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organism/neuron/BEH-AXO.md
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ocrampal 3db11c15a1 nuova PRE
2026-03-19 12:03:22 +01:00

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BEH-AXO.md

Qui comprendiamo:

  • BEH-AXO: Axon
  • BEH-PRE: Presynapse
  • BEH-VCGG: Voltage-Controlled Gated Channels

BEH-AXO: Container

Axon: Axon does not contain specific behavior, here we comprehend it as a “cable” transporting the AP from SOMA to Presynapse. It expands BEH-PRE which:

  • can be developed by DEV-PRE
  • the associations between BEH-PRE, 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: BEH-AXO

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

BEH-PRE: Container

Presynapse: We treat each presynapse as standalone. The vesicle reserve pool is a strictly private, local resource of each individual presynaptic bouton. What is shared between synapses on the same axon are signals (neuromodulators) and metabolic resources (energy), but not the synaptic vesicles themselves.

Behaviors Related to:

  • Voltage (V_pre / membrane state) -- Voltage increase from AP (external spike drive — V_pre = 1) -- Voltage decrease from Na/K-ATPase recharge after each AP (we might need to include in the model)

  • NT (neurotransmitter / vesicle pools) -- NT released from RRP (instead of modeling this as stochastic_release: p = p_release_base *Ca_micro, I'd like to model this as a function of Ca-micro, number of vescicles in RRP, modulated down by NT already released) -- NT replenishment in RRP from RP: (map_trace_to_speed: rate gated by Tr_Ca trace; fast when Tr_Ca > T_high, slow when Tr_Ca < T_low — the Ca2+ trace is the recruitment memory) -- NT replenishment in RP from Astrocyte: (glutamine shuttle: refill_RP = Glutamine_pool * conversion_efficiency, runs once per minute; gated by ATP_level via conversion_efficiency) -- NT degradation / dilution from cleft: (passive: NT_cleft *= 1 - dt/tau_NT_decay each ms) -- NT clearance from cleft by Astrocyte EAATs: (cleared_NT = NT_cleft * 0.3, once per second)

  • VGCC (voltage-gated calcium channels) -- VGCC increase in number by slow activity-dependent upregulation -- VGCC conductance suppressed by eCB (retrograde brake) -- VGCC conductance suppressed by mGluR autoreceptor tracks NT_cleft directly via Michaelis-Menten occupancy, fastest of the three brakes — no postsynaptic relay needed -- VGCC conductance suppressed by CDI (calcium-dependent inactivation) CDI rises with Ca_micro via k_CDI_rise, recovers only when Ca_micro falls — the metabolic silence lock

  • Ca2+ -- Ca2+ intake via VGCC on each AP: only the fraction not captured by buffer enters Ca_micro -- Ca2+ buffered into calbindin / calmodulin (fast, on spike): buffer saturates during sustained bursting: B_free -> 0 -- Ca2+ released back from buffer into cytosol (slow recharge)sustains Ca_micro elevation under pump failure -- Ca2+ extruded by PMCA — primary pump, ATP-dependent: first to fail when ATP drops; largest ATP-dependent clearance term -- Ca2+ extruded by NCX — fast exchanger, NOT ATP-dependent: floor mechanism: keeps clearing during metabolic failure; enables auto-reset when high-frequency drive stops -- Ca2+ pumped into ER by SERCA — slowest pump, ATP-dependent: also loads Ca_ER store; fails alongside PMCA under low ATP -- Ca2+ stored in ER (Ca_ER) (Ca_ER += cleared_SERCA; ER store is a future IP3-release target)

  • CDI (calcium-dependent inactivation of VGCCs) -- CDI rises with Ca_micro each ms: accumulates across inter-spike intervals under pump failure -- CDI recovers when Ca_micro is low: rate -> 0 when Ca_micro is high — the self-locking feedback of CASCADE 5

  • ATP -- ATP decrease by PMCA / SERCA pumping: (each ms of Ca2+ clearance consumes ATP; modelled implicitly via the demand that sustains Glucose_level depletion in Loop 3) -- ATP decrease by vesicle re-docking (RP -> RRP recruitment): (each refill_amount of vesicles moved to RRP costs ATP for priming/docking machinery; modelled implicitly in CASCADE 2 demand) -- ATP decrease by Na/K-ATPase recharge after each AP (largest single ATP cost per spike; drives CASCADE 2 during high firing) -- ATP increase from Astrocyte metabolic support: glucose delivery is the root input — set Glucose_level < 1.0 to engage the full metabolic silencing cascade

Tubs:

  • Ca2+: Calcium Ion entering the Presynapse when VCGG open. They are key to check the concentration, release vescicles and modulation
  • ReadyReleasablePool: Readily Releasable Pool: The Readily Releasable Pool consists of the vesicles that are "docked" and "primed" at the active zone of the synapse.
    -- Location: Directly touching the presynaptic membrane.
    -- Function: These are the first to be released when an action potential arrives.
    -- Characteristics: 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.
  • RecyclingPool: Recycling Pool
    --The Recycling Pool is the next line of reinforcement.
    -- Location: Slightly further back from the membrane than the RRP.
    -- Function: These vesicles maintain release during moderate, physiological levels of stimulation.
    -- Characteristics: They are continuously refilled as the neuron "recycles" the membranes of used vesicles through endocytosis. This pool is larger than the RRP (roughly 5% to 20% of the total).
  • ReservePool: The "Reserve Pool" (The true RP)
    -- In many textbooks, RP specifically stands for the Reserve Pool. -- Location: The bulk of the vesicles held further back in the terminal, often tethered by a protein called synapsin.
    -- Function: These are only mobilized during intense, prolonged stimulation once the RRP and Recycling pools are depleted.
    -- Characteristics: This makes up the vast majority of the vesicles (up to 80% or 90%).
  • Nt: Neuro Transmitter, released in the synapse by the vescicles
  • CaTraces: sono le tracce di permanenza della concentrazione di Ca2+. Servono alla modulazione (TUN)
  • TagRelease: forse non serve, ma indica il rilascio di NT da parte di una Pre.

Behaviors: L'idea e' che:

  • Fast Timing -- i VCGG si aprono all'arrivo di un AP dal SOMA. Il numero dei VCGG presenti e' stato modulato (TUN) in una fase di non attivita' della presynapse
    -- I VCGG fanno entrare Ca2+ che ne aumenta la concentrazione
    -- ad un certo livello di concentrazione, viene liberata una vescica, se ci sono ReadyReleasablePool disponibili. La vescica libera xxx Nt nella sinsapsi
  • Medium timing
    -- clearance dei Ca2+ che depolarizza la Presinapsi
    -- riciclo delle vesciche, prendendole dalla Sinapsi e mettenedole dentro a RecyclingPool
  • Slow Timing -- riempimento vesciche di Nt e mettendole dentro Rp
    -- spostamento da ReservePool a ReadyReleasablePool
container: BEH-PRE

  expansion: BEH-PRE-VGCC ( fullness: 10x, active: 5x, emptiness: 2x )
              # tuned_by: TUN-PRE-VGCC from TUN.N

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

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

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

    - TagRelease ( fullness: 1x, active: 0x, emptiness: 0x ) 

    - CaTraces ( fullness: 50x, active: 0x, emptiness: 0x )

  tub_intricated:
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