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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