User Publications

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Our users do some really cool stuff! Check out the list below for publications that were made possible by UArizona's HPC systems.

Steward Observatory, Department of Astronomy

Tamadoni Saray, M., Yurkiv, V., & Shahbazian-Yassar, R. (2023). Role of Kinetics and Thermodynamics in Controlling the Crystal Structure of Nickel Nanoparticles Formed on Reduced Graphene Oxide: Implications for Energy Storage and Conversion Applications. ACS Applied Nano Materials.

Boruah, S. S., Eifler, T., Miranda, V., & Krishanth, P. S. (2023). Accelerating cosmological inference with Gaussian processes and neural networks--an application to LSST Y1 weak lensing and galaxy clustering. Monthly Notices of the Royal Astronomical Society, 518(4)), 4818-4831.

Xu, J., Eifler, T., Huff, E., Huang, H. J., Everett, S., & Krause, E. (2022). Kinematic Lensing with the Roman Space Telescope. arXiv preprint arXiv:2201.00739.

Kong, S., Whitworth, D. J., Smith, R. J., & Hamden, E. T. (2022). Filament formation via collision-induced magnetic reconnection–formation of a star cluster. Monthly Notices of the Royal Astronomical Society, 517(4), 4679-4695.

Woodrum, C., Williams, C. C., Rieke, M., Leja, J., Johnson, B. D., Bezanson, R., ... & Tacchella, S. (2022). Molecular Gas Reservoirs in Massive Quiescent Galaxies at $\mathrm {z\sim0. 7} $ Linked to Late Time Star Formation. arXiv preprint arXiv:2210.03832.

Yung, L. Y., Somerville, R. S., Finkelstein, S. L., Behroozi, P., Davé, R., Ferguson, H. C., ... & Koekemoer, A. M. (2022). Semi-analytic forecasts for Roman--the beginning of a new era of deep-wide galaxy surveys. arXiv preprint arXiv:2210.04902.

Long, J. D., Males, J. R., Haffert, S. Y., Close, L. M., Morzinski, K. M., Van Gorkom, K., ... & Otten, G. P. (2022). XPipeline: Starlight subtraction at scale for MagAO-X. arXiv preprint arXiv:2208.07354.

Wenzl, L., Doux, C., Heinrich, C., Bean, R., Jain, B., Doré, O., ... & Fang, X. (2022). Cosmology with the Roman Space Telescope–Synergies with CMB lensing. Monthly Notices of the Royal Astronomical Society, 512(4), 5311-5328.

Fang, X., Eifler, T., Schaan, E., Huang, H. J., Krause, E., & Ferraro, S. (2022). Cosmology from clustering, cosmic shear, CMB lensing, and cross correlations: combining Rubin observatory and Simons Observatory. Monthly Notices of the Royal Astronomical Society, 509(4), 5721-5736.

Eifler, T., Simet, M., Krause, E., Hirata, C., Huang, H. J., Fang, X., ... & Wu, H. Y. (2021). Cosmology with the Roman Space Telescope: synergies with the Rubin Observatory Legacy Survey of Space and Time. Monthly Notices of the Royal Astronomical Society, 507(1), 1514-1527.

Eifler, T., Miyatake, H., Krause, E., Heinrich, C., Miranda, V., Hirata, C., ... & Wu, H. Y. (2021). Cosmology with the Roman Space Telescope–multiprobe strategies. Monthly Notices of the Royal Astronomical Society, 507(2), 1746-1761.

Fang, X., Eifler, T., & Krause, E. (2020). 2D-FFTLog: efficient computation of real-space covariance matrices for galaxy clustering and weak lensing. Monthly Notices of the Royal Astronomical Society, 497(3), 2699-2714.

Eifler, T., Simet, M., Krause, E., Hirata, C., Huang, H. J., Fang, X., ... & Wu, H. Y. (2020). Cosmology with the Wide-Field Infrared Survey Telescope–Synergies with the Rubin Observatory Legacy Survey of Space and Time. arXiv e-prints, art. arXiv preprint arXiv:2004.04702.

Besla, G., Peter, A. H. G., & Garavito-Camargo, N. (2019). The highest-speed local dark matter particles come from the Large Magellanic Cloud. Journal of Cosmology and Astroparticle Physics, 2019(11), 013.

Garavito-Camargo, N., Besla, G., Laporte, C. F., Johnston, K. V., Gómez, F. A., & Watkins, L. L. (2019). Hunting for the dark matter wake induced by the large magellanic cloud. The Astrophysical Journal, 884(1), 51.

Behroozi, P., Wechsler, R. H., Hearin, A. P., & Conroy, C. (2019). UniverseMachine: The correlation between galaxy growth and dark matter halo assembly from z= 0− 10. Monthly Notices of the Royal Astronomical Society, 488(3), 3143-3194.

Bozzola, G., Espino, P. L., Lewin, C. D., & Paschalidis, V. (2019). Maximum mass and universal relations of rotating relativistic hybrid hadron-quark stars. The European Physical Journal A, 55(9), 1-18.

Bozzola, G., & Paschalidis, V. (2019). Initial data for general relativistic simulations of multiple electrically charged black holes with linear and angular momenta. Physical Review D, 99(10), 104044.

Chan, C. K., Medeiros, L., Özel, F., & Psaltis, D. (2018). GRay2: a general purpose geodesic integrator for kerr spacetimes. The Astrophysical Journal, 867(1), 59.

Jeon, M., Besla, G., & Bromm, V. (2017). Connecting the first galaxies with ultrafaint dwarfs in the Local Group: chemical signatures of Population III stars. The Astrophysical Journal, 848(2), 85.

Raithel, C. A., Özel, F., & Psaltis, D. (2017). From Neutron Star Observables to the Equation of State. II. Bayesian Inference of Equation of State Pressures. The Astrophysical Journal, 844(2), 156.

Schneider, E. E., & Robertson, B. E. (2017). Hydrodynamical coupling of mass and momentum in multiphase galactic winds. The Astrophysical Journal, 834(2), 144.

Ball, D., Özel, F., Psaltis, D., & Chan, C. K. (2016). Particle Acceleration and the Origin of X-Ray Flares in GRMHD Simulations of SGR A. The Astrophysical Journal, 826(1), 77.

Smullen, R. A., Kratter, K. M., & Shannon, A. (2016). Planet scattering around binaries: ejections, not collisions. Monthly Notices of the Royal Astronomical Society, 461(2), 1288-1301.

Raithel, C. A., Özel, F., & Psaltis, D. (2016). Model-independent inference of neutron star radii from moment of inertia measurements. Physical Review C, 93(3), 032801.

Schneider, E. E., & Robertson, B. E. (2015). CHOLLA: a new massively parallel hydrodynamics code for astrophysical simulation. The Astrophysical Journal Supplement Series, 217(2), 24.

Schwartz Research Group

Luft, C. M., Munusamy, E., Pemberton, J. E., & Schwartz, S. D. (2018). Molecular dynamics simulation of the oil sequestration properties of a nonionic rhamnolipid. The Journal of Physical Chemistry B, 122(14), 3944-3952.

McConnell, M., Tal Grinspan, L., Williams, M. R., Lynn, M. L., Schwartz, B. A., Fass, O. Z., ... & Tardiff, J. C. (2017). Clinically divergent mutation effects on the structure and function of the human cardiac tropomyosin overlap. Biochemistry, 56(26), 3403-3413.

Munusamy, E., Luft, C. M., Pemberton, J. E., & Schwartz, S. D. (2017). Structural properties of nonionic monorhamnolipid aggregates in water studied by classical molecular dynamics simulations. The Journal of Physical Chemistry B, 121(23), 5781-5793.

Harijan, R. K., Zoi, I., Antoniou, D., Schwartz, S. D., & Schramm, V. L. (2017). Catalytic-site design for inverse heavy-enzyme isotope effects in human purine nucleoside phosphorylase. Proceedings of the National Academy of Sciences, 114(25), 6456-6461.

Pan, X., & Schwartz, S. D. (2016). Conformational heterogeneity in the michaelis complex of lactate dehydrogenase: An analysis of vibrational spectroscopy using markov and hidden markov models. The Journal of Physical Chemistry B, 120(27), 6612-6620.

Dzierlenga, M. W., Varga, M. J., & Schwartz, S. D. (2016). Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions. Methods in enzymology, 578, 21-43.

Zoi, I., Suarez, J., Antoniou, D., Cameron, S. A., Schramm, V. L., & Schwartz, S. D. (2016). Modulating enzyme catalysis through mutations designed to alter rapid protein dynamics. Journal of the American Chemical Society, 138(10), 3403-3409.

Williams, M. R., Lehman, S. J., Tardiff, J. C., & Schwartz, S. D. (2016). Atomic resolution probe for allostery in the regulatory thin filament. Proceedings of the National Academy of Sciences, 113(12), 3257-3262.

Pan, X., & Schwartz, S. D. (2015). Free energy surface of the Michaelis complex of lactate dehydrogenase: a network analysis of microsecond simulations. The Journal of Physical Chemistry B, 119(17), 5430-5436.

Dzierlenga, M. W., Antoniou, D., & Schwartz, S. D. (2015). Another look at the mechanisms of hydride transfer enzymes with quantum and classical transition path sampling. The journal of physical chemistry letters, 6(7), 1177-1181.

Others

Burrell, D. J., Spencer, M. F., & Driggers, R. G. (2024). Open-loop wavefront sensing in the presence of speckle and weak scintillation. Optics Communications, 130960.

Das Goswami, B. R., Jabbari, V., Shahbazian-Yassar, R., Mashayek, F., & Yurkiv, V. (2023). Unraveling Ion Diffusion Pathways and Energetics in Polycrystalline SEI of Lithium-Based Batteries: Combined Cryo-HRTEM and DFT Study. The Journal of Physical Chemistry C.

Gonzalez, E., Zarei, A., Hendler, N., Simmons, T., Zarei, A., Demieville, J., ... & Pauli, D. (2023). PhytoOracle: Scalable, modular phenomics data processing pipelines. Frontiers in Plant Science, 14.

Gong, Z., Rodriguez, N., Gagatsos, C. N., Guha, S., & Bash, B. A. (2022) Quantum-Enhanced Transmittance Sensing. IEEE Journal of Selected Topics in Signal Processing, 17(2), 473-490.

Benowitz, K. M., Allan, C. W., Jaworski, C. C., Sanderson, M. J., Diaz, F., Chen, X., & Matzkin, L. M. (2022). Chromosome-length genome assemblies of cactophilic Drosophila illuminate links between structural and sequence evolution. bioRxiv.

Manga, V. R., Muralidharan, K., & Zega, T. J. (2022). The interplay between twinning and cation inversion in MgAl2O4-spinel: Implications for a nebular thermochronometer. American Mineralogist, 107(8), 1470-1476.

Zanetta, P. M. (2022). The Unrestrained Use of Python Libraries for Bridging the Gap Between Planetary and Material Sciences. Microscopy and Microanalysis, 28(S1), 2686-2688.

Song, J. P., Clay, R. T., & Mazumdar, S. (2022). Valence Transition Theory of the Pressure-Induced Dimensionality Crossover in Superconducting Sr $ _ {14-x} $ Ca $ _x $ Cu $ _ {24} $ O $ _ {41} $. arXiv preprint arXiv:2207.00628.

Dunham, A. M., Kiser, E., Kargel, J. S., Haritashya, U. K., Watson, C. S., Shugar, D. H., ... & DeCelles, P. G. (2022). Topographic control on ground motions and landslides from the 2015 Gorkha earthquake. Geophysical Research Letters, e2022GL098582.

Hviding, R. E., Hainline, K. N., Rieke, M., Juneau, S., Lyu, J., & Pucha, R. (2022). A New Infrared Criterion for Selecting Active Galactic Nuclei to Lower Luminosities. The Astronomical Journal, 163(5), 224.

Thakur, A. K., Muralidharan, K., Zega, T. J., & Ziurys, L. M. (2022). A nanometric window on fullerene formation in the interstellar medium: Insights from molecular dynamics studies. The Journal of Chemical Physics, 156(15), 154704.

Bamberger, N. D., Dyer, D., Parida, K. N., El-Assaad, T. H., Pursell, D., McGrath, D. V., ... & Monti, O. L. (2022). Beyond Simple Structure–Function Relationships: The Interplay of Geometry, Electronic Structure, and Molecule/Electrode Coupling in Single-Molecule Junctions. The Journal of Physical Chemistry C, 126(15), 6653-6661.

Román‐Palacios, C., Moraga‐López, D., & Wiens, J. J. (2022). The origins of global biodiversity on land, sea and freshwater. Ecology letters.

Lin, A. S., Monson, A., Mahadevan, S., Ninan, J. P., Halverson, S., Nitroy, C., ... & Stefansson, G. (2022). Observing the Sun as a star: Design and early results from the NEID solar feed. The Astronomical Journal, 163(4), 184.

Gorelik, R., Asaduzzaman, A., Manga, V. R., Thakur, A., & Muralidharan, K. (2022). A First-Principles Investigation of Lithium and Sodium Ion Diffusion in C60 Molecular Solids. The Journal of Physical Chemistry C, 126(9), 4259-4266.

Yang, B., Balazs, K. R., Butterfield, B. J., Laushman, K. M., Munson, S. M., Gornish, E. S., & Barberán, A. (2022). Does restoration of plant diversity trigger concomitant soil microbiome changes in dryland ecosystems?. Journal of Applied Ecology, 59(2), 560-573.

Kinney, A. C., Current, S., & Lega, J. (2021). Aedes-AI: Neural network models of mosquito abundance. PLoS computational biology, 17(11), e1009467.

Spotnitz, M., Kwong, N. H., & Binder, R. (2021)Terahertz spectroscopy of semiconductor microcavity lasers: Photon lasers. Physical Review B, 104(11), 115305.

Song, J. P., Mazumdar, S., & Clay, R. T. (2021). Absence of Luther-Emery superconducting phase in the three-band model for cuprate ladders. Physical Review B, 104(10), 104504.

Hosseinverdi, S., & Fasel, H. F. (2022). Towards understanding of natural boundary-layer transition for low-speed flows via random excitation. In IUTAM Laminar-Turbulent Transition (pp. 391-405). Springer, Cham.

Chen, Y., Martinez, A., Cleavenger, S., Rudolph, J., & Barberán, A. (2021). Changes in soil microbial communities across an urbanization gradient: A local-scale temporal study in the arid southwestern usa. Microorganisms, 9(7), 1470.

Gillan, J. K., Ponce‐Campos, G. E., Swetnam, T. L., Gorlier, A., Heilman, P., & McClaran, M. P. (2021). Innovations to expand drone data collection and analysis for rangeland monitoring. Ecosphere, 12(7), e03649.

He, W., Guha, S., Shapiro, J. H., & Bash, B. A. (2021). Performance analysis of free-space quantum key distribution using multiple spatial modes. Optics Express, 29(13), 19305-19318.

Li, H., & Bredas, J. L. (2021). Impact of structural defects on the elastic properties of two-dimensional covalent organic frameworks (2D COFs) under tensile stress. Chemistry of Materials, 33(12), 4529-4540.

Zhou, Z., Daly, A. M., & Kukolich, S. G. (2021). Microwave measurements of rotational transitions and nitrogen quadrupole coupling for 2-aminopyridine. Journal of Molecular Spectroscopy, 378, 111457.

Li, H., Evans, A. M., Dichtel, W. R., & Bredas, J. L. (2021). Quantitative Description of the Lateral Growth of Two-Dimensional Covalent Organic Frameworks Reveals Self-Templation Effects. ACS Materials Letters, 3(4), 398-405.

Klein, K. G., Verniero, J. L., Alterman, B., Bale, S., Case, A., Kasper, J. C., ... & Whittlesey, P. (2021). Inferred Linear Stability of Parker Solar Probe Observations Using One-and Two-component Proton Distributions. The Astrophysical Journal, 909(1), 7.

Chen, Y., Neilson, J. W., Kushwaha, P., Maier, R. M., & Barberán, A. (2021). Life-history strategies of soil microbial communities in an arid ecosystem. The ISME journal, 15(3), 649-657.

Xiong, Z., Potter, C. J., & McLeod, E. (2021). High-speed lens-free holographic sensing of protein molecules using quantitative agglutination assays. ACS sensors, 6(3), 1208-1217.

Zhang, Y., Weeks, R. R., Lecaplain, C., Harilal, S. S., Yeak, J., Phillips, M. C., & Jones, R. J. (2021). Burst-mode dual-comb spectroscopy. Optics letters, 46(4), 860-863.

Luk, S. M., Vergnet, H., Lafont, O., Lewandowski, P., Kwong, N. H., Galopin, E., ... & Baudin, E. (2021). All-optical beam steering using the polariton lighthouse effect. ACS Photonics, 8(2), 449-454.

Ivie, J. A., Bamberger, N. D., Parida, K. N., Shepard, S., Dyer, D., Saraiva-Souza, A., ... & Monti, O. L. (2021). Correlated energy-level alignment effects determine substituent-tuned single-molecule conductance. ACS Applied Materials & Interfaces, 13(3), 4267-4277.

Lemoine, D. (2021). The climate risk premium: how uncertainty affects the social cost of carbon. Journal of the Association of Environmental and Resource Economists, 8(1), 27-57.

Tanjaroon, C., Mills, D. D., Hoyos, C. A. J., & Kukolich, S. G. (2021). Calculations and analysis of 55Mn nuclear quadrupole coupling for asymmetric top acyl methyl manganese pentacarbonyl. Chemical Physics Letters, 762, 138151.

Jaworski, C. C., Allan, C. W., & Matzkin, L. M. (2020). Chromosome‐level hybrid de novo genome assemblies as an attainable option for nonmodel insects. Molecular ecology resources, 20(5), 1277-1293.

Tanjaroon, C., Zhou, Z., Mills, D., Keck, K., & Kukolich, S. G. (2020). Microwave Spectra and Theoretical Calculations for Two Structural Isomers of Methylmanganese Pentacarbonyl. Inorganic chemistry, 59(9), 6432-6438.

Pyarelal, A., & Su, S. (2020). Higgs assisted razor search for Higgsinos at a 100 TeV pp collider. SCIENCE CHINA Physics, Mechanics & Astronomy, 63(10), 1-9.

Klein, K. G., Martinović, M., Stansby, D., & Horbury, T. S. (2019). Linear stability in the inner heliosphere: Helios re-evaluated. The Astrophysical Journal, 887(2), 234.

Yazdi, E. T., Limaye, A., Akoglu, A., Adegbija, T., & Buntzman, A. (2019, December). Bit-wise and Multi-GPU Implementations of the DNA Recombination Algorithm. In 2019 IEEE 26th International Conference on High Performance Computing, Data, and Analytics (HiPC) (pp. 131-140). IEEE.

Sarid, G., Volk, K., Steckloff, J. K., Harris, W., Womack, M., & Woodney, L. M. (2019). 29P/Schwassmann–Wachmann 1, a centaur in the gateway to the Jupiter-family comets. The Astrophysical Journal Letters, 883(1), L25.

Grant, A. D., Vail, P., Padi, M., Witkiewicz, A. K., & Knudsen, E. S. (2019). Interrogating mutant allele expression via customized reference genomes to define influential cancer mutations. Scientific reports, 9(1), 1-15.

Volk, K., & Malhotra, R. (2019). Not a simple relationship between Neptune’s migration speed and Kuiper belt inclination excitation. The Astronomical Journal, 158(2), 64.

Kling, F., Li, H., Pyarelal, A., Song, H., & Su, S. (2019). Exotic Higgs decays in Type-II 2HDMs at the LHC and future 100 TeV hadron colliders. Journal of High Energy Physics, 2019(6), 1-33.

Esmaili, E., Akoglu, A., Hariri, S., & Moukabary, T. (2019). Implementation of scalable bidomain-based 3d cardiac simulations on a graphics processing unit cluster. The Journal of Supercomputing, 75(8), 5475-5506.

Schissler, A. G., Piegorsch, W. W., & Lussier, Y. A. (2018). Testing for differentially expressed genetic pathways with single-subject N-of-1 data in the presence of inter-gene correlation. Statistical methods in medical research, 27(12), 3797-3813.

Alsayoud, A. Q., Manga, V. R., Muralidharan, K., Vita, J., Bringuier, S., Runge, K., & Deymier, P. (2018). Atomistic insights into the effect of polymerization on the thermophysical properties of 2-D C-60 molecular solids. Carbon, 133, 267-274.

Gladstein, A. L., Quinto-Cortés, C. D., Pistorius, J. L., Christy, D., Gantner, L., & Joyce, B. L. (2018). SimPrily: A Python framework to simplify high-throughput genomic simulations. SoftwareX, 7, 335-340.

Lucas, P., Coleman, G. J., Venkateswara Rao, M., Edwards, A. N., Devaadithya, C., Wei, S., ... & Deymier, P. A. (2017). Structure of ZnCl2 melt. Part II: Fragile-to-strong transition in a tetrahedral liquid. The Journal of Physical Chemistry B, 121(49), 11210-11218.

Vasquez, M. M., Hu, C., Roe, D. J., Chen, Z., Halonen, M., & Guerra, S. (2016). Least absolute shrinkage and selection operator type methods for the identification of serum biomarkers of overweight and obesity: simulation and application. BMC medical research methodology, 16(1), 1-19.

Hendler, N. P., Mulders, G. D., Pascucci, I., Greenwood, A., Kamp, I., Henning, T., ... & Evans II, N. J. (2017). Hints for Small Disks around Very Low Mass Stars and Brown Dwarfs∗. The Astrophysical Journal, 841(2), 116.

Li, Q., Schissler, A. G., Gardeux, V., Achour, I., Kenost, C., Berghout, J., ... & Lussier, Y. A. (2017). N-of-1-pathways MixEnrich: advancing precision medicine via single-subject analysis in discovering dynamic changes of transcriptomes. BMC Medical Genomics, 10(1), 5-16.

Lorenzo, A. T., Morzfeld, M., Holmgren, W. F., & Cronin, A. D. (2017). Optimal interpolation of satellite and ground data for irradiance nowcasting at city scales. Solar Energy, 144, 466-474.

Li, Q., Schissler, A. G., Gardeux, V., Berghout, J., Achour, I., Kenost, C., ... & Lussier, Y. A. (2017). kMEn: Analyzing noisy and bidirectional transcriptional pathway responses in single subjects. Journal of biomedical informatics, 66, 32-41.

Schlawin, E., Rieke, M., Leisenring, J., Walker, L. M., Fraine, J., Kelly, D., ... & Stansberry, J. (2016). Two NIRCam channels are better than one: how JWST can do more science with NIRCam’s short-wavelength dispersed Hartmann sensor. Publications of the Astronomical Society of the Pacific, 129(971), 015001.

Danford, F., Welch, E., Cárdenas-Ródriguez, J., & Strout, M. M. (2016, September). Analyzing parallel programming models for magnetic resonance imaging. In International Workshop on Languages and Compilers for Parallel Computing (pp. 188-202). Springer, Cham.

Schissler, A. G., Li, Q., Chen, J. L., Kenost, C., Achour, I., Billheimer, D. D., ... & Lussier, Y. A. (2016). Analysis of aggregated cell–cell statistical distances within pathways unveils therapeutic-resistance mechanisms in circulating tumor cells. Bioinformatics, 32(12), i80-i89.