Supercomputers Map the Coronavirus

In a video interview with Stony Brook University more than a year ago, Carlos Simmerling, Ph.D., presented a 3D printed model of a spike found on the surface of the coronavirus. The chemistry professor’s excitement was obvious as he explained that the colorful parts of the red, blue and yellow model represented the “fingers” of the virus, which it uses to attach itself to human cells. He showed another model that demonstrated what those fingers look like when they open. Since then, nearly all of Simmerling’s research has been devoted to these models. 

Working in his eponymous lab in the Laufer Center for Physical and Quantitative Biology at Stony Brook University, Simmerling and his team of researchers and graduate students have been creating 3D computer models of the coronavirus. Unlike most models, which are static and don’t show important molecular movement, his team is using supercomputers to create models that simulate the movement of these viruses in order to gain a deeper understanding of exactly how they attach to cells. 

“It’s the same thing as taking a picture with a camera,” said Simmerling, who is the Marsha Laufer Endowed Professor of Physical and Quantitative Biology. “If you’re sitting still it’s going to be fine, but if you’re running, the photos are going to be blurry. We take in data from these experiments, and then simulate the parts that are fuzzy.”

A depiction of the protein spike found on the coronavirus. Provided by the Laufer Center

By focusing on the specific interaction virus spikes have when connecting to ACE2 receptors – proteins found on the surface of many common cells – Simmerling’s team found a pocket that opens on the coronavirus during this process. This opening could potentially allow small-molecule drugs to enter and effectively target the virus itself before a person is infected – unlike drugs such as remdesivir that aim to stop the virus from replicating after it has infected someone. This treatment could one day be more effective than vaccines, especially if new mutations of the virus make them ineffective. But such potential treatments are still far away. 

“We are still working on this, trying to understand how the spike mediates membrane fusion to allow the virus to get inside the cell,” Simmerling explained. “There is very little experimental detail on this process, but a better understanding could lead to treatments that are effective against all coronaviruses”

Simmerling has a way of making his complex research understandable. “Imagine you teach someone to recognize a car – if you teach them color or shape, that won’t work for different cars, but if you teach them that it has four wheels and doors it is much more general.”

Carlos Simmerling. Photo provided by Stony Brook University

The research has received funding from various grants and organizations, including the Research Corporation for Science Advancement – a private Arizona-based foundation that funds innovative research in the physical sciences – as well as seed money from Stony Brook and the State University of New York, and a pending National Science Foundation proposal for approximately $200,000. 

In addition, Simmerling’s team has been authorized to use supercomputers through the COVID-19 HPC Consortium – a national collaboration between the White House Office of Science and Technology Policy, the U.S. Department of Energy and IBM, which offers use of supercomputers across the country to various researchers. He says time on the supercomputers is “worth far more than the dollars.”

Simmerling was part of a national research team that used a supercomputer named Summit to simulate the coronavirus spike protein and viral envelope using 305 million atoms. Summit resides at the Department of Energy’s Oak Ridge National Laboratory in Tennessee, where it takes up the space of two tennis courts, weighs more than a commercial aircraft, is connected by 185 miles of fiber optic cable and can do 200,000 trillion calculations per second. 

The Stony Brook professor and his human colleagues won the 2020 Gordon Bell Special Prize for High Performance Computing-Based COVID-19 Research. The Gordon Bell Prize is known as the “Nobel Prize for Supercomputing” and comes with a $10,000 award.