Member Publications

Publications that acknowledge the STF allocation on Hyak

  1. F. Egidi, S. Sun, J. J. Goings, G. Scalmani, M. J. Frisch, X. Li, “Two-Component Non-Collinear Time-Dependent Spin Density Functional Theory for Excited State Calculations,” J. Chem. Theory Comput., 2017, 13, 2591–2603.
  2. A. Petrone, D. B. Williams-Young, D. B. Lingerfelt, X. Li, “Ab Initio Excited State Transient Raman Analysis,” J. Phys. Chem. A, 2017, 121, 3958–3965.
  3. H. D. Nelson, S. Hinterding, R. Fainblat, S. Creutz, X. Li, D. R. Gamelin, “Mid-Gap States and Normal vs Inverted Bonding in Luminescent Cu+– and Ag+-Doped CdSe Nanocrystals,” J. Am. Chem. Soc., 2017, 139, 6411–6421.
  4. Y. Liu, K. Miao, N. P. Dunham, H. Liu, M. Fares, A. K. Boal, X. Li, X. Zhang, “The Cation-π Interaction Enables a Halo-Tag Fluorogenic Probe for Fast No-Wash Live Cell Imaging and Gel-Free Protein Quantification,” Biochemistry, 2017, 56, 1585–1595.
  5. D. B. Lingerfelt, P. J. Lestrange, J. J. Radler, S. E. Brown-Xu, P. Kim, F. N. Castellano, L. X. Chen, X. Li, “Can Excited State Electronic Coherence be Tuned via Molecular Structural Modification? A First-Principles Quantum Electronic Dynamics Study of Pyrazolate-Bridged Pt(II) Dimers,” J. Phys. Chem. A, 2017, 121, 1932-1939.
  6. A. Kingsland, S. Samai, Y. Yan, D. S. Ginger, L. Maibaum, “Local Density Fluctuations Predict Photoisomerization Quantum Yield of Azobenzene-Modified DNA,” J. Phys. Chem. Lett., 2016, 7 (15), 3027–3031.
  7. A.C. Walls, et. al., “Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy,” Nature Structural & Molecular Biology, 2016, 23, 899–905.
  8. K.G. Sprenger, A. Choudhury, J. L. Kaar, J. Pfaendtner, “ Lytic Polysaccharide Monooxygenases ScLPMO10B and ScLPMO10C Are Stable in Ionic Liquids As Determined by Molecular Simulations,” J. Phys. Chem. B, 2016, 120 (16), 3863–3872.
  9. K. G. Sprenger, Y. He, J. Pfaendtner, “Probing How Defects in Self-assembled Monolayers Affect Peptide Adsorption with Molecular Simulation,” Foundations of Molecular Modeling and Simulation, Ed. R. Q. Snurr, C. S. Adjiman, D. A. Kofke, Springer Singapore 2016, 21-35.
  10. J. M. Resnick, J. T. Rubinstein. (2016) Encoding implications of pathological auditory nerve fiber demyelination during electrical stimulation. Presentation at the Northwest Auditory and Vestibular Research Meeting.
  11. D. P. Fleming, T. R. Quinn, “Coevolution of binaries and circumbinary gaseous discs,” MNRAS, 2016, 464 (3), 3343-3356.
  12. J. Aljadeff, B. J. Lansdell, A. L. Fairhall, D. Kleinfeld, “Analysis of Neuronal Spike Trains, Deconstructed,” Neuron, 91 (2), 2016, 221-259.
  13. D. B. Williams-Young, J. Goings, X. Li, “Accelerating Real-Time Time-Dependent Density Functional Theory with a Nonrecursive Chebyshev Expansion of the Quantum Propagator,” J. Chem. Theory Comput., 2016, 12 (11), 5333-5338.
  14. D. B. Williams-Young, F. Egidi, X. Li, “Relativistic Two-Component Particle–Particle Tamm–Dancoff Approximation,” J. Chem. Theory Comput., 2016, 12 (11), 5379-5384.
  15. D. C. Gary, A. Petrone, X. Li, B. M. Cossairt, “Investigating the Role of Amine in InP Nanocrystal Synthesis: Destabilizing Cluster Intermediates by Z-type Ligand Displacement,” Chem. Commun., 2016, 53, 161-164.
  16. A. Petrone, D. B. Lingerfelt, D. B. Williams-Young, X. Li, “Ab Initio Transient Vibrational Spectral Analysis,” J. Phys. Chem. Lett., 2016, 7, 4501.
  17. N. Li, Z. Zhu, C.-C. Chueh, H. Liu, B. Peng, A. Petrone, X. Li, L. Wang, A. K.-Y. Jen, “Mixed Cation FAxPEA1–xPbI3 with Enhanced Phase and Ambient Stability toward High-Performance Perovskite Solar Cells,” Adv. Energy Mater., 2016, 1601307.
  18. A. Petrone, J. J. Goings, X. Li, “Quantum Confinement Effects on Optical Transitions in Nanodiamonds Containing Nitrogen Vacancies,” Phys. Rev. B, 2016, 94, 165402.
  19. L. X. Chen, M. L. Shelby, P. J. Lestrange, N. E. Jackson, K. Haldrup, M. W. Mara, A. B. Stickrath, D. Zhu, H. Lemke, M. Chollet, B. M. Hoffman, X. Li, “Imaging Ultrafast Excited State Pathways in Transition Metal Complexes by X-ray Transient Absorption and Scattering using X-ray Free Electron Laser Source,” Farad. Discuss., 2016, 194, 639-658.
  20. G. Donati, D. B. Lingerfelt, A. Petrone, N. Rega, X. Li, ““Watching” Polaron Pair Formation from First-Principles Electron-Nuclear Dynamics,” J. Phys. Chem. A, 2016, 120, 7255–7261.
  21. E. Q. Chong, D. B. Lingerfelt, A. Petrone, X. Li, “Classical or Quantum? A Computational Study of Small Ion Diffusion in II-VI Semiconductor Quantum Dots,” J. Phys. Chem. C, 2016, 120, 19434.
  22. M. L. Shelby, P. J. Lestrange, N. E. Jackson, K. Haldrup, M. W. Mara, A. B. Stickrath, D. Zhu, H. Lemke, B. M. Hoffman, X. Li, L. X. Chen, “Ultrafast Excited State Relaxation of a Metalloporphyrin Revealed by Femtosecond X-ray Absorption Spectroscopy,” J. Am. Chem. Soc., 2016, 138, 8752-8764.
  23. D. B. Lingerfelt, D. B. Williams-Young, A. Petrone, X. Li, “Direct Ab Initio (Meta-)Surface-Hopping Dynamics,”J. Chem. Theory Comput., 2016, 12, 935–945.
  24. A.C. Walls, M. A. Tortorici, B.J. Bosch, B. Frenz, P.J.M. Rottier, F. DiMaio, F.A. Rey, D. Veesler. Cyro-electron microscopy structure of a coronavirus spike glycoprotein trimerNature, 2016, 531, 114-117.
  25. H. D. Nelson, X. Li, and D. R. Gamelin. Computational Studies of the Electronic Structures of Copper-Doped CdSe Nanocrystals: Oxidation States, Jahn–Teller Distortions, Vibronic Bandshapes, and Singlet–Triplet Splittings J. Phys. Chem. C, 2016, 120, 5714-5723.
  26. C. L. Baldwin, C. R. Laumann, A. Pal, and A. Scardicchio. The many-body localized phase of the quantum random energy model. Phys. Rev. B, 2016, 93, 024202.
  27. D. C. Gary, S. E. Flowers, W. Kaminsky, A. Petrone, X. Li, B. M. Cossairt, Single Crystal and Electronic Structure of a 1.3 nm Indium Phosphide Nanocluster, J. Am. Chem. Soc., 2016, 138, 1510-1513.
  28. P. J. Lestrange, F. Egidi, X. Li, The Consequences of Improperly Describing Oscillator Strengths Beyond the Electric Dipole Approximation, J. Chem. Phys., 2015143, 234103.
  29. Sale, D.C. and Aliseda, A. (2016) Computational simulation of tidal energy generation estuary-scale scenarios Proceedings of the 4th Marine Energy Technology Symposium, Washington, D.C., April 25-27
  30. Sale, D.C. and Aliseda, A. (2016) The flow field of a two-bladed horizontal axis turbine via comparison of LES and RANS simulations against experimental PIV flume measurements Proceedings of the 4th Marine Energy Technology Symposium, Washington, D.C., April 25-27
  31. B. Peng, P. J. Lestrange, J. J. Goings, M. Caricato, X. Li, Energy-Specific Equation-of-Motion Coupled-Cluster Methods for High-Energy Excited States: Application to K-edge X-ray Absorption SpectroscopyJ. Chem. Theory Comput., 2015, 11, 4146-4153.