PLANNING AND LEADERSHIP FOR A BETTER WORLD
PLANNING AND LEADERSHIP FOR A BETTER WORLD
When you were in high school biology, you probably had to build models of cells using poster board, gummy worms and glue. Now, researchers have created a much more accurate model—a computerized version that accurately simulates cell behavior.
The cell models were created by a collaborative team of researchers from the Max Planck Institute of Biology in Germany and the University of Illinois in Champaign, Ill. To build the models, they used the latest powerful graphics processing unit (GPU) computing technology. GPU technology is the same imaging tool behind video games and projects like radiation reduction for cancer patients.
"This is the first time that we're modeling entire cells with the complete contents of the cellular cytoplasm represented," said University of Illinois postdoctoral researcher and lead author of the study Elijah Roberts in a statement. "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."
In the computer models of what are called "in silico cells," the simulation accurately replicates the interior behavior of a cell reacting to sugar in its environment.
Past research has already successfully modeled tiny individual components within a cell. For instance, Zaida Luthey-Schulten, the University of Illinois chemistry professor who led the research, had previously done modeling of individual molecules and groups of molecules.
Then in 2006, a group of researchers at Max Planck, led by Wolfgang Baumeister, successfully located each of a bacterium's ribosomes, the protein-building components of the cell.
With the help of Baumeister and his colleague Julio Ortiz, Luthey-Schulten and her team developed a three-dimensional model of a typical Escerichia coli (E. coli) cell. The "molecular crowding" shown by the model particularly surprised researchers—very little space remained empty in the cell.
"I think, like everybody else, my perception of the cell up until Wolfgang and Julio's 2006 article had always been that it's a pretty big sack of water where a lot of chemical reactions occur," Luthey-Schulten said in a statement. "But in fact there are a lot of obstacles in the cell, and that is going to affect how individual molecules move around and it's going to affect the reactions that occur."
With fluorescence experiments, studies of live cells can allow researchers to discover protein variations among a population of cells. But because the causes of such variations are so microscopic, they can be difficult to observe in live cells. Computer simulations allow researchers to accurately track every reaction.
The simulation of E. coli cells, for example, helped show that "bacterial cell architecture does indeed affect the reactions that occur within the cells," Luthey-Schulten said. Different strains of the bacteria reacted to sugar in different ways, a discovery that could not have been made without the computer simulation.
According to the researchers, the new simulation is a big leap toward an accurate model of an entire working cell, with its many complex structures and behaviors.
This research was supported by the Department of Energy Office of Science, the National Science Foundation and the Foundation Fourmentin-Guibert, with additional resources from the NSF through the TeraGrid and the National Center for Supercomputing Applications, and also by the CUDA Center of Excellence at Illinois.
The paper, "Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study," was published by PLoS Computational Biology and is available online.
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