Team:Tokyo Tech/Modeling Details

• 
• 
• 
  • 
    • 
    • 
    • 
    • 
  • 
    • 
    • 
    • 
  • 
  • 
    • 
    • 
• 
• 
  • 
  • 
  • 
  • 
• 
  • 
  • 
  • 
• 
• 
  • 
  • 
  • 
  • 
  • 
  • 

Detail Descriptions

Model Development

Team:Tokyo Tech/tpl/head Team:Tokyo Tecj/tpl/fortables

Parameters

No model is complete without parameters. Our exhaustive list of parameters are summarised in the table below.

Parameter	Value	Description	Reference
g	0.0123	Growth rate of each cells	[ここにリンク先 Fitted to experimental data]
Pmax	3.6641	Carrying capacity	[ここにリンク先 Fitted to experimental data]
EDiMazF	0.101715	Effect of MazF dimer on growth rate of each cells	[ここにリンク先 Fitted to experimental data]
k	5 min-1	Transcriptional rate of mRNA under Ptet	Assumed
leakPlux	0.113 nMmin-1	Leakage of Plux	[ここにリンク先 Fitted to experimental data]
leakPrhl	3.5 nMmin-1	Leakage of Prhl	[ここにリンク先 Fitted to experimental data]
κPlux	10.3 nM-1min-1	Maximum transcriptional rate of mRNA under Plux	[ここにリンク先 Fitted to experimental data]
κPrhl	9.73 nM-1min-1	Maximum transcriptional rate of mRNA under Prhl	[ここにリンク先 Fitted to experimental data]
nLux	2.5	Hill coefficient for Plux	[ここにリンク先 Fitted to experimental data]
nRhl	2.5	Hill coefficient for Prhl	[ここにリンク先 Fitted to experimental data]
KmLux	78.32 nM	Lumped parameter for the Lux system	Estimated from Literature
KmRhl	1969 nM	Lumped parameter for the Rhl system	Estimated from Literature
FDiMazF	5 nM-1min-1	Cutting rate at ACA sequences on mRNA by MazF dimer	Assumed
f	0.409213	The probability of distinction of ACA sequences on mRNA by MazF dimer	Estimated
fmRNARFP	10	The number of ACA arrays in mRNARFP	Extraction of data
fmRNAGFP	23	The number of ACA arrays in mRNAGFP	Extraction of data
fmRNARhlI	1	The number of ACA arrays in mRNARhlI	Extraction of data
fmRNALasI	10	The number of ACA arrays in mRNALasI	Extraction of data
fmRNAMazF	2	The number of ACA arrays in mRNAMazF	Extraction of data
fmRNAMazE	10	The number of ACA arrays in mRNAMazE	Extraction of data
α	5 min-1	Translation rate of protein	Assumed
kDiMazF	5.226124 nM-1min-1	Formation rate of MazF dimer	Literature
k-DiMazF	3.151962 min-1	Dissociation rate of MazF dimer	Literature
kDiMazE	6.759816 nM-1min-1	Formation rate of MazE dimer	Literature
k-DiMazE	3.808504 min-1	Dissociation rate of MazE dimer	Literature
kHexa	3.170544 nM-1min-1	Formation rate of Maz hexamer	Literature
k-Hexa	8.344358 min-1	Dissociation rate of Maz hexamer	Literature
pLas	1 min-1	Production rate of 3OC12AHL by LasI	Assumed
pRhl	1 min-1	Production rate of C4AHL by RhlI	Assumed
D	1 nM-1min-1	Decomposition rate of 3OC12AHL by AmiE	[Assumed
d	0.2773 min-1	Degradation rate of mRNA	Literature
dRFP	0.017 min-1	Degradation rate of RFP	Literature
dGFP	0.017 min-1	Degradation rate of GFP	Literature
dRhlI	0.0167 min-1	Degradation rate of RhlI	Literature
dLasI	0.0167 min-1	Degradation rate of LasI	Literature
dMazF	0.173286 min-1	Degradation rate of RhlI	[ここにリンク先 Fitted to experimental data]
dDiMazF	0.700037 min-1	Degradation rate of MazF dimer	[ここにリンク先 Fitted to experimental data]
dMazE	0.340082 min-1	Degradation rate of MazE	[ここにリンク先 Fitted to experimental data]
dDiMazE	0.166615 min-1	Degradation rate of MazE dimer	[ここにリンク先 Fitted to experimental data]
dHexa	0.155088 min-1	Degradation rate of Maz hexamer	[ここにリンク先 Fitted to experimental data]
dC4AHL	0.000222 min-1	Degradation rate of C4AHL	Literature

|d_C12AHL||0.004 min^-1||Degradation rate of 3OC12AHL||Literature |} |d_AmiE||0.01 min^-1||Degradation rate of mRNA||Assumed |}