Using Supercomputers For Cellulosic Ethanol Research

LiveScience:

In a series of linked projects, researchers used the National Science Foundation-supported "Ranger" supercomputer at the Texas Advanced Computing Center and Energy Laboratory's Red Mesa system to simulate the world of enzymes. They explored enzymes from the prodigiously plant-digesting fungus, Trichoderma reesei, and the cellulose-eating bacteria, Clostridium thermocellum. Both of these organisms are effective at converting biomass to energy, though they use different strategies.

"Nature cleverly designed machinery for single-cell organisms to locate cellulose, then secrete large enzyme complexes that hold the cells near biomass while the enzymes degrade it," Beckham said.

The bacteria forms scaffolds for its enzymes, which work together to break apart the plant. The fungal enzymes, on the other hand, are not tethered to a large complex, but act independently.

It isn't clear how the enzyme scaffolds form, so the researchers created a computational model of the active molecules and set them into motion in a virtual environment. Contrary to expectations, the larger, slower-moving enzymes lingered near the scaffold longer, allowing them to bind to the frame more frequently; the smaller ones moved faster and more freely through the solution, but bound less often.

The results of the study, led by National Renewable Energy Laboratory researchers Yannick Bomble and Mike Crowley, were reported in the Journal of Biological Chemistry in February 2011. The insights are being used in the creation of designer enzymes to make biomass conversion faster, more efficient and less expensive.

It would seem like cow stomachs would provide some answers to questions of converting cellulose to sugar.