TABLE 1.

Sample snapshot of the internal_state object during a whole-cell simulation^a

Type	Molecule ID	Data
BulkMolecules	WATER[c]	Total count: 18,512,198,212
	ATP[c]	Total count: 1,192,909
	APORNAP-CPLX[c]	Total count: 3,151
UniqueMolecules	activeRnaPoly	Molecule 1: {“rnaIndex”: 152, “transcriptLength”: 189}
		Molecule 2: {“rnaIndex”: 819, “transcriptLength”: 619}
	activeRibosome	Molecule 1: {“proteinIndex”: 2912, “peptideLength”: 38}
		Molecule 2: {“proteinIndex”: 919, “peptideLength”: 91}

^aMolecules constituting the internal_state can be divided into two types, BulkMolecules and UniqueMolecules, depending on whether the individual molecules can be distinguished from one another based on their unique attributes. For molecules represented as BulkMolecules, the simulation keeps track of only the total counts of the molecular species in each compartment (differentiated by a location tag, such as [c], which would indicate a molecule in the cytoplasm). For molecules represented as UniqueMolecules, the simulation keeps track of the individual attributes of each molecule.