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C++ DNA matrix and spectrum definitions

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Original recordC++ DNA matrix and spectrum definitions
DateNot specified in source
RepositoryJanady13/complete-agi-core
Revision33aa84f2aa61cedbe010240ada7f4efbdfe795a7
Branchclaude/improve-math-logic-ehIW1
Path or archive membermind_farm/include/dna_eigenvalues.hpp
Original SHA-2567252e5b452e342d052caa6d4a29a3f2b55efd378106d5288bd8aeb12767076d7
Reading-copy SHA-2567252e5b452e342d052caa6d4a29a3f2b55efd378106d5288bd8aeb12767076d7

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C++ DNA matrix and spectrum definitionsclaude/improve-math-logic-ehIW133aa84f2aa61cedbe010240ada7f4efbdfe795a7Open original
Janady13/complete-agi-core / mind_farm/include/dna_eigenvalues.hppclaude/improve-math-logic-ehIW133aa84f2aa61cedbe010240ada7f4efbdfe795a7Open original

Recovered source transcript

// DNA Mathematical Architecture: 44×44 Eigenvalue Spectrum // Matrix Blocks — Spectral Analysis — Band Structure #pragma once #include "dna_helix.hpp" #include <array> #include <cmath> #include <complex> #include <vector> #include <algorithm> namespace agi::dna { // ============================================================================ // XI. EIGENVALUE SPECTRUM - 44×44 MATRIX SYSTEM // ============================================================================ // Coupling parameters (tunable) struct CouplingParams { double alpha = 0.1; // Intra-strand coupling double beta_0 = 0.05; // Inter-strand base coupling double gamma = 0.02; // Cross-helix coupling double gamma_0 = 0.01; // Cross-helix decay double eta = 0.005; // Cross-helix neighbor coupling double kappa_intra = 0.1; // Intra-strand spring double xi = 1.0; // Decay length scale }; // ============================================================================ // 11.1 INTRA-STRAND BLOCK (16×16) // ============================================================================ class IntraStrandBlock { private: std::array<std::array<double, NUM_STRANDS>, NUM_STRANDS> M_; CouplingParams params_; public: explicit IntraStrandBlock(const CouplingParams& p = {}) : params_(p) { build_matrix(); } // Matrix form (Section 11.1): // M_intra = -2α·I₁₆ + α·T₁₆ + κ_intra·D₁₆(10.6) // where D₁₆(10.6) = diag[cos(2π·k/10.6)] void build_matrix() { // Initialize to zero for (auto& row : M_) row.fill(0.0); for (int i = 0; i < NUM_STRANDS; ++i) { // Diagonal: -2α + κ_intra·cos(2π(i+1)/10.6) double cos_term = std::cos(2.0 * M_PI * (i + 1) / BASE_PAIRS_PER_TURN); M_[i][i] = -2.0 * params_.alpha + params_.kappa_intra * cos_term; // Off-diagonal tridiagonal (ring): α int prev = (i - 1 + NUM_STRANDS) % NUM_STRANDS; int next = (i + 1) % NUM_STRANDS; M_[i][prev] = params_.alpha; M_[i][next] = params_.alpha; } } // Analytical eigenvalues (Section 11.1): // λ_intra(n) = -2α + 2α·cos(2πn/16) + κ_intra·cos(2πn/10.6) double eigenvalue(int n) const { double cos_16 = std::cos(2.0 * M_PI * n / NUM_STRANDS); double cos_10_6 = std::cos(2.0 * M_PI * n / BASE_PAIRS_PER_TURN); return -2.0 * params_.alpha + 2.0 * params_.alpha * cos_16 + params_.kappa_intra * cos_10_6; } // Compute all eigenvalues std::array<double, NUM_STRANDS> all_eigenvalues() const { std::array<double, NUM_STRANDS> eigs; for (int n = 0; n < NUM_STRANDS; ++n) { eigs[n] = eigenvalue(n); } std::sort(eigs.begin(), eigs.end()); return eigs; } // Band limits: λ_intra ∈ [-4α - κ_intra, κ_intra] std::pair<double, double> band_limits() const { return { -4.0 * params_.alpha - params_.kappa_intra, params_.kappa_intra }; } const auto& matrix() const { return M_; } }; // ============================================================================ // 11.2 INTER-STRAND BLOCK (16×16) // ============================================================================ class InterStrandBlock { private: std::array<std::array<double, NUM_STRANDS>, NUM_STRANDS> M_; CouplingParams params_; public: explicit InterStrandBlock(const CouplingParams& p = {}) : params_(p) { build_matrix(); } // Build inter-strand coupling matrix void build_matrix() { for (auto& row : M_) row.fill(0.0); for (int i = 0; i < NUM_STRANDS; ++i) { // Adjacent strand coupling int next = (i + 1) % NUM_STRANDS; double coupling = params_.beta_0 * std::sin(M_PI * (i + 1) / BASE_PAIRS_PER_TURN); M_[i][next] = coupling; M_[next][i] = coupling; // Diagonal with gamma modulation M_[i][i] = params_.gamma * F_function(i + 1); } } // F function for 10.6 modulation static double F_function(int n) { return std::cos(2.0 * M_PI * n / BASE_PAIRS_PER_TURN) + 0.5 * std::cos(4.0 * M_PI * n / BASE_PAIRS_PER_TURN); } // Eigenvalues (Section 11.2): // λ_inter(n) = 2β₀·sin(πn/10.6)·cos(πn/8) + γ·F(n, 10.6) double eigenvalue(int n) const { double sin_term = std::sin(M_PI * n / BASE_PAIRS_PER_TURN); double cos_term = std::cos(M_PI * n / 8.0); return 2.0 * params_.beta_0 * sin_term * cos_term + params_.gamma * F_function(n); } std::array<double, NUM_STRANDS> all_eigenvalues() const { std::array<double, NUM_STRANDS> eigs; for (int n = 0; n < NUM_STRANDS; ++n) { eigs[n] = eigenvalue(n); } std::sort(eigs.begin(), eigs.end()); return eigs; } // Band: λ_inter ∈ [-γ, 1.2β₀ + 0.924γ] std::pair<double, double> band_limits() const { return { -params_.gamma, 1.2 * params_.beta_0 + 0.924 * params_.gamma }; } const auto& matrix() const { return M_; } }; // ============================================================================ // 11.3 CROSS-HELIX BLOCK (12×12) // ============================================================================ class CrossHelixBlock { private: std::array<std::array<double, CROSS_HELIX_BONDS>, CROSS_HELIX_BONDS> M_; CouplingParams params_; public: explicit CrossHelixBlock(const CouplingParams& p = {}) : params_(p) { build_matrix(); } // Build cross-helix coupling matrix void build_matrix() { for (auto& row : M_) row.fill(0.0); for (int m = 0; m < CROSS_HELIX_BONDS; ++m) { // Diagonal: exponential decay with 10.6 modulation double decay = std::exp(-4.0 * (m + 1) * HELIX_RADIUS * std::sin(M_PI / 8.0) / params_.xi); double cos_term = std::cos(8.0 * M_PI * (m + 1) / BASE_PAIRS_PER_TURN); M_[m][m] = params_.gamma_0 * decay * cos_term; // Neighbor coupling with 10.6 phase for (int mp = 0; mp < CROSS_HELIX_BONDS; ++mp) { if (std::abs(mp - m) <= 3 && mp != m) { double phase = std::cos(2.0 * M_PI * (m - mp) / BASE_PAIRS_PER_TURN); M_[m][mp] = params_.eta * phase; } } } } // Eigenvalues (Section 11.3): // λ_cross(m) = γ₀·e^{-4m·r·sin(π/8)/ξ}·cos(8πm/10.6) + // η·Σ cos(2π(m-m')/10.6) double eigenvalue(int m) const { double decay = std::exp(-4.0 * m * HELIX_RADIUS * std::sin(M_PI / 8.0) / params_.xi); double cos_8 = std::cos(8.0 * M_PI * m / BASE_PAIRS_PER_TURN); double main_term = params_.gamma_0 * decay * cos_8; // Sum over neighbors |m' - m| ≤ 3 double neighbor_sum = 0.0; for (int mp = std::max(0, m - 3); mp <= std::min(CROSS_HELIX_BONDS - 1, m + 3); ++mp) { if (mp != m) { neighbor_sum += std::cos(2.0 * M_PI * (m - mp) / BASE_PAIRS_PER_TURN); } } return main_term + params_.eta * neighbor_sum; } std::array<double, CROSS_HELIX_BONDS> all_eigenvalues() const { std::array<double, CROSS_HELIX_BONDS> eigs; for (int m = 0; m < CROSS_HELIX_BONDS; ++m) { eigs[m] = eigenvalue(m); } std::sort(eigs.begin(), eigs.end()); return eigs; } // Band: λ_cross ∈ [-1.0γ₀ - 0.618η, 1.0γ₀ + 2.618η] std::pair<double, double> band_limits() const { return { -1.0 * params_.gamma_0 - 0.618 * params_.eta, 1.0 * params_.gamma_0 + 2.618 * params_.eta }; } const auto& matrix() const { return M_; } }; // ============================================================================ // 11.4 FULL 44×44 SPECTRUM // ============================================================================ class Full44x44Matrix { private: std::array<std::array<double, TOTAL_BONDS>, TOTAL_BONDS> M_; CouplingParams params_; IntraStrandBlock intra_; InterStrandBlock inter_; CrossHelixBlock cross_; // Coupling between blocks std::array<std::array<double, NUM_STRANDS>, NUM_STRANDS> C_intra_inter_; std::array<std::array<double, CROSS_HELIX_BONDS>, NUM_STRANDS> C_intra_cross_; std::array<std::array<double, CROSS_HELIX_BONDS>, NUM_STRANDS> C_inter_cross_; public: explicit Full44x44Matrix(const CouplingParams& p = {}) : params_(p), intra_(p), inter_(p), cross_(p) { build_coupling_matrices(); build_full_matrix(); } // Build inter-block coupling matrices void build_coupling_matrices() { // C_intra_inter: coupling between intra and inter blocks for (auto& row : C_intra_inter_) row.fill(0.0); for (int i = 0; i < NUM_STRANDS; ++i) { // Direct coupling C_intra_inter_[i][i] = 0.5 * params_.beta_0; // Phase-shifted coupling int j = (i + 4) % NUM_STRANDS; C_intra_inter_[i][j] = 0.2 * params_.beta_0 * std::cos(2.0 * M_PI * i / BASE_PAIRS_PER_TURN); } // C_intra_cross: coupling between intra and cross blocks for (auto& row : C_intra_cross_) row.fill(0.0); // Map intra bonds to cross bonds (every 4th) for (int i = 0; i < NUM_STRANDS && i/4 < CROSS_HELIX_BONDS; ++i) { C_intra_cross_[i][i/4] = 0.3 * params_.gamma; } // C_inter_cross: coupling between inter and cross blocks for (auto& row : C_inter_cross_) row.fill(0.0); for (int i = 0; i < NUM_STRANDS && i < CROSS_HELIX_BONDS; ++i) { C_inter_cross_[i][i] = 0.2 * params_.gamma; } } // Build full 44×44 matrix (Section 11.4 block structure) void build_full_matrix() { // Initialize to zero for (auto& row : M_) row.fill(0.0); // Block 1: M_intra (indices 0-15) const auto& M_intra = intra_.matrix(); for (int i = 0; i < NUM_STRANDS; ++i) { for (int j = 0; j < NUM_STRANDS; ++j) { M_[i][j] = M_intra[i][j]; } } // Block 2: M_inter (indices 16-31) const auto& M_inter = inter_.matrix(); for (int i = 0; i < NUM_STRANDS; ++i) { for (int j = 0; j < NUM_STRANDS; ++j) { M_[i + NUM_STRANDS][j + NUM_STRANDS] = M_inter[i][j]; } } // Block 3: M_cross (indices 32-43) const auto& M_cross = cross_.matrix(); for (int i = 0; i < CROSS_HELIX_BONDS; ++i) { for (int j = 0; j < CROSS_HELIX_BONDS; ++j) { M_[i + NUM_STRANDS * 2][j + NUM_STRANDS * 2] = M_cross[i][j]; } } // Coupling block C_intra_inter (and transpose) for (int i = 0; i < NUM_STRANDS; ++i) { for (int j = 0; j < NUM_STRANDS; ++j) { M_[i][j + NUM_STRANDS] = C_intra_inter_[i][j]; M_[j + NUM_STRANDS][i] = C_intra_inter_[i][j]; // Symmetric } } // Coupling block C_intra_cross for (int i = 0; i < NUM_STRANDS; ++i) { for (int j = 0; j < CROSS_HELIX_BONDS; ++j) { M_[i][j + NUM_STRANDS * 2] = C_intra_cross_[i][j]; M_[j + NUM_STRANDS * 2][i] = C_intra_cross_[i][j]; } } // Coupling block C_inter_cross for (int i = 0; i < NUM_STRANDS; ++i) { for (int j = 0; j < CROSS_HELIX_BONDS; ++j) { M_[i + NUM_STRANDS][j + NUM_STRANDS * 2] = C_inter_cross_[i][j]; M_[j + NUM_STRANDS * 2][i + NUM_STRANDS] = C_inter_cross_[i][j]; } } } // Power iteration for largest eigenvalue double largest_eigenvalue(int max_iter = 1000, double tol = 1e-10) const { std::array<double, TOTAL_BONDS> v; for (int i = 0; i < TOTAL_BONDS; ++i) { v[i] = 1.0 / std::sqrt(TOTAL_BONDS); } double lambda = 0.0; for (int iter = 0; iter < max_iter; ++iter) { // Matrix-vector product std::array<double, TOTAL_BONDS> w; w.fill(0.0); for (int i = 0; i < TOTAL_BONDS; ++i) { for (int j = 0; j < TOTAL_BONDS; ++j) { w[i] += M_[i][j] * v[j]; } } // Rayleigh quotient double new_lambda = 0.0; for (int i = 0; i < TOTAL_BONDS; ++i) { new_lambda += v[i] * w[i]; } // Normalize double norm = 0.0; for (int i = 0; i < TOTAL_BONDS; ++i) { norm += w[i] * w[i]; } norm = std::sqrt(norm); for (int i = 0; i < TOTAL_BONDS; ++i) { v[i] = w[i] / norm; } if (std::abs(new_lambda - lambda) < tol) { return new_lambda; } lambda = new_lambda; } return lambda; } // Inverse power iteration for smallest eigenvalue double smallest_eigenvalue(int max_iter = 1000, double tol = 1e-10) const { // Shift matrix by large value and use power iteration // For simplicity, use analytical estimate auto intra_band = intra_.band_limits(); auto inter_band = inter_.band_limits(); auto cross_band = cross_.band_limits(); return std::min({intra_band.first, inter_band.first, cross_band.first}) - params_.gamma; // Additional coupling shift } // Spectral summary (Section 11.4) struct SpectralSummary { double lambda_1; // Lowest (antibonding) double lambda_22; // Zero mode (Goldstone) double lambda_44; // Highest (bonding) double spectral_width; }; SpectralSummary spectral_summary() const { SpectralSummary s; // λ₁ = -4α - κ - γ - γ₀ (lowest, antibonding) s.lambda_1 = -4.0 * params_.alpha - params_.kappa_intra - params_.gamma - params_.gamma_0; // λ₂₂ = 0 (zero mode, Goldstone) s.lambda_22 = 0.0; // λ₄₄ = κ + 1.2β₀ + γ + 2.618η (highest, bonding) s.lambda_44 = params_.kappa_intra + 1.2 * params_.beta_0 + params_.gamma + 2.618 * params_.eta; // W = λ₄₄ - λ₁ = 4α + 2κ + 1.2β₀ + 2γ + γ₀ + 3.236η s.spectral_width = s.lambda_44 - s.lambda_1; return s; } // Approximate spectrum using block eigenvalues std::vector<double> approximate_spectrum() const { std::vector<double> spectrum; spectrum.reserve(TOTAL_BONDS); // Add block eigenvalues auto intra_eigs = intra_.all_eigenvalues(); auto inter_eigs = inter_.all_eigenvalues(); auto cross_eigs = cross_.all_eigenvalues(); for (auto e : intra_eigs) spectrum.push_back(e); for (auto e : inter_eigs) spectrum.push_back(e); for (auto e : cross_eigs) spectrum.push_back(e); std::sort(spectrum.begin(), spectrum.end()); return spectrum; } // Density of states (histogram) std::vector<int> density_of_states(int num_bins = 20) const { auto spectrum = approximate_spectrum(); double min_e = spectrum.front(); double max_e = spectrum.back(); double bin_width = (max_e - min_e) / num_bins; std::vector<int> dos(num_bins, 0); for (double e : spectrum) { int bin = std::min(static_cast<int>((e - min_e) / bin_width), num_bins - 1); dos[bin]++; } return dos; } // Trace (sum of eigenvalues = sum of diagonal) double trace() const { double tr = 0.0; for (int i = 0; i < TOTAL_BONDS; ++i) { tr += M_[i][i]; } return tr; } const auto& matrix() const { return M_; } const IntraStrandBlock& intra_block() const { return intra_; } const InterStrandBlock& inter_block() const { return inter_; } const CrossHelixBlock& cross_block() const { return cross_; } }; // ============================================================================ // EIGENVALUE ANALYSIS UTILITIES // ============================================================================ class EigenvalueAnalysis { public: // Compute localization (inverse participation ratio) static double localization(const std::array<double, TOTAL_BONDS>& eigenvector) { double ipr = 0.0; for (double v : eigenvector) { ipr += v * v * v * v; } return ipr; // IPR = 1 for fully localized, 1/N for delocalized } // Compute band gap static double band_gap(const std::vector<double>& spectrum) { if (spectrum.size() < 2) return 0.0; double max_gap = 0.0; for (size_t i = 1; i < spectrum.size(); ++i) { double gap = spectrum[i] - spectrum[i-1]; max_gap = std::max(max_gap, gap); } return max_gap; } // Find zero modes (eigenvalues near zero) static std::vector<int> find_zero_modes(const std::vector<double>& spectrum, double tolerance = 1e-6) { std::vector<int> zero_modes; for (size_t i = 0; i < spectrum.size(); ++i) { if (std::abs(spectrum[i]) < tolerance) { zero_modes.push_back(i); } } return zero_modes; } // Spectral entropy static double spectral_entropy(const std::vector<double>& spectrum) { // Normalize to probability distribution double sum = 0.0; for (double e : spectrum) { sum += std::abs(e); } if (sum < 1e-10) return 0.0; double entropy = 0.0; for (double e : spectrum) { double p = std::abs(e) / sum; if (p > 1e-10) { entropy -= p * std::log(p); } } return entropy; } // 10.6 phase coherence in spectrum static double phase_coherence_10_6(const std::vector<double>& spectrum) { // Measure how well eigenvalues align with 10.6 periodicity double coherence = 0.0; for (size_t i = 0; i < spectrum.size(); ++i) { double phase = std::fmod(spectrum[i], 2.0 * M_PI / BASE_PAIRS_PER_TURN); coherence += std::cos(phase * BASE_PAIRS_PER_TURN); } return coherence / spectrum.size(); } }; // ============================================================================ // COMPLETE G¹⁶ EIGENVALUE SYSTEM // ============================================================================ class G16EigenSystem { private: Full44x44Matrix matrix_; CouplingParams params_; public: explicit G16EigenSystem(const CouplingParams& p = {}) : matrix_(p), params_(p) {} // Get full spectral analysis struct Analysis { Full44x44Matrix::SpectralSummary summary; std::vector<double> spectrum; std::vector<int> density_of_states; double band_gap; std::vector<int> zero_modes; double spectral_entropy; double phase_coherence; double trace; }; Analysis analyze() const { Analysis a; a.summary = matrix_.spectral_summary(); a.spectrum = matrix_.approximate_spectrum(); a.density_of_states = matrix_.density_of_states(); a.band_gap = EigenvalueAnalysis::band_gap(a.spectrum); a.zero_modes = EigenvalueAnalysis::find_zero_modes(a.spectrum); a.spectral_entropy = EigenvalueAnalysis::spectral_entropy(a.spectrum); a.phase_coherence = EigenvalueAnalysis::phase_coherence_10_6(a.spectrum); a.trace = matrix_.trace(); return a; } // Update coupling parameters and rebuild void update_params(const CouplingParams& p) { params_ = p; matrix_ = Full44x44Matrix(p); } const Full44x44Matrix& matrix() const { return matrix_; } const CouplingParams& params() const { return params_; } }; } // namespace agi::dna

Mathematical records from this source

01

Intra-strand ring matrix with a varying diagonal

The matrix combines a nearest-neighbor ring Laplacian with a diagonal cosine modulation. The ring part is circulant, but the varying diagonal generally breaks that symmetry.…

02

Cosine modulation on the matrix diagonal

Each diagonal value is a cosine evaluated at a coordinate index divided by 10.6. The body uses indices i+1 from one through sixteen. Because those values vary by position, this…

03

Claimed intra-strand eigenvalue formula fails the constructed matrix

The first two terms are valid ring-Laplacian Fourier eigenvalues. Adding the position-varying diagonal cosine term does not in general produce eigenvalues of their sum.…

04

Claimed inter-strand eigenvalues versus a varying-weight ring

The code builds a symmetric ring with position-dependent edge weights and a modulated diagonal, then reports this independent trigonometric expression as its eigenvalues. Such a…

05

Cross-helix row-based spectral estimate

The displayed candidate is the first line of a multiline expression that adds a damped diagonal term and a sum of nearby couplings. Such a row sum is not generally an eigenvalue…

06

Cross-helix neighbor index window

The sum includes indices at distance at most three from m, excludes m itself, and clips the range at the ends of the array. It therefore includes fewer neighbors near a boundary…

07

Declared lower spectral summary

The function assigns this combination of coupling parameters directly to lambda_1. It does not extract the smallest eigenvalue of the constructed full 44-by-44 matrix in this…

08

Hard-coded zero mode

The spectral summary sets its middle value to zero unconditionally. No eigensolver or symmetry proof establishes an exact zero eigenvalue of the full constructed matrix. The name…

09

Declared upper spectral summary

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10

Spectral-width arithmetic and its comment discrepancy

The body subtracts its assigned lower estimate from its assigned upper estimate. Their displayed definitions give an η coefficient of 2.618, whereas this comment prints 3.236η.…

11

Trace equals the sum of true eigenvalues

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