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Modeling

  Introduction

  E.casso uses the communication between cells made available by quorum sensing. Quorum diffuses away from one cell to the other. Because we wanted to find out how the quorums produced by Brush E.coli diffuse in our model, we applied the reaction-diffusion system to our model and analyzed the distribution and propagation of quorums. This section investigates how the quorums diffuse from one cell to the other which will provide crucial data for our final simulation.

  Objectives

  Answer the following questions,
- How fast does quorum diffuse into adjacent E. coli as rapidly as we predicted?
- How does the produced quorum diffuse with respect to time and space?
- How much quorum does the source E. coli ultimately transfer to neighboring E. coli?

  Modeling Approach

  Fig 1 | (a) Approximation of the dimensions of E.coli as a square having equal area (b) Schematic representation of E.coli distribution model on a grid

According to the statistics on E. coli ^1, the shape of E.coli is oval with 200nm minor axis and 2um major axis. For simulating our random diffusion system in E.casso, we simply the E.coli shape as square having equal area with the area of oval. (Fig 1a)

Based on this calculation, we can assume a two dimensional distribution model in which E.colis are distributed on a grid that consists of squares of side 1.1 micrometer. (Fig 1b) In each square, there may exist a brush E.coli, a paint E.coli, or nothing.

According to the statistics on E. coli ^1, the speed of a small molecule in the cytoplasm is 50 nanometers per millisecond. Also, all molecules move by random walk during diffusion. Using Python, we ran a simulation on the random walk of a quorum molecule. It was assumed that each step takes 0.2 milliseconds. [python code]