Skip to content

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.

1. Single-Material Structures

1.1. 2D Structures

1.1.1. SrTiO3 Slab 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 12

Strontium Titanate Slabs

1.2. 0D Structures

1.2.1. Gold Nanoclusters

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. 3 Gold Nanoparticles

2. Multi-Material Structures

2.1. Interfaces

2.1.1. Interface between Graphene and h-BN

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 Graphene on Hexagonal Boron Nitride

2.1.2. Interface between Graphene and SiO2 (alpha-quartz)

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 Graphene on Silicon Dioxide

2.1.3. Interface between Copper and SiO2 (Cristobalite)

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 4. Copper on Cristobalite

2.1.4. High-k Metal Gate Stack (Si/SiO2/HfO2/TiN)

QuantumATK tutorial: High-k Metal Gate Stack Builder 56 High-k Metal Gate Stack

2.2. Twisted Interfaces

2.2.1. Twisted Bilayer h-BN nanoribbons

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 7 Twisted Bilayer Boron Nitride

2.2.2. Twisted Bilayer MoS2 commensurate lattices

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 89 Twisted Bilayer Molybdenum Disulfide

3. Defects

3.1. Point Defects

3.1.1. Substitutional Point Defects in Graphene

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 Point Defect, Substitution, 0

3.1.2. Vacancy-Substitution Pair Defects in GaN

Giacomo Miceli, Alfredo Pasquarello, "Self-compensation due to point defects in Mg-doped GaN", Physical Review B, 2016.

DOI: 10.1103/PhysRevB.93.165207. 10 Point Pair Defects: Mg Substitution and Vacancy in GaN

3.1.3. Vacancy Point Defect in h-BN

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 Vacancy in h-BN

3.1.4. Interstitial Point Defect in SnO

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. 111213 SnO O-interstitial

3.2. Surface Defects

3.2.1. Island Surface Defect Formation in TiN

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. 14 Surface Defect

3.2.2. Step Surface Defect on Pt(111)

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. 15 Fig. 1.

3.2.3. Adatom Surface Defects on Graphene

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 Adatom on Graphene Surface

3.3. Planar Defects

3.3.1. Grain Boundary in FCC Metals (Copper)

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. 16 Copper Grain Boundary

3.3.2. Grain Boundary (2D) in h-BN

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 h-BN Grain Boundary

4. Passivation

4.1. Edge Passivation

4.1.1. H-Passivated Silicon Nanowire

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 17 Passivated Silicon nanowire

4.2. Surface Passivation

4.2.1. H-Passivated Silicon (100) Surface

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. 181920 Si(100) H-Passivated Surface

5. Perturbations

5.1. Ripples

5.1.1. Ripple perturbation of a Graphene sheet

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. 212223 Rippled Graphene

6. Other

6.1. Interface Optimization

6.1.1. Gr/Ni(111) Interface Optimization

Arjun Dahal, Matthias Batzill "Graphene–nickel interfaces: a review" Nanoscale, 6(5), 2548. (2014)

DOI: 10.1039/c3nr05279f. 242526 Gr/Ni Interface

6.1.2. Pt Adatoms Island on MoS2

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. 2728293031Pt Island on MoS2

  1. 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, May 2008. URL: https://link.aps.org/doi/10.1103/PhysRevB.77.195408. ↩

  2. Atashi B. Mukhopadhyay, Javier F. Sanz, and Charles B. Musgrave. First-principles calculations of structural and electronic properties of monoclinic hafnia surfaces. Phys. Rev. B, 73:115330, Mar 2006. URL: https://link.aps.org/doi/10.1103/PhysRevB.73.115330. ↩

  3. Ask Hjorth Larsen, Jesper Kleis, Kristian Sommer Thygesen, Jens K. Nørskov, and Karsten Wedel Jacobsen. Electronic shell structure and chemisorption on gold nanoparticles. Phys. Rev. B, 84(24):245429, 2011. URL: https://doi.org/10.1103/PhysRevB.84.245429. ↩

  4. T.-R. Shan, B. D. Devine, S. R. Phillpot, and S. B. Sinnott. Molecular dynamics study of the adhesion of cu/sio2interfaces using a variable-charge interatomic potential. Physical Review B, 2011. URL: https://doi.org/10.1103/PhysRevB.83.115327. ↩

  5. D A Muller, N Nakagawa, A Ohtomo, J L Grazul, and H Y Hwang. The electronic structure at the atomic scale of ultrathin gate oxides. Nature, 399:758–761, 1999. URL: https://doi.org/10.1038/21667. ↩

  6. J Robertson. High dielectric constant gate oxides for metal oxide si transistors. Reports on Progress in Physics, 69:327, 2006. URL: https://doi.org/10.1088/0034-4885/69/2/R02. ↩

  7. 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, 2020. URL: https://doi.org/10.1021/acs.nanolett.9b00986. ↩

  8. Kaihui Liu, Liming Zhang, Ting Cao, Chenhao Jin, Diana Qiu, Qin Zhou, Alex Zettl, Peidong Yang, Steve G. Louie, and Feng Wang. Evolution of interlayer coupling in twisted molybdenum disulfide bilayers. Nature Communications, 5:4966, 2014. URL: https://doi.org/10.1038/ncomms5966, doi:10.1038/ncomms5966. ↩

  9. Y. Cao, V. Fatemi, S. Fang, and et al. Unconventional superconductivity in magic-angle graphene superlattices. Nature, 556:43–50, 2018. URL: https://doi.org/10.1038/nature26160. ↩

  10. Giacomo Miceli and Alfredo Pasquarello. Self-compensation due to point defects in mg-doped gan. Physical Review B, 93:165207, 2016. URL: https://link.aps.org/doi/10.1103/PhysRevB.93.165207. ↩

  11. A. Togo, F. Oba, and I. Tanaka. First-principles calculations of native defects in tin monoxide. Physical Review B, 74(19):195128, 2006. URL: https://doi.org/10.1103/PhysRevB.74.195128. ↩

  12. H. Wang, A. Chroneos, C. A. Londos, E. N. Sgourou, and U. Schwingenschlögl. Carbon related defects in irradiated silicon revisited. Scientific Reports, 4:4909, 2014. URL: https://doi.org/10.1038/srep04909. ↩

  13. Sutassana Na-Phattalung, M. F. Smith, Kwiseon Kim, Mao-Hua Du, Su-Huai Wei, S. B. Zhang, and Sukit Limpijumnong. First-principles study of native defects in anatase tio2. Physical Review B, 73:125205, 2006. URL: https://doi.org/10.1103/PhysRevB.73.125205. ↩

  14. D. G. Sangiovanni, A. B. Mei, D. Edström, L. Hultman, V. Chirita, I. Petrov, and J. E. Greene. Effects of surface vibrations on interlayer mass transport: ab initio molecular dynamics investigation of ti adatom descent pathways and rates from tin/tin(001) islands. Physical Review B, 97:035406, 2018. URL: https://link.aps.org/doi/10.1103/PhysRevB.97.035406. ↩

  15. Z. Šljivančanin and B. Hammer. 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, 2002. URL: https://doi.org/10.1016/s0039-6028(02)01908-8. ↩

  16. Timofey Frolov, David L Olmsted, Mark Asta, and Yuri Mishin. Structural phase transformations in metallic grain boundaries. Nature Communications, 4:1899, 2013. URL: https://doi.org/10.1038/ncomms2924. ↩

  17. 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(3):035305, 2007. URL: https://doi.org/10.1103/PhysRevB.76.035305. ↩

  18. U. Hansen and P. Vogl. Hydrogen passivation of silicon surfaces: a classical molecular-dynamics study. Physical Review B, 57(20):13295–13304, 1998. URL: https://doi.org/10.1103/physrevb.57.13295. ↩

  19. J. E. Northrup. Structure of si(100)h: dependence on the h chemical potential. Physical Review B, 44(3):1419–1422, 1991. URL: https://doi.org/10.1103/physrevb.44.1419. ↩

  20. J. J. Boland. Structure of the h‐saturated si(100) surface. Physical Review Letters, 65(26):3325–3328, 1990. URL: https://doi.org/10.1103/physrevlett.65.3325. ↩

  21. R. C. Thompson-Flagg, M. J. B. Moura, and M. Marder. Rippling of graphene. EPL (Europhysics Letters), 85(4):46002, 2009. URL: https://doi.org/10.1209/0295-5075/85/46002. ↩

  22. A. Fasolino, J. H. Los, and M. I. Katsnelson. Intrinsic ripples in graphene. Nature Materials, 6:858–861, 2007. URL: https://doi.org/10.1038/nmat2011. ↩

  23. L. A. Openov and A. I. Podlivaev. Interaction of the stone-wales defects in graphene. Physics of the Solid State, 52(1):2010, 2010. URL: https://doi.org/10.1134/S1063783415070240. ↩

  24. Arjun Dahal and Matthias Batzill. Graphene–nickel interfaces: a review. Nanoscale, 6:2548–2562, 2014. URL: https://doi.org/10.1039/C3NR05279F. ↩

  25. Y. Gamo, A. Nagashima, M. Wakabayashi, M. Terai, and C. Oshima. Atomic structure of monolayer graphite formed on ni(111). Surface Science, 374(1-3):61–64, 1997. URL: https://www.sciencedirect.com/science/article/abs/pii/S0039602896007856. ↩

  26. G. Bertoni, L. Calmels, A. Altibelli, and V. Serin. First-principles calculation of the electronic structure and eels spectra at the graphene/ni(111) interface. Physical Review B, 2004. URL: https://journals.aps.org/prb/abstract/10.1103/PhysRevB.71.075402. ↩

  27. W. A. Saidi. Density functional theory study of nucleation and growth of pt nanoparticles on mos2(001) surface. Crystal Growth & Design, 15(2):642–652, 2015. URL: https://doi.org/10.1021/cg5013395. ↩

  28. M. Jiao, W. Song, H.-J. Qian, Y. Wang, Z. Wu, S. Irle, and K. Morokuma. Qm/md studies on graphene growth from small islands on the ni(111) surface. Nanoscale, 8(5):3067–3074, 2016. URL: https://doi.org/10.1039/c5nr07680c. ↩

  29. Kristen A. Fichthorn and Matthias Scheffler. Island nucleation in thin-film epitaxy: a first-principles investigation. Phys. Rev. Lett., 84:5371, 2000. URL: https://link.aps.org/doi/10.1103/PhysRevLett.84.5371. ↩

  30. Jörg Neugebauer and Matthias Scheffler. Mechanisms of island formation of alkali-metal adsorbates on al(111). Phys. Rev. Lett., 71:577, 1993. URL: https://link.aps.org/doi/10.1103/PhysRevLett.71.577. ↩

  31. Mahbube Hortamani, Peter Kratzer, and Matthias Scheffler. Density-functional study of mn monosilicide on the si(111) surface: film formation versus island nucleation. Phys. Rev. B, 76:235426, 2007. URL: https://link.aps.org/doi/10.1103/PhysRevB.76.235426. ↩