Srinivas Aluru, left, and Steve Nystrom have worked for months to connect cables and cooling hoses and otherwise get Iowa State University’s second supercomputer up to speed. (Credit: Photo by Bob Elbert)

And there’s a lot of raw power in those racks.

Cystorm, a Sun Microsystems machine, boasts a peak performance of 28.16 trillion calculations per second. That’s five times the peak of CyBlue, an IBM Blue Gene/L supercomputer that’s been on campus since early 2006 and uses 2,048 processors to do 5.7 trillion calculations per second.

Aluru, the Ross Martin Mehl and Marylyne Munas Mehl Professor of Computer Engineering and the leader of the Cystorm project, said the new machine also scores high on a more realistic test of a supercomputer’s actual performance: 15.44 trillion calculations per second compared to CyBlue’s 4.7 trillion per second. That measure makes Cystorm 3.3 times more powerful than CyBlue.

Those performance numbers, however, do not earn Cystorm a spot on the TOP500 list of the world’s fastest supercomputers. (When CyBlue went online three years ago, it was the 99th most powerful supercomputer on the list.)

“Cystorm is going to be very good for data-intensive research projects,” Aluru said. “The capabilities of Cystorm will help Iowa State researchers do new, pioneering research in their fields.”

The supercomputer is targeted for work in materials science, power systems and systems biology.

Aluru said materials scientists will use the supercomputer to analyze data from the university’s Local Electrode Atom Probe microscope, an instrument that can gather data and produce images at the atomic scale of billionths of a meter. Systems biologists will use the supercomputer to build gene networks that will help researchers understand how thousands of genes interact with each other. Power systems researchers will use the supercomputer to study the security, reliability and efficiency of the country’s energy infrastructure. And computer engineers will use the supercomputer to build a software infrastructure that helps users make decisions by identifying relevant information sources.

“These research efforts will lead to significant advances in the penetration of high performance computing technology,” says a summary of the Cystorm project. “The project will bring together multiple departments and research centers at Iowa State University and further enrich interdisciplinary culture and training opportunities.”

Joining Aluru on the Cystorm project are five Iowa State researchers: Maneesha Aluru, an associate scientist in electrical and computer engineering and genetics, development and cell biology; Baskar Ganapathysubramanian, an assistant professor and William March Scholar in Mechanical Engineering; James McCalley, the Harpole Professor in Electrical Engineering; Krishna Rajan, a professor of materials science and engineering; and Arun Somani, Anson Marston Distinguished Professor in Engineering and Jerry R. Junkins Endowed Chair of electrical and computer engineering. Steve Nystrom, a systems support specialist for the department of electrical and computer engineering, is the system administrator for Cystorm.

The researchers purchased the computer with a $719,000 grant from the National Science Foundation, $400,000 from Iowa State colleges, departments and researchers, and a $200,000 equipment donation from Sun Microsystems.

Because of Cystorm, the computer company will designate Iowa State a Sun Microsystems Center of Excellence for Engineering Informatics and Systems Biology.

While Cystorm is much more powerful than CyBlue, Aluru said Iowa State’s first supercomputer will still be used by researchers across campus.

“CyBlue will still be around,” Aluru said. “Researchers will use both systems to solve problems. Both systems enhance the research capabilities of Iowa State.”

The new method to create a tiny quantum sized black hole would allow researchers to better understand what physicist Stephen Hawking proposed more than 35 years ago: black holes are not totally void of activity; they emit photons, which is now known as Hawking radiation.

“Hawking famously showed that black holes radiate energy according to a thermal spectrum,” said Paul Nation, an author on the paper and a graduate student at Dartmouth. “His calculations relied on assumptions about the physics of ultra-high energies and quantum gravity. Because we can’t yet take measurements from real black holes, we need a way to recreate this phenomenon in the lab in order to study it, to validate it.”

In this paper, the researchers show that a magnetic field-pulsed microwave transmission line containing an array of superconducting quantum interference devices, or SQUIDs, not only reproduces physics analogous to that of a radiating black hole, but does so in a system where the high energy and quantum mechanical properties are well understood and can be directly controlled in the laboratory. The paper states, “Thus, in principle, this setup enables the exploration of analogue quantum gravitational effects.”

“We can also manipulate the strength of the applied magnetic field so that the SQUID array can be used to probe black hole radiation beyond what was considered by Hawking,” said Miles Blencowe, another author on the paper and a professor of physics and astronomy at Dartmouth.

This is not the first proposed imitation black hole, says Nation. Other proposed analogue schemes have considered using supersonic fluid flows, ultracold bose-einstein condensates and nonlinear fiber optic cables. However, the predicted Hawking radiation in these schemes is incredibly weak or otherwise masked by commonplace radiation due to unavoidable heating of the device, making the Hawking radiation very difficult to detect. “In addition to being able to study analogue quantum gravity effects, the new, SQUID-based proposal may be a more straightforward method to detect the Hawking radiation,” says Blencowe.

In addition to Nation and Blencowe, other authors on the paper include Alexander Rimberg at Dartmouth and Eyal Buks at Technion in Haifa, Israel.

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A diagram (above) and real-life image (inset) of a carbon nanotube. (Credit: CARDEQ Project (www.cardeq.eu))

Carbon nanotubes are ultra-thin fibres of carbon and a nanotechnologist’s dream.

They are made from thin sheets of carbon only one atom thick – known as graphene – rolled into a tube only a few nanometres across. Even the thickest is more than a thousand times thinner than a human hair.

Interest in carbon nanotubes blossomed in the 1990s when they were found to possess impressive characteristics that make them very attractive raw materials for nanotechnology of all kinds.

“They have unique properties,” explains Professor Pertti Hakonen of Helsinki University of Technology. “They are about 1000 times stronger than steel and very good thermal conductors and good electrical conductors.”

Hakonen is coordinator of the EU-funded CARDEQ project (http://www.cardeq.eu/) which is exploiting these intriguing materials to build a device sensitive enough to measure the masses of atoms and molecules.

Vibrating strings

A carbon nanotube is essentially an extremely thin, but stiff, piece of string and, like other strings, it can vibrate. As all guitar players know, heavy strings vibrate more slowly than lighter strings, so if a suspended carbon nanotube is allowed to vibrate at its natural frequency, that frequency will fall if atoms or molecules become attached to it.

It sounds simple and the idea is not new. What is new is the delicate sensing system needed to detect the vibration and measure its frequency. Some nanotubes turn out to be semiconductors, depending on how the graphene sheet is wound, and it is these that offer the solution that CARDEQ has developed.

Members of the consortium have taken the approach of building a semiconducting nanotube into a transistor so that the vibration modulates the current passing through it. “The suspended nanotube is, at the same time, the vibrating element and the readout element of the transistor,” Hakonen explains.

“The idea was to run three different detector plans in parallel and then select the best one,” he says. “Now we are down to two. So we have the single electron transfer concept, which is more sensitive, and the field effect transistor concept, which is faster.”

Single atoms

Last November, CARDEQ partners in Barcelona reported that they had sensed the mass of single chromium atoms deposited on a nanotube. But Hakonen says that even smaller atoms, of argon, can now be detected, though the device is not yet stable enough for such sensitivity to be routine. “When the device is operating well, we can see a single argon atom on short time scales. But then if you measure too long the noise becomes large.”

CARDEQ is not alone in employing carbon nanotubes as mass sensors. Similar work is going on at two centres in California – Berkeley and Caltech – though each has adopted a different method to measuring the mass.

All three groups have announced they can perform mass detection on the atomic level using nanotubes, but CARDEQ researchers provided the most convincing data with a clear shift in the resonance frequency.

But a single atom is nowhere near the limit of what is possible. Hakonen is confident they can push the technology to detect the mass of a single nucleon – a proton or neutron.

“It’s a big difference,” he admits, “but typically the improvements in these devices are jump-like. It’s not like developing some well-known device where we have only small improvements from time to time. This is really front-line work and breakthroughs do occur occasionally.”

Biological molecules

If the resolution can be pared down to a single nucleon, then researchers can look forward to accurately weighing different types of molecules and atoms in real time.

It may then become possible to observe the radioactive decay of a single nucleus and to study other types of quantum mechanical phenomena.

But the real excitement would be in tracking chemical and biological reactions involving individual atoms and molecules reacting right there on the vibrating nanotube. That could have applications in molecular biology, allowing scientists to study the basic processes of life in unprecedented detail. Such practical applications are probably ten years away, Hakonen estimates.

“It will depend very much on how the technology for processing carbon nanotubes develops. I cannot predict what will happen, but I think chemical reactions in various systems, such as proteins and so on, will be the main applications in the future.”

The CARDEQ project received funding from the FET-Open strand of the EU’s Sixth Framework Programme for ICT research.

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This artist’s concept shows the core of an active galaxy, where a feeding supermassive black hole drives oppositely directed particle jets. (Credit: ESA/NASA/AVO/Paolo Padovani)

“Compton showed us that two classes of active galaxies emitted gamma rays — blazars and radio galaxies,” said Luigi Foschini at Brera Observatory of the National Institute for Astrophysics in Merate, Italy. “With Fermi, we’ve found a third — and opened a new window in the field.”

In the Beam

Active galaxies are those with unusually bright centers that show evidence of particle acceleration to speeds approaching that of light itself. In 1943, astronomer Carl Seyfert described the first two types of active galaxy based on the width of spectral lines, a tell-tale sign of rapid gas motion in their cores. Today, astronomers recognize many additional classes, but they now believe these types represent the same essential phenomenon seen at different viewing angles.

At the center of each active galaxy sits a feeding black hole weighing upwards of a million times the sun’s mass. Through processes not yet understood, some of the matter headed for the black hole blasts outward in fast, oppositely directed particle jets. For the most luminous active-galaxy classes — blazars — astronomers are looking right down the particle beam.

Using Fermi’s Large Area Telescope (LAT), Foschini and his colleagues detected gamma rays from a Seyfert 1 galaxy cataloged as PMN J0948+0022, which lies 5.5 billion light-years away in the constellation Sextans. Splitting the light from this source into its component colors shows a spectrum with narrow lines, which indicates slower gas motions and argues against the presence of particle jet.

“But, unlike ninety percent of narrow-line Seyfert 1 galaxies, PMN J0948 also produces strong and variable radio emission,” said Gino Tosti, who leads the Fermi LAT science group studying active galaxies at the University and National Institute of Nuclear Physics in Perugia, Italy. “This suggested the galaxy was indeed producing such a jet.”

“The gamma rays seen by Fermi’s LAT seal the deal,” said team member Gabriele Ghisellini, a theorist at Brera Observatory. “They confirm the existence of particle acceleration near the speed of light in these types of galaxies.” The findings will appear in the July 10 issue of The Astrophysical Journal.

“We are sifting through Fermi LAT data for gamma rays from more sources of this type,” Foschini said. “And we’ve begun a multiwavelength campaign to monitor PMN J0948 across the spectrum, from radio to gamma rays.”

Flare Up

Another case where Fermi sees something new involves NGC 1275, a massive Seyfert galaxy much closer to home. Also known as Perseus A, one of the sky’s loudest radio sources, NGC 1275 lies at the center of the Perseus cluster of galaxies about 225 million light-years away.

The Compton observatory’s high-energy EGRET instrument never detected gamma rays from NGC 1275, although it was detected by another instrument sensitive to lower-energy gamma rays. But Fermi’s LAT clearly shows the galaxy to be a gamma-ray source at the higher energies for which EGRET was designed. “Fermi sees this galaxy shining with gamma rays at a flux about seven times higher than the upper limit of EGRET,” said Jun Kataoka at Waseda University in Tokyo. “If NGC 1275 had been this bright when EGRET was operating, it would have been seen.”

This change in the galaxy’s output suggests that its particle beam was either inactive or much weaker a decade ago. Such changes clue astronomers into the size of the emitting region. “The gamma rays in NGC 1275 must arise from a source no more than two light-years across,” said Teddy Cheung at NASA’s Goddard Space Flight Center in Greenbelt, Md. “That means we’re seeing radiation from the heart of the galaxy — near its black hole — as opposed to emission by hot gas throughout the cluster.”

The Fermi team plans to monitor the galaxy to watch for further changes. The results of the study will appear in the July 1 issue of The Astrophysical Journal.

NASA’s Fermi Gamma-ray Space Telescope is an astrophysics and particle physics partnership mission, developed in collaboration with the U.S. Department of Energy and important contributions from academic institutions and partners in France, Germany, Italy, Japan, Sweden, and the U.S.

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Bacterial assassins Iron-oxide nanoparticles developed at Brown University target an infected prosthesis, penetrate a bacterial film on the implant’s surface and thwart the colony by killing the bacteria. The nanoparticles also are believed to help natural bone cell growth. (Credit: Erik Taylor/Brown University)

Inside the body, the bacteria multiply on the implant’s surface and then build a slimy, protective film to shield the colony from antibiotics. According to a study in the journal Clinical Infectious Diseases, up to 2.5 percent of hip and knee implants alone in the United States become infected, affecting thousands of patients, sometimes fatally.

More ominously, there is no effective antidote for infected implants. The only way to get rid of the bacteria is to remove the implant. “There is no [easy] solution,” said Thomas Webster, a biomedical engineer at Brown University.

Now, Webster and Brown graduate student Erik Taylor have created a nano-sized headhunter that zeroes in on the implant, penetrates S. epidermidis’s defensive wall and kills the bacteria. The finding, published in the International Journal of Nanomedicine, is the first time iron-oxide nanoparticles have been shown to eliminate a bacterial infection on an implanted prosthetic device.

In lab tests, Taylor, the lead author, and Webster, associate professor of engineering and orthopaedics, noted that up to 28 percent of the bacteria on an implant had been eliminated after 48 hours by injecting 10 micrograms of the nanoparticle agents. The same dosage repeated three times over six days destroyed essentially all the bacteria, the experiments showed.

The tests show “there will be a continual killing of the bacteria until the film is gone,” said Webster, who is editor-in-chief of the peer-reviewed journal in which the paper appears.

A surprising added benefit, the scientists learned, is the nanoparticles’ magnetic properties appear to promote natural bone cell growth on the implant’s surface, although this observation needs to be tested further.

To carry out the study, the researchers created iron-oxide particles (they call them “superparamagnetic”) with an average diameter of eight nanometers. They chose iron oxide because the metallic properties mean the particles can be guided by a magnetic field to the implant, while its journey can be tracked using a simple magnetic technique, such as magnetic resonance imaging (MRI). Moreover, previous experiments showed that iron seemed to cause S. epidermidis to die, although researchers are unsure why. (Webster said it may be due to iron overload in the bacteria’s cell.)

Once the nanoparticles arrive at the implant, they begin to penetrate the bacterial shield. The researchers are studying why this happens, but they believe it’s due to magnetic horsepower. In the tests, the researchers positioned a magnet below the implant, producing a strong enough field to force the nanoparticles above to filter through the film and proceed to the implant, Webster explained.

The particles then penetrate the bacterial cells because of their super-small size. A micron-sized particle, a thousand times larger than a nanoparticle, would be too large to penetrate the bacterial cell wall.

The researchers plan to test the iron-oxide nanoparticles on other bacteria and then move on to evaluating the results on implants in animals. The research was funded by the private Hermann Foundation Inc. In addition, Taylor’s tuition and stipend are funded through the National Science Foundation GK-12 program.

LSU’s Wave-Current-Surge Information System for Coastal Louisiana now offers graphic, easy-to-understand model outputs projecting wave height, current depths and tracks, salinity ratios and water temperature measurements that not only provide state-of-the-art guidance to emergency management officials, but also give federal and state agencies new and improved ways to test their own modeling accuracy. (Credit: WAVCIS / Powered by Google Earth / Map data (c) 2009 Tele Atlas)

Drawing from a pool of scientific talent at the university, across the nation and Europe, WAVCIS now offers graphic, easy-to-understand model outputs projecting wave height, current depths and tracks, salinity ratios and water temperature measurements that not only provide state-of-the-art guidance to emergency management officials, but also give federal and state agencies such as the United States Navy, National Oceanic and Atmospheric Administration, the National Weather Service, National Hurricane Center and Louisiana Department of National Resources new and improved ways to test their own modeling accuracy.

“I believe WAVCIS is likely the most comprehensive program in the entire nation,” said Gregory Stone, director of both the WAVCIS program and the Coastal Studies Institute and also the James P. Morgan Distinguished Professor at LSU. “We now have 60 to 84 hour advance forecasting capabilities due to our satellite link-ups with NOAA and our supercomputing capabilities. Because of these advancements, we are in much better shape for the 2009 hurricane season to provide valuable information than we were in the past.”

WAVCIS operates by deploying equipment in the depths of the Gulf of Mexico. Currently, they have sensors attached to numerous oil platforms. Instruments are attached to towers on the platforms and allow meteorological measurements – air temperature, wind speed and direction, visibility – to be made; state-of-the-art oceanographic sensors are placed underwater and on the sea floor.

Advanced technology, including the Acoustic Doppler Profiler, an instrument that Stone’s group has helped perfect in real time with the private sector, provides a very comprehensive overview of current velocities from the sea bed to the surface in addition to wave conditions on the sea surface.

“In a normal weather situation, WAVCIS links with the satellites and retrieves up-to-date information every hour. This information is then immediately supplied to computer models at LSU’s WAVCIS lab and the data are posted on the WAVCIS Web site,” said Stone. “However, during a hurricane or other extreme weather events, we have the capacity to increase the frequency of these link-ups. We won’t have the luxury of waiting an hour during the approach of a hurricane – it’s critical that we can see what’s going on out there in 15 to 30 minute intervals in order to accurately assess the situation.”

The WAVCIS group, a component of LSU’s world famous Coastal Studies Institute, has sensors all throughout the Gulf of Mexico. In fact, most of the equipment used by WAVCIS is developed and maintained in-house at the Coastal Studies Institute’s fabrication shop. Through a close and reciprocal relationship with NOAA’s National Data Buoy Center, WAVCIS can also access that group’s sensors, giving the system a gulf-wide look at emerging trends in waves and currents, which can be very important during the approach of a tropical cyclone.

“Things such as the maximum wave height, wind speeds and storm surge, will play an integral role in issues concerning public safety,” said Stone. “For example, the development of certain currents, such as the Loop current in the Gulf of Mexico, allows for almost immediate intensification of storms. That’s why having an easy-to-understand and comprehensive end product was so important to my team and the Coastal Studies Institute, for example the Earth Scan Lab and the Southern Regional Climate Center, during the development stages. When it’s crunch time and people are nervous, we want the facts to be clear.”

In addition to being a very active research group and providing graduate and undergraduate students with hands-on opportunities in an internationally-acclaimed lab, WAVCIS also provides other entities with the opportunity to test their own modeling accuracy. “By looking at the models they developed and then comparing them to ours and our measurements offshore, they can determine how accurate their models currently are and go about fine-tuning if necessary. This strengthens our knowledge of the oceanographic and coastal environment. Given the vulnerability of, for example coastal Louisiana and the oil and gas infrastructure in the Gulf of Mexico to erosion and hurricane impacts, it is important that the Federal Government, State of Louisiana and the oil and gas industry continue to support this effort,” Stone said.

WAVCIS models are available on http://wavcis.csi.lsu.edu/index.asp.

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