1. Xianfeng Song Lin Wang Sima Setayeshgar
Computational Investigation of Chemotaxis and Surface Motility in Biofilm Monolayer Formation
Xianfeng Song
Lin Wang
Sima Setayeshgar

2. Modeling Framework: Chemotaxis
From experiment [2]:
Realistic, stochastic description of chemotaxis network in E. coli (adapted from StochSim [1])
Reactions treated as collisions between biomolecules
Experimentally-based rates, protein copy numbers
Description of flagellar CCW/CW response (and resulting running/tumbling motion) in good agreement with experiments (adapted from AgentCell[2])
Based on simple CheY-P thresholding
We are currently improving upon this …
Our results:
[1] C. J. Morton-Firth, T. S. Shimizu and D. Bray, J. Mol. Biol. (1999).
[2] T. Emonet, et al. Bioinformatics (2005).
Friday May 18, 2007
Biofilm Group Meeting

3. Modeling Framework: Chemoattractant Diffusion
Diffusion of chemoattractant with cells as sources
r: rate of chemoattractant secretion
(molecules/time)
Solve using finite difference scheme on discrete grid
Distribute cell source term among neighboring grid points
Alternate updating cell positions and chemoattractant field at each time step
Friday May 18, 2007
Biofilm Group Meeting

4. Modeling Framework: Surface Motility
Surface-adhered cells continue to exhibit chemotactic response in two dimensions
Currently neglecting rotational Brownian motion for motion on the surface (this is included for three dimensional motion!)
New run direction following tumble randomly selected (0, 2) (for three-dimensional motion, new run direction selected within cone about old run direction, consistent with experiments)
Friday May 18, 2007
Biofilm Group Meeting

5. Preliminary Results No attractant Friday May 18, 2007
Biofilm Group Meeting

6. Preliminary Results (cont’d)
Chemoattractant secretion by adherent cells (with surface motility): Dynamics on surface
Friday May 18, 2007
Biofilm Group Meeting

7. Preliminary Results (cont’d)
Chemoattractant secretion by adherent cells (with surface motility): Dynamics in bulk
Friday May 18, 2007
Biofilm Group Meeting

8. Preliminary Results (cont’d)
Single cell trajectory
Friday May 18, 2007
Biofilm Group Meeting

9. Computational limitations to be resolved …
Increase system size (eliminate boundary effects)
Increase cell number (improve statistics)
Friday May 18, 2007
Biofilm Group Meeting

10. Future Systematic Investigations
Quantify clustering (beyond “eye-balling”) (for example, using 2D FFT):
No clusters, small versus large clusters
Role of governing biophysical parameters
Rate of chemoattractant secretion (by surface-attached cells, all cells?)
Probability of attachment (to surface, to other cells)
Chemoattractant diffusion constant
Cell speed on surface, in bulk
Role of stochastic versus deterministic description of chemotaxis signal transduction
Friday May 18, 2007
Biofilm Group Meeting