Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

UK e-Science project wins top supercomputing award

18.11.2005


Issued by EPSRC on behalf of the UK e-Science Programme



A UK e-Science project has won a top award at SC05, the world’s premier supercomputing conference in Seattle this week. SPICE (Simulated Pore Interactive Computing Environment) achieved success in the HPC Analytics Challenge for demonstrating the use of innovative techniques in rigorous data analysis and high-end visualisation to solve a complex, real-world problem.

“SPICE shows how the power of supercomputers on both sides of the Atlantic can be harnessed to simulate and visualise biological processes of unprecedented complexity. We’re delighted with this award,” says Professor Peter Coveney, principal investigator for the SPICE project from University College London.


The SPICE team convinced the judges with their simulation of DNA strands passing through a cell membrane. Knowledge of this important biological process is crucial for understanding the transfer of genetic information during cell division, and for applications such as the design of high-throughput DNA screening devices. However, it takes place over a much longer timescale than is possible to simulate using conventional computational methods.

“Many biological processes take longer than a nanosecond – that’s what makes them so computationally difficult,” says Dr Shantenu Jha, technical lead on the SPICE team.

SPICE uses technology developed under another UK e-Science project, RealityGrid, to marshal the resources of supercomputers on the UK National Grid Service (NGS) and the US TeraGrid, connected by dedicated high bandwidth optical channels. Even with resources of this grid-of-grids to hand, the simulation is too large for straight computation. SPICE has overcome this obstacle by dividing the simulation into two stages.

In the first, the researcher gets a rough “feel” for the DNA’s progress from the response of a haptic device (joystick) used to pull it through a protein nanopore embedded in the cell membrane. “You try to pull the DNA through the pore and you can feel the strain on it. It’s a very smart way of probing the DNA’s local energetic environment – and it’s fun,” says Dr Jha.

In the second stage, insight gained from the first is used to set the parameters for a set of full-scale simulations. “By doing some smart exploration first, we’re limiting the computation we need for a detailed, rigorous analysis,” says Dr Jha.

Such complex simulations would not be possible without the use of dedicated optical networks to connect supercomputers in the US and UK. The researchers steer the simulation in real time via the haptic device, each snapshot of the simulation requiring several hundred processors and simultaneous high-end compute and visualization resources. Standard packet-switched networks, even with high bandwidth, cannot guarantee sufficient quality of service for such interactivity.

“Without dedicated optical networks in the US, UK and across the Atlantic, SPICE would be impossible. There’s no loss or re-ordering of data which means that we can steer the simulations interactively,” says Professor Coveney. SPICE is one of the first demonstrations of the UK’s new dedicated optical research network, UKLight.

SPICE is jointly funded by the UK Engineering and Physical Sciences Research Council (EPSRC) and the US National Science Foundation (NSF) as one component of a bi-national collaboration to exploit state of the art optical (lambda) networks to tackle scientific problems that would otherwise remain out of reach. Two US projects, NeKTAR and VORTRONICS, are using the same infrastructure to simulate blood flow through the entire network of human arteries and to tackle highly computationally-intensive problems in turbulent fluid dynamics.

Judy Redfearn | alfa
Further information:
http://www.realitygrid.org/Spice/
http://www.rcuk.ac.uk/escience
http://sc05.supercomputing.org/about/home.php

More articles from Science Education:

nachricht Starting school boosts development
11.05.2017 | Max-Planck-Institut für Bildungsforschung

nachricht New Master’s programme: University of Kaiserslautern educates experts in quantum technology
15.03.2017 | Technische Universität Kaiserslautern

All articles from Science Education >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Wafer-thin Magnetic Materials Developed for Future Quantum Technologies

Two-dimensional magnetic structures are regarded as a promising material for new types of data storage, since the magnetic properties of individual molecular building blocks can be investigated and modified. For the first time, researchers have now produced a wafer-thin ferrimagnet, in which molecules with different magnetic centers arrange themselves on a gold surface to form a checkerboard pattern. Scientists at the Swiss Nanoscience Institute at the University of Basel and the Paul Scherrer Institute published their findings in the journal Nature Communications.

Ferrimagnets are composed of two centers which are magnetized at different strengths and point in opposing directions. Two-dimensional, quasi-flat ferrimagnets...

Im Focus: World's thinnest hologram paves path to new 3-D world

Nano-hologram paves way for integration of 3-D holography into everyday electronics

An Australian-Chinese research team has created the world's thinnest hologram, paving the way towards the integration of 3D holography into everyday...

Im Focus: Using graphene to create quantum bits

In the race to produce a quantum computer, a number of projects are seeking a way to create quantum bits -- or qubits -- that are stable, meaning they are not much affected by changes in their environment. This normally needs highly nonlinear non-dissipative elements capable of functioning at very low temperatures.

In pursuit of this goal, researchers at EPFL's Laboratory of Photonics and Quantum Measurements LPQM (STI/SB), have investigated a nonlinear graphene-based...

Im Focus: Bacteria harness the lotus effect to protect themselves

Biofilms: Researchers find the causes of water-repelling properties

Dental plaque and the viscous brown slime in drainpipes are two familiar examples of bacterial biofilms. Removing such bacterial depositions from surfaces is...

Im Focus: Hydrogen Bonds Directly Detected for the First Time

For the first time, scientists have succeeded in studying the strength of hydrogen bonds in a single molecule using an atomic force microscope. Researchers from the University of Basel’s Swiss Nanoscience Institute network have reported the results in the journal Science Advances.

Hydrogen is the most common element in the universe and is an integral part of almost all organic compounds. Molecules and sections of macromolecules are...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Dortmund MST Conference presents Individualized Healthcare Solutions with micro and nanotechnology

22.05.2017 | Event News

Innovation 4.0: Shaping a humane fourth industrial revolution

17.05.2017 | Event News

Media accreditation opens for historic year at European Health Forum Gastein

16.05.2017 | Event News

 
Latest News

New approach to revolutionize the production of molecular hydrogen

22.05.2017 | Materials Sciences

Scientists enlist engineered protein to battle the MERS virus

22.05.2017 | Life Sciences

Experts explain origins of topographic relief on Earth, Mars and Titan

22.05.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>