Model Mathematics

Component based math viewer is available

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 = \frac{bagVolume}{bagSurfaceArea} bagConcentrationToDensityConversionFactor = 0.6022 bagVolumeToAreaRatio

Component: Time

Component: ho1pcyA_Promoter

Component: Template_Promoter_Constitutive

JRNA = \frac{k 1.0 e 9}{localVolume 1.0 e -15 avogadrosConstant}

Component: Template_Species

\frac{d}{d time} (concentration) = JGain

Component: Bioenvironment_Degradation_ho1pcyA_mRNA

Component: Template_RxR1P1

J = k concentration

Component: ho1_RBS

Component: Template_RBS

RNARiPs = 1 e 9 k RNA localVolume 1 e -15

Component: ho1_CDS

Component: Template_ProteinCDS

J = \frac{1.0 e 6 hostRNARiPs}{localVolume}

Component: pcyA_RBS

Component: Template_RBS

RNARiPs = 1 e 9 k RNA localVolume 1 e -15

Component: pcyA_CDS

Component: Template_ProteinCDS

J = \frac{1.0 e 6 hostRNARiPs}{localVolume}

Component: Template_Species

\frac{d}{d time} (concentration) = JGain

Component: Bioenvironment_Degradation_Ho1

Component: Template_RxR1P1

J = k concentration

Component: Template_Species

\frac{d}{d time} (concentration) = JGain

Component: Bioenvironment_Degradation_PcyA

Component: Template_RxR1P1

J = k concentration

Component: Template_Species

\frac{d}{d time} (concentration) = JGain

Component: Bioenvironment_Degradation_BV

Component: Template_RxR1P1

J = k concentration

Component: Bioenvironment_Haem

Component: Bioenvironment_BVFormation

Component: Template_RxR1P1MM

J = \frac{k catalyst reactant}{reactant + Km}

Component: Template_Species

\frac{d}{d time} (concentration) = JGain

Component: Bioenvironment_Degradation_PCB

Component: Template_RxR1P1

J = k concentration

Component: Bioenvironment_PCBFormation

Component: Template_RxR1P1MM

J = \frac{k catalyst reactant}{reactant + Km}

Component: Template_BoundSpecies

\frac{d}{d time} (density) = JGain

Component: Bioenvironment_Degradation_Cph8

Component: Template_RxBoundR1BoundP1

J = k density

Component: Bioenvironment_Cph8_no_PCB

Component: Bioenvironment_Cph8Formation

Jdensity_timeless = 1 Jdensity Jconcentration = \frac{Jconcentration_timeless}{1}

Component: Template_RxBoundR2BoundP1Rev

J = kf reactant1 reactant2 - (kb product)

Component: Template_ConcentrationToDensityConversion

density = concentration Ccm

Component: Template_DensityToConcentrationConversion

concentration = \frac{density}{Ccm}

Component: Bioenvironment_PeriodicLightSource

lightIntensity = switchValue 1 switchFirstPeriodValue = lowLightValue 1 switchSecondPeriodValue = highLightValue 1

Component: Template_PeriodicSwitch

period = {-1}^{⌈ \frac{time}{timeInterval} ⌉} value = \{\begin{matrix} firstPeriodValue if period = -1 \\ secondPeriodValue otherwise \end{matrix}

Component: Template_BoundSpecies

\frac{d}{d time} (density) = JGain

Component: Bioenvironment_LightDependentPhosphorylation_Cph8

k = calculated_k

Component: Template_RxBoundR1BoundP1

J = k density

Component: Template_LightDependentFirstOrderRateConstant

k = \{\begin{matrix} kMax \frac{lightIntensity}{kMax_lightIntensity} if lightIntensity > 0 \land lightIntensity < kMax_lightIntensity \\ kMax if lightIntensity \geq kMax_lightIntensity \\ 0 otherwise \end{matrix}

Component: ompR_Promoter

Component: Template_Promoter_Constitutive

JRNA = \frac{k 1.0 e 9}{localVolume 1.0 e -15 avogadrosConstant}

Component: Template_Species

\frac{d}{d time} (concentration) = JGain

Component: Bioenvironment_Degradation_ompR_mRNA

Component: Template_RxR1P1

J = k concentration

Component: ompR_RBS

Component: Template_RBS

RNARiPs = 1 e 9 k RNA localVolume 1 e -15

Component: ompR_CDS

Component: Template_ProteinCDS

J = \frac{1.0 e 6 hostRNARiPs}{localVolume}

Component: Template_Species

\frac{d}{d time} (concentration) = JGain

Component: Bioenvironment_Degradation_OmpR

Component: Template_RxR1P1

J = k concentration

Component: Bioenvironment_OmpRpFormation

Jconcentration_timeless = 1 Jconcentration Jdensity = \frac{Jdensity_timeless}{1}

Component: Template_RxR2P2Rev

J = reactant1 reactant2 kf - (kb product1 product2)

Component: Template_ConcentrationToDensityConversion

density = concentration Ccm

Component: Template_DensityToConcentrationConversion

concentration = \frac{density}{Ccm}

Component: Template_DensityToConcentrationConversion

concentration = \frac{density}{Ccm}

Component: Template_Species

\frac{d}{d time} (concentration) = JGain

Component: Bioenvironment_Degradation_OmpRp

Component: Template_RxR1P1

J = k concentration

Component: ompC_lacZ_Promoter

Component: Template_Promoter_PartiallyInductive

JRNA = \frac{(\frac{(1 - basalProportion) k {tFactor}^{n}}{{Km}^{n} + {tFactor}^{n}} + basalProportion k) 1.0 e 9}{localVolume 1.0 e -15 avogadrosConstant}

Component: Template_Species

\frac{d}{d time} (concentration) = JGain

Component: Bioenvironment_Degradation_ompC_lacZ_mRNA

Component: Template_RxR1P1

J = k concentration

Component: beta_galactosidase_RBS

Component: Template_RBS

RNARiPs = 1 e 9 k RNA localVolume 1 e -15

Component: beta_galactosidase_CDS

Component: Template_ProteinCDS

J = \frac{1.0 e 6 hostRNARiPs}{localVolume}

Component: Template_Species

\frac{d}{d time} (concentration) = JGain

Component: Bioenvironment_Degradation_Beta_Galactosidase

Component: Template_RxR1P1

J = k concentration

Component: Bioenvironment_S_Galactosidase

Component: Template_Species

\frac{d}{d time} (concentration) = JGain

Component: Bioenvironment_PrecipitateFormation

Component: Template_RxR1P1MM

J = \frac{k catalyst reactant}{reactant + Km}