Difference between revisions of "Team:Tokyo Tech/Modeling Details"

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{{:Team:Tokyo_Tech/tpl/head|Parameters and Tools}}
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{{:Team:Tokyo _Tecj/tpl/fortables}}
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==Parameters==
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No model is complete without parameters. Our exhaustive list of parameters are summarised in the table below.
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{|class="wikitable sortable"
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!Parameter!!Value!!Description!!Reference
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|-
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|g||0.0123||Growth rate of each cells||[ここにリンク先 Fitted to experimental data]
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|-
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|P<sub>max</sub>||3.6641||Carrying capacity||[ここにリンク先 Fitted to experimental data]
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|-
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|E<sub>DiMazF</sub>||0.101715||Effect of MazF dimer on growth rate of each cells||[ここにリンク先 Fitted to experimental data]
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|-
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|k||5 min<sup>-1</sup>||Transcriptional rate of mRNA under P<sub>tet</sub>||Assumed
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|-
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|leak<sub>P<sub>lux</sub></sub>||0.113 nMmin<sup>-1</sup>||Leakage of P<sub>lux</sub>||[ここにリンク先 Fitted to experimental data]
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|-
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|leak<sub>P<sub>rhl</sub></sub>||3.5 nMmin<sup>-1</sup>||Leakage of P<sub>rhl</sub>||[ここにリンク先 Fitted to experimental data]
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|-
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|κ<sub>P<sub>lux</sub></sub>||10.3 nM<sup>-1</sup>min<sup>-1</sup>||Maximum transcriptional rate of mRNA under P<sub>lux</sub>||[ここにリンク先 Fitted to experimental data]
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|-
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|κ<sub>P<sub>rhl</sub></sub>||9.73 nM<sup>-1</sup>min<sup>-1</sup>||Maximum transcriptional rate of mRNA under P<sub>rhl</sub>||[ここにリンク先 Fitted to experimental data]
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|-
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|n<sub>Lux</sub>||2.5||Hill coefficient for P<sub>lux</sub>||[ここにリンク先 Fitted to experimental data]
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|-
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|n<sub>Rhl</sub>||2.5||Hill coefficient for P<sub>rhl</sub>||[ここにリンク先 Fitted to experimental data]
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|-
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|K<sub>mLux</sub>||78.32 nM||Lumped parameter for the Lux system||Estimated from Literature
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|-
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|K<sub>mRhl</sub>||1969 nM||Lumped parameter for the Rhl system||Estimated from Literature
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|-
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|F<sub>DiMazF</sub>||5 nM<sup>-1</sup>min<sup>-1</sup>||Cutting rate at ACA sequences on mRNA by MazF dimer||Assumed
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|-
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|f||0.409213||The probability of distinction of ACA sequences on mRNA by MazF dimer||Estimated
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|-
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|f<sub>mRNA<sub>RFP</sub></sub>||10||The number of ACA arrays in mRNA<sub>RFP</sub>||Extraction of data
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|-
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|f<sub>mRNA<sub>GFP</sub></sub>||23||The number of ACA arrays in mRNA<sub>GFP</sub>||Extraction of data
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|-
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|f<sub>mRNA<sub>RhlI</sub></sub>||1||The number of ACA arrays in mRNA<sub>RhlI</sub>||Extraction of data
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|-
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|f<sub>mRNA<sub>LasI</sub></sub>||10||The number of ACA arrays in mRNA<sub>LasI</sub>||Extraction of data
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|-
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|f<sub>mRNA<sub>MazF</sub></sub>||2||The number of ACA arrays in mRNA<sub>MazF</sub>||Extraction of data
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|-
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|f<sub>mRNA<sub>MazE</sub></sub>||10||The number of ACA arrays in mRNA<sub>MazE</sub>||Extraction of data
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|-
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|α||5 min<sup>-1</sup>||Translation rate of protein||Assumed
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|-
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|k<sub>DiMazF</sub>||5.226124 nM<sup>-1</sup>min<sup>-1</sup>||Formation rate of MazF dimer||Literature
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|-
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|k<sub>-DiMazF</sub>||3.151962 min<sup>-1</sup>||Dissociation rate of MazF dimer||Literature
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|-
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|k<sub>DiMazE</sub>||6.759816 nM<sup>-1</sup>min<sup>-1</sup>||Formation rate of MazE dimer||Literature
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|-
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|k<sub>-DiMazE</sub>||3.808504 min<sup>-1</sup>||Dissociation rate of MazE dimer||Literature
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|-
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|k<sub>Hexa</sub>||3.170544 nM<sup>-1</sup>min<sup>-1</sup>||Formation rate of Maz hexamer||Literature
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|-
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|k<sub>-Hexa</sub>||8.344358 min<sup>-1</sup>||Dissociation rate of Maz hexamer||Literature
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|-
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|p<sub>Las</sub>||1 min<sup>-1</sup>||Production rate of 3OC12AHL by LasI||Assumed
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|-
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|p<sub>Rhl</sub>||1 min<sup>-1</sup>||Production rate of C4AHL by RhlI||Assumed
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|-
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|D||1 nM<sup>-1</sup>min<sup>-1</sup>||Decomposition rate of 3OC12AHL by AmiE||[Assumed
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|-
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|d||0.2773 min<sup>-1</sup>||Degradation rate of mRNA||Literature
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|-
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|d<sub>RFP</sub>||0.017 min<sup>-1</sup>||Degradation rate of RFP||Literature
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|-
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|d<sub>GFP</sub>||0.017 min<sup>-1</sup>||Degradation rate of GFP||Literature
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|-
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|d<sub>RhlI</sub>||0.0167 min<sup>-1</sup>||Degradation rate of RhlI||Literature
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|-
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|d<sub>LasI</sub>||0.0167 min<sup>-1</sup>||Degradation rate of LasI||Literature
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|-
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|d<sub>MazF</sub>||0.173286 min<sup>-1</sup>||Degradation rate of RhlI||[ここにリンク先 Fitted to experimental data]
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|-
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|d<sub>DiMazF</sub>||0.700037 min<sup>-1</sup>||Degradation rate of MazF dimer||[ここにリンク先 Fitted to experimental data]
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|-
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|d<sub>MazE</sub>||0.340082 min<sup>-1</sup>||Degradation rate of MazE||[ここにリンク先 Fitted to experimental data]
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|-
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|d<sub>DiMazE</sub>||0.166615 min<sup>-1</sup>||Degradation rate of MazE dimer||[ここにリンク先 Fitted to experimental data]
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|-
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|d<sub>Hexa</sub>||0.155088 min<sup>-1</sup>||Degradation rate of Maz hexamer||[ここにリンク先 Fitted to experimental data]
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|-
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|d<sub>C4AHL</sub>||0.000222 min<sup>-1</sup>||Degradation rate of C4AHL||Literature
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|}
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|d<sub>C12AHL</sub>||0.004 min<sup>-1</sup>||Degradation rate of 3OC12AHL||Literature
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|}
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|d<sub>AmiE</sub>||0.01 min<sup>-1</sup>||Degradation rate of mRNA||Assumed
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|}
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Revision as of 14:24, 12 October 2016

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

|dC12AHL||0.004 min-1||Degradation rate of 3OC12AHL||Literature |} |dAmiE||0.01 min-1||Degradation rate of mRNA||Assumed |}