universal-physics-tensor 7.0.0 → 9.0.0

package/dist/bridges/equations/be-24-foerster-fret.d.ts

@@ -1,87 +0,0 @@
-/**
- * Bridge Equation 24 — Förster Resonance Energy Transfer (FRET) efficiency.
- *
- *   η = R_0⁶ / (R_0⁶ + R⁶)  ≡  1 / (1 + (R/R_0)⁶)
- *
- * R is the donor-acceptor distance, R_0 is the Förster radius (typically
- * 2-10 nm; defined as the distance at which η = 1/2). η ∈ [0,1] by
- * construction.
- *
- * BE-24's catalog `formula_latex` carries TWO formulas — the
- * dipole-dipole transfer rate `k_FRET = (1/τ_D)·(R_0/R)⁶` (dim [T^-1])
- * and the bound-respecting efficiency `η` (dimensionless). We encode
- * the EFFICIENCY here because:
- *   - it is the natural FRET observable in donor-acceptor distance
- *     measurements;
- *   - η ∈ [0,1] by construction (no bound-violation regime to worry
- *     about);
- *   - it round-trips cleanly to `[1]` through the validator without
- *     needing a τ_D dimensional symbol.
- *
- * Reference: Förster 1948 *Ann. Phys. (Leipzig)* 437:55 (canonical FRET
- * derivation). Lakowicz 2006 *Principles of Fluorescence Spectroscopy*
- * 3rd ed. Ch. 13 (textbook reference for both k_FRET and η forms).
- *
- * Status: speculative.
- *
- * Honest-claude scope notes:
- *   - The Förster formulas are canonical; the *bridge framing* (using
- *     FRET as a UPT quantum ↔ biological bridge) is the speculative
- *     element. Same convention as BE-22 (Kitaev-Preskill canonical,
- *     QG framing speculative) and BE-38 (Milgrom MOND canonical, UPT
- *     framing speculative).
- *   - FRET is incoherent (incoherent dipole-dipole rate, no
- *     quantum-coherent enhancement); the long-running quantum-coherence-
- *     in-photosynthesis question (Engel 2007 vs. Cao 2020 / Duan 2017
- *     / Thyrhaug 2018) is contested. UPT pins FRET as the canonical
- *     baseline — see BE-24 `known_issues` for the contested-coherence
- *     reformulation candidate.
- *   - The Förster radius R_0 is itself set by `R_0⁶ ∝ κ² Q_D J / n⁴`
- *     (orientation factor κ², donor quantum yield Q_D, spectral overlap
- *     J, refractive index n). UPT does not commit to a specific
- *     R_0-decomposition; R_0 is treated as a free input.
- *
- * @see docs/specification/Part-II.md ("Bridge Equation 24: Quantum Coherence in Photosynthesis Efficiency")
- * @see src/bridges/index.ts BRIDGE_EQUATIONS.find(e => e.id === 24)
- * @module bridges/equations/be-24-foerster-fret
- */
-import type { ExprNode, DimensionValidationReport } from '../../dimensional/validator.js';
-/**
- * RHS of the FRET efficiency:
- *   η = R_0⁶ / (R_0⁶ + R⁶)
- *
- * Encoded directly: numerator R_0⁶ and denominator R_0⁶ + R⁶, both with
- * dim [L^6]. The ratio is dimensionless. The sextic powers use the `^`
- * op with literal-numeric exponent 6.
- */
-export declare const BE24_FRET_EFFICIENCY_RHS: ExprNode;
-/** LHS: η is dimensionless. */
-/** @internal */
-export declare const BE24_FRET_EFFICIENCY_LHS: ExprNode;
-/**
- * @internal — typed-arg shape for the file-local `evaluateFRETEfficiency` function; not in the v0.7 public surface. See `docs/architecture/archive/v0.7-be-module-exports-audit.md` §4.
- */
-interface FRETEfficiencyInputs {
-    /** Donor-acceptor distance R (m). Must be > 0 and finite. */
-    R: number;
-    /** Förster radius R_0 (m). Must be > 0 and finite. */
-    R_0: number;
-}
-/**
- * Evaluate the FRET transfer efficiency
- *
- *   η = 1 / (1 + (R/R_0)⁶)  ∈ [0, 1]
- *
- * Equivalent canonical form: η = R_0⁶/(R_0⁶ + R⁶).
- *
- * @returns Dimensionless efficiency η ∈ [0, 1].
- */
-export declare function evaluateFRETEfficiency(input: FRETEfficiencyInputs): number;
-/**
- * Run the AST through the dimensional analyzer; both sides should be
- * dimensionless.
- */
-/** @internal */
-export declare function validateBE24Dimensions(): DimensionValidationReport;
-export {};
-//# sourceMappingURL=be-24-foerster-fret.d.ts.map

package/dist/bridges/equations/be-24-foerster-fret.d.ts.map

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package/dist/bridges/equations/be-24-foerster-fret.js

@@ -1,113 +0,0 @@
-/**
- * Bridge Equation 24 — Förster Resonance Energy Transfer (FRET) efficiency.
- *
- *   η = R_0⁶ / (R_0⁶ + R⁶)  ≡  1 / (1 + (R/R_0)⁶)
- *
- * R is the donor-acceptor distance, R_0 is the Förster radius (typically
- * 2-10 nm; defined as the distance at which η = 1/2). η ∈ [0,1] by
- * construction.
- *
- * BE-24's catalog `formula_latex` carries TWO formulas — the
- * dipole-dipole transfer rate `k_FRET = (1/τ_D)·(R_0/R)⁶` (dim [T^-1])
- * and the bound-respecting efficiency `η` (dimensionless). We encode
- * the EFFICIENCY here because:
- *   - it is the natural FRET observable in donor-acceptor distance
- *     measurements;
- *   - η ∈ [0,1] by construction (no bound-violation regime to worry
- *     about);
- *   - it round-trips cleanly to `[1]` through the validator without
- *     needing a τ_D dimensional symbol.
- *
- * Reference: Förster 1948 *Ann. Phys. (Leipzig)* 437:55 (canonical FRET
- * derivation). Lakowicz 2006 *Principles of Fluorescence Spectroscopy*
- * 3rd ed. Ch. 13 (textbook reference for both k_FRET and η forms).
- *
- * Status: speculative.
- *
- * Honest-claude scope notes:
- *   - The Förster formulas are canonical; the *bridge framing* (using
- *     FRET as a UPT quantum ↔ biological bridge) is the speculative
- *     element. Same convention as BE-22 (Kitaev-Preskill canonical,
- *     QG framing speculative) and BE-38 (Milgrom MOND canonical, UPT
- *     framing speculative).
- *   - FRET is incoherent (incoherent dipole-dipole rate, no
- *     quantum-coherent enhancement); the long-running quantum-coherence-
- *     in-photosynthesis question (Engel 2007 vs. Cao 2020 / Duan 2017
- *     / Thyrhaug 2018) is contested. UPT pins FRET as the canonical
- *     baseline — see BE-24 `known_issues` for the contested-coherence
- *     reformulation candidate.
- *   - The Förster radius R_0 is itself set by `R_0⁶ ∝ κ² Q_D J / n⁴`
- *     (orientation factor κ², donor quantum yield Q_D, spectral overlap
- *     J, refractive index n). UPT does not commit to a specific
- *     R_0-decomposition; R_0 is treated as a free input.
- *
- * @see docs/specification/Part-II.md ("Bridge Equation 24: Quantum Coherence in Photosynthesis Efficiency")
- * @see src/bridges/index.ts BRIDGE_EQUATIONS.find(e => e.id === 24)
- * @module bridges/equations/be-24-foerster-fret
- */
-import { DIMENSIONLESS, LENGTH, } from '../../dimensional/types.js';
-import { sym, validateFiniteInputs, validateBEDimensions } from './_be-helpers.js';
-/**
- * RHS of the FRET efficiency:
- *   η = R_0⁶ / (R_0⁶ + R⁶)
- *
- * Encoded directly: numerator R_0⁶ and denominator R_0⁶ + R⁶, both with
- * dim [L^6]. The ratio is dimensionless. The sextic powers use the `^`
- * op with literal-numeric exponent 6.
- */
-export const BE24_FRET_EFFICIENCY_RHS = {
-    kind: 'op', op: '/',
-    args: [
-        {
-            // R_0^6
-            kind: 'op', op: '^',
-            args: [sym('R_0', LENGTH), sym('6', DIMENSIONLESS)],
-        },
-        {
-            // R_0^6 + R^6  (both terms are [L^6])
-            kind: 'op', op: '+',
-            args: [
-                {
-                    kind: 'op', op: '^',
-                    args: [sym('R_0', LENGTH), sym('6', DIMENSIONLESS)],
-                },
-                {
-                    kind: 'op', op: '^',
-                    args: [sym('R', LENGTH), sym('6', DIMENSIONLESS)],
-                },
-            ],
-        },
-    ],
-};
-/** LHS: η is dimensionless. */
-/** @internal */
-export const BE24_FRET_EFFICIENCY_LHS = sym('eta_transfer', DIMENSIONLESS);
-/**
- * Evaluate the FRET transfer efficiency
- *
- *   η = 1 / (1 + (R/R_0)⁶)  ∈ [0, 1]
- *
- * Equivalent canonical form: η = R_0⁶/(R_0⁶ + R⁶).
- *
- * @returns Dimensionless efficiency η ∈ [0, 1].
- */
-export function evaluateFRETEfficiency(input) {
-    validateFiniteInputs(input, [
-        { name: 'R', min: 0, excludeMin: true },
-        { name: 'R_0', min: 0, excludeMin: true },
-    ], 'evaluateFRETEfficiency');
-    const { R, R_0 } = input;
-    const ratio = R / R_0;
-    const ratio6 = Math.pow(ratio, 6);
-    return 1 / (1 + ratio6);
-}
-// --- Self-validation ---
-/**
- * Run the AST through the dimensional analyzer; both sides should be
- * dimensionless.
- */
-/** @internal */
-export function validateBE24Dimensions() {
-    return validateBEDimensions(BE24_FRET_EFFICIENCY_LHS, BE24_FRET_EFFICIENCY_RHS, 'BE24');
-}
-//# sourceMappingURL=be-24-foerster-fret.js.map

package/dist/bridges/equations/be-24-foerster-fret.js.map

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package/dist/bridges/equations/be-25-iit-phi.d.ts

@@ -1,222 +0,0 @@
-/**
- * Bridge Equation 25 — Consciousness ↔ Information Integration (IIT Φ).
- *
- * Encodes the **inner intrinsic-information form** from Integrated
- * Information Theory (Tononi; Oizumi-Albantakis-Tononi 2014 IIT 3.0;
- * Albantakis et al. 2023 IIT 4.0):
- *
- *   ii(s, s̃) = p(s̃ | s) · log₂[ p(s̃ | s) / p(s̃) ]
- *
- * where `s` is a candidate-substrate state and `s̃` a successor state
- * in its transition probability matrix (TPM). `ii(s, s̃)` measures, in
- * bits, the irreducibility of the conditional probability `p(s̃|s)`
- * against the substrate-marginal `p(s̃)`.
- *
- * The full canonical Φ_max formula is
- *
- *   Φ_max(S) = min_{θ ∈ partitions(S)} [ ii(s, s̃) - ii_θ(s, s̃) ]
- *
- * The outer `min_θ` is the **minimum information partition (MIP)** —
- * a discrete optimization over the set of bipartitions of the
- * substrate. The UPT AST grammar (`symbol | op (* / + - ^) | integral |
- * derivative`) has no `min` primitive over a discrete index set, so the
- * MIP outer structure is **deferred grammar-extension** (same status
- * as BE-15 stochastic noise and BE-28 Lagrange multipliers). This
- * module encodes the **inner** ii(s, s̃) — the kernel that the MIP
- * minimizes — as DIMENSIONLESS.
- *
- * **Bits is a pseudo-unit, not an SI dimension.** Φ and ii have units
- * of bits when log₂ is used (or nats with ln, hartleys with log₁₀).
- * Bits is not in the SI 7-base system; it is the LHS of a unit-free
- * pure number when measured in the canonical IIT convention. The
- * dimensional analyzer therefore types ii as DIMENSIONLESS `[1]`. The
- * encoding committee preserves the "bits" semantics by docstring
- * convention; the validator only enforces that all components are
- * dimensionally consistent.
- *
- * **Faithful `transcendental` log₂ (v0.19).** `log₂[p(s̃|s)/p(s̃)]` is encoded
- * as a `transcendental` `log2` node over the inner ratio, which is exposed
- * separately as `BE25_LOG_RATIO_ARG` so a lemma test can verify the argument is
- * dimensionless directly. (dimensionless → dimensionless, so the round-trip
- * dimensional_signature is unchanged.)
- *
- * **AST structure (multiplicative, not additive — note the difference
- * from BE-45).** BE-45's RHS `log(M_P/H_inf) − γ·log(r/0.01)` is a
- * *sum* of two log-stubs. BE-25's `p(s̃|s) · log₂[p(s̃|s)/p(s̃)]` is a
- * *product* — a probability times a log-stub. Both are encoded with
- * the same fresh-symbol-stub convention; only the outer operator
- * differs.
- *
- * Bracket-checks (numerical evaluator computes ii(s,s̃) = p_cond ·
- * log₂(p_cond/p_marg)):
- *   - Maximum irreducibility (p_cond = 1, p_marg → 0⁺): ii → +∞;
- *   - No irreducibility (p_cond = p_marg, e.g. both 0.5):
- *     ii = 0.5 · log₂(1) = 0;
- *   - "Surprise" case (p_cond = 0.5, p_marg = 0.25):
- *     ii = 0.5 · log₂(2) = 0.5 bits;
- *   - Shannon-zero (p_cond = 0, p_marg arbitrary): ii = 0 (limit);
- *   - Impossible-joint (p_cond > 0, p_marg = 0): KL-divergence
- *     diverges — caller error (RangeError thrown).
- *
- * References:
- *   - Tononi 2008 *Biol. Bull.* 215:216 (canonical original IIT
- *     formulation; integrated information as a measure of
- *     consciousness).
- *   - Oizumi, Albantakis & Tononi 2014 *PLoS Comput. Biol.* 10:e1003588
- *     (IIT 3.0; calculable Φ via earth-mover's distance / Wasserstein
- *     metric over partitions; minimum information partition; the
- *     canonical computational-IIT reference).
- *   - Albantakis, Barbosa, Findlay, Grasso, Haun, Marshall, Mayner,
- *     Zaeemzadeh, Boly, Juel, Sasai, Fujii, David, Bjørndahl, Lemmon,
- *     Allen, Mosquera, Ladd, Hassan, Hendren, Kim, Yu, Tian, Chen,
- *     Tsuchiya & Tononi 2023 *PLoS Comput. Biol.* 19:e1011465
- *     (arXiv:2212.14787; IIT 4.0 with explicit axiom-postulate
- *     framework).
- *   - Wikipedia "Phi (integrated information theory)" / "Integrated
- *     information theory" (canonical Φ formula via MIP and intrinsic
- *     information ii(s,s̃) = p(s̃|s) log₂[p(s̃|s)/p(s̃)]).
- *   - Aaronson 2014 blog "Why I am not an integrated information
- *     theorist" (computational counterexamples yielding arbitrarily
- *     large Φ for systems generally not regarded as conscious;
- *     canonical contested-framework citation).
- *
- * Status: speculative (NOT lifted by this encoding).
- *
- * Honest-claude scope notes:
- *   - This module encodes the **inner** ii(s, s̃) only. The outer
- *     `min_θ` over partitions (MIP) and the partition-conditional
- *     `ii_θ` lemma are NOT encoded — both require a `min`-over-index-
- *     set grammar extension that the UPT AST does not currently
- *     support. The same deferral applies to BE-15 (stochastic noise)
- *     and BE-28 (Lagrange multipliers).
- *   - Status 'speculative' is **not lifted by this encoding**. IIT
- *     itself is calculable and well-defined; the bridge framing
- *     (consciousness ↔ maximally-integrated-information) is contested
- *     by Aaronson 2014 (computational counterexamples) and Doerig
- *     2019 (unfolding argument). Pinning a Tier-5 AST does not
- *     promote the bridge claim.
- *   - The 0·log(0) = 0 limit (p_cond → 0) is enforced by the
- *     numerical evaluator following Shannon's canonical convention
- *     and Oizumi-Albantakis-Tononi 2014. The p_marg = 0 with
- *     p_cond > 0 case (KL-divergence singularity) is rejected with
- *     RangeError because the joint outcome is physically inconsistent
- *     (the system did transition to s̃ but the marginal says s̃ is
- *     impossible).
- *   - Φ_max is exponential in substrate size (EXPTIME); the numerical
- *     evaluator here only computes ii for a single (s, s̃) pair, not
- *     the outer MIP minimization. Computing Φ_max for substrates with
- *     more than ~10 elements is intractable in practice.
- *   - **Encoded form vs. IIT 4.0 canonical metric (Wave-Z final-review
- *     scope note, 2026-05-11):** the encoded
- *     `ii(s,s̃) = p(s̃|s) · log₂[p(s̃|s)/p(s̃)]` is the *pointwise-KL*
- *     / Wikipedia / IIT-pedagogical simplified form of the intrinsic
- *     information. IIT 3.0 (Oizumi-Albantakis-Tononi 2014) and IIT 4.0
- *     (Albantakis et al. 2023) use the **earth-mover's distance**
- *     (Wasserstein metric) as the canonical irreducibility measure on
- *     the cause-effect repertoire, NOT the pointwise log-ratio. The
- *     two agree in spirit and give qualitatively similar Φ rankings
- *     for small systems but differ quantitatively. The encoded log-
- *     ratio is preferred here because (a) it has a closed-form scalar
- *     reduction the AST grammar can express, and (b) it is the form
- *     most commonly cited in introductory IIT references. Encoding
- *     the Wasserstein metric would require a transport-plan primitive
- *     the UPT AST does not have.
- *
- * @see docs/specification/Part-II.md ("Bridge Equation 25: Consciousness — Information Integration Bridge")
- * @see src/bridges/index.ts BRIDGE_EQUATIONS.find(e => e.id === 25)
- * @see src/bridges/equations/be-25-orch-or.ts (archived; legacy Penrose-Hameroff form)
- * @module bridges/equations/be-25-iit-phi
- */
-import type { ExprNode, DimensionValidationReport } from '../../dimensional/validator.js';
-/**
- * Lemma AST: the conditional probability `p(s̃|s)` (DIMENSIONLESS,
- * ∈ [0, 1]).
- *
- * Exposed as a separate node so it can be reused inside both
- * `BE25_LOG_RATIO_ARG` and `BE25_INTRINSIC_INFORMATION_RHS`. The
- * validator only sees its dimension (DIMENSIONLESS); the [0, 1] range
- * is a semantic property enforced by the numerical evaluator's
- * input-validation guards, not the type system.
- */
-export declare const BE25_P_CONDITIONAL: ExprNode;
-/**
- * Lemma AST: the marginal probability `p(s̃)` (DIMENSIONLESS, ∈ [0, 1]).
- *
- * Same convention as `BE25_P_CONDITIONAL`: dimension is DIMENSIONLESS;
- * the [0, 1] range is enforced numerically, not type-theoretically.
- */
-export declare const BE25_P_MARGINAL: ExprNode;
-/**
- * Lemma AST: the log₂ argument `p(s̃|s) / p(s̃)` (DIMENSIONLESS, the
- * ratio of two probabilities).
- *
- * Exposed for the lemma test that verifies the argument is
- * dimensionless (per the dimensionless-stub convention; see
- * `src/dimensional/README.md` "Encoding transcendental functions").
- */
-export declare const BE25_LOG_RATIO_ARG: ExprNode;
-/**
- * Lemma AST: the `log₂[p(s̃|s) / p(s̃)]` factor, encoded as a faithful
- * `transcendental` `log2` node (v0.19) over the inner ratio. The log argument
- * is exposed separately via `BE25_LOG_RATIO_ARG` so the lemma test can verify
- * it is dimensionless.
- */
-export declare const BE25_LOG2_FACTOR: ExprNode;
-/**
- * RHS of `ii(s, s̃) = p(s̃|s) · log₂[p(s̃|s) / p(s̃)]` as a typed
- * ExprNode tree:
- *
- *   p_cond · log2_ratio_ii
- *
- * `BE25_LOG2_FACTOR` is a faithful `transcendental` `log2` node; its
- * argument `p_cond / p_marg` is exposed via `BE25_LOG_RATIO_ARG` and
- * verified dimensionless directly. The product of a dimensionless probability
- * and a dimensionless log is DIMENSIONLESS — same shape as BE-46's `A · exp_factor`.
- */
-export declare const BE25_INTRINSIC_INFORMATION_RHS: ExprNode;
-/**
- * LHS: ii(s, s̃) is in bits (DIMENSIONLESS in the SI sense — bits is
- * a pseudo-unit not in the SI 7-base system).
- */
-/** @internal */
-export declare const BE25_INTRINSIC_INFORMATION_LHS: ExprNode;
-/**
- * @internal — typed-arg shape for the file-local `evaluateIntrinsicInformation` function; not in the v0.7 public surface. See `docs/architecture/archive/v0.7-be-module-exports-audit.md` §4.
- */
-interface IntrinsicInformationInputs {
-    /** Conditional probability p(s̃|s) ∈ [0, 1]. Must be finite. */
-    p_cond: number;
-    /** Marginal probability p(s̃) ∈ (0, 1]. Must be finite. When `p_cond > 0`, must be > 0 (KL-divergence singularity rejected). */
-    p_marg: number;
-}
-/**
- * Evaluate the inner intrinsic information of a (s, s̃) transition
- * pair:
- *
- *   ii(s, s̃) = p_cond · log₂(p_cond / p_marg)
- *
- * Edge cases (Shannon convention; matches Oizumi-Albantakis-Tononi
- * 2014 IIT 3.0):
- *
- *   - p_cond = 0: returns 0 (the canonical limit 0 · log(0) = 0).
- *     The value of p_marg is not consulted in this branch.
- *   - p_cond > 0 and p_marg = 0: throws RangeError. The joint outcome
- *     is physically inconsistent — the system did transition to s̃
- *     but the marginal says s̃ has zero probability; the KL-divergence
- *     diverges to +∞.
- *   - p_cond = p_marg: returns 0 (no irreducibility — conditional
- *     equals marginal means s̃ was no more or less likely given s).
- *
- * @returns Intrinsic information in bits (dimensionless; can be
- *   negative when p_cond < p_marg — i.e., conditioning on s makes s̃
- *   less likely than the unconditional marginal).
- */
-export declare function evaluateIntrinsicInformation(input: IntrinsicInformationInputs): number;
-/**
- * Run the AST through the dimensional analyzer; LHS and RHS should
- * both be DIMENSIONLESS.
- */
-/** @internal */
-export declare function validateBE25Dimensions(): DimensionValidationReport;
-export {};
-//# sourceMappingURL=be-25-iit-phi.d.ts.map

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