organism/neuron/soma-sergio.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.

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

```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: 
```

#### RefractorySpill: interacting

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

```Gen
interacting: RefractorySpill
  contained_by: SOMA

  context: any
  rf: ( active: 16x )

  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, ReadyH 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
```