In this paper we take an extended reaction scheme framework to model general genetic regulatory pathways. Extended reaction schemes are an extension of normal chemical reaction schemes. Extended reaction schemes allow molecules to be structured not only by type (or species) and their copy numbers, but in addition allow to attach to any type of molecule discrete internal states.
Biological and (Bio)Medical Complexity
One of the most important open problems in ecosystem modeling is explaining the origin of biodiversity in competitive ecosystems: these are most commonly described mathematically using MacArthur's consumer-resource model, leading to the ‘‘competitive exclusion principle’’ which limits the number of coexisting competing species to the number of available resources. Nevertheless, several empirical evidences - like the ‘‘paradox of the plankton’’, but also bacterial community culture experiments - show that this principle is violated in real ecosystems.