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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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‘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.”

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B.C. sets up a panel on bear deaths, will review conservation officer training

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VICTORIA – The British Columbia government is partnering with a bear welfare group to reduce the number of bears being euthanized in the province.

Nicholas Scapillati, executive director of Grizzly Bear Foundation, said Monday that it comes after months-long discussions with the province on how to protect bears, with the goal to give the animals a “better and second chance at life in the wild.”

Scapillati said what’s exciting about the project is that the government is open to working with outside experts and the public.

“So, they’ll be working through Indigenous knowledge and scientific understanding, bringing in the latest techniques and training expertise from leading experts,” he said in an interview.

B.C. government data show conservation officers destroyed 603 black bears and 23 grizzly bears in 2023, while 154 black bears were killed by officers in the first six months of this year.

Scapillati said the group will publish a report with recommendations by next spring, while an independent oversight committee will be set up to review all bear encounters with conservation officers to provide advice to the government.

Environment Minister George Heyman said in a statement that they are looking for new ways to ensure conservation officers “have the trust of the communities they serve,” and the panel will make recommendations to enhance officer training and improve policies.

Lesley Fox, with the wildlife protection group The Fur-Bearers, said they’ve been calling for such a committee for decades.

“This move demonstrates the government is listening,” said Fox. “I suspect, because of the impending election, their listening skills are potentially a little sharper than they normally are.”

Fox said the partnership came from “a place of long frustration” as provincial conservation officers kill more than 500 black bears every year on average, and the public is “no longer tolerating this kind of approach.”

“I think that the conservation officer service and the B.C. government are aware they need to change, and certainly the public has been asking for it,” said Fox.

Fox said there’s a lot of optimism about the new partnership, but, as with any government, there will likely be a lot of red tape to get through.

“I think speed is going to be important, whether or not the committee has the ability to make change and make change relatively quickly without having to study an issue to death, ” said Fox.

This report by The Canadian Press was first published Sept. 9, 2024.

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