Minnesota/9 June 2009

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Revision as of 18:45, 29 July 2009

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Today Patrick arrived and began working on getting up to speed on the team's TTL model and creating the TTN model he will eventually be working on.
The model created was similar to that described previously except with the addition of a second tet operon (tetO2):

Reaction	Forward Kinetic Constant	Reverse Kinetic Constant
RNAp + lacP + tetO1 + tetO2 ↔ RNAp:lacP	1E+07	1
RNA:lacP -> RNAp:lacP*	.01
RNAp:lacP* -> lacP + tetO1 + tetO2 + RNAp:DNAgfp	30
RNAp:DNAgfp -> RNAp + gfp_mRNA	30
gfp_mRNA + rib -> rib:gfp_mRNA	100000
rib:gfp_mRNA -> rib:gfp_mRNA_1 + gfp_mRNA	33
rib:gfp_mRNA_1 -> rib + gfp	33
tetR2 + aTc ↔ tetR2:aTc	2E+09	4E-04
tetR2:aTc + aTc ↔ tetR2:aTc2	1E+08	1E-03
tetR2:aTc + tetO1 ↔ tetR2:tetO1:aTc	1E+08	1
tetR2:aTc2 + tetO1 ↔ tetR2:tetO1:aTc2	1E+08	1E+05
tetR2:tetO1 + aTc ↔ tetR2:tetO1:aTc	1E+08	1E-03
tetR2:tetO1:aTc + aTc ↔ tetR2:tetO1:aTc2	1E+08	1E-03
tetR2:aTc + tetO2 ↔ tetR2:tetO2:aTc	1E+08	1
tetR2:aTc2 + tetO2 ↔ tetR2:tetO2:aTc2	1E+08	1E+05
tetR2:tetO2 + aTc ↔ tetR2:tetO2:aTc	1E+08	1E-03
tetR2:tetO2:aTc + aTc ↔ tetR2:tetO2:aTc2	1E+08	1E-03
tetR2 -> Ø	2.89E-04
tetR2:aTc -> aTc	2.89E-04
tetR2:aTc2 -> 2 aTc	2.89E-04
tetR2 + nsDNA ↔ tetR2:nsDNA	1000	3.2409
tetR2:aTc + nsDNA ↔ tetR2:aTc:nsDNA	1000	3.2409
tetR2:aTc:nsDNA -> aTc + nsDNA	1.93E-04
tetR2:nsDNA -> nsDNA	1.93E-04
Ø -> tetR2	1E-11
Ø -> aTc	3.3E-04
gfp_mRNA -> Ø	1.16E-03
gfp -> Ø	3.21E-05

@@ Line 13: / Line 13: @@
 ! Reverse Kinetic Constant
 |-
-| RNAp + lacP + lacI4:lacO1 ->  RNAp:lacP||6.23E+05||
+| RNAp + lacP + tetO1 + tetO2 ↔ RNAp:lacP||1E+07|| 1
-|-
-| RNAp + lacP + lacO1 ↔ RNAp:lacP||1E+07|| 1
 |-
 |RNA:lacP -> RNAp:lacP* || .01 ||
 |-
-|RNAp:lacP* -> lacP + lacO1 + RNAp:DNAgfp||30||
+|RNAp:lacP* -> lacP + tetO1 + tetO2 + RNAp:DNAgfp||30||
 |-
 |RNAp:DNAgfp -> RNAp + gfp_mRNA||30||
@@ Line 40: / Line 38: @@
 |-
 |tetR2:tetO1:aTc + aTc ↔ tetR2:tetO1:aTc2||1E+08||1E-03
+|-
+|tetR2:aTc + tetO2 ↔ tetR2:tetO2:aTc||1E+08||1
+|-
+|tetR2:aTc2 + tetO2 ↔ tetR2:tetO2:aTc2||1E+08||1E+05
+|-
+|tetR2:tetO2 + aTc ↔ tetR2:tetO2:aTc||1E+08||1E-03
+|-
+|tetR2:tetO2:aTc + aTc ↔ tetR2:tetO2:aTc2||1E+08||1E-03
 |-
 |tetR2 -> Ø||2.89E-04||