Source Code and Dataset for: A Computational Framework for Non-Markovian Quantum Dynamics in 3D Microtubule Tryptophan Networks

Update: Included full 400-coordinate phase-space sweep data (11.4 hours computation) and updated ENAQT mapping figures. This study is an undergraduate-level exploratory research project investigating the physical conditions for long-lived quantum coherence in biological systems. We specifically focus on the tryptophan molecular networks within microtubules, as empirically reported by Kalra et al. (2022). Traditional Markovian models predict immediate quantum decay in warm biological environments. To address this limitation, this proposal adopts an open quantum systems framework with non-Markovian thermal bath characteristics. This project strictly focuses on numerical simulations rather than macroscopic cognitive behaviors. We utilize Python-based QuTiP frameworks and Hierarchical Equations of Motion (HEOM) to inverse-trace the effective parameter bounds (e.g., spectral density profiles, coupling strengths, and memory timescales). The goal is to identify the conditions that permit extended electronic coherence in the picosecond to nanosecond regime. As a prospective undergraduate researcher, the primary objective is to acquire rigorous computational skills and assist the host research group's ongoing simulations, integrating this exploratory project within the framework of the group's advanced research on open quantum dynamics.