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Atomic-scale materials design (Assembled)

Contact: Dr Damien Thompson 
Tel. +353-61-237734

We model advanced materials for applications in health, electronics, and green energy.

L-R: Dr Jose Luis Dominguez, Shayon Bhattacharya, Dr. Adam Orlowski, Dr Pierre-Andre Cazade, Dr Damien Thompson, Sarah Guerin, Melissa Gunnoo, and Shane O’Mahony.

We design novel architectures and assemblies based on the directed self-assembly of nanoscale building blocks (molecules, monolayers, nanoparticles, and proteins) in collaboration with leading experimental and industry partners in European Framework, Science Foundation Ireland and Enterprise Ireland funded projects.  Atomic-resolution modelling of assemblies containing up to a few million atoms is performed using high performance computing facilities at the Materials and Surface Science Institute UL, the Irish Centre for High End Computing and supercomputing centres throughout mainland Europe. We use modelling techniques including molecular and periodic density functional theory, replica exchange, metadynamics, and steered molecular dynamics to compute properties such as binding free energies, diffusion coefficients, and electron transport, and use more coarse-grained models where necessary to approximate larger length (micron+) and time (millisecond+) scales.






Selected recent publications include:

  1. Gunnoo, M.; Cazade, P.A.; Galera-Prat, A.; Nash, M.A.; Czjzek, M.; Cieplak, M.; Alvarez, B.;  Aguilar, M.; Karpol, A.; Gaub, H.; Carrión-Vázquez, M.; Bayer, E.A.; Thompson, D. (2015) Nano-scale engineering of designer cellulosomes Advanced Materials, accepted. IF = 15.4. Invited review on nano-bio engineering with co-authors from EU CellulosomePlus project.
  2.  Song, P.; Sangeeth, C.S.S.; Thompson, D.; Du, W.; Loh, K.P.; Nijhuis, C.A. (2015) NonCovalent Self-Assembled Monolayers on Graphene as a Highly Stable Platform for Molecular Tunnel Junctions. Advanced Materials, accepted. IF = 15.4. Selected as VIP paper by Advanced Functional Materials (<5% of printed papers).
  3. Jiang, L.; Sangeeth, C.S.S.; Yuan, L.; Thompson, D.; Nijhuis, C.A. (2015)  One-Nanometer Thin Monolayers Remove the Deleterious Effect of Substrate Defects in Molecular Tunnel Junctions. Nano Letters, 15, 6643. IF = 13.6. The first demonstration that molecules can compensate for defects in metal electrodes, removing the need for expensive template stripping.
  4. Yuan, L.; Nerngchamnong, N.; Cao, L.; Hamoudi, H.; Del Barco, E.; Roemer, M.; Sriramula, R.K.; Thompson, D.; Nijhuis, C.A. (2015) Controlling the direction of rectification in a molecular diode. Nature Communications, 6, 6324. IF = 11.5. Demonstration that weak molecule-surface binding can dramatically change device properties.
  5. 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, 947. IF = 36.5. Demonstration that molecular energy levels can be reliably measured under robust conditions of room temperature liquids.
  6. Yuan, L.; Jiang, L.; Thompson, D.; Nijhuis, C.A. (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, 6554. IF = 12.1.
  7. Nerngchamnong, N.; Li, Y.; Qi, D.; Jian, L.; Thompson, D.;  Nijhuis, C.A. (2013) The role of van der Waals forces in the performance of molecular diodes. Nature Nanotechnology, 8, 113-118. IF = 34.0.
  8. Thompson, D.; Hermes, J.P.; Quinn, A.J.; 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, 3007. IF = 12.9.
  9. Perl, A.; Gomez-Casado, A.;  Thompson, D.; Dam, H.; Jonkheijm, P.; Reinhoudt, D.; Huskens, J. (2011). Gradient-driven motion of multivalent ligand molecules along a surface functionalized with multiple receptors. Nature Chemistry, 3, 317-322. IF = 25.3.
  10. Gannon, G.; Larsson, J.A.; Greer, J.C.; Thompson, D. (2010). Molecular dynamics study of naturally-occurring defects in self-assembled monolayer formation. ACS Nano, 4, 921-932. IF = 12.9.


A full listing of publications for PI Damien Thompson can be viewed using Google Scholar Damien Thompson or Researcher ID: G-6138-2015.


Meet the team:

Group leader Damien Thompson is a lecturer in the Department of Physics and Energy at UL since 2013 and is a member of the Materials and Surface Science Institute (MSSI). He has a PhD in computational chemistry (2003) and performed postdoctoral studies in biophysics with Prof Tom Simonson at Ecole Polytechnique France (2003-2005) before working for eight years as a research scientist in Prof Jim Greer’s electronic structure theory group at the Tyndall National Institute and lecturing at University College Cork. He models a wide range of materials using molecular dynamics and electronic structure methods. He is married with Irish twins and remembers when he had time to listen to rock music and read existentialist novels.


Pierre Andre Cazade obtained his PhD in 2008 at the University of Pau, France. He worked on chromophores encapsulated in solgel by means of QM calculations and MD simulations, combined with fluorescence experiments. He did his first postdoc with Dr. Benoit Coasne at the University of Montpellier, working on nanofiltration. In 2010, he joined the group of Prof. Markus Meuwly at the University of Basel. There he modelled the conversion of toxic NO into harmless nitrate by haemoglobin. He also modelled 2D IR spectra using MD simulations. He joined the team in 2014 and is currently studying the dynamics of linkers in the cellulosome complex in an effort to redesign an industrially efficient version of this nanomachine that can produce biofuel from feedstock wastes, in the EU FP7 CellulosomePlus project. Pierre enjoys reading, mostly historical novels and fantasy, and particularly likes the music of J. S. Bach, Beethoven, and Ravel.


Jose Luis Dominguez Meijide was born in Galicia, Spain, on the 24th of December of 1984. His parents resisted the urge to name him Natividad. After completing high school he moved to Santiago de Compostela where he obtained his Bachelor Degree in Organic Chemistry. He followed that with a PhD in Computational Chemistry, where he took his first steps in the field of neurodegenerative diseases. He arrived in our group in the summer of 2015 and currently studies the dynamics of neurotoxic proteins in research funded by Science Foundation Ireland.


Adam Orlowski got his Master’s degree in biophysics at the Jagiellonian University in Krakow. During his studies he had the pleasure to spend some time working at the Centre for Drug Research at the University of Helsinki and Tampere University of Technology in Finland. He then started PhD studies in the group of Prof. Ilpo Vattulainen at the Tampere University of Technology. His PhD thesis research focused mainly on studies of lipid-protein interactions using biomolecular simulations, but he also found time to participate in projects from other fields, ranging from neurochemistry to nanotechnology to protein-sugar interactions. After his PhD, Adam took a short break from research and worked for a while as an analyst in the Forensic Technology division of one of the “big four” consulting companies. He joined our group in late 2015 and is currently studying protein-sugar interactions in the EU FP7 CellulosomePlus project and will continue these studies in an Enterprise Ireland funded project starting in early 2016. Before he got involved in scientific research, his passion was athletics and he specialised in running 110/400 meters hurdles. Nowadays, in his free time he still likes to run (without hurdles though), travel, scuba dive in cold lakes, and drink Smithwicks in real Irish pubs.

Shane O’Mahony graduated with a BSc in Physics from University College Cork in 2010 and graduated from there in 2012 with an MSc in plasma physics. He started his Science Foundation Ireland funded PhD work in 2012 and he is currently using molecular dynamics simulations to investigate various methods of immobilising proteins on surfaces. Shane enjoys baking and running and recently completed his first half-marathon.





Melissa Gunnoo received her B.Sc. in Physics with Biomedical sciences from Dublin City University, Ireland in 2013. She joined the group in 2014 to study for a PhD in computational protein design, funded through the EU FP7 CellulosomePlus project. When she is not playing with proteins, you will find Melissa either baking or enjoying long walks in the lovely Irish weather.


After completing his Bachelor’s degree in Pharmaceutical Sciences, Shayon Bhattacharya received his MSc degree in Pharmacoinformatics from National Institute of Pharmaceutical Education and Research (NIPER), India. His Master’s thesis was focussed on understanding the biological role of the ligand-binding sites of tubulin protein across eukaryotic families, using bioinformatics tools and molecular modelling. He also had a short stint at University of Cincinnati, USA, where he underwent various laboratory rotations. On one of his rotations in Experimental Neuroscience, he worked on microscopic identification of cells in rat brain sections to study regulation of adult forebrain neurogenesis by Ciliary Neurotropic Factor Receptor – alpha (CNTFR-a), work published in Journal of Neuroscience. Shayon joined us mid 2015 to study for a PhD in the design of inhibitors of neurotoxic proteins, funded through Science Foundation Ireland in the EU Joint Programme for Neurodegenerative Disease Research (JPND). Shayon enjoys photography (especially landscape and macro), loves to travel, and is always eager to try his hand at cooking delicacies.

Sarah Guerin started her PhD studies in September 2015 funded through the Science Foundation Ireland Cúram centre for research in medical devices. Her research aims to model piezoelectricity in biomolecules such as prestin and lysozyme. She graduated in August 2015 with a first class honours BSc in Applied Physics. Her final year project, which characterised polymers for industrial applications, was highly commended in the 2015 Undergraduate Awards. A proud Kerry woman, she enjoys climbing very high mountains and is climbing Kilimanjaro in 2016.