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XSEDE IMPACT MAY 2020

 
May 2020 | Science Highlights, Announcements & Upcoming Events
 
XSEDE helps the nation's most creative minds discover breakthroughs and solutions for some of the world's greatest scientific challenges. Through free, customized access to the National Science Foundation's advanced digital resources, consulting, training, and mentorship opportunities, XSEDE enables you to Discover More. Get started here.
 
Science Highlights
 
COVID-19 Analysis Performed on XSEDE-Allocated Resources with Galaxy Bioinformatics Platform
 
Large-scale compute infrastructure analyzes thousands of genomes
 
 
The Galaxy project is one of the world's largest, most successful, web-based bioinformatics platforms. With regard to Covid-19, researchers perform the majority of their parallel processing and analyses on the XSEDE-allocated Stampede2 and Jetstream supercomputers located at TACC. In addition, Galaxy employs the XSEDE-allocated Bridges platform at PSC for genome assembly jobs that require large amounts of shared memory. "We can essentially solve all genomic data analysis needs for the worldwide research community when it comes to SARS-CoV-2."  Anton Nekrutenko, Penn State.
 
 
This CDC illustration (top) reveals ultrastructural morphology exhibited by coronaviruses. Credit: CDC. Logo via the Galaxy project.
 
XSEDE-Allocated Resources Used to Create Simulations for Natural Disaster Case Studies
 
Supercomputers illustrate details for tsunamis, volcanoes, landslides
 
 
High-performance computer modeling has been found to accurately simulate tsunamis from volcanic events a discovery which could lead to early-warning systems that could save lives and help minimize catastrophic property damage. Researchers at the University of Rhode Island used XSEDE-allocated supercomputers to create detailed simulations of recent and prehistoric natural disasters. The researchers hope that their work allows for the improvement of early warning systems so that people have time to reach safety before a tsunami hits.
 
 
A supercomputer-generated model of the tsunami from the December 22, 2018 lateral collapse of th e Anak Krakatau volcano in the Sunda Straits, Ind onesia. Credit: Grilli et al.
 
Supercomputer Simulations Help Advance Electrochemical Reaction Research
 
New insights for nickel-embedded graphene revealed
 
 
Single-atom catalysts have recently emerged as promising innovations for solving environmental and energy issues. One such example, nickel embedded in graphene, has been shown to convert carbon dioxide, a molecule that causes the greenhouse effect, into carbon monoxide, an important feedstock for chemical engineering. However, a better understanding of the atomic structure of this concoction is needed before we can use nickel-embedded graphene on a regular basis. To help with this challenge, researchers from the University of Texas at Austin recently simulated the catalytic mechanism and atomic structure of nickel-doped graphene with XSEDE-allocated resources. The simulations showed a clear picture of the catalyst's atomic structure so that researchers were able to better understand critical effects of surface change and hydrogen bonding, which were overlooked in previous models.
 
 
Electrochemical reduction of carbon dioxide catalyzed by single nickel atom embedded in graphene with nitrogen dopant. Credit: X. Zhao and Y. Liu.
 
XSEDE Resources Aid International Engineering Team on Wave Energy Project
 
Supercomputers validate novel simulation tool
 
 
Similar to solar panels and wind turbines, wave energy converters harness energy from Mother Nature's resources—specifically ocean waves—and turn them into electricity. Although several challenges must be overcome before wave energy becomes a realistic option for mainstream power, one step toward a solution was recently studied and validated by an international team of engineering researchers focused on modeling complex fluid-structure interaction problems with support from XSEDE-allocated resources.
 
 
This simulation shows the interaction of an inertial sea wave energy converter device with incoming ocean waves in a "numerical" wave tank. Credit: Bhalla Group.
 
Microscopic... and Huge
 
XSEDE-allocated supercomputer powers visualization of whole viruses at atomic level
 
 
An image can help human beings make connections. That's why a scientist from Catholic University of America is using the large-memory nodes of the XSEDE-allocated Bridges system to put together some of the largest assemblies of proteins ever pictured. Thanks to Bridges' powerful nodes with large amounts of memory, he has created images of whole viruses with atomic-level detail. These images will help engineer those viruses as vaccines or other medical therapies.
 
 
The T4 virus (left), modified to contain coat proteins from HIV, the AIDS virus (center), and the plague bacterium (right). Credit: Padilla-Sanchez.
 
Supercomputing Future Wind Power Rise
 
XSEDE helps simulate promises and pitfalls of wind power expansion
 
 
Researchers at Cornell University conducted the first detailed study that developed scenarios for how wind energy can expand to 20 percent of total U.S. electrical supply by 2030. The simulations were conducted on the DOE NERSC Cori supercomputer, and analyzed on XSEDE-allocated supercomputers. Improved calculations of U.S. wind resources can ensure better decision making and a better, more robust energy supply. 
 
 
A scanning Doppler LIDAR is operated to characterize wakes in the lee of wind turbines. Credit: S. C. Pryor.
 
Experimental Introduction
 
Introducing experimental data into molecular simulations on XSEDE-allocated resource improves predictions of metallic glass structure
 
 
Metallic glass is useful in many practical applications, including medicine, electronics, nanotechnology and even sporting goods. Scientists don't agree on how the atoms in metallic glasses are arranged, limiting the ability to engineer new metallic glasses for expanded uses. Ohio University scientists employed XSEDE-allocated resources to carry out a new type of molecular simulation on a metallic glass that introduces lab-derived data in the simulation process. The method better agreed with lab results than former simulation methods, and predicted unexpected properties that may help guide future applications of the material.
 
 
A phosphorus atom (top, center) rattling inside a cage of palladium and nickel, from the AIFEAR simulations. Credit: Bhattarai, Thapa, and Drabold.
 
Program Announcements
 
XSEDE and the HPC Consortium for COVID-19
 
 
XSEDE is proud to manage the scientific review process for the COVID-19 HPC Consortium from  The White House's Office of Science and Technology Policy , a consortium of private, government, and academic partners that seeks to expedite applications for advanced computing research to combat the COVID-19 pandemic. The consortium uses the XSEDE Resource Allocations System ( XRAS ) platform for proposal submission and review. At the time of this writing, the consortium is currently supporting 41 active projects. Researchers who are interested in conducting this timely work are asked to  submit research proposals to the COVID-19 Online Portal here , which is handled by the XRAS team.
 
 
Fight COVID-19 While Improving the Utility of Your Campus Computing Resources
 
The XSEDE Cyberinfrastructure Resource Integration team and the National Center for Genome Analysis Support are offering the following types of consulting and software services to operators of campus-based computational resources to aid you in supporting your campus researchers in their work on COVID-19:
  • Consulting and help in accessing and installing relevant bioinformatics software on your local compute systems so that you can more effectively support your local researchers who are taking part in research related to COVID-19 through teleconferences and other remote facilitation methods
  • Consulting with bioinformatics software and system administration experts in support of your local research needs related to COVID-19, including use of containerized applications
  • Consulting on data movement and management
  • Assistance with the process of applying for and implementing the operational activities required to become a functioning member of the COVID-19 HPC Consortium
  • Assistance in applying for resources available through XSEDE and NCGAS
 
For assistance, please fill out the form at  https://forms.gle/kkQFp9yWHnoY2uy79  and we will reply as soon as possible to discuss your needs.
 
XSEDE Cyberinfrastructure Integration (XCI) Updates
 
 
The XSEDE Cyberinfrastructure Integration (XCI) team is providing remote support to Bentley University in support of COVID-19 protein-folding research and has released new documentation for 1) campuses to leverage XSEDE's authentication and login services including two-factor for access to their local HPC resources, 2) users to discover data analysis resources on XSEDE resources, and 3) application developers that leverage XSEDE Web SSO to access and use a user's affiliated institution information to customize the user's experience or log the information for statistical purposes.
 
 
Community Announcements
 
Trusted CI Webinar "Is Your Code Safe from Attack?"
 
 
Tune in to Trusted CI's webinar on Monday, May 18 at 10 a.m. CST to hear University of Wisconsin-Madison's Barton Miller and Elisa Heymann presenting the talk, "Is Your Code Safe from Attack?." Their presentation will focus on how and why to conduct in-depth code reviews. Register in advance and learn more at the link below.
 
 
Trustworthy Data Working Group Needs Your Input
 
The  Trustworthy Data Working Group , a collaboration between several organizations within our community, invites scientific researchers and the cyberinfrastructure professionals who support them to complete a short survey about scientific data security concerns and practices. Responses are requested by May 31. Survey results, along with the analysis and applicable guidance, will be published by the Trustworthy Data Working Group as a freely available report by the end of 2020.
 
 
Deadlines Extended for Gateways 2020
 
 
Gateways 2020 (October 19–21, Bethesda, Maryland) is still accepting submissions of short papers, demos, panels, and posters on the topic of gateways for science, engineering, or other disciplines. The deadline for s hort papers, demos, and panels has been extended until May 18. Poster abstracts will be accepted until September 11.
 
 
Upcoming Dates and Deadlines