ocrampal/organism

Fork 0

Files

T

Sergio Marchetti f20ad82954 Edit soma.md

2026-05-10 14:22:53 +00:00

11 KiB

Raw Blame History

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 ( full: 50x, active: 20x, empty: 10x ) 
      # modulated_by: VGSC-SOMA-H-TUN # possible/actual

    - VGSC-SOMA-M ( full: 50x, active: 20x, empty: 10x ) 
      # modulated_by: VGSC-SOMA-M-TUN # possible/actual

    - VGSC-SOMA-L ( full: 50x, active: 20x, empty: 10x ) 
      # modulated_by: VGSC-SOMA-L-TUN # possible/actual


  tub_local:
    - VDB
    - Na
    - Ca2+
    - RefractorySoma

  tub_intricated:  
    - SpikeTrainTraces ( contained_in: DAY-N )

ms: SOMA

SOMA-Status: 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

  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

  condition: NOT ( RefractorySoma empty )
    out_context: RefractorySoma_ctx

SomaSpike: 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 RefractorySoma rappresenta la lunghezza del refractory.

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

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

ActiveAP: 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 RefractorySoma per fase di refractory
riempiamo Ca2+ per le tracce medio termine di potenziamento/depotenziamento.

ActiveAP: ( active: 8x )
  type: accumulator
  contained_by: SOMA

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

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

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

NaSpill: accumulator

Questo potrebbe non servire se eliminiamo tutti Na durante ActiveAP.

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

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

RefractorySomaSpill: accumulator

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

RefractorySomaSpill: ( active: 16x )
  type: accumulator
  contained_by: SOMA

  in_context: RefractorySoma_ctx
    hypothesis: NOT ( RefractorySoma empty )
      action: [ decrease RefractorySoma ]
      trace:

sec: SOMA

min: SOMA

VGSC-SOMA-H: container

Voltage Gated Sodium Channel: difficult to open (High)

container: VGSC-SOMA-H

  tub_local:
    RefractoryH ( 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: contextor

Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di Refractory. 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 ( RefractoryH emptiness ) 
      out_context: NaEnterH_Ctx

    condition: ( RefractoryH mediumness ) OR ( RefractoryH fullness )
      out_context: RefractoryHSpill_ctx

NaEnterH: 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 RefractoryH full )
      action: [ RefractoryH increase ]
      trace: None

RefractoryHSpill: accumulator

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

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

  in_context: RefractoryHSpill_ctx
    hypothesis: NOT ( RefractoryH empty )  
      action: [ RefractoryH decrease ]
      trace: None

VGSC-SOMA-M: container

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

container: VGSC-SOMA-M

  tub_local:
    RefractoryM ( 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: contextor

Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di Refractory. 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: ( RefractoryH emptiness ) 
      out_context: NaEnterM_Ctx

NaEnterM: accumulator

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 RefractoryM full )
      action: [ RefractoryH increase ]
      trace: None

RefractoryMSpill: accumulator

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

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

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

VGSC-SOMA-L: container

Voltage Gated Sodium Channel: easy to open (Low)

container: VGSC-SOMA-L

  tub_local:
    RefractoryL ( 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: contextor

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.

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

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

NaEnterL: accumulator

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 RefractoryL full )
      action: [ RefractoryL increase ]
      trace: None

RefractoryLSpill: accumulator

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

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

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

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: check_tpc

context: check_tpc
  contained_by: VGSC-SOMA-TUN

  rf: ( active: 60x )
  in_context: TunPossible

  condition:  
    out_context: TunSomaVcgg

?: interacting

interacting: ?
  contained_by: TUN-PRE-VGCC

  rf: ( active: x )
  context: TunSomaVcgg

 hypothesis:  
  action: 
  trace:

11 KiB Raw Blame History Unescape Escape

soma.md

SOMA: container

ms: SOMA

SOMA-Status: contextor

SomaSpike: contextor

ActiveAP: accumulator

NaSpill: accumulator

RefractorySomaSpill: accumulator

sec: SOMA

min: SOMA

VGSC-SOMA-H: container

sec: VGSC-SOMA-H

VGSC-H_Status: contextor

NaEnterH: accumulator

RefractoryHSpill: accumulator

VGSC-SOMA-M: container

sec: VGSC-SOMA-M

VGSC-M_TPC: contextor

NaEnterM: accumulator

RefractoryMSpill: accumulator

VGSC-SOMA-L: container

sec: VGSC-SOMA-L

VGSC-L_TPC: contextor

NaEnterL: accumulator

RefractoryLSpill: accumulator

VGSC-SOMA-TUN: Tuner

Check: check_tpc

?: interacting

11 KiB

Raw Blame History