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cdi traces

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ocrampal
2026-03-22 16:28:09 +01:00
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neuron/BEH-AXO.md
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@@ -39,7 +39,7 @@ container: BEH-AXO
-- CDI rises with Ca2+ each ms: accumulates across inter-spike intervals under pump failure
-- CDI recovers when Ca2+ is low: rate -> 0 when Ca2+ is high — the self-locking feedback
- Ca²⁺ trace integrates toward CaTraces
- Vesicles release from RRP, based on CaMicro and RRP, suppressed by NT_cleft
- Vesicles release from RRP, based on Ca2+ and RRP, suppressed by NT_cleft
- NT added to cleft
- NT_released_this_window accumulates (feeds Medium)
- NT passively diffuses out of cleft (Astrocyte behavior)
@@ -133,25 +133,25 @@ context: RRPConcentration
out_context: RRPFull
```
#### Ca2MicroConcentration: Context
#### Ca2+Concentration: Context
```Gen
context: Ca2MicroConcentration
context: Ca2+Concentration
contained_by: BEH-PRE
in_context: AP
rf: ( active: 60x )
condition: (Ca2Micro medium)
out_context: Ca2MicroMedium
condition: (Ca2+ medium)
out_context: Ca2+Medium
condition: (Ca2Micro full)
out_context: Ca2MicroFull
condition: (Ca2+ full)
out_context: Ca2+Full
```
#### NTrelease: Episodes
Ci sono 4 casi che dipendono da RRP, Ca2+ e NT. L'idea e' che la quantita' di RRP sia il driver principale. Gli NT liberati sono di piu' al crescere di RRP e CaMicro e di meno al crescere di NT. 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 NT. 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 al crescere di NT. 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.
ATP cost of Na/K-ATPase recharge on each AP. The cost is per action potential. Here we charge it at every release of NT. This is the dominant ATP drain at high firing rates.
@@ -161,7 +161,7 @@ ATP cost of Na/K-ATPase recharge on each AP. The cost is per action potential. H
episode: NTreleaseMaximum
contained_by: BEH-PRE
in_context: (Ca2MicroFull AND RRPFull)
in_context: (Ca2+Full AND RRPFull)
rf: ( active: 6x ) # Maximum
hypothesis: (NT empty)
@@ -175,7 +175,7 @@ episode: NTreleaseMaximum
episode: NTreleaseHigh
contained_by: BEH-PRE
in_context: (Ca2MicroFull AND RRPFull)
in_context: (Ca2+Full AND RRPFull)
rf: ( active: 6x ) # High
hypothesis: NOT (NT empty) # solo in questo caso NT modera!
@@ -189,7 +189,7 @@ episode: NTreleaseHigh
episode: NTreleaseMedium
contained_by: BEH-PRE
in_context: (Ca2MicroFull AND RRPMedium) OR (Ca2MicroMedium AND RRPFull)
in_context: (Ca2+Full AND RRPMedium) OR (Ca2+Medium AND RRPFull)
rf: ( active: 6x ) # Medium
hypothesis: (NT empty) OR NOT (NT empty) # In tutti i casi
@@ -203,7 +203,7 @@ episode: NTreleaseMedium
episode: NTreleaseLow
contained_by: BEH-PRE
in_context: (Ca2MicroMedium AND RRPMedium)
in_context: (Ca2+Medium AND RRPMedium)
rf: ( active: 6x ) # Low
hypothesis: (NT empty) OR NOT (NT empty) # In tutti i casi
@@ -233,9 +233,36 @@ Limita rilascio NT: Dipende da quanti NT sono stati gia' rilasciati nella Syn
Limita rilascio NT: Dipende da POST che tende a bloccare rialascio di NT se non servono
#### CDI/CaTraces concentration
#### CDIs concentration
Limita rilascio NT: Dipende dalla concentrazione alta di Ca2+ nella PRE.
probabilmente sta dentro VGCC? Possiamo metterlo come un controllo su fullness di Ca2+ e cmq spiegare che e' un floor a questo comportamento di CDI
CDI is calcium-dependent inactivation of VGCCs. The inactivation happens because Ca²⁺ enters through the channel and binds to a calmodulin tethered to the channel's intracellular face, physically blocking it from reopening. This is a local, channel-specific event — it requires Ca²⁺ to be flowing through that channel right now, not residual Ca²⁺ drifting in the cytosol between spikes.
So the rise increment should only fire when V_pre == 1 (the spike window when channels are actually open and Ca²⁺ is entering). The recovery, by contrast, should run every millisecond unconditionally — CDI de-inactivation is a continuous process that proceeds whenever Ca²⁺ dissociates from calmodulin, which depends on the ambient Ca_micro level at all times.
Limita rilascio NT: Dipende dalla concentrazione alta di Ca2+ nella PRE. Driver Ca2+ > 0 between spikes CDI -> 1, effective_conductance -> 0.
```Gen
context: CDIConcentration
contained_by: BEH-PRE
in_context: NOT AP # prima volta NOT in un contesto
rf: ( active: 60x )
condition: (Ca2+ full)
out_context: IncreaseCDIFast
condition: (Ca2+ medium)
out_context: IncreaseCDIMedium
condition: (Ca2+ empty)
out_context: DecreaseCDI
```
#### CaTrace concentration
Serve a dare la velocita' al trasporto di vesicles da RP a RRP. Ha un decadimento proprio il che dice alla Presinapsi di accellerare se da poco c'e' stata una spike, altrimenti di andare piu' piano. So after one second of silence Tr_Ca has fallen to ~37% of its peak value, after two seconds to ~14%, after three seconds to ~5%. It asymptotes toward zero but never exactly reaches it. Between spikes, Ca2+ falls toward zero as the pumps clear it.
#### RP->RRP shuttling