Quantum-Biological Communication Channels (QBCC): simulations and data

Reproducibility package (simulation code and data) for the paper

An Open-Quantum-Systems Theory of Quantum-Biological Communication Channels Liang Dong, IEEE Transactions on Molecular, Biological, and Multi-Scale Communications (Special Feature on Quantum Biology Computing and Communications, Series IV). Manuscript TMBMC-QB-26-0001.

This repository contains the simulation scripts, raw inputs, simulation outputs, and verification suites needed to reproduce the numerical results reported in the paper. It contains code and data only; the manuscript and its figure sources are not included here. All code is pure Python (NumPy + SciPy).

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Repository structure

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├── code/                       Python simulation and verification scripts
│   ├── common.py               shared utilities (units, table I/O, binary capacity)
│   ├── exp_interference.py     four-site dephasing-assisted interference network
│   ├── exp_fmo.py              seven-site FMO complex (Adolphs--Renger)
│   ├── exp_radical_pair.py     cryptochrome FAD/Trp radical pair
│   ├── exp_dna_tunnelling.py   G--C proton-tunnelling mutation channel
│   ├── exp_ion_channel.py      KcsA-inspired ion-throughput loop
│   ├── exp_fmo_pdb.py          FMO couplings from PDB 3EOJ (structure check)
│   ├── exp_kcsa_pdb.py         KcsA geometry from PDB 1BL8 (structure check)
│   ├── exp_classical_null.py   quantum-vs-classical BIC/Delta-ell comparison
│   ├── exp_nai_sensitivity.py  NAI reference-level sensitivity sweep
│   ├── audit_theorems.py       13 theorem-vs-simulation regression tests
│   └── verify_theory_support.py  extended parameter-range theory checks
├── data/                       raw inputs
│   ├── 3EOJ.pdb                FMO trimer crystal structure (RCSB PDB)
│   └── 1BL8.pdb                KcsA channel crystal structure (RCSB PDB)
├── results/                    simulation outputs (*.dat tables, *.json summaries)
├── requirements.txt
├── run.sh                      one-command reproduction + verification
├── CITATION.cff
└── LICENSE

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Requirements

Python 3.10+ with the packages in requirements.txt:

pip install -r requirements.txt

Only numpy (>= 2.0) and scipy (>= 1.10) are needed.

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Quick start

Reproduce every result and run both verification suites with one command:

bash run.sh

This regenerates results/, runs the 13-test theorem-vs-simulation regression suite (audit_theorems.py), and runs the extended parameter-range verification (verify_theory_support.py). It exits with a non-zero status if any check fails.

To run an individual experiment (writing its outputs to results/):

cd code
python3 exp_fmo.py

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Verification

Suite	What it checks
code/audit_theorems.py	13 regression tests pinning each theoretical claim at a representative operating point: Proposition 1 (data-processing / quantum-Fisher bound), Corollary 1 (Holevo bound), Proposition 2 (dark-state lock), Proposition 3 (serial-composition bottleneck), the WKB kinetic-isotope scaling, CPTP trace conservation, the Haberkorn yield budget, and the BIC/Delta-ell quantum-vs-classical discrimination.
code/verify_theory_support.py	The same claims stress-tested across parameter ranges: the Fisher bound across magnetic-field amplitude, the Holevo chain across dephasing rate, the dark-state lock and its linear onset, the first-passage-density identity, and the serial bottleneck over 500 random channel pairs.

Each check computes the two sides of an inequality or identity independently, so a PASS is genuine evidence rather than a tautology.

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Script -> output -> paper-figure map

Script	Key outputs (results/)	Figure in the paper
exp_interference.py	interference_curve.dat, interference_traj_*.dat	Fig. 3 (Sec. V-A)
exp_fmo.py	fmo_dephasing_curve.dat, fmo_traj_*.dat	Fig. 4 (Sec. V-B)
exp_radical_pair.py	rp_compass_theta.dat, rp_fisher_B.dat, rp_zeno_kT.dat	Fig. 5 (Sec. V-C)
exp_dna_tunnelling.py	dna_temperature_curve.dat, dna_asymmetry.dat	Fig. 6 (Sec. V-D)
exp_ion_channel.py	ion_dephasing.dat, ion_iv.dat, ion_impulse.dat	Fig. 7 (Sec. V-E)
exp_fmo_pdb.py	fmo_J_compare.dat, fmo_pdb_dephasing.dat	Fig. 8 (Sec. V-F); Fig. 4(a) overlay
exp_kcsa_pdb.py	kcsa_pdb_dephasing.dat, kcsa_distances.dat	Sec. V-F (KcsA)
exp_classical_null.py	classical_null_interference.dat, classical_null_fmo.dat	Fig. 9 (Sec. V-G)
exp_nai_sensitivity.py	nai_sensitivity_interference.dat, nai_sensitivity_fmo.dat	Sec. III-D (NAI sensitivity)

The figures themselves are typeset in the manuscript and are not part of this repository; the table above maps each script and its data files to the corresponding figure number in the paper. The two exp_*_pdb.py scripts require the corresponding files in data/.

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Data provenance

The two crystal structures in data/ are obtained from the RCSB Protein Data Bank (https://www.rcsb.org) and are redistributed here for convenience:

• 3EOJ -- FMO antenna protein trimer (Tronrud, Wen, Gay, Blankenship, Photosynth. Res. 100, 79, 2009).
• 1BL8 -- KcsA potassium channel (Doyle et al., Science 280, 69, 1998).

All other inputs are numerical parameters drawn from the cited literature (see the manuscript). The simulation outputs in results/ are produced entirely by the scripts in code/.

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License

• Code (code/): MIT License (see LICENSE).
• Simulation outputs (results/): Creative Commons Attribution 4.0 (CC-BY-4.0).
• Crystal structures (data/*.pdb): redistributed from the RCSB PDB under its terms of use.

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How to cite

If you use this software or data, please cite the paper:

L. Dong, "An Open-Quantum-Systems Theory of Quantum-Biological Communication Channels," IEEE Transactions on Molecular, Biological, and Multi-Scale Communications, 2026.

The archived software and data have their own DOI: 10.5281/zenodo.20646427.

Machine-readable citation metadata for this repository is in CITATION.cff.

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Author

Liang Dong (liangdng@gmail.com). ORCID: 0000-0002-8585-1087. Department of Electrical and Computer Engineering, Baylor University; and Department of Radiology, The University of Texas Southwestern Medical Center.