Scientists open their eyes
to visualization's potential
(Page 3 of 4)
A simulation of an enzyme found in white rot digesting a million atoms of plant cellulose, for example, models a process that humans would like to recreate to make fuel from wood waste. (See the visualization "Cellobiohydrolase Action on Cellulose.")
Michael Crowley, senior scientist at the National Renewable Energy Laboratory in Golden, Colo., created the simulation in collaboration with Cornell and Pennsylvania State universities. Crowley is lead principal investigator for a SciDAC life sciences project and NREL is a partner in the BioEnergy Science Center (BESC) under DOE's Office of Biological and Environmental Research (BER).
"You don't see all the million atoms because you wouldn't be able to see anything," Crowley says. "But in the calculation it's all there."
The simulation takes into account the angles and distances of all the chemical bonds among atoms, along with physical forces that govern the reactions.
"For each atom there are many thousands of interactions with other atoms that have to be calculated," Crowley says. "You end up needing a lot of compute power for every single time step, and we need to take many millions of time steps to make any sense of what's happening."
Crowley doesn't yet know exactly how the enzyme cellulase breaks down plant cellulose. That's a goal of the simulation. "Once we have some ideas of the mechanisms based on the physics we have put into the model, we can make suggestions to the experimentalists &ndash 'Try changing this amino acid to this one.'"
Experimental mutations to the organism may either destroy its functionality or increase the rate of cellulose conversion into sugar, the feedstock for ethanol fuel. The former would challenge the model while the latter would validate it but either result would generate data to improve the model. "It's extremely exciting, and it's something that you can't get out in other ways," Crowley says.
