Supersized Science

This podcast is part of our inaugural yearly magazine called Texascale, available at www.tacc.utexas.edu/texascale. Host Jorge Salazar interviews Charlie Dey, Director of Training and Professional Development at TACC. Dey outlined the the TACC Institutes, which work to educate the next generation of supercomputing professionals. Full Q&A at this link:www.tacc.utexas.edu/texascale/2018/…e-workforce-gap Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

Change is in the air, and water, of the Arctic Ocean. Scientists are keeping an eye out on shrinking sea ice, five million square miles of floating ice surrounding the North Pole. It bounces sunlight back to space, which keeps polar regions cool and helps moderate global climate. An award-winning simulation shows the complex changes in circulation happening at one of Earth’s most remote and inaccessible places, the Arctic Ocean. The Texas Advanced Computing Center (TACC) shared an award with UT Austin’s Institute for Computational Engineering and Sciences (ICES) for the Best Scientific Visualization & Data Analytics Showcase, "Circulation in the Arctic Ocean and its Marginal Seas: From Low Latitudes to the Pole and Back." The supercomputing conference SC18 gave the award in November of 2018 to the team of lead author Greg Foss and Briana Bradshaw of TACC; and An Nguyen, Arash Bigdeli, Victor Ocaña and Patrick Heimbach of ICES. Podcast host Jorge Salazar interviews Greg Foss of TACC about the Arctic Ocean simulation and creating visualizations for science. Story: www.tacc.utexas.edu/-/award-winning…to-arctic-ocean Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/  

It’s easy to take a lot for granted. Scientists do this when they study stress, the force per unit area on an object. Scientists handle stress mathematically by assuming it to have symmetry. That means the components of stress are identical if you transform the stressed object with something like a turn or a flip. Supercomputer simulations show that at the atomic level, material stress doesn’t behave symmetrically. That’s according to a study published September of 2018 in the Proceedings of the Royal Society A. The findings could help scientists come up with new materials such as glass or metal that doesn’t ice up. On the podcast to talk more about the stress study is Liming Xiong, Assistant Professor, Department of Aerospace Engineering, Iowa State University. Dr. Xiong used supercomputer allocations on XSEDE, the Extreme Science and Engineering Discovery Environment, funded by the National Science Foundation. That gave Xiong access to the Comet system at the San Diego Supercomputer Center; and Jetstream, a cloud environment supported by Indiana University, the University of Arizona, and the Texas Advanced Computing Center. Podcast host Jorge Salazar interviewed Liming Xiong. Story: https://www.tacc.utexas.edu/-/a-new-way-to-see-stress-using-supercomputers Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

Any truck operator knows that hydraulics do the heavy lifting. Water does the work because it’s nearly incompressible at normal scales. But things behave strangely in nanotechnology, the control of materials at the scale of atoms and molecules. Using supercomputers, scientists found a surprising amount of water compression at the nanoscale. These findings could help advance medical diagnostics through creation of nanoscale systems that detect, identify, and sort biomolecules. The unexpected effect comes from the action of an electric field on water in very narrow pores and in very thin materials. That’s according to research by Aleksei Aksimentiev and James Wilson of the Department of Physics at the University of Illinois at Urbana–Champaign. They published their findings in Physical Review Letters, June of 2018. Aksimentiev and Wilson used supercomputer time awarded through XSEDE, the Extreme Science and Engineering Discover Environment, funded by the National Science. Foundation. XSEDE allocations allowed the researchers use of the Stampede1 and Stampede2 systems at the Texas Advanced Computing Center; and Blue Waters at the National Center for Supercomputer Applications. Aleksei Aksimentiev joins podcast host Jorge Salazar to talk more about the study. Story: www.tacc.utexas.edu/-/simulations-s…-dna-sequencing Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

The National Science Foundation announced on August 29, 2018 an award of 60 million dollars to the Texas Advanced Computing Center (TACC) at UT Austin for the acquisition and deployment of a new supercomputer that will be the fastest at any U.S. university and among the most powerful in the world. The new system is called Frontera , Spanish for "frontier," and it will begin operations in 2019. On this TACC podcast, host Jorge Salazar interviewed Manish Parashar, Office Director for the the Office of Advanced Cyberinfrastructure at the National Science Foundation. Dr. Parashar took time out during the announcement event at TACC to talk more about the Frontera supercomputer. Story Link: www.tacc.utexas.edu/-/a-new-fronter…nce-discoveries Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/

Scientists have used supercomputers to engineer an enzyme that breaks down plastic. It’s called polyethylene terephthalate, or PET, and it’s used to make things like carpets and bottles for soda and water. This plastic pollutes the soil and the oceans. The scientists say it’s a first step toward recycling PET and other plastics into commercially valuable materials at industrial scale. They published their results March of 2018 in the Proceedings of the National Academy of Sciences. The researchers took advantage for this study of computational resources of XSEDE, the Extreme Science and Engineering Discovery Environment, funded by the National Science Foundation. They used the Stampede2 supercomputer at the Texas Advanced Computing Center, and they used the Comet supercomputer at the San Diego Supercomputer Center. These systems helped them simulate the interactions of the plastic-degrading enzyme with PET. On the podcast to talk about their study are co-authors Gregg Beckham and Lee Woodcock. Gregg Beckham is a senior research fellow and group leader at the US National Renewable Energy Laboratory. Lee Woodcock is an associate professor of chemistry at the University of South Florida. Jorge Salazar of TACC hosts the podcast. Music Credit: Raro Bueno, Chuzausen freemusicarchive.org/music/Chuzausen/    

What makes kevlar stop a bullet, at the atomic level? The properties of materials emerge from their molecular or atomic structure. Yet many details between the micro and the macro remain a mystery to science. Scientists are actively researching the rational design of targeted supramolecular architectures, with the goal of engineering their structural dynamics and their response to environmental cues. A team of chemists at the University of California, San Diego has now designed a two-dimensional protein crystal that toggles between states of varying porosity and density. This is a first in biomolecular design that combined experimental studies with computation done on supercomputers through an allocation on XSEDE, the Extreme Science And Engineering Discovery Environment, funded by the National Science Foundation. XSEDE awarded the UCSD researchers over a million core hours on the Maverick supercomputer, a dedicated visualization and data analysis resource that uses graphics processing units at the Texas Advanced Computing Center. The research, published in April of 2018 in Nature Chemistry, could help create new materials for renewable energy, medicine, water purification, and more. Study co-authors and chemists Akif Tezcan, Francesco Paesani, and Robert Alberstein of the University of California, San Diego join podcast host Jorge Salazar to discuss the findings.    

Scientists have made the best computational modeling yet of mantle plumes. These are hypothesized, mushroom-shaped upwellings of hot rock from deep in the Earth that reach more than a thousand kilometers down. The scientists modeled mantle plumes on the Stampede supercomputer of the Texas Advanced Computing Center through an allocation on XSEDE, the eXtreme Science and Engineering Discovery Environment funded by the National Science Foundation. And through XSEDE they also took advantage of Science Gateways and of the Campus Champions program at the University of Michigan. With that support they showed, for the first time, details of how mantle plumes form and how they rise from Earth's mantle. What's more, the researchers say their work could guide future experiments with seismic imaging and help get to the bottom of mysteries like the origin of Hawaii's volcanos. The international science team published their results on mantle plumes in January of 2018 in the American Geophysical Union's Journal of Geophysical Research, Solid Earth. Podcast host Jorge Salazar interviews study authors Ross Maguire and Jeroen Ritsema of the University of Michigan.

Scientists have used big data to catch a big fish genome. Researchers assembled and annotated for the first time the genome of Seriola dorsalis, also known as California Yellowtail, a fish of high value to the sashimi, or raw seafood industry. The science team members were from the U.S. National Marine Fisheries Service, Iowa State University, and the Instituto Politécnico Nacional in Mexico. They published their results January of 2018 in the journal BMC Genomics. Assembling and annotating a genome is like building a three dimensional jigsaw puzzle, and the Seriola dorsalis genome had 685 million pieces - its base pairs of DNA - to put together. The researchers were awarded computational allocations from XSEDE, the eXtreme Science and Engineering Discovery Environment funded by the National Science Foundation. That gave them access to the Blacklight system at the Pittsburg Supercomputing Center to assemble the Seriola dorsalis genome. XSEDE also allocated use of the Stampede1 supercomputer at the Texas Advanced Computing Center to analyze and annotate the fish genome. What's more, the science team got direct help from workflow experts through the XSEDE Campus Champions program at PSC. Podcast host Jorge Salazar interviews two scientists and co-authors of the first-ever genomics work - Andrew Severin, Facility Manager; and Arun Seetharam, Associate Scientist. They're both at the Genome Informatics Facility of Iowa State University.

Imagine a new kind of computer that can quickly solve problems that would stump even the world’s most powerful supercomputers. Quantum computers are fundamentally different. They can store information as not only just ones and zeros, but in all the shades of gray in-between. Several companies and government agencies are investing billions of dollars in the field of quantum information. But what will quantum computers be used for? South by Southwest 2018 hosts a panel on March 10th called Quantum Computing: Science Fiction to Science Fact. Experts on quantum computing make up the panel, including Jerry Chow of IBM; Bo Ewald of D-Wave Systems; Andrew Fursman of 1QBit; and Antia Lamas-Linares of the Texas Advanced Computing Center at UT Austin. Dr. Lamas-Linares is a Research Associate in the High Performance Computing group at TACC. Her background is as an experimentalist with quantum computing systems, including work done with them at the Centre for Quantum Technologies in Singapore. She joins podcast host Jorge Salazar to talk about her South by Southwest panel and about some of her latest research on quantum information.

Artificial intelligence - or AI - is helping people make better decisions about how to manage water resources. That’s because scientists are taking the best tools of advanced computing to help make science-based decisions about complex and pressing problems in how to manage Earth’s resources, including water. A science panel on AI and water management meets in Austin, Texas on February 17th at the 2018 meeting of the American Association for the Advancement of Science. Suzanne Pierce moderates and co-organized the panel. Pierce is a Research Scientist in Dynamic Decision Support Systems and part of the Data Management & Collections Group of the Texas Advanced Computing Center. Podcast host Jorge Salazar interviews Suzanne Pierce of TACC about the Intelligent Systems for Geosciences community, of which she is on the steering committee; her panel on AI and water management at the AAAS, and the work TACC is doing to support efforts to bridge advanced computing with Earth science.

Some scientists think there might be light at the end of the tunnel in the hunt for better semiconductor materials for solar cells and LEDs. That’s according to an August 2017 study that used supercomputer simulations with graphics processing units to model nanocrystals of silicon. Solar cells have a problem with heat. Photovoltaics on solar panels lose some energy as heat in when they convert sunlight to electricity. The reverse holds true for LED lights, which convert electricity into light. Scientists call the heat loss in LEDs and solar cells non-radiative recombination. And they’ve struggled to understand the basic physics of this heat loss, especially for materials with molecules of over 20 atoms. Podcast host Jorge Salazar interviews Benjamin Levine, an associate professor in the Department of Chemistry at Michigan State University. Dr. Levine models the behavior caused by defects in materials, such as doping bulk silicon to transform it into semiconductors in transistors, LEDs, and solar cells. Levine and has used over 975,000 compute hours on the Maverick supercomputer, a dedicated visualization and data analysis resource architected with 132 NVIDIA Tesla K40 "Atlas" GPUs for remote visualization and GPU computing to the national community. XSEDE, the eXtreme Science and Engineering Discovery Environment funded by the National Science Foundation, provided the allocation.

Some secrets of our skeletons might be found in the silky webs of golden orb weaver spiders, according to experiments guided by supercomputers. Scientists don’t yet understand the details of osteogenesis, or how bones form. A study found that silica combined with engineered silk derived from the dragline of golden orb weaver spider webs could be fine-tuned to activate genes in human stem cells that initiated biomineralization, a key step in bone formation. The study appeared September 2017 in the journal Advanced Functional Materials. The authors used supercomputers through and allocation from XSEDE, the Xtreme Science and Engineering Discovery Environment, funded by the National Science Foundation. Stampede at the Texas Advanced Computing Center (TACC) and Comet at the San Diego Supercomputing Center helped scientists model the protein folding of integrin, an essential step in the intracellular pathways that lead to osteogenesis. This research will help larger efforts to cure bone disorders such as osteoporosis or calcific aortic valve disease. Joining host Jorge Salazar of TACC on the podcast to talk about the bone formation study are Zaira Martín-Moldes of the Kaplan Lab at Tufts University and Davoud Ebrahimi at the Laboratory for Atomistic and Molecular Mechanics of the Massachusetts Institute of Technology.

Black holes make for a great space mystery. They're so massive that nothing, not even light, can escape a black hole once it gets close enough. A great mystery for scientists is the evidence of powerful jets of electrons and protons that shoot out of the top and bottom of some black holes. Yet no one knows how these jets form. Computer code called Cosmos now fuels supercomputer simulations of black hole jets and is starting to reveal the mysteries of black holes and other space oddities. Cosmos code developer Chris Fragile joins host Jorge Salazar on the TACC podcast. Fragile is a professor in the Physics and Astronomy Department of the College of Charleston. Also featured on the podcast is Damon McDougall, a Research Associate in the HPC Applications at the Texas Advanced Computing Center, also appointed jointly at the Institute for Computational Engineering and Sciences of the University of Texas at Austin. McDougall spoke more about XSEDE Extended Collaborative Support Services.

How do you make a building that can stand up to an earthquake? A summer camp at TACC smoothed the way for high school students to learn about the science behind building design for earthquakes. It's called Code @ TACC DesignSafe. The summer camp was funded by DesignSafe, a national program supported by the National Science Foundation. DesignSafe is a web-based research platform of the Natural Hazards Engineering Research Infrastructure Network that helps engineers build safer structures that can better withstand natural hazards such as earthquakes and windstorms. The Code @ TACC DesignSafe Camp students were given a project under budget to design their own custom building models outfitted with sensors that recorded their movement as they were shaken under laboratory conditions based on historical earthquake data. TACC Podcast host Jorge Salazar interviews Joon-Yee Chuah, Outreach Coordinator at the Texas Advanced Computing Center; Chunxiao Ge, a physics and biology teacher at the Colorado River Collegiate Academy of Bastrop ISD; and Patty Hill, an algebra teacher at Kealing Middle School at Austin ISD.