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This work was facilitated though the use of advanced computational, storage, and networking infrastructure provided by the Hyak supercomputer system at the University of Washington.

Below list is not complete but it shows the wide variety of scientific work which has been done by using Hyak.

All Sciences

Google Scholar

Student Technology Fee Funded Work


  • Armstrong, J. C.; Barnes, R.; Domagal-Goldman, S., Breiner, J.; Quinn, T. R.; Meadows, V. S., (2014) Effects of Extreme Obliquity Variations on the Habitability of Exoplanets, Astrobiology, vol. 14, issue 4, pp. 277-291. doi: 10.1089/ast.2013.1129
  • Arney, G., Meadows, V., Crisp, D., Schmidt, S. J., Bailey, J. and Robinson, T. (2014), Spatially resolved measurements of H2O, HCl, CO, OCS, SO2, cloud opacity, and acid concentration in the Venus near-infrared spectral windows, JGR: Planets 119(8) 1860–1891. doi 10.1002/2014JE004662
  • Arney, G., Meadows, V., Domagal-Goldman, S., Claire, M., Schwieterman, E. 2015. Hazy Archean Earth as an Analog for Hazy Earthlike Exoplanets. American Astronomical Society Meeting #225, #224.02.
  • Kopparapu, R.K., Ramirez, R., Kasting, J.F., Eymet, V., Robinson, T.D., Mahadevan, S., Terrien, R., Domagal-Goldman, S., Meadows, V., Deshpande, R. 2013. Habitable Zones Around Main Sequence Stars: New Estimates. The Astrophysical Journal 765:131. doi: 10.1088/0004-637X/765/2/131
  • Schwieterman, E.W., Robinson, T.D., Meadows, V.S., Misra, A., Domagal-Goldman, S.D. 2015. Detecting and Constraining N2 Abundances in Planetary Atmospheres Using Collisional Pairs. The Astrophysical Journal 810, 57. doi:10.1088/0004-637X/810/1/57
  • Schwieterman, E.W., Cockell, C.S., Meadows, V.S. 2015. Nonphotosynthetic Pigments as Potential Biosignatures. Astrobiology, 15(5): 341-361. doi:
  • Schwieterman, E.W., Meadows, V.S., Robinson, T.D., Misra, A., Domagal-Goldman, S.D., Luger, R., Barnes, R., Crisp, D. 2015. Using Dimers to Constrain Planetary Habitability and Discriminate Against False Positives for Life. Astrobiology Science Conference 2015 #7486.
  • Shields, A., Meadows, V.S., Bitz, C.M, Pierrehumbert, R.T., Joshi, M.M., Robinson, T.D. 2013. The Effect of Host Star Spectral Energy Distribution and Ice-Albedo Feedback on the Climate of Extrasolar Planets. Astrobiology, 13(8): 715-739. doi: 10.1089/ast.2012.0961
  • Shields, A. L., Bitz, C. M., Meadows, V. S., Joshi, M. M., Robinson, T. D. 2014 Spectrum-driven Planetary Deglaciation Due to Increases in Stellar Luminosity, Astrophysical Journal Letters, 785, 9. doi: 10.1088/2041-8205/785/1/L9
  • Timpe, M., Barnes, R., Kopparapu, R., Raymond, S.N., Greenberg, R., Gorelick, N. 2013. Secular Behavior of Exoplanets: Self-Consistency and Comparisons with the Planet-Planet Scattering Hypothesis. The Astronomical Journal 146, 63. doi: 10.1088/0004-6256/146/3/63
  • The Starspots of HAT-P-11: Evidence for a Solar-like Dynamo, Brett Morris et al accepted by ApJ
  • Haqq-Misra, J., Wolf, E. T., Joshi, M., Zhang, X., & Kopparapu, R. K. (2018). Demarcating Circulation Regimes of Synchronously Rotating Terrestrial Planets within the Habitable Zone. *The Astrophysical Journal*, *852*(2), 67.


  • Warfield, B.M., Anderson, P.C. Molecular simulations and Markov state modeling reveal the structural diversity and dynamics of a theophylline-binding RNA aptamer in its unbound state. PLoS ONE 12(4): e0176229 (2017).
  • Opuni, K.F.M., Solomon, S., Metzen, F., Frommholz, D., Koy, C., Röwer, C., Glocker, M.O., Illges, H., Anderson, P.C. In silico epitope mapping of glucose-6-phosphate isomerase, a rheumatoid arthritis autoantigen. J. Proteomics Bioinform. 10, 60-72 (2017).
  • Alexandra C. Walls, M. Alejandra Tortorici, Berend-Jan Bosch, Brandon Frenz, Peter J. M. Rottier, Frank DiMaio, Félix A. Rey and David Veesler (2016) Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer
  • Aaron Y. Lee, Cecilia S. Lee and Russell N. Van Gelder (2016) Scalable metagenomics alignment research tool (SMART): a scalable, rapid, and complete search heuristic for the classification of metagenomic sequences from complex sequence populations
  • Vorobev, A., Beck, D. A. C., Kalyuzhnaya, M. G., Lidstrom, M. E., & Chistoserdova, L. (2013). Comparative transcriptomics in three Methylophilaceae species uncover different strategies for environmental adaptation. PeerJ, 1, e115. doi:10.7717/peerj.115

  • Beck D. A. C., Kalyuzhnaya MG, Malfatti S, Tringe SG, Glavina Del Rio T, Ivanova N, Lidstrom ME, Chistoserdova L. A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation* between the Methylococcaceae and the Methylophilaceae. PeerJ. 2013 Feb 19;1:e23.
  • Hirano, T., Beck, D. A. C., Wright, C. J., Demuth, D. R., Hackett, M., & Lamont, R. J. (2013). Regulon controlled by the GppX hybrid two component system in Porphyromonas gingivalis. Molecular oral microbiology, 28(1), 70–81. doi:10.1111/omi.12007
  • Hirano, T., Beck, D. A. C., Demuth, D. R., Hackett, M., & Lamont, R. J. (2012). Deep Sequencing of Porphyromonas gingivalis and Comparative Transcriptome Analysis of a LuxS Mutant. Frontiers in Cellular and Infection Microbiology. doi:10.3389/fcimb.2012.00079
  • Beck D.A.C., Hendrickson E.L., Wang T., Lamont, R. J., Hackett, M. Protein database construction for microbial community proteomics and impacts on peptide and protein assignments, confidence, quantitation and differential analysis. 10th Int. Symp. on Mass Spec. in the Health & Life Sciences: Mol. & Cell. Proteomic, San Francisco, 2011.
  • Hendrickson E.L., Beck D.A.C., Want, T., Yoon, S. H., Chistoserdova L., Baliga, N. S., Lamont, R. J., Leigh, J. A., Hackett, M. Proteomic and Transcriptomic Correlations for Microbial Species: Methanococcus maripaludis and Methylotenera mobilis. 10th Int. Symp. on Mass Spec. in the Health & Life Sciences: Mol. & Cell. Proteomic, San Francisco, 2011.
  • Beck D.A.C., Hendrickson E.L., Vorobev A., Wang T., Lim S., Kalyuzhnaya M.G., Lidstrom M.E., Hackett M., Chistoserdova L. An integrated proteomics/transcriptomics approach points to oxygen as the main electron sink for methanol metabolism in Methylotenera mobilis. J Bacteriol. 2011, Jul 15.
  • Kalyuzhnaya, M.G., Beck, D.A.C., and L. Chistoserdova. Functional metagenomics of methylotrophs. Methods in Enzymology, 495:81-98, 2011.
  • Hendrickson E.L., Beck D.A.C., Wang T., Lidstrom M. E., Hackett. M., and L. Chistoserdova. The expressed genome of Methylobacillus flagellatus defined through proteogenomics and new insights into methylotrophy. Journal of Bacteriology, 192: 4859-4867, 2010.
  • Kalyuzhnaya, M.G., Beck, D.A.C., Suciu, D., Pozhitkov, A., Lidstrom M.E., and L. Chistoserdova. Functioning in situ: gene expression in Methylotenera mobilis in its native environment as assessed via transcriptomics. ISME Journal,4: 388-398, 2009.


  • G. Donati, A. Wildman, S. Caprasecca, D.B. Lingerfelt, F. Lipparini, B. Mennucci, X. Li, "Coupling Real-Time Time-Dependent Density Functional Theory with Polarizable Force Field," J. Phys. Chem. Lett., *2017*, 8, 5283–5289, DOI: 10.1021/acs.jpclett.7b02320
  • Local Density Fluctuations Predict Photoisomerization Quantum Yield of Azobenzene-Modified DNA Addie Kingsland, Soumyadyuti Samai, Yunqi Yan, David S. Ginger, and Lutz Maibaum J. Phys. Chem. Lett., 2016, 7 (15), pp 3027–3031

Climate Science

  • Livneh, B. and D.P. Lettenmaier, 2012: Multi-criteria parameter estimation for the unified land model, Hydrol. Earth Syst. Sci., 16, 3029-3048, doi:10.5194/hess-16-3029-2012.
  • Livneh B., and D.P. Lettenmaier, 2013: Regional parameter estimation for the Unified Land Model, Water Resources Research, doi:10.1029/2012WR012220.
  • Siedlecki, S.A., Banas, N., Davis, K.A., Giddings, S., P. MacCready, Connolly, T., & B. Hickey. The role of slope currents in determining the chemistry of upwelling source waters –A closer look at seasonal oxygen variation in the Pacific Northwest.  Gordon Research Conference on Coastal Oceanography, Massachusetts, 2011
  • Siedlecki, S.A., Banas, N., Davis, K.A., Giddings, S., P. MacCready, Connolly, T., & B. Hickey. The role of slope currents in determining the chemistry of upwelling source waters –A closer look at seasonal oxygen variation in the Pacific Northwest.  Pacific Northwest Climate Conference, Seattle, 2011.
  • Siedlecki, S.A., Banas, N., Davis, K.A., Giddings, S., P. MacCready, Connolly, T., & B. Hickey. The Role of the Slope Currents in Seasonal Oxygen variability on the Pacific Northwest Continental Shelves. AGU/ASLO Ocean Sciences Meeting, Salt Lake City, 2012.
  • Shukla, S., Sheffield, J., Wood, E. F., and Lettenmaier, D. P., (2013): On the sources of global land surface hydrologic predictability, Hydrol. Earth Syst. Sci., 17, 2781-2796, doi:10.5194/hess-17-2781-2013. (
  • Shukla, S. and Lettenmaier, D. P., (2013): Multi-RCM ensemble downscaling of NCEP CFS winter season forecasts: Implications for seasonal hydrologic forecast skill, Journal of Geophysical Research (Atmospheres), DOI: 10.1002/jgrd.50628. (Early online publication:
    Shi, Xiaoming, Dale R. Durran, 2014: The Response of Orographic Precipitation over Idealized Midlatitude Mountains Due to Global Increases in CO2. *J. Climate, 27, 3938–3956. doi:
  • Shi, X., and C. S. Bretherton (2014), Large-scale character of an atmosphere in rotating radiative-convective equilibrium, J. Adv. Model. Earth Syst., 06, doi:10.1002/2014MS000342 <>.
  • A. Muhlbauer, E. Berry, J. M. Comstock3 and G. G. Mace, "Perturbed physics ensemble simulations of cirrus on the cloud system-resolving scale," Journal of Geophysical Research: Atmospheres, Volume 119, Issue 8, pages 4709–4735, 27 April 2014
    Siedlecki, S.A., Banas, N., Davis, K.A., Giddings, S., Hickey, B.M., MacCready, P., Connolly, T., and S. Geier, Seasonal and interannual oxygen variability on the Washington and Oregon continental shelves, (2015), J. Geophys. Res. Oceans, 120, DOI: 10.1002/2014JC010254 <>
    Davis, K. A., N. S. Banas, S. N. Giddings, *S. A. Siedlecki, P. MacCready, E. J. Lessard, R. M. Kudela, and B. M. Hickey (2014), Estuary-enhanced upwelling of marine nutrients fuels coastal productivity in the U.S. Pacific Northwest, J. Geophys. Res. Oceans, 119, 8778–8799, doi:10.1002/2014JC010248. <>
    Giddings, SN, MacCready, P, Hickey, BM, Banas, NS, Davis, KA, *Siedlecki, SA, Trainer, VL, Kudela, RM, Pelland, NA, and Connolly, TP. (2014) Hindcasts of harmful algal bloom transport on the Pacific Northwest coast, JGR-oceans, 119(4), 2439-2461. doi: 10.1002/2013/JC009622. <>
    Siedlecki, S.A., Kaplan, I.C., Hermann, A., Nguyen, T., Bond, N., Williams, G., Newton, J., Peterson, W. T., Alin, S., and R.A. Feely (*2016) Experiments with Seasonal Forecasts of ocean conditions for the Northern region of the California Current upwelling system, Nature: Scientific Reports <> 6, doi:10.1038/srep27203
    Kaplan, I, Williams, G, Bond, N, Hermann, A, and *Siedlecki, SA (2016) Cloudy with a chance of sardines: forecasting sardine distributions using regional climate models, Fisheries Oceanography 25:1, 15-27. doi: 10.1111/fog.12131


  • Michael Deighan, Massimiliano Bonomi, and Jim Pfaendtner, "Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble", Journal of Chemical Theory and Computation 2012 8 (7), 2189-2192
  • Ferrante A. & Baraldi A. (2011) "A mass-conserving volume of fluid method: volume tracking in incompressible isotropic turbulence", 20th AIAA Computational Fluid Dynamics Conference, Honolulu, Hawaii
  • Baraldi A. & Ferrante A. (2011) "DNS of droplet-laden incompressible turbulence: surface tension in a VoF method", Proceedings 64th American Physical Society Meeting, Division of Fluid Dynamics, Baltimore, MD | Abstract
  • Baraldi A. & Ferrante A. (2010) "A mass-conserving volume of fluid method for two-phase incompressible isotropic turbulence", Proceedings 63rd American Physical Society Meeting, Division of Fluid Dynamics, Long Beach, CA | Abstract
  • Ferrante A. & Webster K. (2010) "DNS of turbulent boundary layer over a flat plate at Reθ=5200", Proceedings 63rd American Physical Society Meeting, Division of Fluid Dynamics, Long Beach, CA | Abstract
  • Patrick R Burney and Jim Pfaendtner, "Structural and Dynamic Features of Candida rugosa Lipase1 in Water, Octane, Toluene and Ionic Liquids BMIM-PF6 and BMIM-NO3", The Journal of Physical Chemistry
  • Motley, Michael R., and Ramona B. Barber. "Passive Control of Marine Hydrokinetic Turbine Blades." Composite Structures (2013).
  • Burney PR, White N, Pfaendtner J (2014) Structural Effects of Methionine Oxidation on Isolated Subdomains of Human Fibrin D and αC Regions. PLoS ONE 9(1): e86981. doi:10.1371/journal.pone.0086981
  • Marafi, N. A., Berman, J. W., and Eberhard, M. O. (2015) Ductility-dependent intensity measure that accounts for ground-motion spectral shape and duration. Earthquake Engineering & Structural Dynamics, doi: 10.1002/eqe.2678 <>.
  • Dodd, M. S. & Ferrante, A. "On the interaction of Taylor length scale size droplets and isotropic turbulence." *Journal of Fluid Mechanics*, *806*, 356-412, 2016

  • Adams, D. K., Dodd, M. S. & Ferrante, A. "PSH3D: A Petascale Solver of the Helmholtz Equation in 3D." *27th International Conference on Parallel Computational Fluid Dynamics*, Montreal, Canada, 2015
  • Dodd, M. S. & Ferrante, A. "A fast pressure-correction method for incompressible two-fluid flows." *Journal of Computational Physics*, *273*, 416-434, 2014
  • Baraldi, A., Dodd, M. S. & Ferrante, A. "A mass-conserving volume-of-fluid method: Volume tracking and droplet surface-tension in incompressible isotropic turbulence." *Computers and Fluids*, *96*, 322-337, 2014
  • J Liu, X Xu, MP Anantram  "Role of inelastic electron–phonon scattering in electron transport through ultra-scaled amorphous phase change material nanostructures"  Journal of Computational Electronics, 2014
  • J Liu, MP Anantram, "Low-bias electron transport properties of germanium telluride ultrathin films" Journal of Applied Physics, 2013
  • X Xu, J Liu, MP Anantram "Conduction in alumina with atomic scale copper filaments" Journal of Applied Physics, 2014
  • J Liu, X Xu, L Brush, MP Anantram "A multi-scale analysis of the crystallization of amorphous germanium telluride using ab initio simulations and classical crystallization theory" Journal of Applied Physics, 2014
  • J Liu "Microscopic Origin of Electron Transport Properties and Ultrascalability of Amorphous Phase Change Material Germanium Telluride" IEEE Transactions on Electron Devices 2017


Interdisciplinary Social Sciences (Statistics,  Sociology, Anthropology)

(Center for Studies in Demography and Ecology)

  • Moody J, Adams J, Morris M. Epidemic potential by sexual activity distributions. Network Science. 2017;5(4):461-75. doi: 10.1017/nws.2017.3. PubMed PMID: WOS:000416732200003.
  •  Jenness SM, Goodreau SM, Morris M. EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks. Journal of Statistical Software. 2017;(forthcoming).
  • Armbruster B, Wang L, Morris M. Forward reachable sets: Analytically derived properties of connected components for dynamic networks. Network Science. 2017;5(3):328-54. doi: 10.1017/nws.2017.10. PubMed PMID: WOS:000408564600005.
  •  Jenness SM, Goodreau SM, Morris M, Cassels S. Effectiveness of combination packages for HIV-1 prevention in sub-Saharan Africa depends on partnership network structure: a mathematical modelling study. Sexually Transmitted Infections. 2016;92(8):619-24. doi: 10.1136/sextrans-2015-052476. PubMed PMID: WOS:000388826500015.
  • Hamilton DT, Morris M. The racial disparities in STI in the U.S.: Concurrency, STI prevalence, and heterogeneity in partner selection. Epidemics. 2015;11:56-61. doi:


  • Nuclear Physics from Lattice QCD. Martin J. Savage., arXiv:1110.5943 nucl-th
  • Hyperon-Nucleon Interactions and the Composition of Dense Nuclear Matter from Quantum Chromodynamics. S.R. Beane, E. Chang, S.D. Cohen, W. Detmold, H. -W. Lin, T.C. Luu, K. Orginos, A. Parreno, M.J. Savage, A. Walker-Loud., arXiv:1204.3606 hep-lat
  • High Statistics Analysis using Anisotropic Clover Lattices: (IV) Volume Dependence of Light Hadron Masses. S.R. Beane, E. Chang, W. Detmold, H.W. Lin, T.C. Luu, K. Orginos, A. Parreno, M.J. Savage, A. Torok, A. Walker-Loud.
  • A. Bulgac, Y.-L. Luo, and K.J. Roche, Quantum Shock Waves and Domain Walls in Real-Time Dynamics of a Superfluid Unitary Fermi Gas.
  • A. Bulgac, Y.-L. Luo, P. Magierski, K.J. Roche, and Y. Yu, Real-Time Dynamics of Quantized Vortices in a Unitary Fermi Superfluid, Science, 332, 1288 (2011).
  • Evidence for a Bound H-dibaryon from Lattice QCD. By NPLQCD Collaboration (S.R. Beane et al.). Dec 2010. (Published Apr 22, 2011). 4pp. Published in Phys.Rev.Lett.106:162001,2011.
  • I. Stetcu, A. Bulgac, P. Magierski, and K.J. Roche, Isovector Giant Dipole Resonance from 3D Time-Dependent Density Functional Theory for Superfluid Nuclei.
  • J. de Vries, R. Higa, C.-P. Liu, E. Mereghetti, I. Stetcu, R. G. E.Timmermans, U. van Kolck, Electric Dipole Moments of Light Nuclei From Chiral Effective Field Theory, submitted to Phys. Rev. C, arXiv:1109.3604v1 hep-ph (2011).
  • The I=2 pipi S-wave Scattering Phase Shift from Lattice QCD,Silas R. Beane, Emmanuel Chang, William Detmold, Huey-Wen Lin, Tom C. Luu, Kostas Orginos, Assumpta Parreno, Martin J. Savage,  Aaron Torok, and Andre Walker-Loud., arXiv:1107.5023
  • The Deuteron and Exotic Two-Body Bound States from Lattice QCD, Silas R. Beane, Emmanuel Chang, William Detmold, Huey-Wen Lin, Tom C. Luu, Kostas Orginos, Assumpta Parreno, Martin J. Savage,  Aaron Torok, and Andre Walker-Loud., arXiv:1109.2889
  • Light Nuclei and Hypernuclei from Quantum Chromodynamics in the Limit of SU(3) Flavor Symmetry. S.R. Beane, E. Chang, S.D. Cohen, W. Detmold, H.W. Lin, T.C. Luu, K. Orginos, A. Parreno, M.J. Savage, A. Walker-Loud. Jun 2012. 33 pp. ICCUB-12-309, JLAB-THY-12-1581, NT@UW-12-09, NT-LBNL-12-012, UCB-NPAT-12-011, UNH-12-04 e-Print: arXiv:1206.5219 hep-lat PDF
  • Nucleon-Nucleon Scattering Parameters in the Limit of SU(3) Flavor Symmetry, S.R. Beane, E. Chang, S.D. Cohen, W. Detmold, P. Junnarkar, H.W. Lin, T.C. Luu, K. Orginos, A. Parreno, M.J. Savage, and A. Walker-Loud, Phys. Rev., C88 (2013) 024003, arXiv:1301.5790.
  • Nuclear sigma-terms and Scalar-Isoscalar WIMP-Nucleus Interactions from Lattice QCD, S.R. Beane,S.D. Cohen, W. Detmold, H.W. Lin, and M.J. Savage., Phys. Rev., D89 (2014) 07450., arXiv:1306.6939
  • Magnetic Moments of Light Nuclei from Lattice Quantum Chromodynamics, S.R. Beane, E. Chang, S. Cohen, W. Detmold, H.W. Lin, K. Orginos, A. Parreno, M.J. Savage, and B.C. Tiburzi., Phys. Rev. Lett., 113} (2014) 25, 252001, arXiv:1409.3556.
  • Quarkonium-Nucleus Bound States from Lattice QCD, S.R. Beane, E. Chang, S. D. Cohen, W. Detmold, H.-W. Lin, K. Orginos, A. Parreno, and M. J. Savage., INT-PUB-14-049, arXiv:1410.7069 submitted to PRD
  • Nucleon Helicity and Transversity Parton Distributions from Lattice QCD, Jiunn-Wei Chen, Saul D. Cohen, Xiangdong Ji, Huey-Wen Lin, Jian-Hui Zhang., INT-PUB-16-009, arXiv:1603.06664.