162548
constant: false
value: NaN
name: V_ATPase
type: Parameter

162609
constant: true
value: 0.92
name: Q_adk
type: Parameter

162560
constant: true
value: 0.355
name: Vlac_0
type: Parameter

162503
constant: true
value: 5.0
name: Vmax_pk
type: Parameter

W3 CDTF: Fri Jun 25 13:26:04 BST 2010

277962
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

162458
constant: true
value: 2.5
name: Vmax_hk
type: Parameter

277890
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

162569
constant: false
value: NaN
name: ADP
type: Parameter

162464
constant: true
value: 0.068
name: KI_F6P
type: Parameter

277865
unit: 277902
unit: 277890
unit: 277878
name: per_mM_s
type: SBMLUnitsDef

162598
constant: true
value: 1.0
name: stim
type: Parameter

162437
constant: false
value: 0.001
name: F26P
type: Parameter

277731
exponent: 1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

162360
constant: true
units: litre
size: 1.0
spatial dimensions: 3.0
type: Compartment

278132
unit: 278144
name: mV
type: SBMLUnitsDef

162601
constant: true
value: 50.0
name: to
type: Parameter

162578
constant: false
value: NaN
name: AMP
type: Parameter

278107
exponent: 1.0
scale: -3
multipler: 1.0
kind: SIEMENS
type: SBMLUnit

277998
unit: 278011
name: per_cm
type: SBMLUnitsDef

277792
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

162539
constant: true
value: 0.0
name: kr_ck
type: Parameter

162443
constant: false
value: 0.1
name: PYR
type: Parameter

277914
unit: 277926
name: per_s
type: SBMLUnitsDef

162530
constant: true
value: 0.0
name: kr_ldh
type: Parameter

277878
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

277950
exponent: 1.0
scale: -2
multipler: 1.0
kind: METRE
type: SBMLUnit

277744
unit: 277768
unit: 277756
name: mM
type: SBMLUnitsDef

162446
constant: false
value: 0.5
name: LAC
type: Parameter

162476
constant: true
value: 0.18
name: Km_F6P_pfk
type: Parameter

162557
constant: false
value: NaN
name: V_lac
type: Parameter

162536
constant: true
value: 0.0
name: kf_ck
type: Parameter

162595
constant: true
value: 0.05
name: Ka_AMP
type: Parameter

278144
exponent: 1.0
scale: -3
multipler: 1.0
kind: VOLT
type: SBMLUnit

162596
constant: false
value: NaN
name: v_stim
type: Parameter

162491
constant: true
value: 0.05
name: Km_ATP_pfk2
type: Parameter

278011
exponent: -1.0
scale: -2
multipler: 1.0
kind: METRE
type: SBMLUnit

162509
constant: true
value: 0.4
name: Km_GAP_pk
type: Parameter

162581
constant: false
value: NaN
name: ATP_inh
type: Parameter

162563
constant: true
value: 0.71
name: K_LAC_eff
type: Parameter

162603
constant: true
value: 200.0
name: tend
type: Parameter

162500
constant: false
value: NaN
name: V_pk
type: Parameter

162521
constant: true
value: 0.5
name: Km_PYR_op
type: Parameter

162455
constant: false
value: NaN
name: V_hk
type: Parameter

162614
constant: true
value: 2.0
name: nh_amp
type: Parameter

162597
constant: false
value: NaN
name: unitpulseSB
type: Parameter

162604
constant: true
value: 0.5
name: v1_n
type: Parameter

277719
unit: 277731
name: s
type: SBMLUnitsDef

W3 CDTF: Fri Jun 25 13:26:04 BST 2010

162542
constant: false
value: NaN
name: Cr
type: Parameter

162488
constant: true
value: 0.0
name: Vmaxr_pfk2
type: Parameter

162518
constant: true
value: 0.005
name: Km_ADP_op
type: Parameter

277902
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

278095
unit: 278120
unit: 278107
name: mS_per_cm2
type: SBMLUnitsDef

278083
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

278023
unit: 278047
unit: 278035
name: C_per_mole
type: SBMLUnitsDef

162593
constant: true
value: 0.5
name: nAMP
type: Parameter

162494
constant: true
value: 0.01
name: Km_F6P_pfk2
type: Parameter

278156
unit: 278168
name: time
type: SBMLUnitsDef

162605
constant: true
value: 0.0
name: v2_n
type: Parameter

162473
constant: true
value: 0.05
name: Km_ATP_pfk
type: Parameter

162527
constant: true
value: 0.0
name: kf_ldh
type: Parameter

277756
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

162611
constant: true
value: 0.005
name: Kamp_pfk2
type: Parameter

277804
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

162545
constant: true
value: 20.0
name: PCrtot
type: Parameter

162506
constant: true
value: 0.005
name: Km_ADP_pk
type: Parameter

162575
constant: false
value: NaN
name: dAMP_dATP
type: Parameter

277938
unit: 277986
unit: 277974
unit: 277962
unit: 277950
name: cm_per_mM_s
type: SBMLUnitsDef

162485
constant: true
value: 0.0
name: Vmaxf_pfk2
type: Parameter

MODEL1006230016
parameter: 162572
parameter: 162542
rule: 162408
parameter: 162446
units def: 278156
parameter: 162584
rule: 162366
parameter: 162539
parameter: 162512
rule: 162387
parameter: 162533
time units: 278156
parameter: 162458
parameter: 162524
parameter: 162485
parameter: 162611
parameter: 162593
parameter: 162563
units def: 277744
parameter: 162470
rule: 162369
parameter: 162449
units def: 277998
type: SBMLModel
parameter: 162604
rule: 162432
parameter: 162554
rule: 162375
parameter: 162482
parameter: 162598
rule: 162420
is described by: http://identifiers.org/pubmed/19828503
parameter: 162614
parameter: 162566
rule: 162363
parameter: 162494
rule: 162414
units def: 278132
parameter: 162440
units def: 277816
parameter: 162506
parameter: 162590
parameter: 162575
rule: 162402
units def: 277865
parameter: 162452
rule: 162378
units def: 277780
parameter: 162587
notes: This a model from the article: The control systems structures of energy metabolism. Cloutier M, Wellstead P. J R Soc Interface 2010 Apr 6;7(45):651-65 19828503 , Abstract: The biochemical regulation of energy metabolism (EM) allows cells to modulate their energetic output depending on available substrates and requirements. To this end, numerous biomolecular mechanisms exist that allow the sensing of the energetic state and corresponding adjustment of enzymatic reaction rates. This regulation is known to induce dynamic systems properties such as oscillations or perfect adaptation. Although the various mechanisms of energy regulation have been studied in detail from many angles at the experimental and theoretical levels, no framework is available for the systematic analysis of EM from a control systems perspective. In this study, we have used principles well known in control to clarify the basic system features that govern EM. The major result is a subdivision of the biomolecular mechanisms of energy regulation in terms of widely used engineering control mechanisms: proportional, integral, derivative control, and structures: feedback, cascade and feed-forward control. Evidence for each mechanism and structure is demonstrated and the implications for systems properties are shown through simulations. As the equivalence between biological systems and control components presented here is generic, it is also hypothesized that our work could eventually have an applicability that is much wider than the focus of the current study. This model was taken from the CellML repository and automatically converted to SBML. The original model was: Cloutier M, Wellstead P. (2009) - version=1.0 The original CellML model was created by: Catherine Lloyd c.lloyd@auckland.ac.nz The University of Auckland This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent…
parameter: 162461
parameter: 162527
parameter: 162479
parameter: 162521
parameter: 162473
rule: 162423
parameter: 162610
parameter: 162609
parameter: 162518
units def: 277938
rule: 162411
parameter: 162603
parameter: 162434
parameter: 162545
rule: 162390
units def: 278095
units def: 277719
parameter: 162500
units def: 278023
rule: 162426
parameter: 162497
rule: 162384
parameter: 162491
rule: 162365
name: Cloutier2009_EnergyMetabolism_ModelB
rule: 162372
compartment: 162360
parameter: 162488
parameter: 162596
area units: area

162606
constant: true
value: 2.0
name: t_n_stim
type: Parameter

162554
constant: true
value: 0.5
name: Km_ATP
type: Parameter

162452
constant: false
value: 18.14
name: PCr
type: Parameter

278059
unit: 278083
unit: 278071
name: L_per_millimole
type: SBMLUnitsDef

162467
constant: false
value: NaN
name: V_pfk
type: Parameter

162584
constant: true
value: 0.4
name: nATP
type: Parameter

162512
constant: false
value: NaN
name: V_op
type: Parameter

162434
constant: false
value: 0.2
name: F6P
type: Parameter

277816
unit: 277852
unit: 277840
unit: 277828
name: mM_per_s
type: SBMLUnitsDef

277840
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

162590
constant: false
value: NaN
name: AMP_act
type: Parameter

278168
exponent: 1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

277780
unit: 277804
unit: 277792
name: per_mM
type: SBMLUnitsDef

278071
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

278035
exponent: 1.0
scale: 0
multipler: 1.0
kind: COULOMB
type: SBMLUnit

162482
constant: false
value: NaN
name: V_pfk2
type: Parameter

277768
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

162533
constant: false
value: NaN
name: V_ck
type: Parameter

277974
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

162515
constant: true
value: 1.0
name: Vmax_op
type: Parameter

162461
constant: true
value: 0.5
name: Km_ATP_hk
type: Parameter

162497
constant: true
value: 1.0E-4
name: Km_F26P_pfk2
type: Parameter

277986
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

162440
constant: false
value: 0.0405
name: GAP
type: Parameter

162566
constant: true
value: 0.641
name: K_LAC
type: Parameter

162449
constant: false
value: 2.402
name: ATP
type: Parameter

162608
constant: true
value: 2.51
name: ANP
type: Parameter

277926
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

278120
exponent: -2.0
scale: -2
multipler: 1.0
kind: METRE
type: SBMLUnit

162587
constant: true
value: 1.0
name: KI_ATP
type: Parameter

162524
constant: false
value: NaN
name: V_ldh
type: Parameter

277828
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

277852
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

162551
constant: true
value: 0.9355
name: Vmax_ATPase
type: Parameter

162470
constant: true
value: 3.85
name: Vmax_pfk
type: Parameter

162479
constant: true
value: 0.01
name: Km_F26P_pfk
type: Parameter

278047
exponent: -1.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

162610
constant: false
value: NaN
name: AMP_pfk2
type: Parameter

162572
constant: false
value: NaN
name: u
type: Parameter

orgname: University of Auckland

given: Catherine
family: Lloyd

orgname: University of Auckland

W3 CDTF: Fri Jun 25 13:26:04 BST 2010

W3 CDTF: Fri Jun 25 13:26:04 BST 2010

given: Catherine
family: Lloyd

given: Catherine
family: Lloyd

ORG:
  orgname: University of Auckland