$c_i$	Species (i) concentration
$c_x$	Biomass concentration
$c_{GLC}^{feed}$	Glucose feeding solution concentration
$c_{glc,j}^{feed}$	Glucose feeding solution concentration over the time-arc “J”
$c_{glc,0}^{ext}=c_{GLC}^{ext}(t=0)$	Initial glucose concentration in the bioreactor
$c_{GLC}^{ext}$	Glucose concentration in the bulk phase
$F_L$	Liquid feed flow rate in the bioreactor
k, $k_j$, $K_j$, K, n, $V_{2m}$, $V_{4m}$, $r_j^{\max }$, ${\mathrm{a}}_{\mathrm{x}}$, ${\mathrm{b}}_{\mathrm{x}}$, ${\mathrm{N}}_{\mathrm{x}}$, $r_{uptake}^{\max }$, $K_{PTS,a1}$, $K_{PTS,a2}$, $K_{PTS,a3}$, $V_{2m}$ g,, $K_R^{amp}$, $K_T^{atp}$, ${\mu }_T$, ${\mathrm{a}}_{\mathrm{T}}$, ${\mathrm{b}}_{\mathrm{T}}$, ${\mathrm{N}}_{\mathrm{T}}$, etc.-	Reaction rates and/or equilibrium constants of the kinetic model
$r_i$	Species (i) reaction rate
$t$, $t_{{}_f}$	Time, batch time
$V_1 - V_6$	Metabolic fluxes in the glycolysis (Table 2 and Table 3, Figure 3)
$V_L$	Liquid volume in the bioreactor
$y_{tca} , y_{trp}$	Stoichiometric coefficients
Greeks
α, β, γ, δ	Reaction rate constants
μ	Cell content dilution rate, that is $\ln (2)/t_c$, where $t_c$ denotes the cell cycle
Ω	FBR optimization objective function, Equation (10)
${\rho }_x$	Biomass density
Subscripts
0,o	Initial
cell	Referring to the cell (inside)
ext	External to cell (i.e., in the bulk phase)
f	Final
inlet	In the feed
x	Biomass
Abbreviations
13dpg, pgp	1,3-Diphosphoglycerate
3pg	3-Phosphoglycerate
2pg	2-Phosphoglycerate
AA	Amino acid
Accoa, acetyl-CoA	Acetyl-coenzyme A
AC	acetate
ADP, adp	Adenosine diphosphate
AK-ase	Adenylate kinase
ALE	Adaptive laboratory evolution
AMP, amp	Adenosine monophosphate
ATP, atp	Adenosine triphosphate
ATP-ase	ATP monophosphatase
CCM	Central carbon metabolism
CIT	Citrate
CSTR	Continuously stirred tank reactor
DO	Dissolved oxygen
DW	Dry mass
E	Enzyme anthranilate synthase in TRP synthesis model
ETOH	Ethanol
ext	External to the cell (i.e., in the bulk phase)
FBR	Fed-batch bioreactor
FDP, fdp	Fructose-1,6-biphosphate
F6P, f6p	Fructose-6-phosphate
GalP/Glk	Galactose permease/glucokinase
G3P, g3p, GAP, gap, 3PG, 3pg	Glyceraldehyde-3-phosphate
2PG, 2pg	2-Phosphoglycerate
G6P, g6p	Glucose-6-phosphate
GLC, glc	Glucose
Glc(ex), [GLC]ext	Glucose in the environment (bulk phase)
GMO	Genetically modified microorganisms
GRC	Genetic regulatory circuits
HK-ase	Hexokinase
JWS	Silicon Cell project of Olivier and Snoep [55]
LAC, lac	Lactate
Max (x)	Maxim of (x)
MMA	The adaptive random optimization algorithm of Maria [93]; Mihail and Maria [99]
mRNA	Tryptophan messenger ribonucleic acid during its encoding gene dynamic transcription and translation
NAD(P)H	Nicotinamide adenine dinucleotide (phosphate) reduced
NLP	Nonlinear programming
ODE	Ordinary differential equations set
OR	The complex between O and R (aporepressor of the TRP gene)
OT	The total TRP operon
P, Pi	Phosphoric acid
PEP, pep	Phosphoenolpyruvate
13DPG=PGP	1,3-Diphosphoglycerate
PFK-ase	Phosphofructokinase
PK-ase	Pyruvate kinase
PTS	Phosphotransferase or the phosphoenolpyruvate–glucose phosphotransferase system
PYR, pyr	Pyruvate
QSS	Quasi-steady state
R5P	Ribose 5-phosphate
mRNA	Messenger ribonucleic acid
SUCC, suc	Succinate
TCA, tca	Tricarboxylic acid cycle
TF	Gene expression transcription factors
TRP, Trp, trp	Tryptophan
X	Biomass
Wt.	Weight
[x]	Concentration of species x