CSM

Agarwal appointed editor for biomedical publication

Pratul Agarwal, of the Computational Biology Institute and Computer Science & Mathematics Division, has been appointed specialty editor and editorial board member to WebmedCentral Plus, a publishing platform that publishes biomedical scientific content. As a specialty editor, Agarwal will handle manuscripts submitted to the biochemistry section. Members of the specialty editorial board are specialists in their respective fields and have had some previous experience reviewing manuscripts.

Patent Awarded

CSMD Researcher Travis Humble (along with ORNL researchers Ryan Bennink and Warren Grice) have been awarded a patent for their invention "Tampering Detection System Using Quantum-Mechanical Systems."

According to Dr. Humble -"The patent describes a method for detecting unauthorized physical access to a protected environment. The novelty of the method lies in its use of feedback from a quantum mechanical system to indicate the presence of the intruder. The feedback derives from the non-local correlations, i.e., entanglement, inherent to these systems and the assurance that such measurement signatures can not be spoofed. The ORNL team has experimentally confirmed these ideas using polarization entangled photon pairs as the quantum mechanical probe, and they are currently extending the development of these quantum optical seals for future use in technical verification of nonproliferation treaties."

Software Tools Will Need Refresh for ORNL's Titan Supercomputer

Richard Graham, Group leader for CSMD's/OLCF's Application Performance Tools Group, discusses with HPCWire the challenges presented by new hybrid computer architectures used in Supercomputers such as ORNL's Titan. Read the interview HERE.

American Chemical Society Award

The American Chemical Society has awarded CSMD researcher Ariana Beste (along with ORNL researchers Michelle Kidder and AC Buchanan) the Glenn award for best paper presented before the FUEL division at ACS' spring national meeting in San Franscisco. The title of their paper is "Pyrolysis Behavior of Lignin Model Compounds."

The researchers will receive there award at the ACS' national fall meeting in Denver.

Patent Awarded

CSMD Researcher Pratul Agarwal has been awarded a patent for his invention "Fast Computational Methods for Predicting Protein Structure from Primary Amino Acid Sequence."

According to the US Patent Office, "the invention provides a method utilizing primary amino acid sequence of a protein, energy minimization, molecular dynamics and protein vibrational modes to predict three-dimensional structure of a protein."

Packing the ions: Discovery boosts supercapacitor energy storage

DOE recognizes ORNL’s outstanding mentors

Four researchers from ORNL’s Computer Science and Mathematics Division were selected by DOE as winners of the Office of Science’s Outstanding Mentor Awards.  The winners were: Ralf Deiterding, George Ostrouchov, John Cobb, and Pat Worley

The DOE Outstanding Mentor Award program, coordinated through the Office of Science Workforce Development for Teachers and Scientists, began in 2002 as an effort to establish a culture that values mentorship within the DOE national laboratories.

ORNL team aids State of the Birds report

Ornithology joined forces with high-performance computing to support a new report on bird habitat released Wednesday by the Secretary of the Interior Ken Salazar and Agriculture Under Secretary Harris Sherman.

The State of the Birds report relied on lab staff who helped analyze more than 600,000 bird observations collected and logged in Cornell Universitys eBird database by citizen birders. The report evaluates the distribution of birds on nearly 850 million acres of public land and will be used to set policy agendas for governmental and non-governmental conservation efforts.

Through the DataONE (Observation Network for Earth) project, ORNL team members helped integrate environmental data from land use databases and satellite data from ORNLs Distributed Active Archive Center with the volunteer-collected eBird observations. With access to TeraGrid, a collaborative high-performance computing network, the team was able to calculate bird migration maps with unprecedented detail and accuracy, says CMSDs John Cobb.

Maps of this detail are useful in making land use and other policy decisions that affect habitat for important species, said Cobb, who leads ORNLs participation in TeraGrid.

While this years report focused on the relationship between land use and bird habitat, Cobb says future plans include conducting multi-year analyses to better understand how bird migration patterns vary over time as an indicator of climate change.

ORNL collaborators include Robert Cook and Suresh Santhana Vannan from the Environmental Sciences Division, Bruce Wilson from the Information Technology Services Division, and Line Pouchard from the Computer Science and Mathematics Division.

10 Questions for a Climate Scientist

Climate scientist Kate Evans works in the CSMD on a variety of projects from using supercomputers to study the movements of ice sheets to developing a model to explore the impacts of storms on ocean currents. The DOE ENERGYBLOG recently interviewed Kate about her work advancing climate simulations and modeling and why an Indiana storm sparked her interest in Earth sciences. Read the article HERE.

ORHS Student Wins

Gloria DAzevedo, a senior at Oak Ridge High School, won first place in the Tennessee Junior Science & Humanities Symposium for her research on improving elimination orderings for tree decompositions. She was awarded a $2000 college scholarship and an all-expense paid trip to the national JSHS, where she will compete for additional scholarships. Glorias research was conducted at Oak Ridge National Laboratory with Blair D. Sullivan and Chris Groer as part of the DOE ASCR Applied Mathematics project Scalable Graph Decompositions & Algorithms to Support the Analysis of Petascale Data. Gloria showed computationally that incorporating graph parameters such as the number of second neighbors of a vertex into traditional degree- and fill-based algorithms for choosing an elimination ordering can lead to significantly lower tree-widths. The impact of tree-width on the complexity of tree-decomposition based graph analysis algorithms is exponential, so this new idea for improving orderings could lead to significant speed-up.

Colony Team Boots Advanced Kernel

The Colony team reached a milestone this month by booting a new operating system kernel. Through successfully bringing up the advanced kernel on a Cray XT with a Seastar interconnect, the team paves the way for the next phase of performance and scalability testing. Unlike the typical Linux kernel which suffers performance drawbacks, the new kernel is designed to provide a full featured environment with excellent scalability on the worlds most capable machines. As coordinated stop-lights are able to improve traffic flow, the Colony system software stack is able to co-schedule parallel jobs and thus remove the harmful effects of operating system noise or interference through the use of an innovative kernel scheduler. The kernel utilizes a high precision clock synchronization algorithm developed by the Colony team to provide federated nodes with a sufficient global time source for the required coordination. The Colony Project is led by ORNL computer scientist Terry Jones.

Applied mathematicians include land ice in global climate models

Recently, Rhode-Island-sized chunks of ice have separated from Greenland and Antarctica, garnering worldwide attention. But is this calving due to typical seasonal variations or a long-term warmer world? Climate scientists already use ice sheet models to better understand how ice loss affects sea levels; however, those models are not easily adapted for use in global climate models. In August the Scalable, Efficient, and Accurate Community Ice Sheet Model (SEACISM) project began on Jaguar, one of the worlds fastest supercomputers, at Oak Ridge National Laboratory (ORNL). SEACISMs aim is to use state-of-the-art simulation to predict the behavior of ice sheets under a changing climate by developing scalable algorithms. Continue reading...

Award recognizes achievement in scaling computational chemistry application

CSMD's computational chemist Edoardo Apr is winner of this year’s HPCwire Reader’s Choice Award in supercomputing achievement.

The awards were passed out Monday, November 10, in New Orleans at the 2010 International Conference for High Performance Computing, Networking, Storage and Analysis, better known as SC10.

Apr was honored for his work with a computational chemistry application known as NWChem, which was developed at Pacific Northwest National Laboratory. Under Apr’s guidance, the application reached 1.39 thousand trillion calculations per second, or 1.39 petaflops, on ORNL’s Cray XT5 Jaguar system.

NWChem helped Apr and his colleagues uncover the electronic structure of water using a quantum chemistry technique called coupled cluster. They published some of their scientific results in the October 12 issue of the Journal of Physical Chemistry Letters (pubs.acs.org/doi/full/10.1021/jz101245s). The team was also a finalist for the prestigious 2009 Gordon Bell Prize, which recognizes the world’s top supercomputing application.

“Top supercomputing achievement” is one of about 20 categories offered in the awards. The Readers’ Choice winners are determined through polling among HPCwire’s online audience. The site’s 30,000 newsletter subscribers are also asked to vote.

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Employment/Student Opportunities with CSM

CSM currently has a number of job openings and postdoc opportunties — check out our jobs page. For undergraduate and graduate students, there are a number of opportunites for employment through ORNL's Research Alliance in Math and Science Program.