6.6 KiB
soma.md
Qui comprendiamo:
- SOMA: il soma
- VGSC-SOMA-H: Na ion channels. Open only when VDB high
- VGSC-SOMA-M: Na ion channels. Open only when VDB medium
- VGSC-SOMA-L: Na ion channels. Open only when VDB low
SOMA: Container
Simplified verifiable behaviors:
— ms:
- Resting at -70 mV: Leak channels + pumps (keep at resting)
- VDB Depolarization : ~1-2 ms: Na⁺ enters (some VGSCs open)
- Opened VGSC and then remain closed for a refractory period
- Spike if depolarized above threshold: to -50 mV
- Ca2+ enter
- Repolarization to -70 mV: ~1-2 ms: K⁺ exits (VG K⁺ channels open) ← NOT pumps!
- After-hyperpolarization: ~5-20 ms: K⁺ channels still open
— secs:
- Return to exact -70 mV: ~100-1000 ms: Na⁺/K⁺ pumps restore gradients
- Ca2+ accumulation
— mins:
- VGSC modulation
G expression:
— ms:
-
based on VDB, VGSC open and let Na+ in. VGSG then go into refractory
-
if Na fullness then ApCtx. Here the threshold is based only on the integration of Na+
-
increase SpikeTrainTraces (fast at spike)
-
increase Ca2+ traces
-
decrease Na: fast pump which decreases Na+, we do not model K+ -- there is a tug of war between Na entering and exiting. Na can reach fullness only if VDB increases fast (derivative)
-
there are 2 context: ApCtx and RefractorySoma imlemented with timers and tunable
-
decrease SpikeTraintraces slow, only if away from spiketrain this is empty
-
Tune: -- The threshold is tuned during the spiketrain. Low threshold at rest, to increase sensitivity, threshold increase during spike to increase discrimination
— secs:
- SpikeTrainTraces
— mins:
- Tune: -- refractory lenght
Tubs:
-
VDB: dendrites deliver current
-
Na: are a proxy for the Coulombs of charge building up on the somatic membrane. They are used to check threshold, but also to mimic Na+ and K+ pumping
-
Ca2+: Medium term traces to guide tuning and Night development. It is a local trace, ATP is a global (Astrocyte)
-
SpikeTrainTraces: sono le tracce che consentono al neurone di far partire il Tuning neuronale, quando e' lontano da uno spike-train, ovvero e' in riposo.
container: SOMA
expansion:
- VGSC-SOMA-H ( fullness: 50x, active: 20x, emptiness: 10x )
# modulated_by: VGSC-SOMA-H-TUN # possible/actual
- VGSC-SOMA-M ( fullness: 50x, active: 20x, emptiness: 10x )
# modulated_by: VGSC-SOMA-M-TUN # possible/actual
- VGSC-SOMA-L ( fullness: 50x, active: 20x, emptiness: 10x )
# modulated_by: VGSC-SOMA-L-TUN # possible/actual
tub_local:
- VDB
- Na
- Ca2+
tub_intricated:
- SpikeTrainTraces ( contained_in: DAY-N )
ms: SOMA
CheckVDB: Episode
As dendrites deliver current (VDB), the soma acts like a capacitor. It "stores" this charge in the form of membrane potential. This contextualizes VGSC-SOMA to open ion channels that let Na+ ions in.
This only applies if not ApCtx, or in other words, SOMA is not in refractory period.
episode: CheckVDB
contained_by: SOMA
context: Fixed
rf: ( active: 60x )
condition: (VDB fullness ) AND NOT ApCtx
out_context: VDBMax
condition: ( VDB mediumness ) AND NOT ApCtx
out_context: VDBMedium
condition: ( VDB emptiness ) AND NOT ApCtx
out_context: VDBLow
SomaSpike: Episode
Qui siamo nella fase effettiva di spike, non refractory che viene dopo. Fa da contesto di durata fra un RF ed un altro.
episode: SomaSpike
contained_by: SOMA
context: Fixed
rf: ( active: 60x )
condition: ( Na fullness ) AND ( NOT SomaRefractory )
out_context: ApCtx
out_context: bApCtx
APInteracting: Interacting
Durante la fase effettiva di spike, eliminiamo Na accumulati e riempiamo per fase di refractory
interacting: APInteracting
contained_by: SOMA
context: ApCtx
rf: ( active: 8x )
hypothesis: NOT Na empty
action: [ decrease Na ]
trace:
hypothesis: NOT RefractorySoma full
action: [ increase RefractorySoma ]
trace:
ClearRefractorySoma: Interacting
interacting: ClearRefractorySoma
contained_by: SOMA
context: Fixed
rf: ( active: 8x )
hypothesis: NOT RefractorySoma empty
action: [ decrease RefractorySoma ]
trace:
sec: SOMA
min: SOMA
VGSC-SOMA-TUN: Tuner
tuner: VGSC-SOMA-TUN
contained_by: SOMA
tunes: SOMA/expansion/VGSC-SOMA
context_intricated:
- TunPossible ( contained_by: DAY-N )
tub_local:
tub_intricated:
Check: Episode
context: episode
contained_by: VGSC-SOMA-TUN
context: TunPossible
rf: ( active: 60x )
condition:
out_context: TunSomaVcgg
?: Interacting
interacting: ?
contained_by: TUN-PRE-VGCC
context: TunSomaVcgg
rf: ( active: x )
hypothesis:
action:
trace:
VGSC-SOMA-H: Container
Voltage Gated Sodium Channel: difficult to open (High)
container: VGSC-SOMA-H
tub_local:
Ready ( )
tub_intricated:
Na ( contained_in: SOMA)
sec: VGSC-SOMA-H
NaEnterH: Interacting
Se metto il controllo sulla (NOT Ready fullness) il VGSC puo' far entrare un numero di Na non superiore ad un massimo.
interacting: NaEnterH
contained_by: VGSC-H-SOMA
context: VDBMax AND ( NOT RefractoryH )
rf: ( active: 1x )
hypothesis: ( NOT Na fullness ) AND ( NOT ReadyH fullness )
action: [ Na increase, ReadyH increase ]
trace: None
CheckRefractoryH: Episode
Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di Refractory. Questo perche' e' un era nella qualle avviene l'episodio.
episode: CheckRefractoryH
contained_by: VGSC-H-SOMA
context: NOT RefractoryH
rf: ( active: 60x )
condition: ( ReadyH fullness )
out_context: RefractoryH
RefractoryH: Interacting
Questo episodio deve girare varie volte nell'ambito del contesto di refractory che viene controllato ad un RF maggiore.
interacting: RefractoryH
contained_by: VGSC-H-SOMA
context: RefractoryH
rf: ( active: 1x )
hypothesis: NOT ( Ready emptyness )
action: [ Ready decrease ]
trace: None
VGSC-SOMA-M: Container
Voltage Gated Sodium Channel
container: VGSC-SOMA-M
sec: VGSC-SOMA-M
Interacting2
interacting: ??
contained_by: VGSC-M-SOMA
context: xxx
rf: ( active: 1x )
hypothesis:
action:
trace: None
VGSC-SOMA-L: Container
Voltage Gated Sodium Channel
container: VGSC-SOMA-M
sec: VGSC-SOMA-L
Interacting3
interacting: ??
contained_by: VGSC-L-SOMA
context: xxx
rf: ( active: 1x )
hypothesis:
action:
trace: None