Physiology
Reaction Diagram
Cross-References
Annotations
Structures
Name | Type | Electrical |
---|---|---|
aMem | Membrane | cytosol(+) apical_lumen(-) |
bMem | Membrane | basolateral_lumen(+) cytosol(-) |
mMem | Membrane | mitochondria(+) cytosol(-) |
mitochondria | Compartment | (+) (-) |
apical_lumen | Compartment | (+) (-) |
cytosol | Compartment | (+) (-) |
basolateral_lumen | Compartment | (+) (-) |
aMem Universal ID's
aMem Text Annotations
bMem Universal ID's
bMem Text Annotations
mMem Universal ID's
mMem Text Annotations
mitochondria Universal ID's
mitochondria Text Annotations
apical_lumen Universal ID's
apical_lumen Text Annotations
cytosol Universal ID's
cytosol Text Annotations
basolateral_lumen Universal ID's
basolateral_lumen Text Annotations
Species
Name | Structure | BioNetGen Definition | Depiction |
---|---|---|---|
Mt_mitochondria | mitochondria | ||
Mt_basolateral_lumen | basolateral_lumen | ||
Mt_apical_lumen | apical_lumen | ||
Mt_cytosol | cytosol |
Mt_mitochondria Universal ID's
Mt_mitochondria Text Annotations
Mt_basolateral_lumen Universal ID's
Mt_basolateral_lumen Text Annotations
Mt_apical_lumen Universal ID's
Mt_apical_lumen Text Annotations
Mt_cytosol Universal ID's
Mt_cytosol Text Annotations
Applications
Name | Properties | Math Type | Annotation |
---|---|---|---|
Matching w/ Matlab data |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | 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 |
10x10x10 numbered geometry |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | (copied from Matching w/ Matlab data) 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 |
Matching w/ Matlab data Universal ID's
Matching w/ Matlab data Text Annotations
10x10x10 numbered geometry Universal ID's
10x10x10 numbered geometry Text Annotations
Specifications (Species) - Matching w/ Matlab data go to Simulations
Specifications (Reaction) - Matching w/ Matlab data go to Simulations
Simulations - Matching w/ Matlab data go to Specifications
Name | End Time | Output Options |
---|---|---|
logKow impact on c=1,0,-1 | 300.0 |
KeepEvery 1 KeepAtMost 1000 |
Fig 6A influx pKa 9.6, logKow=1.88, c=1 | 100.0 |
KeepEvery 1 KeepAtMost 1000 |
Fig 6B efflux pKa 9.6, logKow=1.88, c=1 | 100.0 |
KeepEvery 1 KeepAtMost 1000 |
Matching w/ Matlab data Universal ID's
Matching w/ Matlab data Text Annotations
Matching w/ Matlab data Universal ID's
Matching w/ Matlab data Text Annotations
Matching w/ Matlab data Universal ID's
Matching w/ Matlab data 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 | mMem |
Events
Name | Variable | Rate Expression |
---|
Specifications (Species) - 10x10x10 numbered geometry go to Simulations
Specifications (Reaction) - 10x10x10 numbered geometry go to Simulations
Simulations - 10x10x10 numbered geometry go to Specifications
Name | End Time | Output Options |
---|---|---|
acid, base, neutral scan for logKow -2, 0, 2 | 300.0 |
KeepEvery 1 KeepAtMost 1000 |
Fig6A Influx, pKa 9.6, logKow=1.88, c=1 | 100.0 |
KeepEvery 1 KeepAtMost 1000 |
Fig6B Efflux, pKa 9.6, logKow=1.88, c=1 | 100.0 |
KeepEvery 1 KeepAtMost 1000 |
Fig6C Efflux pHa=6.5 vs 7.4, pKa 9.6, logKow=1.88, c=1 | 100.0 |
KeepEvery 1 KeepAtMost 1000 |
10x10x10 numbered geometry Universal ID's
10x10x10 numbered geometry Text Annotations
10x10x10 numbered geometry Universal ID's
10x10x10 numbered geometry Text Annotations
10x10x10 numbered geometry Universal ID's
10x10x10 numbered geometry Text Annotations
10x10x10 numbered geometry Universal ID's
10x10x10 numbered geometry 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 | mMem |
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 | Matching w/ Matlab data.bngl , 10x10x10 numbered geometry.bngl |
SBML | Matching w/ Matlab data.sbml , 10x10x10 numbered geometry.sbml |
Matlab | Matching w/ Matlab data.m , 10x10x10 numbered geometry.m |
NFSim XML | Matching w/ Matlab data.xml , 10x10x10 numbered geometry.xml |