Overview

The single cell model is a mathematical model of the species involved in our synthetic system of a single SmoColi cell. The change of the species concentrations in time is given by non-linear ordinary differential equations (ODEs), most of which follow Hill kinetics. The parameters we used in the model are derived from literature supported by experimental evidence. Some of the parameters are slightly adjusted to meet our own experimental approaches. The single cell model was simulated using numerical Matlab solvers.

Our model has several important strengths which are:

1. MODULARITY

Our system consists of three modules:

Sensor Module
Band Detector Module
Filter (Alarm) Module

The modules are almost independent, related between each other just by a single species. Most of the parameter values used within the modules do not depend on the other modules as well. The independence of the three modules enables their reusage in other systems. So if we want for example to add another sensor module to the existing band detector, the only thing we should change in the band detector is few parameter values for the linker species. This important property allows us to use the band detector + alarm with different sensors, making our synthetic cells a biological quantifiers of a range of substances.

2. ROBUSTNESS

We did a robustness analysis for our system and found out that it is indeed robust. This means that even upon parameter variation, the GFP band do not dissapear, just gets shifted or varies in its thickness. Each of our species eventually end up in a single stable steady states, there are no bufurcations nor oscillations in our system. So, we can freely vary the parameters found in literature to meet our experimental approaches and we can be sure that our system will still show the same global behaviour.

3. CONSISTENCY WITH BIOLOGY (will have to make sure this is correct)