Xianfeng Song Lin Wang Sima Setayeshgar

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Presentation transcript:

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

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

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

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

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

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

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

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

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

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