I have been fascinated by two tools simulating cellular progresses. Well, I should have said that one with explicit ability and the other with potential. They are MCell and Matlab. I’ll talk about Matlab later and am concetrating on one application of MCell, which has been published in 2005.

**Division accuracy in a stochastic model of Min oscillations in Escherichia coli**

Rex Kerr, Herbert Levine, Terrence Sejnowski, and Wouter-Jan Rappel

PNAS 103, 347-352, 2006 [link]

The observed biological fact is that E. coli, the rod-shaped bacterium reproduces in a characteristic way. The cell elongates along its long axis and duplicate its genomes, then divides symmetrically into two daughter cells. The dividing plane in wild-type E.coli is at 0.5 with 0.013 deviation of the distance along the long axis of the cell. As stated in the paper, there are numbers of approaching to explain the phenomena from deterministic and stochastic models. The authors introduce a stochastic model starting with the reaction-diffusion scheme.

It is known that in simulations, essentially there are three steps, the first step is to construct models, which includes choosing parameters, building targets and their inner and inter relations, and algorithm to simulate the event. The second step is initializing and iterating the simulation process by implement the algorithm. The last step is then to analyze the simulation results, nowadays, it means we need show the results in a very attractive visual way.

They identified the parameters–proteins involved in the cell division process, the key players are FtsZ protein which forms a ring and mechanically implement the division and determine the division site. In the meantime, the factor which inhibit the formation of the FtsZ ring is the presence of the nucleoids, which is the precursor of the formation of two daughter cells. The Min proteins are also actively involved, MinC inhibits the formation of the FtsZ ring while MinD functions as a recruiter of MinC. The concentration of MinD is higher at then ends of the cell than at the center, and MinD oscillates from end to end of the cell. MinE is required for the oscillation of MinD.

The algorithm here is a series of chemical reactions. The system is then consists of a rode-shape container, lots of proteins (5400 proteins), their relation is quantized by the chemical reactions. And the algorithm to simulate the dynamic process is MCell. Using this stochastic model, the authors were able to simulate the precise position of the cell division.

MCell could also be used to simulate other cellular dynamics, such as signal transduction, cytoskeletal motion, etc. Very impressive tool.