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

EUGENE, Ore. -- (Sept. 21, 2011) -- University of Oregon researchers have devised a mathematically rich analytic approach to account for often-missing thermodynamic and molecular parameters in molecular dynamic simulations.

The new approach, which returns atomistic-level data into the time frame of the macroscopic world, is detailed in a paper appearing online ahead of regular publication in the journal Physical Review E. The method is all about timing, says Marina G. Guenza, professor of theoretical physical chemistry, and may help reduce trial-and-error experimentation required in manufacturing when such information is missing.

Molecular dynamic simulations are indispensable tools -- a natural partner of experiments and theory -- that help scientists understand the properties of new materials and processes by providing a view at the resolution of atoms. Simulations expedite the development of new materials by showing how those with a specific atomistic structure behave in various conditions, for example when they are strained or frozen.

Simulations of polymers and biological systems have been used since the 1990s. That effort has focused on the short-time motion of macromolecules described in atomistic detail, which, in addition to plastics and glasses, also applies to DNA and proteins, Guenza said.

However, modelers remove critical pieces of information, such as atom-level activity, to scale back simulations to cover only generic components and access longer times in an accessible simulation run. This technique provides helpful but incomplete data about behavioral responses, Guenza said. Simulations in which atomistic information is withheld are called coarse-grained models.

"These are big molecules," she said. "They move slowly. It is difficult to set up a simulation where the atomistic definition is included and still be able to see things happen on the long time scale, which can be really important.
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Contact: Jim Barlow
jebarlow@uoregon.edu
541-346-3481
University of Oregon
Source:Eurekalert  

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