Hyak Publications

Publications that acknowledge Hyak Resources Funded by STF on Hyak

Have a new publication to report? Tell us about it here: https://forms.gle/HZpQGQv2fTM7DD4w7


Agol, E., Dorn, C., Grimm, S. L., Turbet, M., Ducrot, E., Delrez, L., … & Van Grootel, V. Refining the Transit-timing and Photometric Analysis of TRAPPIST-1: Masses, Radii, Densities, Dynamics, and Ephemerides. The Planetary Science Journal, 2(1), 1 (2021).

2020 (56 publications)

Chen, T., & Carson, E. Predict-and-recompute conjugate gradient variants. SIAM Journal on Scientific Computing, 42(5), A3084-A3108 (2020).

Gordon, T. A., Agol, E., & Foreman-Mackey, D. A Fast, Two-dimensional Gaussian Process Method Based on Celerite: Applications to Transiting Exoplanet Discovery and Characterization. The Astronomical Journal, 160(5), 240 (2020).

Tran, C., Champion, K., Forte, A., Hill, B. M., & Greenstadt, R. Are anonymity-seekers just like everybody else? An analysis of contributions to Wikipedia from Tor. In 2020 IEEE Symposium on Security and Privacy (SP) (pp. 186-202). IEEE (2020).

Guzewich, S. D., Lustig-Yaeger, J., Davis, C. E., Kopparapu, R. K., Way, M. J., & Meadows, V. S. The Impact of Planetary Rotation Rate on the Reflectance and Thermal Emission Spectrum of Terrestrial Exoplanets around Sunlike Stars. The Astrophysical Journal, 893(2), 140 (2020).

Fillingham, P., & Novosselov, I. V. Wall jet similarity of impinging planar underexpanded jets. International Journal of Heat and Fluid Flow, 81, 108516 (2020).

Moeyens, J., Myhrvold, N., & Ivezić, Ž. ATM: An open-source tool for asteroid thermal modeling and its application to NEOWISE data. Icarus, 341, 113575 (2020).

Basanta, B., Bick, M. J., Bera, A. K., Norn, C., Chow, C. M., Carter, L. P., … & Baker, D. An enumerative algorithm for de novo design of proteins with diverse pocket structures. Proceedings of the National Academy of Sciences, 117(36), 22135-22145 (2020).

Luo, Y., & Maibaum, L. Modulated and spiral surface patterns on deformable lipid vesicles. The Journal of Chemical Physics, 153(14), 144901 (2020).

Brandão, A. F., Bonet, I. J. M., Pagliusi Jr, M., Zanetti, G. G., Pho, N., Tambeli, C. H., … & Sartori, C. R. Physical activity induces nucleus accumbens genes expression changes preventing chronic pain susceptibility promoted by high-fat diet and sedentary behavior in mice. Frontiers in neuroscience, 13, 1453 (2020).

Soldatova, A. V., & Spiro, T. G. Alternative modes of O2 activation in P450 and NOS enzymes are clarified by DFT modeling and resonance Raman spectroscopy. Journal of inorganic biochemistry, 207, 111054 (2020).

Aithal, A. B., & Ferrante, A. A fast pressure-correction method for incompressible flows over curved walls. Journal of Computational Physics, 421, 109693 (2020).

Fillingham, P., Vaddi, R. S., Bruning, A., Israel, G., & Novosselov, I. V. Drag, lift, and torque on a prolate spheroid resting on a smooth surface in a linear shear flow. Powder Technology, 377, 958-965.

Venkataraman, Y. R., Downey-Wall, A. M., Ries, J., Westfield, I., White, S. J., Roberts, S. B., & Lotterhos, K. E. General DNA methylation patterns and environmentally-induced differential methylation in the eastern oyster (Crassostrea virginica). Frontiers in Marine Science, 7, 225 (2020).

Zhao, L., Wildman, A., Tao, Z., Schneider, P., Hammes-Schiffer, S., & Li, X. Nuclear–electronic orbital Ehrenfest dynamics. The Journal of Chemical Physics, 153(22), 224111 (2020).

Fujiwara, G. E., Bragg, M. B., & Broeren, A. P. Comparison of Computational and Experimental Ice Accretions of Large Swept Wings. Journal of Aircraft, 57(2), 342-359 (2020).

Hoyer, C. E., & Li, X. Relativistic two-component projection-based quantum embedding for open-shell systems. The Journal of Chemical Physics, 153(9), 094113 (2020).

Branch, R. A., Horner‐Devine, A. R., Kumar, N., & Poggioli, A. R. River plume liftoff dynamics and surface expressions. Water resources research, 56(7), e2019WR026475 (2020).

Leung, M., Meadows, V. S., & Lustig-Yaeger, J. High-resolution Spectral Discriminants of Ocean Loss for M-dwarf Terrestrial Exoplanets. The Astronomical Journal, 160(1), 11 (2020).

Kasper, J. M., Gamelin, D. R., & Li, X. Theoretical investigation of quantum confinement on the Rashba effect in ZnO semiconductor nanocrystals. The Journal of chemical physics, 152(1), 014308. (2020).

Pavlovicz, R. E., Park, H., & DiMaio, F. Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination. PLoS computational biology, 16(9), e1008103 (2020).

Lu, D., Aithal, A. B., & Ferrante, A. Law of Incipient Separation over Curved Ramps as Inferred by Reynolds-Averaged Navier–Stokes. AIAA Journal, 1-19 (2020).

Ashraf, C., & Pfaendtner, J. Assessing the Performance of Various Stochastic Optimization Methods on Chemical Kinetic Modeling of Combustion. Industrial & Engineering Chemistry Research, 59(43), 19212-19225 (2020).

Collette, R., Garfinkel, D. A., Hu, Z., Masiello, D. J., & Rack, P. D. Near field excited state imaging via stimulated electron energy gain spectroscopy of localized surface plasmon resonances in plasmonic nanorod antennas. Scientific reports, 10(1), 1-9 (2020).

Buenaflor, J., Sommerville, P., Qian, H., & Luscombe, C. Investigation of Bimetallic Nickel Catalysts in Catalyst‐Transfer Polymerization of π‐Conjugated Polymers. Macromolecular Chemistry and Physics, 221(2), 1900363 (2020).

Sampath, J., Kullman, A., Gebhart, R., Drobny, G., & Pfaendtner, J. Molecular recognition and specificity of biomolecules to titanium dioxide from molecular dynamics simulations. npj Computational Materials, 6(1), 1-8 (2020).

Benedett, T. E., Hansen, C. J., Morgan, K. D., & Jarboe, T. R. Effects of temperature and density evolution in MHD simulations of HIT-SI. Physics of Plasmas, 27(4), 042508 (2020).

Boyer, M. A., Chiu, C. S., McDonald, D. C., Wagner, J. P., Colley, J. E., Orr, D. S., … & McCoy, A. B. The Role of Tunneling in the Spectra of H5+ and D5+ up to 7300 cm–1. The Journal of Physical Chemistry A, 124(22), 4427-4439 (2020).

Finney, J. M., DiRisio, R. J., & McCoy, A. B. Guided Diffusion Monte Carlo: A Method for Studying Molecules and Ions That Display Large Amplitude Vibrational Motions. The Journal of Physical Chemistry A, 124(46), 9567-9577 (2020).

Sun, S., & Li, X. Relativistic Effects in Magnetic Circular Dichroism: Restricted Magnetic Balance and Temperature Dependence. Journal of Chemical Theory and Computation, 16(7), 4533-4542 (2020).

Kessenich, B. L., Pokhrel, N., Kibue, J. K., Flury, M., Maibaum, L., & De Yoreo, J. J. Negatively charged lipids exhibit negligible effects on the water repellency of montmorillonite films. ACS omega, 5(21), 12154-12161 (2020).

Winter, A. O., & Motley, M. R. Development of a Fluid-Structure Interaction Model of an Oscillating Wave Surge Converter Using OpenFOAM. In ASME 2020 39th International Conference on Ocean, Offshore and Arctic Engineering. American Society of Mechanical Engineers Digital Collection (2020).

Mulligan, V. K., Kang, C. S., Sawaya, M. R., Rettie, S., Li, X., Antselovich, I., … & Baker, D. Computational design of mixed chirality peptide macrocycles with internal symmetry. Protein Science, 29(12), 2433-2445 (2020).

Beckner, W., Ashraf, C., Lee, J., Beck, D. A., & Pfaendtner, J. Continuous Molecular Representations of Ionic Liquids. The Journal of Physical Chemistry B, 124(38), 8347-8357. (2020).

Fleming, D. P., Barnes, R., Luger, R., & VanderPlas, J. T. On the XUV luminosity evolution of TRAPPIST-1. The Astrophysical Journal, 891(2), 155 (2020).

Zhang, L., Kang, C., Zhang, G., Pan, Z., Huang, Z., Xu, S., … & Jen, A. K. Y. All‐Inorganic CsPbI3 Quantum Dot Solar Cells with Efficiency over 16% by Defect Control. Advanced Functional Materials, 2005930. (2020).

Hill, A. H., Manifold, B., & Fu, D. (2020). Tissue imaging depth limit of stimulated Raman scattering microscopy. Biomedical optics express, 11(2), 762-774 (2020).

Hu, H., Jenkins, A. J., Liu, H., Kasper, J. M., Frisch, M. J., & Li, X. Relativistic two-component multireference configuration interaction method with tunable correlation space. Journal of chemical theory and computation, 16(5), 2975-2984 (2020).

West, C. A., Olafsson, A., Pakeltis, G., Garfinkel, D. A., Rack, P. D., Masiello, D. J., … & Idrobo, J. C. Plasmon Hybridization in Nanorhombus Assemblies. The Journal of Physical Chemistry C, 124(49), 27009-27016. (2020).

Jin, K., Wilson, K. A., Beck, J. N., Nelson, C. S., Brownridge III, G. W., Harrison, B. R., … & Promislow, D. Genetic and metabolomic architecture of variation in diet restriction-mediated lifespan extension in Drosophila. PLoS genetics, 16(7), e1008835 (2020).

Richie-Halford, A., Drut, J. E., & Bulgac, A. Emergence of a Pseudogap in the BCS-BEC Crossover. Physical Review Letters, 125(6), 060403 (2020).

Sommerville, P. J., Li, Y., Dong, B. X., Zhang, Y., Onorato, J. W., Tatum, W. K., … & Luscombe, C. K. Elucidating the Influence of Side-Chain Circular Distribution on the Crack Onset Strain and Hole Mobility of Near-Amorphous Indacenodithiophene Copolymers. Macromolecules, 53(17), 7511-7518 (2020).

Liu, T., Zhang, J., Wu, X., Liu, H., Li, F., Deng, X., … & Jen, A. K. Y. Interfacial Modification through a Multifunctional Molecule for Inorganic Perovskite Solar Cells with over 18% Efficiency. Solar RRL, 4(9), 2000205 (2020).

Kasper, J. M., & Li, X. Natural transition orbitals for complex two‐component excited state calculations. Journal of computational chemistry, 41(16), 1557-1563 (2020).

Beck, R. A., Lu, L., Petrone, A., Ong, A. C., Pauzauskie, P. J., & Li, X. Spectroscopic Signatures of the B and H4 Polyatomic Nitrogen Aggregates in Nanodiamond. The Journal of Physical Chemistry C, 124(33), 18275-18283 (2020).

Zhao, L., Tao, Z., Pavošević, F., Wildman, A., Hammes-Schiffer, S., & Li, X. Real-Time Time-Dependent Nuclear− Electronic Orbital Approach: Dynamics beyond the Born–Oppenheimer Approximation. The journal of physical chemistry letters, 11(10), 4052-4058 (2020).

Lu, L., Wildman, A., Jenkins, A. J., Young, L., Clark, A. E., & Li, X. The “Hole” Story in Ionized Water from the Perspective of Ehrenfest Dynamics. The Journal of Physical Chemistry Letters, 11(22), 9946-9951 (2020).

Rabe, E. J., Goldwyn, H. J., Hwang, D., Masiello, D. J., & Schlenker, C. W. Intermolecular Hydrogen Bonding Tunes Vibronic Coupling in Heptazine Complexes. The Journal of Physical Chemistry B. (2020).

Summers, S., Kraft, C., Alamdari, S., Pfaendtner, J., & Kaar, J. L. Enhanced Activity and Stability of Acidothermus cellulolyticus Endoglucanase 1 in Ionic Liquids via Engineering Active Site Residues and Non-Native Disulfide Bridges. ACS Sustainable Chemistry & Engineering, 8(30), 11299-11307 (2020).

Komp, E., & Valleau, S. Machine Learning Quantum Reaction Rate Constants. The Journal of Physical Chemistry A (2020).

Gibson, L. D., & Pfaendtner, J. Solvent oligomerization pathways facilitated by electrolyte additives during solid-electrolyte interphase formation. Physical Chemistry Chemical Physics, 22(37), 21494-21503 (2020).

Lee, V. G., Vetterli, N. J., Boyer, M. A., & McCoy, A. B. Diffusion Monte Carlo Studies on the Detection of Structural Changes in the Water Hexamer upon Isotopic Substitution. The Journal of Physical Chemistry A, 124(34), 6903-6912 (2020).

Kaptanoglu, A. A., Benedett, T. E., Morgan, K. D., Hansen, C. J., & Jarboe, T. R. Two-temperature effects in Hall-MHD simulations of the HIT-SI experiment. Physics of Plasmas, 27(7), 072505 (2020).

Kaptanoglu, A.A. Morgan, K.D. Hansen, C.J. Brunton, S.L. Characterizing magnetized plasmas with dynamic mode decomposition. Physics of Plasmas. 27, 032108 (2020).

Hellner, B. Alamdari, S. Pyles, H. Zhang, S. Prakash, A. Sprenger, K.G. De Yoreo, J. J. Baker, D. Pfaendtner, J. Baneyx, F. Sequence-structure-binding relationships reveal adheasion behavior of the Car9 solid-binding peptide: an integraded experimental and simulation study. J. Am. Chem. Soc. 142, 5, 2355-2363 (2020).

Perfect, B. Kumar, N. Riley, J.J. Energetics of Seamount Wakes, Part 2: Wave Fluxes. Journal of the Physical Oceanography. DOI 10.1175/JPO-D-19-0104.1.

Wang, J. Zhu, Z. Jen. K. Y. A. Highly efficient all-inorganic perovskite solar cells with suppressed non-radiative recombination by a Lewis base. Nat. Commun. 11, 177 (2020).

2019 (33 Publications)

Alamdari, S., Pfaendtner, J. Impact of glutamate carboxylation in the adsoprtion of the α-1 domain of the osteocalcin to hydroxyapatite and titania. Mol. Syst. Des. Eng. DOI: 10.1039/c9me00158a (2019).

Lee, V.G.M., McCoy, A.B. An Efficient Approach for Studies of Water Clusters Using Diffusion Monte Carlo. J. Phys. Chem. A. 123, 8063-8070 (2019).

Bai, F. A 0D/3D Heterostructured All-Inorganic Halide Perovskite Solar Cell with High Performance and Enhanced Phase Stability. Advanced Materials. 31, 48 (2019).

Sun, S., et. al. Simulating Magnetic Circular Dichroism Spectra with Real-Time Time-Dependent Density Functional Theory in Gauge Including Atomic Orbitals. J. Chem. Theory Comput. 15, 6824-6831 (2019).

Valentine, A.J.S., et. al. Resolving the ultrafast intersystem crossing in a bimetallic platinum complex. J. Chem. Phys. 151, 114303 (2019).

Valentine, A.J.S. & Li, X. Toward the evaluation of the intersystem crossing rates with variational relativistic methods. J. Chem. Phys. 151, 084107 (2019).

De Siena, M.C., et. al. Spinodal Decomposition During Anion Exchange in Colloidal Mn2+-Doped CsPBX3 (X=Cl, Br) Perovskite Nanocrystals. Chem. Mater. 31, 7711-7722 (2019).

Manifold, B., et. al. Denoising of stimulated Raman scattering microscopy images via deep learning. Biomed. Opt. Express. 10, 3860-3874 (2019).

Koulias, L.N., et. al. Relativistic Real-Time Time-Dependent Equation-of-Motion Coupled-Cluster. J. Chem. Theory Comput. 15, 6617-6624 (2019).

Stetina, T.F., et. al. Modeling L 2,3 -edge X-ray absorption spectroscopy with linear response exact two-component relativistic time-dependent density functional theory. J. Chem. Phys. 150, 234103 (2019).

Stetina, T.F., et. al. The Role of Excited-State Proton Relays in the Photochemical Dynamics of Water Nanodroplets. J. Phys. Chem. Lett. 10, 3694-3698 (2019).

Creutz, S.E., et. al. Structural Diversity in Cesium Bismuth Halide Nanocrystals. Chem. Mater. 31, 46850-4697 (2019).

Crane, M.J., et. al. High-pressure, high-temperature molecular doping of nanodiamond. Sci. Adv. 5, 5, (2019).

Stetina, T.F., et. al. Modeling Magneto-Photoabsorption Using Time-Dependent Complex Generalized Hartree-Fock. ChemPhotoChem. 3, 9 (2019).

Chen, Z. Self-Assembling 2D Arrays with de Novo Protein Building Blocks. J. Am. Chem. Soc. 141, 8891-8895 (2019).

Jenkins, A.J., et. al. Variational Relativistic Two-Component Complete-Active-Space Self-Consistent Field Method. J. Chem. Theory Comput. 15, 2974-2982 (2019).

Hoyer, C.E., et. al. Embedding non-collinear two-component electronic structure in a collinear quantum environment. J. Chem. Phys. 150, 174114 (2019).

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).

Fu, W., et. al. Tailoring the Functionality of Organic Spacer Cations for Efficient and Stable Quasi-2D Perovskite Solar Cells. Adv. Func. Mater. 29, 25 (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).

Davis, J., et. al. Soot morphology and nanostructure in complex flame flow patterns via secondary particle surface growth. Fuel. 245447-457 (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).

Beckner, W., & Pfaendtner, J. Fantastic Liquids and Where to Find Them: Optimizations of Discrete Chemical Space. J. Chem. Inf. Model. 59, 2617-2625 (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).

Leger, J.D., et. al. Carboxylate Anchors Act as Exciton Reporters in 1.3 nm Indium Phosphide Nanoclusters. J. Phys. Chem. Lett. 10, 1833-1839 (2019).

Stansfield, S.E., et. al. Sexual role and HIV-1 set point viral load among men who have sex with men. Epidemics. 26, 68-76 (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).

Sun, S. et. al. An ab Initio Linear Response Method for Computing Magnetic Circular Dichrosim Spectra with Nonperturbative Treatment of Magnetic Field. J. Chem. Theory Comput. 15, 3162-3169 (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

Liu, H., et. al. Time-Dependent Complete Active Space Embedded in a Polarizable Force Field. J. Chem. Theory Comput. 15, 1633-1641 (2019).

Buckle, E.L., et. al. Solid-State NMR and MD Study of the Structure of the Statherin Mutant SNa15 on Mineral Surfaces. J. Am. Chem. Soc. 141, 1998-2011 (2019).

2018 (35 Publications)

Winter, A. O., Motley, M. R., & Eberhard, M. O. Tsunami-Like Wave Loading of Individual Bridge Components. Journal of Bridge Engineering. 23, 2, 2018.

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 (31 Publications)

Stephens, M. T., Winter, A. O., Motley, M. R., & Lehman, D. E. Comparing Seismic and Tsunami Load Demands on Reinforced Concrete and Concrete Filled Steel Tube Bridges. IABSE Symposium Report169, 61, 683-690.

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 (18 Publications)

Motley, M.R. Wong, H.K. Qin, X. Winter, A.O. Eberhard, M.O. Tsunami-induced forces on skewed bridges. Journal of Waterway, Port, Coastal, and Ocean Engineering. 142, 2016.

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).