.Bodylight.Chemical.Components.Speciation

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.

Revisions

2013

Marek Matejak, Charles University, Prague, Czech Republic