1D-Dyad-Model-RyR-IP3R

Single dyad model configuration

LTCC-triggered spark simulations

1. Perform LTCC-triggered spark simulations
   • Run: one_dyad_Mult_clusters_mult_runs_save_RyR_IP3R_6State.m (with IP3R model) or;
   • Run: one_dyad_Mult_clusters_mult_runs_save_RyR_ConstJSR.m (constant JSR leak) or;
   • Run: one_dyad_Mult_clusters_mult_runs_save_RyR_StochJSR.m (randomly occurring JSR leak) or;
   • Run: one_dyad_Mult_clusters_mult_runs_save_rand_RyR_IP3R.m (random cluster arrangement in dyad)
   • Run: one_dyad_Mult_clusters_mult_runs_save_RyR_Sheep.m (Sheep RyR, varying SERCA activity, no IP3R)
   • With dependencies:
     • RxnDiffusion_parameters.m
     • IP3R_parameters.m
     • EulerMethod.m
     • RxnDiffusion_Fluxes.m
     • Update_IP3R_vars.m
     • parsave.m
2. Result analysis & figure generation
   • Run: plot_Triggered_Spark_Cai_profile.m (temporal evolution of: dyad Ca²⁺, JSR Ca²⁺, n(RyR open), n(IP3R open))
   • For sheep RyR model - Run: one_dyad_SheepRyR_plots.m (temporal evolution of dyad Ca²⁺, JSR Ca²⁺, n(RyR open))
   • With dependencies:
     • data_shade.m
   • Run: extract_Triggered_spark_data.m (identifies and extracts spark statistics into one file)
   • Run: plot_Triggered_Spark_Stats.m (swarm plots of spark amp and FDHM, statistical analysis)
   • With dependencies:
     • plotSpread.m
     • myErrorbar.m
     • isEven.m
     • repeatEntries.m

Spontaneous spark simulations

1. Perform spontaneous spark simulations
   • Run: Coupl_rep_uncoupl_Mult_clusters_mult_runs_save_1Dyad_NoStim.m (with IP3R model) or;
   • Run: Coupl_rep_uncoupl_Mult_clusters_mult_runs_save_1Dyad_ConstJSR.m (constant JSR leak) or;
   • Run: Coupl_rep_uncoupl_Mult_clusters_mult_runs_save_1Dyad_StochJSR.m (randomly occurring JSR leak)
   • With same dependencies as 1 above
2. Result analysis & figure generation
   • Run: extract_Spont_spark_data.m (identifies and extracts spark statistics into one file)
   • Run: plot_Spont_Spark_Stats.m (swarm plots of spark amp and FDHM, statistical analysis)
   • With same dependencies as 2 above