Publications
Some key publications arising from use of the Legion HPC service, from several of the Research Computing Consortia are listed below.
Papers preceded by *** resulted from research conducted on the Legion cluster via 'non‑standard' use of resources (see Requests for Additional Resources or Resource Reservations)
Contents
Astrophysics and Remote Sensing
Bioinformatics and Computational
Biology
Earth Materials
Epidemiology
Molecular Quantum Dynamics and
Electronic Structure
Nanoscience and Defects
Neuroscience
Surface Science and Catalysis
Systems Biomedicine
Other
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.http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2966.2011.20247.x/abstrac
‘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.
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2966.2012.20719.x/abstract
‘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.
http://iopscience.iop.org/0004-637X/731/1/16/
‘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.
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2966.2011.18261.x/abstract
‘Maser
Sources in Astrophysics’ by Gray,
M. D. Cambridge University Press (2012).
http://www.cambridge.org/gb/knowledge/isbn/item2709668/?site_locale=en_GB
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.
http://www.nejm.org/doi/full/10.1056/NEJMoa1008020
‘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.
http://www.sciencemag.org/content/326/5949/137.abstract
‘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). doi:10.1073/pnas.1120036109.
http://www.pnas.org/content/109/24/E1540.full
‘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.
http://nar.oxfordjournals.org/content/38/3/720.full
***
‘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.
http://mbe.oxfordjournals.org/content/27/10/2257.short
'Lattice electrical
resistivity of magnetic bcc iron from first-principles calculations' by D. Alfè, M. Pozzo, and M. P. Desjarlais. Physical Review B 85, 024102 1-5 (2012).
http://www.homepages.ucl.ac.uk/~ucfbdxa/pubblicazioni/PhysRevB.85.024102.pdf
‘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.
http://journals.lww.com/aidsonline/Fulltext/2011/0327/Effect_on_transmission_of_HIV_1_resistance_of.15.aspx
‘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.
http://journals.lww.com/aidsonline/Fulltext/2012/01280/Projected_life_expectancy_of_people_with_HIV.9.aspx
‘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.
http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.1001245
‘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.
http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.1000439
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.
http://pubs.acs.org/doi/abs/10.1021/ja2019492
‘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.
http://pubs.rsc.org/en/Content/ArticleLanding/2010/CC/B910499B
‘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.
http://pubs.acs.org/doi/abs/10.1021/ja301042u
Work subsequently highlighted in
Nature 485 (2012) 49.
http://www.nature.com/nature/journal/v485/n7396/full/485049a.html
‘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.
http://jcp.aip.org/resource/1/jcpsa6/v135/i3/p034113_s1
‘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.
http://www.sciencedirect.com/science/article/pii/S0022407312000878
'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. http://www.pnas.org/content/107/28/12429.full
‘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.
http://pubs.acs.org/doi/abs/10.1021/cm100847p
‘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.
http://pubs.acs.org/doi/abs/10.1021/cs100068t
‘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. http://pubs.acs.org/doi/abs/10.1021/jz201583n
‘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.
http://www.pnas.org/content/109/17/6399.full
‘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. http://www.cell.com/neuron/fulltext/S0896-6273(10)00512-X?switch=standard
‘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. http://pubs.acs.org/doi/abs/10.1021/cm103164w
‘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. http://pubs.rsc.org/en/content/articlelanding/2012/ra/c2ra00832g
‘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. http://onlinelibrary.wiley.com/doi/10.1002/chem.201090227/abstract
‘A
molecular dynamics study of the interprotein interactions in collagen fibrils’ by I. Streeter and N.H. de Leeuw. Soft Matter 7 (2011) 3373.
http://pubs.rsc.org/en/content/articlelanding/2011/sm/c0sm01192d
‘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.
http://pubs.acs.org/doi/abs/10.1021/cg201092s
‘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.
http://pubs.acs.org/doi/abs/10.1021/ci200308r
‘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.
http://rsif.royalsocietypublishing.org/content/8/61/1114.long
‘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.
http://pubs.acs.org/doi/abs/10.1021/ja104106y
‘Universality
of Performance Parameters in Vehicular ad hoc Networks’ by T. Hewer, M. Nekovee and P. V. Coveney. IEEE Communications Letters 15 (2011) 947.
http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=5955146
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