PAGE 0 (Importance to Project)

Modeling plays a key role in our project and many other biological projects, due to the ability to change
parameters and see what changing these conditions would do to the overall system. In our project,
mathematical modeling allows us to obtain numerical values for each of the important processes that
take place. The two models created will allow our team to determine how diffusion will affect the
concentration of each bacteria in the biofilm. Modeling the concentration of nhaR and GFP for our
biofilm will give us a physical equation in which we can test scenarios that may not be able to be safely
replicated in a lab.

PAGE 1
For our project, diffusion plays an important role in how GFP is expressed in the biofilm. Due to the
complicated structure of mucosal biofilms, our model simplified the structure into a slab. This allows for
diffusion to be measured consistently throughout the biofilm.

PAGE 2
Our parameters for the diffusion model were length, diffusivity coefficient, and initial concentration. In
order to model the change in concentration, we used Fick’s Second law. Fick’s Second Law pertains to
changes in concentration with time and distance. The change in concentration at location x is given by
the difference in flux into and out of an element of a certain width.

Page 3
The plot shown is a percentage concentration of cation for a given depth of 10 x 10^6 nano-meters.
Each line on the plot represents the concentration at a different final time.

Page 4
The diffusion model was created to help more realistically model the primary model, a sodium biosensor
of a single cell. The model is currently a very simplified model, more research much be done in order to
add further variables, increasing the sophistication and accuracy of the model. Our model attempts to
model the concentration of GFP in the cell. Currently, we assume that nhaR operates as a repressor,
although current journals are unknown. we assume that the concentration of GFP is directly
proportional to the concentration of the binded repressor.
Page 5
The first plot shows an arbitrary amount of repressor in the cell at a certain time. When more
information is known about the amount of initial repressor in the cell, we can change the parameters to
better fit the model.

Page 6
The second plot shows the number of binded repressor in the cell. It is important to note that as
number of binded repressor increases, the amount of repressor decreases. Because we assumed that
the concentration of GFP is directly proportional to the concentration of binded repressor, the GFP
expression will be exactly the same as the plot shown. Repressor = Cation Responsive Protein.

What’s Next?
The next objectives in terms of modeling is to increase the accuracy of our sodium biosensor model,
combine the two models together, and use base splines in order to create a function using the data
points received for fluorescence of GFP. Determine how much we need to fine tune the sensor in order
to know when there is an overwhelming influx of sodium and whether the cell is performing its regular
operations.