Damien Thompson
Education:
1999-2003
1995-1999
Telephone: +353-21-490-extension or +353-21-490-4177
Employment:
September 2003 - March 2005
2005 - date
Projects:
Project Name Summary
NaPa Emerging Nanopatterning Methods
Teaching:
"Fundamentals of molecular dynamics (MD) modelling and its
applications in simulations of nanopatterning processes"
at PANAMA Summer School on Emerging Nanopatterning Methods
(EU Project NaPa):
2006 lecture (PDF, 11 MB) ,
2007 lecture (PDF, 5 MB)
"A Practical Course in
Atomistic Electronics Theory" held at Tyndall, June 2007;
lectures on molecular modelling and molecular dynamics (MD):
MD overview (PDF, 2.1 MB) ,
MD of self-assembled
monolayers (PDF, 1.6 MB) ,
MD of proteins (PDF, 3.3 MB) ,
Steered MD (PDF, 2.2 MB) .Molecular modelling (CM3109) practicals held at Tyndall
for UCC Chemistry Department
Publications:
Publication Volume Pages Year Publication Title List of Authors
J BIOL CHEM
281
23792-23803
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 D. Thompson, T. Simonson
J PHYS CHEM B
110
16640
2006
Modeling Competitive Guest Binding to beta-Cyclodextrin Molecular Printboards D. Thompson, J.A. Larsson
CHEMBIOCHEM
7
337-344
2006
Free-Energy Simulations and Experiments Reveal Long-Range Electrostatic Interactions and Substrate-Assisted Specificity in an Aminoacyl-tRNA Synthetase D. Thompson, P. Plateau, T. Simonson
LANGMUIR
23
8441-8451
2007
Free Energy Balance Predicates Dendrimer Binding Multivalency at Molecular Printboards D. Thompson
J BIOL CHEM
282
30856-30868
2007
Ammonium Scanning in an Enzyme Active Site: The Chiral Specificity of Aspartyl-tRNA synthetase D. Thompson, C. Lazennec, P. Plateau, T. Simonson
CHEMPHYSCHEM
8
1684-1693
2007
In Silico Engineering of Tailored Ink-Binding Ability at Molecular Printboards D. Thompson
J PHYS CHEM B
112
4994-4999
2008
The Effective Concentration of Unbound Ink Anchors at the Molecular Printboard D. Thompson
J CHEM PHYS
128
234906
2008
Coarse-grained molecular dynamics simulations of nanopatterning with multivalent inks M. Cieplak, D. Thompson
PROTEINS
71
1450-1460
2008
Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations D. Thompson, C. Lazennec, P. Plateau, T. Simonson
BIOCHEMISTRY-US
47
10333-10344
2008
Computer Simulations Reveal a Novel Nucleotide-Type Binding Orientation for Ellipticine-Based Anticancer c-kit Kinase Inhibitors D. Thompson, C. Miller, F.O. McCarthy
TOP CATAL
50
116-123
2008
Hydrocarbon Selective Oxidation on Vanadium Phosphorus Oxide Catalysts: Insights from Electronic Structure Calculations D. Thompson, B.K. Hodnett
J PHYS CHEM B
112
8906 8911
2008
Guanidinium Chloride Molecular Diffusion in Aqueous and Mixed Water−Ethanol Solutions G. Gannon, J.A. Larsson, J.C. Greer, D. Thompson
DRUG FUTURE
34
102
2009
Design and synthesis of novel ellipticine c-Kit kinase inhibitors C. Miller, D. Thompson, F.O. McCarthy
J PHYS CHEM C
113
7298
2009
Monolayer Packing, Dehydration, and Ink-Binding Dynamics at the Molecular Printboard G. Gannon, J.A. Larsson, D. Thompson
LANGMUIR
25
242-247
2009
Quantification of Ink Diffusion in Microcontact Printing with Self-Assembled Monolayers G. Gannon, J.A. Larsson, J.C. Greer, D. Thompson
J MOL RECOGNIT
23
117-127
2010
Alchemical free energy simulations for biological complexes: powerful but temperamental A. Aleksandrov, D. Thompson, T. Simonson
ELECTROCHIM ACTA
55
3348-3354
2010
Interaction of acridine-calix[4]arene with DNA at the electrified liquid|liquid interface F. Kivlehan, M. Lefoix, H.A. Moynihan, D. Thompson, V.I. Ogurtsov, G. Herzog, D.W.M. Arrigan
ACS NANO
4(2)
921-932
2010
Molecular Dynamics Study of Naturally Occurring Defects in Self-Assembled Monolayer Formation G. Gannon, J.C. Greer, J.A. Larsson, D. Thompson
Electronic structure of the extended vanadyl
pyrophosphate (1 0 0) surface
D.J. Thompson, I.M. Ciobica, B.K. Hodnett, R.A. van Santen,
and M.O. Fanning
Catalysis Today, 91-92, 177 (2004)
A DFT periodic study of the vanadyl
pyrophosphate (1 0 0) surface
D.J. Thompson, I.M. Ciobica, B.K. Hodnett, R.A. van Santen,
and M.O. Fanning
Surface Science, 547, 438 (2003)
The interplay of electrostatic and covalent effects in
1-butene oxidation over vanadyl pyrophosphate
D.J. Thompson, M.O. Fanning, and B.K. Hodnett
Journal of Molecular Catalysis A: Chemical, 206, 435 (2003)
Modelling the active sites in vanadyl pyrophosphate
D.J. Thompson, M.O. Fanning, and B.K. Hodnett
Journal of Molecular Catalysis A: Chemical, 198, 125 (2003)
contact Tyndall National Institute
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