MODEL1006230059
type: SBMLModel
parameter: 387304
compartment: 387222
parameter: 387324
rule: 387226
rule: 387258
rule: 387256
parameter: 387356
parameter: 387336
parameter: 387273
parameter: 387289
rule: 387246
rule: 387252
rule: 387239
rule: 387244
units def: 471438
units def: 471570
rule: 387243
parameter: 387359
parameter: 387322
parameter: 387279
parameter: 387342
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: 387363
parameter: 387301
parameter: 387307
parameter: 387327
rule: 387231
parameter: 387362
parameter: 387354
rule: 387259
parameter: 387313
parameter: 387266
parameter: 387319
parameter: 387286
parameter: 387339
volume units: 290956
length unit: 076409
parameter: 387348
parameter: 387285
parameter: 387298
rule: 387250
parameter: 387280
units def: 471666
parameter: 387268
parameter: 387331
units def: 471729
rule: 387228
parameter: 387292
time units: 471729
parameter: 387316
parameter: 387271
parameter: 387325
rule: 387265
parameter: 387345
parameter: 387282
rule: 387255
rule: 387253
parameter: 387337
parameter: 387300
units def: 471353
parameter: 387274
parameter: 387357
parameter: 387294
rule: 387234
units def: 471317
units def: 471293
parameter: 387365
parameter: 387360
parameter: 387351
parameter: 387343
is described by: http://identifiers.org/pubmed/19828503
units def: 471390
units def: 471594
parameter: 387328
rule: 387249
parameter: 387283
curated: false
parameter: 387276
rule: 387262

387304
type: Parameter
constant: false
value: NaN
name: V_op

387222
type: Compartment
constant: true
units: litre
size: 1.0
spatial dimensions: 3.0

387324
type: Parameter
constant: true
value: 0.9355
name: Vmax_ATPase

387356
type: Parameter
constant: true
value: 0.5
name: v1_n

387336
type: Parameter
constant: false
value: NaN
name: dAMP_dATP

387273
type: Parameter
constant: false
value: 2.402
name: ATP

387289
type: Parameter
constant: false
value: NaN
name: V_pfk2

471438
type: SBMLUnitsDef
unit: 471474
unit: 471462
unit: 471450
name: per_mM_s

471474
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

471462
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

471450
type: SBMLUnit
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE

471570
type: SBMLUnitsDef
unit: 471582
name: per_cm

471582
type: SBMLUnit
exponent: -1.0
scale: -2
multipler: 1.0
kind: METRE

387359
type: Parameter
constant: true
value: 2.0
name: t_n_stim

387322
type: Parameter
constant: false
value: NaN
name: V_ATPase

387279
type: Parameter
constant: true
value: 0.5
name: Km_ATP_hk

387342
type: Parameter
constant: true
value: 1.0
name: KI_ATP

387363
type: Parameter
constant: false
value: NaN
name: AMP_pfk2

387301
type: Parameter
constant: true
value: 0.005
name: Km_ADP_pk

387307
type: Parameter
constant: true
value: 0.005
name: Km_ADP_op

387327
type: Parameter
constant: false
value: NaN
name: V_lac

387362
type: Parameter
constant: true
value: 0.92
name: Q_adk

387354
type: Parameter
constant: true
value: 200.0
name: tend

387313
type: Parameter
constant: true
value: 0.0
name: kr_ldh

387266
type: Parameter
constant: false
value: 0.2
name: F6P

387319
type: Parameter
constant: false
value: NaN
name: Cr

387286
type: Parameter
constant: true
value: 0.18
name: Km_F6P_pfk

387339
type: Parameter
constant: false
value: NaN
name: ATP_inh

387348
type: Parameter
constant: false
value: NaN
name: v_stim

387285
type: Parameter
constant: true
value: 0.05
name: Km_ATP_pfk

387298
type: Parameter
constant: false
value: NaN
name: V_pk

387280
type: Parameter
constant: true
value: 0.068
name: KI_F6P

471666
type: SBMLUnitsDef
unit: 471691
unit: 471678
name: mS_per_cm2

471691
type: SBMLUnit
exponent: -2.0
scale: -2
multipler: 1.0
kind: METRE

471678
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: SIEMENS

387268
type: Parameter
constant: false
value: 0.0405
name: GAP

387331
type: Parameter
constant: true
value: 0.641
name: K_LAC

471729
type: SBMLUnitsDef
unit: 471742
name: time

471742
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: SECOND

387292
type: Parameter
constant: true
value: 1.036E-4
name: Vmaxr_pfk2

387316
type: Parameter
constant: true
value: 3.0
name: kf_ck

387271
type: Parameter
constant: false
value: 0.5
name: LAC

387325
type: Parameter
constant: true
value: 0.5
name: Km_ATP

387345
type: Parameter
constant: true
value: 0.5
name: nAMP

387282
type: Parameter
constant: false
value: NaN
name: V_pfk

387337
type: Parameter
constant: false
value: NaN
name: AMP

387300
type: Parameter
constant: true
value: 5.0
name: Vmax_pk

471353
type: SBMLUnitsDef
unit: 471377
unit: 471365
name: per_mM

471377
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

471365
type: SBMLUnit
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE

387274
type: Parameter
constant: false
value: 18.14
name: PCr

387357
type: Parameter
constant: true
value: 0.0
name: v2_n

387294
type: Parameter
constant: true
value: 0.05
name: Km_ATP_pfk2

471317
type: SBMLUnitsDef
unit: 471341
unit: 471329
name: mM

471341
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

471329
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

471293
type: SBMLUnitsDef
unit: 471305
name: s

471305
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: SECOND

387365
type: Parameter
constant: true
value: 0.005
name: Kamp_pfk2

387360
type: Parameter
constant: true
value: 2.51
name: ANP

387351
type: Parameter
constant: true
value: 1.0
name: stim

387343
type: Parameter
constant: false
value: NaN
name: AMP_act

471390
type: SBMLUnitsDef
unit: 471426
unit: 471414
unit: 471402
name: mM_per_s

471426
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

471414
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

471402
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

471594
type: SBMLUnitsDef
unit: 471618
unit: 471606
name: C_per_mole

471618
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: MOLE

471606
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: COULOMB

387328
type: Parameter
constant: true
value: 0.355
name: Vlac_0

387283
type: Parameter
constant: true
value: 3.85
name: Vmax_pfk

387276
type: Parameter
constant: false
value: NaN
name: V_hk

387334
type: Parameter
constant: false
value: NaN
name: u

387267
type: Parameter
constant: false
value: 0.001
name: F26P

387295
type: Parameter
constant: true
value: 0.01
name: Km_F6P_pfk2

W3 CDTF: Fri Jun 25 14:19:49 BST 2010

W3 CDTF: Fri Jun 25 14:19:49 BST 2010

471703
type: SBMLUnitsDef
unit: 471716
name: mV

471716
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: VOLT

387349
type: Parameter
constant: false
value: NaN
name: unitpulseSB

387288
type: Parameter
constant: true
value: 0.01
name: Km_F26P_pfk

387346
type: Parameter
constant: true
value: 0.05
name: Ka_AMP

471486
type: SBMLUnitsDef
unit: 471498
name: per_s

471498
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

387321
type: Parameter
constant: true
value: 20.0
name: PCrtot

471630
type: SBMLUnitsDef
unit: 471654
unit: 471642
name: L_per_millimole

471654
type: SBMLUnit
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE

471642
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

387366
type: Parameter
constant: true
value: 2.0
name: nh_amp

387306
type: Parameter
constant: true
value: 1.0
name: Vmax_op

387340
type: Parameter
constant: true
value: 0.4
name: nATP

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

387333
type: Parameter
constant: false
value: NaN
name: ADP

387270
type: Parameter
constant: false
value: 0.1
name: PYR

387353
type: Parameter
constant: true
value: 50.0
name: to

387309
type: Parameter
constant: true
value: 0.5
name: Km_PYR_op

387312
type: Parameter
constant: true
value: 0.0
name: kf_ldh

387318
type: Parameter
constant: true
value: 1.26
name: kr_ck

387303
type: Parameter
constant: true
value: 0.4
name: Km_GAP_pk

471510
type: SBMLUnitsDef
unit: 471558
unit: 471546
unit: 471534
unit: 471522
name: cm_per_mM_s

471558
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

471546
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

471534
type: SBMLUnit
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE

471522
type: SBMLUnit
exponent: 1.0
scale: -2
multipler: 1.0
kind: METRE

387277
type: Parameter
constant: true
value: 2.5
name: Vmax_hk

387315
type: Parameter
constant: false
value: NaN
name: V_ck

387297
type: Parameter
constant: true
value: 1.0E-4
name: Km_F26P_pfk2

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

387310
type: Parameter
constant: false
value: NaN
name: V_ldh

387330
type: Parameter
constant: true
value: 0.71
name: K_LAC_eff

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

387291
type: Parameter
constant: true
value: 2.0E-4
name: Vmaxf_pfk2

W3 CDTF: Fri Jun 25 14:19:49 BST 2010

W3 CDTF: Fri Jun 25 14:19:49 BST 2010