MODEL1006230010
type: SBMLModel
length unit: 335510
time units: 249252
curated: false
rule: 188269
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: 188251
area units: area
parameter: 188317
parameter: 188288
parameter: 188338
rule: 188263
parameter: 188333
parameter: 188353
parameter: 188281
parameter: 188354
parameter: 188305
units def: 249156
rule: 188246
parameter: 188348
parameter: 188321
parameter: 188341
units def: 248963
parameter: 188285
parameter: 188315
parameter: 188336
rule: 188260
rule: 188245
parameter: 188302
substance units: 178797
parameter: 188303
parameter: 188293
parameter: 188323
rule: 188249
rule: 188253
units def: 248914
parameter: 188287
rule: 188271
compartment: 188240
rule: 188265
units def: 248817
parameter: 188275
parameter: 188300
parameter: 188329
parameter: 188320
parameter: 188349
units def: 249120
parameter: 188292
rule: 188272
parameter: 188309
parameter: 188280
parameter: 188351
parameter: 188296
parameter: 188326
rule: 188247
parameter: 188347
units def: 249228
parameter: 188313
parameter: 188284
parameter: 188314
rule: 188259
parameter: 188334
rule: 188261
parameter: 188278
parameter: 188308
parameter: 188298
parameter: 188328
parameter: 188299
rule: 188254
parameter: 188344
parameter: 188286
parameter: 188316
parameter: 188311
parameter: 188331
rule: 188266
parameter: 188332
units def: 248841
rule: 188273
is described by: http://identifiers.org/pubmed/19828503
parameter: 188337

249252
type: SBMLUnitsDef
unit: 249264
name: time

249264
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: SECOND

188317
type: Parameter
constant: false
value: NaN
name: Cr

188288
type: Parameter
constant: true
value: 3.85
name: Vmax_pfk

188338
type: Parameter
constant: true
value: 0.5
name: nAMP

188333
type: Parameter
constant: false
value: NaN
name: ATP_inh

188353
type: Parameter
constant: false
value: NaN
name: AMP_pfk2

188281
type: Parameter
constant: false
value: 18.14
name: PCr

188354
type: Parameter
constant: true
value: 0.005
name: Kamp_pfk2

188305
type: Parameter
constant: false
value: NaN
name: V_op

249156
type: SBMLUnitsDef
unit: 249180
unit: 249168
name: L_per_millimole

249180
type: SBMLUnit
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE

249168
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

188348
type: Parameter
constant: true
value: 0.0
name: v2_n

188321
type: Parameter
constant: true
value: 0.9355
name: Vmax_ATPase

188341
type: Parameter
constant: false
value: NaN
name: v_stim

248963
type: SBMLUnitsDef
unit: 248999
unit: 248987
unit: 248975
name: per_mM_s

248999
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

248987
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

248975
type: SBMLUnit
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE

188285
type: Parameter
constant: true
value: 0.5
name: Km_ATP_hk

188315
type: Parameter
constant: true
value: 0.0
name: kf_ck

188336
type: Parameter
constant: true
value: 1.0
name: KI_ATP

188302
type: Parameter
constant: true
value: 5.0
name: Vmax_pk

188303
type: Parameter
constant: true
value: 0.005
name: Km_ADP_pk

188293
type: Parameter
constant: false
value: NaN
name: V_pfk2

188323
type: Parameter
constant: false
value: NaN
name: V_lac

248914
type: SBMLUnitsDef
unit: 248951
unit: 248939
unit: 248927
name: mM_per_s

248951
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

248939
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

248927
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

188287
type: Parameter
constant: false
value: NaN
name: V_pfk

188240
type: Compartment
constant: true
units: litre
size: 1.0
spatial dimensions: 3.0

248817
type: SBMLUnitsDef
unit: 248829
name: s

248829
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: SECOND

188275
type: Parameter
constant: false
value: 0.2
name: F6P

188300
type: Parameter
constant: false
value: NaN
name: V_pk

188329
type: Parameter
constant: false
value: NaN
name: u

188320
type: Parameter
constant: false
value: NaN
name: V_ATPase

188349
type: Parameter
constant: true
value: 2.0
name: t_n_stim

249120
type: SBMLUnitsDef
unit: 249144
unit: 249132
name: C_per_mole

249144
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: MOLE

249132
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: COULOMB

188292
type: Parameter
constant: true
value: 0.01
name: Km_F26P_pfk

188309
type: Parameter
constant: true
value: 0.5
name: Km_PYR_op

188280
type: Parameter
constant: false
value: 2.402
name: ATP

188351
type: Parameter
constant: true
value: 0.92
name: Q_adk

188296
type: Parameter
constant: true
value: 0.0
name: Vmaxr_pfk2

188326
type: Parameter
constant: true
value: 0.71
name: K_LAC_eff

188347
type: Parameter
constant: true
value: 0.5
name: v1_n

249228
type: SBMLUnitsDef
unit: 249240
name: mV

249240
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: VOLT

188313
type: Parameter
constant: true
value: 0.0
name: kr_ldh

188284
type: Parameter
constant: true
value: 2.5
name: Vmax_hk

188314
type: Parameter
constant: false
value: NaN
name: V_ck

188334
type: Parameter
constant: true
value: 0.4
name: nATP

188278
type: Parameter
constant: false
value: 0.1
name: PYR

188308
type: Parameter
constant: true
value: 0.005
name: Km_ADP_op

188298
type: Parameter
constant: true
value: 0.01
name: Km_F6P_pfk2

188328
type: Parameter
constant: false
value: NaN
name: ADP

188299
type: Parameter
constant: true
value: 1.0E-4
name: Km_F26P_pfk2

188344
type: Parameter
constant: true
value: 50.0
name: to

188286
type: Parameter
constant: true
value: 0.068
name: KI_F6P

188316
type: Parameter
constant: true
value: 0.0
name: kr_ck

188311
type: Parameter
constant: true
value: 0.0
name: kf_ldh

188331
type: Parameter
constant: false
value: NaN
name: dAMP_dATP

188332
type: Parameter
constant: false
value: NaN
name: AMP

248841
type: SBMLUnitsDef
unit: 248865
unit: 248853
name: mM

248865
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

248853
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

188337
type: Parameter
constant: false
value: NaN
name: AMP_act

188350
type: Parameter
constant: true
value: 2.51
name: ANP

188325
type: Parameter
constant: true
value: 0.355
name: Vlac_0

188345
type: Parameter
constant: true
value: 200.0
name: tend

188319
type: Parameter
constant: true
value: 20.0
name: PCrtot

188339
type: Parameter
constant: true
value: 0.05
name: Ka_AMP

188355
type: Parameter
constant: true
value: 2.0
name: nh_amp

188327
type: Parameter
constant: true
value: 0.641
name: K_LAC

188306
type: Parameter
constant: true
value: 1.0
name: Vmax_op

188276
type: Parameter
constant: false
value: 0.001
name: F26P

248877
type: SBMLUnitsDef
unit: 248902
unit: 248890
name: per_mM

248902
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

248890
type: SBMLUnit
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE

188277
type: Parameter
constant: false
value: 0.0405
name: GAP

188297
type: Parameter
constant: true
value: 0.05
name: Km_ATP_pfk2

249096
type: SBMLUnitsDef
unit: 249108
name: per_cm

249108
type: SBMLUnit
exponent: -1.0
scale: -2
multipler: 1.0
kind: METRE

W3 CDTF: Fri Jun 25 13:09:50 BST 2010

W3 CDTF: Fri Jun 25 13:09:50 BST 2010

188322
type: Parameter
constant: true
value: 0.5
name: Km_ATP

249035
type: SBMLUnitsDef
unit: 249084
unit: 249072
unit: 249059
unit: 249047
name: cm_per_mM_s

249084
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

249072
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

249059
type: SBMLUnit
exponent: -1.0
scale: -3
multipler: 1.0
kind: MOLE

249047
type: SBMLUnit
exponent: 1.0
scale: -2
multipler: 1.0
kind: METRE

188342
type: Parameter
constant: false
value: NaN
name: unitpulseSB

188343
type: Parameter
constant: true
value: 1.0
name: stim

188290
type: Parameter
constant: true
value: 0.05
name: Km_ATP_pfk

188291
type: Parameter
constant: true
value: 0.18
name: Km_F6P_pfk

188310
type: Parameter
constant: false
value: NaN
name: V_ldh

188279
type: Parameter
constant: false
value: 0.5
name: LAC

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

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

188304
type: Parameter
constant: true
value: 0.4
name: Km_GAP_pk

188294
type: Parameter
constant: true
value: 0.0
name: Vmaxf_pfk2

249011
type: SBMLUnitsDef
unit: 249023
name: per_s

249023
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

188282
type: Parameter
constant: false
value: NaN
name: V_hk

249192
type: SBMLUnitsDef
unit: 249216
unit: 249204
name: mS_per_cm2

249216
type: SBMLUnit
exponent: -2.0
scale: -2
multipler: 1.0
kind: METRE

249204
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: SIEMENS

W3 CDTF: Fri Jun 25 13:09:50 BST 2010

W3 CDTF: Fri Jun 25 13:09:50 BST 2010

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