1088 lines
50 KiB
Markdown
1088 lines
50 KiB
Markdown
# Tripartite Synapse — Pseudocode v5
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# Energy and material flows explicit. Variables aggregated to minimum set.
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---
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## Part 1 — Conventions
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```
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SCOPE = { DAY, NIGHT }
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CONTEXT = { AP, NOT_AP, bAP, NOT_bAP, CONTINUOUS }
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Variable types:
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FIXED = externally imposed — does not change during simulation
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VAR = changes dynamically
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FAST_TRACE = accumulates and decays within DAY — never reaches NIGHT
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role: biases next behavior within same context
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TAG = set during DAY, decays slowly, survives to NIGHT
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role: gates structural commit in NIGHT
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for POST only: two phases — CANDIDATE (DAY) → STABLE (DAY) → NIGHT
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BUDGET = single energy variable per compartment
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all costs deducted here
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MATERIAL = single structural resource variable per compartment
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all material draws and returns here
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STRUCTURE = slow architectural variable
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READ during DAY, WRITTEN only in NIGHT
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```
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---
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## Part 2 — Fixed Parameters
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```
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// Thresholds
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FIXED Ca_TAG_threshold // Ca²⁺ level sufficient to set post CANDIDATE tag
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FIXED Ca_HIGH // LTP-driving Ca²⁺ amplitude
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FIXED Ca_LOW // LTD-driving Ca²⁺ amplitude
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FIXED spillover_threshold // cleft saturation threshold for mGluR activation
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FIXED eligibility_threshold // minimum fast_trace to be taggable (all components)
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FIXED dopamine_threshold // minimum dopamine for tag stabilization
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FIXED tagging_threshold // minimum possible_tagging for tag accumulation
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FIXED tag_expiry_threshold // minimum tag to survive to NIGHT commit
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FIXED homeostatic_ceiling // max soma firing rate before global downscale
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FIXED disuse_threshold // silence duration before passive depotentiation
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FIXED recycling_fraction // fraction of material recovered after LTD dismantling
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// External signals — organism level
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FIXED dopamine_level // VTA broadcast — reward/save signal
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FIXED NE_level // locus coeruleus — arousal/gain
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FIXED ACh_level // basal forebrain — attention/threshold
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// Physical constraints
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FIXED vascular_glucose_supply // hard energy ceiling — astrocyte root
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FIXED branch_geometry // dendritic topology — affects bAP decay
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FIXED Ca_cooperativity_n // Hill coefficient for Ca²⁺-driven NT release (~3-4)
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FIXED Ca_half_max_K // half-maximal Ca²⁺ for NT release
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```
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---
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## Part 3 — Energy and Material Declarations
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```
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// ── ENERGY: one budget per compartment ────────────────────────────────
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VAR astro_budget // ROOT energy variable for synaptic operations
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// SOURCE: vascular_glucose_supply → glycolysis
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// COSTS: glutamate clearance (EAAT transport)
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// D-serine synthesis (serine racemase)
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// ECM secretion (Glypicans, Thrombospondins)
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// process motility (cytoskeletal remodeling)
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// lactate production (exported to pre, post, dend)
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// (simplifies: astro_ATP_budget + all enzyme running costs)
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VAR astro_lactate // fuel exported by astrocyte → feeds pre, post, dend
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// = min(glycolysis(vascular_glucose_supply), astro_budget × export_fraction)
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// hard cap: vascular_glucose_supply (FIXED)
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VAR pre_budget // bouton energy
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// SOURCE: astro_lactate (primary) — via perisynaptic delivery
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// COSTS: VGCC opening + vesicle fusion + VATPase refill
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// active zone maintenance
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// (simplifies: bouton_ATP + VATPase_running_cost)
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VAR post_budget // spine energy
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// SOURCE: astro_lactate (primary) — via perisynaptic delivery
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// COSTS: NaK pump membrane reset
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// AMPA receptor lateral diffusion + recycling
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// actin remodeling for transient spine changes
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// NMDA current handling
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// (simplifies: spine_ATP + NaK_ATPase_cost + actin_cycling_cost)
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VAR dend_budget // branch energy
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// SOURCE: astro_lactate (primary) + soma organelle delivery (minor)
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// COSTS: bAP propagation along branch
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// local mRNA translation
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// protein and organelle transport to spines
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// branch calcium handling
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// (simplifies: dend_mitochondria_ATP + local_translation_cost)
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VAR soma_budget // somatic energy
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// SOURCE: own mitochondria (self-fueled — not from astrocyte)
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// COSTS: AP generation (Na⁺/K⁺ currents)
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// CREB transcription
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// protein synthesis machinery
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// organelle biogenesis
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// shipping to dend and axon
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// (simplifies: soma_ATP + synthesis_running_cost)
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VAR axon_budget // axonal energy
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// SOURCE: soma_budget (primary) + astro_lactate along shaft (minor)
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// COSTS: AP propagation at each node of Ranvier
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// anterograde motor protein transport
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// myelin maintenance
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// (simplifies: axon_ATP + transport_running_cost)
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// ── MATERIAL: one material variable per compartment ───────────────────
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VAR astro_material // astrosynaptic structural components
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// SOURCE: astrocyte cell body synthesis
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// CONTAINS: EAAT transporter proteins
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// serine racemase enzyme
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// ECM proteins (Glypicans, Thrombospondins)
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// process cytoskeleton components
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// D-serine precursor (serine)
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// COSTS: drawn by DAY D-serine release (serine consumed)
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// drawn by NIGHT ECM secretion and process remodeling
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// (simplifies: astro_ECM_pool + racemase_cap + EAAT_pool
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// + process_extensions + D_serine_precursor)
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VAR pre_material // presynaptic bouton structural components
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// SOURCE: soma_material via axon transport (anterograde)
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// CONTAINS: RIM, Munc13 (AZ scaffold)
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// VGCC subunits
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// vesicle membrane proteins
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// synaptotagmin, SNARE proteins
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// COSTS: drawn by NIGHT active zone expansion
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// RETURNS: to shared axonal pool after LTD dismantling
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// (simplifies: axon_vesicle_protein_pool + AZ_scaffold_proteins)
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VAR post_material // postsynaptic spine structural components
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// SOURCE: dend_material (branch local pool + soma delivery)
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// CONTAINS: AMPA receptor subunits (GluA1, GluA2)
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// PSD scaffold proteins (PSD-95, SHANK)
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// actin monomers + polymerization machinery
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// CaMKII
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// COSTS: drawn by NIGHT receptor anchoring + spine enlargement
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// RETURNS: to branch pool after LTD internalization
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// (simplifies: dend_receptor_reserve + dend_actin_machinery
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// + PSD_scaffold_pool)
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VAR dend_material // dendritic branch structural and supply components
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// SOURCE: soma_material (shipped during DAY NOT_AP + NIGHT)
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// CONTAINS: plasticity proteins (Arc, Homer)
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// mRNA pool (Arc mRNA, BDNF mRNA)
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// AMPA receptor subunits (in transit to spines)
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// organelles (mitochondria for local energy)
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// COSTS: drawn by local translation (mRNA consumed)
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// drawn by spine delivery (post_material replenishment)
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// drawn by NIGHT branch structural expansion
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// (simplifies: dend_protein_flux + dend_mRNA_pool
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// + dend_organelle_store)
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VAR soma_material // somatic production output
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// SOURCE: CREB-driven synthesis (own ribosomes + nucleus)
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// CONTAINS: all structural proteins for downstream compartments
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// mRNA transcripts (Arc, BDNF, receptor subunits)
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// organelles (mitochondria, ribosomes)
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// COSTS: shipped to dend_material during DAY NOT_AP + NIGHT
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// shipped to axon for pre_material replenishment
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// depleted by soma's own NIGHT structural commit
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// (simplifies: soma_protein_synthesis_rate + soma_organelle_pool
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// + soma_receptor_synthesis_rate + mRNA_transcription)
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VAR axon_material // axonal transport and structural components
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// SOURCE: soma_material (motor proteins, myelin components)
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// CONTAINS: kinesin/dynein motor proteins
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// microtubule components
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// myelin maintenance proteins
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// COSTS: drawn by NIGHT axon structural expansion
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// consumed continuously by anterograde transport
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// (simplifies: transport_machinery + myelination_proteins)
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```
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---
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## Part 4 — Structural Variables (Written Only in NIGHT)
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```
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VAR pre_structure // active zone capacity
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// RRP_capacity ∝ pre_structure
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// VGCC_coupling ∝ pre_structure
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// refill_ceiling ∝ pre_structure
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// (simplifies: active_zone_size + VGCC_clustering + RRP_pool_capacity)
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VAR post_structure // spine sensitivity capacity
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// anchoring_slots ∝ post_structure
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// spine_volume ∝ post_structure
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// local_reserve ∝ post_structure
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// (simplifies: AMPA_count_ceiling + spine_volume + receptor_reserve_ceiling)
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VAR dend_structure // branch transmission and supply capacity
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// bAP_fidelity ∝ dend_structure × attenuation(position)
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// translation_ceiling ∝ dend_structure
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// transport_speed ∝ dend_structure
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// (simplifies: mitochondria_density + cytoskeletal_integrity
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// + mRNA_pool_ceiling)
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VAR soma_structure // somatic output and production capacity
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// baseline_threshold ∝ 1/soma_structure
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// AP_reliability ∝ soma_structure
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// synthesis_ceiling ∝ soma_structure
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// (simplifies: ion_channel_density + ribosome_density
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// + CREB_machinery)
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VAR axon_structure // axonal transmission and transport capacity
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// propagation_reliability ∝ axon_structure
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// transport_rate ∝ axon_structure
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// (simplifies: myelination_density + transport_machinery_capacity
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// + axonal_mitochondria_density)
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VAR astro_structure // astrosynaptic environmental capacity
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// perisynaptic_distance ∝ 1/astro_structure
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// EAAT_density ∝ astro_structure
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// D_serine_tonic ∝ astro_structure
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// ECM_integrity ∝ astro_structure
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// SELF-REINFORCING in both directions:
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// LTP → astro_structure ↑ → signal more contained,
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// D-serine tonic ↑ → future LTP easier
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// LTD → astro_structure ↓ → signal dilutes,
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// D-serine tonic = 0 → future LTD easier
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// (simplifies: perisynaptic_distance + ECM_integrity
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// + D_serine_tonic_level + EAAT_density)
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```
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---
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## Part 5 — Trace Variables
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```
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// ── Fast traces: DAY only, decay automatically ────────────────────────
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FAST_TRACE pre_fast_trace
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// += spike_Ca_influx() on each AP
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// *= decay(τ ≈ 100ms)
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// role: (1) biases NT flux in next AP context (residual Ca²⁺)
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// (2) eligibility condition for pre_possible_tagging
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// energy: no direct cost — Ca²⁺ dynamics are passive
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// material: no direct cost
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FAST_TRACE post_fast_trace
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// += NMDA_Ca_influx × rise_speed() in NOT_bAP context
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// += bAP_Ca_boost() if CANDIDATE tag confirmed in bAP context
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// *= decay(τ ≈ tens of ms)
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// role: (1) encodes LTP vs LTD instruction (amplitude × speed)
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// (2) eligibility condition for post CANDIDATE tag
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// energy cost: post_budget -= NMDA_current_cost
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// material: no direct cost
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FAST_TRACE dend_fast_trace
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// += bAP_Ca_influx() + spine_Ca_spillover()
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// *= decay(τ ≈ 300ms)
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// role: (1) integrates branch co-activity
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// (2) eligibility for dend_possible_tagging
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// (3) gates local translation rate when dend_tag set
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// energy cost: dend_budget -= branch_Ca_handling_cost
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// material: no direct cost
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FAST_TRACE soma_fast_trace
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// += nuclear_Ca_influx() on each somatic AP
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// *= decay(τ ≈ seconds)
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// role: (1) adaptation — raises AP_threshold with recent firing
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// (2) eligibility condition for soma CREB gate
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// energy cost: soma_budget -= AP_generation_cost
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// material: no direct cost
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FAST_TRACE axon_fast_trace
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// += AP_propagation_load(input_freq) on each AP
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// *= decay(τ ≈ seconds)
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// role: (1) drives propagation failure at branch points under high freq
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// (2) eligibility for axon_possible_tagging
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// energy cost: axon_budget -= AP_propagation_cost
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// material: no direct cost
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FAST_TRACE astro_fast_trace
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// += mGluR5_Ca_influx() when glutamate > spillover_threshold
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// *= decay(τ ≈ seconds)
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// role: (1) drives D-serine release proportional to magnitude
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// (2) eligibility for astro_possible_tagging
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// (3) triggers global lockdown when > OVERLOAD_threshold
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// energy cost: astro_budget -= D_serine_synthesis_cost
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// material cost: astro_material -= D_serine_precursor_cost
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// ── Possible tagging: intermediate, decays over seconds–minutes ───────
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VAR pre_possible_tagging // += pre_fast_trace when > eligibility_threshold
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// *= decay(τ ≈ seconds)
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VAR post_possible_tagging // += post_fast_trace when > Ca_TAG_threshold (bAP confirmed)
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// *= decay(τ ≈ minutes) — CANDIDATE lifetime
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VAR dend_possible_tagging // += dend_fast_trace when > eligibility_threshold
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// *= decay(τ ≈ seconds–minutes)
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VAR soma_possible_tagging // += soma_fast_trace when > eligibility_threshold
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// *= decay(τ ≈ seconds–minutes)
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VAR axon_possible_tagging // += axon_fast_trace when > eligibility_threshold
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// *= decay(τ ≈ seconds–minutes)
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VAR astro_possible_tagging // += astro_fast_trace when > eligibility_threshold
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// *= decay(τ ≈ seconds–minutes)
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// ── Tags: slow, DAY→NIGHT bridge ──────────────────────────────────────
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TAG pre_tag // += dopamine × pre_possible_tagging when both > threshold
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// *= decay(τ ≈ hours) — survives to NIGHT
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// gates: pre_structure expansion in NIGHT
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// energy cost: none — tag is a molecular state, not a process
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TAG post_tag // TWO-PHASE for POST only:
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// CANDIDATE phase:
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// set when post_fast_trace > Ca_TAG_threshold AND bAP confirmed
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// decays within minutes if dopamine does not arrive
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// STABLE phase:
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// += dopamine × post_possible_tagging when both > threshold
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// *= decay(τ ≈ hours) — survives to NIGHT
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// gates: post_structure expansion in NIGHT
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// energy cost: post_budget -= PKA_phosphorylation_cost (minor)
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// material cost: none
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TAG dend_tag // += dopamine × dend_possible_tagging when both > threshold
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// *= decay(τ ≈ hours)
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// gates: dend_structure expansion + local translation activation in NIGHT
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// energy cost: none
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TAG soma_tag // += dopamine × soma_possible_tagging when both > threshold
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// *= decay(τ ≈ hours)
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// gates: soma_structure expansion + protein synthesis peak in NIGHT
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// energy cost: soma_budget -= CREB_phosphorylation_cost (minor)
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// material cost: none
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TAG axon_tag // += dopamine × axon_possible_tagging when both > threshold
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// *= decay(τ ≈ hours)
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// gates: axon_structure expansion in NIGHT
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// energy cost: none
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TAG astro_tag // += dopamine × astro_possible_tagging when both > threshold
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// *= decay(τ ≈ hours)
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// gates: astro_structure expansion (process retraction + ECM sealing) in NIGHT
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// energy cost: none
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```
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---
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---
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# SCOPE: DAY
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Budgets consumed. Fast traces written and decay. Tags set but not cleared.
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Structures READ only.
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---
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## PRE | CONTEXT: AP
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```
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scope DAY | context AP:
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// Energy gate — release requires ATP
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if pre_budget < AP_release_cost:
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suppress(NT_flux)
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exit context
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// biological basis: ATP depletion → VGCC cannot open reliably
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// Fast trace: residual Ca²⁺ deposit
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pre_fast_trace += spike_Ca_influx(input_freq)
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pre_fast_trace *= decay(τ = 100ms)
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pre_budget -= Ca_handling_cost
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// biological basis: Ca²⁺ enters via VGCCs, pumped out by PMCA/NCX
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// NT flux: continuous release while RRP has content
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// Ca_drive: Hill function — cooperative Ca²⁺ dependence of synaptotagmin
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Ca_drive = pre_fast_trace^Ca_cooperativity_n /
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(Ca_half_max_K^Ca_cooperativity_n + pre_fast_trace^Ca_cooperativity_n)
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if RRP_level > 0:
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NT_flux = RRP_level × Ca_drive // proportional to pool × Ca²⁺
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glutamate += NT_flux × Δt // cleft concentration rises
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RRP_level -= NT_flux × Δt // pool depletes
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pre_budget -= NT_flux × vesicle_fusion_cost // ATP per vesicle equivalent
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// biological basis: SNARE-mediated vesicle fusion, each event costs ATP
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// RRP refill from reserve — rate limited by pre_budget and pre_structure
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RRP_refill = min(refill_rate_constant, pre_structure.refill_ceiling)
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RRP_level += RRP_refill × Δt
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RRP_level = clamp(RRP_level, 0, pre_structure.RRP_capacity)
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pre_budget -= RRP_refill × VATPase_cost
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// biological basis: VATPase pumps refill vesicles with NT, costs ATP
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// Overflow brake — mGluR2/3 Gi-mediated autoinhibition
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if glutamate > spillover_threshold:
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Ca_drive *= mGluR_brake_factor
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// biological basis: extrasynaptic glu activates mGluR2/3 → Gi →
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// adenylyl cyclase ↓ → cAMP ↓ → VGCC opening ↓
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// Refuel from astrocyte lactate
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pre_budget += astro_lactate × pre_fraction
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// biological basis: lactate → pyruvate → TCA → ATP via bouton mitochondria
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```
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## PRE | CONTEXT: NOT_AP
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```
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scope DAY | context NOT_AP:
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// Fast trace decays — eligibility window closing
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pre_fast_trace *= decay(τ = 100ms)
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// RRP refills during silence — STP recovery
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RRP_refill = min(refill_rate_constant, pre_structure.refill_ceiling)
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RRP_level += RRP_refill × Δt
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RRP_level = clamp(RRP_level, 0, pre_structure.RRP_capacity)
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pre_budget -= RRP_refill × VATPase_cost
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// Possible tagging: graded accumulation while eligible
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if pre_fast_trace > eligibility_threshold:
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pre_possible_tagging += pre_fast_trace
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pre_possible_tagging *= decay(τ = seconds)
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// Dopamine decays locally
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dopamine_local *= decay(τ = hundreds_of_ms)
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// biological basis: dopamine reuptake by DAT, enzymatic degradation (MAO, COMT)
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// Tag: set only when BOTH local eligibility AND global validation coincide
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if dopamine_local > dopamine_threshold and
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pre_possible_tagging > tagging_threshold:
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pre_tag += dopamine_local × pre_possible_tagging
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pre_tag *= decay(τ = hours)
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// biological basis: PKA phosphorylation of AZ proteins stabilizes tag
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// requires both residual Ca²⁺ eligibility AND dopamine-driven PKA
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```
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---
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## POST | CONTEXT: NOT_bAP
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```
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scope DAY | context NOT_bAP:
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// AMPA current — gated by post_structure (READ)
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// Occupancy: transient receptor insertion/removal from existing slots
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AMPA_current = glutamate × post_structure.sensitivity
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Vm += AMPA_current
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post_budget -= AMPA_current_cost
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// biological basis: AMPA receptor opening → Na⁺ influx → NaK pump cost
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// NMDA gate: three-way coincidence
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// (1) sufficient depolarization (Mg²⁺ block ejected)
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// (2) D-serine from astrosynapse (co-agonist present)
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// (3) glutamate bound
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if Vm > Mg_eject_threshold and
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astro_D_serine > D_serine_threshold:
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Ca_influx = NMDA_Ca_influx(glutamate)
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post_fast_trace += Ca_influx × rise_speed(Ca_influx)
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post_budget -= NMDA_current_cost
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// biological basis: NMDA Ca²⁺ influx → CaMKII vs PP1 competition
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// fast rise → CaMKII wins → LTP instruction
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||
// slow rise → PP1 wins → LTD instruction
|
||
|
||
// CANDIDATE tag: set when Ca²⁺ crossed tagging threshold
|
||
// This is the Hebbian anticipation — before bAP confirms
|
||
if post_fast_trace > Ca_TAG_threshold:
|
||
post_possible_tagging += post_fast_trace // graded — higher Ca²⁺ → more contribution
|
||
post_possible_tagging *= decay(τ = minutes) // CANDIDATE lifetime — minutes
|
||
// biological basis: early CaMKII activation creates labile tag
|
||
// decays via phosphatase activity if not stabilized
|
||
|
||
// Fast trace decays
|
||
post_fast_trace *= decay(τ = tens_of_ms)
|
||
|
||
// Refuel
|
||
post_budget += astro_lactate × post_fraction
|
||
```
|
||
|
||
## POST | CONTEXT: bAP
|
||
|
||
```
|
||
scope DAY | context bAP:
|
||
|
||
// bAP arrives — strength set by dend_structure.bAP_fidelity (READ)
|
||
Vm += bAP_depolarization × dend_structure.bAP_fidelity
|
||
post_budget -= bAP_reset_cost
|
||
// biological basis: bAP Ca²⁺ entry via VDCCs in spine, NaK reset costs ATP
|
||
|
||
// Coincidence confirmation: bAP finds CANDIDATE already set
|
||
if post_possible_tagging > Ca_TAG_threshold:
|
||
post_fast_trace += bAP_Ca_boost() // trace amplified above Ca_HIGH
|
||
// biological basis: bAP + prior NMDA Ca²⁺ → supralinear Ca²⁺ summation
|
||
// this is the Hebbian coincidence — forward + backward signals
|
||
|
||
// else: bAP arrives but spine was not active — no amplification, no tag
|
||
|
||
// Dopamine decays locally
|
||
dopamine_local *= decay(τ = hundreds_of_ms)
|
||
|
||
// STABLE tag: CANDIDATE stabilized by dopamine within window
|
||
if dopamine_local > dopamine_threshold and
|
||
post_possible_tagging > tagging_threshold:
|
||
post_tag += dopamine_local × post_possible_tagging
|
||
post_tag *= decay(τ = hours)
|
||
post_budget -= PKA_phosphorylation_cost // minor ATP cost for PKA activity
|
||
// biological basis: dopamine → D1R → PKA → GluA1-Ser845 phosphorylation
|
||
// PKA also phosphorylates DARPP-32 → inhibits PP1
|
||
// stabilizes tag against phosphatase-driven decay
|
||
```
|
||
|
||
---
|
||
|
||
## DEND | CONTEXT: CONTINUOUS
|
||
|
||
```
|
||
scope DAY | context CONTINUOUS:
|
||
|
||
// Integrate spines upward toward soma
|
||
branch_Vm = integrate(POST.Vm, all_spines_on_branch)
|
||
|
||
// Propagate bAP downward — fidelity set by dend_structure (READ)
|
||
bAP_local = propagate_bAP(SOMA.AP_fired,
|
||
dend_structure.bAP_fidelity,
|
||
branch_geometry)
|
||
dend_budget -= bAP_propagation_cost
|
||
// biological basis: bAP propagation requires Na⁺ channel re-activation
|
||
// costs ATP via NaK reset along branch length
|
||
|
||
// Fast trace: branch Ca²⁺ from bAP + spine spillover
|
||
dend_fast_trace += bAP_Ca_influx(bAP_local)
|
||
dend_fast_trace += spine_Ca_spillover(active_spines)
|
||
dend_fast_trace *= decay(τ = 300ms)
|
||
dend_budget -= branch_Ca_handling_cost
|
||
// biological basis: Ca²⁺ enters via VDCCs along branch,
|
||
// SERCA pump re-sequestration costs ATP
|
||
|
||
// Possible tagging: branch co-activity threshold
|
||
if dend_fast_trace > eligibility_threshold:
|
||
dend_possible_tagging += dend_fast_trace
|
||
dend_possible_tagging *= decay(τ = seconds)
|
||
|
||
// Dopamine decays
|
||
dopamine_local *= decay(τ = hundreds_of_ms)
|
||
|
||
// Tag
|
||
if dopamine_local > dopamine_threshold and
|
||
dend_possible_tagging > tagging_threshold:
|
||
dend_tag += dopamine_local × dend_possible_tagging
|
||
dend_tag *= decay(τ = hours)
|
||
|
||
// Local translation: activated when tag set, gated by dend_budget
|
||
if dend_tag > tag_expiry_threshold and dend_budget > translation_cost:
|
||
local_proteins = translate(dend_material.mRNA_pool,
|
||
dend_fast_trace) // rate ∝ fast trace
|
||
dend_material.mRNA_pool -= local_proteins × mRNA_cost
|
||
post_material += local_proteins × delivery_fraction
|
||
dend_budget -= translation_cost
|
||
// biological basis: Arc mRNA + polyribosomes at branch
|
||
// fast local protein supply for early structural changes
|
||
// no soma wait required
|
||
|
||
// ACh modulates commit threshold globally
|
||
commit_threshold *= (1 / (1 + ACh_level × ACh_gain))
|
||
|
||
// Branch maintenance cost
|
||
dend_budget -= branch_maintenance_cost
|
||
dend_budget += astro_lactate × dend_fraction
|
||
// material: replenished by soma shipping during NOT_AP
|
||
```
|
||
|
||
---
|
||
|
||
## SOMA | CONTEXT: AP
|
||
|
||
```
|
||
scope DAY | context AP:
|
||
|
||
// Integrate — fires when branch inputs cross threshold
|
||
// Threshold modulated by fast trace (adaptation) and neuromodulators
|
||
AP_threshold = soma_structure.baseline_threshold
|
||
× (1 + adaptation_factor(soma_fast_trace)) // rises with recent firing
|
||
× neuromod_factor(NE_level, ACh_level) // NE lowers, ACh sharpens
|
||
× refractory_factor(time_since_last_AP) // hard block then graded recovery
|
||
|
||
if branch_Vm > AP_threshold:
|
||
AP_fired = True
|
||
soma_budget -= AP_generation_cost
|
||
// biological basis: Na⁺/K⁺ currents for AP, NaK pump reset
|
||
|
||
// Fast trace: nuclear Ca²⁺ accumulation
|
||
soma_fast_trace += nuclear_Ca_influx()
|
||
soma_fast_trace *= decay(τ = seconds)
|
||
// biological basis: L-type VGCC → nuclear Ca²⁺ → CaM kinase nuclear activation
|
||
|
||
// Refractory period
|
||
refractory_timer = absolute_refractory_duration // ~2ms hard block
|
||
|
||
// Possible tagging
|
||
if soma_fast_trace > eligibility_threshold:
|
||
soma_possible_tagging += soma_fast_trace
|
||
soma_possible_tagging *= decay(τ = seconds)
|
||
|
||
// Dopamine decays
|
||
dopamine_local *= decay(τ = hundreds_of_ms)
|
||
|
||
// Tag: nuclear Ca²⁺ AND dopamine coincidence
|
||
if dopamine_local > dopamine_threshold and
|
||
soma_possible_tagging > tagging_threshold:
|
||
soma_tag += dopamine_local × soma_possible_tagging
|
||
soma_tag *= decay(τ = hours)
|
||
soma_budget -= CREB_phosphorylation_cost
|
||
// biological basis: nuclear Ca²⁺ + PKA → CREB phosphorylation
|
||
// requires both activity (Ca²⁺) AND reward (dopamine/PKA)
|
||
```
|
||
|
||
## SOMA | CONTEXT: NOT_AP
|
||
|
||
```
|
||
scope DAY | context NOT_AP:
|
||
|
||
// Integrate dendritic inputs
|
||
branch_Vm = integrate(DEND.branch_Vm, all_branches)
|
||
|
||
// Refractory timer counts down
|
||
refractory_timer = max(0, refractory_timer - Δt)
|
||
|
||
// Fast trace decays — threshold returning to baseline
|
||
soma_fast_trace *= decay(τ = seconds)
|
||
|
||
// Ship material to tagged branches — priority by tag magnitude
|
||
for branch in branches_ranked_by(dend_tag):
|
||
delivery = min(shipping_fraction × soma_material,
|
||
soma_budget × shipping_cost_fraction)
|
||
dend_material[branch] += delivery
|
||
soma_material -= delivery
|
||
soma_budget -= shipping_cost
|
||
// biological basis: kinesin-driven anterograde transport of mRNA + proteins
|
||
// tagged branches receive priority allocation
|
||
|
||
// Ship material to axon for bouton replenishment
|
||
axon_delivery = min(axon_shipping_fraction × soma_material,
|
||
soma_budget × axon_shipping_cost_fraction)
|
||
axon_material += axon_delivery
|
||
soma_material -= axon_delivery
|
||
soma_budget -= axon_shipping_cost
|
||
// biological basis: slow axonal transport — days to reach distal boutons
|
||
|
||
// Neuromodulator context: PKA broadcast amplifies all tagged component traces
|
||
if dopamine_level > dopamine_threshold or NE_level > NE_threshold:
|
||
for each component where possible_tagging > tagging_threshold:
|
||
tag += dopamine_level × possible_tagging × PKA_amplifier
|
||
// biological basis: dopamine → cAMP → PKA → phosphorylates targets
|
||
// throughout neuron simultaneously
|
||
```
|
||
|
||
---
|
||
|
||
## AXON | CONTEXT: CONTINUOUS
|
||
|
||
```
|
||
scope DAY | context CONTINUOUS:
|
||
|
||
// AP propagation — reliability set by axon_structure (READ)
|
||
propagation_reliability = axon_structure.myelination
|
||
× (1 - failure_rate(axon_fast_trace))
|
||
// biological basis: high axon_fast_trace → Na⁺ channel inactivation at branch points
|
||
// → some APs fail to reach distal boutons
|
||
// → this is axonal STD (frequency-dependent filtering)
|
||
|
||
APs_delivered = AP_fired × propagation_reliability
|
||
axon_budget -= AP_propagation_cost × APs_delivered
|
||
|
||
// Fast trace: propagation load
|
||
axon_fast_trace += APs_delivered
|
||
axon_fast_trace *= decay(τ = seconds)
|
||
|
||
// Anterograde transport — delivers pre_material to boutons
|
||
transport_rate = min(axon_structure.transport_capacity,
|
||
axon_budget × transport_fraction)
|
||
pre_material += transport_rate × Δt // boutons receive material
|
||
axon_material -= transport_rate × Δt // axon pool depletes
|
||
axon_budget -= transport_cost × transport_rate × Δt
|
||
// biological basis: kinesin moves cargo at ~1μm/s along microtubules
|
||
// costs ATP per step (kinesin ATPase)
|
||
|
||
// Possible tagging
|
||
if axon_fast_trace > eligibility_threshold:
|
||
axon_possible_tagging += axon_fast_trace
|
||
axon_possible_tagging *= decay(τ = seconds)
|
||
|
||
// Dopamine decays
|
||
dopamine_local *= decay(τ = hundreds_of_ms)
|
||
|
||
// Tag
|
||
if dopamine_local > dopamine_threshold and
|
||
axon_possible_tagging > tagging_threshold:
|
||
axon_tag += dopamine_local × axon_possible_tagging
|
||
axon_tag *= decay(τ = hours)
|
||
|
||
// Refuel from soma budget + local astrocyte
|
||
axon_budget += soma_budget × axon_fuel_fraction
|
||
axon_budget += astro_lactate × axon_astro_fraction
|
||
// biological basis: soma mitochondria supply axon proximally
|
||
// local astrocytes supply along shaft distally
|
||
```
|
||
|
||
---
|
||
|
||
## ASTRO | CONTEXT: CONTINUOUS
|
||
|
||
```
|
||
scope DAY | context CONTINUOUS:
|
||
|
||
// ROOT energy production: glycolysis from vascular glucose
|
||
astro_budget += glycolysis(vascular_glucose_supply) × Δt
|
||
// hard cap: vascular_glucose_supply (FIXED) — cannot be exceeded
|
||
// biological basis: glucose → lactate via glycolysis in astrocyte cytoplasm
|
||
|
||
// Lactate export to neuronal compartments
|
||
astro_lactate = min(astro_budget × lactate_export_fraction,
|
||
vascular_glucose_supply × max_export_fraction)
|
||
astro_budget -= astro_lactate
|
||
deliver(astro_lactate → pre_budget × pre_fraction,
|
||
post_budget × post_fraction,
|
||
dend_budget × dend_fraction,
|
||
axon_budget × axon_fraction)
|
||
// biological basis: lactate released into ECS → absorbed by MCT2 on neurons
|
||
// neurons convert lactate → pyruvate → TCA → ATP
|
||
|
||
// Glutamate clearance — rate set by astro_structure (READ)
|
||
clearance = astro_structure.EAAT_density × glutamate × Δt
|
||
glutamate -= clearance
|
||
astro_budget -= clearance × EAAT_ATP_cost
|
||
// biological basis: EAAT cotransports 3 Na⁺ per glutamate → NaK pump cost
|
||
|
||
// Overflow detection and D-serine release
|
||
if glutamate > spillover_threshold:
|
||
astro_fast_trace += mGluR5_Ca_influx()
|
||
// biological basis: spillover activates mGluR5 → Gq → PLC → IP3
|
||
// → Ca²⁺ release from ER → Ca²⁺-dependent exocytosis
|
||
|
||
// D-serine release: proportional to fast trace, material + budget limited
|
||
D_serine_released = min(proportional_to(astro_fast_trace),
|
||
astro_material.D_serine_precursor,
|
||
astro_budget × Ds_fraction)
|
||
astro_material -= D_serine_released × precursor_cost
|
||
astro_budget -= D_serine_released × synthesis_cost
|
||
astro_D_serine += D_serine_released
|
||
// biological basis: serine racemase converts L-serine → D-serine
|
||
// costs ATP, consumes serine from astro_material
|
||
|
||
// Simultaneous presynaptic brake (cross-compartment, no astro budget cost)
|
||
Ca_drive_pre *= mGluR_brake_factor
|
||
// biological basis: spillover also activates mGluR2/3 on PRE → Gi →
|
||
// suppresses VGCC — brakes release at source
|
||
|
||
// Possible tagging
|
||
if astro_fast_trace > eligibility_threshold:
|
||
astro_possible_tagging += astro_fast_trace
|
||
astro_possible_tagging *= decay(τ = seconds)
|
||
|
||
// Dopamine decays
|
||
dopamine_local *= decay(τ = hundreds_of_ms)
|
||
|
||
// Tag
|
||
if dopamine_local > dopamine_threshold and
|
||
astro_possible_tagging > tagging_threshold:
|
||
astro_tag += dopamine_local × astro_possible_tagging
|
||
astro_tag *= decay(τ = hours)
|
||
|
||
astro_fast_trace *= decay(τ = seconds)
|
||
|
||
// Global overload: circuit breaker
|
||
if astro_fast_trace > OVERLOAD_threshold:
|
||
trigger(shockwave_lockdown)
|
||
// biological basis: global Ca²⁺ wave → GABA + ATP release
|
||
// mass AMPA internalization, hyperpolarization
|
||
|
||
// Tonic D-serine baseline — set by astro_structure (READ)
|
||
astro_D_serine += astro_structure.D_serine_tonic × Δt
|
||
astro_budget -= astro_structure.D_serine_tonic × tonic_synthesis_cost
|
||
astro_material -= astro_structure.D_serine_tonic × tonic_precursor_cost
|
||
// biological basis: constitutive racemase activity maintains baseline
|
||
// D-serine availability independent of overflow events
|
||
```
|
||
|
||
---
|
||
|
||
## Special Case — Shockwave Lockdown (any scope)
|
||
|
||
```
|
||
scope DAY or NIGHT | context OVERLOAD:
|
||
|
||
// Emergency — bypasses budget gates
|
||
// Biological basis: global astrocytic Ca²⁺ wave →
|
||
// GABA release → hyperpolarization
|
||
// ATP release → purinergic inhibition
|
||
post_fast_trace = 0
|
||
Vm = HYPERPOLARIZED
|
||
AMPA_occupancy = mass_internalization() // returned to post_material reserve
|
||
post_material += recovered_AMPA
|
||
axon_fast_trace += overdrive_cluster() // VGCC clustering beneath AZ
|
||
astro_budget -= emergency_cost // large deduction — territory depleted
|
||
```
|
||
|
||
---
|
||
---
|
||
|
||
# SCOPE: NIGHT
|
||
Structural variables WRITTEN. Budgets replenished. Tags evaluated and cleared.
|
||
|
||
---
|
||
|
||
## Step 1 — Replenish Budgets and Material
|
||
|
||
```
|
||
scope NIGHT | step 1:
|
||
|
||
// Astrocyte replenishes first — it fuels everything
|
||
astro_budget += overnight_glycolysis(vascular_glucose_supply) × Δt_night
|
||
astro_material += astrocyte_cellbody_synthesis() × Δt_night
|
||
// biological basis: astrocyte protein synthesis overnight
|
||
// replenishes EAAT, racemase, ECM proteins, process cytoskeleton
|
||
|
||
// Soma replenishes from own mitochondria — self-fueled
|
||
soma_budget += overnight_mitochondria_output() × Δt_night
|
||
|
||
// Soma material production peaks in NIGHT — driven by soma_tag magnitude
|
||
soma_material += CREB_driven_synthesis(soma_tag) × Δt_night
|
||
// biological basis: CREB → Arc, BDNF, GluA1, scaffold proteins
|
||
// peaks during slow-wave sleep replay
|
||
|
||
// Soma ships material to downstream compartments
|
||
dend_material += soma_material × dend_delivery_fraction
|
||
axon_material += soma_material × axon_delivery_fraction
|
||
soma_material -= (dend_delivery_fraction + axon_delivery_fraction) × soma_material
|
||
|
||
// Downstream budgets refilled from soma and astrocyte
|
||
dend_budget += astro_lactate × dend_fraction
|
||
+ soma_budget × soma_to_dend_fraction
|
||
pre_budget += astro_lactate × pre_fraction
|
||
post_budget += astro_lactate × post_fraction
|
||
axon_budget += soma_budget × soma_to_axon_fraction
|
||
+ astro_lactate × axon_fraction
|
||
```
|
||
|
||
---
|
||
|
||
## Step 2 — Structural Commits (Parallel, Independent per Compartment)
|
||
|
||
```
|
||
scope NIGHT | step 2:
|
||
|
||
// Each compartment commits independently based on its own tag
|
||
// No global AND gate — coherence emerges from shared DAY events
|
||
// COHERENCE BONUS: if all tags SET simultaneously → amplified commit
|
||
all_aligned = (pre_tag > tag_expiry_threshold and
|
||
post_tag > tag_expiry_threshold and
|
||
astro_tag > tag_expiry_threshold)
|
||
coherence_bonus = all_aligned ? coherence_factor : 1.0
|
||
|
||
// ── PRE COMMIT ──────────────────────────────────────────────────────
|
||
if pre_tag > tag_expiry_threshold:
|
||
Δpre = min(AZ_expansion_cost,
|
||
pre_material,
|
||
pre_budget × pre_structural_fraction)
|
||
pre_structure += Δpre × coherence_bonus // STRUCTURE WRITTEN
|
||
pre_material -= Δpre // material consumed
|
||
pre_budget -= Δpre × structural_ATP_cost
|
||
if Δpre < AZ_expansion_cost:
|
||
queue(pre_deficit → next NIGHT) // deficit deferred
|
||
// biological basis: RIM + Munc13 incorporation → new docking slots
|
||
// VGCC clustering → tighter Ca²⁺-release coupling
|
||
// LTD: passive decay if maintenance not met (see step 3)
|
||
|
||
// ── POST COMMIT ─────────────────────────────────────────────────────
|
||
if post_tag > tag_expiry_threshold:
|
||
Δpost = min(AMPA_insertion_cost,
|
||
post_material,
|
||
post_budget × post_structural_fraction)
|
||
post_structure += Δpost × coherence_bonus // STRUCTURE WRITTEN
|
||
post_material -= Δpost // material consumed
|
||
post_budget -= Δpost × structural_ATP_cost
|
||
if Δpost < AMPA_insertion_cost:
|
||
queue(post_deficit → next NIGHT)
|
||
// biological basis: CaMKII anchors AMPA receptors into PSD scaffold
|
||
// actin polymerization enlarges spine head
|
||
// new anchoring slots created — not just slots filled
|
||
|
||
// ── DEND COMMIT ─────────────────────────────────────────────────────
|
||
if dend_tag > tag_expiry_threshold:
|
||
Δdend = min(branch_expansion_cost,
|
||
dend_material,
|
||
dend_budget × dend_structural_fraction)
|
||
dend_structure += Δdend × coherence_bonus // STRUCTURE WRITTEN
|
||
dend_material -= Δdend
|
||
dend_budget -= Δdend × structural_ATP_cost
|
||
if Δdend < branch_expansion_cost:
|
||
queue(dend_deficit → next NIGHT)
|
||
// biological basis: mitochondria incorporation → local ATP ceiling raised
|
||
// cytoskeletal reinforcement → better bAP propagation
|
||
// mRNA pool expanded → more local translation capacity
|
||
|
||
// ── SOMA COMMIT ─────────────────────────────────────────────────────
|
||
if soma_tag > tag_expiry_threshold:
|
||
Δsoma = min(soma_expansion_cost,
|
||
soma_material,
|
||
soma_budget × soma_structural_fraction)
|
||
soma_structure += Δsoma // STRUCTURE WRITTEN
|
||
soma_material -= Δsoma
|
||
soma_budget -= Δsoma × structural_ATP_cost
|
||
// biological basis: ion channel density increase at axon initial segment
|
||
// ribosome biogenesis → synthesis ceiling raised
|
||
// CREB machinery expansion
|
||
|
||
// ── AXON COMMIT ─────────────────────────────────────────────────────
|
||
if axon_tag > tag_expiry_threshold:
|
||
Δaxon = min(axon_expansion_cost,
|
||
axon_material,
|
||
axon_budget × axon_structural_fraction)
|
||
axon_structure += Δaxon // STRUCTURE WRITTEN
|
||
axon_material -= Δaxon
|
||
axon_budget -= Δaxon × structural_ATP_cost
|
||
if Δaxon < axon_expansion_cost:
|
||
queue(axon_deficit → next NIGHT)
|
||
// biological basis: myelination density increase
|
||
// motor protein pool expansion
|
||
// microtubule stabilization
|
||
|
||
// ── ASTRO COMMIT ────────────────────────────────────────────────────
|
||
if astro_tag > tag_expiry_threshold:
|
||
Δastro = min(process_retraction_cost,
|
||
astro_material,
|
||
astro_budget × astro_structural_fraction)
|
||
astro_structure += Δastro × coherence_bonus // STRUCTURE WRITTEN
|
||
astro_material -= Δastro // ECM proteins + cytoskeleton consumed
|
||
astro_budget -= Δastro × structural_ATP_cost
|
||
if Δastro < process_retraction_cost:
|
||
queue(astro_deficit → next NIGHT)
|
||
// biological basis: process retraction → perisynaptic_distance ↓
|
||
// ECM secretion (Glypicans, Thrombospondins) → cleft sealed
|
||
// racemase upregulation → D_serine_tonic ↑
|
||
// EAAT density increase → clearance ceiling ↑
|
||
// SELF-REINFORCING: astro_structure ↑ → future signals more contained
|
||
// → future D-serine higher
|
||
// → future LTP easier
|
||
```
|
||
|
||
---
|
||
|
||
## Step 3 — Passive Depotentiation (Resource Conservation)
|
||
|
||
```
|
||
scope NIGHT | step 3:
|
||
|
||
// Potentiation is the primary drive.
|
||
// Depotentiation is its shadow — a consequence of finite resources.
|
||
// Structures decay at a baseline rate.
|
||
// Decay is overcome only if maintenance allocation is sufficient.
|
||
// Maintenance draws from what remains AFTER potentiation has taken its share.
|
||
|
||
remaining_material = total_material - material_consumed_by_potentiation
|
||
remaining_budget = total_budget - budget_consumed_by_potentiation
|
||
|
||
maintenance_per_synapse = remaining_material / total_synapse_count
|
||
|
||
for each synapse:
|
||
// Structural decay — passive, continuous
|
||
pre_structure -= structural_decay_rate × Δt_night
|
||
post_structure -= structural_decay_rate × Δt_night
|
||
dend_structure -= structural_decay_rate × Δt_night
|
||
astro_structure -= structural_decay_rate × Δt_night
|
||
|
||
// Maintenance allocation — overcomes decay if resources available
|
||
if maintenance_per_synapse >= maintenance_cost:
|
||
pre_structure += maintenance_pre
|
||
post_structure += maintenance_post
|
||
dend_structure += maintenance_dend
|
||
astro_structure += maintenance_astro
|
||
// decay fully compensated — structure stable
|
||
|
||
else:
|
||
// maintenance_per_synapse < maintenance_cost
|
||
// partial compensation only — structure drifts downward
|
||
// THIS IS DEPOTENTIATION BY NEGLECT — no active signal required
|
||
// the synapse is not told to weaken
|
||
// it simply does not receive enough to stay where it is
|
||
pre_structure += maintenance_per_synapse × pre_fraction
|
||
post_structure += maintenance_per_synapse × post_fraction
|
||
// net: structure slowly declines toward lower baseline
|
||
|
||
// LTD material recovery: dismantled proteins returned to pools
|
||
// This enriches the remaining pool and partially benefits other synapses
|
||
for each synapse where net_structure_change < 0:
|
||
recovered = structure_loss × recycling_fraction
|
||
pre_material += recovered × pre_fraction
|
||
post_material += recovered × post_fraction
|
||
astro_material += recovered × astro_fraction × recycling_fraction
|
||
// biological basis: ubiquitin-proteasome degradation → amino acids recycled
|
||
// internalized receptors → endosomal reserve
|
||
// dismantled AZ proteins → axonal pool
|
||
```
|
||
|
||
---
|
||
|
||
## Step 4 — Homeostatic Scaling
|
||
|
||
```
|
||
scope NIGHT | step 4:
|
||
|
||
// If soma fired too much overall during DAY — global downscale
|
||
if soma_tag > homeostatic_ceiling:
|
||
scale_factor = homeostatic_ceiling / soma_tag
|
||
for each synapse:
|
||
post_structure *= scale_factor // STRUCTURE WRITTEN
|
||
pre_structure *= scale_factor // STRUCTURE WRITTEN
|
||
// biological basis: global AMPA downscaling during sleep
|
||
// relative differences preserved — absolute excitability restored
|
||
// material recovery: scaled-down proteins returned to soma_material
|
||
soma_material += sum(structure_reduction) × recycling_fraction
|
||
```
|
||
|
||
---
|
||
|
||
## Step 5 — Clear All Traces
|
||
|
||
```
|
||
scope NIGHT | step 5:
|
||
|
||
// FAST_TRACEs: already decayed during DAY — confirm zero
|
||
pre_fast_trace = 0
|
||
post_fast_trace = 0
|
||
dend_fast_trace = 0
|
||
soma_fast_trace = 0
|
||
axon_fast_trace = 0
|
||
astro_fast_trace = 0
|
||
|
||
// POSSIBLE_TAGGING: decayed during DAY — confirm zero
|
||
pre_possible_tagging = 0
|
||
post_possible_tagging = 0
|
||
dend_possible_tagging = 0
|
||
soma_possible_tagging = 0
|
||
axon_possible_tagging = 0
|
||
astro_possible_tagging = 0
|
||
|
||
// TAGS: explicitly cleared after commit
|
||
// Tags above expiry threshold carry forward to next NIGHT (multi-night consolidation)
|
||
if pre_tag < tag_expiry_threshold: pre_tag = 0
|
||
if post_tag < tag_expiry_threshold: post_tag = 0
|
||
if dend_tag < tag_expiry_threshold: dend_tag = 0
|
||
if soma_tag < tag_expiry_threshold: soma_tag = 0
|
||
if axon_tag < tag_expiry_threshold: axon_tag = 0
|
||
if astro_tag < tag_expiry_threshold: astro_tag = 0
|
||
// Tags above threshold: partial commit ran, deficit queued,
|
||
// remaining tag persists to next NIGHT for completion
|
||
```
|
||
|
||
---
|
||
|
||
## Summary of Energy and Material Relations
|
||
|
||
```
|
||
ENERGY FLOW:
|
||
vascular_glucose_supply (FIXED)
|
||
→ astro_budget (glycolysis)
|
||
→ astro_lactate → pre_budget, post_budget, dend_budget, axon_budget
|
||
→ soma_budget (own mitochondria — independent of astrocyte)
|
||
→ axon_budget (partial)
|
||
→ dend_budget (partial, via organelle delivery)
|
||
|
||
MATERIAL FLOW:
|
||
soma (CREB synthesis)
|
||
→ soma_material
|
||
→ dend_material (shipping during DAY NOT_AP + NIGHT)
|
||
→ post_material (local delivery to spines)
|
||
→ axon_material (shipping during DAY NOT_AP + NIGHT)
|
||
→ pre_material (anterograde transport to boutons)
|
||
astrocyte cell body (local synthesis)
|
||
→ astro_material
|
||
→ D-serine (consumed in DAY)
|
||
→ ECM proteins (consumed in NIGHT)
|
||
→ process cytoskeleton (consumed in NIGHT)
|
||
|
||
RECOVERY FLOWS (LTD → returns material to pools):
|
||
post LTD → AMPA receptors → post_material (local reserve)
|
||
pre LTD → AZ proteins → pre_material (axonal pool)
|
||
astro LTD → ECM fragments → astro_material (partial, recycling_fraction)
|
||
```
|