A joint release by the University of Chicago and Argonne National Laboratory (managed by the UC) explains how a simulator will help to study the relationship between intracellular biochemical processes and behavior of individual E. Coli bacteria:
The simulation, called AgentCell, has possible applications in cancer research, drug development and combating bioterrorism. Other simulations of biological systems are limited to the molecular level, the single-cell level or the level of bacterial populations. AgentCell can simultaneously simulate activity on all three scales, something its creators believe no other software can do.
“With AgentCell we can simulate the behavior of entire populations of cells as they sense their environment, respond to stimuli and move in a three-dimensional world,” said Thierry Emonet, a Research Scientist in Philippe Cluzel’s laboratory at the University of Chicago’s Institute for Biophysical Dynamics.
Emonet and his colleagues have verified the accuracy of AgentCell in biological experiments. AgentCell now enables scientists rapidly to run test experiments on the computer, saving them valuable time in the laboratory later…
AgentCell will be used to tackle a major goal in single-cell biology today: to document the connection between internal biochemical fluctuations and cellular behavior. “The belief is that these fluctuations are going to be reflected in the behavior of the cell as shown experimentally by John Spudich and Daniel Koshland in 1976,” Emonet said. They may even reveal why cells sometimes act as individuals and sometimes as part of a community…
Each digital cell in AgentCell is a virtual Escherichia coli, a single-celled bacterium, which is equipped with all the virtual components necessary to search for food. These digital E. coli contain their own chemotaxis system, which transmits the biochemical signals responsible for cellular locomotion. They also have flagella, the whiplike appendages that cells use for propulsion, and the motors to drive them.
Emonet and his associates have designed their digital bacterial system in modules, so that additional components may be added later.
What’s more is that the AgentCell computer code is going to be an open source project, and available for download right here.
