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In early March, when experimental scientists released an important batch of information about the coronavirus, biophysicist Rommie Amaro sent an email to Dan Stanzione at Austin's Texas Advanced Computing Center (TACC). She asked for time on Frontera, the fifth most powerful supercomputer in the world.
She and a team from her computational biology lab at the University of California, San Diego, together with scientists from other labs, were creating a model of the virus. Their goals included simulating its movements, which would provide information about how the virus interacted with human cells and provide structural insights for drug development.
Amaro and her team previously modeled and analyzed an influenza virus. The project, which was finished in 2019, took six years. Now, amid a global pandemic, they were hoping to create the coronavirus model in a matter of weeks. This could only be possible with collaboration in the global community and the use of one of the world's most powerful supercomputers. So she contacted Stanzione, TACC's executive director.
"It took me one email to Dan Stanzione," she says. "He said, 'I know what you guys do. Just go for it.' It turned out to be so critical for this work. It's unprecedented and impressive."
As researchers race to provide important information about the coronavirus and its spread, organizations from the federal government, industry and academia have come together to quickly get researchers free access to supercomputers. They joined forces to create the COVID-19 High Performance Computing Consortium, which carries out a daily review of requests for computing capacity. When Amaro was modeling influenza, it took her a year to get her proposal for supercomputer time funded.
TACC is a member of the consortium. The Austin center is part of the University of Texas-Austin and is funded by the National Science Foundation. It has more than 10 supercomputers, and Frontera is the fastest academic computer in the world.
"We are supporting over 20 projects now that are in some way dealing with the coronavirus response," says Stanzione, "for probably a few hundred researchers around the country."
Some projects come in through the daily review process, while others have been green-lit even more quickly, using a discretionary process similar to that used in emergencies such as a hurricane threat in the Gulf of Mexico. The researchers now receiving this immediate approval are usually those who have worked with the center before. They are able to use elements of past projects to approach the new coronavirus threat.
"Existing capacity matters a lot," he says. "Software has been built. There are data sets you can use. The projects where we are already pushing out results that are helping come from existing relationships."
The supercomputers at TACC have hundreds of thousands of processors networked in such a way that the transmission time between the processors is extremely low. This allows for large, intricate calculations to be done. Stanzione says that in order to simulate the coronavirus over time, processors need to communicate with each other within fractions of a femtosecond, which is a millionth of a billionth of a second.
Amaro and her team, along with several groups from other labs, will create a three-dimensional model of the outside of the new coronavirus, SARS-CoV-2, as well as a simulation of its movements. This should give information about how it interacts with human cells and provide insights for drug and vaccine development. The researchers expect the model to contain about 200 million atoms.
So far, the team has built a three-dimensional model of the spike proteins (which are the red "knobs" seen on coronavirus images), the tether that connects the spikes to the membrane on the outside of the virus, and some of that membrane. They have also been able to model the sugar-like molecules found on the proteins, which may be camouflaging the virus from our immune system.
The team will now apply the laws of physics to model how the virus moves.
"You have to have to understand how it is moving in order to understand its function," she says.
Amaro says that simulations of other viruses have revealed hidden aspects of the coronavirus, such as drug targets, that could not be seen experimentally. Simulation data such as hers is used to augment data collected in experimental labs around the world. It is part of a fast-moving, global effort to conquer coronavirus.
"The sharing and collaboration has been surprising and incredible," says Amaro.
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Austin FC couldn't find the stamina to fight off a 2-0 loss against LAFC for their inaugural match on Saturday.
The match, which saw No. 21 Austin FC go head-to-head with No. 2 LAFC in Los Angeles, was broadcast nationally on FOX and FOX Deportes.
Salute the support. 👏
It's only the beginning for @AustinFC. pic.twitter.com/TduorqYr2y
— Major League Soccer (@MLS) April 18, 2021
Eleven players took the stage as Austin FC players for the first time, with five starters making their MLS debut. "Ringleader" Alex Ring took the captain's armband and wore it well. The defensive midfielder could be seen leading his teammates through their first ever match, but it wasn't enough to stage an Austin takeover in LA.
In the signature style of Head Coach Josh Wolff, the team played with quickness and intensity, nearly connecting on several fast breaks. It was harder for them to stay in front, however, something that Wolff credits with quick decision making and a tough LAFC defense.
"We have a quick attacking team, but I think when you make quick attacks and it fizzles it's just about some decision making," Wolff said. "Are we in position to finish attacks? If not, can we reestablish our attack and get stuff better?"
The club was given some generous breaks from No. 2 LAFC, who had one or both of their star DPs out for the half. While forward Diego Rossi is out for the entire match due to a hamstring injury, Carlos Vela was accidentally pulled too soon on what turned out to be a miscommunication.
"He gave us the sign that he needed to come off," LAFC Head Coach Bob Bradley said on broadcast. "I can't say more than maybe it's my fault."
LA pulled some dramatics and slowly gained more possession throughout the half, but ATXFC's defense wasn't initially as shaky as it seemed in preseason. Jhohan Romana has pulled his weight in getting the ball out of goal, and a 34-year old Matt Besler held his own in center back.
As the second half commenced, however, it became clear that LAFC had the advantage over Austin's first major league team.
Goalkeeper Brad Stuver had his work cut out for him, fending off 24 shot attempts, 11 of which were on goal. He didn't have much time to prepare, either: in the first 30 seconds of play, Stuver had already made a save to keep the match 0-0.
LAFC finally connected in the 61st minute of play as Corey Baird shot one into the bottom right corner. The team capitalized off their momentum and put one past Stuver a second time, drawing roars of approval from the LAFC crowd.
While some last-minute attempts from Jon Gallagher and others were made, Austin FC didn't have the endurance to bring a tie. After seven additional minutes of stoppage time, the club lost their first match 2-0.
While the scoreboard tells one story, Wolff said that the team did well considering the skill of LAFC and the pressure of their club debut.
"We've got to be realistic," Wolff said. "This is the first time this organization has been in front of TV with an opportunity to show itself and I think there were some promising moments. And we're going to maximize those and continue to try to develop those, but there's lots to build on."
The team may have lost, but it still won the support of thousands of Verde fans, dozens of which made it to watch their team's first match. When Stuver and the team made it to bthe stadium, Los Verdes fans were already there to show support, and Stuver said his wife saw the same back in Austin.
"The moment that we pulled into the stadium, we saw Black and Verde fans cheering us on as we got to the stadium," Stuver said. "During warm up, you can just look around and see different groups sitting in different sections of the stadium and it's just truly amazing to see the support in our first game. We know that we want to give the fans everything, because this we play for the city and we play for them."