The term “model” can refer to a number of different concepts depending on the context in which it is used. These vary from complex sets of mathematical equations to attractive, but often overally thin, people walking down runways. For our purposes though we are using the term to mean: An approach for abstracting a complex process such that aspects of the process can be explored for greater understanding.

For our modeling project we have chosen to explore the processes of protein mis-folding and inclusion body formation. These two processes are interrelated to each other and exploring them complements nicely with the wet lab part of our project.

The goals of the modeling project were to:

• Develop an understanding of the sequence of steps that occur as a proteins form inclusion bodies
• Investigate the factors impacting the formation of misfolded proteins and inclusion bodies
• Attempt to quantize the affects that different factors have on the likely hood of inclusion body formation
• Use the developed models to drive hypothesis to be investigated in future wet lab experiments

To achieve those goals two different models were developed. The first model uses MATLAB software to simulate the process of protein production. Qualitative and quantitative data about the protein production process were incorporated into this model to explore how different factors would affect the process. For the second model we have generated a visualization of the process of inclusion body formation.

More detailed information about each of the models can be found in their respective sections