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feature/SOF-8091 Fix: citations in the specific-example notebooks #407

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SOF-8091: fix specific-example citations
VsevolodX Oct 30, 2026
e7771b2
SOF-8091: review fixes
VsevolodX Oct 30, 2026
8f6d8c6
SOF-8091: citation values match references.bib
VsevolodX Oct 30, 2026
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23 changes: 13 additions & 10 deletions other/materials_designer/specific_examples/Introduction.ipynb
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"| `X-2D-PAS` | Passivated Surface | [Silicon Surface Passivation](passivation_surface_silicon.ipynb) | *To be added* | [[21]](#ref21) |\n",
"| `X-1D-PAS` | Passivated Edge | [Si Nanowire Edge Passivation](passivation_edge_nanowire_silicon.ipynb) | *To be added* | [[22]](#ref22) |\n",
"| `X-0D-PAS` | Passivated Edge | *To be added* | — | — |\n",
"| `X-0D-CUT` | Slab Cutout | [Custom Cutout in Etched Silicon](custom_cutout_etched_silicon.ipynb) | *To be added* | — |\n",
"| `X-0D-CUT` | Slab Cutout | [Custom Cutout in Etched Silicon](custom_cutout_etched_silicon.ipynb) | *To be added* | [[25]](#ref25) |\n",
"\n",
"## References\n",
"\n",
"<a id=\"ref1\"></a>[1] Eglitis, R. I., & Vanderbilt, D. (2008). First-principles calculations of atomic and electronic structure of SrTiO₃ (001) and (011) surfaces. *Physical Review B*, 77(19), 195408. https://doi.org/10.1103/PhysRevB.77.195408\n",
"\n",
"<a id=\"ref2\"></a>[2] Larsen, A. H., et al. (2011). Structure optimization of supported gold clusters. *Physical Review B*, 84(24), 245429. https://doi.org/10.1103/PhysRevB.84.245429\n",
"<a id=\"ref2\"></a>[2] Larsen, A. H., et al. (2011). Electronic shell structure and chemisorption on gold nanoparticles. *Physical Review B*, 84(24), 245429. https://doi.org/10.1103/PhysRevB.84.245429\n",
"\n",
"<a id=\"ref3\"></a>[3] Muller, D. A., et al. (1999). The electronic structure at the atomic scale of ultrathin gate oxides. *Nature*, 399(6738), 758-761. https://doi.org/10.1038/21602\n",
"\n",
"<a id=\"ref4\"></a>[4] Jung, J., et al. (2015). Moiré band model and band gaps of graphene on hexagonal boron nitride. *Nature Communications*, 6, 6308. https://doi.org/10.1038/ncomms7308\n",
"<a id=\"ref4\"></a>[4] Jung, J., et al. (2015). Origin of band gaps in graphene on hexagonal boron nitride. *Nature Communications*, 6, 6308. https://doi.org/10.1038/ncomms7308\n",
"\n",
"<a id=\"ref5\"></a>[5] Kang, Y.-J., Kang, J., & Chang, K. J. (2008). Electronic structure of graphene and doping effect on SiO₂. Physical Review B, 78(11), 115404. https://doi.org/10.1103/PhysRevB.78.115404\n",
"\n",
"<a id=\"ref6\"></a>[6] Shan, T. R., et al. (2011). Molecular dynamics study of the adhesion of Cu/SiO₂ interfaces using a variable-charge interatomic potential. *Physical Review B*, 83(11), 115327. https://doi.org/10.1103/PhysRevB.83.115327\n",
"<a id=\"ref6\"></a>[6] Shan, T.-R., et al. (2011). Molecular dynamics study of the adhesion of Cu/SiO₂ interfaces using a variable-charge interatomic potential. *Physical Review B*, 83(11), 115327. https://doi.org/10.1103/PhysRevB.83.115327\n",
"\n",
"<a id=\"ref7\"></a>[7] Dahal, A., & Batzill, M. (2014). Graphene–nickel interfaces: a review. *Nanoscale*, 6(5), 2548-2562. https://doi.org/10.1039/c3nr05279f\n",
"\n",
Expand All @@ -78,19 +78,19 @@
"\n",
"<a id=\"ref12\"></a>[12] Zou, X., et al. (2015). Grain boundary properties of elemental two-dimensional materials. *Nano Letters*, 15(5), 3495-3500. https://doi.org/10.1021/acs.nanolett.5b01852\n",
"\n",
"<a id=\"ref13\"></a>[13] Frolov, T., et al. (2013). Structural phase transformations in metallic grain boundaries. *Nature Communications*, 4, 2919. https://doi.org/10.1038/ncomms2919\n",
"<a id=\"ref13\"></a>[13] Frolov, T., et al. (2013). Structural phase transformations in metallic grain boundaries. *Nature Communications*, 4, 1899. https://doi.org/10.1038/ncomms2919\n",
"\n",
"<a id=\"ref14\"></a>[14] Sangiovanni, D. G., Mei, A. B., Edstrom, D., Hultman, L., Chirita, V., Petrov, I., & Greene, J. E. (2018). Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands. Physical Review B, 97(3), 035406. https://doi.org/10.1103/PhysRevB.97.035406\n",
"<a id=\"ref14\"></a>[14] Sangiovanni, D. G., Mei, A. B., Edström, D., Hultman, L., Chirita, V., Petrov, I., & Greene, J. E. (2018). Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands. Physical Review B, 97(3), 035406. https://doi.org/10.1103/PhysRevB.97.035406\n",
"\n",
"<a id=\"ref15\"></a>[15] Sljivancanin, Z., & Hammer, B. (2002). Oxygen dissociation at close-packed Pt terraces, Pt steps, and Ag-covered Pt steps studied with density functional theory. *Surface Science*, 515(2-3), 235-244. https://doi.org/10.1016/s0039-6028(02)01908-8\n",
"<a id=\"ref15\"></a>[15] Šljivančanin, Ž., & Hammer, B. (2002). Oxygen dissociation at close-packed Pt terraces, Pt steps, and Ag-covered Pt steps studied with density functional theory. *Surface Science*, 515(1), 235-244. https://doi.org/10.1016/s0039-6028(02)01908-8\n",
"\n",
"<a id=\"ref16\"></a>[16] Miceli, G., & Pasquarello, A. (2016). Self-compensation due to point defects in Mg-doped GaN. *Physical Review B*, 93(16), 165207. https://doi.org/10.1103/PhysRevB.93.165207\n",
"\n",
"<a id=\"ref17\"></a>[17] Togo, A., et al. (2006). First-principles calculations of native defects in tin monoxide. *Physical Review B*, 74(19), 195128. https://doi.org/10.1103/PhysRevB.74.195128\n",
"\n",
"<a id=\"ref18\"></a>[18] Lherbier, A., et al. (2011). Electronic and transport properties of unbalanced sublattice N-doping in graphene. *Physical Review B*, 84(24), 245446. https://doi.org/10.1103/PhysRevB.84.245446\n",
"<a id=\"ref18\"></a>[18] Fujimoto, Y., & Saito, S. (2011). Formation, stabilities, and electronic properties of nitrogen defects in graphene. *Physical Review B*, 84(24), 245446. https://doi.org/10.1103/PhysRevB.84.245446\n",
"\n",
"<a id=\"ref19\"></a>[19] Ivády, V., et al. (2022). Ab initio theory of the negatively charged boron vacancy qubit in hexagonal boron nitride. *npj Computational Materials*, 8(1), 1-9. https://doi.org/10.1038/s41524-022-00730-w\n",
"<a id=\"ref19\"></a>[19] Bertoldo, F., Ali, S., Manti, S., & Thygesen, K. S. (2022). Quantum point defects in 2D materials - the QPOD database. *npj Computational Materials*, 8(1), 56. https://doi.org/10.1038/s41524-022-00730-w\n",
"\n",
"<a id=\"ref20\"></a>[20] Thompson-Flagg, R. C., et al. (2009). Rippling of graphene. *EPL (Europhysics Letters)*, 85(4), 46002. https://doi.org/10.1209/0295-5075/85/46002\n",
"\n",
Expand All @@ -99,7 +99,10 @@
"<a id=\"ref22\"></a>[22] Aradi, B., et al. (2007). Theoretical study of the chemical gap tuning in silicon nanowires. *Physical Review B*, 76(3), 035305. https://doi.org/10.1103/PhysRevB.76.035305\n",
"\n",
"<a id=\"ref23\"></a>[23] Van de Walle, C. G., & Martin, R. M. (1986). Theoretical calculations of heterojunction discontinuities in the Si/Ge system. *Physical Review B*, 34(8), 5621. https://doi.org/10.1103/PhysRevB.34.5621\n",
"<a id=\"ref24\"></a>[24] Hinuma, Y., Grüneis, A., Kresse, G., & Oba, F. (2014). Band alignment of semiconductors from density-functional theory and many-body perturbation theory. *Physical Review B*, 90(15), 155405. https://doi.org/10.1103/PhysRevB.90.155405\n"
"\n",
"<a id=\"ref24\"></a>[24] Hinuma, Y., Grüneis, A., Kresse, G., & Oba, F. (2014). Band alignment of semiconductors from density-functional theory and many-body perturbation theory. *Physical Review B*, 90(15), 155405. https://doi.org/10.1103/PhysRevB.90.155405\n",
"\n",
"<a id=\"ref25\"></a>[25] Chen, Y., Fang, F., & Zhang, N. (2024). Advance in additive manufacturing of 2D materials at the atomic and close-to-atomic scale. *npj 2D Materials and Applications*, 8(1), 17. https://doi.org/10.1038/s41699-024-00456-x\n"
]
},
{
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7 changes: 7 additions & 0 deletions other/materials_designer/specific_examples/custom_cutout_etched_silicon.ipynb
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"- Two parallel channels at the top\n",
"- A deeper central cavity\n",
"\n",
"Following the publication:\n",
"\n",
"> **Yixin Chen, Fengzhou Fang, and Nan Zhang**\n",
"> \"Advance in additive manufacturing of 2D materials at the atomic and close-to-atomic scale\"\n",
"> npj 2D Materials and Applications 8, 17 (2024)\n",
"> [DOI: 10.1038/s41699-024-00456-x](https://doi.org/10.1038/s41699-024-00456-x)\n",
"\n",
"<h2 style=\"color:green\">Usage</h2>\n",
"\n",
"1. Make sure to select Input Material (in the outer runtime) before running the notebook.\n",
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2 changes: 1 addition & 1 deletion other/materials_designer/specific_examples/defect_point_interstitial_tin_oxide.ipynb
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"\n",
"This example demonstrates how to create a O interstitial defect in a SnO material. Following the publication:\n",
"\n",
"> **A. Togo, F. Oba, and I. Tanaka**\n",
"> **A. Togo, F. Oba, I. Tanaka, and K. Tatsumi**\n",
"> \"First-principles calculations of native defects in tin monoxide\"\n",
"> Phys. Rev. B 74, 195128 (2006)\n",
"> [DOI: 10.1103/PhysRevB.74.195128](https://doi.org/10.1103/PhysRevB.74.195128)\n",
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4 changes: 2 additions & 2 deletions ...materials_designer/specific_examples/defect_point_interstitial_tin_oxide_SIMULATION.ipynb
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"source": [
"# Formation Energy and DOS of the V_Sn-O_i Defect Pair in SnO\n",
"\n",
"> **A. Togo, F. Oba, and I. Tanaka**\n",
"> **A. Togo, F. Oba, I. Tanaka, and K. Tatsumi**\n",
"> \"First-principles calculations of native defects in tin monoxide\"\n",
"> Phys. Rev. B 74, 195128 (2006)\n",
"> [DOI: 10.1103/PhysRevB.74.195128](https://doi.org/10.1103/PhysRevB.74.195128)\n",
Expand Down Expand Up @@ -718,7 +718,7 @@
"source": [
"## References\n",
"\n",
"[1] Togo, A., Oba, F., & Tanaka, I. (2006). First-principles calculations of native defects in tin monoxide. Phys. Rev. B, 74(19), 195128. https://doi.org/10.1103/PhysRevB.74.195128"
"[1] Togo, A., Oba, F., Tanaka, I., & Tatsumi, K. (2006). First-principles calculations of native defects in tin monoxide. Phys. Rev. B, 74(19), 195128. https://doi.org/10.1103/PhysRevB.74.195128"
]
}
],
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2 changes: 1 addition & 1 deletion other/materials_designer/specific_examples/defect_point_substitution_graphene.ipynb
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"\n",
"[//]: # (<embed src=\"https://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.245446\" width=\"100%\" height=\"300\">)\n",
"\n",
"> **Yoshitaka Fujimoto and Susumu Saito**, \"Formation, stabilities, and electronic properties of nitrogen defects in graphene\", Physical Review B, 2011. [DOI: 10.1103/PhysRevB.84.245446](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.245446).\n",
"> **Yoshitaka Fujimoto and Susumu Saito**, \"Formation, stabilities, and electronic properties of nitrogen defects in graphene\", Physical Review B 84, 245446 (2011). [DOI: 10.1103/PhysRevB.84.245446](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.245446).\n",
"> \n",
"Below is the figure 1 from the manuscript demonstrating the nitrogen substitution defects in graphene.\n",
"\n",
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2 changes: 1 addition & 1 deletion other/materials_designer/specific_examples/defect_point_vacancy_boron_nitride.ipynb
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"This tutorial demonstrates the process of creating materials with vacancy defects, based on the work presented in the following manuscript:\n",
"\n",
"> **Fabian Bertoldo, Sajid Ali, Simone Manti & Kristian S. Thygesen**,\n",
"> \"Quantum point defects in 2D materials - the QPOD database\", npj Computational Materials, 2022. \n",
"> \"Quantum point defects in 2D materials - the QPOD database\", npj Computational Materials 8, 56 (2022). \n",
"> [DOI:10.1038/s41524-022-00730-w](https://doi.org/10.1038/s41524-022-00730-w)\n",
"\n",
"Below is the figure 1 from the manuscript demonstrating the boron vacancy defects in hexagonal boron nitride (h-BN).\n",
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4 changes: 2 additions & 2 deletions .../materials_designer/specific_examples/defect_point_vacancy_boron_nitride_SIMULATION.ipynb
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"# Defect Formation Energy of a Boron Vacancy in h-BN\n",
"\n",
"> **Fabian Bertoldo, Sajid Ali, Simone Manti & Kristian S. Thygesen**,\n",
"> \"Quantum point defects in 2D materials - the QPOD database\", npj Computational Materials, 2022.\n",
"> \"Quantum point defects in 2D materials - the QPOD database\", npj Computational Materials 8, 56 (2022).\n",
"> [DOI:10.1038/s41524-022-00730-w](https://doi.org/10.1038/s41524-022-00730-w)\n",
"\n",
"Computes the neutral formation energy of the vacancy created in the\n",
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"source": [
"## References\n",
"\n",
"[1] Bertoldo, Ali, Manti & Thygesen, \"Quantum point defects in 2D materials — the QPOD database\", npj Comput. Mater. 8, 56 (2022). https://doi.org/10.1038/s41524-022-00730-w\n",
"[1] Bertoldo, Ali, Manti & Thygesen, \"Quantum point defects in 2D materials - the QPOD database\", npj Comput. Mater. 8, 56 (2022). https://doi.org/10.1038/s41524-022-00730-w\n",
"[2] QPOD entry v_B in BN (charge 0): https://qpod.fysik.dtu.dk/material/1BN-1.2d.v_B.0.1"
]
}
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2 changes: 1 addition & 1 deletion other/materials_designer/specific_examples/defect_surface_adatom_graphene.ipynb
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"This tutorial demonstrates creation of metal adatom on graphene hollow site.\n",
"\n",
"> **Chan, K. T., Neaton, J. B., & Cohen, M. L. (2008).** \n",
"> First-principles study of metal adatom adsorption on graphene. Physical Review B, 77(23). \n",
"> First-principles study of metal adatom adsorption on graphene. Physical Review B, 77(23), 235430. \n",
"> [DOI:10.1103/physrevb.77.235430 ](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.77.235430)\n",
" \n",
"\n",
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2 changes: 1 addition & 1 deletion other/materials_designer/specific_examples/defect_surface_island_titanium_nitride.ipynb
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"This tutorial demonstrates the process of creating a rectangular island defect on a slab. \n",
"\n",
"\n",
"> **D. G. Sangiovanni, A. B. Mei, D. Edström, L. Hultman, V. Chirita, I. Petrov, and J. E. Greene**, \"Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands\", Physical Review B, 2018. [DOI: 10.1103/PhysRevB.97.035406](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.97.035406).\n",
"> **D. G. Sangiovanni, A. B. Mei, D. Edström, L. Hultman, V. Chirita, I. Petrov, and J. E. Greene**, \"Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands\", Physical Review B 97, 035406 (2018). [DOI: 10.1103/PhysRevB.97.035406](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.97.035406).\n",
"> \n",
"\n",
"![Fig 2.](https://github.com/Exabyte-io/documentation/raw/12617167278ae3523adc028583b21ea4e8ebd197/images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/0.png)\n",
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4 changes: 2 additions & 2 deletions other/materials_designer/specific_examples/defect_surface_step_platinum.ipynb
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"\n",
"> **Šljivančanin, Ž., & Hammer, B.**\n",
"> \"Oxygen dissociation at close-packed Pt terraces, Pt steps, and Ag-covered Pt steps studied with density functional theory.\"\n",
"> Surface Science, 515(1), 235–244. \n",
"> [DOI: 10.1016/s0039-6028(02)01908-8 ](https://doi:10.1016/s0039-6028(02)01908-8 )\n",
"> Surface Science, 515(1), 235–244 (2002). \n",
"> [DOI: 10.1016/s0039-6028(02)01908-8](https://doi.org/10.1016/s0039-6028(02)01908-8)\n",
"\n",
"Replicating the material from the FIG. 1. B.\n",
"\n",
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4 changes: 2 additions & 2 deletions other/materials_designer/specific_examples/interface_3d_3d_copper_cristobalite.ipynb
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"\n",
"Following the manuscript:\n",
" > **Shan, T.-R., Devine, B. D., Phillpot, S. R., & Sinnott, S. B.** \n",
" > \"Molecular dynamics study of the adhesion of Cu/SiO2interfaces using a variable-charge interatomic potential.\"\n",
" > Physical Review B, 83(11). \n",
" > \"Molecular dynamics study of the adhesion of Cu/SiO2 interfaces using a variable-charge interatomic potential.\"\n",
" > Physical Review B, 83(11), 115327 (2011). \n",
" > [DOI: 10.1103/PhysRevB.83.115327](https://doi.org/10.1103/PhysRevB.83.115327) \n",
"\n",
"\n",
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2 changes: 1 addition & 1 deletion ...pecific_examples/optimization_interface_film_xy_position_graphene_nickel_SIMULATION.ipynb
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"source": [
"## References\n",
"\n",
"[1] Arjun Dahal, Matthias Batzill, \"Graphene-nickel interfaces: a review\",\n",
"[1] Arjun Dahal, Matthias Batzill, \"Graphene–nickel interfaces: a review\",\n",
"Nanoscale 6(5), 2548 (2014). [DOI: 10.1039/c3nr05279f](https://doi.org/10.1039/c3nr05279f)\n",
"\n",
"[2] Jayeeta Lahiri, Travis S. Miller, Andrew J. Ross, Lyudmyla Adamska, Ivan I. Oleynik,\n",
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