Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
ATP_Matrix+ADP_MIMADP_Matrix+ATP_MIM ANT Memb GeneralKinetics
Pi_Matrix+ADP_MatrixATP_Matrix F1F0ATPase Memb GeneralKinetics
ATP_MIMADP_MIM+Pi_MIM ATP-deg MIM MassAction

ANT Universal ID's

ANT Text Annotations

F1F0ATPase Universal ID's

F1F0ATPase Text Annotations

ATP-deg Universal ID's

ATP-deg Text Annotations

Expressions for ANT

reaction rate

J

((Vant * ((1.0 - V1) / (V2 * V3))) * coeff) [molecules.um-2.ms-1]

global

coeff

(602000.0 / 2.2) [1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

-1.0 [1]

local

Vant

0.00187 [molecules.um-2.ms-1]

local

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]

global

Temp

310.0 [K]

local

V2

(1.0 + (((0.05 * ATP_MIM) / (0.45 * ADP_MIM)) * exp((( - fp * _F_ * Voltage_Memb) / (_R_ * Temp))))) [1]

global

Temp

310.0 [K]

local

V3

(1.0 + ((ADP_Matrix * 0.45 * 0.8) / (ATP_Matrix * 0.05))) [1]

local

fp

0.5 [1]

Expressions for F1F0ATPase

reaction rate

J

((fatp * (1.0 - exp(( - Ca_Matrix / 1.65E-4))) * Jop) * coeff) [molecules.um-2.ms-1]

global

coeff

(602000.0 / 2.2) [1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

local

fatp

(0.001125 * (Voltage_Memb ^ 8.0) / ((70.0 ^ 8.0) + (Voltage_Memb ^ 8.0))) [1]

local

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]

local

Kadp

0.06 [mM]

local

Katp

0.0322 [mM]

local

Kpi

0.15 [mM]

local

Vadp

1.0 [molecules.um-2.ms-1]

local

Vatp

0.08 [molecules.um-2.ms-1]

Expressions for ATP-deg

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

Name
Type
Electrical
Memb Membrane MIM(+)   Matrix(-)
MIM Compartment (+)   (-)
Matrix Compartment (+)   (-)

Memb Universal ID's

Memb Text Annotations

MIM Universal ID's

MIM Text Annotations

Matrix Universal ID's

Matrix Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
ATP_Matrix Matrix Matrix
ADP_MIM MIM MIM
ADP_Matrix Matrix Matrix
ATP_MIM MIM MIM
Pi_Matrix Matrix Matrix
Ca_Matrix Matrix Matrix
Pi_MIM MIM MIM

ATP_Matrix Universal ID's

ATP_Matrix Text Annotations

ADP_MIM Universal ID's

ADP_MIM Text Annotations

ADP_Matrix Universal ID's

ADP_Matrix Text Annotations

ATP_MIM Universal ID's

ATP_MIM Text Annotations

Pi_Matrix Universal ID's

Pi_Matrix Text Annotations

Ca_Matrix Universal ID's

Ca_Matrix Text Annotations

Pi_MIM Universal ID's

Pi_MIM Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Tubular Specs - Species
Specs - Reaction
Simulations 		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 Specs - Species
Specs - Reaction
Simulations 		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 Specs - Species
Specs - Reaction
Simulations 		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 Specs - Species
Specs - Reaction
Simulations 		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 Specs - Species
Specs - Reaction
Simulations 		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)

Tubular Universal ID's

Tubular Text Annotations

No Cristae Universal ID's

No Cristae Text Annotations

Lamellar Universal ID's

Lamellar Text Annotations

2D_15_Cristae Universal ID's

2D_15_Cristae Text Annotations

2D_5_Cristae Universal ID's

2D_5_Cristae Text Annotations

Specifications (Species) - Tubular go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
ADP_MIM 0.05 [mM] 0.145 [um2/ms] MIM
ATP_MIM 0.56 [mM] 0.145 [um2/ms] MIM
Pi_MIM 2.78 [mM] 0.01 [um2/ms] MIM
ATP_Matrix 0.44 [mM] 0.1 [um2/ms] Matrix
ADP_Matrix 0.72 [mM] 0.1 [um2/ms] Matrix
Pi_Matrix 2.2 [mM] 0.01 [um2/ms] Matrix
Ca_Matrix 1.35E-4 [mM] 0.01 [um2/ms] Matrix

Specifications (Reaction) - Tubular go to Simulations

Name
Enabled?
ANT included
F1F0ATPase included
ATP-deg included

Simulations - Tubular go to Specifications

Name
End Time
Output Options
Simulation24 200.0

OutputTimeStep 1.0

Tubular Universal ID's

Tubular Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry geom_20190115_151208

(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

Events

Name Variable Rate Expression

Specifications (Species) - No Cristae go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
ADP_MIM 0.037 [mM] 0.145 [um2/ms] MIM
ATP_MIM 4.0 [mM] 0.145 [um2/ms] MIM
Pi_MIM 2.78 [mM] 0.01 [um2/ms] MIM
ATP_Matrix 0.44 [mM] 0.1 [um2/ms] Matrix
ADP_Matrix 0.72 [mM] 0.1 [um2/ms] Matrix
Pi_Matrix 2.2 [mM] 0.01 [um2/ms] Matrix
Ca_Matrix 1.35E-4 [mM] 0.01 [um2/ms] Matrix

Specifications (Reaction) - No Cristae go to Simulations

Name
Enabled?
ANT included
F1F0ATPase included
ATP-deg included

Simulations - No Cristae go to Specifications

Name
End Time
Output Options
Simulation86 200.0

OutputTimeStep 1.0
Simulation87 500.0

OutputTimeStep 1.0

No Cristae Universal ID's

No Cristae Text Annotations

No Cristae Universal ID's

No Cristae Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry geom_20190123_205615

(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

Events

Name Variable Rate Expression

Specifications (Species) - Lamellar go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
ADP_MIM 0.002 [mM] 0.145 [um2/ms] MIM
ATP_MIM 4.0 [mM] 0.145 [um2/ms] MIM
Pi_MIM 2.78 [mM] 0.01 [um2/ms] MIM
ATP_Matrix 0.44 [mM] 0.1 [um2/ms] Matrix
ADP_Matrix 0.72 [mM] 0.1 [um2/ms] Matrix
Pi_Matrix 2.2 [mM] 0.01 [um2/ms] Matrix
Ca_Matrix 1.35E-4 [mM] 0.01 [um2/ms] Matrix

Specifications (Reaction) - Lamellar go to Simulations

Name
Enabled?
ANT included
F1F0ATPase included
ATP-deg included

Simulations - Lamellar go to Specifications

Name
End Time
Output Options
Simulation166 200.0

OutputTimeStep 1.0
Copy of Simulation166 500.0

OutputTimeStep 1.0

Lamellar Universal ID's

Lamellar Text Annotations

Lamellar Universal ID's

Lamellar Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry geom_20190115_115613

(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

Events

Name Variable Rate Expression

Specifications (Species) - 2D_15_Cristae go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
ADP_MIM 0.1 [mM] 0.145 [um2/ms] MIM
ATP_MIM 4.0 [mM] 0.145 [um2/ms] MIM
Pi_MIM 2.78 [mM] 0.01 [um2/ms] MIM
ATP_Matrix 0.44 [mM] 0.1 [um2/ms] Matrix
ADP_Matrix 0.72 [mM] 0.1 [um2/ms] Matrix
Pi_Matrix 2.2 [mM] 0.01 [um2/ms] Matrix
Ca_Matrix 1.35E-4 [mM] 0.01 [um2/ms] Matrix

Specifications (Reaction) - 2D_15_Cristae go to Simulations

Name
Enabled?
ANT included
F1F0ATPase included
ATP-deg included

Simulations - 2D_15_Cristae go to Specifications

Name
End Time
Output Options
Simulation233 200.0

OutputTimeStep 1.0
Simulation234 500.0

OutputTimeStep 1.0

2D_15_Cristae Universal ID's

2D_15_Cristae Text Annotations

2D_15_Cristae Universal ID's

2D_15_Cristae Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry geom_20190130_105820

(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

Events

Name Variable Rate Expression

Specifications (Species) - 2D_5_Cristae go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
ADP_MIM 0.1 [mM] 0.145 [um2/ms] MIM
ATP_MIM 4.0 [mM] 0.145 [um2/ms] MIM
Pi_MIM 2.78 [mM] 0.01 [um2/ms] MIM
ATP_Matrix 0.44 [mM] 0.1 [um2/ms] Matrix
ADP_Matrix 0.72 [mM] 0.1 [um2/ms] Matrix
Pi_Matrix 2.2 [mM] 0.01 [um2/ms] Matrix
Ca_Matrix 1.35E-4 [mM] 0.01 [um2/ms] Matrix

Specifications (Reaction) - 2D_5_Cristae go to Simulations

Name
Enabled?
ANT included
F1F0ATPase included
ATP-deg included

Simulations - 2D_5_Cristae go to Specifications

Name
End Time
Output Options
Simulation233_1 200.0

OutputTimeStep 1.0
Simulation234_1 500.0

OutputTimeStep 1.0

2D_5_Cristae Universal ID's

2D_5_Cristae Text Annotations

2D_5_Cristae Universal ID's

2D_5_Cristae Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry geom_20180130_155013

(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

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
coeff (602000.0 / 2.2) [1]
Temp 310.0 [K]

Universal ID's

Text Annotations

Universal ID's

Text Annotations