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

This repository contains the 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). Update for Revised Manuscript:This repository has been substantially updated to address peer review critiques regarding Courant-Friedrichs-Lewy (CFL) stability and the topological constraints of classical force fields (Supplementary Section S3). It explicitly details the methodological distinction between the raw classical MD baselines (V1, V2) and the stochastic Langevin projection (V3) necessitated by the inability of fixed-charge models (AMBER) to dynamically rehybridize orbitals during field-driven chiral inversion. 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 ⟨Ex⟩ = -0.0052 simulation units. Multiphysics Triad (V1 & V2): Raw GROMACS molecular dynamics accurately modeling static field entrapment (V1) and localized dielectric relaxation of the hydration shell (V2). Langevin Projection (V3): A non-equilibrium stochastic projection parameterized by the FDTD field magnitude, explicitly mapping the deterministic symmetry breaking to the 125.86° attractor while overriding rigid classical topological constraints. CFL Stability & Standard MD Control: Rigorous integration stability checks (dt = 0.25 to 2.0 fs) under the peak FDTD-derived local field (2.925 V/nm). Explicitly proves that without the FDTD spatial boundary coupling, standard uniform-field MD fails to achieve deterministic steering, resulting instead in chaotic, symmetric athermal racemization. Repository Structure & Files: 1. Rendered Figures (Publication Ready) Figure_1_FDTD_Field_Map.png: Photonic Jet Intensity Heatmap. Figure2_Hybrid_V1_V3.png: Comparative kinetic overlay isolating macroscopic drift from the thermodynamic noise floor. S3_CFL_Convergence_Plot.png: Visualizes the chaotic athermal racemization of the failed standard MD control. 2. Python Analysis & Cloud Pipelines fig2_langevin_projection.py: Hybrid Python pipeline that extracts V1/V2 physical trajectories via MDAnalysis and mathematically synthesizes the V3 Langevin stochastic projection to generate Figure 2. cfl_control_colab.py: A fully automated Google Colab execution script that proves standard periodic boundary MD fails to deterministically steer the dihedral under uniform AC application (allows 1-click cloud verification without local software installation). fdtd_field_map_generator.py: Synthesizes the Figure 1 spatial intensity matrix. 3. Raw Computational Data (GROMACS) c4_ace_ala_null_run_v1.tar.gz: Raw GROMACS V1 (Static Field Entrapment) dataset. c4_thz_run_v2.tar.gz: Raw GROMACS V2 (Dielectric Relaxation) dataset.