added preliminary notes on mechanisms

map.typ

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+= Collected notes on simulation
+
+== Broad Overview
+Simplified model of AP:
+  1. Input current causes potential to reach threshold
+  2. Threshold casues voltage gated ("charged protein domains")
+      Na+ channels to open (depol)
+  3. Voltage gated K+ channels open (opening assisted by Ca) ("delayed rectifier") and flow (repol, hyperpol)
+== Mechanisms
+
+General .mod notes:
+  - PARAMETERs aren't changed during the simulation, but can be set by user
+  - ASSIGNEDs are variables that change dynamically (like per-section voltage),
+    and local variables used in computation.
+  - STATEs are evolved via diffeq's, and are persistent between timesteps
+  - DERIVATIVEs are the diffeq's
+  - BREAKPOINT is the computation run at every timestep
+  - Neuron functions additively: several writes will sum (NOT FOR nonspecific)
+
+=== Global State (append as I read):
+  - `v` - membrane potential (per section)
+  - `e[ca|k|na]` - equilibrium potential for [Ca|K|Na] (managed by ion mechanism)
+  - `i[ca|k|na]` - intracellular [Ca|K|Na] level
+  - `ihcn` - HCN (mixed cation channels, permeable to both Na and K)
+  - `imcn` - nonspecific inactivation current
+
+=== Module Summaries
+`mech/Ca.mod`
+- Basic HH Ca model, writes to the calcium current
+`mech/CaDynamics_E2.mod`
+- Takes Ca current and uses it to determine new level of intracellular calcium
+`mech/CaDynamics_E2_soma.mod`
+- Same as CaDynamics_E2.mod but adapted for soma
+`mech/Ca_HVA.mod`
+- High-Voltage-Activation Ca channels
+- Similar to Ca.mod, but with much higher maximum conductance (0.684 $"mS"/"cm"^2$ vs 0.01 $"mS"/"cm"$)
+`mech/Ca_HVA_soma.mod`
+- Specific soma dynamics for HVA Ca channel
+`mech/Ca_LVAst.mod`
+- Low-Voltage-Activation Ca channels
+`mech/Ca_LVAst_soma.mod`
+- Specific soma dynamics for LVA Ca Channel
+`mech/hhqt.mod`
+- Squid axon HH (the og model) for Ca, K, L channels in squit giant axon membrane
+`mech/Ih.mod`
+- HCN current
+- _note: Check later if this is addressed in any of the Ca and K dynamics_
+`mech/Im.mod`
+- Potassium channel current
+`mech/K_Pst.mod`
+- Persistent (very slowly inactivating) component of the potassium current
+- Continues conducting through sustained depolarization
+`mech/K_Tst.mod`
+- Transient (activates rapidly during depol)
+- Inactivates rapidly during repol
+- Turns off quickly even if depol continues
+`mech/Nap_Et2.mod`
+- Persistent sodium current
+`mech/NaTa_t.mod`
+- Transient sodium current
+`mech/NaTa_t_myel.mod`
+- Transient sodium current for myelinated
+`mech/NaTa_t_nor.mod`
+`mech/NaTs2_t_apic.mod`
+`mech/NaTs2_t.mod`
+`mech/NaTs2_t_soma.mod`
+`mech/SK_E2.mod`
+`mech/SK_E2_soma.mod`
+`mech/SKv3_1_apic.mod`
+`mech/SKv3_1.mod`
+`mech/SKv3_1_soma.mod`
+`mech/xtra.mod`