Research

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 451 publications:

2013

Title	Authors	Publication
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

2012

Title	Authors	Publication
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
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
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'2012
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
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
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
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 C_nH_2n+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 GaN_xAs_1-x	G. Stenuit, S. Fahy	Physical Review
Effect of indium-nitrogen bonding on the localized vibrational mode in In_yGa_1-yN_xAs_1-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