Biochar Molecular Modelling Tutorials

By Valentina Erastova, University of Edinburgh, June 2026.

Contact: valentina.erastova@ed.ac.uk

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These tutorials support the biochar modelling methodology introduced in the 2024 papers by Wood, Masek & Erastova (10.1016/j.xcrp.2024.102036, 10.1016/j.xcrp.2024.102037) and Ngambia, Masek & Erastova (10.1016/j.biombioe.2024.107199). They show how to build biochar molecular models from experimental descriptors, and how to use those models in GROMACS adsorption studies, using a recent example from Wood, Masek & Erastova (10.1016/j.biombioe.2026.109080).

Assumed Background

These tutorial assume that you are comfortable with:

• Running GROMACS workflows from the command line
• Preparing and editing topology files
• Running energy minimisation, equilibration, and production simulations
• Submitting jobs to an HPC system
• Inspecting structures and trajectories in VMD
• Plotting and interpreting standard MD outputs

These tutorials build on that foundation to focus on the additional challenges specific to biochar: chemically heterogeneous surfaces, porous carbon-rich structures, experimental validation targets, and interfacial adsorption analysis.

If you want to revise the above basics, MD Research Techniques workshop (github.com/Edinburgh-Chemistry-Teaching/MD_ResearchTechniques) is a good starting point. That workshop provides the GROMACS, HPC, topology, .mdp, visualisation, and analysis background assumed here. These tutorials do not repeat the full introductory setup.

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Tutorials

1. biochar_model_building_tutorial.md

   Build a biochar molecular model from experimental targets using the iterative approach developed by Wood, Masek & Erastova and extended by Ngambia, Masek & Erastova. The tutorial covers target selection, building-block design, model assembly, condensation, validation against experimental properties, and preparation of a surface-exposed model.

2. biochar_solvated_gromacs_tutorial.md

   Set up and analyse adsorption simulations using published biochar surface models in GROMACS. The tutorial covers selecting a biochar model, solvating the surface, adding solutes and ions, running the simulation, checking convergence, and analysing adsorption at the biochar-water interface.

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Supporting Repositories

The tutorials refer to files, examples, and workflows from the following repositories:

• MD Research Techniques workshop: github.com/Edinburgh-Chemistry-Teaching/MD_ResearchTechniques
• Published biochar molecular models: github.com/Erastova-group/Biochar_MolecularModels
• Example 2,4-D adsorption simulations: github.com/Erastova-group/24D_biochar
• Mn(II)-biochar simulation materials: github.com/Erastova-group/Mn_Biochar
• DynDen convergence analysis: github.com/Erastova-group/DynDen

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Citation

We hope these tutorials were useful for you! If you use our models or approach in your published work, please cite our works that enabled these tutorials.

Adsorption studies:

1. Wood R, Mašek O & Erastova V. Unravelling 2,4-D – biochar interactions by molecular dynamics: adsorption modes and surface functionalities. Biomas and Bioenergy 210, 109080 (2025). DOI: 10.1016/j.biombioe.2026.109080

2. Ngambia A, Gavrilova A, Huang H, Lyu Z, Mašek O, Graham M & Erastova V. Decoupling Precipitation and Surface Complexation during Mn (II) Removal by Biochar via Experiments and Atomistic Simulations. arXiv preprint (2026). DOI: 10.48550/arXiv.2603.22144

Biochar model development:

3. Wood R, Mašek O & Erastova V. Developing a molecular-level understanding of biochar materials using public characterization data. Cell Reports Physical Science 5(7), 102036 (2024). DOI: 10.1016/j.xcrp.2024.102036

4. Wood R, Mašek O & Erastova V. Developing realistic molecular models of biochars. Cell Reports Physical Science 5(7), 102037 (2024). DOI: 10.1016/j.xcrp.2024.102037

5. Ngambia A, Mašek O & Erastova V. Development of biochar molecular models with controlled porosity. Biomass and Bioenergy 184, 107199 (2024). DOI: 10.1016/j.biombioe.2024.107199

Convergence analysis:

6. Degiacomi MT, Tian S, Greenwell HC & Erastova V. DynDen: Assessing convergence of molecular dynamics simulations of interfaces. Computer Physics Communications 269 (2021). DOI: 10.1016/j.cpc.2021.108126