Electronic Notebook: pH-Dependent Stability and Thermodynamics of Insulin's Native and Fibril States

This repository contains supporting information, molecular dynamics (MD) simulation data, and analysis scripts accompanying the following scientific manuscripts by Hervø-Hansen et al.:

1. Characterization of the pH-Dependent Stabilizing Forces of Insulin's Native and Fibril States ACS Physical Chemistry Au, 2026. DOI: 10.1021/acsphyschemau.6c00045.
2. pH-Dependent Free Energies of Insulin Fibrillation from Protonation Ensemble Statistics 2026 (Submitted).

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Repository Layout

Data Directories

• monomer/ — Simulation data and trajectories for the insulin monomer system.
• fibril_1/ to fibril_8/ — Simulation data for insulin fibril fragments ranging from 1-mer to 8-mer lengths.
• Figures/ — Publication-ready figures generated during data analysis.

Jupyter Notebooks

• Simulations.ipynb — Detailed workflow describing how the molecular dynamics simulations were prepared, configured, and executed.
• Analysis_monomer.ipynb — Analysis of the insulin monomer simulations.
• Analysis_fibril_1mer.ipynb — Analysis of the fibril 1-mer system.
• Analysis_fibril_3mer.ipynb — Analysis of the fibril 3-mer system.
• Analysis_fibril_7mer.ipynb — Analysis of the fibril 7-mer system.
• Analysis_fibrillation_thermodynamics.ipynb — Thermodynamics analysis evaluating pH-dependent free energies from protonation ensemble statistics.

Miscellaneous

• LICENSE — The text of the BSD 3-Clause License.
• README.md — This file.

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License

This project is licensed under the BSD 3-Clause License.