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XSEDE IMPACT January 2021

 

 

 

 

 
January 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
 
Supercomputers Simulate New Pathways for Potential RNA Virus Treatment
 
XSEDE allocations lead to important viral inhibitor discovery
 
 
University of New Hampshire (UNH) researchers recently used the XSEDE-allocated Comet at the San Diego Supercomputer Center (SDSC) and Stampede2 at the Texas Advanced Computing Center (TACC) to identify new inhibitor binding/unbinding pathways in an RNA-based virus. The findings could be beneficial in understanding how these inhibitors react and potentially help develop a new generation of drugs to target viruses with high death rates, such as HIV-1, Zika, Ebola, and SARS-CoV2, the virus that causes COVID-19.
 
 
Structural changes in RNA on drug binding/unbinding. Credit: Lev Levintov, University of New Hampshire.
 
Powering COVID-19 Collaborations and Communicating Risks to Public
 
Support from XSEDE's Novel and Innovative Projects initiative helps re-tool critical epidemiological models for HPC applications
 
 
UT Austin COVID-19 Modeling Consortium, led by Lauren Ancel Meyers, has developed some of the leading epidemiological models of how the disease spreads. The models, which were re-tooled for HPC with support from XSEDE's Novel and Innovative Projects initiative, incorporate the latest science on virus transmission and real-time data on social distancing from cell phone data. Researchers have shared the results of pandemic forecasts with the public through the COVID-19 Portal, which hosts models that state, local, and national decision-makers, media, and the public have used during the pandemic to inform their understanding of risk.
 
 
The portal's School Risk dashboard projects the expected number of students or staff who will arrive infected in a given week based on recent estimates for COVID-19 prevalence in each US county and the size of a school or pod. Credit: UT-Austin COVID-19 Modeling Consortium.
 
Targeting the Deadly Coils of Ebola
 
XSEDE EMPOWER program and XSEDE compute allocations support research showing weak spots in virus nucleocapsid
 
 
Ebola outbreaks continue to flare up in West Africa, although a vaccine developed in December 2019 and improvements in care and containment have helped keep Ebola in check. Supercomputer simulations by a University of Delaware team that included an undergraduate supported by the XSEDE EMPOWER program are adding to the mix and helping to crack the defenses of Ebola's coiled genetic material. This new research could help lead to breakthroughs in treatment and improved vaccines for Ebola and other deadly viral diseases such as COVID-19.
 
 
The deadly Ebola virus shields its RNA genetic material in coils of proteins called nucleocapsids (above). The lab of Juan Perilla at the University of Delaware completed all-atom simulations of the nucleocapsid with (R) and without (L) RNA, showing that the RNA confers stability vs. disorder without. Credit: Juan R. Perilla, University of Delaware.
 
Supercomputer Models Describe Chloride's Role in Corrosion
 
XSEDE-enabled simulations show how chloride degrades iron
 
 
Researchers have been studying chloride's corrosive effects on various materials for decades. Thanks to XSEDE allocations on the high-performance computers at the San Diego Supercomputer Center (SDSC) and the Texas Advanced Computing Center (TACC), detailed models have now been simulated to model the nanoscale processes that lead to chloride-induced breakdown of iron passive films. However, researchers have found that protective passive films can help the design of effective alloys and corrosion inhibitors to increase the service life of structures.
 
 
Surface structural changes to iron passive films caused by the adsorption of OH and/or Cl. (a) Fe(OH)3, (b) Fe(OH)2Cl, (c) Fe(OH)Cl2, d FeCl3. Credit: Oregon State University College of Engineering.
 
XSEDE Aids Sickle Cell Research Discovery
 
New models show details of stress caused by malformed red blood cells
 
 
Although there has yet to be a cure for sickle cell disease, researchers recently used XSEDE allocations to create detailed simulations on the Comet system at the San Diego Supercomputer Center (SDSC) showing how these stiff red blood cells flow through blood vessels, deforming and colliding along the way. The study, recently published in the Physical Review Fluids journal, reveals new information regarding the ways in which sickle cells collide with one another as well as healthy cells and blood vessel walls. These collisions generate large forces that impact healthy cells on the blood vessel walls — causing harmful inflammation.
 
 
Researchers used XSEDE allocations on SDSC's Comet supercomputer to simulate the forces caused by sickle cells upon vessel walls. These snapshots show a front view of healthy red blood cells (red) and sickle red blood cells (blue) as they are distributed during flow. Credit: Michael Graham, University of Wisconsin – Madison, et al.
 
Program Announcements
 
XSEDE Welcomes New Service Providers
 
 
XSEDE has recently welcomed five resources into the XSEDE Federation: the University of Kentucky's KyRIC, Purdue University's Anvil, Texas A&M's FASTER, Johns Hopkins University's Rockfish, and the Open Storage Network (OSN). 
 
Of these newly-added resources, KyRIC and OSN are currently accepting allocation requests for the current deadline of January 15, 2021, along with two other recently-added members of the XSEDE Federation: San Diego Supercomputer Center's Expanse and Pittsburgh Supercomputing Center's Bridges-2. The others expect to begin accepting requests later in 2021.
 
 
XSEDE's Terminology Statement
 
 
Words matter. XSEDE's commitment to fostering and promoting an inclusive environment for all users, staff, and the wider community extends to all language and terminology in all of our materials. We encourage you to reach out to the XSEDE Terminology Task Force with any feedback, recognizing that some third-party materials may be beyond our editorial control.
 
Register Today for XSEDE Student Programs Info Session
 
 
Register today for the XSEDE Student Programs Info Session on Wednesday, January 19, 2021 at 2 PM CST.
 
Attendees will learn about internships, fellowships, trainings, and student research opportunities in data science. XSEDE advanced computing resources help students and researchers across all disciplines to explore, create, and innovate. Join a team that is decoding genomes, modeling climate change, designing transportation systems, tracking the spread of epidemic movements, and supporting social action that depends on computation, data analytics, and information visualizations for breakthrough results and insights.
 
 
Community Announcements
 
Upcoming Virtual Opportunities at SDSC
 
 
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
 
 
Trusted CI Webinar: Trustworthy Data Panel
 
 
Trusted CI, the NSF Cybersecurity Center of Excellence, is launching the 2021 webinar series with a presentation on SciTokens. The SciTokens project is building a federated ecosystem for authorization on distributed scientific computing infrastructures, including XSEDE. The webinar will be held on Monday, January 25 at 10 AM CST.
 
 
Registration Is Now Open for GlobusWorld 2021
 
 
Come engage with the Globus team and community at GlobusWorld 2021, which will be held May 12-14 as a virtual event. Learn about best practices in research data management and hear about our product development plans.
 
GlobusWorld is free to attend, but registration is required. So be sure to mark your calendar, spread the word, and register today!
 
 
Upcoming Dates and Deadlines