MODEL1006230068
type: SBMLModel
parameter: 937708
parameter: 937722
parameter: 937690
parameter: 937677
parameter: 937673
units def: 501883
parameter: 937681
rule: 937640
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: 937648
rule: 937638
rule: 937635
parameter: 937693
parameter: 937665
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

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

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

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

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

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

501883
type: SBMLUnitsDef
unit: 501895
name: s

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

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

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

502064
type: SBMLUnit
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kind: SECOND

502052
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kind: LITRE

502040
type: SBMLUnit
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scale: -3
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kind: MOLE

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

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

502222
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unit: 502235
name: L_per_millimole

502247
type: SBMLUnit
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multipler: 1.0
kind: MOLE

502235
type: SBMLUnit
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kind: LITRE

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

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

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

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

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

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

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

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

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

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

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

501943
type: SBMLUnitsDef
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unit: 501955
name: per_mM

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

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

502324
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unit: 502337
name: time

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

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

502150
type: SBMLUnit
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scale: 0
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kind: SECOND

502138
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502126
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kind: MOLE

502113
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scale: -2
multipler: 1.0
kind: METRE

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

502162
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name: per_cm

502174
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kind: METRE

937713
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value: NaN
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501907
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501931
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501919
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937726
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value: NaN
name: unitpulseSB

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

937676
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value: 0.0
name: Vmaxr_pfk2

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

937740
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constant: true
value: 0.005
name: Kamp_pfk2

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

502186
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unit: 502198
name: C_per_mole

502210
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kind: MOLE

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

937672
type: Parameter
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value: 0.01
name: Km_F26P_pfk

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

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

502076
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502088
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

502259
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unit: 502272
name: mS_per_cm2

502285
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kind: METRE

502272
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scale: -3
multipler: 1.0
kind: SIEMENS

937737
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constant: true
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name: Q_adk

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

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

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

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

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

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

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

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

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

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

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

502016
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multipler: 1.0
kind: SECOND

502004
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multipler: 1.0
kind: LITRE

501992
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multipler: 1.0
kind: MOLE

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

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

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

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

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

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

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

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

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

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

502298
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name: mV

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

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

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

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

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

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

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

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

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