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Sergio Marchetti
2026-04-25 15:19:18 +00:00
parent 8107bff7d5
commit 15489815a7
1 changed files with 60 additions and 87 deletions
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neuron/axon.md
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@@ -86,7 +86,7 @@ VGCC-PRE
-- Ca Influx -- Ca Influx
Ca2+enterLow: interacting Ca2+enterLow: interacting
Ca2+enterMedium: interacting Ca2+enterMedium: interacting
Ca2+enterSuppressed: interacting Ca2+enterHigh: interacting
``` ```
@@ -109,13 +109,10 @@ container: PRESYNAPSE
tub_local: tub_local:
- Ca2+ ( full: 60x, active: 30x, empty: 0x ) - Ca2+ ( full: 60x, active: 30x, empty: 0x )
# developed_by: DEV-PRE-CA2+FULL from DEV.N # developed_by: DEV-PRE-CA2+FULL from DEV.N
- Rrp ( full: 30x, active: 15x, empty: 0x ) - Rrp ( full: 30x, active: 15x, empty: 0x )
# developed_by: DEV-PRE-RRP-FULL from DEV.N # developed_by: DEV-PRE-RRP-FULL from DEV.N
- Rp ( full: 30x, active: 15x, empty: 0x ) - Rp ( full: 30x, active: 15x, empty: 0x )
# developed_by: DEV-PRE-RRP-FULL from DEV.N # developed_by: DEV-PRE-RRP-FULL from DEV.N
- CaTraces ( full: 50x, active: 0x, empty: 0x ) - CaTraces ( full: 50x, active: 0x, empty: 0x )
tub_intricated: tub_intricated:
@@ -129,8 +126,7 @@ container: PRESYNAPSE
### ms: behaviors ### ms: behaviors
#### PRE_Status_ms: check_tpc #### PRE_Status_ms: check_tpc !!! DA ELINMINARE !!!
Il rilascio di NT lo facciamo nel contesto di AP. Biologicamente dovrebbe avvenire solo in base alle concentrazioni, quindi anche al difuori degli AP. Il rilascio di NT lo facciamo nel contesto di AP. Biologicamente dovrebbe avvenire solo in base alle concentrazioni, quindi anche al difuori degli AP.
RF di interacting deve essere MOLTO piu' basso di un RF di AP. In maniera da essere attivo varie volte nel contesto di un episodio di AP. Il che ha senso perche' un AP e' SOMA ad un tempo piu' alto che i comportamenti di PRE. Questo poi per permettere la diversa contestualizzazione degli episodi di NTrelease, a piu' o meno alta velocita'. RF di interacting deve essere MOLTO piu' basso di un RF di AP. In maniera da essere attivo varie volte nel contesto di un episodio di AP. Il che ha senso perche' un AP e' SOMA ad un tempo piu' alto che i comportamenti di PRE. Questo poi per permettere la diversa contestualizzazione degli episodi di NTrelease, a piu' o meno alta velocita'.
@@ -163,35 +159,20 @@ Non consideriamo le vesicles come liberate, ma direttamente gli NT. Questo perme
Ci sono 4 casi che dipendono da RRP, Ca2+ e indirettamente da concentrazione di NT nella SYN che diventa mGLur che limita in VGCC l'entrata di Ca2+. L'idea e' che la quantita' di RRP sia il driver principale. Gli NT liberati sono di piu' al crescere di RRP e Ca2+ e di meno (indirettamente) al crescere della concentrazione di NT gia' liberati nella SYN. Gli NT nella sinapsi fanno da moderazione alla ulteriore liberazione di NT, ma non bloccano mai totalmente. NT suppression only matters when everything else is already at maximum, which is exactly the biological purpose: it prevents runaway release during peak activity, not during moderate activity. Ci sono 4 casi che dipendono da RRP, Ca2+ e indirettamente da concentrazione di NT nella SYN che diventa mGLur che limita in VGCC l'entrata di Ca2+. L'idea e' che la quantita' di RRP sia il driver principale. Gli NT liberati sono di piu' al crescere di RRP e Ca2+ e di meno (indirettamente) al crescere della concentrazione di NT gia' liberati nella SYN. Gli NT nella sinapsi fanno da moderazione alla ulteriore liberazione di NT, ma non bloccano mai totalmente. NT suppression only matters when everything else is already at maximum, which is exactly the biological purpose: it prevents runaway release during peak activity, not during moderate activity.
##### NTreleaseMaximum: interacting
NT empty. Qui siamo contestualizzati se Ca2+ full, il che dovrebbe significare indirettamente che non ci sono NT nella SYN.
```Gen
interacting: NTreleaseMaximum
contained_by: PRESYNAPSE
in_context: NTreleaseMax_ctx
rf: ( active: 3x ) # Maximum
hypothesis: NOT (NT empty)
action: [Rrp decrease, Nt increase, ATP decrease]
trace: None
```
##### NTreleaseHigh: interacting ##### NTreleaseHigh: interacting
Solo in questo caso NT modera! NT NOT empty, perche' Ca2+ fullness non full. NT empty. Qui siamo contestualizzati se Ca2+ full, il che dovrebbe significare indirettamente che non ci sono NT nella SYN.
```Gen ```Gen
interacting: NTreleaseHigh interacting: NTreleaseHigh
contained_by: PRESYNAPSE contained_by: PRESYNAPSE
in_context: NTreleaseHigh_ctx in_context: AP_ctx
rf: ( active: 6x ) # High rf: ( active: 3x ) # High
hypothesis: NOT (NT empty) hypothesis: ( Ca2+ fullness ) AND ( Rrp fullness ) AND
action: [Rrp decrease, Nt increase, ATP decrease] NOT( ATP empty )
action: [Rrp decrease, NT increase, ATP decrease]
trace: None trace: None
``` ```
@@ -203,10 +184,12 @@ In tutti i casi di NT
interacting: NTreleaseMedium interacting: NTreleaseMedium
contained_by: PRESYNAPSE contained_by: PRESYNAPSE
in_context: NTreleaseMed_ctx in_context: AP_ctx
rf: ( active: 9x ) # Mediumness rf: ( active: 9x ) # Medium
hypothesis: (NT empty) OR NOT (NT empty) hypothesis: (( Ca2+ fullness ) AND ( Rrp mediumness ) OR
( Ca2+ mediumness ) AND ( Rrp fullness )) AND
NOT( ATP empty )
action: [Rrp decrease, Nt increase, ATP decrease] action: [Rrp decrease, Nt increase, ATP decrease]
trace: None trace: None
``` ```
@@ -219,9 +202,12 @@ In tutti i casi di NT
interacting: NTreleaseLow interacting: NTreleaseLow
contained_by: PRESYNAPSE contained_by: PRESYNAPSE
in_context: NTreleaseLow_ctx in_context: AP_ctx
rf: ( active: 12x ) # Low
hypothesis: (NT empty) OR NOT (NT empty) hypothesis: ( Ca2+ mediumness ) AND
( Rrp mediumness ) AND
NOT( ATP empty )
action: [Rrp decrease, Nt increase, ATP decrease] action: [Rrp decrease, Nt increase, ATP decrease]
trace: None trace: None
``` ```
@@ -244,7 +230,7 @@ Abbiamo il caso di clearance nel contesto di un AP e non nel contesto di AP, per
interacting: AP-CaClearanceHigh interacting: AP-CaClearanceHigh
contained_by: PRESYNAPSE contained_by: PRESYNAPSE
in_context: AP in_context: AP_ctx
rf: ( active: 3x ) # High rf: ( active: 3x ) # High
hypothesis: (Ca2+ fullness) hypothesis: (Ca2+ fullness)
@@ -258,7 +244,7 @@ interacting: AP-CaClearanceHigh
interacting: AP-CaClearanceMediumness interacting: AP-CaClearanceMediumness
contained_by: PRESYNAPSE contained_by: PRESYNAPSE
in_context: AP in_context: AP_ctx
rf: ( active: 6x ) # mediumness rf: ( active: 6x ) # mediumness
hypothesis: (Ca2+ mediumness) hypothesis: (Ca2+ mediumness)
@@ -320,7 +306,7 @@ interacting: CaTracesAccumulationSlow
### sec: behaviors ### sec: behaviors
#### PRE_Status_sec: check_tpc #### PRE_Status_sec: check_tpc !!! DA ELINMINARE !!!
Contestualizziamo in maniera Fixed ogni mezzo secondo? Contestualizziamo in maniera Fixed ogni mezzo secondo?
@@ -331,13 +317,13 @@ check_tpc: PRE_Status_sec
in_context: NOT AP_ctx in_context: NOT AP_ctx
rf: ( active: 600x ) rf: ( active: 600x )
condition: NOT (RP empty) AND NOT (RRP full) condition: NOT(RP empty) AND NOT(RRP full)
out_context: RPShuttle_ctx out_context: RPShuttle_ctx
condition: NOT (CaTrace empty) condition: NOT(CaTrace empty)
out_context: CaTracesNotEmpty_ctx out_context: CaTracesNotEmpty_ctx
condition: NOT (eCB empy) condition: NOT(eCB empy)
out_context: eCBNotEmpty_ctx out_context: eCBNotEmpty_ctx
``` ```
@@ -351,7 +337,7 @@ Qui non facciamo un flush di eCB, riduciamo ogni mezzo secondo (context) di un R
interacting: eCBClearance interacting: eCBClearance
contained_by: PRESYNAPSE contained_by: PRESYNAPSE
in_context: eCBNotEmpty_ctx in_context: NOT AP_ctx
rf: ( active: 24x ) # Slow rf: ( active: 24x ) # Slow
hypothesis: NOT (eCB empty) hypothesis: NOT (eCB empty)
@@ -367,7 +353,7 @@ Qui non facciamo un flush di Catrace, riduciamo ogni mezzo secondo (context) di
interacting: CaTracesClearance interacting: CaTracesClearance
contained_by: PRESYNAPSE contained_by: PRESYNAPSE
in_context: CaTracesNotEmpty_ctx in_context: NOT AP_ctx
rf: ( active: 24x ) # Slow rf: ( active: 24x ) # Slow
hypothesis: NOT (CaTrace empty) hypothesis: NOT (CaTrace empty)
@@ -386,72 +372,56 @@ The "Hard Bottleneck" State. Recruitment is throttled by a lack of signal, a lac
Rate: 0.00 – 0.25 Rate: 0.00 – 0.25
```Gen ```Gen
interacting: RPShuttleSlow interacting: RPShuttleLow
contained_by: PRESYNAPSE contained_by: PRESYNAPSE
in_context: RPShuttle_ctx in_context: NOT AP_ctx
rf: ( active: 48x ) # Slow rf: ( active: 48x ) # Low
hypothesis: (CaTrace emptiness) OR (RP emptiness) OR (RRP fullness) hypothesis: (CaTrace emptiness) OR
(RP emptiness) OR
(RRP fullness)
action: [RP decrease, RRP increase] action: [RP decrease, RRP increase]
trace: None trace: None
``` ```
##### RPShuttleModerate: interacting ##### RPShuttleMedium: interacting
The "Sub-Optimal" State. The machinery is working, but it's held back by partial limitations. This covers cases where the signal is steady but the "piston" isn't firing at full speed, or where a high vacancy in the RRP (emptiness) forces a low signal to work a bit harder. The "Sub-Optimal" State. The machinery is working, but it's held back by partial limitations. This covers cases where the signal is steady but the "piston" isn't firing at full speed, or where a high vacancy in the RRP (emptiness) forces a low signal to work a bit harder.
Rate: 0.50 – 0.97 Rate: 0.50 – 0.97
```Gen ```Gen
interacting: RPShuttleModerate interacting: RPShuttleMedium
contained_by: PRESYNAPSE contained_by: PRESYNAPSE
in_context: RPShuttle_ctx in_context: AP_ctx
rf: ( active: 24x ) # Slow rf: ( active: 24x ) # Medium
hypothesis: ((CaTrace mediumness) AND (RP mediumness) AND (RRP mediumness)) OR hypothesis: (CaTrace mediumness) AND (RP mediumness) AND (RRP mediumness) OR
((CaTrace fullness) AND (RP mediumness) AND (RRP mediumness)) OR # signal boost (CaTrace fullness) AND (RP mediumness) AND (RRP mediumness) OR # signal boost
((CaTrace mediumness) AND (RP fullness) AND (RRP mediumness)) OR # supply boost (CaTrace mediumness) AND (RP fullness) AND (RRP mediumness) OR # supply boost
((CaTrace mediumness) AND (RP mediumness) AND (RRP emptiness)) # vacancy boost (CaTrace mediumness) AND (RP mediumness) AND (RRP emptiness) # vacancy boost
action: [RP decrease, RRP increase] action: [RP decrease, RRP increase]
trace: None trace: None
``` ```
##### RPShuttleFast: interacting ##### RPShuttleHigh: interacting
The "High Performance" State. Multiple systems are optimized, but one is still at a "mediumness" level. This represents an active synapse that hasn't reached its absolute peak because either the supply is only 50% or the RRP isn't empty enough to create that "maximal vacuum" pull. The "High Performance" State. Multiple systems are optimized, but one is still at a "mediumness" level. This represents an active synapse that hasn't reached its absolute peak because either the supply is only 50% or the RRP isn't empty enough to create that "maximal vacuum" pull.
Rate: 1.25 – 1.94 Rate: 1.25 – 1.94
```Gen ```Gen
interacting: RPShuttleFast interacting: RPShuttleHigh
contained_by: PRESYNAPSE contained_by: PRESYNAPSE
in_context: RPShuttle_ctx in_context: AP_ctx
rf: ( active: 12x ) # Fast rf: ( active: 12x ) # Fast
hypothesis: ((CaTrace fullness) AND (RP fullness) AND (RRP mediumness)) OR # signal + supply hypothesis: (CaTrace fullness) AND (RP fullness) AND (RRP mediumness) OR # signal + supply
((CaTrace fullness) AND (RP mediumness) AND (RRP emptiness)) OR # signal + vacancy (CaTrace fullness) AND (RP mediumness) AND (RRP emptiness) OR # signal + vacancy
((CaTrace mediumness) AND (RP fullness) AND (RRP emptiness)) # supply + vacancy (CaTrace mediumness) AND (RP fullness) AND (RRP emptiness) # supply + vacancy
action: [RP decrease, RRP increase]
trace: None
```
##### RPShuttleMaximal: interacting
The "Total Recovery" State. All systems are at their theoretical peak for speed.
Rate: 2.50 – 5.00
```Gen
interacting: RPShuttleMaximal
contained_by: PRESYNAPSE
in_context: RPShuttle_ctx
rf: ( active: 6x ) # Maximal
hypothesis: (CaTrace fullness) AND (RP fullness) AND RRP (emptiness)
action: [RP decrease, RRP increase] action: [RP decrease, RRP increase]
trace: None trace: None
``` ```
@@ -580,41 +550,44 @@ Devo controllare che le condizioni sotto siano esaustive.
##### Ca2+enterOpen: interacting ##### Ca2+enterOpen: interacting
```Gen ```Gen
interacting: Ca2+enterOpen interacting: Ca2+enterLow
contained_by: VGCC-PRE contained_by: VGCC-PRE
in_context: AP_ctx in_context: AP_ctx
rf: ( active: 6x ) rf: ( active: 12x ) # Low
hypothesis: (Ca2+ empty) and (eCB empty) hypothesis: (Ca2+ empty) AND (eCB empty)
action: [Ca2+ increase, ATP decrease] action: [Ca2+ increase, ATP decrease]
trace: None trace: None
``` ```
##### Ca2+enterReduced-partial: interacting ##### Ca2+enterMedium: interacting
```Gen ```Gen
interacting: Ca2+enterReduced-partial interacting: Ca2+enterMedium
contained_by: VGCC-PRE contained_by: VGCC-PRE
in_context: AP_ctx in_context: AP_ctx
rf: ( active: 6x ) rf: ( active: 6x ) # Medium
hypothesis: (Ca2+ mediumness) OR ((eCB mediumness) AND (Ca2+ empty)) OR ((eCB full) AND (Ca2+ empty) AND (NT empty)) hypothesis: (Ca2+ mediumness) OR
(eCB mediumness) AND (Ca2+ empty) OR
(eCB full) AND (Ca2+ empty) AND (NT empty)
action: [Ca2+ increase, ATP decrease] action: [Ca2+ increase, ATP decrease]
trace: None trace: None
``` ```
##### Ca2+enterSuppressed: interacting ##### Ca2+enterHigh: interacting
```Gen ```Gen
interacting: Ca2+enterSupressed interacting: Ca2+enterHigh
contained_by: VGCC-PRE contained_by: VGCC-PRE
in_context: AP_ctx in_context: AP_ctx
rf: ( active: 6x ) rf: ( active: 3x ) # High
hypothesis: ((Ca2+ mediumness) AND (eCB full) OR (eCB mediumness)) hypothesis: (Ca2+ mediumness) AND (eCB full) OR
(eCB mediumness))
action: [Ca2+ increase, ATP decrease] action: [Ca2+ increase, ATP decrease]
trace: None trace: None
``` ```