Research-Stack/6-Documentation/docs/GLOSSARY.md

Project-Wide Glossary — Sovereign Research Stack

Authority: docs/VOCABULARY_LOCK.md, CONCEPTS.md, docs/gcl/GLOSSARY.md Ground Truth: Lean 4 (0-Core-Formalism/lean/Semantics/)

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Core Formalism

Term	Definition
bind	The single universal primitive: (A × B × Metric) → Bind A B. All algorithms collapse to this. Five allowed classes: informational, geometric, thermodynamic, physical, control.
Q16_16	32-bit fixed-point (UInt32, 0x00010000 = 1.0). Mixed integer + fraction. Last-resort only; requires documented deterministic overflow.
Q0_16	16-bit fixed-point (UInt16), pure fraction [-1, 1 - 2^-16]. Default for all dimensionless quantities (losses, scores, probabilities, phase angles).
Q0_64	64-bit 0D scalar [0, 1). Universal scalar for cross-substrate communication.
FixedPoint	The formal module (Semantics.FixedPoint) defining both Q16_16 and Q0_16 arithmetic. All operations must match bit-exactly across Lean/Verilog/Python.
AMMR	Algebraic Merkle Mountain Range — hierarchical cryptographic accumulator over equation forest nodes.
AVMR	Adaptive Vector Manifest Roll-up — hierarchical summary of vector manifolds across substrates.
O-AMMR	Ordered AMMR — AMMR with explicit dependency ordering on the equation DAG.
BraidField	Path-sensitive field B(t) through which information carriers are rotated to expose phase/charge instability. Basis of the Charged-Mass Braid Sieve.
BracketedCalculus	Gap-conserving bound calculus: ⟨l, u, v, g_l, g_u⟩ where g_l + g_u = u − l. Substrate #35.
bindPreservesInvariant	Core theorem: every lawful bind operation preserves the domain's declared invariant.
MasterEquation	S_{t+1} = MLGRU(Gossip(Prune(Stabilize(Score_{Σ+NK}(Expand(S_t)))))) — the universal state transition across all agent substrates.

Geometry

Term	Definition
PIST	Perfectly Imperfect Square Theory — witness/audit surface with shell coordinate transform. States: (k, t) ∈ ℕ². Invariant: mass conservation.
DIAT	Dynamic Integer-Address Transform — shell coordinate system for energy cell quantization.
NUVMAP	Non-Uniform Variable Mapping — 2D spectral projection (u, v) where u = f(t) = t×1000, v = g(n) = n.
GWL	Gravitational-Wave-Like topology — 5-factor rotational coupling geometry (θ, φ, τ, χ, proximity).
S3C	Shell/Topological Codec — energy cell quantization into n² + m integer shells.
SSMS_nD	Nested self-similar manifold shell — recursive fractal dimension descent. Substrate #5.
Goxel	Geometric voxel — an N-space shape primitive whose derived math must be auditable in a declared field.
Torus	Toroidal manifold on which PIST operations wrap via (k, t) mod T. Substrate #9.
BettiCycle	Topological cycle (β₀, β₁, β₂) used as fingerprint of manifold connectivity.
SolitonTensor	Nonlinear persistent wave on the manifold with conserved identity (Sine-Gordon energy). Substrate #7.
TorsionalPIST	Quaternion-valued PIST extension: (q₁, q₂, q₃) ∈ ℚ³ with quaternion geodesic distance. Substrate #8.
GWLThroat	Multi-factor GWL threshold traversal: holonomy bounded, Φ_topo >> Φ_metric. Substrate #24.

Compression

Term	Definition
GCCL	Geometric-Coded Compression Language — the unified compression theory spanning all substrates.
GCLang	Executable notation / compiler substrate for GCL.
GCCL-Rep	GCCL representation format — the serialized interchange format.
MISC	Manifold-Invariant Shell Compression — compression via shell coordinate encoding on the manifold.
GENSIS	Genetic-Natured N-Space universal encoding substrate — MISC extended with every known biological/genetic coding system generalized to N-dimensional hypercubic shells.
DeltaGCL	Differential GCL — compact representation of differences (deltas) between successive manifold states. Substrate #19.
PTOS	Photonic Topological Optical Storage — photon-pulse-based read/write of crystal substrate topology.
KOT	Kinetic Optical Transform — the optical pulse modulation mechanism for substrate state update.
VLE	Variable-Length Encoding — adaptive symbol encoding based on frequency/basin statistics.
ΔφγKλ	Delta-phase-gamma-kappa-lambda — the complete differential encoding across phase (φ), gamma (γ), curvature (κ), and wavelength (λ).

Biology / Neural

Term	Definition
SpikingNeuron	Izhikevich model: (v, u, I) with membrane potential dynamics dv/dt, du/dt. Substrate #20.
STDP	Spike-Timing-Dependent Plasticity: Δw = A·exp(-Δt/τ). Weight update depends on relative spike timing. Substrate #21.
GeneticCode	Codon → amino acid mapping with Hamming distance d_H = Σ[b_i ≠ b_j]. Includes 30+ variant tables. Substrate #16.
CodonOptimization	Codon reassignment driven by CAI (Codon Adaptation Index): CAI = Π(w_i)^(1/L). Substrate #18.
DNAmethylation	Epigenetic mark — methyl group addition to cytosine, altering expression without changing sequence.
HistoneMod	Histone tail modification (acetylation, methylation, phosphorylation) — encodes regulatory state on chromatin.
Prion	Misfolded protein acting as conformational template — a physical instantiation of the Reverse-Sisyphus structural-memory principle.
Genome18	18-bit genome address space: 6 bins × 3 bits per bin.
r_vs_SAE	Pearson correlation between codon bias and SAE neural feature alignment — a project-specific manifold-capacity proxy.

Thermodynamics

Term	Definition
Trixal	Multi-axis thermodynamic quality state: (thermal, work, irrev) with `
HomeostaticGovernor	Control dynamics: stress = α·surprise + β·regret, pressure evolution p_{t+1} = γ·p_t + s_t. Fixed-point condition: `
DynamicCanal	Adaptive canal that deforms under pressure: λ(p, pressure) with width ≥ 0. Substrate #27.
Landauer	Landauer's principle: minimum energy kT·ln2 per bit erasure. Grounds AngrySphinx thermodynamic asymmetry.
HyperFlow	Navier-Stokes on the manifold: ∂F/∂t = ν∇²F - (F·∇)F + ∇p. Fixed-point convergence with bounded pressure. Substrate #10.
TSM	Thermal State Machine — Builder (ADD), Judge (PAUSE), Warden (SUBTRACT) clock triad.
Reverse-Sisyphus	Property: dC/dt = f(W, C) AND E[W(t+Δ)] < E[W(t)] — work persistently reduces future work on the same pattern class.
CognitiveLoad	5-component load model: (L_I, L_E, L_G, L_R, L_M) with efficiency η = Î/(total+ε). Substrate #14.

Security

Term	Definition
AngrySphinx	Lattice-based PQC primitive. Exponential energy asymmetry: E_attack = n ⟹ E_solve ≥ 2^n. NaN boundary at F → 0. Substrate #3.
FAMM	Frustration-Aware Manifold Mesh — frustration-aligned memory policy that stores failed/partial/successful routes as basin/scar signals. Substrate #6.
FrustrationTensor	Triadic frustration tensor (i, j, k) storing route constraint violation as geometric torsion.
NaNBoundary	The limit surface where AngrySphinx frustration metric F → 0, returning undefined — a deliberate defense mechanism.
PodAccumulator	Distributed attestation accumulator that collects and verifies PIST witness signatures across swarm pods.
Waveprobe	Hysteretic mode-switch security sensor: risk = (1+γ·(1-cosθ))/d² + η·h with barriers B_lock > B_warn > B_recover. Substrate #30.
stark_trace	STARK-based validation trace used by the Warden to verify GCL program execution integrity.
nanokernel_isolation	Theorem: different capabilities map to different physical addresses — non-interference guarantee for MORE FAMM.

Semantics

Term	Definition
CrossDimensionalFilter	Semantic filter operating across dimensions via 12 primal primes. reductionFilter and expansionFilter preserve prime overlap. Substrate #4.
SemanticPrime	One of 12 irreducible semantic dimensions: Identity, Agent, Object, Action, State, Relation, Good, Bad, Want, Know, Place, Time.
reductionFilter	Compresses state to scalar Q0.64 via prime-space projection.
expansionFilter	Reconstructs state from Q0.64 scalar via prime-space interpolation.
PrimeOverlap	The invariant: shared semantic primes must remain non-empty across filtering operations.
Identity / Agent / Object / Action / State / Relation / Good / Bad / Want / Know / Place / Time	The 12 semantic primes — atomic dimensions of the CrossDimensionalFilter.

Meta

Term	Definition
Metatype	The trajectory quality invariant — a formal classification of agent trajectory behavior patterns.
UMUP-λ	Universal Manifold Update Protocol — the λ-parameterized update rule across all manifolds.
IRP	Invariant Receipt Protocol — auditable proof that a transition preserved the declared invariant.
InvariantReceipt	A signed cryptographic receipt proving a specific invariant was preserved through a state transition.
SettlementState	Ladder: SEED → FORMING → STABLE → CRYSTALLIZED → COMPRESSED. Encodes the maturity of a claim, module, or route.
PromotionLadder	Evidence ladder: BEAUTIFUL_PROVISIONAL → CALIBRATED_ENGINEERING_DELTA → REVIEWED → VERIFIED. Each step requires non-LLM evidence.
BLS	BLS signature scheme — aggregate signatures for swarm consensus attestation.
Sigma	Statistical surprise measure (5σ / 6σ / 6.5σ). Applies ONLY to statistical claims, not formal proofs.
FNWH	Formal Non-Wave Harmonic — the underlying harmonic framework for Burgers/Braiding proofs.

Infrastructure

Term	Definition
ENE	Endless Node Edges — distributed, self-replicating credential and node management system with gossip protocol and 2/3 consensus for credential rotation.
OTOM	Ordered Transformation & Orchestration Model — the unifying label for all Research Stack work.
NII	Native Integer ISA — the executable control layer (Semantics.ISA).
SVQF	Spherical Quaternion Vector Field — spherical quaternion geometry for field representation.
PIST	(also listed under Geometry) — serves dual role as witness surface and shell addressing infrastructure.
Substrate	A mathematical layer with: state space, metric, transition, invariant, guard.
FPGA_Warden	FPGA-based Warden node executing stark_trace validation on burned DAG-LUTs.
ASICTopology	Capability-vector topology over ASIC nodes, geodesic distance admissibility check. Substrate #34.
CacheSieve	5×2-bit symbol classifier (PASS/HOLD/REJECT) with sieve invariant. Substrate #36.
DAG-LUT	Burned-in Look-Up Table representing banned/immutable coordinate history. Append-only.
MORE_FAMM	Capability-based memory isolation via BRAM segments. Foundation of the safety architecture.
RcloneIntegration	Formalized TopologicalStorageArea structure — Google Drive as persistent ENE surface.
SubstrateState	Component of VMState — the topological RAM substrate within the virtual machine.

The 36 USTSM Substrates

From docs/roadmaps/UNIVERSAL_SUBSTRATE_ROADMAP.md §1:

#	Substrate	Invariant
1	PIST/DIAT Shell	mass conservation
2	GWL Rotational	dE/dt ≤ 0
3	AngrySphinx	E_solve ≥ 2^n
4	CrossDimensionalFilter	semantic prime preservation
5	SSMS_nD	self-similarity invariant
6	FAMM Frustration	frustration monotonic
7	SolitonTensor	soliton identity
8	TorsionalPIST	quaternion norm
9	HybridTSMPISTTorus	positive mass only
10	HyperFlow	fixed point convergence
11	Q16_16 FixedPoint	totality (no NaN)
12	Q0_64 0D Scalar	stay in [0,1)
13	Trixal Thermodynamic	irrev < threshold
14	Cognitive Load	efficiency ≥ 0
15	Homeostatic Governor	pressure bounded
16	Genetic Code	codon validity
17	Genomic Compression	field invariant
18	Codon Optimization	CAI monotonic
19	Delta GCL	delta(m,m) = empty
20	Spiking Neuron	v < 30 mV until fire
21	STDP Synaptic	bounds conserved
22	Manifold Networking	curvature bounded
23	Quantum Geometry	observational fit
24	GWL Throat	holonomy bounded
25	Braid Field	mergeDebt ≤ threshold
26	Adaptation	isLawful, params in range
27	DynamicCanal	width ≥ 0
28	CompressionMechanics	order contracts
29	PIST Bridge	O(1) per step
30	Waveprobe	B_lock > B_warn > B_recover
31	MasterEquation	probability sum = 1
32	CompressionControl	canonicalized
33	CompressionEvidence	energy decomposes
34	ASICTopology	operation admissible
35	BracketedCalculus	g_l + g_u = u − l
36	CacheSieve	sieve invariant