Team:USTC Software/WhatCooperation

Introduction

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

pConX₂+LuxR+pLux/Tet+GFP

Parts:

Reactions and ODE

A Simplified Model

We employed an ODE model. We defined the input to be AHL_out 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 AHL_in.

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 AHL_out 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 [http://partsregistry.org/Part:BBa_F2620:Experience/Endy/Data_analysis here] to the details.

Identification Results

With the help of USTC Wet Team, we succeeded to estimate the values of k₃, r_AHLin, C₁, C₂, C₃ and C₄. The simulation results as follows.

Parameters

k3=0.8; rAHL=0.001; C1=1.5*10^(-10); C2=1*10^(10); C3=8*10^(-7); C4=5.8*10^(11)

Simulation 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 AHL_out.