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.本仓库包含了用于验证提交至《化学理论与计算杂志》（Journal of Chemical Theory and Computation，JCTC）的时域有限差分-分子动力学（FDTD-MD）多尺度耦合框架的完整计算流程、原始数据集以及出版级渲染图表。本研究阐释了在25 μm水相液滴边界处产生的介观场非均匀性（光子射流，photonic jet）如何将高频太赫兹（terahertz）场整流为持续的有质动力（ponderomotive forces），进而在封端的丙氨酸二肽（Ace-Ala-Nme）中引发可重复的对称性破缺。 研究亮点 FDTD阶段：对介电边界施加双频太赫兹辐照（$f_1 = 2.30$ THz，$f_2 = 4.6$ THz），可获得4.0倍的局域场强增强（光子射流），产生的时间平均整流场矢量为$langle E_x angle = -0.0052$ 模拟单位。 多物理场非平衡分子动力学（NEMD）三联验证：将提取的场参数应用于GROMACS软件中，开展三相验证三联实验（V1：静态场，V2：介电弛豫，V3：确定性对称性破缺）。 构象调控：在高振幅V3方案（2.30 THz共振，0.15 V/nm）下，手性非键二面角（$zeta$）从外消旋中心（0°）偏移至约126°的稳定热力学平均值（125.86°）。 验证流程：本研究采用稳健的统计系综，每个方案均设置3条独立的1 ns轨迹（$N=3$），并严格使用V-rescale温控器以排除非平衡热伪影。 仓库结构与图表 本归档文件包含出版级可视化素材，以及整合三联实验各阶段的全部经过清理、可独立运行的数据结构。 出版级渲染图表 FDTD_Field_Map.png（图1）：光子射流强度热图，展示4.0倍局域场增强与整流场提取坐标。 Figure_2_Conformational_Steering.png（图2）：V1、V2、V3方案的对比时间叠加图，通过稳健的滑动平均（$n=50$）从热力学噪声基底中分离宏观漂移。 原始计算数据（GROMACS与拓扑文件） c4_ace_ala_null_run_v1.tar.gz：V1（静态场束缚）数据集，包含基线失效度量$langle E_x angle = -0.0052$ V/nm。 c4_thz_run_v2.tar.gz：V2（介电弛豫）数据集，包含基于2.30 THz共振模式（0.05 V/nm）的方差阻尼度量。 c4_thz_run_v3.tar.gz：V3（高振幅构象调控）数据集，包含成功实现确定性对称性破缺的度量参数（2.30 THz，0.15 V/nm）。 备注：每个压缩tar包均包含3组独立重复实验的显式AMBER99SB-ILDN拓扑文件（.top）、初始坐标文件（.gro）、二进制运行输入文件（.tpr）、高精度原始轨迹文件（.trr）、压缩轨迹文件（.xtc）以及完整能量日志文件（.edr）。 Python分析流程 generate_fdtd_map.py：用于合成图1的空间强度矩阵。 c4_jctc_final_figure.py：从3个.tar.gz归档文件中提取MDAnalysis分析得到的二面角坐标，并渲染符合JCTC规范的图2动力学叠加图。