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  • Researchers take virus-tracking software worldwide
    pandemic H1N1 and avian influenza H5N1 Using SUPRAMAP we initially developed maps that illustrated the spread of drug resistant influenza and host shifts in H1N1 and H5N1 influenza and in coronaviruses such as SARS said Janies SUPRAMAP allows the user to track strains carrying key mutations in a geospatial browser such as Google EarthTM Our software allows public health scientists to update and view maps on the evolution and spread of pathogens The original implementation of SUPRAMAP was built with a single client that was tightly coupled to the server software We now have decoupled the server from the original client to provide a modular web service for POY poyws org an open source freely available phylogenetic analysis program developed at AMNH The web service can be used by other researchers with new ideas data and clients to create novel applications said Ward Wheeler Ph D curator in charge of scientific computing at AMNH and a coauthor with Janies and others on a recent article about the project in the journal Cladistics To demonstrate the POY web service we have produced a new client software application GEOGENES www geogenes org said Wheeler Unlike in SUPRAMAP in which the user is required to create and upload data files in GEOGENES the user works from a graphical interface to query a curated dataset thus freeing the user from managing files Currently this service is hosted on large shared systems at OSC the center s flagship HP Intel Xeon Oakley Cluster their IBM Opteron Glenn Cluster and on a smaller dedicated cluster at Ohio State s Wexner Medical Center Decoupling the client from the server provides another advantage in that the implementation of the server can change to take advantage of advances in computing technology noted Thomas Bitterman a senior software engineer at OSC and co author of the journal article For example the recent addition of the Oakley Cluster at OSC has made available a large set of GPUs that could result in performance improvements To give their new software implementation a proper road test the researchers examined groups of key mutations in a pathogen they hadn t tracked before the H7 avian influenza virus Infection of humans by the H7 virus is rare but it has occurred among people who have direct contact with infected poultry H7 influenza like H5N1 is largely an avian virus but infects humans periodically and therefore we wanted to see how it evolves said Janies We have shown that pathogenicity of the H7 influenza is highly labile on a molecular evolutionary level and has occurred independently in many places around the world Now that the H5N1 papers detailing transmission among mammals have been published we can next pinpoint the natural geographic distribution of key sets of mutations that could lead to human to human transmission Our maps will allow scientists to better deploy public health resources to protect citizens and forces in the field Grant funding through the U S Army Research Laboratory and Office supports

    Original URL path: http://archive.osc.edu/press/releases/2012/janies2012.shtml (2013-06-13)
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  • Search begins to fill OSC Executive Director position
    Media Kit OSC Media Contacts Staff Directory Visit OSC Supercomputing Support Networking Support OSC Media Contacts Jamie Abel Media Relations Manager 614 292 6495 jabel osc edu Press Room Current News Press Releases by Date Press Releases by Subject OSC in the News by Date OSC in the News by Subject Important Dates Media Kit Search begins to fill OSC Executive Director position A search has commenced to find candidates for the position of Executive Director at the Ohio Supercomputer Center located in Columbus Ohio The Executive Director has responsibility for overseeing and serving as the technology leader of Ohio s advanced computing and research industrial innovation and computational science resources Candidates for this position must have a clear vision for the potential of advanced technology to increase research opportunities and economic competitiveness of the state of Ohio and nationally For more information on the position please visit the full job listing posted by the Human Resources Department at The Ohio State University https www jobsatosu com postings 35936 About the Ohio Supercomputer Center OSC A member of the Ohio Technology Consortium of the Ohio Board of Regents Ohio Supercomputer Center OSC addresses the rising computational demands of academic and

    Original URL path: http://archive.osc.edu/press/releases/2012/Director.shtml (2013-06-13)
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  • Olivucci models potential of toxic algae photoreceptors
    may allow us to engineer this and related organisms to thrive in diverse illumination conditions said Olivucci Such new properties would contribute to the field of alternative energy via the microbial conversion of light energy into biomasses oxygen and hydrogen Biophysical studies of the bacterial photoreceptor and its underlying molecular mechanisms can help us to understand its biotechnological potentials and the associated environmental implications Using sunlight as an energy source a sensory protein within ASR detects light of two different colors and behaves like the eye of Anabaena using its green light sensitivity to activate a cascade of reactions In sophisticated computer simulations Olivucci created at the Ohio Supercomputer Center OSC he found that a short fragment of the long retinal chromophore backbone of ASR undergoes a complete clockwise rotation powered by the energy carried by two photons of light We are constructing quantum mechanical and molecular mechanical models on Ohio Supercomputer Center systems Olivucci explained Past simulations have revealed that light induces a molecular level rotary motion in the protein interior Now the same computer models will be used to engineer hundreds of mutants that display programmed spectroscopic photochemical and photobiological properties and identify which mutants should be prepared in the laboratory This new approach constitutes a unique opportunity for developing computational tools useful for understanding the molecular factors that control the spectra of proteins and their photo responsive properties in general Olivucci s research is expected lead to an unprecedented tool by which hundreds to thousands of mutant models can be screened for wanted properties such as color excited state lifetime or photochemical transformations This will provide tailored genetic materials for generating organisms that for instance can thrive under alternative light conditions and modulate biomass production or be used in engineering applications Ohio is an international player in

    Original URL path: http://archive.osc.edu/press/releases/2012/Olivucci.shtml (2013-06-13)
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  • Better turbine simulation software to yield better engines
    other machines that transfer energy between a rotor and a fluid is especially instrumental in power generation in the aeronautic automotive marine space and industrial sectors For engine designers to achieve the most efficient propulsion and power systems they must understand the physics of very complex air flow fields produced within multiple stages of constantly rotating rotors and stators Jen Ping Chen Jen Ping Chen Ph D an associate professor of mechanical and aerospace engineering at The Ohio State University is working to improve the computational fluid dynamics CFD software that engineers use to simulate and evaluate the operation of turbomachinery Chen was the chief architect of that type of computer code appropriately named TURBO which he developed earlier for NASA Chen is leveraging the computational power of the Ohio Supercomputer Center to refine the software as it validates the flow field of engine components specifically as it applies to high pressure compressors and low pressure turbines The world is demanding increasingly cleaner more efficient and reliable power systems noted Ashok Krishnamurthy interim co executive director of OSC Therefore it is essential that experts like Dr Chen find innovative ways to improve the tools the engineers need to accomplish that goal and we at OSC are proud to be able to provide the computational resources that make that effort successful Each turbomachinery component has unique physical characteristics that present difficulties in design and operation such as stall in a compressor and cooling in a high pressure turbine With a simulation tool that is validated and optimized to run efficiently on a large computer cluster engine designers will have more physical insight to the complex flow field which will lead to reduced testing reduced risk faster time to market and lower costs While traditional wind tunnel testing is often the most straightforward approach it also comes with high costs and severe constraints on placing the measurement probes according to Chen Numerical simulation using CFD has provided an alternative for studying such flows at a lower cost and with unconstrained probe placement Yet the accuracy of a simulation depends on the accuracy of the mathematical model behind the simulation Our goal is to develop a reliable prediction technology to help improve turbomachinery component design said Chen The successful combination of CFD simulation and experimentation can greatly supplement the understanding of fundamental fluid behavior of gas turbine systems thus enhancing the ability of engineers to develop more advanced engine components Chen s team is investigating three specific areas of current industrial interest coupled fluid structure interaction active flow control and turbine film cooling Improved numerical simulation will allow engineers to analyze complex flow fields and aeroelastic phenomena such as flutter limit cycle oscillations forced response nonsynchronous vibrations and separated flow vibrations which arise from fluid structure interaction Application of a newly developed flow control simulation model for vortex generating jets in low pressure turbines will help improve engineers understanding of how flow control can be used to increase the performance and operability of

    Original URL path: http://archive.osc.edu/press/releases/2011/Chen.shtml (2013-06-13)
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  • Researchers get $7.5M grant to combat nerve agents
    ability to destroy a broad array of chemical agents inside the body Magliery is an assistant professor of chemistry and biochemistry and Hadad is a professor of chemistry and associate dean in the Division of Natural and Mathematical Sciences of the College of Arts and Sciences at Ohio State Dr Hadad s research group is consistently one of the largest and most sophisticated user groups of computing cycles at the center said Ashok Krishnamurthy interim co executive director of OSC It is gratifying for OSC to provide him with the resources that helped formalize such an important collaboration Hopefully it will lead to significant steps toward counteracting these toxic agents Nerve agents are chemicals that attack the nervous system causing paralysis and seizures and ultimately killing the victim through asphyxiation They do so by bonding with the enzyme acetylcholinesterase so that it can t transmit chemical messages from the brain to the rest of the body Once attached to the enzyme nerve agents can t be removed explained Magliery So the researchers are focusing on ways to stop the deadly chemicals before they can attach in the first place They have engineered souped up versions of naturally occurring human enzymes that will scavenge nerve agents from the bloodstream No tests involving actual nerve agents will take place at Ohio State Nerve agents like sarin and even related pesticides are a significant threat in the hands of terrorists and we re really lacking in ways to treat mass casualties said Magliery co leader of the new Ohio State center Fortunately there are enzymes already in human blood that can deactivate these agents We just have to engineer them to be more efficient and we have to be able to produce and formulate them as drugs Hadad leads an effort to model the chemical structure of candidate enzymes on the powerful parallel supercomputer systems at OSC while Magliery is producing synthetic versions of the new enzymes for further testing and preclinical evaluation by the Army The preliminary results from the first round of this grant showed that these enzymes can be engineered to have enough activity to use as therapeutic agents said Magliery But there are still challenges ahead There are a lot of related agents and there are few enzymes used as drugs today Hadad outlined one of the main challenges In nature each enzyme generally has only one function one thing that it does very well he said But we need an enzyme that will deactivate many different nerve agents We need one molecule that can do it all Magliery added that the ideal enzyme would remain active for days or weeks at a time pulling toxic agents from the body over and over again It could be administered as an antidote immediately after an attack or as an inoculation against future attacks Soldiers and first responders are among the likely recipients of such a preventive dose but so are people whose jobs regularly expose them to nerve agents even

    Original URL path: http://archive.osc.edu/press/releases/2011/Hadad-Magliery.shtml (2013-06-13)
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  • OSC features partnerships at international conference
    The Research Institute and OSC to harmonize domain experts to battle disease The following outlines the specific partnerships highlighted in the exhibition booth The Research Institute at Nationwide Children s Hospital The Research Institute OSC provides microscopy and biorepository image storage services to hospital s research group as well as other medical research centers in Ohio Working with The Research Institute OSC is providing data storage and a development platform for the remote visualization of memory intensive pathological images for initiatives associated with The Research Institute and the Biopathology Center The OSU Department of Biomedical Informatics BMI OSC supports OSU BMI s clusters and works to mirror their genomics databases installing and supporting software required for analysis of genetic data of human disease and running PhemoLIMS a lab notebook Nimbis Services Inc a cloud computing and application portal consulting company which is working with OSC to develop domain specific portal applications for OSC s BCC program that can be easily embraced by a large cross section of companies These applications develop an online marketplace for on demand portals or application services driven behind the scenes by HPC Total Sim USA OSC s most recent BCC related project with this computational fluid dynamics consulting company whose U S headquarters are in Dublin Ohio is to work with small manufacturers an application called the Manifold Flow Predictor MFP Manifolds involve a large category of industrial applications that use pipes hoses sprinklers or vacuums to move either air or fluids through several openings from spraying glue on a cereal box lid to capturing smoke from a boiler The CFD and visualizations are calculated using OSC resources and displayed to the user via their web browser Alliance for High Performance Digital Manufacturing This cross industry collaborative organization of which OSC is a member is dedicated to changing American manufacturing by bringing the power of advanced computing to the value chain OSC and its partners also have a presence in the SC11 technical program On Nov 16 AHPDM partners from the National Center for Manufacturing Sciences Intel and OSC will present a birds of a feather session that discusses barriers and solutions to the missing middle the 95 of all manufacturers who do not have access to HPC approaches On Nov 15 Billiter from The Research Institute will present a Masterworks session on digital pathology s use to support personalized and translational medicine in the fight against cancer And Tom Lange of Procter Gamble a partner in OSC s state BCC activities will focus on the ways in which HPC can be leveraged to fuel consumer product science and engineering processes In addition OSC staff will demonstrate the capabilities of the Intel MIC Architecture across five high performance computing HPC application classes at the Intel booth Booth 2121 Findings in the research fields of computational chemistry climate and ocean modeling high energy physics image processing and computational material sciences will be jointly presented OSC s participation at the SC11 conference also extends to the education

    Original URL path: http://archive.osc.edu/press/releases/2011/SC11.shtml (2013-06-13)
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  • UC-Berkeley's Miller to deliver 2011 Pitzer Lecture
    significant of his contributions include a comprehensive semiclassical scattering theory the classical S matrix of inelastic and reactive scattering processes the reaction path Hamiltonian for describing polyatomic reactions the S matrix Kohn variational method for state to state reactive scattering and a rigorous quantum theory of chemical reaction rates and its semiclassical limit the instanton model that generalizes transition state theory Most recently his efforts have focused on developing the initial value representation IVR of semiclassical theory into a practical way of adding quantum effects to classical molecular dynamics simulations of chemical processes Miller earned his bachelor s degree in chemistry from the Georgia Institute of Technology in 1963 and a doctorate in chemical physics from Harvard University in 1967 During 1967 69 he was a Junior Fellow in Harvard s Society of Fellows the first year of which was spent as a NATO postdoctoral fellow at the University of Freiburg Germany He joined the chemistry department of the University of California Berkeley in 1969 and has held the rank of professor since 1974 serving as department chairman from 1989 to 1993 and becoming the Kenneth S Pitzer Distinguished Professor in 1999 Miller is a member of the International Academy of Quantum Molecular Sciences the National Academy of Sciences and the American Academy of Arts and Sciences His awards include the Annual Prize of the International Academy of Quantum Molecular Sciences the E O Lawrence Memorial Award the Irving Langmuir Award in Chemical Physics the American Chemical Society Award in Theoretical Chemistry the Hirschfelder Prize in Theoretical Chemistry the Ira Remsen Award the Spiers Medal of the Royal Society of Chemistry the Peter Debye Award in Physical Chemistry the Herschbach Award in the Dynamics of Molecular Collisions the Welch Award in Chemistry and the Ahmed Zewail Prize in Molecular Sciences

    Original URL path: http://archive.osc.edu/press/releases/2011/Miller_Pitzer.shtml (2013-06-13)
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  • Simulations unlock carbon nanotube potential for industry
    with a different structural arrangement and possess extraordinary thermal mechanical and electrical properties Individual nanotubes naturally align themselves into cylindrical ropes held together by van der Waals forces the attraction forces found among atoms molecules and surfaces and caused by correlations in the fluctuating polarity of other nearby particles Sadhan C Jana Ph D professor of Polymer Engineering at the University of Akron UA has been studying the interesting properties of these molecules by simulating these microscopic structures using the powerful systems of the Ohio Supercomputer Center OSC The biggest obstacle in realizing the full potential of CNTs is agglomerate formation owing to van der Waals and electrostatic interactions between individual CNT particles explained Jana Researchers have devised several methodologies to weaken such interactions With access to Ohio Supercomputer Center systems a research team led by University of Akron s Sadhan Jana simulated organic tie molecules on the surface of multi walled carbon nanotubes The red balls represent oxygen white balls represent hydrogen and gray balls represent carbon atoms in tie molecules Two major approaches are followed in applying CNTs to material surfaces covalent and non covalent functionalization In covalent functionalization chemical bonds are formed with the surface carbon atoms a process which often alters the graphitic characteristics of CNTs and compromises the electrical conductivity and mechanical strength of the molecule In contrast non covalent functionalization utilizes uniquely designed tie molecules a molecular segment that helps to improve the stability of CNTs by creating ties between the CNTs and polymer chains or solvent molecules to provide exceptional toughness impact resistance and resistance to cracking The simulations of polymer nanocomposites in solution are CPU intense tasks said Jie Feng a postdoctoral research fellow working with Jana at UA In our approach the resolution of simulation is increased for the parts that are of utmost importance for example the phenomena at or near the nanotube surfaces while low resolution is used for simulation of the parts of the system such as the motion of solvent molecules Jana and Feng conducted simulations of adhering tie molecules onto material surfaces and obtained estimates of improved mechanical properties and thermal conductivity Their research focuses on gaining a fundamental understanding of the mechanism of physical transference or adsorption of such tie molecules from solutions onto surfaces of multi walled carbon nanotubes MWCNTs The tie molecules may include polymers surfactants or biopolymers The CNTs treated with the tie molecules may be used in the fabrication of sensors and devices or may be compounded with the host polymers to create bulk polymer composites The Akron researchers are collaborating with experimentalists at a pair of Ohio based companies Zyvex Technologies and PolyOne Corporation to conduct this research The investigators believe their research will provide industry with guidance and theoretical explanations to aid in the development of tie molecules and value added composite materials for automotive naval and aerospace industry applications With the rich manufacturing history of this state advanced materials is a natural fit for the staff and resources

    Original URL path: http://archive.osc.edu/press/releases/2011/Jana.shtml (2013-06-13)
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