Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction

Structures

Name
Type
Electrical
aMem Membrane c(+)   a(-)
bMem Membrane b(+)   c(-)
mMem Membrane m(+)   c(-)
LMem Membrane l(+)   c(-)
m Compartment (+)   (-)
a Compartment (+)   (-)
c Compartment (+)   (-)
b Compartment (+)   (-)
l Compartment (+)   (-)

aMem Universal ID's

aMem Text Annotations

bMem Universal ID's

bMem Text Annotations

mMem Universal ID's

mMem Text Annotations

LMem Universal ID's

LMem Text Annotations

m Universal ID's

m Text Annotations

a Universal ID's

a Text Annotations

c Universal ID's

c Text Annotations

b Universal ID's

b Text Annotations

l Universal ID's

l Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
Mt_m m m
Mt_b b b
Mt_a a a
Mt_c c c
Mt_l l l

Mt_m Universal ID's

Mt_m Text Annotations

Mt_b Universal ID's

Mt_b Text Annotations

Mt_a Universal ID's

Mt_a Text Annotations

Mt_c Universal ID's

Mt_c Text Annotations

Mt_l Universal ID's

Mt_l Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Imported Zhang et al 2006 Mol Pharm Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental (copied from Import model: Zhang et al 2006 Mol Pharm) Monobasic molecule M transport simulator v.1 Mt is total concentration of M in each compartment. a = apical lumen of intestine, where drug initially is introduced as high concentration. pH = 6.8 aMem = apical side membrane of enterocyte. Membrane potential Eam. -9.3mV c = cytosolic compartment of enterocyte. pH = 7.0 m = mitochondria of enterocyte. pH = 8.0 mMem = mitochondrial membrane Membrane potential Emm = -160mV b = basolateral lumen of enterocyte. pH = 7.4 bMem = basolateral side membrane of enterocyte. Membrane potential Ebm = 119mV
test pH outside Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental (copied from Imported Zhang et al 2006 Mol Pharm) (copied from Import model: Zhang et al 2006 Mol Pharm) Monobasic molecule M transport simulator v.1 Mt is total concentration of M in each compartment. a = apical lumen of intestine, where drug initially is introduced as high concentration. pH = 6.8 aMem = apical side membrane of enterocyte. Membrane potential Eam. -9.3mV c = cytosolic compartment of enterocyte. pH = 7.0 m = mitochondria of enterocyte. pH = 8.0 mMem = mitochondrial membrane Membrane potential Emm = -160mV b = basolateral lumen of enterocyte. pH = 7.4 bMem = basolateral side membrane of enterocyte. Membrane potential Ebm = 119mV

Imported Zhang et al 2006 Mol Pharm Universal ID's

Imported Zhang et al 2006 Mol Pharm Text Annotations

test pH outside Universal ID's

test pH outside Text Annotations

Specifications (Species) - Imported Zhang et al 2006 Mol Pharm go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Mt_m 0.0 [uM] 0.0 [um2/s] m
Mt_a 1000.0 [uM] 0.0 [um2/s] a
Mt_c 0.0 [uM] 0.0 [um2/s] c
Mt_b 0.0 [uM] 0.0 [um2/s] b
Mt_l 0.0 [uM] 0.0 [um2/s] l

Specifications (Reaction) - Imported Zhang et al 2006 Mol Pharm go to Simulations

Name
Enabled?
flux_ac included
flux_cb included
flux_cm included
flux_cl included

Simulations - Imported Zhang et al 2006 Mol Pharm go to Specifications

Name
End Time
Output Options
logKow2 impact on acid, neutral, base 600.0

KeepEvery 1

KeepAtMost 1000
Emm -160 vs -220 pKa 7,9,11 100.0

KeepEvery 1

KeepAtMost 1000

Imported Zhang et al 2006 Mol Pharm Universal ID's

Imported Zhang et al 2006 Mol Pharm Text Annotations

Imported Zhang et al 2006 Mol Pharm Universal ID's

Imported Zhang et al 2006 Mol Pharm Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial

(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment LMem

Events

Name Variable Rate Expression

Specifications (Species) - test pH outside go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Mt_m 0.0 [uM] 0.0 [um2/s] m
Mt_a 1000.0 [uM] 0.0 [um2/s] a
Mt_c 0.0 [uM] 0.0 [um2/s] c
Mt_b 0.0 [uM] 0.0 [um2/s] b
Mt_l 0.0 [uM] 0.0 [um2/s] l

Specifications (Reaction) - test pH outside go to Simulations

Name
Enabled?
flux_ac included
flux_cb included
flux_cm included
flux_cl included

Simulations - test pH outside go to Specifications

Name
End Time
Output Options
Simulation0 600.0

KeepEvery 1

KeepAtMost 1000
Simulation1 100.0

KeepEvery 1

KeepAtMost 1000

test pH outside Universal ID's

test pH outside Text Annotations

test pH outside Universal ID's

test pH outside Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial

(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment LMem

Events

Name Variable Rate Expression

Global Parameters

Name
Expression