Welcome to the XSEDE podcast page! Below are a few audio-recorded feature news segments about XSEDE science success stories.

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XSEDE Science Interviews
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Supercomputing Black Hole Jets

Black holes make one of the great mysteries in physics. You might know that black holes are so massive that nothing, not even light, can escape once it gets close enough.
The great physics mystery is that something is shooting out of some black holes at close to the speed of light. No one knows how these jets form. Supercomputer simulations of black hole jets are starting to shed light on them.
To get a better picture of what's happening, imagine gases, dust, and debris from stars spiraling into a black hole. They form a disc around it. Coming out the top and bottom of the disc are jets - one made of electrons and protons and the other of electrons and positrons - the antimatter twin brother of electrons.
On the podcast host Jorge Salazar talks more about black hole jets with Ken-Ichi Nishikawa, a principal research scientist at The Center for Space Plasma and Aeronomic Research at the University of Alabama in Huntsville. Dr. Nishikawa's team been awarded XSEDE allocations on several supercomputers, including time on Maverick, Ranch, and Stampede at the Texas Advanced Computing Center; Oasis and Gordon at the San Diego Supercomputing Center; and Nautilus at the National Institute for Computational Sciences. His simulations study how black hole jets interact with the plasma environment that surrounds them.
Nishikawa co-authored a study published April of 2016 in the Astrophysical Journal. The study simulations showed for the first time structural differences in one jet compared to the other. He's interviewed by podcast host Jorge Salazar.

How to See Living Machines

Scientists have taken the closest look yet at molecule-sized machinery called the human preinitiation complex. It basically opens up DNA so that genes can be copied and turned into proteins. The science team formed from Northwestern University, Berkeley National Laboratory, Georgia State University, and UC Berkeley. They used a cutting-edge technique called cryo-electron microscopy and combined it with supercomputer analysis. They published their results May of 2016 in the journal Nature.
Over 1.4 million 'freeze frames' of the human preinitiation complex, or PIC, were obtained with cryo-electron microscopy. They were initially processed using supercomputers at the National Energy Research Scientific Computing Center. This sifted out background noise and reconstructed three-dimensional density maps that showed details in the shape of the molecule that had never been seen before.
Study scientists next built an accurate model that made physical sense of the density maps of PIC. For that they XSEDE, the eXtream Science and Engineering Discovery Environment, funded by the National Science Foundation. Through XSEDE, the Stampede supercomputer at the Texas Advanced Computing Center modeled the human pre initiation complex for this study. Their computational work on molecular machines also includes XSEDE allocations on the Comet supercomputer at the San Diego Supercomputing Center.
Podcast host Jorge Salazar interviews Eva Nogales, Professor in the Department of Molecular and Cellular Biology at UC Berkeley and Senior Faculty Scientist and Howard Hughes Medical Investigator at Lawrence Berkeley National Laboratory; and Ivaylo Ivanov, Associate Professor of in the Department of Chemistry at Georgia State University.

Kelly Gaither Starts Advanced Computing for Social Change

 XSEDE identified 20 graduate and undergrad students that participated in a week-long event in November 2016 called Advanced Computing for Social Change. The event is hosted by XSEDE, TACC and SC16.
The SC16 Social Action Network student cohort tackled a computing challenge. They learned how to mine through a variety of data sets such as social media data encompassing a number of years and across large geographic regions. To complete their analysis in a timely fashion they learned how to organize the large data sets to allow fast queries.
The students of the SC16 Social Action Network used a computational modeling tool called risk terrain modeling that has been used to predict crime using crime statistics. This technique was first introduced to TACC in work done with the Cook County Hospital in Chicago, Illinois. The work used statistical data to predict child maltreatment in an effort to put programs in place to prevent it.
Podcast host Jorge Salazar interviewed Kelly Gaither, Director of Visualization at the Texas Advanced Computing Center (TACC). Gaither is also the Director of Community Engagement and Enrichment for XSEDE, the Extreme Science and Engineering Discovery Environment, funded by the National Science Foundation.
Kelly Gaither: Advanced Computing for social change is an initiative that we started to really use our collective capabilities, here at TACC and more broadly at supercomputing centers across the nation, to work on problems that we know have need for advanced computing. You can think of it as data analysis, data collection, all the way to visualization and everything in between to really work on problems of societal benefit. We want to make a positive change using the skill sets we already have.
The SC16 supercomputing conference took place in Salt Lake City, Utah November 13-18, 2016. The event showcases the latest in supercomputing to advance scientific discovery, research, education and commerce. 


It takes a supercomputer to grow a better soybean. A project called the Soybean Knowledge Base, or SoyKB for short, wants to do just that. Scientists at the University of Missouri-Columbia developed SoyKB. They say they've made SoyKB a publicly-available web resource for all soybean data, from molecular data to field data that includes several analytical tools.

SoyKB has grown to be used by thousands of soybean researchers in the U.S. and beyond. They did it with the support of XSEDE, the Extreme Science and Engineering Discovery Environment, funded by the National Science Foundation. The SoyKB team needed XSEDE resources to sequence and analyze the genomes of over a thousand soybean lines using about 370,000 core hours on the Stampede supercomputer at the Texas Advanced Computing Center. They're since moved that work from Stampede to Wrangler, TACC's newest data-intensive system. And they're getting more users onboard with an allocation on XSEDE's Jetstream, a fully configurable cloud environment for science.

Host Jorge Salazar interviews Trupti Joshi and Dong Xu of the University of Missouri-Columbia; and Mats Rynge of the University of Southern California.

Feature Story: www.tacc.utexas.edu/-/soybean-scien…-supercomputers

Recovering Lost History

The story in this podcast revolves around a collaboration of social scientists, humanities scholars, and digital researchers directed at using advanced computing to find and understand the historical experiences of Black women by searching two massive databases (HathiTrust and JSTOR)for written works from the 18th through the 20th centuries. The team also is developing a common toolbox that can help other digital humanities projects.

The research is supported by the National Science Foundation's eXtreme Science and Engineering Discovery Environment (XSEDE), the preeminent collection of integrated digital resources and services in the world. (xsede.org)

Participating in the podcast's discussion are the following: Ruby Mendenhall, an associate professor at the University of Illinois, Urbana-Champaign, and the project's principal investigator; Nicole M. Brown, a postdoctoral researcher at the National Center for Supercomputing Applications (NCSA); Michael Black, an assistant professor of English at the University of Massachusetts, Lowell; and Mark Vanmoer, a senior visualization programmer at NCSA.

Links to stories that have been written about this project:

Tiny Zaps, Big Results: Laser–Materials Research with Guest Leonid Zhigilei

The "small talk" of researchers in nanotechnology is extremely small. Their interest is in the physical phenomena occurring with things one-billionth of a meter in size, a million times shorter than the length of an ant, and up to 100,000 times thinner than a human hair. But the benefits to society of the science, engineering, and technology they're doing at such tiny scales are huge.

In fact, more than 800 everyday commercial products rely on nanoscale materials and processes, according to the National Nanotechnology Initiative (nano.gov). A central aspect of nanotechnology is that it allows essential structures of materials to be tailored to achieve specific properties that improve a variety of applications in medicine, energy, information technology, and many other areas.

One method of nanotechnology research involves the use of short laser pulses at minuscule fractions of a second to produce structural changes in thin, localized surface regions of various materials, such as gold, silver, or silicon.

Leonid Zhigilei, who heads the Computational Materials Research Group at the University of Virginia, says via telephone in this podcast that what attracted him to this type of research is the ability of lasers to excite and change materials in ways not possible with any other technique.

DIrect link to story: https://www.nics.tennessee.edu/zhigilei-laser-nanotechnology