Ultrafast Magnetic Processes Observed 'Live' Using an X-Ray Laser

Detail of the structure of cupric oxide (CuO). The copper atoms (green) carry a magnetic moment, behaving like small compass needles. The direction of the magnetic moment is illustrated by a red arrow. A point means that the arrow is pointing out of the surface (we are looking at its sharp end), a cross shows that the arrow is pointing into the surface (we are looking at its tail end). The magnetic structure changes significantly as the temperature increases above 213 Kelvin (around -60°C). One aspect of this change is a difference in the period of the magnetic order. Unlike the ordering at low temperatures, the magnetic structure in the temperature range 213 K to 230 K is incommensurate: its period does not ‘fit’ with the period of the crystal structure of copper and oxygen atoms. To be precise, a full rotation of the direction of the magnetic moment does not require exactly four atomic separations, but a little more or a little less, depending on the direction. (Credit: Image courtesy of Paul Scherrer Institut (PSI))

ScienceDaily (Jan. 23, 2012) — In first-of-their-kind experiments performed at the American X-ray laser LCLS, a collaboration led by researchers from the Paul Scherrer Institute has been able to precisely follow how the magnetic structure of a material changes.

This is another milestone, because such investigations will also be a major focus of research at the planned Swiss X-ray Laser, Swiss FEL, at PSI. The results could contribute to the development of new technologies for magnetic storage media for the future.The study was carried out on cupric oxide (CuO). The change of structure was initiated by a laser pulse, and then, with the help of short X-ray pulses, near-instantaneous images were obtained at different points in time for individual intermediate steps during the process. It appears as if the structure begins to change 400 femtoseconds after the laser pulse strikes (1 femtosecond = 0.000 000 000 000 001 seconds). Apparently, the fundamental magnets within the material need that much time to communicate with each other and then react. In addition to this scientific result, the work proves that it is actually possible with X-ray lasers to follow certain types of extremely rapid magnetic processes.

The researchers have reported on their work in the latest edition of the technical journal Physical Review Letters (PRL).

Materials with particular magnetic properties are the basis of many current technologies, in particular, data storage on hard discs and in other media. For this, the magnetic orientation in the material is most often used: the atoms in the material behave to some extent like tiny rod magnets ("spins"). These mini-magnets can be oriented in different ways and information can be stored through their orientation. For efficient data storage, it is crucial that old data can be rapidly overwritten. This is possible if the magnetic orientation in a material can be altered in a very short time. To develop innovative materials which can store data quickly, it is therefore important to understand exactly how this change occurs as a function of time.

Magnetic orientation in motion

In experiments performed at the X-ray laser LCLS at Stanford, California, a collaboration led by researchers from the Paul Scherrer Institute have been able to study the magnetic orientation in cupric oxide, CuO. This material demonstrates completely different magnetic orientations depending on temperature: Below -60°C, the spins, which function in the copper atoms (Cu) like magnets, point periodically in one direction and then the opposite; between -60°C and -43°C, they are arranged helically, as if they were forming a spiral staircase. Although the spin orientations for the two arrangements have been known for some time, the time required to move from one arrangement to the other has only now been shown by the experiment.

"In our investigation, we began with a 'cold' sample and then heated it with an intense flash of light from an optical laser," explains Steven Johnson, spokesman for the PSI experiment. "Shortly after this, we determined the structure of the sample by illuminating it with an extremely short pulse from an X-ray laser. When we repeated this at different time intervals between the flash of light and the X-ray pulse, we were able to reconstruct the course of the change in the magnetic structure."

Mini-magnets need 400 femtoseconds to agree amongst themselves.

The results show that it takes about 400 femtoseconds before the magnetic structure begins to alter visibly. Then the structure gradually reaches its final state. The more intense the initiating flash of light, the faster the change of state. "The spins of all copper atoms are involved in the magnetic structure. Thus the atoms at opposite ends of the material must be coordinated before the structure can change. This takes 400 femtoseconds," explains Urs Staub, one of the PSI researchers responsible. "For cupric oxide, that is the fundamental limit; it simply cannot happen faster than that. This depends upon how strongly the spins are coupled between neighbouring atoms."

There is a good reason why the researchers were particularly interested in cupric oxide. Along with the screw-like magnetic orientation that occurs between -60°C and -43°C, the material is also 'multiferroic', a material where electrical and magnetic processes mutually influence one another. These materials have many different potential areas of application where magnetism and electronics interact.

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---

Journal Reference:

1. S. Johnson, R. de Souza, U. Staub, P. Beaud, E. Möhr-Vorobeva, G. Ingold, A. Caviezel, V. Scagnoli, W. Schlotter, J. Turner, O. Krupin, W.-S. Lee, Y.-D. Chuang, L. Patthey, R. Moore, D. Lu, M. Yi, P. Kirchmann, M. Trigo, P. Denes, D. Doering, Z. Hussain, Z.-X. Shen, D. Prabhakaran, A. Boothroyd. Femtosecond Dynamics of the Collinear-to-Spiral Antiferromagnetic Phase Transition in CuO.Physical Review Letters, 2012; 108 (3) DOI:10.1103/PhysRevLett.108.037203

Scientists study 'galaxy zoo' using Google Maps and thousands of volunteers

ScienceDaily (Nov. 3, 2011) — The reddest galaxies with the largest central bulb show the largest bars -- gigantic central columns of stars and dark matter -- according to a scientific study that used Google Maps to observe the sky. A group of volunteers of more than 200,000 participants of the galaxy classification project Galaxy Zoo contributed to this research.

More than two thirds of spiral galaxies, including our own Milky Way, display a central bar that can extend for thousands of light years. These colossal elongated structures are made up of collections of stars and dark matter which are held together by gravity.

Now a team of researchers from Europe and the USA have measured the bar length of some 5000 galaxies with the help of amateur astronomers. The most precise results (those obtained for 3150 galaxies) have been published in the Monthly Notices of the Royal Astronomical Society.

The study comes under the Galaxy Zoo project, a citizen science initiative in which more than 200,000 volunteers assisted in classifying a million galaxies through images provided by the Sloan Digital Sky Survey astronomical catalogue. As for the bars, 150 amateur astronomers have recorded their observations on a webpage specifically created for this purpose. The page is currently still active despite being closed to any further data entry.

Ben Hoyle, researcher at the Institute of Cosmos Sciences (University of Barcelona, Spain) and coordinator of the study, stresses that "this webpage combines Galaxy Zoo classifications with Google Maps technology." More precisely, the team has used the Google Maps Sky interface which allows to see the sky, especially the galaxies, as seen from Earth's surface.

The redness of bars

"In this way we have compiled some 16,000 measurements of the bars of 5000 galaxies, which is a sample a hundred times greater than previous ones. We have also come to many different conclusions, such as the fact that redder galaxies, which are stopping star formation, have longer bars," says Hoyle.

In the electromagnetic spectrum, the colour red comes from older, cooler stars whereas the colour blue is linked to hotter and younger stars. The study also reveals that the bars tend to be redder than the rest of the galaxy, which indicates that they have an older stellar population.

Other conclusions indicate that those galaxies with a larger bulb (a central agglomeration of stars) have longer bars. In addition, barred galaxies are more likely to display spiral arms than unbarred galaxies.

The images provide examples of barred galaxies with spiral arms. In the first row, the arms are connected to the ring around the bar. In the second row, the arms are connected at the end of the bar and the third row shows a mixture of the two. Image: Ben Hoyle et al./Galaxy Zoo.

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Journal Reference:

Ben Hoyle, Karen. L. Masters, Robert C. Nichol, Edward M. Edmondson, Arfon M. Smith, Chris Lintott, Ryan Scranton, Steven Bamford, Kevin Schawinski, Daniel Thomas. Galaxy Zoo: bar lengths in local disc galaxies. Monthly Notices of the Royal Astronomical Society, 2011; 415 (4): 3627 DOI: 10.1111/j.1365-2966.2011.18979.x

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Using photons to manage data

ScienceDaily (Oct. 27, 2011) — Managing light to carry computer data, such as text, audio and video, is possible today with laser light beams that are guided along a fibre-optic cable. These waves consist of countless billions of photons, which carry information down the fibre across continents.

A research team at the University of Alberta wants to refine the optical transmission of information by using a single photon, the fundamental building block of light that can allow unprecedented applications in optical information transfer.

Zubin Jacob, a U of A electrical and computer engineering researcher, says that rather than spreading data over waves of light, the goal is to use single particles of light, photons.

"Unfortunately, the efficient generation of single photons for practical applications is a serious engineering challenge," said Jacob.

Jacob and his research team are looking into metamaterials to tackle this problem. A metamaterial is a medium that has designer nanostructures in it, giving it technical capabilities beyond any materials we currently have. "The metamaterial would efficiently collect single photons of light and allow their transmission," said Jacob.

At other universities, researchers are looking at attaching single photons to waves of electrons. The electrons and photons combine to form a plasmon wave that can be transmitted on a metal nanowire.

Jacob says the benefit of working with single photons for transmitting computer data is the ability to encode much more complex information on an individual particle of light. "A single photon could carry encryption codes, which are far more complex than the security password information we currently use to protect sensitive data."

Jacob says that this technology is at least 10 years away and the products are not aimed at general consumers. "This technology is destined for markets such as the military that requires extremely high levels of data encryption."

The development in this field of research combining nanophotonics and quantum technologies was published Oct. 27 in the journal Science.

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The above story is reprinted from materials provided by University of Alberta. The original article was written by Brian Murphy.

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Z. Jacob, V. M. Shalaev. Plasmonics Goes Quantum. Science, 2011; 334 (6055): 463 DOI: 10.1126/science.1211736

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Emulating -- and surpassing -- nature: Using DNA to build nanomaterials with desired properties

ScienceDaily (Oct. 13, 2011) — Nature is a master builder. Using a bottom-up approach, nature takes tiny atoms and, through chemical bonding, makes crystalline materials, like diamonds, silicon and even table salt. In all of them, the properties of the crystals depend upon the type and arrangement of atoms within the crystalline lattice.

Now, a team of Northwestern University scientists has learned how to top nature by building crystalline materials from nanoparticles and DNA, the same material that defines the genetic code for all living organisms.

Using nanoparticles as "atoms" and DNA as "bonds," the scientists have learned how to create crystals with the particles arranged in the same types of atomic lattice configurations as some found in nature, but they also have built completely new structures that have no naturally occurring mineral counterpart.

The basic design rules the Northwestern scientists have established for this approach to nanoparticle assembly promise the possibility of creating a variety of new materials that could be useful in catalysis, electronics, optics, biomedicine and energy generation, storage and conversion technologies.

The new method and design rules for making crystalline materials from nanostructures and DNA will be published Oct. 14 by the journal Science.

"We are building a new periodic table of sorts," said Professor Chad A. Mirkin, who led the research. "Using these new design rules and nanoparticles as 'artificial atoms,' we have developed modes of controlled crystallization that are, in many respects, more powerful than the way nature and chemists make crystalline materials from atoms. By controlling the size, shape, type and location of nanoparticles within a given lattice, we can make completely new materials and arrangements of particles, not just what nature dictates."

Mirkin is the George B. Rathmann Professor of Chemistry in the Weinberg College of Arts and Sciences and professor of medicine, chemical and biological engineering, biomedical engineering and materials science and engineering and director of Northwestern's International Institute for Nanotechnology (IIN).

"Once we have a certain type of lattice," Mirkin said, "the particles can be moved closer together or farther apart by changing the length of the interconnecting DNA, thereby providing near-infinite tunability."

"This work resulted from an interdisciplinary collaboration that coupled synthetic chemistry with theoretical model building," said coauthor George C. Schatz, a theoretician and the Charles E. and Emma H. Morrison Professor of Chemistry at Northwestern. "It was the back and forth between synthesis and theory that was crucial to the development of the design rules. Collaboration is a special aspect of research at Northwestern, and it worked very effectively for this project."

In the study, the researchers start with two solutions of nanoparticles coated with single-stranded DNA. They then add DNA strands that bind to these DNA-functionalized particles, which then present a large number of DNA "sticky ends" at a controlled distance from the particle surface; these sticky ends then bind to the sticky ends of adjacent particles, forming a macroscopic arrangement of nanoparticles.

Different crystal structures are achieved by using different combinations of nanoparticles (with varying sizes) and DNA linker strands (with controllable lengths). After a process of mixing and heating, the assembled particles transition from an initially disordered state to one where every particle is precisely located according to a crystal lattice structure. The process is analogous to how ordered atomic crystals are formed.

The researchers report six design rules that can be used to predict the relative stability of different structures for a given set of nanoparticle sizes and DNA lengths. In the paper, they use these rules to prepare 41 different crystal structures with nine distinct crystal symmetries. However, the design rules outline a strategy to independently adjust each of the relevant crystallographic parameters, including particle size (varied from 5 to 60 nanometers), crystal symmetry and lattice parameters (which can range from 20 to 150 nanometers). This means that these 41 crystals are just a small example of the near infinite number of lattices that could be created using different nanoparticles and DNA strands.

Mirkin and his team used gold nanoparticles in their work but note that their method also can be applied to nanoparticles of other chemical compositions. Both the type of nanoparticle assembled and the symmetry of the assembled structure contribute to the properties of a lattice, making this method an ideal means to create materials with predictable and controllable physical properties.

Mirkin believes that, one day soon, software will be created that allows scientists to pick the particle and DNA pairs required to make almost any structure on demand.

The Air Force Office of Scientific Research, the U.S. Department of Energy Office of Basic Energy Sciences and the National Science Foundation supported the research.

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The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Northwestern University, via EurekAlert!, a service of AAAS.

Journal Reference:

R. J. Macfarlane, B. Lee, M. R. Jones, N. Harris, G. C. Schatz, C. A. Mirkin. Nanoparticle Superlattice Engineering with DNA. Science, 2011; 334 (6053): 204 DOI: 10.1126/science.1210493

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Using math and light to detect misshapen red blood cells

ScienceDaily (Oct. 31, 2011) — Misshapen red blood cells (RBCs) are a sign of serious illnesses, such as malaria and sickle cell anemia. Until recently, the only way to assess whether a person's RBCs were the correct shape was to look at them individually under a microscope -- a time-consuming process for pathologists. Now researchers from the University of Illinois at Urbana-Champaign (UIUC) have pioneered a technique that will allow doctors to ascertain the healthy shape of red blood cells in just a few seconds, by analyzing the light scattered off hundreds of cells at a time.

The team reports its results in the October issue of the Optical Society's (OSA) open-access journal Biomedical Optics Express.

A healthy RBC looks like a disc with a depression -- called a dimple -- in the top and bottom. Stressed RBCs often have deeper dimples than healthy ones, giving the cells a deflated look; others may have shallow dimples or no dimples at all. The UIUC researchers reasoned that if they shone light on a sample of blood and analyzed the light scattering off that sample, they would get a pattern -- a sort of signature produced by the way light interacts with itself in a three-dimensional space -- that would be different from the pattern collected from blood containing mostly misshapen cells. But these light-cell interactions were too complicated to analyze with the usual mathematical tools. So researchers made use of the Born approximation, a mathematical rule that can be used when the object of interest is small and transparent.

By running Fourier Transform Light Scattering (FTLS) -- a method developed by the same group three years ago -- on individual RBCs, the scientists found that the pattern changed significantly with the diameter and dimple width of the cells. Using this information, the UIUC team applied the Born approximation to their findings and calculated what the appropriate scattering signature for healthy cells should be. They then used this new "healthy cell signature" to identify the correct morphology of cells in a blood smear. The new technique may allow for faster, accurate blood tests that could help doctors diagnose various types of anemia, and could be especially useful in resource-poor areas of the world, the researchers say.

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Bartolomeo Della Ventura, Luigi Schiavo, Carlo Altucci, Rosario Esposito, Raffaele Velotta. Light assisted antibody immobilization for bio-sensing. Biomedical Optics Express, 2011; 2 (11): 3223 DOI: 10.1364/BOE.2.003223

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Monkeys 'move and feel' virtual objects using only their brains

ScienceDaily (Oct. 6, 2011) — In a first ever demonstration of a two-way interaction between a primate brain and a virtual body, two monkeys trained at the Duke University Center for Neuroengineering learned to employ brain activity alone to move an avatar hand and identify the texture of virtual objects.

"Someday in the near future, quadriplegic patients will take advantage of this technology not only to move their arms and hands and to walk again, but also to sense the texture of objects placed in their hands, or experience the nuances of the terrain on which they stroll with the help of a wearable robotic exoskeleton," said Miguel Nicolelis, M.D., Ph.D., professor of neurobiology at Duke University Medical Center and co-director of the Duke Center for Neuroengineering, who was senior author of the study.

Without moving any part of their real bodies, the monkeys used their electrical brain activity to direct the virtual hands of an avatar to the surface of virtual objects and, upon contact, were able to differentiate their textures.

Although the virtual objects employed in this study were visually identical, they were designed to have different artificial textures that could only be detected if the animals explored them with virtual hands controlled directly by their brain's electrical activity.

The texture of the virtual objects was expressed as a pattern of minute electrical signals transmitted to the monkeys' brains. Three different electrical patterns corresponded to each of three different object textures.

Because no part of the animal's real body was involved in the operation of this brain-machine-brain interface (BMBI), these experiments suggest that in the future patients severely paralyzed due to a spinal cord lesion may take advantage of this technology, not only to regain mobility, but also to have their sense of touch restored, said Nicolelis, who was senior author of the study published in the journal Nature on Oct. 5.

"This is the first demonstration of a brain-machine-brain interface that establishes a direct, bidirectional link between a brain and a virtual body," Nicolelis said. "In this BMBI, the virtual body is controlled directly by the animal's brain activity, while its virtual hand generates tactile feedback information that is signaled via direct electrical microstimulation of another region of the animal's cortex."

"We hope that in the next few years this technology could help to restore a more autonomous life to many patients who are currently locked in without being able to move or experience any tactile sensation of the surrounding world," Nicolelis said.

"This is also the first time we've observed a brain controlling a virtual arm that explores objects while the brain simultaneously receives electrical feedback signals that describe the fine texture of objects 'touched' by the monkey's newly acquired virtual hand," Nicolelis said. "Such an interaction between the brain and a virtual avatar was totally independent of the animal's real body, because the animals did not move their real arms and hands, nor did they use their real skin to touch the objects and identify their texture. It's almost like creating a new sensory channel through which the brain can resume processing information that cannot reach it anymore through the real body and peripheral nerves."

The combined electrical activity of populations of 50-200 neurons in the monkey's motor cortex controlled the steering of the avatar arm, while thousands of neurons in the primary tactile cortex were simultaneously receiving continuous electrical feedback from the virtual hand's palm that let the monkey discriminate between objects, based on their texture alone.

"The remarkable success with non-human primates is what makes us believe that humans could accomplish the same task much more easily in the near future," Nicolelis said.

It took one monkey only four attempts and another nine attempts before they learned how to select the correct object during each trial. Several tests demonstrated that the monkeys were actually sensing the object and not selecting them randomly.

The findings provide further evidence that it may be possible to create a robotic exoskeleton that severely paralyzed patients could wear in order to explore and receive feedback from the outside world, Nicolelis said. Such an exoskeleton would be directly controlled by the patient's voluntary brain activity in order to allow the patient to move autonomously. Simultaneously, sensors distributed across the exoskeleton would generate the type of tactile feedback needed for the patient's brain to identify the texture, shape and temperature of objects, as well as many features of the surface upon which they walk.

This overall therapeutic approach is the one chosen by the Walk Again Project, an international, non-profit consortium, established by a team of Brazilian, American, Swiss, and German scientists, which aims at restoring full body mobility to quadriplegic patients through a brain-machine-brain interface implemented in conjunction with a full-body robotic exoskeleton.

The international scientific team recently proposed to carry out its first public demonstration of such an autonomous exoskeleton during the opening game of the 2014 FIFA Soccer World Cup that will be held in Brazil.

Other authors include Joseph E. O'Doherty, Mikhail A. Lebedev, Peter J. Ifft, Katie Z. Zhuang, all from the Duke University Center for Neuroengineering and Solaiman Shokur, and Hannes Bleuler from the Ecole Polytechnic Federale de Lausanne (EPFL), in Lausanne, Switzerland.

This work was funded by the U.S. National Institutes of Health.

A video illustrating the experiment is available at: http://www.youtube.com/watch?v=WTTTwvjCa5g

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Journal Reference:

Joseph E. O’Doherty, Mikhail A. Lebedev, Peter J. Ifft, Katie Z. Zhuang, Solaiman Shokur, Hannes Bleuler, Miguel A. L. Nicolelis. Active tactile exploration using a brain–machine–brain interface. Nature, 2011; DOI: 10.1038/nature10489

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Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Monkeys 'move and feel' virtual objects using only their brains

ScienceDaily (Oct. 6, 2011) — In a first ever demonstration of a two-way interaction between a primate brain and a virtual body, two monkeys trained at the Duke University Center for Neuroengineering learned to employ brain activity alone to move an avatar hand and identify the texture of virtual objects.

"Someday in the near future, quadriplegic patients will take advantage of this technology not only to move their arms and hands and to walk again, but also to sense the texture of objects placed in their hands, or experience the nuances of the terrain on which they stroll with the help of a wearable robotic exoskeleton," said Miguel Nicolelis, M.D., Ph.D., professor of neurobiology at Duke University Medical Center and co-director of the Duke Center for Neuroengineering, who was senior author of the study.

Without moving any part of their real bodies, the monkeys used their electrical brain activity to direct the virtual hands of an avatar to the surface of virtual objects and, upon contact, were able to differentiate their textures.

Although the virtual objects employed in this study were visually identical, they were designed to have different artificial textures that could only be detected if the animals explored them with virtual hands controlled directly by their brain's electrical activity.

The texture of the virtual objects was expressed as a pattern of minute electrical signals transmitted to the monkeys' brains. Three different electrical patterns corresponded to each of three different object textures.

Because no part of the animal's real body was involved in the operation of this brain-machine-brain interface (BMBI), these experiments suggest that in the future patients severely paralyzed due to a spinal cord lesion may take advantage of this technology, not only to regain mobility, but also to have their sense of touch restored, said Nicolelis, who was senior author of the study published in the journal Nature on Oct. 5.

"This is the first demonstration of a brain-machine-brain interface that establishes a direct, bidirectional link between a brain and a virtual body," Nicolelis said. "In this BMBI, the virtual body is controlled directly by the animal's brain activity, while its virtual hand generates tactile feedback information that is signaled via direct electrical microstimulation of another region of the animal's cortex."

"We hope that in the next few years this technology could help to restore a more autonomous life to many patients who are currently locked in without being able to move or experience any tactile sensation of the surrounding world," Nicolelis said.

"This is also the first time we've observed a brain controlling a virtual arm that explores objects while the brain simultaneously receives electrical feedback signals that describe the fine texture of objects 'touched' by the monkey's newly acquired virtual hand," Nicolelis said. "Such an interaction between the brain and a virtual avatar was totally independent of the animal's real body, because the animals did not move their real arms and hands, nor did they use their real skin to touch the objects and identify their texture. It's almost like creating a new sensory channel through which the brain can resume processing information that cannot reach it anymore through the real body and peripheral nerves."

The combined electrical activity of populations of 50-200 neurons in the monkey's motor cortex controlled the steering of the avatar arm, while thousands of neurons in the primary tactile cortex were simultaneously receiving continuous electrical feedback from the virtual hand's palm that let the monkey discriminate between objects, based on their texture alone.

"The remarkable success with non-human primates is what makes us believe that humans could accomplish the same task much more easily in the near future," Nicolelis said.

It took one monkey only four attempts and another nine attempts before they learned how to select the correct object during each trial. Several tests demonstrated that the monkeys were actually sensing the object and not selecting them randomly.

The findings provide further evidence that it may be possible to create a robotic exoskeleton that severely paralyzed patients could wear in order to explore and receive feedback from the outside world, Nicolelis said. Such an exoskeleton would be directly controlled by the patient's voluntary brain activity in order to allow the patient to move autonomously. Simultaneously, sensors distributed across the exoskeleton would generate the type of tactile feedback needed for the patient's brain to identify the texture, shape and temperature of objects, as well as many features of the surface upon which they walk.

This overall therapeutic approach is the one chosen by the Walk Again Project, an international, non-profit consortium, established by a team of Brazilian, American, Swiss, and German scientists, which aims at restoring full body mobility to quadriplegic patients through a brain-machine-brain interface implemented in conjunction with a full-body robotic exoskeleton.

The international scientific team recently proposed to carry out its first public demonstration of such an autonomous exoskeleton during the opening game of the 2014 FIFA Soccer World Cup that will be held in Brazil.

Other authors include Joseph E. O'Doherty, Mikhail A. Lebedev, Peter J. Ifft, Katie Z. Zhuang, all from the Duke University Center for Neuroengineering and Solaiman Shokur, and Hannes Bleuler from the Ecole Polytechnic Federale de Lausanne (EPFL), in Lausanne, Switzerland.

This work was funded by the U.S. National Institutes of Health.

A video illustrating the experiment is available at: http://www.youtube.com/watch?v=WTTTwvjCa5g

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The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Duke University Medical Center.

Journal Reference:

Joseph E. O’Doherty, Mikhail A. Lebedev, Peter J. Ifft, Katie Z. Zhuang, Solaiman Shokur, Hannes Bleuler, Miguel A. L. Nicolelis. Active tactile exploration using a brain–machine–brain interface. Nature, 2011; DOI: 10.1038/nature10489

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Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

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New targets for the control of HIV predicted using a novel computational analysis

ScienceDaily (Sep. 23, 2011) — A new computational approach has predicted numerous human proteins that the human immunodeficiency virus (HIV) requires to replicate itself. These discoveries "constitute a powerful resource for experimentalists who desire to discover new targets for human proteins that can control the spread of HIV," according to the authors of this study that appears in the Sept. 22, 2011 issue of PLoS Computational Biology, a journal published by the Public Library of Science.

The authors of the article are: T. M. Murali, a computer scientist, and Brett Tyler of the Virginia Bioinformatics Institute, both located at Virginia Tech, and Michael G. Katze, a microbiologist and associate director of the Washington National Primate Research Center at the University of Washington.

David Badger of Blacksburg, Va., one of Murali's graduate students, and Matthew D. Dyer of Applied Biosystems of Foster City, Cal., also contributed to the study, which was funded by grants from the National Institutes of Health to Katze, the Virginia Bioinformatics Institute Fellows Program to Murali and Tyler, and the Virginia Tech's Support Program for Innovative Research Strategies to Murali.

When a person contracts HIV, it causes the progressive failure of the body's immune system, with the onset of life threatening infections and diseases such as cancer. Over 25 years of intensive research have failed to create a vaccine for preventing HIV. Moreover, drugs used to cure HIV become rapidly ineffective because HIV is able to develop mutations against drugs, Murali said.

A recent line of research is examining whether human proteins can be targeted to cure HIV. Since viruses such as HIV have very small genomes, they must exploit the cellular machinery of the host to spread. Therefore, disrupting the activity of selected host proteins may impede viruses. Moreover, since human proteins evolve at a much slower rate than HIV proteins, human proteins that are targeted by drugs are very unlikely to develop mutations that render the drugs ineffective.

In fact, three studies published in 2008 systematically silenced virtually every human gene in order to discover HIV Dependency Factors (HDFs), i.e., those genes that are necessary for HIV to survive and replicate. Each of these three studies discovered hundreds of HDFs. However, a puzzling aspect was that only a handful of HDFs were common to two or more experiments.

"We set out to untangle this mystery," Murali said. "We hypothesized that many HDFs have not yet been discovered. Other papers had suggested that HDFs may themselves interact with each other. Inspired by these observations, we hypothesized that we could predict new HDFs by exploiting the proximity between HDFs within networks of interactions between human proteins."

To this end, they used an algorithm called SinkSource developed by Murali and Tyler. Tyler explained the algorithm using this analogy: "We treated the human protein network as if it were a system of tanks connected by pipes carrying water. This arrangement allowed us to study the flow of predictive information (water) from proteins we are certain about (full tanks) to those we are uncertain about (empty tanks). The further you get from the full tanks, the weaker the trickle, and the less water accumulates in the bottom of the tank. Mathematically you can show that, over time, every empty tank accumulates some stable level of water. At the end of the analysis, tanks accumulating lots of water were judged to be good predictions."

"We found that SinkSource and one of its variants made predictions of very high quality," Murali added. "We evaluated predicted HDFS using a number of additional datasets that we did not use during the prediction step."

Their most exciting results used an analysis of HDF activities in two non-human primate species that respond differently to Simian Immunodeficiency Virus (SIV). One species, the African green monkey, does not develop disease when infected by SIV, in contrast to the other species, pig-tailed macaque. Using data already published by Katze, the authors showed that predicted HDFs had very different patterns of expression in the two species, especially in lymph nodes and within 10 days after infection with the virus. They also showed that predicted HDFs participated in human cellular processes that are known to be subverted by the virus, including gene transcription and translation, energy production, protein degradation, and transport across the nuclear membrane. Moreover, many predicted HDFs themselves directly interacted with proteins in HIV.

From these results, Murali, Tyler, and Katze concluded that existing genomic screens are "incomplete and many HDFs are yet to be discovered experimentally. Our results suggest that many HDFs are yet to be discovered and that they have potential value as prognostic markers to determine pathological outcome and the likelihood of Acquired Immune Deficiency Syndrome (AIDS) development."

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Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Virginia Tech, via EurekAlert!, a service of AAAS.

Journal Reference:

T. M. Murali, Matthew D. Dyer, David Badger, Brett M. Tyler, Michael G. Katze. Network-Based Prediction and Analysis of HIV Dependency Factors. PLoS Computational Biology, 2011; 7 (9): e1002164 DOI: 10.1371/journal.pcbi.1002164

Note: If no author is given, the source is cited instead.

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

New targets for the control of HIV predicted using a novel computational analysis

ScienceDaily (Sep. 23, 2011) — A new computational approach has predicted numerous human proteins that the human immunodeficiency virus (HIV) requires to replicate itself. These discoveries "constitute a powerful resource for experimentalists who desire to discover new targets for human proteins that can control the spread of HIV," according to the authors of this study that appears in the Sept. 22, 2011 issue of PLoS Computational Biology, a journal published by the Public Library of Science.

The authors of the article are: T. M. Murali, a computer scientist, and Brett Tyler of the Virginia Bioinformatics Institute, both located at Virginia Tech, and Michael G. Katze, a microbiologist and associate director of the Washington National Primate Research Center at the University of Washington.

David Badger of Blacksburg, Va., one of Murali's graduate students, and Matthew D. Dyer of Applied Biosystems of Foster City, Cal., also contributed to the study, which was funded by grants from the National Institutes of Health to Katze, the Virginia Bioinformatics Institute Fellows Program to Murali and Tyler, and the Virginia Tech's Support Program for Innovative Research Strategies to Murali.

When a person contracts HIV, it causes the progressive failure of the body's immune system, with the onset of life threatening infections and diseases such as cancer. Over 25 years of intensive research have failed to create a vaccine for preventing HIV. Moreover, drugs used to cure HIV become rapidly ineffective because HIV is able to develop mutations against drugs, Murali said.

A recent line of research is examining whether human proteins can be targeted to cure HIV. Since viruses such as HIV have very small genomes, they must exploit the cellular machinery of the host to spread. Therefore, disrupting the activity of selected host proteins may impede viruses. Moreover, since human proteins evolve at a much slower rate than HIV proteins, human proteins that are targeted by drugs are very unlikely to develop mutations that render the drugs ineffective.

In fact, three studies published in 2008 systematically silenced virtually every human gene in order to discover HIV Dependency Factors (HDFs), i.e., those genes that are necessary for HIV to survive and replicate. Each of these three studies discovered hundreds of HDFs. However, a puzzling aspect was that only a handful of HDFs were common to two or more experiments.

"We set out to untangle this mystery," Murali said. "We hypothesized that many HDFs have not yet been discovered. Other papers had suggested that HDFs may themselves interact with each other. Inspired by these observations, we hypothesized that we could predict new HDFs by exploiting the proximity between HDFs within networks of interactions between human proteins."

To this end, they used an algorithm called SinkSource developed by Murali and Tyler. Tyler explained the algorithm using this analogy: "We treated the human protein network as if it were a system of tanks connected by pipes carrying water. This arrangement allowed us to study the flow of predictive information (water) from proteins we are certain about (full tanks) to those we are uncertain about (empty tanks). The further you get from the full tanks, the weaker the trickle, and the less water accumulates in the bottom of the tank. Mathematically you can show that, over time, every empty tank accumulates some stable level of water. At the end of the analysis, tanks accumulating lots of water were judged to be good predictions."

"We found that SinkSource and one of its variants made predictions of very high quality," Murali added. "We evaluated predicted HDFS using a number of additional datasets that we did not use during the prediction step."

Their most exciting results used an analysis of HDF activities in two non-human primate species that respond differently to Simian Immunodeficiency Virus (SIV). One species, the African green monkey, does not develop disease when infected by SIV, in contrast to the other species, pig-tailed macaque. Using data already published by Katze, the authors showed that predicted HDFs had very different patterns of expression in the two species, especially in lymph nodes and within 10 days after infection with the virus. They also showed that predicted HDFs participated in human cellular processes that are known to be subverted by the virus, including gene transcription and translation, energy production, protein degradation, and transport across the nuclear membrane. Moreover, many predicted HDFs themselves directly interacted with proteins in HIV.

From these results, Murali, Tyler, and Katze concluded that existing genomic screens are "incomplete and many HDFs are yet to be discovered experimentally. Our results suggest that many HDFs are yet to be discovered and that they have potential value as prognostic markers to determine pathological outcome and the likelihood of Acquired Immune Deficiency Syndrome (AIDS) development."

Recommend this story on Facebook, Twitter,
and Google +1:

Other bookmarking and sharing tools:

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Virginia Tech, via EurekAlert!, a service of AAAS.

Journal Reference:

T. M. Murali, Matthew D. Dyer, David Badger, Brett M. Tyler, Michael G. Katze. Network-Based Prediction and Analysis of HIV Dependency Factors. PLoS Computational Biology, 2011; 7 (9): e1002164 DOI: 10.1371/journal.pcbi.1002164

Note: If no author is given, the source is cited instead.

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Using waste heat from automobile exhaust

ScienceDaily (June 12, 2011) — With the completion of a successful prototype, engineers at Oregon State University have made a major step toward addressing one of the leading problems in energy use around the world today -- the waste of half or more of the energy produced by cars, factories and power plants.

New technology is being developed at OSU to capture and use the low-to-medium grade waste heat that's now going out the exhaust pipe of millions of automobiles, diesel generators, or being wasted by factories and electrical utilities.

The potential cost savings, improved energy efficiency and broad application of such technology is enormous, experts say. The new systems now being perfected at OSU should be able to use much of that waste heat either in cooling or the production of electricity.

A prototype device has been finished to demonstrate the efficacy of this technology, and the findings just published in Applied Thermal Engineering, a professional journal.

"This could become a very important new energy source and way to improve energy efficiency," said Hailei Wang, a research associate in the School of Mechanical, Industrial and Manufacturing Engineering at OSU. "The prototype shows that these systems work as well as we expected they would."

More than half of the heat generated by industrial activities is now wasted, Wang said, and even very advanced electrical power plants only convert about 40 percent of the energy produced into electricity. The internal combustion engines of automobiles are even worse -- they generally operate around 25-40 percent conversion efficiency. The very function of an automobile radiator is to dissipate wasted heat.

Various approaches have been attempted, and are sometimes used, to capture and use at least some of that waste heat to produce cooling. The new system being developed at OSU may do that as, or more efficiently than past approaches, be more portable, and also have one major advantage -- the ability to also produce electricity.

It's called a "thermally activated cooling system" that gains much of its efficiency by using extraordinarily small microchannels which help to better meet the performance, size and weight challenges. It effectively combines a vapor compression cycle with an "organic Rankine cycle," an existing energy conversion technology.

The new prototype completed at OSU succeeded in turning 80 percent of every kilowatt of waste heat into a kilowatt of cooling capability. Researchers say the conversion efficiency wouldn't be nearly as high if the goal is to produce electricity -- about 15-20 percent -- but it's still much better than the current approach, which is to waste the energy potential of all of the heat.

"This technology would be especially useful if there's a need to have cooling systems where heat is being wasted," Wang said. "That's one reason the research has been supported by the Department of Defense, because they see it being used to provide needed air conditioning for electronics and other purposes when they are using generators in the field."

However, the OSU scientists said that may be just the beginning. Factories often produce enormous amounts of wasted heat in their operations. The systems could also be incorporated into alternative energy technologies such as solar or geothermal, scientists say, in addition to fossil fuel use.

Conceptually, it should also be possible for such systems to be used in hybrid automotive technology, taking waste heat from the gasoline engine and using it not only for air conditioning but also to help recharge the battery that powers the vehicle, Wang said.

Continued research will be needed to perfect the technology and adapt it to different uses, the scientists said.

The work takes advantage of OSU's advanced programs in microchannel technology, a key focus of the Microproducts Breakthrough Institute operated by OSU and the Pacific Northwest National Laboratory. This study was co-authored by Rich Peterson, an OSU professor of mechanical engineering, expert in thermal sciences and energy systems, and associate director of the Microproducts Breakthrough Institute.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Oregon State University.

Journal Reference:

Hailei Wang, Richard B. Peterson. Performance Enhancement of a Thermally Activated Cooling System Using Microchannel Heat Exchangers. Applied Thermal Engineering, 2011; DOI: 10.1016/j.applthermaleng.2011.05.026

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Using magnets to help prevent heart attacks: Magnetic field can reduce blood viscosity, physicist discovers

ScienceDaily (June 8, 2011) — If a person's blood becomes too thick it can damage blood vessels and increase the risk of heart attacks. But a Temple University physicist has discovered that he can thin the human blood by subjecting it to a magnetic field.

Rongjia Tao, professor and chair of physics at Temple University, has pioneered the use of electric or magnetic fields to decrease the viscosity of oil in engines and pipelines. Now, he is using the same magnetic fields to thin human blood in the circulation system.

Because red blood cells contain iron, Tao has been able to reduce a person's blood viscosity by 20-30 percent by subjecting it to a magnetic field of 1.3 Telsa (about the same as an MRI) for about one minute.

Tao and his collaborator tested numerous blood samples in a Temple lab and found that the magnetic field polarizes the red blood cells causing them to link together in short chains, streamlining the movement of the blood. Because these chains are larger than the single blood cells, they flow down the center, reducing the friction against the walls of the blood vessels. The combined effects reduce the viscosity of the blood, helping it to flow more freely.

When the magnetic field was taken away, the blood's original viscosity state slowly returned, but over a period of several hours.

"By selecting a suitable magnetic field strength and pulse duration, we will be able to control the size of the aggregated red-cell chains, hence to control the blood's viscosity," said Tao. "This method of magneto-rheology provides an effective way to control the blood viscosity within a selected range."

Currently, the only method for thinning blood is through drugs such as aspirin; however, these drugs often produce unwanted side effects. Tao said that the magnetic field method is not only safer, it is repeatable. The magnetic fields may be reapplied and the viscosity reduced again. He also added that the viscosity reduction does not affect the red blood cells' normal function.

Tao said that further studies are needed and that he hopes to ultimately develop this technology into an acceptable therapy to prevent heart disease.

Tao and his former graduate student, Ke "Colin" Huang, now a medical physics resident in the Department of Radiation Oncology at the University of Michigan, are publishing their findings in the journal Physical Review E.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Temple University, via EurekAlert!, a service of AAAS.

Note: If no author is given, the source is cited instead.

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Using waste heat from automobile exhaust

ScienceDaily (June 12, 2011) — With the completion of a successful prototype, engineers at Oregon State University have made a major step toward addressing one of the leading problems in energy use around the world today -- the waste of half or more of the energy produced by cars, factories and power plants.

New technology is being developed at OSU to capture and use the low-to-medium grade waste heat that's now going out the exhaust pipe of millions of automobiles, diesel generators, or being wasted by factories and electrical utilities.

The potential cost savings, improved energy efficiency and broad application of such technology is enormous, experts say. The new systems now being perfected at OSU should be able to use much of that waste heat either in cooling or the production of electricity.

A prototype device has been finished to demonstrate the efficacy of this technology, and the findings just published in Applied Thermal Engineering, a professional journal.

"This could become a very important new energy source and way to improve energy efficiency," said Hailei Wang, a research associate in the School of Mechanical, Industrial and Manufacturing Engineering at OSU. "The prototype shows that these systems work as well as we expected they would."

More than half of the heat generated by industrial activities is now wasted, Wang said, and even very advanced electrical power plants only convert about 40 percent of the energy produced into electricity. The internal combustion engines of automobiles are even worse -- they generally operate around 25-40 percent conversion efficiency. The very function of an automobile radiator is to dissipate wasted heat.

Various approaches have been attempted, and are sometimes used, to capture and use at least some of that waste heat to produce cooling. The new system being developed at OSU may do that as, or more efficiently than past approaches, be more portable, and also have one major advantage -- the ability to also produce electricity.

It's called a "thermally activated cooling system" that gains much of its efficiency by using extraordinarily small microchannels which help to better meet the performance, size and weight challenges. It effectively combines a vapor compression cycle with an "organic Rankine cycle," an existing energy conversion technology.

The new prototype completed at OSU succeeded in turning 80 percent of every kilowatt of waste heat into a kilowatt of cooling capability. Researchers say the conversion efficiency wouldn't be nearly as high if the goal is to produce electricity -- about 15-20 percent -- but it's still much better than the current approach, which is to waste the energy potential of all of the heat.

"This technology would be especially useful if there's a need to have cooling systems where heat is being wasted," Wang said. "That's one reason the research has been supported by the Department of Defense, because they see it being used to provide needed air conditioning for electronics and other purposes when they are using generators in the field."

However, the OSU scientists said that may be just the beginning. Factories often produce enormous amounts of wasted heat in their operations. The systems could also be incorporated into alternative energy technologies such as solar or geothermal, scientists say, in addition to fossil fuel use.

Conceptually, it should also be possible for such systems to be used in hybrid automotive technology, taking waste heat from the gasoline engine and using it not only for air conditioning but also to help recharge the battery that powers the vehicle, Wang said.

Continued research will be needed to perfect the technology and adapt it to different uses, the scientists said.

The work takes advantage of OSU's advanced programs in microchannel technology, a key focus of the Microproducts Breakthrough Institute operated by OSU and the Pacific Northwest National Laboratory. This study was co-authored by Rich Peterson, an OSU professor of mechanical engineering, expert in thermal sciences and energy systems, and associate director of the Microproducts Breakthrough Institute.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Oregon State University.

Journal Reference:

Hailei Wang, Richard B. Peterson. Performance Enhancement of a Thermally Activated Cooling System Using Microchannel Heat Exchangers. Applied Thermal Engineering, 2011; DOI: 10.1016/j.applthermaleng.2011.05.026

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Using magnets to help prevent heart attacks: Magnetic field can reduce blood viscosity, physicist discovers

ScienceDaily (June 8, 2011) — If a person's blood becomes too thick it can damage blood vessels and increase the risk of heart attacks. But a Temple University physicist has discovered that he can thin the human blood by subjecting it to a magnetic field.

Rongjia Tao, professor and chair of physics at Temple University, has pioneered the use of electric or magnetic fields to decrease the viscosity of oil in engines and pipelines. Now, he is using the same magnetic fields to thin human blood in the circulation system.

Because red blood cells contain iron, Tao has been able to reduce a person's blood viscosity by 20-30 percent by subjecting it to a magnetic field of 1.3 Telsa (about the same as an MRI) for about one minute.

Tao and his collaborator tested numerous blood samples in a Temple lab and found that the magnetic field polarizes the red blood cells causing them to link together in short chains, streamlining the movement of the blood. Because these chains are larger than the single blood cells, they flow down the center, reducing the friction against the walls of the blood vessels. The combined effects reduce the viscosity of the blood, helping it to flow more freely.

When the magnetic field was taken away, the blood's original viscosity state slowly returned, but over a period of several hours.

"By selecting a suitable magnetic field strength and pulse duration, we will be able to control the size of the aggregated red-cell chains, hence to control the blood's viscosity," said Tao. "This method of magneto-rheology provides an effective way to control the blood viscosity within a selected range."

Currently, the only method for thinning blood is through drugs such as aspirin; however, these drugs often produce unwanted side effects. Tao said that the magnetic field method is not only safer, it is repeatable. The magnetic fields may be reapplied and the viscosity reduced again. He also added that the viscosity reduction does not affect the red blood cells' normal function.

Tao said that further studies are needed and that he hopes to ultimately develop this technology into an acceptable therapy to prevent heart disease.

Tao and his former graduate student, Ke "Colin" Huang, now a medical physics resident in the Department of Radiation Oncology at the University of Michigan, are publishing their findings in the journal Physical Review E.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Temple University, via EurekAlert!, a service of AAAS.

Note: If no author is given, the source is cited instead.

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Using microbes to generate electricity?

ScienceDaily (May 23, 2011) — Using bacteria to generate energy is a significant step closer following a breakthrough discovery by scientists at the University of East Anglia (UEA).

Published May 23 by the scientific journal Proceedings of the National Academy of Sciences (PNAS), the research demonstrates for the first time the exact molecular structure of the proteins which enable bacterial cells to transfer electrical charge.

The discovery means scientists can now start developing ways to 'tether' bacteria directly to electrodes -- creating efficient microbial fuel cells or 'bio-batteries'. The advance could also hasten the development of microbe-based agents that can clean up oil or uranium pollution, and fuel cells powered by human or animal waste.

"This is an exciting advance in our understanding of how some bacterial species move electrons from the inside to the outside of a cell," said Dr Tom Clarke of UEA's School of Biological Sciences.

"Identifying the precise molecular structure of the key proteins involved in this process is a crucial step towards tapping into microbes as a viable future source of electricity."

Funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the US Department of Energy, the project is led by Dr Clarke, Prof David Richardson and Prof Julea Butt of UEA, in collaboration with colleagues at the Pacific Northwest National Laboratory in the US.

In earlier research published by PNAS in 2009, the team demonstrated the mechanism by which bacteria survive in oxygen-free environments by constructing electrical wires that extend through the cell wall and make contact with a mineral -- a process called iron respiration or 'breathing rocks'.

In this latest research, the scientists used a technique called x-ray crystallography to reveal the molecular structure of the proteins attached to the surface of a Shewanella oneidensis cell through which electrons are transferred.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by University of East Anglia.

Journal Reference:

Thomas A. Clarke, Marcus J. Edwards, Andrew J. Gates, Andrea Hall, Gaye F. White, Justin Bradley, Catherine L. Reardon, Liang Shi, Alexander S. Beliaev, Matthew J. Marshall, Zheming Wang, Nicholas J. Watmough, James K. Fredrickson, John M. Zachara, Julea N. Butt and David J. Richardson. Structure of a bacterial cell surface decaheme electron conduit. PNAS, May 23, 2011 DOI: 10.1073/pnas.1017200108

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Using microbes to generate electricity?

ScienceDaily (May 23, 2011) — Using bacteria to generate energy is a significant step closer following a breakthrough discovery by scientists at the University of East Anglia (UEA).

Published May 23 by the scientific journal Proceedings of the National Academy of Sciences (PNAS), the research demonstrates for the first time the exact molecular structure of the proteins which enable bacterial cells to transfer electrical charge.

The discovery means scientists can now start developing ways to 'tether' bacteria directly to electrodes -- creating efficient microbial fuel cells or 'bio-batteries'. The advance could also hasten the development of microbe-based agents that can clean up oil or uranium pollution, and fuel cells powered by human or animal waste.

"This is an exciting advance in our understanding of how some bacterial species move electrons from the inside to the outside of a cell," said Dr Tom Clarke of UEA's School of Biological Sciences.

"Identifying the precise molecular structure of the key proteins involved in this process is a crucial step towards tapping into microbes as a viable future source of electricity."

Funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the US Department of Energy, the project is led by Dr Clarke, Prof David Richardson and Prof Julea Butt of UEA, in collaboration with colleagues at the Pacific Northwest National Laboratory in the US.

In earlier research published by PNAS in 2009, the team demonstrated the mechanism by which bacteria survive in oxygen-free environments by constructing electrical wires that extend through the cell wall and make contact with a mineral -- a process called iron respiration or 'breathing rocks'.

In this latest research, the scientists used a technique called x-ray crystallography to reveal the molecular structure of the proteins attached to the surface of a Shewanella oneidensis cell through which electrons are transferred.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by University of East Anglia.

Journal Reference:

Thomas A. Clarke, Marcus J. Edwards, Andrew J. Gates, Andrea Hall, Gaye F. White, Justin Bradley, Catherine L. Reardon, Liang Shi, Alexander S. Beliaev, Matthew J. Marshall, Zheming Wang, Nicholas J. Watmough, James K. Fredrickson, John M. Zachara, Julea N. Butt and David J. Richardson. Structure of a bacterial cell surface decaheme electron conduit. PNAS, May 23, 2011 DOI: 10.1073/pnas.1017200108

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Teaching algae to make fuel: New process could lead to production of hydrogen using bioengineered microorganisms

ScienceDaily (May 24, 2011) — Many kinds of algae and cyanobacteria, common water-dwelling microorganisms, are capable of using energy from sunlight to split water molecules and release hydrogen, which holds promise as a clean and carbon-free fuel for the future. One reason this approach hasn't yet been harnessed for fuel production is that under ordinary circumstances, hydrogen production takes a back seat to the production of compounds that the organisms use to support their own growth.

But Shuguang Zhang, associate director of MIT's Center for Biomedical Engineering, and postdocs Iftach Yacoby and Sergii Pochekailov, together with colleagues at Tel Aviv University in Israel and the National Renewable Energy Laboratory in Colorado, have found a way to use bioengineered proteins to flip this preference, allowing more hydrogen to be produced.

"The algae are really not interested in producing hydrogen, they want to produce sugar," Yacoby says -- the sugar is what they need for their own survival, and the hydrogen is just a byproduct. But a multitasking enzyme, introduced into the liquid where the algae are at work, both suppresses the sugar production and redirects the organisms' energies into hydrogen production. The work is described in a paper being published online this week in the Proceedings of the National Academy of Sciences, and was supported in part by a European Molecular Biology Organization postdoctoral fellowship, the Yang Trust Fund and the U.S. Department of Energy's National Renewable Energy Laboratory.

Adding the bioengineered enzyme increases the rate of algal hydrogen production by about 400 percent, Yacoby says. The sugar production is suppressed but not eliminated, he explains, because "if it went to zero, it would kill the organism."

The research demonstrates for the first time how the two processes carried out by algae compete with each other; it also shows how that competition could be modified to favor hydrogen production in a laboratory environment. Zhang and Yacoby plan to continue developing the system to increase its efficiency of hydrogen production.

"It's one step closer to an industrial process," Zhang says. "First, you have to understand the science" -- which has been achieved through this experimental work. Now, developing it further -- through refinements to produce a viable commercial system for hydrogen-fuel manufacturing -- is "a matter of time and money," Zhang says.

Ultimately, such a system could be used to produce hydrogen on a large scale using water and sunlight. The hydrogen could be used directly to generate electricity in a fuel cell or to power a vehicle, or could be combined with carbon dioxide to make methane or other fuels in a renewable, carbon-neutral way, the researchers say.

In the long run, "the only viable way to produce renewable energy is to use the sun, [either] to make electricity or in a biochemical reaction to produce hydrogen," Yacoby says. "I believe there is no one solution," he adds, but rather many different approaches depending on the location and the end uses.

This particular approach, he says, is simple enough that it has promise "not just in industrialized countries, but in developing countries as well" as a source of inexpensive fuel. The algae needed for the process exist everywhere on Earth, and there are no toxic materials involved in any part of the process, he says.

"The beauty is in its simplicity," he says.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Massachusetts Institute of Technology. The original article was written by David L. Chandler.

Journal Reference:

I. Yacoby, S. Pochekailov, H. Toporik, M. L. Ghirardi, P. W. King, S. Zhang. Photosynthetic electron partitioning between [FeFe]-hydrogenase and ferredoxin:NADP -oxidoreductase (FNR) enzymes in vitro. Proceedings of the National Academy of Sciences, 2011; DOI: 10.1073/pnas.1103659108

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Teaching algae to make fuel: New process could lead to production of hydrogen using bioengineered microorganisms

ScienceDaily (May 24, 2011) — Many kinds of algae and cyanobacteria, common water-dwelling microorganisms, are capable of using energy from sunlight to split water molecules and release hydrogen, which holds promise as a clean and carbon-free fuel for the future. One reason this approach hasn't yet been harnessed for fuel production is that under ordinary circumstances, hydrogen production takes a back seat to the production of compounds that the organisms use to support their own growth.

But Shuguang Zhang, associate director of MIT's Center for Biomedical Engineering, and postdocs Iftach Yacoby and Sergii Pochekailov, together with colleagues at Tel Aviv University in Israel and the National Renewable Energy Laboratory in Colorado, have found a way to use bioengineered proteins to flip this preference, allowing more hydrogen to be produced.

"The algae are really not interested in producing hydrogen, they want to produce sugar," Yacoby says -- the sugar is what they need for their own survival, and the hydrogen is just a byproduct. But a multitasking enzyme, introduced into the liquid where the algae are at work, both suppresses the sugar production and redirects the organisms' energies into hydrogen production. The work is described in a paper being published online this week in the Proceedings of the National Academy of Sciences, and was supported in part by a European Molecular Biology Organization postdoctoral fellowship, the Yang Trust Fund and the U.S. Department of Energy's National Renewable Energy Laboratory.

Adding the bioengineered enzyme increases the rate of algal hydrogen production by about 400 percent, Yacoby says. The sugar production is suppressed but not eliminated, he explains, because "if it went to zero, it would kill the organism."

The research demonstrates for the first time how the two processes carried out by algae compete with each other; it also shows how that competition could be modified to favor hydrogen production in a laboratory environment. Zhang and Yacoby plan to continue developing the system to increase its efficiency of hydrogen production.

"It's one step closer to an industrial process," Zhang says. "First, you have to understand the science" -- which has been achieved through this experimental work. Now, developing it further -- through refinements to produce a viable commercial system for hydrogen-fuel manufacturing -- is "a matter of time and money," Zhang says.

Ultimately, such a system could be used to produce hydrogen on a large scale using water and sunlight. The hydrogen could be used directly to generate electricity in a fuel cell or to power a vehicle, or could be combined with carbon dioxide to make methane or other fuels in a renewable, carbon-neutral way, the researchers say.

In the long run, "the only viable way to produce renewable energy is to use the sun, [either] to make electricity or in a biochemical reaction to produce hydrogen," Yacoby says. "I believe there is no one solution," he adds, but rather many different approaches depending on the location and the end uses.

This particular approach, he says, is simple enough that it has promise "not just in industrialized countries, but in developing countries as well" as a source of inexpensive fuel. The algae needed for the process exist everywhere on Earth, and there are no toxic materials involved in any part of the process, he says.

"The beauty is in its simplicity," he says.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Massachusetts Institute of Technology. The original article was written by David L. Chandler.

Journal Reference:

I. Yacoby, S. Pochekailov, H. Toporik, M. L. Ghirardi, P. W. King, S. Zhang. Photosynthetic electron partitioning between [FeFe]-hydrogenase and ferredoxin:NADP -oxidoreductase (FNR) enzymes in vitro. Proceedings of the National Academy of Sciences, 2011; DOI: 10.1073/pnas.1103659108

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Transistors reinvented using new 3-D structure

ScienceDaily (May 5, 2011) — Intel Corporation has announced a significant breakthrough in the evolution of the transistor, the microscopic building block of modern electronics. For the first time since the invention of silicon transistors over 50 years ago, transistors using a three-dimensional structure will be put into high-volume manufacturing. Intel will introduce a revolutionary 3-D transistor design called Tri-Gate, first disclosed by Intel in 2002, into high-volume manufacturing at the 22-nanometer (nm) node in an Intel chip codenamed "Ivy Bridge." A nanometer is one-billionth of a meter.

The three-dimensional Tri-Gate transistors represent a fundamental departure from the two-dimensional planar transistor structure that has powered not only all computers, mobile phones and consumer electronics to-date, but also the electronic controls within cars, spacecraft, household appliances, medical devices and virtually thousands of other everyday devices for decades.

"Intel's scientists and engineers have once again reinvented the transistor, this time utilizing the third dimension," said Intel President and CEO Paul Otellini. "Amazing, world-shaping devices will be created from this capability as we advance Moore's Law into new realms."

Scientists have long recognized the benefits of a 3-D structure for sustaining the pace of Moore's Law as device dimensions become so small that physical laws become barriers to advancement. The key to this latest breakthrough is Intel's ability to deploy its novel 3-D Tri-Gate transistor design into high-volume manufacturing, ushering in the next era of Moore's Law and opening the door to a new generation of innovations across a broad spectrum of devices.

Moore's Law is a forecast for the pace of silicon technology development that states that roughly every 2 years transistor density will double, while increasing functionality and performance and decreasing costs. It has become the basic business model for the semiconductor industry for more than 40 years.

Unprecedented Power Savings and Performance Gains

Intel's 3-D Tri-Gate transistors enable chips to operate at lower voltage with lower leakage, providing an unprecedented combination of improved performance and energy efficiency compared to previous state-of-the-art transistors. The capabilities give chip designers the flexibility to choose transistors targeted for low power or high performance, depending on the application.

The 22nm 3-D Tri-Gate transistors provide up to 37 percent performance increase at low voltage versus Intel's 32nm planar transistors. This incredible gain means that they are ideal for use in small handheld devices, which operate using less energy to "switch" back and forth. Alternatively, the new transistors consume less than half the power when at the same performance as 2-D planar transistors on 32nm chips.

"The performance gains and power savings of Intel's unique 3-D Tri-Gate transistors are like nothing we've seen before," said Mark Bohr, Intel Senior Fellow. "This milestone is going further than simply keeping up with Moore's Law. The low-voltage and low-power benefits far exceed what we typically see from one process generation to the next. It will give product designers the flexibility to make current devices smarter and wholly new ones possible. We believe this breakthrough will extend Intel's lead even further over the rest of the semiconductor industry."

Continuing the Pace of Innovation -- Moore's Law

Transistors continue to get smaller, cheaper and more energy efficient in accordance with Moore's Law -- named for Intel co-founder Gordon Moore. Because of this, Intel has been able to innovate and integrate, adding more features and computing cores to each chip, increasing performance, and decreasing manufacturing cost per transistor.

Sustaining the progress of Moore's Law becomes even more complex with the 22nm generation. Anticipating this, Intel research scientists in 2002 invented what they called a Tri-Gate transistor, named for the three sides of the gate. This announcement follows further years of development in Intel's highly coordinated research-development-manufacturing pipeline, and marks the implementation of this work for high-volume manufacturing.

The 3-D Tri-Gate transistors are a reinvention of the transistor. The traditional "flat" two-dimensional planar gate is replaced with an incredibly thin three-dimensional silicon fin that rises up vertically from the silicon substrate. Control of current is accomplished by implementing a gate on each of the three sides of the fin -- two on each side and one across the top -- rather than just one on top, as is the case with the 2-D planar transistor. The additional control enables as much transistor current flowing as possible when the transistor is in the "on" state (for performance), and as close to zero as possible when it is in the "off" state (to minimize power), and enables the transistor to switch very quickly between the two states (again, for performance).

Just as skyscrapers let urban planners optimize available space by building upward, Intel's 3-D Tri-Gate transistor structure provides a way to manage density. Since these fins are vertical in nature, transistors can be packed closer together, a critical component to the technological and economic benefits of Moore's Law. For future generations, designers also have the ability to continue growing the height of the fins to get even more performance and energy-efficiency gains.

"For years we have seen limits to how small transistors can get," said Moore. "This change in the basic structure is a truly revolutionary approach, and one that should allow Moore's Law, and the historic pace of innovation, to continue."

World's First Demonstration of 22nm 3-D Tri-Gate Transistors

The 3-D Tri-Gate transistor will be implemented in the company's upcoming manufacturing process, called the 22nm node, in reference to the size of individual transistor features. More than 6 million 22nm Tri-Gate transistors could fit in the period at the end of this sentence.

Intel has demonstrated the world's first 22nm microprocessor, codenamed "Ivy Bridge," working in a laptop, server and desktop computer. Ivy Bridge-based Intel® Core™ family processors will be the first high-volume chips to use 3-D Tri-Gate transistors. Ivy Bridge is slated for high-volume production readiness by the end of this year.

This silicon technology breakthrough will also aid in the delivery of more highly integrated Intel® Atom™ processor-based products that scale the performance, functionality and software compatibility of Intel® architecture while meeting the overall power, cost and size requirements for a range of market segment needs.

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The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Intel Corporation.

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Scientists design new anti-flu virus proteins using computational methods

ScienceDaily (May 14, 2011) — A research article May 12 in Science demonstrates the use of computational methods to design new antiviral proteins not found in nature, but capable of targeting specific surfaces of flu virus molecules.

One goal of such protein design would be to block molecular mechanisms involved in cell invasion and virus reproduction.

Computationally designed, surface targeting, antiviral proteins might also have diagnostic and therapeutic potential in identifying and fighting viral infections.

The lead authors of the study are Sarel J. Fleishman and Timothy Whitehead of the University of Washington (UW) Department of Biochemistry, and Damian C. Ekiert from the Department of Molecular Biology and the Skaggs Institute for Chemical Biology at The Scripps Research Institute. The senior authors are Ian Wilson from Scripps and David Baker from the UW and the Howard Hughes Medical Institute.

The researchers note that additional studies are required to see if such designed proteins can help in diagnosing, preventing or treating viral illness. What the study does suggest is the feasibility of using computer design to create new proteins with antiviral properties.

"Influenza presents a serious public health challenge," the researchers noted, "and new therapies are needed to combat viruses that are resistant to existing anti-viral medications or that escape the body's defense systems."

They focused their attention on the section of the flu virus known as the hemagglutinin stem region. They concentrated on trying to disable this part because of its function in invading the cells of the human respiratory tract.

Their approach was somewhat similar to engineering a small space shuttle with the right configuration and construction, as well as recognizance and interlocking mechanisms, to dock with a troublesome space station and upset its mission. Only these scientists attempted their engineering feat at an atomic and molecular level.

Central to their approach is the ability of biological molecules to recognize certain other molecules or their working parts, and to have an affinity for binding to them at pre-determined locations. This recognition has both physical and chemical bases. Protein-protein interactions underlie many biological activities, including those that disarm and deactivate viruses.

In their report, the researchers described their general computational methods for designing new, tiny protein molecules that could bind to a certain spot on large protein molecules. They took apart some protein structures and watched how these disembodied sections interacted with a target surface. They analyzed particular high-affinity interactions, and used this information to further refine computer-generated designs for interfaces.

"Protein surfaces are never flat, but have many crevices and bulges at the atomic scale," lead author Sarel Fleishman explained. "The challenge is to identify amino acid side chains that would fit perfectly into these surfaces. The fit must be precise both in shape and in other chemical properties such as electrostatic charge. This geometrical and biophysical problem can be computationally solved, but requires large computational resources."

The researchers made use of a peer-to-peer computing platform called Rosetta@Home for going through the hundreds of millions of possible interactions of designed proteins and the surface of hemagglutinin to solve this challenge.

Following optimization, the designed proteins bound hemagglutinin very tightly.

Through this method, the researchers created two designs for new proteins that could bind to a surface patch on the stem of the influenza hemagglutinin from the 1918 H1N1 pandemic flu virus.

The shortcomings of the approach, due to approximations, meant that the researchers started out with 73 possibilities of which just two were successful.

One of the disease-causing characteristics of the influenza hemagglutinin stem is that it changes shape by refolding when in an acidic environment. This reconfiguration appears to allow the virus reproduce itself inside of cells.

In this study, one of the newly designed proteins was shown to block a conformational change, not only in H1 influenza hemagglutinin, but also in a similar component in H5 avian influenza.

"This finding suggests that this new protein design may have virus-neutralizing effects against multiple influenza subtypes," the researchers reported.

What was unusual about the workable designs was that they had helical binding modes, roughly shaped like a spiral staircase, rather than the loop binding that naturally occurring antibodies employ.

X-ray crystallography of the proteins complex showed that the actual orientation of the bound proteins was almost identical to the way the binding mode was designed. The modified surface of the main recognition helix on the designed protein was packed into a groove on the desired region of the virus protein.

"Overall, the crystal structure is in excellent agreement with the designed interface," the researchers noted, "with no significant deviations at any of the contact points." The design and the actual formation were nearly identical.

The scientists were encouraged by this finding. Despite their limitations, the design methods, the scientists believe, capture the essential features of the desired protein-protein interaction.

In addition to Fleishman, Whitehead, Ekiert, Wilson and Baker, other scientists on the research team were Cyrille Dreyfus of The Scripps Research Institute, Jacob E. Corn, previously at the UW but now with Genentech in San Francisco, and Eva-Maria Strauch of the UW Department of Biochemistry.

Computational designs for this study were generated on resources provided by people around the world who donate their unused home computer time as part of Rosetta@Home and by the Argonne National Leadership Computing Facility.

The project was supported by a fellowship from the Human Frontier Science Program, the Jane Coffin Child's Memorial Fund, and a career development award from the National Institute of Allergy and Infectious Disease at the National Institutes of Health. Additional support came from the Defense Advanced Research Projects Agency, the NIH yeast resource center, the Defense Threat Reduction Agency, the Howard Hughes Medical Institute, the Achievement Rewards for College Scientists Foundation, the NIH Molecular Evolution Training Program and the Skaggs Institute for Chemical Biology.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by University of Washington. The original article was written by Leila Gray.

Journal Reference:

S. J. Fleishman, T. A. Whitehead, D. C. Ekiert, C. Dreyfus, J. E. Corn, E.-M. Strauch, I. A. Wilson, D. Baker. Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin. Science, 2011; 332 (6031): 816 DOI: 10.1126/science.1202617

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Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

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