Physiology
Reaction Diagram
Cross-References
Annotations
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
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
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
Specifications (Reaction) - Imported Zhang et al 2006 Mol Pharm go to Simulations
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
Specifications (Reaction) - test pH outside go to Simulations
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 |
---|
Downloads
Model Format | Model Downloads |
---|---|
Virtual Cell Markup Language | VCML File |
PDF Report | Report |
COMBINE Archive | OMEX File |
SEDML | SEDML File |
File Format | Application Downloads |
BNGL | Imported Zhang et al 2006 Mol Pharm.bngl , test pH outside.bngl |
SBML | Imported Zhang et al 2006 Mol Pharm.sbml , test pH outside.sbml |
Matlab | Imported Zhang et al 2006 Mol Pharm.m , test pH outside.m |
NFSim XML | Imported Zhang et al 2006 Mol Pharm.xml , test pH outside.xml |