Given the challenges of 2020, society has encountered distinguished heroes in many new and sometimes unexpected places. Professor Carlos Simmerling, Stony Brook University’s Marsha Laufer Professor of Physical and Quantitative Biology, worked with a team to develop a groundbreaking AI-driven simulation of the COVID-19 virus, analyzing its infectious effect on host cells. The research has gained significant traction, earning their paper “AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics” the prestigious Gordon Bell Prize.
The Gordon Bell Prize is known as the Nobel Prize of Supercomputing, recognizing innovative and remarkable achievements in high-performance computing with $10,000 to stimulate further research. It brings to light the extraordinary research conducted by Professor Simmerling and his team on research that can transform the state of the pandemic.
“The team has been working tirelessly on the development of a model for the behavior of the spike protein of coronaviruses,” says Professor Simmerling. Investigating how spike proteins conduct themselves provides an understanding on how the virus changes within the host cell. The evolving behavior of the virus is the crux of this global issue.
“If we can figure out how the virus changes its shape when it gets into the host cells, the mappings of said behavior are what we can use and share with other experimental collaborators to figure out ways in which we can interfere with coronaviruses,” says Professor Simmerling.
The primary concern is that vaccines will not be enough to hinder the spread of coronaviruses, since “vaccines only remedy specific versions of the virus,” says Professor Simmerling. Through this research, Professor Simmerling and his team are paving the way for a more dependable cure of coronaviruses, not just the current strain, SARS-CoV-2.
Professor Simmerling’s research shows the interdependence between several scientific disciplines, with AI as a critical ingredient of its success. It can be difficult to cultivate meaningful information, since coronaviruses are often in their ground state. Experiments and simulations are not enough to produce sufficient data, and that is where AI steps up to the plate.
“AI accelerates the motions of the virus, which we can’t get out of experiments or simulations, and pulls out which simulations we can enhance and run,” says Professor Simmerling. In effect, AI tags the virus in its active state and assembles reduced descriptions of the system, which highlight the most important changes within the model. Through AI, the behavior of the virus when attaching to the host cell has been classified as flexible, which is a significant step towards a fuller understanding of coronaviruses, and eventually, a cure.
Professor Simmerling’s area of expertise, computational structural biology, is another academic cornerstone of this research. “My role on the team is being able to simulate how molecules change in time. I train the physics models and then develop hypotheses for how the structure might be changing, and ways we can explore this in the simulations.” Without Professor Simmerling’s insight, the current knowledge of coronaviruses’ behavior would not be possible.
Through receiving the Gordon Bell Prize his work of computational structural biology has been professionally validated. “Personally, the award has shown me that it’s worth eight months of not taking off weekends. It’s an encouragement that we should keep going, and that we’re on the right track,” says Professor Simmerling.
Professor Kenneth Dill, Director of the Laufer Center for Physical and Quantitative Biology extended his admiration to Professor Simmerling for his research and service.
“Carlos is a sweet person and he is an outstanding teacher. He’s what a lot of people in academics would call a triple threat. Professor Simmerling is a productive member of the scientific research community, he’s a valuable member of the staff because of his outstanding teaching skill, and at the end of the day he’s a loyal community member, always working on community service. The Stony Brook community appreciates him for all of the work he does, and the Gordon Bell Prize is just another indicator of how admirable Professor Simmerling is,” says Professor Dill.
Professor Simmerling and his team’s research acts as a beacon of hope, and reminds us of the necessity for different scientific disciplines to work together. “Modern science is about being at the interface between traditional disciplines,” says Professor Simmerling, and that is the means by which we find a cure to coronaviruses.
-Alyssa Dey, Communications Assistant