News

CCS Member wins Wellcome Image Award 2008

CCS member Mary-Ann Thyveetil has won a Wellcome Image Award 2008. The winning image (displayed above) will be displayed in the Atrium of the Wellcome Collection along with the other Award winners for several months.

The visualisation shows the lowest of three sheets of an anionic clay (otherwise known as a layered double hydroxide) comprised of a positively charged Mg/Alhydroxide, between two sheets of which is intercalated a 480 base pair double stranded circular anionic DNA plasmid; the molecular simulation model from which this snapshot has been taken contains more than one million atoms. This image was a "by product" of our investigations into the nature of the structural stability and properties of DNA intercalated in these clay nanomaterials. Such DNA intercalates are of interest for drug delivery, gene therapy and, by no means least, in origins of life studies. Indeed, we have been able to show that such intercalated double-stranded DNA (in linear and plasmid forms) has greatly enhanced structural stability compared to DNA in bulk water, retaining its integrity at high temperatures and pressures, of the kind associated with the vicinity of deep ocean hydrothermal vents.

The award ceremony took place at the Wellcome Trust, Euston Road, London on 11th March 2008. The pictures below show Mary-Ann receiving her award from science broadcaster Vivienne Parry.

For further details see:

• The Wellcome Image Awards 2008
• M. Thyveetil, P. V. Coveney, H. C. Greenwell, J. Suter, "Computer Simulation Study of the Structural Stability and Materials Properties of DNA-Intercalated Layered Double Hydroxides", Journal of the American Chemical Society, in press, (2008).

SPICE has won the ISC Life Sciences Award at International Supercomputer Conference 2006

The EPSRC and NSF funded SPICE project has won the ISC Life Sciences Award for 2006. More information on SPICE can be found here.

Version 1.0.0 of the Application Hosting Environment released

Version 1.0.0 of the Application Hosting Environment (AHE) is released. The AHE is a lightweight hosting environment that allows scientists to run applications on grid resources in a quick, transparent manner. The AHE provides resource selection, application launching, workflow execution, provenance and data-recovery, exposing a WSRF compatible interface to job management on remote grid resources using WSRF::Lite as its middleware. The development of the AHE is funded by the EPSRC "Rapid Prototyping of Usable Grid Middleware" Project, GR/T27488/01, and by OMII under the Managed Programme RAHWL project. Find out more and download the latest release here.

Recent publications

• G. De Fabritiis, R. Delgado-Buscalioni and P. V. Coveney, " Multiscale modelling of liquids with molecular specificity", Physical Review Letters, 97(13), 134501(2006), DOI:10.1103/PhysRevLett.97.134501. Published online, 29 September 2006 at http://link.aps.org/abstract/PRL/v97/e134501. Available for download here.
• J. Chin and P. V. Coveney, "Chirality and domain growth in the gyroid mesophase", Proceedings of the Royal Society of London Series A (2006). Published online, 23 June 2006. DOI: 10.1098/rspa.2006.1741. Available for download here.
• M. J. Harvey, D. Scott and P. V. Coveney, "An Integrated Instrument Control and Informatics System for Combinatorial Materials Research", J. Chem. Inf. Model., 46(3), 1026-1033(2006)DOI: 10.1021/ci050399g. Available for download here.
• A tutorial on "Building Secure WS-Resources with WSRF::Lite and WS-Security" has been published on IBM developerWorks. You can access it here. You will have to sign up for a developerWorks account to access this.
• A joint paper entitled "NekTAR, SPICE and VORTONICS: Using Federated Grids for Large Scale Scientific Applications", which describes the three projects in a Joint US/UK High End Computing Project involving RealityGrid, can be downloaded here.
• The position paper: B.M. Boghosian, L.I. Finn and P.V. Coveney, "Moving the data to the computation: multi-site distributed parallel computation" has been recently issued and can be downloaded here.
  The paper describes recent findings within the Joint US/UK High End Computing Project (NekTAR, SPICE and VORTONICS) in which "meta-computing" applications are being run across several sites in the US and UK. It introduces the new concept of Geographically Distributed Domain Decomposition to utilise a high-performance computing grid to run a single large-scale application over multiple, geographically remote sites, to address "grand challenge" problems that will otherwise always remain beyond the scope of a single supercomputer.
• A paper presenting "HARC: A Highly-Available Robust Co-scheduler" is available for download.
  The paper describes a co-scheduling framework suitable for any resource under the control of a scheduler supporting reservations. The co-scheduling of resources is becoming essential in Distributed High-Performance Computing Applications, which require the allocation of multiple resources; often, these resources will belong to multiple administrative domains, and so will not be under centralized control. Typically, dedicated resources of different types will be required, usually including high performance computers and networks, storage systems, vsualization systems, AccessGrid nodes and haptic devices. Distributed applications require these resources to be co-scheduled, i.e. to be made available at the same time or at some coordinated set of times. HARC is an external co-scheduling system, which is highly fault-tolerant through its use of Gray and Lamport's Paxos Commit protocol , and therefore suitable for use in a distributed environment or Grid.
• A paper on "Usable Middleware for Grid Based Computational Science" is available for download (doc).
  The paper describes different usable middleware schemes which are transparent, portable and modular, and are designed to overcome the difficulties posed by "heavyweight" middleware and to encourage application users to utilize grid resources. The paper will be presented at the e-Science Usability Meeting at NeSC (26-27 January 2006), http://www.nesc.ac.uk/esi/events/613/ and http://mytea.org.uk/uws/.
• P. Stansell, K. Stratford, J.-C.Desplat, R. Adhikari, M. E. Cates, "Nonequilibrium Steady States in Sheared Binary Fluids", accepted for publication in Physical Review Letters cond-mat/0511745.
• The August 2005 issue of Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences contains papers of a Theme Issue entitled "Scientific Grid Computing", compiled and edited by Peter V. Coveney.

RealityGrid Platform Grant

SuperComputing 2005

RealityGrid was involved in some major activities at Supercomputing 2005 (SC|05), which took place in Seattle 12-18 November 2005: http://sc05.supercomputing.org/.

The EPSRC and NSF funded SPICE project has won the HPC Analytics Challenge Award at SC|05.

SPICE is part of a joint US/UK collaboration, with the associated US projects NekTAR and VORTONICS.
For more information on these projects see here.
A press release on these projects at SC|05 can be downloaded here (pdf) and is available online on the TeraGrid website.

Official release of WEDS: a WSRF-based Environment for Distributed Simulation

RealityGrid: the musical