= 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`