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 the Journal of Chemical Theory and Computation (JCTC). The study demonstrates how mesoscopic field heterogeneity (photonic jets) generated at the boundary of a 25 $\mu$m 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 ($f_1 = 2.30$ THz, $f_2 = 4.6$ THz) of a dielectric boundary yields a 4.0$\times$ localized field intensity enhancement (photonic jet), producing a time-averaged, rectified field vector of $\langle E_x \rangle = -0.0052$ 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 ($0^\circ$) to a persistent thermodynamic mean near $126^\circ$ ($125.86^\circ$).

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 4.0$\times$ 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 ($\langle E_x \rangle = -0.0052$ 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_jctc_final_figure.py: Extracts the MDAnalysis dihedral coordinates from the three .tar.gz archives and renders the JCTC-compliant Figure 2 kinetic overlay.