EE Times delivers reports from the University of Massachusetts at Amherst of “observing and measuring the conductivity of long wires, 3 to 5 nanometers in diameter, emanating [what an interesting choice of verbs] from the Geobacter bacteria.” Researchers have known for years of Geobacters ability to metabolize metals from soils and water, applying it to environmental cleanup.

“‘The microbial world never stops surprising us,’ said Aristides Patrinos, associate director of the DOE’s Office of Biological and Environmental Research. ‘This discovery illustrates the continuing relevance of the physical sciences to today’s biological investigations.’”

Find out more from UMass’ Derek Lovely’s team and read the research group’s article (.pdf) in Nature.

The unveiling of the new Pittsburgh Supercomputing Center Cray XT3, called Big Ben, represents another step in the goal of increasing the rate of educational capacity and emerging technologies for computational science especially since its another resource added to the TeraGrid. Sporting 2090 processors, Big Ben is somewhat smaller than its brethren at ORNL. However the ORNL machine proves the XT3 has substantial scalability, having gone from 3700 processors to over 5000 in just a few weeks. CTWatch caught up with HPC Challenge benchmark suite co-developer Dr. Piotr Luszczek and asked him about the new Cray. While discussing differences between the higher end supercomputers and clusters, Luszczek pointed out Cray’s use of AMD processors with Hypertransport technology as an advantage over other machines that rely on some form of PCI and the resulting bottlenecks in processor data throughput. He further stated that

Big Ben’s bandwidth performance is an example of good use of existing technology by Cray since it’s a system that could not be easily replicated with other processors.

More detailed information about Big Ben and PSC can be found here.

The tragedy that befell the shuttle Columbia in 2003 resulted in numerous changes within NASA’s shuttle program. One of these changes, as outlined at SiliconValley.com, is greater intra-agency collaboration within the shuttle program itself. Experts at NASA’s Ames Center in California are now involved in certain aspects of the shuttle program, once reserved for NASA’s Johnson Space Center in Texas and the Kennedy Space Center in Florida. Taking advantage of it’s institutional-wide expertise, NASA now involves all of its centers in shuttle processes. The Ames Center has specifically been called upon to run simulations using it’s supercomputer (the third fastest in the world based on June’s Top500 list), appropriately named Columbia, to test scenarios involving the thermal tiles and other components. Personnel at Ames will also be on call to use the Columbia supercomputer to run immediate simulations during missions to find the best solution to specific problems.

NASA leveraging its overall talent, expertise, and multiple resources for a common goal represents an approach that should be utilized in greater frequency, not only within other agencies, but between separate organizations as well (such as academia and government). Such a paradigm would, in many ways, accelerate the nation’s cyberinfrastructure efforts.

Thanks to SiliconValley.com for the article.

An extensive, ongoing discussion on Slashdot regarding the merits of Itanium. You’ll have to turn on your pure drivel filter, and the discussion often focuses on the consumer aspects. But there’s a lot there, and it was provoked by the status of Itanium on the Top 500 list, so it might be worth a look.

It seems only fitting as hurricane season is well underway that some news about weather forecasting get the spotlight. The Pittsburgh Supercomputing Center, in a multiple partnership led by NOAA, successfully demonstrated never before achieved storm forecasting by producing higher resolution results than currently used forecasting models are capable of. Over a three month period from April to June, PSC utilized a new forecasting model on its Terascale Computing System to generate three forecasts a day over an area of the Great Plains in the midwest. According to Kelvin Droegemeier, director of the Center for Analysis and Prediction of Storms at the University of Oklahoma and one of the partners of the effort,

Results from the spring experiment suggest that the atmosphere may be fundamentally more predictable at the scale of individual storms and especially organized storm systems than previously thought. Real time daily forecasts over such a large area and with such high spatial resolution have never been attempted before.

It’s good to see a parallel software success story as is the case with this new weather modeling system called the Weather Research and Forecasting (WRF) Model, especially given the fact that high performance software development lags well behind the much publicized advances in computing power.

The full story can be found on PSC’s website here.

Technology Review covers the emerging realm of silicon-based optical connections in its current issue.

The take:

[E]xisting optical components, which are made out of such exotic semiconductors as gallium arsenide and indium phosphide, are far too expensive for use in individual computers or even local networks. If you could make optical devices out of silicon, which is cheap and, at least for a company like Intel, easy to manufacture, that would change everything… Companies would likely exploit that capability first by replacing copper connections with optical links in networks. But eventually, silicon photonics might also replace copper wires between processors within a single chip.

Pat Gelsinger, a senior VP at Intel, has a vision: “Silicon to us, it’s maybe not a religious experience, but it’s pretty close. Silicon has proven cost effective, scalable, durable, manufacturable and has all sorts of other wonderful characteristics… Today, optics is a niche technology. Tomorrow it’s the mainstream of every chip that we build.”