Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
X_CMX_CM+X_CM r2 CM GeneralKinetics
Y_CMY_CM+Y_CM r3 CM GeneralKinetics
L_sourceL_EC rx EC GeneralKinetics
L_EC+R_CMS_CM r1 CM GeneralKinetics

r2 Universal ID's

r2 Text Annotations

r3 Universal ID's

r3 Text Annotations

rx Universal ID's

rx Text Annotations

r1 Universal ID's

r1 Text Annotations

Expressions for r2

reaction rate

J

(0.04 + (0.4 * N_CM) + (2.0 * X_CM * X_CM / (1.0 + (X_CM * X_CM))) - (0.4 * X_CM * Y_CM) + (0.008 * X_CM * S_CM)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

0.0 [1]

Expressions for r3

reaction rate

J

((0.4 * X_CM) - (0.028 * Y_CM)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

0.0 [1]

Expressions for rx

reaction rate

J

((kf * L_source) - (kr * L_EC)) [uM.s-1]

local

kr

1.0 [s-1]

local

kf

10.0 [s-1]

Expressions for r1

reaction rate

J

((kf * L_EC * R_CM) - (kr * S_CM)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

0.0 [1]

local

kr

1.0 [s-1]

local

kf

2.0 [s-1.uM-1]

Structures

Name
Type
Electrical
CM Membrane IC(+)   EC(-)
IC Compartment (+)   (-)
EC Compartment (+)   (-)

CM Universal ID's

CM Text Annotations

IC Universal ID's

IC Text Annotations

EC Universal ID's

EC Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
L_EC EC EC
L_source EC EC
N_CM CM CM
Y_CM CM CM
X_CM CM CM
S_CM CM CM
R_CM CM CM

L_EC Universal ID's

L_EC Text Annotations

L_source Universal ID's

L_source Text Annotations

N_CM Universal ID's

N_CM Text Annotations

Y_CM Universal ID's

Y_CM Text Annotations

X_CM Universal ID's

X_CM Text Annotations

S_CM Universal ID's

S_CM Text Annotations

R_CM Universal ID's

R_CM Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Needle Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (3D)

Needle Universal ID's

Needle Text Annotations

Specifications (Species) - Needle go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
L_EC 0.0 [uM] 15.0 [um2/s] EC
L_source (((( - 5.0 + x) * ( - 5.0 + x)) + (( - 5.0 + y) * ( - 5.0 + y)) + (( - 2.5 + z) * ( - 2.5 + z))) < 1.0) [uM] 10.0 [um2/s] EC
N_CM (0.2 * ((t >= 15.0) && (t <= 16.0))) [uM] 0.1 [um2/s] CM
Y_CM 2.0 [uM] 0.0 [um2/s] CM
X_CM 0.14 [uM] 0.0 [um2/s] CM
S_CM 0.0 [uM] 0.0 [um2/s] CM
R_CM 100.0 [uM] 0.0 [um2/s] CM

Specifications (Reaction) - Needle go to Simulations

Name
Enabled?
r2 included
r3 included
rx included
r1 included

Simulations - Needle go to Specifications

Name
End Time
Output Options
Simulation0 100.0

OutputTimeStep 1.0

Needle Universal ID's

Needle Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry 3DLEGI_BEN

(Origin: 0.0, 0.0, 0.0; Extent: 5.0, 5.0, 5.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical IC 11.821125 [um3] IC
Volume Analytical EC 113.17887499999999 [um3] EC
Surface EC_IC_membrane EC | IC 25.03574790171551 [um2] CM

Events

Name Variable Rate Expression

Global Parameters

Name
Expression

Downloads

Model Format
Model Downloads
Virtual Cell Markup Language VCML File
PDF Report Report
COMBINE Archive OMEX File
SEDML SEDML File
File Format
Application Downloads
BNGL Needle.bngl
SBML Needle.sbml
Matlab Needle.m
NFSim XML Needle.xml