Back to Table of contents

Primeur weekly 2012-04-23

Exascale supercomputing

Heading toward Exascale: ISC'12 sessions to look at global progress, plans and programmes ...

The Cloud

VENUS-C - Empowering emergency crews with the Cloud ...

Amazon Web Services introduces AWS Marketplace where customers can find and buy pre-configured software for the AWS Cloud ...

EMC introduces VSPEX proven infrastructure ...

Cisco Intelligent Automation for Cloud selected by Data#3 for its Cloud services in Australia ...

Netelligent introduces Desktop as a Service (DaaS) powered by Desktone, Cisco and NetApp ...

Cycle Computing ramps global 50,000-core cluster for Schrodinger molecular research ...

SoftLayer adds high-performance computing to global platform ...

Desktop Grids

IBM enables water quality predictions for major waterways in partnership between World Community Grid and University of Virginia ...

EuroFlash

Russia turns to HPC to revive national defense industry ...

PRACE celebrates 2nd anniversary and launches 5th Call for Proposals ...

PRACE to issue Call for Proposals for 5th Project Access and Multi-year Access (Tier-0) and synchronized Call for DECI-9 (Tier-1) ...

SARA to launch tender for new Dutch national supercomputer ...

Innovative Nordic supercomputer in Iceland ...

First description of a triple DNA helix in a vacuum ...

Queen's aims to change the future of car manufacturing with supercomputer ...

The final frontier: space centre launch facility chooses projectiondesign ...

Data mining opens the door to predictive neuroscience ...

USFlash

Cray names William C. Blake Senior Vice President and Chief Technology Officer ...

DataDirect Networks lowers Big Data total cost of ownership & deployment with new NAS scaler file storage system enhancements ...

Lustre made simple by DataDirect Networks ...

CSIRO chooses Xenon for supercomputing upgrade ...

SDSC announces Center of Excellence for Predictive Analytics ...

Baylor doctoral student awarded National Science Foundation Fellowship ...

12 companies join Stanford and Berkeley to launch new Open Networking Research Center ...

First description of a triple DNA helix in a vacuum

18 Apr 2012 Barcelona - A team of researchers at the Institute for Research in Biomedicine (IRB Barcelona) and the Barcelona Supercomputing Center (BSC) have managed for the first time to extract trustworthy structural information from a triple helix DNA in gas phase, that is to say in conditions in which DNA is practically in a vacuum. The study has appeared in theJournal of the American Chemical Society(JACS), one of the journals with greatest impact in chemistry.

"Until now these special DNA structures were almost impossible to detect and it was not known whether they preserved structural memory in solution when they were evaporated. With this study we have characterized this structure and demonstrated that it maintains a surprising memory of its previous biological environment, aqueous solution, in which it is normally very difficult to characterize", explained Modesto Orozco, principal investigator at IRB Barcelona, senior professor at the University of Barcelona and director of Life Sciences at the BSC. Modesto Orozco's team has combined computational simulation techniques with experimental validation through mass spectrometry. This was the last structure pending to complete the atlas of classical DNA structures in gas phase, work that has taken Dr. Orozco's group more than ten years of dedication.

One of the most relevant biomedical consequences of this study is that it could avail the development of the so-called antigen therapy. This therapeutic approach, which is based on DNA triple helix structures, would switch off the activity of the genes involved in a given disease.

"There is still no drug based on gene therapy in the market but several are under development", explained the researcher. One of the main obstacles blocking the availability of these therapies was in the difficulty to experimentally detect these triple helix structures. "Demonstration that the structure is maintained in gas phase will allow these DNA structures to be detected more easily", affirmed Dr. Orozco.

Furthermore, these results pave the way for the implementation of new structural resolution techniques based on the use of x-ray free-electron lasers (X-FEL). The X-FEL is a large scientific facility being built in Germany that produces intense light pulses, similar to a synchrotron. "If our calculations are correct X-FEL could be used to obtain structural data in gas phase about the behaviour of a molecule in its natural biological environment and X-FEL would become a very powerful tool to resolve the structure of macromolecules", Modesto Orozco went on to say.

Computational simulation has been performed using the supercomputer MareNostrum at the BSC while the experimental validation has been undertaken by the Mass Spectrometry Core Facility at IRB Barcelona, the Experimental Bioinformatics Lab (EBL) - a joint IRB Barcelona and BSC facility, and with the collaboration of Valerie Gabelica's group at the University of Liège, Belgium.

Source: Institute for Research in Biomedicine - IRB Barcelona

Back to Table of contents

Primeur weekly 2012-04-23

Exascale supercomputing

Heading toward Exascale: ISC'12 sessions to look at global progress, plans and programmes ...

The Cloud

VENUS-C - Empowering emergency crews with the Cloud ...

Amazon Web Services introduces AWS Marketplace where customers can find and buy pre-configured software for the AWS Cloud ...

EMC introduces VSPEX proven infrastructure ...

Cisco Intelligent Automation for Cloud selected by Data#3 for its Cloud services in Australia ...

Netelligent introduces Desktop as a Service (DaaS) powered by Desktone, Cisco and NetApp ...

Cycle Computing ramps global 50,000-core cluster for Schrodinger molecular research ...

SoftLayer adds high-performance computing to global platform ...

Desktop Grids

IBM enables water quality predictions for major waterways in partnership between World Community Grid and University of Virginia ...

EuroFlash

Russia turns to HPC to revive national defense industry ...

PRACE celebrates 2nd anniversary and launches 5th Call for Proposals ...

PRACE to issue Call for Proposals for 5th Project Access and Multi-year Access (Tier-0) and synchronized Call for DECI-9 (Tier-1) ...

SARA to launch tender for new Dutch national supercomputer ...

Innovative Nordic supercomputer in Iceland ...

First description of a triple DNA helix in a vacuum ...

Queen's aims to change the future of car manufacturing with supercomputer ...

The final frontier: space centre launch facility chooses projectiondesign ...

Data mining opens the door to predictive neuroscience ...

USFlash

Cray names William C. Blake Senior Vice President and Chief Technology Officer ...

DataDirect Networks lowers Big Data total cost of ownership & deployment with new NAS scaler file storage system enhancements ...

Lustre made simple by DataDirect Networks ...

CSIRO chooses Xenon for supercomputing upgrade ...

SDSC announces Center of Excellence for Predictive Analytics ...

Baylor doctoral student awarded National Science Foundation Fellowship ...

12 companies join Stanford and Berkeley to launch new Open Networking Research Center ...