IGEM:IMPERIAL/2007/Projects/Cell by date/Modelling

Cell by Date: Modelling

• Introduction
• Specifications
• Design
• Modelling
• Implementation
• Testing/Validation
• Notes
• References

Summary:

In the design section we outlined which variants of Cell By Date we would like to implement in different Chassis, as shown in the table below.

Chassis	Level 1	Level 2	Level 3
E.coli	X
In-Vitro	X	X	X
In-Veso	X	X	X

In this section we modify the variants of Cell by Date so that they can be implemented advantageously in each chassis. We also model these modified variants in order to understand the behaviour we expect or to tune the system to realise a particular behaviour. This leads us to write up experiments to determine if our system behaves the way our models predict.

Ant - Think about using Arrhenius Equation to model temperature response of system

Overview of Modelling

Overall our modelling for this project will take the form of

[math]\displaystyle{ \frac{dFP}{dt}=k_{FP}(t)-d_{FP}[GFP] }[/math]

1. kFP : Function of Temperature. k is based on the promoter used as promoters take time to turn on.
2. dFP : Function of System. May be considered to be a function of temperature as proteins may degrade at high temperatures.

With this in mind we will look at two graphs of k vs. time (special pt is kON.) and [FP] vs. time key point is [FP]ss

• Our major problem at the moment is estimating the errosrs involved with our fluorometer and Pipette we hope to address these through calibration curves.

For each experiment we will do the following

1. Calibration curve to determine error in Fluorometer
2. Decay Experiment @ Varying temperatures
3. Plug Together to find transient response and k
4. Find these parameters as a function of Temperature

Construct Specific modelling

Picture5

Apply the above general equation to this specific construct.

[math]\displaystyle{ \frac{d[GFP]}{dt}=k_{Ptet}(t)-d_{GFP}[GFP] }[/math]

1. calibration curve to determine error in Fluorometer - we are trying to get this infromation from BertholdTech
2. Decay Experiment at varying temperatues:
   1. This is to determine [math]\displaystyle{ d_{GFP} }[/math]

The Fluroresence of a pure sample of GFP kept at 'constant temperature' will be measured at time intervals. We expect the fluroesence to decay exponentially with time. We plan to determine the decay constant in the following way.

1. Having found [math]\displaystyle{ d_{GFP} }[/math] we look at transient respone of construct at several constant temperatuers to find k
2. Find k & d as functions of temperature