Dashboard

Name - FDAP diffusion

BioModel ID - 101962320

Reaction Diagram

reactionDiagram

Physiology

Universal ID's Text Annotations

Applications

Applications See in Dashboard
Name Math Type Annotation
Application half-cell Deterministic (ODE) Spatial (3D) (copied from Application1)
half-cell-smaller+tall Deterministic (ODE) Spatial (3D) (copied from Application half-cell) (copied from Application1)

Application - Application half-cell

Specifications(Species) - Application half-cell See in Dashboard
Species Initial Condition Diffusion Constant
laser (sqrt(((x * x) + (( - 10.0 + y) * ( - 10.0 + y)))) < 1.0) [uM] 0.0 [um2/s]
Gactin_PA 0.0 [uM] 10.0 [um2/s]
Gactin 100.0 [uM] 10.0 [um2/s]
Specifications(Reaction) - Application half-cell See in Dashboard
Name Reaction Mapping
r_PAforGa included
Simulations - Application half-cell See in Dashboard
Name End Time Output Options
short D between 2 and 10 Gactin=100 0.2 [s]

OutputTimeStep 0.002
D=2 - 10 2.0 [s]

OutputTimeStep 0.002
short D= from 2 to 10 Gactin=1 0.2 [s]

OutputTimeStep 0.002
Copy of D=2 - 10 2.0 [s]

OutputTimeStep 0.002
Geometry 3D-half lamel cali-1 See in Dashboard
(Origin: -20.0, 0.0, -3.5; Extent: 40.0, 20.0, 3.5[um])
Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical subVolume1 707.3967921228407 [um3] c0
Volume Analytical subVolume0 2092.6032078771595 [um3] c1
Surface subVolume0_subVolume1_membrane subVolume0 | subVolume1 1270.7539854953793 [um2] Membrane0

Application - half-cell-smaller+tall

Specifications(Species) - half-cell-smaller+tall See in Dashboard
Species Initial Condition Diffusion Constant
laser (sqrt(((x * x) + (( - 10.0 + y) * ( - 10.0 + y)))) < 1.0) [uM] 0.0 [um2/s]
Gactin_PA 0.0 [uM] 10.0 [um2/s]
Gactin 100.0 [uM] 10.0 [um2/s]
Specifications(Reaction) - half-cell-smaller+tall See in Dashboard
Name Reaction Mapping
r_PAforGa included
Simulations - half-cell-smaller+tall See in Dashboard
Name End Time Output Options
Simulation0 0.2 [s]

OutputTimeStep 0.002
Simulation1 2.0 [s]

OutputTimeStep 0.002
Simulation2 0.2 [s]

OutputTimeStep 0.002
Simulation3 2.0 [s]

OutputTimeStep 0.002
Geometry 3D-half lamel cali-1 See in Dashboard
(Origin: -15.0, 0.0, -7.0; Extent: 30.0, 15.0, 7.0[um])
Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical subVolume1 641.8342290585618 [um3] c0
Volume Analytical subVolume0 2508.165770941438 [um3] c1
Surface subVolume0_subVolume1_membrane subVolume0 | subVolume1 745.886799368184 [um2] Membrane0

Global Parameters

Global Parameters See in Dashboard
Name Expression
t_start 0.0[s]
t_finish 0.063[s]
k_forw 0.1[uM-1.s-1]
k_f 0.1[uM-1.s-1]
k_r 0.1[s-1]
K_PA 1.0[uM-1.s-1]
K_polym 0.0[uM-1.s-1]
K_depol 1.0[uM-1.s-1]