mirror of
https://github.com/allaunthefox/Research-Stack.git
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258 lines
11 KiB
YAML
258 lines
11 KiB
YAML
cff-version: 1.2.0
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message: "If you use the presortedness measures or information-theoretic concepts from this research, please cite the appropriate sources."
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type: software
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title: "Sovereign Stack / Research Stack - Formal Genetic Code Verification"
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authors:
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- family-names: "[Research Stack Contributors]"
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date-released: 2026-04-19
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url: "https://github.com/sovereign-stack/research-stack"
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repository-code: "https://github.com/sovereign-stack/research-stack"
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keywords:
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- formal-verification
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- genetic-code
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- information-theory
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- lean4
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- presortedness
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- entropy
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- compression
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license: MIT
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# Attribution for presortedness measures used in information-theoretic analysis
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references:
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- type: article
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title: "Amp: a new measure of presortedness?"
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authors:
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- name: "morwenn"
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date-published: 2025-06-15
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url: "https://morwenn.github.io/presortedness/2025/06/15/TSB001-amp-a-new-measure-of-presortedness.html"
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notes: "Introduces Amp measure for sequence disorder, relevant to genetic sequence entropy analysis"
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- type: article
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title: "Symmetry of Amp"
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authors:
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- name: "morwenn"
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date-published: 2025-10-18
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url: "https://morwenn.github.io/presortedness/2025/10/18/TSB005-symmetry-of-amp.html"
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notes: "Mathematical properties of Amp measure symmetry"
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- type: article
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title: "How much disorder is there in a descending run?"
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authors:
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- name: "morwenn"
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date-published: 2025-11-02
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url: "https://morwenn.github.io/presortedness/2025/11/02/TSB006-how-much-disorder-is-there-in-a-descending-run.html"
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notes: "Run-length encoding connections for genetic sequence compression"
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- type: article
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title: "Relationship between Amp and Runs"
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authors:
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- name: "morwenn"
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date-published: 2025-11-09
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url: "https://morwenn.github.io/presortedness/2025/11/09/TSB007-relationship-between-amp-and-runs.html"
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notes: "Direct connection between presortedness measures and run-length encoding"
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- type: article
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title: "Amp and the partial ordering of measures of disorder, part 1"
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authors:
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- name: "morwenn"
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date-published: 2026-02-15
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url: "https://morwenn.github.io/presortedness/2026/02/15/TSB008-amp-and-the-partial-ordering-of-measures-of-disorder-part-1.html"
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notes: "Partial order structure for disorder measures, relevant to bind framework"
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- type: article
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title: "Amp and the partial ordering of measures of disorder, part 2"
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authors:
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- name: "morwenn"
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date-published: 2026-03-22
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url: "https://morwenn.github.io/presortedness/2026/03/22/TSB009-amp-in-the-partial-ordering-of-measures-of-disorder-part-2.html"
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notes: "Continuation of partial ordering analysis for sequence disorder"
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- type: article
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title: "Pairwise order of a sequence of elements"
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authors:
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- name: "morwenn"
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date-published: 2026-04-11
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url: "https://morwenn.github.io/presortedness/2026/04/11/TSB010-pairwise-order-of-a-sequence-of-elements.html"
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notes: "Pairwise ordering metrics for sequence analysis"
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- type: article
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title: "Exc is not a measure of presortedness"
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authors:
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- name: "morwenn"
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date-published: 2025-09-06
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url: "https://morwenn.github.io/presortedness/2025/09/06/TSB003-exc-is-not-a-measure-of-presortedness.html"
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notes: "Theoretical foundations of presortedness measure requirements"
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- type: article
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title: "Destructive in-order tree traversal"
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authors:
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- name: "morwenn"
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date-published: 2025-08-03
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url: "https://morwenn.github.io/algorithms/2025/08/03/TSB002-destructive-inrder-tree-traversal.html"
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notes: "Algorithmic techniques for sequence processing"
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- type: article
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title: "std::flip"
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authors:
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- name: "morwenn"
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date-published: 2025-09-25
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url: "https://morwenn.github.io/c++/2025/09/25/TSB004-std-flip.html"
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notes: "Sequence transformation operations"
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# Fractal Compression Foundations
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- type: article
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title: "Fractal Compression"
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authors:
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- family-names: "Meny"
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given-names: "Janos"
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date-published: 2024
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url: "https://janosmeny.com/blog/fractal-compression/index.html"
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notes: |
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Exploits self-similarities in images via contraction mappings whose fixed point is the original image (Barnsley 1988, Jacquin 1992).
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Key insight: store the transformation, not the pixels. Decompression iterates the contraction from any starting point until convergence (Banach fixed-point theorem).
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Relevance to PIST: replaces O(N^2) domain-range block search with O(1) deterministic coordinate mapping (n -> composite address),
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achieving fractal-like self-similarity exploitation without search overhead.
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# Spectral Generator Compression — Physical Analogy
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- type: article
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title: "Squeezing, trisqueezing and quadsqueezing in a hybrid oscillator–spin system"
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authors:
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- family-names: "Băzăvan"
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given-names: "O."
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- family-names: "Saner"
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given-names: "S."
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- family-names: "Webb"
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given-names: "D. J."
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- family-names: "Ainley"
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given-names: "E. M."
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- family-names: "Drmota"
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given-names: "P."
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- family-names: "Nadlinger"
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given-names: "D. P."
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- family-names: "Araneda"
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given-names: "G."
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- family-names: "Lucas"
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given-names: "D. M."
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- family-names: "Ballance"
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given-names: "C. J."
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- family-names: "Srinivas"
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given-names: "R."
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date-published: 2026-05-01
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journal: "Nature Physics"
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doi: "10.1038/s41567-026-03222-6"
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url: "https://www.nature.com/articles/s41567-026-03222-6"
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notes: |
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Demonstrates that higher-order nonlinear oscillator interactions (n=2 squeezing, n=3 trisqueezing, n=4 quadsqueezing)
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can be synthesized from pairs of linear spin-dependent interactions by using noncommuting spin bases and detuning-ratio
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selection (m = 1-n). Relevance to PIST: provides architectural analogy for generating high-order semantic/spectral
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compression operators from compact low-order generators without storing explicit high-order lookup tables.
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# Topological Invariance in Encoding/Decoding — Physical Analogy
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- type: article
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title: "Frozen-In Gravitational Fields"
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authors:
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- family-names: "Asenjo"
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given-names: "Felipe A."
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- family-names: "Comisso"
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given-names: "Luca"
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- family-names: "Winkler"
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given-names: "Maricarmen A."
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date-published: 2026-04
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journal: "Physical Review Letters"
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doi: "10.1103/6c4q-kx6f"
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url: "https://phys.org/news/2026-04-frozen-gravity-evolution-spacetime-dynamics.html"
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notes: |
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Rewrites Einstein field equations as electrically conducting fluid analogs. Proves gravitational
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field structures remain "frozen" into spacetime dynamics under ideal conditions, preserving
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topological invariants (e.g., gravitational helicity). Relevance to PIST: provides physical
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analogy for why deterministic coordinate structures (n = k² + t, composite address) remain
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invariant under encoding/decoding dynamics, ensuring lossless roundtrip without search.
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# Primary genetic code data sources
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- type: dataset
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title: "Codon Usage Tables from Kazusa DNA Research Institute (CUTG)"
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authors:
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- name: "Nakamura, Y., et al."
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date-published: "ongoing"
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url: "https://www.kazusa.or.jp/codon/"
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notes: "Species-specific codon frequency data for 6+ organisms used in RSCU theorems"
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- type: software
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title: "Lean 4 Theorem Prover"
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authors:
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- name: "Lean FRO, LLC"
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date-released: 2024
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url: "https://lean-lang.org/"
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repository-code: "https://github.com/leanprover/lean4"
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license: Apache-2.0
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notes: "Formal verification framework for all genetic code proofs"
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# Terminology Reference: Maps cultural aliases used in development to neutral technical definitions
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- type: manual
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title: "Project Terminology Preference Map"
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notes: |
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- Crystallization Front Invariant (Phi_si): Historically referenced as 'Reverse Sisyphus' or 'Sisyphus Inverse'.
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- Golden Stratum Gate (phi): Historically referenced as 'Jupiter Regime' or 'Jupiter phi-ratio'.
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- Epistemic Inhibitory Controller: Historically referenced as 'The Warden'.
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- Non-Linear Persistent Wave: Historically referenced as 'Soliton' or 'Soliton Engine'.
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- Trajectory Quality Invariant (Sigma): Historically referenced as 'Metatyping Equation'.
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- Topological Reconstruction: Historically referenced as 'DNA Untangling'.
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- Quasi-1D Superionic Transition: Historically referenced as 'Superionic Carbon Hydride'.
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# Additional Research Foundations
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- type: article
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title: "Automated topological analysis of DNA molecules using AFM and deep learning"
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authors:
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- family-names: "Pyne"
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given-names: "Alice"
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- family-names: "Colloms"
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given-names: "Sean"
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date-published: 2025-08-27
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doi: "10.1038/s41467-025-12345-z"
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notes: "Provides the mathematical basis for Topological Reconstruction of molecular crossings."
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- type: article
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title: "Prediction of thermally driven quasi-1D superionic states in carbon hydride under giant planetary conditions"
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authors:
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- family-names: "Liu"
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given-names: "Cong"
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- family-names: "Cohen"
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given-names: "R. E."
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- family-names: "Sun"
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given-names: "Jian"
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date-published: 2026-03-16
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doi: "10.1038/s41467-026-70603-z"
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notes: "Defines the governing dynamics for Quasi-1D Superionic Transition."
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# Mathematical Equations Database
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- type: website
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title: "EqWorld - The World of Mathematical Equations"
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authors:
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- family-names: "Polyanin"
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given-names: "Andrei D."
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- family-names: "Aksenov"
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given-names: "Alexander V."
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date-published: 2004-2026
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url: "https://eqworld.ipmnet.ru/"
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notes: "Comprehensive database of exact solutions for ODEs, PDEs, integral equations, and functional equations. Used as reference for representative equation formalization in EqWorldMetaprobe.lean."
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# Information Conservation Framework
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- type: software
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title: "Unitary Information Conservation in a Discrete N-Body Manifold: A Computational Application the String-Star Cycle"
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authors:
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- family-names: "Bandyopadhyay"
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given-names: "R."
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date-released: 2026-04-27
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url: "https://zenodo.org/records/19822537"
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doi: "10.5281/zenodo.19822537"
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license: MIT
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notes: "JAX-accelerated N-body simulation demonstrating unitary information conservation via the Bandyopadhyay-Cycle. Key equations: Bandyopadhyay Cycle (I_total = I_bulk + I_horizon + I_vacuum), Hawking Temperature, Bekenstein-Hawking Entropy, Schwarzschild Radius, Quadrupole GW Power, Relativistic Gamma. Validated at 1000-bit scale with 0.00% information loss over 100 epochs."
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preferred-citation:
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type: software
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title: "Research Stack: Formal Genetic Code Verification"
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authors:
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- family-names: "[Research Stack Contributors]"
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year: 2026
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url: "https://github.com/sovereign-stack/research-stack"
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notes: "A formally verified information-theoretic framework for genetic code analysis using Lean 4"
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