Table 1.

Agents, the rules they execute, and the agents they interact with

Agent	Rules	Interacts with
Promoter	transcription	ComK, ComX, DegU, Repressor
Repressor	move, bind	Promoter
Ribosome	move, bind, translation	mRNA
mRNA	move, death	Ribosome
ComK	move, bind	Promoter, ComK, MecA
ComS	move	MecA
ComX	move, bind	Promoter
DegU	move, bind	Promoter
MecA	move, bind	ComK, ComS, ClpC/ClpP
ClpC/ClpP	move, bind, death	MecA
Culture Model	diffusion	Nutrients, ComX Peptides
Cell ABM	move, shove, generatePeptide, consumePeptide, consumeNutrients, life, death	Nutrients, ComX Peptides