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ocrampal
2026-06-01 15:49:46 +02:00
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elements/neuron/soma.md
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@@ -4,64 +4,28 @@ include_toc: true
# soma.md
Qui comprendiamo:
## SOMA: Comprehension
- 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
Expansions and modulations:
- is expanded by: [NEURON](neuron.md)
- expands: SOMA_VGSC
---
```Gen
SOMA
type: comprehension
**Simplified verifiable behaviors**:
expand_comprehension:
&SOMA_VGSC-H: SOMA_VGSC (full: 50x, active: 20x, empty: 10x)
&SOMA_VGSC-M: SOMA_VGSC (full: 50x, active: 20x, empty: 10x)
&SOMA_VGSC_L: SOMA_VGSC (full: 50x, active: 20x, empty: 10x)
— 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 SomaRefractory 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
---
instantiate_container:
MAIN-SOMA []
SOMA_VGSC_H_TUN [pass: &SOMA_VGSC_H]
SOMA_VGSC_M_TUN [pass: &SOMA_VGSC_M]
SOMA_VGSC_L_TUN [pass: &SOMA_VGSC_L]
```
**Tubs:**
@@ -75,31 +39,10 @@ Qui comprendiamo:
- **SomaRefractory**: tracce di refractory
---
## SOMA: Comprehension
### MAIN-SOMA: Container
```Gen
SOMA
type: comprehension
expand_comprehension:
&VGSC-SOMA-H: VGSC-SOMA (full: 50x, active: 20x, empty: 10x)
&VGSC-SOMA-M: VGSC-SOMA (full: 50x, active: 20x, empty: 10x)
&VGSC-SOMA-L: VGSC-SOMA (full: 50x, active: 20x, empty: 10x)
instantiate_container:
SOMA-BEH []
VGSC-SOMA-H-TUN [pass: &VGSC-SOMA-H]
VGSC-SOMA-M-TUN [pass: &VGSC-SOMA-M]
VGSC-SOMA-L-TUN [pass: &VGSC-SOMA-L]
```
### SOMA-BEH: Container
```Gen
SOMA-BEH
MAIN-SOMA
type: container
activity_scope: !DAY
@@ -116,14 +59,14 @@ SOMA-BEH
##### SOMA-Status: ( active: 60x ) contextor
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.
As dendrites deliver current (VDB​), the soma acts like a capacitor. It "stores" this charge in the form of membrane potential. This contextualizes SOMA_VGSC 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
SOMA-Status: ( active: 60x )
type: contextor
contained_by: SOMA-BEH
contained_by: MAIN-SOMA
in_context: any
condition: ( VDB fullness ) AND NOT AP_ctx
@@ -147,7 +90,7 @@ La fullness di Na rappresenta il threshold e puo' essere modificato. La fullness
```Gen
SomaSpike: ( active: 30x )
type: contextor
contained_by: SOMA-BEH
contained_by: MAIN-SOMA
in_context: any
condition: ( Na fullness ) AND ( SomaRefractory emptiness )
@@ -162,7 +105,7 @@ Lo spill deve essere piu' lento dell'increase che avviene in ActiveAP
```Gen
SomaRefractorySpill: ( active: 16x )
type: accumulator
contained_by: SOMA-BEH
contained_by: MAIN-SOMA
in_context: any
hypothesis: NOT ( SomaRefractory empty )
@@ -183,7 +126,7 @@ Durante la fase effettiva di spike:
```Gen
ActiveAP: ( active: 8x )
type: accumulator
contained_by: SOMA-BEH
contained_by: MAIN-SOMA
in_context: Ap_ctx
hypothesis: NOT Na empty
@@ -208,7 +151,7 @@ Questo potrebbe non servire se eliminiamo tutti Na durante ActiveAP.
```Gen
NaSpill: ( active: 8x )
type: accumulator
contained_by: SOMA-BEH
contained_by: MAIN-SOMA
in_context: NaSpill_ctx
hypothesis: NOT ( Na emptiness )
@@ -216,12 +159,12 @@ NaSpill: ( active: 8x )
trace:
```
## VGSC-SOMA: Comprehension
## SOMA_VGSC: Comprehension
Voltage Gated Sodium Channel: difficult to open (High)
```Gen
container: VGSC-SOMA-H
container: SOMA_VGSC-H
tub_local:
VGSCRefractoryH ( full: 60x, active: 30x, empty: 0x )
@@ -233,7 +176,7 @@ container: VGSC-SOMA-H
VDBMaxCtx ( contained_by: SOMA )
```
### sec: VGSC-SOMA-H
### sec: SOMA_VGSC-H
#### VGSC-H_Status: ( active: 60x ) contextor
@@ -242,7 +185,7 @@ Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di
```Gen
VGSC-H_Status: ( active: 60x )
type: contextor
contained_by: VGSC-SOMA-H
contained_by: SOMA_VGSC-H
in_context: any
condition: VDBMaxCtx AND ( VGSCRefractoryH emptiness )
@@ -260,7 +203,7 @@ Questo sopra è il commmento della versione precedente, ora la quantità di NA i
```Gen
NaEnterH: ( active: 1x )
type: accumulator
contained_by: VGSC-SOMA-H
contained_by: SOMA_VGSC-H
in_context: NaEnterH_ctx
hypothesis: ( NOT Na full )
@@ -279,7 +222,7 @@ Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractor
```Gen
VGSCRefractoryHSpill: ( active: 1x )
type: accumulator
contained_by: VGSC-SOMA-H
contained_by: SOMA_VGSC-H
in_context: VGSCRefractoryHSpill_ctx
hypothesis: NOT ( VGSCRefractoryH empty )
@@ -287,12 +230,12 @@ VGSCRefractoryHSpill: ( active: 1x )
trace: None
```
## VGSC-SOMA-M: container
## SOMA_VGSC-M: container
Voltage Gated Sodium Channel: less difficult to open (Medium)
```Gen
container: VGSC-SOMA-M
container: SOMA_VGSC-M
tub_local:
VGSCRefractoryM ( full: 60x, active: 30x, empty: 0x )
@@ -304,7 +247,7 @@ container: VGSC-SOMA-M
VDBMedCtx ( contained_by: SOMA )
```
### sec: VGSC-SOMA-M
### sec: SOMA_VGSC-M
#### VGSC-M_TPC: ( active: 60x ) contextor
@@ -313,7 +256,7 @@ Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di
```Gen
VGSC-M_Status: ( active: 60x )
type: contextor
contained_by: VGSC-SOMA-M
contained_by: SOMA_VGSC-M
in_context: VDBMediumCtx OR VDBMaxCtx
condition: ( VGSCRefractoryH emptiness )
@@ -328,7 +271,7 @@ Questo sopra è il commmento della versione precedente, ora la quantità di NA i
```Gen
NaEnterM: ( active: 1x )
type: accumulator
contained_by: VGSC-SOMA-M
contained_by: SOMA_VGSC-M
in_context: NaEnterM_ctx
hypothesis: ( NOT Na full )
@@ -347,7 +290,7 @@ Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractor
```Gen
VGSCRefractoryMSpill: ( active: 1x )
type: accumulator
contained_by: VGSC-SOMA-M
contained_by: SOMA_VGSC-M
in_context: any
hypothesis: NOT ( VGSCRefractoryM empty )
@@ -355,12 +298,12 @@ VGSCRefractoryMSpill: ( active: 1x )
trace: None
```
## VGSC-SOMA-L: container
## SOMA_VGSC_L: container
Voltage Gated Sodium Channel: easy to open (Low)
```Gen
container: VGSC-SOMA-L
container: SOMA_VGSC_L
tub_local:
VGSCRefractoryL ( full: 60x, active: 30x, empty: 0x )
@@ -372,7 +315,7 @@ container: VGSC-SOMA-L
VDBLowCtx ( contained_by: SOMA )
```
### sec: VGSC-SOMA-L
### sec: SOMA_VGSC_L
#### VGSC-L_TPC: ( active: 60x ) contextor
@@ -381,7 +324,7 @@ Il check su refractory deve essere fatto ad un RF maggiore della eliminazione di
```Gen
VGSC-L_Status: ( active: 60x )
type: contextor
contained_by: VGSC-SOMA-L
contained_by: SOMA_VGSC_L
in_context: VDBLowCtx OR VDBMediumCtx OR VDBMaxCtx
condition: ( VGSCRefractoryH emptiness )
@@ -396,7 +339,7 @@ Questo sopra è il commmento della versione precedente, ora la quantità di NA i
```Gen
NaEnterL: ( active: 1x )
type: accumulator
contained_by: VGSC-SOMA-L
contained_by: SOMA_VGSC_L
in_context: NaEnterL_ctx
hypothesis: ( NOT Na full )
@@ -415,6 +358,7 @@ Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractor
```Gen
VGSCRefractoryLSpill: ( active: 1x )
type: accumulator
contained_by: VGSC-L-SOMA
in_context: any
@@ -424,14 +368,14 @@ VGSCRefractoryLSpill: ( active: 1x )
```
## VGSC-SOMA-TUN: Tuner
## SOMA_VGSC_TUN: Tuner
```Gen
VGSC-SOMA-TUN
SOMA_VGSC_TUN
type: tuner
contained_by: SOMA
tunes: SOMA/expansion/VGSC-SOMA
tunes: SOMA/expansion/SOMA_VGSC
context_intricated:
- TunPossible ( contained_by: DAY-N )
@@ -446,7 +390,7 @@ VGSC-SOMA-TUN
```Gen
check_tpc: ( active: 60x )
type: contextor
contained_by: VGSC-SOMA-TUN
contained_by: SOMA_VGSC-TUN
in_context: TunPossible
condition: ??