Team:Paris/Analysis/Construction2

From 2008.igem.org

(Difference between revisions)
(→Model Construction)
(→Model Construction)
Line 1: Line 1:
== Model Construction ==
== Model Construction ==
-
description
+
why use a chemostat
 +
 
 +
which model of chemostat we choose
 +
 
 +
 
equations
equations
 +
 +
d[c]/dt=alpha_cell*[c]*(c_max-[c])/c_max-(D_renewal+death)*[c]
 +
d[LasI]/dt=beta_FlhDC*theta_FlhDC^n_FlhDC/(theta_FlhDC^n_FlhDC+[TetR]^n_FlhDC)-gamma*[LasI]
 +
d[TetR]/dt=beta_TetR*[HSL]^n_TetR/(theta_TetR^n_TetR+[HSL]^n_TetR)-gamma*[TetR]
 +
d[HSL::ext]/dt=eta*v_cell*[c]*([HSL]-[HSL::ext])-(D_renewal+gamma_HSLext)*[HSL::ext]
 +
d[HSL]/dt=beta_HSL*[LasI]+eta*[HSL::ext]-(gamma+gamma_HSLint+eta)*[HSL]
parameters
parameters
Line 61: Line 71:
|Source  
|Source  
|- style="background: #dddddd;"|     
|- style="background: #dddddd;"|     
-
| ! rowspan="5" style="background: #ffffff;" | figure / equations of Quorum Sensing
+
| ! rowspan="6" style="background: #ffffff;" | figure / equations of Quorum Sensing
-
|style="background: #D4E2EF;" | α<sub>cell</sub>
+
| style="background: #D4E2EF;" |γ<sub>HSL</sub>  
-
|style="background: #dddddd;"| Growth rate
+
| style="background: #dddddd;"|Degradation rate
-
| style="background: #dddddd;"|0.0198
+
| style="background: #dddddd;"|0.0053
-
| style="background: #dddddd;"|1
+
| style="background: #dddddd;"|0.2690
-
|style="background: #dddddd;"|min<sup>-1</sup>
+
| style="background: #dddddd;"|min<sup>-1</sup>
-
|style="background: #dddddd;"| [[Team:Paris/Modeling/BOB#Remarks|wet-lab]]  
+
| style="background: #dddddd;"|[[Team:Paris/Modeling/BOB#Remarks|wet-lab]]  
-
|- style="background: #dddddd;"|    
+
|- style="background: #dddddd;"|  
-
| style="background: #D4E2EF;"| c<sub>max</sub>
+
| style="background: #D4E2EF;"|γ<sub>HSL<sub>ext</sub></sub> <br> <br>
-
| style="background: #dddddd;"| Carrying capacity for cell growth
+
| style="background: #dddddd;"|Degradation rate
-
| style="background: #dddddd;"| 0.1
+
| style="background: #dddddd;"|0.0106
-
| style="background: #dddddd;"| 0.1
+
| style="background: #dddddd;"|0.5380
-
| style="background: #dddddd;"| µm<sup>3</sup>
+
|style="background: #dddddd;"| min<sup>-1</sup>
-
| style="background: #dddddd;"| [[Team:Paris/Modeling/BOB#Bibliography|[3]]]
+
| style="background: #dddddd;"|[[Team:Paris/Modeling/BOB#Bibliography|[6]]]
-
|- style="background: #dddddd;"|  
+
|- style="background: #dddddd;"|  
-
| style="background: #D4E2EF;"| D<sub>renewal</sub>
+
| style="background: #D4E2EF;" |β<sub>HSL</sub>  
-
| style="background: #dddddd;"| Dilution rate
+
| style="background: #dddddd;"|Production rate
-
| style="background: #dddddd;"| 0.00198
+
| style="background: #dddddd;"|0.3168
-
| style="background: #dddddd;"| 0.1
+
| style="background: #dddddd;"|16
-
| style="background: #dddddd;"| min<sup>-1</sup>
+
| style="background: #dddddd;"|min<sup>-1</sup>
-
| style="background: #dddddd;"| [[Team:Paris/Modeling/BOB#Remarks|wet-lab]] ([[Team:Paris/Modeling/BOB#Bibliography|[3]]])
+
| style="background: #dddddd;"|[[Team:Paris/Modeling/BOB#Bibliography|∅]]
-
|- style="background: #dddddd;"|  
+
|- style="background: #dddddd;"|
-
| style="background: #D4E2EF;"| d
+
| style="background: #D4E2EF;" |η
-
| style="background: #dddddd;"| Death rate
+
| style="background: #dddddd;"|Diffusion rate
-
| style="background: #dddddd;"| 0.0099
+
| style="background: #dddddd;"|10
-
| style="background: #dddddd;"| 0.5
+
| style="background: #dddddd;"|505
-
| style="background: #dddddd;"| min<sup>-1</sup>
+
| style="background: #dddddd;"|min<sup>-1</sup>
-
| style="background: #dddddd;"|[[Team:Paris/Modeling/BOB#Remarks|wet-lab]]
+
| style="background: #dddddd;"|[[Team:Paris/Modeling/BOB#Bibliography|[2]]]
 +
|- style="background: #dddddd;"|  
 +
| style="background: #D4E2EF;" |n<sub>HSL</sub>
 +
| style="background: #dddddd;"|Hill coefficient
 +
| style="background: #dddddd;"|&nbsp;
 +
| style="background: #dddddd;"|4
 +
| style="background: #dddddd;"|&nbsp;
 +
| style="background: #dddddd;"|[[Team:Paris/Modeling/BOB#Bibliography|[3]]]
 +
|- style="background: #dddddd;"|
 +
| style="background: #D4E2EF;" |θ<sub>HSL</sub>
 +
| style="background: #dddddd;"|Hill characteristic concentration for the second operator
 +
| style="background: #dddddd;"|&nbsp;
 +
| style="background: #dddddd;"|0.5
 +
| style="background: #dddddd;"|[[Team:Paris/Modeling/BOB#Remarks|c.u]]
 +
| style="background: #dddddd;"|[[Team:Paris/Modeling/BOB#Bibliography|[3]]]
|}</center>
|}</center>

Revision as of 20:34, 25 October 2008

Model Construction

why use a chemostat

which model of chemostat we choose


equations

d[c]/dt=alpha_cell*[c]*(c_max-[c])/c_max-(D_renewal+death)*[c] d[LasI]/dt=beta_FlhDC*theta_FlhDC^n_FlhDC/(theta_FlhDC^n_FlhDC+[TetR]^n_FlhDC)-gamma*[LasI] d[TetR]/dt=beta_TetR*[HSL]^n_TetR/(theta_TetR^n_TetR+[HSL]^n_TetR)-gamma*[TetR] d[HSL::ext]/dt=eta*v_cell*[c]*([HSL]-[HSL::ext])-(D_renewal+gamma_HSLext)*[HSL::ext] d[HSL]/dt=beta_HSL*[LasI]+eta*[HSL::ext]-(gamma+gamma_HSLint+eta)*[HSL]

parameters

Parameters
 
Chemostat Parameter Meaning Original Value Normalized Value Unit Source
figure / equations of Chemostat αcell Growth rate 0.0198 1 min-1 wet-lab
cmax Carrying capacity for cell growth 0.1 0.1 µm3 [3]
Drenewal Dilution rate 0.00198 0.1 min-1 wet-lab ([3])
d Death rate 0.0099 0.5 min-1 wet-lab
 
Quorum Sensing Parameter Meaning Original Value Normalized Value Unit Source
figure / equations of Quorum Sensing γHSL Degradation rate 0.0053 0.2690 min-1 wet-lab
γHSLext

Degradation rate 0.0106 0.5380 min-1 [6]
βHSL Production rate 0.3168 16 min-1 ∅
η Diffusion rate 10 505 min-1 [2]
nHSL Hill coefficient   4   [3]
θHSL Hill characteristic concentration for the second operator   0.5 c.u [3]
Retrieved from "http://2008.igem.org/Team:Paris/Analysis/Construction2"