details]

Peer Reviewed Journals

Year Publication
2014 'Nanoelectrical analysis of single molecules and atomic-scale materials at the solid/liquid interface'
Nirmalraj P, Thompson D, Molina-Ontoria A, Sousa M, Martín N, Gotsmann B, Riel H (2014) 'Nanoelectrical analysis of single molecules and atomic-scale materials at the solid/liquid interface'. Nature materials, 13 (10):947-953 [DOI] [Details]
2014 'On the remarkable role of surface topography of the bottom electrodes in blocking leakage currents in molecular diodes'
Yuan L, Jiang L, Thompson D, Nijhuis CA (2014) 'On the remarkable role of surface topography of the bottom electrodes in blocking leakage currents in molecular diodes'. Journal of the American Chemical Society, 136 (18):6554-6557 [DOI] [Details]
2014 'On the hydration of subnanometric antifouling organosilane adlayers: A molecular dynamics simulation'
Sheikh S, Blaszykowski C, Nolan R, Thompson D, Thompson M (2014) 'On the hydration of subnanometric antifouling organosilane adlayers: A molecular dynamics simulation'. Journal of colloid and interface science, 437C :197-204 [DOI] [Details]
2014 'Reassigning the most stable surface of hydroxyapatite to the water resistant hydroxyl terminated (010) surface'
Zeglinski, Jacek,Nolan, Michael,Thompson, Damien,Tofail, Syed A.M. (2014) 'Reassigning the most stable surface of hydroxyapatite to the water resistant hydroxyl terminated (010) surface'. Surface Science, 623 (0):55-63 [DOI] [Details]
2013 'The role of van der Waals forces in the performance of molecular diodes'
Nerngchamnong N, Yuan L, Qi DC, Li J, Thompson D, Nijhuis CA (2013) 'The role of van der Waals forces in the performance of molecular diodes'. Nature nanotechnology, 8 (2):113-118 [DOI] [Details]
2013 'Large directional conductivity change in chemically stable layered thin films of vanadium oxide and a 1D metal complex'
Glynn, C,Thompson, D,Paez, J,Collins, G,Benavente, E,Lavayen, V,Yutronic, N,Holmes, JD,Gonzalez, G,O'Dwyer, C (2013) 'Large directional conductivity change in chemically stable layered thin films of vanadium oxide and a 1D metal complex'. Journal Of Materials Chemistry C, 1 :5675-5684 [DOI] [Details]
2013 'Nanoscale dynamics and protein adhesivity of alkylamine self-assembled monolayers on graphene'
O'Mahony S, O'Dwyer C, Nijhuis CA, Greer JC, Quinn AJ, Thompson D (2013) 'Nanoscale dynamics and protein adhesivity of alkylamine self-assembled monolayers on graphene'. Langmuir, 29 (24):7271-7282 [DOI] [Details]
2013 'A multi-scale molecular dynamics study of the assembly of micron-size supraparticles from 30 nm alkyl-coated nanoparticles'
Thompson D, Sikora M, Szymczak P, Cieplak M (2013) 'A multi-scale molecular dynamics study of the assembly of micron-size supraparticles from 30 nm alkyl-coated nanoparticles'. Physical chemistry chemical physics : PCCP, 15 (21):8132-8143 [DOI] [Details]
2012 'Nanoparticle-based drug delivery: case studies for cancer and cardiovascular applications'
Galvin P, Thompson D, Ryan KB, McCarthy A, Moore AC, Burke CS, Dyson M, Maccraith BD, Gun'ko YK, Byrne MT, Volkov Y, Keely C, Keehan E, Howe M, Duffy C, MacLoughlin R (2012) 'Nanoparticle-based drug delivery: case studies for cancer and cardiovascular applications'. Cellular and molecular life sciences : CMLS, 69 (3):389-404 [DOI] [Details]
2012 'Scanning the potential energy surface for synthesis of dendrimer-wrapped gold clusters: design rules for true single-molecule nanostructures'
Thompson D, Hermes JP, Quinn AJ, Mayor M (2012) 'Scanning the potential energy surface for synthesis of dendrimer-wrapped gold clusters: design rules for true single-molecule nanostructures'. Acs Nano, 6 (4):3007-3017 [DOI] [Details]
2012 'Monofunctionalized gold nanoparticles stabilized by a single dendrimer form dumbbell structures upon homocoupling'
Hermes JP, Sander F, Fluch U, Peterle T, Thompson D, Urbani R, Pfohl T, Mayor M (2012) 'Monofunctionalized gold nanoparticles stabilized by a single dendrimer form dumbbell structures upon homocoupling'. Journal of the American Chemical Society, 134 (36):14674-14677 [DOI] [Details]
2012 'Accommodating Curvature in a Highly Ordered Functionalized Metal Oxide Nanofiber: Synthesis, Characterization, and Multiscale Modeling of Layered Nanosheets'
O’Dwyer, C.,Gannon, G.,McNulty, D.,Buckley, D. N.,Thompson, D. (2012) 'Accommodating Curvature in a Highly Ordered Functionalized Metal Oxide Nanofiber: Synthesis, Characterization, and Multiscale Modeling of Layered Nanosheets'. Chemistry of Materials, 24 (20):3981-3992 [Details]
2012 'Non-Covalent Functionalization of Graphene Using Self-Assembly of Alkane-Amines'
Long, Brenda and Manning, Mary and Burke, Micheal and Szafranek, Bartholomaeus N. and Visimberga, Giuseppe and Thompson, Damien and Greer, James C. and Povey, Ian M. and MacHale, John and Lejosne, Guaylord and Neumaier, Daniel and Quinn, Aidan J. (2012) 'Non-Covalent Functionalization of Graphene Using Self-Assembly of Alkane-Amines'. Advanced Functional Materials, 22 (4):717-725 [DOI] [Details]
2011 'Molecular dynamics of the hydrophobic patch that immobilizes hydrophobin protein HFBII on silicon'
Moldovan C, Thompson D (2011) 'Molecular dynamics of the hydrophobic patch that immobilizes hydrophobin protein HFBII on silicon'. Journal of molecular modeling, 17 (9):2227-2235 [DOI] [Details]
2011 'Interdigitating Organic Bilayers Direct the Short Inter layer Spacing in Hybrid Organic-Inorganic Layered Vanadium Oxide Nanostructures'
Gannon, G; O'Dwyer, C; Larsson, JA; Thompson, D (2011) 'Interdigitating Organic Bilayers Direct the Short Inter layer Spacing in Hybrid Organic-Inorganic Layered Vanadium Oxide Nanostructures'. Journal Of Physical Chemistry B, 115 :14518-14525 [DOI] [Details]
2011 'Electronic structure calculations and physicochemical experiments quantify the competitive liquid ion association and probe stabilisation effects for nitrobenzospiropyran in phosphonium-based ionic liquids'
Thompson D, Coleman S, Diamond D, Byrne R (2011) 'Electronic structure calculations and physicochemical experiments quantify the competitive liquid ion association and probe stabilisation effects for nitrobenzospiropyran in phosphonium-based ionic liquids'. Physical chemistry chemical physics : PCCP, 13 (13):6156-6168 [DOI] [Details]
2011 'Linker-mediated assembly of gold nanoparticles into multimeric motifs'
Sikora M, Szymczak P, Thompson D, Cieplak M (2011) 'Linker-mediated assembly of gold nanoparticles into multimeric motifs'. Nanotechnology, 22 (44) [DOI] [Details]
2011 'Gradient-driven motion of multivalent ligand molecules along a surface functionalized with multiple receptors'
Perl A, Gomez-Casado A, Thompson D, Dam HH, Jonkheijm P, Reinhoudt DN, Huskens J (2011) 'Gradient-driven motion of multivalent ligand molecules along a surface functionalized with multiple receptors'. Nature chemistry, 3 (4):317-322 [DOI] [Details]
2011 'Gold nanoparticles stabilized by thioether dendrimers'
Hermes JP, Sander F, Peterle T, Urbani R, Pfohl T, Thompson D, Mayor M (2011) 'Gold nanoparticles stabilized by thioether dendrimers'. Chemistry (Weinheim an der Bergstrasse, Germany), 17 (48):13473-13481 [DOI] [Details]
2010 'Alchemical free energy simulations for biological complexes: powerful but temperamental'
Aleksandrov A, Thompson D, Simonson T (2010) 'Alchemical free energy simulations for biological complexes: powerful but temperamental'. Journal of molecular recognition : JMR, 23 (2):117-127 [DOI] [Details]
2010 'Interaction of acridine-calix [4] arene with DNA at the electrified liquid| liquid interface'
F Kivlehan, M Lefoix, HA Moynihan, D Thompson, VI Ogurtsov, G Herzog, DWM Arrigan (2010) 'Interaction of acridine-calix [4] arene with DNA at the electrified liquid| liquid interface'. Electrochimica Acta, 55 [DOI] [Details]
2010 'Molecular dynamics study of naturally occurring defects in self-assembled monolayer formation'
Gannon G, Greer JC, Larsson JA, Thompson D (2010) 'Molecular dynamics study of naturally occurring defects in self-assembled monolayer formation'. Acs Nano, 4 (2):921-932 [DOI] [Details]
2009 'Monolayer Packing, Dehydration, and Ink-Binding Dynamics at the Molecular Printboard'
Gannon, Greg,Larsson, J. Andreas,Thompson, Damien (2009) 'Monolayer Packing, Dehydration, and Ink-Binding Dynamics at the Molecular Printboard'. The Journal of Physical Chemistry C, 113 (17):7298-7304 [Details]
2009 'Quantification of ink diffusion in microcontact printing with self-assembled monolayers'
Gannon G, Larsson JA, Greer JC, Thompson D (2009) 'Quantification of ink diffusion in microcontact printing with self-assembled monolayers'. Langmuir, 25 (1):242-247 [DOI] [Details]
2008 'Hydrocarbon Selective Oxidation on Vanadium Phosphorus Oxide Catalysts: Insights from Electronic Structure Calculations'
Thompson, D; Hodnett, BK (2008) 'Hydrocarbon Selective Oxidation on Vanadium Phosphorus Oxide Catalysts: Insights from Electronic Structure Calculations'. TOPICS IN CATALYSIS, 50 (1-4):116-123 [DOI] [Details]
2008 'The Effective Concentration of Unbound Ink Anchors at the Molecular Printboard'
Thompson, D. (2008) 'The Effective Concentration of Unbound Ink Anchors at the Molecular Printboard'. The Journal of Physical Chemistry B, 112 (16):4994-4999 [Details]
2008 'Guanidinium chloride molecular diffusion in aqueous and mixed water-ethanol solutions'
Gannon G, Larsson JA, Greer JC, Thompson D (2008) 'Guanidinium chloride molecular diffusion in aqueous and mixed water-ethanol solutions'. The journal of physical chemistry. B, 112 (30):8906-8911 [DOI] [Details]
2008 'Computer Simulations Reveal a Novel Nucleotide-Type Binding Orientation for Ellipticine-Based Anticancer c-kit Kinase Inhibitors†'
Thompson, Damien,Miller, Charlotte,McCarthy, Florence O. (2008) 'Computer Simulations Reveal a Novel Nucleotide-Type Binding Orientation for Ellipticine-Based Anticancer c-kit Kinase Inhibitors†'. Biochemistry, 47 (39):10333-10344 [Details]
2008 'Coarse-grained molecular dynamics simulations of nanopatterning with multivalent inks'
Cieplak, Marek and Thompson, Damien (2008) 'Coarse-grained molecular dynamics simulations of nanopatterning with multivalent inks'. The Journal of Chemical Physics, 128 (23) [DOI] [Details]
2008 'Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations'
Thompson D, Lazennec C, Plateau P, Simonson T (2008) 'Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations'. Proteins-Structure Function And Bioinformatics, 71 (3):1450-1460 [DOI] [Details]
2007 'In silico engineering of tailored ink-binding ability at molecular printboards'
Thompson D (2007) 'In silico engineering of tailored ink-binding ability at molecular printboards'. Chemphyschem, 8 (11):1684-1693 [DOI] [Details]
2007 'Free energy balance predicates dendrimer binding multivalency at molecular printboards'
Thompson D (2007) 'Free energy balance predicates dendrimer binding multivalency at molecular printboards'. Langmuir, 23 (16):8441-8451 [DOI] [Details]
2007 'Ammonium scanning in an enzyme active site. The chiral specificity of aspartyl-tRNA synthetase'
Thompson D, Lazennec C, Plateau P, Simonson T (2007) 'Ammonium scanning in an enzyme active site. The chiral specificity of aspartyl-tRNA synthetase'. The Journal of biological chemistry, 282 (42):30856-30868 [DOI] [Details]
2006 'Free-energy simulations and experiments reveal long-range electrostatic interactions and substrate-assisted specificity in an aminoacyl-tRNA synthetase'
Thompson D, Plateau P, Simonson T (2006) 'Free-energy simulations and experiments reveal long-range electrostatic interactions and substrate-assisted specificity in an aminoacyl-tRNA synthetase'. Chembiochem, 7 (2):337-344 [DOI] [Details]
2006 'Molecular dynamics simulations show that bound Mg2+ contributes to amino acid and aminoacyl adenylate binding specificity in aspartyl-tRNA synthetase through long range electrostatic interactions'
Thompson D, Simonson T (2006) 'Molecular dynamics simulations show that bound Mg2+ contributes to amino acid and aminoacyl adenylate binding specificity in aspartyl-tRNA synthetase through long range electrostatic interactions'. The Journal of biological chemistry, 281 (33):23792-23803 [DOI] [Details]
2006 'Modeling competitive guest binding to beta-cyclodextrin molecular printboards'
Thompson D, Larsson JA (2006) 'Modeling competitive guest binding to beta-cyclodextrin molecular printboards'. The journal of physical chemistry. B, 110 (33):16640-16645 [DOI] [Details]
2004 'Electronic structure of the extended vanadyl pyrophosphate (1 0 0) surface'
Thompson, D.J,Ciobı̂cǎ, I.M,Hodnett, B.K,van Santen, R.A,Fanning, M.O (2004) 'Electronic structure of the extended vanadyl pyrophosphate (1 0 0) surface'. Catalysis Today, 91–92 (0):177-180 [Details]
2003 'The interplay of electrostatic and covalent effects in 1-butene oxidation over vanadyl pyrophosphate'
Thompson, D.J,Fanning, M.O,Hodnett, B.K (2003) 'The interplay of electrostatic and covalent effects in 1-butene oxidation over vanadyl pyrophosphate'. Journal of Molecular Catalysis A: Chemical, 206 (1–2):435-439 [Details]
2003 'Modelling the active sites in vanadyl pyrophosphate'
Thompson, D.J.,Fanning, M.O.,Hodnett, B.K. (2003) 'Modelling the active sites in vanadyl pyrophosphate'. Journal of Molecular Catalysis A: Chemical, 198 (1–2):125-137 [Details]
2003 'A DFT periodic study of the vanadyl pyrophosphate (1 0 0) surface'
Thompson, D.J,Ciobı̂că, I.M,Hodnett, B.K,van Santen, R.A,Fanning, M.O (2003) 'A DFT periodic study of the vanadyl pyrophosphate (1 0 0) surface'. Surface Science, 547 (3):438-451 [Details]