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BIOMD0000000162 - Hernjak2005_Calcium_Signaling

 

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Reference Publication
Publication ID: 16169982
Hernjak N, Slepchenko BM, Fernald K, Fink CC, Fortin D, Moraru II, Watras J, Loew LM.
Modeling and analysis of calcium signaling events leading to long-term depression in cerebellar Purkinje cells.
Biophys. J. 2005 Dec; 89(6): 3790-3806
Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, Connecticut.  [more]
Model
Original Model: VCell logo
Submitter: Harish Dharuri
Submission ID: MODEL1629310283
Submission Date: 30 Jan 2008 23:07:54 UTC
Last Modification Date: 20 Feb 2014 17:06:51 UTC
Creation Date: 28 Jan 2008 11:44:38 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:occursIn Brenda Tissue Ontology cerebellar Purkinje cell
set #2
bqbiol:hasTaxon Taxonomy Chordata
set #3
bqbiol:isPartOf KEGG Pathway Long-term depression - Homo sapiens (human)
Gene Ontology regulation of synaptic activity
Gene Ontology calcium ion transport
Notes

The model reproduces the time profiles of Calcium in the spine and dendrites as depicted in Fig 8 and Fig 9 of the paper for CF activation.

The model was reproduced using MathSBML.

Please note that the units of volume species is molecules/micrometer cubed as against the units of microMolar given in the paper. To convert the units to microMolar multiply the species concentration by the conversion factor 1/602.


This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels Team.
For more information see the terms of use .
To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.

Model
Publication ID: 16169982 Submission Date: 30 Jan 2008 23:07:54 UTC Last Modification Date: 20 Feb 2014 17:06:51 UTC Creation Date: 28 Jan 2008 11:44:38 UTC
Mathematical expressions
Reactions
CD28k_highDbinding PA_Dbinding CG_deg IP3deg
D28kB_deg D28k_deg PA_MgD PA_Ca
PABMg_deg D28k_high_deg Ca_d D28kB_high_deg
CG_d D28kB_d reaction1 CGbinding
CaD28k_med PABCa_deg IP3_d D28k_high_d
reaction0 PABMg_d CD28k_high D28kBDbinding
PABCa_d PA_d CGB_deg PA_Mg
PA_deg IP3_degr D28kB_high_d D28k_d
CGB_d CG_Dbinding IP3_degr1 Ca_deg
pulses ER_leak_flux SERCA_fluxD IP3R_fluxD
SERCA_flux flux0 IP3R_flux flux1
ER_leak_fluxD      
Rules
Assignment Rule (variable: pulses_ar) Assignment Rule (variable: flux0_ar) Assignment Rule (variable: flux1_ar)  
Physical entities
Compartments Species
Extracellular Ca_Extracellular Ca_D_Extracellular  
Cytosol PA_D_Cytosol PABCa_D_Cytosol PABMg_D_Cytosol
CG_D_Cytosol D28kB_D_Cytosol PA_Cytosol
CG_Cytosol PABCa_Cytosol Mg_Cytosol
D28k_high_Cytosol D28k_high_D_Cytosol D28kB_high_D_Cytosol
CGB_D_Cytosol Ca_D_Cytosol CGB_Cytosol
D28k_Cytosol D28kB_high_Cytosol PABMg_Cytosol
IP3_Cytosol D28k_D_Cytosol IP3_D_Cytosol
Mg_D_Cytosol Ca_Cytosol D28kB_Cytosol
ER Ca_D_ER Ca_ER  
PM      
ERM ERDensity_ERM h_D_ERM ERDensity_D_ERM
h_ERM    
Global parameters
KMOLE pulses0 p0 delta
tau Ks A1 B1
flux0_ar Jch t1 t2
flux1_ar JchD pulses_ar p1
p2 p3 p4 p5
p6 p7 p8 p9
p10 p11 p12 p13
Reactions (45)
 
 CD28k_highDbinding [Ca_D_Cytosol] + [D28k_high_D_Cytosol] ↔ [D28kB_high_D_Cytosol];  
 
 PA_Dbinding [PA_D_Cytosol] + [Ca_D_Cytosol] ↔ [PABCa_D_Cytosol];  
 
 CG_deg [CG_D_Cytosol] ↔ ;   {CG_Cytosol}
 
 IP3deg [IP3_D_Cytosol] ↔ ;   {IP3_Cytosol}
 
 D28kB_deg [D28kB_D_Cytosol] ↔ ;   {D28kB_Cytosol}
 
 D28k_deg [D28k_D_Cytosol] ↔ ;   {D28k_Cytosol}
 
 PA_MgD [Mg_D_Cytosol] + [PA_D_Cytosol] ↔ [PABMg_D_Cytosol];  
 
 PA_Ca [PA_Cytosol] + [Ca_Cytosol] ↔ [PABCa_Cytosol];  
 
 PABMg_deg [PABMg_D_Cytosol] ↔ ;   {PABMg_Cytosol}
 
 D28k_high_deg [D28k_high_D_Cytosol] ↔ ;   {D28k_high_Cytosol}
 
 Ca_d [Ca_Cytosol] ↔ ;   {Ca_D_Cytosol}
 
 D28kB_high_deg [D28kB_high_D_Cytosol] ↔ ;   {D28kB_high_Cytosol}
 
 CG_d [CG_Cytosol] ↔ ;   {CG_D_Cytosol}
 
 D28kB_d [D28kB_Cytosol] ↔ ;   {D28kB_D_Cytosol}
 
 reaction1 [h_D_ERM] ↔ ;   {Ca_D_Cytosol}
 
 CGbinding [Ca_Cytosol] + [CG_Cytosol] ↔ [CGB_Cytosol];  
 
 CaD28k_med [D28k_Cytosol] + [Ca_Cytosol] ↔ [D28kB_Cytosol];  
 
 PABCa_deg [PABCa_D_Cytosol] ↔ ;   {PABCa_Cytosol}
 
 IP3_d [IP3_Cytosol] ↔ ;   {IP3_D_Cytosol}
 
 D28k_high_d [D28k_high_Cytosol] ↔ ;   {D28k_high_D_Cytosol}
 
 reaction0 [h_ERM] ↔ ;   {Ca_Cytosol}
 
 PABMg_d [PABMg_Cytosol] ↔ ;   {PABMg_D_Cytosol}
 
 CD28k_high [Ca_Cytosol] + [D28k_high_Cytosol] ↔ [D28kB_high_Cytosol];  
 
 D28kBDbinding [D28k_D_Cytosol] + [Ca_D_Cytosol] ↔ [D28kB_D_Cytosol];  
 
 PABCa_d [PABCa_Cytosol] ↔ ;   {PABCa_D_Cytosol}
 
 PA_d [PA_Cytosol] ↔ ;   {PA_D_Cytosol}
 
 CGB_deg [CGB_D_Cytosol] ↔ ;   {CGB_Cytosol}
 
 PA_Mg [PA_Cytosol] + [Mg_Cytosol] ↔ [PABMg_Cytosol];  
 
 PA_deg [PA_D_Cytosol] ↔ ;   {PA_Cytosol}
 
 IP3_degr [IP3_Cytosol] ↔ ;  
 
 D28kB_high_d [D28kB_high_Cytosol] ↔ ;   {D28kB_high_D_Cytosol}
 
 D28k_d [D28k_Cytosol] ↔ ;   {D28k_D_Cytosol}
 
 CGB_d [CGB_Cytosol] ↔ ;   {CGB_D_Cytosol}
 
 CG_Dbinding [Ca_D_Cytosol] + [CG_D_Cytosol] ↔ [CGB_D_Cytosol];  
 
 IP3_degr1 [IP3_D_Cytosol] ↔ ;  
 
 Ca_deg [Ca_D_Cytosol] ↔ ;   {Ca_Cytosol}
 
 pulses  ↔ [IP3_Cytosol];  
 
 ER_leak_flux [Ca_Cytosol] ↔ [Ca_ER];   {ERDensity_ERM}
 
 SERCA_fluxD [Ca_D_Cytosol] ↔ [Ca_D_ER];   {ERDensity_D_ERM}
 
 IP3R_fluxD [Ca_D_Cytosol] ↔ [Ca_D_ER];   {IP3_D_Cytosol} , {ERDensity_D_ERM} , {h_D_ERM}
 
 SERCA_flux [Ca_Cytosol] ↔ [Ca_ER];   {ERDensity_ERM}
 
 flux0 [Ca_Extracellular] ↔ [Ca_Cytosol];  
 
 IP3R_flux [Ca_Cytosol] ↔ [Ca_ER];   {IP3_Cytosol} , {h_ERM} , {ERDensity_ERM}
 
 flux1 [Ca_D_Extracellular] ↔ [Ca_D_Cytosol];  
 
 ER_leak_fluxD [Ca_D_Cytosol] ↔ [Ca_D_ER];   {ERDensity_D_ERM}
 
Rules (3)
 
 Assignment Rule (name: pulses_ar) pulses_ar = piecewise(p0*exp(-(t+(-delta))*Ks), t > delta, 0)+piecewise(p1*exp(-(t+(-(tau+delta)))*Ks), t > tau+delta, 0)+piecewise(p2*exp(-Ks*(t+(-(2*tau+delta)))), t > 2*tau+delta, 0)+piecewise(p3*exp(-Ks*(t+(-(3*tau+delta)))), t > 3*tau+delta, 0)+piecewise(p4*exp(-Ks*(t+(-(4*tau+delta)))), t > 4*tau+delta, 0)+piecewise(p5*exp(-Ks*(t+(-(5*tau+delta)))), t > 5*tau+delta, 0)+piecewise(p6*exp(-Ks*(t+(-(6*tau+delta)))), t > 6*tau+delta, 0)+piecewise(p7*exp(-Ks*(t+(-(7*tau+delta)))), t > 7*tau+delta, 0)+piecewise(p8*exp(-Ks*(t+(-(8*tau+delta)))), t > 8*tau+delta, 0)+piecewise(p9*exp(-Ks*(t+(-(9*tau+delta)))), t > 9*tau+delta, 0)+piecewise(p10*exp(-Ks*(t+(-(10*tau+delta)))), t > 10*tau+delta, 0)+piecewise(p11*exp(-Ks*(t+(-(11*tau+delta)))), t > 11*tau+delta, 0)
 
 Assignment Rule (name: flux0_ar) flux0_ar = piecewise(Jch*(0.0016611295681*Ca_Extracellular+(-0.0016611295681*Ca_Cytosol)), (t > t1) && (t < t2), 0)
 
 Assignment Rule (name: flux1_ar) flux1_ar = piecewise(JchD*(0.0016611295681*Ca_D_Extracellular+(-0.0016611295681*Ca_D_Cytosol)), (t > t1) && (t < t2), 0)
 
 Extracellular Spatial dimensions: 3.0  Compartment size: 1.0
 
 Ca_Extracellular
Compartment: Extracellular
Initial concentration: 602000.0  (Units: molecules)
 
 Ca_D_Extracellular
Compartment: Extracellular
Initial concentration: 602000.0  (Units: molecules)
 
 Cytosol Spatial dimensions: 3.0  Compartment size: 14169.5000044198
 
 PA_D_Cytosol
Compartment: Cytosol
Initial concentration: 1928.19396  (Units: molecules)
 
 PABCa_D_Cytosol
Compartment: Cytosol
Initial concentration: 9827.53562  (Units: molecules)
 
 PABMg_D_Cytosol
Compartment: Cytosol
Initial concentration: 36404.27644  (Units: molecules)
 
 CG_D_Cytosol
Compartment: Cytosol
Initial concentration: 84566.35334  (Units: molecules)
 
 D28kB_D_Cytosol
Compartment: Cytosol
Initial concentration: 2510.04502  (Units: molecules)
 
 PA_Cytosol
Compartment: Cytosol
Initial concentration: 1928.19396  (Units: molecules)
 
 CG_Cytosol
Compartment: Cytosol
Initial concentration: 84566.35334  (Units: molecules)
 
 PABCa_Cytosol
Compartment: Cytosol
Initial concentration: 9827.53562  (Units: molecules)
 
 Mg_Cytosol
Compartment: Cytosol
Initial concentration: 355180.0  (Units: molecules)
 
 D28k_high_Cytosol
Compartment: Cytosol
Initial concentration: 43952.64608  (Units: molecules)
 
 D28k_high_D_Cytosol
Compartment: Cytosol
Initial concentration: 43952.64608  (Units: molecules)
 
 D28kB_high_D_Cytosol
Compartment: Cytosol
Initial concentration: 4207.35392  (Units: molecules)
 
 CGB_D_Cytosol
Compartment: Cytosol
Initial concentration: 11753.6286  (Units: molecules)
 
 Ca_D_Cytosol
Compartment: Cytosol
Initial concentration: 27.09  (Units: molecules)
 
 CGB_Cytosol
Compartment: Cytosol
Initial concentration: 11753.6286  (Units: molecules)
 
 D28k_Cytosol
Compartment: Cytosol
Initial concentration: 45649.95498  (Units: molecules)
 
 D28kB_high_Cytosol
Compartment: Cytosol
Initial concentration: 4207.35392  (Units: molecules)
 
 PABMg_Cytosol
Compartment: Cytosol
Initial concentration: 36404.27644  (Units: molecules)
 
 IP3_Cytosol
Compartment: Cytosol
Initial concentration: 96.32  (Units: molecules)
 
 D28k_D_Cytosol
Compartment: Cytosol
Initial concentration: 45649.95498  (Units: molecules)
 
 IP3_D_Cytosol
Compartment: Cytosol
Initial concentration: 96.32  (Units: molecules)
 
 Mg_D_Cytosol
Compartment: Cytosol
Initial concentration: 355180.0  (Units: molecules)
 
 Ca_Cytosol
Compartment: Cytosol
Initial concentration: 27.09  (Units: molecules)
 
 D28kB_Cytosol
Compartment: Cytosol
Initial concentration: 2510.04502  (Units: molecules)
 
 ER Spatial dimensions: 3.0  Compartment size: 2500.0
 
 Ca_D_ER
Compartment: ER
Initial concentration: 240800.0  (Units: molecules)
 
 Ca_ER
Compartment: ER
Initial concentration: 240800.0  (Units: molecules)
 
 PM Spatial dimensions: 2.0  Compartment size: 16669.5000051998  (Units: um2)
 ERM Spatial dimensions: 2.0  Compartment size: 50000.0  (Units: um2)
 
 ERDensity_ERM
Compartment: ERM
Initial concentration: 1.0  (Units: molecules)
 
 h_D_ERM
Compartment: ERM
Initial concentration: 0.8  (Units: molecules)
 
 ERDensity_D_ERM
Compartment: ERM
Initial concentration: 1.0  (Units: molecules)
 
 h_ERM
Compartment: ERM
Initial concentration: 0.8  (Units: molecules)
 
Global Parameters (28)
 
   KMOLE
Value: 0.00166112956810631   (Units: uM_um3_molecules_1)
Constant
 
   pulses0  
 
   p0
Value: 1.0
Constant
 
   delta
Constant
 
   tau
Value: 0.012
Constant
 
   Ks
Value: 1.188
Constant
 
   A1
Value: 1.0
Constant
 
   B1
Value: 2.0
Constant
 
   flux0_ar  
 
   Jch
Value: 13.25
Constant
 
   t1
Value: 0.1
Constant
 
   t2
Value: 0.105
Constant
 
   flux1_ar  
 
   JchD
Value: 6.25
Constant
 
   pulses_ar  
 
   p1
Value: 1.0
Constant
 
   p2
Value: 1.0
Constant
 
   p3
Value: 1.0
Constant
 
   p4
Value: 1.0
Constant
 
   p5
Value: 1.0
Constant
 
   p6
Value: 1.0
Constant
 
   p7
Value: 1.0
Constant
 
   p8
Value: 1.0
Constant
 
   p9
Value: 1.0
Constant
 
   p10
Value: 1.0
Constant
 
   p11
Value: 1.0
Constant
 
   p12
Value: 1.0
Constant
 
   p13
Value: 1.0
Constant
 
CD28k_highDbinding (2)
 
   Kf
Value: 5.5   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 2.6   (Units: s_1)
Constant
 
PA_Dbinding (2)
 
   Kf
Value: 107.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 0.95   (Units: s_1)
Constant
 
CG_deg (7)
 
   D
Value: 15.0   (Units: um2_s_1)
Constant
 
   r_n
Value: 0.1   (Units: um)
Constant
 
   l_n
Value: 0.66   (Units: um)
Constant
 
   r_d
Value: 1.0   (Units: um)
Constant
 
   l_star
Value: 27.9812   (Units: um)
Constant
 
   CG_F
Value: 140.47567   (Units: uM)
Constant
 
   lc
Value: 5.6265   (Units: um)
Constant
 
IP3deg (7)
 
   D
Value: 283.0   (Units: um2_s_1)
Constant
 
   r_n
Value: 0.1   (Units: um)
Constant
 
   l_n
Value: 0.66   (Units: um)
Constant
 
   r_d
Value: 1.0   (Units: um)
Constant
 
   l_star
Value: 27.9812   (Units: um)
Constant
 
   IP3_F
Value: 0.16   (Units: uM)
Constant
 
   lc
Value: 5.6265   (Units: um)
Constant
 
D28kB_deg (7)
 
   D
Value: 28.0   (Units: um2_s_1)
Constant
 
   r_n
Value: 0.1   (Units: um)
Constant
 
   l_n
Value: 0.66   (Units: um)
Constant
 
   r_D
Value: 1.0   (Units: um)
Constant
 
   l_star
Value: 27.9812   (Units: um)
Constant
 
   D28kB_F
Value: 4.16951   (Units: uM)
Constant
 
   lc
Value: 5.6265   (Units: um)
Constant
 
D28k_deg (7)
 
   D
Value: 28.0   (Units: um2_s_1)
Constant
 
   r_n
Value: 0.1   (Units: um)
Constant
 
   l_n
Value: 0.66   (Units: um)
Constant
 
   r_D
Value: 1.0   (Units: um)
Constant
 
   l_star
Value: 27.9812   (Units: um)
Constant
 
   D28k_F
Value: 75.83049   (Units: uM)
Constant
 
   lc
Value: 5.6265   (Units: um)
Constant
 
PA_MgD (2)
 
   Kf
Value: 0.8   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 25.0   (Units: s_1)
Constant
 
PA_Ca (2)
 
   Kf
Value: 107.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 0.95   (Units: s_1)
Constant
 
PABMg_deg (7)
 
   D
Value: 43.0   (Units: um2_s_1)
Constant
 
   r_n
Value: 0.1   (Units: um)
Constant
 
   l_n
Value: 0.66   (Units: um)
Constant
 
   r_d
Value: 1.0   (Units: um)
Constant
 
   l_star
Value: 27.9812   (Units: um)
Constant
 
   PABMg_F
Value: 60.47222   (Units: uM)
Constant
 
   lc
Value: 5.6265   (Units: um)
Constant
 
D28k_high_deg (7)
 
   D
Value: 28.0   (Units: um2_s_1)
Constant
 
   r_n
Value: 0.1   (Units: um)
Constant
 
   l_n
Value: 0.66   (Units: um)
Constant
 
   r_D
Value: 1.0   (Units: um)
Constant
 
   l_star
Value: 27.9812   (Units: um)
Constant
 
   D28k_high_F
Value: 73.01104   (Units: uM)
Constant
 
   lc
Value: 5.6265   (Units: um)
Constant
 
Ca_d (4)
 
   D
Value: 223.0   (Units: um2_s_1)
Constant
 
   r_neck
Value: 0.1   (Units: um)
Constant
 
   l
Value: 0.66   (Units: um)
Constant
 
   r_spine
Value: 0.288   (Units: um)
Constant
 
D28kB_high_deg (7)
 
   D
Value: 28.0   (Units: um2_s_1)
Constant
 
   r_n
Value: 0.1   (Units: um)
Constant
 
   l_n
Value: 0.66   (Units: um)
Constant
 
   r_D
Value: 1.0   (Units: um)
Constant
 
   l_star
Value: 27.9812   (Units: um)
Constant
 
   D28kB_high_F
Value: 6.98896   (Units: uM)
Constant
 
   lc
Value: 5.6265   (Units: um)
Constant
 
CG_d (4)
 
   D
Value: 15.0   (Units: um2_s_1)
Constant
 
   r_neck
Value: 0.1   (Units: um)
Constant
 
   l
Value: 0.66   (Units: um)
Constant
 
   r_spine
Value: 0.288   (Units: um)
Constant
 
D28kB_d (4)
 
   D
Value: 28.0   (Units: um2_s_1)
Constant
 
   r_neck
Value: 0.1   (Units: um)
Constant
 
   l
Value: 0.66   (Units: um)
Constant
 
   r_spine
Value: 0.288   (Units: um)
Constant
 
reaction1 (3)
 
   I
Constant
 
   Kinh
Value: 0.2   (Units: uM)
Constant
 
   Kon
Value: 2.7   (Units: molecules_um_2_uM_1_s_1)
Constant
 
CGbinding (2)
 
   Kf
Value: 430.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 140.0   (Units: s_1)
Constant
 
CaD28k_med (2)
 
   Kf
Value: 43.5   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 35.8   (Units: s_1)
Constant
 
PABCa_deg (7)
 
   D
Value: 43.0   (Units: um2_s_1)
Constant
 
   r_n
Value: 0.1   (Units: um)
Constant
 
   l_n
Value: 0.66   (Units: um)
Constant
 
   r_d
Value: 1.0   (Units: um)
Constant
 
   l_star
Value: 27.9812   (Units: um)
Constant
 
   PABCa_F
Value: 16.32481   (Units: uM)
Constant
 
   lc
Value: 5.6265   (Units: um)
Constant
 
IP3_d (4)
 
   D
Value: 283.0   (Units: um2_s_1)
Constant
 
   r_neck
Value: 0.1   (Units: um)
Constant
 
   l
Value: 0.66   (Units: um)
Constant
 
   r_spine
Value: 0.288   (Units: um)
Constant
 
D28k_high_d (4)
 
   D
Value: 28.0   (Units: um2_s_1)
Constant
 
   r_neck
Value: 0.1   (Units: um)
Constant
 
   l
Value: 0.66   (Units: um)
Constant
 
   r_spine
Value: 0.288   (Units: um)
Constant
 
reaction0 (3)
 
   I
Constant
 
   Kinh
Value: 0.2   (Units: uM)
Constant
 
   Kon
Value: 2.7   (Units: molecules_um_2_uM_1_s_1)
Constant
 
PABMg_d (4)
 
   D
Value: 43.0   (Units: um2_s_1)
Constant
 
   r_neck
Value: 0.1   (Units: um)
Constant
 
   l
Value: 0.66   (Units: um)
Constant
 
   r_spine
Value: 0.288   (Units: um)
Constant
 
CD28k_high (2)
 
   Kf
Value: 5.5   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 2.6   (Units: s_1)
Constant
 
D28kBDbinding (2)
 
   Kf
Value: 43.5   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 35.8   (Units: s_1)
Constant
 
PABCa_d (4)
 
   D
Value: 43.0   (Units: um2_s_1)
Constant
 
   r_neck
Value: 0.1   (Units: um)
Constant
 
   l
Value: 0.66   (Units: um)
Constant
 
   r_spine
Value: 0.288   (Units: um)
Constant
 
PA_d (4)
 
   D
Value: 43.0   (Units: um2_s_1)
Constant
 
   r_neck
Value: 0.1   (Units: um)
Constant
 
   l
Value: 0.66   (Units: um)
Constant
 
   r_spine
Value: 0.288   (Units: um)
Constant
 
CGB_deg (7)
 
   D
Value: 15.0   (Units: um2_s_1)
Constant
 
   r_n
Value: 0.1   (Units: um)
Constant
 
   l_n
Value: 0.66   (Units: um)
Constant
 
   r_d
Value: 1.0   (Units: um)
Constant
 
   l_star
Value: 27.9812   (Units: um)
Constant
 
   CGB_F
Value: 19.5243   (Units: uM)
Constant
 
   lc
Value: 5.6265   (Units: um)
Constant
 
PA_Mg (2)
 
   Kf
Value: 0.8   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 25.0   (Units: s_1)
Constant
 
PA_deg (7)
 
   D
Value: 43.0   (Units: um2_s_1)
Constant
 
   r_n
Value: 0.1   (Units: um)
Constant
 
   l_n
Value: 0.66   (Units: um)
Constant
 
   r_d
Value: 1.0   (Units: um)
Constant
 
   l_star
Value: 27.9812   (Units: um)
Constant
 
   PA_F
Value: 3.20298   (Units: uM)
Constant
 
   lc
Value: 5.6265   (Units: um)
Constant
 
IP3_degr (2)
 
   Kdegr
Value: 0.14   (Units: s_1)
Constant
 
   IP3_CytosolS
Value: 0.16   (Units: uM)
Constant
 
D28kB_high_d (4)
 
   D
Value: 28.0   (Units: um2_s_1)
Constant
 
   r_neck
Value: 0.1   (Units: um)
Constant
 
   l
Value: 0.66   (Units: um)
Constant
 
   r_spine
Value: 0.288   (Units: um)
Constant
 
D28k_d (4)
 
   D
Value: 28.0   (Units: um2_s_1)
Constant
 
   r_neck
Value: 0.1   (Units: um)
Constant
 
   l
Value: 0.66   (Units: um)
Constant
 
   r_spine
Value: 0.288   (Units: um)
Constant
 
CGB_d (4)
 
   D
Value: 15.0   (Units: um2_s_1)
Constant
 
   r_neck
Value: 0.1   (Units: um)
Constant
 
   l
Value: 0.66   (Units: um)
Constant
 
   r_spine
Value: 0.288   (Units: um)
Constant
 
CG_Dbinding (2)
 
   Kf
Value: 430.0   (Units: uM_1_s_1)
Constant
 
   Kr
Value: 140.0   (Units: s_1)
Constant
 
IP3_degr1 (2)
 
   Kdegr
Value: 0.14   (Units: s_1)
Constant
 
   IP3_CytosolD
Value: 0.16   (Units: uM)
Constant
 
Ca_deg (7)
 
   D
Value: 223.0   (Units: um2_s_1)
Constant
 
   r_n
Value: 0.1   (Units: um)
Constant
 
   l_n
Value: 0.66   (Units: um)
Constant
 
   r_D
Value: 1.0   (Units: um)
Constant
 
   l_star
Value: 27.9812   (Units: um)
Constant
 
   Ca_F
Value: 0.045   (Units: uM)
Constant
 
   lc
Value: 5.6265   (Units: um)
Constant
 
pulses (3)
 
   SVR
Value: 3.0   (Units: um_1)
Constant
 
   Js
Constant
 
   Rs
Value: 0.288   (Units: _one_)
Constant
 
ER_leak_flux (2)
 
   I
Constant
 
   vL
Value: 0.12396   (Units: uM_um3_molecules_1_s_1)
Constant
 
SERCA_fluxD (3)
 
   I
Constant
 
   vP
Value: 3.75   (Units: uM_um3_molecules_1_s_1)
Constant
 
   kP
Value: 0.27
Constant
 
IP3R_fluxD (4)
 
   I
Constant
 
   Jmax2
Value: 21000.0   (Units: _one__0E_57_item_4_m6_mol_s_1)
Constant
 
   dI
Value: 20.0   (Units: uM)
Constant
 
   Kact
Value: 0.3   (Units: uM)
Constant
 
SERCA_flux (3)
 
   I
Constant
 
   vP
Value: 3.75   (Units: uM_um3_molecules_1_s_1)
Constant
 
   kP
Value: 0.27
Constant
 
flux0 (1)
 
   I
Constant
 
IP3R_flux (4)
 
   I
Constant
 
   Jmax2
Value: 21000.0   (Units: _one__0E_57_item_4_m6_mol_s_1)
Constant
 
   dI
Value: 20.0   (Units: uM)
Constant
 
   Kact
Value: 0.3   (Units: uM)
Constant
 
flux1 (1)
 
   I
Constant
 
ER_leak_fluxD (2)
 
   I
Constant
 
   vL
Value: 0.12396   (Units: uM_um3_molecules_1_s_1)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000162

Curator's comment: (updated: 27 Aug 2009 20:00:34 BST)

The model reproduces Figure 8a of the reference publication. The species are defined in molecules/micrometer cubed units in the model. The top 2 plots are in molecules/micrometer cubed units. The bottom two plots corresponds to that of the paper which are in microMolars (obtained by converting molecules/micrometer cubed to microMolars by multiplying by the converting factor 1/602).

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