Team:UT-Tokyo/Sudoku modeling

From 2010.igem.org

(Difference between revisions)
(→4C3leak switch)
(→4C3leak switch)
Line 33: Line 33:
====''' Parameters  '''====
====''' Parameters  '''====
-
k0 :
+
k0 : mRNA translation rate
-
k1 :  
+
 
 +
k1 : protein degradation rate
 +
 
 +
k2 : mRNA translation rate
 +
 
 +
k3 : cre protein degradation rate
 +
 
 +
l0 : transcription speed per unit concentration of RNA polymearase
 +
 
 +
l1 : mRNA degradation rate
 +
 
 +
l2 : cre mRNA degradation rate
 +
 
 +
K : recombinase binding constant
 +
 
 +
v : recombinase reaction rate
 +
 
 +
pT7 : concentration o T7 polymerase
 +
 
 +
p : terminator leak probability
 +
-
unit value meaning
 
-
k0 1/s 0.1 mRNA translation speed
 
-
k2 1/s 0.05 mRNA translation speed for external mRNA
 
-
k1 1/s 0.0002 protein degradation constant
 
-
k3 1/s 0.02 cre protein degradation constant
 
-
l1 1/s 0.003 mRNA degradation constant
 
-
l2 1/s 0.01 cre mRNA degradation rate
 
-
l0 1/(s*uM) 0.05 translation speed per unit concentration o polymerase
 
-
K uM^2 0.0001 binding constants of DNA recombinases
 
-
pT7 uM 0.6 concentration of T7 promoter
 
-
p unitless 0.01 terminator leak probability
 
-
v 1/s 0.01 recombinase turnover rate
 
Line 59: Line 67:
==='''Results'''===
==='''Results'''===
 +
 +
==='''Discussion'''===
 +
 +
==='''conclusion'''===
=='''MS2 phage infection'''==
=='''MS2 phage infection'''==

Revision as of 15:22, 27 October 2010

UT-Tokyo

Sudoku

Introduction System Modeling Lab note Result Reference

4C3leak switch

We modeled our 4C3 leak switch as ODE system.

Modelling

Variable

Basically, "pn" denotes for protein concentration and "rn" denotes for mRNA concentration

p1,p2,p3,p4 : concentration of 4 recombinase protein

r1,r2,r3,r4 : concentration of 4 recombinass mRNA

pc,rc : concentration of cre recombinase protein and mRNA

ps,rs : concentration of SP6 polymerase protein and mRNA

Besides, we treated DNA as continuous variabl, since there could be hundreds of plasmid in one E.coli (multicopy plasmid). There are 32 kinds of variables that stand for DNA corresponding to their different internal states.


Parameters

k0 : mRNA translation rate

k1 : protein degradation rate

k2 : mRNA translation rate

k3 : cre protein degradation rate

l0 : transcription speed per unit concentration of RNA polymearase

l1 : mRNA degradation rate

l2 : cre mRNA degradation rate

K : recombinase binding constant

v : recombinase reaction rate

pT7 : concentration o T7 polymerase

p : terminator leak probability



Equations

Methods

We used original python program (Runge-Kutta) to solve this equation.

Results

Discussion

conclusion

MS2 phage infection

Whole system

What's Sudoku?




Retrieved from "http://2010.igem.org/Team:UT-Tokyo/Sudoku_modeling"