Dashboard
Name - Baik & Rosania 2013 JPP - 03 Transcellular model with lysosome
BioModel ID - 94538871
Reaction Diagram
Physiology
| Universal ID's | Text Annotations |
|---|---|
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| Reaction |
Name
Structure
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Kinetics | Depiction |
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| Name |
Type
Electrical (Membrane Polarity)
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|---|---|
| m |
Compartment
(+) (-)
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| a |
Compartment
(+) (-)
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| c |
Compartment
(+) (-)
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| b |
Compartment
(+) (-)
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| l |
Compartment
(+) (-)
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| aMem |
Membrane
N/A
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| bMem |
Membrane
N/A
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| mMem |
Membrane
N/A
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| LMem |
Membrane
N/A
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| Name | Structure | BioNetGen Definition |
|---|---|---|
| Mt_m | m | |
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| Mt_b | b | |
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| Mt_a | a | |
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| Mt_c | c | |
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| Mt_l | l | |
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| Name | Text Annotations | BioNetGen Definition |
|---|
| Name |
Type
Count
|
BioNetGen Definition |
|---|
Applications
| Name | Math Type | Annotation |
|---|---|---|
| Imported Zhang et al 2006 Mol Pharm | 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 | 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 |
Application - Imported Zhang et al 2006 Mol Pharm
| Species | Initial Condition | Diffusion Constant | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Mt_m | 0.0 [uM] | 0.0
[um2/s] | Mt_a |
1000.0
[uM]
|
0.0
[um2/s] | Mt_c |
0.0
[uM]
|
0.0
[um2/s] | Mt_b |
0.0
[uM]
|
0.0
[um2/s] | Mt_l |
0.0
[uM]
|
0.0
[um2/s]
|
|
| Name | Reaction Mapping |
|---|---|
| flux_ac | included |
| flux_cb | included |
| flux_cm | included |
| flux_cl | included |
| Name | End Time | Output Options |
|---|---|---|
| logKow2 impact on acid, neutral, base | 600.0 [s] |
KeepEvery 1 KeepAtMost 1000 |
| Emm -160 vs -220 pKa 7,9,11 | 100.0 [s] |
KeepEvery 1 KeepAtMost 1000 |
| Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
|---|---|---|---|---|---|
| Compartmental | Compartment | LMem |
Application - test pH outside
| Species | Initial Condition | Diffusion Constant | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Mt_m | 0.0 [uM] | 0.0
[um2/s] | Mt_a |
1000.0
[uM]
|
0.0
[um2/s] | Mt_c |
0.0
[uM]
|
0.0
[um2/s] | Mt_b |
0.0
[uM]
|
0.0
[um2/s] | Mt_l |
0.0
[uM]
|
0.0
[um2/s]
|
|
| Name | Reaction Mapping |
|---|---|
| flux_ac | included |
| flux_cb | included |
| flux_cm | included |
| flux_cl | included |
| Name | End Time | Output Options |
|---|---|---|
| Simulation0 | 600.0 [s] |
KeepEvery 1 KeepAtMost 1000 |
| Simulation1 | 100.0 [s] |
KeepEvery 1 KeepAtMost 1000 |
| Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
|---|---|---|---|---|---|
| Compartmental | Compartment | LMem |
Global Parameters
| Name | Expression |
|---|