Stampede2

DNA Capture by Nanopores

Surprising things happen when an electric field is applied to water near narrow pores in very thin materials, according to research on Stampede2 by Aleksei Aksimentiev, a computational biophysicist from the University of Illinois at Urbana–Champaign.

His team found that an electric field can compress water locally, preventing molecules from being transported through small pores. This effect, he believes, can be harnessed to create a new type of DNA sequencer. Aksimentiev and his team published their findings in the Physical Review Letters in June 2018.

The simulations took into account the motion of more than 100,000 atoms, which was critically important for the discovery of the phenomenon.

"It's been amazing how fast and how accurate the Stampede2 machine works," Aksimentiev said.

James Wilson, a post-doc working with Aksimentiev, added that "by running the simulations on Stampede2, we were able to finish twenty simulations in a couple of days, cutting down our time to solution immensely."

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Sediment Transport

Stampede2 has allowed researchers to perform grain-resolving simulations of cohesive sediment dynamics involving thousands of discrete particles, in work co-authored by Eckart Meiburg, director of the Center for Interdisciplinary Research in Fluids at the University of California at Santa Barbara.

"These simulations provide insight into a wide range of situations of great importance to the environment, such as the transport of mud, silt, clay, and nutrients by flows in rivers, lakes and the oceans," Meiburg said.

The simulations were carried out in parallel with experiments conducted on the International Space Station. The researchers expect this combination of simulations and experiments to lead to the development of novel models for cohesive sediment transport that will enhance our predictive modeling capabilities for rivers, lakes, and estuaries.

"Stampede2 has enabled us to perform computational simulations for problems that had been intractable to date, and to address parameter regimes in our simulations that have so far been inaccessible," Meiburg said.

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Astrophysical Accretion Discs

Magnetized winds and turbulence drive the growth, or accretion, of disks in space, be they around black holes or protoplanets. Zhaohuan Zhu of the University of Nevada, Las Vegas, modeled the relative importance of turbulence and disk wind in accretion using numerical simulations on Stampede2. He co-authored work that appeared in the Astrophysical Journal in April 2018.

"In the field of astronomy, to do cutting edge research and advance our knowledge, we need the best tools. For observers, they need big telescopes. For theorists, we need large computers to understand physical processes in more detail," Zhu said.

For research on protoplanetary disks and planet formation, recent observations provide so much detail that previous low-resolution simulations are not sufficient to explain them.

"Stampede2 is absolutely essential for both observational and theoretical astronomy," Zhu said.

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Turbulent Flow

Stampede2 simulations are helping Diego Donzis, an aerospace engineer at Texas A&M University, study shock turbulence interactions, a critical phenomenon that must be accounted for when designing supersonic and hypersonic aircraft.

"Stampede2 is allowing us to run simulations, some of them at unprecedented levels of realism, needed to study processes that depend both on the large and the small scales of turbulent flows," Donzis said.

Stampede2 lets Donzis and his team run a wide range of simulations and conditions for a range of problems.

"Some of these simulations ended up forming some of the largest databases of their kind," he added. These in turn will help engineers design the high-speed aircraft of the future.

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Inside the Proton

Scientists will take what they've learned from particle physics simulations on Stampede2 and test their results on the planned Electron-Ion Collider at Brookhaven National Laboratory.

"Stampede2 enabled me and my collaborators to calculate new aspects of the gluon structure of the proton for the first time," said Phiala Shanahan, assistant professor of Physics at the Massachusetts Institute of Technology. Gluons are the force-carrying particle of the strong force that bind the proton together.

"The quantities we calculated will be able to be measured for the first time at the planned Electron-Ion Collider, a new particle collider that's currently in development. Being able to set theory benchmarks ahead of first experimental measurements is extremely exciting," Shanahan said.

Resources such as Stampede2 are exactly what are needed to do groundbreaking scientific calculations efficiently. "They're essential tools," Shanahan added.

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HIV-1 Targets

Stampede2 helped model a key building block in the HIV-1 protective capsid, which could lead to strategies for potential therapeutic intervention in its replication. Scientists found the naturally-occurring compound inositol hexakisphosphate (IP6) promotes both the assembly and the maturation of HIV-1.

"We discovered, in collaboration with other researchers, that HIV-1 uses this small molecule to complete its function," said Juan R. Perilla, Department of Chemistry and Biochemistry, University of Delaware. "HIV-1 has evolved to make use of these small molecules present in our cells to essentially be infectious." Perilla co-authored the study in the journal Nature in August 2018.

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