modelSpeciation
Extends from Icons.Speciation, SteadyStates.Interfaces.SteadyStateSystem (Global abstract class, for additional global state equations), Interfaces.ConditionalVolume (Chemical processes can be modeled with or without(normalized to 1 liter) variable solution volume).
Information
This block identifies one specific chemical form of one macromolecule defined by forms of its subunits (one chosen chemical species - called specie).
Only main connector called species is designed for inflow and outflow of macromolecule to/from system. The concentration in this connector is the concentration of its specific specie.
Connectors subunitSpecies[:] represent specific forms of the macromolecule subunit types. If the subnunit type occures n-times in macromolecule, the inflow is n-time greater than the inflow of macromolecule.
Initial total concentrations of subunits must be set to be right distribution of total macromolecule concentration. So the ratios between subunit concentrations are the ratios of their occurrence in macromolecule. In equilibrium are this proporties fulfilled.
For example: If the macromolecule has four identical independent subunits and each subunit can occur in two form F1 and F2, then the concentration of macromolecule specie composed only from four subunits in form F1 is species.conc=conc*fF1^4.
Where:
conc is totat concentration of macromolecule in system accumulated by species.q,
fF1 = F1/(F1+F2) is fraction of form F1 in subsystem of subunit,
4 is number of subunits (numberOfSubunit).
This block can be connected to chemical reactions such as it was the chosen species with subsystem behind. It is recommended to use this block only as an equilibrated subsystem.
Heat of chemical system.
Enthalpy of each subunit species can be presented as subunitEnthalpies[:]. Then the total enthalpy of the chemical system can be calculated by equation:
systemEnthalpy = sum(subunitEnthalpies[i] * totalSubunitAmount[i]) / totalSubsystemAmount
And the stored heat as enthalpy is systemEnthalpy*totalSubsystemAmount.
Parameters
| Type | Name | Default | Description |
|---|---|---|---|
| Types.Volume | NormalVolume (from ConditionalVolume) | 0.001 | 1 liter |
| Integer | NumberOfSubunits | 1 | Number of independent subunits occurring in molecule |
| Simulation › Simulation type | |||
| Types.SimulationType | Simulation (from SteadyStateSystem) | Dynamic with Initialization or Steady State | |
| Simulation › Equilibrium | |||
| Integer | NumberOfDependentStates (from SteadyStateSystem) | 1 | Number of additional steady state equation of the system |
| External inputs/outputs | |||
| Boolean | useNormalizedVolume (from ConditionalVolume) | true | Normalized volume of solution is 1 liter |
| Heat › External inputs/outputs | |||
| Boolean | useInternalHeatsInput | false | =true, if subunitInternalHeat inputs are used instead of parameter SubunitEnthalpies |
| Heat | |||
| Types.MolarEnergy[NumberOfSubunits] | SubunitEnthalpies | zeros(NumberOfSubunits) | Enthalpy changes of substances (can relative to one chosen specific form of chemical substance in the system) if useEnthalpiesInput=false |
Connectors
| Type | Name | Default | Description |
|---|---|---|---|
| Types.RealIO.VolumeInput | solutionVolume (from ConditionalVolume) | volume | Volume of solution |
| Interfaces.ChemicalPort_a | specificForm | Specific form composed with subunits form of subunitSpiecies | |
| Interfaces.ChemicalPort_a[NumberOfSubunits] | specificSubunitForm | Specific form of subunits of specific molecule form in connector called spieces | |
| Types.RealIO.AmountOfSubstanceInput[NumberOfSubunits] | amountOfSubunit | Total amount of the subunits in all forms | |
| Types.RealIO.AmountOfSubstanceOutput | amount | Total amount of macromolecules in this system | |
| Types.RealIO.EnergyOutput | internalHeat | Relative internal heat of all chemical forms in this system | |
| Types.RealIO.EnergyInput[NumberOfSubunits] | subunitInternalHeat | internalHeatOfSubunit |
Components
| Type | Name | Default | Description |
|---|---|---|---|
| Real[NumberOfDependentStates] | normalizedState (from SteadyStateSystem) | Normalized independent masses of the system/Normalized independent energies of the system/... This variables must always equals to ones. | |
| Types.Volume | volume (from ConditionalVolume) | Solution volume | |
| Types.Energy[NumberOfSubunits] | internalHeatOfSubunit | Internal heat of subunits |
Revisions
2013
Marek Matejak, Charles University, Prague, Czech Republic