'What's New in XSEDE' - archives

What's New in XSEDE

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"What's New in XSEDE" is a monthly e-newsletter providing information on scientific discoveries made possible by the Extreme Science and Engineering Discovery Environment, as well as the people, places, and programs involved. XSEDE is a five-year high-performance computing project supported by the National Science Foundation.


Harnessing fusion energy

lithiated graphite surface
Dynamic in lithiated graphite: a) Experiments show that deuterium bombardment dramatically increases the surface oxygen

XSEDE-allocated resources have aided in answering the question of how the behavior of plasma—the extremely hot gases of nuclear fusion—can be controlled with ultra-thin lithium films on graphite walls lining thermonuclear magnetic fusion devices. This multi-institutional team from the U.S., Japan, and France, led by Predrag S. Krstic of the Joint Institute for Computational Sciences and Jean Paul Allain of Purdue University, turned to Kraken to run their quantum-mechanical simulations. After 1 million hours on the supercomputer, the team combined predictions from the simulations with experimental results to find that seemingly insignificant lithium depositions can profoundly influence the behavior of fusion plasmas. Krstic says this work could lead to improvement of the hydrogen-recycling properties of the fusion materials facing plasma, as well as advancements in other areas.

Read more about lithium coatings unlocking the mystery surrounding the harnessing of fusion energy arrow to link

Rapid vegetation green-up and the food chain

XSEDE-allocated resources have become the key to analyzing and drawing meaningful results for estimating the rate and extent to which the patterns of vegetation growth are changing across the Greater Yellowstone Ecosystem (GYE). The early onset of spring caused by warmer temperatures and melting snow, coupled with changes in the recurring lifecycle stages of plants, can ripple across the food chain, affecting pollinators, herbivores, and their predators by creating a mismatch in timing of life-history events.

Karthik Ram of the University of California, Berkeley and his research team had 1.25 million data points for each year, spanning an 11-year period. Measuring inter-annual changes in the green wave and estimating the rate and extent of green-up not only required comparing data across years but also within a year, to extract seasonal trends. As the volume of data continues to grow, so does the team's need for supercomputing resources.

The researchers turned to the XSEDE-allocated Nautilus supercomputer, managed by the National Institute for Computational Sciences (NICS), with resources and support provided by the Remote Data Analysis and Visualization Center (RDAV) of NICS. They discovered that under the warmer conditions, the green wave progressed significantly faster, with what could be termed "high-quality" forage occurring at higher elevations as compared with cool years. The researchers hypothesize that the rapid green wave could lead to complex dynamics in the elk populations and, consequently, the wolf populations, as well.

Read more about research on rate and extent of green-up of high-elevation landscapes and effects on the food chain arrow to link

Make mine a double... spinal endplate

double vs single layer endplate
A double layer endplate is made up of a porous, thin top layer (red) and thicker second layer (green). The double and single layer endplates (orange) that were examined had a very similar overall thickness.

Researchers at The University of California, San Francisco (UCSF) have confirmed the existence of a tissue that has historically been overlooked, unnoticed, or inadvertently sliced up in the dissection or sampling process, the double layer vertebral endplate. XSEDE enabled access to the processing power of Ranger at the Texas Advanced Computing Center (TACC), allowing the researchers to use the micro-CT data to perform high-resolution finite element simulations—virtual "stress tests."

These simulations also allowed the researchers to carry out permeability experiments with the endplates. According to the results, double endplates appear to have a distinct MRI scanning signature that could be used clinically to identify those with and without the double structure. Discovery of the double endplate spinal structure could mean an impact on personalized spinal treatments of the future, with spinal implants being designed to take advantage of a patient's unique spinal anatomy.

Read more about XSEDE-allocated resources helping visualize and test strength of double spinal endplate arrow to link

XSEDE13 panel to address importance of computation, data analytics in biosciences

A panel of distinguished experts will discuss the role of computation and data analytics in supporting biological discovery when XSEDE13—the annual conference focusing on science, education, outreach, software, and technology related to XSEDE—is held July 22-25 at the Marriott Marquis and Marina in downtown San Diego.

Moderating the panel will be Kevin Patrick, professor of Family and Preventive Medicine at the University of California, San Diego and director of the Center for Wireless and Population Health Systems at the California Institute for Telecommunications and Information Technology. Panelists include Alex Dickinson, senior vice president, Cloud Genomics, Illumina; Donald Jones, chief digital officer at the Scripps Translational Science Institute and vice president of global strategy and market development for Qualcomm Life; Darryl León, associate director, product management, Life Technologies; Karen Nelson, president, J. Craig Venter Institute; Glen Otero, Life Sciences HPC Solution Architect, Dell; and Nicholas Schork, director of bioinformatics and biostatistics at the Scripps Translational Science Institute.

Learn more about this biosciences panel at XSEDE13 arrow to link

What's behind the bias?

A study out of University of Tennessee, Knoxville is using XSEDE-allocated resources to employ computational methods to extract biologically meaningful information from the genome of Saccharomyces cevevisiae, baker's or brewer's yeast. Specifically, the researchers are seeking to gain a quantitative understanding of a phenomenon called codon usage bias (CUB), which relates to protein translation, one of the most fundamental and universal biological processes. Additionally, the leader of the research, Michael Gilchrist, says he and his team are looking closely at gene expression, the process by which the information in a gene is used to assemble a functional gene product, often a protein.

Gilchrist's team developed software in the R programming language that models the efficiency of a ribosome at translating messenger ribonucleic acids (mRNA) in relation to the evolution of CUB. Through their work with XSEDE and the data analysis team at the Remote Data Analysis and Visualization Center (RDAV), the team was able to improve the efficiency of the R code and optimize it to run on the Nautilus supercomputer, a system managed by the National Institute for Computational Sciences (NICS) and housed at Oak Ridge National Laboratory. Preliminary results showed that calculations that took 24 hours on the desktop computer could be executed in less than an hour on Nautilus. The RDAV data analysis team is continuing to work on improving the efficiency of the code.

Read more about why ribosomes choose certain chemical particles over others in manufacturing proteins arrow to link

Fluorish representing nutshell.XSEDE in a nutshell

Following are events, deadlines and opportunities related to XSEDE.

Submissions for the XSEDE13 conference are due March 8. XSEDE13, July 22-25 in San Diego arrow to link

Submission deadline EXTENDED for XSEDE and European Grid Infrastructure use cases. Now due March 8  arrow to link

Applications for International Summer School on HPC Challenges in Computational Sciences due March 18 arrow to link

XSEDE seeking use cases from the humanities, social sciences, and arts arrow to link

Extreme Scaling Workshop 2013 Call for Presentations due May 15. Workshop Aug. 15-16 in Boulder, CO arrow to link