The day may be getting a little closer when robots will perform surgery on patients in dangerous situations or in remote locations, such as on the battlefield or in space, with minimal human guidance.

Engineers at Duke University believe that the results of feasibility studies conducted in their laboratory represent the first concrete steps toward achieving this space age vision of the future. Also, on a more immediate level, the technology developed by the engineers could make certain contemporary medical procedures safer for patients, they said.

For their experiments, the engineers started with a rudimentary tabletop robot whose “eyes” used a novel 3-D ultrasound technology developed in the Duke laboratories. An artificial intelligence program served as the robot’s “brain” by taking real-time 3-D information, processing it, and giving the robot specific commands to perform.

“In a number of tasks, the computer was able to direct the robot’s actions,” said Stephen Smith, director of the Duke University Ultrasound Transducer Group and senior member of the research team. “We believe that this is the first proof-of-concept for this approach. Given that we achieved these early results with a rudimentary robot and a basic artificial intelligence program, the technology will advance to the point where robots — without the guidance of the doctor — can someday operate on people.”

The results of a series of experiments on the robot system directing catheters inside synthetic blood vessels was published online in the journal IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control. A second study, published in April in the journal Ultrasonic Imaging, demonstrated that the autonomous robot system could successfully perform a simulated needle biopsy.

Advances in ultrasound technology have made these latest experiments possible, the researchers said, by generating detailed, 3-D moving images in real-time.

The Duke laboratory has a long track record of modifying traditional 2-D ultrasound — like that used to image babies in utero — into the more advanced 3-D scans. After inventing the technique in 1991, the team also has shown its utility in developing specialized catheters and endoscopes for real-time imaging of blood vessels in the heart and brain.

In the latest experiment, the robot successfully performed its main task: directing a needle on the end of the robotic arm to touch the tip of another needle within a blood vessel graft. The robot’s needle was guided by a tiny 3-D ultrasound transducer, the “wand” that collects the 3-D images, attached to a catheter commonly used in angioplasty procedures.

“The robot was able to accurately direct needle probes to target needles based on the information sent by the catheter transducer,” said John Whitman, a senior engineering student in Smith’s laboratory and first author on both papers. “The ability of the robot to guide a probe within a vascular graft is a first step toward further testing the system in animal models.”

While the research will continue to refine the ability of robots to perform independent procedures, the new technology could also have more direct and immediate applications.

“Currently, cardiologists doing catheter-based procedures use fluoroscopy, which employs radiation, to guide their actions,” Smith said. “Putting a 3-D ultrasound transducer on the end of the catheter could provide clearer images to the physician and greatly reduce the need for patients to be exposed to radiation.”

In the earlier experiments, the tabletop robot arm successfully touched a needle on the arm to another needle in a water bath. Then it performed a simulated biopsy of a cyst, fashioned out of a liquid-filled balloon in a medium designed to simulate tissue.

“These experiments demonstrated the feasibility of autonomous robots accomplishing simulated tasks under the guidance of 3-D ultrasound, and we believe that it warrants additional study,” Whitman said.

The researchers said that adding this 3-D capability to more powerful and sophisticated surgical robots already in use at many hospitals could hasten the development of autonomous robots that could perform complex procedures on humans.

[Richard Merritt @ Duke University]

An undergraduate student at Rensselaer Polytechnic Institute has learned very quickly that a spoonful of sugar really does help the medicine go down. In fact, with his invention, the sugar may actually be the medicine.

Among the most important and complex molecules in the human body, sugars control not just metabolism but also how cells communicate with one another. Graduating senior Jeffery Martin has put his basic knowledge of sugars to exceptional use by creating a lab-on-a-chip device that builds complex, highly specialized sugar molecules, mimicking one of the most important cellular structures in the human body — the Golgi Apparatus.

“Almost completely independently he has been able to come closer than researchers with decades more experience to creating an artificial Golgi,” said Robert Linhardt, the Ann and John H. Broadbent Jr. ‘59 Senior Constellation Professor of Biocatalysis and Metabolic Engineering at Rensselaer and Martin’s adviser. “He saw a problem in the drug discovery process and almost instantly devised a way to solve it.”

Cells build sugars in a cellular organelle known as the Golgi Apparatus. Under a microscope, the Golgi looks similar to a stack of pancakes. The strange-looking organelle finishes the process of protein synthesis by decorating the proteins with highly specialized arrangements of sugars. The final sugar-coated molecule is then sent out into the cell to aid in cell communication and to help determine the cell’s function in the body.

Martin’s artificial Golgi functions in a surprisingly similar way to the natural Golgi, but he gives the ancient organelle a very high-tech makeover. His chip looks similar to a miniature checker board where sugars, enzymes, and other basic cell materials are suspended in water and can be transported and mixed by applying electric currents to the destination squares on the checker board. Through this process sugars can be built in an automated fashion where they are exposed to a variety of enzymes found in the natural Golgi. The resulting sugars can then be tested on living cells either on the chip or in the lab to determine their effects. With the chip’s ability to process many combinations of sugars and enzymes, it could help researchers quickly uncover new sugar-based drugs, according to Martin.

Scientists have known for years that certain sugars can serve as extremely beneficial therapeutics for humans. One well-known example is heparin, which is among the most widely used drugs in the world. Heparin is formed naturally in the Golgi organelle in cells of the human body as well as in other animals like pigs. Heparin acts as an anticoagulant preventing blood clots, which makes it a good therapeutic for heart, stroke, and dialysis patients.

The main source of heparin is currently the intestines of foreign livestock and, as recent news reports highlight, the risk of contamination from such sources is high. So researchers are working around the clock to develop a safer, man-made alternative to the drug that will prevent outside contamination. A synthetic alternative would build the sugar from scratch, helping eliminate the possibility of contamination he explained.

“I am very grateful to have the privilege of working with Dr. Linhardt who has discovered the recipe to make fully synthetic heparin,” Martin said. “Because we know the recipe, I am going to use it as a model to test the device. If our artificial Golgi can build fully functional heparin, we can then use the artificial organelle to produce many different sugar variants by altering the combination of enzymes used to synthesize them. Another great thing about these devices is that they are of microscale size, so that if needed we could fill an entire room with them to increase throughput for drug discovery.”

There are millions of possible sugar combinations that can be formed and scientists currently only know the function of very few of them like heparin. “Since it is known that these types of sugars play a part in many important biological processes such as cell growth, cell differentiation, blood coagulation, and viral defense mechanisms, we feel that that this artificial Golgi will help our team to develop a next generation of sugar-based drugs, known as glycotheraputics,” Martin said. “We are going to start making new combinations and we simply don’t know what we are going to find. We could find a sugar whose signal blocks the spread of cancer cells or initiates the differentiation of stem cells. We just don’t know.”

Martin, a Barry M. Goldwater Scholar and native of the small town of Boylston, Mass., is graduating from Rensselaer on May 17, 2008 with a nearly perfect GPA. He plans to continue on at Rensselaer as a graduate student, working with Linhardt to test and further develop his artificial Golgi.

[Gabrielle DeMarco @ Rensselaer Polytechnic Institute]

Research led by Iowa State University limnologist, or lake scientist, John Downing finds that ponds around the globe could absorb as much carbon as the world’s oceans.

Professor Downing found that constructed ponds and lakes on farmland in the United States bury carbon at a much higher rate than expected; as much as 20-50 times the rate at which trees trap carbon. In addition, ponds were found to take up carbon at a higher rate than larger lakes.

“Aquatic ecosystems play a disproportionately large role in the global carbon budget,” Downing said. “Despite being overlooked in the past, it’s small bodies of water that are important because they take up carbon at a high rate and there are more of them than previously thought. The combined effect is that farm ponds could be burying as much carbon as the world’s oceans, each year.”

Ponds capture carbon in two main ways:

The research estimated there are 304 million natural lakes and ponds in the world, covering an area of 4.2 million square kilometers, twice the area previously thought. As many as 90 percent of these water bodies are one hectare (two acres) or less in area.

Downing’s research team published its most recent findings in the Feb. 15 issue of the journal Global Biogeochemical Cycles in a paper titled, “Sediment organic carbon burial in agriculturally eutrophic impoundments over the last century.” The team included members from Europe, the United States and Canada. The work was sponsored by the National Center for Ecological Analysis and Synthesis and the Iowa Department of Natural Resources.

Downing has presented invited seminars on this research to the International Society of Limnology, the American Society of Limnology and Oceanography, and at several major research institutions in North America and Europe. Most recently, he was invited to discuss his research by the Pond Conservation, a charity in the United Kingdom dedicated to creating and protecting ponds and the wildlife they support. He will spoke today at University College London. An upcoming presentation is scheduled for the annual meeting of the European Pond Conservation Network in Valencia, Spain.

Jeremy Biggs, Pond Conservation director of policy and research, said the research has exciting implications. “It may be that ponds will be the modern equivalent of the swamps that formed coal in the past. But before we all rush into making ponds to trap carbon we need to do some basic research here in the UK. If the rate of carbon uptake in ponds in Europe is the same as that found in the USA study, we may well have discovered an important new natural way of trapping carbon,” he said.

Downing’s ongoing research, partnering with the United States Geological Survey, and his contributions to the Iowa Lakes Survey will investigate the role of small Iowa lakes in the absorption of atmospheric carbon dioxide and other important gases such as methane.

[John Downing @ Iowa State University]

High gasoline prices could lead to a dramatic saving in US greenhouse-gas emissions. That’s the conclusion of economists in the US, who suggest high fuel prices are turning consumers off SUVs and onto smaller, more fuel-efficient vehicles.

What’s more, car owners are predicted to cut back on driving in order to save money. Together, these changes in consumer behaviour could make an important dent in the US contribution to global warming, reducing annual carbon dioxide emissions by tens of millions of tonnes per year. The impact will be dramatic, says Chris Knittel, an economist at the University of California, Davis, who was involved in one of the studies.

The changes are being driven by record fuel prices in the US, where, at the end of April, the average price of gasoline stood at $3.65 per gallon, 20 percent more than in January and treble the price of a decade ago. Until recently, these increases did not seem to be having a consistent effect on the car market and fuel use. Though sales of SUVs in the US have been falling over the past few years, this decline has come on the back of years of rapid growth, and overall gasoline consumption has been increasing every year since 1991.

That could be about to change. Knittel and colleagues looked at data on 1.4 million car purchases over the past 10 years, comparing sales patterns with gas prices. They found that sales of the least fuel-efficient cars, such as SUVs and pick-up trucks, fell by 13 percent for every $1 per gallon increase in the price of gasoline. The biggest SUVs suffered the most, with sales dropping by over 25 percent for every dollar by which the gas price rose. And for every $1 hike in gas prices there was a corresponding 17 percent sales boost for the most efficient vehicles, such as compact cars and hybrids. Knittel estimates that over about a decade, such changes in buying habits could cut the amount of gasoline used by US drivers by around 7 percent for every $1 increase in its price.

Knittel’s findings, presented last month at the University of California Energy Institute in Berkeley, are in broad agreement with those of economist Kenneth Small of the University of California, Irvine. Small looked at data on US fuel consumption and prices over the past 40 years, and projected last year that the recent doubling in fuel prices would quickly lead to a 4 percent drop in the total mileage covered on the roads. In the longer term, as drivers continue to react to rising prices, he projects the size of the reduction will grow to around 20 percent (The Energy Journal, vol 28, p 25).

This would lead to a substantial reduction in carbon emissions. Small says that a $1 per gallon rise in gasoline prices, roughly that seen over the past two years, will result in motorists using 14 percent less fuel in the long term. That would avoid the release of some tens of millions of tonnes of CO2 per year, equivalent to roughly 2 percent of the country’s greenhouse-gas emissions for 2006. That is a hugely significant drop, close to the level of cuts that some nations are required to make under the Kyoto protocol.

Small’s prediction comes with major caveats, however. Gasoline prices are not expected to return to the lows of a decade ago, but could fall by 10 or 20 percent in coming years. And any US economic recovery will boost fuel consumption, partly through raising incomes, which would dilute the pressure on motorists to drive less. So while expensive fuel will rein in consumption, Small and other economists question whether this will be enough to cause an overall fall in emissions from cars.

It is also possible that politics will intervene before any of these effects has a chance to kick in. Presidential hopefuls John McCain and Hillary Clinton have reacted to consumer protests over soaring fuel prices by declaring that they would suspend federal gasoline taxes. “It’s a fantastically stupid idea,” says Roberton Williams, an economist at the University of Texas at Austin.

“But people don’t like high gas taxes, so it’s popular.”

[Claire Bowles @ New Scientist]

When students have the opportunity to participate in “Socratic seminars” on a regular basis, a different classroom culture evolves. The students collaborate more and more voices are heard. The students develop their thinking skills in a cooperative and investigative atmosphere. This is shown in a new dissertation in Pedagogy by Ann S. Pihlgren at the Stockholm University in Sweden.

The Socratic dialogue is a particular way of developing children’s, as well as adults’, thinking skills through cooperative dialogue where significant human ideas and values are discussed. By participating in Socratic seminars regularly every other week, preschool children and older students develop their thinking skills. The seminars address literature and art work, with questions such as these: is Pippi Longstocking a good friend, is Jack stupid or smart when he sells his mother’s cow for some beans, or are we born good or evil? In the beginning the students have difficulty expressing their thoughts, but with time their ability to express themselves and to examine ideas critically and logically develops.

The study included seven groups of children, five to sixteen years old. The groups were filmed during three years of philosophizing in the classroom and the films were analyzed. The interaction in the classroom was positively influenced, according to Ann S Pihlgren. The teacher dominated less, more students spoke and the students gradually took over the responsibilities of the teacher to promote exploration in the dialogue. The ability to use the Socratic seminar is learned by students and teachers through practice and by testing the rules of the seminar. The students construct a supportive group culture through their silent interaction, where gestures, glances, and body language are used to show not only support or sympathy for each other, but also cooperation with each other when someone attempts to disturb or to provoke the dialogue. The teacher role changes to one of support, ensuring that the analysis is fruitful and that the dialogue is respectful.

Socratic methods have developed independently in various countries. They all describe a set of methodological steps to attain similar objectives. An opening question is answered by all participants and followed by cooperative, critical analysis. Finally, the new ideas are connected to the everyday life experience of the participants.

It seems as if this ritualized structure and the nurturing culture of the seminar provide a safe circle, helping the participants to try new, bold ideas that they might otherwise not have tested, Ann S. Pihlgren says. By cooperating when examining the ideas they also seem to learn a way to address problems on their own without teacher intervention.

To work with methods connected to the ancient philosopher Socrates may seem out-of-date in a modern school, but that is absolutely not the case, Ann S. Pihlgren states.

The Socratic seminars have been seen as a complement to traditional classroom teaching for hundreds of years. But it is not easy to learn how to stage them to get positive effects. It is especially hard for teachers, who often fall back to their traditional, controlling “teacher” roles. The dissertation offers excellent tools for teachers who want to develop students’ thinking and to foster cooperative group dialogue.

The name of the dissertation: Socrates in the Classroom. Rationales and Effects of Philosophizing with Children. The dissertation can be downloaded as a pdf here.

[Jonas Ablad @ Swedish Research Council]

Being obese can increase the risk of Alzheimer’s Disease by as much as 80 percent, according to a study in the May issue of Obesity Reviews.

But it’s not just weight gain that poses a risk. People who are underweight also have an elevated risk of dementia, unlike people who are normal weight or overweight.

US researchers carried out a detailed review of 10 international studies published since 1995, covering just over 37,000 people, including 2,534 with various forms of dementia. Subjects were aged between 40 and 80 years when the studies started, with follow-up periods ranging from three to 36 years.

The review, which included studies from the USA, France, Finland, Sweden and Japan, also included a sophisticated meta-analysis of seven of the studies, published between 2003 and 2007 with a follow-up period of at least five years.

All kinds of dementia were included, with specific reference to Alzheimer’s Disease and to vascular dementia — where areas of the brain stop functioning because the blood vessels that supply them are damaged by conditions such as high blood pressure or heart disease.

“Our meta-analysis showed that obesity increased the relative risk of dementia, for both sexes, by an average of 42 percent when compared with normal weight” says Dr Youfa Wang, Associate Professor of International Health and Epidemiology at Johns Hopkins Bloomberg School of Public Health, Baltimore.

“And being underweight increased the risk by 36 percent.

“But when we looked specifically at Alzheimer’s Disease, the increased risk posed by obesity was 80 percent. The increased risk for people with vascular dementia was 73 percent.

“The risks were greater in studies where sufferers developed Alzheimer’s Disease or vascular dementia before the age of 60 or in studies with follow-up periods of more than 10 years.

“We also found that obesity was more likely to be a risk factor for women when it came to developing Alzheimer’s Disease and for men when it came to vascular dementia.”

The authors estimate that 12 percent of the dementia risk in the study population could be attributed to obesity, with this rising to just over 21 percent in patients with Alzheimer’s Disease.

It’s estimated that up to 10 percent of people aged 65 or more suffer from some form of dementia and two-thirds of those have Alzheimer’s Disease.

“There has been controversy about the links between obesity and dementia for a number of years, but previous findings have been mixed and inconclusive” says Dr Wang.

“The advantage of carrying out a meta-analysis is that it provides researchers with access to a large number of study subjects and it is possible to iron out the inconsistencies and come to overarching conclusions.

“Our detailed analysis clearly shows a U-shaped relationship between weight and dementia, with people who are obese or underweight facing a greater risk.

“We believe that our results show that reducing the prevalence of obesity is a promising strategy for preventing the progression of normal ageing into Alzheimer’s Disease.”

[Annette Whibley @ Wiley-Blackwell]

An international consortium of scientists, led by Washington University School of Medicine in St. Louis, has decoded the genome of the platypus, showing that the animal’s peculiar mix of features is reflected in its DNA. An analysis of the genome, published today in the journal Nature, can help scientists piece together a more complete picture of the evolution of all mammals, including humans.

The platypus, classified as a mammal because it produces milk and is covered in a coat of fur, also possesses features of reptiles, birds and their common ancestors, along with some curious attributes of its own. One of only two mammals that lays eggs, the platypus also sports a duck-like bill that holds a sophisticated electrosensory system used to forage for food underwater. Males possess hind leg spurs that can deliver pain-inducing venom to its foes competing for a mate or territory during the breeding season.

“The fascinating mix of features in the platypus genome provides many clues to the function and evolution of all mammalian genomes,” says Richard K. Wilson, Ph.D., director of the The Genome Center at Washington University and the paper’s senior author. “By comparing the platypus genome to other mammalian genomes, we’ll be able to study genes that have been conserved throughout evolution.”

The platypus represents the earliest offshoot of the mammalian lineage some 166 million years ago from primitive ancestors that had features of both mammals and reptiles. “What is unique about the platypus is that it has retained a large overlap between two very different classifications, while later mammals lost the features of reptiles,” says Wes Warren, Ph.D., an assistant professor of genetics, who led the project.

Comparison of the platypus genome with the DNA of humans and other mammals, which diverged later, and the genomes of birds, whose ancestors branched off an estimated 315 million years ago, can help scientists fill gaps in their understanding of mammalian evolution. The comparison also will allow scientists to date the emergence of genes and traits specific to mammals.

The Nature paper analyzes the genome sequence of a female platypus named Glennie from New South Wales, Australia. The project was largely funded by the National Human Genome Research Institute, part of the National Institutes of Health, and includes scientists from the United States, Australia, England, Germany, Israel, Japan, New Zealand and Spain.

“At first glance, the platypus appears as if it was the result of an evolutionary accident,” says Francis S. Collins, M.D., Ph.D., director of NHGRI. “But as weird as this animal looks, its genome sequence is priceless for understanding how mammalian biological processes evolved.”

“While we’ve always been able to compare and consider all of these creatures on the basis of their physical characteristics, internal anatomy and behavior, it’s truly amazing to be able to compare their genetic blueprints and begin to get a close-up look at how evolution brings about change,” Wilson says.

As part of their analysis, the researchers compared the platypus genome with genomes of the human, mouse, dog, opossum and chicken. They found that the platypus shares 82 percent of its genes with these animals. The chicken genome was chosen because it represents a group of egg-laying animals, including extinct reptiles, which passed on much of their DNA to the platypus and other mammals over the course of evolution.

The researchers also found genes that support egg laying - a feature of reptiles - as well as lactation - a characteristic of all mammals. Interestingly, the platypus lack nipples, so its young nurse through the abdominal skin.

The researchers also attempted to determine which characteristics of the platypus were linked to reptiles at the DNA level. When they analyzed the genetic sequences responsible for venom production in the male platypus, they found it arose from duplications in a group of genes that evolved from ancestral reptile genomes. Amazingly, duplications in the same genes appear to have evolved independently in venomous reptiles.

The platypus swims with its eyes, ears and nostrils closed, relying on electrosensory receptors in its bill to detect faint electric fields emitted by underwater prey. Surprisingly, the researchers found the genome contains an expansion of genes that code for a particular type of odor receptor. “We were expecting very few of these odor receptor genes because the animals spend the majority of their life in the water,” Warren says.

Similar genes are found in animals that rely on a sense of smell, such as rodents and dogs, and the scientists suspect that their addition in the platypus allows the animals to detect odors while foraging underwater.

At roughly 2.2 billion base pairs, the platypus genome is about two-thirds the size of the human genome and contains about 18,500 genes, similar to other vertebrates. The animal has 52 chromosomes, including an unusual number of sex chromosomes: 10. The platypus X chromosome bears resemblance to the sex chromosome of a bird, known as Z.

Sequencing and assembling the platypus genome proved far more daunting than sequencing any other mammalian genome to date. About 50 percent of the genome is composed of repetitive elements of DNA, which makes it a challenge to assemble properly.

The platypus genome sequence, along with those for other organisms, such as the mouse, dog, cow, and many other animals can be accessed at GenBank (www.ncbi.nih.gov/Genbank) at NIH’s National Center for Biotechnology Information.

[Caroline Arbanas @ Washington University School of Medicine]

Three researchers from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) have proposed an innovative way to improve global climate change predictions by using a supercomputer with low-power embedded microprocessors, an approach that would overcome limitations posed by today’s conventional supercomputers.

Berkeley Lab has signed a collaboration agreement with Tensilica, Inc. to explore the use of Tensilica’s Xtensa processor cores as the basic building blocks in a massively parallel system design. Tensilica’s Xtensa processor is about 400 times more efficient in floating point operations per watt than the conventional server processor chip shown here.

In a paper published in the May issue of the International Journal of High Performance Computing Applications, Michael Wehner and Lenny Oliker of Berkeley Lab’s Computational Research Division, and John Shalf of the National Energy Research Scientific Computing Center (NERSC) lay out the benefit of a new class of supercomputers for modeling climate conditions and understanding climate change. Using the embedded microprocessor technology used in cell phones, iPods, toaster ovens and most other modern day electronic conveniences, they propose designing a cost-effective machine for running these models and improving climate predictions.

In April, Berkeley Lab signed a collaboration agreement with Tensilica, Inc. to explore such new design concepts for energy-efficient high-performance scientific computer systems. The joint effort is focused on novel processor and systems architectures using large numbers of small processor cores, connected together with optimized links, and tuned to the requirements of highly-parallel applications such as climate modeling.

Understanding how human activity is changing global climate is one of the great scientific challenges of our time. Scientists have tackled this issue by developing climate models that use the historical data of factors that shape the earth’s climate, such as rainfall, hurricanes, sea surface temperatures and carbon dioxide in the atmosphere. One of the greatest challenges in creating these models, however, is to develop accurate cloud simulations.

Although cloud systems have been included in climate models in the past, they lack the details that could improve the accuracy of climate predictions. Wehner, Oliker and Shalf set out to establish a practical estimate for building a supercomputer capable of creating climate models at 1-kilometer (km) scale. A cloud system model at the 1-km scale would provide rich details that are not available from existing models.

To develop a 1-km cloud model, scientists would need a supercomputer that is 1,000 times more powerful than what is available today, the researchers say. But building a supercomputer powerful enough to tackle this problem is a huge challenge.

Historically, supercomputer makers build larger and more powerful systems by increasing the number of conventional microprocessors — usually the same kinds of microprocessors used to build personal computers. Although feasible for building computers large enough to solve many scientific problems, using this approach to build a system capable of modeling clouds at a 1-km scale would cost about $1 billion. The system also would require 200 megawatts of electricity to operate, enough energy to power a small city of 100,000 residents.

In their paper, Towards Ultra-High Resolution models of Climate and Weather, the researchers present a radical alternative that would cost less to build and require less electricity to operate. They conclude that a supercomputer using about 20 million embedded microprocessors would deliver the results and cost $75 million to construct. This “climate computer” would consume less than 4 megawatts of power and achieve a peak performance of 200 petaflops.

“Without such a paradigm shift, power will ultimately limit the scale and performance of future supercomputing systems, and therefore fail to meet the demanding computational needs of important scientific challenges like the climate modeling,” Shalf said.

The researchers arrive at their findings by extrapolating performance data from the Community Atmospheric Model (CAM). CAM, developed at the National Center for Atmospheric Research in Boulder, Colorado, is a series of global atmosphere models commonly used by weather and climate researchers.

The “climate computer” is not merely a concept. Wehner, Oliker and Shalf, along with researchers from UC Berkeley, are working with scientists from Colorado State University to build a prototype system in order to run a new global atmospheric model developed at Colorado State.

“What we have demonstrated is that in the exascale computing regime, it makes more sense to target machine design for specific applications,” Wehner said. “It will be impractical from a cost and power perspective to build general-purpose machines like today’s supercomputers.”

Under the agreement with Tensilica, the team will use Tensilica’s Xtensa LX extensible processor cores as the basic building blocks in a massively parallel system design. Each processor will dissipate a few hundred milliwatts of power, yet deliver billions of floating point operations per second and be programmable using standard programming languages and tools. This equates to an order-of-magnitude improvement in floating point operations per watt, compared to conventional desktop and server processor chips. The small size and low power of these processors allows tight integration at the chip, board and rack level and scaling to millions of processors within a power budget of a few megawatts.

Berkeley Lab is a U.S. Department of Energy national laboratory located in Berkeley, California. It conducts unclassified scientific research and is managed by the University of California. Visit our Website at www.lbl.gov.

[Ucilia Wang @ DOE/Lawrence Berkeley National Laboratory]

Scientists at the University of Konstanz in Germany and the National Institute of Standards and Technology (NIST) have demonstrated an ultrafast laser that offers a record combination of high speed, short pulses and high average power. The same NIST group also has shown that this type of laser, when used as a frequency comb — an ultraprecise technique for measuring different colors of light — could boost the sensitivity of astronomical tools searching for other Earthlike planets as much as 100 fold.

The dime-sized laser, to be described Thursday, May 8, at the Conference on Lasers and Electro-Optics, emits 10 billion pulses per second, each lasting about 40 femtoseconds (quadrillionths of a second), with an average power of 650 milliwatts. For comparison, the new laser produces pulses 10 times more often than a standard NIST frequency comb while producing much shorter pulses than other lasers operating at comparable speeds. The new laser is also 100 to 1000 times more powerful than typical high-speed lasers, producing clearer signals in experiments. The laser was built by Albrecht Bartels at the Center for Applied Photonics of the University of Konstanz.

Among its applications, the new laser can be used in searches for planets orbiting distant stars. Astronomers look for slight variations in the colors of starlight over time as clues to the presence of a planet orbiting the star. The variations are due to the small wobbles induced in the star’s motion as the orbiting planet tugs it back and forth, producing minute shifts in the apparent color (frequency) of the starlight. Currently, astronomers’ instruments are calibrated with frequency standards that are limited in spectral coverage and stability. Frequency combs could be more accurate calibration tools, helping to pinpoint even smaller variations in starlight caused by tiny Earthlike planets. Such small planets would cause color shifts equivalent to a star wobble of just a few centimeters per second. Current instruments can detect, at best, a wobble of about 1 meter per second.

Standard frequency combs have “teeth” that are too finely spaced for astronomical instruments to read. The faster laser is one approach to solving this problem. In a separate paper, the NIST group and astronomer Steve Osterman at the University of Colorado at Boulder describe how, by bouncing the light between sets of mirrors a particular distance apart, they can eliminate periodic blocks of teeth to create a gap-toothed comb. This leaves only every 10th or 20th tooth, making an ideal ruler for astronomy.

Both approaches have advantages for astronomical planet finding and related applications. The dime-sized laser is very simple in construction and produces powerful and extremely well-defined comb teeth. On the other hand, the filtering approach can cover a broader range of wavelengths. Four or five filtering cavities in parallel would provide a high-precision comb of about 25,000 evenly spaced teeth that spans the visible to near-infrared wavelengths (400 to 1100 nanometers), NIST physicist Scott Diddams says.

Osterman says he is pursuing the possibility of testing such a frequency comb at a ground-based telescope or launching a comb on a satellite or other space mission. Other possible applications of the new laser include remote sensing of gases for medical or atmospheric studies, and on-the-fly precision control of high-speed optical communications to provide greater versatility in data and time transmissions. The application of frequency combs to planet searches is of international interest and involves a number of major institutions such as the Max-Planck Institute for Quantum Optics and Harvard Smithsonian Center for Astrophysics.

[Laura Ost @ National Institute of Standards and Technology (NIST)]

If you use one of America’s top Internet service providers, you may share server space with an organization that enables worldwide terrorism, says a new study by Tel Aviv University.

A workshop on terrorist organizations and the Internet was organized for the North American Treaty Organization (NATO) by the Netvision Institute for Internet Studies (NIIS) and the Interdisciplinary Center for Technology Analysis & Forecasting, both of Tel Aviv University. Berlin’s Institute for Cooperation Management and Interdisciplinary Research (NEXUS), affiliated with the Technical University of Berlin, also participated in the workshop.

The findings were presented in Berlin to a closed audience of high-ranking representatives from NATO in February 2008.

Organizing and Recruiting Online

Enlisted by NATO officials to study the web activity of terrorist organizations, researchers found that some of the world’s most dangerous organizations are operating on American turf. Hezbollah, the Islamic Jihad, and al-Qaeda all have websites hosted by popular American Internet service providers — the same companies that most of us use every day.

“These websites hosted in America are targeting Muslim mothers in America, Canada, the U.K. and all over the world, convincing them that being ‘Shahid’ or a suicide bomber is particularly good and very important for their sons,” says Prof. Niv Ahituv of the NIIS.

Available in English, Arabic, Spanish and other languages, the websites also provide tutorials on bomb building and enlist impressionable American and British Muslim women and men into a life of terror activity.

Free-Speech for Terrorists

Prof. Ahituv acknowledges the dilemma that America’s First Amendment creates — free-speech protections may foster propaganda directed towards the U.S. “America’s First Amendment protects these websites from being shut down,” he says, recognizing the irony of waging a war on terror when some of the most dangerous propaganda is being created at home.

According to the study, the Islamic Jihad operates 15 websites in Arabic and English, hosted by both U.S. and Canadian companies. Hamas operates 20 websites in eight languages, a portion of which are based in the U.S and Canada, while Hezbollah operates 20 websites, also hosted by companies in the U.S. and Canada.

Limited Successes and American Law

The FBI has shut down a few websites, but American law prevents the closure of most, says Prof. Ahituv. Terrorists could coordinate a 9/11-scale attack via these websites, he warns. There are, however, some people who believe that leaving those websites intact is desired in order to monitor content, trends and policy. It is hard to tell which side is right, adds Prof. Ahituv.

An issue of great concern is that terrorist organizations are using the Internet to bypass the role of the established press, he notes. “Since those organizations do not possess TV stations, radio stations and printed press outlets, they use the Internet to impart their views and events to the public and to the media.”

More information about the Netvision Institute for Internet Studies here.

[George Hunka @ American Friends of Tel Aviv University]

As microchips shrink, even tiny defects in the lines, dots and other shapes etched on them become major barriers to performance. Princeton engineers have now found a way to literally melt away such defects, using a process that could dramatically improve chip quality without increasing fabrication cost.

The method, published in the May 4 issue of Nature Nanotechnology, enables more precise shaping of microchip components than what is possible with current technology. More precise component shapes could help manufacturers build smaller and better microchips, the key to more powerful computers and other devices.

“We are able to achieve a precision and improvement far beyond what was previously thought achievable,” said electrical engineer Stephen Chou, the Joseph C. Elgin Professor of Engineering, who developed the method along with graduate student Qiangfei Xia. Chou’s lab has previously pioneered a number of innovative chip making techniques, including a revolutionary method for making nanometer-scale patterns using imprinting.

Microchips work best when the structures fabricated on them are straight, thin and tall. Rough edges and other defects can degrade or even ruin chip performance in most applications. In integrated circuits, for instance, such flaws could cause current to leak and voltage to fluctuate. In optic devices, they could interfere with the transmission of light. In biological devices, they could impede the flow of DNA and other biomaterials.

“These chip defects pose serious roadblocks to future advances in many industries,” Chou said.

To deal with this problem, researchers try to improve the process used to make the microchips. However, Chou said such an approach works only to a point; eventually chip makers will run up against fundamental physical limits of current manufacturing techniques. In particular, the electrons and photons that are used like chisels to carve out the microscopic features on a chip always have some random behavior. This effect becomes pronounced at very small scales and limits the accuracy of component shapes.

“What we propose instead is a paradigm shift: Rather than struggle to improve fabrication methods, we could simply fix the defects after fabrication,” said Chou. ???And fixing the defects could be automatic — a process of self-perfection.???

Chou’s method, termed Self-Perfection by Liquefaction (SPEL), achieves this by melting the structures on a chip momentarily, and guiding the resulting flow of liquid so that it re-solidifies into the desired shapes. This is possible because natural forces acting on the molten structures, such as surface tension — the force that allows some insects to walk on water — smooth the structures into geometrically more accurate shapes. Lines, for instance, become straighter, and dots become rounder.

Simple melting by direct heating has previously been shown to smooth out the defects in plastic structures. This process can’t be applied to a microchip, for two reasons. First, the key structures on a chip are not made of plastic, which melts at temperatures close to the boiling point of water, but from semiconductors and metals, which have much higher melting points. Heating the chip to such temperatures would melt not just the structures, but nearly everything else on the chip. Secondly, the melting process would widen the structures and round off their top and side surfaces, all of which would be detrimental to the chip.

Chou’s team overcame the first obstacle by using a light pulse from so-called excimer laser, similar to those used in laser eye surgery, because it heats only a very thin surface layer of a material and causes no damage to the structures underneath. The researchers carefully designed the pulse so that it would melt only semiconductor and metal structures, and not damage other parts of the chip. The structures need to be melted for only a fraction of a millionth of a second, because molten metal and semiconductors can flow as easily as water and have high surface tension, which allows them to change shapes very quickly.

To overcome the second obstacle, Chou’s team placed a plate on top of the melting structures to guide the flow of liquid. The plate prevents a molten structure from widening, and keeps its top flat and sides vertical, Chou said. In one experiment, it made the edges of 70 nanometer-wide chromium lines more than five times smoother. The resulting line smoothness was far more precise than what semiconductor researchers believe to be attainable with existing technology.

The conventional approach to fixing chip defects is to measure the exact shape of each defect, and provide a correction precisely tailored to it — a slow and expensive process, Chou said. In contrast, Chou’s guided melting process fixes all defects on a chip in a single quick and inexpensive step. “Regardless of the shape of each defect, it always gets fixed precisely and with no need for individual shape measurement or tailored correction,” Chou said.

One of the big surprises from this work is observed when the guiding plate is placed not in direct contact with the molten structures, but at a distance above it. In this situation, the liquid material from the structures rises up and reaches the plate by itself, causing line structures to become taller and narrower — both highly desirable outcomes from a chip design perspective.

“The authors demonstrate improved edge roughness and dramatically altered aspect ratios in nanoscale features,” said Donald Tennant, director of operations at the NanoScale Science and Technology Facility at Cornell University. The techniques “may be a way forward when nanofabricators bump up against the limits of lithography and pattern transfer,” he said.

Next, Chou’s group plans to demonstrate this technique on large (8-inch) wafers. Several leading semiconductor manufacturers have expressed keen interest in the technique, Chou said.

[Steven Schultz @ Princeton University Engineering School]