This article details a modification in the identification of volumes related to reversible reactions within the QSP software, aimed at simplifying their use.
Key Enhancements in QSP Software for Reversible Reactions
A key component of most models built within the QSP software is reaction nodes, which can represent chemical or biological reactions or, more generally, any process that can be described as a term in an ordinary differential equation (ODE). A chemical or biological reaction typically simplifies the transitions between two different states of a system, corresponding to different local bonds or bindings between the smaller, indivisible elements comprising the system. These different states generally have different free energies and a free energy barrier between them. Often, the free energies are such that the system is always in a mixed state where, locally, some parts have bonds or bindings corresponding to one state and others to the other state. In such situations, there may be significant overall fluxes in both directions, making the reaction reversible.
In the previous version of the QSP software, a new property of reaction nodes, "Reverse Rate," was introduced, along with an associated visual indication of when it is in use. This property allows for clear and uncluttered modeling of reversible reactions.
Another feature of the QSP software's handling of reactions is that the corresponding ODEs are always solved for amounts rather than concentrations. To enable this, while still allowing users to enter equations for concentrations, the software automatically determines compartments and corresponding volumes associated with reactions for multiplying reaction rates in cases where there is a mismatch in dimensionalities between reactions and updated species. In the previous version of the QSP software, only one compartment/volume would be determined for both the forward and reverse rates of a reversible reaction.
The previous implementation restricted the application of reversible reactions in cases where reactions represented transfer between two different compartments. Users could work around this restriction by including explicit reaction rates. This document describes changes that enable the automatic determination of compartments/volumes for reversible reactions to be performed separately for the forward and reverse terms, allowing easier use of reversible reactions in cases of transfer between two different compartments.
Enhanced Automatic Reaction Compartment Determination
The automatic determination of reaction compartments has been modified to identify compartments separately for the forward and reverse components according to the following rules:
Species Referenced in Rate Expression: For a given component (forward or reverse), if species are referenced in the corresponding rate expression, the reaction compartment is determined to be equal to their compartment. An error occurs if the determination of a compartment is required and not all such species are in the same compartment.
No Species Referenced: If the rate expression does not reference any species (a very unusual case), all in-scope species are considered instead. If there are none, all connected species are considered.
The second rule is included to maintain behavior consistency with previous releases as much as possible, although it will likely only affect very unusual cases.
Nonetheless, a small change compared to the behavior of previous releases will occur, but only in that some workspaces that would previously have failed verification will now pass verification and simulate. Any workspaces that would have previously passed verification and simulated will still do so, and the results will remain the same.