051958
constant: false
value: NaN
name: v_stim
type: Parameter

634858
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

634870
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

051936
constant: true
value: 0.5
name: Km_ATP
type: Parameter

634809
unit: 634833
unit: 634821
name: mM
type: SBMLUnitsDef

051963
constant: true
value: 50.0
name: to
type: Parameter

051879
constant: false
value: 0.0405
name: GAP
type: Parameter

634821
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

051943
constant: false
value: NaN
name: ADP
type: Parameter

635185
exponent: -2.0
scale: -2
multipler: 1.0
kind: METRE
type: SBMLUnit

051916
constant: true
value: 1.0
name: Vmax_op
type: Parameter

051906
constant: true
value: 0.01
name: Km_F6P_pfk2
type: Parameter

051957
constant: true
value: 0.05
name: Ka_AMP
type: Parameter

635029
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

051925
constant: false
value: NaN
name: V_ck
type: Parameter

051976
constant: true
value: 2.0
name: nh_amp
type: Parameter

634907
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

051883
constant: false
value: 2.402
name: ATP
type: Parameter

051895
constant: true
value: 0.05
name: Km_ATP_pfk
type: Parameter

051877
constant: false
value: 0.001
name: F26P
type: Parameter

051942
constant: true
value: 0.641
name: K_LAC
type: Parameter

051915
constant: false
value: NaN
name: V_op
type: Parameter

635041
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

635221
unit: 635233
name: time
type: SBMLUnitsDef

635125
unit: 635149
unit: 635137
name: L_per_millimole
type: SBMLUnitsDef

051924
constant: true
value: 2.5355
name: kr_ldh
type: Parameter

051975
constant: true
value: 0.005
name: Kamp_pfk2
type: Parameter

051946
constant: false
value: NaN
name: dAMP_dATP
type: Parameter

051894
constant: true
value: 3.85
name: Vmax_pfk
type: Parameter

635101
exponent: 1.0
scale: 0
multipler: 1.0
kind: COULOMB
type: SBMLUnit

634931
unit: 634968
unit: 634955
unit: 634943
name: per_mM_s
type: SBMLUnitsDef

051882
constant: false
value: 0.5
name: LAC
type: Parameter

634882
unit: 634919
unit: 634907
unit: 634895
name: mM_per_s
type: SBMLUnitsDef

051918
constant: true
value: 0.005
name: Km_ADP_op
type: Parameter

635089
unit: 635113
unit: 635101
name: C_per_mole
type: SBMLUnitsDef

051966
constant: true
value: 0.5
name: v1_n
type: Parameter

635209
exponent: 1.0
scale: -3
multipler: 1.0
kind: VOLT
type: SBMLUnit

635173
exponent: 1.0
scale: -3
multipler: 1.0
kind: SIEMENS
type: SBMLUnit

051904
constant: true
value: 0.05
name: Km_ATP_pfk2
type: Parameter

051955
constant: true
value: 0.5
name: nAMP
type: Parameter

051945
constant: false
value: NaN
name: u
type: Parameter

051937
constant: false
value: NaN
name: V_lac
type: Parameter

634919
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

051964
constant: true
value: 200.0
name: tend
type: Parameter

635233
exponent: 1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

634895
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

051832
constant: true
units: litre
size: 1.0
spatial dimensions: 3.0
type: Compartment

635113
exponent: -1.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

051903
constant: true
value: 1.036E-4
name: Vmaxr_pfk2
type: Parameter

051954
constant: false
value: NaN
name: AMP_act
type: Parameter

635053
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

051888
constant: true
value: 2.5
name: Vmax_hk
type: Parameter

051930
constant: false
value: NaN
name: Cr
type: Parameter

634968
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

635161
unit: 635185
unit: 635173
name: mS_per_cm2
type: SBMLUnitsDef

635077
exponent: -1.0
scale: -2
multipler: 1.0
kind: METRE
type: SBMLUnit

634943
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

635005
unit: 635053
unit: 635041
unit: 635029
unit: 635017
name: cm_per_mM_s
type: SBMLUnitsDef

051891
constant: true
value: 0.068
name: KI_F6P
type: Parameter

051912
constant: true
value: 0.005
name: Km_ADP_pk
type: Parameter

051889
constant: true
value: 0.5
name: Km_ATP_hk
type: Parameter

051973
constant: false
value: NaN
name: AMP_pfk2
type: Parameter

051919
constant: true
value: 0.5
name: Km_PYR_op
type: Parameter

051939
constant: true
value: 0.355
name: Vlac_0
type: Parameter

051921
constant: false
value: NaN
name: V_ldh
type: Parameter

051910
constant: true
value: 5.0
name: Vmax_pk
type: Parameter

635197
unit: 635209
name: mV
type: SBMLUnitsDef

051931
constant: true
value: 20.0
name: PCrtot
type: Parameter

051909
constant: false
value: NaN
name: V_pk
type: Parameter

635149
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

634833
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

051892
constant: false
value: NaN
name: V_pfk
type: Parameter

051952
constant: true
value: 1.0
name: KI_ATP
type: Parameter

051948
constant: false
value: NaN
name: AMP
type: Parameter

051901
constant: true
value: 2.0E-4
name: Vmaxf_pfk2
type: Parameter

634797
exponent: 1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

051922
constant: true
value: 12.5
name: kf_ldh
type: Parameter

051972
constant: true
value: 0.92
name: Q_adk
type: Parameter

051967
constant: true
value: 0.0
name: v2_n
type: Parameter

634980
unit: 634993
name: per_s
type: SBMLUnitsDef

MODEL1006230096
units def: 635161
parameter: 051877
units def: 634845
parameter: 051886
parameter: 051907
parameter: 051943
parameter: 051916
parameter: 051952
units def: 635089
parameter: 051969
rule: 051872
rule: 051862
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…
rule: 051854
parameter: 051901
parameter: 051934
parameter: 051898
parameter: 051910
parameter: 051897
rule: 051868
units def: 634980
rule: 051847
parameter: 051964
parameter: 051928
parameter: 051963
parameter: 051927
parameter: 051937
parameter: 051973
parameter: 051936
parameter: 051972
rule: 051839
name: Cloutier2009_EnergyMetabolism_ModelF
volume units: 290956
curated: false
time units: 635221
substance units: 178797
type: SBMLModel
parameter: 051879
parameter: 051889
parameter: 051946
parameter: 051888
parameter: 051945
parameter: 051909
parameter: 051919
parameter: 051955
parameter: 051918
parameter: 051954
parameter: 051880
units def: 635197
units def: 635125
parameter: 051948
units def: 634809
parameter: 051883
parameter: 051882
parameter: 051904
parameter: 051940
parameter: 051903
parameter: 051913
rule: 051871
parameter: 051912
rule: 051851
rule: 051853
rule: 051857
rule: 051842
parameter: 051966
parameter: 051939
parameter: 051975
rule: 051874
rule: 051838
rule: 051836
parameter: 051922
rule: 051866
parameter: 051921
parameter: 051931
parameter: 051894
parameter: 051930
units def: 635221
length unit: 821056
units def: 634931
units def: 635005

051886
constant: false
value: NaN
name: V_hk
type: Parameter

051898
constant: true
value: 0.01
name: Km_F26P_pfk
type: Parameter

635065
unit: 635077
name: per_cm
type: SBMLUnitsDef

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

051928
constant: true
value: 1.26
name: kr_ck
type: Parameter

051876
constant: false
value: 0.2
name: F6P
type: Parameter

051933
constant: false
value: NaN
name: V_ATPase
type: Parameter

051961
constant: true
value: 1.0
name: stim
type: Parameter

051949
constant: false
value: NaN
name: ATP_inh
type: Parameter

051951
constant: true
value: 0.4
name: nATP
type: Parameter

051900
constant: false
value: NaN
name: V_pfk2
type: Parameter

634993
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

W3 CDTF: Fri Jun 25 14:47:33 BST 2010

634955
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

635017
exponent: 1.0
scale: -2
multipler: 1.0
kind: METRE
type: SBMLUnit

051885
constant: false
value: 18.14
name: PCr
type: Parameter

051907
constant: true
value: 1.0E-4
name: Km_F26P_pfk2
type: Parameter

051897
constant: true
value: 0.18
name: Km_F6P_pfk
type: Parameter

051927
constant: true
value: 3.0
name: kf_ck
type: Parameter

051960
constant: false
value: NaN
name: unitpulseSB
type: Parameter

051934
constant: true
value: 0.9355
name: Vmax_ATPase
type: Parameter

051880
constant: false
value: 0.1
name: PYR
type: Parameter

635137
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

634845
unit: 634870
unit: 634858
name: per_mM
type: SBMLUnitsDef

051969
constant: true
value: 2.0
name: t_n_stim
type: Parameter

051940
constant: true
value: 0.71
name: K_LAC_eff
type: Parameter

634785
unit: 634797
name: s
type: SBMLUnitsDef

051970
constant: true
value: 2.51
name: ANP
type: Parameter

051913
constant: true
value: 0.4
name: Km_GAP_pk
type: Parameter

given: Catherine
family: Lloyd

W3 CDTF: Fri Jun 25 14:47:33 BST 2010

ORG:
  orgname: University of Auckland

W3 CDTF: Fri Jun 25 14:47:33 BST 2010

orgname: University of Auckland

given: Catherine
family: Lloyd

W3 CDTF: Fri Jun 25 14:47:33 BST 2010