SARS-Cov-2 virus

Arizona universities join forces to contribute to COVID-19 modeling and simulation efforts

By

Marisa Brazil

While the COVID-19 pandemic continues to impact the world, the research computing centers at Arizona State University, Northern Arizona University and University of Arizona have united as a team to contribute to the Folding@home project. The project utilizes idle computing power to significantly contribute to vital scientific research and therapeutic drug discovery. 

The Arizona Research Computing consortium is contributing to this collective effort by using advanced computing resources to perform complex protein modeling computations during brief idle periods on local supercomputers. By running these computations only during downtime, contributions to COVID-19 modeling and simulation efforts can be made through the Folding@home project without impacting everyday research.  

What is the Folding@home project?

The Folding@home project provides people around the world the opportunity to make active contributions to a variety of scientific research efforts including COVID-19. Volunteers, or “citizen scientists,” can download the Folding@home software to their personal computers, allowing simulations of complex scientific processes to run in the background while their personal computers are not in use. The Folding@home project is crowdsourcing at its best, using shared computing power at a massive scale to help solve grand challenges in biomedical research. 

In addition to mobilizing citizen scientists across the globe, many institutions and corporations are contributing their own computational resources such as high performance workstations and servers. This distributed computational power is estimated to be 10 times faster than the world’s fastest individual supercomputer. 

How is the Folding@home project impacting COVID-19 research?

The onslaught of COVID-19 has raised the visibility of the Folding@home project, highlighting a unique opportunity to fight the virus. The project seeks to understand how proteins, which are large, complex molecules that play an important role in how our bodies function, “fold” to perform their biological functions. This helps researchers understand diseases that result from protein “misfolding” and identify novel ways to develop new drug therapies.

How proteins fold or misfold can help us understand what causes diseases like cancer, Alzheimer's disease and diabetes. It might also lend insight into viruses such as SARS-CoV-2, the cause of the recent COVID-19 pandemic. 

“Imagine if I told 100 people to fold a pipe cleaner. They are going to fold it in 100 different ways because there’s an infinite number of combinations of how to take something that is straight and fold it," said Blake Joyce, assistant director of research computing at the University of Arizona. "That’s what viruses and living things do with proteins. They make copies of themselves and fold them up in their own particular way.”  

Using computational modeling, researchers can explore the mechanics of proteins of the virus and predict every possible way it might fold, or physically change shape. 

“In biology, shape is function. … If you can disrupt that shape, the virus is inactive or can’t do its thing. If you disrupt any of the mechanisms that can damage us, you have a cure, or at least something you can treat. And that is what we’re after. It just takes a lot of computing to come up with every possible way to bend a pipe cleaner,” Joyce said. 

By running computer simulations, researchers can take the virus and see how it interacts with various compounds or drugs and narrow down which ones might work to interrupt one of the critical mechanisms the virus needs to survive. 

Folding@home “assigns” pieces of a protein simulation to each computer and the results are returned to create an overall simulation. Folding@home computations for COVID-19 research seem to be most productive on the kind of computers found in facilities like Arizona’s research computing centers, making their contributions even more valuable. 

What is the impact? 

Volunteers can track their contributions on the Folding@home website and combine their efforts as a team, receiving points for completing work assigned to them and even earning bonus points for work that is more computationally demanding or that might have a greater scientific priority. 

The Arizona Research Computing team has risen quickly in the ranks, highlighting the powerful computing capabilities at Arizona’s state universities and the effectiveness of regional collaborations. As of mid-June, the Arizona Research Computing team was ranked in the top 100 out of nearly a quarter of a million teams, surpassing Hewlett Packard, Cisco Systems, Apple Computer, Inc., Google, Ireland and Poland, as well as many other university, industry and national or international contributors. 

The Folding@home project “investigates many research questions that require an enormous amount of computing, but this specific use for COVID-19 provides a unique opportunity, spurring many computing centers to participate in Folding@home for the first time,” said Gil Speyer, lead scientific software engineer for Arizona State University’s research computing center. 

Today’s biomedical research requires vast amounts of time and computing power. While the Arizona Research Computing team may directly impact COVID-19 research in a small way, the overall impact of the Folding@home project is much broader and will continue to have applications beyond the COVID-19 pandemic. 

Contributors

ASU:

Sean Dudley, assistant vice president and chief research information officer, Research Technology Office

Douglas Jennewein, senior director, research computing, Research Technology Office 

Gil Speyer, lead scientific software engineer, Research Technology Office

Marisa Brazil, associate director, research computing, Research Technology Office

Jason Yalim, postdoc, research computing, Research Technology Office

Lee Reynolds, systems analyst principal, research computing, Research Technology Office

Eric Tannenhill, senior software engineer, research computing, Research Technology Office

NAU: 

Chris Coffey, team lead, HPC 

UArizona: 

Blake Joyce, assistant director, research computing 

Todd Merritt, information technology manager, principal 

Ric Anderson, systems administrator, principal

Chris Reidy, systems administrator, principal

Adam Michel, systems administrator, principal