From ba17c03ec71b8216266777b11a11cc53b680842c Mon Sep 17 00:00:00 2001 From: VsevolodX Date: Sun, 9 Feb 2025 14:44:28 -0800 Subject: [PATCH 1/8] update: ... --- .../tutorials/materials/specific/overview.md | 80 +++++++++++++++++++ 1 file changed, 80 insertions(+) create mode 100644 lang/en/docs/tutorials/materials/specific/overview.md diff --git a/lang/en/docs/tutorials/materials/specific/overview.md b/lang/en/docs/tutorials/materials/specific/overview.md new file mode 100644 index 00000000..f5bd6a22 --- /dev/null +++ b/lang/en/docs/tutorials/materials/specific/overview.md @@ -0,0 +1,80 @@ +# Specific Materials Examples + +This section contains tutorials that demonstrate how to reproduce material structures from published scientific manuscripts. Each tutorial provides step-by-step instructions for creating and analyzing specific material configurations. + +## Point Defects + +### Substitutional Defects +- [Substitutional Point Defects in Graphene](defect-point-substitution-graphene.md) + > **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) + +### Vacancy Defects +- [Vacancy Point Defect in h-BN](defect-point-vacancy-boron-nitride.md) + > **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) + +### Surface Defects +- [Adatom Surface Defects on Graphene](defect-surface-adatom-graphene.md) + > **Kevin T. Chan, J. B. Neaton, and Marvin L. Cohen** + > "First-principles study of metal adatom adsorption on graphene" + > Phys. Rev. B 77, 235430, 2008 + > [DOI: 10.1103/PhysRevB.77.235430](https://doi.org/10.1103/PhysRevB.77.235430) + +### Planar Defects +- [Grain Boundary (2D) in h-BN](defect-planar-grain-boundary-2d-boron-nitride.md) + > **Qiucheng Li, et al.** + > "Grain Boundary Structures and Electronic Properties of Hexagonal Boron Nitride on Cu(111)" + > ACS Nano 2015 9 (6), 6308-6315 + > [DOI: 10.1021/acs.nanolett.5b01852](https://doi.org/10.1021/acs.nanolett.5b01852) + +## Interface Structures + +### 2D-2D Interfaces +- [Interface between Graphene and h-BN](interface-2d-2d-graphene-boron-nitride.md) + > **Jeil Jung, Ashley M. DaSilva, Allan H. MacDonald & Shaffique Adam** + > "Origin of the band gap in graphene on hexagonal boron nitride" + > Nature Communications volume 6, Article number: 6308 (2015) + > [DOI: 10.1038/ncomms7308](https://doi.org/10.1038/ncomms7308) + +### 2D-3D Interfaces +- [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 78, 115404 (2008) + > [DOI: 10.1103/PhysRevB.78.115404](https://doi.org/10.1103/PhysRevB.78.115404) + +## Surface Modifications +- [Pt Adatoms Island on MoS2](defect-point-adatom-island-molybdenum-disulfide-platinum.md) + > **Saidi, W. A.** + > "Density Functional Theory Study of Nucleation and Growth of Pt Nanoparticles on MoS2(001) Surface" + > Crystal Growth & Design, 15(2), 642–652. (2015) + > [DOI: 10.1021/cg5013395](https://doi.org/10.1021/cg5013395) + +## Heterostructures and Multi-layer Systems +- [High-k Metal Gate Stack (Si/SiO2/HfO2/TiN)](heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md) +- [Twisted Bilayer MoS2 commensurate lattices](interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md) + +## Surface Modifications and Passivation +- [H-Passivated Silicon Nanowire](passivation-edge-nanowire-silicon.md) +- [H-Passivated Silicon (100) Surface](passivation-surface-silicon.md) +- [SrTiO3 Slab](slab-strontium-titanate.md) + +## Nanostructures +- [Gold Nanoclusters](nanocluster-gold.md) + +## Interface Optimization +- [Gr/Ni(111) Interface Optimization](optimization-interface-film-xy-position-graphene-nickel.md) + +## Material Perturbations +- [Ripple perturbation of a Graphene sheet](perturbation-ripples-graphene.md) + +## 3D Interfaces +- [Interface between Copper and SiO2 (Cristobalite)](interface-3d-3d-copper-silicon-dioxide.md) +- [Grain Boundary in FCC Metals (Copper)](defect-planar-grain-boundary-3d-fcc-metals-copper.md) + +Each tutorial provides detailed steps for reproducing the material structures from these published works. The tutorials include interactive JupyterLite notebooks and step-by-step instructions for creating and analyzing the specific material configurations. \ No newline at end of file From c3770fba3d24cfccc0b1f82ec074e7915525c292 Mon Sep 17 00:00:00 2001 From: VsevolodX Date: Sun, 9 Feb 2025 15:02:00 -0800 Subject: [PATCH 2/8] update: add refs with script --- .../tutorials/materials/specific/overview.md | 172 +++++++++++++----- 1 file changed, 122 insertions(+), 50 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/overview.md b/lang/en/docs/tutorials/materials/specific/overview.md index f5bd6a22..c54447c8 100644 --- a/lang/en/docs/tutorials/materials/specific/overview.md +++ b/lang/en/docs/tutorials/materials/specific/overview.md @@ -1,80 +1,152 @@ # Specific Materials Examples -This section contains tutorials that demonstrate how to reproduce material structures from published scientific manuscripts. Each tutorial provides step-by-step instructions for creating and analyzing specific material configurations. +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 where available. -## Point Defects +--- -### Substitutional Defects -- [Substitutional Point Defects in Graphene](defect-point-substitution-graphene.md) +## 1. Single-Material Structures + +### 1.1. 3D Structures +- [SrTiO3 Slab](slab-strontium-titanate.md) + > Manuscript Reference: 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] + +### 1.2. 0D Structures +- [Gold Nanoclusters](nanocluster-gold.md) + > Manuscript Reference: > **A. H. Larsen, J. Kleis, K. S. Thygesen, J. K. Nørskov, and K. W. Jacobsen**, +> "Electronic shell structure and chemisorption on gold nanoparticles", +> *Phys. Rev. B 84, 245429 (2011)*, +> [DOI: 10.1103/PhysRevB.84.245429](https://doi.org/10.1103/PhysRevB.84.245429){:target='_blank'}. [@Larsen2011] + +--- + +## 2. Multi-Material Structures + +### 2.1. Interfaces +- [Interface between Graphene and h-BN](interface-2d-2d-graphene-boron-nitride.md) + > **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) + +- [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) + +- [Interface between Copper and SiO2 (Cristobalite)](interface-3d-3d-copper-silicon-dioxide.md) + > Manuscript Reference: **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]. + +- [High-k Metal Gate Stack (Si/SiO2/HfO2/TiN)](heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md) + > Manuscript Reference: [Placeholder – Reference not provided] + +### 2.2. Twisted Interfaces +- [Twisted Bilayer h-BN nanoribbons](interface-bilayer-twisted-nanoribbons-boron-nitride.md) + > Manuscript Reference: **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] + +- [Twisted Bilayer MoS2 commensurate lattices](interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md) + > Manuscript Reference: **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] + +--- + +## 3. Defects + +### 3.1. Point Defects +- [Substitutional Point Defects in Graphene](defect-point-substitution-graphene.md) > **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) -### Vacancy Defects -- [Vacancy Point Defect in h-BN](defect-point-vacancy-boron-nitride.md) +- [Vacancy-Substitution Pair Defects in GaN](defect-point-pair-gallium-nitride.md) + > Manuscript Reference: **Giacomo Miceli, Alfredo Pasquarello**, +"Self-compensation due to point defects in Mg-doped GaN", Physical Review B, 2016. +[DOI: 10.1103/PhysRevB.93.165207](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.93.165207){:target='_blank'}. [@Miceli2016] + +- [Vacancy Point Defect in h-BN](defect-point-vacancy-boron-nitride.md) > **Fabian Bertoldo, Sajid Ali, Simone Manti & Kristian S. Thygesen** - > "Quantum point defects in 2D materials - the QPOD database" + > "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) + +- [Interstitial Point Defect in SnO](defect-point-interstitial-tin-oxide.md) + > Manuscript Reference: A. Togo, F. Oba, and I. Tanaka +"First-principles calculations of native defects in tin monoxide" +Physical Review B 74, 195128 (2006) +[DOI: 10.1103/PhysRevB.74.195128](https://doi.org/10.1103/PhysRevB.74.195128){:target='_blank'}. [@Togo2006; @Wang2014; @Na-Phattalung2006] + +### 3.2. Surface Defects +- [Island Surface Defect Formation in TiN](defect-surface-island-titanium-nitride.md) + > Manuscript Reference: **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] + +- [Step Surface Defect on Pt(111)](defect-surface-step-platinum.md) + > Manuscript Reference: 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] -### Surface Defects -- [Adatom Surface Defects on Graphene](defect-surface-adatom-graphene.md) +- [Adatom Surface Defects on Graphene](defect-surface-adatom-graphene.md) > **Kevin T. Chan, J. B. Neaton, and Marvin L. Cohen** > "First-principles study of metal adatom adsorption on graphene" - > Phys. Rev. B 77, 235430, 2008 + > Phys. Rev. B, 2008 > [DOI: 10.1103/PhysRevB.77.235430](https://doi.org/10.1103/PhysRevB.77.235430) -### Planar Defects -- [Grain Boundary (2D) in h-BN](defect-planar-grain-boundary-2d-boron-nitride.md) +### 3.3. Planar Defects +- [Grain Boundary in FCC Metals (Copper)](defect-planar-grain-boundary-3d-fcc-metals-copper.md) + > Manuscript Reference: Timofey Frolov, David L. Olmsted, Mark Asta & Yuri Mishin, "Structural phase transformations in metallic grain boundaries", Nature Communications, volume 4, Article number: 1899 (2013). [DOI: 10.1038/ncomms2919](https://www.nature.com/articles/ncomms2919){:target='_blank'}. [@Frolov2013] + +- [Grain Boundary (2D) in h-BN](defect-planar-grain-boundary-2d-boron-nitride.md) > **Qiucheng Li, et al.** > "Grain Boundary Structures and Electronic Properties of Hexagonal Boron Nitride on Cu(111)" - > ACS Nano 2015 9 (6), 6308-6315 + > ACS Nano, 2015 > [DOI: 10.1021/acs.nanolett.5b01852](https://doi.org/10.1021/acs.nanolett.5b01852) -## Interface Structures +--- -### 2D-2D Interfaces -- [Interface between Graphene and h-BN](interface-2d-2d-graphene-boron-nitride.md) - > **Jeil Jung, Ashley M. DaSilva, Allan H. MacDonald & Shaffique Adam** - > "Origin of the band gap in graphene on hexagonal boron nitride" - > Nature Communications volume 6, Article number: 6308 (2015) - > [DOI: 10.1038/ncomms7308](https://doi.org/10.1038/ncomms7308) +## 4. Passivation -### 2D-3D Interfaces -- [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 78, 115404 (2008) - > [DOI: 10.1103/PhysRevB.78.115404](https://doi.org/10.1103/PhysRevB.78.115404) +- [H-Passivated Silicon Nanowire](passivation-edge-nanowire-silicon.md) + > Manuscript Reference: 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] -## Surface Modifications -- [Pt Adatoms Island on MoS2](defect-point-adatom-island-molybdenum-disulfide-platinum.md) - > **Saidi, W. A.** - > "Density Functional Theory Study of Nucleation and Growth of Pt Nanoparticles on MoS2(001) Surface" - > Crystal Growth & Design, 15(2), 642–652. (2015) - > [DOI: 10.1021/cg5013395](https://doi.org/10.1021/cg5013395) +- [H-Passivated Silicon (100) Surface](passivation-surface-silicon.md) + > Manuscript Reference: Hansen, U., & Vogl, P. +"Hydrogen passivation of silicon surfaces: A classical molecular-dynamics study." +Physical Review B, 57(20), 13295–13304. (1998) +[DOI: 10.1103/PhysRevB.57.13295](https://doi.org/10.1103/PhysRevB.57.13295){:target='_blank'}. [@Hansen1998; @Northrup1991; @Boland1990] -## Heterostructures and Multi-layer Systems -- [High-k Metal Gate Stack (Si/SiO2/HfO2/TiN)](heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md) -- [Twisted Bilayer MoS2 commensurate lattices](interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md) +--- -## Surface Modifications and Passivation -- [H-Passivated Silicon Nanowire](passivation-edge-nanowire-silicon.md) -- [H-Passivated Silicon (100) Surface](passivation-surface-silicon.md) -- [SrTiO3 Slab](slab-strontium-titanate.md) +## 5. Perturbations -## Nanostructures -- [Gold Nanoclusters](nanocluster-gold.md) +- [Ripple perturbation of a Graphene sheet](perturbation-ripples-graphene.md) + > Manuscript Reference: Thompson-Flagg, R. C., Moura, M. J. B., & Marder, M. +"Rippling of graphene" +EPL (Europhysics Letters), 85(4), 46002 (2009) +[DOI: 10.1209/0295-5075/85/46002](https://doi.org/10.1209/0295-5075/85/46002){:target='_blank'}. [@ThompsonFlagg2009; @Fasolino2007; @Openov2010] -## Interface Optimization -- [Gr/Ni(111) Interface Optimization](optimization-interface-film-xy-position-graphene-nickel.md) +--- -## Material Perturbations -- [Ripple perturbation of a Graphene sheet](perturbation-ripples-graphene.md) +## 6. Other -## 3D Interfaces -- [Interface between Copper and SiO2 (Cristobalite)](interface-3d-3d-copper-silicon-dioxide.md) -- [Grain Boundary in FCC Metals (Copper)](defect-planar-grain-boundary-3d-fcc-metals-copper.md) +- [Gr/Ni(111) Interface Optimization](optimization-interface-film-xy-position-graphene-nickel.md) + > Manuscript Reference: Arjun Dahal, Matthias Batzill +"Graphene–nickel interfaces: a review" +Nanoscale, 6(5), 2548. (2014) +[DOI: 10.1039/c3nr05279f](https://doi.org/10.1039/c3nr05279f){:target='_blank'}. [@Dahal2014; @Gamo1997; @Bertoni2004] -Each tutorial provides detailed steps for reproducing the material structures from these published works. The tutorials include interactive JupyterLite notebooks and step-by-step instructions for creating and analyzing the specific material configurations. \ No newline at end of file +- [Pt Adatoms Island on MoS2](defect-point-adatom-island-molybdenum-disulfide-platinum.md) + > Manuscript Reference: Saidi, W. A. +"Density Functional Theory Study of Nucleation and Growth of Pt Nanoparticles on MoS2(001) Surface" +Crystal Growth & Design, 15(2), 642–652. (2015) +[DOI: 10.1021/cg5013395](https://doi.org/10.1021/cg5013395){:target='_blank'}. [@Saidi2015; @Jiao2016; @Fichthorn2000; @Neugebauer1993; @Hortamani2007] \ No newline at end of file From 7ffa1d35176b3a8f21f2abf97f034beccc191f77 Mon Sep 17 00:00:00 2001 From: VsevolodX Date: Sun, 9 Feb 2025 15:03:26 -0800 Subject: [PATCH 3/8] chore: format --- lang/en/docs/tutorials/materials/specific/overview.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lang/en/docs/tutorials/materials/specific/overview.md b/lang/en/docs/tutorials/materials/specific/overview.md index c54447c8..3d4f8c6a 100644 --- a/lang/en/docs/tutorials/materials/specific/overview.md +++ b/lang/en/docs/tutorials/materials/specific/overview.md @@ -1,6 +1,6 @@ # Specific Materials Examples -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 where available. +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. --- From caf2804f874bd6c3b3aa130cb5ab2ab086bc9c4b Mon Sep 17 00:00:00 2001 From: VsevolodX Date: Sun, 9 Feb 2025 18:47:00 -0800 Subject: [PATCH 4/8] update :add images --- .../tutorials/materials/specific/overview.md | 30 ++++++++++++++++--- 1 file changed, 26 insertions(+), 4 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/overview.md b/lang/en/docs/tutorials/materials/specific/overview.md index 3d4f8c6a..534773f3 100644 --- a/lang/en/docs/tutorials/materials/specific/overview.md +++ b/lang/en/docs/tutorials/materials/specific/overview.md @@ -6,19 +6,22 @@ This document contains links to the tutorials that demonstrate how to reproduce ## 1. Single-Material Structures -### 1.1. 3D Structures -- [SrTiO3 Slab](slab-strontium-titanate.md) - > Manuscript Reference: R. I. Eglitis and David Vanderbilt +### 1.1. 2D Structures +#### 1.1.1. [SrTiO3 Slab](slab-strontium-titanate.md) +Manuscript Reference: 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] +![Strontium Titanate Slabs](../../../images/tutorials/materials/2d_materials/slab_strontium_titanate/0-figure-from-manuscript.webp "Strontium Titanate Slabs, FIG. 2.") + ### 1.2. 0D Structures - [Gold Nanoclusters](nanocluster-gold.md) > Manuscript Reference: > **A. H. Larsen, J. Kleis, K. S. Thygesen, J. K. Nørskov, and K. W. Jacobsen**, > "Electronic shell structure and chemisorption on gold nanoparticles", > *Phys. Rev. B 84, 245429 (2011)*, > [DOI: 10.1103/PhysRevB.84.245429](https://doi.org/10.1103/PhysRevB.84.245429){:target='_blank'}. [@Larsen2011] +![Gold Nanoparticles](../../../images/tutorials/materials/0d_materials/nanocluster_gold/0-manuscript-image.webp "Fig. 2. Gold Nanoparticles") --- @@ -30,32 +33,38 @@ Phys. Rev. B 77, 195408 (2008) > "Origin of the band gap in graphene on hexagonal boron nitride" > Nature Communications, 2015 > [DOI: 10.1038/ncomms7308](https://doi.org/10.1038/ncomms7308) +![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") - [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) +![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) - [Interface between Copper and SiO2 (Cristobalite)](interface-3d-3d-copper-silicon-dioxide.md) > Manuscript Reference: **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]. +![Copper on Cristobalite](../../../images/tutorials/materials/interfaces/interface_3d_3d_copper_cristobalite/0-figure-from-manuscript.webp "Copper on Cristobalite, FIG. 1") - [High-k Metal Gate Stack (Si/SiO2/HfO2/TiN)](heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md) > Manuscript Reference: [Placeholder – Reference not provided] +![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") ### 2.2. Twisted Interfaces - [Twisted Bilayer h-BN nanoribbons](interface-bilayer-twisted-nanoribbons-boron-nitride.md) > Manuscript Reference: **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] +![Twisted Bilayer Boron Nitride](../../../images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/tbbn-paper-image.png "Twisted Bilayer Boron Nitride") - [Twisted Bilayer MoS2 commensurate lattices](interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md) > Manuscript Reference: **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] +![Twisted Bilayer Molybdenum Disulfide](../../../images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/MoS2-twisted-bilayers.png "Twisted Bilayer Molybdenum Disulfide") --- @@ -67,47 +76,56 @@ Physical Review B, 83(11). > "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) +![Point Defect, Substitution, 0](../../../images/tutorials/materials/defects/defect_creation_point_substitution_graphene/0-figure-from-manuscript.webp "Point Defect, Substitution, FIG. 1.") - [Vacancy-Substitution Pair Defects in GaN](defect-point-pair-gallium-nitride.md) > Manuscript Reference: **Giacomo Miceli, Alfredo Pasquarello**, "Self-compensation due to point defects in Mg-doped GaN", Physical Review B, 2016. [DOI: 10.1103/PhysRevB.93.165207](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.93.165207){:target='_blank'}. [@Miceli2016] +![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.") - [Vacancy Point Defect in h-BN](defect-point-vacancy-boron-nitride.md) > **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) +![Vacancy in h-BN](../../../images/tutorials/materials/defects/defect_point_vacancy_boron_nitride/0-figure-from-manuscript.webp "Vacancy in h-BN") - [Interstitial Point Defect in SnO](defect-point-interstitial-tin-oxide.md) > Manuscript Reference: A. Togo, F. Oba, and I. Tanaka "First-principles calculations of native defects in tin monoxide" Physical Review B 74, 195128 (2006) [DOI: 10.1103/PhysRevB.74.195128](https://doi.org/10.1103/PhysRevB.74.195128){:target='_blank'}. [@Togo2006; @Wang2014; @Na-Phattalung2006] +![SnO O-interstitial](../../../images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/0-figure-from-manuscript.webp "O-interstitial defect in SnO") ### 3.2. Surface Defects - [Island Surface Defect Formation in TiN](defect-surface-island-titanium-nitride.md) > Manuscript Reference: **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) - [Step Surface Defect on Pt(111)](defect-surface-step-platinum.md) > Manuscript Reference: 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] +![Fig. 1.](../../../images/tutorials/materials/defects/defect_surface_step_platinum/0-figure-from-manuscript.webp "Fig. 1.") - [Adatom Surface Defects on Graphene](defect-surface-adatom-graphene.md) > **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) +![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 - [Grain Boundary in FCC Metals (Copper)](defect-planar-grain-boundary-3d-fcc-metals-copper.md) > Manuscript Reference: Timofey Frolov, David L. Olmsted, Mark Asta & Yuri Mishin, "Structural phase transformations in metallic grain boundaries", Nature Communications, volume 4, Article number: 1899 (2013). [DOI: 10.1038/ncomms2919](https://www.nature.com/articles/ncomms2919){:target='_blank'}. [@Frolov2013] +![Copper Grain Boundary](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/0-figure-from-manuscript.webp "Copper Grain Boundary, FIG. 1") - [Grain Boundary (2D) in h-BN](defect-planar-grain-boundary-2d-boron-nitride.md) > **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) +![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.") --- @@ -118,12 +136,14 @@ Physical Review B 74, 195128 (2006) "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] +![Passivated Silicon nanowire](../../../images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/0-figure-from-manuscript.webp "Passivated Silicon nanowire, FIG. 1.") - [H-Passivated Silicon (100) Surface](passivation-surface-silicon.md) > Manuscript Reference: Hansen, U., & Vogl, P. "Hydrogen passivation of silicon surfaces: A classical molecular-dynamics study." Physical Review B, 57(20), 13295–13304. (1998) [DOI: 10.1103/PhysRevB.57.13295](https://doi.org/10.1103/PhysRevB.57.13295){:target='_blank'}. [@Hansen1998; @Northrup1991; @Boland1990] +![Si(100) H-Passivated Surface](../../../images/tutorials/materials/passivation/passivation_surface_silicon/0-figure-from-manuscript.webp "H-Passivated Silicon (100) --- @@ -134,6 +154,7 @@ Physical Review B, 57(20), 13295–13304. (1998) "Rippling of graphene" EPL (Europhysics Letters), 85(4), 46002 (2009) [DOI: 10.1209/0295-5075/85/46002](https://doi.org/10.1209/0295-5075/85/46002){:target='_blank'}. [@ThompsonFlagg2009; @Fasolino2007; @Openov2010] +![Rippled Graphene](../../../images/tutorials/materials/defects/perturbation_ripple_graphene/0-figure-from-manuscript.webp "Rippled Graphene, FIG. 1.") --- @@ -144,9 +165,10 @@ EPL (Europhysics Letters), 85(4), 46002 (2009) "Graphene–nickel interfaces: a review" Nanoscale, 6(5), 2548. (2014) [DOI: 10.1039/c3nr05279f](https://doi.org/10.1039/c3nr05279f){:target='_blank'}. [@Dahal2014; @Gamo1997; @Bertoni2004] +![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) - [Pt Adatoms Island on MoS2](defect-point-adatom-island-molybdenum-disulfide-platinum.md) > Manuscript Reference: Saidi, W. A. "Density Functional Theory Study of Nucleation and Growth of Pt Nanoparticles on MoS2(001) Surface" Crystal Growth & Design, 15(2), 642–652. (2015) -[DOI: 10.1021/cg5013395](https://doi.org/10.1021/cg5013395){:target='_blank'}. [@Saidi2015; @Jiao2016; @Fichthorn2000; @Neugebauer1993; @Hortamani2007] \ No newline at end of file +[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") From 6a4caf97bf2574ca791329f8fdee908bab8080fd Mon Sep 17 00:00:00 2001 From: VsevolodX Date: Sun, 9 Feb 2025 18:57:03 -0800 Subject: [PATCH 5/8] update: reformat numbering --- .../tutorials/materials/specific/overview.md | 137 +++++++++--------- 1 file changed, 72 insertions(+), 65 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/overview.md b/lang/en/docs/tutorials/materials/specific/overview.md index 534773f3..d694d1e2 100644 --- a/lang/en/docs/tutorials/materials/specific/overview.md +++ b/lang/en/docs/tutorials/materials/specific/overview.md @@ -7,8 +7,7 @@ This document contains links to the tutorials that demonstrate how to reproduce ## 1. Single-Material Structures ### 1.1. 2D Structures -#### 1.1.1. [SrTiO3 Slab](slab-strontium-titanate.md) -Manuscript Reference: R. I. Eglitis and David Vanderbilt +#### 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] @@ -16,11 +15,11 @@ Phys. Rev. B 77, 195408 (2008) ![Strontium Titanate Slabs](../../../images/tutorials/materials/2d_materials/slab_strontium_titanate/0-figure-from-manuscript.webp "Strontium Titanate Slabs, FIG. 2.") ### 1.2. 0D Structures -- [Gold Nanoclusters](nanocluster-gold.md) - > Manuscript Reference: > **A. H. Larsen, J. Kleis, K. S. Thygesen, J. K. Nørskov, and K. W. Jacobsen**, -> "Electronic shell structure and chemisorption on gold nanoparticles", -> *Phys. Rev. B 84, 245429 (2011)*, -> [DOI: 10.1103/PhysRevB.84.245429](https://doi.org/10.1103/PhysRevB.84.245429){:target='_blank'}. [@Larsen2011] +#### 1.2.1. [Gold Nanoclusters](nanocluster-gold.md) +**A. H. Larsen, J. Kleis, K. S. Thygesen, J. K. Nørskov, and K. W. Jacobsen**, +"Electronic shell structure and chemisorption on gold nanoparticles", +*Phys. Rev. B 84, 245429 (2011)*, +[DOI: 10.1103/PhysRevB.84.245429](https://doi.org/10.1103/PhysRevB.84.245429){:target='_blank'}. [@Larsen2011] ![Gold Nanoparticles](../../../images/tutorials/materials/0d_materials/nanocluster_gold/0-manuscript-image.webp "Fig. 2. Gold Nanoparticles") --- @@ -28,40 +27,40 @@ Phys. Rev. B 77, 195408 (2008) ## 2. Multi-Material Structures ### 2.1. Interfaces -- [Interface between Graphene and h-BN](interface-2d-2d-graphene-boron-nitride.md) - > **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) +#### 2.1.1. [Interface between Graphene and h-BN](interface-2d-2d-graphene-boron-nitride.md) +**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) ![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") -- [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) +#### 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) ![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) -- [Interface between Copper and SiO2 (Cristobalite)](interface-3d-3d-copper-silicon-dioxide.md) - > Manuscript Reference: **Shan, T.-R., Devine, B. D., Phillpot, S. R., & Sinnott, S. 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]. ![Copper on Cristobalite](../../../images/tutorials/materials/interfaces/interface_3d_3d_copper_cristobalite/0-figure-from-manuscript.webp "Copper on Cristobalite, FIG. 1") -- [High-k Metal Gate Stack (Si/SiO2/HfO2/TiN)](heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md) - > Manuscript Reference: [Placeholder – Reference not provided] +#### 2.1.4. [High-k Metal Gate Stack (Si/SiO2/HfO2/TiN)](heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md) +[Placeholder – Reference not provided] ![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") ### 2.2. Twisted Interfaces -- [Twisted Bilayer h-BN nanoribbons](interface-bilayer-twisted-nanoribbons-boron-nitride.md) - > Manuscript Reference: **Lede Xian, Dante M. Kennes, Nicolas Tancogne-Dejean, Massimo Altarelli, and Angel Rubio**, +#### 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] ![Twisted Bilayer Boron Nitride](../../../images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/tbbn-paper-image.png "Twisted Bilayer Boron Nitride") -- [Twisted Bilayer MoS2 commensurate lattices](interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md) - > Manuscript Reference: **Kaihui Liu, Liming Zhang, Ting Cao, Chenhao Jin, Diana Qiu, Qin Zhou, Alex Zettl, Peidong Yang, Steve G. Louie & Feng Wang**, +#### 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] ![Twisted Bilayer Molybdenum Disulfide](../../../images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/MoS2-twisted-bilayers.png "Twisted Bilayer Molybdenum Disulfide") @@ -71,75 +70,79 @@ Physical Review B, 83(11). ## 3. Defects ### 3.1. Point Defects -- [Substitutional Point Defects in Graphene](defect-point-substitution-graphene.md) - > **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) +#### 3.1.1. [Substitutional Point Defects in Graphene](defect-point-substitution-graphene.md) +**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) ![Point Defect, Substitution, 0](../../../images/tutorials/materials/defects/defect_creation_point_substitution_graphene/0-figure-from-manuscript.webp "Point Defect, Substitution, FIG. 1.") -- [Vacancy-Substitution Pair Defects in GaN](defect-point-pair-gallium-nitride.md) - > Manuscript Reference: **Giacomo Miceli, Alfredo Pasquarello**, +#### 3.1.2. [Vacancy-Substitution Pair Defects in GaN](defect-point-pair-gallium-nitride.md) +**Giacomo Miceli, Alfredo Pasquarello**, "Self-compensation due to point defects in Mg-doped GaN", Physical Review B, 2016. [DOI: 10.1103/PhysRevB.93.165207](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.93.165207){:target='_blank'}. [@Miceli2016] ![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.") -- [Vacancy Point Defect in h-BN](defect-point-vacancy-boron-nitride.md) - > **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) +#### 3.1.3. [Vacancy Point Defect in h-BN](defect-point-vacancy-boron-nitride.md) +**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) ![Vacancy in h-BN](../../../images/tutorials/materials/defects/defect_point_vacancy_boron_nitride/0-figure-from-manuscript.webp "Vacancy in h-BN") -- [Interstitial Point Defect in SnO](defect-point-interstitial-tin-oxide.md) - > Manuscript Reference: A. Togo, F. Oba, and I. Tanaka +#### 3.1.4. [Interstitial Point Defect in SnO](defect-point-interstitial-tin-oxide.md) +A. Togo, F. Oba, and I. Tanaka "First-principles calculations of native defects in tin monoxide" Physical Review B 74, 195128 (2006) [DOI: 10.1103/PhysRevB.74.195128](https://doi.org/10.1103/PhysRevB.74.195128){:target='_blank'}. [@Togo2006; @Wang2014; @Na-Phattalung2006] ![SnO O-interstitial](../../../images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/0-figure-from-manuscript.webp "O-interstitial defect in SnO") ### 3.2. Surface Defects -- [Island Surface Defect Formation in TiN](defect-surface-island-titanium-nitride.md) - > Manuscript Reference: **D. G. Sangiovanni, A. B. Mei, D. Edström, L. Hultman, V. Chirita, I. Petrov, and J. E. Greene**, +#### 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) -- [Step Surface Defect on Pt(111)](defect-surface-step-platinum.md) - > Manuscript Reference: 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] +#### 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] ![Fig. 1.](../../../images/tutorials/materials/defects/defect_surface_step_platinum/0-figure-from-manuscript.webp "Fig. 1.") -- [Adatom Surface Defects on Graphene](defect-surface-adatom-graphene.md) - > **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) +#### 3.2.3. [Adatom Surface Defects on Graphene](defect-surface-adatom-graphene.md) +**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) ![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 -- [Grain Boundary in FCC Metals (Copper)](defect-planar-grain-boundary-3d-fcc-metals-copper.md) - > Manuscript Reference: Timofey Frolov, David L. Olmsted, Mark Asta & Yuri Mishin, "Structural phase transformations in metallic grain boundaries", Nature Communications, volume 4, Article number: 1899 (2013). [DOI: 10.1038/ncomms2919](https://www.nature.com/articles/ncomms2919){:target='_blank'}. [@Frolov2013] +#### 3.3.1. [Grain Boundary in FCC Metals (Copper)](defect-planar-grain-boundary-3d-fcc-metals-copper.md) +Timofey Frolov, David L. Olmsted, Mark Asta & Yuri Mishin, "Structural phase transformations in metallic grain boundaries", Nature Communications, volume 4, Article number: 1899 (2013). [DOI: 10.1038/ncomms2919](https://www.nature.com/articles/ncomms2919){:target='_blank'}. [@Frolov2013] ![Copper Grain Boundary](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/0-figure-from-manuscript.webp "Copper Grain Boundary, FIG. 1") -- [Grain Boundary (2D) in h-BN](defect-planar-grain-boundary-2d-boron-nitride.md) - > **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) +#### 3.3.2. [Grain Boundary (2D) in h-BN](defect-planar-grain-boundary-2d-boron-nitride.md) +**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) ![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.") --- ## 4. Passivation -- [H-Passivated Silicon Nanowire](passivation-edge-nanowire-silicon.md) - > Manuscript Reference: B. Aradi, L. E. Ramos, P. Deák, Th. Köhler, F. Bechstedt, R. Q. Zhang, and Th. Frauenheim, + +### 4.1. Edge Passivation +#### 4.1.1. [H-Passivated Silicon Nanowire](passivation-edge-nanowire-silicon.md) +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] ![Passivated Silicon nanowire](../../../images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/0-figure-from-manuscript.webp "Passivated Silicon nanowire, FIG. 1.") -- [H-Passivated Silicon (100) Surface](passivation-surface-silicon.md) - > Manuscript Reference: Hansen, U., & Vogl, P. + +### 4.2. Surface Passivation +#### 4.2.1. [H-Passivated Silicon (100) Surface](passivation-surface-silicon.md) +Hansen, U., & Vogl, P. "Hydrogen passivation of silicon surfaces: A classical molecular-dynamics study." Physical Review B, 57(20), 13295–13304. (1998) [DOI: 10.1103/PhysRevB.57.13295](https://doi.org/10.1103/PhysRevB.57.13295){:target='_blank'}. [@Hansen1998; @Northrup1991; @Boland1990] @@ -149,8 +152,10 @@ Physical Review B, 57(20), 13295–13304. (1998) ## 5. Perturbations -- [Ripple perturbation of a Graphene sheet](perturbation-ripples-graphene.md) - > Manuscript Reference: Thompson-Flagg, R. C., Moura, M. J. B., & Marder, M. + +### 5.1. Ripples +#### 5.1.1. [Ripple perturbation of a Graphene sheet](perturbation-ripples-graphene.md) +Thompson-Flagg, R. C., Moura, M. J. B., & Marder, M. "Rippling of graphene" EPL (Europhysics Letters), 85(4), 46002 (2009) [DOI: 10.1209/0295-5075/85/46002](https://doi.org/10.1209/0295-5075/85/46002){:target='_blank'}. [@ThompsonFlagg2009; @Fasolino2007; @Openov2010] @@ -160,15 +165,17 @@ EPL (Europhysics Letters), 85(4), 46002 (2009) ## 6. Other -- [Gr/Ni(111) Interface Optimization](optimization-interface-film-xy-position-graphene-nickel.md) - > Manuscript Reference: Arjun Dahal, Matthias Batzill + +### 6.1. Interface Optimization +#### 6.1.1. [Gr/Ni(111) Interface Optimization](optimization-interface-film-xy-position-graphene-nickel.md) +Arjun Dahal, Matthias Batzill "Graphene–nickel interfaces: a review" Nanoscale, 6(5), 2548. (2014) [DOI: 10.1039/c3nr05279f](https://doi.org/10.1039/c3nr05279f){:target='_blank'}. [@Dahal2014; @Gamo1997; @Bertoni2004] ![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) -- [Pt Adatoms Island on MoS2](defect-point-adatom-island-molybdenum-disulfide-platinum.md) - > Manuscript Reference: Saidi, W. A. +#### 6.1.2. [Pt Adatoms Island on MoS2](defect-point-adatom-island-molybdenum-disulfide-platinum.md) +Saidi, W. A. "Density Functional Theory Study of Nucleation and Growth of Pt Nanoparticles on MoS2(001) Surface" Crystal Growth & Design, 15(2), 642–652. (2015) [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") From f2ac2e2b024f9707dbd875611ae5a2a53ecacce7 Mon Sep 17 00:00:00 2001 From: VsevolodX Date: Sun, 9 Feb 2025 19:21:15 -0800 Subject: [PATCH 6/8] update: add mkdcos --- mkdocs.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/mkdocs.yml b/mkdocs.yml index 5fd29282..23d86f03 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -225,6 +225,7 @@ nav: - Import materials from files in various formats: tutorials/materials/import-from-files.md - Reproducing Specific Manuscripts: + - Overview: tutorials/materials/specific/overview.md - Substitutional Point Defects in Graphene: tutorials/materials/specific/defect-point-substitution-graphene.md - Vacancy-Substitution Pair Defects in GaN: tutorials/materials/specific/defect-point-pair-gallium-nitride.md - Vacancy Point Defect in h-BN: tutorials/materials/specific/defect-point-vacancy-boron-nitride.md From e25af6ee7a87ce971f860d293c0c2d1c08572891 Mon Sep 17 00:00:00 2001 From: VsevolodX Date: Sun, 9 Feb 2025 19:23:19 -0800 Subject: [PATCH 7/8] chore: cleanups --- .../tutorials/materials/specific/overview.md | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/overview.md b/lang/en/docs/tutorials/materials/specific/overview.md index d694d1e2..541036a0 100644 --- a/lang/en/docs/tutorials/materials/specific/overview.md +++ b/lang/en/docs/tutorials/materials/specific/overview.md @@ -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.") @@ -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) @@ -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") --- @@ -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) @@ -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) @@ -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] @@ -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 @@ -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.") --- @@ -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.") From 958c208b1bbc16d4140c1648d5a9823666cd01ac Mon Sep 17 00:00:00 2001 From: VsevolodX Date: Sun, 9 Feb 2025 19:35:14 -0800 Subject: [PATCH 8/8] chore: cleanups 2 --- .../tutorials/materials/specific/overview.md | 36 +++++++++++++++---- 1 file changed, 29 insertions(+), 7 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/overview.md b/lang/en/docs/tutorials/materials/specific/overview.md index 541036a0..419d0eb1 100644 --- a/lang/en/docs/tutorials/materials/specific/overview.md +++ b/lang/en/docs/tutorials/materials/specific/overview.md @@ -10,6 +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){: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.") @@ -19,6 +20,7 @@ Phys. Rev. B 77, 195408 (2008) **A. H. Larsen, J. Kleis, K. S. Thygesen, J. K. Nørskov, and K. W. Jacobsen**, "Electronic shell structure and chemisorption on gold nanoparticles", *Phys. Rev. B 84, 245429 (2011)*, + [DOI: 10.1103/PhysRevB.84.245429](https://doi.org/10.1103/PhysRevB.84.245429){:target='_blank'}. [@Larsen2011] ![Gold Nanoparticles](../../../images/tutorials/materials/0d_materials/nanocluster_gold/0-manuscript-image.webp "Fig. 2. Gold Nanoparticles") @@ -31,6 +33,7 @@ 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){: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") @@ -38,30 +41,34 @@ Nature Communications, 2015 **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){: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) +![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){: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) -[Placeholder – Reference not provided] +QuantumATK tutorial: [High-k Metal Gate Stack Builder](https://docs.quantumatk.com/tutorials/hkmg_builder/hkmg_builder.html) [@Muller1999; @Robertson2006] ![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") ### 2.2. Twisted Interfaces #### 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){: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){: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") @@ -74,12 +81,14 @@ 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){: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) **Giacomo Miceli, Alfredo Pasquarello**, "Self-compensation due to point defects in Mg-doped GaN", Physical Review B, 2016. + [DOI: 10.1103/PhysRevB.93.165207](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.93.165207){:target='_blank'}. [@Miceli2016] ![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.") @@ -87,6 +96,7 @@ 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){:target='_blank'} ![Vacancy in h-BN](../../../images/tutorials/materials/defects/defect_point_vacancy_boron_nitride/0-figure-from-manuscript.webp "Vacancy in h-BN") @@ -94,35 +104,43 @@ Nature, 2022 A. Togo, F. Oba, and I. Tanaka "First-principles calculations of native defects in tin monoxide" Physical Review B 74, 195128 (2006) + [DOI: 10.1103/PhysRevB.74.195128](https://doi.org/10.1103/PhysRevB.74.195128){:target='_blank'}. [@Togo2006; @Wang2014; @Na-Phattalung2006] ![SnO O-interstitial](../../../images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/0-figure-from-manuscript.webp "O-interstitial defect in SnO") ### 3.2. Surface Defects #### 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] +"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") #### 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] +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] ![Fig. 1.](../../../images/tutorials/materials/defects/defect_surface_step_platinum/0-figure-from-manuscript.webp "Fig. 1.") #### 3.2.3. [Adatom Surface Defects on Graphene](defect-surface-adatom-graphene.md) **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){: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 #### 3.3.1. [Grain Boundary in FCC Metals (Copper)](defect-planar-grain-boundary-3d-fcc-metals-copper.md) -Timofey Frolov, David L. Olmsted, Mark Asta & Yuri Mishin, "Structural phase transformations in metallic grain boundaries", Nature Communications, volume 4, Article number: 1899 (2013). [DOI: 10.1038/ncomms2919](https://www.nature.com/articles/ncomms2919){:target='_blank'}. [@Frolov2013] +Timofey Frolov, David L. Olmsted, Mark Asta & Yuri Mishin, "Structural phase transformations in metallic grain boundaries", Nature Communications, volume 4, Article number: 1899 (2013). + +[DOI: 10.1038/ncomms2919](https://www.nature.com/articles/ncomms2919){:target='_blank'}. [@Frolov2013] ![Copper Grain Boundary](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/0-figure-from-manuscript.webp "Copper Grain Boundary, FIG. 1") #### 3.3.2. [Grain Boundary (2D) in h-BN](defect-planar-grain-boundary-2d-boron-nitride.md) **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){: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.") @@ -145,8 +163,9 @@ DOI: [10.1103/PhysRevB.76.035305](https://doi.org/10.1103/PhysRevB.76.035305){:t Hansen, U., & Vogl, P. "Hydrogen passivation of silicon surfaces: A classical molecular-dynamics study." Physical Review B, 57(20), 13295–13304. (1998) + [DOI: 10.1103/PhysRevB.57.13295](https://doi.org/10.1103/PhysRevB.57.13295){:target='_blank'}. [@Hansen1998; @Northrup1991; @Boland1990] -![Si(100) H-Passivated Surface](../../../images/tutorials/materials/passivation/passivation_surface_silicon/0-figure-from-manuscript.webp "H-Passivated Silicon (100) +![Si(100) H-Passivated Surface](../../../images/tutorials/materials/passivation/passivation_surface_silicon/0-figure-from-manuscript.webp "H-Passivated Silicon (100)") --- @@ -158,6 +177,7 @@ Physical Review B, 57(20), 13295–13304. (1998) Thompson-Flagg, R. C., Moura, M. J. B., & Marder, M. "Rippling of graphene" EPL (Europhysics Letters), 85(4), 46002 (2009) + [DOI: 10.1209/0295-5075/85/46002](https://doi.org/10.1209/0295-5075/85/46002){:target='_blank'}. [@ThompsonFlagg2009; @Fasolino2007; @Openov2010] ![Rippled Graphene](../../../images/tutorials/materials/defects/perturbation_ripple_graphene/0-figure-from-manuscript.webp "Rippled Graphene, FIG. 1.") @@ -171,11 +191,13 @@ EPL (Europhysics Letters), 85(4), 46002 (2009) Arjun Dahal, Matthias Batzill "Graphene–nickel interfaces: a review" Nanoscale, 6(5), 2548. (2014) + [DOI: 10.1039/c3nr05279f](https://doi.org/10.1039/c3nr05279f){:target='_blank'}. [@Dahal2014; @Gamo1997; @Bertoni2004] -![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) +![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)") #### 6.1.2. [Pt Adatoms Island on MoS2](defect-point-adatom-island-molybdenum-disulfide-platinum.md) Saidi, W. A. "Density Functional Theory Study of Nucleation and Growth of Pt Nanoparticles on MoS2(001) Surface" Crystal Growth & Design, 15(2), 642–652. (2015) + [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")