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For up-to-date publication information, please visit Prof. Kim’s Google Scholar or ORCID pages.

Select Publications

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Three-dimensional imaging of individual carbon atoms

arXiv.2504.08228
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Modeling Temperature-Dependent Electron Thermal Diffuse Scattering via Machine-Learned Interatomic Potentials and Path-Integral Molecular Dynamics

Phys. Rev. Lett. 132, 086301 (2024)
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Three-dimensional atomic packing in amorphous solids with liquid-like structure

Nat. Mater. 21, 95 (2022)
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Correlating the three-dimensional atomic defects and electronic properties of two-dimensional transition metal dichalcogenides

Nat. Mater. 19, 867 (2020)
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Capturing 3D atomic defects and phonon localization at the 2D heterostructure interface

Sci. Adv., 7, 38, eabi6699 (2021)
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Observing crystal nucleation in four dimensions using atomic electron tomography

Nature, 570, 7762, 500 (2019)
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Nuclear quantum effect with pure anharmonicity and the anomalous thermal expansion of silicon

Proc. Natl. Acad. Sci. USA 115, 1992 (2018)

All publications


† denote equal contribution, ‡ denote corresponding authorship, bold names denote PERL Team member

25. Y. Yuan, S. Moniri, Y. Yang, J. Zhou, A. Yuan, D.S. Kim, Y. Yang, C. Li, W. Chen, P. Ercius,

J. Miao, “Crystal nucleation and growth in high-entropy alloys revealed by atomic electron

tomography”, arXiv:2504.11325 (2025).

24. N.Y. Kim, H. Zhong, J. Zhang, C. O’Leary, Y. Liao, J. Zou, H. Sha, M. Pham, W. Li, Y. Yuan, J.H.

Park, D.S. Kim, H. Jiang, J. Kong, M. Chi, J. Miao, “Determining 3D atomic coordinates of light-element quantum materials using ptychographic electron tomography”, arXiv:2504.08228 (2025).

23. C.N. Saunders, V.V. Ladygin, D.S. Kim, D.L. Abernathy, B.T. Fultz, “Diffuse inelastic neutron

scattering from anharmonic vibrations in cuprite”, Phys. Rev. Mater. 9, 024602 (2025).

22. D.S. Kim, C. Harris, M.D. Hanwell, B. Zhou, D. Chang, C. Ophus, P. Ercius, and J. Miao, “Ma-

terials Data Bank, a modern open-source database for experimental atomic structure dissemination”, under review at Sci. Data (2025).

21. D.S. Kim‡, M. Xu, and J.M. LeBeau, “Modeling Temperature-Dependent Electron Thermal

Diffuse Scattering via Machine-Learned Interatomic Potentials and Path-Integral Molecular

Dynamics”, Phys. Rev. Lett. 132 (8), 086301 (2024).

20. F. Knoop, N. Shulumba, A. Castellano, J.P. Alvarinhas Batista, R. Farris, M.J. Verstraete, M.

Heine, D. Broido, D.S. Kim, J. Klarbring, I. Abrikosov, S.I. Simak, O. Hellman, “TDEP: Tem-

perature Dependent Effective Potentials”, J. Open Source Softw., 9(94), 6150 (2024).

19. C.M. Bernal-Choban, H.L. Smith, C. Saunders, D.S. Kim, D.L. Abernathy, and B. Fultz, “Non-

harmonic contributions to the high-temperature phonon thermodynamics of Cr”, Phys. Rev. B, 107, 054312 (2023).

18. H.G. Seo, A. Staerz, D.S. Kim, J.M. LeBeau, H.L. Tuller. “Tuning surface acidity of mixed

conducting electrodes: Recovery of Si-induced degradation of oxygen exchange rate and

area specific resistance”, Adv. Mater., 35, 2208182 (2023).

17. X. Chen, D.S. Kim†, and J.M. LeBeau, “A Comparison of Molecular Dynamics Potentials

Used to Incorporate Thermal Diffuse Scattering in Multislice Simulations”, Ultramicroscopy,240, 113644 (2023).

16. H.G. Seo, A. Staerz, D.S. Kim, D. Klotz, C. Nicollet, M. Xu, J.M. LeBeau, H.L. Tuller. “Reacti-

vation of chromia poisoned oxygen exchange kinetics in mixed conducting solid oxide fuel

cell electrodes by serial infiltration of lithia”, Energy Environ. Sci. 15, 4038-4047 (2022).

MIT News: “A simple way to significantly increase lifetimes of fuel cells and other devices”

news.mit.edu (2022).

15. C. Saunders, D.S. Kim, O. Hellman, H.L. Smith, N.J. Weadock, S.T. Omelchenko, G.E. Granroth,

C.M. Bernal, S.H. Lohaus, D.L. Abernathy, and B. Fultz, “Thermal expansion and phonon an-

harmonicity of cuprite (Cu2O)”, Phys. Rev. B 105, 174308 (2022).

14. A. Staerz, H.G. Seo, D. Klotz, D.S. Kim, J.M. LeBeau, H.L. Tuller. “The influence of Cr-

additives on the polarization resistance of praseodymium-doped ceria cathodes for solid

oxide fuel cells”, J. Electrochem. Soc 169 044530 (2022).

13. Y. Yuan, D.S. Kim†, J. Zhou, D.J. Chang, F. Zhu, Y. Nagaoka, Y. Yang, M. Pham, S.J. Os-

her, O. Chen, P. Ercius, A.K. Schmid, and J. Miao, “Three-dimensional atomic packing in

amorphous solids with liquid-like structure”, Nat. Mater. 21, 95–102 (2022).

12. X. Tian, X. Yan, G. Varnavides, Y. Yuan, D.S. Kim, C.J. Ciccarino, P. Anikeeva, P. Narang,

X. Pan, and J. Miao, “Capturing 3D atomic defects and phonon localization at the 2D het-

erostructure interface”, Sci. Adv. 7, 38 (2021).

11. Y. Yang, J. Zhou, F. Zhu, Y. Yuan, D.J. Chang, D.S. Kim, M. Pham, A. Rana, X. Tian, Y. Yao,

S. Osher, A.K. Schmid, L. Hu, P. Ercius, and J. Miao, “Determining the three-dimensional

atomic structure of an amorphous solid”, Nature, 592, 60–64 (2021).

News & Views in Nature 592, 31-32 (2021).

10. D.S. Kim‡, O. Hellman, N. Shulumba, C. Saunders, J.Y.Y. Lin, H.L. Smith, J. Herriman, J.L.

Niedziela, D.L. Abernathy, C.W. Li, and B. Fultz, “Temperature-dependent phonon lifetimes

and thermal conductivity of silicon by inelastic neutron scattering and ab initio calculation”,

Phys. Rev. B, 102, 174311 (2020).

9. D. Chang, D.S. Kim, X. Tian, J. Zhou, P. Ercius, and J. Miao, “Ptychographic Atomic Electron

Tomography: Towards 3D Imaging of Individual Light Atoms in Materials”, Phys. Rev. B.,102, 174101 (2020).

8. X. Tian, D.S. Kim†, S. Yang, C.J. Ciccarino, Y. Gong, Y. Yang, Y. Yang, Y. Yuan, B. Duschatko,

P.M. Ajayan, J-C. Idrobo, P. Narang, and J. Miao, “Correlating the three-dimensional atomic

defects and electronic properties of two-dimensional transition metal dichalcogenides ”,

Nat. Mater. 19, 867–873 (2020).

News & Views in Nat. Mater. 19, 827–828 (2020).

 

7. J. Zhou, Y.S. Yang, Y. Yang, D.S. Kim, A. Yuan, X. Tian, C. Ophus, F. Sun, A.K. Schmid, M.

Nathanson, H. Heinz, Q. An, H. Zeng, P. Ercius, and J. Miao, “Observing crystal nucleation in

four dimensions using Atomic electron tomography”, Nature, 570, 500-503 (2019).

News & View in Nature 570, 450-452 (2019)

6. D.S. Kim†‡, O. Hellman, J. Herriman, H.L. Smith, J.Y.Y. Lin, N. Shulumba, J.L. Niedziela, C.W.

Li, D.L. Abernathy, and B. Fultz, “Nuclear quantum effect with pure anharmonicity causes

the anomalous thermal expansion of silicon”, Proc. Natl. Acad. Sci. U.S.A. 115 (9) 1992-1997 (2018).

Editor’s Choice in “Silicon sheds its harmonicity” Science ,360, 6385 (2018).

5. H.L. Smith, Y. Shen, D.S. Kim, F.C. Yang, C.P. Adams, C.W. Li, D.L. Abernathy, M.B. Stone and

B. Fultz, “The temperature dependence of phonons in FeGe2”, Phys. Rev. Mater. 2, 103602 (2018).

4. H.L. Smith, C.W. Li, A. Hoff, G.R. Garrett, D.S. Kim, F.C. Yang, M.S. Lucas, T. Swan-Wood, J.Y.Y.

Lin, M.B. Stone, D.L. Abernathy, M. Demetriou, and B. Fultz, “Separating the configurational

and vibrational entropy contributions in metallic glasses”, Nat. Phys. 13, 900-905 (2017).

3. T. Lan, C.W. Li, O. Hellman, D.S. Kim, J.A. Muñoz, H.L Smith, D.L. Abernathy, and B. Fultz,

“Phonon quarticity induced by changes in phonon-tracked hybridization during lattice ex-

pansion and its stabilization of rutile TiO2”, Phys. Rev. B 92, 054304 (2015).

2. D.S. Kim‡, H.L Smith, J.L. Niedziela, C.W. Li, D.L. Abernathy, and B. Fultz, “Phonon Anhar-

monicity in Silicon from 100 to 1500 K”, Phys. Rev. B 91, 014307 (2015).

1. T. Lan, C.W. Li, O. Hellman, D.S. Kim, J.A. Muñoz, H.L Smith, D.L. Abernathy, and B. Fultz,

“Phonon quarticity induced by changes in phonon-tracked hybridization during lattice ex-

pansion and its stabilization of rutile TiO2”, Phys. Rev. B 92, 054304 (2015).