organism/neuron/soma.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 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. 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.

---

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+

  tub_intricated:  
    - SpikeTrainTraces ( contained_in: DAY-N )

ms: SOMA

CheckVDB: Context

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 AP, or in other words, SOMA is not in refractory period.

context: CheckVDB
  contained_by: SOMA

  in_context: Fixed
  rf: ( active: 60x )

  condition: (VDB fullness ) AND NOT AP
    out_context: VDBMax

  condition: ( VDB mediumness ) AND NOT AP
    out_context: VDBMedium 

  condition: ( VDB emptiness ) AND NOT AP
    out_context: VDBLow

CheckSomaSpike: Context

The initiation and duration of a spike

context: CheckSomaSpike
  contained_by: SOMA

  in_context: Fixed
  rf: ( active: 60x )

  condition: ( Na fullness OR APRefractory )
    out_context: AP
    out_context: bAP

SomaSpike: Episode

episode: SomaSpike
  contained_by: SOMA

  in_context: AP
  rf: ( active: 8x )

 hypothesis: 
  action: 
  trace: 

ClearNa: Episode

episode: ClearNa
  contained_by: SOMA

  in_context: AP
  rf: ( active: 8x )

 hypothesis: 
  action: 
  trace: 

sec: SOMA

min: SOMA

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:

Context

context: Check
  contained_by: VGSC-SOMA-TUN

  in_context: TunPossible
  rf: ( active: 60x )

  condition:  
  out_context: TunSomaVcgg

Episode

episode: ?
  contained_by: TUN-PRE-VGCC

  in_context: TunSomaVcgg
  rf: ( active: x )

 hypothesis:  
  action: 
  trace: 

VGSC-SOMA-H: Container

Voltage Gated Sodium Channel

container: VGSC-SOMA-H

sec: VGSC-SOMA-H

Episode1

episode: ??
  contained_by: VGSC-H-SOMA

  in_context: xxx
  rf: ( active: 1x )

  hypothesis:  
  action: 
  trace: None

VGSC-SOMA-M: Container

Voltage Gated Sodium Channel

container: VGSC-SOMA-M

sec: VGSC-SOMA-M

Episode2

episode: ??
  contained_by: VGSC-M-SOMA

  in_context: xxx
  rf: ( active: 1x )

  hypothesis:  
  action: 
  trace: None

VGSC-SOMA-L: Container

Voltage Gated Sodium Channel

container: VGSC-SOMA-M

sec: VGSC-SOMA-L

Episode3

episode: ??
  contained_by: VGSC-L-SOMA

  in_context: xxx
  rf: ( active: 1x )

  hypothesis:  
  action: 
  trace: None