Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction

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 (+)   (-)

Species

Name
Structure
BioNetGen Definition
Depiction
Mt_m m m
Mt_b b b
Mt_a a a
Mt_c c c
Mt_l l l

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

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

Specifications (Species) - Imported Zhang et al 2006 Mol Pharm go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Mt_m 0.0 [uM] 0.0 [um2/s] m
Mt_a 1000.0 [uM] 0.0 [um2/s] a
Mt_c 0.0 [uM] 0.0 [um2/s] c
Mt_b 0.0 [uM] 0.0 [um2/s] b
Mt_l 0.0 [uM] 0.0 [um2/s] l

Specifications (Reaction) - Imported Zhang et al 2006 Mol Pharm go to Simulations

Name
Enabled?
flux_ac included
flux_cb included
flux_cm included
flux_cl included

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

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

Species
Initial Condition
Diffusion Constant
Structure
Mt_m 0.0 [uM] 0.0 [um2/s] m
Mt_a 1000.0 [uM] 0.0 [um2/s] a
Mt_c 0.0 [uM] 0.0 [um2/s] c
Mt_b 0.0 [uM] 0.0 [um2/s] b
Mt_l 0.0 [uM] 0.0 [um2/s] l

Specifications (Reaction) - test pH outside go to Simulations

Name
Enabled?
flux_ac included
flux_cb included
flux_cm included
flux_cl included

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

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

Global Parameters

Name
Expression