organism/neuron/axon.md

axon.md

Qui comprendiamo:

• AXON: Axon
• PRESYNAPSE: Presynapse
• VGCC-PRE: Voltage-Controlled Gated Channels

AXON: Container

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:

• can be developed by DEV-PRE
• the associations between PRESYNAPSE, BEH-POST e BEH-SYN is performed by the module that instantiate the Neurons and the Atrocytes, for example BEH-EXH or BEH-INH from winnertakeall.

container: AXON

  expansion: PRESYNAPSE ( full: 50x, active: 0x, empty: 10x ) 
    # managed_by: BEH-EXH or BEH-INH from winnertakeall
    # developed_by: DEV-AXO-PRESYNAPSE-TUB from DEV-N

PRESYNAPSE: Container

Discursive description:

The presynapse is the sending terminal of a neuron — a small bulb at the tip of an axon whose job is to release chemical signals, called neurotransmitters (NT), into the synaptic cleft, the narrow gap that separates it from the receiving neuron's postsynapse.

To do this, the presynapse maintains a stockpile of NT packed inside small membrane bubbles called vesicles. These vesicles are organised in two pools: a reserve pool (RP), which is the deep storage, and a readily-releasable pool (RRP), which is the small set of vesicles docked at the membrane and ready to fire immediately. When a spike arrives — an electrical pulse called an action potential — it briefly opens specialised calcium channels (VGCCs) in the membrane. Calcium (Ca²⁺) rushes in, and the sudden local surge of calcium triggers the docked vesicles to fuse with the membrane and pour their NT into the cleft.

But the presynapse does not just release blindly. It runs several interlocking feedback loops that continuously regulate how much it releases, how quickly it recovers, and when it should stop entirely to protect itself.

The amount of Ca²⁺ that enters is itself regulated. Three brakes — CDI, eCB, and mGluR — each reduce the effective number of open channels in their own way and on their own timescale. CDI (calcium-dependent inactivation) is a channel-level self-brake: Ca²⁺ that enters during a spike physically blocks the same channels from reopening, accumulating gradually across repeated spikes. eCB (endocannabinoids) is a retrograde signal synthesised by the receiving neuron when it is over-stimulated; it travels backward across the cleft to suppress the presynaptic channels. mGluR is a presynaptic autoreceptor that senses accumulated NT in the cleft and reduces channel conductance through a slower chemical signalling cascade.

The release of vesicles itself is regulated by two separate NT-sensing mechanisms. One acts locally at the release site in the same millisecond: high NT already in the cleft reduces how many docked vesicles fuse, trimming the current release event. The other is the mGluR pathway described above, which acts more slowly and suppresses the next spike's Ca²⁺ influx rather than the current one.

After release the vesicle stockpile must be replenished. The RRP is refilled from the RP on a timescale of seconds, at a speed that depends on recent calcium history — the synapse replenishes faster when it has been active recently. The RP itself is replenished over minutes via a chemical shuttle from the neighbouring astrocyte, a support cell that recycles the released NT back into a precursor form and ships it back to the presynapse.

The astrocyte is also the gateway to the energy supply. All of the active processes — pumping Ca²⁺ back out, docking vesicles, running the membrane pumps that restore the electrical gradient after each spike — consume ATP, the cell's energy currency. The astrocyte delivers glucose, which sets the rate of ATP replenishment. Under sustained high-frequency firing, this energy demand can outpace supply: ATP falls, the Ca²⁺ pumps slow, residual Ca²⁺ accumulates between spikes, CDI cannot recover, and the VGCCs lock shut. The synapse goes silent — not because it is broken, but because it is protecting itself from the toxic consequence of uncontrolled Ca²⁺ overload, a process known as excitotoxicity. This self-imposed silence is the central emergent behaviour we want to comprehend.

The presynapse does not release blindly. Its behaviour is governed by three interlocking closed loops — the NT loop, the Ca²⁺ loop, and the ATP loop — each operating on a different timescale and each feeding back on the others.

---

The NT loop is the supply chain of the synapse, operating across all three timescales.

• On the millisecond scale, action potentials trigger Ca²⁺-driven release of NT from the RRP into the cleft. NT in the cleft feeds back on itself within the same millisecond — high cleft concentration suppresses further release, acting as a local brake.
• On the seconds scale, the astrocyte's EAATs actively clear NT from the cleft, and the accumulated clearance load drives the IP3 signal that tells the astrocyte how hard the synapse has been working. EEATs only captures 30% of NT?. The rest is dispersed.
• On the minutes scale, the astrocyte converts the captured glutamate into glutamine and ships it back to the presynapse, which repackages it into vesicles and restores the RP. The RP then feeds the RRP on the seconds scale via Ca²⁺-trace-gated recruitment.
• The loop closes when those recycled vesicles are released again at the next burst.
• The critical asymmetry is timescale: release takes milliseconds, full replenishment takes minutes. Sustained firing depletes faster than the loop can replenish.

The Ca²⁺ loop is the timing and intensity controller of the synapse, operating entirely within the millisecond scale with a slow integration tail that reaches into seconds.

• Ca²⁺ enters through VGCCs at every spike and immediately drives two things in parallel:
  • vesicle release (the higher the Ca²⁺, the more vesicles fuse)
  • the Tr_Ca trace integrator (which accumulates the recent Ca²⁺ history).
• Ca²⁺ is then cleared by a single slow decay term, returning toward baseline between spikes.
• The loop closes through Tr_Ca: a high trace — reflecting a recent burst — accelerates RP→RRP recruitment in the seconds loop, meaning that Ca²⁺ activity directly speeds up the resupply of the very vesicles that Ca²⁺ triggered.
• The Ca²⁺ loop is also where the eCB retrograde signal from the postsynapse intersects: sustained postsynaptic depolarisation generates eCB on the seconds scale, which travels back and suppresses VGCC opening at the next spike, reducing Ca²⁺ influx. This makes the Ca²⁺ loop the primary interface between the presynapse and the postsynapse — it is the channel through which the receiving neuron tells the sending terminal to ease off.

The ATP loop (not included in the coprehension yet) is the metabolic backbone of the synapse, operating on the minutes scale but with consequences that reach back into every millisecond.

• ATP is consumed continuously by three processes:
  • the Na/K-ATPase pump that restores the membrane gradient after each spike (the largest cost, proportional to firing rate)
  • the PMCA and SERCA pumps that clear Ca²⁺ from the cytosol
  • the molecular machinery that docks and primes vesicles for release.
• These costs accumulate in an ATP demand register that grows with every spike and every Ca²⁺ clearance event in the millisecond loop.
• The creation side of the loop runs on the minutes scale and is entirely astrocyte-dependent. The astrocyte delivers glucose from the bloodstream to both itself and the presynapse. Glucose enters glycolysis and the mitochondrial oxidative phosphorylation chain, producing ATP. The astrocyte also produces lactate as an intermediate, which it shuttles directly to the presynaptic terminal as an additional fuel source. The rate of ATP production is therefore set by glucose availability — the root input of the loop.
• The loop closes through Ca²⁺ clearance. If firing is sustained long enough that ATP demand outpaces glucose-driven production, ATP falls, the PMCA and SERCA pumps slow, and residual Ca²⁺ builds between spikes. This elevated residual Ca²⁺ suppresses CDI recovery, causing VGCCs to gradually lock shut and silencing the synapse. Silence stops consuming ATP, allowing the production side to catch up and ATP to recover. The ATP loop therefore has a natural self-resetting property: the same mechanism that causes silence also triggers recovery.
• The ATP loop intersects both other loops. It shares Ca²⁺ clearance with the Ca²⁺ loop — pump failure is what connects ATP depletion to VGCC inactivation. It shares the glutamine shuttle with the NT loop — when the astrocyte is energy-starved, conversion efficiency falls and RP replenishment slows, making vesicle depletion more severe and prolonged. ATP depletion is therefore the single point of failure that can cascade across all three loops simultaneously, which is why it is the mechanistic basis of excitotoxic protection.

---

Behaviors:

— ms:

• AP fires → membrane jumps to peak, decays toward rest (Na/K-ATPase)
• ATP cost charged per AP (Na/K-ATPase recharge)
• Ca²⁺ enters via VGCCs, gated by CDI, eCB, and mGluR suppression
• Ca²⁺ buffered by calbindin / calmodulin (fast capture, slow release)
• Ca²⁺ cleared by NCX (always), PMCA and SERCA (ATP-dependent)
• ATP cost charged per unit Ca²⁺ extruded by PMCA and SERCA
• SERCA loads Ca_ER store as a side-effect of clearance
• CDI rises with Ca²⁺ — only during spike (channels open and Ca²⁺ entering)
• CDI recovers every ms — rate suppressed when Ca²⁺ is high (self-locking)
• Ca²⁺ trace (Tr_Ca) integrates every ms, including between spikes
• Vesicles release from RRP — driven by Ca²⁺ Hill sensor, suppressed by NT_cleft
• NT added to cleft
• NT_released_this_window accumulates (feeds mGluR and IP3 in seconds loop)
• NT passively diffuses out of cleft (physical, not astrocyte)
• Observed behaviors: -- STD: exhaustion of NT momentarly stops presynapse from releasing NT -- STP: Ca2+ left in the presynapse beteween spikes primes next NT release.

— seconds:

• Astrocyte EAATs actively clear 30% of remaining NT_cleft
• IP3 integrates NT_released_this_window (cumulative burst load)
• If IP3 exceeds threshold → astrocyte Ca²⁺ wave triggered
• mGluR autoreceptor activation updates from NT_released_this_window
• eCB retrograde signal updates from V_post history (postsynaptic input)
• RP → RRP recruitment runs (rate gated by Tr_Ca, costs ATP)
• NT_released_this_window resets to zero

— mins:

• ATP_demand (accumulated from ms loop) reduces ATP_level
• ATP_demand resets to zero
• Glucose level sets metabolic health and conversion_efficiency
• conversion_efficiency gates glutamine shuttle throughput
• Glutamine shuttle refills N_RP from astrocyte store

---

Semplified comprehension:

In this comprehension, we decide to simplify:

• The VCGG are active while the AP is active, we do not comprehend the Voltage increase and decay
• We do not comprehend the ATP
• We do not comprehend CDI, we check just for Ca2+ concentration
• We do not comprehend mGlur, we check for the concentration of NT in the cleft
• We do not comprehend Ca2+ buffering
• We do not comprehend PMCA, NCX, and SERCA, we comprehend Ca2+ clearing as a slow process
• We do not comprehend vesicles, we comprehend them as processes releasing NT, fast, mediumness and slow based on conditions

The simplification impies that:

• Removing CDI and mGluR means Ca²⁺ concentration and NT in the cleft are now the only two conditions controlling release rate.
• Removing ATP removes the metabolic silencing cascade entirely. The mins behavior now only does one thing: replenish the NT reserve. If we want the synapse to still be able to fail under sustained firing, the mechanism would have to come from NT depletion alone (RP exhausted, nothing to replenish) rather than from pump failure and Ca²⁺ accumulation.
• "Ca²⁺ cleared slowly" replaces PMCA, NCX, and SERCA with a single exponential decay. This means Ca²⁺ will still accumulate under high firing if the decay is slow relative to the spike rate, which preserves some of the residual-Ca²⁺ dynamic even without the full pump machinery.

Simplified Behaviors:

— ms:

• AP fires → VGCCs open, Ca²⁺ enters
• Ca²⁺ cleared slowly (single decay term, no pump detail)
• Ca²⁺ trace (Tr_Ca) integrates every ms
• NT released into cleft — rate determined by Ca²⁺ level and NT already in cleft
• NT released accumulates (feeds sec behavior)
• NT passively diffuses out of cleft
• Observed behaviors: -- STD: exhaustion of NT momentarly stops presynapse from releasing NT -- STP: Ca2+ left in the presynapse beteween spikes primes next NT release.

— seconds:

• Astrocyte EAATs clear 30% of remaining NT in the cleft (Atrocyte behavior)
• eCB retrograde signal updates from postsynapsis (postsynaptic input)
• eCB suppresses NT release (feeds back into ms behavior release rate)
• RP → RRP recruitment runs (rate gated by Tr_Ca)
• NT released in sec resets to zero

— mins:

• Glucose level sets base conversion_efficiency (Atrocyte behavior)
• If astrocyte wave was triggered → conversion_efficiency boosted temporarily
• Glutamine shuttle refills NT reserve from astrocyte store (faster if wave active, baseline if not)
• Wave boost decays back to baseline over subsequent cycles

---

Tubs:

• Ca2+: Calcium Ion entering the Presynapse when VCGG open that influence NT release. Normally returns to ~0 between spikes; stays elevated when pumps fail. They are key to check the concentration, release NT and modulation
• Rrp: Readily Releasable Pool: The Readily Releasable Pool consists of the vesicles that are "docked" and "primed" at the active zone of the synapse. This pool is very small (usually only about 0.5% to 5% of total vesicles) and can be exhausted quickly during high-frequency firing, leading to "short-term depression" of the signal. Here we consider them as NT ready to be released.
• Rp: Reserve Pool: The bulk of the vesicles held further back in the terminal, often tethered by a protein called synapsin. These are only mobilized during intense, prolonged stimulation. This makes up the vast majority of the vesicles (up to 80% or 90%). Here we consider them NT in reserve that can be transfered to RRP and created using Glutamine from Astorcyte.
• NT: Neuro Transmitter, released in the synapse by the vescicles. The release increses NT and decreases RRP
• CaTraces: sono le tracce di permanenza della concentrazione di Ca2+. Servono alla modulazione (TUN)
• eCB: retrograde signal updates from postsynapsis (postsynaptic input)

---

container: PRESYNAPSE

  expansion: VGCC-PRE ( full: 10x, active: 5x, empty: 2x )

  tub_local:
    - Ca2+ ( full: 60x, active: 30x, empty: 0x )
       # developed_by: DEV-PRE-CA2+FULL from DEV.N

    - Rrp ( full: 30x, active: 15x, empty: 0x )
       # developed_by: DEV-PRE-RRP-FULL from DEV.N

    - Rp ( full: 30x, active: 15x, empty: 0x )
       # developed_by: DEV-PRE-RRP-FULL from DEV.N

    - CaTraces ( full: 50x, active: 0x, empty: 0x )

  tub_intricated:
    - NT # SYN
    - ATP? # 
    - eCB # from POST

  context_intricated:
  - AP ( contained_by: BEH-SOMA ) 

ms: behaviors

AP-RRPConcentration: Context

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 deve essere MOLTO piu' basso della durata di un 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'.

context: AP-RRPConcentration
  contained_by: PRESYNAPSE

  in_context: AP
  rf: ( active: 60x )

  condition: (Rrp mediumness) 
    out_context: RRPmediumness

  condition: (Rrp fullness) 
    out_context: RRPFull

AP-Ca2+Concentration: Context

Qui controlliamo la concentrazione nel contesto di un AP.

context: AP-Ca2+Concentration
  contained_by: PRESYNAPSE

  in_context: AP
  rf: ( active: 60x )

  condition: (Ca2+ mediumness) 
    out_context: Ca2+mediumness

  condition: (Ca2+ fullness) 
    out_context: Ca2+Full

NTrelease

Non consideriamo le vesicles come liberate, ma direttamente gli NT. Questo permette di gestire la quantita' rilasciata di NT, invece di gestire un numero di vescicles. Nella realta' ciascuna vesicle contiene migliaia di NT. Qui mettiamo un floor a questo tipo di comprensione.

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.

NTreleaseMaximum: Episode

NT empty

episode: NTreleaseMaximum
  contained_by: PRESYNAPSE

  in_context: (Ca2+Full AND RRPFull)
  rf: ( active: 3x ) # Maximum

  hypothesis: NOT (NT empty)
    action: [Rrp decrease, Nt increase, ATP decrease]
    trace: None

NTreleaseHigh: Episode

Solo in questo caso NT modera! NT NOT empty

episode: NTreleaseHigh
  contained_by: PRESYNAPSE

  in_context: (Ca2+Full AND RRPFull)
  rf: ( active: 6x ) # High

  hypothesis: NOT (NT empty) 
    action: [Rrp decrease, Nt increase, ATP decrease]
    trace: None

NTreleaseMediumness: Episode

In tutti i casi di NT

episode: NTreleaseMediumness
  contained_by: PRESYNAPSE

  in_context: (Ca2+Full AND RRPMediumness) OR (Ca2+Mediumness AND RRPFull)
  rf: ( active: 9x ) # Mediumness

  hypothesis: (NT empty) OR NOT (NT empty) 
    action: [Rrp decrease, Nt increase, ATP decrease]
    trace: None

NTreleaseLow: Episode

In tutti i casi di NT

episode: NTreleaseLow
  contained_by: PRESYNAPSE

  in_context: (Ca2+Mediumness AND RRPMediumness)
  rf: ( active: 12x ) # Low

  hypothesis: (NT empty) OR NOT (NT empty)
    action: [Rrp decrease, Nt increase, ATP decrease]
    trace: None

CaClearance

Qui eliminiamo Ca2+. Non comprendiamo per ora:

• PMCA: primary, ATP-dependent
• NCX: fast, NOT ATP-dependent
• SERCA: slowest, ATP-dependent

Quindi non comprendiamo anche il ristabilimento del Voltage, con altri Ioni entranti e uscenti, per ora tutto dipende da AP del SOMA.

Abbiamo il caso di clearance nel contesto di un AP e non nel contesto di AP, per eliminare il Ca2+ fra le spike.

AP-CaClearanceHigh: Episode

episode: AP-CaClearanceHigh
  contained_by: PRESYNAPSE

  in_context: Ca2+Full
  rf: ( active: 3x ) # High

  hypothesis: NOT (Ca2+ empty)
    action: [Ca2+ decrease]
    trace: None

AP-CaClearanceMediumness: Episode

episode: AP-CaClearanceMediumness
  contained_by: PRESYNAPSE

  in_context: Ca2+Mediumness
  rf: ( active: 6x ) # mediumness

  hypothesis: NOT (Ca2+ empty)
    action: [Ca2+ decrease]
    trace: None

NotAP-CaClearance: Episode

episode: NotAP-CaClearance
  contained_by: PRESYNAPSE

  in_context: NOT AP
  rf: ( active: 24x ) # Low

  hypothesis: NOT (Ca2+ empty)
    action: [Ca2+ decrease]
    trace: None

CaTraces accumulation

Serve a dare la velocita' al trasporto di vesicles da RP a RRP. The biological meaning is that a synapse that has just been through a burst is primed for fast recovery — the molecular machinery for vesicle docking is already engaged, calcium-dependent priming factors are still elevated, and the system is in a ready state. A synapse that has been silent for several seconds has cooled down and replenishes slowly.

So after one second of silence CaTrace 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.

The result is that Tr_Ca encodes not the instantaneous calcium level but the recent history of calcium activity — a smoothed, time-averaged measure of how active the synapse has been over the past one to two seconds.

CaTracesAccumulationFast: Episode

episode: CaTracesAccumulationFast
  contained_by: PRESYNAPSE

  in_context: Ca2+Full
  rf: ( active: 12x ) # fast

  hypothesis: (Ca2+ fullness)
    action: [CaTrace increase]
    trace: None

CaTracesAccumulationSlow: Episode

episode: CaTracesAccumulationSlow
  contained_by: PRESYNAPSE

  in_context: Ca2+Full
  rf: ( active: 24x ) # Slow

  hypothesis: (Ca2+ mediumness)
    action: [CaTrace increase]
    trace: None

sec: behaviors

CheckConditionsPreSec: Context

Contestualizziamo in maniera Fixed ogni mezzo secondo?

context: CheckConditionsPreSec
  contained_by: PRESYNAPSE

  in_context: Fixed
  rf: ( active: 600x )

  condition: NOT (RP empty) AND NOT (RRP full)
    out_context: RPShuttle

  condition: NOT (CaTrace empty) 
    out_context: CaTracesNotEmpty

  condition: NOT (eCB empy) 
    out_context: eCBNotEmpty

eCB clearance: Episode

eCB dipende da POST. Tende a modulare l'entrata di Ca2+ degli VGCC.

Qui non facciamo un flush di eCB, riduciamo ogni mezzo secondo (context) di un RF di questo episodio.

episode: eCBClearance
  contained_by: PRESYNAPSE

  in_context: eCBNotEmpty
  rf: ( active: 24x ) # Slow

  hypothesis: NOT (eCB empty)
    action: [eCB decrease]
    trace: None

CaTraces clearance: Episode

Qui non facciamo un flush di Catrace, riduciamo ogni mezzo secondo (context) di un RF di questo episodio.

episode: CaTracesClearance
  contained_by: PRESYNAPSE

  in_context: CaTracesNotEmpty
  rf: ( active: 24x ) # Slow

  hypothesis: NOT (CaTrace empty)
    action: [CaTRace decrease]
    trace: None

RPShuttling

This happens in the seconds loop, once per second.

RPShuttleSlow: Episode

The "Hard Bottleneck" State. Recruitment is throttled by a lack of signal, a lack of supply, or a lack of space. If even one of these "Near-Stop" conditions is met, the rate cannot exceed "Slow," regardless of the other two conditions.

Rate: 0.00 – 0.25

episode: RPShuttleSlow
  contained_by: PRESYNAPSE

  in_context: RPShuttle
  rf: ( active: 48x ) # Slow

  hypothesis: (CaTrace emptiness) OR (RP emptiness) OR (RRP fullness)  
    action: [RP decrease, RRP increase]
    trace: None

RPShuttleModerate: Episode

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

episode: RPShuttleModerate
  contained_by: PRESYNAPSE

  in_context: RPShuttle
  rf: ( active: 24x ) # Slow

  hypothesis: ((CaTrace mediumness) AND (RP mediumness) AND (RRP mediumness)) OR 
              ((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 mediumness) AND (RRP emptiness)) # vacancy boost
    action: [RP decrease, RRP increase]
    trace: None

RPShuttleFast: Episode

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

episode: RPShuttleFast
  contained_by: PRESYNAPSE

  in_context: RPShuttle
  rf: ( active: 12x ) # Fast

  hypothesis: ((CaTrace fullness) AND (RP fullness) AND (RRP mediumness)) OR # signal + supply
              ((CaTrace fullness) AND (RP mediumness) AND (RRP emptiness)) OR # signal + vacancy
              ((CaTrace mediumness) AND (RP fullness) AND (RRP emptiness)) # supply + vacancy
    action: [RP decrease, RRP increase]
    trace: None

RPShuttleMaximal: Episode

The "Total Recovery" State. All systems are at their theoretical peak for speed.

Rate: 2.50 – 5.00

episode: RPShuttleMaximal
  contained_by: PRESYNAPSE

  in_context: RPShuttle
  rf: ( active: 6x ) # Maximal

  hypothesis: (CaTrace fullness) AND (RP fullness) AND RRP (emptiness)
    action: [RP decrease, RRP increase]
    trace: None

min: behaviors

Refill RP from Glutamine

This happens in the minutes loop, once per minute, via the glutamine shuttle from the astrocyte. It is a two-step process across two cells.

Step 1 — astrocyte side The astrocyte has been accumulating cleared glutamate from the cleft since the last minutes-loop execution. Its glutamine synthetase enzyme converts that glutamate into glutamine, filling the Glutamine_pool. The fraction successfully converted per cycle is conversion_efficiency, which is set by glucose availability and boosted temporarily if the astrocyte calcium wave fired during the preceding seconds:

refill_RP = Glutamine_pool * conversion_efficiency Glutamine_pool = max(0.0, Glutamine_pool - refill_RP)

Step 2 — presynapse side

The glutamine crosses into the presynapse, where glutaminase converts it back into glutamate. That glutamate is immediately repackaged into vesicles and added to N_RP:

The asymmetry that makes depletion possible:

The chain reveals why sustained high-frequency firing eventually depletes the synapse even with all replenishment mechanisms running.

The RRP holds at most Max_RRP = 20 vesicles. At 20 Hz with strong Ca²⁺, release can draw 2-4 vesicles per spike — potentially exhausting the RRP in under a second. The seconds loop can move vesicles from RP to RRP at a maximum rate of k_rec_fast = 5 /s, meaning at most 5 vesicles per second under ideal conditions. Release outpaces recruitment by roughly an order of magnitude during a burst.

The RP holds up to Max_RP = 200 vesicles — ten times the RRP. At sustained 20 Hz the RP can sustain firing for tens of seconds even after the RRP is repeatedly emptied, as long as recruitment keeps pace. But the minutes loop only refills N_RP once per minute at a rate limited by Glutamine_pool * conversion_efficiency. If glucose is low or the astrocyte wave has not fired, this replenishment may add only a fraction of what was consumed.

The result is a three-tier buffer with mismatched timescales:

RRP — depletes in seconds, refilled in seconds (fast but shallow) RP — depletes in minutes, refilled in minutes (deep but slow) Gln — depletes over bursts, refilled by glucose (slowest, astrocyte-dependent)

Each tier buys time for the one below it to respond. When all three are depleted simultaneously — which only happens under prolonged high-frequency firing with insufficient glucose — the synapse has no remaining buffer and goes silent until the minutes loop restores the Glutamine_pool.

VGCC-PRE-TUN: Tuner

tuner: VGCC-PRE-TUN

 contained_by: PRESYNAPSE

 tunes: PRESYNAPSE/expansion/PRESYNAPSE-VCGG
  
 tub_modulation: # in TUN agiamo su POS/ACT
   - posMod ( fullness: None, active: PRESYNAPSE-VCGG/fullness, empty: 0x)  # riferimento a possible di PRESYNAPSE-VCGG
   - actMod ( fullness: None, active: PRESYNAPSE-VCGG/active, empty: PRESYNAPSE-VCGG/emptiness)  # riferimento a active di PRESYNAPSE-VCGG
# qui stiamo modulando possible e actual di PRESYNAPSE-VCGG associandoli
# a posMod e actMod. Non serve associare una fullness perche' 
# la modulazione e' una pompa fra posMod e actMod e controlliamo
# solo empty

 context_intricated:
  - TunPossible ( contained_by: DAY-N )

 tub_local:

 tub_intricated:

Context

context: Check
  contained_by: VGCC-PRE-TUN

  in_context: TunPossible
  rf: ( active: 60x )

  condition:  
  out_context: TunPreVcgg

Episode

episode: Tun
  contained_by: VGCC-PRE-TUN

  in_context: TunPreVcgg
  rf: ( active: x )

 hypothesis:  
  action: 
  trace: 

VGCC-PRE: Container

Voltage-Controlled Gated Channels: Qui per ora non gestiamo l'evoluzione della depolarizzazione. Alla scomparsa dell'AP, i VGCC smettono di funzionare.

container: VGCC-PRE

  tub_intricated:
    - Ca2+ ( contained_by: PRESYNAPSE )

  context_intricated:
    - AP ( contained_by: BEH-SOMA )

ms: behavior

Ca2+enter

Here we comprehend the breaking activity on VGCC by: CDI,eCB and mGluR:

Qui sostituiamo:

• CDI con concentrazione Ca2+ -- 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. -- 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.

• mGluR con concentrazione NT (forse su tempi di sec e quindi avremmo bisono di un altro Tub)

• Open — zero active brakes. mGluR alone never escapes this group because its ceiling is alpha_mGluR = 0.4, meaning even at full it only removes 40% of conductance, leaving 60% — still above the 85% threshold. So mGluR is irrelevant to the open/not-open boundary. Only CDI and eCB decide.

• Reduced/partial — exactly one meaningful brake active. Either CDI has started building (mediumness), or eCB has risen from sustained postsynaptic activity, but not both simultaneously. The system is aware something is happening but has not compounded yet. This is the normal operating range during moderate sustained firing.

• Suppressed — two brakes multiplying. The compounding is what defines this zone — no single variable alone produces it (except CDI approaching full). 0.5 × 0.5 = 0.25 remaining is where the synapse starts losing significant transmission efficacy. Biologically this is the pre-silence warning zone: CDI is building from residual Ca²⁺ while eCB is already engaged from postsynaptic activity.

• Closed — CDI = full is the only reliable hard rule. Because CDI can reach 1.0 and appears as (1 - CDI_factor) in the formula, it alone drives conductance to zero regardless of eCB and mGluR state. The three-brake overlap corner case (eCB=full + CDI=mediumness + mGluR=full) also reaches here, but in practice CDI reaching full is the primary biological mechanism.

Devo controllare che le condizioni sotto siano esaustive.

Ca2+enterOpen: Episode

episode: Ca2+enterOpen
  contained_by: VGCC-PRE

  in_context: AP
  rf: ( active: 6x )

  hypothesis: (Ca2+ empty) and (eCB empty)
    action: [Ca2+ increase, ATP decrease]
    trace: None

Ca2+enterReduced-partial: Episode

episode: Ca2+enterReduced-partial
  contained_by: VGCC-PRE

  in_context: AP
  rf: ( active: 6x )

  hypothesis: (Ca2+ mediumness) OR ((eCB mediumness) AND (Ca2+ empty)) OR ((eCB full) AND (Ca2+ empty) AND (mGluR empty))
    action: [Ca2+ increase, ATP decrease]
    trace: None

Ca2+enterSuppressed: Episode

episode: Ca2+enterSupressed
  contained_by: VGCC-PRE

  in_context: AP
  rf: ( active: 6x )

  hypothesis: ((Ca2+ mediumness) AND (eCB full) OR (eCB mediumness))
    action: [Ca2+ increase, ATP decrease]
    trace: None