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organism/elements/neuron/soma.md
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sergio 27068b36d8 Update elements/neuron/soma.md
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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

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 SomaRefractory 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.

  • SomaRefractory: tracce di refractory

SOMA: Comprehension

SOMA
  type: comprehension

  expand_comprehension: 
    &VGSC-SOMA-H: VGSC-SOMA (full: 50x, active: 20x, empty: 10x) 
    &VGSC-SOMA-M: VGSC-SOMA (full: 50x, active: 20x, empty: 10x) 
    &VGSC-SOMA-L: VGSC-SOMA (full: 50x, active: 20x, empty: 10x) 

  instantiate_container:
    SOMA-BEH []
    VGSC-SOMA-H-TUN [pass: &VGSC-SOMA-H]
    VGSC-SOMA-M-TUN [pass: &VGSC-SOMA-M]
    VGSC-SOMA-L-TUN [pass: &VGSC-SOMA-L]

SOMA-BEH: Container

SOMA-BEH
  type: container
  activity_scope: !DAY
  
  tub_local:
    - VDB
    - Na
    - Ca2+
    - SomaRefractory

  tub_intricated:  
    - SpikeTrainTraces ( contained_in: DAY-N )

any

SOMA-Status: ( active: 60x ) contextor

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.

SOMA-Status: ( active: 60x )
  type: contextor
  contained_by: SOMA-BEH

  in_context: any
    condition: ( VDB fullness ) AND NOT AP_ctx
      out_context: VDBMax_Ctx
    condition: ( VDB mediumness ) AND NOT AP_ctx
      out_context: VDBMedium_ctx 
    condition: ( VDB emptiness ) AND NOT Ap_ctx
      out_context: VDBLow_ctx
    condition: NOT ( Na empty )
      out_context: NaSpill_ctx
SomaSpike: ( active: 30x ) contextor

Il fatto che mettiamo il check di AP separato dal check del Soma-Status, e' perche' vogliamo poter avere un RF specifico per AP, eventualmente tunabile.

Qui siamo nella fase effettiva di spike, non refractory che viene dopo. Fa da contesto di durata fra un RF ed un altro.

La fullness di Na rappresenta il threshold e puo' essere modificato. La fullness di SomaRefractory rappresenta la lunghezza del refractory.

SomaSpike: ( active: 30x )
  type: contextor
  contained_by: SOMA-BEH

  in_context: any
    condition: ( Na fullness ) AND ( SomaRefractory emptiness )
      out_context: AP_ctx
      out_context: bAp_ctx

SomaRefractorySpill: ( active: 16x ) accumulator

Lo spill deve essere piu' lento dell'increase che avviene in ActiveAP

SomaRefractorySpill: ( active: 16x )
  type: accumulator
  contained_by: SOMA-BEH

  in_context: any
    hypothesis: NOT ( SomaRefractory empty )
      action: [ decrease SomaRefractory ]
      trace:

Ap_ctx

ActiveAP: ( active: 8x ) accumulator

Durante la fase effettiva di spike:

  • eliminiamo Na accumulati. Qui ad un RF molto maggiore che con NaSpill. In teoria qui dovremmo eliminare tutti gli Na e NaSpill potrebbe non servire.
  • riempiamo SomaRefractory per fase di refractory
  • riempiamo Ca2+ per le tracce medio termine di potenziamento/depotenziamento.
ActiveAP: ( active: 8x )
  type: accumulator
  contained_by: SOMA-BEH

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

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

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

NaSpill_ctx

NaSpill: ( active: 8x ) accumulator

Questo potrebbe non servire se eliminiamo tutti Na durante ActiveAP.

NaSpill: ( active: 8x )
  type: accumulator
  contained_by: SOMA-BEH

  in_context: NaSpill_ctx
    hypothesis: NOT ( Na emptiness )
      action: [ decrease Na ]
      trace:

VGSC-SOMA: Comprehension

Voltage Gated Sodium Channel: difficult to open (High)

container: VGSC-SOMA-H

  tub_local:
    VGSCRefractoryH ( full: 60x, active: 30x, empty: 0x )

  tub_intricated:
    Na ( contained_in: SOMA)

   context_intricated:
    VDBMaxCtx ( contained_by: SOMA )

sec: VGSC-SOMA-H

VGSC-H_Status: ( active: 60x ) contextor

Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di VGSCRefractory. Questo perche' e' un era nella quale avviene l'episodio.

VGSC-H_Status: ( active: 60x )
  type: contextor
  contained_by: VGSC-SOMA-H

  in_context: any
    condition: VDBMaxCtx AND ( VGSCRefractoryH emptiness ) 
      out_context: NaEnterH_Ctx

    condition: ( VGSCRefractoryH mediumness ) OR ( VGSCRefractoryH fullness )
      out_context: VGSCRefractoryHSpill_ctx

NaEnterH: ( active: 1x ) accumulator

Se metto il controllo sulla (NOT Ready fullness) il VGSC puo' far entrare un numero di Na non superiore ad un massimo. Questo sopra è il commmento della versione precedente, ora la quantità di NA increase dipende dal rf di VGSC-H_TPC dato che li c'è la condition sulla presenza delle traccie di refractory

NaEnterH: ( active: 1x )
  type: accumulator
  contained_by: VGSC-SOMA-H

  in_context: NaEnterH_ctx
    hypothesis: ( NOT Na full )
      action: [ Na increase]
      trace: None

    hypothesis: ( NOT VGSCRefractoryH full )
      action: [ VGSCRefractoryH increase ]
      trace: None

VGSCRefractoryHSpill: ( active: 1x ) accumulator

Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractoryH (interactor precedente)

VGSCRefractoryHSpill: ( active: 1x )
  type: accumulator
  contained_by: VGSC-SOMA-H

  in_context: VGSCRefractoryHSpill_ctx
    hypothesis: NOT ( VGSCRefractoryH empty )  
      action: [ VGSCRefractoryH decrease ]
      trace: None

VGSC-SOMA-M: container

Voltage Gated Sodium Channel: less difficult to open (Medium)

container: VGSC-SOMA-M

  tub_local:
    VGSCRefractoryM ( full: 60x, active: 30x, empty: 0x )

  tub_intricated:
    Na ( contained_in: SOMA)

  context_intricated:
    VDBMedCtx ( contained_by: SOMA )

sec: VGSC-SOMA-M

VGSC-M_TPC: ( active: 60x ) contextor

Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di VGSCRefractory. Questo perche' e' un era nella quale avviene l'episodio.

VGSC-M_Status: ( active: 60x )
  type: contextor
  contained_by: VGSC-SOMA-M

  in_context: VDBMediumCtx OR VDBMaxCtx
    condition: ( VGSCRefractoryH emptiness ) 
      out_context: NaEnterM_Ctx

NaEnterM: ( active: 1x ) accumulator

Se metto il controllo sulla (NOT Ready fullness) il VGSC puo' far entrare un numero di Na non superiore ad un massimo. Questo sopra è il commmento della versione precedente, ora la quantità di NA increase dipende dal rf di VGSC-H_TPC dato che li c'è la condition sulla presenza delle traccie di refractory

NaEnterM: ( active: 1x )
  type: accumulator
  contained_by: VGSC-SOMA-M

  in_context: NaEnterM_ctx
    hypothesis: ( NOT Na full )
      action: [ Na increase]
      trace: None

    hypothesis: ( NOT VGSCRefractoryM full )
      action: [ VGSCRefractoryH increase ]
      trace: None

VGSCRefractoryMSpill: ( active: 1x ) accumulator

Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractoryH (interactor precedente)

VGSCRefractoryMSpill: ( active: 1x )
  type: accumulator
  contained_by: VGSC-SOMA-M

  in_context: any
    hypothesis: NOT ( VGSCRefractoryM empty )  
      action: [ VGSCRefractoryM decrease ]
      trace: None

VGSC-SOMA-L: container

Voltage Gated Sodium Channel: easy to open (Low)

container: VGSC-SOMA-L

  tub_local:
    VGSCRefractoryL ( full: 60x, active: 30x, empty: 0x )

  tub_intricated:
    Na ( contained_in: SOMA)

  context_intricated:
    VDBLowCtx ( contained_by: SOMA )

sec: VGSC-SOMA-L

VGSC-L_TPC: ( active: 60x ) contextor

Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di VGSCRefractory. Questo perche' e' un era nella qualle avviene l'episodio.

VGSC-L_Status: ( active: 60x )
  type: contextor
  contained_by: VGSC-SOMA-L

  in_context: VDBLowCtx OR VDBMediumCtx OR VDBMaxCtx
    condition: ( VGSCRefractoryH emptiness ) 
      out_context: NaEnterL_ctx

NaEnterL: ( active: 1x ) accumulator

Se metto il controllo sulla (NOT Ready fullness) il VGSC puo' far entrare un numero di Na non superiore ad un massimo. Questo sopra è il commmento della versione precedente, ora la quantità di NA increase dipende dal rf di VGSC-H_TPC dato che li c'è la condition sulla presenza delle traccie di refractory

NaEnterL: ( active: 1x )
  type: accumulator
  contained_by: VGSC-SOMA-L

  in_context: NaEnterL_ctx
    hypothesis: ( NOT Na full )
      action: [ Na increase]
      trace: None

    hypothesis: ( NOT VGSCRefractoryL full )
      action: [ VGSCRefractoryL increase ]
      trace: None

VGSCRefractoryLSpill: ( active: 1x ) accumulator

Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractoryH (interactor precedente)

VGSCRefractoryLSpill: ( active: 1x )
  type: accumulator
  contained_by: VGSC-L-SOMA

  in_context: any
    hypothesis: NOT ( VGSCRefractoryL empty )  
      action: [ VGSCRefractoryL decrease ]
      trace: None

VGSC-SOMA-TUN: Tuner

VGSC-SOMA-TUN
 type: tuner
 contained_by: SOMA

 tunes: SOMA/expansion/VGSC-SOMA

 context_intricated:
  - TunPossible ( contained_by: DAY-N )

 tub_local:

 tub_intricated:

check_tpc: ( active: 60x ) contextor

check_tpc: ( active: 60x )
  type: contextor
  contained_by: VGSC-SOMA-TUN

  in_context: TunPossible
      condition:  ??
        out_context: TunSomaVcgg

?: ( active: x ) accumulator

?: ( active: x )
  type: accumulator
  contained_by: TUN-PRE-VGCC

  in_context: TunSomaVcgg
     hypothesis:  
      action: 
      trace:
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