Table 1.

Summary of Standard Parameters for the Simulations Reported in This Work

Category	Parameter	Valuea
Genetic algorithm	Tournament size	2
	Promoter region mutation rate (μp)	0.001 mutations/bp/generation
	Recognizer mutation rate (μr)	0.005 mutations/weight/generation
	Population size	500
	Maximum number of generations	15,000
	Stopping criteria	Max generation & optimal fitness
	Recognizer weight initialization	0
	Promoter region base initialization	Uniform
Regulatory network	Promoter regions	16
	Size of promoter regions	32 bp
	Length of binding sites	16 bp
Genome	Size	10,000 bp
	Sequence	Random 50% GC/E. coli
Fitness model	Wild-type enzyme concentration	1 μM
	Benefit parameter (δ)	0.17
	Cost parameter (η)	0.02
	Maximum enzyme concentration (M)	1.8
	Michaelis constant of LacY (KY)	0.4 mM
Occupancy model	Distribution of transcription factor	Boltzmann
	Temperature	30°C
	Nonspecific binding	−8 kcal/mol
	Expression function	Max occupancy in promoter

^aVariations to these parameters are explicitly noted in the text.