ETHZ/Simulations

From 2007.igem.org

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Revision as of 20:31, 11 September 2007

Contents

Basic Model

Constitutively produced proteins

Model01.png

Learning system

Model02.png

Reporter system

Model03.png

System Equations

Constitutively produced proteins

Eq01.png


Learning system

Eq02.png


Reporter system

Eq03.png


Allosteric regulation

Eq04.png

Model Parameters

Parameter Value Description Comments
aR basic production of lacI
aS basic production of tetR
aL basic production of luxR
aQ1 basic production of cI
aQ2 basic production of p22cII
aGFP basic production of GFP
aRFP basic production of RFP
dR 0.06 degradation of lacI Ref. [4]
dS degradation of tetR
dL degradation of luxR
dQ1 degradation of cI
dQ2 degradation of p22cII
dGFP degradation of GFP
dRFP degradation of RFP
kR 0.22 [mM/h] promoter strength (Promoter R0010)
kS promoter strength (Promoter R0040)
kL promoter strength (Promoter R0062)
kQ1 0.20 [mM/h] promoter strength (Promoter R0051)
kQ2 promoter strength (Promoter R0053)
KR 1.3e-3 - 2e-3 [mM/h] lacI repressor dissociation constant lower value is from Ref. [2], higher value is from Ref. [?]
KIR 1.5e-10 [mM/h] IPTG-lacI repressor dissociation constant
KS tetR repressor dissociation constant
KIS aTc-tetR repressor dissociation constant
KL luxR activator dissociation constant
KIL AHL-luxR activator dissociation constant
KQ1 2e-3 [mM/h] cI repressor dissociation constant
KQ2 p22cII repressor dissociation constant
nR 1 lacI repressor Hill cooperativity
nIR 2 IPTG-lacI repressor Hill cooperativity
nS 3 tetR repressor Hill cooperativity Ref. [3]
nIS aTc-tetR repressor Hill cooperativity
nL 1 luxR activator Hill cooperativity Ref. [3]
nIL 1 AHL-luxR activator Hill cooperativity Ref. [3]
nQ1 1.9 cI repressor Hill cooperativity
nQ2 p22cII repressor Hill cooperativity

References

  1. A synthetic time-delay circuit in mammalian cells and mice (http://www.pnas.org/cgi/content/abstract/104/8/2643)
  2. Detailed map of a cis-regulatory input function (http://www.pnas.org/cgi/content/full/100/13/7702?ck=nck)
  3. Parameter Estimation for two synthetic gene networks (http://ieeexplore.ieee.org/iel5/9711/30654/01416417.pdf)

Variable Mapping

Variable Compound
R lacI
IR IPTG
S tetR
IS aTc
L luxR
IL AHL
Q1 cI
Q2 p22cII