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  • Biophysicist uses supercomputer to help fight brain tumors
    frame and the lines indicate key drug interacting chemical groups Both portions of the molecule within the dotted circles can be modified to improve its drug potential COLUMBUS March 10 2010 An Ohio State University biophysicist is using supercomputer simulations to search tens of thousands of molecular compounds to discover drugs that will block an enzyme that inhibits the human body s ability to suppress brain tumors Chenglong Li Ph D an assistant professor in the medicinal chemistry and pharmacognosy division of the College of Pharmacy is using computational chemistry to help develop a genetically targeted drug that could surpass current approaches to treating a type of aggressive brain tumor called glioblastoma multiforme GBM In contrast to many cancers the survival outcome of patients diagnosed with a GBM is relatively poor and has improved only marginally over the past several decades In general GBMs are the most common tumors that attack the central nervous system afflicting nearly 10 000 pediatric and adult patients each year in North America alone Combinations of surgery radiation and chemotherapy currently remain the most common therapy for these tumors yet surgeons often can t completely remove the highly invasive tumors without causing serious damage to the brain radiation is rarely effective and chemotherapy usually produces serious side effects My group has been conducting molecular dynamics simulations of the PRMT5 enzyme to gain insights on its catalytic mechanisms in order to understand how to manipulate it effectively and specifically said Li We then conducted virtual screenings of more than 100 000 pharmaceutical compounds to identify drugs that prevent that enzyme from blocking the body s cancer suppression genes This novel approach is called epigenetic cancer therapy where the identified molecular compounds reawaken natural human tumor fighting genes that stay dormant in many types of cancers Kiran Mahasenan a graduate student on Li s research team developed molecular models using the IBM Cluster 1350 system at the Ohio Supercomputer Center which the team also used to screen drug candidates The center s flagship supercomputer system nicknamed the Glenn Cluster features 9 500 cores 24 terabytes of memory and a peak computational capability of 75 teraflops For these very important computational approaches we typically use 32 to 64 nodes of the OSC system Li said Having access to the OSC supercomputers allows us to run these routines much quicker which allows us to optimize our results In addition very few places in the world have the combination of an NIH comprehensive cancer center and a top notch supercomputer center like we have here with OSC and OSU s James Cancer Hospital together Li and his research team represented one of the top user groups of OSC supercomputer cycles in each of the last two years In earlier research projects Li s research team has conducted similar molecular modeling studies to improve treatment for breast cancer prostate cancer and leukemia as well as for neurological disorders such as Parkinson s Alzheimer s and autism We are excited that these

    Original URL path: http://archive.osc.edu/press/releases/2010/brainTumors.shtml (2013-06-13)
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  • Metro High School student discovers “world of supercomputing”
    get some performance values and begin to debug and optimize the program Last week I conducted two interviews one with Kathryn Kelley Director of the Outreach Program and one with Doug Johnson Senior Systems Engineer of HPC Operations I asked them questions such as How does what you do relate to the mission of the OSC and What did you have to do in order to get to where you are now I will be incorporating their responses into a paper for a school assignment Well that s how my time has been spent thus far here at the Ohio Supercomputer Center in a nutshell I really like being here and helping out a big thank you to Jim specifically for taking the time to allow me to work with him and to Dr Gordon for being my mentor and allowing me to be a part here and I can t wait for what this week and the next weeks will bring January 22 2010 9 41 a m Well after a log and hard thought session I have decided to keep my posts with the snazzy title of Weekly Blog Entry The compilation of OpenFOAM was a success and I was able to begin testing it Jim and I ran into some problems with certain required libraries not being accessible by normal users however that was just a permissions error We also found a problem with the paraFoam package and are trying to work that out I think it happened because the machine tried to use two different versions of the package qmake to make paraFoam however I guess I ll find out I feel sort of taken over by OpenFOAM now wanting to compile it on my new desktop machine to give it a real computational test Oh well such is my life My Internship advisor Mr Bluel will be here on Tuesday I m hoping that he likes whatever it is that he s looking for in my progress Have a good weekend everyone January 29 2010 9 29 a m This week was another productive week for OpenFOAM although it s not quite done yet break Early on we ran into a problem with paraFoam not being able to find the ZN11QHeaderView5resetEv symbol I found that the problem may have been caused by accidentally using two different versions of qmake provided by the Qt software package during the compilation of paraview It is currently being recompiled and hopefully we ll have a fully functional OpenFOAM 1 6 installation come later today and begin testing on Monday I was able to learn more as to how OpenFOAM using multiple processors and the performance benefits or negatives that can come as a result I now have this urge to build a five computer cluster at my house just so I can get some more experience as to how to use design and administer a cluster although mine would probably suffer from severe communications lag because I d be

    Original URL path: http://archive.osc.edu/press/releases/2010/kochs_metro.shtml (2013-06-13)
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  • Researchers work to refine calculations of ocean levels
    are using powerful supercomputers to further refine satellite measurements of the surface height of the world s oceans With more than 70 percent of its surface covered in water the Earth s oceans greatly influence global climate and weather Studying ocean topography provides data that is vital to researchers who produce atmospheric models for hurricane forecasting optimizing routes for commercial shipping tracking floating debris and helping manage marine mammal and fish populations To measure the surface height of oceans scientists today analyze data that comes primarily from satellite sensors called altimeters which bounce microwave pulses off the water s surface and record the returning signals While these high tech methods produce highly accurate measurements small but important errors occur because waves are not symmetrical wide shallow wave troughs reflect electromagnetic energy more strongly than the narrow sharp wave crests Because of this variance altimeter measurements report sea heights that can be several centimeters too low requiring additional corrections Joel Johnson a professor of Electrical and Computer Engineering and Praphun Naenna a graduate research assistant there have turned to high performance computers at the Ohio Supercomputer Center OSC to help correct this electromagnetic EM bias Our study uses a method for hydrodynamic simulations that can better capture these effects than models previous studies employed said Johnson This method however comes with far more computational burden so we use supercomputing resources at OSC to produce a deterministic set of sea surface profiles and the corresponding altimeter pulse returns Last summer officials at OSC and ESL signed a collaboration agreement to develop parallel software codes for computational electromagnetics especially for layered sensing research While the numerical method used for these simulations is very efficient the total problem is still very computationally intensive said Ashok Krishnamurthy OSC s interim co executive director We granted

    Original URL path: http://archive.osc.edu/press/releases/2010/ocean.shtml (2013-06-13)
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  • OSC engineer supports materials modeling research
    at Louisiana State University the interdisciplinary team has been awarded 17 million supercomputing processor hours on Oak Ridge National Laboratory s Cray XT supercomputer for a project on Next Generation Multi Scale Quantum Simulation Software for Strongly Correlated Materials The team is supported by Karen Tomko Ph D a senior systems developer engineer at OSC and also includes researchers from Oak Ridge National Laboratory and University of California Davis This method and the opportunity to use the Cray Jaguar XT5 machine gives us a chance to study model systems with the precision that was previously impossible Jarrell stated in an LSU release We hope our research will provide a more comprehensive understanding of the makeup and basic properties of these materials We want this work to lead to materials that companies such as Goodyear Battelle or Procter Gamble can use to develop better technology for areas such as electronic devices or medical science According to the U S DOE Projects receiving INCITE awards utilize complex simulations to accelerate discoveries in ground breaking technologies such as lithium air batteries and nano solar cells The awards also include projects designed to close the nuclear fuel cycle develop advanced propulsion systems improve DNA sequencing and explore phenomena on the tiny scale of nanostructured superconductors The team will use the massive power of the Jaguar supercomputer to model strongly correlated materials using computing codes that were first fine tuned on OSC s flagship Glenn IBM Cluster 1350 system located in Columbus on the west campus of The Ohio State University Over the past year the team has worked on a similar project with a 15 million CPU hour award from the National Center for Computational Sciences Oak Ridge National Laboratory Jarrell Tomko and the team of applied mathematicians computational physicists and computer scientists are

    Original URL path: http://archive.osc.edu/press/releases/2010/materials_research.shtml (2013-06-13)
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  • Organization honors OSC leader as a model planner
    executive director of the Ohio Supercomputer Center has been honored by the American Institute of Certified Planners with the announcement of his selection to its College of Fellows Gordon will be inducted in April at the American Planning Association APA Conference in New Orleans APA is a nonprofit education and membership organization whose members include practicing planners planning students elected and appointed officials planning commissioners and interested citizens The American Institute of Certified Planners AICP is the APA s professional institute providing recognized leadership nationwide in the certification of professional planners ethics professional development planning education and the standards of planning practice Fellows of AICP are honored in recognition of the achievements of the planner as an individual elevating the Fellow before the public and the profession as a model planner who has made significant contributions to planning and society The Ohio Supercomputer Center OSC is a statewide high performance computing center that offers Ohio researchers access to sophisticated computing storage and software as well as cyberinfrastructure and education resources As senior director of Education and Client Support Gordon oversees training programs for OSC users and leads workshops for undergraduate faculty and graduate students at OSC and national conferences He has played a significant role in several OSC education programs in Science Technology Engineering and Mathematics for high school and middle school students including the Summer Engineering STEM Academy and Young Women s Summer Institute Gordon is the founding director of the center s Ralph Regula School of Computational Science a virtual school that coordinates inter disciplinary inter institutional programs for computational science education The school features programs that lead to a baccalaureate minor associate concentration and workforce certification In 1997 2003 Gordon served as deputy director of OSC As a professor of City and Regional Planning at The Ohio

    Original URL path: http://archive.osc.edu/press/releases/2010/gordon.shtml (2013-06-13)
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  • Dublin named among worlds top intelligent communities'
    designation were Arlington County Va Dublin Ohio Dundee Scotland Eindhoven Netherlands Ottawa Ontario Canada Suwon South Korea and Tallinn Estonia According to the ICF Intelligent Communities are those which have whether through crisis or foresight come to understand the challenges of the broadband economy and have taken conscious steps to create an economy capable of prospering in it In a study funded by the Province of Ontario Canada the Intelligent Community Forum defined five critical success factors for the creation of Intelligent Communities broadband connectivity knowledge workforce digital inclusion innovation and marketing and advocacy According to the ICF Intelligent Communities are those which have whether through crisis or foresight come to understand the enormous challenges of the Broadband Economy and have taken conscious steps to create an economy capable of prospering in it In a study funded by the Province of Ontario Canada the Intelligent Community Forum defined five critical success factors for the creation of Intelligent Communities broadband connectivity knowledge workforce digital inclusion innovation and marketing and advocacy In 2005 Dublin leveraged its innovative underground fiber optic network DubLink to connect to the Ohio Academic Resources Network OARnet to establish the Central Ohio Research Network CORN The research network links government businesses and schools to the Ohio Supercomputer Center OSC and other powerful online resources for research and economic development DubLINK encompasses nearly 100 miles of fiber optic cable while OARnet provides a statewide network backbone of more than 1 850 miles linking Ohio s K 12 schools colleges universities educational medical centers public broadcasting stations and state and local governments OSC a statewide resource funded through the Ohio Board of Regents provides client organizations with valuable high performance computing and storage systems software and services It is a great honor to be considered in league with these global

    Original URL path: http://archive.osc.edu/press/releases/2010/dublin.shtml (2013-06-13)
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  • X-ray researchers turn focus from black holes to cancer
    Now they and their interdisciplinary colleagues are repositioning their scientific methodology to peer into the human body to enhance cancer therapy and diagnostics theranostics Led by OSU s Anil Pradhan Ph D and Sultana Nahar Ph D an international research team is using new computer based models and high end X ray spectroscopy to minimize radiation risks and enhance therapeutic efficiency for cancer patients The X ray irradiation process causes embedded nanoparticles of iron gold and other heavy elements to release photons and low energy electrons to help break up the DNA in malignant tumors The researchers are also experimenting with bromine iodine and platinum The resonant nano plasma theranostics or RNPT could revolutionise X ray diagnostics and therapy Pradhan told the science magazine Nature The RNPT approach would reduce radiation exposure by factors from 10 to 100 he added The Ohio Supercomputer Center with our flagship IBM Cluster 1350 system is well positioned to help researchers with this sort of ground breaking critically important investigation said Ashok Krishnamurthy interim co executive director of OSC Nature recently reported on Pradhan and Nahar s cancer project in its India edition while just last month OSC highlighted the duo s recent astronomy work in an annual research publication Black holes are invisible but a plasma sea of super hot atoms spiraling into black holes betrays their existence Astronomers study the plasma to collect telltale radiation readings from the visible to the X ray using satellites and large telescopes such as the Large Binocular Telescope Pradhan Nahar and their team leveraged OSC resources to perform high accuracy energy calculations to compare with the radiation readings The most precise large scale calculations ever made for iron were done by Nahar who thus is known among astronomers as the Iron Lady Astrophysicists also use supercomputers

    Original URL path: http://archive.osc.edu/press/releases/2010/xray.shtml (2013-06-13)
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  • Obama lauds early-stage OSU chemist for simulations
    leverages supercomputers to help fill in the rest of the story with computer modeling and simulation For his outstanding work as a theoretical chemist President Barack Obama last week bestowed upon Herbert a 2009 Presidential Early Career Award for Scientists and Engineers along with 99 other early stage researchers from across the country The PECASE awards established by President Clinton in 1996 are coordinated by the Office of Science and Technology Policy within the Executive Office of the President These extraordinarily gifted young scientists and engineers represent the best in our country the President said in a statement With their talent creativity and dedication I am confident that they will lead their fields in new breakthroughs and discoveries and help us use science and technology to lift up our nation and our world Herbert was among twenty awardees nominated by the National Science Foundation for the award the highest honor that beginning researchers can receive in the United States for exemplary integration of research and education within the context of the mission of their organization He was recognized for his work in developing novel algorithms for the simulation of electronically excited states consisting of hundreds of atoms and for applying these techniques to the characterization of photochemical processes in DNA and for his work in developing open ended research projects to be integrated into undergraduate teaching laboratories Herbert s work also was highlighted last fall in an annual research publication of the Ohio Supercomputer Center OSC Herbert leverages the power of OSC s flagship system the Glenn IBM Cluster 1350 to accomplish the complex modeling and simulation work his research group conducts We are thrilled for the recognition John has deservedly received at the highest levels early in his career said Ashok Krishnamurthy interim co executive director of OSC John

    Original URL path: http://archive.osc.edu/press/releases/2010/obama_chemist.shtml (2013-06-13)
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