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The Computational Science Journal Club is an informal, fortnightly meeting where a volunteer will present an interesting paper on something to do with computational science followed by a group discussion about the merits (or otherwise) of the article. We usually meet on Wednesdays at 11am in the Christopher Ingold Building (Chemistry) in room 124c or 124d.

The journal club will be on hiatus for the summer following the meeting on the 4th of July. An announcement will be made later in the year concerning its recommencement.

It is organised by Rupert Nash and Dave Wright in the Centre for Computational Science. All are welcome. If you would like to be added to our mailing list or to present a paper, please email us.

Forthcoming Journal Clubs

Date

Time

Speaker

Room

Paper

22/04/2013

10.30

Hans Koss

124d

Solution structure, dynamics and interdomain communication of
PI-phospholipase Cg1. Poster

08/05/2013

11.00

Shunzhou Wan & Dave Wright

124c

Recent molecular dynamics studies of EGFR:
Y. Shan et al. "Oncogenic Mutations Counteract Intrinsic Disorder in the EGFR Kinase and Promote Receptor Dimerization" http://www.sciencedirect.com/science/article/pii/S0092867412004163
Wan et al. "Mechanism of Drug Efficacy Within the EGF Receptor Revealed by Microsecond Molecular Dynamics Simulation" http://mct.aacrjournals.org/content/11/11/2394.long

TBC

11.00

TBC

124c

TBC

Past Journal Clubs

Date

Time

Speaker

Room

Paper

24/10/2012

11.00

Miguel Bernabeu

124c

"Point: CFD---Computational Fluid Dynamics or Confounding Factor Dissemination" http://www.ajnr.org/content/33/3/395.full 
"Counterpoint: Realizing the Clinical Utility of Computational Fluid Dynamics---Closing the Gap" http://www.ajnr.org/content/33/3/396.full

04/07/2012

11.00

Shunzhou Wan

124c

Large-scale prediction and testing of drug activity on side-effect targets, Nature, 486, 361--36 (2012) http://www.nature.com/nature/journal/v486/n7403/abs/nature11159.html

13/06/2012

11.00

Lev Shamardin

124c

The OPERA Collaboration (T. Adam et al.), "Measurement of the neutrino velocity with the OPERA detector in the CNGS beam". http://arxiv.org/abs/1109.4897

30/05/2012

11.00

Jacob Swadling

124c

Talk rehearsal "Interaction of Nucleic-Acids at the Aqueous Mineral Interface"

16/05/2012

11.00

James Suter

124c

Davies, R. J. (2011). "Methane contamination of drinking water caused by hydraulic fracturing remains unproven", PNAS, 108(43), E871--E871. doi:10.1073/pnas.1113299108

02/05/2012

11.00

Nour Shublaq

124c

Bearer et al., "Multiparameter Computational Modeling of Tumor Invasion", Cancer Research, 69, 4493--4501 (2009). doi:10.1158/0008-5472.CAN-08-3834

18/04/2012

11.00

Kevin Lau

124c

van Nierop, Alben & Brenner, "How Bumps on Whale Flippers Delay Stall: An Aerodynamic Model", Phys. Rev. Lett., 100, 054502 (2008). doi:10.1103/PhysRevLett.100.054502

21/03/2012

15.00

Liberty Foreman

124c

S. Price, "Computed Crystal Energy Landscapes for Understanding and Predicting Organic Crystal Structures and Polymorphism", Accounts of Chemical Research, 42(1), 117--126 (2009). DOI:10.1021/ar800147t

07/03/2012

11.00

Ben Jefferys

124c

Barrett et al., "National survey of British public's views on use of identifiable medical data by the National Cancer Registry", BMJ, doi:10.1136/bmj.38805.473738.7C (2006)

22/02/2012

11.00

Rupert Nash

124c

Smallenburg et al., "Vacancy-stabilized crystalline order in hard cubes", arXiv:1111.3466v2.

08/02/2012

11.00

Oliver Henrich

124c

Frijters, Günther and Harting, "Deformation of fluid droplets stabilized by colloids or surfactant", arXiv:1201.6562v1.

25/01/2012

11.00

Ben Hall & Derek Groen

124c

Fraud Special

14/12/2011

11.00

Hans Koss

124c

Gupta et al., "Emergence of Drug Resistance in HIV Type 1-Infected Patients after Receipt of First-Line Highly Active Antiretroviral Therapy: A Systematic Review of Clinical Trials", Clinical Infectious Diseases. 47, 712--722 (2008). DOI:10.1086/590943

29/11/2011

11.00

James Hetherington

124c

Moreau et al., "The Open Provenance Model core specification (v1.1)", Future Generation Comput. Sys., 27, 743-756 (2011). DOI: 10.1016/j.future.2010.07.005

16/11/2011

11.00

Ben Hall

124c

Hall et al., "Transmembrane Helix Dynamics of Bacterial Chemoreceptors Supports a Piston Model of Signalling", PLoS Comput. Biol. 7, e1002204 (2011). DOI: 10.1371/journal.pcbi.1002204

02/11/2011

11.00

Shunzhou Wan

124c

David Nesvorny, "Young Solar System's Fifth Giant Planet?", arXiv, 1109.2949v1 (2011). Link: http://arxiv.org/abs/1109.2949

19/10/2011

11.00

Maiki Bem

124c

Benjamin Snyder et al., "A Statistical Model for Lost Language Decipherment", Proceeding ACL '10 Proceedings of the 48th Annual Meeting of the Association for Computational Linguistics. Link: http://dl.acm.org/citation.cfm?id=1858788

05/10/2011

11.00

Miguel Bernabeu

124c

Denis Noble, "Modeling the heart--from genes to cells to the whole organ", Science, 295, 1678-1682 (2002). DOI: 10.1126/science.1069881

21/09/2011

11.00

David Chang

124c

Wong et al., "Optical Imaging of Electrically Evoked Visual Signals in Cats", in Proc. IEEE EMBS, 29, 1635--1638 (2007). DOI: 10.1109/IEMBS.2007.4352620

07/09/2011

11.00

James Suter

124c

Walsh et al., "Microsecond Simulations of Spontaneous Methane Hydrate Nucleation and Growth", Science, 326, 1095--1098 (2009). DOI: 10.1126/science.1174010

24/08/2011

11.00

Gary Doctors

Cruciform Foyer Seminar Room 2

IA Hasnain and AM Donald, "Microrheological characterization of anisotropic materials", Phys. Rev. E, 73, 031901 (2006). DOI: 10.1103/PhysRevE.73.031901

13/07/2011

11.00

Jacob Swadling

124c

Lane, Nick. "Chance or Necessity? Bioenergetics and the Probability of Life" Journal of Cosmology, 10, 3286-3304, 2010. Link: http://journalofcosmology.com/Abiogenesis107.html
Lane, Nick. "Genesis Revisited", New Scientist, 7 August 2010. Link: http://www.nick-lane.net/Lane%20hydrogen%20animals.pdf

18/05/2011

11.00

Oliver Henrich

124c

Eric Lauga, "Life around the scallop theorem", Soft Matter, 7, 3060, 2011. DOI:10.1039/C0SM00953A

04/05/2011

11.00

Derek Groen

124c

Simon Portegies Zwart, "The Lost Siblings of the Sun", Astrophys. J. Lett., 696, L13, 2009. DOI:10.1088/0004-637X/696/1/L13
Simon Portegies Zwart, Sci. Am., 301, 40, 2009. DOI:10.1038/scientificamerican1109-40

20/04/2011

11.00

David Wright

124c

Tracey Chapman et al., "Stalk-eyed flies", Curr Biol., 5, 533-535, 2005. DOI:10.1016/j.cub.2005.07.015
Patrice David et al., "Condition-dependent signalling of genetic variation in stalk-eyed flies", Nature, 406, 2000. DOI:10.1038/35018079

07/04/2011

11.00

Ben Jeffreys

124c

Seth Cooper et al. "Predicting protein structures with a multiplayer online game", Nature, 466, 756--760, 2010. DOI:10.1038/nature09304

23/03/2011

11.00

Rupert Nash

124c

Angelani, Di Leonardo & Ruocco. "Self-Starting Micromotors in a Bacterial Bath.", Phys. Rev. Lett., 102, 048104, 2009. DOI: 10.1103/PhysRevLett.102.048104
Di Leonardo et al.. "Bacterial ratchet motors.", PNAS, 107, 9541, 2010. DOI:10.1073/pnas.0910426107

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