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 208 publications:

2010

Title	Authors	Publication
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.
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
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	Jonathan Mackey, Andrew J. Lim	MNRAS
Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations	Edina Rosta, Nicolae-Viorel Buchete, Gerhard Hummer	J. Chem. Theory Comput., 2009
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
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
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
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
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