Supersized Science

Plastic waste is a big problem in the environment. About 300 million tons of plastic waste are produced every year, according to the United Nations. Much of that is polyethylene terephthalate (PET), a plastic in single-use bottles, carpets, and clamshell packaging. In the U.S., the Environmental Protection Agency estimates annually that only about 29 percent of PET bottles are recycled. In 2016, Japanese scientists discovered that the bacteria Ideonella sakaiensis had evolved digestive enzymes called PETase that breakdown PET. And in October of 2020, a study came out in the Proceedings of the National Academy of Sciences. It used supercomputers allocated by XSEDE, the Extreme Science and Engineering Discovery Environment. They revealed more about a sidekick enzyme, called MHETase, that helps PETase breakdown PET plastic. Stampede2 here at TACC; Comet at the San Diego Supercomputer Center, and the Eagle system of the National Renewable Energy Laboratory were use in the PETase-MHETase study. While dealing with plastic pollution at scale remains daunting, in the words of Jeff Goldblum’s character in the movie Jurassic Park, “Life finds a way.” Podcast host and TACC science writer Jorge Salazar is joined by study co-authors Brandon Knott and Erika Erickson, both scientists at the National Renewable Energy Laboratory, where Knott is a staff engineer and Erickson is a post-doctoral researcher. Supersized Science is part of the Texas Podcast Network – the conversations changing the world – brought to you by The University of Texas at Austin. The opinions expressed in this podcast represent the views of the hosts, and not of The University of Texas at Austin. Story Link: www.tacc.utexas.edu/-/supercomputer…stic-eating-duo Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

The Supersized Science podcast hosted by science writer Jorge Salazar features research and discoveries enabled by advanced computing technology and expertise of the Texas Advanced Computing Center of the University of Texas at Austin. High above your head right now, it's raining dirt. Day or night, every second, millions of pieces of dirt that are smaller than a grain of sand strike Earth's upper atmosphere. At an altitude of about 100 kilometers, bits of dust, mainly debris from asteroid collisions, zing through the sky vaporizing as they go 10 to 100 times the speed of a bullet. The bigger ones can make streaks in the sky, meteors that can take one’s breath away. Scientists are using TACC’s Stampede2 supercomputer, allocated through XSEDE, the Extreme Science and Engineering Discovery Environment funded by the National Science Foundation, to help understand how tiny meteors liberate electrons that can be detected by radar and can characterize the speed, direction and rate of meteor deceleration with high precision, allowing its origin to be determined. Because this falling space dust helps seed rain-making clouds, this basic research on meteors will help scientists more fully understand the chemistry of Earth's atmosphere. What's more, meteor composition helps astronomers characterize the space environment of our solar system. The meteor research was published in June 2021 in the Journal of Geophysical Research: Space Physics of the American Geophysical Society. Study co-author Meers Oppenheim, a professor of Astronomy at Boston University. Dr. Oppenheim, describes his meteor study on Supersized Science.

Viruses lurk in the grey area between the living and the nonliving, according to scientists. Like living things, they replicate but they don't do it on their own. Viruses needs a host cell. And through infection, they hijack it and force it to make copies of itself. Supercomputer simulations have helped uncover the mechanism for how the HIV-1 virus imports into its core the nucleotides it needs to fuel DNA synthesis, a key step in its replication. It's the first example found where a virus performs an activity such as recruiting small molecules from a cellular environment into its core to conduct a process beneficial for its life cycle. The simulation work was supported by XSEDE, the Extreme Science and Engineering Discovery Environment funded by the National Science Foundation. And it was carried out on the Stampede2 system here at the Texas Advanced Computing Center, as well as on the Bridges system at the Pittsburgh Supercomputing Center. XSEDE awarded supercomputing access and expertise to biophysical chemist Juan R. Perilla and his lab at the University of Delaware. Chaoyi Xu, a graduate student in the Perilla Lab, was the lead author on the HIV viral capsid work, published with Perilla and other scientists December 2020 in PLOS Biology. Xu and Perilla join host Jorge Salazar on the Supersized Science podcast to talk about their research.

The COVID-19 virus holds some mysteries. Scientists remain in the dark on details of its behavior such as how it fuses and enters the host cell; how it assembles itself; and how it buds off the host cell to spread infection. Computational modeling combined with experimental data can provide insights into these behaviors. But modeling over timescales long enough to mean anything has so far been limited to bits and pieces of the coronavirus, like its spike protein, which is a target for the current round of vaccines. A new multiscale coarse-grained model of the complete SARS-CoV-2 virion, its core genetic material and capsid shell, has been developed using supercomputers. The new model offers scientists potential to gain new insights and vulnerabilities in the coronavirus’s large-scale behavior. The Supersized Science podcast features interviews with Gregory Voth of the University of Chicago; and Rommie Amaro of the University of California, San Diego. They’re coauthors of a study that details the new computer model of the complete coronavirus, published in November 2020 in the Biophysical Journal.

In the midst of a global pandemic with COVID-19, it’s hard to appreciate how lucky those outside of Africa have been to avoid the deadly Ebola virus disease. It incapacitates its victims soon after infection with massive vomiting or diarrhea, leading to death from fluid loss in about 50 percent of the afflicted. The Ebola virus transmits only through bodily fluids, marking a key difference from the COVID-19 virus and one that has helped contain Ebola’s spread. Ebola outbreaks continue to flare up in West Africa, although a vaccine developed in December 2019 and improvements in care and containment have helped keep Ebola in check. Supercomputer simulations by a University of Delaware team that included an undergraduate supported by the XSEDE EMPOWER program are adding to the mix and helping to crack the defenses of Ebola’s coiled genetic material. This new research could help lead to breakthroughs in treatment and improved vaccines for Ebola and other deadly viral diseases such as COVID-19. Podcast host Jorge Salazar talks with the research team about their findings on Ebola - Juan Perilla, Chaoyi Xu, Tanya Nesterova, and Nidhi Katyal. Perilla is an Assistant Professor, Xu a PhD student, Nesterova an undergraduate researcher, and Katyal a postdoctoral researcher, all in the Perilla Lab, Department of Chemistry and Biochemistry, University of Delaware.

The coronavirus infects its host cell by first binding one of its spike proteins and then fusing its helical core to the host cell. The virus makes its own molecular version of the mythical Jacob’s Ladder that reaches for the heavens. It builds a far-reaching ladder-like apparatus from core helical amino acids that latch on to its host cell, leading to infection. Scientists don’t yet fully understand the details of how the coronavirus binds and fuses. Numan Oezguen is an instructor at the Microbiome Center of Texas Children’s Hospital and also at the Baylor College of Medicine. He’s developed a model simulating coronavirus binding and fusing on Longhorn, the graphics processing unit subsystem of the Frontera supercomputer at the Texas Advanced Computing Center (TACC). Dr. Oezguen joins host Jorge Salazar on the TACC podcast. Story Link: https://www.tacc.utexas.edu/-/corona-s-ladderMusic Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

They say you can’t judge a book by its cover. But the human immune system does just that when it comes to finding and attacking harmful microbes such as the coronavirus. It relies on being able to recognize foreign intruders and generate antibodies to destroy them. Unfortunately, the coronavirus uses a sugary coating of molecules called glycans to camouflage itself as harmless from the defending antibodies. Simulations on the National Science Foundation (NSF)-funded Frontera supercomputer at the Texas Advanced Computing Center (TACC) have revealed the atomic makeup of the coronavirus’s sugary shield. What’s more, simulation and modeling show that glycans also prime the coronavirus for infection. Scientists hope this basic research will add to the arsenal of knowledge needed to defeat the COVID-19 virus. Podcast host Jorge Salazar interviews Rommie Amaro, a professor of chemistry and biochemistry at the University of California, San Diego to talk about her science team’s latest findings. Story Link: www.tacc.utexas.edu/-/sugar-coating…s-for-infectionMusic Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

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 Texas Advanced Computing Center of UT Austin. The knowledge gained from the full model can help researchers design new drugs and vaccines to combat the coronavirus. Podcast host Jorge Salazar interviews Rommie Amaro, a professor of chemistry and biochemistry at the University of California, San Diego. She’s leading efforts to build the first complete all-atom model of the SARS-COV-2 coronavirus envelope, its exterior component. Story Link: www.tacc.utexas.edu/-/coronavirus-m…a-supercomputerMusic Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

For scientists, natural systems can try one’s patience. For a long time, nothing. Then all of a sudden, something. Wonderful things in nature can burst on the scene after long periods of dullness - rare events such as protein folding, chemical reactions, or even the seeding of clouds. Path sampling techniques employ computer algorithms that deal with the dullness in data by focusing on transitions. Scientists are using supercomputers to help understand the relatively rare event of salts in water passing through atomically-thin nanoporous membranes. This research could not only help make progress in desalination for fresh water; it has applications in decontaminating the environment, better pharmaceuticals, and more. Advanced path sampling techniques and molecular dynamics simulations captured the kinetics of solute transport through nanoporous membranes, according to a study published online in the Cell journal Matter, January 2020. Supercomputers supported the research through allocations on XSEDE, the Extreme Science and Engineering Discovery Environment, funded by the National Science Foundation. Researchers ran simulations on the Stampede2 system at TACC . Joining host Jorge Salazar on the podcast is study co-author Amir Haji-Akbari, an assistant professor of chemical and environmental engineering at Yale University. Story Link: www.tacc.utexas.edu/-/supercomputer…nsport-research Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

The spacefaring Romulans of Star Trek science fiction have inspired some astrophysicists to develop cosmological simulations called RomulusC, where the ‘C’ stands for galaxy cluster. With a focus on black hole physics, RomulusC has produced some of the finest resolution simulations ever of galaxy clusters, which can contain hundreds or even thousands of galaxies. On Star Trek, the Romulans powered their spaceships with an artificial black hole. In reality, it turns out that black holes can drive the formation of stars and the evolution of whole galaxies. An October 2019 study yielded results from RomulusC simulations, published in the Monthly Notices of the Royal Astronomical Society. Supercomputer simulations helped probe the ionized gas within and surrounding the intracluster medium, which fills the space between galaxies in a galaxy cluster. The Stampede2 supercomputer at TACC and the Comet supercomputer at the San Diego Supercomputer Center played a role, through allocation awarded by XSEDE, the Extreme Science and Engineering Discovery Environment, funded by the National Science Foundation. The scientists also used the NASA Pleiades supercomputer, eventually completing the simulation on 32,000 processors of the Blue Waters system at the National Center for Supercomputing Applications. On the podcast are two study co-authors, Iryna Butsky and Tom Quinn, both in the Department of Astronomy at the University of Washington. Iryna Butsky is a PhD Student, and Tom Quinn is a Professor of Astronomy. Podcast host Jorge Salazar with the Texas Advanced Computing Center conducts the Q&A. Story Link: www.tacc.utexas.edu/-/simulations-r…lusters-details Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

Scientists are using powerful supercomputers to uncover the mechanism that activates cell mutations found in about 50 percent of melanomas, the most serious type of human skin cancer because it can spread throughout the body. The scientists say they’re hopeful their study can help lead to a better understanding of skin cancer and to the design of better drugs. On the podcast are Yasushi Kondo and Deepti Karandur, both postdoctoral researchers in the John Kuriyan Lab at UC Berkeley. Karandur is also a postdoctoral fellow at the Howard Hughes Medical Institute. Kondo and Karandur are co-authors of a study published October of 2019 in the journal Science that determined the structure of a complex of proteins called B-Raf kinase, short for Rapidly Accelerated Fibrosarcoma. B-Raf kinase is a protein that’s part of the signal chain that starts outside the cell and goes inside to direct cell growth. This larger signal pathway is important for cancer research, which seeks to understand out-of-control cell growth. About 50 percent of melanomas have a specific single mutation on B-Raf, and it’s became an important drug target. Strangely though, drugs that inhibit the mutant had a down side. They activated other undesired proteins, called wild-type B-Raf kinases, which again triggered melanoma. The science team modeled the B-Raf protein and other proteins in the chemical pathway using supercomputer allocations on XSEDE, the Extreme Science and Engineering Discovery Environment funded by the National Science Foundation. They used the Stampede2 system at TACC as well as the Bridges system at the Pittsburgh Supercomputer Center. This new research by Kondo and Karandur’s science team has found how the paradoxical B-Raf activation happens. Drs. Kondo and Karandur are interviewed by podcast host Jorge Salazar, with the Texas Advanced Computing Center.

The Texas Advanced Computing Center (TACC) celebrated the official launch of its newest supercomputing system, Frontera, funded by a $60 million award from the National Science Foundation. Frontera aims to help scientists with the cyberinfrastructure resources to tackle some of the biggest unknowns in science. And it’s made a promising start, with an initial rank of #5 fastest supercomputer in the world and #1 fastest academic system, according to the June 2019 Top500 rankings. Fleming Crim, the Chief Operating Officer of the National Science Foundation, gave opening remarks at the dedication event for the launch of Frontera. TACC Podcast host Jorge Salazar interviewed Crim about the NSF-funded Frontera system and the value of supercomputers for fundamental research.

The University of Texas at Austin has claimed a leadership role in supercomputing with the top academic system in the world, Frontera, located at the Texas Advanced Computing Center (TACC). The National Science Foundation awarded TACC $60 million for building and operating Frontera, the fifth fastest computer in the world according to the June 2019 Top500 rankings. Frontera’s dedication event on September 3, 2019 was marked by an address from UT Austin President Greg Fenves. TACC podcast host Jorge Salazar interviewed President Fenves shortly afterwards, where he spoke on the impact the NSF-funded Frontera supercomputer will have on the university and the world at large.

Trust, but verify. The well-known proverb speaks to the heart of the scientific method, which builds on the results of others but requires that data be collected in a way that can be repeated with the same results. Beyond just recreating the conditions of a physical experiment, the computational analysis of data also factors into scientific reproducibility. Joining host Jorge Salazar on the podcast are Dan Stanzione, Executive Director of the Texas Advanced Computing Center and Associate Vice-President for Research at the University of Texas at Austin; and Doug James, former Deputy Director for High Performance Computing at the Texas Advanced Computing Center. Most of the computational resources mentioned on the podcast such as the Stampede2 supercomputer are funded by the National Science Foundation.

Using supercomputers, scientists are just starting to design proteins that self-assemble to combine and resemble life-giving molecules like hemoglobin. Hemoglobin molecules in red blood cells transport oxygen by changing their shape. Four copies of the same protein in hemoglobin open and close like flower petals, structurally coupled to respond to each other. A science team from the University of Texas at Austin and the University of Michigan made a flower-like structured molecule by supercharging proteins, which means they changed the subunits of proteins called amino acids to give them an overall artificially high positive or negative charge. The scientists first reported their findings in January of 2019 in the Journal Nature Chemistry. The scientists say their methods could be applied to useful technologies such as pharmaceutical targeting, artificial energy harvesting, 'smart' sensing and building materials, and more. Host Jorge Salazar interviews Jens Glaser and Vyas Ramasubramani of the University of Michigan; and Anna Simon of UT Austin. Story: www.tacc.utexas.edu/-/supercomputer…rotein-assembly Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/