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Some key publications arising from use of the Legion HPC service.

Papers preceded by *** resulted from research conducted on the Legion cluster via 'non‑standard' use of resources (see Requesting Additional or Unusual Resources).

Astrophysics and Remote Sensing§

‘Cosmological simulations using GCMHD+’ by Barnes, David J., Kawata, Daisuke and Wu, Kinwah. Monthly Notices of the Royal Astronomical Society 420 (2012) 3195. 1

‘Axial symmetry breaking of Saturn's thermosphere’ by Smith, C. G. A. and Achilleos, N. Monthly Notices of the Royal Astronomical Society 422 (2012) 1460. 2

‘Methane in the atmosphere of the transiting hot Neptune GJ436b?’ by Beaulieu JP, Tinetti G, Kipping DM, Ribas I, Barber RJ, Cho JYK, Polichtchouk I, Tennyson J, Yurchenko SN, Griffith CA, Batista V, Waldmann I, Miller S, Carey S, Mousis O and Fossey SJ. Astrophysical Journal 731 (2011) 2041. 3

‘A variationally computed line list for hot NH3’ by Yurchenko SN, Barber RJ and Tennyson J. Monthly Notices of the Royal Astronomical Society 413 (2011) 1828. 4

‘Maser Sources in Astrophysics’ by Gray, M. D. Cambridge University Press (2012). 5

Bioinformatics and Computational Biology§

‘AIP Mutation in Pituitary Adenomas in the 18th Century and Today’ by Chahal HS, Stals K, Unterlander M, Balding DJ, Thomas MG, Kumar AV, Besser GM, Atkinson AB, Morrison PJ, Howlett TA, Levy MJ, Orme SM, Akker SA, Abel RL, Grossman AB, Burger J, Ellard S, and Korbonits M. New England Journal of Medicine 364 (2011) 43. 6

‘Genetic Discontinuity Between Local Hunter-Gatherers and Central Europe's First Farmers’ by Bramanti B, Thomas MG, Haak W, Unterlaender M, Jores P, Tambets K, Antanaitis-Jacobs I, Haidle MN, Jankauskas R, Kind C-J, Lueth F, Terberger T, Hiller J, Matsumura S, Forster P and Burger J. Science 326 (2009) 137. 7

‘Accurate de novo structure prediction of large transmembrane protein domains using fragment assembly and correlated mutation analysis’ by Nugent T and Jones DT. Proceedings of the National Academy of Sciences (2012). . 8

‘GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains’ by Lee DA, Rentzsch R and Orengo C. Nucleic Acids Research 38 (2010) 720. 9

*** ‘The effect of insertions, deletions and alignment errors on the branch-site test of positive selection’ by Fletcher W and Yang Z. Molecular Biology and Evolution 27 (2010) 2257. 10

Earth Materials§

'Lattice electrical resistivity of magnetic bcc iron from first-principles calculations' by D. Alfè, M. Pozzo, and M. P. Desjarlais. Physical Review B 85, (2012) 024102 1-5. 11


‘Effect on transmission of HIV-1 resistance of timing of implementation of viral load monitoring to determine switches from first to second line antiretroviral regimens in resource-limited settings’ by Phillips AN, Pillay D, Garnett G, Bennett D, Vitoria M, Cambiano V and Lundgren JD. AIDS 25 (2011) 843. 12

‘Projected life expectancy of people with HIV according to timing of diagnosis’ by Nakagawa F, Lodwick RK, Smith CJ, Smith R, Cambiano V, Lundgren JD, Delpech V and Phillips AN. AIDS 26 (2012) 335. 13

‘HIV Treatment as Prevention: Systematic Comparison of Mathematical Models of the Potential Impact of Antiretroviral Therapy on HIV Incidence in South Africa’ by Jeffrey W. Eaton, Leigh F. Johnson, Joshua A. Salomon, Till Bärnighausen, Eran Bendavid, Anna Bershteyn, David E. Bloom, Valentina Cambiano, Christophe Fraser, Jan A. C. Hontelez, Salal Humair, Daniel J. Klein, Elisa F. Long, Andrew N. Phillips, Carel Pretorius, John Stover, Edward A. Wenger, Brian G. Williams and Timothy B. Hallett. Public Library of Science Medicine Medicine 9 (2012) e1001245. 14

‘Threshold Haemoglobin Levels and the Prognosis of Stable Coronary Disease: Two New Cohorts and a Systematic Review and Meta-Analysis’ by Anoop D. Shah, Owen Nicholas, Adam D. Timmis, Gene Feder, Keith R. Abrams, Ruoling Chen, Aroon D. Hingorani and Harry Hemingway. Public Library of Science Medicine 8 (2011) e1000439. 15

Molecular Quantum Dynamics and Electronic Structure§

‘Experimental and computational studies of small molecule activation by uranium tris(aryloxides): binding of N2, coupling of CO and deoxygenation insertion of CO2 under ambient conditions’ by Stephen M. Mansell, Nikolas Kaltsoyannis and Polly L. Arnold. Journal of the American Chemical Society 133 (2011) 9036. 16

‘A combined NMR/MD/QM approach for structure and dynamics elucidations in the solution state: pilot studies using tetrapeptides’ by Aliev, A. E., Courtier-Murias, D., Bhandal, S. and Zhou, S. Chemical Communications 46 (2010) 695. 17

‘A stable two-coordinate acyclic silylene’ by Andrey V. Protchenko, Krishna Hassomal Birjkumar, Deepak Dange, Andrew D. Schwarz, Dragoslav Vidovic, Cameron Jones, Nikolas Kaltsoyannis, Philip Mountford and Simon Aldridge. Journal of the American Chemical Society 134 (2012) 6500. 18
Work subsequently highlighted in Nature 485 (2012) 49. 19

‘A global, high accuracy ab initio dipole moment surface for the electronic ground state of the water molecule’ by Lorenzo Lodi, Jonathan Tennyson and Oleg L. Polyanski. Journal of Chemical Physics 135 (2011) 034113. 20

‘Line lists for H218O and H217O based on empirical line positions and ab initio intensities’ by Lorenzo Lodi and Jonathan Tennyson. Journal of Quantitative Spectroscopy & Radiative Transfer 113 (2012) 850. 21

Nanoscience and Defects§

'Point defects at the ice (0001) surface’ by Matthew Watkin, Joost VandeVondele and Ben Slater. Proceedings of the National Academy of Sciences 107 (2010) 12429. 22

‘Aluminosilicate glasses as yttrium vectors for in-situ radiotherapy: understanding composition-durability effects through molecular dynamics simulations’ by J. K. Christie and A. Tilocca. Chem. Mater. 22 (2010) 3725.23

‘Aerobic Oxidation of Hydrocarbons Catalyzed by Mn-Doped Nanoporous Aluminophosphates(I): Preactivation of the Mn Sites’ by Gomez-Hortiguela, L and Cora, F and Catlow, CRA. ACS Catalysis 1 (2011) 18. (Cover article in the first ever edition of this journal.) 24

‘Protonated Carboxyl Anchor for Stable Adsorption of Ru N749 Dye (Black Dye) on a TiO2 Anatase (101) Surface’ by K. Sodeyama, M. Sumita, C. O'Rourke, U. Terranova, A. Islam, L. Han, D. R. Bowler and Y. Tateyama. J. Phys. Chem. Lett. 3 (2012) 472. 25

‘Mechanistic insight into the blocking of CO diffusion in [NiFe]-hydrogenase mutants through multiscale simulation’ by P. Wang and J. Blumberger. Proceedings of the National Academy of Sciences 109 (2012) 6399. 26



‘Rapid Desynchronization of an Electrically Coupled Interneuron Network with Sparse Excitatory Synaptic Input’ by Koen Vervaeke, Andrea Lőrincz, Padraig Gleeson, Matteo Farinella, Zoltan Nusser, R. Angus Silver. Neuron 67 (2010) 435. 28

Surface Science and Catalysis§

‘Ab initio molecular dynamics simulations of the cooperative adsorption of hydrazine and water on copper surfaces: Implications for shape control of nanoparticles’ by T.D. Daff and N.H. de Leeuw.Chemistry of Materials 23 (2011) 2718. 29

‘Density functional theory and interatomic potential study of structural, mechanical and surface properties of calcium oxalate materials’ by D. Di Tommaso, S.E. Ruiz-Hernandez, Z. Du and N.H. de Leeuw. RSC Advances 2 (2012) 4664. 30

‘Catalytic Reaction Mechanism of Mn-Doped Nanoporous Aluminophosphates for the Aerobic Oxidation of Hydrocarbons’ by Luis Gómez-Hortigüela, Furio Corà, Gopinathan Sankar, Claudio M. Zicovich-Wilson, and C. Richard A. Catlow. Chemistry, A European Journal 16 (2010) 13553. (Cover article.) 31

‘A molecular dynamics study of the interprotein interactions in collagen fibrils’ by I. Streeter and N.H. de Leeuw. Soft Matter 7 (2011) 3373. 32

‘Molecular Dynamics simulation of the early stages of nucleation of hydroxyapatite at a collagen template’ by N. Almora-Barrios and N.H. de Leeuw. Crystal Growth & Design 12 (2012) 756. 33

Systems Biomedicine§

‘Resolution of Discordant HIV-1 Protease Resistance Rankings Using Molecular Dynamics Simulations’ by D. Wright and P. V. Coveney. Journal of Chemical Information and Modeling 51 (2011) 2636. 34

‘Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs’ by S. Wan and P. V. Coveney. J. R. Soc. Interface 8 (2011) 1114. 35

‘Clay Minerals Mediate Folding and Regioselective Interactions of RNA: A Large-Scale Atomistic Simulation Study’ by J. B. Swadling, P. V. Coveney and H. C. Greenwell. Journal of the American Chemical Society 132 (2010) 13750.36


‘Universality of Performance Parameters in Vehicular ad hoc Networks’ by T. Hewer, M. Nekovee and P. V. Coveney. IEEE Communications Letters 15 (2011) 947. 37