modelMichaelisMenten
Extends from Chemical.Icons.EnzymeKinetics, Chemical.Processes.Internal.PartialReactionWithProductsDefinition (Chemical Reaction), Chemical.Interfaces.PartialSolutionSensor.
Information
s1·S1 + .. + snS·SnS <-> p1·P1 + .. + pnP·PnP
By redefinition of stoichometry as vi = -si, Ai = Si for i=1..nS vi = pi-nS, Ai = Pi-nS for i=nS+1..nS+nP
So the reaction can be written also as 0 = ∑ (vi · Ai)
Equilibrium equation
K = product(a(S).^s) / product( a(P).^s ) = product(a(A).^v) |
dissociation constant |
ΔrG = ∑ (vi · ΔfGi) = ΔrH - T·ΔrS = -R·T·log(K) |
molar Gibb's energy of the reaction |
ΔrH = ∑ (vi · ΔfHi) |
molar enthalpy of the reaction |
molar entropy of the reaction |
Notations
Ai |
i-th substance |
vi |
stochiometric coefficients of i-th substance |
K |
dissociation constant (activity based) |
a(Ai)=fi*xi |
activity of the substance A |
fi |
activity coefficient of the substance A |
xi |
mole fraction of the substance A |
ΔfHi |
molar enthalpy of formation of i-th substance |
ΔfGi |
molar Gibbs energy of formation of i-th substance |
ΔfSi |
molar entropy of formation of i-th substance |
Δrω |
change of number of microstates of particles by reaction |
Parameters
| Type | Name | Default | Description |
|---|---|---|---|
| Modelica.Units.SI.StoichiometricNumber[nS] | s (from PartialReaction) | ones(nS) | Stoichiometric coefficients for substrates |
| Modelica.Units.SI.StoichiometricNumber[nP] | p (from PartialReaction) | ones(nP) | Stoichiometric numbers for products |
| Chemical.Interfaces.Definition | process (from PartialReactionWithProductsDefinition) | Chemical.Interfaces.processData(1) | Process definition |
| Real | k_cat | ||
| Real | Km | ||
| Advanced | |||
| Modelica.Units.SI.MolarFlowRate | n_flow_reg (from PartialReaction) | dropOfCommons.n_flow_reg | Regularization threshold of mass flow rate |
| StateSelect | n_flowStateSelect (from PartialReaction) | StateSelect.default | State select for n_flow |
| Modelica.Units.SI.Time | TC (from PartialReaction) | dropOfCommons.TC | Time constant for electro-chemical potential adaption |
| Utilities.Units.Inertance | L (from PartialReaction) | dropOfCommons.L | Inertance of the flow |
| Initialization › Molar flow | |||
| InitializationMethods | initN_flow (from PartialReaction) | Chemical.Utilities.Types.InitializationMethods.none | Initialization method for n_flow |
| Modelica.Units.SI.MolarFlowRate | n_flow_0 (from PartialReaction) | 0 | Initial value for n_flow |
| Utilities.Units.MolarFlowAcceleration | n_acceleration_0 (from PartialReaction) | 0 | Initial value for der(n_flow) |
| General › Ports | |||
| Integer | nS (from PartialReaction) | 0 | Number of substrate types |
| Integer | nP (from PartialReaction) | 0 | Number of product types |
| Products definitions | |||
| FirstProductChoice | firstProductFrom (from PartialReactionWithProductsDefinition) | FirstProductChoice.Process | First product definition comes from? |
| Chemical.Interfaces.Definition | firstProduct (from PartialReactionWithProductsDefinition) | dropOfCommons.DefaultSubstance | First product definition as Substance |
| Chemical.Interfaces.Definition[:] | nextProducts (from PartialReactionWithProductsDefinition) | fill(((s*ones(nS))/(p*ones(nP)))*dropOfCommons.DefaultSubstance, max(1, nP - 1)) | Definitions of next products |
| Chemical solution (of products) | |||
| SolutionChoice | solutionFrom (from PartialSolutionSensor) | Chemical.Utilities.Types.SolutionChoice.FirstSubstrate | Chemical solution comes from? |
| Chemical.Interfaces.SolutionState | solutionParam (from PartialSolutionSensor) | Chemical.Interfaces.SolutionState(phase = Chemical.Interfaces.Phase.Incompressible) | Chemical solution state as Parameter |
Connectors
| Type | Name | Default | Description |
|---|---|---|---|
| Chemical.Interfaces.Rear[nS] | substrates (from PartialReaction) | ||
| Chemical.Interfaces.Fore[nP] | products (from PartialReaction) | ||
| Chemical.Interfaces.SolutionPort | solution (from PartialSolutionSensor) | To connect substance with solution, where is pressented | |
| Modelica.Blocks.Interfaces.RealInput | e0 | Initial enzyme concentration |
Components
| Type | Name | Default | Description |
|---|---|---|---|
| Modelica.Units.SI.MolarFlowRate | rr (from PartialReaction) | Reaction molar flow rate | |
| Chemical.Interfaces.SolutionState | solutionState (from PartialSolutionSensor) |
Revisions
2013-2020 by Marek Matejak, Charles University, Prague, Czech Republic