Dataset and Code for: Multiphysics Simulation Framework Coupling FDTD Electromagnetics with Molecular Dynamics

This repository contains the complete computational pipeline, raw datasets, and rendered publication-quality figures used to validate the FDTD-MD multiscale coupling framework. The study demonstrates how mesoscopic field heterogeneity (photonic jets) in a 25 μm water droplet can deterministically break chiral symmetry in a capped Alanine dipeptide (Ace-Ala-Nme). Research Highlights FDTD Phase: Bi-harmonic terahertz rectification ($f_1=2.3$ THz, $f_2=4.6$ THz) extracted a localized rectified field vector of $E_x = -0.0052$ (simulation units). NEMD Phase: Application of the extracted field in GROMACS induced a shift in the chiral improper dihedral angle ($\zeta$) from 0° to a persistent mean of 125.86°. Validation: 1 ns production run (500,000 steps) confirmed a strong, persistent chiral bias under high-intensity field conditions, consistent with the Resonant Enantioselective Synthesis (RES) hypothesis. Repository Structure & Figures In addition to the raw simulation data, this repository now includes the four primary figures submitted for peer review: Rendered Figures (Publication Ready) Figure_1.tiff: Multiscale Pipeline Schematic showing the FDTD-to-MD data flow. Figure_2.tiff: Thermodynamic Stability Analysis including Backbone RMSD and Energy Drift metrics. Figure_3.tiff: Photonic Jet Intensity Heatmap showing the 4.0x localized field enhancement at the droplet boundary. Figure_4.tiff: Chiral Bias Distribution Plot showing the 125.86° shift compared to racemic control. Raw Computational Data production.trr: Raw high-precision GROMACS trajectory (The "Movie"). topol.top: Full system topology using AMBER99SB-ILDN parameters. em.gro: Final equilibrated starting structure used for the production run. production.mdp: Complete simulation parameter file, including the electric-field-x coupling constant. RES_Experiment_Full_Backup.zip: A comprehensive archive containing all logs (production.log), energy files (production.edr), and temporary processing files. Software Requirements GROMACS 2021.4 or newer Meep (FDTD Engine) MDAnalysis (Python analysis library) Matplotlib/NumPy (For figure rendering and data processing) Usage These datasets are provided for the purpose of scientific transparency and reproducibility. The .trr and .mdp files allow for the exact reconstruction of the non-equilibrium ensemble used to identify the "Enantiomeric Lockdown" effect.