Science Highlights Spring/Summer 2020
A bi-annual summary of projects conducted and supported by PSC computational resources, educational programs, and staff expertise
WELCOME TO THE SPRING / SUMMER 2020 ISSUE
From the Director
I am Shawn Brown, and in November 2019, I was named the new Director of the Pittsburgh Supercomputing Center. I am extremely humbled and honored to be taking this position. When I started at PSC in 2005 as a Senior Chemistry Support Specialist, I never imagined then that I would be given the opportunity to lead such a storied and wonderful organization.
FEATURE: Big Waves Happen Here, Too
Recent tsunamis have killed hundreds of thousands and done vast economic damage. But even areas not known for big waves, such as the East Coast of
the U.S., are at risk. Working for the U.S. National Tsunami Hazard Mitigation Program, scientists at the universities of Rhode Island and Delaware have leveraged the large capacity and data analytics capabilities of PSC’s Bridges platform to simulate worst-case scenarios of tsunami damage on the eastern seaboard.
The NMDA receptor protein underlies memory formation, an important target of drugs for conditions as different as depression, Alzheimer’s disease and tinnitus. Scientists might be able to design better medications for these conditions if they understood better how the receptor works. Using Anton 2 at PSC, Johns Hopkins scientists simulated the receptor and the neurotransmitter chemicals that activate it. They discovered a curious difference in how the different neurotransmitters work that may be biologically important and offers new targets for drug development.
Picking Up the Beat
Irregular heartbeat—arrhythmia—causes a lot of sickness and death in the U.S. Some medications can treat arrhythmia, but they carry potentially serious side effects. Using Anton 2 at PSC a team from the University of California, Davis has performed previously impossible simulations of how the anti-arrhythmic drug lidocaine enters the cardiac sodium channel that initiates heart-muscle contraction. The results revealed an unexpected path of entry for the drug. The results may help scientists design better anti-arrythmia medications with fewer side effects.
Looking a Hominid in the Mouth
Oral health may have a surprising impact on overall health. But scientists still don’t fully understand which of the bacteria in our mouths cause disease. Scientists used data-intensive computation on PSC’s Bridges platform to identify the bacteria of the “oral microbiome.” The project sequenced bacterial DNA from the tooth surfaces of chimpanzees and compared it to those of humans and Neanderthals. The scientists discovered that relatively rare bacteria associated with disease in human mouths are common in our close evolutionary relatives.
Freedom, they Printed
In the 17th century, you could get jailed or even executed for criticizing the government of England. But a flood of books on civil liberties, produced at great risk by anonymous printers, helped change that. An artificial intelligence (AI) analysis of irregular letters using PSC’s Bridges platform has helped a Carnegie Mellon team solve the mystery of who printed nine of these seminal works.
A Galactic Choice
New telescope surveys are discovering hundreds of millions of new galaxies—far more than humans can classify. A National Center for Supercomputing Applications (NCSA)-led team has employed “deep learning” artificial intelligence (AI) on the graphics processing units (GPUs) of PSC’s Bridges platform to produce a galaxy-classifying artificial intelligence with better-than-human accuracy and capacity.
Microscopic and Huge
An image can help human beings make connections. That’s why a scientist from Catholic University of America is using the large-memory nodes of PSC’s Bridges platform to put together some of the largest assemblies of proteins ever pictured. Thanks to Bridges’ powerful nodes with large amounts of memory, Victor Padilla-Sanchez has created images of whole viruses with atomic-level detail. These images will help engineer those viruses as vaccines or other medical therapies.