Dashboard

Name - Baik & Rosania 2013 JPP - 02 Transcellular model no lysosome

BioModel ID - 83932806

Reaction Diagram

reactionDiagram

Physiology

Universal ID's Text Annotations

Applications

Applications See in Dashboard
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

Specifications(Species) - Matching w/ Matlab data See in Dashboard
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]
Specifications(Reaction) - Matching w/ Matlab data See in Dashboard
Name Reaction Mapping
flux_cm included
flux_ac included
flux_cb included
Simulations - Matching w/ Matlab data See in Dashboard
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
Geometry non-spatial See in Dashboard
(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

Application - 10x10x10 numbered geometry

Specifications(Species) - 10x10x10 numbered geometry See in Dashboard
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]
Specifications(Reaction) - 10x10x10 numbered geometry See in Dashboard
Name Reaction Mapping
flux_cm included
flux_ac included
flux_cb included
Simulations - 10x10x10 numbered geometry See in Dashboard
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
Geometry non-spatial See in Dashboard
(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

Global Parameters

Global Parameters See in Dashboard
Name Expression