organism/neuron/soma.md

# soma.md

Qui comprendiamo:

- BEH-SOMA: il soma

## BEH-SOMA: Container

**Simplified behaviors**:

— ms:

- Resting at -70 mV: Leak channels + pumps (keep at resting)
-- ?
- VDB Depolarization : ~1-2 ms: Na⁺ enters (some VGSCs open)
- Opened VGSC remain closed for a refractory period
 Spike if depolarized above threshold: to -50 mV
 -- Here the threshold is based only on the integration of Na+
 -- The threshold is tuned during the spiketrain. Low threshold at rest, to increase sensitivity, threshold increase during spike to increase discrimination
 -- increase SpikeTrainTraces (fast at spike)
 -- increase Ca2+ traces
- Repolarization to -70 mV:  ~1-2 ms: K⁺ exits (VG K⁺ channels open) ← NOT pumps!
-- fast pump which decreases Na+, we do not model K+
- After-hyperpolarization: ~5-20 ms: K⁺ channels still open
-- must figure out how to deal with deoplarization
-- decrease SpikeTraintraces slow, only if away from spiketrain this is empty

— seconds:

- Return to exact -70 mV: ~100-1000 ms: Na⁺/K⁺ pumps restore gradients
-- slow pump
- Ca2+ accumulation: SpikeTrainTraces
-- ?
— mins:

- VGSC modulation

---

**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

- **AP**:

- **bAP**:

- **Ca2+**: Medium term traces to guide tuning and Night development

- **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.

---

```Gen
container: BEH-SOMA

  expansion: 
    - VGSC-SOMA ( fullness: 50x, active: 20x, emptiness: 10x ) 
      # modulated_by: TUN-SOMA-VCGG # possible/actual

  tub_local:

    - VDB

    - Na

    - AP

    - bAP

    - Ca2+

  tub_intricated:  
    - SpikeTrainTraces ( contained_in: DAY-N )
```

### ms: behaviors SOMA

#### CheckVDB: Context

As dendrites deliver current (VDB​), the soma acts like a capacitor. It "stores" this charge in the form of membrane potential. VSOMA is proxy for the Coulombs of charge building up on the somatic membrane.

Contestualizziamo in maniera Fixed?

```Gen
context: CheckVDB
  contained_by: BEH-SOMA

  in_context: Fixed
  rf: ( active: 60x )

  condition: (VDB fullness)
    out_context: VDBMax

  condition: (VDB mediumness)
    out_context: VDBMedium 

  condition: (VDB emptiness)
    out_context: VDBLow
```

##### AddVSOMAMax: Episode

```Gen
episode: AddVSOMAMax
  contained_by: BEH-SOMA

  in_context: VDBMax
  rf: ( active: 2x )

 hypothesis: NOT (VSOMA full)
  action: [VSOMA increase]
  trace: 
```

##### AddVSOMAMed: Episode

```Gen
episode: AddVSOMAMed
  contained_by: BEH-SOMA

  in_context: VDBMedium
  rf: ( active: 4x )

 hypothesis: NOT (VSOMA full)
  action: [VSOMA increase]
  trace: 
```

##### AddVSOMALow: Episode

```Gen
episode: AddVSOMALow
  contained_by: BEH-SOMA

  in_context: VDBLow
  rf: ( active: 8x )

 hypothesis: NOT (VSOMA full)
  action: [VSOMA increase]
  trace: 
```

#### SomaSpike: Episode

```Gen
episode: SomaSpike
  contained_by: BEH-SOMA

  in_context: 
  rf: ( active: 8x )

 hypothesis: 
  action: 
  trace: 
```

#### ClearVSOMA: Episode

```Gen
episode: ClearVSOMA
  contained_by: BEH-SOMA

  in_context: 
  rf: ( active: 8x )

 hypothesis: 
  action: 
  trace: 
```

### sec: behaviors SOMA

### min: behaviors SOMA

#### TUN-SOMA-VCGG: 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:
```

##### Context

```Gen
context: Check
  contained_by: TUN-SOMA-VCGG

  in_context: TunPossible
  rf: ( active: 60x )

  condition:  
  out_context: TunSomaVcgg
```

##### Episode

```Gen
episode: ?
  contained_by: TUN-PRE-VGCC

  in_context: TunSomaVcgg
  rf: ( active: x )

 hypothesis:  
  action: 
  trace: 
```

## VGSC-SOMA: Container

Voltage Gated Sodium Channel

```Gen
container: VGSC-SOMA

```

### ms: behaviors SOMA-VGSC

#### Episode1

```Gen
episode: ??
  contained_by: VGSC-SOMA

  in_context: xxx
  rf: ( active: 1x )

  hypothesis:  
  action: 
  trace: None
```

##