GTC DAY 2 KEYNOTE: GPUS ENABLING MOLECULAR BIOLOGY RESEARCH

by Tony Kontzer

The impact of NVIDIA’s GPU technology has reached into the molecular frontier, enabling scientific researchers to observe everything from protein folding to photosynthesis in more detail than ever before. Such was the message renowned computational biologist Dr. Klaus Schulten sent during his morning keynote presentation on day two of NVIDIA's GPU Technology Conference. Since 2006, Schulten and his team of researchers at University of Illinois, Urbana-Champaign, where he’s a professor, have tapped the power of GPU-powered computing to get a better look at some of the molecular processes that have long vexed the scientific community. “We’ve benefitted a lot from this technology,” Schulten said. “It’s led to several scientific discoveries.”

Klaus Schulten

GPUs are aiding Schulten’s research in three important ways: by increasing the speed of simulations, improving their accuracy and opening doors to new fields that were unfathomable using GPU technology. They’re doing this by enabling far more powerful microscopy, and, by pairing GPUs with powerful molecular dynamics codes and molecular visualization programs, enabling heretofore time-consuming computational analysis of these detailed images.

Here are some of the ways Schulten’s team has put GPUs to work:

  • They’ve discovered Tamiflu drug resistance in the H1-N1 Swine Flu virus. Also were able to observe that a two-step binding process is necessary, via microscopic views far greater in detail than anything possible prior to GPGPU. This information will allow them to reconfigure Tamiflu to make it more effective in battling H1-N1.
  • They’ve made important discoveries about how viruses attach themselves to cells and respond to atomic microscopy, during which the viruses are prodded to see how they respond to pressure.
  • They’ve shortened to 90 seconds from one hour the time required to analyze electrostatics, which provide electrical charges during the photosynthesis process, opening the door to new insights on harnessing solar energy.
  • They’ve observed ribosomes in action—as opposed to the low-resolution static images possible via CPU-only configurations—providing a snapshot of a protein being born. Schulten likened this to watching a football game rather than just seeing pre-game pictures of the teams.
  • They’ve detected subtle differences in DNA strands, providing more information on the genetics of diseases like cancer and depression, and have reduced the time required to compute radial distribution functions, which are measurements of atomic density, from 15 hours to 10 minutes.
  • They’ve rendered electron clouds in real time, speeding the computing of molecular dynamics by up to 400x. By comparison, CPUs require an entire working day to get a snapshot of an electron cloud.  “This turns out to be heaven for GPUs,” Schulten said. “(Chemists and GPUs) go hand-in-hand—they love each other.”
  • They’ve observed the process of protein folding in unprecedented details, an important advance in being able to combat diseases that result from the unfolding of proteins.

Not surprisingly, such widespread impact led Schulten to conduct a recent workshop on how GPU computing can be used to further molecular dynamics. Based on the impact GPUs have had on Schulten’s work thus far, the sky’s the limit.