Recovered source transcript
1// DNA Mathematical Architecture: 44×44 Eigenvalue Spectrum
2// Matrix Blocks — Spectral Analysis — Band Structure
3#pragma once
4
5#include "dna_helix.hpp"
6#include <array>
7#include <cmath>
8#include <complex>
9#include <vector>
10#include <algorithm>
11
12namespace agi::dna {
13
14// ============================================================================
15// XI. EIGENVALUE SPECTRUM - 44×44 MATRIX SYSTEM
16// ============================================================================
17
18// Coupling parameters (tunable)
19struct CouplingParams {
20 double alpha = 0.1; // Intra-strand coupling
21 double beta_0 = 0.05; // Inter-strand base coupling
22 double gamma = 0.02; // Cross-helix coupling
23 double gamma_0 = 0.01; // Cross-helix decay
24 double eta = 0.005; // Cross-helix neighbor coupling
25 double kappa_intra = 0.1; // Intra-strand spring
26 double xi = 1.0; // Decay length scale
27};
28
29// ============================================================================
30// 11.1 INTRA-STRAND BLOCK (16×16)
31// ============================================================================
32
33class IntraStrandBlock {
34private:
35 std::array<std::array<double, NUM_STRANDS>, NUM_STRANDS> M_;
36 CouplingParams params_;
37
38public:
39 explicit IntraStrandBlock(const CouplingParams& p = {}) : params_(p) {
40 build_matrix();
41 }
42
43 // Matrix form (Section 11.1):
44 // M_intra = -2α·I₁₆ + α·T₁₆ + κ_intra·D₁₆(10.6)
45 // where D₁₆(10.6) = diag[cos(2π·k/10.6)]
46 void build_matrix() {
47 // Initialize to zero
48 for (auto& row : M_) row.fill(0.0);
49
50 for (int i = 0; i < NUM_STRANDS; ++i) {
51 // Diagonal: -2α + κ_intra·cos(2π(i+1)/10.6)
52 double cos_term = std::cos(2.0 * M_PI * (i + 1) / BASE_PAIRS_PER_TURN);
53 M_[i][i] = -2.0 * params_.alpha + params_.kappa_intra * cos_term;
54
55 // Off-diagonal tridiagonal (ring): α
56 int prev = (i - 1 + NUM_STRANDS) % NUM_STRANDS;
57 int next = (i + 1) % NUM_STRANDS;
58 M_[i][prev] = params_.alpha;
59 M_[i][next] = params_.alpha;
60 }
61 }
62
63 // Analytical eigenvalues (Section 11.1):
64 // λ_intra(n) = -2α + 2α·cos(2πn/16) + κ_intra·cos(2πn/10.6)
65 double eigenvalue(int n) const {
66 double cos_16 = std::cos(2.0 * M_PI * n / NUM_STRANDS);
67 double cos_10_6 = std::cos(2.0 * M_PI * n / BASE_PAIRS_PER_TURN);
68 return -2.0 * params_.alpha + 2.0 * params_.alpha * cos_16 +
69 params_.kappa_intra * cos_10_6;
70 }
71
72 // Compute all eigenvalues
73 std::array<double, NUM_STRANDS> all_eigenvalues() const {
74 std::array<double, NUM_STRANDS> eigs;
75 for (int n = 0; n < NUM_STRANDS; ++n) {
76 eigs[n] = eigenvalue(n);
77 }
78 std::sort(eigs.begin(), eigs.end());
79 return eigs;
80 }
81
82 // Band limits: λ_intra ∈ [-4α - κ_intra, κ_intra]
83 std::pair<double, double> band_limits() const {
84 return {
85 -4.0 * params_.alpha - params_.kappa_intra,
86 params_.kappa_intra
87 };
88 }
89
90 const auto& matrix() const { return M_; }
91};
92
93// ============================================================================
94// 11.2 INTER-STRAND BLOCK (16×16)
95// ============================================================================
96
97class InterStrandBlock {
98private:
99 std::array<std::array<double, NUM_STRANDS>, NUM_STRANDS> M_;
100 CouplingParams params_;
101
102public:
103 explicit InterStrandBlock(const CouplingParams& p = {}) : params_(p) {
104 build_matrix();
105 }
106
107 // Build inter-strand coupling matrix
108 void build_matrix() {
109 for (auto& row : M_) row.fill(0.0);
110
111 for (int i = 0; i < NUM_STRANDS; ++i) {
112 // Adjacent strand coupling
113 int next = (i + 1) % NUM_STRANDS;
114 double coupling = params_.beta_0 * std::sin(M_PI * (i + 1) / BASE_PAIRS_PER_TURN);
115 M_[i][next] = coupling;
116 M_[next][i] = coupling;
117
118 // Diagonal with gamma modulation
119 M_[i][i] = params_.gamma * F_function(i + 1);
120 }
121 }
122
123 // F function for 10.6 modulation
124 static double F_function(int n) {
125 return std::cos(2.0 * M_PI * n / BASE_PAIRS_PER_TURN) +
126 0.5 * std::cos(4.0 * M_PI * n / BASE_PAIRS_PER_TURN);
127 }
128
129 // Eigenvalues (Section 11.2):
130 // λ_inter(n) = 2β₀·sin(πn/10.6)·cos(πn/8) + γ·F(n, 10.6)
131 double eigenvalue(int n) const {
132 double sin_term = std::sin(M_PI * n / BASE_PAIRS_PER_TURN);
133 double cos_term = std::cos(M_PI * n / 8.0);
134 return 2.0 * params_.beta_0 * sin_term * cos_term +
135 params_.gamma * F_function(n);
136 }
137
138 std::array<double, NUM_STRANDS> all_eigenvalues() const {
139 std::array<double, NUM_STRANDS> eigs;
140 for (int n = 0; n < NUM_STRANDS; ++n) {
141 eigs[n] = eigenvalue(n);
142 }
143 std::sort(eigs.begin(), eigs.end());
144 return eigs;
145 }
146
147 // Band: λ_inter ∈ [-γ, 1.2β₀ + 0.924γ]
148 std::pair<double, double> band_limits() const {
149 return {
150 -params_.gamma,
151 1.2 * params_.beta_0 + 0.924 * params_.gamma
152 };
153 }
154
155 const auto& matrix() const { return M_; }
156};
157
158// ============================================================================
159// 11.3 CROSS-HELIX BLOCK (12×12)
160// ============================================================================
161
162class CrossHelixBlock {
163private:
164 std::array<std::array<double, CROSS_HELIX_BONDS>, CROSS_HELIX_BONDS> M_;
165 CouplingParams params_;
166
167public:
168 explicit CrossHelixBlock(const CouplingParams& p = {}) : params_(p) {
169 build_matrix();
170 }
171
172 // Build cross-helix coupling matrix
173 void build_matrix() {
174 for (auto& row : M_) row.fill(0.0);
175
176 for (int m = 0; m < CROSS_HELIX_BONDS; ++m) {
177 // Diagonal: exponential decay with 10.6 modulation
178 double decay = std::exp(-4.0 * (m + 1) * HELIX_RADIUS *
179 std::sin(M_PI / 8.0) / params_.xi);
180 double cos_term = std::cos(8.0 * M_PI * (m + 1) / BASE_PAIRS_PER_TURN);
181 M_[m][m] = params_.gamma_0 * decay * cos_term;
182
183 // Neighbor coupling with 10.6 phase
184 for (int mp = 0; mp < CROSS_HELIX_BONDS; ++mp) {
185 if (std::abs(mp - m) <= 3 && mp != m) {
186 double phase = std::cos(2.0 * M_PI * (m - mp) / BASE_PAIRS_PER_TURN);
187 M_[m][mp] = params_.eta * phase;
188 }
189 }
190 }
191 }
192
193 // Eigenvalues (Section 11.3):
194 // λ_cross(m) = γ₀·e^{-4m·r·sin(π/8)/ξ}·cos(8πm/10.6) +
195 // η·Σ cos(2π(m-m')/10.6)
196 double eigenvalue(int m) const {
197 double decay = std::exp(-4.0 * m * HELIX_RADIUS *
198 std::sin(M_PI / 8.0) / params_.xi);
199 double cos_8 = std::cos(8.0 * M_PI * m / BASE_PAIRS_PER_TURN);
200 double main_term = params_.gamma_0 * decay * cos_8;
201
202 // Sum over neighbors |m' - m| ≤ 3
203 double neighbor_sum = 0.0;
204 for (int mp = std::max(0, m - 3); mp <= std::min(CROSS_HELIX_BONDS - 1, m + 3); ++mp) {
205 if (mp != m) {
206 neighbor_sum += std::cos(2.0 * M_PI * (m - mp) / BASE_PAIRS_PER_TURN);
207 }
208 }
209
210 return main_term + params_.eta * neighbor_sum;
211 }
212
213 std::array<double, CROSS_HELIX_BONDS> all_eigenvalues() const {
214 std::array<double, CROSS_HELIX_BONDS> eigs;
215 for (int m = 0; m < CROSS_HELIX_BONDS; ++m) {
216 eigs[m] = eigenvalue(m);
217 }
218 std::sort(eigs.begin(), eigs.end());
219 return eigs;
220 }
221
222 // Band: λ_cross ∈ [-1.0γ₀ - 0.618η, 1.0γ₀ + 2.618η]
223 std::pair<double, double> band_limits() const {
224 return {
225 -1.0 * params_.gamma_0 - 0.618 * params_.eta,
226 1.0 * params_.gamma_0 + 2.618 * params_.eta
227 };
228 }
229
230 const auto& matrix() const { return M_; }
231};
232
233// ============================================================================
234// 11.4 FULL 44×44 SPECTRUM
235// ============================================================================
236
237class Full44x44Matrix {
238private:
239 std::array<std::array<double, TOTAL_BONDS>, TOTAL_BONDS> M_;
240 CouplingParams params_;
241
242 IntraStrandBlock intra_;
243 InterStrandBlock inter_;
244 CrossHelixBlock cross_;
245
246 // Coupling between blocks
247 std::array<std::array<double, NUM_STRANDS>, NUM_STRANDS> C_intra_inter_;
248 std::array<std::array<double, CROSS_HELIX_BONDS>, NUM_STRANDS> C_intra_cross_;
249 std::array<std::array<double, CROSS_HELIX_BONDS>, NUM_STRANDS> C_inter_cross_;
250
251public:
252 explicit Full44x44Matrix(const CouplingParams& p = {})
253 : params_(p), intra_(p), inter_(p), cross_(p) {
254 build_coupling_matrices();
255 build_full_matrix();
256 }
257
258 // Build inter-block coupling matrices
259 void build_coupling_matrices() {
260 // C_intra_inter: coupling between intra and inter blocks
261 for (auto& row : C_intra_inter_) row.fill(0.0);
262 for (int i = 0; i < NUM_STRANDS; ++i) {
263 // Direct coupling
264 C_intra_inter_[i][i] = 0.5 * params_.beta_0;
265 // Phase-shifted coupling
266 int j = (i + 4) % NUM_STRANDS;
267 C_intra_inter_[i][j] = 0.2 * params_.beta_0 *
268 std::cos(2.0 * M_PI * i / BASE_PAIRS_PER_TURN);
269 }
270
271 // C_intra_cross: coupling between intra and cross blocks
272 for (auto& row : C_intra_cross_) row.fill(0.0);
273 // Map intra bonds to cross bonds (every 4th)
274 for (int i = 0; i < NUM_STRANDS && i/4 < CROSS_HELIX_BONDS; ++i) {
275 C_intra_cross_[i][i/4] = 0.3 * params_.gamma;
276 }
277
278 // C_inter_cross: coupling between inter and cross blocks
279 for (auto& row : C_inter_cross_) row.fill(0.0);
280 for (int i = 0; i < NUM_STRANDS && i < CROSS_HELIX_BONDS; ++i) {
281 C_inter_cross_[i][i] = 0.2 * params_.gamma;
282 }
283 }
284
285 // Build full 44×44 matrix (Section 11.4 block structure)
286 void build_full_matrix() {
287 // Initialize to zero
288 for (auto& row : M_) row.fill(0.0);
289
290 // Block 1: M_intra (indices 0-15)
291 const auto& M_intra = intra_.matrix();
292 for (int i = 0; i < NUM_STRANDS; ++i) {
293 for (int j = 0; j < NUM_STRANDS; ++j) {
294 M_[i][j] = M_intra[i][j];
295 }
296 }
297
298 // Block 2: M_inter (indices 16-31)
299 const auto& M_inter = inter_.matrix();
300 for (int i = 0; i < NUM_STRANDS; ++i) {
301 for (int j = 0; j < NUM_STRANDS; ++j) {
302 M_[i + NUM_STRANDS][j + NUM_STRANDS] = M_inter[i][j];
303 }
304 }
305
306 // Block 3: M_cross (indices 32-43)
307 const auto& M_cross = cross_.matrix();
308 for (int i = 0; i < CROSS_HELIX_BONDS; ++i) {
309 for (int j = 0; j < CROSS_HELIX_BONDS; ++j) {
310 M_[i + NUM_STRANDS * 2][j + NUM_STRANDS * 2] = M_cross[i][j];
311 }
312 }
313
314 // Coupling block C_intra_inter (and transpose)
315 for (int i = 0; i < NUM_STRANDS; ++i) {
316 for (int j = 0; j < NUM_STRANDS; ++j) {
317 M_[i][j + NUM_STRANDS] = C_intra_inter_[i][j];
318 M_[j + NUM_STRANDS][i] = C_intra_inter_[i][j]; // Symmetric
319 }
320 }
321
322 // Coupling block C_intra_cross
323 for (int i = 0; i < NUM_STRANDS; ++i) {
324 for (int j = 0; j < CROSS_HELIX_BONDS; ++j) {
325 M_[i][j + NUM_STRANDS * 2] = C_intra_cross_[i][j];
326 M_[j + NUM_STRANDS * 2][i] = C_intra_cross_[i][j];
327 }
328 }
329
330 // Coupling block C_inter_cross
331 for (int i = 0; i < NUM_STRANDS; ++i) {
332 for (int j = 0; j < CROSS_HELIX_BONDS; ++j) {
333 M_[i + NUM_STRANDS][j + NUM_STRANDS * 2] = C_inter_cross_[i][j];
334 M_[j + NUM_STRANDS * 2][i + NUM_STRANDS] = C_inter_cross_[i][j];
335 }
336 }
337 }
338
339 // Power iteration for largest eigenvalue
340 double largest_eigenvalue(int max_iter = 1000, double tol = 1e-10) const {
341 std::array<double, TOTAL_BONDS> v;
342 for (int i = 0; i < TOTAL_BONDS; ++i) {
343 v[i] = 1.0 / std::sqrt(TOTAL_BONDS);
344 }
345
346 double lambda = 0.0;
347 for (int iter = 0; iter < max_iter; ++iter) {
348 // Matrix-vector product
349 std::array<double, TOTAL_BONDS> w;
350 w.fill(0.0);
351 for (int i = 0; i < TOTAL_BONDS; ++i) {
352 for (int j = 0; j < TOTAL_BONDS; ++j) {
353 w[i] += M_[i][j] * v[j];
354 }
355 }
356
357 // Rayleigh quotient
358 double new_lambda = 0.0;
359 for (int i = 0; i < TOTAL_BONDS; ++i) {
360 new_lambda += v[i] * w[i];
361 }
362
363 // Normalize
364 double norm = 0.0;
365 for (int i = 0; i < TOTAL_BONDS; ++i) {
366 norm += w[i] * w[i];
367 }
368 norm = std::sqrt(norm);
369 for (int i = 0; i < TOTAL_BONDS; ++i) {
370 v[i] = w[i] / norm;
371 }
372
373 if (std::abs(new_lambda - lambda) < tol) {
374 return new_lambda;
375 }
376 lambda = new_lambda;
377 }
378 return lambda;
379 }
380
381 // Inverse power iteration for smallest eigenvalue
382 double smallest_eigenvalue(int max_iter = 1000, double tol = 1e-10) const {
383 // Shift matrix by large value and use power iteration
384 // For simplicity, use analytical estimate
385 auto intra_band = intra_.band_limits();
386 auto inter_band = inter_.band_limits();
387 auto cross_band = cross_.band_limits();
388
389 return std::min({intra_band.first, inter_band.first, cross_band.first}) -
390 params_.gamma; // Additional coupling shift
391 }
392
393 // Spectral summary (Section 11.4)
394 struct SpectralSummary {
395 double lambda_1; // Lowest (antibonding)
396 double lambda_22; // Zero mode (Goldstone)
397 double lambda_44; // Highest (bonding)
398 double spectral_width;
399 };
400
401 SpectralSummary spectral_summary() const {
402 SpectralSummary s;
403
404 // λ₁ = -4α - κ - γ - γ₀ (lowest, antibonding)
405 s.lambda_1 = -4.0 * params_.alpha - params_.kappa_intra -
406 params_.gamma - params_.gamma_0;
407
408 // λ₂₂ = 0 (zero mode, Goldstone)
409 s.lambda_22 = 0.0;
410
411 // λ₄₄ = κ + 1.2β₀ + γ + 2.618η (highest, bonding)
412 s.lambda_44 = params_.kappa_intra + 1.2 * params_.beta_0 +
413 params_.gamma + 2.618 * params_.eta;
414
415 // W = λ₄₄ - λ₁ = 4α + 2κ + 1.2β₀ + 2γ + γ₀ + 3.236η
416 s.spectral_width = s.lambda_44 - s.lambda_1;
417
418 return s;
419 }
420
421 // Approximate spectrum using block eigenvalues
422 std::vector<double> approximate_spectrum() const {
423 std::vector<double> spectrum;
424 spectrum.reserve(TOTAL_BONDS);
425
426 // Add block eigenvalues
427 auto intra_eigs = intra_.all_eigenvalues();
428 auto inter_eigs = inter_.all_eigenvalues();
429 auto cross_eigs = cross_.all_eigenvalues();
430
431 for (auto e : intra_eigs) spectrum.push_back(e);
432 for (auto e : inter_eigs) spectrum.push_back(e);
433 for (auto e : cross_eigs) spectrum.push_back(e);
434
435 std::sort(spectrum.begin(), spectrum.end());
436 return spectrum;
437 }
438
439 // Density of states (histogram)
440 std::vector<int> density_of_states(int num_bins = 20) const {
441 auto spectrum = approximate_spectrum();
442 double min_e = spectrum.front();
443 double max_e = spectrum.back();
444 double bin_width = (max_e - min_e) / num_bins;
445
446 std::vector<int> dos(num_bins, 0);
447 for (double e : spectrum) {
448 int bin = std::min(static_cast<int>((e - min_e) / bin_width), num_bins - 1);
449 dos[bin]++;
450 }
451 return dos;
452 }
453
454 // Trace (sum of eigenvalues = sum of diagonal)
455 double trace() const {
456 double tr = 0.0;
457 for (int i = 0; i < TOTAL_BONDS; ++i) {
458 tr += M_[i][i];
459 }
460 return tr;
461 }
462
463 const auto& matrix() const { return M_; }
464 const IntraStrandBlock& intra_block() const { return intra_; }
465 const InterStrandBlock& inter_block() const { return inter_; }
466 const CrossHelixBlock& cross_block() const { return cross_; }
467};
468
469// ============================================================================
470// EIGENVALUE ANALYSIS UTILITIES
471// ============================================================================
472
473class EigenvalueAnalysis {
474public:
475 // Compute localization (inverse participation ratio)
476 static double localization(const std::array<double, TOTAL_BONDS>& eigenvector) {
477 double ipr = 0.0;
478 for (double v : eigenvector) {
479 ipr += v * v * v * v;
480 }
481 return ipr; // IPR = 1 for fully localized, 1/N for delocalized
482 }
483
484 // Compute band gap
485 static double band_gap(const std::vector<double>& spectrum) {
486 if (spectrum.size() < 2) return 0.0;
487
488 double max_gap = 0.0;
489 for (size_t i = 1; i < spectrum.size(); ++i) {
490 double gap = spectrum[i] - spectrum[i-1];
491 max_gap = std::max(max_gap, gap);
492 }
493 return max_gap;
494 }
495
496 // Find zero modes (eigenvalues near zero)
497 static std::vector<int> find_zero_modes(const std::vector<double>& spectrum,
498 double tolerance = 1e-6) {
499 std::vector<int> zero_modes;
500 for (size_t i = 0; i < spectrum.size(); ++i) {
501 if (std::abs(spectrum[i]) < tolerance) {
502 zero_modes.push_back(i);
503 }
504 }
505 return zero_modes;
506 }
507
508 // Spectral entropy
509 static double spectral_entropy(const std::vector<double>& spectrum) {
510 // Normalize to probability distribution
511 double sum = 0.0;
512 for (double e : spectrum) {
513 sum += std::abs(e);
514 }
515 if (sum < 1e-10) return 0.0;
516
517 double entropy = 0.0;
518 for (double e : spectrum) {
519 double p = std::abs(e) / sum;
520 if (p > 1e-10) {
521 entropy -= p * std::log(p);
522 }
523 }
524 return entropy;
525 }
526
527 // 10.6 phase coherence in spectrum
528 static double phase_coherence_10_6(const std::vector<double>& spectrum) {
529 // Measure how well eigenvalues align with 10.6 periodicity
530 double coherence = 0.0;
531 for (size_t i = 0; i < spectrum.size(); ++i) {
532 double phase = std::fmod(spectrum[i], 2.0 * M_PI / BASE_PAIRS_PER_TURN);
533 coherence += std::cos(phase * BASE_PAIRS_PER_TURN);
534 }
535 return coherence / spectrum.size();
536 }
537};
538
539// ============================================================================
540// COMPLETE G¹⁶ EIGENVALUE SYSTEM
541// ============================================================================
542
543class G16EigenSystem {
544private:
545 Full44x44Matrix matrix_;
546 CouplingParams params_;
547
548public:
549 explicit G16EigenSystem(const CouplingParams& p = {}) : matrix_(p), params_(p) {}
550
551 // Get full spectral analysis
552 struct Analysis {
553 Full44x44Matrix::SpectralSummary summary;
554 std::vector<double> spectrum;
555 std::vector<int> density_of_states;
556 double band_gap;
557 std::vector<int> zero_modes;
558 double spectral_entropy;
559 double phase_coherence;
560 double trace;
561 };
562
563 Analysis analyze() const {
564 Analysis a;
565 a.summary = matrix_.spectral_summary();
566 a.spectrum = matrix_.approximate_spectrum();
567 a.density_of_states = matrix_.density_of_states();
568 a.band_gap = EigenvalueAnalysis::band_gap(a.spectrum);
569 a.zero_modes = EigenvalueAnalysis::find_zero_modes(a.spectrum);
570 a.spectral_entropy = EigenvalueAnalysis::spectral_entropy(a.spectrum);
571 a.phase_coherence = EigenvalueAnalysis::phase_coherence_10_6(a.spectrum);
572 a.trace = matrix_.trace();
573 return a;
574 }
575
576 // Update coupling parameters and rebuild
577 void update_params(const CouplingParams& p) {
578 params_ = p;
579 matrix_ = Full44x44Matrix(p);
580 }
581
582 const Full44x44Matrix& matrix() const { return matrix_; }
583 const CouplingParams& params() const { return params_; }
584};
585
586} // namespace agi::dna
587