Venus Dimer Theory Figures (Exact Scripts + Non-interactive Saving)

Abrahams, Ian T. "Excitonic Coupling and Photon Antibunching in Venus Yellow Fluorescent Protein Dimers: A Lindblad Master Equation Approach" arXiv:2508.14233 [quant-ph]

This release supersedes v1.2.0-arxiv with a full reorganization of figure scripts, corrected coherence extraction, and standardized constants/units for reproducibility.

Includes:

Figure scripts (restructured & standardized)

Fig. 1: Homodimer in energy basis with both site dephasing and thermal transfer; removed unwanted/incorrect population/coherence dynamics.

Fig. 2: Heterodimer relaxation from a bright–dark mixture; bright/dark now energy-based (no dipole heuristic).

Fig. 3: PyMOL alignment (1MYW vs 1GFL), renamed for clarity.

Fig. 4: Cryogenic coherence (1×2 layout, 250 mK & 400 mK). Uses expect() to correctly compute ρ; plots Im[ρ₊₋] for clear oscillatory decay and half-life; removed unwanted/incorrect population/coherence dynamics.

Save wrappers for batch PNG generation at publication resolution.

Unified constants (ħ, k_B, λ_fast, simulation-unit) and grid definitions across figures.

Cleanup of duplicate functions and comment typos.

Usage: conda env create -f environment.yml conda activate venus-dimer make all

Version:

Tag: v2.0.0-arxiv

Target: main

Changes vs. v1.2.0-arxiv:

Reorganized script names and outputs

Energy-based bright/dark definition in Fig. 2

Corrected coherence calculation in Fig. 4

Unified constants & units across all figures

Standardized output filenames (*_v2.0.0-arxiv.png)

Version DOI: 10.5281/zenodo.16892122  Latest version DOI: 10.5281/zenodo.16887703