organism/neuron/somaSergio.md

# 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

---

```Gen
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

#### VDB-Concentration: check_tpc

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.

```Gen
check_tpc: VDB-Concentration
  contained_by: SOMA

  tpc: any
  rf: ( active: 60x )

  condition: (VDB fullness ) AND NOT ApCtx
    out_tpc: VDBMaxCtx

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

  condition: ( VDB emptiness ) AND NOT ApCtx
    out_tpc: VDBLowCtx
```

#### SomaSpill: interacting

```Gen
interacting: SomaSpill
  contained_by: SOMA

  context: any
  rf: ( active: 8x )

  hypothesis: NOT NA emptiness
    action: [ decrease NA ]
    trace:
```

#### SomaSpike: check_tpc

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

```Gen
check_tpc: SomaSpike
  contained_by: SOMA

  context: fixed
  rf: ( active: 60x )

  condition: ( Na fullness ) AND ( RefractorySoma emptiness )
    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.

```Gen
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

```Gen
interacting: RefractoryBeh
  contained_by: SOMA

  context: any
  rf: ( active: 8x )

  hypothesis: NOT RefractorySoma empty
    action: [ decrease RefractorySoma ]
    trace: 
```

### sec: SOMA

### min: SOMA

#### VGSC-SOMA-TUN: Tuner

```Gen
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

```Gen
context: check_tpc
  contained_by: VGSC-SOMA-TUN

  context: TunPossible
  rf: ( active: 60x )

  condition:  
  out_context: TunSomaVcgg
```

##### ?: interacting

```Gen
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)

```Gen
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.

```Gen
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: check_tpc

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.

```Gen
check_tpc: 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.

```Gen
interacting: RefractoryH
  contained_by: VGSC-H-SOMA

  context: RefractoryH
  rf: ( active: 1x )

  hypothesis: NOT ( ReadyH emptyness )  
    action: [ ReadyH decrease ]
    trace: None
```

## VGSC-SOMA-M: container

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

```Gen
container: VGSC-SOMA-M

  tub_local:
    Ready ( )

  tub_intricated:
    Na ( contained_in: SOMA)
```

### sec: VGSC-SOMA-M

#### NaEnterM: interacting

Se metto il controllo sulla (NOT Ready fullness) il VGSC puo' far entrare un numero di Na non superiore ad un massimo.

```Gen
interacting: NaEnterM
  contained_by: VGSC-M-SOMA

  context: (VDBMediumCtx OR VDBMaxCtx) AND ( NOT RefractoryM )
  rf: ( active: 1x )

  hypothesis: ( NOT Na fullness ) AND ( NOT ReadyM fullness )
    action: [ Na increase, ReadyM increase ]
    trace: None
```

##### CheckRefractoryM: check_tpc

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.

```Gen
check_tpc: CheckRefractoryM
  contained_by: VGSC-M-SOMA

  context: NOT RefractoryM
  rf: ( active: 60x )

  condition: ( ReadyM fullness )
    out_context: RefractoryM
```

##### RefractoryM: interacting

Questo episodio deve girare varie volte nell'ambito del contesto di refractory che viene controllato ad un RF maggiore.

```Gen
interacting: RefractoryM
  contained_by: VGSC-M-SOMA

  context: RefractoryM
  rf: ( active: 1x )

  hypothesis: NOT ( ReadyM emptyness )  
    action: [ ReadyM decrease ]
    trace: None
```

## VGSC-SOMA-L: container

Voltage Gated Sodium Channel: easy to open (Low)

```Gen
container: VGSC-SOMA-L

  tub_local:
    Ready ( )

  tub_intricated:
    Na ( contained_in: SOMA)
```

### sec: VGSC-SOMA-L

#### NaEnterL: interacting

Se metto il controllo sulla (NOT Ready fullness) il VGSC puo' far entrare un numero di Na non superiore ad un massimo.

```Gen
interacting: NaEnterL
  contained_by: VGSC-L-SOMA

  context: ( VDBLowCtx OR VDBMediumCtx OR VDBMaxCtx) AND ( NOT RefractoryL )
  rf: ( active: 1x )

  hypothesis: ( NOT Na fullness ) AND ( NOT ReadyL fullness )
    action: [ Na increase, ReadyL increase ]
    trace: None
```

##### CheckRefractoryL: check_tpc

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.

```Gen
check_tpc: CheckRefractoryL
  contained_by: VGSC-L-SOMA

  context: NOT RefractoryL
  rf: ( active: 60x )

  condition: ( ReadyL fullness )
    out_context: RefractoryL
```

##### RefractoryL: interacting

Questo episodio deve girare varie volte nell'ambito del contesto di refractory che viene controllato ad un RF maggiore.

```Gen
interacting: RefractoryL
  contained_by: VGSC-L-SOMA

  context: RefractoryL
  rf: ( active: 1x )

  hypothesis: NOT ( ReadyL emptyness )  
    action: [ ReadyL decrease ]
    trace: None
```