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 j^{th} 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 | m_{0} × 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 |