I'm really glad you're getting into this stuff, you're obviously a smart guy and I think it's going to be great having you on the team.
Alongside that I want to say that this is not a new model, we have been talking about this stuff for quite a while now. If you are interested you can check out this thread
or have a look at what I wrote about the CPA model in the gdd channel on slack (about 3 posts up). We have already decided on a L-K type model for predation alongside a chemical model (both of which are based on random collisions between particles, interestingly) for the processes inside the microbes. I'll try to describe the chemical part of the system now. So yes there is some stuff that needs to be fleshed out and formalised however this is not a new problem. Once you've understood where we are at then I'll happily listen to what you have to say about improvements and upgrades to the system (or even large changes) as you obviously have the expertise to help.
So yes as you say this is a separate system from the "swimming around" which the player does in the single player. When we talk about patches there is some debate about size but we could be talking about 100,000 sq km and all the microbes that live in an area that big (to keep the numbers more manageable we may be talking about a representative sample of a smaller size). However the CPA model is designed for populations in the billions, and as such the swimming around will have no impact on it.
So this model will run in the background of the patch the player is playing in. The players experience will then be slaved to the CPA model for that patch. So if species A is dominant in the model then the player will meet a lot of species A as it swims around. As you evolve your microbe in the editor you will need to think both about what you want as the player and what will help your species (you will get some info on the plight of your species in the editor) that's the main reason why it's important to model the swimming around as closely as possible with the CPA system because, ideally, you want the best choice for your species to be the best choice for you as the player. So that's how the two parts will be related. This relationship will be the same for all the creature stages up to society where things really change.
The species is basically considered as a giant sack of compounds and the sack has two sub-divisions or pools. One is compounds locked and one is compounds free. So at the start all the compounds are in the free pool and then they are transferred to the locked pool proportionally to how many there are. This represents the microbes locking compounds away in their cytoskeletons and cell membranes etc. There is also a flow from the compounds locked pool into the environment representing the death of the species. So for a one compound system
d(Compounds Free)/dt = + (Compounds in from the environment) - (growth rate)* (Compounds Free)
d(Compounds Locked)/dt = + (growth rate)* (Compounds Free) - (death rate)* (Compounds Locked)
Now obviously things are more complicated than this, there are many compounds all being converted from one type to another and locked away in proportion to the "blueprint" of the species (number of organelles of different types).
The population number is then derived from the (compounds locked)/(mass of a single member).
The problem then becomes using this population number and the blueprint of the species use an L-K style model to build a food web for transferring compounds from one species (both pools) to another or to the environment. And that's what I was suggesting we work on when I posed the problem to you the other day.
So yes I misunderstood some of your notation, apologies, I mixed up d_xy and c_xy. What we want finally is, as you say, "the overall compound transfer over a certain period of time". Once we have that we are pretty much set as we can plug it into the other half of the model and we are done.
I'm not exactly sure what you mean when you say mass-action (do you mean it's based on a the chance of randomly moving individuals bumping into each other?) or implicit vs explicit.
For pack hunters I would suggest we consider them to just be larger blobs. So they are less likely to encounter other species but whenever they do (as prey or predators) they get a boost to their "fight power", however we end up determining that.
Does this all make sense? Please ask if you have any questions about it.