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InTheLoop | 02.27.2012

February 27, 2012

New Mathematical Method Reveals Where Genes Switch On or Off

Developmental biologists at Stanford University, using computing resources at NERSC, have taken a new mathematical method used in signal processing and applied it to biochemistry, using it to reveal the atomic-level details of protein–DNA interactions with unprecedented accuracy. They hope this method, called “compressed sensing,” will speed up research into where genes are turned on and off, and they expect it to have applications in many other scientific domains as well. Read more.


A Roadmap for Engineering Piezoelectricity in Graphene

With the help of supercomputers at NERSC, researchers at Stanford University have uncovered yet another hidden talent of graphene—with a little chemical doping, it can be transformed into a controllable piezoelectric material. This discovery could lead to a wide variety of graphene-based nanoscale devices. Read more.


Two States Climb Aboard New, 100-Gigabit Fast Train

Indiana and Ohio are the first states to take advantage of the next-generation backbone being built out by Internet2 and ESnet, linking in-state academic research networks to the 100-gigabits/sec cross-country network. Read more.


John Shalf’s Paper Is Among the Best in History of HPDC Conference

“The Cactus Code: A Problem Solving Environment for the Grid,” a paper co-authored by John Shalf, head of the Computer and Data Sciences Department in the Computational Research Division, has been selected as one of the top 20 papers in the 20 years of publications from HPDC, the International ACM Symposium on High-Performance Parallel and Distributed Computing. Other authors of the paper, written in 2000, are Gabrielle Allen, Werner Benger, Tom Goodale, Hans-Christian Hege, Gerd Lanfermann, André Merzky, Thomas Radke, and Edward Seidel.

The team used Cactus to perform simulations of the spiraling coalescence of two black holes, a problem of particular importance for interpreting the gravitational wave signatures being measured by detectors such as the Laser Interferometer Gravitational-Wave Observatory. Detection of the first gravitational waves (or failure to do so) will strongly test Einstein’s Theory of General Relativity, the results of which will have ramifications that extend throughout the world of physics. Using Cactus, the team created the first-ever accurate simulation of a spiraling merger of this type. Read more.


Berkeley Lab Staff Mentor Teen Girls in App Development

On Tuesday afternoons, a group of more than 60 high school girls from Berkeley and Albany head to Berkeley Lab for a series of 10 two-hour workshops to develop science education apps for Android smart phones. Split into five-member teams, the girls are being mentored by 20 women who work at Berkeley Lab. Mentors from the Computational Research Division (CRD) include Deb Agarwal, Sowmya Balasubramanian, Amy Chen, Orianna Demasi, Krishnaveni Palaniappan and Taghrid Samak. Katie Antypas of NERSC is serving as a mentor at the program being held on the UC Berkeley campus. Read more.


Howard Walter Retiring in June

NERSC Division Deputy Howard Walter will be retiring at the end of June 2012. While he will be greatly missed at NERSC, he is looking forward to spending more time with his wife, and going on more hiking, camping, and geocaching trips. In announcing Howard’s retirement, NERSC Division Director Kathy Yelick said, “Howard has been invaluable to me as Director, both in my initial transition into the position when I did not know many of the NERSC staff, and again in the last year as my time has been stretched even more than usual.”

Given the active search for a new NERSC Director and the role of deputies as “at will” positions by the Director, Kathy is deferring the decision about Howard’s replacement to the next NERSC Director.


John Bell and Kirsten Fagnan Featured on AMS Website

A photo of John Bell and Kirsten Fagnan of CRD’s Center for Computational Sciences and Engineering—neither of whom are in fact faculty—is featured on the American Mathematical Society’s web page titled “Information for Faculty.”


This Week’s Computing Sciences Seminars

2012 Bowen Lectures: Many Particle-Systems and Plasma Physics: Overview
Monday, February 27, 4:10–5:00 pm, 105 Stanley Hall, UC Berkeley
Cédric Villani, Université de Lyon et Institut Henri Poincaré, Fields Medalist 2010

In this lecture I shall present some of the basic problems in the mathematical theory of many-particle systems in classical physics, including in particular plasma physics.

(Reception to follow, 5:15 pm, Room 1015, Evans Hall.)

2012 Bowen Lectures: Many Particle Systems and Plasma Physics: Landau Damping — Problems and Results
Tuesday, February 28, 4:10–5:00 pm, 105 Stanley Hall, UC Berkeley
Cédric Villani, Université de Lyon et Institut Henri Poincaré, Fields Medalist 2010

In this lecture I explain about the physical and mathematical theory of Landau damping, and the recent progress by Mouhot and myself about Landau damping in the nonlinear, close-to-equilibrium regime.

2012 Bowen Lectures: Many Particle Systems and Plasma Physics: Landau Damping — Proofs and Problems
Wednesday, February 29, 4:10–5:00 pm, 1 LeConte Hall, UC Berkeley
Cédric Villani, Université de Lyon et Institut Henri Poincaré, Fields Medalist 2010

In this lecture I shall go more deeply into some of the proofs of the nonlinear Landau damping, and evoke some of the many problems in the area which have hardly been touched so far.

TRUST Security Seminar: Cybersecurity for High-Performance Computing Systems
Thursday, March 1, 1:00–2:00 pm, Soda Hall, Wozniak Lounge, UC Berkeley
David Bailey, LBNL/CRD

Large high-performance computing (HPC) systems pose some unique challenges and opportunities for cybersecurity. To begin with, large HPC systems are very expensive, and outages are very disruptive to the scientists and others who rely on them. Secondly, the advent of “BitCoin” and the like has added a new dimension of threat: The very large computational power of these systems might be subverted by intruders for financial gain. On the other hand, an HPC environment does simplify some things, since there are typically only a limited number of users, a limited portal to the outside world, and typically only a few types of scientific applications are run (which applications typically have very distinctive signatures of interprocessor communication). In this talk, we will present some techniques we have developed to identify scientific computations by their communication signatures.


Link of the Week: Recycling Is Not Always Good: The Dangers of Self-Plagiarism

Plagiarism is an act of academic fraud that implies “taking over the ideas, methods, or written words of another, without acknowledgment and with the intention that they be taken as the work of the deceiver.” If one “borrows” one’s own ideas from one’s own publication(s) without attribution, is the deception still academic fraud? Yes, it is, according to an editorial in ACS Nano, because it is an intentional attempt to deceive a reader by implying that new information is being presented. Read more.



About Computing Sciences at Berkeley Lab

The Lawrence Berkeley National Laboratory (Berkeley Lab) Computing Sciences organization provides the computing and networking resources and expertise critical to advancing the Department of Energy's research missions: developing new energy sources, improving energy efficiency, developing new materials and increasing our understanding of ourselves, our world and our universe.

ESnet, the Energy Sciences Network, provides the high-bandwidth, reliable connections that link scientists at 40 DOE research sites to each other and to experimental facilities and supercomputing centers around the country. The National Energy Research Scientific Computing Center (NERSC) powers the discoveries of 6,000 scientists at national laboratories and universities, including those at Berkeley Lab's Computational Research Division (CRD). CRD conducts research and development in mathematical modeling and simulation, algorithm design, data storage, management and analysis, computer system architecture and high-performance software implementation. NERSC and ESnet are DOE Office of Science User Facilities.

Lawrence Berkeley National Laboratory addresses the world's most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab's scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the DOE’s Office of Science.

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.