Record-breaking supercomputing performance
On November 4, 2004, Department of Energy (DOE) Secretary Spencer Abraham announced that a supercomputer developed for the nation’s Stockpile Stewardship Program (SSP) has attained a record-breaking performance of 70.72 trillion operations per second (teraops) on the industry standard LINPACK benchmark. Although the supercomputer is running at one-quarter its final size for DOE, the BlueGene/L beta system is already asserting U.S. leadership in supercomputing. The product of a multiyear research and development partnership between DOE’s National Nuclear Security Administration and IBM, BlueGene/L will support the SSP’s mission to ensure the safety, security, and reliability of the nation’s nuclear weapons stockpile without underground nuclear testing.
Secretary Abraham, who has since stepped down, said, “The delivery of the first quarter of the Blue/GeneL system to Lawrence Livermore this month shows how a partnership between government and industry can effectively advance national agendas in science, technology, security, and industrial competitiveness. High-performance computing is the backbone of the nation’s science and technology enterprise, which is why the department has made supercomputing a top priority investment. Breakthroughs in applied scientific research are possible with the tremendous processing capabilities provided by extremely scalable computer systems such as BlueGene/L.”
The final BlueGene/L system will exceed the performance of the Japanese Earth Simulator by a factor of about nine while requiring one-seventh as much electrical power and one-fourteenth the floor space.
Contact: Dona Crawford (925) 422-1985 (firstname.lastname@example.org).
Genome reveals role in mediating global warming
The DOE Joint Genome Institute (JGI) has generated the first genetic instruction manual for a diatom. The diatom belongs to a family of microscopic ocean algae that are among Earth’s most prolific carbon dioxide assimilators. This work, published in the October 1, 2004, issue of Science, has yielded insight on how the creature Thalassiosira pseudonana absorbs the major greenhouse gas carbon dioxide in amounts comparable to all the world’s tropical rain forests combined. Don Rokhsar, one of the coauthors and head of computational genomics at JGI, says, “Now that we have a glimpse at the inner workings of diatoms, we’re better positioned to understand the role they and other phytoplankton play in mediating global warming.”
Virginia Armbrust, a University of Washington associate professor of oceanography and the paper’s lead author, says that the growth of single-cell diatoms accounts for as much as 40 percent of the 50 to 55 billion tons of organic carbon produced each year in the sea. The diatoms are just 3 or 4 micrometers wide and are encased by a frustule, a rigid cell wall delicately marked with pores in patterns distinctive enough for scientists to tell the species apart. “We discovered they have a urea cycle, something no one ever suspected,” says Ambrust. A urea cycle is a nitrogen waste pathway that has been found in animals but has never before been seen in a diatom. Nitrogen is crucial for diatom growth and is often in short supply in seawater.
Forty-six researchers from 26 institutions are working on the project, including four from Livermore.
Contact: David E. Gilbert (925) 296-5643 (email@example.com).
Agreement to develop an artificial retinal device
A consortium of DOE national laboratories, including Livermore, and universities has signed an agreement with Second Sight Medical Products, Inc., to jointly develop technology that could restore sight to those who have lost their vision later in life. The Cooperative Research and Development Agreement allows Second Sight of Sylmar, California, to obtain a limited exclusive license for inventions developed during the DOE Retinal Prosthesis Project.
Attached to and functioning as part of the eye’s retina, the retinal prosthesis device promises hope for those with age-related macular degeneration, retinitis pigmentosa, or related diseases where photoreceptors are damaged but the optic nerve and its connections to the brain are still intact. Engineers from Livermore’s Center for Micro and Nanotechnology are developing a flexible silicone-based microelectrode array. The implantable retinal prosthesis is based on a system that converts a video camera signal into a simulation pattern. This pattern can then be applied directly to the intraocular retinal surface. (See S&TR, November 2003, Retinal Prosthesis Provides Hope for Restoring Sight.)
Although the device will not restore full vision, it is expected to provide enough optical resolution for patients to read and recognize fine shapes. The Laboratory’s pioneering use of polydimethlsiloxane (PDMS) allows the microelectrode array to conform to the curved shape of the retina. Courtney Davidson, Livermore’s principal investigator, says, “PDMS is biocompatible, which makes it a good candidate material for long-term implants.”
Contact: Courtney Davidson (925) 423-7168 (firstname.lastname@example.org).