Model Mathematics

Component: SpeciesInitialValues

Component: ho1pcyA_mRNA_Interface

JGain=JPlusPromoter-JMinusDegradation

Component: Ho1_Interface

JGain=JPlusProduction-JMinusDegradation

Component: PcyA_Interface

JGain=JPlusProduction-JMinusDegradation

Component: BV_Interface

JGain=JPlusProduction-JMinusDegradation-JMinusPCBFormation

Component: PCB_Interface

JGain=JPlusProduction-JMinusDegradation+JMinusCph8Addition

Component: Cph8_Interface

JGain=JPlusPCBAddition+JPlusOmpRpFormation-JMinusDegradation+JMinusCph8Phosphorylation

Component: Cph8p_Interface

JGain=JPlusCph8Phosphorylation-JMinusOmpRpFormation

Component: ompR_mRNA_Interface

JGain=JPlusPromoter-JMinusDegradation

Component: OmpR_Interface

JGain=JPlusProduction-JMinusDegradation+JMinusOmpRpFormation

Component: OmpRp_Interface

JGain=JPlusFormation-JMinusDegradation

Component: ompC_lacZ_mRNA_Interface

JGain=JPlusPromoter-JMinusDegradation

Component: Beta_Galactosidase_Interface

JGain=JPlusProduction-JMinusDegradation

Component: Precipitate_Interface

JGain=JPlusProduction

Component: Chassis_EColi

Component: Template_Chassis_BoundedWellStirredBag

bagVolumeToAreaRatio=bagVolumebagSurfaceArea bagConcentrationToDensityConversionFactor=0.6022bagVolumeToAreaRatio

Component: Time

Component: ho1pcyA_Promoter

Component: Template_Promoter_Constitutive

JRNA=k1.0e9localVolume1.0e-15avogadrosConstant

Component: Template_Species

ddtimeconcentration=JGain

Component: Bioenvironment_Degradation_ho1pcyA_mRNA

Component: Template_RxR1P1

J=kconcentration

Component: ho1_RBS

Component: Template_RBS

RNARiPs=1e9kRNAlocalVolume1e-15

Component: ho1_CDS

Component: Template_ProteinCDS

J=1.0e6hostRNARiPslocalVolume

Component: pcyA_RBS

Component: Template_RBS

RNARiPs=1e9kRNAlocalVolume1e-15

Component: pcyA_CDS

Component: Template_ProteinCDS

J=1.0e6hostRNARiPslocalVolume

Component: Template_Species

ddtimeconcentration=JGain

Component: Bioenvironment_Degradation_Ho1

Component: Template_RxR1P1

J=kconcentration

Component: Template_Species

ddtimeconcentration=JGain

Component: Bioenvironment_Degradation_PcyA

Component: Template_RxR1P1

J=kconcentration

Component: Template_Species

ddtimeconcentration=JGain

Component: Bioenvironment_Degradation_BV

Component: Template_RxR1P1

J=kconcentration

Component: Bioenvironment_Haem

Component: Bioenvironment_BVFormation

Component: Template_RxR1P1MM

J=kcatalystreactantreactant+Km

Component: Template_Species

ddtimeconcentration=JGain

Component: Bioenvironment_Degradation_PCB

Component: Template_RxR1P1

J=kconcentration

Component: Bioenvironment_PCBFormation

Component: Template_RxR1P1MM

J=kcatalystreactantreactant+Km

Component: Template_BoundSpecies

ddtimedensity=JGain

Component: Bioenvironment_Degradation_Cph8

Component: Template_RxBoundR1BoundP1

J=kdensity

Component: Bioenvironment_Cph8_no_PCB

Component: Bioenvironment_Cph8Formation

Jdensity_timeless=1Jdensity Jconcentration=Jconcentration_timeless1

Component: Template_RxBoundR2BoundP1Rev

J=kfreactant1reactant2-kbproduct

Component: Template_ConcentrationToDensityConversion

density=concentrationCcm

Component: Template_DensityToConcentrationConversion

concentration=densityCcm

Component: Bioenvironment_PeriodicLightSource

lightIntensity=switchValue1 switchFirstPeriodValue=lowLightValue1 switchSecondPeriodValue=highLightValue1

Component: Template_PeriodicSwitch

period=-1timetimeInterval value=firstPeriodValueifperiod=-1secondPeriodValueotherwise

Component: Template_BoundSpecies

ddtimedensity=JGain

Component: Bioenvironment_LightDependentPhosphorylation_Cph8

k=calculated_k

Component: Template_RxBoundR1BoundP1

J=kdensity

Component: Template_LightDependentFirstOrderRateConstant

k=kMaxlightIntensitykMax_lightIntensityiflightIntensity>0lightIntensity<kMax_lightIntensitykMaxiflightIntensitykMax_lightIntensity0otherwise

Component: ompR_Promoter

Component: Template_Promoter_Constitutive

JRNA=k1.0e9localVolume1.0e-15avogadrosConstant

Component: Template_Species

ddtimeconcentration=JGain

Component: Bioenvironment_Degradation_ompR_mRNA

Component: Template_RxR1P1

J=kconcentration

Component: ompR_RBS

Component: Template_RBS

RNARiPs=1e9kRNAlocalVolume1e-15

Component: ompR_CDS

Component: Template_ProteinCDS

J=1.0e6hostRNARiPslocalVolume

Component: Template_Species

ddtimeconcentration=JGain

Component: Bioenvironment_Degradation_OmpR

Component: Template_RxR1P1

J=kconcentration

Component: Bioenvironment_OmpRpFormation

Jconcentration_timeless=1Jconcentration Jdensity=Jdensity_timeless1

Component: Template_RxR2P2Rev

J=reactant1reactant2kf-kbproduct1product2

Component: Template_ConcentrationToDensityConversion

density=concentrationCcm

Component: Template_DensityToConcentrationConversion

concentration=densityCcm

Component: Template_DensityToConcentrationConversion

concentration=densityCcm

Component: Template_Species

ddtimeconcentration=JGain

Component: Bioenvironment_Degradation_OmpRp

Component: Template_RxR1P1

J=kconcentration

Component: ompC_lacZ_Promoter

Component: Template_Promoter_PartiallyInductive

JRNA=1-basalProportionktFactornKmn+tFactorn+basalProportionk1.0e9localVolume1.0e-15avogadrosConstant

Component: Template_Species

ddtimeconcentration=JGain

Component: Bioenvironment_Degradation_ompC_lacZ_mRNA

Component: Template_RxR1P1

J=kconcentration

Component: beta_galactosidase_RBS

Component: Template_RBS

RNARiPs=1e9kRNAlocalVolume1e-15

Component: beta_galactosidase_CDS

Component: Template_ProteinCDS

J=1.0e6hostRNARiPslocalVolume

Component: Template_Species

ddtimeconcentration=JGain

Component: Bioenvironment_Degradation_Beta_Galactosidase

Component: Template_RxR1P1

J=kconcentration

Component: Bioenvironment_S_Galactosidase

Component: Template_Species

ddtimeconcentration=JGain

Component: Bioenvironment_PrecipitateFormation

Component: Template_RxR1P1MM

J=kcatalystreactantreactant+Km
Source
Derived from workspace Virtual Bacterial Photography at changeset fb8422a520b9.
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License

This work is licensed under a Creative Commons Attribution 3.0 Unported License.