Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction

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 mitochondria
Mt_basolateral_lumen basolateral_lumen basolateral_lumen
Mt_apical_lumen apical_lumen apical_lumen
Mt_cytosol 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

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

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

Species
Initial Condition
Diffusion Constant
Structure
Mt_mitochondria 0.0 [uM] 0.0 [um2/s] mitochondria
Mt_apical_lumen 10.0 [uM] 0.0 [um2/s] apical_lumen
Mt_cytosol 0.0 [uM] 0.0 [um2/s] cytosol
Mt_basolateral_lumen 0.0 [uM] 0.0 [um2/s] basolateral_lumen

Specifications (Reaction) - Matching w/ Matlab data go to Simulations

Name
Enabled?
flux_cm included
flux_ac included
flux_cb included

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

Species
Initial Condition
Diffusion Constant
Structure
Mt_mitochondria 0.0 [uM] 0.0 [um2/s] mitochondria
Mt_apical_lumen 10.0 [uM] 0.0 [um2/s] apical_lumen
Mt_cytosol 0.0 [uM] 0.0 [um2/s] cytosol
Mt_basolateral_lumen 0.0 [uM] 0.0 [um2/s] basolateral_lumen

Specifications (Reaction) - 10x10x10 numbered geometry go to Simulations

Name
Enabled?
flux_cm included
flux_ac included
flux_cb included

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

Global Parameters

Name
Expression