A Matter of Scale
University of Illinois at Urbana-Champaign
Brookhaven National Laboratory
Story by Alan S. Brown
For Ashlee Ford, it’s all about scale.
On one hand, Ford’s doctoral research involves events that occur on vastly different scales of time. Her cutting-edge computational techniques show how interactions measured in picoseconds — one-millionth of one-millionth of a second — determine events weeks and even months later.
On the other hand, Ford has experienced similar differences of scale in her personal life. She grew up in Snyder, Oklahoma, a town of 1,500 where her graduating class of 60 was the high school’s largest ever. It sits 100 miles southwest of Oklahoma City, surrounded by farmland in every direction.
Yet, in summer 2007 the chemical engineering doctoral student at the University of Illinois found herself in greater New York City. She was there to complete her DOE CSGF practicum at Brookhaven National Laboratory, located on Long Island.
Ford went there to work with James Davenport, whose research focuses on using Newton’s laws of motion and quantum mechanics to explain how molecules bond with one another. “I was not familiar with it at all,” Ford says.
Ford used the techniques to model how enzymes make sugars from cellulose, one of the substances that give plants their stiffness. The sugars can be used to make ethanol, making it possible to use woody materials like corn stalks and husks instead of grain for biofuel production.
It’s tricky, however. Cellulose doesn’t yield its sugars readily, making the process energy-intensive and expensive. That’s why numerous researchers are focusing on improving the enzymes’ performance.
At Brookhaven, Ford created molecular dynamics simulations of small glucose clusters representing cellulose. The models showed how the glucose interacted with molecules of benzene, which stood in for protein residues that play a role in enzyme-cellulose interaction. Other researchers have used molecular dynamics to study similar models, but for a span of only 150 picoseconds. Davenport and Ford wanted to increase the simulation’s sampling time to see if the system’s thermodynamic properties remained stable.