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Publications

Publications resulting from research assisted by ICHEC are displayed here. We strongly encourage all ICHEC researchers with submitted, accepted or published research in science journals or conference proceedings to submit a copy of their research to us at info@ichec.ie.

In some instances, the level of ICHEC involvement in user research projects has resulted in members of ICHEC staff included as co-authors of publications (see Co-authored Publications).

Since ICHEC started offering its services to the Irish academic community on September 1st, 2005, it has been credited in at least 527 publications:

2014

Title Authors Publication
Enabling Smeagol on Xeon Phi: Lessons Learned Alin M. Elena, Ivan Rungger PRACE whitepaper
Enabling the UCD-SPH code on the Xeon Phi Christian Lalanne, Ashkan Rafiee, Denys Dutykh, Michael Lysaght, Frederic Dias PRACE
Investigating Performance Benefits from OpenACC Kernel Directives Benjamin Eagan, Gilles Civario, Renato Miceli Advances in Parallel Computing
Conformational Changes in Acetylcholine Binding Protein Investigated by Temperature Accelerated Molecular Dynamics Zeynab Mohammad Hosseini Naveh, Therese E. Malliavin, Luca Maragliano, Grazia Cottone, Giovanni Ciccotti PLOS ONE
Influence of History of Solution in Crystal Nucleation of Fenoxycarb: Kinetics and Mechanisms Manuel Kuhs, Jacek Zeglinski, and Åke C. Rasmuson Cryst. Growth Des.
Reassigning the most stable surface of hydroxyapatite to the water resistant hydroxyl terminated (010) surface Jacek Zeglinski, Michael Nolan, Damien Thompson, Syed A.M. Tofail Surface Science
Modelling bearing failure in countersunk composite joints under quasi-static loading using 3D explicit finite element analysis B. Egan, M.A. McCarthy, R.M. Frizzell, P.J. Gray, C.T. McCarthy Composite Structures

2013

Title Authors Publication
Equilibrium and Rate Constants, and Reaction Mechanism of the HF Dissociation in the HF (H2O) 7 Cluster by ab Initio Rare Event Simulations Alin Marin Elena, Simone Meloni, Giovanni Ciccotti J PhyS Chem A
Wind Forecasting Using HARMONIE with Bayes Model Averaging for Fine-tuning Martin B. Peters, Enda O'Brien, Alastair McKinstry, Adam Ralph Energy Procedia
Failure modelling of trabecular bone using a non-linear combined damage and fracture voxel finite element approach Noel M. Harrison, Pat McDonnell, Liam Mullins, Niall Wilson, Denis O'Mahoney, Peter E. McHugh Biomech Model Mechanobiol
The State-of-the-Art in Directive-Guided Auto-Tuning for Accelerator and Heterogeneous Many-Core Architectures Renato Miceli, François Bodin PRACE
Opportunities and Strategies for I/O Auto-Tuning Renato Miceli Dagstuhl
AutoTune: Plugin-based Tuning of Parallel Codes Renato Miceli HiPEAC
AutoTune: A Plugin-Driven Approach to the Automatic Tuning of Parallel Applications Renato Miceli, Gilles Civario, Anna Sikora, Eduardo César, Michael Gerndt, Houssam Haitof, Carmen Navarrete, Siegfried Benkner, Martin Sandrieser, Laurent Morin, François Bodin LNCS
Strain effects on the ionic conductivity of Y-doped ceria: A simulation study Mario Burbano, Dario Marrocchelli, Graeme W. Watson J. Chem. Inf. Model.
Structure-Activity Relationships in novel non ligand-binding pocket (non-LBP) Diarylhydrazide Antiandrogens Caboni, L, Egan, B, Kelly, B, Blanco, F, Fayne, D, Meegan, MJ, Lloyd, DG. J. Chem. Inf. Model.
De-Peptidising Protein-Protein Interactions – big jobs for small molecules Fayne, D. Drug Discovery Today: Technologies
Ligand-Based Molecular Design using Pseudoreceptors Fayne, D De Novo Design
An AIPS-based, distributed processing method for large radio interferometric datasets Stephen Bourke, Huib Jan van Langevelde, Karl Torstensson, Aaron Golden Experimental Astronomy
Enhancement of DFT-calculations at petascale: Nuclear Magnetic Resonance, Hybrid Density Functional Theory and Car–Parrinello calculations Nicola Varini, Davide Ceresoli, Layla Martin-Samos, Ivan Girotto, Carlo Cavazzoni Computer Physics Communications
Effects of Li-ion vacancies on the ionic conduction mechanism of LiMgSO4F Dario Marrocchelli, Mathieu Salanne and Graeme W Watson Modelling Simul. Mater. Sci. Eng.
PbO2: from semi-metal to transparent conducting oxide by defect chemistry control Aron Walsh, Aoife B. Kehoe, Douglas J. Temple, Graeme W. Watson and David O. Scanlon Chem. Commun.
Computational testing of trivalent dopants in CeO2 for improved high-K dielectric behaviour Patrick R. L. Keating, David O. Scanlon and Graeme W. Watson J. Mater. Chem. C
Origin of the bipolar doping behavior of SnO from x-ray spectroscopy and density functional theory N. F. Quackenbush, J. P. Allen, D. O. Scanlon, S. Sallis, J. A. Hewlett, A. S. Nandur, B. Chen, K. E. Smith, C. Weiland, D. A. Fischer, J. C. Woicik, B. E. White, G. W. Watson, and L. F. J. Piper Chem. Mater.
Understanding the defect chemistry of tin monoxide Jeremy P. Allen, David O. Scanlon, Louis F. J. Piper and Graeme W. Watson J. Mater. Chem. C
Electronic structures of antimony oxides Jeremy P. Allen, John J. Carey, Aron Walsh, David O. Scanlon, and Graeme W. Watson J. Phys. Chem. C.
Effects of knee flexion on the femoropopliteal artery: A computational study Ríona Ní Ghriallais, Mark Bruzzi Medical Engineering & Physics
Investigation of the Effect of Stent Length and Stent Location on the Deformation Characteristics of the Femoropopliteal Artery After Knee Flexion: A Finite Element Study Ríona Ní Ghriallais, Mark Bruzzi Proceedings of the ASME/FDA 2013
Optimizing the design of a bioabsorbable metal stent using computer simulation methods J.A. Grogan, S.B. Leen, P.E. McHugh Biomaterials
Spectroscopic observations of unbound asteroid pairs using the WHT Duddy, S. R., Lowry, S. C., Christou, A., Wolters, S. D., Rozitis, B., Green, S. F., Weissman, P. R. Monthly Notices of the Royal Astronomical Society
Orbital clustering of Martian Trojans: An asteroid family in the inner solar system? Apostolos A. Christou Icarus
Theoretical and Kinetic Study of the Hydrogen Atom Abstraction Reactions of Esters with HO2 Radicals J. Mendes, C.-W. Zhou, H. J. Curran J. Phys. Chem. A
Theoretical and Kinetic Study of the Reactions of Ketones with HO2 Radicals. Part I: Abstraction Reaction Channels Jorge Mendes, Chong-Wen Zhou and Henry J. Curran J. Phys. Chem. A
Theoretical and Kinetic Study of the Reaction of Ethyl Methyl Ketone with HO2 for T = 600-1,600 K. Part II: Addition Reaction Channels Chong-Wen Zhou, Jorge Mendes and Henry J. Curran J. Phys. Chem. A
A high temperature and atmospheric pressure experimental and detailed chemical kinetic modelling study of 2-methyl furan oxidation K.P. Somers, J.M. Simmie, F. Gillespie, U. Burke, J. Connolly, W.K. Metcalfe, F. Battin-Leclerc, P. Dirrenberger, O. Herbinet, P.-A. Glaude, H.J. Curran Proc. Combust. Inst.
The reaction of 2,5-dimethylfuran with hydrogen atoms - An experimental and theoretical study Philipp Friese, John M. Simmie, Matthias Olzmann Proc. Combust. Inst.
Rate constants of hydrogen abstraction by methyl radical from n-butanol and a comparison of CanTherm, MultiWell and Variflex D. Katsikadakos, C.-W. Zhou, J.M. Simmie, H.J. Curran, P.A. Hunt, Y. Hardalupas, A.M.K.P. Taylor Proc. Combust. Inst.
Theoretical kinetics for the decomposition of iso-butanol and related (CH3)2CH + CH2OH reactions Chong-Wen Zhou, Stephen J. Klippenstein, John M. Simmie, Henry J. Curran Proc. Combust. Inst.
Substituent Effects in the Thermochemistry of Furans: A Theoretical (CBS-QB3, CBS-APNO and G3) Study John. M. Simmie, Kieran P. Somers, Wayne K. Metcalfe, Henry J. Curran J. Chemical Thermodynamics
A Quantum Chemical Study of the Abnormal Reactivity of 2-Methoxyfuran J. M. Simmie, K. P. Somers, K. Yasunaga, H. J. Curran Int. J. of Chemical Kinetics
Dynamical exchange interaction from time-dependent spin density functional theory Maria Stamenova and Stefano Sanvito Phys. Rev. B
An investigation of the inelastic behaviour of trabecular bone during the press-fit implantation of a tibial component in total knee arthroplasty. Nicola Kelly, Derek T. Cawley, Fintan J. Shannon, J. Patrick McGarry Medical Engineering & Physics
An experimental and computational investigation of the post-yield behaviour of trabecular bone during vertebral device subsidence. Nicola Kelly, Noel M. Harrison, Pat McDonnell, J. Patrick McGarry Biomech Model Mechanobiol
A genome-wide association study for somatic cell score using the Illumina high-density bovine beadchip identifies several novel QTL potentially related to mastitis susceptibility Meredith B., Berry D., Kearney F., Finlay, E.K., Fahey, A.G., Bradley D.G. and Lynn D.J. Front. Genet.
Referential translation machines for quality estimation Ergun Bicici ACL 2013
Feature decay algorithms for fast deployment of accurate statistical machine translation systems Ergun Bicici ACL 2013
SnO-nanocluster modified anatase TiO2 photocatalyst: exploiting the Sn(II) lone pair for a new photocatalyst material with visible light absorption and charge carrier separation Anna Iwaszuk and Michael Nolan J. Mater. Chem. A
Lead oxide-modified TiO2 photocatalyst: tuning light absorption and charge carrier separation by lead oxidation state Anna Iwaszuk and Michael Nolan Catal. Sci. Technol.
Finite element analysis of balloon-expandable coronary stent deployment: Influence of angioplasty balloon configuration D. Martin and F. Boyle Int J Numer Method Biomed Eng
CNGL: Grading student answers by acts of translation Ergun Bicici and Josef van Genabith SemEval 2013
CNGL-CORE: Referential translation machines for measuring semantic similarity Ergun Bicici and Josef van Genabith *SEM 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. Phys Chem Chem Phys
On Watts' cascade model with random weights Hurd TR and Gleeson JP J Complex Networks
Binary-state dynamics on complex networks: pair approximation and beyond Gleeson JP Phys. Rev.
Anisotropic mode-dependent damage of cortical bone using the extended finite element method (XFEM) Emer M Feerick, Xiangyi (Cheryl) Liu, Patrick McGarry J Mech Behav Biomed
Influence of statistical size effects on the plastic deformation of coronary stents J.A. Grogan, S.B. Leen, P.E McHugh J MECH BEHAV BIOMED
The Origin of the Visible Light Response of Nickel(II)Oxide Cluster-Surface Modified Titanium(IV) Dioxide A. Iwaszuk, M. Nolan, Q. Jin, M. Fujishima and H. Tada Journal of Physical Chemistry C
TiO2 Nanocluster Modified-Rutile TiO2 Photocatalyst: A first Principles Investigation A. Iwaszuk, P. A. Mulheran and M. Nolan Journal of Materials Chemistry A
Nanoscale dynamics and protein adhesivity of alkylamine self-assembled monolayers on graphene O’Mahony, S.; O’Dwyer, C.; Nijhuis, C.A.; Greer, J.C.; Quinn, A.J.; Thompson, D. Langmuir
The Role of van der Waals Forces in the Performance of Molecular Diodes Nerngchamnong, N.; Li, Y.; Qi, D.; Jian, L.; Thompson, D.; Nijhuis, C.A. Nat. Nanotechnol.
A theoretical quantification of the possible improvement in the mechanical properties of carbon nanotube bundles by carbon ion irradiation N.P. O’Brien, M.A. McCarthy, W.A. Curtin Carbon
Improved inter-tube coupling in CNT bundles through carbon ion irradiation N.P. O’Brien, M.A. McCarthy, W.A. Curtin Carbon
Probing the Structures of Hydrated Nafion in Different Morphologies Using Temperature Accelerated Molecular Dynamics Simulations Lucid, Jeremy, Simone Meloni, Donal MacKernan, Eckhard Spohr, and Giovanni Ciccotti J. Phys. Chem. C
Gene Expression and epigenetic discovery screen reveal methylation of SFRP2 in prostate cancer Perry A., O'Hurley G., Raheem O.A., Brennan K., Wong S., O'Grady A., Kennedy A.-M., Marignol L., Murphy T.M., Sullivan L., Barrett C., Loftus B., Thornhill J., Hewitt S.M., Lawler M., Kay E., Lynch T. and Hollywood D. Int. J. Cancer

2012

Title Authors Publication
AutoTune: Automatic Online Code Tuning Renato Miceli, Gilles Civario, François Bodin GTC
Business-driven short-term management of a hybrid IT infrastructure Paulo Ditarso Maciel Jr., Francisco Brasileiro, Ricardo Araújo Santos, David Candeia, Raquel Lopes, Marcus Carvalho, Renato Miceli, Nazareno Andrade, Miranda Mowbray JPDC
Study of E/Z Isomerization in a Series of Novel Non-ligand Binding Pocket Androgen Receptor Antagonists Blanco F, Egan B, Caboni L, Elguero J, O'Brien J, McCabe T, Fayne D, Meegan MJ, Lloyd DG. J Chem Inf Model.
On the possibility of p-type SnO2 David O. Scanlon and Graeme W. Watson J. Mater. Chem.
Cooperative mechanism for the diffusion of Li+ ions in LiMgSO4F Mathieu Salanne, Dario Marrocchelli, and Graeme W. Watson J. Phys. Chem. C
Geometry, electronic structure, and bonding in CuMCh2 (M = Sb, Bi; Ch = S, Se): Alternative solar cell absorber materials? Douglas J. Temple, Aoife B. Kehoe, Jeremy P. Allen, Graeme W. Watson, and David O. Scanlon J. Phys. Chem. C
Analysis of Intrinsic Defects in CeO2 Using a Koopmans-Like GGA+U Approach Patrick R. L. Keating, David O. Scanlon, Benjamin J. Morgan, Natasha M. Galea, and Graeme W. Watson J. Phys. Chem. C
Physical and dynamical characterisation of low ΔV NEA (190491) 2000 FJ10 Christou, A. A., Kwiatkowski, T., Butkiewicz, M.; Gulbis, A.; Hergenrother, C. W.; Duddy, S.; Fitzsimmons, A. Astronomy & Astrophysics
High Level ab Initio Enthalpies of Formation of 2,5-Dimethylfuran, 2-Methylfuran, and Furan David Feller and John M. Simmie J. Phys. Chem. A
Simulating the future wind energy resource of Ireland using the COSMO-CLM model Nolan, P., Lynch, P. and Sweeney, C. Wind Energy
Investigation of metallic and carbon fibre PEEK fracture fixation devices for three-part proximal humeral fractures Emer M. Feerick, Jim Kennedy, Hannan Mullett, David FitzPatrick, Patrick McGarry Med Eng Phys
Regional modelling of the 21st century climate changes in the Irish Sea Agnieszka I. Olbert, Tomasz Dabrowski, Stephen Nash, Michael Hartnett Cont. Shelf Res.
Comparing coronary stent material performance on a common geometric platform through simulated bench testing J.A. Grogan, S.B. Leen, P.E McHugh J MECH BEHAV BIOMED
Near IR emitting BODIPY fluorophores with mega-stokes shifts Martin, Aaron; Long, Conor; Forster, Robert J.; Keyes, Tia E. Chem. Commun.
Wavelength dependent photocatalytic H-2 generation using iridium-Pt/Pd complexes Soman, Suraj; Bindra, Gurmeet Singh; Groarke, Avishek Paul Robert; Manton, Jennifer C.; Connaughton, Finn M.; Schulz, Martin; Dini, Danilo; Long, Conor; Pryce, Mary T.; Vos, Johannes G. Dalton Trans.
Potential Energy Mapping of the Excited-States of (eta(6)-Arene)Cr(CO)(3) Complexes: the Evolution Toward CO-Loss or Haptotropic Shift Processes Long, Conor J. Phys. Chem. A
Surface Orientation Effects in Crystalline-Amorphous Silicon Interfaces M. Nolan, M. Legesse and G. Fagas Phys. Chem. Chem. Phys.
Photocatalytic Activities of Tin (IV) Oxide Surface-Modified Titanium (IV) Dioxide Show a Strong Sensitivity to the TiO2 Crystal Form Q. Jin, M. Fujishima, M. Nolan, A. Iwaszuk and H. Tada J. Phys. Chem. C
Molecular Metal Oxide Cluster-Surface Modified Titanium (IV) Dioxide Photocatalysts M. Nolan, A. Iwaszuk and H. Tada Aust. J. Chem.
First Principles Prediction of New Photocatalyst Materials with Visible Light Absorption and Improved Charge Separation: Surface Modification of Rutile TiO2 with Nanoclusters of MgO and Ga2O3 M. Nolan ACS Appl. Mater. Interfaces
The effect of remodelling and contractility of the actin cytoskeleton on the shear resistance of single cells: A computational and experimental investigation Dowling, E. P., Ronan, W., Ofek, G., Deshpande, V., McMeeking, R. M., Athanasiou, K. A. and McGarry, J. P. J R Soc Interface
Computational investigation of in situ chondrocyte deformation and actin cytoskeleton remodelling under physiological loading Enda P. Dowling, William Ronan, J. Patrick McGarry Acta Biomaterialia
Cassie–Baxter and Wenzel States on a Nanostructured Surface: Phase Diagram, Metastabilities, and Transition Mechanism by Atomistic Free Energy Calculations Giacomello, Alberto, Simone Meloni, Mauro Chinappi, and Carlo Massimo Casciola Langmuir
Metazoan opsin evolution reveals a simple route to animal vision Fueda R., Hamilton S.C., McInerney J.O. and Pisani D. Proc. Natl. Acad. Sci. USA
Effects of Strong Magnetic Fields on Photoionised Clouds Jonathan Mackey and Andrew J. Lim High Energy Density Physics
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. Chem. Mater., 2012, 24 (20), pp 3981–3992
Prediction of energy absorption characteristics of aligned carbon nanotube/epoxy nanocomposites D Weidt, Ł Figiel1 and M Buggy IOP Conference Series: Materials Science and Engineering
Molecular Dynamics Simulations of Clathrate Hydrates on Specialised Hardware Platforms Nicola Varini, Niall J English and Christian R Trott Energies
A Computational Test-Bed to Assess Coronary Stent Implantation Mechanics Using a Population-Specific Approach C. Conway, F. Sharif, J. P. McGarry and P. E. McHugh CVET
Detecting grammatical errors with treebank-induced, probabilistic parsers Wagner, J DORAS
Search for variable gamma-ray emission from the Galactic plane in the Fermi data A. Neronov, D. Malyshev, M. Chernyakova, A. Lutovinov A&A
A TD-DFT study of the effects of structural variations on the photochemistry of polyene dyes Saurabh Agrawal, Pratibha Dev, Niall J. English, K. Ravindranathan Thampi, J. M. D. MacElroy Chem. Sci.
Effects of external electromagnetic fields on the conformational sampling of a short alanine peptide Gleb Y. Solomentsev, Niall J. English, Damian A. Mooney J. Comput. Chem.
Mechanism of Atmospheric CO2 Fixation in the Cavities of a Dinuclear Cryptate Morad M. El-Hendawy, Niall J. English, Damian A. Mooney Inorg. Chem.
Band gap engineering of (N, Si)-codoped TiO2 from hybrid density functional theory calculations Run Long, Niall J. English New J. Phys.
Development of the finite volume particle method for internal flow with rigid body dynamics Nathan J. Quinlan, Libor Lobovský, Mihai Basa, Ruairi M. Nestor Proc. SPHERIC7
Parallelisation of a finite volume particle method code Mihai Basa, Libor Lobovský, Nathan J. Quinlan Proc. SPHERIC7
Self-expanding stent modelling and radial force accuracy Ríona Ní Ghriallais, Mark Bruzzi Comput Methods Biomech Biomed Engin
The implementation of a visco-hyperelastic numerical material model for simulating the behaviour of polymer foam materials Conor Briody, Barry Duignan, Steve Jerrams, John Tiernan Comput. Mater. Sci.
Supersymmetric lattice fermions on the triangular lattice: superfrustration and criticality L. Huijse, D. Mehta, N. Moran, K. Schoutens, J. Vala New J. Phys.
Gut microbiota composition correlates with diet and health in the elderly Claesson M.J., Jeffery I.B., Conde S., Power S.E., O'Connor E.M., Cusack S., Harris H.M.B., Coakley M., Lakshminarayanan B., O'Sullivan O., Fitzgerald G.F., Deane J., O'Connor M., Harnedy N., O'Connor K., O'Mahony D., van Sinderen D., Wallace M., Brennan L., Stanton C., Marchesi J.R., Fitzgerald A.P., Shanahan F., Hill C., Ross P.R. and O'Toole P.W. Nature
Increased genome sampling reveals a dynamic relationship between gene duplicability and the structure of the primate protein–protein interaction network Doherty A., Alvarez-Ponce D. and McInerney J.O. Mol. Biol. Evol.
Many-electron scattering applied to atomic point contacts S. McDermott and J.C. Greer J. Phys.: Condens. Matter
Subthreshold behavior of junctionless silicon nanowire transistors from atomic scale simulations L. Ansari, B. Feldman, G. Fagas, J.-P. Colinge and J.C. Greer Solid State Electronics
A Proposed Confinement Modulated Gap Nanowire Transistor Based on a Metal (Tin) Lida Ansari, Giorgos Fagas, Jean-Pierre Colinge, and J. C. Greer Nano Letters
An OpenCL implementation for the solution of the time-dependent Schrödinger equation on GPUs and CPUs Cathal Ó Broin, , L.A.A. Nikolopoulos Comput Phys Commun
INVESTIGATING DUCTILE FAILURE AT THE MICROSCALE IN ENGINEERING STEELS: A MICROMECHANICAL FINITE ELEMENT MODEL Dong-Feng Li, Noel P. O'Dowd ASME 2012 Conf. Proc.
The effect of remodelling and contractility of the actin cytoskeleton on the shear resistance of single cells: A computational and experimental investigation Dowling, E. P., Ronan, W., Ofek, G., Deshpande, V., McMeeking, R. M., Athanasiou, K. A. and McGarry, J. P Journal of the Royal Society Interface
Superorbital modulation of X-ray emission from gamma-ray binary LSI +61 303 M. Chernyakova, A. Neronov, S. Molkov, D. Malyshev, A. Lutovinov, G. Pooley ApJ
Multiphoton Absorption of Myoglobin–Nitric Oxide Complex: Relaxation by D-NEMD of a Stationary State Grazia Cottone, Gianluca Lattanzi, Giovanni Ciccotti, Ron Elber J. Phys. Chem. B
Rigorous calculations of non-Abelian statistics in the Kitaev honeycomb model Bolukbasi A.T. and Vala J. New J. Phys.
FOXL2 Is Regulated During the Bovine Estrous Cycle and Its Expression in the Endometrium Is Independent of Conceptus-Derived Interferon Tau Eozenou C., Carvalho A.V., Forde N., Giraud-Delville C., Gall L., Lonergan P., August A., Charpigny G., Richard C., Pannetier M. and Sandra O. Biol. Reprod.
Rate constants for hydrogen abstraction by HȮ2 from n-butanol C-W. Zhou, J. M. Simmie and H. J. Curran Int. J. Chem. Kinet.
Kinetics and Thermochemistry of 2,5-Dimethyltetrahydrofuran and Related Oxolanes: Next Next-Generation Biofuels John M. Simmie J. Phys. Chem. A
Conformational dynamics of human IAPP monomers Murphy R.D., Conlon J., Mansoor T., Luca S., Vaiana S.M. and Buchete N.-V. Biophys. Chem.
Genome-wide associations for milk production and somatic cell score in Holstein-Friesian cattle in Ireland Meredith B.K., Kearney F.J., Finlay E.K., Bradley D.G., Fahey A.G., Berry D.P. and Lynn D.J. BMC Genetics
Full and surface tibial cementation in total knee arthroplasty: A biomechanical investigation of stress distribution and remodeling in the tibia Derek T. Cawley, Nicola Kelly, Andrew Simpkin, Fintan J. Shannon, J. Patrick McGarry Clinical Biomechanics
Smoothed particle hydrodynamics modelling of the fluid flow and heat transfer in the weld pool during laser spot welding Mingming Tong, David J. Browne IOP Conf. Ser.: Mater. Sci. Eng.
Mechanisms for Substrate-Enhanced Growth during the Early Stages of Atomic Layer Deposition of Alumina onto Silicon Nitride Surfaces Luca Lamagna, Claudia Wiemer, Michele Perego, Sabina Spiga, Jesús Rodríguez, David Santiago Coll, Maria Elena Grillo, Sylwia Klejna, Simon D. Elliott Chem. Mater.
Structural systematics and conformational analyses of a 3 × 3 isomer grid of fluoro-N-(pyridyl)benzamides: physicochemical correlations, polymorphism and isomorphous relationships Pavle Mocilac, Katie Donnelly, John F. Gallagher Acta Cryst.
A Combined Theoretical and Experimental Study on the Wavelength-Dependent Photophysics of (eta(6)-benzene)Mo(CO)(3) George, Michael W. Long, Conor Pryce, Mary T. Sun, Xue-Zhong Vuong, Khuong Q. Organometallics
Photochemistry of (eta(6)-Anisole)Cr(CO)(3) and (eta(6)-Thioanisole)Cr(CO)(3): Evidence for a Photoinduced Haptotropic Shift of the Thioanisole Ligand, a Picosecond Time-Resolved Infrared Spectroscopy and Density Functional Theory Investigation Clark, Ian P. George, Michael W. Greetham, Gregory M. Harvey, Emma C. Long, Conor Manton, Jennifer C. McArdle, Hazel Pryce, Mary T. Journal of Physical Chemistry A
Functional consequence of positive selection revealed through rational mutagenesis of human myeloperoxidase Loughran NB, McCormick-Hill S, Hinde S, Leidal KG, Bloomberg S, Loughran ST, O'Connor B, Fagan C, Nauseef WM*, and O'Connell MJ* Molecular Biology and Evolution
Investigation of strain hardening effects under in-plane shear of unidirectional composite materials D.J. O’Dwyer, N.P. O’Dowd, C.T. McCarthy Computational Material Science
Integrated Virtual Screening for the Identification of Novel and Selective Peroxisome Proliferator-Activated Receptor (PPAR) Scaffolds Daniel K. Nevin, Martin B. Peters, Giorgio Carta, Darren Fayne, and David G. Lloyd J. Med. Chem.
Utilizing Sulfoxide...Iodine Halogen Bonding for Cocrystallization Kevin S. Eccles, Robin E. Morrison, Stephen P. Stokes, Graham E. O’Mahony, John A. Hayes, Dawn M. Kelly, Noel M. O'Boyle, László Fábián, Humphrey A. Moynihan, Anita R. Maguire, and Simon E. Lawrence Cryst. Growth Des.
A new time-dependent finite-difference method for relativistic shock acceleration S. Delaney*, P. Dempsey, P. Duffy, T. P. Downes MNRAS
Scanning the Potential Energy Surface for Synthesis of Dendrimer-Wrapped Gold Clusters: Design Rules for True Single-Molecule Nanostructures. Damien Thompson, Jens P. Hermes, Aidan J. Quinn, and Marcel Mayor. ACS Nano
Atomic basis sets for first-principles studies of Si nanowires Dimpy Sharma, Hadi Hassanian Arefi, Giorgos Fagas Computational and Theoretical Chemistry
Charge transfer and formation of reduced Ce3+ upon adsorption of metal atoms at the ceria (110) surface Michael Nolan J. Chem. Phys.
Modelling a single-bolt countersunk composite joint using implicit and explicit finite element analysis Egan, B., McCarthy, C.T., McCarthy, M.A., Gray, P.J., Frizzell, R.F. Computational Materials Science
"Understanding 'Clean-Up' of III-V Native Oxides During Atomic Layer Deposition Using Bulk First Principles Models S. Klejna, S. D. Elliott J. Nanosci. Nanotechn.
Non-Covalent Functionalization of Graphene Using Self-Assembly of Alkane-Amines B. Long, M. Manning, M. Burke, B.N. Szafranek, G. Visimberga, D. Thompson, J.C. Greer, I.M. Povey, J. MacHale, G. Lejosne, D. Neumaier, A.J. Quinn Advanced Functional Materials
Unravelling the specific site preference in doping of calcium hydroxyapatite with strontium from ab initio investigations and Rietveld analyses Jacek Zeglinski, Michael Nolan, Michael Bredol, Andrea Schatte, Syed A. M. Tofail Phys. Chem. Chem. Phys.
A molecular analysis of desiccation tolerance mechanisms in the anhydrobiotic nematode Panagrolaimus superbus using expressed sequenced tags Tyson T., O'Mahony Zamora G., Wong S., Skelton M., Daly B., Jones J.T., Mulvihill E.D., Elsworth B., Phillips M., Blaxter M. and Burnell A.M. BMC Res. Notes
First-Principles Modeling of the “Clean-Up” of Native Oxides during Atomic Layer Deposition onto III–V Substrates Sylwia Klejna, Simon D. Elliott J. Phys. Chem. C
Real-Time Risk Simulation: The GPU Revolution In Profit Margin Analysis Gilles Civario, Renato Miceli GTC
Enabling faster material science modeling using the accelerated Quantum ESPRESSO Filippo Spiga, Ivan Girotto, Carlo Cavazzoni NVIDIA GPU Computing Conference
On the interaction of Mg with the (111) and (110) surfaces of ceria M Nolan, Y Lykhach, N Tsud, T Skála, T Staudt, KC Prince, V Matolín, J Libuda Phys. Chem. Chem. Phys.
Tin oxide-surface modified anatase titanium(iv) dioxide with enhanced UV-light photocatalytic activity Musashi Fujishima, Qiliang Jin, Hironori Yamamoto, Hiroaki Tada and Michael Nolan Phys. Chem. Chem. Phys.
The impact of Arctic sea ice on the Arctic energy budget and on the climate of the Northern mid- latitudes Tido Semmler, Raymond McGrath, Shiyu Wang Climate Dynamics

2011

Title Authors Publication
Electronic structures of silver oxides Jeremy P. Allen, David O. Scanlon, and Graeme W. Watson Phys. Rev. B
Nature of the band gap and origin of conductivity in PbO2 revealed by theory and experiment David O. Scanlon, Aoife B. Kehoe, Graeme W. Watson, Martin O. Jones, William I. F. David, David J. Payne, Russell G. Egdell, Peter P. Edwards and Aron Walsh Phys. Rev. Lett.
Sources of conductivity and doping limits in CdO from hybrid density functional theory Mario Burbano, David O. Scanlon, and Graeme W. Watson J. Am. Chem. Soc.
Comparison of the defective pyrochlore and ilmenite polymorphs of AgSbO3 using GGA and hybrid DFT Jeremy P. Allen, M. Kristin Nilsson, David O. Scanlon, and Graeme W. Watson Phys. Rev. B
Uncovering the Complex Behavior of Hydrogen in Cu2O David O. Scanlon and Graeme W. Watson Phys. Rev. Lett.
Role of Lattice Distortions in the Oxygen Storage Capacity of Divalently Doped CeO2 Aoife B. Kehoe, David O. Scanlon, and Graeme W. Watson Chem. Mater.
The origin of the enhanced oxygen storage capacity of Ce1-x(Pd/Pt)xO2 David O. Scanlon, Benjamin J. Morgan and Graeme W. Watson Phys. Chem. Chem. Phys.
Tin monoxide: Structural prediction from first principles calculations with van der Waals corrections Jeremy P. Allen, David O. Scanlon, Stephen C. Parker, and Graeme W. Watson J. Phys. Chem. C
Chemical bonding in copper-based transparent conducting oxides: CuMO2 (M = In, Ga, Sc) K G Godinho, B J Morgan, J P Allen, D O Scanlon and G W Watson J. Phys.: Condens. Matter
Reducing errors of wind speed forecasts by an optimal combination of post-processing methods Sweeney, Conor, Peter Lynch and Paul Nolan Meteorological Applications
Simulating Climate Change and its Effects on the Wind Energy Resource of Ireland Nolan, P., Lynch, P. and Sweeney, C Wind Energy
Long-term inter-annual variability of a cyclonic gyre in the western Irish Sea Agnieszka I. Olbert, Michael Hartnett, Tomasz Dabrowski, Uwe Mikolajewicz Cont. Shelf Res.
Electrical control of spin dynamics in finite one-dimensional systems A. Pertsova, M. Stamenova, and S. Sanvito Phys. Rev. B
Combining Rare Events Techniques: Phase Change in Si Nanoparticles Orlandini, Sergio, Simone Meloni, and Giovanni Ciccotti J. Stat. Phys.
Atomistic Structure of Amorphous Silicon Nitride From Classical Molecular Dynamics Simulations Ippolito, Mariella, and Simone Meloni Phys. Rev.
Temperature Accelerated Monte Carlo (TAMC): A Method for Sampling the Free Energy Surface of Non-analytical Collective Variables Ciccotti, Giovanni, and Simone Meloni Phys. Chem. Chem. Phys
Hydrodynamics From Statistical Mechanics: Combined Dynamical-NEMD and Conditional Sampling to Relax An Interface Between Two Immiscible Liquids Orlandini, Sergio, Simone Meloni, and Giovanni Ciccotti Phys. Chem. Chem. Phys
Hydrodynamics From Dynamical Non‐equilibrium MD Orlandini, Sergio, Simone Meloni, and Giovanni Ciccotti AIP Conf. Proc.
Radiation-MHD Simulations of Pillars and Globules in HII Regions Mackey, J. 459, 6th International Conference of Numerical Modeling of Space Plasma Flows (ASTRONUM 2011)
Density Fluctuations in Liquid Water Niall J. English, John S. Tse Phys. Rev. Lett.
Human aquaporin 4 gating dynamics in dc and ac electric fields: A molecular dynamics study J.-A. Garate, Niall J. English, J. M. D. MacElroy J. Chem. Phys.
A theoretical thermodynamic investigation of cascade reactions in dinuclear octa-azacryptates involving carbon dioxide Morad M. El-Hendawy, Niall J. English, Damian A. Mooney J. Molec. Model.
First-principles study of the excited-state properties of coumarin-derived dyes in dye-sensitized solar cells Saurabh Agrawal, Pratibha Dev, Niall J. English, K. Ravindranathan Thampi, J. M. D. MacElroy J. Mater. Chem.
Electrophoretic Deposition of Poly(3-decylthiophene) onto Gold-Mounted Cadmium Selenide Nanorods José-Antonio Garate, Niall J. English, Ajay Singh, Kevin M. Ryan, Damian A. Mooney, J. M. D. MacElroy Langmuir
Study of translational, librational and intra-molecular motion of adsorbed liquid water monolayers at various TiO2 interfaces Ritwik S. Kavathekar, Niall J. English, J. M. D. MacElroy Mol. Phys.
Band gap engineering of double-cation-impurity-doped anatase-titania for visible-light photocatalysts: a hybrid density functional theory approach Run Long, Niall J. English Phys. Chem. Chem. Phys
Extreme-ultraviolet pump–probe studies of one-femtosecond-scale electron dynamics P. Tzallas, E. Skantzakis, L. A. A. Nikolopoulos, G. D. Tsakiris and D. Charalambidis Nature Phys.
On the evolution of lattice deformation in austenitic stainless steels—The role of work hardening at finite strains Dong-Feng Li , Noel P. O'Dowd, J Mech Phys Solids
Microscale prediction of deformation in an austenitic stainless steel under uniaxial loading Dong-Feng Li a, Noel P. O’Dowd a, *, Catrin M. Davies b, Shu-Yan Zhang c EUR J MECH A-SOLID
Electronic properties of anatase-TiO2 codoped by cation-pairs from hybrid density functional theory calculations Run Long, Niall J. English Chem. Phys. Lett.
New Insights into the Band-Gap Narrowing of (N, P)-Codoped TiO2 from Hybrid Density Functional Theory Calculations Run Long, Niall J. English ChemPhysChem
Electronic structure of cation-codoped TiO2 for visible-light photocatalyst applications from hybrid density functional theory calculations Run Long, Niall J. English Appl. Phys. Lett.
Tailoring the electronic structure of TiO2 by cation codoping from hybrid density functional theory calculations Run Long, Niall J. English Phys. Rev. B
Rate constants for hydrogen-abstraction by from n-butanol Chong-Wen Zhou, John. M. Simmie and Henry J. Curran Combust. Flame
Ab initio and kinetic study of the reaction of ketones with OH for T="500-2,000" K. Part I: hydrogen-abstraction from H3CC(O)CH(3-x)CH3, x="0-2" C-W. Zhou, J. M. Simmie and H. J. Curran Phys. Chem. Chem. Phys.
Ab Initio Study of the Decomposition of 2,5-Dimethylfuran John M. Simmie and Wayne K. Metcalfe J. Phys. Chem. A
Adaptive postprocessing of short-term wind forecasts for energy applications. Conor Sweeney, Peter Lynch Wind Energy
Reducing errors of wind speed forecasts by an optimal combination of post-processing methods. Conor Sweeney, Peter Lynch, Paul Nolan Meteorological Applications
Defect-trapped electrons and ferromagnetic exchange in ZnO Aurab Chakrabarty, Charles H. Patterson Phys. Rev. B
Explorations on template-directed genetic repair using ancient ancestors and other templates Donagh Hatton, Diarmuid P. O'Donoghue GECCO '11
A look at the ocean in the EC-Earth climate model Andreas Sterl, Richard Bintanja, Laurent Brodeau, Emily Gleeson, Torben Koenigk, Torben Schmith, Tido Semmler, Camiel Severijns, Klaus Wyser, Shuting Yang Clim Dyn
Structural systematics and conformational analyses of a 3 × 3 isomer grid of nine N-(tolyl)pyridinecarboxamides and three chlorinated relatives Pavle Mocilac, John F. Gallagher CrystEngComm
Structures and conformational analysis of a 3 × 3 isomer grid of nine N-(fluorophenyl)pyridinecarboxamides Pavle Mocilac, Alan J. Lough, John F. Gallagher CrystEngComm
Photochemistry of (eta(6)-Arene)Cr(CO)(3) (Arene = Methylbenzoate, Naphthalene, or Phenanthrene) in n-Heptane Solution: Population of Two Excited States Following 400 nm Excitation As Detected by Picosecond Time-Resolved Infrared Spectroscopy Clark, Ian P. George, Michael W. Greetham, Gregory M. Harvey, Emma C. Long, Conor Manton, Jennifer C. Pryce, Mary T. Journal of Physical Chemistry A
Probing the Metal-to-Ligand Charge Transfer First Excited State in (eta(6)-Naphthalene)Cr(CO)(3) and (eta(6)-Phenanthrene)Cr(CO)(3) by Resonance Raman Spectroscopy and Density Functional Theory Calculations Picardi, Gennaro Keyes, Tia E. Forster, Robert J. Long, Conor Journal of Physical Chemistry A
Catalytic Mechanism and Roles of Arg197 and Thr183 in the Staphylococcus aureus Sortase A Enzyme. B. Tian, L.A. Eriksson Journal of Physical Chemistry B
Diagonalisation of quantum observables on regular lattices and general graphs Niall Moran, Graham Kells, Jiri Vala CPC
Exact ground states of a staggered supersymmetric model for lattice fermions L. Huijse, N. Moran J. Vala and K. Schoutens Phys. Rev. B
Interdigitating Organic Bilayers Direct the Short Interlayer Spacing in Hybrid Organic–Inorganic Layered Vanadium Oxide Nanostructures G. Gannon, C. O’Dwyer, J. A. Larsson, and D. Thompson J. Phys. Chem. B
phiGEMM: a CPU-GPU library for porting Quantum ESPRESSO on hybrid systems Filippo Spiga, Ivan Girotto Proc PDP2012
The Eyjafjallajökull ash plume – Part 2: Simulating ash cloud dispersion with REMOTE C. O'Dowd, S. Varghese, D. Martin, R. Flanagan, A. McKinstry, D. Ceburnis, J. Ovadnevaite, G. Martucci, J. Bialek, C. Monahan, H. Berresheim, A. Vaishya, T. Grigas, Z. McGraw, S.G. Jennings, B. Langmann, T. Semmler, R. McGrath Atmos Env.
Surface modification of TiO2 with metal oxide nanoclusters: a route to composite photocatalytic materials M Nolan Chem. Commun.
Electronic coupling in iron oxide-modified TiO2 leads to a reduced band gap and charge separation for visible light active photocatalysis M Nolan Phys. Chem. Chem. Phys.
Charge compensation in trivalent cation doped bulk rutile TiO2 A Iwaszuk, M Nolan J. Phys.: Condens. Matter
Transitioning a message passing interface wavefront sensor model to a graphics processor environment Michael T. Browne, Renato Miceli Proc. SPIE
EC-Earth V2.2: description and validation of a new seamless earth system prediction model W. Hazeleger, X. Wang, C. Severijns, S. Stefănescu, R. Bintanja, A. Sterl, K. Wyser, T. Semmler, S. Yang, B. van den Hurk, T. van Noije, E. van der Linden and K. van der Wiel Climate Dynamics
A look at the ocean in the EC-Earth climate model Andreas Sterl, Richard Bintanja, Laurent Brodeau, Emily Gleeson, Torben Koenigk, Torben Schmith, Tido Semmler, Camiel Severijns, Klaus Wyser and Shuting Yang Climate Dynamics
The Cambrian Conundrum: Early Divergence and Later Ecological Success in the Early History of Animals Erwin D.H., Laflamme M., Tweedt S.M., Sperling E.A., Pisani D. and Peterson K.J. Science
Stress Analysis of Single-Bolt, Single-Lap, Countersunk Composite Joints with Variable Bolt-Hole Clearance B. Egan, C.T. McCarthy, M.A. McCarthy, R.F. Frizzell J. Comp Struct
MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda Campbell L.I., Rota-Stabelli O., Edgecombe G.D., Marchioro T., Longhorn S.J., Telford M.J., Philippe H., Rebecchi L., Peterson K.J. and Pisani D. Proc. Natl. Acad. Sci. USA
Molecular dynamics of the “hydrophobic patch” that immobilizes hydrophobin protein HFBII on silicon Clara Moldovan & Damien Thompson J. Mol Model
Are peptides good two-state folders? Alexander M. Berezhkovskii, Florentina Tofoleanu, and Nicolae-Viorel Buchete J. Chem. Theory Comput.
The Electronic Structure and Reactivity of Ce and Zr Doped TiO2: Assessing the Sensitivity to Density Functional Theory Approaches Anna Iwaszuk and Michael Nolan J. Phys. Chem. C
Computational Design and Selection of Optimal Organic Photovoltaic Materials Noel M. O’Boyle, Casey M. Campbell, and Geoffrey R. Hutchison J. Phys. Chem. C
A finite element study of microstructure-sensitive plasticity and crack nucleation in fretting O.J. McCarthy, J.P. McGarry and S.B. Leen J. Comp Materials Science
Hybrid density functional theory description of N- and C-doping of NiO Michael Nolan, Run Long, Niall J. English, Damian A. Mooney J. Chem. Phys.
Enhanced Oxygen Vacancy Formation on Ceria (111) and (110) Surfaces Doped With Divalent Cations Michael Nolan J. Mater. Chem.
A Corrosion Model for Bioabsorbable Metallic Stents J.A. Grogan, B.J. O'Brien, S.B. Leen and P.E. McHugh Acta Biomaterialia
Molecular paleobiological insights into the origin of the Brachiopoda Sperling E.A., Pisani D. and Peterson K.J. Evol. Dev.
Time reverse location of seismic long-period events recorded on Mt Etna G. S. O'Brien, I. Lokmer, L. De Barros, C. J. Bean, G. Saccorotti, J-P Metaxian and D. Patane Geophysical Journal International
Source Mechanism of Long Period events recorded by a high density seismic network during the 2008 eruption on Mt Etna De Barros, L., I. Lokmer, C.J. Bean, G. S. O'Brien, G. Saccorotti, J.-P. Metaxian, L. Zuccarello, and D. Patane J. Geophys. Res.
Charge Compensation and Ce3+ Formation in Trivalent Doping of the CeO2(110) Surface: The Key Role of Dopant Ionic Radius Michael Nolan J Phys Chem C
Effects of magnetic fields on photoionized pillars and globules Jonathan Mackey, Andrew J. Lim MNRAS
Gradient-driven motion of multivalent ligand molecules along a surface functionalized with multiple receptors András Perl, Alberto Gomez-Casado, Damien Thompson, Henk H. Dam, Pascal Jonkheijm, David N. Reinhoudt & Jurriaan Huskens Nat. Chem.
Electronic structure calculations and physicochemical experiments quantify the competitive liquid ion association and probe stabilisation effects for nitrobenzospiropyran in phosphonium-based ionic liquids Damien Thompson, Simon Coleman, Dermot Diamond and Robert Byrne Phys. Chem. Chem. Phys.
Reactivity of sub 1 nm supported clusters: (TiO2)n clusters supported on rutile TiO2 (110) Anna Iwaszuk and Michael Nolan Phys. Chem. Chem. Phys.
Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana Donoghue M.T.A., Keshavaiah C., Swamidatta S.H. and Spillane C. BMC Evol. Biol.
A case-by-case evolutionary analysis of four imprinted retrogenes McCole R.B., Loughran N.B., Chahal M., Fernandes L.P., Roberts R.G., Fraternali F., O'Connell M.J. and Oakey R.J. Int. J. Org. Evol.
Multifluid magnetohydrodynamic turbulent decay Downes, T.P., O'Sullivan, S. ApJ
Radiation-MHD models of elephant trunks and globules in H II regions Jonathan Mackey and Andrew J. Lim BSRSL
Structural and energetic origin of defects at the interface between germanium and a high-k dielectric from first principles S. D. Elliott and J. C. Greer Appl. Phys. Lett.
Finite-bias electronic transport of molecules in water solution I. Rungger, X. Chen, Udo Schwingenschl¨ogl, and Stefano Sanvito Phys. Rev. B

2010

Title Authors Publication
Stability, geometry, and electronic structure of an alternative I-III-VI2 material, CuScS2: A hybrid density functional theory analysis David O. Scanlon, and Graeme W. Watson Appl. Phys. Lett.
Effects of complex hydrodynamic processes on the horizontal and vertical distribution of Tc-99 in the Irish Sea Agnieszka I. Olbert,Michael Hartnett, Tomasz Dabrowski, Kevin Kellehe Sci. Total Env.
Assessment of Tc-99 monitoring within the western Irish Sea using a numerical model Agnieszka I. Olbert, Michael Hartnett, Tomasz Dabrowski Science of the Total Environment
Judging grammaticality: experiments in sentence classification Wagner et al. The Computer Assisted Language Instruction Consortium
The effect of correcting grammatical errors on parse probabilities Wagner, J; Foster, J Association for Computational Linguistics
A simple model for electron plasma heating in supernova remnants D. Malyshev, S. Gabici, L. O'C. Drury, F. A. Aharonian A&A
Deformation Potentials and Electron−Phonon Coupling in Silicon Nanowires F. Murphy-Armando*, G. Fagas and J. C. Greer Nano Lett., 2010, 10 (3), pp 869–873
Simulation of junctionless Si nanowire transistors with 3 nm gate length Lida Ansari, Baruch Feldman, Giorgos Fagas, Jean-Pierre Colinge, and James C. Greer Appl. Phys. Lett.
Spin-Polarization Mechanisms of the Nitrogen-Vacancy Center in Diamond P. Delaney, J.C. Greer, and J.A. Larsson Nano Letters
Evaluating the mechanical behaviour of 316 stainless steel at the microscale using finite element modelling and in-situ neutron scattering Au. D Li, Au. N O'Dowd, Au. C Davies, Au. SY Zhang ASME Conf. Proc.
THE HIGH-ENERGY, ARCMINUTE-SCALE GALACTIC CENTER GAMMA-RAY SOURCE Chernyakova, M.; Malyshev, D.; Aharonian, F. A.; Crocker, R. M., Jones, D. I. ApJ
Ab Initio Chemical Kinetics of Methyl Formate Decomposition: The Simplest Model Biodiesel Wayne K. Metcalfe, John M. Simmie and Henry J. Curran J. Phys. Chem. A
Effects of molecular structure on oxidation reactivity of cyclic hydrocarbons: Experimental observations and conformational analysis Y. Yang, A.L. Boehman, J.M. Simmie Combust. Flame
Uniqueness in the low temperature oxidation of cycloalkanes Y. Yang, A.L. Boehman, J.M. Simmie Combust. Flame
Synthesis, structural and conformational analysis of a 3 × 3 isomer grid based on nine methyl-N-(pyridyl)benzamides Pavle Mocilac, Mark Tallon, Alan J. Lough, John F. Gallagher CrystEngComm
Rational Design of Highly Cytotoxic η6-Arene β-Diketiminato-Ruthenium Complexes Phillips, Andrew D.; Zava, Olivier; Scopelitti, Rosario; Nazarov, Alexey A.; Dyson, Paul J. Organometallics
Discover DL_POLY. 1. DL_POLY: an MD code ICHEC has ported to CUDA Gilles Civario NVIDIA GPU Computing Conference
Porting the DL POLY molecular dynamics package to GPGPUs R. Nestor, C. Kartsaklis, W. Smith, and I. T. Todorov Workshop on GPUs and Accelerators in HPC
Dynamics of protein folding: Probing the kinetic network of folding–unfolding transitions with experiment and theory Ginka S. Buchner,Ronan D. Murphy, Nicolae-Viorel Buchete and Jan Kubelka Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics
Statistical selection of the "best" seismic source mechanisms from inversions of synthetic volcanic long-period events G. S. O'Brien, I. Lokmer, and C. J. Bean J. Geophys. Res.
Computational micromodel for epigenetic mechanisms Raghavan K., Ruskin H.J., Perrin, D., Goasmat F. and Burns J. PloS ONE
A computationally efficient method for calculating the maximum conductance of disordered networks: Application to one-dimensional conductors Luiz F. C. Pereira, C. G. Rocha, A. Latgé, and M. S. Ferreira J. Appl. Phys.
Selection and the Cell Cycle: Positive Darwinian Selection in a Well-Known DNA Damage Response Pathway Mary J. O’Connell J Mol Evol
The enumeration of Costas arrays of order 28 K. Drakakis, F. Iorio, and S. Rickard IEEE Information Theory Workshop (ITW) 2010
GECCO '10 Proceedings of the 12th annual conference companion on Genetic and evolutionary computation Amy FitzGerald, Diarmuid P. O'Donoghue GECCO Conference
First-principles calculation of electronic structure of V-doped anatase TiO2 R. Long and N.J. English Chem.Phys.Chem.
First-principles calculation of synergistic (N, P) codoping effects on the visible-light photocatalytic activity of anatase TiO2 R. Long and N.J. English J. Phys. Chem. C
Electronic structure and origin of visible-light activity of C-doped cubic In2O3 from first-principles calculations R. Long and N.J. English J. Phys. Chem. C
Electronic Properties of F/Zr Co-doped anatase TiO2 photocatalysts from GGA+U calculations R. Long and N.J. English Chem. Phys. Lett.
Model refinement through high-performance computing: an agent-based HIV example Dimitri Perrin, Heather J. Ruskin and Martin Crane Immunome Research
Epitaxial strain effects in the spinel ferrites CoFe2O4 and NiFe2O4 from first principles D. Fritsch and C. Ederer Phys. Rev. B
Excited State Dynamics and Activation Parameters of Remarkably Slow Photoinduced CO Loss from (η6-Benzene)Cr(CO)3 in n-Heptane Solution: A DFT and Picosecond-Time-Resolved Infrared Study Ian P. Clark, Michael W. George, Gregory M. Greetham, Emma C. Harvey, Conor Long, Jennifer C. Manton, and Mary T. Pryce J. Phys Chem A
Evidence for Cobalt−Cobalt Bond Homolysis and Wavelength-Dependent CO Loss in (μ2-Alkyne)Co2(CO)6 Complexes Nicola M. Boyle, Anthony C. Coleman, Conor Long, Kate L. Ronayne, Wesley R. Browne, Ben L. Feringa, and Mary T. Pryce Inorg. Chem.
Comparison of trabecular bone behavior in core and whole bone samples using high-resolution modeling of a vertebral body Harrison NM, McHugh PE Biomech Model Mechanobiol.
Investigation of the Conducting Properties of a Photoswitching Dithienylethene Molecule Anders Odell, Anna Delin, Brje Johansson, Ivan Rungger, and Stefano Sanvito ACS Nano
Computational modeling of a carbon nanotube-based DNA nanosensor R. Kalantari-Nejad, M. Bahrami, H. Rafii-Tabar, I. Rungger, and Stefano Sanvito Nanotechnology
Oxygen defect origin of ferromagnetism in ZnCoO Ruairi Hanafin and Stefano Sanvito J. Magn. Magn. Mater.
Magnetism of wurtzite CoO nanoclusters Ruairi Hanafin, Thomas Archer, and Stefano Sanvito Phys. Rev. B
Polaronic distortion and vacancy-induced magnetism in MgO A. Droghetti, C.D. Pemmaraju, and S. Sanvito Phys. Rev. B
The rise of spinterface science S. Sanvito Nature Physics
Magnetic interaction of Co ions near the {10Ŋ10} ZnO surface T. Archer, C.D. Pemmaraju, and S. Sanvito New. J. Phys.
Ab initio study of electron transport in dry poly(G)-poly(C) A-DNA strands C.D. Pemmaraju, I. Rungger, X. Chen, A.R. Rocha, and S. Sanvito Phys. Rev. B
Controlled sequential dehydrogenation of single molecules by scanning tunneling microscopy Nadjib Baadji, Stefan Kuck, Jens Brede, Germar Hoffmann, Roland Wiesendanger, and Stefano Sanvito Phys. Rev. B
Surface science: Seeing the spin through Stefano Sanvito Nature
Meta-analysis to test the association of HIV-1 nef amino acid differences and deletions with disease progression Pushker R, Jacqué JM, Shields DC J Virol
Nutrient exposure of chemotactic organisms in small-scale turbulent flows J. Munoz-Garcia, Z. Neufeld, C. Torney New J. Phys.
Barrier heights for H-atom abstraction by HȮ2 from n-butanol—A simple yet exacting test for model chemistries? Gráinne Black, John M. Simmie Journal of Computational Chemistry
Bio-butanol: Combustion properties and detailed chemical kinetic model G. Black, H. J. Curran, S. Pichon, J.M. Simmie, V. Zhukov Combustion and Flame
Hydrogen Abstraction from n-Butanol by the Hydroxyl Radical: High Level Ab Initio Study of the Relative Significance of Various Abstraction Channels and the Role of Weakly Bound Intermediates Jerzy Moc and John M. Simmie J. Phys. Chem. A
An ab initio/Rice-Ramsperger-Kassel-Marcus study of the hydrogen-abstraction reactions of methyl ethers, H3COCH3−x(CH3)x, x = 0–2, by ˙OH; mechanism and kinetics Chong-Wen Zhou, John M. Simmie and Henry J. Curran Phys. Chem. Chem. Phys.
Magnetic vortex growth in the transition layer of a mildly relativistic plasma shock Gareth C. Murphy, Mark E. Dieckmann and Luke O'C Drury Phys. Plasmas
A phylogenetic approach to test for evidence of parental conflict or gene duplications associated with protein-encoding imprinted orthologous genes in placental mammals O'Connell M.J., Loughran N.B., Walsh T.A., Donoghue M.T.A., Schmid K.J. and Spillane C. Mamm. Genome
Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins Morgan C.C., Loughran N.B., Walsh T.A., Harrison A.J. and O'Connell M.J. BMC Evol. Biol.
Multidimensional Simulations of Magnetic Field Amplification and Electron Acceleration to Near-Energy Equipartition With Ions by a Mildly Relativistic Quasi-Parallel Plasma Collision Murphy, G. C.; Dieckmann, M. E.; Drury, L. O. IEEE TPS
Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function Cotton J.A. and McInerney J.O. Proc. Natl. Acad. Sci. USA
Magnetic field amplification and electron acceleration to near-energy equipartition with ions by a mildly relativistic quasi-parallel plasma protoshock G. C. Murphy, M. Dieckmann, A. Bret, L. Drury A&A
Effects of complex hydrodynamic processes on the horizontal and vertical distribution of Tc-99 in the Irish Sea Olbert, A.I., Hartnett, M., Dabrowski, T., Kelleher, K. Sci. Total Environment
Assessment of Tc-99 monitoring within the western Irish Sea using a numerical model Olbert, A.I., Hartnett, M. , Dabrowski, T. Sci. Total Environment
Deep genomic-scale analyses of the Metazoa reject Coelomata: evidence from single and multi gene families analysed under a supertree and supermatrix paradigm. Holton, T.A. and Pisani, D. Genome Biol. Evol.
Hybrid Density Functional Theory Description of Oxygen Vacancies in the CeO2 (110) and (100) Surfaces Michael Nolan Chem. Phys. Lett.
Kinetic Particle-In-Cell Simulations of Asymmetric Quasi-Parallel Mildly Relativistic Plasma Collisions: Field and Electron Dynamics Gareth C. Murphy, Mark E. Dieckmann and Luke O'C Drury Int J Mod Phys
Interactions of the melanocortin-4 receptor with the peptide agonist NDP-MSH Chapman KL, Kinsella GK, Cox A, Donnelly D, Findlay JB J Mol Biol.
3D rotated and standard staggered finite-difference solutions to Biot's poroelastic wave equations: Stability condition and dispersion analysis O'Brien, G.S. Geophysics
Moment tensor inversion of explosive long period events recorded on Arenal volcano, Costa Rica, constrained by synthetic tests Davi, R., G.S. O'Brien, I. Lokmer, C.J. Bean, P. Lesage, M.M. Mora J. Volcanol. Geotherm. Res.
Exciton: a code for excitations in materials Charles H. Patterson Mol. Phys.
Surface and interstitial Ti diffusion at the rutile TiO2(110) surface P. A. Mulheran, M. Nolan, C. S. Browne, M. Basham, E. Sanville and R. A. Bennett Phys. Chem. Chem. Phys.
The Atomic Level Structure of the TiO2-NiTi Interface M. Nolan and S. A. M. Tofail Phys. Chem. Chem. Phys.
Local and regional mechanical characterisation of a collagen-glycosaminoglycan scaffold using high-resolution finite element analysis A.J.F. Stops, N.M. Harrison, M.G. Haugh, F.J. O’Brien, and P.E. McHugh J Mech Behav Biomed Mater.
Density Functional Theory Studies of Doping in Titania R. Long and N.J. English Molec. Sim.
Electronic structures of N- and C-doped NiO from first-principles calculations R. Long, N.J. English and D.A. Mooney Phys. Lett. A
Synergistic effects on band gap-narrowing in titania by codoping from first-principles calculations R. Long and N.J. English Chem. Mater.
Formation of Ce3+ at the cerium dioxide (1 1 0) surface by doping Michael Nolan Chem. Phys. Lett.
Cell type-dependent, infection-induced, aberrant DNA methylation in gastric cancer Perrin D., Ruskin H.J. and Niwa T. J. Theor. Biol.
Understanding conductivity anomalies in CuI-based delafossite transparent conducting oxides: Theoretical insights Scanlon D.O., Godinho K.G., Morgan B.J. and Watson G.W. J. Chem. Phys.
Understanding conductivity in SrCu2O2: stability, geometry and electronic structure of intrinsic defects from first principles Godinho K.G., Carey J.J., Morgan B.J. Scanlon D.O. and Watson G.W. J. Mater. Chem.
Large scale magnetic fields in viscous resistive accretion disks I. Ejection from weakly magnetized disks G. C. Murphy, J. Ferreira and C. Zanni A&A
Doping of ceria surfaces with lanthanum: a DFT+U study I. Yeriskin and M. Nolan J. Phys. Cond. Matt.
Intrinsic n-type Defect Formation in TiO2: A Comparison of Rutile and Anatase from GGA+U Calculations Benjamin J. Morgan and Graeme W. Watson J. Phys. Chem. C
Particle-in-cell simulation of a mildly relativistic collision of an electron-ion plasma carrying a quasi-parallel magnetic field - Electron acceleration and magnetic field amplification at supernova shocks M. E. Dieckmann, G. C. Murphy, A. Meli and L. O. C. Drury A&A
Interaction of acridine-calix[4]arene with DNA at the electrified liquid | liquid interface Francine Kivlehan, Myriam Lefoix, Humphrey A. Moynihan, Damien Thompson, Vladimir I. Ogurtsov, Grégoire Herzog, Damien W.M. Arrigan Electrochimica Acta
Molecular dynamics study of naturally-occurring defects in self-assembled monolayer formation Greg Gannon, James C. Greer, J. Andreas Larsson, Damien Thompson ACS Nano
Density functional theory simulation of titanium migration and reaction with oxygen in the early stages of oxidation of equiatomic NiTi alloy Michael Nolan, Syed A M Tofail Biomaterials
Competing Mechanisms in Atomic Layer Deposition of Er2O3 versus La2O3 from Cyclopentadienyl Precursors Michael Nolan and Simon Elliott Chem. Mater.
EC-EARTH: A seamless earth system prediction approach in action Hazeleger, W., Severijns, C., Semmler, T., Stefanescu, S., Yang, S., Wang, X., Wyser, K., Baldasano, J. M., Bintanja, R., Bougeault, P., Caballero, R., Dutra, E., Ekman, A. M. L., Christensen, J. H., van den Hurk, B., Jimenez, P., Jones, C., Kallberg, P., Koenigk, T., McGrath, R., Miranda, P., van Noije, T., Parodi, J. A., Schmith, T., Selten, F., Storelvmo, T., Sterl, A., Tapamo, H., Vancoppenolle, M., Viterbo, P., and Willen, U. BAMS
A prediction of cell differentiation and proliferation within a collagen-glycosaminoglycan scaffold subjected to mechanical strain and perfusive fluid flow AJF Stops, KB Heraty, M Browne, FJ O’Brien, PE McHugh Journal of Biomechanics

2009

Title Authors Publication
Ring currents in azulene AT Paxton, TN Todorov, AM Elena Chem Phys Lett
Defect Ceria Surfaces: Comparing Interatomic Potentials with Density Functional Theory Natasha M. Galea, David O. Scanlon, Paul Martin and Graeme W. Watson e-J. Surf. Sci. Nanotech
Testing Interatomic Potentials for QM/MM Embedded-Cluster Calculations on Ceria Surfaces Natasha M. Galea, David O. Scanlon, Paul Martin, Graeme W. Watson, Paul Sherwood e-J. Surf. Sci. Nanotech.
Stochastic particle acceleration in the lobes of giant radio galaxies O'Sullivan, S.; Reville, B.; Taylor Monthly Notices of the Royal Astronomical Society
Tunnel Currents across Silane Diamines/Dithiols and Alkane Diamines/Dithiols: A Comparative Computational Study Shane McDermott, Chris George, Giorgos Fagas, J. C. Greer, and M. A. Ratner J. Phys. Chem. C
Influence of ion pairing on styrene hydrogenation using a cationic η6-arene β-diketiminato-ruthenium complex Moreno, Aitor; Pregosin, Paul S.; Laurenczy, Gabor; Phillips, Andrew D.; Dyson, Paul J. Organometallics
A Java Library for the Generation and Scheduling of PTX Assembly C. Kartsaklis and G. Civario NVIDIA GPU Computing Conference
Atomistic Spin Dynamics. in “The Oxford Handbook of Nanoscience and Nanotechnology: Vol. I” M. Stamenova and S. Sanvito Oxford University Press, Oxford
Valence-bond states: Link models E. Rico, R. Hübener, S. Montangero, N. Moran, B. Pirvu, J. Vala, and H.J. Briegel Annals Phys. Volume 324, Issue 9, September 2009, Pages 1875-1896
Electron transport across electrically switchable magnetic molecules Sujeet K. Shukla and Stefano Sanvito Phys. Rev. B
MgN: a new promising material for spintronic applications Andrea Droghetti, Nadjib Baadji, and Stefano Sanvito Phys. Rev. B
Discovery of small molecule inhibitors of protein-protein interactions using combined ligand and target score normalization Casey FP, Pihan E, Shields DC J Chem Inf Model
Formation Enthalpies and Bond Dissociation Energies of Alkylfurans. The Strongest CX Bonds Known? John M. Simmie and Henry J. Curran J. Phys. Chem. A
The elimination of water from a conformationally complex alcohol: A computational study of the gas phase dehydration of n-butanol Jerzey Moc, John M. Simmie, Henry J. Curran Journal of Molecular Structure
Energy Barriers for the Addition of H, H3, and 2H5 to CH2═CHX [X = H, CH3, OH] and for H-Atom Addition to RCH═O [R = H, CH3, 2H5, n-C3H7]: Implications for the Gas-Phase Chemistry of Enols John M. Simmie and Henry J. Curran J. Phys. Chem. A
The Unimolecular Decomposition and H Abstraction Reactions by HO and HO2 from n-Butanol, Computational Methods in Science and Engineering, Advances in Computational Science Jerzy Moc, Gráinne Black, John M. Simmie and Henry J. Curran American Inst. of Physics
Multifluid Simulations of the Kelvin-Helmholtz Instability in a Weakly Ionised Plasma Jones, Aoife C.; Shadmehri, Mohsen; Downes, Turlough P. n/a
Non-ideal MHD turbulent decay in molecular clouds Downes, T.P., O'Sullivan, S. ApJ
Density functional theory description of the mechanism of ferromagnetism in nitrogen-doped SnO2 R. Long and N.J. English Phys. Lett. A
Mechanisms for thermal conduction in various polymorphs of methane hydrate N.J. English, J.S. Tse and D. Carey Phys. Rev. B
Static and alternating electric field and distance-dependent effects on carbon nanotube-assisted water self-diffusion across lipid membranes J.-A. Garate, N.J. English and J.M.D. MacElroy J. Chem. Phys.
Magnetic properties of first-row element-doped ZnS semiconductors: a density functional theory investigation R. Long and N.J. English Phys. Rev. B
First-Principles Study of S Doping at the Rutile TiO_2 (110) Surface R. Long, N.J. English and Y. Dai J. Phys. Chem. C
Molecular dynamics study of thermal-driven methane hydrate dissociation N.J. English and G.M. Phelan J. Chem. Phys.
Band gap engineering of (N, Ta)-codoped TiO_2 : A first-principles calculation R. Long and N.J. English Chem. Phys. Lett.
Electromagnetic field effects on binary dimethylimidazolium-based ionic liquid/water solutions N.J. English and D.A. Mooney Phys. Chem. Chem. Phys.
Non-equilibrium molecular dynamics study of electric and low-frequency microwave fields on hen egg white lysozyme N.J. English, G.Y. Solomentsev and P. O’Brien J. Chem. Phys.
Very Different Responses to Electromagnetic Fields in Binary Ionic Liquid-Water Solutions N.J. English and D.A. Mooney J. Phys. Chem. B
Estimation of zeta potentials of titania nanoparticles by molecular simulation N.J. English and W.F. Long Physica A
Energetic and electronic properties of P doping at the rutile TiO_2 (110) surface from first-principles R. Long and N.J. English Phys. Chem C.
Mechanisms for thermal conduction in methane hydrate N.J. English and J.S. Tse Phys. Rev. Lett.
Synergistic Effects of Bi/S Codoping on Visible Light-Activated Anatase TiO2 Photocatalysts from First Principles R. Long and N.J. English J. Phys. Chem. C
First-principles calculation of nitrogen-tungsten codoping effects on the band structure of anatase-titania R. Long and N.J. English Appl. Phys. Lett.
Carbon nanotube assisted water self-diffusion across lipid membranes in the absence and presence of electric fields J.-A. Garate, N.J. English, J.M.D. MacElroy Molec. Sim.
(Cu2S2)(Sr3SC2O5)-A Layered, Direct Band Gap, p-Type Transparent Conducting Oxychalcogenide: A Theoretical Analysis. Scanlon D.O. and Watson, G.W. Chem. Mater.
Comparative study of bandwidths in copper delafossites from x-ray emission spectroscopy Shin D, Foord J.S., Payne D.J., Arnold T., Aston D.J., Egdell R.G., Godinho K.G., Scanlon D.O., Morgan B.J., Watson G.W., Mugnier E., Yaicle C., Rougier A., Colakerol L., Glans P.A., Piper L.F.J. and Smith, K.E. Phys. Rev. B
Source geometry from exceptionally high resolution long period event observations at Mt Etna during the 2008 eruption De Barros, L., C. J. Bean, I. Lokmer, G. Saccorotti, L. Zuccarello, G. S. O'Brien, J.-P. Métaxian, and D. Patanè Geophys. Res. Lett.
Aggregation of chemotactic organisms in a differential flow Muñoz-García J. and Neufeld Z. Phys. Rev. E
Plankton bloom controlled by horizontal stirring McKiver W., Neufeld Z. and Scheuring I. Nonlin. Processes Geophys.
Positional Information Generated by Spatially Distributed Signaling Cascades Munoz-Garcia J., Neufeld Z. & Kholodenko B.N. PLoS Comput. Biol.
Influence of turbulent advection on a phytoplankton ecosystem with nonuniform carrying capacity McKiver W.J. and Neufeld Z. Phys. Rev. E
Polaronic trapping of electrons and holes by native defects in anatase TiO2 Benjamin J. Morgan and Graeme W. Watson Phys. Rev. B
Effect of La doping on CO adsorption at ceria surfaces I. Yeriskin, M. Nolan J CHEM PHYS
Context-dependent interaction leads to emergent search behavior in social aggregates Torney C., Neufeld Z. and Couzin I.D. Proc. Natl. Acad. Sci. USA
Dynamical Models for the Formation of Elephant Trunks in H II Regions Mackey, Jonathan; Lim, Andrew J. MNRAS
Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations Edina Rosta, Nicolae-Viorel Buchete, Gerhard Hummer J. Chem. Theory Comput., 2009
Locating volcano-seismic signals in the presence of rough topography: wave simulations on Arenal volcano, Costa Rica Métaxian J.P., O'Brien G.S., Bean C.J., Valette B. and Mora M. Geophys. J. Int.
Tracking Relevant Alignment Characteristics for Machine Translation Patrik Lambert, Yanjun Ma, Sylwia Ozdowska, Andy Way Proc. of Machine Translation
Understanding the p-Type Conduction Properties of the Transparent Conducting Oxide CuBO2: A Density Functional Theory Analysis Scanlon D.O., Walsh A. and Watson G.W. Chem. Mater.
Modeling the polaronic nature of p-type defects in Cu2O: The failure of GGA and GGA+U Scanlon D.O., Morgan B.J. and Watson G.W. J. Chem. Phys.
Upper bound for the conductivity of nanotube networks Pereira L.F.C., Rocha C.G., Latge A., Coleman J.N. and Ferreira M.S. Appl. Phys. Lett.
Switching a Single Spin on Metal Surfaces by a STM Tip: Ab Initio Studies Kun Tao, V. S. Stepanyuk, W. Hergert, I. Rungger, Sanvito and P. Bruno Phys. Rev. Lett.
Electrostatic spin crossover effect in polar magnetic molecules Baadji N., Piacenza M., Tugsuz T., Della Sala F., Maruccio G. and Sanvito S. Nat. Mater.
A spin of their own Szulczewski G., Sanvito S. and Coey M. Nat. Mater.
Electron doping and magnetic moment formation in N- and C-doped MgO Droghetti A. and Sanvito S. Appl. Phys. Lett.
Comment on “Theoretical Description of Carrier Mediated Magnetism in Cobalt Doped ZnO” Stefano Sanvito and C.D. Pemmara ju Phys. Rev. Lett.
Exploring the limits of the self-consistent Born approximation for inelastic electronic transport W. Lee, N. Jean, and S. Sanvito Phys. Rev. B
Resonant electronic states and I-V curves of Fe/MgO/Fe(100) tunnel junctions I. Rungger, O. Mryasov, and S. Sanvito Phys. Rev. B
Simulating STM transport in alkanes from first principles C. Toher, I. Rungger, and S. Sanvito Phys. Rev. B
Ab initio calculation of the bias-dependent transport properties of Mn12 molecules C.D. Pemmaraju, I. Rungger, and S. Sanvito Phys. Rev. B
Intrinsic ferromagnetism in CeO2: dispelling the myth of vacancy site localization mediated superexchange Keating P.R.L., Scanlon D.O. and Watson G.W. J. Phys.: Condens. Matter
Reactivity on the (110) Surface of Ceria: A GGA+U Study of Surface Reduction and the Adsorption of CO and NO2 Scanlon D.O., Galea N.M., Morgan B.J. and Watson G.W. J. Phys. Chem. C
Acceptor Levels in p-Type Cu2O: Rationalizing Theory and Experiment Scanlon D.O., Morgan B.J., Watson G.W. and Walsh A. Phys. Rev. Lett.
Simulation of vertebral trabecular bone loss using voxel finite element analysis McDonnell P., Harrison N., Liebschner M.A.K. and McHugh P.E. J. Biomech.
Investigation of the mechanical interaction of the trabecular core with an external shell using rapid prototype and finite element models McDonnell P., Harrison N., Lohfeld S., Kennedy O., Zhang Y. and McHugh P.E. J. Mech. Behav. Biomed. Mater.
Electrostatically immobilised BOX and PYBOX metal catalysts: application to ene reactions McDonagh C. and O'Leary P. Tetrahedron Lett.
Modeling the population dynamics of antibiotic-resistant bacteria: an agent-based approach Murphy J.T., Walshe R. and Devocelle M. IJMPC
Volcano topography, structure and intrinsic attenuation: their relative influences on a simulated 3D visco-elastic wavefield O'Brien G.S. and Bean C.J. J. Volcanol. Geotherm. Res.
Time reversal imaging of synthetic volcanic tremor sources Lokmer, I., G. S. O'Brien, D. Stich, and C. J. Bean Geophys. Res.
Small polarons in Nb- and Ta-doped rutile and anatase TiO2 Morgan B.J., Scanlon D.O. and Watson G.W. J. Mater. Chem.
Bilingually Motivated Domain-Adapted Word Segmentation for Statistical Machine Translation Ma Y. and Way A. EACL 2009
Codon Size Reduction as the Origin of the Triplet Genetic Code Baranov P.V., Venin M. and Provan G. PLoS ONE
Lines of Evidence for Horizontal Gene Transfer of a Phenazine Producing Operon into Multiple Bacterial Species Fitzpatrick D.A. J. Mol. Evol.
Monolayer Packing, Dehydration, and Ink-Binding Dynamics at the Molecular Printboard Gannon G., Larsson J.A. and Thompson D. J. Phys. Chem. C
Ballistic Conductance in Oxidized Si Nanowires G. Fagas, J.C. Greer Nano Lett
Healing of oxygen vacancies on reduced surfaces of gold-doped ceria Nolan M. J. Chem. Phys.
Finite size effects in the Kitaev honeycomb lattice model on a torus Kells G., Moran N. and Vala J. J. Stat. Mech.
OpenDDA: a Novel High-Performance Computational Framework for the Discrete Dipole Approximation McDonald J., Golden A. and Jennings S.G. Int. J. High Perform. Comput. Appl.
Charge Transfer in Cr Adsorption and Reactions at the Rutile TiO2(110) Surface Nolan M., Mulley J.S. and Bennett R.A. Phys. Chem. Chem. Phys.
Quantification of Ink Diffusion in Microcontact Printing with Self-Assembled Monolayers Gannon G., Larsson J.A., Greer J.C. and Thompson D. Langmuir
Molecular Adsorption on the Doped Ceria (110) Surface Nolan M. J. Phys. Chem. C
Dispersion analysis and computational efficiency of elastic lattice methods for seismic wave propagation O'Brien G.S., Bean C.J. and Tapamo H. Comput. Geosci.
Non-stoichiometric oxide and metal interfaces and reactions Bennett R.A., Mulley J.S., Basham M., Nolan M., Elliott S.D. and Mulheran P.A. Appl. Phys. A

2008

Title Authors Publication
Parser-based retraining for domain adaptation of probabilistic generators Hogan et al. Association for Computational Linguistics
Monte Carlo configuration interaction predictions for the electronic spectra of Ne, CH2, C2, N2, and H2O compared to full configuration interaction calculations W. Győffry, R. J. Bartlett and J. C. Greer J. Chem. Phys.
Orientation of Individual C60 Molecules Adsorbed on Cu(111): Low-Temperature Scanning Tunneling Microscopy and Theoretical Investigation J. A. Larsson, S. D. Elliott, J. C. Greer, J. Repp, G. Meyer, and R. Allensprach, Phys Rev B
The formation of relativistic plasma structures and their potential role in the generation of cosmic ray electrons M E Dieckmann Nonlinear Processes in Geophysics
Results of the enumeration of Costas arrays of order 27 K. Drakakis, S. Rickard, J. Beard, R. Caballero, F. Iorio, G. O’Brien, and J. Walsh Volume 54, Issue 1, pp. 4684–4687
Parser-Based Retraining for Domain Adaptation of Probabilistic Generators Deirdre Hogan, Jennifer Foster, Joachim Wagner and Josef van Genabith INLG 08 - 5th International Natural Language Generation Conference
Optimal stepwise experimental design for pairwise functional interaction studies Casey FP, Cagney G, Krogan N, Shields DC Bioinformatics
Effect of electrostatics techniques on the estimation of thermal conductivity via equilibrium molecular dynamics simulation: application to methane hydrate N.J. English Molec. Phys.
Newtonian origin of the spin motive force in ferromagnetic atomic wires M. Stamenova, T.N. Todorov, and S. Sanvito Phys. Rev. B
Polarizability of molecular chains: A self-interaction correction approach. Chaitanya Das Pemmaraju, S. Sanvito, and K. Burke. Phys. Rev. B
Effects of self-interaction corrections on the transport properties of phenyl-based molecular junctions. C. Toher and S. Sanvito Phys. Rev. B
Magnetism of CoO polymorphs: density functional theory and Monte Carlo simulations. T. Archer, R. Hanafin, and S. Sanvito. Phys. Rev. B
Algorithm for the construction of self-energies for electronic transport calculations based on singularity elimination and singular value decomposition. I. Rungger and S. Sanvito Phys. Rev. B
Impurity-Ion pair induced high-temperature ferromagnetism in Co-doped ZnO. Chaitanya Das Pemmaraju, R. Hanafin, T. Archer, B.H. Braun, and S. Sanvito. Phys. Rev. B
Electronic properties of bulk and thin film SrRuO3: a search for the metal-insulator transition. J.M. Rondinelli, N.M. Caffrey, S. Sanvito, and N.A. Spaldin. Phys. Rev. B
Predicting d0 magnetism Andrea Droghetti, C.D. Pemmaraju and Stefano Sanvito. Phys. Rev. B
On the Development of Coarse-Grained Protein Models: Importance of Relative Side-Chain Orientations and Backbone Interactions Buchete, N.V., Straub, J.E. and Thirumalai, D. in "Coarse-Graining of Condensed Phase and Biomolecular Systems"
Multi-agent simulations of the immune response to HIV during the acute stage of infection Walshe R., Ruskin H.J. and Callaghan A. IJMPC
The tree of genomes: An empirical comparison of genome-phylogeny reconstruction methods McCann A., Cotton J.A. and O McInerney J. BMC Evol. Biol.
Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis Fitzpatrick D.A., Logue M.E. and Butler G. BMC Evol. Biol.
Fainter and closer: finding planets by symmetry breaking Burke D., Devaney N., Gladysz S., Barrett H., Whitaker M.K. and Caucci L. Proc. SPIE
Detection of Faint Companions through Stochastic Speckle Discrimination Gladysz S. and Christou, J. C. Astrophys. J.
Temporal Variability and Statistics of the Strehl Ratio in Adaptive-Optics Images Gladysz S., Christou J.C., Bradford L.W. and Roberts Jr. L.C. Publ. Astron. Soc. Pac.
Topological Degeneracy and Vortex Dynamics in the Kitaev Honeycomb Model Kells G., Bolukbasi A.T., Lahtinen V., Slingerland J., Pachos J.K. and Vala J. Phys. Rev. Lett.
Genetic repair for optimization under constraints inspired by Arabidopsis thaliana FitzGerald A. and O’Donoghue D.P. PPSN X
Phototactic clustering of swimming microorganisms in a turbulent velocity field Torney C. and Neufeld Z. Phys. Rev. Lett.
Exploiting alignment techniques in MaTrEx: the DCU Machine Translation System for IWSLT08 Ma Y., Tinsley J., Hassan H., Du J. and Way A. Proc. IWSLT 2008
Automatic Generation of Parallel Treebanks Zhechev V. and Way A. Proc. Coling 2008
Temporal evolution of long-period seismicity at Etna Volcano, Italy, and its relationships with the 2004 2005 eruption Lokmer I., Saccorotti G., di Lieto B. and Bean C.J. Earth Planet. Sci. Lett.
Influence of near-surface volcanic structure on long-period seismic signals and on moment tensor inversions: Simulated examples from Mount Etna Bean C., Lokmer I. and O'Brien G. J. Geophys. Res.
Seismicity on volcanoes generated by gas slug ascent O'Brien G.S. and Bean C.J. Geophys. Res. Lett.
Computer simulations reveal a novel nucleotide-type binding orientation for ellipticine-based anticancer c-kit kinase inhibitors Thompson D., Miller C. and McCarthy F.O. Biochemistry
Copper/molybdenum nanocomposite particles as catalysts for the growth of bamboo-structured carbon nanotubes Li Z., Larsson J.A., Larsson P., Ahuja R., Tobin J.M., O’Byrne J., Morris M.A., Attard G. and Holmes J.D. J. Phys. Chem. C
Autoignition measurements and a validated kinetic model for the biodiesel surrogate, methyl butanoate Dooley S., Curran H.J. and Simmie J.M. Combust. Flame
Thermochemistry and kinetics of acetonylperoxy radical isomerisation and decomposition: a quantum chemistry and CVT/SCT approach El-Nahas A.M., Simmie J.M., Navarro M.V., Bozzelli J.W., Black G. and Curran H.J. Phys. Chem. Chem. Phys.
Enthalpies of Formation and Bond Dissociation Energies of Lower Alkyl Hydroperoxides and Related Hydroperoxy and Alkoxy Radicals John M. Simmie, Grainne Black, Henry J. Curran, John P. Hinde J Phys Chem A
Accurate Benchmark Calculation of the Reaction Barrier Height for Hydrogen Abstraction by the Hydroperoxyl Radical from Methane. Implications for CnH2n+2 where n = 2 → 4 Aguilera-Iparraguirre J., Curran H.J., Klopper W. and Simmie J.M. J. Phys. Chem. A
The mechanism of nanobump formation in femtosecond pulse laser nanostructuring of thin metal films Ivanov D.S., Rethfeld B., O'Connor G.M., Glynn T.J., Volkov A.N. and Zhigilei L.V. J. Appl. Phys. A
Explanation of the different preferential binding sites for Ce and La in M2@C80 (M = Ce, La)—a density functional theory prediction Muthukumar K. and Larsson J.A. J. Mater. Chem.
A Density Functional Study of Ce@C82: Explanation of the Ce Preferential Bonding Site Muthukumar K. and Larsson J.A. J. Phys. Chem. A
Tuning the transparency of Cu2O with substitutional cation doping Nolan M. and Elliott S.D. Chem. Mater.
Vacancy formation and CO adsorption on gold-doped ceria surfaces Nolan M., Verdugo V.S. and Metiu H. Surf. Sci.
Defects in Cu2O, CuAlO2 and SrCu2O2 transparent conducting oxides Nolan M. Thin Solid Films
Effect of chlorine doping on electrical and optical properties of ZnO thin films Chikoidze E., Nolan M., Modreanu M., Sallet V. and Galtier P. Thin Solid Films
Thermochemistry of methyl and ethyl nitro, RNO2, and nitrite, RONO, organic compounds Asatryan R., Bozzelli J.W. and Simmie J.M. J. Phys. Chem. A
Ketene Thermochemistry Simmie J., Metcalfe W.K. and Curran H.J. ChemPhysChem
Speaker identification using instantaneous frequencies Grimaldi M. and Cummins F. IEEE Trans. Audio Speech Lang. Processing
Electronic structure of point defects in controlled self-doping of the TiO2 (110) surface: Combined photoemission spectroscopy and density functional theory study Nolan M., Elliott S.D., Mulley J.S., Bennett R.A., Basham M. and Mulheran P. Phys. Rev. B
Guanidinium chloride molecular diffusion in aqueous and mixed water-ethanol solutions Greg Gannon, J. Andreas Larsson, James C. Greer and Damien Thompson J Phys Chem B
Spectrum of the non-abelian phase in Kitaev’s honeycomb lattice model Lahtinen V., Kells G., Carollo A., Stitt T., Vala J. and Pachos J.K. Ann. Phys.
The phylogeny of the Mammalian Heme Peroxidases and the evolution of their diverse functions Noeleen B Loughran, Brendan O'Connor, Ciaran O'Fagain and Mary J O'Connell BMC Evol. Biol.
The effective concentration of unbound ink anchors at the molecular printboard Thompson D. J. Phys. Chem. B
The transport of cosmic rays in self-excited magnetic turbulence Reville B., O'Sullivan S., Duffy P. and Kirk J.G. MNRAS
The formation of a relativistic partially electromagnetic planar plasma shock M.E. Dieckmann, P.K. Shukla and L.O.C. Drury Astrophysical Journal
Discrete visco-elastic lattice methods for seismic wave propagation O'Brien, G. S. Geophys. Res. Lett.
Interacting jets from binary protostars G.C. Murphy, T. Lery, S. OSullivan, D. Spicer, F. Bacciotti, and A. Rosen Astronomy and astrophysics

2007

Title Authors Publication
C-Structures and F-Structures for the British National Corpus (In Proceedings of the Twelfth International Lexical Functional Grammar Conference LFG07) Joachim Wagner, Djamé Seddah, Jennifer Foster and Josef van Genabith CSLI Publications, Stanford University,
Exchange parameters from approximate self-interaction correction scheme A. Akande and S. Sanvito J. Chem. Phys.
Efficient Atomic Self-Interaction Correction Scheme for Nonequilibrium Quantum Transport C. Toher and S. Sanvito Phys. Rev. Lett.
Search for magnetoresistance in excess of 1000% in Ni point contacts: Density functional calculations A. R. Rocha, T. Archer, and S. Sanvito Phys. Rev. B
Injecting and controlling spins in organic materials S. Sanvito J. Mater. Chem.
Organic electronics: Spintronics goes plastic Sanvito S. Nat. Mater.
Thermochemistry for enthalpies and reaction paths of nitrous acid isomers R. Asatryan, J. W.Bozzelli, J. M. Simmie International Journal of Chemical Kinetics
Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations Thompson D., Lazennec C., Plateau P. and Simonson T. Proteins
Moment-tensor inversion of LP events recorded on Etna in 2004 using constraints obtained from wave simulation tests Lokmer, I., C. J. Bean, G. Saccorotti, and D. Patanè Geophys. Res. Lett.
Micro-seismic activity within a serac zone in an Alpine glacier (Glacier d’Argentiere, Mont-Blanc, France) Roux, P.-F., D. Marsan, J.-P. Metaxian, G. O’Brien, L. Moreau Journal of Glaciology
Supertrees Disentangle the Chimerical Origin of Eukaryotic Genomes Davide Pisani, James A. Cotton, and James O. McInerney Molecular Biology and Evolution
Capturing Translational Divergences with a Statistical Tree-to-Tree Aligner Mary Hearne, John Tinsley, Ventsislav Zhechev and Andy Way Proc. TMI-07
Robust Language Pair-Independent Sub-Tree Alignment John Tinsley, Ventsislav Zhechev, Mary Hearne and Andy Way Proc. MT-Summit-XI
Comparing electrostatic instabilities driven by mildly and highly relativistic proton beams M E Dieckmann, A Bret and P K Shukla Plasma Phys. Control. Fusion
Tunnelling in Alkanes Anchored to Gold Electrodes via Amine Groups G. Fagas and J. C. Greer Nanotechnology
Ammonium Scanning in an Enzyme Active Site: The Chiral Specificity of Aspartyl-tRNA synthetase Damien Thompson, Christine Lazennec, Pierre Plateau, Thomas Simonson J Biol Chem
Solvent effects and hydration of a tripeptide in sodium halide aqueous solutions: an in silico study Maxim V. Fedorov, Jonathan M. Goodman and Stephan Schum Phys. Chem. Chem. Phys.
Optical and microstructural properties of p-type SrCu2O2: First principles modeling and experimental studies M. Modreanu, M. Nolan, S.D. Elliott, O. Durand, B. Servet, G. Garry, H. Gehan, G. Huyberechts, E.L. Papadopoulou, M. Androulidaki, E. Aperathitis Thin Solid Films
Binary fluids under steady shear in three dimensions K. Stratford, J.-C. Desplat, P. Stansell, M.E. Cates Physical Review E
Adapting WSJ-Trained Parsers to the British National Corpus using In-Domain Self-Training Jennifer Foster, Joachim Wagner, Djamé Seddah and Josef van Genabith Proc. IWPT 2007
A Comparative Evaluation of Deep and Shallow Approaches to the Automatic Detection of Common Grammatical ErrorsEMNLP-CoNLL Joachim Wagner, Jennifer Foster and Josef van Genabith Proc. EMNLP-CoNLL
Free Energy Balance Predicates Dendrimer Binding Multivalency at Molecular Printboards D. Thompson Langmuir
In Silico Engineering of Tailored Ink-Binding Ability at Molecular Printboards D. Thompson ChemPhysChem
Atomic scale model interfaces between high-k hafnium silicates and silicon S. Monaghan, J. C. Greer, S. D. Elliott Phys. Rev. B
Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication Scannell, D.R., Frank, A.C., Conant, G.C., Byrne, K.P., Woolfit, M. and Wolfe, K.H. Proc. Natl. Acad. Sci. USA
Memoirs of a spin S. Sanvito Nature Nanotech.
Resonant magnetoresistance in organic spin-valves A.R. Rocha and S. Sanvito J. Appl. Phys.
Observation of van der Waals driven self-assembly of MoSI nanowires into a low symmetry structure using aberration corrected electron microscopy V. Nicolosi, P.D. Nellist, S. Sanvito, E.C. Cosgriff, S. Krishnamurthy, W.J. Blau, M.L.H. Green, D. Vengust, D. Dvorsek, D. Mihailovic, G. Compagnini, J. Sloan, V. Stolo jan, J.D. Carey, S.J. Pennycook, and J.N. Coleman Adv. Mater.
Atomic-orbital-based approximate self-interaction correction scheme for molecules and solids C. Das Pemmaraju, T. Archer, D. Sanchez-Portal, and S. Sanvito Phys. Rev. B
Identification of Potential Small Molecule Peptidomimetics Similar to Motifs in Proteins Ivan Baran, Radka Svobodova Varekova, Laavanya Parthasarathi, Simon Suchomel, Fergal Casey, Denis C. Shields Journal of Chemical Information and Modeling
Stress in slicon interlayers at the SiO_x/Ge interface S. O'Callaghan, S. Monaghan, S.D. Elliott, and J.C. Greer Applied Physics Letters
Aspects of self-similar current distributions resulting from the plasma filamentation instability M.E. Dieckmann, I. Lerche, P.K. Shukla, and L.O.C. Drury New Journal of Physics
Silicon Nanowire Band Gap Modification Michael Nolan, Sean O' Callaghan, Giorgos Fagas, James C. Greer and Thomas Frauenheim Nanoletters
Enthalpies of formation, bond dissociation energies and reaction paths for the decomposition of model biofuels: ethyl propanoate and methyl butanoate A. El-Nahas, M.V. Navarro, J.M. Simmie, J.W. Bozzelli, G. Black, H.J. Curran, S. Dooley, W. Metcalfe J. Phys. Chem. A
Thermochemistry of acetonyl and related radicals A. El-Nahas, J.W. Bozzelli, J.M. Simmie, M.V. Navarro, G. Black, H.J. Curran J. Phys. Chem. A
Shoreline approximation for unstructured mesh generation G.J. Gorman, D. Piggott, and C.C. Pain Computers & Geosciences
Molecular dynamics study of structural properties of beta-sheet assemblies formed by synthetic de novo oligopeptides Giovanni Bellesia, Maxim V. Fedorov and Edward G. Timoshenko Physica A: Statistical and Theoretical Physics

2006

Title Authors Publication
Independent particle descriptions of tunneling using the many-body quantum transport approach G. Fagas, P. Delaney and J. C. Greer Phys. Rev. B
Oxygen Vacancies at the Si(001)/SiO2 Interface J.C. Greer, T.M. Henderson, G. Bersuker, R.J. Bartlett, and A. Korkin Electrochemical Society Transactions
Computational Design of Silicon Suboxides: Chemical and Mechanical Forces on the Atomic Scale Anatoli Korkin, Rodney J. Bartlett, V. V. Karasiev, J. C. Greer, T. M. Henderson and Gennadi Bersuker J. Comput. Aided Mater. Des.
Computational design of Si∕SiO2 interfaces: Stress and strain on the atomic scale A. Korkin, J. C. Greer, G. Bersuker, V. Karasiev, and R. J. Bartlett Phys. Rev. B
Analysis of the relative importance of the humoral versus the cellular response during the acute stage of HIV infection: Results from multi-agent computer simulations Callaghan A., Ruskin H.J. and Walshe R. ESM'2006
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis Fitzpatrick D.A., Logue M.E., Stajich J.E. and Butler G. BMC Evol. Biol.
Absolute net charge and the biological activity of oligopeptides Parthasarathi L, Devocelle M, Sondergaard C, Baran I, O’Dushlaine CT, Davey NE, Edwards RJ, Moran N, Kenny D, Shields DC Journal of Chemical Information and Modeling
Solvent Effects and Conformational Stability of a Tripeptide Maxim V. Fedorov, Stephan Schumm, and Jonathan M. Goodman CompLife 2006, Lecture Notes in Bionformatics
Modelling of size dependent failure in Cardiovascular Stent Struts under Tension and Bending F. Harewood and P.E. McHugh Annals of Biomedical Engineering
The use of rapid prototype models for investigation of failure mechanisms in trabecular bone P. McDonnell, N. Harrison, D. O'Mahoney, P. McHugh and S. Lohfeld Journal of Biomechanics
Damage and failure of trabecular bone with non-linear geometry and inhomogeneous material properties N. Harrison, D. O'Mahoney, P. McDonnell and P. McHugh Journal of Biomechanics
The p-type Conduction Mechanism in Cu2O: a First Principles Study Michael Nolan and Simon D. Elliott Physical Chemistry Chemical Physics
Tuning the Electronic Structure of the Transparent Conducting Oxide Cu2O Michael Nolan and Simon D. Elliott Thin Solid Films
Rotational modulation of the radio emission from the M9 dwarf TVLM 513-46546: broadband coherent emission at the substellar boundary? G. Hallinan, A. Antonova, J.G. Doyle, S. Bourke, W. F. Brisken, A. Golden APJ
Calculated mechanical properties of GaNxAs1-x G. Stenuit, S. Fahy Physical Review
Effect of indium-nitrogen bonding on the localized vibrational mode in InyGa1-yNxAs1-x A. M. Teweldeberhan, S. Fahy Physical Review
Spin and molecular electronics in atomically-generated orbital landscapes A.R. Rocha, V.M. Garcia Suarez, S.W. Bailey, C.J. Lambert, J. Ferrer, S. Sanvito Physical Review
Inelastic transport in molecular spin valves N. Jean, S.Sanvito Physical Review
Magneto-mechanical interplay in spin-polarized point contacts M. Stamenova, S. Sahoo, C. G. Sánchez, T. N. Todorov, S. Sanvito Physical Review
Molecular conduction: Do time-dependent simulations tell you more than the Landauer approach? C. Sanchez, M. Stamenova, S. Sanvito, D.R. Bowler, A.P. Horsfield, T. Todorov Journal of Chemical Physics
Molecular-Spintronics: the art of driving spin through molecules S. Sanvito, A.R. Rocha J. Comput. Theor. Nanosci.
Magnetization of electrodeposited nickel: Role of interstitial carbon C. O’Reilly, S. Sanvito, F.M.F. Rhen, P. Stamenov, J.M.D. Coey Journal of Applied Physics
Ab initio study on the magnetostructural properties of MnAs I. Rungger, S. Sanvito Physical Review
On-site approximation for spin-orbit interaction in DFT L. Fernandez Seivane, M.A. Oliveira, S. Sanvito, J. Ferrer Journal of Physics
Modelling competitive guest binding to beta-cyclodextrin molecular printboards D. Thompson and J.A. Larsson Journal of Physical Chemistry B
Statistical Estimates of Electron Correlations W. Gyorffy, T.M. Henderson, J.C. Greer Journal of Chemical Physics
3D MHD Simulations of Laboratory Plasma Jets Andrea Ciardi Astrophysics and Space Science
Self-organizing neural networks to support the discovery of DNA-binding motifs Shaun Mahony, Panayiotis V. Benos, Terry J. Smith, Aaron Golden Neural Networks
A two-stage approach for improved prediction of residue contact maps Alessandro Vullo, Ian Walsh & Gianluca Pollastri BMC Bioinformatics
The effect of pion mass on Skyrme Conor Houghton & Shane Magee Physics Letters B
Harnessing the latent computing power of many desktop machines to create a high-throughput phylogenetics supercomputer Thomas M. Keane, Matthew Goode, Thomas J. Naughton, James O. McInerney BMC Bioinformatics
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified Thomas M. Keane, Christopher J. Creevey, Melissa M. Pentony, Thomas J. Naughton, James O. McInerney BMC Evolutionary Biology
Magneto-mechanical interplay in spin-polarized point contacts Maria Stamenova, Sudhakar Sahoo, Cristian G. Sanchez, Tchavdar N. Todorov, Stefano Sanvito Physical Review B
Particle-in-cell simulation studies of the non-linear evolution of ultrarelativistic two-stream instabilities M.E. Dieckmann, P.K. Shukla, L.O.C. Drury MNRAS
On the ultrarelativistic two-stream instability, electrostatic turbulence and Brownian motion M.E. Dieckmann, L.O.C. Drury and P.K. Shukla New Journal of Physics
Multiple Lineage Specific Expansions in the Guanylyl Cyclase Gene Family Fitzpatrick, D.A., O'Halloran, D.M. and Burnell, A.M BMC Evolutionary Biology
The Molecular Phylogeny and Functional Significance of a Nematode Specific Clade of Heterotrimeric G-protein α-Subunit Genes O'Halloran, D.M., Fitzpatrick, D.A., McCormack, G.P., McInerney, J.O. Journal of molecular evolution
Nonequilibrium steady states in sheared binary fluids P. Stansell, K. Stratford, J.-C. Desplat, R. Adhikari, and M.E. Cates Physical Review Letters

2005

Title Authors Publication
Onset of rigidity for stretched string networks G. W. Delaney, D. Weaire and S. Hutzler Europhysics Letters