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How computers push on the molecules they simulate
Date:1/3/2013

Because modern computers have to depict the real world with digital representations of numbers instead of physical analogues, to simulate the continuous passage of time they have to digitize time into small slices. This kind of simulation is essential in disciplines from medical and biological research, to new materials, to fundamental considerations of quantum mechanics, and the fact that it inevitably introduces errors is an ongoing problem for scientists.

Scientists at the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) have now identified and characterized the source of tenacious errors and come up with a way to separate the realistic aspects of a simulation from the artifacts of the computer method. The research was done by David Sivak and his advisor Gavin Crooks in Berkeley Lab's Physical Biosciences Division and John Chodera, a colleague at the California Institute of Quantitative Biosciences (QB3) at the University of California at Berkeley. The three report their results in Physical Review X.

"Our group uses a theoretical method called nonequilibrium statistical mechanics to study molecular machines, the protein complexes essential to processes like photosynthesis and DNA repair," says Sivak. "But when we applied common algorithms to model the behavior in biological molecules, we found persistent, significant errors in the simulation results."

Systems in equilibrium are relatively easy to simulate, but natural systems are often driven far from equilibrium by absorbing light, burning energy-dense chemical fuel, or other driving forces. Sivak, who recently joined the University of California at San Francisco as a Systems Biology Fellow, describes nonequilibrium statistical mechanics as "a way of understanding situations where conditions change abruptly and the system has to play catch-up," a kind of problem in which there are few exact analytical results.

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Contact: Paul Preuss
paul_preuss@lbl.gov
510-486-6249
DOE/Lawrence Berkeley National Laboratory
Source:Eurekalert  

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