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This document contains links to the tutorials that demonstrate how to reproduce material structures from published scientific manuscripts. Each entry lists the tutorial name and the corresponding manuscript reference.
44

5-
---
6-
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## 1. Single-Material Structures
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97
### 1.1. 2D Structures
10-
#### 1.1.1. [SrTiO3 Slab](slab-strontium-titanate.md) R. I. Eglitis and David Vanderbilt
11-
"First-principles calculations of atomic and electronic structure of SrTiO3 (001) and (011) surfaces"
12-
Phys. Rev. B 77, 195408 (2008)
13-
8+
#### 1.1.1. [SrTiO3 Slab](slab-strontium-titanate.md)
149
[DOI: 10.1103/PhysRevB.77.195408](https://doi.org/10.1103/PhysRevB.77.195408){:target='_blank'} [@Eglitis2008; @Mukhopadhyay2006]
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![Strontium Titanate Slabs](../../../images/tutorials/materials/2d_materials/slab_strontium_titanate/0-figure-from-manuscript.webp "Strontium Titanate Slabs, FIG. 2.")
11+
![Strontium Titanate Slabs](../../../images/tutorials/materials/2d_materials/slab_strontium_titanate/0-figure-from-manuscript.webp "Strontium Titanate Slabs, FIG. 2."){ style="max-height:500px;width:auto;" }
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### 1.2. 0D Structures
19-
#### 1.2.1. [Gold Nanoclusters](nanocluster-gold.md)
20-
**A. H. Larsen, J. Kleis, K. S. Thygesen, J. K. Nørskov, and K. W. Jacobsen**,
21-
"Electronic shell structure and chemisorption on gold nanoparticles",
22-
*Phys. Rev. B 84, 245429 (2011)*,
23-
14+
#### 1.2.1. [Gold Nanoclusters](nanocluster-gold.md)
2415
[DOI: 10.1103/PhysRevB.84.245429](https://doi.org/10.1103/PhysRevB.84.245429){:target='_blank'}. [@Larsen2011]
25-
![Gold Nanoparticles](../../../images/tutorials/materials/0d_materials/nanocluster_gold/0-manuscript-image.webp "Fig. 2. Gold Nanoparticles")
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27-
---
17+
![Gold Nanoparticles](../../../images/tutorials/materials/0d_materials/nanocluster_gold/0-manuscript-image.webp "Fig. 2. Gold Nanoparticles"){ style="max-height:500px;width:auto;" }
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## 2. Multi-Material Structures
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### 2.1. Interfaces
3224
#### 2.1.1. [Interface between Graphene and h-BN](interface-2d-2d-graphene-boron-nitride.md)
33-
**Jeil Jung, Ashley M. DaSilva, Allan H. MacDonald & Shaffique Adam**
34-
"Origin of the band gap in graphene on hexagonal boron nitride"
35-
Nature Communications, 2015
25+
[DOI: 10.1038/ncomms7308](https://doi.org/10.1038/ncomms7308){:target='_blank'} [@Jung2015]
3626

37-
[DOI: 10.1038/ncomms7308](https://doi.org/10.1038/ncomms7308){:target='_blank'}
38-
![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")
27+
![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"){ style="max-height:500px;width:auto;" }
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#### 2.1.2. [Interface between Graphene and SiO2 (alpha-quartz)](interface-2d-3d-graphene-silicon-dioxide.md)
41-
**Yong-Ju Kang, Joongoo Kang, and K. J. Chang**
42-
"Electronic structure of graphene and doping effect on SiO2"
43-
Physical Review B, 2008
44-
4530
[DOI: 10.1103/PhysRevB.78.115404](https://doi.org/10.1103/PhysRevB.78.115404){:target='_blank'}
46-
![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)")
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#### 2.1.3. [Interface between Copper and SiO2 (Cristobalite)](interface-3d-3d-copper-silicon-dioxide.md)
49-
**Shan, T.-R., Devine, B. D., Phillpot, S. R., & Sinnott, S. B.**
50-
"Molecular dynamics study of the adhesion of Cu/SiO2interfaces using a variable-charge interatomic potential."
51-
Physical Review B, 83(11).
32+
![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)"){ style="max-height:500px;width:auto;" }
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#### 2.1.3. [Interface between Copper and SiO2 (Cristobalite)](interface-3d-3d-copper-silicon-dioxide.md)
5335
[DOI: 10.1103/PhysRevB.83.115327](https://doi.org/10.1103/PhysRevB.83.115327){:target='_blank'} [@Shan2011].
54-
![Copper on Cristobalite](../../../images/tutorials/materials/interfaces/interface_3d_3d_copper_cristobalite/0-figure-from-manuscript.webp "Copper on Cristobalite, FIG. 1")
36+
37+
![Copper on Cristobalite](../../../images/tutorials/materials/interfaces/interface_3d_3d_copper_cristobalite/0-figure-from-manuscript.webp "Copper on Cristobalite, FIG. 1"){ style="max-height:500px;width:auto;" }
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#### 2.1.4. [High-k Metal Gate Stack (Si/SiO2/HfO2/TiN)](heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md)
5740
QuantumATK tutorial: [High-k Metal Gate Stack Builder](https://docs.quantumatk.com/tutorials/hkmg_builder/hkmg_builder.html) [@Muller1999; @Robertson2006]
58-
![High-k Metal Gate Stack](../../../images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/original-figure.webp "High-k Metal Gate Stack")
41+
![High-k Metal Gate Stack](../../../images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/original-figure.webp "High-k Metal Gate Stack"){ style="max-height:500px;width:auto;" }
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5943

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### 2.2. Twisted Interfaces
6145
#### 2.2.1. [Twisted Bilayer h-BN nanoribbons](interface-bilayer-twisted-nanoribbons-boron-nitride.md)
62-
**Lede Xian, Dante M. Kennes, Nicolas Tancogne-Dejean, Massimo Altarelli, and Angel Rubio**,
63-
"Multiflat Bands and Strong Correlations in Twisted Bilayer Boron Nitride: Doping-Induced Correlated Insulator and Superconductor" Phys. Rev. Lett. 125, 086402, 20 August 2020
64-
6546
[DOI: 10.1021/acs.nanolett.9b00986](https://doi.org/10.1021/acs.nanolett.9b00986){:target='_blank'} [@Xian2020]
66-
![Twisted Bilayer Boron Nitride](../../../images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/tbbn-paper-image.png "Twisted Bilayer Boron Nitride")
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#### 2.2.2. [Twisted Bilayer MoS2 commensurate lattices](interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md)
69-
**Kaihui Liu, Liming Zhang, Ting Cao, Chenhao Jin, Diana Qiu, Qin Zhou, Alex Zettl, Peidong Yang, Steve G. Louie & Feng Wang**,
70-
"Evolution of interlayer coupling in twisted molybdenum disulfide bilayers" Nature Communications volume 5, Article number: 4966 (2014)
48+
![Twisted Bilayer Boron Nitride](../../../images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/tbbn-paper-image.png "Twisted Bilayer Boron Nitride"){ style="max-height:500px;width:auto;" }
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#### 2.2.2. [Twisted Bilayer MoS2 commensurate lattices](interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md)
7251
[DOI: 10.1038/ncomms5966](https://doi.org/10.1038/ncomms5966){:target='_blank'} [@Liu2014; @Zhang2016; @Cao2018]
73-
![Twisted Bilayer Molybdenum Disulfide](../../../images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/MoS2-twisted-bilayers.png "Twisted Bilayer Molybdenum Disulfide")
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75-
---
53+
![Twisted Bilayer Molybdenum Disulfide](../../../images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/MoS2-twisted-bilayers.png "Twisted Bilayer Molybdenum Disulfide"){ style="max-height:500px;width:auto;" }
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7656

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## 3. Defects
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### 3.1. Point Defects
8060
#### 3.1.1. [Substitutional Point Defects in Graphene](defect-point-substitution-graphene.md)
81-
**Yoshitaka Fujimoto and Susumu Saito**
82-
"Formation, stabilities, and electronic properties of nitrogen defects in graphene"
83-
Physical Review B, 2011
84-
8561
[DOI: 10.1103/PhysRevB.84.245446](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.245446){:target='_blank'}
86-
![Point Defect, Substitution, 0](../../../images/tutorials/materials/defects/defect_creation_point_substitution_graphene/0-figure-from-manuscript.webp "Point Defect, Substitution, FIG. 1.")
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#### 3.1.2. [Vacancy-Substitution Pair Defects in GaN](defect-point-pair-gallium-nitride.md)
89-
**Giacomo Miceli, Alfredo Pasquarello**,
90-
"Self-compensation due to point defects in Mg-doped GaN", Physical Review B, 2016.
63+
![Point Defect, Substitution, 0](../../../images/tutorials/materials/defects/defect_creation_point_substitution_graphene/0-figure-from-manuscript.webp "Point Defect, Substitution, FIG. 1."){ style="max-height:500px;width:auto;" }
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#### 3.1.2. [Vacancy-Substitution Pair Defects in GaN](defect-point-pair-gallium-nitride.md)
9266
[DOI: 10.1103/PhysRevB.93.165207](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.93.165207){:target='_blank'}. [@Miceli2016]
93-
![Point Pair Defects: Mg Substitution and Vacancy in GaN](../../../images/tutorials/materials/defects/defect_point_pair_gallium_nitride/0-figure-from-manuscript.webp "Point Defect Pair: Substitution, Vacancy in GaN, FIG. 2.")
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#### 3.1.3. [Vacancy Point Defect in h-BN](defect-point-vacancy-boron-nitride.md)
96-
**Fabian Bertoldo, Sajid Ali, Simone Manti & Kristian S. Thygesen**
97-
"Quantum point defects in 2D materials – the QPOD database"
98-
Nature, 2022
68+
![Point Pair Defects: Mg Substitution and Vacancy in GaN](../../../images/tutorials/materials/defects/defect_point_pair_gallium_nitride/0-figure-from-manuscript.webp "Point Defect Pair: Substitution, Vacancy{ style="max-height:500px;width:auto;" } in GaN, FIG. 2.")
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70+
#### 3.1.3. [Vacancy Point Defect in h-BN](defect-point-vacancy-boron-nitride.md)
10071
[DOI: 10.1038/s41524-022-00730-w](https://doi.org/10.1038/s41524-022-00730-w){:target='_blank'}
101-
![Vacancy in h-BN](../../../images/tutorials/materials/defects/defect_point_vacancy_boron_nitride/0-figure-from-manuscript.webp "Vacancy in h-BN")
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103-
#### 3.1.4. [Interstitial Point Defect in SnO](defect-point-interstitial-tin-oxide.md)
104-
A. Togo, F. Oba, and I. Tanaka
105-
"First-principles calculations of native defects in tin monoxide"
106-
Physical Review B 74, 195128 (2006)
73+
![Vacancy in h-BN](../../../images/tutorials/materials/defects/defect_point_vacancy_boron_nitride/0-figure-from-manuscript.webp "Vacancy in h-BN"){ style="max-height:500px;width:auto;" }
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#### 3.1.4. [Interstitial Point Defect in SnO](defect-point-interstitial-tin-oxide.md)
10876
[DOI: 10.1103/PhysRevB.74.195128](https://doi.org/10.1103/PhysRevB.74.195128){:target='_blank'}. [@Togo2006; @Wang2014; @Na-Phattalung2006]
109-
![SnO O-interstitial](../../../images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/0-figure-from-manuscript.webp "O-interstitial defect in SnO")
77+
78+
![SnO O-interstitial](../../../images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/0-figure-from-manuscript.webp "O-interstitial defect in SnO"){ style="max-height:500px;width:auto;" }
79+
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### 3.2. Surface Defects
11282
#### 3.2.1. [Island Surface Defect Formation in TiN](defect-surface-island-titanium-nitride.md)
113-
**D. G. Sangiovanni, A. B. Mei, D. Edström, L. Hultman, V. Chirita, I. Petrov, and J. E. Greene**,
114-
"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.
11583
[DOI: 10.1103/PhysRevB.97.035406](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.97.035406){:target='_blank'}. [@Sangiovanni2018]
116-
![Surface Defect](../../../images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/0.png "Surface Defect, Island FIG. 2. a")
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118-
#### 3.2.2. [Step Surface Defect on Pt(111)](defect-surface-step-platinum.md)
119-
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.
85+
![Surface Defect](../../../images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/0.png "Surface Defect, Island FIG. 2. a"){ style="max-height:500px;width:auto;" }
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#### 3.2.2. [Step Surface Defect on Pt(111)](defect-surface-step-platinum.md)
12188
[DOI: 10.1016/s0039-6028(02)01908-8](https://doi.org/10.1016/s0039-6028(02)01908-8){:target='_blank'}. [@Sljivancanin2002]
122-
![Fig. 1.](../../../images/tutorials/materials/defects/defect_surface_step_platinum/0-figure-from-manuscript.webp "Fig. 1.")
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124-
#### 3.2.3. [Adatom Surface Defects on Graphene](defect-surface-adatom-graphene.md)
125-
**Kevin T. Chan, J. B. Neaton, and Marvin L. Cohen**
126-
"First-principles study of metal adatom adsorption on graphene"
127-
Phys. Rev. B, 2008
90+
![Step Surface Defect on Pt](../../../images/tutorials/materials/defects/defect_surface_step_platinum/0-figure-from-manuscript.webp "Fig. 1."){ style="max-height:500px;width:auto;" }
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#### 3.2.3. [Adatom Surface Defects on Graphene](defect-surface-adatom-graphene.md)
12993
[DOI: 10.1103/PhysRevB.77.235430](https://doi.org/10.1103/PhysRevB.77.235430){:target='_blank'}
130-
![Adatom on Graphene Surface](../../../images/tutorials/materials/defects/defect-surface-adatom-graphene/me_adatom_on_hollow_graphene.webp "Fig. 1. Adatom on Graphene Surface")
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### 3.3. Planar Defects
133-
#### 3.3.1. [Grain Boundary in FCC Metals (Copper)](defect-planar-grain-boundary-3d-fcc-metals-copper.md)
134-
Timofey Frolov, David L. Olmsted, Mark Asta & Yuri Mishin, "Structural phase transformations in metallic grain boundaries", Nature Communications, volume 4, Article number: 1899 (2013).
95+
![Adatom on Graphene Surface](../../../images/tutorials/materials/defects/defect-surface-adatom-graphene/me_adatom_on_hollow_graphene.webp "Fig. 1. Adatom on Graphene Surface"){ style="max-height:500px;width:auto;" }
96+
13597

98+
### 3.3. Planar Defects
99+
#### 3.3.1. [Grain Boundary in FCC Metals (Copper)](defect-planar-grain-boundary-3d-fcc-metals-copper.md)
136100
[DOI: 10.1038/ncomms2919](https://www.nature.com/articles/ncomms2919){:target='_blank'}. [@Frolov2013]
137-
![Copper Grain Boundary](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/0-figure-from-manuscript.webp "Copper Grain Boundary, FIG. 1")
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139-
#### 3.3.2. [Grain Boundary (2D) in h-BN](defect-planar-grain-boundary-2d-boron-nitride.md)
140-
**Qiucheng Li, et al.**
141-
"Grain Boundary Structures and Electronic Properties of Hexagonal Boron Nitride on Cu(111)"
142-
ACS Nano, 2015
102+
![Copper Grain Boundary](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/0-figure-from-manuscript.webp "Copper Grain Boundary, FIG. 1"){ style="max-height:500px;width:auto;" }
143103

104+
#### 3.3.2. [Grain Boundary (2D) in h-BN](defect-planar-grain-boundary-2d-boron-nitride.md)
144105
[DOI: 10.1021/acs.nanolett.5b01852](https://doi.org/10.1021/acs.nanolett.5b01852){:target='_blank'}
145-
![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.")
146106

147-
---
107+
![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."){ style="max-height:500px;width:auto;" }
108+
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## 4. Passivation
150110

111+
## 4. Passivation
151112

152113
### 4.1. Edge Passivation
153114
#### 4.1.1. [H-Passivated Silicon Nanowire](passivation-edge-nanowire-silicon.md)
154-
B. Aradi, L. E. Ramos, P. Deák, Th. Köhler, F. Bechstedt, R. Q. Zhang, and Th. Frauenheim,
155-
"Theoretical study of the chemical gap tuning in silicon nanowires"
156-
Phys. Rev. B 76, 035305 (2007)
157-
DOI: [10.1103/PhysRevB.76.035305](https://doi.org/10.1103/PhysRevB.76.035305){:target='_blank'} [@Aradi2007]
158-
![Passivated Silicon nanowire](../../../images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/0-figure-from-manuscript.webp "Passivated Silicon nanowire, FIG. 1.")
115+
[DOI: 10.1103/PhysRevB.76.035305](https://doi.org/10.1103/PhysRevB.76.035305){:target='_blank'} [@Aradi2007]
159116

117+
![Passivated Silicon nanowire](../../../images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/0-figure-from-manuscript.webp "Passivated Silicon nanowire, FIG. 1."){ style="max-height:500px;width:auto;" }
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161-
### 4.2. Surface Passivation
162-
#### 4.2.1. [H-Passivated Silicon (100) Surface](passivation-surface-silicon.md)
163-
Hansen, U., & Vogl, P.
164-
"Hydrogen passivation of silicon surfaces: A classical molecular-dynamics study."
165-
Physical Review B, 57(20), 13295–13304. (1998)
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### 4.2. Surface Passivation
121+
#### 4.2.1. [H-Passivated Silicon (100) Surface](passivation-surface-silicon.md)
167122
[DOI: 10.1103/PhysRevB.57.13295](https://doi.org/10.1103/PhysRevB.57.13295){:target='_blank'}. [@Hansen1998; @Northrup1991; @Boland1990]
168-
![Si(100) H-Passivated Surface](../../../images/tutorials/materials/passivation/passivation_surface_silicon/0-figure-from-manuscript.webp "H-Passivated Silicon (100)")
169123

170-
---
124+
![Si(100) H-Passivated Surface](../../../images/tutorials/materials/passivation/passivation_surface_silicon/0-figure-from-manuscript.webp "H-Passivated Silicon (100)"){ style="max-height:500px;width:auto;" }
125+
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## 5. Perturbations
173127

128+
## 5. Perturbations
174129

175130
### 5.1. Ripples
176131
#### 5.1.1. [Ripple perturbation of a Graphene sheet](perturbation-ripples-graphene.md)
177-
Thompson-Flagg, R. C., Moura, M. J. B., & Marder, M.
178-
"Rippling of graphene"
179-
EPL (Europhysics Letters), 85(4), 46002 (2009)
180-
181132
[DOI: 10.1209/0295-5075/85/46002](https://doi.org/10.1209/0295-5075/85/46002){:target='_blank'}. [@ThompsonFlagg2009; @Fasolino2007; @Openov2010]
182-
![Rippled Graphene](../../../images/tutorials/materials/defects/perturbation_ripple_graphene/0-figure-from-manuscript.webp "Rippled Graphene, FIG. 1.")
183133

184-
---
134+
![Rippled Graphene](../../../images/tutorials/materials/defects/perturbation_ripple_graphene/0-figure-from-manuscript.webp "Rippled Graphene, FIG. 1."){ style="max-height:500px;width:auto;" }
185135

186136
## 6. Other
187137

188-
189138
### 6.1. Interface Optimization
190139
#### 6.1.1. [Gr/Ni(111) Interface Optimization](optimization-interface-film-xy-position-graphene-nickel.md)
191-
Arjun Dahal, Matthias Batzill
192-
"Graphene–nickel interfaces: a review"
193-
Nanoscale, 6(5), 2548. (2014)
194-
195140
[DOI: 10.1039/c3nr05279f](https://doi.org/10.1039/c3nr05279f){:target='_blank'}. [@Dahal2014; @Gamo1997; @Bertoni2004]
196-
![Gr/Ni Interface](../../../images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/0-figure-from-manuscript.webp "Optimal position of graphene on Ni(111)")
141+
142+
![Gr/Ni Interface](../../../images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/0-figure-from-manuscript.webp "Optimal position of graphene on Ni(111)"){ style="max-height:500px;width:auto;" }
197143

198144
#### 6.1.2. [Pt Adatoms Island on MoS2](defect-point-adatom-island-molybdenum-disulfide-platinum.md)
199-
Saidi, W. A.
200-
"Density Functional Theory Study of Nucleation and Growth of Pt Nanoparticles on MoS2(001) Surface"
201-
Crystal Growth & Design, 15(2), 642–652. (2015)
145+
[DOI: 10.1021/cg5013395](https://doi.org/10.1021/cg5013395){:target='_blank'}. [@Saidi2015; @Jiao2016; @Fichthorn2000; @Neugebauer1993; @Hortamani2007]
146+
147+
![Pt Island on MoS2](../../../images/tutorials/materials/defects/defect_point_adatom_island_molybdenum_disulfide_platinum/0-figure-from-manuscript.webp "Pt island formation on MoS2"){ style="max-height:500px;width:auto;" }
148+
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[DOI: 10.1021/cg5013395](https://doi.org/10.1021/cg5013395){:target='_blank'}. [@Saidi2015; @Jiao2016; @Fichthorn2000; @Neugebauer1993; @Hortamani2007]![Pt Island on MoS2](../../../images/tutorials/materials/defects/defect_point_adatom_island_molybdenum_disulfide_platinum/0-figure-from-manuscript.webp "Pt island formation on MoS2")
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## References

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