Team:EPF-Lausanne/ODEmodeling

The model

The simulation of the expression of the RFP protein activated by the lovTAP in the Read Out 2 circuit was obtained by the following model:

1. LacI --> LovTAP

2. LovTAP --> LovTAP* (activated form of LovTAP due to a light-induced conformational change)

3. lovTAP* --> TetR

4. TetR --> RFP

5. RFP --> RFP* (activated, fluorescent)

Where:

• L is the concentration of lovTAP [um]

• L* is the concentration of the activated lovTAP (all lovTAP molecules become activated when exposed to light stimulation) [um]

• T is the concentration of TetR [um]

• R is the concentration of RFP [um]

• R* is the concentration of activated RFP [um]

• is the function of light exposure

• is the basal expression of the given promoter

• K is the affinity of the given repressor for its target promoter [um]

• n is the cooperativity coefficient of the Hill function

• is the molecule degradation rate [min -1]

• is the dilution rate [min -1]

Parameters values

The values used for these parameters are listed below:

• L = 7 [um]

• = 0.05 for TetR and 0.3 for RFP

• K = 7 [um] for L*, 7 [um] for TetR and 7 [um] for RFP [um]

• n = 2 for L, 2 for TetR and 2 for RFP

• = 0.069 [min -1] for LovTAP, 0.069 [min -1] for TetR and 0.012 [min -1] for RFP

• = log(2)/20, since a division occurs every 20 min for E. Coli