023945
constant: true
value: 0.005
name: Km_ADP_pk
type: Parameter

023939
constant: true
value: 0.05
name: Km_ATP_pfk2
type: Parameter

630413
unit: 630461
unit: 630449
unit: 630437
unit: 630425
name: cm_per_mM_s
type: SBMLUnitsDef

023925
constant: true
value: 0.5
name: Km_ATP_hk
type: Parameter

023992
constant: true
value: 500.0
name: tend
type: Parameter

023931
constant: true
value: 0.05
name: Km_ATP_pfk
type: Parameter

024001
constant: true
value: 0.005
name: Kamp_pfk2
type: Parameter

630461
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

023972
constant: true
value: 0.641
name: K_LAC
type: Parameter

023951
constant: true
value: 0.005
name: Km_ADP_op
type: Parameter

023965
constant: true
value: 0.9355
name: Vmax_ATPase
type: Parameter

630245
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

630545
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

023944
constant: true
value: 5.0
name: Vmax_pk
type: Parameter

630317
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

023959
constant: true
value: 3.0
name: kf_ck
type: Parameter

023924
constant: true
value: 2.5
name: Vmax_hk
type: Parameter

023919
constant: false
value: 0.5
name: LAC
type: Parameter

023993
constant: true
value: 0.5
name: v1_n
type: Parameter

023973
constant: false
value: NaN
name: ADP
type: Parameter

630377
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

023964
constant: false
value: NaN
name: V_ATPase
type: Parameter

023983
constant: false
value: NaN
name: AMP_act
type: Parameter

630593
exponent: -2.0
scale: -2
multipler: 1.0
kind: METRE
type: SBMLUnit

630449
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

023913
constant: false
value: 0.2
name: F6P
type: Parameter

630197
unit: 630209
name: s
type: SBMLUnitsDef

630425
exponent: 1.0
scale: -2
multipler: 1.0
kind: METRE
type: SBMLUnit

023943
constant: false
value: NaN
name: V_pk
type: Parameter

023933
constant: true
value: 0.01
name: Km_F26P_pfk
type: Parameter

024003
constant: true
value: 2.0
name: nh_amp
type: Parameter

630605
unit: 630617
name: mV
type: SBMLUnitsDef

023923
constant: false
value: NaN
name: V_hk
type: Parameter

023963
constant: true
value: 20.0
name: PCrtot
type: Parameter

023953
constant: false
value: NaN
name: V_ldh
type: Parameter

630233
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

630569
unit: 630593
unit: 630581
name: mS_per_cm2
type: SBMLUnitsDef

023984
constant: true
value: 0.5
name: nAMP
type: Parameter

630305
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

630497
unit: 630521
unit: 630509
name: C_per_mole
type: SBMLUnitsDef

023932
constant: true
value: 0.18
name: Km_F6P_pfk
type: Parameter

630557
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

023979
constant: false
value: NaN
name: ATP_inh
type: Parameter

023991
constant: true
value: 50.0
name: to
type: Parameter

630581
exponent: 1.0
scale: -3
multipler: 1.0
kind: SIEMENS
type: SBMLUnit

023971
constant: true
value: 0.71
name: K_LAC_eff
type: Parameter

023999
constant: true
value: 0.92
name: Q_adk
type: Parameter

023985
constant: true
value: 0.05
name: Ka_AMP
type: Parameter

630437
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

630365
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

023952
constant: true
value: 0.5
name: Km_PYR_op
type: Parameter

023976
constant: false
value: NaN
name: dAMP_dATP
type: Parameter

023941
constant: true
value: 1.0E-4
name: Km_F26P_pfk2
type: Parameter

023996
constant: true
value: 2.0
name: t_n_stim
type: Parameter

630641
exponent: 1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

630221
unit: 630245
unit: 630233
name: mM
type: SBMLUnitsDef

023961
constant: false
value: NaN
name: Cr
type: Parameter

630389
unit: 630401
name: per_s
type: SBMLUnitsDef

023915
constant: false
value: 0.001
name: F26P
type: Parameter

630509
exponent: 1.0
scale: 0
multipler: 1.0
kind: COULOMB
type: SBMLUnit

023920
constant: false
value: 2.402
name: ATP
type: Parameter

630281
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

023969
constant: true
value: 0.355
name: Vlac_0
type: Parameter

023948
constant: false
value: NaN
name: V_op
type: Parameter

630209
exponent: 1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

023955
constant: true
value: 0.0
name: kf_ldh
type: Parameter

MODEL1006230095
parameter: 023927
rule: 023903
parameter: 023920
is described by: http://identifiers.org/pubmed/19828503
rule: 023881
parameter: 023929
parameter: 023989
units def: 630413
parameter: 023913
parameter: 023945
parameter: 023995
rule: 023894
rule: 023892
rule: 023884
parameter: 024003
parameter: 023951
parameter: 023960
parameter: 023975
parameter: 023948
parameter: 023947
parameter: 023931
units def: 630341
rule: 023897
rule: 023889
parameter: 023985
rule: 023909
parameter: 023941
parameter: 023957
rule: 023878
parameter: 023956
parameter: 023965
rule: 023902
parameter: 023921
parameter: 023971
parameter: 023980
name: Cloutier2009_EnergyMetabolism_ModelD
parameter: 023959
compartment: 023874
parameter: 023915
rule: 023905
units def: 630533
parameter: 023924
parameter: 023923
units def: 630389
parameter: 023996
rule: 023893
parameter: 023917
parameter: 023952
parameter: 023961
parameter: 023977
parameter: 023976
parameter: 023949
rule: 023880
units def: 630497
parameter: 023933
parameter: 023932
units def: 630473
rule: 023886
area units: 237671
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: 023991
units def: 630221
parameter: 024000
rule: 023906
parameter: 023935
parameter: 023968
parameter: 023967
rule: 023911
rule: 023901
units def: 630197
rule: 023899
parameter: 023973
units def: 630293
parameter: 023972
volume units: 290956
parameter: 023981
parameter: 023997
parameter: 023953
parameter: 023916
parameter: 023925

023874
constant: true
units: litre
size: 1.0
spatial dimensions: 3.0
type: Compartment

023977
constant: false
value: NaN
name: AMP
type: Parameter

630257
unit: 630281
unit: 630269
name: per_mM
type: SBMLUnitsDef

023940
constant: true
value: 0.01
name: Km_F6P_pfk2
type: Parameter

630353
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

023997
constant: true
value: 2.51
name: ANP
type: Parameter

023987
constant: false
value: NaN
name: v_stim
type: Parameter

023960
constant: true
value: 1.26
name: kr_ck
type: Parameter

023921
constant: false
value: 18.14
name: PCr
type: Parameter

023968
constant: false
value: NaN
name: V_lac
type: Parameter

630521
exponent: -1.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

023935
constant: false
value: NaN
name: V_pfk2
type: Parameter

023949
constant: true
value: 1.0
name: Vmax_op
type: Parameter

630485
exponent: -1.0
scale: -2
multipler: 1.0
kind: METRE
type: SBMLUnit

630629
unit: 630641
name: time
type: SBMLUnitsDef

023929
constant: true
value: 3.85
name: Vmax_pfk
type: Parameter

023927
constant: true
value: 0.068
name: KI_F6P
type: Parameter

023988
constant: false
value: NaN
name: unitpulseSB
type: Parameter

630401
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

023980
constant: true
value: 0.4
name: nATP
type: Parameter

023936
constant: true
value: 0.0
name: Vmaxf_pfk2
type: Parameter

023967
constant: true
value: 0.5
name: Km_ATP
type: Parameter

023928
constant: false
value: NaN
name: V_pfk
type: Parameter

630293
unit: 630329
unit: 630317
unit: 630305
name: mM_per_s
type: SBMLUnitsDef

023957
constant: false
value: NaN
name: V_ck
type: Parameter

024000
constant: false
value: NaN
name: AMP_pfk2
type: Parameter

023995
constant: true
value: 0.0
name: v2_n
type: Parameter

023975
constant: false
value: NaN
name: u
type: Parameter

630473
unit: 630485
name: per_cm
type: SBMLUnitsDef

023916
constant: false
value: 0.0405
name: GAP
type: Parameter

630269
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

023989
constant: true
value: 1.0
name: stim
type: Parameter

630617
exponent: 1.0
scale: -3
multipler: 1.0
kind: VOLT
type: SBMLUnit

630341
unit: 630377
unit: 630365
unit: 630353
name: per_mM_s
type: SBMLUnitsDef

023981
constant: true
value: 1.0
name: KI_ATP
type: Parameter

023937
constant: true
value: 0.0
name: Vmaxr_pfk2
type: Parameter

023917
constant: false
value: 0.1
name: PYR
type: Parameter

630329
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

630533
unit: 630557
unit: 630545
name: L_per_millimole
type: SBMLUnitsDef

023956
constant: true
value: 0.0
name: kr_ldh
type: Parameter

023947
constant: true
value: 0.4
name: Km_GAP_pk
type: Parameter

given: Catherine
family: Lloyd

given: Catherine
family: Lloyd

orgname: University of Auckland

ORG:
  orgname: University of Auckland

W3 CDTF: Fri Jun 25 14:47:05 BST 2010

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

W3 CDTF: Fri Jun 25 14:47:05 BST 2010

W3 CDTF: Fri Jun 25 14:47:05 BST 2010

W3 CDTF: Fri Jun 25 14:47:05 BST 2010