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December 2007 Staff Research Notes

December 10, 2007

Nano Poster Wins AwardThree researchers from won the Best Poster Award at the November SC07 supercomputing conference in Reno. Zhengji Zhao, Juan Meza and Lin-Wang Wang were recognized for their poster describing "A New O(N) Method for Petascale Nanoscience Simulations,” which describes new linear scaling three-dimensional fragment (LS3DF) method for ab initio electronic structure calculations. The poster was one of 39 accepted for the conference from more than 150 submissions. SC07 is the… Read More »

Science Journal Features Research On Petascale Enabling Technologies

December 5, 2007

The November 2007 issue of the Cyberinfrastructure Technology Watch (CTWatch) Quarterly included significant contributions – five out of the nine articles – from CRD researchers, who authored papers on code performance, software tools, visualization, scientific data management and data placement solutions for distributed petascale science. The issue featured articles written by dozens of researchers about SciDAC’s Centers for Enabling Technologies. SciDAC (Scientific Discovery through… Read More »

Deconstructing Microbes

November 22, 2007

A metagenome data management and analysis system developed and managed by CRD researchers contributed to a breakthrough research recently published in Nature that probed the genetic materials of microbes in a termite’s gut. Understanding how these microbes convert wood to energy for sustaining a termite’s life would help researchers figure out better ways to convert biomass to biofuels in factories. The microbes exude enzymes that efficiently break down the wood’s cellular structure, but… Read More »

Lab Authors' Paper in Nano Letters Draws Strong Interest

October 15, 2007

A research paper showing how zinc oxide can be manipulated to become a good material for photovoltaic devices was among the most-accessed paper published by Nano Letters in the third quarter. The paper, written by Joshua Schrier, Denis Demchenko and Lin-Wang Wang in CRD’s Scientific Computing Group, laid out the calculations that narrowed the band gap – the energy difference between the top of the valence band and the bottom of the conduction band – of zinc oxide. To effectively absorb… Read More »

Algorithm Solves Key Energy-reduction Issue in Describing Complex System

September 28, 2007

The SIAM Journal on Scientific Computing recently published the work by three CRD researchers that incorporated an algorithm they developed in computing the ground state energy and wave functions for describing the mechanics of a complex physical system. The paper, “A Trust Region Direct Constrained Minimization Algorithm for the Kohn-Sham Equation,” described the use of the direct constrained minimization (DCM) algorithm with the “trust region” technique to compute single electron… Read More »

June 2007 Staff Research Notes

June 14, 2007

New Money, New AlgorithmsXiaoye “Sherry” Li has been awarded $10,000 from the France-Berkeley Fund, which aims to stimulate research exchanges among scientists from the University of California and France. Li, who is a researcher in CRD’s Scientific Computing Group, and her project co-leader from France, plan to use the money to further their work on developing novel algorithms for solving large sparse linear systems, used in many time-consuming computations in fields such as fluid… Read More »

CCSE's Marc Day Awarded NASA Allocation for Combustion Research

April 18, 2007

Research to quantify the formation of pollutants during natural gas combustion has received 1.5 million computing hours from NASA. Led by Marc Day in CRD’s Center for Computational Sciences and Engineering, the project, “Flames Dynamics and Emission Chemistry in High-Pressure Industrial Burners,” was one of the four awarded by NASA last month under its National Leadership Computing System initiative. The initiative sets out to support computationally intensive projects that advance a… Read More »

Nanowire’s Novel Properties Could Increase Power Output In Solar Cells

April 5, 2007

A CRD scientist has designed a nanowire with potential of generating electricity more efficiently than many conventional materials currently used for solar cells. Using gallium nitride and gallium phosphide, Lin-Wang Wang and two collaborators at the National Renewable Energy Laboratory in Colorado have modeled the nanowire—a coaxial cable—that overcomes several key problems encountered in bulk material solar cells and hydrogen fuel production today. “Bulk materials have lots of… Read More »

Serving Up a Smoother Flow of Water Resources Data

March 12, 2007

A collaboration among Microsoft, Berkeley Lab and UC Berkeley is underway to develop a scientific data server for amassing and organizing water data from diverse sources, a system that will accelerate research in the increasingly important areas of water and climate change. Called Microsoft e-Science, the project is part of the Berkeley Water Center’s effort to marshal expertise from public institutions and the private sector and support projects that enable researchers to easily access and… Read More »

Supercomputing Report Card

February 15, 2007

A comprehensive supercomputer performance evaluation undertaken by CRD scientists has won a Best Paper award in the Application track at the IEEE International Parallel and Distributed Processing Symposium (IPDPS), underscoring the significant contribution the research makes to improving scientific applications for the arrival of petascale computing. The paper, “Scientific Application Performance on Candidate PetaScale Platforms,” is an accumulation of four years of exhaustive study that… Read More »

CRD Staff Have Strong Presence at SIAM Conference

February 15, 2007

This year’s SIAM Conference on Computational Science and Engineering (CSE) featured a strong showing from CRD scientists, who spent a week in Costa Mesa, California this month to discuss topics that ranged from nanoscience simulations to scientific data management. SIAM is the Society for Industrial and Applied Mathematics. In all, 13 researchers from the division attended the week-long conference, which also ran concurrently with the SIAM Workshop on Combinatorial Scientific Computing. Read More »

February 2007 Staff Research Notes

February 15, 2007

Paxson Named ACM FellowVern Paxson, a researcher in CRD’s Distributed Systems Department, has been named a fellow of the Association for Computing Machinery (ACM). The fellowship is given to scientists who have made “outstanding technical and professional achievements in the field of information technology,” according to ACM. Paxson is probably best known for his original development work on Bro, the Lab’s intrusion detection system, which monitors incoming and outgoing traffic and… Read More »

CRD Takes Lead at DOE Cybersecurity Workshop

February 1, 2007

CRD scientists co-chaired and led discussions in a DOE Office of Science workshop last month that defined the research and development goals for cybersecurity in the global scientific community. The three-day workshop, sponsored by the Office of Advanced Scientific Computing Research and titled, “DOE Cybersecurity R&D Challenges for Open Science,” pooled knowledge and experiences from about 40 cybersecurity production personnel and cybersecurity researchers from across the DOE Office of… Read More »

BDMTC, JGI Announce IMG/M Upgrade

January 15, 2007

The DOE Joint Genome Institute (JGI), collaborating with CRD’s Biological Data Management and Technology Center (BDMTC), announced last month an upgrade of the metagenome data management and analysis system, IMG/M, on the anniversary of its launch. Developed by BDMTC’s data management and software engineers and scientists of JGI’s Genome Biology and Microbial Ecology Programs, IMG/M is a valuable asset for a growing community of biologists. Metagenomics refers to the genomic study of… Read More »