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We help USTC Wet Team identify the kinetic parameters in pConX2+LuxR+pLux/Tet+GFP device. The completion of this model are a result of collaboration. With the permission from both teams, we share the source code of this description page together
Reactions and ODE
A Simplified Model
We employed an ODE model. We defined the input to be AHLout the and the output to be the synthesis rate of mature GFP. In this system,we assumed the concentration of the LuxR was constant.
To simplify the model, the (Recation S2-4), (Recation S2-5) and (Recation S2-6) were considered to be able to get balance in a very short time.
From above equations, we can the change of PoPS respond to the AHLin.
For this system, the value of parameter d, 0.00847, could be estimated based on the measurement of the OD. For instance, when the concentration of AHLout was zero, the value of d was 0.00368 per minute. The values of 4.8E-3 per sec for rmG, 1.8E-3 per sec for a and 0.4 per sec for pG were got from the experiment conducted by Barry Canton and Anna Labno in 2004, click here to the details.
With the help of USTC Wet Team, we succeeded to estimate the values of k3, rAHLin, C1, C2, C3 and C4. The simulation results as follows.
k3=0.8; rAHL=0.001; C1=1.5*10^(-10); C2=1*10^(10); C3=8*10^(-7); C4=5.8*10^(11)
Identification Results Comparison With Raw Data
In this picture, the dots were the measuring poingts in our system and the curves were the corresponding simulations to a particular concentration of AHLout.
In picture below, the dots were the measuring poingts in our system and the surface was the corresponding simulation.