1. Modeling Nisin-Induced Bacterial Fluorescence Key properties of the system –Certain types of bacteria are sensitive to nisin (peptide) –High levels of nisin induce cell death –We can engineer the bacteria to fluoresce (produce GFP) for intermediate levels of nisin 1 Nisin source

2. Modeling Nisin-Induced Bacterial Fluorescence Experimental setup –We can grow a population of nisin sensitive bacteria in a petri dish –We then place a chemical mask (high nisin concenration) on top of the cell layer –The nisin diffuses down to the cells and causes fluorescence 2

3. Modeling Nisin-Induced Bacterial Fluorescence Modeling diffusion on a computer –Diffusion Molecules are in constant motion, and they move in all directions The constant motion tends to eliminate areas of high/low concentration (think about how you can smell someone cooking in a different room – gas molecules can diffuse freely throughout your house) –Computer Model We can model diffusion on a computer by simulating the movement of each molecule We model space as a grid of points Each molecule can move to an adjacent point at each time step with an equal probability We also incorporate the degradation of molecules by decreasing the total number at each time step 3

4. Modeling Nisin-Induced Bacterial Fluorescence Modeling fluorescence on a computer –We model our petri dish and cell layer as a 3-dimensional grid –The top layer of the dish has a high initial nisin concentration in some specific shape –We then simulate diffusion of the nisin down to the cell layer –The cell layer then fluoresces for a certain amount of nisin reaching the bottom layer If the nisin concentration is above a certain threshold value, the cells do not fluoresce (because of cell death) If the nisin concentration is below a certain threshold value, the cells are not stimulated to fluoresce 4

5. Modeling Nisin-Induced Bacterial Fluorescence 5 Diffusion Top View – Initial Setup Indicator Layer