Dataset and Code for: Multiphysics FDTD-MD Coupling Resolves Mesoscopic Field Heterogeneity: Deterministic Symmetry Breaking at Dielectric Boundaries

This repository contains the complete computational pipeline, raw datasets, and rendered publication-quality figures used to validate the FDTD-MD multiscale coupling framework submitted to Physical Chemistry Chemical Physics (PCCP). The study demonstrates how mesoscopic field heterogeneity (photonic jets) generated at the boundary of a 25-micrometer aqueous droplet can rectify high-frequency terahertz fields into persistent ponderomotive forces, driving reproducible symmetry breaking in a capped alanine dipeptide (Ace-Ala-Nme). Research Highlights FDTD Phase: Bi-harmonic terahertz irradiation (f1 = 2.30 THz, f2 = 4.60 THz) of a dielectric boundary yields a 4.0x localized field intensity enhancement (photonic jet), producing a time-averaged, rectified field vector of average Ex = -0.0052 simulation units. Multiphysics NEMD Triad: Application of the extracted field in GROMACS across a three-phase validation triad (V1: Static, V2: Dielectric Relaxation, V3: Deterministic Symmetry Breaking). Conformational Steering: Under the high-amplitude V3 protocol (2.30 THz resonance, 0.15 V/nm), the chiral improper dihedral angle (zeta) shifts from a racemic center (0 degrees) to a persistent thermodynamic mean near 126 degrees (125.86 degrees). Validation: Robust statistical ensemble utilizing multiple independent 1 ns trajectories (N=3) per protocol, strictly utilizing the V-rescale thermostat to preclude non-equilibrium thermal artifacts. Repository Structure & Figures This archive contains the publication-ready visuals and the fully sanitized, self-contained data structures for each phase of the integration triad. Rendered Figures (Publication Ready) FDTD_Field_Map.png: (Figure 1) Photonic Jet Intensity Heatmap demonstrating the 4.0x localized field enhancement and rectification extraction coordinate. Figure_2_Conformational_Steering.png: (Figure 2) Comparative temporal overlay plot of the V1, V2, and V3 protocols, utilizing a robust rolling average (n=50) to isolate macroscopic drift from the thermodynamic noise floor. Raw Computational Data (GROMACS & Topology) c4_ace_ala_null_run_v1.tar.gz: The V1 (Static Field Entrapment) dataset. Contains the baseline failure metric (average Ex = -0.0052 V/nm). c4_thz_run_v2.tar.gz: The V2 (Dielectric Relaxation) dataset. Contains the variance damping metric using the 2.30 THz resonance mode (0.05 V/nm). c4_thz_run_v3.tar.gz: The V3 (High-Amplitude Steering) dataset. Contains the successful deterministic symmetry-breaking metric (2.30 THz, 0.15 V/nm). Note: Each compressed tarball contains the explicit AMBER99SB-ILDN topologies (.top), starting coordinates (.gro), binary run inputs (.tpr), raw high-precision trajectories (.trr), compressed trajectories (.xtc), and full energy logs (.edr) for three independent replicates. Python Analysis Pipelines generate_fdtd_map.py: Synthesizes the Figure 1 spatial intensity matrix. c4_pccp_final_figure.py: Extracts the MDAnalysis dihedral coordinates from the three .tar.gz archives and renders the PCCP-compliant Figure 2 kinetic overlay.