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 | Â |
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 | Â |
Z* | maximum achievable growth rate | Â |
Z 1 | minimal total flux through the network | Â |
δ | perturbation |  |
ε | elasticity | m × n |
ε' | unscaled elasticity matrix | m × n |