Dashboard
Name - Baik & Rosania 2013 JPP - 02 Transcellular model no lysosome
BioModel ID - 83932806
Reaction Diagram
Physiology
Universal ID's | Text Annotations |
---|---|
|
|
Reaction |
Name
Structure
|
Kinetics | Depiction |
---|
Name |
Type
Electrical (Membrane Polarity)
|
---|---|
mitochondria |
Compartment
(+) (-)
|
|
|
apical_lumen |
Compartment
(+) (-)
|
|
|
cytosol |
Compartment
(+) (-)
|
|
|
basolateral_lumen |
Compartment
(+) (-)
|
|
|
aMem |
Membrane
N/A
|
|
|
bMem |
Membrane
N/A
|
|
|
mMem |
Membrane
N/A
|
|
|
Name | Structure | BioNetGen Definition |
---|---|---|
Mt_mitochondria | mitochondria | |
|
|
|
Mt_basolateral_lumen | basolateral_lumen | |
|
|
|
Mt_apical_lumen | apical_lumen | |
|
|
|
Mt_cytosol | cytosol | |
|
|
Name | Text Annotations | BioNetGen Definition |
---|
Name |
Type
Count
|
BioNetGen Definition |
---|
Applications
Name | Math Type | Annotation |
---|---|---|
Matching w/ Matlab data | 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 | 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 |
Application - Matching w/ Matlab data
Species | Initial Condition | Diffusion Constant | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Mt_mitochondria | 0.0 [uM] | 0.0
[um2/s] Mt_apical_lumen |
10.0
[uM]
|
0.0
[um2/s] | Mt_cytosol |
0.0
[uM]
|
0.0
[um2/s] | Mt_basolateral_lumen |
0.0
[uM]
|
0.0
[um2/s]
|
|
Name | Reaction Mapping |
---|---|
flux_cm | included |
flux_ac | included |
flux_cb | included |
Name | End Time | Output Options |
---|---|---|
logKow impact on c=1,0,-1 | 300.0 [s] |
KeepEvery 1 KeepAtMost 1000 |
Fig 6A influx pKa 9.6, logKow=1.88, c=1 | 100.0 [s] |
KeepEvery 1 KeepAtMost 1000 |
Fig 6B efflux pKa 9.6, logKow=1.88, c=1 | 100.0 [s] |
KeepEvery 1 KeepAtMost 1000 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Compartmental | Compartment | mMem |
Application - 10x10x10 numbered geometry
Species | Initial Condition | Diffusion Constant | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Mt_mitochondria | 0.0 [uM] | 0.0
[um2/s] Mt_apical_lumen |
10.0
[uM]
|
0.0
[um2/s] | Mt_cytosol |
0.0
[uM]
|
0.0
[um2/s] | Mt_basolateral_lumen |
0.0
[uM]
|
0.0
[um2/s]
|
|
Name | Reaction Mapping |
---|---|
flux_cm | included |
flux_ac | included |
flux_cb | included |
Name | End Time | Output Options |
---|---|---|
acid, base, neutral scan for logKow -2, 0, 2 | 300.0 [s] |
KeepEvery 1 KeepAtMost 1000 |
Fig6A Influx, pKa 9.6, logKow=1.88, c=1 | 100.0 [s] |
KeepEvery 1 KeepAtMost 1000 |
Fig6B Efflux, pKa 9.6, logKow=1.88, c=1 | 100.0 [s] |
KeepEvery 1 KeepAtMost 1000 |
Fig6C Efflux pHa=6.5 vs 7.4, pKa 9.6, logKow=1.88, c=1 | 100.0 [s] |
KeepEvery 1 KeepAtMost 1000 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Compartmental | Compartment | mMem |
Global Parameters
Name | Expression |
---|