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Taking Great Ideas from the Lab to the Fab

aarondubrow aarondubrow writes  |  about a week ago

aarondubrow (1866212) writes "The "valley of death" is well-known to entrepreneurs — the lull between government funding for research and industry support for prototypes and products. To confront this problem, in 2013 the National Science Foundation created a new program called InTrans to extend the life of the most high-impact NSF-funded research and help great ideas transition from lab to practice.Today, in partnership with Intel, NSF announced the first InTrans award of $3 million to a team of researchers who are designing customizable, domain-specific computing technologies for use in healthcare. The work could lead to less exposure to dangerous radiation during x-rays by speeding up the computing side of medicine. It also could result in patient-specific cancer treatments."
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Computing a Cure for HIV

aarondubrow aarondubrow writes  |  about a month ago

aarondubrow (1866212) writes "The tendency of HIV to mutate and resist drugs has made it particularly difficult to eradicate. But in the last decade scientists have begun using a new weapon in the fight against HIV: supercomputers. Using some of the nation's most powerful supercomputers, teams of researchers are pushing the limits of what we know about HIV and how we can treat it. The Huffington Post describes nine ways supercomputers are helping scientists understand and treat the disease."
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A High Performance First Year for Stampede

aarondubrow aarondubrow writes  |  about a month ago

aarondubrow (1866212) writes "Sometimes, the laboratory just won't cut it. After all, you can't recreate an exploding star, manipulate quarks, or forecast the climate in the lab. In cases like these, scientists rely on supercomputing simulations to capture the physical reality of these phenomena — minus the extraordinary cost, dangerous temperatures or millennium-long wait times. This week, the Texas Advanced Computing Center released a Special Report on Stampede, the 7th most powerful computing system in the world. The report describes 8 example of how scientists are using the supercomputer to make discoveries in genetics, hurricane forecasting, renewable fuels and other fields."
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The Internet's broken. Who's going to invent a new one?

aarondubrow aarondubrow writes  |  about 2 months ago

aarondubrow (1866212) writes "The Internet has evolved to support an incredibly diverse set of needs, but we may be reaching a point at which new solutions and new infrastructure are needed in particular to improve security, connect with the Internet of Things and address an increasingly mobile computing landscape. Today, NSF announced $15 million in awards to develop, deploy and test future Internet architecture in challenging real-world environments. These clean-slate designs explore novel network architectures and networking concepts and also consider the larger societal, economic and legal issues that arise from the interplay between the Internet and society.

Each project will partner with cities, non-profit organizations, academic institutions and industrial partners across the nation to test their Internet architectures. Some of the test environments include: a vehicular network deployment in Pittsburgh, a context-aware weather emergency notification system for Dallas/Fort Worth, and a partnership with Open mHealth, a patient-centric health ecosystem based in San Francisco."

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Making graphene work for real-world devices

aarondubrow aarondubrow writes  |  about 3 months ago

aarondubrow (1866212) writes "Graphene, a one-atom-thick form of the carbon material graphite, is strong, light, nearly transparent and an excellent conductor of electricity and heat, but a number of practical challenges must be overcome before it can emerge as a replacement for silicon in electronics or energy devices. One particular challenge concerns the question of how graphene diffuses heat, in the form of phonons. Thermal conductivity is critical in electronics, especially as components shrink to the nanoscale. Using the Stampede supercomputer at the Texas Advanced Computing Center, Professor Li Shi simulated how phonons (heat-carrying vibrations in solids) scatter as a function of the thickness of the graphene layers. He also investigated how graphene interacts with substrate materials and how phonon scattering can be controlled. The results were published in the Proceedings of the National Academy of Sciences, Applied Physical Letters and Energy and Environmental Science."
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Cosmic Slurp

aarondubrow aarondubrow writes  |  about 3 months ago

aarondubrow (1866212) writes "A “tidal disruption” occurs when a star orbits too close to a black hole and gets sucked in. The phenomenon is accompanied by a bright flare with a unique signature that changes over time. Researchers at the Georgia Institute of Technology are using Stampede and other NSF-supported supercomputers to simulate tidal disruptions in order to better understand the dynamics of the process. Doing so helps astronomers find many more possible candidates of tidal disruptions in sky surveys and will reveal details of how stars and black holes interact."
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Investigating the Dark Matter of Life

aarondubrow aarondubrow writes  |  1 year,6 days

aarondubrow (1866212) writes "Metagenomics makes it possible to investigate microbes in their natural environments and in the complex communities in which they normally live, but requires massive computing power. Researchers from the J. Craig Ventor Institute used the Ranger supercomputer at TACC to determine the bacterial and viral diversity of the Indian Ocean as part of the Global Ocean Sampling Expedition. They reported their results in PLOS One in October 2012. They are now applying a metagenomic approach to the human esophagus and the microbial imbalances there that may play a role in certain kinds of gastric acid reflux and esophageal cancer."
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Sculpting Flow

aarondubrow aarondubrow writes  |  1 year,13 days

aarondubrow (1866212) writes "Researchers reported results in Nature Communications on a new way of sculpting tailor-made fluid flows by placing tiny pillars in microfluidic channels. The method could allow clinicians to better separate white blood cells in a sample, increase mixing in industrial applications, and more quickly perform lab-on-a-chip-type operation. Using the Ranger and Stampede supercomputers, the researchers ran more than 1,000 simulations representing combinations of speeds, thicknesses, heights or offsets that produce unique flows. This library of transformations will help the broader community design and use sculpted fluid flows."
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"Shields to Maximum, Mr. Scott"

aarondubrow aarondubrow writes  |  1 year,26 days

aarondubrow (1866212) writes "Researchers at The University of Texas at Austin developed a fundamentally new way of simulating fabric impacts that captures the fragmentation of the projectiles and the shock response of the target. Running hundreds of simulations on supercomputers at the Texas Advanced Computing Center, they assisted NASA in the development of ballistic limit curves that predict whether a shield will be perforated when hit by a projectile of a given size and speed. The framework they developed also allows them to study the impact of projectiles on body armor materials and to predict the response of different fabric weaves upon impact."
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A Database of Brains

aarondubrow aarondubrow writes  |  about a year ago

aarondubrow (1866212) writes "Researchers recently created OpenfMRI, a web-based, supercomputer-powered tool that makes it easier for researchers to process, share, compare and rapidly analyze fMRI brain scans from many different studies. Applying supercomputing to the fMRI analysis allows researchers to conduct larger studies, test more hypotheses, and accommodate the growing spatial and time resolution of brain scans. The ultimate goal is to collect enough brain data to develop a bottom-up understanding of brain function."
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When Will My Computer Understand Me?

aarondubrow aarondubrow writes  |  about a year ago

aarondubrow (1866212) writes "For more than 50 years, linguists and computer scientists have tried to get computers to understand human language by programming semantics as software, with mixed results. Enabled by supercomputers at the Texas Advanced Computing Center, University of Texas researchers are using new methods to more accurately represent language so computers can interpret it. Recently, they were awarded a grant from DARPA to combine distributional representation of word meanings with Markov logic networks to better capture the human understanding of language."
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Hip-Hip-Hadoop: Data Mining for Science

aarondubrow aarondubrow writes  |  about a year ago

aarondubrow (1866212) writes "In 2010, the Texas Advanced Computing Center began experimenting with Hadoop to test the technology's applicability for scientific problems. Researchers who are not C++ or Fortran programmers can quickly harness the power of Hadoop on the Longhorn remote visualization cluster to query massive collections and databases in new ways. Using TACC's Longhorn Hadoop system, researchers improved biomarker analysis, natural language processing and data mining of online health forums."
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Texas Unleashes Stampede for Science

aarondubrow aarondubrow writes  |  about a year ago

aarondubrow (1866212) writes "You hear it before you see it — a roar like a factory in full production. But instead of cars or washing machines, this factory produces scientific knowledge.

Stampede, the newest supercomputer at the Texas Advanced Computing Center (TACC) and one of the most advanced scientific research instruments in the world, fills aisle after aisle of a new 11,000-square-foot data center on the J.J. Pickle Research Campus of The University of Texas at Austin. Over the past year TACC staff designed, built and deployed Stampede, working closely with Dell and Intel engineers and university researchers.

According to the November 2012 Top 500 list of supercomputers, Stampede is the seventh-most powerful advanced computing system on the planet, but it is the most powerful in the U.S. dedicated to academic research, capable of outperforming 100,000 home computers. In the first three months of operations, approximately 600 projects and more than 1,200 scientists have run on Stampede. These include top researchers in every field of inquiry from earthquake prediction to brain tumor imaging to CO2 capture and conversion."

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Garden Variety Mutants

aarondubrow aarondubrow writes  |  about 2 years ago

aarondubrow writes "Geraniums are one of two plant groups known to have mutable genomes. The organization of the geranium's chloroplast genome and the genes within it are highly rearranged in comparison to other plants and the rates of change for certain gene sequences are highly elevated. Leading geranium scholars are using the Ranger supercomputer to better understand why the geranium has evolved to be so radically different from other plants and what this can tell us about genomic function in general."
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Exposing the Machinery of the Resistome

aarondubrow aarondubrow writes  |  about 2 years ago

aarondubrow (1866212) writes "2011 Nobel Prize Winner, Bruce Beutler, is using the Ranger supercomputer at The University of Texas at Austin for an ambitious new project to discover all of the genes involved in the mammalian immune response – the so-called "resistome." Over several years, Beutler's lab will sequence the protein coding portions of genes in 8,000 mice to detect the impact of mutations on immunity. This means scanning, enriching and sequencing 500 billion base pairs every week. The project represents a "Big Data" problem of the highest order."
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Monogamy and the Immune System

aarondubrow aarondubrow writes  |  about 2 years ago

aarondubrow (1866212) writes "Researchers from UC Berkeley examined the differences between two species of mice – one monogamous and one promiscuous – on a microscopic and molecular level. They discovered that the lifestyles of the two mice had a direct impact on the bacterial communities that reside within the female reproductive tract of the species. These differences correlate with enhanced diversifying selection on genes related to immunity against bacterial diseases."
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Mapping the Future of Climate Change in Africa

aarondubrow aarondubrow writes  |  about 2 years ago

aarondubrow writes "The Climate Change and African Political Stability Program (CCAPS) has created a web tool that uses historical data to map the different levels of vulnerability to climate change at the sub-national level. The web tool will soon incorporate vulnerability measurements based on future climate projections, derived from simulations run on TACC's Ranger supercomputer."
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Small Molecule May Play Big Role in Alzheimer's Disease

aarondubrow aarondubrow writes  |  about 2 years ago

aarondubrow writes "Researchers from UC Santa Barbara used the Ranger supercomputer to simulate small forms of amyloid peptides that are believed to be a primary cause of toxicity in Alzheimer's disease. They found that hairpin-shaped forms of the peptide initiated the aggregation of oligomers that ultimately led to the formation of a fibril. The simulations are leading to new diagnostic and treatment options they may stop the disease."
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Molecular Matchmaking for Drug Discovery

aarondubrow aarondubrow writes  |  more than 2 years ago

aarondubrow writes "For millennia, mankind has discovered new drugs either through educated guesswork or blind luck. But with the proliferation of advanced computing, a new paradigm has emerged whereby one can find drug targets through simulation and modeling...As a consequence of improvements to the image reconstruction and modeling algorithms, researchers can now identify secondary structures of molecules, like individual side-chains — floppy but crucial limbs that extend from the central spine of molecule. This level of detail is required to accurately predict binding."
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