model info

docs/index.md

@@ -5,21 +5,32 @@
 
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-- CaMKII model: "Mechanisms of Ca2+/calmodulin-dependent kinase II activation in single dendritic spines" (Chang et al., 2019, Nature Communications); https://doi.org/10.1038/s41467-019-10694-z
-- ROS activation model: Oxidized Calmodulin Kinase II Regulates Conduction Following Myocardial Infarction: A Computational Analysis (Christensen et al. 2009); https://doi.org/10.1371/journal.pcbi.1000583
-- Isoproterenol and CaMKII effects: A novel computational model of mouse myocyte electrophysiology to assess the synergy between Na+ loading and CaMKII. (Moritti et al. 2014); https://doi.org/10.1113/jphysiol.2013.266676
-- Neonatal rat ventricular myocyte model: Model of Excitation-Contraction Coupling of Rat Neonatal Ventricular Myocytes (Korhonen et al. 2009); https://pmc.ncbi.nlm.nih.gov/articles/PMC2716686/
+[Chang(2019)]:  https://doi.org/10.1038/s41467-019-10694-z
+[Christensen(2019)]: https://doi.org/10.1371/journal.pcbi.1000583
+[Moritti(2014)]: https://doi.org/10.1113/jphysiol.2013.266676
+[Korhonen(2009)]: https://pmc.ncbi.nlm.nih.gov/articles/PMC2716686/
+
+- CaMKII model: "Mechanisms of Ca2+/calmodulin-dependent kinase II activation in single dendritic spines" (Chang et al., 2019, Nature Communications); [Chang(2019)][]
+- ROS activation model: Oxidized Calmodulin Kinase II Regulates Conduction Following Myocardial Infarction: A Computational Analysis (Christensen et al. 2009); [Christensen(2019)][]
+- Isoproterenol and CaMKII effects: A novel computational model of mouse myocyte electrophysiology to assess the synergy between Na+ loading and CaMKII. (Moritti et al. 2014); [Moritti(2014)][]
+- Neonatal rat ventricular myocyte (NRVM) model: Model of Excitation-Contraction Coupling of Rat Neonatal Ventricular Myocytes (Korhonen et al. 2009); [Korhonen(2009)][]
 
 ## Adjusted from the original models
 
-- Caffeine activation of RyR: increasing sensitivity to Sub-SR Ca instead of constant opening.
-- Corrected compartment volumes for SR Ca and Sub-SR Ca ODEs.
-- Added a simplified beta-adrenergic system with a steady-state algebraic representation.
-- Fast sodium channel recovery rate increased by 3 times to accomodate 2Hz and 3Hz pacing.
+### Beta-adrenergic system
+
+The activities of PKACI, PKACII, PP1, and their downstream targets (SERCA, LCC, RyR, and NCX) are described by Hill functions, fitted to the activities in the original beta-adrenergic system in [Moritti(2014)][] across a range of isoproterenol.
+
+### CaMKII system
 
-### Parameters adjusted
+![Image](https://github.com/user-attachments/assets/37a18568-99f4-4b97-b410-f9052f6b58e7)
 
-- kCaM4_on: 30 -> 15Hz / μM
-- kCaM2C_on: 0.92 -> 0.5Hz / μM
-- k_phosCaM: 30 -> 10Hz
-- CmdnTotal: 50 -> 30μM
+- Association/dissociation rates of CaMKII and CaM-calcium (kf, kb) is fitted to [Chang(2019)][] model across a range of cytosolic calcium.
+- Autophosphorylation/dephosphorylation rates of CaMKII (kdp, kph) are adapted from [Chang(2019)][] model.
+- Oxidation/reduction rates of CaMKII (kox, krd) are adapted from [Christensen(2019)][] model.
+
+### Neonatal rat ventricular cardiomyocyte (NRVM)
+
+- Caffeine activation of RyR: increasing sensitivity to Sub-SR Ca instead of constant opening.
+- Compartment corrections for SR Ca and Sub-SR Ca ODEs.
+- Fast sodium channel gating variable recovery rates increased by 3 times to accomodate 2Hz and 3Hz pacing.