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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.
RefractorySoma: tracce di refractory

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+

    - RefractorySoma

  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: VDBMaxCtx

  condition: ( VDB mediumness ) AND NOT ApCtx
    out_context: VDBMediumCtx 

  condition: ( VDB emptiness ) AND NOT ApCtx
    out_context: VDBLowCtx

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 SomaRefractoryCtx )
    out_context: ApCtx
    out_context: bApCtx

ApBeh: Interacting

Durante la fase effettiva di spike, eliminiamo Na accumulati, riempiamo RefractorySoma per fase di refractory e riempiamo Ca2+ per le tracce medio termine di potenziamento/depotenziamento.

interacting: ApBeh
  contained_by: SOMA

  context: ApCtx
  rf: ( active: 8x )

  hypothesis: NOT Na empty
    action: [ decrease Na ]
    trace: 

  hypothesis: NOT RefractorySoma full
    action: [ increase RefractorySoma ]
    trace: 

  hypothesis: NOT Ca2+ full
    action: [ increase Ca2+ ]
    trace:

RefractoryBeh: Interacting

interacting: RefractoryBeh
  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: VDBMaxCtx 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