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Table 6 Nomenclature

From: Towards a genome-scale kinetic model of cellular metabolism

Index Description Size
i species/metabolites m
j reactions n
BM subset of j: reactions with fluxes defined in BioModels 55
r subset of i: all independent metabolites m 0
Variable Description Dimensions
A N·ε' m × m
c compartment volumes m × 1
C J scaled flux control coefficients n × n
C J ' unscaled flux control coefficients n × n
C S ' unscaled concentration control coefficients m × n
e j denotes the jth standard basis vector n × 1
f vector specifying the optimized fluxes n × 1
N stoichiometric matrix m × n
L link matrix m × m 0
t time  
x metabolite concentrations m × 1
x* reference metabolite concentrations m × 1
x r independent metabolite concentrations m0 × 1
v flux vector n × 1
v* reference flux vector n × 1
v min lower bounds vector n × 1
v max upper bounds vector n × 1
v T fluxes defined in the Biomodels database 55 × 1
Z optimization objective  
Z* maximum achievable growth rate  
Z 1 minimal total flux through the network  
δ perturbation  
ε elasticity m × n
ε' unscaled elasticity matrix m × n