Klaus Schulten
The Computational Microscope
(jnk)Sep 2016 - Aug 2017
Investigating Dynamic Instability of Microtubules Using MD Simulations
(jq6)Feb 2016 - Jan 2017
PAID-Load balancing and topology in NAMD
(gkq)Sep 2015 - Jun 2017
Development of rapid in-field Ebola infection screening guided by biomolecular simulation and collaborative remote visualization
(jtz)May 2015 - Apr 2016
The 26S Proteasome: A computational study of the waste recycler of the cell
(jse)Nov 2014 - Dec 2015
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2015
Till Rudack: Molecular Dynamics Simulations of Large Macromolecular Complexes
Blue Waters Symposium 2016, Jun 15, 2016
Juan R. Perilla, B. C. Goh, J. Stone, and K. Schulten: Chemical Visualization of Human Pathogens: the Retroviral Capsids
Scientific Visualization & Data Analytics Showcase at the International Conference for High Performance Computing, Networking, Storage and Analysis (SC '15); Austin, Texas, U.S.A., Nov 18, 2015
Juan Perilla: Atomistic Characterization of the HIV Capsid from Molecular Dynamics Simulations
Blue Waters Symposium 2015, May 13, 2015
James Phillips: Attacking HIV with Petascale Molecular Dynamics Simulations on Titan and Blue Waters
2015 GPU Technology Conference; San Jose, California, U.S.A., Mar 17, 2015
Melih Sener, J. E. Stone, A. Barragan, A. Singharoy, I. Teo, K. L. Vandivort, B. Isralewitz, B. Liu, B. C. Goh, J. C. Phillips, L. F. Kourkoutis, C. N. Hunter, and K. Schulten: Visualization of Energy Conversion Processes in a Light Harvesting Organelle at Atomic Detail
Scientific Visualization & Data Analytics Showcase at the International Conference for High Performance Computing, Networking, Storage and Analysis (SC '14); New Orleans, Louisiana, U.S.A., Nov 19, 2014
John E. Stone: Fighting HIV with GPU-Accelerated Petascale Computing
International Conference for High Performance Computing, Networking, Storage and Analysis (SC '13); Denver, Colorado, U.S.A., Nov 19, 2013
John E. Stone: Interactive molecular visualization and analysis with GPU computing
246th ACS National Meeting, fall 2013; Indianapolis, Indiana, U.S.A., Sep 11, 2013
John E. Stone: VMD: GPU-Accelerated Visualization and Analysis of Petascale Molecular Dynamics Simulations
2013 GPU Technology Conference; San Jose, California, U.S.A., Mar 20, 2013
A view of a virus: research reveals new insights into hepatitis B
May 31, 2018
Researchers at the University of Delaware, working with colleagues at Indiana University, have gained new insights into the virus that causes hepatitis B — a life-threatening and incurable infection that afflicts more than 250 million people worldwide. The discovery, which was published April 27 in the journal eLife, reveals previously unknown details about the capsid, or protein shell, that encloses the virus’ genetic blueprint. Scientists believe that the capsid, which drives the delivery of that blueprint to infect a host cell, is a key target in developing drugs to treat hepatitis B. “With hepatitis B, the structure of the capsid has been known for years, but we wanted to study its motion and its influence on its surroundings,” said Jodi A. Hadden, an independent postdoctoral researcher in UD’s Department of Chemistry and Biochemistry and the lead author of the new paper.
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Molecular mechanism of extreme mechanostability in a pathogen adhesin
Mar 29, 2018
Researchers have characterized the physical mechanism that enables a widespread bacterial pathogen to adhere to the tissues of its human host.
Sources:
- http://science.sciencemag.org/content/359/6383/1527
- https://www.sciencedaily.com/releases/2018/03/180329141022.htm
- https://www.eurekalert.org/pub_releases/2018-03/lm-bba032718.php
- https://phys.org/news/2018-03-bacterial-adhesion-vitro-silico.html
- https://www.hpcwire.com/off-the-wire/blue-waters-reveals-how-staph-bacteria-cling-to-human-cells/
- https://scicasts.com/channels/disease-processes/1872-medical-microbiology/13576-research-shows-how-gpus-aid-fight-against-zombie-like-bugs/
- https://www.nanowerk.com/spotlight/spotid=49991.php
- https://blogs.nvidia.com/blog/2018/04/17/antibiotic-resistant-staph-infection/
Team brings subatomic resolution to computational microscope
Mar 26, 2018
Scientists have built a “computational microscope” that can simulate the atomic and subatomic forces that drive molecular interactions. This tool will streamline efforts to understand the chemistry of life, model large molecular systems and develop new pharmaceutical and industrial agents, the researchers say. They report their findings in the journal Nature Methods. ... Both molecular mechanics and quantum mechanics programs have been available for years, and other teams have worked to combine them, said University of Illinois chemistry professor Zaida (Zan) Luthey-Schulten, who led the new research with her husband, U. of I. physics professor Klaus Schulten. But the new effort streamlines the process of setting up, performing and analyzing the simulations.
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- https://news.illinois.edu/view/6367/630024
- https://www.hpcwire.com/off-the-wire/team-uses-blue-waters-to-bring-subatomic-resolution-to-computational-microscope/
- https://www.scientificcomputing.com/news/2018/04/team-uses-blue-waters-supercomputer-bring-subatomic-resolution-computational-microscope
Supercomputer Visualization Shows 1.2 Microseconds in the Life of a 4-Million-Atom HIV Capsid
Jul 21, 2017
While some researchers look for drugs to treat HIV, other scientists delve deep into the virus itself for answers on how it causes infections. Using two supercomputers, University of Illinois research scientist Juan R. Perilla and late physics professor Klaus Schulten simulated 1.2 microseconds of the life of the HIV capsid, the structure that contains the virus's genetic material. The simulation, which took two years to complete, gives us a view of the virus on a molecular level and provides us with insight into how HIV senses its environment and becomes infective.
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Massive Simulation Shows HIV Capsid Interacting with its Environment
Jul 20, 2017
It took two years on a supercomputer to simulate 1.2 microseconds in the life of the HIV capsid, a protein cage that shuttles the HIV virus to the nucleus of a human cell. The 64-million-atom simulation offers new insights into how the virus senses its environment and completes its infective cycle. The findings are reported in the journal Nature Communications. "We are learning the details of the HIV capsid system, not just the structure but also how it changes its environment and responds to its environment," said University of Illinois research scientist Juan R. Perilla, who led the study with U. of I. physics professor Klaus Schulten. Such details could help scientists find new ways to defeat the virus, Perilla said.
Sources:
- https://www.laboratoryequipment.com/news/2017/07/massive-simulation-shows-hiv-capsid-interacting-its-environment
- http://trendintech.com/2017/07/31/supercomputer-simulation-of-hiv-virus-may-provide-new-treatment-options/
- https://news.developer.nvidia.com/supercomputers-reveal-how-the-hiv-virus-moves/
- https://www.eurekalert.org/pub_releases/2017-07/uoia-mss071317.php
- https://phys.org/news/2017-07-massive-simulation-hiv-capsid-interacting.html
- http://www.labmanager.com/news/2017/07/massive-simulation-shows-hiv-capsid-interacting-with-its-environment#.WYNrRdPyuEI
- http://www.infectioncontroltoday.com/news/2017/07/simulation-shows-hiv-capsid-interacting-with-its-environment.aspx
- https://www.healio.com/infectious-disease/hiv-aids/news/in-the-journals/%7B2dba1905-6c07-4518-b878-7fe759c04d82%7D/hiv-capsid-computer-simulation-may-yield-clues-to-fighting-virus
- https://cosmosmagazine.com/biology/simulating-the-inner-life-of-an-hiv-virus
- http://news.illinois.edu/view/6367/532452
A cure for HIV takes a step closer after supercomputers reveal how the virus moves
Jul 19, 2017
A brief glimpse into how HIV travels through the body has been simulated for the first time on supercomputers in the US. For two years, multiple supercomputers at the University of Illinois modelled the behaviour of 64 million atoms to capture 1.2 microseconds of the life of an HIV capsid, a protein cage that transports the HIV virus to the nucleus of a human cell. The capsid simulation was performed on the Department of Energy's Titan supercomputer, while analysis was made using the Blue Waters supercomputer at the National Center for Supercomputing Applications at the university.
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Rock Stars of HPC: James Phillips
Apr 27, 2017
Recipient of a Gordon Bell Award in 2002, James Phillips has been a full-time research programmer for almost 20 years. Since 1998, he has been the lead developer of NAMD, a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales beyond 200,000 cores, and is undoubtedly a Rock Star of HPC. ... InsideHPC: That advice led you to Professor Klaus Schulten – what impact did he have on your career? When Schulten came here from Germany he had a couple of grad students and a home-built parallel computer that they used to run the first simulation of a membrane back in early 1990s. He was very much dedicated to the idea that we can use parallel computing to do science and he largely dedicated his life to running this place. In fact he rarely slept – I remember at one point I was working on something and I sent him an email at 3am to try and impress him, and he wrote back.
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First atomic-scale view of interaction between HIV capsid and host protein cyclophilin A
Mar 7, 2016
A new study offers the first atomic-scale view of an interaction between the HIV capsid - the protein coat that shepherds HIV into the nucleus of human cells - and a host protein known as cyclophilin A. This interaction is key to HIV infection, researchers say. A paper describing the research appears in the journal Nature Communications. ... "We have known for some time that cyclophilin A plays a role in HIV infection," said University of Illinois physics professor Klaus Schulten, who led the new study with postdoctoral researcher Juan R. Perilla and University of Pittsburgh professor Peijun Zhang and postdoctoral researcher Chuang Liu.
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- https://www.news-medical.net/news/20160307/First-atomic-scale-view-of-interaction-between-HIV-capsid-and-host-protein-cyclophilin-A.aspx
- http://www.laboratoryequipment.com/news/2016/03/understanding-how-hiv-defeats-cellular-defender
- http://www.sciencecodex.com/study_offers_clearest_picture_yet_of_how_hiv_defeats_a_cellular_defender-177136
Researchers resolve structure of a key component of bacterial decision-making
Dec 8, 2015
For bacteria that swim, determining whether to stay the course or head in a new direction is vital to survival. A new study offers atomic-level details of the molecular machinery that allows swimming bacteria to sense their environment and change direction when needed. The study, reported in the journal eLife, represents a major step in understanding the "bacterial brain," said University of Illinois physics professor Klaus Schulten, who led the new research.
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- http://www.eurekalert.org/pub_releases/2015-12/uoia-rrs120815.php
- https://news.illinois.edu/blog/view/6367/290048
Researchers Construct Atomic Model of an Immature Retrovirus
Aug 12, 2015
Using molecular modeling and large-scale molecular dynamic simulation, University of Illinois researchers constructed an atomic model of an immature retrovirus. The researchers, from the Theoretical and Computational Biophysics Group at the Beckman Institute for Advanced Science and Technology at Illinois, published their work in the journal Structure.
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Attacking HIV with Titan and Blue Waters
May 13, 2015
In this video from the GPU Technology Conference, James Phillips Senior Research Programmer from the University of Illinois at Urbana-Champaign presents: Attacking HIV with Petascale Molecular Dynamics Simulations on Titan and Blue Waters.
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Celebrating Blue Waters
Apr 7, 2015
On April 6, U.S. Sen. Mark Kirk (R-IL) convened a celebration in honor of the second birthday of NCSA’s Blue Waters supercomputer, which is used by scientists and engineers across the country to tackle challenging research for the benefit of science and society. In kicking off the event, Kirk highlighted the importance of Blue Waters—and of continuing investment in high-performance computing. ... A panel of Blue Waters users—four from among the 200 teams across the country that have used the system—then briefly described how the supercomputer accelerates their research:
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Blue Waters to help researchers tackle Ebola
Apr 7, 2015
NCSA’s Blue Waters supercomputer will be used by three research teams to gain new understanding of the deadly Ebola virus, thanks to allocations provided through the National Science Foundation’s Rapid Response Research program. “As the nation’s most powerful and productive supercomputer for open science, Blue Waters plays a vital role in a wide range of research that impacts our lives,” said Blue Waters leader Bill Kramer. “Blue Waters is helping scientists better understand Alzheimer’s disease, HIV, earthquakes, and dangerous tornadoes, and we’re gratified that now we can help address the global threat of Ebola.”
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18 general, 9 exploratory allocations on Blue Waters awarded to Illinois researchers
Nov 24, 2014
Eighteen researchers at the University of Illinois at Urbana-Champaign received allocations on the Blue Waters petascale supercomputer at the National Center for Supercomputing Applications (NCSA). A portion of available time on Blue Waters is reserved for University faculty and staff projects like these that require the system’s unique capabilities. Ten of the awards will continue projects already running on Blue Waters, related to a wide variety of topics like tornadoes, steel casting, and cell function, among others. Eight allocations are for new projects.
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(Cloud + super) computing = results
Oct 29, 2014
Can cloud computing replace supercomputers like Blue Waters in the future? No, says Vijay Pande, director of the biophysics program at Stanford University. He says both are critical to his study of serious diseases like Alzheimer's and cancer. Pande's lab uses cloud computing through Folding@home and Google Exacycle to run many detailed molecular dynamics (MD) simulations of protein folding independent of one another. "A lot of what we do is run the raw trajectories on Folding@home, or Google Exacycle, analyze it on Blue Waters, and spit it back out to Folding@home," says Pande.
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- http://www.ncsa.illinois.edu/news/story/cloud_super_computing_results
- http://www.ncsa.illinois.edu/news/story/cloud_and_supercomputing_cooperate_in_molecular_dynamics_research
NSF awards time on Blue Waters to seven new projects
Oct 1, 2014
The National Science Foundation (NSF) has awarded 14 new allocations on the Blue Waters petascale supercomputer at the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign. Seven of the awards are for new projects.
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Bolstering Extreme Scale Computational Biology
Jul 31, 2014
According to Dr. Klaus Schulten from the University of Illinois, the molecular dynamics and visualization programs NAMD and VMD, which serve over 300,000 registered users in many fields of biology and medicine, are pushing the limits of extreme scale computational biology. Schulten says these programs can operate on a wide variety of hardware and offer new inroads to medical discovery. In addition to outlining NAMD and VMD on ARM and GPU developments over the last several years that led to the programs’ extreme performance on Blue Waters, Titan and Stampede, Schulten is known for shedding light on how these fields and programs are enabled by petascale computing.
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Computing a Cure for HIV: 9 Ways Supercomputers Help Scientists Understand and Treat the Virus
Jun 20, 2014
The tendency of HIV to mutate and resist drugs has made it particularly difficult to eradicate. Some treatments have shown progress in slowing or even stopping the progress of the virus, but no cure or vaccine has been discovered that can truly stamp out the disease. In the last decade scientists have begun using a new weapon in the fight against HIV: supercomputers. ... Among the researchers using supercomputers to study HIV is Klaus Schulten, the keynote speaker at the 2014 International Supercomputing Conference in Leipzig, Germany. Schulten, a professor of physics at the University of Illinois at Urbana-Champaign, invented the Nanoscale Molecular Dynamics (NAMD) software program, one of the most widely used tools for understanding diseases at a molecular level.
Sources:
- https://www.huffingtonpost.com/aaron-dubrow/computing-a-cure-for-hiv-_b_5512311.html
- https://scienceblog.com/73053/computing-cure-hiv/
- https://www.nsf.gov/discoveries/disc_summ.jsp?cntn_id=131779&org=OAC&from=news
Blue Waters Symposium a success
May 28, 2014
The symposium, held May 13-15 in Champaign, Ill., gathered many of the country’s leading supercomputer users to share what they have learned using Blue Waters and discuss the future of supercomputing. On May 13, 2014, Blue Waters supercomputer users and many of the NCSA staff who support their work converged in Champaign, Ill., for the second annual Blue Waters Symposium. The ensuing three days were filled with what many of them would later refer to as a wonderful variety of science talks and opportunities for networking and collaboration.
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House briefing highlights value of supercomputers for science, industry
May 2, 2014
On April 28 the four co-chairs of the House Science and National Labs Caucus—Reps. Randy Hultgren, Chaka Fattah, Ben Ray Luján, and Alan Nunnelee—sponsored a briefing on the value of federal investment in high-performance computing. The event was held in conjunction with the one-year anniversary of NCSA’s Blue Waters supercomputer, a petascale powerhouse capable of performing quadrillions of calculations per second that supports a wide range of science and engineering research across the country. ... Several scientists described the breakthrough research they have been able to achieve thanks to high-performance computing systems like Blue Waters: Patrick Reed (Cornell University) uses the Blue Waters supercomputer to better model the forces that act on the satellites we rely on for communication, navigation, and environmental monitoring. Klaus Schulten (University of Illinois at Urbana-Champaign) refers to his research as using a “computational microscope” because using supercomputers to simulate the interactions of biomolecules provides an unprecedented view of the dynamic activities occurring in living cells.
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12 Illinois faculty awarded prestigious Blue Waters Professorships
Feb 4, 2014
Twelve University of Illinois faculty members from a range of fields have been selected as Blue Waters Professors, an honor that comes with substantial computing and data resources on the Blue Waters supercomputer at the university’s National Center for Supercomputing Applications (NCSA).
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The Top Supercomputing Led Discoveries of 2013
Jan 2, 2014
2013 has been an incredible year for the entire ecosystem around supercomputing; from vendors pushing new technologies to boost performance, capacity, and programmability to researchers turning over new insights with fresh techniques. While exascale has taken more of a backseat than we might have predicted at the year’s end of 2010, there are plenty of signs that production HPC environments are blazing plenty of new trails. ...
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NCSA Receives Honors in 2013 HPCwire Readers’ and Editors’ Choice Awards
Nov 18, 2013
NCSA announced today that it received the HPCwire Editors’ Choice Award for Best Use of HPC in Life Sciences for the use of the Blue Waters supercomputer to achieve a significant breakthrough in the understanding of HIV. The 2013 HPCwire Readers’ and Editors’ Choice Awards were announced at the start of the Opening Reception at the 2013 International Conference for High Performance Computing, Networking, Storage and Analysis (SC13), in Denver, Colorado. The award recognizes research conducted by biophysicist Klaus Schulten of the University of Illinois at Urbana-Champaign and his collaborators.
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Wit, grit and a supercomputer yield chemical structure of HIV capsid
May 29, 2013
Researchers report that they have determined the precise chemical structure of the HIV capsid, a protein shell that protects the virus's genetic material and is a key to its virulence. The capsid has become an attractive target for the development of new antiretroviral drugs. ... "This is a big structure, one of the biggest structures ever solved," said U. of I. physics professor Klaus Schulten, who, with postdoctoral researcher Juan R. Perilla, conducted the molecular simulations that integrated data from laboratory experiments performed by colleagues at the University of Pittsburgh and Vanderbilt University. "It was very clear that it would require a huge amount of simulation - the largest simulation ever published - involving 64 million atoms."
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Advances in Computational Research Transform Scientific Process and Discovery
Mar 25, 2013
Not every scientific discovery originates in the lab, or from the field. Scientists increasingly are turning to powerful new computers to perform calculations they couldn't do with earlier generation machines, and at breathtaking speed, resulting in groundbreaking computational insights across a range of research fields. .... Last October, NSF inaugurated Yellowstone, one of the world's most powerful computers, based at NCAR in Cheyenne, Wyo., and later this month will dedicate two additional supercomputers, Blue Waters, located at the National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign, and Stampede, headquartered at the Texas Advanced Computing Center 9TACC) at The University of Texas at Austin. ... "The computer is excellent in permitting us to test a hypothesis," says Klaus Schulten, a professor of physics at the University of Illinois at Urbana-Champaign, who uses large-scale computing to study the molecular assembly of biological cells, most recently HIV, the virus that causes AIDS. "But if you want to test a hypothesis, you need to have a hypothesis."
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Virus unmasked
Feb 1, 2013
Simulations carried out using the Blue Waters petascale supercomputer have determined the structure of the rabbit hemorrhagic disease virus (RHDV), which causes a highly infectious and often fatal illness in domestic and wild rabbits. This research, carried out collaboratively by researchers at the University of Illinois, the University of California-San Diego and several Chinese research institutions, has been published in PLOS Pathogens. ... University of Illinois biophysicist Klaus Schulten, a co-author of the published study, says the computational power of Blue Waters and the NAMD molecular dynamics code developed at the University of Illinois were vital to achieving this result.
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Blue Waters petascale supercomputer now in friendly user phase
Nov 6, 2012
The full Blue Waters petascale computing system is now available in "friendly-user" mode to the National Science Foundation-approved science and engineering teams. These groups from across the country will use Blue Waters for challenging research in weather and climate, astrophysics, biomolecular systems, and other fields. ... Selected "friendly users" will have access to the entire system during this window in order to help the Blue Waters team test and evaluate the full system and to expedite the Petascale Computing Resource Allocation (PRAC) teams' ability to use the full Blue Waters system productively as soon as it is in full production status.
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Making history
Sep 24, 2012
A brief but tantalizing test run of the Blue Waters sustained petascale supercomputer earlier this year has left researchers eagerly awaiting full deployment. The Blue Waters Early Science System (BW-ESS) was only about 15 percent of the full machine as it consisted of 48 cabinets with 4,512 XE6 compute nodes and 96 service nodes and a Sonexion Lustre Storage Appliance provided two petabytes of disk storage. But that was enough to allow researchers to test the technology used in Blue Waters and identify and fix software bugs and other issues that prevented some codes from successfully scaling.
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6 science teams begin using Blue Waters Early Science System
Mar 20, 2012
Six research teams have begun using the first phase of the Blue Waters sustained-petascale supercomputer to study some of the most challenging problems in science and engineering, from supernovae to climate change to the molecular mechanism of HIV infection. The Blue Waters Early Science System, which is made up of 48 Cray XE6 cabinets, represents about 15 percent of the total Blue Waters computational system and is currently the most powerful computing resource available through the National Science Foundation.
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- http://www.ncsa.illinois.edu/news/story/6_science_teams_begin_using_blue_waters_early_science_system
What will scientists do with Blue Waters?
Dec 9, 2009
Many scientists are working now with the Blue Waters team so they are ready to use the massive sustained-petaflop supercomputer when it comes online in 2011. These teams will use Blue Waters to improve our understanding of tornadoes, earthquakes, the spread of contagious diseases, the formation of galaxies, the behavior of molecules and more.
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Getting viral
Sep 1, 2009
"In the planning world, we work with policymakers to design studies of particular outcomes," says Virginia Tech's Keith Bisset. Months of planning, collaboration, and modeling might go into strategies for what a city, county, or entire country might do when facing a disease outbreak. "But now we also have tools that allow for a quick turnaround. We can do a situational assessment that shows them what a particular [outbreak] might look like tomorrow or next week as it unfolds. They describe the situation, and we can tell them the outcomes of various interventions," he says. This spring Bisset and a group from Virginia Tech joined forces with the Pittsburgh Supercomputing Center's Shawn Brown and Douglas Roberts and Diglio Simoni of North Carolina's Research Triangle Institute to win one of the first Petascale Computing Resource Allocations awards. With that support and with computing time on Blue Waters, they expect to model global epidemics, as well as smaller-scale outbreaks. Instead of looking at a few hundred million people, as the team members do with their current codes, they'll look at more than 6 billion people.
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