From 464011b858dfd7148141a6bcde60de14dcc3769d Mon Sep 17 00:00:00 2001 From: Sergio Marchetti Date: Sat, 18 Apr 2026 21:24:35 +0000 Subject: [PATCH] Update 2 files - /neuron/soma.md - /neuron/somaSergio.md --- neuron/soma.md | 0 neuron/somaSergio.md | 435 +++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 435 insertions(+) create mode 100644 neuron/soma.md create mode 100644 neuron/somaSergio.md diff --git a/neuron/soma.md b/neuron/soma.md new file mode 100644 index 0000000..e69de29 diff --git a/neuron/somaSergio.md b/neuron/somaSergio.md new file mode 100644 index 0000000..f0cddf4 --- /dev/null +++ b/neuron/somaSergio.md @@ -0,0 +1,435 @@ +# 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, 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 +``` +