Team:ETH Zurich/modeling/int

From 2014.igem.org

(Difference between revisions)
(Characterization: KSABxb1)
Line 131: Line 131:
[[File:ETH Zurich Bonnet S4.jpg|center|800px|thumb|Transfer function from aTc to Bxb1. The experimental data corresponds to the points. They fitted this data with their own model. Supplementary figure S4 of Bonnet's paper ''Amplifying Genetic Logic Gates'']]
[[File:ETH Zurich Bonnet S4.jpg|center|800px|thumb|Transfer function from aTc to Bxb1. The experimental data corresponds to the points. They fitted this data with their own model. Supplementary figure S4 of Bonnet's paper ''Amplifying Genetic Logic Gates'']]
-
To use their experimental data, we have to model their induction mechanism using aTc. We use a simplify version of it proposed by the [https://2013.igem.org/Team:UCSF/Modeling 2013 iGEM team UCSF]. They modeled the induction with aTc as a leaky Hill function. We then obtain the following set of differential equations:
+
To use their experimental data, we have to model their induction mechanism using aTc. We use a simplify version of it proposed by the [https://2013.igem.org/Team:UCSF 2013 iGEM team UCSF]. They modeled the induction with aTc as a leaky Hill function. In the following table are the set of parameters introduced to model induction.
-
\begin{align*}
+
{| class="wikitable"
-
\frac{d[Bxb1]}{dt} &= a_{F2}*(A_L + B_L * \frac{[aTc]^n}{[aTc]^n+K_L^n})- 2 k_{DBxb1}*[Bxb1]^2 + 2k_{-DBxb1}*[DBxb1] - d_{I}*[Bxb1] \\
+
|-
-
\frac{d[DBxb1]}{dt} &= k_{DBxb1}*[Bxb1]^2 - k_{-DBxb1}*[DBxb1] - k_{SABxb1}*[DBxb1]*[SI_{Bxb1}] + k_{-SABxb1}*[SA_{Bxb1}] - d_J*[DBxb1] \\
+
!Name
 +
!Value
 +
!Description
 +
!Reference
 +
|-
 +
|A<sub>L</sub>
 +
|8.904 mRNA min<sup>-1</sup>
 +
|Basal expression level of tet promoter
 +
|[[https://2013.igem.org/Team:UCSF/Modeling 2013 iGEM team UCSF]]
 +
|-
 +
|B<sub>L</sub>
 +
|443.7 mRNA min<sup>-1</sup>
 +
|Maximal expresion level of tet promoter
 +
|[[https://2013.igem.org/Team:UCSF/Modeling 2013 iGEM team UCSF]]
 +
|-
 +
|n
 +
|2.551 (no units)
 +
|Hill exponent
 +
|[[https://2013.igem.org/Team:UCSF/Modeling 2013 iGEM team UCSF]]
 +
|-
 +
|K<sub>m</sub>
 +
|11.45 µmoles
 +
|Half-maximal effective concentration of aTc
 +
|[[https://2013.igem.org/Team:UCSF/Modeling 2013 iGEM team UCSF]]
 +
|-
 +
|k<sub>mRNA<sub>Bxb1</sub></sub>
 +
|Unknown
 +
|Translation rate of Bxb1
 +
|
 +
|}
 +
 
 +
We obtain the following set of differential equations:
 +
 
 +
$$\begin{align*}
 +
\frac{d[Bxb1]}{dt} &= a_{}*(A_L + B_L * \frac{[aTc]^n}{[aTc]^n+K_L^n})- 2 k_{DBxb1}*[Bxb1]^2 + 2k_{-DBxb1}*[DBxb1] - d_{Bxb1}*[Bxb1] \\
 +
\frac{d[DBxb1]}{dt} &= k_{DBxb1}*[Bxb1]^2 - k_{-DBxb1}*[DBxb1] - k_{SABxb1}*[DBxb1]*[SI_{Bxb1}] + k_{-SABxb1}*[SA_{Bxb1}] - d_{DBxb1}*[DBxb1] \\
\frac{d[SA_{Bxb1}]}{dt} &= k_{SABxb1}*[DBxb1]*[SI_{Bxb1}] - k_{-SABxb1}*[SA_{Bxb1}]
\frac{d[SA_{Bxb1}]}{dt} &= k_{SABxb1}*[DBxb1]*[SI_{Bxb1}] - k_{-SABxb1}*[SA_{Bxb1}]
-
\end{align*}
+
\end{align*}$$
=== Assumptions ===
=== Assumptions ===
 +
 +
Line 150: Line 187:
<html><article id="Parameters2"></html>
<html><article id="Parameters2"></html>
 +
== Characterization ==
== Characterization ==

Revision as of 10:51, 12 October 2014

iGEM ETH Zurich 2014