NCSA’s Delta Assists potential staph infection breakthrough

Computers sometimes have their own bugs to deal with, but the GPU-based Delta system at the National Center for Supercomputing Applications chipped in to help researchers learn more about what makes staph infections so resilient and challenging to treat.

Auburn University biophysicists relied on the Delta supercomputer at NCSA to uncover new details on the bacterial grip strength of Staphylococcus aureus on human skin. In a recent article published in ScienceAdvances, researchers from the Computational Biophysics Group at Auburn University’s Department of Physics found the adhesion of staph bacteria to skin to be “one of the strongest noncovalent biomolecular interactions ever recorded” and that “calcium is a critical regulator” in lowering that bond and preventing infection.

“It is the strongest non-covalent protein-protein bond ever reported,” said Associate Professor of Physics Rafael Bernardi. “This is what makes staph so persistent, and it helps us understand why these infections are so difficult to get rid of.”

Molecular dynamics simulations performed with Delta GPU allocations at NCSA enabled a key part of the findings, which allowed researchers to model, atom by atom, how bacterial adhesin locks onto the human protein with unprecedented strength. These simulations, combined with scientists measuring the force of a single staph bacterium attaching to the human skin, led to the extraordinary conclusion that this is the strongest protein bond known in biology.

“Most of the molecular dynamics packages used in biomolecular modeling take advantage of the computing power of GPU accelerators,” said Greg Bauer, NCSA technical assistant director and co-principal investigator for Delta. “The NCSA Delta system provides a range of GPU types for researchers to use for accelerated computing such as molecular dynamics.”

The research also found that calcium plays a significant part in the bond, explaining why infections are so persistent in eczema and pointing toward new therapies that block adhesion rather than relying solely on antibiotics.

“We were surprised to see how much calcium contributed to the strength of this interaction,” explains Priscila Gomes, a researcher in Auburn’s Department of Physics and co-author of the study. “It not only stabilized the bacterial protein, it made the whole complex much more resistant to breaking.”

Delta continues to be an invaluable tool for groundbreaking research.

“We are deeply grateful for the computational resources provided by NCSA,” Gomes said. “They were essential to uncovering how calcium stabilizes this interaction and solving a long-standing mystery in staph pathogenesis.”

ABOUT DELTA AND DELTAAI

NCSA’s Delta and DeltaAI are part of the national cyberinfrastructure ecosystem through the U.S. National Science FoundationACCESS program. Delta (OAC 2005572) is a powerful computing and data-analysis resource combining next-generation processor architectures and NVIDIA graphics processors with forward-looking user interfaces and file systems. The Delta project partners with the Science Gateways Community Institute to empower broad communities of researchers to easily access Delta and with the University of Illinois Division of Disability Resources & Educational Services and the School of Information Sciences to explore and reduce barriers to access. DeltaAI (OAC 2320345) maximizes the output of artificial intelligence and machine learning (AI/ML) research. Tripling NCSA’s AI-focused computing capacity and greatly expanding the capacity available within ACCESS, DeltaAI enables researchers to address the world’s most challenging problems by accelerating complex AI/ML and high-performance computing applications running terabytes of data. Additional funding for DeltaAI comes from the State of Illinois.