2016

2015

Advancing Flu Virus Research with GPUs

A modern twist on a World War II combat method is aiding the fight against the deadly Ebola virus — and could help avoid a catastrophic influenza pandemic. Eric Jakobsson from the University of Illinois at Urbana-Champaign and the National Center for Supercomputing Applications, and Amir Barati Farimani from Stanford University, took their inspiration from the Blitz, and the randomly determined automatic firing patterns of anti-aircraft guns to protect London from German war planes. They’ve used similar stochastic algorithms, powered by GPUs, to develop multiple simulated molecular models that predict which antibodies would best combat certain strains of Ebola.

• http://www.dabcc.com/advancing-flu-virus-research-with-gpus/
• https://blogs.nvidia.com/blog/2017/01/18/flu-virus-research/?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+nvidiablog+%28The+NVIDIA+Blog%29

Researchers Using Blue Waters Make Strides in Researching Treatment for Ebola

Who would have thought that a method that enabled the automatic firing of anti-aircraft guns in World War II would be applicable over 70 years later? This time, though, instead of protecting London's citizens from German warplanes, it’s creating antibodies to protect humans from infectious viruses. Even the method of viral infection is similarly violent to warplanes—viruses like Ebola punch a hole in the surface of a cell to inject genetic material. This method, called smart Monte Carlo or biased random walk, can be explained in terms of evolution: Random mutations occur, but there's a bias toward those mutations that improve survival, since the lethal mutations won't get passed on. A team of researchers at the University of Illinois at Urbana-Champaign and Stanford University used this method to predict what antibody would most likely pair best with a protein that coats a virus. Their work focuses on two strains of the Ebola virus, and multiple possible mutants of both strains. "Part of our simulation was to emulate that process in the coat protein. Every time we wanted to try a new coat protein, we threw dice, but we threw loaded dice," team member and senior research scientist at the National Center for Supercomputing Applications (NCSA) Eric Jakobsson, says.

• https://www.hpcwire.com/off-the-wire/researchers-using-blue-waters-make-strides-researching-treatment-ebola/
• http://www.ncsa.illinois.edu/news/story/researchers_using_blue_waters_supercomputer_make_strides_in_researching_tre

18 general, 9 exploratory allocations on Blue Waters awarded to Illinois researchers

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.

• http://www.ncsa.illinois.edu/news/story/18_general_9_exploratory_allocations_on_blue_waters_awarded_to_illinois_res