Sergio Marchetti
465 lines
10 KiB
Markdown
465 lines
10 KiB
Markdown
# soma.md
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Qui comprendiamo:
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- SOMA: il soma
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- VGSC-SOMA-H: Na ion channels. Open only when VDB high
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- VGSC-SOMA-M: Na ion channels. Open only when VDB medium
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- VGSC-SOMA-L: Na ion channels. Open only when VDB low
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## SOMA: container
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---
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**Simplified verifiable behaviors**:
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— ms:
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- Resting at -70 mV: Leak channels + pumps (keep at resting)
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- VDB Depolarization : ~1-2 ms: Na⁺ enters (some VGSCs open)
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- Opened VGSC and then remain closed for a refractory period
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- Spike if depolarized above threshold: to -50 mV
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- Ca2+ enter
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- Repolarization to -70 mV: ~1-2 ms: K⁺ exits (VG K⁺ channels open) ← NOT pumps!
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- After-hyperpolarization: ~5-20 ms: K⁺ channels still open
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— secs:
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- Return to exact -70 mV: ~100-1000 ms: Na⁺/K⁺ pumps restore gradients
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- Ca2+ accumulation
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— mins:
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- VGSC modulation
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---
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**G expression**:
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— ms:
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- based on VDB, VGSC open and let Na+ in. VGSG then go into refractory
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- if Na fullness then ApCtx. Here the threshold is based only on the integration of Na+
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- increase SpikeTrainTraces (fast at spike)
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- increase Ca2+ traces
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- decrease Na: fast pump which decreases Na+, we do not model K+
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-- there is a tug of war between Na entering and exiting. Na can reach fullness only if VDB increases fast (derivative)
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- there are 2 context: ApCtx and RefractorySoma imlemented with timers and tunable
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- decrease SpikeTraintraces slow, only if away from spiketrain this is empty
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- Tune:
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-- The threshold is tuned during the spiketrain. Low threshold at rest, to increase sensitivity, threshold increase during spike to increase discrimination
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— secs:
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- SpikeTrainTraces
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— mins:
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- Tune:
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-- refractory lenght
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---
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**Tubs:**
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- **VDB**: dendrites deliver current
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- **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
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- **Ca2+**: Medium term traces to guide tuning and Night development. It is a local trace, ATP is a global (Astrocyte)
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- **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.
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- **RefractorySoma**: tracce di refractory
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---
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```Gen
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container: SOMA
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expansion:
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- VGSC-SOMA-H ( fullness: 50x, active: 20x, emptiness: 10x )
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# modulated_by: VGSC-SOMA-H-TUN # possible/actual
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- VGSC-SOMA-M ( fullness: 50x, active: 20x, emptiness: 10x )
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# modulated_by: VGSC-SOMA-M-TUN # possible/actual
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- VGSC-SOMA-L ( fullness: 50x, active: 20x, emptiness: 10x )
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# modulated_by: VGSC-SOMA-L-TUN # possible/actual
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tub_local:
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- VDB
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- Na
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- Ca2+
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- RefractorySoma
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tub_intricated:
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- SpikeTrainTraces ( contained_in: DAY-N )
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```
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### ms: SOMA
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#### VDB-Concentration: check_tpc
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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.
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This only applies if not ApCtx, or in other words, SOMA is not in refractory period.
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```Gen
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check_tpc: VDB-Concentration
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contained_by: SOMA
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tpc: any
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rf: ( active: 60x )
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condition: (VDB fullness ) AND NOT ApCtx
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out_tpc: VDBMaxCtx
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condition: ( VDB mediumness ) AND NOT ApCtx
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out_tpc: VDBMediumCtx
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condition: ( VDB emptiness ) AND NOT ApCtx
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out_tpc: VDBLowCtx
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```
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#### SomaSpill: interacting
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```Gen
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interacting: SomaSpill
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contained_by: SOMA
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context: any
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rf: ( active: 8x )
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hypothesis: NOT NA emptiness
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action: [ decrease NA ]
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trace:
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```
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#### SomaSpike: check_tpc
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Qui siamo nella fase effettiva di spike, non refractory che viene dopo. Fa da contesto di durata fra un RF ed un altro.
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La fullness di Na rappresenta il threshold e puo' essere modificato. La fullness di RefractorySoma rappresenta la lunghezza del refractory.
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```Gen
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check_tpc: SomaSpike
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contained_by: SOMA
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context: fixed
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rf: ( active: 60x )
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condition: ( Na fullness ) AND ( RefractorySoma emptiness )
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out_context: ApCtx
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out_context: bApCtx
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```
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#### ApBeh: interacting
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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.
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```Gen
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interacting: ApBeh
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contained_by: SOMA
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context: ApCtx
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rf: ( active: 8x )
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hypothesis: NOT Na empty
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action: [ decrease Na ]
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trace:
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hypothesis: NOT RefractorySoma full
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action: [ increase RefractorySoma ]
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trace:
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hypothesis: NOT Ca2+ full
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action: [ increase Ca2+ ]
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trace:
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```
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#### RefractorySpill: interacting
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Lo spill deve essere piu' lento dell'increase che avviene in APBeh
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```Gen
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interacting: RefractorySpill
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contained_by: SOMA
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context: any
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rf: ( active: 16x )
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hypothesis: NOT RefractorySoma empty
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action: [ decrease RefractorySoma ]
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trace:
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```
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### sec: SOMA
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### min: SOMA
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#### VGSC-SOMA-TUN: Tuner
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```Gen
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tuner: VGSC-SOMA-TUN
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contained_by: SOMA
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tunes: SOMA/expansion/VGSC-SOMA
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context_intricated:
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- TunPossible ( contained_by: DAY-N )
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tub_local:
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tub_intricated:
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```
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##### Check: check_tpc
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```Gen
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context: check_tpc
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contained_by: VGSC-SOMA-TUN
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context: TunPossible
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rf: ( active: 60x )
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condition:
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out_context: TunSomaVcgg
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```
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##### ?: interacting
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```Gen
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interacting: ?
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contained_by: TUN-PRE-VGCC
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context: TunSomaVcgg
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rf: ( active: x )
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hypothesis:
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action:
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trace:
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```
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## VGSC-SOMA-H: container
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Voltage Gated Sodium Channel: difficult to open (High)
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```Gen
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container: VGSC-SOMA-H
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tub_local:
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Ready ( )
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tub_local:
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RefractoryH ( full: 60x, active: 30x, empty: 0x )
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tub_intricated:
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Na ( contained_in: SOMA)
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```
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### sec: VGSC-SOMA-H
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##### VGSC-H_TPC: check_tpc
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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.
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```Gen
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check_tpc: VGSC-H_TPC
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contained_by: VGSC-SOMA-H
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tpc: VDBMaxCtx
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rf: ( active: 60x )
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condition: ( RefractoryH emptiness )
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out_context: NaEnterH_Ctx
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```
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#### NaEnterH: interacting
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Se metto il controllo sulla (NOT Ready fullness) il VGSC puo' far entrare un numero di Na non superiore ad un massimo.
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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
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```Gen
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interacting: NaEnterH
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contained_by: VGSC-H-SOMA
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context: NaEnterH_Ctx
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rf: ( active: 1x )
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hypothesis: ( NOT Na full )
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action: [ Na increase]
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trace: None
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hypothesis: ( NOT RefractoryH full )
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action: [ RefractoryH increase ]
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trace: None
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```
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##### RefractoryHSpill: interacting
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Lo Spill deve avere un rf maggiore dell'interacting che incrementa RefractoryH (interactor precedente)
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```Gen
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interacting: RefractoryHSpill
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contained_by: VGSC-H-SOMA
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context: any
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rf: ( active: 1x )
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hypothesis: NOT ( RefractoryH empty )
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action: [ RefractoryH decrease ]
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trace: None
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```
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## VGSC-SOMA-M: container
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Voltage Gated Sodium Channel: less difficult to open (Medium)
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```Gen
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container: VGSC-SOMA-M
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tub_local:
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Ready ( )
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tub_local:
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RefractoryM ( full: 60x, active: 30x, empty: 0x )
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tub_intricated:
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Na ( contained_in: SOMA)
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```
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### sec: VGSC-SOMA-M
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##### VGSC-M_TPC: check_tpc
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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.
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```Gen
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check_tpc: VGSC-M_TPC
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contained_by: VGSC-SOMA-M
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tpc: VDBMediumCtx OR VDBMaxCtx
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rf: ( active: 60x )
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condition: ( RefractoryH emptiness )
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out_context: NaEnterM_Ctx
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```
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#### NaEnterM: interacting
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Se metto il controllo sulla (NOT Ready fullness) il VGSC puo' far entrare un numero di Na non superiore ad un massimo.
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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
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```Gen
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interacting: NaEnterM
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contained_by: VGSC-M-SOMA
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context: NaEnterM_Ctx
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rf: ( active: 1x )
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hypothesis: ( NOT Na full )
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action: [ Na increase]
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trace: None
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hypothesis: ( NOT RefractoryM full )
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action: [ RefractoryH increase ]
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trace: None
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```
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##### RefractoryMSpill: interacting
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Lo Spill deve avere un rf maggiore dell'interacting che incrementa RefractoryH (interactor precedente)
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```Gen
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interacting: RefractoryMSpill
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contained_by: VGSC-M-SOMA
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context: any
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rf: ( active: 1x )
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hypothesis: NOT ( RefractoryM empty )
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action: [ RefractoryM decrease ]
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trace: None
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```
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## VGSC-SOMA-L: container
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Voltage Gated Sodium Channel: easy to open (Low)
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```Gen
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container: VGSC-SOMA-L
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tub_local:
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Ready ( )
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tub_local:
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RefractoryL ( full: 60x, active: 30x, empty: 0x )
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tub_intricated:
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Na ( contained_in: SOMA)
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```
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### sec: VGSC-SOMA-L
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##### VGSC-L_TPC: check_tpc
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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.
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```Gen
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check_tpc: VGSC-L_TPC
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contained_by: VGSC-SOMA-L
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tpc: VDBLowCtx OR VDBMediumCtx OR VDBMaxCtx
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rf: ( active: 60x )
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condition: ( RefractoryH emptiness )
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out_context: NaEnterL_Ctx
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```
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#### NaEnterL: interacting
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Se metto il controllo sulla (NOT Ready fullness) il VGSC puo' far entrare un numero di Na non superiore ad un massimo.
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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
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```Gen
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interacting: NaEnterL
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contained_by: VGSC-L-SOMA
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context: NaEnterL_Ctx
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rf: ( active: 1x )
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hypothesis: ( NOT Na full )
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action: [ Na increase]
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trace: None
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hypothesis: ( NOT RefractoryL full )
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action: [ RefractoryL increase ]
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trace: None
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```
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##### RefractoryLSpill: interacting
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Lo Spill deve avere un rf maggiore dell'interacting che incrementa RefractoryH (interactor precedente)
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```Gen
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interacting: RefractoryLSpill
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contained_by: VGSC-L-SOMA
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context: any
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rf: ( active: 1x )
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hypothesis: NOT ( RefractoryL empty )
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action: [ RefractoryL decrease ]
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trace: None
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```
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