clancy2
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000126) Biomodels notes: The model is according to the paper "Na+ Channel Mutation That Causes Both Brugada and Long-QT Syndrome Phenotypes: A Simulation Study of Mechanism". Original model comes from ModelDB with accession number: 62661. This is the wide type model. All the values and reactions obtained from Data Supplement6: Appendix of the paper. Figure3 has been reproduced by MathSBML. The stimulus v=-30mV during the time from 5ms to 20 ms displayed in the event. The meaning for the keyword, C: Close states; O: Open states; IF: Fast inactivation states; IC: Closed-Inactivation states; IM: Intermediat Inactivation states. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.
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| Simulation | |
|---|---|
| clancy2002_Fig3B |
Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.
| Name | Definition | |
|---|---|---|
| — | 0.001 second | |
| — | 0.001 volt |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| cell | — | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| C1 | — | 0.0 | cell | ✘ | |
| C2 | — | 0.0 | cell | ✘ | |
| C3 | — | 1.0 | cell | ✘ | |
| IC2 | — | 0.0 | cell | ✘ | |
| IC3 | — | 0.0 | cell | ✘ | |
| IF | — | 0.0 | cell | ✘ | |
| IM1 | — | 0.0 | cell | ✘ | |
| IM2 | — | 0.0 | cell | ✘ | |
| O | open states | 0.0 | cell | ✘ |
Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.
| Definition |
|---|
| Id | Name | Objective coefficient | Reaction Equation and Kinetic Law | Flux bounds | |
|---|---|---|---|---|---|
| reaction_0000001 | IC3=IC2 | IC3 = IC2 cell * (IC3 * a11 - IC2 * b11) | |||
| reaction_0000002 | IC2=IF | IC2 = IF cell * (IC2 * a12 - IF * b12) | |||
| reaction_0000003 | IF=IM1 | IF = IM1 cell * (IF * a4 - IM1 * b4) | |||
| reaction_0000004 | IM1=IM2 | IM1 = IM2 cell * (IM1 * a5 - IM2 * b5) | |||
| reaction_0000005 | C3=IC3 | C3 = IC3 cell * (C3 * b3 - IC3 * a3) | |||
| reaction_0000006 | C2=C3 | C2 = C3 cell * (C2 * b11 - C3 * a11) | |||
| reaction_0000007 | C2=IC2 | C2 = IC2 cell * (C2 * b3 - IC2 * a3) | |||
| reaction_0000008 | C1=C2 | C1 = C2 cell * (C1 * b12 - C2 * a12) | |||
| reaction_0000009 | C1=IF | C1 = IF cell * (C1 * b3 - IF * a3) | |||
| reaction_0000010 | IF=O | IF = O cell * (IF * b2 - a2 * O) | |||
| reaction_0000011 | O=C1 | O = C1 cell * (-C1 * a13 + O * b13) |
| Id | Value | |
|---|---|---|
| Ena | 0.0 | |
| Fara | 96485.0 | |
| Gna | 23.5 | |
| Ina | 0.0 | |
| Rk | 8314.0 | |
| Temp | 310.0 | |
| a11 | 0.0 | |
| a12 | 0.0 | |
| a13 | 0.0 | |
| a2 | 0.0 | |
| a3 | 0.0 | |
| a4 | 0.0 | |
| a5 | 0.0 | |
| b11 | 0.0 | |
| b12 | 0.0 | |
| b13 | 0.0 | |
| b2 | 0.0 | |
| b3 | 0.0 | |
| b4 | 0.0 | |
| b5 | 0.0 | |
| nai | 15.0 | |
| nao | 140.0 | |
| scale | 1000.0 | |
| v | 0.0 | |
| vhold | -80.0 | |
| vtest | -30.0 |
| Id | Value | Reaction |
|---|
| Definition | |
|---|---|
| a11 = 3.802 / (0.1027 * exp(-v / 17.0) + 0.2 * exp(-v / 150.0)) | |
| a12 = 3.802 / (0.1027 * exp(-v / 15.0) + 0.23 * exp(-v / 150.0)) | |
| a2 = 9.178 * exp(v / 29.68) | |
| b13 = 0.22 * exp(-(v - 10.0) / 20.3) | |
| b3 = 0.0084 + 2.000000e-05 * v | |
| a4 = (9.178 * exp(v / 29.68)) / 100.0 | |
| b4 = 3.7933 * 1.000000e-07 * exp(-v / 7.7) | |
| b5 = (3.7933 * 1.000000e-07 * exp(-v / 7.7)) / 50.0 | |
| a5 = (9.178 * exp(v / 29.68)) / (9.5 * 10000.0) | |
| Ena = Rk * Temp / Fara * log(nao / nai) | |
| b11 = 0.1917 * exp(-v / 20.3) | |
| b2 = (3.802 / (0.1027 * exp(-v / 12.0) + 0.25 * exp(-v / 150.0))) * (9.178 * exp(v / 29.68)) * (3.7933 * 1.000000e-07 * exp(-v / 7.7)) / ((0.22 * exp(-(v - 10.0) / 20.3)) * (0.0084 + 2.000000e-05 * v)) | |
| b12 = 0.2 * exp(-(v - 5.0) / 20.3) | |
| Ina = Gna * (O / (IC3 + IC2 + IF + IM1 + IM2 + C3 + C2 + C1 + O)) * (v - (Rk * Temp / Fara * log(nao / nai))) / scale | |
| a3 = 3.7933 * 1.000000e-07 * exp(-v / 7.7) | |
| a13 = 3.802 / (0.1027 * exp(-v / 12.0) + 0.25 * exp(-v / 150.0)) | |
| v = piecewise(vtest,5.0<time<=300.0,vhold) |
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| Definition |
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| Trigger | Assignments |
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