"
Team:UT-Tokyo/Sudoku modeling
From 2010.igem.org
(→4C3leak switch) |
(→4C3leak switch) |
||
| Line 14: | Line 14: | ||
We modeled our 4C3 leak switch as ODE system. | We modeled our 4C3 leak switch as ODE system. | ||
| - | ==='''Variable'''=== | + | ==='''Modelling'''=== |
| + | |||
| + | ===='''Variable'''==== | ||
Basically, "pn" denotes for protein concentration and "rn" denotes for mRNA concentration | Basically, "pn" denotes for protein concentration and "rn" denotes for mRNA concentration | ||
| Line 27: | Line 29: | ||
Besides, we treated DNA as continuous variabl, since there could be hundreds of plasmid in one E.coli (multicopy plasmid). | 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 : | ||
| + | k1 : | ||
| + | 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 | ||
| - | |||
| - | ===''' | + | |
| + | ===='''Equations'''==== | ||
| + | |||
| + | |||
| + | ==='''Methods'''=== | ||
| + | |||
| + | We used original python program (Runge-Kutta) to solve this equation. | ||
| + | |||
| + | ==='''Results'''=== | ||
=='''MS2 phage infection'''== | =='''MS2 phage infection'''== | ||
Revision as of 15:18, 27 October 2010
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 : k1 :
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
Equations
Methods
We used original python program (Runge-Kutta) to solve this equation.
Results
MS2 phage infection
Whole system
