Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
CaRNE1CaIn leakRNE RNEmem MassAction
CaInCaRNE1 SPCA RNEmem GeneralKinetics
CaIn CatSper Cytosole GeneralKinetics
IP3 PLCd m0 GeneralKinetics
IP3 IP3K Cytosole GeneralKinetics
CaIn LeakPP m0 GeneralLumpedKinetics
CaIn+CaPrCaBuf CalMod Cytosole MassAction
CaRNE1+CaReticCaReticCal CaRetFast RNE MassAction
CaRNE1+CaRet_SlowCaRetSlow_Calcium CaRetSlow RNE MassAction
CaIn PMCA m0 GeneralKinetics
CaIn+caMSlowCaMSlowCa CaM_slow Cytosole MassAction

Structures

Name
Type
Electrical
m0 Membrane Cytosole(+)   outside(-)
RNEmem Membrane RNE(+)   Cytosole(-)
RNE Compartment (+)   (-)
outside Compartment (+)   (-)
Cytosole Compartment (+)   (-)

Species

Name
Structure
BioNetGen Definition
Depiction
CaIn Cytosole Cytosole
CaRNE1 RNE RNE
IP3 Cytosole Cytosole
Ip3buf Cytosole Cytosole
CaPr Cytosole Cytosole
CaBuf Cytosole Cytosole
CaRetic RNE RNE
CaReticCal RNE RNE
CaRet_Slow RNE RNE
CaRetSlow_Calcium RNE RNE
caMSlow Cytosole Cytosole
CaMSlowCa Cytosole Cytosole

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Application0 Specs - Species
Specs - Reaction
Simulations
Deterministic (ODE) Spatial (3D)

Specifications (Species) - Application0 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
CaRNE1 1000.0 [uM] 20.0 [um2/s] RNE
CaRetic ((3000.0 * 18.0 / 602.0 / RNE) * 1.0) [uM] 20.0 [um2/s] RNE
CaReticCal 0.0 [uM] 20.0 [um2/s] RNE
CaRet_Slow ((3000.0 * 18.0 / 602.0 / RNE) * 18.0) [uM] 20.0 [um2/s] RNE
CaRetSlow_Calcium 0.0 [uM] 20.0 [um2/s] RNE
CaIn 0.1 [uM] Diffusion [um2/s] Cytosole
IP3 0.0 [uM] 8.0 [um2/s] Cytosole
Ip3buf 0.0 [uM] 0.0 [um2/s] Cytosole
CaPr ((1000.0 * 2.0) * 18.0 / 602.0 / Cytosole) [uM] Diffusion [um2/s] Cytosole
CaBuf 0.0 [uM] Diffusion [um2/s] Cytosole
caMSlow ((1000.0 * 2.0) * 18.0 / 602.0 / Cytosole) [uM] Diffusion [um2/s] Cytosole
CaMSlowCa 0.0 [uM] Diffusion [um2/s] Cytosole

Specifications (Reaction) - Application0 go to Simulations

Name
Enabled?
leakRNE included
SPCA included
CatSper included
PLCd included
IP3K included
LeakPP included
CalMod included
CaRetFast included
CaRetSlow included
PMCA included
CaM_slow included
IP3R included

Simulations - Application0 go to Specifications

Name
End Time
Output Options
Calcium diffusionvariationosc 1000.0

OutputTimeStep 1.0

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry1120118915

(Origin: -12.5, 3.0, 3.9; Extent: 50.0, 3.5, 2.5 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical subdomain2 0.12512500000000001 [um3] RNE
Volume Analytical subdomain1 18.032437500000004 [um3] Cytosole
Volume Analytical subdomain0 419.3424375000001 [um3] outside
Surface subdomain0_subdomain1_membrane subdomain0 | subdomain1 96.30630517752202 [um2] m0
Surface subdomain1_subdomain2_membrane subdomain1 | subdomain2 1.033529612708134 [um2] RNEmem

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
kcatABHD 3.0[tbd]
Vabhd 0.0[tbd]
KmABHD 66.0[tbd]
CatSper_0 0.0[tbd]
CatSper0 0.0[tbd]
IC50AG 0.35[tbd]
K_abhdProgf 0.0[tbd]
K_abhdProgb 0.0[tbd]
K_CatSperf 0.0[tbd]
Popen 0.0[tbd]
K2 30.0[tbd]
K3 0.005[tbd]
K5 0.25[tbd]
Z (1.0 + (CaIn * K3 / (K1 * K2)) + (CaIn / K5) + ((CaIn ^ 2.0) * K3 / (K5 * K1 * K2)) + (IP3 / K1) + (IP3 * CaIn / (K1 * K2)) + (IP3 * CaIn / (K1 * K5)) + (IP3 * CaIn * CaIn / (K1 * K2 * K5)))[tbd]
w11 (IP3 * CaIn * 1.0 / (K1 * K5 * Z))[tbd]
K1 0.13[tbd]
DOLYA (CaIn / (CaIn + 0.7))[tbd]
NIP3R 1850.0[tbd]
Kserca 0.27[tbd]
Vserca 0.92[tbd]
kleakrne 0.1[tbd]
g0 0.0[tbd]
leakparam ((x < 28.0) * (t < 700.0))[tbd]
Vcatsperfake 0.7[tbd]
Diffusion 4.0[tbd]
Kd_CaRetic_slow 1.0[uM]
Vspca 0.93[tbd]
p_k 1.8[1]

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 Application0.bngl
SBML Application0.sbml
Matlab Application0.m
NFSim XML Application0.xml