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Catching molecular motion at just the right time
Date:9/21/2011

Coarse-graining allows one to simulate macromolecules for longer time, but, because some information is eliminated, the motion measured is unrealistically fast."

Entropy -- a loss of thermodynamic energy -- and surface friction are lost in these simulations, she said. Simulations at the atomistic level depict motion occurring in femtoseconds. (A femtosecond is a millionth of a nanosecond; a nanosecond, a billionth of a second.)

To understand what happens in macroscopic systems, you have to look at movement over longer periods of time -- over seconds, says Ivan Lyubimov, a UO doctoral student in chemistry and lead author. "When you try to simulate a second's worth of information at the atomistic level, with all the details included, it might take one or two years for the computer to run the simulation, and you'd still have errors due to numerical algorithms," he said.

Guenza and Lyubimov looked at simulations where thousands of macromolecules of polyethelene are represented as interacting soft particle, i.e. a coarse-grained model, and applied an original theory that refocuses the information missing in the simulations.

Guenza -- a member of the UO's Institute of Theoretical Science, Materials Science Institute and Institute of Molecular Biology and Lyubimov first detailed the basics of their theoretical formula in 2010 in the Journal of Chemical Physics.

Their "first-principle" approach looks at the loss of energy, due to the change in entropy, caused by the coarse-graining of the molecule in simulations. Coarse-graining also affects the surface of molecules in simulation, so the formalism accounts for the loss of friction as well.

"We were able to show that if you run your simulation with less detail, we can correct for these factors, and you'll produce the correct motion -- the dynamics -- of the real system," Guenza said. "We have done a lot of tests with different experiments and simulations, and our
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Contact: Jim Barlow
jebarlow@uoregon.edu
541-346-3481
University of Oregon
Source:Eurekalert  

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