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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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NASA Scientists Find Secret in Decades-Old Voyager 2 Data About the Ice Giant Uranus – SciTechDaily

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Voyager 2 took this image as it approached the planet Uranus on January 14, 1986. The planet’s hazy bluish color is due to the methane in its atmosphere, which absorbs red wavelengths of light. Credit: NASA/JPL-Caltech

The ice giant Uranus appears to be losing a bit of its atmosphere to space, perhaps siphoned away by the planet’s magnetic field.

Eight and a half years into its grand tour of the solar system, NASA’s Voyager 2 spacecraft was ready for another encounter. It was January 24, 1986, and soon it would meet the mysterious seventh planet, icy-cold Uranus.

Over the next few hours, Voyager 2 flew within 50,600 miles (81,433 kilometers) of Uranus’ cloud tops, collecting data that revealed two new rings, 11 new moons and temperatures below minus 353 degrees Fahrenheit (minus 214 degrees Celsius). The dataset is still the only up-close measurements we have ever made of the planet.

Three decades later, scientists reinspecting that data found one more secret.

Unbeknownst to the entire space physics community, 34 years ago Voyager 2 flew through a plasmoid, a giant magnetic bubble that may have been whisking Uranus’ atmosphere out to space. The finding, reported in Geophysical Research Letters, raises new questions about the planet’s one-of-a-kind magnetic environment.

A Wobbly Magnetic Oddball

Planetary atmospheres all over the solar system are leaking into space. Hydrogen springs from Venus to join the solar wind, the continuous stream of particles escaping the Sun. Jupiter and Saturn eject globs of their electrically-charged air. Even Earth’s atmosphere leaks. (Don’t worry, it will stick around for another billion years or so.)

The effects are tiny on human timescales, but given long enough, atmospheric escape can fundamentally alter a planet’s fate. For a case in point, look at Mars.

“Mars used to be a wet planet with a thick atmosphere,” said Gina DiBraccio, space physicist at NASA’s Goddard Space Flight Center and project scientist for the Mars Atmosphere and Volatile Evolution, or MAVEN mission. “It evolved over time” — 4 billion years of leakage to space — “to become the dry planet we see today.”

Uranus Magnetic Field

More Secret
An animated GIF showing Uranus’ magnetic field. The yellow arrow points to the Sun, the light blue arrow marks Uranus’ magnetic axis, and the dark blue arrow marks Uranus’ rotation axis. Credit: NASA/Scientific Visualization Studio/Tom Bridgman

Atmospheric escape is driven by a planet’s magnetic field, which can both help and hinder the process. Scientists believe magnetic fields can protect a planet, fending off the atmosphere-stripping blasts of the solar wind. But they can also create opportunities for escape, like the giant globs cut loose from Saturn and Jupiter when magnetic field lines become tangled. Either way, to understand how atmospheres change, scientists pay close attention to magnetism.

That’s one more reason Uranus is such a mystery. Voyager 2’s 1986 flyby revealed just how magnetically weird the planet is.

“The structure, the way that it moves … ,” DiBraccio said, “Uranus is really on its own.”

Unlike any other planet in our solar system, Uranus spins almost perfectly on its side — like a pig on a spit roast — completing a barrel roll once every 17 hours. Its magnetic field axis points 60 degrees away from that spin axis, so as the planet spins, its magnetosphere — the space carved out by its magnetic field — wobbles like a poorly thrown football. Scientists still don’t know how to model it.

This oddity drew DiBraccio and her coauthor Dan Gershman, a fellow Goddard space physicist, to the project. Both were part of a team working out plans for a new mission to the “ice giants” Uranus and Neptune, and they were looking for mysteries to solve.

Uranus’ strange magnetic field, last measured more than 30 years ago, seemed like a good place to start.

So they downloaded Voyager 2’s magnetometer readings, which monitored the strength and direction of the magnetic fields near Uranus as the spacecraft flew by. With no idea what they’d find, they zoomed in closer than previous studies, plotting a new datapoint every 1.92 seconds. Smooth lines gave way to jagged spikes and dips. And that’s when they saw it: a tiny zigzag with a big story.

“Do you think that could be … a plasmoid?” Gershman asked DiBraccio, catching sight of the squiggle.

Little known at the time of Voyager 2’s flyby, plasmoids have since become recognized as an important way planets lose mass. These giant bubbles of plasma, or electrified gas, pinch off from the end of a planet’s magnetotail — the part of its magnetic field blown back by the Sun like a windsock. With enough time, escaping plasmoids can drain the ions from a planet’s atmosphere, fundamentally changing its composition.

They had been observed at Earth and other planets, but no one had detected plasmoids at Uranus — yet.

DiBraccio ran the data through her processing pipeline, and the results came back clean. “I think it definitely is,” she said.

The Bubble Escapes

The plasmoid DiBraccio and Gershman found occupied a mere 60 seconds of Voyager 2’s 45-hour-long flight by Uranus. It appeared as a quick up-down blip in the magnetometer data. “But if you plotted it in 3D, it would look like a cylinder,” Gershman said.

Comparing their results to plasmoids observed at Jupiter, Saturn and Mercury, they estimated a cylindrical shape at least 127,000 miles (204,000 kilometers) long, and up to roughly 250,000 miles (400,000 kilometers) across. Like all planetary plasmoids, it was full of charged particles — mostly ionized hydrogen, the authors believe.?

Readings from inside the plasmoid — as Voyager 2 flew through it — hinted at its origins. Whereas some plasmoids have a twisted internal magnetic field, DiBraccio and Gershman observed smooth, closed magnetic loops. Such loop-like plasmoids are typically formed as a spinning planet flings bits of its atmosphere to space. “Centrifugal forces take over, and the plasmoid pinches off,” Gershman said. According to their estimates, plasmoids like that one could account for between 15% and 55% of atmospheric mass loss at Uranus, a greater proportion than either Jupiter or Saturn. It may well be the dominant way Uranus sheds its atmosphere to space.

How has plasmoid escape changed Uranus over time? With only one set of observations, it’s hard to say.

“Imagine if one spacecraft just flew through this room and tried to characterize the entire Earth,” DiBraccio said. “Obviously it’s not going to show you anything about what the Sahara or Antarctica is like.”

But the findings help focus new questions about the planet. The remaining mystery is part of the draw. “It’s why I love planetary science,” DiBraccio said. “You’re always going somewhere you don’t really know.”

Reference: “Voyager 2 constraints on plasmoid‐based transport at Uranus” by Gina A. DiBraccio and Daniel J. Gershman, 9 August 2019, Geophysical Research Letters.
DOI: 10.1029/2019GL083909

The twin Voyager spacecraft were built by and continue to be operated by NASA’s Jet Propulsion Laboratory. JPL is a division of Caltech in Pasadena. The Voyager missions are a part of the NASA Heliophysics System Observatory, sponsored by the Heliophysics Division of the Science Mission Directorate in Washington.

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Uranus is losing its atmosphere because of its weird wobbly magnetic field – Yahoo Tech

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<p class="canvas-atom canvas-text Mb(1.0em) Mb(0)–sm Mt(0.8em)–sm" type="text" content="Voyager 2 may have long ago left our solar system and headed out into interstellar space to explore the unknown, but scientists are still learning from the data it collected as it passed by the other planets in our system. A new analysis of 30-year-old data has revealed a surprising finding about the planet Uranus — the huge magnetic bubble surrounding it is siphoning its atmosphere off into space.” data-reactid=”12″>Voyager 2 may have long ago left our solar system and headed out into interstellar space to explore the unknown, but scientists are still learning from the data it collected as it passed by the other planets in our system. A new analysis of 30-year-old data has revealed a surprising finding about the planet Uranus — the huge magnetic bubble surrounding it is siphoning its atmosphere off into space.

<p class="canvas-atom canvas-text Mb(1.0em) Mb(0)–sm Mt(0.8em)–sm" type="text" content="Atmospheres being lost into space can have a profound effect on the development of a planet. As an example, Mars is thought to have started out as an ocean-covered planet similar to Earth but lost its atmosphere over time. “Mars used to be a wet planet with a thick atmosphere,” Gina DiBraccio, space physicist at NASA’s Goddard Space Flight Center and project scientist for the Mars Atmosphere and Volatile Evolution, or MAVEN mission, said in a statement. “It evolved over time to become the dry planet we see today.”” data-reactid=”13″>Atmospheres being lost into space can have a profound effect on the development of a planet. As an example, Mars is thought to have started out as an ocean-covered planet similar to Earth but lost its atmosphere over time. “Mars used to be a wet planet with a thick atmosphere,” Gina DiBraccio, space physicist at NASA’s Goddard Space Flight Center and project scientist for the Mars Atmosphere and Volatile Evolution, or MAVEN mission, said in a statement. “It evolved over time to become the dry planet we see today.”

Uranus’s atmospheric loss is driven by its strange magnetic field, the axis of which points at an angle compared to the axis on which the planet spins. That means its magnetosphere wobbles as it moves, which makes it very difficult to model. “The structure, the way that it moves,” DiBraccio said, “Uranus is really on its own.”

Voyager 2 took this image as it approached the planet Uranus on Jan. 14, 1986. The planet's hazy bluish color is due to the methane in its atmosphere, which absorbs red wavelengths of light.
<figcaption class="C($c-fuji-grey-h) Fz(13px) Py(5px) Lh(1.5)" title="Voyager 2 took this image as it approached the planet Uranus on Jan. 14, 1986. The planet’s hazy bluish color is due to the methane in its atmosphere, which absorbs red wavelengths of light. NASA/JPL-Caltech” data-reactid=”22″>

Voyager 2 took this image as it approached the planet Uranus on Jan. 14, 1986. The planet’s hazy bluish color is due to the methane in its atmosphere, which absorbs red wavelengths of light. NASA/JPL-Caltech

Due to the wobbling of the magnetosphere, bits of the atmosphere are drained away in what are called plasmoids — bubbles of plasma which pinch off from the magnetic field as it is blown around by the Sun. Although these plasmoids have been seen on Earth and on some other planets, they had never been observed on Uranus before the recent analysis of old Voyager 2 data.

“Imagine if one spacecraft just flew through this room and tried to characterize the entire Earth,” DiBraccio said. “Obviously it’s not going to show you anything about what the Sahara or Antarctica is like.”

“It’s why I love planetary science,” DiBraccio said. “You’re always going somewhere you don’t really know.”

<p class="canvas-atom canvas-text Mb(1.0em) Mb(0)–sm Mt(0.8em)–sm" type="text" content="The research is published in the journal Geophysical Research Letters.” data-reactid=”29″>The research is published in the journal Geophysical Research Letters.

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Sunlit Peaks in the Himalayas – NASA

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As the International Space Station (ISS) was traveling over India towards the day-night terminator, an astronaut shot this photograph of Earth’s third-highest summit, Kangchenjunga, and its surrounding peaks warmly lit by the setting Sun. With the Sun low in the sky, the light was passing through more atmosphere, which scatters it towards the red end of the visible spectrum.

Kangchenjunga rises more than 8500 meters (28,000 feet) above sea level. It stands on the border of Nepal and India about 120 kilometers (75 miles) east-southeast of Mount Everest. The apex of Kangchenjunga is surrounded by valley glaciers, some of which (like Yalung) are discernable in the shadows of this image. Just out of reach of the Sun’s rays, a deck of low-lying clouds lingers over the valley floors.

Thirteen other mountain peaks on Earth rise higher than 8000 meters (26,000 feet). These are known by mountaineers and climbers as the “eight-thousanders.” Oblique views such as this one give the dauntingly dangerous terrain a three-dimensional appearance and depth.

Astronaut photograph ISS061-E-92131 was acquired on December 16, 2019, with a Nikon D5 digital camera using a 500 millimeter lens and is provided by the ISS Crew Earth Observations Facility and the Earth Science and Remote Sensing Unit, Johnson Space Center. The image was taken by a member of the Expedition 61 crew. The image has been cropped and enhanced to improve contrast, and lens artifacts have been removed. The International Space Station Program supports the laboratory as part of the ISS National Lab to help astronauts take pictures of Earth that will be of the greatest value to scientists and the public, and to make those images freely available on the Internet. Additional images taken by astronauts and cosmonauts can be viewed at the NASA/JSC Gateway to Astronaut Photography of Earth. Caption by Andrew Britton, Jacobs, JETS Contract at NASA-JSC.

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