soma description
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@@ -41,14 +41,14 @@ In this model we decide to simplify:
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The simplifications imply that:
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- Removing spine neck resistance means all spines contribute equally to V_dend regardless of their geometry or location. The physical basis of synaptic weighting by dendritic position is lost. All EPSPs are treated as equivalent inputs to the shared pool.
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- Removing active conductances means the dendrite cannot generate dendritic spikes. Summation is strictly linear — two spines together produce exactly twice the V_dend of one spine alone. There is no threshold event within the dendrite itself, only at the soma.
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- Removing active conductances means the dendrite cannot generate dendritic spikes. Integration is nearly linear — two spines together produce exactly twice the VDB of one spine alone. There is no threshold event within the dendrite itself, only at the soma.
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- Removing bAP attenuation means all spines have equal access to the coincidence signal regardless of distance from the soma. Proximal and distal synapses have identical plasticity thresholds. The functional gradient that makes dendritic location matter is absent.
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- Removing structural plasticity means the geometry of the dendrite is fixed. LTP and LTD change AMPA receptor density at each spine but do not change how well those spines couple electrically to the dendrite. The structural component of long-term potentiation — which in biology is arguably more important than the receptor component for sustained changes — is not captured.
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The only behavior we model:
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- Linear summation of spine EPSPs into V_dend each ms
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- Uniform bAP distribution to all spines on soma firing. In this case the dendrites acts as a cable, relaying the bAp to Postsynapse. No modelling needed.
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- Integrations of spine EPSPs into VDB
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- Uniform bAP distribution to all spines on soma firing. In this case the dendrites acts as a cable, relaying the bAp to Postsynapse. bAp arrives here and directly to each spine, no distance from SOMA and attenuation.
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---
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@@ -56,14 +56,9 @@ The only behavior we model:
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— ms:
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- Each active spine contributes an EPSP to V_dend
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V_dend += receptor_conductance_i * AMPA_weight
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(summed across all spines; no neck attenuation)
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- V_dend decays passively each ms
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V_dend *= (1 - dt / tau_dend)
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tau_dend is the membrane time constant of the branch
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- V_dend passed to soma each ms (read externally)
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- Each active spine contributes VPost (EPSP) to VDB
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- VDB decays passively each ms
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— secs:
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- nothing in the simplified model
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@@ -71,8 +66,7 @@ The only behavior we model:
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— mins:
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- nothing in the simplified model
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(structural remodelling of spine neck geometry
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under LTP/LTD would live here if added later)
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(structural remodelling of spine neck geometry under LTP/LTD would live here if added later)
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---
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@@ -99,7 +93,7 @@ Container: BEH-BD
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**Tubs:**
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- **??**: ..
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- **VPost**: e' l'integrazione degli EPSP della postsinapse
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---
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@@ -172,6 +166,8 @@ episode: VDBLow
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Qui facciamo il clearance del VDB. Lo facciamo in questo modo perche' abbiamo semplificato quello che succede fra BD e SOMA.
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Qui posso aggiungere il flush, clearance veloce quando c'e' il bAP.
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```Gen
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episode: VDBClearance
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contained_by: BEH-BD
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+9
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@@ -53,8 +53,8 @@ ATP is a simplification of convenience — at this stage we do not comprehend th
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— ms:
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- VDB is integrated (each Dendratites acts as leaky integrator)
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- Threshold check -condition VDB fullness - (only when not in AP waveform phase and not in absolute refractory)
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- VDB is integrated (each Dendrites acts as leaky integrator)
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- Threshold check - condition VDB fullness - (only when not in AP waveform phase and not in absolute refractory)
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-- AP
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-- bAP
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-- VSOMA
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@@ -62,11 +62,9 @@ ATP is a simplification of convenience — at this stage we do not comprehend th
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--- (tau_AP_fall = 1.5 ms) - V_soma falls toward V_AHP - K⁺ channels open — repolarisation
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--- (tau_AHP = 5.0 ms) - V_soma recovers from V_AHP toward V_soma_reset - K⁺ channels close — after-hyperpolarisation
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- V_bAP decays each ms (from dendrite loop)
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V_bAP += (0 - V_bAP) * dt / tau_bAP
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decay runs independently of soma state
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- V_bAP as a context is active during ?
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- SpikeTrainTraces
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- SpikeTrainTraces ?
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-- creation
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-- destruction
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@@ -104,7 +102,7 @@ ATP is a simplification of convenience — at this stage we do not comprehend th
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container: BEH-SOMA
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expansion:
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- BEH-SOMA-VCGG ( fullness: 50x, active: 20x, emptiness: 10x )
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- BEH-SOMA-VGSC ( fullness: 50x, active: 20x, emptiness: 10x )
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# modulated_by: TUN-SOMA-VCGG # possible/actual
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tub_local:
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@@ -152,8 +150,10 @@ episode: ??
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## BEH-SOMA-VCGG: Container
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Voltage Gated Sodium Channel
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```Gen
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container: BEH-SOMA-VCGG
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container: BEH-SOMA-VGSC
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```
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@@ -161,7 +161,7 @@ container: BEH-SOMA-VCGG
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```Gen
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episode: ??
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contained_by: BEH-SOMA-VCGG
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contained_by: BEH-SOMA-VGSC
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in_context: xxx
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rf: ( active: 1x )
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@@ -0,0 +1,68 @@
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This document synthesizes our discussion on the **SOMA** as a high-stakes, metabolically-constrained control center. Rather than a simple switch, the soma is a dynamic arena where electrical signals, ion gradients, and energy reserves engage in a constant "tug-of-war."
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---
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## 1. The Core Identity: The "Tug-of-War"
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The state of the soma is defined by the balance between **Inward Currents** (seeking to trigger a spike) and **Outward Currents/Pumps** (seeking to maintain stability).
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- **The Players:**
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- **Inward:** Sodium ($Na^+$) via Voltage-Gated Sodium Channels (VGSC).
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- **Outward:** Potassium ($K^+$) via Leak channels and Voltage-Gated Potassium Channels (VGKC).
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- **The Maintainer:** The **Na/K-ATPase Pump**, which burns **ATP** to reset the field.
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---
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## 2. The Anatomy of an Action Potential (AP)
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When the "Inward" team wins, a non-linear event occurs across four distinct stages:
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| Phase | Ion Movement | Voltage Change | Timing |
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|----------------------|-----------------------------------|-----------------------------------|---------------------|
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| **Rising** | $Na^+$ rushes **IN** | Depolarization (toward +40mV) | \~0.5 ms |
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| **Falling** | $K^+$ rushes **OUT** | Repolarization (back toward rest) | \~1.5 ms |
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| **Undershoot (AHP)** | $K^+$ continues to exit | Hyperpolarization (below rest) | 5–10 ms |
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| **Recovery** | Pump pushes $Na^+$ out / $K^+$ in | Returns to Resting Potential | Variable (ATP-dep.) |
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---
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## 3. The Dynamic Threshold: A Moving Target
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The "Threshold" is the voltage where the $Na^+$ current finally overcomes the $K^+$ leak. It is not a fixed number because it is sensitive to:
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- **Slope Sensitivity:**
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- **Fast Rise:** Catching $Na^+$ channels "by surprise" before they can inactivate, **lowering** the threshold.
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- **Slow Rise:** Allowing $Na^+$ channels to inactivate and $K^+$ to leak out, **raising** the threshold (Accommodation).
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- **Channel Density:** Increasing the number of VGSCs **lowers** the threshold because the statistical probability of enough channels opening to "win" the tug-of-war occurs at more negative voltages.
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- **AIS Geometry:** The Axon Initial Segment (the trigger zone) can physically move. Moving it away from the soma increases the threshold; moving it closer decreases it.
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---
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## 4. Metabolic Constraints: The ATP Loop
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The AP itself is "electrically free" (it uses potential energy), but the **cleanup is expensive.**
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- **The Na/K-ATPase Pump:** This is the biological battery recharger. It burns ATP to move ions against their gradients.
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- **The Speed Gap:** A single channel moves 10 million ions/sec; a pump moves only hundreds. During a spike, the pump is invisible. After the spike, it works at max velocity to prevent "Sodium Overload."
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- **Metabolic Silencing:** If ATP levels drop or the firing rate is too high for the pumps to keep up, the $Na^+/K^+$ ratio fails. The neuron will eventually enter **Depolarization Block**—staying at a high voltage but unable to spike—to prevent cell death (Excitotoxicity).
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---
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## 5. Homeostatic Scaling: Self-Tuning
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The neuron uses long-term feedback loops to keep its activity in a "Goldilocks Zone":
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- **Chronic Overactivity:** The neuron removes VGSCs or moves the AIS away to **raise** the threshold and protect its energy.
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- **Chronic Silence:** The neuron adds VGSCs to **lower** the threshold, becoming hypersensitive to find a signal.
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---
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## 6. The Unified View: The Multi-Scale Loop
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To understand the SOMA, one must see it as a hierarchy of loops:
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1. **The Fast Loop (ms):** Ion channels opening and closing (Information processing).
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2. **The Medium Loop (sec):** Accumulation of ions and pump acceleration (Short-term plasticity/recovery).
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3. **The Slow Loop (mins/hours):** ATP replenishment and channel density scaling (Sustainability and Homeostasis).
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**This unified picture shows the SOMA not just as a processor, but as a living system constantly balancing its computational needs against its metabolic bank account.**
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