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chore: cleanups
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Expand Up @@ -10,7 +10,7 @@ This document contains links to the tutorials that demonstrate how to reproduce
#### 1.1.1. [SrTiO3 Slab](slab-strontium-titanate.md) R. I. Eglitis and David Vanderbilt
"First-principles calculations of atomic and electronic structure of SrTiO3 (001) and (011) surfaces"
Phys. Rev. B 77, 195408 (2008)
[DOI: 10.1103/PhysRevB.77.195408](https://doi.org/10.1103/PhysRevB.77.195408) [@Eglitis2008; @Mukhopadhyay2006]
[DOI: 10.1103/PhysRevB.77.195408](https://doi.org/10.1103/PhysRevB.77.195408){:target='_blank'} [@Eglitis2008; @Mukhopadhyay2006]

![Strontium Titanate Slabs](../../../images/tutorials/materials/2d_materials/slab_strontium_titanate/0-figure-from-manuscript.webp "Strontium Titanate Slabs, FIG. 2.")

Expand All @@ -31,21 +31,21 @@ Phys. Rev. B 77, 195408 (2008)
**Jeil Jung, Ashley M. DaSilva, Allan H. MacDonald & Shaffique Adam**
"Origin of the band gap in graphene on hexagonal boron nitride"
Nature Communications, 2015
[DOI: 10.1038/ncomms7308](https://doi.org/10.1038/ncomms7308)
[DOI: 10.1038/ncomms7308](https://doi.org/10.1038/ncomms7308){:target='_blank'}
![Graphene on Hexagonal Boron Nitride](../../../images/tutorials/materials/interfaces/interface_2d_2d_graphene_boron_nitride/0-figure-from-manuscript.webp "Graphene on Hexagonal Boron Nitride, FIG. 7")

#### 2.1.2. [Interface between Graphene and SiO2 (alpha-quartz)](interface-2d-3d-graphene-silicon-dioxide.md)
**Yong-Ju Kang, Joongoo Kang, and K. J. Chang**
"Electronic structure of graphene and doping effect on SiO2"
Physical Review B, 2008
[DOI: 10.1103/PhysRevB.78.115404](https://doi.org/10.1103/PhysRevB.78.115404)
[DOI: 10.1103/PhysRevB.78.115404](https://doi.org/10.1103/PhysRevB.78.115404){:target='_blank'}
![Graphene on Silicon Dioxide](../../../images/tutorials/materials/interfaces/interface_2d_3d_graphene_silicon_dioxide/0-figure-from-manuscript.webp "Graphene on Silicon Dioxide, FIG. 1(b)

#### 2.1.3. [Interface between Copper and SiO2 (Cristobalite)](interface-3d-3d-copper-silicon-dioxide.md)
**Shan, T.-R., Devine, B. D., Phillpot, S. R., & Sinnott, S. B.**
"Molecular dynamics study of the adhesion of Cu/SiO2interfaces using a variable-charge interatomic potential."
Physical Review B, 83(11).
[DOI: 10.1103/PhysRevB.83.115327](https://doi.org/10.1103/PhysRevB.83.115327) [@Shan2011].
[DOI: 10.1103/PhysRevB.83.115327](https://doi.org/10.1103/PhysRevB.83.115327){:target='_blank'} [@Shan2011].
![Copper on Cristobalite](../../../images/tutorials/materials/interfaces/interface_3d_3d_copper_cristobalite/0-figure-from-manuscript.webp "Copper on Cristobalite, FIG. 1")

#### 2.1.4. [High-k Metal Gate Stack (Si/SiO2/HfO2/TiN)](heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md)
Expand All @@ -56,13 +56,13 @@ Physical Review B, 83(11).
#### 2.2.1. [Twisted Bilayer h-BN nanoribbons](interface-bilayer-twisted-nanoribbons-boron-nitride.md)
**Lede Xian, Dante M. Kennes, Nicolas Tancogne-Dejean, Massimo Altarelli, and Angel Rubio**,
"Multiflat Bands and Strong Correlations in Twisted Bilayer Boron Nitride: Doping-Induced Correlated Insulator and Superconductor" Phys. Rev. Lett. 125, 086402, 20 August 2020
[DOI: 10.1021/acs.nanolett.9b00986](https://doi.org/10.1021/acs.nanolett.9b00986) [@Xian2020]
[DOI: 10.1021/acs.nanolett.9b00986](https://doi.org/10.1021/acs.nanolett.9b00986){:target='_blank'} [@Xian2020]
![Twisted Bilayer Boron Nitride](../../../images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/tbbn-paper-image.png "Twisted Bilayer Boron Nitride")

#### 2.2.2. [Twisted Bilayer MoS2 commensurate lattices](interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md)
**Kaihui Liu, Liming Zhang, Ting Cao, Chenhao Jin, Diana Qiu, Qin Zhou, Alex Zettl, Peidong Yang, Steve G. Louie & Feng Wang**,
"Evolution of interlayer coupling in twisted molybdenum disulfide bilayers" Nature Communications volume 5, Article number: 4966 (2014)
[DOI: 10.1038/ncomms5966](https://doi.org/10.1038/ncomms5966) [@Liu2014; @Zhang2016; @Cao2018]
[DOI: 10.1038/ncomms5966](https://doi.org/10.1038/ncomms5966){:target='_blank'} [@Liu2014; @Zhang2016; @Cao2018]
![Twisted Bilayer Molybdenum Disulfide](../../../images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/MoS2-twisted-bilayers.png "Twisted Bilayer Molybdenum Disulfide")

---
Expand All @@ -74,7 +74,7 @@ Physical Review B, 83(11).
**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)
[DOI: 10.1103/PhysRevB.84.245446](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.245446){:target='_blank'}
![Point Defect, Substitution, 0](../../../images/tutorials/materials/defects/defect_creation_point_substitution_graphene/0-figure-from-manuscript.webp "Point Defect, Substitution, FIG. 1.")

#### 3.1.2. [Vacancy-Substitution Pair Defects in GaN](defect-point-pair-gallium-nitride.md)
Expand All @@ -87,7 +87,7 @@ Physical Review B, 2011
**Fabian Bertoldo, Sajid Ali, Simone Manti & Kristian S. Thygesen**
"Quantum point defects in 2D materials – the QPOD database"
Nature, 2022
[DOI: 10.1038/s41524-022-00730-w](https://doi.org/10.1038/s41524-022-00730-w)
[DOI: 10.1038/s41524-022-00730-w](https://doi.org/10.1038/s41524-022-00730-w){:target='_blank'}
![Vacancy in h-BN](../../../images/tutorials/materials/defects/defect_point_vacancy_boron_nitride/0-figure-from-manuscript.webp "Vacancy in h-BN")

#### 3.1.4. [Interstitial Point Defect in SnO](defect-point-interstitial-tin-oxide.md)
Expand All @@ -101,7 +101,7 @@ Physical Review B 74, 195128 (2006)
#### 3.2.1. [Island Surface Defect Formation in TiN](defect-surface-island-titanium-nitride.md)
**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){:target='_blank'}. [@Sangiovanni2018]
![Surface Defect](../../../images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/0.png "Surface Defect, Island FIG. 2. a)
![Surface Defect](../../../images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/0.png "Surface Defect, Island FIG. 2. a")

#### 3.2.2. [Step Surface Defect on Pt(111)](defect-surface-step-platinum.md)
Šljivančanin, Ž., & Hammer, B., "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. [DOI: 10.1016/s0039-6028(02)01908-8](https://doi.org/10.1016/s0039-6028(02)01908-8){:target='_blank'}. [@Sljivancanin2002]
Expand All @@ -111,7 +111,7 @@ Physical Review B 74, 195128 (2006)
**Kevin T. Chan, J. B. Neaton, and Marvin L. Cohen**
"First-principles study of metal adatom adsorption on graphene"
Phys. Rev. B, 2008
[DOI: 10.1103/PhysRevB.77.235430](https://doi.org/10.1103/PhysRevB.77.235430)
[DOI: 10.1103/PhysRevB.77.235430](https://doi.org/10.1103/PhysRevB.77.235430){:target='_blank'}
![Adatom on Graphene Surface](../../../images/tutorials/materials/defects/defect-surface-adatom-graphene/me_adatom_on_hollow_graphene.webp "Fig. 1. Adatom on Graphene Surface")

### 3.3. Planar Defects
Expand All @@ -123,7 +123,7 @@ Timofey Frolov, David L. Olmsted, Mark Asta & Yuri Mishin, "Structural phase tra
**Qiucheng Li, et al.**
"Grain Boundary Structures and Electronic Properties of Hexagonal Boron Nitride on Cu(111)"
ACS Nano, 2015
[DOI: 10.1021/acs.nanolett.5b01852](https://doi.org/10.1021/acs.nanolett.5b01852)
[DOI: 10.1021/acs.nanolett.5b01852](https://doi.org/10.1021/acs.nanolett.5b01852){:target='_blank'}
![h-BN Grain Boundary](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/0-figure-from-manuscript.webp "h-BN Grain Boundary, FIG. 2c.")

---
Expand All @@ -136,7 +136,7 @@ ACS Nano, 2015
B. Aradi, L. E. Ramos, P. Deák, Th. Köhler, F. Bechstedt, R. Q. Zhang, and Th. Frauenheim,
"Theoretical study of the chemical gap tuning in silicon nanowires"
Phys. Rev. B 76, 035305 (2007)
DOI: [10.1103/PhysRevB.76.035305](https://doi.org/10.1103/PhysRevB.76.035305) [@Aradi2007]
DOI: [10.1103/PhysRevB.76.035305](https://doi.org/10.1103/PhysRevB.76.035305){:target='_blank'} [@Aradi2007]
![Passivated Silicon nanowire](../../../images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/0-figure-from-manuscript.webp "Passivated Silicon nanowire, FIG. 1.")


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