W3 CDTF: Thu Feb 02 21:34:55 GMT 2012

W3 CDTF: Thu Feb 02 21:34:55 GMT 2012

metaid_0000040
constant: true
value: 3.31131121482591E-7
name: k_dHatp
type: Parameter

045239
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

metaid_0000096
constant: false
value: NaN
name: J_MgADPi
type: Parameter

metaid_0000134
constant: true
value: 1.0E-6
name: C_im
type: Parameter

metaid_0000030
constant: true
value: -69.37
name: dG_C1o
type: Parameter

metaid_0000124
constant: false
value: 0.0
name: ATP_mx
type: Parameter

045106
exponent: 1.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

045202
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

metaid_0000058
constant: true
value: 4.5082E-4
name: k_PiH
type: Parameter

metaid_0000063
constant: true
value: 3.2562E-5
name: x_C4
type: Parameter

044986
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

metaid_0000077
constant: false
value: NaN
name: dG_H
type: Parameter

045082
exponent: 1.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000078
constant: false
value: NaN
name: J_DH
type: Parameter

metaid_0000010
unit: 044986
unit: 044974
name: micron_per_second
type: SBMLUnitsDef

metaid_0000083
constant: false
value: NaN
name: J_C4
type: Parameter

metaid_0000009
unit: 044962
unit: 044950
name: per_M
type: SBMLUnitsDef

metaid_0000104
constant: false
value: NaN
name: H2PIx
type: Parameter

045166
exponent: 1.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

044866
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

metaid_0000020
unit: 045239
unit: 045227
unit: 045214
name: mole_per_second_per_l_mito_per_molar_per_molar
type: SBMLUnitsDef

metaid_0000114
constant: false
value: NaN
name: Mg_e
type: Parameter

044950
exponent: -1.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000041
constant: true
value: 5.12861383991365E-7
name: k_dHadp
type: Parameter

metaid_0000135
constant: false
value: 2.6E-5
name: O2
type: Parameter

metaid_0000039
constant: true
value: 1.77827541003892E-7
name: k_dHPi
type: Parameter

metaid_0000097
constant: false
value: NaN
name: ADP_fi
type: Parameter

metaid_0000125
constant: false
value: 0.0
name: ADP_mx
type: Parameter

metaid_0000031
constant: true
value: -32.53
name: dG_C3o
type: Parameter

metaid_0000049
constant: true
value: 0.0027
name: Ctot
type: Parameter

metaid_0000057
constant: true
value: 0.02531
name: k_Pi4
type: Parameter

metaid_0000076
constant: true
value: 327.0
name: x_Pi2
type: Parameter

metaid_0000062
constant: true
value: 0.091737
name: x_C3
type: Parameter

metaid_0000012
unit: 045022
unit: 045010
name: kilojoule_per_mole
type: SBMLUnitsDef

metaid_0000011
unit: 044998
name: per_micron
type: SBMLUnitsDef

metaid_0000029
constant: true
value: 3.0
name: n_A
type: Parameter

045034
exponent: 1.0
scale: -3
multipler: 1.0
kind: VOLT
type: SBMLUnit

044938
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000082
constant: false
value: NaN
name: dG_C3op
type: Parameter

metaid_0000105
constant: false
value: NaN
name: J_AKi
type: Parameter

metaid_0000115
constant: false
value: NaN
name: Mg_i
type: Parameter

metaid_0000019
unit: 045202
name: mole_per_second_per_l_mito_per_molar
type: SBMLUnitsDef

metaid_0000021
unit: 045275
unit: 045263
unit: 045251
name: mole_per_l_mito_per_millivolt
type: SBMLUnitsDef

metaid_0000038
constant: true
value: 0.0
name: AMP_e
type: Parameter

metaid_0000136
constant: true
units: litre
size: 1.0
spatial dimensions: 3.0
type: Compartment

metaid_0000042
constant: true
value: 2.4E-5
name: K_DT
type: Parameter

metaid_0000098
constant: false
value: NaN
name: J_ATP
type: Parameter

045118
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000051
constant: true
value: 0.00297
name: NADtot
type: Parameter

metaid_0000023
constant: true
value: NaN
name: t
type: Parameter

044998
exponent: -1.0
scale: -6
multipler: 1.0
kind: METRE
type: SBMLUnit

045287
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

metaid_0000061
constant: true
value: 0.36923
name: x_C1
type: Parameter

metaid_0000003
unit: 044805
name: mg_per_mitochondria
type: SBMLUnitsDef

044805
exponent: 1.0
scale: -3
multipler: 1.0
kind: GRAM
type: SBMLUnit

metaid_0000122
constant: false
value: 0.0
name: ATP_x
type: Parameter

045154
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

metaid_0000121
constant: false
value: 0.001
name: Cred
type: Parameter

metaid_0000081
constant: false
value: NaN
name: J_C3
type: Parameter

metaid_0000102
constant: false
value: NaN
name: J_Pi1
type: Parameter

045094
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000022
unit: 045300
unit: 045287
name: mole_per_second_per_l_mito_per_molar_per_millivolt
type: SBMLUnitsDef

metaid_0000018
unit: 045190
unit: 045178
unit: 045166
name: mole_per_second_per_l_mito
type: SBMLUnitsDef

metaid_0000071
constant: true
value: 0.0
name: x_AK
type: Parameter

metaid_0000116
constant: false
value: 6.30957344480193E-8
name: H_x
type: Parameter

metaid_0000069
constant: true
value: 0.0
name: x_K
type: Parameter

metaid_0000043
constant: true
value: 3.47E-4
name: K_DD
type: Parameter

metaid_0000099
constant: false
value: NaN
name: J_ADP
type: Parameter

metaid_0000088
constant: false
value: NaN
name: Psi_i
type: Parameter

metaid_0000037
constant: true
value: 0.0
name: ATP_e
type: Parameter

metaid_0000024
constant: true
value: 0.005
name: Mg_tot
type: Parameter

metaid_0000050
constant: true
value: 0.00135
name: Qtot
type: Parameter

metaid_0000060
constant: true
value: 0.09183
name: x_DH
type: Parameter

W3 CDTF: Thu Feb 02 21:34:55 GMT 2012

metaid_0000004
unit: 044829
unit: 044817
name: M
type: SBMLUnitsDef

metaid_0000123
constant: false
value: 0.01
name: ADP_x
type: Parameter

metaid_0000059
constant: true
value: 4.5807
name: r
type: Parameter

044853
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000079
constant: false
value: NaN
name: J_C1
type: Parameter

metaid_0000103
constant: false
value: NaN
name: H2PIi
type: Parameter

metaid_0000017
unit: 045154
unit: 045142
unit: 045130
name: mole_per_second_per_l_cyto
type: SBMLUnitsDef

044926
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000089
constant: true
value: 1.0E-12
name: mincond
type: Parameter

045022
exponent: -1.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000070
constant: true
value: 3.5E-6
name: k_mADP
type: Parameter

metaid_0000117
constant: false
value: 0.14
name: K_x
type: Parameter

metaid_0000080
constant: false
value: NaN
name: dG_C1op
type: Parameter

metaid_0000108
constant: false
value: NaN
name: J_KH
type: Parameter

metaid_0000118
constant: false
value: 0.005
name: Mg_x
type: Parameter

metaid_0000005
unit: 044866
unit: 044853
unit: 044841
name: M_per_second
type: SBMLUnitsDef

metaid_0000128
constant: false
value: 0.0
name: ADP_i
type: Parameter

metaid_0000090
constant: false
value: NaN
name: J_MgATPx
type: Parameter

metaid_0000130
constant: false
value: 0.0
name: ATP_mi
type: Parameter

metaid_0000120
constant: false
value: 8.0E-4
name: QH2
type: Parameter

metaid_0000092
constant: false
value: NaN
name: J_MgADPx
type: Parameter

045142
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000068
constant: true
value: 250.0
name: x_Hle
type: Parameter

metaid_0000044
constant: true
value: 0.4331
name: K_AK
type: Parameter

metaid_0000073
constant: true
value: 1.2E-4
name: k_O2
type: Parameter

045275
exponent: -1.0
scale: -3
multipler: 1.0
kind: VOLT
type: SBMLUnit

metaid_0000045
constant: true
value: 0.72376
name: W_m
type: Parameter

metaid_0000016
unit: 045118
unit: 045106
name: molar_per_mito
type: SBMLUnitsDef

metaid_0000087
constant: false
value: NaN
name: Psi_x
type: Parameter

metaid_0000100
constant: false
value: NaN
name: J_AMP
type: Parameter

045058
exponent: -1.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000035
constant: false
value: NaN
name: H_e
type: Parameter

metaid_0000053
constant: false
value: NaN
name: K_i
type: Parameter

metaid_0000026
constant: true
value: 0.0013
name: ADP_e
type: Parameter

045010
exponent: 1.0
scale: 3
multipler: 1.0
kind: JOULE
type: SBMLUnit

metaid_0000006
unit: 044890
unit: 044878
name: M_2
type: SBMLUnitsDef

metaid_0000109
constant: false
value: NaN
name: NAD_x
type: Parameter

045070
exponent: -1.0
scale: -3
multipler: 1.0
kind: VOLT
type: SBMLUnit

044914
exponent: -3.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000091
constant: false
value: NaN
name: ATP_fx
type: Parameter

metaid_0000129
constant: false
value: 0.0
name: AMP_i
type: Parameter

metaid_0000093
constant: false
value: NaN
name: ADP_fx
type: Parameter

metaid_0000110
constant: false
value: NaN
name: Q
type: Parameter

045300
exponent: -1.0
scale: -3
multipler: 1.0
kind: VOLT
type: SBMLUnit

metaid_0000067
constant: true
value: 2.9802E7
name: x_KH
type: Parameter

metaid_0000119
constant: false
value: 0.0015
name: NADH_x
type: Parameter

metaid_0000015
unit: 045094
unit: 045082
name: molar_per_cyto
type: SBMLUnitsDef

metaid_0000066
constant: true
value: 339430.0
name: x_Pi1
type: Parameter

metaid_0000046
constant: false
value: NaN
name: W_x
type: Parameter

metaid_0000072
constant: true
value: 85.0
name: p_A
type: Parameter

W3 CDTF: Wed Mar 25 10:27:18 GMT 2009

044817
exponent: 1.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000111
constant: false
value: NaN
name: Cox
type: Parameter

044974
exponent: 1.0
scale: -6
multipler: 1.0
kind: METRE
type: SBMLUnit

metaid_0000101
constant: false
value: NaN
name: J_Pi2
type: Parameter

metaid_0000086
constant: false
value: NaN
name: J_ANT
type: Parameter

metaid_0000025
constant: true
value: 0.001
name: Pi_e
type: Parameter

metaid_0000036
constant: true
value: 0.15
name: K_e
type: Parameter

metaid_0000052
constant: false
value: NaN
name: H_i
type: Parameter

metaid_0000132
constant: false
value: 0.001
name: Pi_i
type: Parameter

metaid_0000126
constant: false
value: 0.001
name: Pi_x
type: Parameter

045130
exponent: 1.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000007
unit: 044914
unit: 044902
name: M_3
type: SBMLUnitsDef

metaid_0000056
constant: true
value: 1.9172E-4
name: k_Pi3
type: Parameter

metaid_0000032
constant: true
value: -122.94
name: dG_C4o
type: Parameter

045190
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

044841
exponent: 1.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000106
constant: false
value: NaN
name: J_Hle
type: Parameter

044878
exponent: 2.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000094
constant: false
value: NaN
name: J_MgATPi
type: Parameter

metaid_0000112
constant: false
value: NaN
name: ADP_me
type: Parameter

metaid_0000075
constant: true
value: 1000000.0
name: x_MgA
type: Parameter

045046
exponent: 1.0
scale: 3
multipler: 1.0
kind: JOULE
type: SBMLUnit

metaid_0000014
unit: 045070
unit: 045058
unit: 045046
name: kilojoule_per_mole_per_millivolt
type: SBMLUnitsDef

metaid_0000065
constant: true
value: 0.0079204
name: x_ANT
type: Parameter

metaid_0000047
constant: false
value: NaN
name: W_i
type: Parameter

045227
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

045263
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000055
constant: true
value: 6.7668E-4
name: k_Pi2
type: Parameter

metaid_0000028
constant: true
value: 0.096485
name: F
type: Parameter

metaid_0000133
constant: false
value: 160.0
name: dPsi
type: Parameter

metaid_0000085
constant: false
value: NaN
name: J_F1
type: Parameter

metaid_0000127
constant: false
value: 0.0
name: ATP_i
type: Parameter

metaid_0000131
constant: false
value: 0.0
name: ADP_mi
type: Parameter

metaid_0000033
constant: true
value: 36.03
name: dG_F1o
type: Parameter

metaid_0000008
unit: 044938
unit: 044926
name: microM
type: SBMLUnitsDef

metaid_0000107
constant: false
value: NaN
name: J_K
type: Parameter

MODEL4151491057
parameter: metaid_0000073
parameter: metaid_0000024
rule: metaid_0000196
rule: metaid_0000170
notes: This is the model described in the article: A biophysical model of the mitochondrial respiratory system and oxidative phosphorylation. Beard DA. PLoS Comput Biol. 2005 Sep;1(4):e36. Pubmed ID: 16163394 , doi: 10.1371/journal.pcbi.0010036 . Abstract: A computational model for the mitochondrial respiratory chain that appropriately balances mass, charge, and free energy transduction is introduced and analyzed based on a previously published set of data measured on isolated cardiac mitochondria. The basic components included in the model are the reactions at complexes I, III, and IV of the electron transport system, ATP synthesis at F1F0 ATPase, substrate transporters including adenine nucleotide translocase and the phosphate-hydrogen co-transporter, and cation fluxes across the inner membrane including fluxes through the K+/H+ antiporter and passive H+ and K+ permeation. Estimation of 16 adjustable parameter values is based on fitting model simulations to nine independent data curves. The identified model is further validated by comparison to additional datasets measured from mitochondria isolated from rat heart and liver and observed at low oxygen concentration. To obtain reasonable fits to the available data, it is necessary to incorporate inorganic-phosphate-dependent activation of the dehydrogenase activity and the electron transport system. Specifically, it is shown that a model incorporating phosphate-dependent activation of complex III is able to reasonably reproduce the observed data. The resulting validated and verified model provides a foundation for building larger and more complex systems models and investigating complex physiological and pathophysiological interactions in cardiac energetics. This model was taken from the CellML repository and automatically converted to SBML. The original model was: Beard, 2005 version 03 The original CellML model was created and curated by: Geoffrey Nunns The University of Auckland, Bioengineering Research Group This model…
rule: metaid_0000154
rule: metaid_0000181
parameter: metaid_0000104
units def: metaid_0000013
parameter: metaid_0000127
parameter: metaid_0000061
is described by: http://identifiers.org/pubmed/16163394
rule: metaid_0000174
parameter: metaid_0000074
parameter: metaid_0000108
parameter: metaid_0000097
parameter: metaid_0000048
rule: metaid_0000147
rule: metaid_0000185
rule: metaid_0000145
rule: metaid_0000143
rule: metaid_0000180
parameter: metaid_0000031
units def: metaid_0000014
parameter: metaid_0000034
parameter: metaid_0000115
units def: metaid_0000020
parameter: metaid_0000128
parameter: metaid_0000062
parameter: metaid_0000080
rule: metaid_0000163
parameter: metaid_0000085
parameter: metaid_0000119
area units: area
parameter: metaid_0000098
parameter: metaid_0000101
rule: metaid_0000184
units def: metaid_0000005
parameter: metaid_0000071
rule: metaid_0000142
parameter: metaid_0000032
rule: metaid_0000169
parameter: metaid_0000035
parameter: metaid_0000055
units def: metaid_0000021
parameter: metaid_0000116
parameter: metaid_0000058
rule: metaid_0000162
parameter: metaid_0000086
parameter: metaid_0000102
units def: metaid_0000015
parameter: metaid_0000125
length unit: length
parameter: metaid_0000072
parameter: metaid_0000023
parameter: metaid_0000043
parameter: metaid_0000095
parameter: metaid_0000046
rule: metaid_0000193
units def: metaid_0000010
parameter: metaid_0000059
rule: metaid_0000151
rule: metaid_0000138
units def: metaid_0000016
parameter: metaid_0000110
rule: metaid_0000178
parameter: metaid_0000113
rule: metaid_0000159
units def: metaid_0000022
parameter: metaid_0000126
parameter: metaid_0000060
rule: metaid_0000197
rule: metaid_0000171
parameter: metaid_0000083
parameter: metaid_0000044
parameter: metaid_0000096
parameter: metaid_0000047
rule: metaid_0000157
units def: metaid_0000007
parameter: metaid_0000030

metaid_0000095
constant: false
value: NaN
name: ATP_fi
type: Parameter

044902
exponent: 3.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000074
constant: true
value: 4.253
name: r_buff
type: Parameter

045214
exponent: -1.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

044890
exponent: -2.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000113
constant: false
value: NaN
name: ADP_fe
type: Parameter

metaid_0000048
constant: true
value: 5.99
name: gamma
type: Parameter

metaid_0000064
constant: true
value: 150.93
name: x_F1
type: Parameter

metaid_0000013
unit: 045034
name: millivolt
type: SBMLUnitsDef

metaid_0000054
constant: true
value: 1.3413E-4
name: k_Pi1
type: Parameter

ORG:
  orgname: Auckland Bioengineering Institute, The Auckland University
n:
  given: Geoffrey
  family: Nunns

metaid_0000084
constant: false
value: NaN
name: dG_C4op
type: Parameter

metaid_0000034
constant: true
value: 7.1
name: pH_e
type: Parameter

045251
exponent: 1.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

044962
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000027
constant: true
value: 2.4734
name: RT
type: Parameter

044829
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

045178
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

W3 CDTF: Thu Feb 02 21:34:55 GMT 2012