( is the cheapest and most abundant plan...)Meeting the ethanol challenge: Scientists use supercomputer to target cellulose bottleneck

"Our simulations have given us a better understanding of the interactions between the enzyme complex and cellulose at the molecular level -- the computer model showed us how the binding portion of this enzyme changes shape, which hadn't been anticipated by the scientific community," said first author Mark Nimlos, a Senior Scientist at NREL. "These results are important because they can provide crucial guidance as scientists formulate selective experiments to modify the enzyme complex for improved efficiency."

What the scientists found in their simulations ?a "virtual microscope" that let them zoom in on previously invisible details -- is that initially the binding part of the enzyme moves freely and randomly across the cellulose surface, searching for a broken cellulose chain. When it encounters an available chain, the cellulose itself seems to prompt a change in the shape of the enzyme complex so that it can straddle the broken end of the cellulose chain. This gives the enzyme a crucial foothold to begin the process of digesting or "unzipping" the cellulose into sugar molecules.

To the scientists, the simulation is like a stop-motion film of a baseball pitcher throwing a curveball. In real-life the process occurs far too quickly to evaluate visually, but by using the supercomputer simulations to break the throw down into a step-by-step process, the scientists can see the precise details of the role of velocity, trajectory, movement, and arm angle. To undertake the large-scale simulations, the researchers used the CHARMM (Chemistry at HARvard Molecular Mechanics) suite of modeling software.

According to the researchers, an accurate understanding of the key molecular events required the simulations to run for some six million time steps over 12 nanoseconds (a nanosecond is one billionth
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Source:University of California - San Diego