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  • richardmitnick 12:44 pm on March 29, 2013 Permalink | Reply
    Tags: , , , Computer Science, , ,   

    From PNNL Lab: “Striking While the Iron Is Hot” 

    Chromatography combined with database search strategy identifies hard-to-find heme proteins

    March 2013
    Suraiya Farukhi
    Christine Sharp

    Results: Heme c is an important iron-containing post-translational modification found in many proteins. It plays an important role in respiration, metal reduction, and nitrogen fixation, especially anaerobic respiration of environmental microbes. Such bacteria and their c-type cytochromes are studied extensively because of their potential use in bioremediation, microbial fuel cells, and electrosynthesis of valuable biomaterials.

    heme c
    Heme C

    Until recently, these modifications were hard to find using traditional proteomic methods. Scientists at Pacific Northwest National Laboratory combined a heme c tag protein affinity purification strategy called histidine affinity chromatography (HAC) with enhanced database searching. This combination confidently identified heme c peptides in liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments-by as much as 100-fold in some cases.”

    Why It Matters: Iron is a critical part of many biological processes; however, it is often not biologically available or it can be toxic in high quantities. So, biological systems have developed intricate methods to use and store iron. Many environmentally important microbes and microbial communities are rich in c-type cytochromes. Combining HAC and data analysis tailored to the unique properties of heme c peptides should enable more detailed study of the role of c-type cytochromes in these microbes and microbial communities.

    ‘Several proteomics studies have analyzed the expression of c-type cytochromes under various conditions,’ said PNNL postdoctoral researcher Dr. Eric Merkley, and lead author of a paper that appeared in the Journal of Proteome Research. ‘A shared feature of these studies is that the cytochrome-rich fractions, the cell envelope or extracellular polymeric substance, were purified and explicitly analyzed to efficiently detect cytochromes. Analyses of large-scale proteomics datasets have typically suggested that c-type cytochromes, particularly the heme c peptides, are under-represented.'”

    See the full article here.

    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

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  • richardmitnick 7:22 pm on February 4, 2013 Permalink | Reply
    Tags: , , Computer Science   

    From CERN: “CERN and Oracle celebrate 30 years of collaboration” 

    CERN New Masthead

    4 Feb 2013
    Andrew Purcell

    On Friday 1 February, 2013, CERN and Oracle celebrated 30 years of collaboration. In addition to providing hardware and software to CERN for three decades, Oracle has now been involved in the CERN openlab project for 10 years.

    cake
    Rolf Heuer and Loïc le Guisquet cut cake to celebrate 30 years of collaboration between CERN and Oracle (Image: CERN)

    The celebration, which capped off the ‘IT requirements for the next generation of research infrastructures workshop’ held at CERN, saw CERN Director-General Rolf Heuer present Loïc le Guisquet, executive vice president of Oracle Europe, Middle East, and Africa with a small award to mark the occasion. Heuer presented Guisquet with an Oracle tape mounted in glass and marked with the following inscription: ‘LHC data are stored on Oracle tapes similar to the one presented on this award. This specific tape stores the videos of the announcement of the discovery of the new boson, which took place at CERN on 4th July 2012′.

    ‘It is important that IT infrastructures for research embrace new technologies in a manner that is not only useful for researchers, but also improves the competitiveness of many business sectors,’ says Heuer, who cites the collaboration between Oracle and CERN as an excellent example of this. ‘CERN has been working continuously with Oracle over the last 30 years,’ he adds. ‘Oracle is also a long-standing partner of CERN openlab and I think it has developed into a successful model over the last decade now of public-private partnerships in the IT domain.

    CERN openlab is a unique public-private partnership between CERN and a range of leading IT companies. Its mission is to accelerate the development of cutting-edge solutions to be used by the worldwide LHC community. ‘By using CERN openlab as a showcase, companies can then promote their products and their services to other labs and different business sectors,’ says Bob Jones, head of the organization. ‘We are proud to be part of this collaboration,’ says Le Guisquet. ‘We are energised by it and we want it to go on because it always stretches our limits.'”.

    See the full article here.

    Meet CERN in a variety of places:

    Cern Courier

    THE FOUR MAJOR PROJECT COLLABORATIONS

    ATLAS
    CERN ATLAS New

    ALICE
    CERN ALICE New

    CMS
    CERN CMS New

    LHCb
    CERN LHCb New

    LHC

    CERN LHC New

    LHC particles

    Quantum Diaries


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  • richardmitnick 7:32 pm on January 29, 2013 Permalink | Reply
    Tags: , Computer Science, , ,   

    From Stanford University: “Stanford Researchers Break Million-core Supercomputer Barrier” 

    Stanford Engineering plate

    Researchers at the Center for Turbulence Research set a new record in supercomputing, harnessing a million computing cores to model supersonic jet noise. Work was performed on the newly installed Sequoia IBM Bluegene/Q system at Lawrence Livermore National Laboratories.

    Friday, January 25, 2013
    Andrew Myers

    Stanford Engineering’s Center for Turbulence Research (CTR) has set a new record in computational science by successfully using a supercomputer with more than one million computing cores to solve a complex fluid dynamics problem—the prediction of noise generated by a supersonic jet engine.

    Joseph Nichols, a research associate in the center, worked on the newly installed Sequoia IBM Bluegene/Q system at Lawrence Livermore National Laboratories (LLNL) funded by the Advanced Simulation and Computing (ASC) Program of the National Nuclear Security Administration (NNSA). Sequoia once topped list of the world’s most powerful supercomputers, boasting 1,572,864 compute cores (processors) and 1.6 petabytes of memory connected by a high-speed five-dimensional torus interconnect.

    seq
    A floor view of the newly installed Sequoia supercomputer at the Lawrence Livermore National Laboratories. (Photo: Courtesy of Lawrence Livermore National Laboratories)

    Because of Sequoia’s impressive numbers of cores, Nichols was able to show for the first time that million-core fluid dynamics simulations are possible—and also to contribute to research aimed at designing quieter aircraft engines.

    jet
    An image from the jet noise simulation. A new design for an engine nozzle is shown in gray at left. Exhaust tempertures are in red/orange. The sound field is blue/cyan. Chevrons along the nozzle rim enhance turbulent mixing to reduce noise. (Illustration: Courtesy of the Center for Turbulence Research, Stanford University)

    Andrew Myers is associate director of communications for the Stanford University School of Engineering.”

    See the full article here.

    Leland and Jane Stanford founded the University to “promote the public welfare by exercising an influence on behalf of humanity and civilization.” Stanford opened its doors in 1891, and more than a century later, it remains dedicated to finding solutions to the great challenges of the day and to preparing our students for leadership in today’s complex world. Stanford, is an American private research university located in Stanford, California on an 8,180-acre (3,310 ha) campus near Palo Alto. Since 1952, more than 54 Stanford faculty, staff, and alumni have won the Nobel Prize, including 19 current faculty members

     
  • richardmitnick 1:00 pm on January 7, 2013 Permalink | Reply
    Tags: , , , Computer Science,   

    From ESA Space Engineering: “LEON: the space chip that Europe built” 

    ESA Space Engineering Banner

    ESASpaceForEuropeBanner
    European Space Agency

    XMM Newton
    XMM-Newton

    herschelHerschel


    Planck

    7 January 2013
    No Writer Credit

    Just like home computers, the sophisticated capabilities of today’s space missions are made possible by the power of their processor chips. ESA’s coming Alphasat telecom satellite, the Proba-V microsatellite, the Earth-monitoring Sentinel family and the BepiColombo mission to Mercury are among the first missions to use an advanced 32-bit microprocessor – engineered and built in Europe.

    leon2
    Layout of the LEON2-FT chip, alias AT697

    All of them incorporate the new LEON2-FT chip, commercially known as the AT697. Engineered to operate within spacecraft computers, this microprocessor is manufactured by Atmel in France but originally designed by ESA.

    The underlying LEON design has also been made available to Europe’s space industry as the basis for company-owned ‘system-on-chip’ microprocessors optimised for dedicated tasks. For instance, Astrium is using it to create a space-based GPS/Galileo satnav receiver.

    chip
    LEON2-FT chip within Proba-2’s computer

    Independence from non-European parts is also a driver of our European Components Initiative, in place for the last decade, which is working with European industry to bring new components to market.”

    See the full article here.

    The European Space Agency (ESA), established in 1975, is an intergovernmental organization dedicated to the exploration of space, currently with 19 member states. Headquartered in Paris, ESA has a staff of more than 2,000. ESA’s space flight program includes human spaceflight, mainly through the participation in the International Space Station program, the launch and operations of unmanned exploration missions to other planets and the Moon, Earth observation, science, telecommunication as well as maintaining a major spaceport, the Guiana Space Centre at Kourou, French Guiana, and designing launch vehicles. ESA science missions are based at ESTEC in Noordwijk, Netherlands, Earth Observation missions at ESRIN in Frascati, Italy, ESA Mission Control (ESOC) is in Darmstadt, Germany, the European Astronaut Centre (EAC) that trains astronauts for future missions is situated in Cologne, Germany, and the European Space Astronomy Centre is located in Villanueva de la Cañada, Spain.


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  • richardmitnick 12:03 pm on December 20, 2012 Permalink | Reply
    Tags: , , Computer Science, sandia, ,   

    From Sandia Lab: “Supercomputing on the XPRESS track” 

    Sandia aims to create exascale computing operating system

    December 20, 2012

    “In the stratosphere of high-performance supercomputing, a team led by Sandia National Laboratories is designing an operating system that can handle the million trillion mathematical operations per second of future exascale computers, and then create prototypes of several programming components.

    Called the XPRESS project (eXascale Programming Environment and System Software), the effort to achieve a major milestone in million-trillion-operations-per-second supercomputing is funded at $2.3 million a year for three years by DOE’s Office of Science. The team includes Indiana University and Louisiana University; the Universities of North Carolina, Oregon and Houston; and Oak Ridge and Lawrence Berkeley national laboratories. Work began Sept. 1.

    ‘The project’s goal is to devise an innovative operating system and associated components that will enable exascale computing by 2020, making contributions along the way to improve current petaflop (a million billion operations a second) systems,’ said Sandia program lead Ron Brightwell.”

    See the full post here.

    Sandia National Laboratories is a multiprogram laboratory operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy’s National Nuclear Security Administration. With main facilities in Albuquerque, N.M., and Livermore, Calif., Sandia has major R&D responsibilities in national security, energy and environmental technologies, and economic competitiveness.
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  • richardmitnick 12:17 pm on January 6, 2012 Permalink | Reply
    Tags: , , , Clean Energy Project (CEP2), Computer Science, , , ,   

    From SLAC Today: “Organic Semiconductor” 

    January 6, 2012
    Diane Rezendes Khirallah

    “Simply put, an organic semiconductor is an organic material whose conductivity can be switched on and off at will. This helpful property gives semiconductors a critical role in the on-off switches at the heart of digital devices.

    Many associate the word organic with pesticide-free farm products. But in chemistry, organic refers to compounds that contain the element carbon.

    Today’s most common semiconductor is silicon, which, being its own element, contains no carbon. By controlling conditions such as the percentage and type of impurities in the material and varying the amount of electrical current and the intensity of light – whether visible, infrared or X-ray – scientists can control how the semiconductor behaves.

    But while silicon crystals are durable and allow electrical current to flow rapidly, they are also rigid and expensive to produce, making large-scale implementation cost-prohibitive (for example, in a large-scale solar array).

    In contrast, organic semiconductors – typically plastics and polymers that can be produced in sheets as little as one molecule thick – offer an inexpensive, lightweight, more flexible option. But they don’t yet conduct electricity as efficiently as silicon or operate for as long, which has limited their commercial use.”

    The full article is here.

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    Magnified view of organic semiconductor crystals recently grown by Stanford chemical engineers, who studied their structural properties at SLAC’s Stanford Synchrotron Radiation Lightsource.Image courtesy Gaurav Giri, Chemical Engineering, Stanford University

    Now, here is an example of how this research is being applied today-

    The Clean Energy Project (CEP2), at Harvard University is doing work in collaboration with research teams at SLAC.

    CEP2 is a project in Public Distributed Computing under the World Community Grid (WCG) arm of IBM’s Smarter Planet initiative. You can make a contribution to this project with the idle CPU cycles on your computer(s). WCG projects run on a small piece of software from UC Berkeley, called BOINC - the Berkeley Open Infrastructure for Network Computing. Just visit the WCG web site or the BOINC web site, download and install the BOINC software. Visit the WCG web site to attach to the project. While you are at WCG, take a look at the other very worthwhile projects and attach to as many as you wish.

    Also, at the BOINC web site, you will find a whole host of other projects in the Physical Sciences, Astronomy and Cosmology, Mathematics and other areas. Again, you can attach to as many projects as you like.

    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science. i1

     
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