Physically inaccurate ModifierConnector

[AtiyahElsheikh]

The connector ModifierConnector is not precise and includes excessive unnecessary information regarding the molar flow rate of the connected reaction component.

Reasoning

• A Modifier is either an inhibitor or an activator. A Modifier (of a reaction) alone does not give enough information for the reaction component to be considered in its physical implementation. Thus, in order to prevent a client of using this connector, this connector should be declared as partial and extended by an InhibitorConnector or ActivatorConnector
• It is excessive to include the molar flow rate r as a flow variable in the connector. This is because the reaction component connected to the modifier does not influence the concentration of the modifier. The modifier does not imploy r in anyway. Thus, an accurate implementation should not consider r.

[AtiyahElsheikh]

Ok, concerning the second point, the reason why a ModifierConnector has r is to allow a substance to be connected directly to a reaction. A substance has currently a standard connector with c & r. This is graphically better than having two connectors one acting as a reactant in a reaction and another acting as a modifier.

Consequently, modifier reactions set the r of a ModifierConnector to 0, e.g. Interfaces.Reactions.Modifiers.Activator.

Now another problem arises in the package Interfaces.Reactions.Modifiers. There are many components with the name Modifier. This is meaningless, since a substance is either inhibiting or activating a reaction. A modification is generic and does not specify the physical mathematical formulation of an enzyme kinetic.

[AtiyahElsheikh]

Unfortionately, leaving the unnecessary models out, few apparently automatically generated examples within BioChem are not compiling any more as they use some of these models (with explicit implementation of enzyme kinetics).

[AtiyahElsheikh]

Now another problem arises in the package Interfaces.Reactions.Modifiers. There are many components with the name Modifier. This is meaningless, since a substance is either inhibiting or activating a reaction. A modification is generic and does not specify the physical mathematical formulation of an enzyme kinetic.

The use of the models "Modifier" would make sense if we have hierarchies of model components, e.g. for examining a modifier once as an activator and another as an inhibitor (and once without being as an influenceable modifier). Even in that case, declared connectors s.a. a1 or i1 need to be renamed, e.g. mc1 etc. Unfortunately, this may require modification of many components.