Hyak Publications

Publications that acknowledge Hyak Resources Funded by STF on Hyak

2019 (7 since April 30th)

Clark, A., Machicoane, N. & Aliseda, A. A quantitative study of track initialization of the four-frame best estimate algorithm for three-dimensional Lagrangian particle tracking. Meas. Sci. Technol. 30, 045302 (2019).

Liu, Q., Quillin, S. C., Masiello, D. J. & Crozier, P. A. Nanoscale probing of resonant photonic modes in dielectric nanoparticles with focused electron beams. Phys. Rev. B 99, 165102 (2019).

Wildman, A., Donati, G., Lipparini, F., Mennucci, B. & Li, X. Nonequilibrium Environment Dynamics in a Frequency-Dependent Polarizable Embedding Model. J. Chem. Theory Comput. 15, 43–51 (2019).

Stetina, T. F., Clark, A. E. & Li, X. X-ray absorption signatures of hydrogen-bond structure in water-alcohol solutions. Int. J. Quantum Chem. 119, e25802 (2019).

Jin, R. & Maibaum, L. Mechanisms of DNA hybridization: Transition path analysis of a simulation-informed Markov model. J. Chem. Phys. 150, 105103 (2019).

Cheng, X. et al. Plasmon Heating Promotes Ligand Reorganization on Single Gold Nanorods. J. Phys. Chem. Lett. 10, 1394–1401 (2019).

Mao, C. M., Sampath, J., Sprenger, K. G., Drobny, G. & Pfaendtner, J. Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces. Langmuir acs.langmuir.8b01392 (2019). doi:10.1021/acs.langmuir.8b01392

Lee, V. G. M., Madison, L. R. & McCoy, A. B. Evaluation of Matrix Elements Using Diffusion Monte Carlo Wave Functions. J. Phys. Chem. A acs.jpca.8b11213 (2019). doi:10.1021/acs.jpca.8b11213

2018 (34 Publications)

Nelson, H. D. & Gamelin, D. R. Valence-Band Electronic Structures of Cu + -Doped ZnS, Alloyed Cu–In–Zn–S, and Ternary CuInS 2 Nanocrystals: A Unified Description of Photoluminescence across Compositions. J. Phys. Chem. C 122, 18124–18133 (2018).

Montoni, N. P., Quillin, S. C., Cherqui, C. & Masiello, D. J. Tunable Spectral Ordering of Magnetic Plasmon Resonances in Noble Metal Nanoclusters. ACS Photonics 5, 3272–3281 (2018).

Henn, B. et al. Spatiotemporal patterns of precipitation inferred from streamflow observations across the Sierra Nevada mountain range. J. Hydrol. 556, 993–1012 (2018).

83       Gao, K. et al. Di-Spiro-Based Hole-Transporting Materials for Highly Efficient Perovskite Solar Cells. Adv. Energy Mater. 8, 1800809 (2018).

Ziffer, M. E. et al. Long-Lived, Non-Geminate, Radiative Recombination of Photogenerated Charges in a Polymer/Small-Molecule Acceptor Photovoltaic Blend. J. Am. Chem. Soc. 140, 9996–10008 (2018).

Beck, R. A. et al. Effect of Surface Passivation on Nanodiamond Crystallinity. J. Phys. Chem. C 122, 8573–8580 (2018).

Cherqui, C. et al. Multipolar Nanocube Plasmon Mode-Mixing in Finite Substrates. J. Phys. Chem. Lett. 9, 504–512 (2018).

Kasper, J. M., Williams-Young, D. B., Vecharynski, E., Yang, C. & Li, X. A Well-Tempered Hybrid Method for Solving Challenging Time-Dependent Density Functional Theory (TDDFT) Systems. J. Chem. Theory Comput. 14, 2034–2041 (2018).

Kang, C., Aguilar, B. & Shmulevich, I. Emergence of diversity in homogeneous coupled Boolean networks. Phys. Rev. E 97, 052415 (2018).

Zhao, T. et al. Realization of a Highly Oriented MAPbBr 3 Perovskite Thin Film via Ion Exchange for Ultrahigh Color Purity Green Light Emission. ACS Energy Lett. 3, 1662–1669 (2018).

Curtis, C., Toghani, D., Wong, B. & Nance, E. Colloidal stability as a determinant of nanoparticle behavior in the brain. Colloids Surfaces B Biointerfaces 170, 673–682 (2018).

Kingsland, A. & Maibaum, L. DNA Base Pair Mismatches Induce Structural Changes and Alter the Free-Energy Landscape of Base Flip. J. Phys. Chem. B 122, 12251–12259 (2018).

Ju, D. et al. Tunable Band Gap and Long Carrier Recombination Lifetime of Stable Mixed CH 3 NH 3 Pb x Sn 1– x Br 3 Single Crystals. Chem. Mater. 30, 1556–1565 (2018).

Donati, G., Lingerfelt, D. B., Aikens, C. M. & Li, X. Anisotropic Polarizability-Induced Plasmon Transfer. J. Phys. Chem. C 122, 10621–10626 (2018).

Radler, J. J., Lingerfelt, D. B., Castellano, F. N., Chen, L. X. & Li, X. Role of Vibrational Dynamics on Excited-State Electronic Coherence in a Binuclear Platinum Complex. J. Phys. Chem. A 122, 5071–5077 (2018).

Crane, M. J. et al. High pressure, high temperature molecular doping of nanodiamond. (2018).

Marcos, E. et al. De novo design of a non-local β-sheet protein with high stability and accuracy. Nat. Struct. Mol. Biol. 25, 1028–1034 (2018).

Lestrange, P. J., Hoffmann, M. R. & Li, X. in 295–313 (2018). doi:10.1016/bs.aiq.2017.06.003

Goldwyn, H. J., Smith, K. C., Busche, J. A. & Masiello, D. J. Mislocalization in Plasmon-Enhanced Single-Molecule Fluorescence Microscopy as a Dynamical Young’s Interferometer. ACS Photonics 5, 3141–3151 (2018).

Lestrange, P. J., Williams-Young, D. B., Petrone, A., Jiménez-Hoyos, C. A. & Li, X. Efficient Implementation of Variation after Projection Generalized Hartree–Fock. J. Chem. Theory Comput. 14, 588–596 (2018).

Goodreau, S. M. et al. Relational concurrency, stages of infection, and the evolution of HIV set point viral load. Virus Evol. 4, (2018).

Liu, Y. et al. Modulation of Fluorescent Protein Chromophores To Detect Protein Aggregation with Turn-On Fluorescence. J. Am. Chem. Soc. 140, 7381–7384 (2018).

Resnick, J. M., O’Brien, G. E. & Rubinstein, J. T. Simulated auditory nerve axon demyelination alters sensitivity and response timing to extracellular stimulation. Hear. Res. 361, 121–137 (2018).

Edwards, T. H. & Stoll, S. Optimal Tikhonov regularization for DEER spectroscopy. J. Magn. Reson. 288, 58–68 (2018).

Perfect, B., Kumar, N. & Riley, J. J. Vortex Structures in the Wake of an Idealized Seamount in Rotating, Stratified Flow. Geophys. Res. Lett. 45, 9098–9105 (2018).

Oleson, K. R., Sprenger, K. G., Pfaendtner, J. & Schwartz, D. T. Inhibition of the Exoglucanase Cel7A by a Douglas-Fir-Condensed Tannin. J. Phys. Chem. B 122, 8665–8674 (2018).

Sprenger, K. G., Prakash, A., Drobny, G. & Pfaendtner, J. Investigating the Role of Phosphorylation in the Binding of Silaffin Peptide R5 to Silica with Molecular Dynamics Simulations. Langmuir 34, 1199–1207 (2018).

Kasper, J. M., Lestrange, P. J., Stetina, T. F. & Li, X. Modeling L 2,3 -Edge X-ray Absorption Spectroscopy with Real-Time Exact Two-Component Relativistic Time-Dependent Density Functional Theory. J. Chem. Theory Comput. 14, 1998–2006 (2018).

Goldwyn, H. J., Smith, K. C., Busche, J. A. & Masiello, D. J. Mislocalization in Plasmon-Enhanced Single-Molecule Fluorescence Microscopy as a Dynamical Young’s Interferometer. ACS Photonics 5, 3141–3151 (2018).

Prakash, A., Sprenger, K. G. & Pfaendtner, J. Essential slow degrees of freedom in protein-surface simulations: A metadynamics investigation. Biochem. Biophys. Res. Commun. 498, 274–281 (2018).

Thakkar, N., Montoni, N. P., Cherqui, C. & Masiello, D. J. Plasmonic Landau damping in active environments. Phys. Rev. B 97, 121403 (2018).

Winter, A. O., Motley, M. R. & Eberhard, M. O. Tsunami-Like Wave Loading of Individual Bridge Components. J. Bridg. Eng. 23, 04017137 (2018).

Wildman, A. et al. Anticorrelated Contributions to Pre-edge Features of Aluminate Near-Edge X-ray Absorption Spectroscopy in Concentrated Electrolytes. J. Phys. Chem. Lett. 9, 2444–2449 (2018).

Sommer, D. E. & Dunham, S. T. Atomistic models of Cu diffusion in CuInSe 2 under variations in composition. J. Appl. Phys. 123, 115116 (2018).

Hu, H., Wolstenholme, C. H., Zhang, X. & Li, X. Inverted solvatochromic Stokes shift in GFP-like chromophores with extended conjugation. Chinese J. Chem. Phys. 31, 599–607 (2018).

2017 (30 Publications)

Stein, J. L. et al. Cation Exchange Induced Transformation of InP Magic-Sized Clusters. Chem. Mater. 29, 7984–7992 (2017).

Li, N. et al. Mixed Cation FA x PEA 1- x PbI 3 with Enhanced Phase and Ambient Stability toward High-Performance Perovskite Solar Cells. Adv. Energy Mater. 7, 1601307 (2017).

Lutz, H., Jaeger, V., Bonn, M., Pfaendtner, J. & Weidner, T. Acetylation dictates the morphology of nanophase biosilica precipitated by a 14-amino acid leucine-lysine peptide. J. Pept. Sci. 23, 141–147 (2017).

Donati, G. et al. Coupling Real-Time Time-Dependent Density Functional Theory with Polarizable Force Field. J. Phys. Chem. Lett. 8, 5283–5289 (2017).

47       Fu, C. D., L. Oliveira, L. F. & Pfaendtner, J. Determining energy barriers and selectivities of a multi-pathway system with infrequent metadynamics. J. Chem. Phys. 146, 014108 (2017).

Egidi, F. et al. Two-Component Noncollinear Time-Dependent Spin Density Functional Theory for Excited State Calculations. J. Chem. Theory Comput. 13, 2591–2603 (2017).

Lingerfelt, D. B. et al. 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 121, 1932–1939 (2017).

Liu, Y. et al. The Cation−π Interaction Enables a Halo-Tag Fluorogenic Probe for Fast No-Wash Live Cell Imaging and Gel-Free Protein Quantification. Biochemistry 56, 1585–1595 (2017).

Xu, B. et al. 4- Tert -butylpyridine Free Organic Hole Transporting Materials for Stable and Efficient Planar Perovskite Solar Cells. Adv. Energy Mater. 7, 1700683 (2017).

Petrone, A., Williams-Young, D. B., Lingerfelt, D. B. & Li, X. Ab Initio Excited-State Transient Raman Analysis. J. Phys. Chem. A 121, 3958–3965 (2017).

McGibbon, J. & Bretherton, C. S. Skill of ship‐following large‐eddy simulations in reproducing <scp>MAGIC</scp> observations across the northeast <scp>P</scp> acific stratocumulus to cumulus transition region. J. Adv. Model. Earth Syst. 9, 810–831 (2017).

Palunas, K., Sprenger, K. G., Weidner, T. & Pfaendtner, J. Effect of an ionic liquid/air Interface on the structure and dynamics of amphiphilic peptides. J. Mol. Liq. 236, 404–413 (2017).

Petrone, A., Williams-Young, D. B., Lingerfelt, D. B. & Li, X. Ab Initio Excited-State Transient Raman Analysis. J. Phys. Chem. A 121, 3958–3965 (2017).

38       Gander, M. W., Vrana, J. D., Voje, W. E., Carothers, J. M. & Klavins, E. Digital logic circuits in yeast with CRISPR-dCas9 NOR gates. Nat. Commun. 8, 15459 (2017).

Smith, J. K., Jiang, S. & Pfaendtner, J. Redefining the Protein–Protein Interface: Coarse Graining and Combinatorics for an Improved Understanding of Amino Acid Contributions to the Protein–Protein Binding Affinity. Langmuir 33, 11511–11517 (2017).

Smith, J. et al. Determining dominant driving forces affecting controlled protein release from polymeric nanoparticles. Biointerphases 12, 02D412 (2017).

Bischak, C. G. et al. Noninvasive Cathodoluminescence-Activated Nanoimaging of Dynamic Processes in Liquids. ACS Nano 11, 10583–10590 (2017).

Nelson, H. D. et al. Mid-Gap States and Normal vs Inverted Bonding in Luminescent Cu + – and Ag + -Doped CdSe Nanocrystals. J. Am. Chem. Soc. 139, 6411–6421 (2017).

Liu, H. et al. A Hybrid Quantum-Classical Model of Electrostatics in Multiply Charged Quantum Dots. J. Phys. Chem. C 121, 26086–26095 (2017).

Li, N. et al. Enhanced efficiency and stability of inverted perovskite solar cells by interfacial engineering with alkyl bisphosphonic molecules. RSC Adv. 7, 42105–42112 (2017).

Nelson, H. D. et al. Mid-Gap States and Normal vs Inverted Bonding in Luminescent Cu + – and Ag + -Doped CdSe Nanocrystals. J. Am. Chem. Soc. 139, 6411–6421 (2017).

Gary, D. C., Petrone, A., Li, X. & Cossairt, B. M. Investigating the role of amine in InP nanocrystal synthesis: destabilizing cluster intermediates by Z-type ligand displacement. Chem. Commun. 53, 161–164 (2017).

Frenz, B., Walls, A. C., Egelman, E. H., Veesler, D. & DiMaio, F. RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps. Nat. Methods 14, 797–800 (2017).

Fu, C. D., Oliveira, L. F. L. & Pfaendtner, J. Assessing Generic Collective Variables for Determining Reaction Rates in Metadynamics Simulations. J. Chem. Theory Comput. 13, 968–973 (2017).

Sprenger, K. G., Plaks, J. G., Kaar, J. L. & Pfaendtner, J. Elucidating sequence and solvent specific design targets to protect and stabilize enzymes for biocatalysis in ionic liquids. Phys. Chem. Chem. Phys. 19, 17426–17433 (2017).

Donovan, M. A. et al. LK peptide side chain dynamics at interfaces are independent of secondary structure. Phys. Chem. Chem. Phys. 19, 28507–28511 (2017).

Morgan, K. D., Jarboe, T. R., Hossack, A. C., Chandra, R. N. & Everson, C. J. Validation of extended magnetohydrodynamic simulations of the HIT-SI3 experiment using the NIMROD code. Phys. Plasmas 24, 122510 (2017).

Fleming, D. P. & Quinn, T. R. Coevolution of binaries and circumbinary gaseous discs. Mon. Not. R. Astron. Soc. 464, 3343–3356 (2017).

Chevalier, A. et al. Massively parallel de novo protein design for targeted therapeutics. Nature 550, 74–79 (2017).

Liu, Y. et al. The Cation−π Interaction Enables a Halo-Tag Fluorogenic Probe for Fast No-Wash Live Cell Imaging and Gel-Free Protein Quantification. Biochemistry 56, 1585–1595 (2017).

Chen, L. X. in X-Ray Free Electron Lasers: Applications in Materials, Chemistry and Biology 201–224 (2017). doi:10.1039/9781782624097-00201

2016 (17 Publications)

Walls, A. C. et al. Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy. Nat. Struct. Mol. Biol. 23, 899–905 (2016).

Chen, L. X. et al. Imaging ultrafast excited state pathways in transition metal complexes by X-ray transient absorption and scattering using X-ray free electron laser source. Faraday Discuss. 194, 639–658 (2016).

Shelby, M. L. et al. Ultrafast Excited State Relaxation of a Metalloporphyrin Revealed by Femtosecond X-ray Absorption Spectroscopy. J. Am. Chem. Soc. 138, 8752–8764 (2016).

Petrone, A., Lingerfelt, D. B., Williams-Young, D. B. & Li, X. Ab Initio Transient Vibrational Spectral Analysis. J. Phys. Chem. Lett. 7, 4501–4508 (2016).

Petrone, A., Goings, J. J. & Li, X. Quantum confinement effects on optical transitions in nanodiamonds containing nitrogen vacancies. Phys. Rev. B 94, 165402 (2016).

Nelson, H. D., Li, X. & Gamelin, D. R. 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 120, 5714–5723 (2016).

Lingerfelt, D. B., Williams-Young, D. B., Petrone, A. & Li, X. Direct ab Initio (Meta )Surface-Hopping Dynamics. J. Chem. Theory Comput. 12, 935–945 (2016).

Williams-Young, D., Goings, J. J. & Li, X. Accelerating Real-Time Time-Dependent Density Functional Theory with a Nonrecursive Chebyshev Expansion of the Quantum Propagator. J. Chem. Theory Comput. 12, 5333–5338 (2016).

12..     Sprenger, K. G., Choudhury, A., Kaar, J. L. & Pfaendtner, J. Lytic Polysaccharide Monooxygenases Sc LPMO10B and Sc LPMO10C Are Stable in Ionic Liquids As Determined by Molecular Simulations. J. Phys. Chem. B 120, 3863–3872 (2016).

Kingsland, A., Samai, S., Yan, Y., Ginger, D. S. & Maibaum, L. Local Density Fluctuations Predict Photoisomerization Quantum Yield of Azobenzene-Modified DNA. J. Phys. Chem. Lett. 7, 3027–3031 (2016).

Aljadeff, J., Lansdell, B. J., Fairhall, A. L. & Kleinfeld, D. Analysis of Neuronal Spike Trains, Deconstructed. Neuron 91, 221–259 (2016).

Donati, G., Lingerfelt, D. B., Petrone, A., Rega, N. & Li, X. “Watching” Polaron Pair Formation from First-Principles Electron–Nuclear Dynamics. J. Phys. Chem. A 120, 7255–7261 (2016).

Williams-Young, D., Egidi, F. & Li, X. Relativistic Two-Component Particle–Particle Tamm–Dancoff Approximation. J. Chem. Theory Comput. 12, 5379–5384 (2016).

Baldwin, C. L., Laumann, C. R., Pal, A. & Scardicchio, A. The many-body localized phase of the quantum random energy model. Phys. Rev. B 93, 024202 (2016).

Sprenger, K. G., He, Y. & Pfaendtner, J. in 21–35 (2016). doi:10.1007/978-981-10-1128-3_2

Gary, D. C. et al. Single-Crystal and Electronic Structure of a 1.3 nm Indium Phosphide Nanocluster. J. Am. Chem. Soc. 138, 1510–1513 (2016).

Chong, E. Q., Lingerfelt, D. B., Petrone, A. & Li, X. Classical or Quantum? A Computational Study of Small Ion Diffusion in II–VI Semiconductor Quantum Dots. J. Phys. Chem. C 120, 19434–19441 (2016).

Walls, A. C. et al. Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer. Nature 531, 114–117 (2016).

2015 (2 Publications)

Lestrange, P. J., Egidi, F. & Li, X. The consequences of improperly describing oscillator strengths beyond the electric dipole approximation. J. Chem. Phys. 143, 234103 (2015).

Peng, B., Lestrange, P. J., Goings, J. J., Caricato, M. & Li, X. Energy-Specific Equation-of-Motion Coupled-Cluster Methods for High-Energy Excited States: Application to K -edge X-ray Absorption Spectroscopy. J. Chem. Theory Comput. 11, 4146–4153 (2015).