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Name - Energy-production-pathway-reduced-model-01132021

BioModel ID - 201022999

Reaction Diagram

reactionDiagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
ATP_Matrix+ADP_MIMADP_Matrix+ATP_MIM	ANT Memb	GeneralKinetics	ATP_Matrix+ADP_MIMADP_Matrix+ATP_MIM
		reaction rate (J): ((Vant * ((1.0 - V1) / (V2 * V3))) * coeff)[molecules.um-2.ms-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): -1.0[1] user defined (Vant): 0.00187[molecules.um-2.ms-1] user defined (V1): (((0.05 * ATP_MIM) / (0.45 * ADP_MIM)) * ((ADP_Matrix * 0.45 * 0.8) / (ATP_Matrix * 0.05)) * exp((( - _F_ * Voltage_Memb) / (_R_ * Temp))))[1] user defined (V2): (1.0 + (((0.05 * ATP_MIM) / (0.45 * ADP_MIM)) * exp((( - fp * _F_ * Voltage_Memb) / (_R_ * Temp)))))[1] user defined (V3): (1.0 + ((ADP_Matrix * 0.45 * 0.8) / (ATP_Matrix * 0.05)))[1] user defined (fp): 0.5[1]
Pi_Matrix+ADP_MatrixATP_Matrix	F1F0ATPase Memb	GeneralKinetics	Pi_Matrix+ADP_MatrixATP_Matrix
		reaction rate (J): ((fatp * (1.0 - exp(( - Ca_Matrix / 1.65E-4))) * Jop) * coeff)[molecules.um-2.ms-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (fatp): (0.001125 * (Voltage_Memb ^ 8.0) / ((70.0 ^ 8.0) + (Voltage_Memb ^ 8.0)))[1] user defined (Jop): (((Vadp * (ADP_Matrix / Kadp) * (Pi_Matrix / Kpi)) - (Vatp * (ATP_Matrix / Katp))) / (((1.0 + (ADP_Matrix / Kadp)) * (1.0 + (Pi_Matrix / Kpi))) + (ATP_Matrix / Katp)))[molecules.um-2.ms-1] user defined (Kadp): 0.06[mM] user defined (Katp): 0.0322[mM] user defined (Kpi): 0.15[mM] user defined (Vadp): 1.0[molecules.um-2.ms-1] user defined (Vatp): 0.08[molecules.um-2.ms-1]
ATP_MIMADP_MIM+Pi_MIM	ATP-deg MIM	MassAction	ATP_MIMADP_MIM+Pi_MIM
		reaction rate (J): ((Kf * ATP_MIM) - ((Kr * ADP_MIM) * Pi_MIM))[mM.ms-1] forward rate constant (Kf): 0.003[ms-1] reverse rate constant (Kr): 1.0[ms-1.mM-1]

Structures See in Dashboard
Name	Type Electrical (Membrane Polarity)
MIM	Compartment (+) (-)

Matrix	Compartment (+) (-)

Memb	Membrane N/A

Species See in Dashboard
Name	Structure	BioNetGen Definition
ATP_Matrix	Matrix

ADP_MIM	MIM

ADP_Matrix	Matrix

ATP_MIM	MIM

Pi_Matrix	Matrix

Ca_Matrix	Matrix

Pi_MIM	MIM

Molecules See in Dashboard
Name	Text Annotations	BioNetGen Definition

Observables See in Dashboard
Name	Type Count	BioNetGen Definition

Applications

Applications See in Dashboard
Name	Math Type	Annotation
Tubular	Deterministic (ODE) Spatial (3D)	(copied from Model3-sizes-3D-3-reactions-diffusion-coeff-ADP0.002) (copied from Model2-sizes-3D-3-reactions-diffusion-coeff) (copied from Model1-sizes-3D-3-reactions-diffusion-coeff) (copied from 3-reactions-Model1-sizes)
No Cristae	Deterministic (ODE) Spatial (3D)	(copied from Model6-sizes-3D-3-reactions-diffusion-coeff-ADP0.002-psi172) (copied from Model5-sizes-3D-3-reactions-diffusion-coeff-ADP0.002) (copied from Model4-sizes-3D-3-reactions-diffusion-coeff-ADP0.002) (copied from Model3-sizes-3D-3-reactions-diffusion-coeff-ADP0.002) (copied from Model2-sizes-3D-3-reactions-diffusion-coeff) (copied from Model1-sizes-3D-3-reactions-diffusion-coeff) (copied from 3-reactions-Model1-sizes)
Lamellar	Deterministic (ODE) Spatial (3D)	(copied from Model1-sizes-3D-3-reactions-diffusion-coeff-Resting-psi172) (copied from Model1-sizes-3D-3-reactions-diffusion-coeff-ADP0.002-psi172) (copied from 3-reactions-Model1-sizes)
2D_15_Cristae	Deterministic (ODE) Spatial (2D)	(copied from 2D-Nom3-wide-3-reactions-diff-coeff-Resting-psi172-ADP0.1) (copied from 2D-Nom3-wide-3-reactions-diff-coeff-Resting-psi172-ADP0.01) (copied from 2D-Nom3-wide-3-reactions-diff-coeff-Resting-psi172-ADP0.0037) (copied from 2D-Nom3-wide-3-reactions-diff-coeff-Resting-psi172) (copied from 2D-Nom3-wide-3-reactions-diff-coeff-ADP0.002) (copied from 2D-Nom3-wide-3-reactions-diff-coeff-ADP0.05) (copied from 2D-Nom2-wide-3-reactions-diff-coeff-ADP0.05) (copied from 2D-Nom2-wide-3-reactions-diff-coeff-ADP0.002) (copied from 2D-Nom1-wide-3-reactions-diff-coeff-ADP0.002) (copied from 2D-Nom3-Narrow-3-reactions-diff-coeff) (copied from Copy of 2D-3-reactions-Nom3) (copied from 2D-3-reactions-Nom3) (copied from 2D-3-reactions) (copied from 3-reactions)
2D_5_Cristae	Deterministic (ODE) Spatial (2D)	(copied from 2D_15_Cristae) (copied from 2D-Nom3-wide-3-reactions-diff-coeff-Resting-psi172-ADP0.1) (copied from 2D-Nom3-wide-3-reactions-diff-coeff-Resting-psi172-ADP0.01) (copied from 2D-Nom3-wide-3-reactions-diff-coeff-Resting-psi172-ADP0.0037) (copied from 2D-Nom3-wide-3-reactions-diff-coeff-Resting-psi172) (copied from 2D-Nom3-wide-3-reactions-diff-coeff-ADP0.002) (copied from 2D-Nom3-wide-3-reactions-diff-coeff-ADP0.05) (copied from 2D-Nom2-wide-3-reactions-diff-coeff-ADP0.05) (copied from 2D-Nom2-wide-3-reactions-diff-coeff-ADP0.002) (copied from 2D-Nom1-wide-3-reactions-diff-coeff-ADP0.002) (copied from 2D-Nom3-Narrow-3-reactions-diff-coeff) (copied from Copy of 2D-3-reactions-Nom3) (copied from 2D-3-reactions-Nom3) (copied from 2D-3-reactions) (copied from 3-reactions)

Application - Tubular

Specifications(Species) - Tubular See in Dashboard
Species	Initial Condition	Diffusion Constant
ADP_MIM	0.05 [mM]	0.145 [um2/ms]
ATP_MIM	0.56 [mM]	0.145 [um2/ms]
Pi_MIM	2.78 [mM]	0.01 [um2/ms]
ATP_Matrix	0.44 [mM]	0.1 [um2/ms]
ADP_Matrix	0.72 [mM]	0.1 [um2/ms]
Pi_Matrix	2.2 [mM]	0.01 [um2/ms]
Ca_Matrix	1.35E-4 [mM]	0.01 [um2/ms]

Specifications(Reaction) - Tubular See in Dashboard
Name	Reaction Mapping
ANT	included
F1F0ATPase	included
ATP-deg	included

Simulations - Tubular See in Dashboard
Name	End Time	Output Options
Simulation24	200.0 [ms]	OutputTimeStep 1.0

Geometry geom_20190115_151208 See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 0.22, 0.21, 0.22[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Image	MIM		0.0051292384000000005 [um3]	MIM
Volume	Image	Matrix		0.005034761600000001 [um3]	Matrix
Surface		MIM_Matrix_membrane	MIM \| Matrix	0.3710654836488362 [um2]	Memb

Application - No Cristae

Specifications(Species) - No Cristae See in Dashboard
Species	Initial Condition	Diffusion Constant
ADP_MIM	0.037 [mM]	0.145 [um2/ms]
ATP_MIM	4.0 [mM]	0.145 [um2/ms]
Pi_MIM	2.78 [mM]	0.01 [um2/ms]
ATP_Matrix	0.44 [mM]	0.1 [um2/ms]
ADP_Matrix	0.72 [mM]	0.1 [um2/ms]
Pi_Matrix	2.2 [mM]	0.01 [um2/ms]
Ca_Matrix	1.35E-4 [mM]	0.01 [um2/ms]

Specifications(Reaction) - No Cristae See in Dashboard
Name	Reaction Mapping
ANT	included
F1F0ATPase	included
ATP-deg	included

Simulations - No Cristae See in Dashboard
Name	End Time	Output Options
Simulation86	200.0 [ms]	OutputTimeStep 1.0
Simulation87	500.0 [ms]	OutputTimeStep 1.0

Geometry geom_20190123_205615 See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 0.22, 0.21, 0.22[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Image	MIM		0.004022257800000001 [um3]	MIM
Volume	Image	Matrix		0.0061417422000000004 [um3]	Matrix
Surface		MIM_Matrix_membrane	MIM \| Matrix	0.19664892983634283 [um2]	Memb

Application - Lamellar

Specifications(Species) - Lamellar See in Dashboard
Species	Initial Condition	Diffusion Constant
ADP_MIM	0.002 [mM]	0.145 [um2/ms]
ATP_MIM	4.0 [mM]	0.145 [um2/ms]
Pi_MIM	2.78 [mM]	0.01 [um2/ms]
ATP_Matrix	0.44 [mM]	0.1 [um2/ms]
ADP_Matrix	0.72 [mM]	0.1 [um2/ms]
Pi_Matrix	2.2 [mM]	0.01 [um2/ms]
Ca_Matrix	1.35E-4 [mM]	0.01 [um2/ms]

Specifications(Reaction) - Lamellar See in Dashboard
Name	Reaction Mapping
ANT	included
F1F0ATPase	included
ATP-deg	included

Simulations - Lamellar See in Dashboard
Name	End Time	Output Options
Simulation166	200.0 [ms]	OutputTimeStep 1.0
Copy of Simulation166	500.0 [ms]	OutputTimeStep 1.0

Geometry geom_20190115_115613 See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 0.22, 0.21, 0.22[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Image	MIM		0.005717661400000001 [um3]	MIM
Volume	Image	Matrix		0.0044463386 [um3]	Matrix
Surface		MIM_Matrix_membrane	MIM \| Matrix	0.39676044817813544 [um2]	Memb

Application - 2D_15_Cristae

Specifications(Species) - 2D_15_Cristae See in Dashboard
Species	Initial Condition	Diffusion Constant
ADP_MIM	0.1 [mM]	0.145 [um2/ms]
ATP_MIM	4.0 [mM]	0.145 [um2/ms]
Pi_MIM	2.78 [mM]	0.01 [um2/ms]
ATP_Matrix	0.44 [mM]	0.1 [um2/ms]
ADP_Matrix	0.72 [mM]	0.1 [um2/ms]
Pi_Matrix	2.2 [mM]	0.01 [um2/ms]
Ca_Matrix	1.35E-4 [mM]	0.01 [um2/ms]

Specifications(Reaction) - 2D_15_Cristae See in Dashboard
Name	Reaction Mapping
ANT	included
F1F0ATPase	included
ATP-deg	included

Simulations - 2D_15_Cristae See in Dashboard
Name	End Time	Output Options
Simulation233	200.0 [ms]	OutputTimeStep 1.0
Simulation234	500.0 [ms]	OutputTimeStep 1.0

Geometry geom_20190130_105820 See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 0.7, 0.72, 9.0E-7[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Image	MIM		0.2934127130175598 [um2]	MIM
Volume	Image	Matrix		0.21058728698244022 [um2]	Matrix
Surface		MIM_Matrix_membrane	MIM \| Matrix	21.074730492752657 [um]	Memb

Application - 2D_5_Cristae

Specifications(Species) - 2D_5_Cristae See in Dashboard
Species	Initial Condition	Diffusion Constant
ADP_MIM	0.1 [mM]	0.145 [um2/ms]
ATP_MIM	4.0 [mM]	0.145 [um2/ms]
Pi_MIM	2.78 [mM]	0.01 [um2/ms]
ATP_Matrix	0.44 [mM]	0.1 [um2/ms]
ADP_Matrix	0.72 [mM]	0.1 [um2/ms]
Pi_Matrix	2.2 [mM]	0.01 [um2/ms]
Ca_Matrix	1.35E-4 [mM]	0.01 [um2/ms]

Specifications(Reaction) - 2D_5_Cristae See in Dashboard
Name	Reaction Mapping
ANT	included
F1F0ATPase	included
ATP-deg	included

Simulations - 2D_5_Cristae See in Dashboard
Name	End Time	Output Options
Simulation233_1	200.0 [ms]	OutputTimeStep 1.0
Simulation234_1	500.0 [ms]	OutputTimeStep 1.0

Geometry geom_20180130_155013 See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 0.3, 0.42, 9.0E-7[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Image	MIM		0.08323334546778305 [um2]	MIM
Volume	Image	Matrix		0.042766654532216966 [um2]	Matrix
Surface		MIM_Matrix_membrane	MIM \| Matrix	4.314972474467289 [um]	Memb

Global Parameters

Global Parameters See in Dashboard
Name	Expression
coeff	(602000.0 / 2.2) [1]

Temp	310.0 [K]