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 (+)   (-)

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

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

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

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

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