Minnesota/8 June 2009

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Revision as of 20:45, 28 July 2009

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Today the first model of the TNN system was created. In order to do this, the previous work of the Kaznessis group was used to provide a basis for a a lot of the reactions. This allowed us to easily obtain reasonable kinetic constants for almost all the reactions in the model. Here is the first incarnation of the model (many future models will simply change this one):

Reaction	Forward Kinetic Constant	Reverse Kinetic Constant
RNAp + lacP + lacI4:lacO1 -> RNAp:lacP	6.23E+05
RNAp + lacP + lacO1 ↔ RNAp:lacP	1E+07	1
RNA:lacP -> RNAp:lacP*	.01
RNAp:lacP* -> lacP + lacO1 + 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	number
tetR2:aTc + tetO1 ↔ tetR2:tetO1:aTc	n
tetR2:aTc2 + tetO1 ↔ tetR2:tetO1:aTc2	n
tetR2:tetO1 + aTc ↔ tetR2:tetO1:aTc	n
tetR2:tetO1:aTc + aTc ↔ tetR2:tetO1:aTc2	n
tetR2 -> Ø	n
tetR2:aTc -> aTc	n
tetR2:aTc2 -> 2 aTc	n
tetR2 + nsDNA ↔ tetR2:nsDNA	n
tetR2:aTc + nsDNA ↔ tetR2:aTc:nsDNA	n
tetR2:aTc:nsDNA -> aTc + nsDNA	n
tetR2:nsDNA -> nsDNA	n
Ø -> tetR2	n
aTc -> Ø	n
Ø -> aTc	n
gfp_mRNA -> Ø	1.16E-03
gfp -> Ø	3.21E-05

@@ Line 49: / Line 49: @@
 |-
 |tetR2 + nsDNA ↔  tetR2:nsDNA||n||
+|-
+|tetR2:aTc + nsDNA ↔ tetR2:aTc:nsDNA||n||
+|-
+|tetR2:aTc:nsDNA -> aTc + nsDNA||n||
+|-
+|tetR2:nsDNA -> nsDNA||n||
+|-
+|Ø -> tetR2||n||
+|-
+|aTc -> Ø||n||
+|-
+|Ø -> aTc||n||
+|-
+|gfp_mRNA -> Ø||1.16E-03||
+|-
+|gfp -> Ø||3.21E-05||
 |}
-tetR2:aTc + nsDNA ↔ tetR2:aTc:nsDNA
-tetR2:aTc:nsDNA -> aTc + nsDNA
-tetR2:nsDNA -> nsDNA
-Ø -> tetR2
-aTc -> Ø
-Ø -> aTc
-gfp_mRNA -> Ø 	k = 1.16E-03
-gfp -> Ø		k = 3.21E-05