This month’s topics include: bug battles, bird watching, medical discoveries, and other surprising behavior.
COMPUTING – Battling bugs . . . . . .
The software-writing mistakes known as “bugs” can be a pain for even the simplest applications, forcing developers to go through their code line by line to find and fix errors. These bugs become far more serious when the applications are written for the world’s most powerful supercomputers, as leading scientific applications can be tens of thousands of lines long and run on hundreds of thousands of processors simultaneously. In response, a collaboration between Oak Ridge National Laboratory (ORNL) and software toolmaker Allinea Software has produced a formidable weapon in the fight against application bugs. When it is released this summer, Allinea DDT will allow programmers to analyze applications running 220,000 simultaneous processes and identify problems as they arise. “This project means application developers have a chance to debug their code in a reasonable amount of time at scale,” said ORNL Application Performance Tools Group leader Richard Graham. “They won’t have to write special case code to debug things, and go through the process of debugging the debug code. It lets you get at information that’s very time-consuming to get at otherwise.”
DATA – Bird watching by satellite . . . . . .
By using a data analysis tool developed at Oak Ridge National Laboratory, satellites can help researchers study birds flying through your backyard. Scientists from ORNL’s Distributed Active Archive Center, or DAAC, are collaborating with Cornell University researchers through a project called DataONE (Observation Network for Earth) to enable advanced analysis of bird species distribution and migration patterns. The ORNL tool allows the Cornell investigators to pull specific data generated by NASA’s MODIS satellite sensor and link it to field observations archived in Cornell’s eBird database. “The combination of satellite data with the bird observations is a novelty,” said Suresh Santhana Vannan, an ORNL DAAC scientist. “They’re normally two separate research areas.” By incorporating data extracted from MODIS such as the normalized vegetation density index, or “greenness” of the local area, researchers can conduct more complex analyses, such as modeling how variations in vegetation linked to climate change can affect bird migration.
HEALTH CARE – Strength in numbers . . . . . .
Medical advances made in laboratories and clinical settings could reach patients sooner because of a $38 million grant from the National Institutes of Health to nine institutions. The world’s most powerful computers at Oak Ridge National Laboratory will play a role in the effort, as will the lab’s capabilities in nanotechnology, genetics and particle science. Through a partnership with the Georgetown-Howard Universities Center for Clinical and Translational Science, ORNL’s task is to offer unparalleled opportunity in high-speed, high-volume computing to develop novel translational methodologies in drug discovery and genome-environment interactions. The funds were awarded as part of the Clinical and Translational Science Awards program (www.CTSAweb.org).
PHYSICS – Surprising nucleon behavior . . . . . .
Data from DOE’s Oak Ridge National Laboratory on neutron interactions with isotopes of platinum contradict a basic assumption underpinning random matrix theory, nuclear physics models and quantum chaos. For more than a half century, scientists have assumed that highly excited states in intermediate- to heavy-mass nuclides are chaotic, and that data support this assumption. However, new data from the Oak Ridge Electron Linear Accelerator strongly disagree. The new results suggest that the roughly 200 nucleons inside the platinum nuclei studied act in unison to exhibit regular rather than chaotic properties. Given the relatively high energy and large number of nucleons involved, such collective behavior is totally unexpected and unexplained. A possible explanation is that an even more fundamental tenet of theory–something known as form invariance–is violated. “Either way, as these assumptions underpin the nuclear statistical model, the impact of these new findings could be very broad throughout nuclear physics, nuclear astrophysics and in applications such as nuclear energy,” said ORNL physicist Paul Koehler.
DNA REPAIR – Molecular machines . . . . . .
Ivaylo Ivanov of Georgia State University and colleagues used Jaguar http://www.nccs.gov/computing-resources/jaguar/, a Cray XT high-performance computing system at Oak Ridge National Laboratory, to elucidate the mechanism by which accessory proteins called sliding clamps are loaded onto DNA strands and coordinate enzymes that enable gene repair or replication. “This research has direct bearing on understanding the molecular basis of genetic integrity and the loss of this integrity in cancer and degenerative diseases,” says Ivanov, whose work appeared in a recent issue of the Journal of the American Chemical Society. Although clamp loaders from the different kingdoms of life (bacteria, viruses, animals, etc.) share many architectural features, they differ mechanistically. Drugs targeted to the clamp loader could selectively inhibit replication of viral DNA in diseases such as chickenpox, herpes, and AIDS without interfering with DNA replication in normal human cells. Similarly, in processes with increased DNA replication, such as cancer, inhibiting clamp loading might produce therapeutic effects without unwanted side effects.
Click here to read the full article.
Source: Oak Ridge National Laboratory
Photo: Oak Ridge National Laboratoy