502247
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

937684
constant: true
value: 0.005
name: Km_ADP_pk
type: Parameter

502337
exponent: 1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

502101
unit: 502150
unit: 502138
unit: 502126
unit: 502113
name: cm_per_mM_s
type: SBMLUnitsDef

937722
constant: true
value: 0.5
name: nAMP
type: Parameter

937664
constant: true
value: 0.5
name: Km_ATP_hk
type: Parameter

502272
exponent: 1.0
scale: -3
multipler: 1.0
kind: SIEMENS
type: SBMLUnit

937674
constant: true
value: 0.0
name: Vmaxf_pfk2
type: Parameter

502028
unit: 502064
unit: 502052
unit: 502040
name: per_mM_s
type: SBMLUnitsDef

937716
constant: false
value: NaN
name: AMP
type: Parameter

501943
unit: 501967
unit: 501955
name: per_mM
type: SBMLUnitsDef

937693
constant: true
value: 0.0
name: kf_ldh
type: Parameter

937702
constant: false
value: NaN
name: V_ATPase
type: Parameter

937740
constant: true
value: 0.005
name: Kamp_pfk2
type: Parameter

937654
constant: false
value: 0.0405
name: GAP
type: Parameter

937737
constant: true
value: 0.92
name: Q_adk
type: Parameter

502174
exponent: -1.0
scale: -2
multipler: 1.0
kind: METRE
type: SBMLUnit

501895
exponent: 1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

502235
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

937653
constant: false
value: 0.001
name: F26P
type: Parameter

937673
constant: false
value: NaN
name: V_pfk2
type: Parameter

502040
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

937741
constant: true
value: 2.0
name: nh_amp
type: Parameter

937694
constant: true
value: 0.0
name: kr_ldh
type: Parameter

502113
exponent: 1.0
scale: -2
multipler: 1.0
kind: METRE
type: SBMLUnit

937736
constant: true
value: 2.51
name: ANP
type: Parameter

937717
constant: false
value: NaN
name: ATP_inh
type: Parameter

937710
constant: true
value: 0.641
name: K_LAC
type: Parameter

937652
constant: false
value: 0.2
name: F6P
type: Parameter

937686
constant: false
value: NaN
name: V_op
type: Parameter

502222
unit: 502247
unit: 502235
name: L_per_millimole
type: SBMLUnitsDef

W3 CDTF: Fri Jun 25 14:28:59 BST 2010

502259
unit: 502285
unit: 502272
name: mS_per_cm2
type: SBMLUnitsDef

502186
unit: 502210
unit: 502198
name: C_per_mole
type: SBMLUnitsDef

502088
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

937672
constant: true
value: 0.01
name: Km_F26P_pfk
type: Parameter

937708
constant: true
value: 0.355
name: Vlac_0
type: Parameter

937720
constant: true
value: 1.0
name: KI_ATP
type: Parameter

502126
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

937666
constant: false
value: NaN
name: V_pfk
type: Parameter

937700
constant: false
value: NaN
name: Cr
type: Parameter

937728
constant: true
value: 1.0
name: stim
type: Parameter

937718
constant: true
value: 0.4
name: nATP
type: Parameter

501955
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

937685
constant: true
value: 0.4
name: Km_GAP_pk
type: Parameter

501883
unit: 501895
name: s
type: SBMLUnitsDef

937615
constant: true
units: litre
size: 1.0
spatial dimensions: 3.0
type: Compartment

937721
constant: false
value: NaN
name: AMP_act
type: Parameter

937709
constant: true
value: 0.71
name: K_LAC_eff
type: Parameter

937665
constant: true
value: 0.068
name: KI_F6P
type: Parameter

937692
constant: false
value: NaN
name: V_ldh
type: Parameter

937729
constant: true
value: 50.0
name: to
type: Parameter

937701
constant: true
value: 20.0
name: PCrtot
type: Parameter

502298
unit: 502311
name: mV
type: SBMLUnitsDef

937738
constant: false
value: NaN
name: AMP_pfk2
type: Parameter

MODEL1006230068
parameter: 937708
parameter: 937722
parameter: 937690
parameter: 937677
parameter: 937673
units def: 501883
parameter: 937681
rule: 937640
type: SBMLModel
rule: 937631
rule: 937644
units def: 502028
parameter: 937738
parameter: 937733
units def: 502222
parameter: 937697
parameter: 937669
parameter: 937692
rule: 937623
parameter: 937657
parameter: 937652
rule: 937629
parameter: 937729
rule: 937650
parameter: 937725
parameter: 937694
curated: false
parameter: 937688
parameter: 937654
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: 937684
units def: 501943
units def: 502324
rule: 937619
rule: 937630
rule: 937634
units def: 502101
parameter: 937720
parameter: 937709
rule: 937639
parameter: 937678
parameter: 937674
length unit: 725586
parameter: 937668
parameter: 937682
rule: 937620
is described by: http://identifiers.org/pubmed/19828503
parameter: 937736
rule: 937643
parameter: 937710
name: Cloutier2009_EnergyMetabolism_ModelC
parameter: 937704
parameter: 937700
rule: 937618
parameter: 937734
parameter: 937706
parameter: 937702
rule: 937638
rule: 937635
parameter: 937693
parameter: 937665
rule: 937648
time units: 502324
parameter: 937653
parameter: 937661
parameter: 937717
units def: 502162
parameter: 937713
rule: 937622
units def: 501907
parameter: 937726
parameter: 937721
rule: 937628
parameter: 937676
compartment: 937615
parameter: 937740
parameter: 937689
units def: 502186
parameter: 937672
area units: 291053

502052
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

937670
constant: true
value: 0.18
name: Km_F6P_pfk
type: Parameter

937706
constant: false
value: NaN
name: V_lac
type: Parameter

937726
constant: false
value: NaN
name: unitpulseSB
type: Parameter

937688
constant: true
value: 1.0
name: Vmax_op
type: Parameter

ORG:
  orgname: University of Auckland
n:
  given: Catherine
  family: Lloyd

502138
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

937678
constant: true
value: 0.01
name: Km_F6P_pfk2
type: Parameter

937712
constant: false
value: NaN
name: ADP
type: Parameter

937690
constant: true
value: 0.5
name: Km_PYR_op
type: Parameter

502150
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

937680
constant: true
value: 1.0E-4
name: Km_F26P_pfk2
type: Parameter

502210
exponent: -1.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

502076
unit: 502088
name: per_s
type: SBMLUnitsDef

937660
constant: false
value: 18.14
name: PCr
type: Parameter

937658
constant: false
value: 2.402
name: ATP
type: Parameter

502324
unit: 502337
name: time
type: SBMLUnitsDef

937733
constant: true
value: 0.0
name: v2_n
type: Parameter

937697
constant: true
value: 0.0
name: kf_ck
type: Parameter

937668
constant: true
value: 3.85
name: Vmax_pfk
type: Parameter

502004
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

937698
constant: true
value: 0.0
name: kr_ck
type: Parameter

937713
constant: false
value: NaN
name: u
type: Parameter

501919
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

937730
constant: true
value: 200.0
name: tend
type: Parameter

937677
constant: true
value: 0.05
name: Km_ATP_pfk2
type: Parameter

501979
unit: 502016
unit: 502004
unit: 501992
name: mM_per_s
type: SBMLUnitsDef

937657
constant: false
value: 0.5
name: LAC
type: Parameter

937732
constant: true
value: 0.5
name: v1_n
type: Parameter

937724
constant: true
value: 0.05
name: Ka_AMP
type: Parameter

502064
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

502162
unit: 502174
name: per_cm
type: SBMLUnitsDef

501931
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

937682
constant: true
value: 5.0
name: Vmax_pk
type: Parameter

937704
constant: true
value: 0.9355
name: Vmax_ATPase
type: Parameter

937676
constant: true
value: 0.0
name: Vmaxr_pfk2
type: Parameter

502285
exponent: -2.0
scale: -2
multipler: 1.0
kind: METRE
type: SBMLUnit

937714
constant: false
value: NaN
name: dAMP_dATP
type: Parameter

W3 CDTF: Fri Jun 25 14:28:59 BST 2010

937656
constant: false
value: 0.1
name: PYR
type: Parameter

937662
constant: true
value: 2.5
name: Vmax_hk
type: Parameter

501907
unit: 501931
unit: 501919
name: mM
type: SBMLUnitsDef

937689
constant: true
value: 0.005
name: Km_ADP_op
type: Parameter

937725
constant: false
value: NaN
name: v_stim
type: Parameter

501992
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

501967
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

937705
constant: true
value: 0.5
name: Km_ATP
type: Parameter

502016
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

937681
constant: false
value: NaN
name: V_pk
type: Parameter

502198
exponent: 1.0
scale: 0
multipler: 1.0
kind: COULOMB
type: SBMLUnit

937734
constant: true
value: 2.0
name: t_n_stim
type: Parameter

937661
constant: false
value: NaN
name: V_hk
type: Parameter

937696
constant: false
value: NaN
name: V_ck
type: Parameter

502311
exponent: 1.0
scale: -3
multipler: 1.0
kind: VOLT
type: SBMLUnit

937669
constant: true
value: 0.05
name: Km_ATP_pfk
type: Parameter

W3 CDTF: Fri Jun 25 14:28:59 BST 2010

orgname: University of Auckland

given: Catherine
family: Lloyd

W3 CDTF: Fri Jun 25 14:28:59 BST 2010

given: Catherine
family: Lloyd

ORG:
  orgname: University of Auckland