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Scientists use world's fastest supercomputer to create the largest HIV evolutionary tree
October 28, 2009Mapping Darwinian evolutionary relationships results in an HIV family tree that may lead researchers to new vaccine focus areas
Supporting Los Alamos National Laboratory's role in the international Center for HIV/AIDS Vaccine Immunology (CHAVI) consortium, researchers are using the Roadrunner supercomputer to analyze vast quantities of genetic sequences from HIV infected people in the hope of zeroing in on possible vaccine target areas.
Physicist Tanmoy Bhattacharya and HIV researcher Bette Korber have used samples taken by CHAVI across the globe - from both chronic and acute HIV patients - and created an evolutionary genetic family tree, known as a phylogenetic tree, to look for similarities in the acute versus chronic sequences that may identify areas where vaccines would be most effective.
In this study the evolutionary history of more than 10,000 sequences from more than 400 HIV-infected individuals was compared.
The idea, according to Korber, is to identify common features of the transmitted virus, and attempt to create a vaccine that enables recognition the original transmitted virus before the body's immune response causes the virus to react and mutate.
"DNA Sequencing technology, however, is currently being revolutionized, and we are at the cusp of being able to obtain more than 100,000 viral sequences from a single person," said Korber. "For this new kind data to be useful, computational advances will have to keep pace with the experimental, and the current study begins to move us into this new era."
"The petascale supercomputer gives us the capacity to look for similarities across whole populations of acute patients," said Bhattacharya. "At this scale we can begin to figure out the relationships between chronic and acute infections using statistics to determine the interconnecting branches - and it is these interconnections where a specially-designed vaccine might be most effective.
DOE/Los Alamos National Laboratory
In this study the evolutionary history of more than 10,000 sequences from more than 400 HIV-infected individuals was compared.
The idea, according to Korber, is to identify common features of the transmitted virus, and attempt to create a vaccine that enables recognition the original transmitted virus before the body's immune response causes the virus to react and mutate.
"DNA Sequencing technology, however, is currently being revolutionized, and we are at the cusp of being able to obtain more than 100,000 viral sequences from a single person," said Korber. "For this new kind data to be useful, computational advances will have to keep pace with the experimental, and the current study begins to move us into this new era."
"The petascale supercomputer gives us the capacity to look for similarities across whole populations of acute patients," said Bhattacharya. "At this scale we can begin to figure out the relationships between chronic and acute infections using statistics to determine the interconnecting branches - and it is these interconnections where a specially-designed vaccine might be most effective.
DOE/Los Alamos National Laboratory
Supercomputer Current Events and Supercomputer News RSSLANL Roadrunner models nonlinear physics of high-power lasers
For years scientists have struggled with the difficult physics of inertial confinement fusion. This is the attempt to compress a target capsule containing isotopes of hydrogen with high-powered lasers to high enough pressure and temperature to initiate fusion burn.
Science at the Petascale: Roadrunner Results Unveiled
The world's fastest supercomputer, Roadrunner, at Los Alamos National Laboratory has completed its initial "shakedown" phase doing accelerated petascale computer modeling and simulations of a variety of unclassified, fundamental science projects.
Key new ingredient in climate model refines global predictions
For the first time, climate scientists from across the country have successfully incorporated the nitrogen cycle into global simulations for climate change, questioning previous assumptions regarding carbon feedback and potentially helping to refine model forecasts about global warming.
Kraken becomes first academic machine to achieve petaflop
The National Institute for Computational Sciences' (NICS's) Cray XT5 supercomputer-Kraken-has been upgraded to become the first academic system to surpass a thousand trillion calculations a second, or one petaflop, a landmark achievement that will greatly accelerate science and place Kraken among the top five computers in the world.
Research Team Finds First Evolutionary Branching for Bilateral Animals
In the most computationally intensive phylogenetic analysis to date, an international research team led by Brown University has found the first evolutionary branching for bilateral animals.
Berkeley Lab Scientists' Computer Code Gives Astrophysicists First Full Simulation of Star's Final Hours
The precise conditions inside a white dwarf star in the hours leading up to its explosive end as a Type Ia supernova are one of the mysteries confronting astrophysicists studying these massive stellar explosions.
Hot and cold moves of cyanide and water
Scientists have long known that molecules dance about as the temperature rises, but now researchers know the exact steps that water takes with a certain molecule.
SLAC Researchers Reveal the Dance of Water
Water is familiar to everyone-it shapes our bodies and our planet. But despite this abundance, the molecular structure of water has remained a mystery, with the substance exhibiting many strange properties that are still poorly understood.
First Black Holes Born Starving
The first black holes in the universe had dramatic effects on their surroundings despite the fact that they were small and grew very slowly, according to recent supercomputer simulations carried out by astrophysicists Marcelo Alvarez and Tom Abel of the Kavli Institute for Particle Astrophysics and Cosmology, jointly located at the Department of Energy's SLAC National Accelerator Laboratory and Stanford University, and John Wise, formerly of KIPAC and now of NASA Goddard Space Flight Center.
First black holes kept to a strict diet, study shows
A new supercomputer simulation designed to track the fate of the universe's first black holes finds that, counter to expectations, they couldn't efficiently gorge themselves on nearby gas.
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