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ocrampal
2026-06-01 09:46:05 +02:00
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elements/neuron/axon.md
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@@ -5,9 +5,9 @@ Qui comprendiamo:
- AXON: Axon - AXON: Axon
## AXON: Container ## AXON: Container
Modulation: Intro:
- develops: - is expanded by: [NEURON](neuron.md)
- [PRESYNAPSE](presynapse.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:
@@ -16,11 +16,9 @@ The axon does not contain specific behavior.
```Gen ```Gen
AXON AXON
type: comprehension type: comprehension
expansion: expansion:
_@presynapse: TUB [ comprehension: PRESYNAPSE, full: 50x, active: 0x, empty: 10x ]
_presynapse: TUB [ comprehension: PRESYNAPSE, full: 50x, active: 0x, empty: 10x ]
# managed_by: EXCITATION or INHIBITION from winnertakeall # managed_by: EXCITATION or INHIBITION from winnertakeall
``` ```
elements/neuron/d-branch.md
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@@ -1,10 +1,14 @@
---
include_toc: true
---
# d-branch.md # d-branch.md
Qui comprendiamo: Qui comprendiamo:
- D-BRANCH: Dendritic Branch - D-BRANCH: Dendritic Branch
## D-BRANCH: Container ## D-BRANCH
**Simplified behaviors**: **Simplified behaviors**:
@@ -23,24 +27,41 @@ Qui comprendiamo:
(structural remodelling of spine neck geometry under LTP/LTD would live here if added later) (structural remodelling of spine neck geometry under LTP/LTD would live here if added later)
--- ---
Intro:
- is expanded by: [NEURON](neuron.md)
- expands: [POSTSYNAPSE](posynapse.md)
```Gen ```Gen
Container: D-BRANCH D-BRANCH
type: comprehension
include:
BEH-POST.md
include: posynapse.md
expansion: expansion:
- BEH-POST ( full: 50x, active: 0x, empty: 10x ) _@postsynapse: TUB [ comprehension: POSTSYNAPSE, full: 50x, active: 0x, empty: 10x ]
# managed_by: BEH-EXH or BEH-INH from winnertakeall
# developed_by: DEV-BD-BEH-POST-TUB from DEV-N
tub_local: intrication:
- VPost ( full: 50x, active: 0x, empty: 10x )
tub_intricated: # Scope
- VDB ( contained_by: BEH-SOMA ) !DAY: INTRICATION [ ref: &ORGANISM.!DAY ]
!NIGHT: INTRICATION [ ref: &ORGANISM.!NIGHT ]
# Context
*VPostMax: CONTEXT []
*VPostMedium: CONTEXT []
*VPostLow: CONTEXT []
# Tub
_VDB: INTRICATION [ ref: &SOMA._VDB )
instantiation:
# Tub
_VPost: TUB [ full: 50x, active: 0x, empty: 10x ]
# Behaviour
$: BEHAVIOUR [ behaviour: MAIN_DBRANCH ]
``` ```
--- ---
@@ -51,85 +72,86 @@ Container: D-BRANCH
--- ---
### ms: behaviors BD ### MAIN_DBRANCH: !DAY
#### CheckVPost:Context ```Gen
MAIN_DBRANCH
type: behaviour
within_scope: !DAY
snippet:
# *Fixed
@: CONTEXTOR [ snippet: CheckVPost, rf: active 60x ]
@: ACCUMULATOR [ snippet: VDBClearance, rf: active 2x ]
# *VPostMax
@: ACCUMULATOR [ snippet: VDBMax, rf: active 2x ]
# *VPostMedium
@: ACCUMULATOR [ snippet: VDBMed, rf: active 4x ]
# *VPostLow
@: ACCUMULATOR [ snippet: VDBMin, rf: active 8x ]
```
#### *Fixed
##### CheckVPost
Contestualizziamo in maniera Fixed? Contestualizziamo in maniera Fixed?
```Gen ```Gen
context: CheckVPost CheckVPost
contained_by: D-BRANCH type: contextor
in_context: Fixed in_context: *Fixed
rf: ( active: 60x ) condition: _VPost fullness
out_context: *VPostMax
condition: (VPost fullness) condition: _VPost mediumness
out_context: VPostMax out_context: *VPostMedium
condition: _VPost emptiness
condition: (VPost mediumness) out_context: *VPostLow
out_context: VPostMedium
condition: (VPost emptiness)
out_context: VPostLow
``` ```
##### VDBMax: Episode ##### VDBClearance
```Gen
episode: VDBMax
contained_by: D-BRANCH
in_context: VPostMax
rf: ( active: 2x )
hypothesis: NOT (VDB full)
action: [VDB increase]
trace:
```
##### VDBMed: Episode
```Gen
episode: VDBMed
contained_by: D-BRANCH
in_context: VPostMed
rf: ( active: 2x )
hypothesis: NOT (VDB full)
action: [VDB increase]
trace:
```
##### VDBLow: Episode
```Gen
episode: VDBLow
contained_by: D-BRANCH
in_context: VPostLow
rf: ( active: 2x )
hypothesis: NOT (VDB full)
action: [VDB increase]
trace:
```
#### VDBlearance: Episode
Qui facciamo il clearance del VDB. Lo facciamo in questo modo perche' abbiamo semplificato quello che succede fra BD e SOMA. Qui facciamo il clearance del VDB. Lo facciamo in questo modo perche' abbiamo semplificato quello che succede fra BD e SOMA.
Qui posso aggiungere il flush, clearance veloce quando c'e' il bAP. Qui posso aggiungere il flush, clearance veloce quando c'e' il bAP.
```Gen ```Gen
episode: VDBClearance VDBClearance
contained_by: D-BRANCH in_context: *Fixed
in_context: Fixed hypothesis: NOT _VDB empty
rf: ( active: 2x ) action: [ _VDB decrease ]
trace:
hypothesis: NOT (VDB empty) ```
action: [VDB decrease] #### *VPostMax
trace: ##### VDBMax
```Gen
VDBMax
in_context: *VPostMax
hypothesis: NOT _VDB full
action: [ _VDB increase ]
trace:
```
#### *VPostMedium
##### VDBMed
```Gen
VDBMed
in_context: *VPostMedium
hypothesis: NOT _VDB full
action: [ _VDB increase ]
trace:
```
#### *VPostLow
##### VDBLow
```Gen
in_context: *VPostLow
hypothesis: NOT _VDB full
action: [ _VDB increase ]
trace:
``` ```
elements/neuron/post_ampa.md
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@@ -0,0 +1,71 @@
---
include_toc: true
---
# post_ampa.md
## POST-AMPA
Intro:
- is expanded and tuned by: [POSTSYNAPSE](postsynapse.md)
```Gen
POST-AMPA
type: comprehension
expansion:
intrication:
# Scope
!DAY: INTRICATION [ ref: &ORGANISM.!DAY ]
!NIGHT: INTRICATION [ ref: &ORGANISM.!NIGHT ]
# Context
*bAP: INTRICATION [ ref: &SOMA.*bAP ]
# Tub
_NT: INTRICATION [ ref: &ASTROSYNAPSE._NT ]
_Na: INTRICATION [ ref: &POSTSYNAPSE._Na ]
instantiation:
$: BEHAVIOUR [ behaviour: POST-AMPA-BHE ]
```
### POST-AMPA: !DAY
```Gen
POST-AMPA-BHE
type: behavior
within_scope: !DAY
snippet:
# NOT *bAP
@: ACCUMULATOR [ snippet: NaInAMPAMax, rf: active 2x ]
@: ACCUMULATOR [ snippet: NaInAMPAMed, rf: active 4x ]
```
#### NOT *bAP
##### NaInAMPAMax
```Gen
NaInAMPAMax
type: accumulator
in_context: NOT *bAP
hypothesis: _NT fullness
action: [ _Na increase ]
trace:
```
##### NaInAMPAMed
```Gen
NaInAMPAMed
type: accumulator
in_context: NOT *bAP
hypothesis: _NT mediumness
action: [ _Na increase ]
trace:
```
elements/neuron/postsynapse.md
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@@ -39,63 +39,30 @@ Qui comprendiamo:
--- ---
**G expression**:
```Gen
*bAP
POSTSYNAPSE (ms)
-- Ca Influx
CaNDMAEnterMax: ( active: 2x ) accumulator
CaNDMAEnterMed: ( active: 4x ) accumulator
NOT *bAP:
POSTSYNAPSE (ms)
-- Ca Influx
CaNDMAEnterMedNotBap: ( active: 4x ) accumulator
CaNDMAEnterLow: ( active: 12x ) accumulator
-- Ca Clearence
CaClearance: ( active: 24x ) accumulator
-- V Influx
VPostMax: ( active: 4x ) accumulator ->VPost
VPostMed: ( active: 8x ) accumulator ->VPost
VPostLow: ( active: 16x ) accumulator ->VPost
-- V Clearence
VPostClearance: ( active: 18x ) accumulator ~->VPost
POST-AMPA (ms) ~ NT
-- Na Influx
NaAMPAEnterMax: ( active: 2x ) accumulator ~NT
NaAMPAEnterMed: ( active: 4x ) accumulator ~NT
POST-NA-CLEAR (ms)
-- Na Clearence
NaClearanceHigh: ( active: 4x ) accumulator
NaClearanceLow: ( active: 16x ) accumulator
TunPossible_ctx
TUN-POST-AMPA (sec)
CheckTunPostAmpa: ( active: 60x ) contexting
TryTunUpPostAmpa_ctx
PossibleUpPostAmpaTun: ( active: 10x ) accumulator
TryTunDownPostAmpa_ctx
PossibleDownPostAmpaTun: ( active: 10x ) accumulator
```
**Tubs:** **Tubs:**
- **Na**: Ioni entranti tramite AMPA receptors - **_Na**: Ioni entranti tramite AMPA receptors
- **NT**: - **_NT**: Neuro Trasmettitori
- **_Ca2**: Ioni entranti tramite NMDA - **_Ca2**: Ioni entranti tramite NMDA
- **VPost**: il voltage che viene sentito in DB - **_VPost**: il voltage che viene sentito in DB
- **eCB**: - **_eCB**:
- **Nox**:? - **_Nox**:?
--- ---
## POSTSYNAPSE: Comprehension Intro:
- is expanded and developed by: [D_BRANCH](d-branch.md)
- is tuned by: ORGANISM, organs, modules
- expands and tunes: [POST-AMPA](post_ampa.md)
- develops [_posMod](??), [_actMod](??)
## POSTSYNAPSE
```Gen ```Gen
POSTSYNAPSE POSTSYNAPSE
type: comprehension type: comprehension
include: post_ampa.md
expansion: expansion:
_@PostAmpaAll: TUB [ comprehension: POST-AMPA, full: 10x, active: 5x, empty: 2x ] _@PostAmpaAll: TUB [ comprehension: POST-AMPA, full: 10x, active: 5x, empty: 2x ]
@@ -131,7 +98,7 @@ POSTSYNAPSE
``` ```
### MAIN_POST: Behaviour ### MAIN_POST: !DAY
``` ```
MAIN_POST MAIN_POST
type: behaviour type: behaviour
@@ -161,7 +128,7 @@ MAIN_POST
![post-ltp-ltd.png](.attachments/post-ltp-ltd.png) ![post-ltp-ltd.png](.attachments/post-ltp-ltd.png)
##### CaNDMAEnterMax: ( active: 2x ) accumulator ##### CaNDMAEnterMax
```Gen ```Gen
CaNDMAEnterMax CaNDMAEnterMax
@@ -175,7 +142,7 @@ CaNDMAEnterMax
trace: trace:
``` ```
##### CaNDMAEnterMed: ( active: 4x ) accumulator ##### CaNDMAEnterMed
```Gen ```Gen
CaNDMAEnterMed CaNDMAEnterMed
@@ -190,7 +157,7 @@ CaNDMAEnterMed
#### NOT *bAP #### NOT *bAP
##### CaNDMAEnterLow: ( active: 12x ) accumulator ##### CaNDMAEnterLow
```Gen ```Gen
CaNDMAEnterLow CaNDMAEnterLow
@@ -203,7 +170,7 @@ CaNDMAEnterLow
trace: trace:
``` ```
##### CaNDMAEnterMedNotBap: ( active: 4x ) accumulator ##### CaNDMAEnterMedNotBap
```Gen ```Gen
CaNDMAEnterMedNotBap CaNDMAEnterMedNotBap
@@ -216,7 +183,7 @@ CaNDMAEnterMedNotBap
trace: trace:
``` ```
##### CaClearance: ( active: 24x ) accumulator ##### CaClearance
```Gen ```Gen
CaClearance # Low CaClearance # Low
@@ -229,7 +196,7 @@ CaClearance # Low
trace: None trace: None
``` ```
##### VPostMax: ( active: 4x ) accumulator ##### VPostMax
```Gen ```Gen
VPostMa VPostMa
type: accumulator type: accumulator
@@ -241,7 +208,7 @@ VPostMa
trace: None trace: None
``` ```
##### VPostMed: ( active: 8x ) accumulator ##### VPostMed
```Gen ```Gen
VPostMed VPostMed
type: accumulator type: accumulator
@@ -253,7 +220,7 @@ VPostMed
trace: None trace: None
``` ```
##### VPostMin: ( active: 16x ) accumulator ##### VPostMin
```Gen ```Gen
VPostMin VPostMin
type: accumulator type: accumulator
@@ -266,7 +233,7 @@ VPostMin
``` ```
Il VPost clearance lo facciamo qui nel container dove creaiamo anche i VPost, perche' altrimenti, se lo facessimo in DB, perderemmo l'aspetto temporale della contribuzione dei singoli POST. Il VPost clearance lo facciamo qui nel container dove creaiamo anche i VPost, perche' altrimenti, se lo facessimo in DB, perderemmo l'aspetto temporale della contribuzione dei singoli POST.
##### VPostClearance: ( active: 18x ) accumulator ##### VPostClearance
```Gen ```Gen
VPostClearance VPostClearance
type: accumulator type: accumulator
@@ -280,7 +247,7 @@ VPostClearance
Il NA clearance lo mettiamo qui come sniplet, perche' gli AMPA creano, e questi pompano fuori. Qui non e' un problema di perdere l'integrazione temporale, perche' gli AMPA sono tutti uguali nel loro behavior. Abbiamo messo gli AMPA come container perche' cosi' possiamo modularne la numerosita'. Il NA clearance lo mettiamo qui come sniplet, perche' gli AMPA creano, e questi pompano fuori. Qui non e' un problema di perdere l'integrazione temporale, perche' gli AMPA sono tutti uguali nel loro behavior. Abbiamo messo gli AMPA come container perche' cosi' possiamo modularne la numerosita'.
##### NaClearanceHigh: ( active: 4x ) accumulator ##### NaClearanceHigh
```Gen ```Gen
NaClearanceHigh NaClearanceHigh
type: accumulator type: accumulator
@@ -292,7 +259,7 @@ NaClearanceHigh
trace: None trace: None
``` ```
##### NaClearanceLow: ( active: 16x ) accumulator ##### NaClearanceLow
```Gen ```Gen
NaClearanceLow NaClearanceLow
type: accumulator type: accumulator
@@ -304,7 +271,7 @@ NaClearanceLow
trace: None trace: None
``` ```
### TUN-POST-AMPA: Behaviour ### TUN-POST-AMPA: !DAY
```Gen ```Gen
TUN-POST-AMPA TUN-POST-AMPA
type: behaviour type: behaviour
@@ -323,9 +290,9 @@ TUN-POST-AMPA
``` ```
#### TunPossible_ctx #### *TunPossible
##### CheckTunPostAmpa: ( active: 60x ) contextor ##### CheckTunPostAmpa
```Gen ```Gen
CheckTunPostAmpa CheckTunPostAmpa
type: contextor type: contextor
@@ -338,7 +305,7 @@ CheckTunPostAmpa
out_context: *TryTunDownPostAmpa out_context: *TryTunDownPostAmpa
``` ```
##### PossibleUpPostAmpaTun: ( active: 10x ) accumulator ##### PossibleUpPostAmpaTun
```Gen ```Gen
PossibleUpPostAmpaTun: ( active: 10x ) PossibleUpPostAmpaTun: ( active: 10x )
type: accumulator type: accumulator
@@ -349,7 +316,7 @@ PossibleUpPostAmpaTun: ( active: 10x )
trace: trace:
``` ```
##### PossibleDownPostAmpaTun: ( active: 10x ) accumulator ##### PossibleDownPostAmpaTun
```Gen ```Gen
PossibleDownPostAmpaTun PossibleDownPostAmpaTun
type: accumulator type: accumulator
@@ -359,58 +326,3 @@ PossibleDownPostAmpaTun
action: action:
trace: trace:
``` ```
## POST-AMPA: Comprehension
```Gen
POST-AMPA
type: comprehension
expansion:
intrication:
# Tub
_NT: INTRICATION [ ref: &ASTROSYNAPSE._NT ]
_Na: INTRICATION [ ref: &POSTSYNAPSE._Na ]
instantiation:
$: BEHAVIOUR [ behaviour: POST-AMPA-BHE ]
```
### POST-AMPA: Behaviour
```Gen
POST-AMPA-BHE
type: behavior
within_scope: !DAY
snippet:
# NOT *bAP
@: ACCUMULATOR [ snippet: NaAMPAEnterMax, rf: active 2x ]
@: ACCUMULATOR [ snippet: NaAMPAEnterMed, rf: active 4x ]
```
#### NOT *bAP
##### NaAMPAEnterMax: ( active: 2x ) accumulator
```Gen
NaAMPAEnterMax
type: accumulator
in_context: NOT *bAP
hypothesis: _NT fullness
action: [ _Na increase ]
trace:
```
##### NaAMPAEnterMed: ( active: 4x ) accumulator
```Gen
NaAMPAEnterMed
type: accumulator
in_context: NOT *bAP
hypothesis: _NT mediumness
action: [ _Na increase ]
trace:
```
elements/neuron/pre_vgcc.md
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@@ -6,7 +6,7 @@ include_toc: true
## PRE_VGCC ## PRE_VGCC
- modulation: Intro:
- is expanded and tuned by: [PRESYNAPSE](presynapse.md) - is expanded and tuned by: [PRESYNAPSE](presynapse.md)
Voltage-Controlled Gated Channels: Qui per ora non gestiamo l'evoluzione della depolarizzazione. Alla scomparsa dell'AP, i VGCC smettono di funzionare. Voltage-Controlled Gated Channels: Qui per ora non gestiamo l'evoluzione della depolarizzazione. Alla scomparsa dell'AP, i VGCC smettono di funzionare.