Biochar Molecular Models with Microporocity

By Audrey Ngambia (a.l.noumbissi-ngambia@sms.ed.ac.uk) and Valentina Erastova (valentina.erastova@ed.ac.uk), University of Edinburgh

Please cite as: 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

If you would like to build your own biochar model -- please follow our Biochar Tutorials

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Molecular models of porous woody biochars produced at 600ºC - 650ºC highest treatment temperatures

The structure of the shared files as follows:

Model_BCMA - BCMA model, using uniform sizes of building blocks

• model.gro - gromacs structure
• topol.top- full OPLS-AA topology, including all building blocks assigned with PolyParGen

Model_BCMB - BCMB model, using two types of building blocks with different sizes

• model_II.gro - gromacs structure
• topol.top- full OPLS-AA topology, including all building blocks assigned with PolyParGen

Model_BCMA_V10 - BCMA model simulated with virtual atom V10-6

• model_with_VA.gro - gromacs structure, including VAs.
• model_VA_removed.gro - gromacs structure generated with VAs, with VAs removed.
• topol_with_VA.top- full OPLS-AA topology, including VAs.

Model_BCMA_V30 - BCMA model simulated with virtual atom V30-6

• model_with_VA.gro - gromacs structure, including VAs.
• model_VA_removed.gro - gromacs structure generated with VAs, with VAs removed.
• topol_with_VA.top- full OPLS-AA topology, including VAs.

Model_BCMB_V10 - BCMB model simulated with virtual atom V10-6

• model_with_VA.gro - gromacs structure, including VAs.
• model_VA_removed.gro - gromacs structure generated with VAs, with VAs removed.
• topol_with_VA.top- full OPLS-AA topology, including VAs.

Model_BCMB_V30 - BCMB model simulated with virtual atom V30-6

• model_with_VA.gro - gromacs structure, including VAs.
• model_VA_removed.gro - gromacs structure generated with VAs, with VAs removed.
• topol_with_VA.top- full OPLS-AA topology, including VAs.

Please note that the VA V10-6 and V30-6 in the manuscript correspond to V4 and V14, respectively, in the these shared structures.

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--> To simulate the models without VAs, comment out the corresponding line in the .top file, i.e.:

[ molecules ]
; Compound        #mols
# VS                49
B_14              280
8G11C             120 

--> To model a surface-exposed biochar, extend the simulation box of a bulk system in one of the directions (typically z-direction) by creating an empty space above/below the layer of biochar. Make sure to run the simulation with semi-isotropic pressure coupling to allow de-coupling of z-direction from the xy-plane.

--> If you would like to set up your own biochar models following our approach:

The data collection of experimental measures and a selection of molecular building blocks are given at: github.com/Erastova-group/Biochar_MolecularModels

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For more information on the set-up of biochar molecular models, please see the following publications.

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

Or follow our Biochar Tutorials