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Dr. Damien Thompson

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

Publications

Book Chapters

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 pp. 99-113
DOI: 10.1007/978-1-4614-9176-7_5

Peer Reviewed Journals

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.
In Journal of the American Chemical Society; pp. 6554-6557
DOI: 10.1021/ja5007417

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.
In Nature materials; pp. 947-953
DOI: 10.1038/nmat4060

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.
In Journal of colloid and interface science; pp. 197-204
DOI: 10.1016/j.jcis.2014.09.025

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
In Surface Science; pp. 55-63
DOI: 10.1016/j.susc.2014.01.008

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
In Journal Of Materials Chemistry C; pp. 5675-5684
DOI: 10.1039/c3tc31104j

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.
In Physical chemistry chemical physics : PCCP; pp. 8132-8143
DOI: 10.1039/c3cp50523e

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.
In Nature nanotechnology; pp. 113-118
DOI: 10.1038/nnano.2012.238

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.
In Langmuir; pp. 7271-7282
DOI: 10.1021/la304545n

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.
In Cellular and molecular life sciences : CMLS; pp. 389-404
DOI: 10.1007/s00018-011-0856-6

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
In Chemistry of Materials; American Chemical Society pp. 3981-3992

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.
In Acs Nano; pp. 3007-3017
DOI: 10.1021/nn204470g

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.
In Journal of the American Chemical Society; pp. 14674-14677
DOI: 10.1021/ja306253t

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
In Advanced Functional Materials; pp. 717-725
DOI: 10.1002/adfm.201101956

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.
In Nature chemistry; pp. 317-322
DOI: 10.1038/nchem.1005

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
In Journal Of Physical Chemistry B; pp. 14518-14525
DOI: 10.1021/jp207709c

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.
In Physical chemistry chemical physics : PCCP; pp. 6156-6168
DOI: 10.1039/c0cp02717k

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.
In Nanotechnology;
DOI: 10.1088/0957-4484/22/44/445601

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.
In Journal of molecular modeling; pp. 2227-2235
DOI: 10.1007/s00894-010-0887-1

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.
In Chemistry (Weinheim an der Bergstrasse, Germany); pp. 13473-13481
DOI: 10.1002/chem.201101837

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
In Electrochimica Acta; pp. 3348-
DOI: 10.1016/j.electacta.2010.01.042

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.
In Acs Nano; pp. 921-932
DOI: 10.1021/nn901821h

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....
In Journal of molecular recognition : JMR; pp. 117-127
DOI: 10.1002/jmr.980

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
In The Journal of Physical Chemistry C; American Chemical Society pp. 7298-7304

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.
In Langmuir; pp. 242-247
DOI: 10.1021/la802548u

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
In The Journal of Chemical Physics;
DOI: http://dx.doi.org/10.1063/1.2939247

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.
In Proteins-Structure Function And Bioinformatics; pp. 1450-1460
DOI: 10.1002/prot.21834

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
In Topics In Catalysis; pp. 116-123
DOI: 10.1007/s11244-008-9100-5

2008

Computer Simulations Reveal a Novel Nucleotide-Type Binding Orientation for Ellipticine-Based Anticancer c-kit Kinase Inhibitorsâ€
Thompson, Damien,Miller, Charlotte,McCarthy, Florence O.
(2008) Computer Simulations Reveal a Novel Nucleotide-Type Binding Orientation for Ellipticine-Based Anticancer c-kit Kinase Inhibitorsâ€
In Biochemistry; American Chemical Society pp. 10333-10344

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.
In The journal of physical chemistry. B; pp. 8906-8911
DOI: 10.1021/jp8030336

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
In The Journal of Physical Chemistry B; American Chemical Society pp. 4994-4999

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.
In The Journal of biological chemistry; pp. 30856-30868
DOI: 10.1074/jbc.M704788200

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.
In Chemphyschem; pp. 1684-1693
DOI: 10.1002/cphc.200700288

2007

Free energy balance predicates dendrimer binding multivalency at molecular printboards.
Thompson D
(2007) Free energy balance predicates dendrimer binding multivalency at molecular printboards.
In Langmuir; pp. 8441-8451
DOI: 10.1021/la700878y

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.
In The Journal of biological chemistry; pp. 23792-23803
DOI: 10.1074/jbc.M602870200

2006

Modeling competitive guest binding to beta-cyclodextrin molecular printboards.
Thompson D, Larsson JA
(2006) Modeling competitive guest binding to beta-cyclodextrin molecular printboards.
In The journal of physical chemistry. B; pp. 16640-16645
DOI: 10.1021/jp062553n

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.
In Chembiochem; pp. 337-344
DOI: 10.1002/cbic.200500364

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
In Catalysis Today; pp. 177-180

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
In Surface Science; pp. 438-451

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
In Journal of Molecular Catalysis A: Chemical; pp. 435-439

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
In Journal of Molecular Catalysis A: Chemical; pp. 125-137