It was just about this time last year that we first learned of the virus termed H1N1. Most of us will remember the initial alert—we didn't know it as H1N1 at the time, and it seemed like a distant threat. But what began as a remote nuisance quickly snowballed into an all-out fear-fest as the beast smashed against our shores. Ultimately, one in every six Americans felt the sting of the “Swine Flu,” and the death toll worldwide has already topped the 13,000 mark.

One of the most maddening and frightening aspects of the H1N1 flu pandemic was its penchant for surprise. Though an otherwise healthy Person A may have incurred little more than a sore throat and a cough, an otherwise healthy Person B might well have been thrust into a life-threatening spiral.

Researching and effectively battling such a virus isn’t easy, and as H1N1 climbed toward its peak, we were flooded with reports of the frantic work going on behind the scenes to combat its spread and effects. And now, even as it recedes from our continent, the exploration continues—not merely for a better understanding of how and why H1N1 acts as it does, but for answers to other potential future health crises, too.

One of the organizations involved in that research is the Theoretical and Computational Biophysics Group (TCBG) at the University of Illinois. A key “technology resource” of the National Institutes of Health, TCBG focuses on the structure and function of the intricacies of the living cell and the development of algorithms and efficient physical biology computing tools. It is, in essence, a place where highly learned people use highly advanced technologies, highly sophisticated scientific principles, and highly powerful computing gear to investigate the infinitesimally tiny building blocks that make up our world. It is also an entity that was very much on the front lines when the name H1N1 lay justifiably on the tip of everyone’s tongue.

Klaus Schulten, Swanlund Professor of Physics and director of TCBG, said the H1N1 threat gave theoretical scientists a chance to apply something he refers to as “emergency computing” to help solve a real-world problem. “Emergency computing is computing in the service of society that addresses societal issues of great urgency,” says Schulten. “The actual computing is of the type usually undertaken for less pressing issues like study in biomedicine or the investigation of earthquakes. But it has now begun to play an essential role in assisting society in cases of emergency, when fast yet complex decisions need to be made.”

But where Schulten and his crew had in the past turned to standard CPU-based PC and supercomputing technology to run the immense calculations that are an everyday part of their research, the emergency computing burdens of the H1N1 crisis demanded a new, faster weapon. That weapon, as it turned out, was a fleet of NVIDIA GPUs.

Schulten explains, “GPUs excel at accelerating arithmetic-intensive problems that can be expressed in a highly parallel form, where tens of thousands of individual calculations can be performed concurrently by multiplexing them onto hundreds of GPU processing units. Some of the tasks that run on GPU-enhanced computers range from calculations of multi-million atom electrostatics, biomolecular dynamics like protein folding, diffusion-reaction processes in biological cells, and visualization of quantum chemistry simulations, just to name a few.”

In battling H1N1, the TCBG team utilizes highly specialized NAMD (Nanoscale Molecular Dynamics) and VMD (Visual Molecular Dynamics) software to help answer questions about the immediate and distant future of the cells that make up the virus. How will they react to certain drugs? Will they adapt to or resist treatments? Will they evolve on their own? How can we better deal with future outbreaks? Using NAMD and VMD in conjunction with extreme high-end computers and the parallel processing of GPUs gives Schulten and his compatriots a chance to simulate and visualize cell modifications faster and with more accuracy than ever before. And that’s good news for everybody.

But surely they don't use straight-up gaming cards, do they? Actually, yes, they do. Schulten tells us his lab—and in particular the researchers' PCs—is a game card haven. But for the big jobs, they pull out the big guns. “We use professional 4GB Quadro GPUs for driving high-end stereoscopic visualization workstations and projection systems. We use professional Tesla GPUs within our GPU cluster nodes and in several of the GPU-accelerated visualization workstations in our lab. The Teslas are compute-specific cards, so they are accompanied with one of the other types of cards when used as accelerators in visualization workstations.”

According to Schulten, adding GPUs to the equation—a concept he and his crew debuted in 2007—has increased the speed of applicable calculations by factors of ten (on multi-use parallel supercomputing machines) to 200 (by adding GPUs to single-CPU setups). And that, says Schulten, saves a ton of time. “Electrostatic calculation is an example among many where calculations that once took days now take minutes. This permits one now to carry out calculations that are crucial for scientific understanding, but were unachievable earlier.”

Schulten, for one, is convinced that GPU-accelerated computing at this level is not only preferable, but downright essential as the future unfolds. “GPU acceleration will extend computer simulations to the time-scale and size-scale of living cells, such that computers, as partners of experiments, become microscopes showing the inner working of living systems at unprecedented resolution. Definitely, GPU-accelerated computing is here to stay in life science and biomedical research. This development will be the basis of biomedical treatment of human diseases in circumventing drug resistance of bacteria and viruses, fighting viral infection, and improving cardiovascular diseases through new intervention strategies.”

So, the next time you're busy perforating a gang of rogue aliens at 60 frames per second, give a nod to the gang at the University of Illinois, which is using the same technology to fight the real enemy.