Supersized Science

Sometimes a container isn’t just a container, not when it comes to the deadly HIV-1 virus The HIV-1 virus is wrapped in a double layer of fatty molecules called lipids that not only serves as its container but also plays a key role in HIV-1’s replication and infectivity. Scientists have used supercomputers to complete the first-ever biologically authentic computer model of the HIV-1 virus liposome...

It takes two to tango, as the saying goes. This is especially true for scientists studying what’s inside of a cell. Protein molecules inside a cell interact with other proteins, and in a sense the proteins dance with a partner to respond to signals and regulate each other's activities. Crucial to giving cells energy for life is the migration of a compound called adenosine triphosphate or ATP, out...

Scientists are looking deeper into the mysterious characteristics of vortexes and turbulence, in recent studies by Texas Tech University scientists that used the Frontera, Stampede2, and Lonestar5 supercomputers here at TACC, allocated through the Extreme Science and Engineering Discovery Environment, funded by the National Science Foundation. A possible application of the Texas Tech vortex resear...

The Hawaiian-Emperor seamount chain spans almost four thousand miles from the Hawaiian Islands to the Detroit Seamount in the north Pacific, an L- shaped chain that goes west then abruptly north. The 60-degree bend in the line of mostly undersea mountains and volcanic islands has puzzled scientists since it was first identified in the 1940s from the data of numerous echo sounding ships. A team of...

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, J...

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...

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...

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 lim...

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 th...

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 underst...

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 a...

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...

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...

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...

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...

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...

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 S...

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 podcas...

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...

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-wo...

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 inacce...

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 beh...

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 thr...

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...

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 publish...