For up-to-date publication information, please visit Prof. Kim’s Google Scholar page.
Select Publications
Modeling Temperature-Dependent Electron Thermal Diffuse Scattering via Machine-Learned Interatomic Potentials and Path-Integral Molecular Dynamics
Phys. Rev. Lett. 132, 086301 (2024)
Machine-learned interatomic potentials (MLIPs) show promise in accurately describing the physical properties of materials, but there is a need for a higher throughput method of validation. Here, we demonstrate using that MLIPs and molecular dynamics can accurately capture the potential energy landscape and lattice dynamics that are needed to describe electron thermal diffuse scattering. Using SrTiO3 as a test-bed at cryogenic and room temperatures, we compare electron thermal diffuse scattering simulations using different approximations to incorporate thermal motion. Only when the simulations are based on quantum mechanically accurate MLIPs in combination with path-integral molecular dynamics that include nuclear quantum effects, there is excellent agreement with experiment.
DOI:10.1103/PhysRevLett.132.086301
A Comparison of molecular dynamics potentials used to account for thermal diffuse scattering in multislice simultions
Ultramicroscopy, 244, 113644 (2023)
Here we investigate electron scattering simulations with thermal displacements incorporated using molecular dynamics potentials. Specifically, we explore the sensitivity of electron scattering to the phonon band structure, or more explicitly interatomic forces. Silicon serves as the model material where we introduce thermal atomic displacements via empirical and machine-learned molecular dynamics interatomic potentials and compare them to finite-temperature density functional theory interatomic forces. We demonstrate that when molecular dynamics potentials do not sufficiently reproduce the correct phonon band structure, significant errors in the simulated diffraction and image intensities can occur. Moreover, for Si, we find that multislice simulations using machine-learned interatomic potentials are more accurate than empirical ones. In addition to the selected atomic potential, we demonstrate that the sensitivity to the phonon band structure also depends on the crystal zone axis, which can be used to enhance sensitivity to thermal displacements. Finally, we provide a sensitivity analysis with angle-resolved scanning transmission electron microscopy (STEM) to enhance image sensitivity to the details of the phonon band structure.
DOI:10.1016/j.ultramic.2022.113644
Three-dimensional atomic packing in amorphous solids with liquid-like structure
Nat. Mater. 21, 95 (2022)
Here we investigate electron scattering simulations with thermal displacements incorporated using molecular dynamics potentials. Specifically, we explore the sensitivity of electron scattering to the phonon band structure, or more explicitly interatomic forces. Silicon serves as the model material where we introduce thermal atomic displacements via empirical and machine-learned molecular dynamics interatomic potentials and compare them to finite-temperature density functional theory interatomic forces. We demonstrate that when molecular dynamics potentials do not sufficiently reproduce the correct phonon band structure, significant errors in the simulated diffraction and image intensities can occur. Moreover, for Si, we find that multislice simulations using machine-learned interatomic potentials are more accurate than empirical ones. In addition to the selected atomic potential, we demonstrate that the sensitivity to the phonon band structure also depends on the crystal zone axis, which can be used to enhance sensitivity to thermal displacements. Finally, we provide a sensitivity analysis with angle-resolved scanning transmission electron microscopy (STEM) to enhance image sensitivity to the details of the phonon band structure.
DOI:10.1038/s41563-021-01114-z
Temperature-dependent phonon lifetimes and thermal conductivity of silicon by inelastic neurtron scattering and ab initio calculations
Phys. Rev. B. 102, 174311 (2022)
Here we investigate electron scattering simulations with thermal displacements incorporated using molecular dynamics potentials. Specifically, we explore the sensitivity of electron scattering to the phonon band structure, or more explicitly interatomic forces. Silicon serves as the model material where we introduce thermal atomic displacements via empirical and machine-learned molecular dynamics interatomic potentials and compare them to finite-temperature density functional theory interatomic forces. We demonstrate that when molecular dynamics potentials do not sufficiently reproduce the correct phonon band structure, significant errors in the simulated diffraction and image intensities can occur. Moreover, for Si, we find that multislice simulations using machine-learned interatomic potentials are more accurate than empirical ones. In addition to the selected atomic potential, we demonstrate that the sensitivity to the phonon band structure also depends on the crystal zone axis, which can be used to enhance sensitivity to thermal displacements. Finally, we provide a sensitivity analysis with angle-resolved scanning transmission electron microscopy (STEM) to enhance image sensitivity to the details of the phonon band structure.
DOI:10.1103/PhysRevB.102.174311
Correlating the three-dimensional atomic defects and electronic properties of two-dimensional transition metal dichalcogenides
Nat. Mater. 19, 867 (2020)
The electronic, optical and chemical properties of two-dimensional transition metal dichalcogenides strongly depend on their three-dimensional atomic structure and crystal defects. Using Re-doped MoS
2 as a model system, here we present scanning atomic electron tomography as a method to determine three-dimensional atomic positions as well as positions of crystal defects such as dopants, vacancies and ripples with a precision down to 4 pm. We measure the three-dimensional bond dis- tortion and local strain tensor induced by single dopants. By directly providing these experimental three-dimensional atomic coordinates to density functional theory, we obtain more accurate electronic band structures than derived from conventional density functional theory calculations that relies on relaxed three-dimensional atomic coordinates. We anticipate that scan- ning atomic electron tomography not only will be generally applicable to determine the three-dimensional atomic coordinates of two-dimensional materials, but also will enable ab initio calculations to better predict the physical, chemical and electronic properties of these materials.
Nuclear quantum effect with pure anharmonicity and the anomalous thermal expansion of silicon
Proc. Natl. Acad. Sci. USA 115, 1992 (2018)
Despite the widespread use of silicon in modern technology, its peculiar thermal expansion is not well understood. Adapt- ing harmonic phonons to the specific volume at temperature, the quasiharmonic approximation, has become accepted for sim- ulating the thermal expansion, but has given ambiguous inter- pretations for microscopic mechanisms. To test atomistic mech- anisms, we performed inelastic neutron scattering experiments from 100 K to 1,500 K on a single crystal of silicon to mea- sure the changes in phonon frequencies. Our state-of-the-art ab initio calculations, which fully account for phonon anharmonic- ity and nuclear quantum effects, reproduced the measured shifts of individual phonons with temperature, whereas quasiharmonic shifts were mostly of the wrong sign. Surprisingly, the accepted quasiharmonic model was found to predict the thermal expan- sion owing to a large cancellation of contributions from individual phonons.
Phonon anharmonicity in silicon from 100 to 1500 K
Phys. Rev. B 91, 014307 (2015)
Inelastic neutron scattering was performed on silicon powder to measure the phonon density of states (DOS) from 100 to 1500 K. The mean fractional energy shifts with temperature of the modes were 〈Δεi/εiΔT〉= − 0.07, giving a mean isobaric Grüneisen parameter of + 6.95 ± 0.67, which is significantly different from the isothermal parameter of + 0.98. These large effects are beyond the predictions from quasiharmonic models using density functional theory or experimental data, demonstrating large effects from phonon anharmonicity. At 1500 K the anharmonicity contributes 0.15kB/atom to the vibrational entropy, compared to 0.03kB/atom from quasiharmonicity. Excellent agreement was found between the entropy from phonon DOS measurements and the reference NIST-JANAF thermodynamic entropy from calorimetric measurements.
DOI:10.1103/PhysRevB.91.014307
† denote equal contribution, ‡ denote corresponding authorship, bold names denote PERL Team member
All Publications
Crystal nucleation and growth in high-entropy alloys revealed by atomic electron tomography
Y. Yuan, S. Moniri, Y. Yang, J. Zhou, A. Yuan, D.S. Kim, Y. Yang, C. Li, W. Chen, P. Ercius, J. Miao, Under Review (2025)
Determining 3D atomic coordinates of light-element quantum materials using ptchographic electron tomography
N. Kim, H. Zhong, J. Zhang, C. O’Leary, Y. Liao, J. Zou, H. Sha, M. Pham, W. Li, Y. Yuan, J. Park, D.S. Kim, H. Jiang, J. Kong, M. Chi, J. Miao Under Review, (2025)
Diffuse intensity from phonon noise in inelastic neutron scattering
C.N. Saunders, V.V. Ladygin, D.S. Kim, C.M. Bernal-Choban, S.H. Lohaus, G.E. Granroth, D. L. Abernathy, B.T. Fultz, Phys. Rev. Mater., 9, 024602 (2025)
TDEP: Temperature Dependent Effective Potentials
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. A. Abrikosov, S. I. Simak, O. Hellman, JOSS, 9(94), 6150 (2024)
Modeling Temperature-Dependent Electron Thermal Diffuse Scattering via Machine-Learned Interatomic Potentials and Path-Integral Molecular Dynamics
D.S. Kim‡, M. Xu, and J.M. LeBeau‡, Phys. Rev. Lett. 132, 086301 (2024)
Diffuse inelastic neutron scattering from anharmonic vibrations in cuprite
C.N. Saunders, V.V. Ladygin, D.S. Kim, D.L. Abernathy, B. Fultz‡, under review at Phys. Rev. B (2024)
Nonharmonic contributions to the high-temperature phonon thermodynamics of Cr
C.M. Bernal-Choban, H.L. Smith, C.N. Saunders, D.S. Kim, L. Mauger, D.L. Abernathy, and B. Fultz, Phys. Rev. B, 107, 5, 054312 (2023)
A comparison of molecular dynamics potentials used to account for thermal diffuse scattering in multislice simulations
X. Chen† , D.S. Kim† , and J.M. LeBeau, Ultramicroscopy, 244, 113644 (2023)
Tuning surface acidity of mixed conducting electrodes: Recovery of Si-induced degradation of oxygen exchange rate and area specific resistance
H.G. Seo, A. Staerz, D.S. Kim, J.M. LeBeau, and H.L. Tuller, Adv. Mater., e2208182 (2022)
Reactivation of chromia poisoned oxygen exchange kinetics in mixed conducting solid oxide fuel cell electrodes by serial infiltration of lithia
H.G. Seo, A. Staerz, D.S. Kim, D. Klotz, C. Nicollet, M. Xu, J.M. LeBeau, and H.L. Tuller, Energy Environ. Sci., 15, 10, 4038 (2022)
Reactivation of chromia poisoned oxygen exchange kinetics in mixed conducting solid oxide fuel cell electrodes by serial infiltration of lithia
H.G. Seo, A. Staerz, D.S. Kim, D. Klotz, C. Nicollet, M. Xu, J.M. LeBeau, and H.L. Tuller, Energy Environ. Sci., 15, 10, 4038 (2022)
Thermal expansion and phonon anharmonicity of cuprite studied by inelastic neutron scattering
C.N. Saunders, D.S. Kim, O. Hellman, H.L. Smith, N.J. Weadock, S.T. Omelchenko, G.E. Granroth, C.M. Bernal-Choban, S.H. Lohaus, D.L. Abernathy, and B. Fultz, Phys. Rev. B, 105, 17, 174308 (2022)
The influence of Cr-additives on the polarization resistance of praseodymium-doped Ceria cathodes for solid oxide fuel cells
A. Staerz, H.G. Seo, D. Klotz, D.S. Kim, J.M. LeBeau, and H.L. Tuller, J. Electrochem. Soc., 169, 4, 044530, (2022)
Three-dimensional atomic packing in amorphous solids with liquid-like structure
Y. Yuan† , D.S. Kim† , J. Zhou† , D.J. Chang, F. Zhu, Y. Nagaoka, Y. Yang, M. Pham, S.J. Osher, O. Chen, P. Ercius, A.K. Schmid, and J. Miao, Nat. Mater., 21, 1, 95 (2022)
Capturing 3D atomic defects and phonon localization at the 2D heterostructure interface
X. Tian, X. Yan, G. Varnavides, Y. Yuan, D.S. Kim , C.J. Ciccarino, P. Anikeeva, M.Y. Li, L.J. Li, P. Narang, X. Pan, and J. Miao, Sci. Adv., 7, 38, eabi6699 (2021)
Determining the three-dimensinoal atomic structure of an amorphous solid
Y. Yang, J. Zhou, F. Zhu, Y. Yuan, D.J. Chang, D.S. Kim , M. Pham, A. Rana, X. Tian, Y. Yao, S.J. Osher, A.K. Schmid, L. Hu, P. Ercius, and J. Miao, Nature, 592, 7852, 60 (2021)
Temperature-dependent phonon lifetimes and thermal conductivity of silicon by inelastic neutron scattering and ab initio calculations
D.S. Kim‡, O. Hellman, N. Shulumba, C.N. Saunders, J.Y. Lin, H.L. Smith, J.E. Herriman, J.L. Niedziela, D.L. Abernathy, C.W. Li, B. Fultz‡, Phys. Rev. B, 102, 17, 174311 (2022)
Ptychographic atomic electron tomography: Towards three-dimensional imaging of individual light atoms in materials
D. J. Chang, D.S. Kim, A. Rana, X. Tian, J. Zhou, P. Ercius, and J. Miao, Phys. Rev. B, 102, 17, 174101 (2020)
Correlating the three-dimensional atomic defects and electronic properties of two-dimensional transition metal dichalcogenides
X. Tian† , D.S. Kim† , S. Yang† , C.J. Ciccarino, Y. Gong, Y. Yang, Y. Yang, B. Duschatko, Y. Yuan, P.M. Ajayan, J.C. Idrogo, P. Narang, and J. Miao, Nat. Mater., 19, 8, 867 (2020)
Observing crystal nucleation in four dimensions using atomic electron tomography
J. Zhou, Y. Yang, D.S. Kim, A. Yuan, C. Ophus, F. Sun, A.K. Schmid, M. Nathanson, H. Heinz, Q. An, H. Zeng, P. Ercius, and J. Miao, Nature, 570, 7762, 500 (2019)
Temperature dependence of phonons in FeGe2
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, Phys. Rev. Materials, 2, 10, 103603, (2018)
Nuclear quantum effect with pure anharmonicity and the anomalous thermal expansion of silicon
D.S. Kim†‡O. Hellman†, J. Herriman, H.L. Smith, J.Y.Y. Lin, N. Shulumba, J.L. Niedziela, C.W. Lin, D.L. Abernathy, and B. Fultz‡ Proc Natl. Acad. Sci. U.S.A. 115, 9, 1992, (2018)
Separating the configurational and vibrational entropy contributions in metallic glasses
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. Lin, M.B. Stone, D.L. Abernathy, M.D. Demetriou, and B. Fultz, Nat. Phys. 13, 9, 900 (2017)
Phonon quarticity induced by changes in phonon-tracked hybridization during lattice expansion and its stabilization of rutile TiO2
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. Lin, M.B. Stone, D.L. Abernathy, M.D. Demetriou, and B. Fultz, Phys. Rev. B, 92, 054304 (2015)
Phonon anharmonicity in silicon from 100 to 1500 K
D.S. Kim‡H.L. Smith, J.L. Niedziela, C.W. Li, D.L. Abernathy, and B. Fultz‡ Phys. Rev. B, 91, 014307 (2015)