diff --git a/neuron/somaSergio.md b/neuron/somaSergio.md deleted file mode 100644 index 0e385d3..0000000 --- a/neuron/somaSergio.md +++ /dev/null @@ -1,435 +0,0 @@ -# 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, ReadyL 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 -``` -