DSD system requirements

Automated compilation of DSD system requires DSD systems to follow a particular format. First, all involved species and complexes need to be free of pseudo-knots. Second, we distinguish signal species and fuel species. Signal species are at low concentrations and they present the information (input/output) unit. Fuel species are at high (ideally constant) concentrations and they mediate the information transfer by consuming and/or releasing signal species. After compilation, every species in the formal CRN corresponds to one signal species. Thus, all signal species must have the same domain-level constitution and structure, but they need to be independent of each other. A signal species may be a complex composed of multiple molecules.

History domains are common in many translation schemes. A history domain is considered to be an inert domain of a signal species, but it is unique to the reaction that has produced the signal species. Hence, multiple species that differ only by their history domains map to the same formal species. In the translation scheme language, a history domain is a wildcard: ?. Together with the remainder of the molecule, a species with a wildcard forms a regular-expression, matching every other species in the system that differs only by a single domain instead of ?.