Track A - Intrinsic Transition Measures (v8.1): Threshold-Free Characterization of Coexistence Dynamics in the Two-Mode Jaynes-Cummings Model

# Two-Mode Jaynes–Cummings Model of Endogenous and Exogenous Phase Coherence **Complete Zenodo record with historical development** **DOI:** [10.5281/zenodo.22904994](https://doi.org/10.5281/zenodo.22904994) **Authors:** Miguel Angel Percudani (corresponding: miguel_percudani@yahoo.com.ar, ORCID [0009-0007-1748-3212](https://orcid.org/0009-0007-1748-3212)) & Jorge Iván Díaz **Affiliation:** Independent Research Collaboration **Publication date:** 22 September 2026 **Related records:**- Binary Universe Ontology: [10.5281/zenodo.18015439](https://doi.org/10.5281/zenodo.18015439) (2025)- UAT framework: [10.5281/zenodo.17886549](https://doi.org/10.5281/zenodo.17886549) (2025)- Antifrequency datasets: [10.5281/zenodo.17861265](https://doi.org/10.5281/zenodo.17861265) (2025) --- ## 1. Central paper — read this first > **`track_A_formal.pdf`** (746 kB, 7 pages) > *A Two-Mode Jaynes–Cummings Model of Endogenous and Exogenous Phase Coherence: Falsifiable Predictions for Neural Dynamics* This is the **formal, falsifiable Track A**. The model contains **no geometric constants** (ΦUAT, kUAT, κcrit). The coupling strength g₀ is a free parameter to be fitted to EEG/fMRI data. **This PDF is the one to cite.** All other files in this record are complementary or supplementary. --- ## 2. Two-track structure The record is organized in two independent tracks: ### Track A — Formal, falsifiable, testable now A two-mode Jaynes–Cummings model with Lindblad dissipation and Default Mode Network modulation. The model produces a two-dimensional phase diagram in the plane (α = g/δ,\ γ_φ) and four falsifiable predictions for EEG/fMRI experiments. All parameters are free and listed in the paper. **Track A remains valid even if Track B is refuted.** Documents:- **`track_A_formal.pdf`** (7 pages) — main paper, 4 falsifiable predictions, phase diagram- **`track_A_field_equations.pdf`** (15 pages) — technical appendix: complete field equations, Hilbert space, operator algebra, Lindblad dissipator, master equation, reduced dynamics, BDF numerical scheme- **`track_A_Extended_version_full_derivation.pdf`** (20 pages) — extended appendix that **supersedes** the previous one: it contains all the material of `track_A_field_equations.pdf` plus three new sections with full step-by-step derivations: - (i) mean-field closure of the reduced dynamics - (ii) expansion of the density matrix in the Jaynes–Cummings eigenbasis (dressed states) - (iii) linear stability analysis of the Liouvillian superoperator and spectral gap Δ Both appendix versions are provided for convenience. **The extended version is the recommended reference.** ### Track B — Speculative research program An ontological interpretation of Track A in terms of the Binary Universe Ontology (Bit 1 = analytic qubit, Bit 0 = substrate oscillator, causal friction = Jaynes–Cummings exchange, homeostasis = Lindblad dissipation, DMN = baryonic filter). Contains the constants ΦUAT = π²/8, kUAT ≈ 10.90677, κcrit ≈ 10⁻⁷⁸ **explicitly labeled as speculative hypotheses, not derived results.** Document:- **`track_B_speculative.pdf`** (6 pages) — *Binary Universe Ontology as an Interpretation of Two-Mode Coupling: The Geometric Origin of kUAT as a Speculative Research Program* The two tracks are independent. Track A does not use any of the constants from Track B. Track B does not modify the numerical results of Track A. --- ## 3. Figures (stand-alone PNGs for reuse) - **`v5_run1_rabi.png`** (130 kB) — Rabi oscillation: σz, n₀, SvN, purity for $g = 17$ Hz, 10 periods- **`v6_scan2D.png`** (150 kB) — Phase diagram in (α = g/δ,\ γ_φ) plane, four steady-state observables- **`v6_cortes1D.png`** (173 kB) — One-dimensional cuts at γ_φ ∈ \0.09, 0.44, 2.26, 11.60\ Hz --- ## 4. LaTeX sources (for reproducibility) - `LaTex_track_A_formal.tex` (16 kB) — source of the central paper- `LaTex_track_A_field_equations.tex` (31 kB) — source of the 15-page field-equations appendix- `LaTex_track_A_Extended_version_full_derivation.tex` (45 kB) — source of the 20-page extended appendix- `LaTex_track_B_speculative.tex` (17 kB) — source of the speculative interpretation All sources compile with `pdflatex` (two passes required for cross-references). No external dependencies beyond the standard TeX Live distribution. --- ## 5. Code archives (historical development) The numerical results were developed over six versions. Each `trackA_vN.zip` contains the scripts and data as they were at that stage. Historical versions are included for transparency; **only v5 and v6 are needed to reproduce the published results.** ### Historical / supplementary - **`trackA_v2.zip`** (326 kB) — v2: manual RK4 integrator, initial dark state |0,0 bug, crashes for γ_φ 10 due to stiffness- **`trackA_v3.zip`** (426 kB) — v3: fix with BDF implicit solver (`scipy.integrate.solve_ivp`), first stable runs- **`trackA_v4.zip`** (630 kB) — v4: first sweep in (α, γ_φ) plane- **`trackA_v4_1.zip`** (643 kB) — v4.1: JC coupling corrected (standard Jaynes–Cummings, not anti-JC) ### Final — use these to reproduce - **`trackA_v5.zip`** (1,626 kB) — **IMPORTANT**: Rabi runs and endogen/exogen contrast at equal Rabi period. Generated `v5_run1_rabi.png`.- **`trackA_v6.zip`** (510 kB) — **IMPORTANT**: Final 2D scan and 1D cuts, phase diagram, boundary αcruce(γ_φ), empirical scaling gcruce · γ_φ0.62 ≈ 3.95. **This is the version used in `track_A_formal.pdf`.** --- ## 6. How to reproduce the central result ### Numerical ```bash# Main result (phase diagram + Rabi)unzip trackA_v6.zip && cd trackA_v6python -m venv venv && source venv/bin/activatepip install numpy scipy pandas matplotlibpython main.py # BDF solver, rtol=1e-7, atol=1e-9# Outputs: v6_scan2D.png, v6_cortes1D.png ## 12. Update: intrinsic transition measures (v8.1) In September 2026, the numerical exploration was extended with v8.1, which replaces the threshold-based definition of the "coexistence window" used in earlier versions (v7.x) with threshold-free intrinsic measures based on the product P(t) = R(t) · I(t). Key result: two distinct coexistence regimes emerge: - Vigilance: slow, weak, sustained (P_max = 0.006, W_half = 46, eta = 0.87) - Flow / Endogenous / Sleep: fast, intense, brief (P_max ≈ 0.013-0.016, W_half ≈ 8-15, eta ≈ 0.24-0.38) The trade-off between peak intensity and effective duration is quantified. See trackA_v8_1.zip for code, data, and figures. Licencia: CC BY 4.0 para manuscritos, MIT para código.