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June 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
XSEDE Aids Drug Screening for Heart Arrhythmias
Computational pipeline tests for cardiotoxicity
Death from sudden cardiac arrest makes headlines when it strikes athletes. But it also causes the most deaths by natural causes in the U.S.,  estimated  at 325,000 per year. According to the Cleveland Clinic , the heart's bioelectrical system goes haywire during arrest. The malfunction can send heartbeats racing out of control, cutting off blood to the body and brain. This differs from a heart attack, which is caused by a blockage of the heart's arteries. The leading risk factors for sudden cardiac arrest are a past attack and the presence of disease. Another risk factor is the side effects from medications, which can potentially cause deadly arrhythmias.
Using XSEDE-allocated supercomputers, scientists have developed for the first time a way to screen drugs through their chemical structures for induced arrhythmias.
A computational pipeline to screen drugs for cardiotoxicity has been developed with the use of supercomputers. The pipeline connects atomistic scale information to protein, cell, and tissue scales by predicting drug-binding affinities and rates from simulation of hERG ion channel and drug structure interactions and then using these values to model drug effects on the hERG ion channel function and an emergent cardiac electrical activity alteration. Credit: Yang et al., Circulation Research.
XSEDE-Allocated Resources Used for High Tech Materials Science Study
Supercomputing advances zirconia research for future applications
For thousands of years, humans have produced ceramics by simply combining specific minerals with water or other solvents to create ceramic slurries that cure at room temperature and become some of the hardest known materials. In more recent times, zirconia-based ceramics have been useful for an array of applications ranging from dental implants and artificial joints to jet engine parts.
With help from XSEDE, researchers are conducting simulations to assess zirconia-based ceramic's ability to withstand harsh conditions as well as its fracture and fatigue limitations.
Stress-strain relations of four-, five-, seven-twin boundaries (TB) YSTZ nanopillars. Credit: N. Zhang and M. Asle Zaeem.
Settling In
XSEDE-allocated resources correct computer-predicted protein simulations, approaching lab accuracy
To understand how the tiny machinery of life works in health and disease, scientists need accurate pictures of how proteins fold and move. But laboratory methods for imaging proteins are slow, and so the structures of hundreds of thousands of proteins that have been discovered are still unknown. Scientists have used a number of methods for predicting structures via computer simulation. But sometimes even high-quality simulations aren't as accurate as drug designers may want. A research team used the GPU nodes in XSEDE-allocated supercomputers to optimize predictions made by other scientists. In the process, they made predictions of the structures for a number of proteins with accuracy that approached the most precise, X-ray based lab measurements.
An example of refinement in a portion of one of the proteins simulated. Credit: Heo L, Feig M.
Graphene-Reinforced Carbon Fiber May Lead to Affordable, Stronger Car Materials
Simulations via XSEDE allocation offer insight into chemical reactions
A new way of creating carbon fibers — which are typically expensive to make — could one day lead to using these lightweight, high-strength materials to improve safety and reduce the cost of producing cars, according to a team of researchers. Using a mix of computer simulations (enabled by an XSEDE allocation) and laboratory experiments, the team found that adding small amounts of the 2D graphene to the production process both reduces the production cost and strengthens the fibers.
Credit: Z. Gao et. al.
XSEDE-Allocated Resources Simulate Solar Cells
Perovskite research shows promise for future inexpensive, efficient solar options
Solar energy has become a popular renewable source of electricity around the world with silicon serving as the primary source due to its efficiency and stability. Because of silicon's relatively high cost, hybrid organic-inorganic perovskites (HOIPs) have emerged as a lower-cost and highly efficient option for solar power. A search for stable, efficient, and environmentally safe perovskites has shaped an active avenue in current materials research with new findings relying on simulations made possible through access to supercomputers provided by XSEDE.
Simulations of four lead-free perovskites show that these materials exhibit promising features for solar energy options. They are now being synthesized for further investigation. Credit: H. Tran, et al, and V. Ngoc Tuoc.
Program Announcements
XSEDE EMPOWER Now Accepting Applications for Fall Internships and Mentorships
XSEDE EMPOWER (Expert Mentoring Producing Opportunities for Work, Education, and Research) provides undergraduate students with the opportunity to work on a variety of XSEDE projects, such as computational and/or data analytics research and education in all fields of study, networking, system maintenance and support, visualization, and more. Mentors help engage undergrads in the work of XSEDE. The EMPOWER program aims to enable a diverse group of students to participate in the actual work of XSEDE. To apply to mentor one or more students, create one or more positions by following the link below. If you also have a student in mind to work with, that student should also submit an application.  The deadline for mentors and students to apply for Fall 2020 participation is July 10, 2020.
Check out this video to learn more about  XSEDE   EMPOWER  and what two recent interns have to say about the program.
Computing4Change Application Deadline Extended
For undergraduate students who want to enhance their skillset and create positive change in their community, XSEDE is accepting applications for Computing4Change (C4C).   C4C is a competition for students from diverse disciplines and backgrounds who want to work collaboratively to learn to apply data analysis and computational thinking to a social challenge. Currently it is planned to be co-located at SC20 in Atlanta, GA from November 14-20, 2020 (but may become virtual).  The deadline to apply has been extended until July 19, 2020
XSEDE Cyberinfrastructure Integration (XCI) Updates
XSEDE's InCommon Identity Provider (IdP) enables XSEDE users to sign in to web sites that are part of the InCommon Federation (for example, GENI and ORCID) using their XSEDE accounts and is especially useful for users who do not have an existing InCommon IdP provided by their home institution. Several configuration updates have been made recently to comply with community standards and maintain effective operational security. Please be sure your web browser is up-to-date.
Community Announcements
Jumpstart Your Sustainability Plan with SGCI's Free Virtual Mini-Course
Interested in developing a sustainability strategy for your gateway?  Register by June 12, 2020  for the Science Gateway Community Institute's Jumpstart Your Sustainability Plan mini-course! It's free, and offered virtually. This course will take place June 16-18, 2020, with main presentations from 12-1:30 pm ET each day, and optional office hours and special topics presentations from 2-5 pm ET.
Given that COVID-19 has, for now, limited the ability to travel and gather in person, SGCI is making the best of the situation and offering this free new mini-course instead of Gateway Focus Week, one of SGCI's most popular programs. Jumpstart Your Sustainability Plan will focus solely on offering practical and effective steps for developing a sustainability strategy. The mini-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.
Upcoming Dates and Deadlines