Antibiotic vs TCM Antimicrobial Geometric Pharmacology Atlas: Paper 9 of the Genesis Geometric Medicine Series -- Three-Layer Analysis of Molecular Geometry, Bacterial Infection NS Mapping, and Pulse Trajectory

Paper 9 of the Genesis Geometric Medicine Series presents the first systematic three-layer geometric comparison of antibiotics (n=21, 17 classes) and TCM antimicrobial compounds (n=18: berberine, baicalein, andrographolide, emodin, honokiol, etc.). Layer 1 (Molecular): Antibiotics have significantly higher TPSA (157 vs 75 A^2, p=0.0005) and lower logP (0.07 vs 2.29, p<0.0001), placing them in the Yin geometric zone. TCM antimicrobials have better membrane penetration geometry despite Cold thermal nature -- the Berberine Paradox (TPSA=40, logP=3.34), resolved by the Three-Layer principle. Layer 2 (Infection-NS mapping): 14 bacterial infection scenarios mapped to TCM syndromes and NS zones. Severe infections (sepsis NS=-1.67, meningitis NS=-1.67) require NS depth that no antibiotic NS_equiv (<-0.8) reaches -- the infection NS gap. Layer 3 (Pulse trajectory): 6 treatment trajectories with HRV proxy data; NS shift -0.4 to -0.8 toward neutral with effective treatment. Genesis Framework v4.