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elements/neuron/README.md
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@@ -329,6 +329,55 @@ In this model we decide to simplify:
- We do not model subthreshold oscillations — VSOMA is a simple leaky integrator - We do not model subthreshold oscillations — VSOMA is a simple leaky integrator
- We do not model somatic ATP - We do not model somatic ATP
**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 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
The simplifications imply that: The simplifications imply that:
Removing the axon hillock as a separate compartment means the threshold comparison is applied directly to VSOMA rather than to a spatially distinct zone with its own channel density. In biology the hillock has a lower threshold than the soma body because of its higher Na⁺ channel density — this gradient is absent here. A single fixed threshold applied to VSOMA is a reasonable approximation for a single-compartment model, but it means the model cannot capture phenomena that depend on the hillock's spatial separation from the dendritic integration zone, such as the ability of strong distal dendritic inputs to bypass somatic inhibition. Removing the axon hillock as a separate compartment means the threshold comparison is applied directly to VSOMA rather than to a spatially distinct zone with its own channel density. In biology the hillock has a lower threshold than the soma body because of its higher Na⁺ channel density — this gradient is absent here. A single fixed threshold applied to VSOMA is a reasonable approximation for a single-compartment model, but it means the model cannot capture phenomena that depend on the hillock's spatial separation from the dendritic integration zone, such as the ability of strong distal dendritic inputs to bypass somatic inhibition.
@@ -371,6 +420,20 @@ In this model we decide to simplify:
- We do not model bAP distance attenuation — all spines receive the bAP at full amplitude regardless of their position - We do not model bAP distance attenuation — all spines receive the bAP at full amplitude regardless of their position
- We do not model structural plasticity — spine neck widening and retraction are not implemented - We do not model structural plasticity — spine neck widening and retraction are not implemented
— ms:
- Each active spine contributes VPost (EPSP) to VDB
- VDB decays passively each ms
— secs:
- nothing in the simplified model
— mins:
- nothing in the simplified model
(structural remodelling of spine neck geometry under LTP/LTD would live here if added later)
The simplifications imply that: The simplifications imply that:
- 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. - 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.
elements/neuron/axon.md
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@@ -6,15 +6,15 @@ include_toc: true
## AXON: Container ## AXON: Container
Expansions and modulations:
- is expanded by: [NEURON](neuron.md)
- expands: [PRESYNAPSE](presynapse.md)
The axon does not contain specific behavior. The axon does not contain specific behavior.
- We might add balancing of ATP within PRE later. Here we comprehend it as a “cable” transporting the AP from SOMA to Presynapse. It expands PRESYNAPSE which: - We might add balancing of ATP within PRE later. Here we comprehend it as a “cable” transporting the AP from SOMA to Presynapse. It expands PRESYNAPSE which:
- l'equivalente del tuning della PRESYNAPSE, come espansione dell'AXON, e' fatta da excitation/inhibition in winnertakeall. Per equivalente si intende che e' uno spostare PRESYNAPSE da actual, come se fosse un tuning. - l'equivalente del tuning della PRESYNAPSE, come espansione dell'AXON, e' fatta da excitation/inhibition in winnertakeall. Per equivalente si intende che e' uno spostare PRESYNAPSE da actual, come se fosse un tuning.
- the associations between PRESYNAPSE, POSTSYNAPSE e SYNAPSE is performed by the "bind" in excitation/inhibition in winnertakeall. Because we have to make sure that the correct binding is performed when intricating actuals. - the associations between PRESYNAPSE, POSTSYNAPSE e SYNAPSE is performed by the "bind" in excitation/inhibition in winnertakeall. Because we have to make sure that the correct binding is performed when intricating actuals.
Expansions and modulations:
- is expanded by: [NEURON](neuron.md)
- expands: [PRESYNAPSE](presynapse.md)
```Gen ```Gen
AXON AXON
elements/neuron/d-branch.md
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@@ -4,30 +4,9 @@ include_toc: true
# d-branch.md # d-branch.md
Qui comprendiamo:
- D-BRANCH: Dendritic Branch
## D-BRANCH ## D-BRANCH
**Simplified behaviors**: Expansions and modulations:
— ms:
- Each active spine contributes VPost (EPSP) to VDB
- VDB decays passively each ms
— secs:
- nothing in the simplified model
— mins:
- nothing in the simplified model
(structural remodelling of spine neck geometry under LTP/LTD would live here if added later)
---
Intro:
- is expanded by: [NEURON](neuron.md) - is expanded by: [NEURON](neuron.md)
- expands: [POSTSYNAPSE](posynapse.md) - expands: [POSTSYNAPSE](posynapse.md)
elements/neuron/neuron.md
+2 -2
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@@ -6,12 +6,12 @@ include_toc: true
## NEURON ## NEURON
Nel folder Appunti ci sono i comportamenti osservabili, dai quali siamo partiti, riducendone il numero per semplificare in questa prima fase. La forza della comprensione G. e' che possiamo aggiungere man mano nuovi comportamenti, senza gettare via nulla per ripartire da zero, come saremmo costretti a fare in una comprensione tradizionale.In questa prima comprensione, cerchiamo di fare un'espressione la piu' semplice possibile per valutare la sintassi e la grammatica e l'enliving dell'espressione.
Expansions and modulations: Expansions and modulations:
- is expanded by: modules - is expanded by: modules
- expands: [AXON](axon.md), [SOMA](soma.md), [D_BRANCH](d-branch.md) - expands: [AXON](axon.md), [SOMA](soma.md), [D_BRANCH](d-branch.md)
Nel folder Appunti ci sono i comportamenti osservabili, dai quali siamo partiti, riducendone il numero per semplificare in questa prima fase. La forza della comprensione G. e' che possiamo aggiungere man mano nuovi comportamenti, senza gettare via nulla per ripartire da zero, come saremmo costretti a fare in una comprensione tradizionale.In questa prima comprensione, cerchiamo di fare un'espressione la piu' semplice possibile per valutare la sintassi e la grammatica e l'enliving dell'espressione.
```Gen ```Gen
include: include:
elements/neuron/soma.md
+47 -103
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@@ -4,64 +4,28 @@ include_toc: true
# soma.md # soma.md
Qui comprendiamo: ## SOMA: Comprehension
- SOMA: il soma Expansions and modulations:
- VGSC-SOMA-H: Na ion channels. Open only when VDB high - is expanded by: [NEURON](neuron.md)
- VGSC-SOMA-M: Na ion channels. Open only when VDB medium - expands: SOMA_VGSC
- VGSC-SOMA-L: Na ion channels. Open only when VDB low
--- ```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: 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]
- 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
---
**Tubs:** **Tubs:**
@@ -75,31 +39,10 @@ Qui comprendiamo:
- **SomaRefractory**: tracce di refractory - **SomaRefractory**: tracce di refractory
--- ### MAIN-SOMA: Container
## SOMA: Comprehension
```Gen ```Gen
SOMA MAIN-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
type: container type: container
activity_scope: !DAY activity_scope: !DAY
@@ -116,14 +59,14 @@ SOMA-BEH
##### SOMA-Status: ( active: 60x ) contextor ##### 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. This only applies if not ApCtx, or in other words, SOMA is not in refractory period.
```Gen ```Gen
SOMA-Status: ( active: 60x ) SOMA-Status: ( active: 60x )
type: contextor type: contextor
contained_by: SOMA-BEH contained_by: MAIN-SOMA
in_context: any in_context: any
condition: ( VDB fullness ) AND NOT AP_ctx 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 ```Gen
SomaSpike: ( active: 30x ) SomaSpike: ( active: 30x )
type: contextor type: contextor
contained_by: SOMA-BEH contained_by: MAIN-SOMA
in_context: any in_context: any
condition: ( Na fullness ) AND ( SomaRefractory emptiness ) condition: ( Na fullness ) AND ( SomaRefractory emptiness )
@@ -162,7 +105,7 @@ Lo spill deve essere piu' lento dell'increase che avviene in ActiveAP
```Gen ```Gen
SomaRefractorySpill: ( active: 16x ) SomaRefractorySpill: ( active: 16x )
type: accumulator type: accumulator
contained_by: SOMA-BEH contained_by: MAIN-SOMA
in_context: any in_context: any
hypothesis: NOT ( SomaRefractory empty ) hypothesis: NOT ( SomaRefractory empty )
@@ -183,7 +126,7 @@ Durante la fase effettiva di spike:
```Gen ```Gen
ActiveAP: ( active: 8x ) ActiveAP: ( active: 8x )
type: accumulator type: accumulator
contained_by: SOMA-BEH contained_by: MAIN-SOMA
in_context: Ap_ctx in_context: Ap_ctx
hypothesis: NOT Na empty hypothesis: NOT Na empty
@@ -208,7 +151,7 @@ Questo potrebbe non servire se eliminiamo tutti Na durante ActiveAP.
```Gen ```Gen
NaSpill: ( active: 8x ) NaSpill: ( active: 8x )
type: accumulator type: accumulator
contained_by: SOMA-BEH contained_by: MAIN-SOMA
in_context: NaSpill_ctx in_context: NaSpill_ctx
hypothesis: NOT ( Na emptiness ) hypothesis: NOT ( Na emptiness )
@@ -216,12 +159,12 @@ NaSpill: ( active: 8x )
trace: trace:
``` ```
## VGSC-SOMA: Comprehension ## SOMA_VGSC: Comprehension
Voltage Gated Sodium Channel: difficult to open (High) Voltage Gated Sodium Channel: difficult to open (High)
```Gen ```Gen
container: VGSC-SOMA-H container: SOMA_VGSC-H
tub_local: tub_local:
VGSCRefractoryH ( full: 60x, active: 30x, empty: 0x ) VGSCRefractoryH ( full: 60x, active: 30x, empty: 0x )
@@ -233,7 +176,7 @@ container: VGSC-SOMA-H
VDBMaxCtx ( contained_by: SOMA ) VDBMaxCtx ( contained_by: SOMA )
``` ```
### sec: VGSC-SOMA-H ### sec: SOMA_VGSC-H
#### VGSC-H_Status: ( active: 60x ) contextor #### 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 ```Gen
VGSC-H_Status: ( active: 60x ) VGSC-H_Status: ( active: 60x )
type: contextor type: contextor
contained_by: VGSC-SOMA-H contained_by: SOMA_VGSC-H
in_context: any in_context: any
condition: VDBMaxCtx AND ( VGSCRefractoryH emptiness ) condition: VDBMaxCtx AND ( VGSCRefractoryH emptiness )
@@ -260,7 +203,7 @@ Questo sopra è il commmento della versione precedente, ora la quantità di NA i
```Gen ```Gen
NaEnterH: ( active: 1x ) NaEnterH: ( active: 1x )
type: accumulator type: accumulator
contained_by: VGSC-SOMA-H contained_by: SOMA_VGSC-H
in_context: NaEnterH_ctx in_context: NaEnterH_ctx
hypothesis: ( NOT Na full ) hypothesis: ( NOT Na full )
@@ -279,7 +222,7 @@ Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractor
```Gen ```Gen
VGSCRefractoryHSpill: ( active: 1x ) VGSCRefractoryHSpill: ( active: 1x )
type: accumulator type: accumulator
contained_by: VGSC-SOMA-H contained_by: SOMA_VGSC-H
in_context: VGSCRefractoryHSpill_ctx in_context: VGSCRefractoryHSpill_ctx
hypothesis: NOT ( VGSCRefractoryH empty ) hypothesis: NOT ( VGSCRefractoryH empty )
@@ -287,12 +230,12 @@ VGSCRefractoryHSpill: ( active: 1x )
trace: None trace: None
``` ```
## VGSC-SOMA-M: container ## SOMA_VGSC-M: container
Voltage Gated Sodium Channel: less difficult to open (Medium) Voltage Gated Sodium Channel: less difficult to open (Medium)
```Gen ```Gen
container: VGSC-SOMA-M container: SOMA_VGSC-M
tub_local: tub_local:
VGSCRefractoryM ( full: 60x, active: 30x, empty: 0x ) VGSCRefractoryM ( full: 60x, active: 30x, empty: 0x )
@@ -304,7 +247,7 @@ container: VGSC-SOMA-M
VDBMedCtx ( contained_by: SOMA ) VDBMedCtx ( contained_by: SOMA )
``` ```
### sec: VGSC-SOMA-M ### sec: SOMA_VGSC-M
#### VGSC-M_TPC: ( active: 60x ) contextor #### 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 ```Gen
VGSC-M_Status: ( active: 60x ) VGSC-M_Status: ( active: 60x )
type: contextor type: contextor
contained_by: VGSC-SOMA-M contained_by: SOMA_VGSC-M
in_context: VDBMediumCtx OR VDBMaxCtx in_context: VDBMediumCtx OR VDBMaxCtx
condition: ( VGSCRefractoryH emptiness ) condition: ( VGSCRefractoryH emptiness )
@@ -328,7 +271,7 @@ Questo sopra è il commmento della versione precedente, ora la quantità di NA i
```Gen ```Gen
NaEnterM: ( active: 1x ) NaEnterM: ( active: 1x )
type: accumulator type: accumulator
contained_by: VGSC-SOMA-M contained_by: SOMA_VGSC-M
in_context: NaEnterM_ctx in_context: NaEnterM_ctx
hypothesis: ( NOT Na full ) hypothesis: ( NOT Na full )
@@ -347,7 +290,7 @@ Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractor
```Gen ```Gen
VGSCRefractoryMSpill: ( active: 1x ) VGSCRefractoryMSpill: ( active: 1x )
type: accumulator type: accumulator
contained_by: VGSC-SOMA-M contained_by: SOMA_VGSC-M
in_context: any in_context: any
hypothesis: NOT ( VGSCRefractoryM empty ) hypothesis: NOT ( VGSCRefractoryM empty )
@@ -355,12 +298,12 @@ VGSCRefractoryMSpill: ( active: 1x )
trace: None trace: None
``` ```
## VGSC-SOMA-L: container ## SOMA_VGSC_L: container
Voltage Gated Sodium Channel: easy to open (Low) Voltage Gated Sodium Channel: easy to open (Low)
```Gen ```Gen
container: VGSC-SOMA-L container: SOMA_VGSC_L
tub_local: tub_local:
VGSCRefractoryL ( full: 60x, active: 30x, empty: 0x ) VGSCRefractoryL ( full: 60x, active: 30x, empty: 0x )
@@ -372,7 +315,7 @@ container: VGSC-SOMA-L
VDBLowCtx ( contained_by: SOMA ) VDBLowCtx ( contained_by: SOMA )
``` ```
### sec: VGSC-SOMA-L ### sec: SOMA_VGSC_L
#### VGSC-L_TPC: ( active: 60x ) contextor #### 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 ```Gen
VGSC-L_Status: ( active: 60x ) VGSC-L_Status: ( active: 60x )
type: contextor type: contextor
contained_by: VGSC-SOMA-L contained_by: SOMA_VGSC_L
in_context: VDBLowCtx OR VDBMediumCtx OR VDBMaxCtx in_context: VDBLowCtx OR VDBMediumCtx OR VDBMaxCtx
condition: ( VGSCRefractoryH emptiness ) condition: ( VGSCRefractoryH emptiness )
@@ -396,7 +339,7 @@ Questo sopra è il commmento della versione precedente, ora la quantità di NA i
```Gen ```Gen
NaEnterL: ( active: 1x ) NaEnterL: ( active: 1x )
type: accumulator type: accumulator
contained_by: VGSC-SOMA-L contained_by: SOMA_VGSC_L
in_context: NaEnterL_ctx in_context: NaEnterL_ctx
hypothesis: ( NOT Na full ) hypothesis: ( NOT Na full )
@@ -415,6 +358,7 @@ Lo Spill deve avere un rf maggiore dell'interacting che incrementa VGSCRefractor
```Gen ```Gen
VGSCRefractoryLSpill: ( active: 1x ) VGSCRefractoryLSpill: ( active: 1x )
type: accumulator type: accumulator
contained_by: VGSC-L-SOMA contained_by: VGSC-L-SOMA
in_context: any in_context: any
@@ -424,14 +368,14 @@ VGSCRefractoryLSpill: ( active: 1x )
``` ```
## VGSC-SOMA-TUN: Tuner ## SOMA_VGSC_TUN: Tuner
```Gen ```Gen
VGSC-SOMA-TUN SOMA_VGSC_TUN
type: tuner type: tuner
contained_by: SOMA contained_by: SOMA
tunes: SOMA/expansion/VGSC-SOMA tunes: SOMA/expansion/SOMA_VGSC
context_intricated: context_intricated:
- TunPossible ( contained_by: DAY-N ) - TunPossible ( contained_by: DAY-N )
@@ -446,7 +390,7 @@ VGSC-SOMA-TUN
```Gen ```Gen
check_tpc: ( active: 60x ) check_tpc: ( active: 60x )
type: contextor type: contextor
contained_by: VGSC-SOMA-TUN contained_by: SOMA_VGSC-TUN
in_context: TunPossible in_context: TunPossible
condition: ?? condition: ??
organs/tectum/tectum.md
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@@ -6,13 +6,13 @@ include_toc: true
## TECTUM ## TECTUM
Qui comprendiamo il collegamento fra moduli tipo winnertakeall che mettono a disposizione delle interfacce che devono essere collegate fra moduli. I neuroni sono gia' dichiarati nei moduli, quello che manca sono gli ASTROCYTE. Consideriamo che gli ASTROCYTE sono interni ad un organo.
Expansions and modulations: Expansions and modulations:
- is expanded by: [ORGANISM](../../organism.md) - is expanded by: [ORGANISM](../../organism.md)
- expands: [WINNERTAKEALL](../../modules/winnertakeall/winnertakeall.md), [ASTROCYTE](../../elements/astrocyte/astrocyte.md) - expands: [WINNERTAKEALL](../../modules/winnertakeall/winnertakeall.md), [ASTROCYTE](../../elements/astrocyte/astrocyte.md)
- tunes: [PRESYNAPSE](../../elements/neuron/presynapse.md), [POSTSYNAPSE](../../elements/neuron/postsynapse.md), [ASTROSYNAPSE](../../elements/astrocyte/astrosynapse.md) - tunes: [PRESYNAPSE](../../elements/neuron/presynapse.md), [POSTSYNAPSE](../../elements/neuron/postsynapse.md), [ASTROSYNAPSE](../../elements/astrocyte/astrosynapse.md)
Qui comprendiamo il collegamento fra moduli tipo winnertakeall che mettono a disposizione delle interfacce che devono essere collegate fra moduli. I neuroni sono gia' dichiarati nei moduli, quello che manca sono gli ASTROCYTE. Consideriamo che gli ASTROCYTE sono interni ad un organo.
```Gen ```Gen
include: include: