The most detailed computer model of damaged DNA to date shows that banged up DNA becomes flexible. Further, this flexibility explains how the body's enzymes recognize and fix damaged DNA. The model surveyed a DNA fragment made up of 350 atoms, a large complex simulated on the supercomputer at DOE's W.R. Wiley Environmental Molecular Sciences Laboratory on the Pacific Northwest National Laboratory campus. In the model, damage triggered a reorganization of the sugar-phosphate in the DNA's backbone, causing the DNA to thin and become bendable. It appears to be this difference in flexibility between damaged and intact DNA that the repair enzymes zero in on. The results were reported recently at the American Chemical Society national meeting in Philadelphia.

[Bill Cannon, 509/375-3732;
cannon@pnl.gov]

BaBar produces penguin modes

Asymmetry in “penguin modes” is one of the more intriguing results from the incredible 64 papers the BaBar collaboration presented at the International Conference on High Energy Physics in Beijing this summer. The BaBar experiment at DOE's Stanford Linear Accelerator Center is pursuing hints that penguin modes—a rare class of decay from B mesons to other particles—reveal new physics beyond the Standard Model, perhaps supersymmetry. If the Standard Model is correct, penguin modes should have the exact same amount of asymmetry as in another, well-studied decay process. But experimental data from BaBar and Belle in Japan show the penguin modes appear to have less asymmetry. To be statistically convincing, BaBar will collect two more years of data, starting with a new run Oct. 15.

[Neil Calder, 650/926-8707;
neil.calder@slac.stanford.edu]

Trimming water needs, adding solar power sources

FRUGAL FORAGE — Ron Pate of Sandia National Laboratories checks a tray of forage in a greenhouse just north of the U.S.-Mexico border in Santa Teresa, New Mexico.

A method that uses roughly just one percent of the fresh water customarily needed to grow forage for livestock may leave much more water available for human consumption, as well as help avert future wars. As a byproduct, the method being overseen by DOE's Sandia National Laboratories at a greenhouse barely a stone's throw from the US-Mexican border also may add formerly untapped solar energy to the electrical grid. Peter Davies, director of Sandia's Geoscience and Environment Center, says, “A large proportion of freshwater usage around the world is agricultural. The ability to reduce the amount of water needed for it and thus lessen the possibility of international conflict is extremely important to the security of the United States and the world.”

[Howard Kercheval, 505/844-7842;
hckerch@sandia.gov]

Light Reading

Proteins pass messages to other proteins much like fly-fishermen flicker their lines against water. The repeated weak slapping of protein surfaces against each other is the critical first step in a chain of events that rule all subsequent cellular behavior. But this vital exchange between single molecules has defied direct observation because that line-flicking and message-passing happen randomly at such a small scale. Now, a technique called single-molecule photon stamping spectroscopy, developed at DOE's Pacific Northwest National Laboratory, reveals real-time interactions of single proteins and supports the fly-fishing theory of protein communication. Each peak seen here (image above) depicts a fluorescing protein interacting with another protein. An analysis of the intensity, duration and other physical properties of the photon peaks provides a sequence of subtle and sublime communication between cellular proteins.

[Bill Cannon, 509/375-3732;
cannon@pnl.gov]

ORNL's Jennifer Ryan: Developing Numerical Methods for Real World Applications

ORNL's Jennifer K. Ryan

Developing numerical methods to solve real-world problems is the forte of Alston S. Householder Fellow Jennifer K. Ryan, the latest in a line of outstanding mathematics researchers at DOE's Oak Ridge National Laboratory.

Ryan, a native of Houston, Texas, is an applied mathematician working on numerical algorithms. Her primary research focuses on developing accurate numerical solutions to physical and chemical models represented by partial differential equations.

Ryan's current research is on accuracy enhancement techniques and higher order numerical methods such as the discontinuous Galerkin method. Using those methods, she has investigated real-world issues in areas such as computational fluid dynamics, computational chemistry, aero-acoustics, and climate modeling.

She previously held a graduate fellowship at NASA-Langley. At ORNL, she collaborates with a number of researchers mostly in the area of computational chemistry. Recently, she completed three scientific papers where she is the lead author.

Originally destined to be an engineer, Ryan's interest in math emerged with higher level math courses and a computer programming class during her last years at Rutgers University . She went on to receive her master's degree from New York University 's Courant Institute for Mathematical Sciences and her doctorate from the Division of Applied Mathematics at Brown University , where she earned the Stella Dafermos Award for excellence in graduate studies.

The Householder Fellowship is named for a renowned pioneer in the field of linear algebra who was also the founder of what is now the Computer Science and Mathematics Division at ORNL. Ryan is well aware of the reputation for excellence that her fellowship represents.

"Alston Householder made many important contributions to the field of Linear Algebra. As an applied mathematician I am well aware of his legacy," Ryan says. "Coming to ORNL on this fellowship is a privilege."

Submitted by DOE's Oak Ridge National Laboratory