alcuni sniplet Soma e indentation

neuron/BEH-BD.md

@@ -120,7 +120,7 @@ context: CheckVPost
     out_context: VPostLow
 ```
 
-#### VDBMax: Episode
+##### VDBMax: Episode
 
 ```Gen
 episode: VDBMax
@@ -134,7 +134,7 @@ episode: VDBMax
   trace: 
 ```
 
-#### VDBMed: Episode
+##### VDBMed: Episode
 
 ```Gen
 episode: VDBMed
@@ -148,7 +148,7 @@ episode: VDBMed
   trace: 
 ```
 
-#### VDBLow: Episode
+##### VDBLow: Episode
 
 ```Gen
 episode: VDBLow

neuron/BEH-POST.md

@@ -195,7 +195,7 @@ container: BEH-POST
 
 ![post-ltp-ltd.png](.attachments/post-ltp-ltd.png)
 
-#### CheckNa:Context
+#### CheckNa: Context
 
 Contestualizziamo in maniera Fixed?
 
@@ -216,7 +216,7 @@ context: CheckNa
     out_context: NaLow
 ```
 
-#### CaNDMAEnterMax: Episode
+##### CaNDMAEnterMax: Episode
 
 ```Gen
 episode: CaNDMAEnterMax
@@ -230,7 +230,7 @@ episode: CaNDMAEnterMax
   trace: 
 ```
 
-#### CaNDMAEnterMed: Episode
+##### CaNDMAEnterMed: Episode
 
 ```Gen
 episode: CaNDMAEnterMed
@@ -244,7 +244,7 @@ episode: CaNDMAEnterMed
   trace: 
 ```
 
-#### CaNDMAEnterLow: Episode
+##### CaNDMAEnterLow: Episode
 
 ```Gen
 episode: CaNDMAEnterLow
@@ -258,9 +258,7 @@ episode: CaNDMAEnterLow
     trace: 
 ```
 
-#### CaClearance
+#### CaClearance: Episode
-
-##### CaClearance: Episode
 
 ```Gen
 episode: CaClearance
@@ -345,7 +343,7 @@ context: CheckNTPost
     out_context: NTFull
 ```
 
-#### NaAMPAEnterMax: Episode
+##### NaAMPAEnterMax: Episode
 
 ```Gen
 episode: NaAMPAEnterMax
@@ -359,7 +357,7 @@ episode: NaAMPAEnterMax
   trace: 
 ```
 
-#### NaAMPAEnterMed: Episode
+##### NaAMPAEnterMed: Episode
 
 ```Gen
 episode: NaAMPAEnterMed

neuron/BEH-SOMA.md

@@ -33,6 +33,18 @@ The soma does not fire randomly or continuously. Under no input it sits at rest,
 
 The soma is therefore not a simple threshold device. It is a dynamic integrator with memory encoded in its current membrane potential, a nonlinear decision mechanism encoded in its channel kinetics, a refractory mechanism that shapes its temporal output, and a metabolic dependence that links its firing capacity to the health of its local environment. It is, in miniature, a complete signal processing unit — and the action potential it produces is the one binary output that all of this continuous analogue computation ultimately reduces to.
 
+Event                     Time Scale      Responsible Mechanism
+─────────────────────────────────────────────────────────────────
+Resting at -70 mV         steady          Leak channels + pumps (balance)
+    ↓
+Depolarization to -50 mV  ~1-2 ms         Na⁺ enters (VGSCs open)
+    ↓
+Repolarization to -70 mV  ~1-2 ms         K⁺ exits (VG K⁺ channels open) ← NOT pumps!
+    ↓
+After-hyperpolarization   ~5-20 ms        K⁺ channels still open
+    ↓
+Return to exact -70 mV    ~100-1000 ms    Na⁺/K⁺ pumps restore gradients
+
 ---
 
 **Simplified comprehension**:
@@ -60,48 +72,28 @@ ATP is a simplification of convenience — at this stage we do not comprehend th
 
 — ms:
 
-- VDB is integrated (each Dendrites acts as leaky integrator)
-- Threshold check - condition VDB fullness - (only when not in AP waveform phase and not in absolute refractory)
--- AP
--- bAP
--- VSOMA
---- tau_AP_rise = 0.5 ms - Na⁺ channels open — explosive depolarisation
---- (tau_AP_fall = 1.5 ms) - VSOMA falls toward V_AHP - K⁺ channels open — repolarisation
---- (tau_AHP = 5.0 ms) - VSOMA recovers from V_AHP toward VSOMA_reset - K⁺ channels close — after-hyperpolarisation
-
-- V_bAP as a context is active during ?
-
-- SpikeTrainTraces ?
--- creation
--- destruction
-
-- SOMA-VCGG servono a modificare il comportamento del SOMA: refractory period.
-
-- threshold AP: da capire come lo modifico, forse con una modifica ad una fullness
 
 — seconds:
 
-- nothing — no slow integration in the soma
+- Ca2+ accumulation: SpikeTrainTraces
-  (firing rate statistics could be computed here as a diagnostic
-   but they do not feed back into any other variable)
 
 — mins:
 
-- nothing in the simplified model
+- VGSC modulation
-  (homeostatic threshold regulation would live here if added:
-   sustained low firing rate → VSOMA_threshold decreases
-   sustained high firing rate → VSOMA_threshold increases
-   this is the somatic equivalent of postsynaptic AMPA scaling —
-   the neuron adjusts its own excitability to maintain a target
-   firing rate in the face of changing input statistics)
 
 ---
 
 **Tubs:**
 
-- **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.
+- **VDB**: dendrites deliver current
 
-- **??**: ...
+- **VSOMA**: are a proxy for the Coulombs of charge building up on the somatic membrane.
+
+- **AP**:
+
+- **bAP**:
+
+- **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.
 
 ---
 
@@ -126,36 +118,74 @@ container: BEH-SOMA
     - SpikeTrainTraces ( contained_by: TUN-N )
 ```
 
-## : Context
+### ms: behaviors SOMA
 
-Qui mettiamo lo spike Dendritico. Sempre se vogliamo comprenderlo.
+#### 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: ???...
+context: CheckVDB
- contained_by: BEH-SOMA
-
- in_context: Fixed
- rf: 60x
-
- condition: 
-  activate: xxx
-```
-
-## : Episode
-
-```Gen
-episode: ??
   contained_by: BEH-SOMA
 
-  in_context: xxx
+  in_context: Fixed
-  rf: ( active: 1x )
+  rf: ( active: 60x )
 
-  hypothesis:  
+  condition: (VDB fullness)
-  action: 
+    out_context: VDBMax
-  trace: None
+
+  condition: (VDB mediumness)
+    out_context: VDBMedium 
+
+  condition: (VDB emptiness)
+    out_context: VDBLow
 ```
 
-## BEH-SOMA-VCGG: Container
+##### VDBMax: Episode
+
+```Gen
+episode: VDBMax
+  contained_by: BEH-SOMA
+
+  in_context: VDBMax
+  rf: ( active: 2x )
+
+ hypothesis: NOT (VSOMA full)
+  action: [VSOMA increase]
+  trace: 
+```
+
+##### VDBMed: Episode
+
+```Gen
+episode: VDBMed
+  contained_by: BEH-SOMA
+
+  in_context: VDBMedium
+  rf: ( active: 4x )
+
+ hypothesis: NOT (VSOMA full)
+  action: [VSOMA increase]
+  trace: 
+```
+
+##### VDBLow: Episode
+
+```Gen
+episode: VDBLow
+  contained_by: BEH-SOMA
+
+  in_context: VDBLow
+  rf: ( active: 8x )
+
+ hypothesis: NOT (VSOMA full)
+  action: [VSOMA increase]
+  trace: 
+```
+
+## BEH-SOMA-VGSC: Container
 
 Voltage Gated Sodium Channel
 
@@ -164,7 +194,9 @@ container: BEH-SOMA-VGSC
 
 ```
 
-### Episode1
+### ms: behaviors SOMA-VGSC
+
+#### Episode1
 
 ```Gen
 episode: ??