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THE CONSCIOUSNESS ATLAS
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ConsciousnessLearn · Explore · Joseph Anady

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. Consequently its eigenvalues cannot generally be obtained by simply adding a Fourier-mode ring…

Implementation mathematicsSource recovered; runtime not executed
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gh-eq-305c562b1eda0383source-comment-equation
Mintra=−2α⋅I16+α⋅T16+κintra⋅D16(10.6)M_intra = -2α·I₁₆ + α·T₁₆ + κ_intra·D₁₆(10.6)

Read the equation

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. Consequently its eigenvalues cannot generally be obtained by simply adding a Fourier-mode ring eigenvalue to a diagonal entry.

Terms & definitions

TermMeaning in this source
alpha

Ring coupling

kappa_intra

Diagonal-modulation amplitude

I_16

Identity matrix

T_16

Ring neighbor adjacency

D_16

Cosine diagonal

How it works

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Original context

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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;
Exact original notation
M_intra = -2α·I₁₆ + α·T₁₆ + κ_intra·D₁₆(10.6)

Related builds

Sources & provenance

01
C++ DNA matrix and spectrum definitions
Lines 44–44 · 33aa84f2aa61
02
C++ DNA matrix and spectrum definitions
Lines 44–44 · 33aa84f2aa61

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