This repository contains molecular simulation inputs, analysis scripts, and data processing tools used in:
“How Surface Functionalization Controls Confined Electrolyte Structure and Dynamics at Graphene Interfaces”
Lyndon T. M. Hess, Nhi P. T. Nguyen, et al.
Cornell University
This study explores how chemical functionalization of graphene surfaces modulates the structure and dynamics of confined aqueous NaCl electrolytes. Using molecular dynamics (MD) simulations, we investigate a matrix of functional group types (–COOH, –OH, =O, –CH₃), surface coverages, and electrolyte concentrations.
We also introduce carbonstructures, an open-source Python tool developed to generate functionalized graphene structures for simulation.
carbon-electrolyte-interface/
├── simulation/ # LAMMPS input scripts and run templates
├── analysis/ # Python scripts to analyze trajectories
├── figures/ # Publication-ready figures
├── requirements.txt # Python dependencies for simulation and analysis
├── .gitignore # Ignored files (e.g., dumps, logs)
└── README.md # This file
This external package was used to build functionalized graphene surfaces. Clone and install from its own repository if needed.
Use carbonstructures to generate graphene sheets with desired functional groups and coverage.
Use the files in simulation/ to run LAMMPS MD simulations. Example job scripts are provided for HPC environments.
Run scripts in analysis/ to compute:
- Water and ion density profiles
- Interfacial and bulk diffusion coefficients
- Figure generation (e.g., heatmaps, line plots)
All plots shown in the manuscript are available in figures/. Each figure corresponds to a panel in the Results & Discussion section. See figures/README.md for descriptions.
This repository is released under the MIT License. See LICENSE file for details.
If you use this toolkit or structure generation method in your work, please cite:
Hess, Nguyen, et al. Tuning Interfacial Electrolyte Structure and Dynamics via Surface Functionalization of Graphene. 2025.
All data and scripts are available via this GitHub repository. For questions, contact: