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XSEDE IMPACT February 2021

 
February 2021 | 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
 
Rapid ID of Potential Anti-COVID-19 Agents Powered by XSEDE
 
Bridges-AI identifies more than 20,000 compounds with possible anti-virus activity, thousands of times faster than earlier methods
 
 
COVID-19 has shown that speed can be as important as quality in medical research.
A team from Carnegie Mellon University has developed a new computational pipeline for greatly speeding up the identification of possible anti-SARS-CoV-2 virus candidates using artificial intelligence.
Using the XSEDE-allocated Bridges-AI system, they screened about five billion chemical compounds to select a small number of candidates for combating the disease, thousands of times faster than possible with previous methods.
 
 
COVID protease with an inhibitor molecule (light blue) in the active site.
 
XSEDE-Allocated Supercomputers Advance Longer-Lasting, Faster-Charging Batteries
 
Researchers at multiple universities collectively advance battery technologies
 
 
In an effort to curb the rise in overall carbon vehicle emissions, the state of California recently announced a plan to ban new sales of gasoline-powered vehicles in less than 15 years — if the current governor's order holds strong. Now, thanks to supercomputers funded by the National Science Foundation and allocated, in part, by XSEDE, researchers at UC San Diego, Washington University in Saint Louis, and Washington State University have made progress on developing more reliable and efficient electric cars, by focusing on the lithium-sulfur, lithium-air, and lithium-ion batteries that power them.
 
 
Green represents electrons present in a layered material called electride. Fluorine ions (shown in bright yellow) can easily replace the electrons and hop from one site to another to enable a better electrode for fluoride intercalation batteries. Credit: Rohan Mishra Lab, Washington University.
 
Cell 'Bones' Mystery Solved with Supercomputers
 
XSEDE Stampede2 simulates polarized elongation of actin filaments
 
 
Our cells are filled with ‘bones,' in a sense. Thin, flexible protein strands called actin filaments help support and move around the bulk of the cells of eukaryotes, which includes all plants and animals. Always on the go, actin filaments constantly grow, shrink, bind with other things, and branch off when cells move. Supercomputer simulations conducted by researchers at Yale and the University of Chicago have helped solve the mystery of how actin filaments polymerize, or chain together. This fundamental research could be applied to treatments to stop cancer spread, develop self-healing materials, and more.
 
 
Space-filling model from molecular dynamics simulation showing actin filament barbed end (blue) and pointed end (red). Credit: Vilmos Zsolnay, University of Chicago.
 
AI Uses Language Rules to Simulate Molecular Motions on XSEDE-Allocated Bridges
 
Recreates known chemical rules, opens door to improved vaccines, drugs, industrial processes
 
 
Better predictions of molecular motions could lead to improved vaccines, drugs, and any number of improved industrial chemical processes. A team from the University of Maryland used natural language processing artificial intelligence (AI) on the XSEDE-allocated Bridges platform at the Pittsburgh Supercomputing Center (PSC) to recreate known chemistry. The work showed that AI may be able to reduce molecular dynamics to rules of grammar and syntax, offering the potential for leaping ahead of current computational limits in the field.
 
 
The AI-based method successfully predicted which amino acids (in red, labeled with their symbol letters and their number in the protein's amino-acid chain) would be critical for the binding of benzene (cyan spheres) to the lysozyme protein. Credit: Wang Y et al. 
 
Program Announcements
 
Apply by Feb. 26 for XSEDE EMPOWER Internships
 
 
An XSEDE-wide effort is underway to expand the community by recruiting and enabling a diverse group of students who have the skills — or are interested in acquiring the skills — to participate in the work of XSEDE. The name of this effort is XSEDE EMPOWER (Expert Mentoring Producing Opportunities for Work, Education, and Research). To participate, undergraduate students from any US degree-granting institutions are matched with mentors who have projects that contribute to the work of XSEDE. Participation is strongly encouraged for mentors and students belonging to groups traditionally underrepresented in computing. The application deadline for summer 2021 participation is February 26, 2021.
 
 
XSEDE Cyberinfrastructure Integration (XCI) Updates
 
 
XSEDE has improved the ability for science gateways and other research software providers and integrators to install, advertise, share, and support their own software on XSEDE resources using a feature called Community Software Areas or "CSAs."
 
 
Community Announcements
 
Upcoming Virtual Opportunities at SDSC
 
 
March 4, 9:00 AM - 1:00 PM PST
SDSC's new supercomputer, Expanse, went into full production in late 2020 as a follow-on to Comet. Although the transition should be straightforward for most users, there are some key differences in both the hardware and software between these systems, which will be explored in this virtual tutorial.
 
May 4 -13 (Application Deadline: Mar. 4) This virtual event is designed to help teams of three to six developers accelerate their own codes on GPUs using a programming model or machine learning framework of their choice. Each team is assigned mentors for the duration of the event. 
 
Student Fellowship and Research Opportunities Available at TACC
 
 
June 1, 2021 – May 31, 2022
Application Deadline: February 12, 2021
The year-long Frontera Fellowship Program provides an opportunity for graduate students to compute on the most powerful academic supercomputer in the world, and collaborate with experts at the Texas Advanced Computing Center.
 
June 7 – August 6, 2021 (Virtual)
Application Deadline: March 1, 2021
The REU Site: CI Research 4 Social Change is now recruiting undergraduates for the paid 9-week summer research experience at the Texas Advanced Computing Center at The University of Texas at Austin.
 
PEARC21 Call for Participation
 
 
ACM PEARC21 Conference — Evolution Across All Dimensions will take place virtually from July 18-22, 2021 and will explore the current practice and experience in advanced research computing including workforce development, training, diversity, applications and software, and systems and software. 
 
Submission Deadlines:
 
Tutorials and Workshops: February 9, 2021
Full Papers: March 9, 2021
Short Papers: April 13, 2021
Invited resubmissions: April 20, 2021
Panels: May 9, 2021
Birds of a Feather: May 9, 2021
Posters: May 16, 2021
Visualizations: May 23, 2021
 
 
Jumpstart your sustainability plan with SGCI's free virtual mini-course!
 
 
Monday-Wednesday, March 1-3, 2021
Main presentations will take place 12-1:30 pm ET each day.
 
The Jumpstart Your Sustainability Plan mini-course offered by the Science Gateways Community Institute will focus solely on offering practical and effective steps for developing a sustainability strategy for your gateway. The free and virtual course offers PIs of research and teaching-focused gateways and their teams the perfect way to kick off sustainability planning, whether you are writing a new grant or ready to get to the next level with a more mature project.
 
 
News from Globus
 
 
Globus now supports recurring and scheduled transfers
Globus now supports recurring and scheduled transfers. The new feature allows you to submit a job that will reliably request periodic transfers with a defined start time. Read their blog and give it a try using the new command-line client.
 
Someone just shared data with me, now what? (February 23, 3-4 p.m. CT) 
Secure sharing for Globus endpoint admins (March 16, 3-4 p.m. CT)
What data does the Globus service store and how is it protected? (April 13, 3-4 p.m. CT)
 
Save the date! GlobusWorld 2021
 
Upcoming Dates and Deadlines