Team:KULeuven/Model/Inverter

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Pictogram inverter.png

Contents

Inverter

Position in the system

The inverter part receives its input from the filter, T7. The inverter's function is to produce HSL when no INPUT is present, so a low T7 input gives rise to a high HSL output and vice versa. A high output of HSL will be used in the celldeath-subsystem to produce ccdB, meaning that the cell will start a timer and eventually die off if no INPUT remains present.

Describing the system

Inverter BioBrick.jpg

ODE's

Parameters

Parameter values (Inverter)
Name Value Comments Reference
Degradation Rates
dLuxI 0.00231 s-1
dRNA_LuxI 0.0025 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dLuxI_antimRNA 0.00125 s-1
dLacI 0.00231 s-1 [http://www.biophysj.org/cgi/content/full/89/6/3873?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&searchid=1&FIRSTINDEX=0&volume=89&firstpage=3873&resourcetype=HWCIT link]
dLacI (closed mRNA) 0.0046209812 s-1 estimate: because this mRNA isn't translated, it degrades faster
dLacI (open mRNA) 0.0023104906 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dLacI_mRNA (open complex) 0.0023104906 s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]
dHSL 1.02E-6 s-1 [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]
Dissociation Rates
KmRNA_LuxI:antisense_mRNA 4.22E14 Complex of LuxI mRNA with antisense mRNA
Transcription Rates
kmRNA_LacI 0.0011 s-1
kmRNA_LuxI 0.0025 s-1
Hill Cooperativity
KLuxI 1.0E-10 s-1
nLuxI 2.0
kmaxT7 0.044 s-1 [http://www.jbc.org/cgi/content/full/279/5/3239#FIG2 link]
nT7 1
Translation Rates
kLuxI 0.167 s-1 RBs is B0032 (efficiency 0.3)
kLacI 0.167 s-1 RBS is situated in the keylock
kT7 182 s-1
Equilibrium Constants
KmRNA_LacI 0.015 equilibrium between open and closed mRNA LacI
KmRNA_LacI_Key 0.0212 /M equilibrium between closed mRNA LacI and complex of mRNA with keymRNA
Reaction Rates
kLuxI:HSL 0.0167 s-1 [http://www.pnas.org/content/93/18/9505.full.pdf+html link Vmax]

Models

CellDesigner (SBML file)

Inverter

Matlab (SBML file)

Remark: not yet up to date to latest (final) version

Inverter

Simulations

Remark: simulation is not from latest version.

filter

Sensitivity Analysis

Sens Inverter.png