SRE Topology Auditing Nutrition Source Phase I Validation Report

Abstract

This paper finishes the Phase I verification of the Status-Relational Entropy (SRE) atomic topology auditing framework for nutritional substitution research. The calculation pipeline uses Operator 4, 5, 6, 9, 10 and depends on three compiled .pyd modules. Raw structural data are obtained from AFLOW REST API, Materials Project REST v2 and local deterministic generation. Four benchmark biomolecules are adopted: water tetramer, glycine, glucose and ATP. Anisotropic Gaussian pseudo-MD noise ranging from 0 to 0.15 angstrom is used to simulate room-temperature thermal vibration. A Watts-Strogatz VHC small-world network is constructed to carry out Monte Carlo tests under three oxidative stress levels (mild ROS, moderate inflammation, severe cytotoxicity). Core evaluation indicators include Fiedler eigenvalue lambda2, normalized conditioning number Cond_norm, topological defect coefficient Delta beta1, compensation efficiency eta_comp and TCR compensation rate. Experimental results show that all four biomolecules keep Delta beta1 = 0 under physiological thermal perturbation without topological fracture. The hierarchy of eta_comp matches their biological roles clearly: water tetramer (eta_comp = 1.000) > glycine > glucose > ATP. Severe oxidative stress leads to a 93.3 uncompensated defect ratio of the VHC network, and only water can repair topological damage with TCR = +0.274. Five Si/C/O inorganic demo clusters are screened as potential substitutes. All clusters have spectral matching coefficient Phi_match below the 0.95 standard threshold, and SiC has the maximum value of 0.594. CO2 is the best suboptimal candidate with the lowest residual noise Psi_residue and weak positive repair effect under severe stress. Periodic inorganic lattices and asymmetric biomolecules have inherent gaps on Cond_norm and alpha_n, so complete topological equivalence cannot be achieved in this sample set. All basic SRE axioms pass data verification. This experiment has obvious limitations: pseudo-MD simulation deviation, insufficient inorganic samples and lack of statistical confidence intervals. Corresponding Phase II optimization plans are put forward, including real molecular dynamics simulation, expansion of multi-type molecular & multi-element cluster libraries and mathematical improvement of evaluation indicators.