Scientists at a U.S. nuclear weapons lab are using the world's fastest computer in an effort to defeat one of the world's wiliest and deadliest diseases"HIV, the human immunodeficiency virus.
Roadrunner, the supercomputer built for Los Alamos National Laboratory to perform nuclear weapons research and modeling, was used to analyze more than 10,000 genetic sequences from HIV samples in a search for vulnerabilities in the virus that could lead to an effective vaccine.
The computer, which can perform more than a quadrillion calculations per second, created an HIV genetic family tree that sheds light on the evolution of virus strains from 400 infected individuals, some with acute HIV infections, others with chronic forms of the disease.
By identifying similarities and differences between the strains, researchers hope they will find weak spots in the virus that can be exploited by a vaccine.
For decades that's been a frustrating search. A bedeviling trait of HIV is that it changes form so quickly and frequently that the human immune system can't keep up and defeat it.
The aim of the research with Roadrunner, say Los Alamos researchers, is to develop a vaccine that will block HIV before it mutates.By analyzing the HIV samples, the supercomputer was able to sort them into families, then infer how the viruses evolved. Thus, the computer was able to digitally recreate the ancestors of current viruses, even though those forms of the virus no longer exist, said Marcus Daniels, a computer scientist in the Theoretical Biology and Biophysics Group at Los Alamos.
Recreating HIV ancestors is important, he said, because knowing the form of the viruses at the onset of infection could suggest ways to create a vaccine that would activate the immune system to block HIV before it mutates.
Meanwhile, studying the differences between the HIV strains that cause acute infection and those that cause chronic infections could also reveal new avenues for attacking the virus, Daniels said.
But even with help from the world's fastest computer, the answers are not obvious. Researchers must comb through Roadrunner's data, searching for "anything that might seem relevant to a virologist. In this study we are looking at virus change as it relates the patient's clinical progression," Daniels said.
Why is such a powerful computer necessary?
The computer must be able to model virus mutations that take place in the span of a millisecond, and which may have been triggered by any of a multitude of factors, said Dave Turek, IBM's vice president for deep computing.
To fully understand what's occurring as the virus changes form, researchers may have to model the mutations "in time steps that are 1 million or 100 million times smaller than that," he said.
That requires a lot of computing power.
"The advantage with this computer is that it can simulate huge amounts of activity in a reasonably short amount of time. You can get a second or two seconds of information on the viruses in couple of hours. So you can run it for hundreds and hundreds of hours and get some sense for how the virus is evolving.
"To perform that much analysis on more than 10,000 genetic sequences "you need a peta-scale computer," Turek said.
To turn the information gleaned by Roadrunner into HIV vaccines, researchers will undoubtedly turn again to computers, this time to create digital vaccines.
"We are able to run quite a bit of analysis against digital models before developing the actual vaccine," Turek said.
"You can hypothesize vaccines in silico" and assess fairly quickly in a digital environment how they are likely to act against an invading virus, he said. The most promising virtual vaccines then can then be created and tested for real.
