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Researchers make the leap to whole-cell simulations
Date:3/30/2011

CHAMPAIGN, lll. Researchers have built a computer model of the crowded interior of a bacterial cell that in a test of its response to sugar in its environment accurately simulates the behavior of living cells.

The new "in silico cells" are the result of a collaboration between experimental scientists at the Max Planck Institute of Biology in Germany and theoretical scientists at the University of Illinois using the newest GPU (graphics processing unit) computing technology.

Their study appears in the journal PLoS Computational Biology.

"This is the first time that we're modeling entire cells with the complete contents of the cellular cytoplasm represented," said Illinois postdoctoral researcher and lead author Elijah Roberts. "We're looking at the influence of the whole cellular architecture instead of modeling just a portion of the cell, as people have done previously."

University of Illinois chemistry professor Zaida Luthey-Schulten, who led the research, had done molecular dynamics simulations of individual molecules or groups of molecules involved in information processing, but never of a system as large and complex as the interior of an entire cell.

Then in 2006 she saw a paper by Wolfgang Baumeister and his colleagues at Max Planck that located every one of a bacterium's ribosomes, its protein-building machines, inside the cell.

That image spurred Luthey-Schulten to think about modeling an entire cell, and she asked Baumeister and his colleague Julio Ortiz if they would repeat the study in Escherichia coli (E. coli), a bacterium that has been the subject of numerous molecular studies.

Once the new ribosome data were available, Roberts looked to ot
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Contact: Diana Yates, Life Sciences Editor
diya@illinois.edu
217-333-5802
University of Illinois at Urbana-Champaign
Source:Eurekalert  

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