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Coronavirus Massive Simulations Completed on Supercomputer – Lab Manager Magazine

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A coronavirus envelope all-atom computer model is being developed by the Amaro Lab of UC San Diego on the NSF-funded Frontera supercomputer of TACC at UT Austin. Biochemist Rommie Amaro hopes to build on her recent success with all-atom in?uenza virus simulations (left) and apply them to the coronavirus (right).

Lorenzo Casalino (UCSD), TACC

Scientists are preparing a massive computer model of the coronavirus that they expect will give insight into how it infects in the body. They’ve taken the first steps, testing the first parts of the model and optimizing code on the Frontera supercomputer at the University of Texas at Austin’s Texas Advanced Computing Center (TACC). The knowledge gained from the full model can help researchers design new drugs and vaccines to combat the coronavirus.

Rommie Amaro is leading efforts to build the first complete all-atom model of the SARS-COV-2 coronavirus envelope, its exterior component. “If we have a good model for what the outside of the particle looks like and how it behaves, we’re going to get a good view of the different components that are involved in molecular recognition.” Molecular recognition involves how the virus interacts with the angiotensin converting enzyme 2 (ACE2) receptors and possibly other targets within the host cell membrane. Amaro is a professor of chemistry and biochemistry at the University of California, San Diego.

The coronavirus model is anticipated by Amaro to contain roughly 200 million atoms, a daunting undertaking, as the interaction of each atom with one another has to be computed. Her team’s workflow takes a hybrid, or integrative modeling approach.

“We’re trying to combine data at different resolutions into one cohesive model that can be simulated on leadership-class facilities like Frontera,” Amaro said. “We basically start with the individual components, where their structures have been resolved at atomic or near atomic resolution. We carefully get each of these components up and running and into a state where they are stable. Then we can introduce them into the bigger envelope simulations with neighboring molecules.”

On March 12-13, 2020, the Amaro Lab ran molecular dynamics simulations on up to 4,000 nodes, or about 250,000 processing cores, on Frontera. Frontera, the #5 top supercomputer in the world and #1 academic supercomputer according to November 2019 rankings of the Top500 organization, is the leadership-class high performance computing system supported by the National Science Foundation.


Related Article: Current COVID-19 Vaccine Efforts


SARS-CoV-2 spike protein of the coronavirus was simulated by the Romaro Lab of UC San Diego on the NSF-funded Frontera supercomputer of TACC at UT Austin. It’s the main viral protein involved in host-cell coronavirus infection. Physics-based molecular dynamics simulations can predict how the coronavirus molecular machine moves, which allows researchers insight into its vulnerabilities to potential vaccines and drugs. Coronavirus spike head based on pdb 6vsb; spike stalk using homology modeling; glycoprofile designed according to Walls et al. 2019 Cell, and Watanabe et al. 2020 bioRxiv.

Rommie Amaro, UCSD

“Simulations of that size are only possible to run on a machine like Frontera or on a machine possibly at the Department of Energy,” Amaro said. “We straightaway contacted the Frontera team, and they’ve been very gracious in giving us priority status for benchmarking and trying to optimize the code so that these simulations can run as efficiently as possible, once the system is actually up and running.”

“It’s exciting to work on one of these brand new machines, for sure. Our experience so far has been very good. The initial benchmarks have been really impressive for this system. We’re going to continue to optimize the codes for these ultra large systems so that we can ultimately get even better performance. I would say that working with the team at Frontera has also been fantastic. They’re at the ready to help and have been extremely responsive during this critical time window. It’s been a very positive experience,” Amaro said.

“TACC is proud to support this critical and groundbreaking research,” said Dan Stanzione, Executive Director of TACC and Principal Investigator of the Frontera supercomputer project. “We will continue to support Amaro’s simulations and other important work related to understanding and finding a way to defeat this new threat.”

Amaro’s work with the coronavirus builds on her success with an all-atom simulation of the influenza virus envelope, published in ACS Central Science, February 2020. She said that the influenza work will have a remarkable number of similarities to what they’re now pursuing with the coronavirus.

“It’s a brilliant test of our methods and our abilities to adapt to new data and to get this up and running right off the fly,” Amaro said. “It took us a year or more to build the influenza viral envelope and get it up and running on the national supercomputers. For influenza, we used the Blue Waters supercomputer, which was in some ways the predecessor to Frontera. The work, however, with the coronavirus obviously is proceeding at a much, much faster pace. This is enabled, in part because of the work that we did on Blue Waters earlier.”

Said Amaro: “These simulations will give us new insights into the different parts of the coronavirus that are required for infectivity. And why we care about that is because if we can understand these different features, scientists have a better chance to design new drugs; to understand how current drugs work and potential drug combinations work. The information that we get from these simulations is multifaceted and multidimensional and will be of use for scientists on the front lines immediately and also in the longer term. Hopefully the public will understand that there’s many different components and facets of science to push forward to understand this virus. These simulations on Frontera are just one of those components, but hopefully an important and a gainful one.”

This press release was originally published on the Texas Advanced Computing Center website

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Here’s how Helene and other storms dumped a whopping 40 trillion gallons of rain on the South

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More than 40 trillion gallons of rain drenched the Southeast United States in the last week from Hurricane Helene and a run-of-the-mill rainstorm that sloshed in ahead of it — an unheard of amount of water that has stunned experts.

That’s enough to fill the Dallas Cowboys’ stadium 51,000 times, or Lake Tahoe just once. If it was concentrated just on the state of North Carolina that much water would be 3.5 feet deep (more than 1 meter). It’s enough to fill more than 60 million Olympic-size swimming pools.

“That’s an astronomical amount of precipitation,” said Ed Clark, head of the National Oceanic and Atmospheric Administration’s National Water Center in Tuscaloosa, Alabama. “I have not seen something in my 25 years of working at the weather service that is this geographically large of an extent and the sheer volume of water that fell from the sky.”

The flood damage from the rain is apocalyptic, meteorologists said. More than 100 people are dead, according to officials.

Private meteorologist Ryan Maue, a former NOAA chief scientist, calculated the amount of rain, using precipitation measurements made in 2.5-mile-by-2.5 mile grids as measured by satellites and ground observations. He came up with 40 trillion gallons through Sunday for the eastern United States, with 20 trillion gallons of that hitting just Georgia, Tennessee, the Carolinas and Florida from Hurricane Helene.

Clark did the calculations independently and said the 40 trillion gallon figure (151 trillion liters) is about right and, if anything, conservative. Maue said maybe 1 to 2 trillion more gallons of rain had fallen, much if it in Virginia, since his calculations.

Clark, who spends much of his work on issues of shrinking western water supplies, said to put the amount of rain in perspective, it’s more than twice the combined amount of water stored by two key Colorado River basin reservoirs: Lake Powell and Lake Mead.

Several meteorologists said this was a combination of two, maybe three storm systems. Before Helene struck, rain had fallen heavily for days because a low pressure system had “cut off” from the jet stream — which moves weather systems along west to east — and stalled over the Southeast. That funneled plenty of warm water from the Gulf of Mexico. And a storm that fell just short of named status parked along North Carolina’s Atlantic coast, dumping as much as 20 inches of rain, said North Carolina state climatologist Kathie Dello.

Then add Helene, one of the largest storms in the last couple decades and one that held plenty of rain because it was young and moved fast before it hit the Appalachians, said University of Albany hurricane expert Kristen Corbosiero.

“It was not just a perfect storm, but it was a combination of multiple storms that that led to the enormous amount of rain,” Maue said. “That collected at high elevation, we’re talking 3,000 to 6000 feet. And when you drop trillions of gallons on a mountain, that has to go down.”

The fact that these storms hit the mountains made everything worse, and not just because of runoff. The interaction between the mountains and the storm systems wrings more moisture out of the air, Clark, Maue and Corbosiero said.

North Carolina weather officials said their top measurement total was 31.33 inches in the tiny town of Busick. Mount Mitchell also got more than 2 feet of rainfall.

Before 2017’s Hurricane Harvey, “I said to our colleagues, you know, I never thought in my career that we would measure rainfall in feet,” Clark said. “And after Harvey, Florence, the more isolated events in eastern Kentucky, portions of South Dakota. We’re seeing events year in and year out where we are measuring rainfall in feet.”

Storms are getting wetter as the climate change s, said Corbosiero and Dello. A basic law of physics says the air holds nearly 4% more moisture for every degree Fahrenheit warmer (7% for every degree Celsius) and the world has warmed more than 2 degrees (1.2 degrees Celsius) since pre-industrial times.

Corbosiero said meteorologists are vigorously debating how much of Helene is due to worsening climate change and how much is random.

For Dello, the “fingerprints of climate change” were clear.

“We’ve seen tropical storm impacts in western North Carolina. But these storms are wetter and these storms are warmer. And there would have been a time when a tropical storm would have been heading toward North Carolina and would have caused some rain and some damage, but not apocalyptic destruction. ”

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Follow AP’s climate coverage at https://apnews.com/hub/climate

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Follow Seth Borenstein on Twitter at @borenbears

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Associated Press climate and environmental coverage receives support from several private foundations. See more about AP’s climate initiative here. The AP is solely responsible for all content.

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‘Big Sam’: Paleontologists unearth giant skull of Pachyrhinosaurus in Alberta

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It’s a dinosaur that roamed Alberta’s badlands more than 70 million years ago, sporting a big, bumpy, bony head the size of a baby elephant.

On Wednesday, paleontologists near Grande Prairie pulled its 272-kilogram skull from the ground.

They call it “Big Sam.”

The adult Pachyrhinosaurus is the second plant-eating dinosaur to be unearthed from a dense bonebed belonging to a herd that died together on the edge of a valley that now sits 450 kilometres northwest of Edmonton.

It didn’t die alone.

“We have hundreds of juvenile bones in the bonebed, so we know that there are many babies and some adults among all of the big adults,” Emily Bamforth, a paleontologist with the nearby Philip J. Currie Dinosaur Museum, said in an interview on the way to the dig site.

She described the horned Pachyrhinosaurus as “the smaller, older cousin of the triceratops.”

“This species of dinosaur is endemic to the Grand Prairie area, so it’s found here and nowhere else in the world. They are … kind of about the size of an Indian elephant and a rhino,” she added.

The head alone, she said, is about the size of a baby elephant.

The discovery was a long time coming.

The bonebed was first discovered by a high school teacher out for a walk about 50 years ago. It took the teacher a decade to get anyone from southern Alberta to come to take a look.

“At the time, sort of in the ’70s and ’80s, paleontology in northern Alberta was virtually unknown,” said Bamforth.

When paleontogists eventually got to the site, Bamforth said, they learned “it’s actually one of the densest dinosaur bonebeds in North America.”

“It contains about 100 to 300 bones per square metre,” she said.

Paleontologists have been at the site sporadically ever since, combing through bones belonging to turtles, dinosaurs and lizards. Sixteen years ago, they discovered a large skull of an approximately 30-year-old Pachyrhinosaurus, which is now at the museum.

About a year ago, they found the second adult: Big Sam.

Bamforth said both dinosaurs are believed to have been the elders in the herd.

“Their distinguishing feature is that, instead of having a horn on their nose like a triceratops, they had this big, bony bump called a boss. And they have big, bony bumps over their eyes as well,” she said.

“It makes them look a little strange. It’s the one dinosaur that if you find it, it’s the only possible thing it can be.”

The genders of the two adults are unknown.

Bamforth said the extraction was difficult because Big Sam was intertwined in a cluster of about 300 other bones.

The skull was found upside down, “as if the animal was lying on its back,” but was well preserved, she said.

She said the excavation process involved putting plaster on the skull and wooden planks around if for stability. From there, it was lifted out — very carefully — with a crane, and was to be shipped on a trolley to the museum for study.

“I have extracted skulls in the past. This is probably the biggest one I’ve ever done though,” said Bamforth.

“It’s pretty exciting.”

This report by The Canadian Press was first published Sept. 25, 2024.

The Canadian Press. All rights reserved.

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The ancient jar smashed by a 4-year-old is back on display at an Israeli museum after repair

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TEL AVIV, Israel (AP) — A rare Bronze-Era jar accidentally smashed by a 4-year-old visiting a museum was back on display Wednesday after restoration experts were able to carefully piece the artifact back together.

Last month, a family from northern Israel was visiting the museum when their youngest son tipped over the jar, which smashed into pieces.

Alex Geller, the boy’s father, said his son — the youngest of three — is exceptionally curious, and that the moment he heard the crash, “please let that not be my child” was the first thought that raced through his head.

The jar has been on display at the Hecht Museum in Haifa for 35 years. It was one of the only containers of its size and from that period still complete when it was discovered.

The Bronze Age jar is one of many artifacts exhibited out in the open, part of the Hecht Museum’s vision of letting visitors explore history without glass barriers, said Inbal Rivlin, the director of the museum, which is associated with Haifa University in northern Israel.

It was likely used to hold wine or oil, and dates back to between 2200 and 1500 B.C.

Rivlin and the museum decided to turn the moment, which captured international attention, into a teaching moment, inviting the Geller family back for a special visit and hands-on activity to illustrate the restoration process.

Rivlin added that the incident provided a welcome distraction from the ongoing war in Gaza. “Well, he’s just a kid. So I think that somehow it touches the heart of the people in Israel and around the world,“ said Rivlin.

Roee Shafir, a restoration expert at the museum, said the repairs would be fairly simple, as the pieces were from a single, complete jar. Archaeologists often face the more daunting task of sifting through piles of shards from multiple objects and trying to piece them together.

Experts used 3D technology, hi-resolution videos, and special glue to painstakingly reconstruct the large jar.

Less than two weeks after it broke, the jar went back on display at the museum. The gluing process left small hairline cracks, and a few pieces are missing, but the jar’s impressive size remains.

The only noticeable difference in the exhibit was a new sign reading “please don’t touch.”

The Canadian Press. All rights reserved.

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