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