Publications citing W&M HPC resources

2018
  1. Kaufman, D. E., Friedrichs, M. A. M., Hemmings, J. C. P., and Smith Jr., W. O.: Assimilating bio-optical glider data during a phytoplankton bloom in the southern Ross Sea, Biogeosciences, 15, 73-90, https://doi.org/10.5194/bg-15-73-2018, (2018). 
  2. H. Wang, F. Luo, M. Ibrahim, O. Kayiran, A. Jog. Efficient and Fair Multi-programming in GPUs via Effective Bandwidth Management. Proceedings of the 24th IEEE Symposium on
    High-Performance Computer Architecture (HPCA), Vienna, Austriahttp://adwaitjog.github.io/docs/pdf/pbs-hpca18.pdf, Feb 2018.
  3. G. Kadam, D. Zhang, A. Jog. RCoal: Mitigating GPU Timing Attack via Subwarp-based Randomized Coalescing TechniquesProceedings of 24th IEEE Symposium on High-Performance Computer Architecture (HPCA), Vienna, Austria, http://adwaitjog.github.io/docs/pdf/rcoal-hpca18.pdf, Feb 2018.
  4. Du, J., Shen, J., Zhang, Y. J., Ye, F., Liu, Z., Wang, Z., Wang, Y. P., Yu, X., Sisson, M., Wang, H. V. (2018). Tidal response to sea-level rise in different types of estuaries: The importance of length, bathymetry, and geometry. Geophysical Research Letters, 45. https://doi.org/10.1002/2017GL075963
  5. J. Hindes, I. B. Schwartz, and L. B. Shaw. Enhancement of large fluctuations to extinction in adaptive networks. Phys. Rev. E, 97, 012308 (2018).
  6. Santos, B.S., D.M. Kaplan, M.A.M. Friedrichs, S.G. Barco, K.L. Mansfield, J.P. Manning. 2018. Consequences of drift and carcass decomposition for estimating sea turtle mortality hotspots. Ecological Indicators 84:319-336. doi: 10.1016/j.ecolind.2017.08.064
  7. Jasmin C. Green, Faraz Rahman, Matthew A. Saxton and Kurt E. Williamson, Quantifying aquatic viral community change associated with stormwater runoff in a wet retention pond using metagenomic time series data. Aquatic Microbial Ecology, Vol. 81: 19–35, 2018
    https://doi.org/10.3354/ame01856
2017
  1. St-Laurent, P., M.A.M Friedrichs, R.G. Najjar, D.K. Martins, M. Herrmann, S.K. Miller and J. Wilkin. Impacts of atmospheric nitrogen deposition on surface waters of the western North Atlantic mitigated by multiple feedbacks J. Geophys. Res. Oceans, vol. 122, doi:10.1002/2017jc013072, VIMS Contribution No. 3665.
  2. BenYishay, A., Heuser, S., Runfola, D.M., Trichler, R. 2017. Indigenous land rights and deforestation: Evidence from the Brazilian Amazon. Journal of Environmental Economics and Management. https://doi.org/10.1016/j.jeem.2017.07.008
  3. Zhao, J., Runfola, D., Kemper, P., 2017. Quantifying Heterogeneous Causal Treatment Effects in World Bank Development Finance Projects. Data Mining and Knowledge Discovery (ECML PKDD). http://ecmlpkdd2017.ijs.si/papers/paperID507.pdf
  4. Zhao, J., Runfola, D., Kemper, P. 2017. Simulation Study in Quantifying Heterogeneous Causal Effects. WSC Proceedings. Available online at:                                                http://informs-sim.org/wsc17papers/.
  5. Runfola, D., BenYishay,  A., Tanner, J., Buchanan, G., Nagol, J.,  Leu, M., Goodman, M.,Trichler, R., and Marty, R. 2017. A Top-Down Approach to Estimating Spatially Heterogeneous Impacts of Development Aid on Vegetative Carbon Sequestration. Sustainability 9(3), 409. doi:10.3390/su9030409. http://www.mdpi.com/2071-1050/9/3/409
  6. Tan, J.A., Garakyaraghi, S., Tagami, K.A., Frano, K.A., Crockett, H.M., Ogata, A.F., Patterson, J.D. and Wustholz, K.L. Contributions from Excited-State Proton and Electron Transfer to the Blinking and Photobleaching Dynamics of Alizarin and Purpurin. J. Phys. Chem. C. 2017, 121 (1), 97 - 106. Article ASAP DOI: 10.1021/acs.jpcc.6b09818
  7. Richter, A.W., Throckmorton, N.A. A New Way to Quantify the Effect of Uncertainty. Federal Reserve Bank of Dallas Working Paper 1705. May 2017.
  8. Moriarty, J. M., Harris, C. K., Rabouille, C., Fennel, K., Friedrichs, M.A.M, and Xu, K. (2017). The Roles of Resuspension, Diffusion and Biogeochemical Processes on Oxygen Dynamics Offshore of the Rhone River, France: A Numerical Modeling Study. Biogeosciences, 14, p. 1919-1946.
  9. Kaufman, D. E., M. A. M. Friedrichs, W. O. Smith Jr., E. E. Hofmann, M. S. Dinniman, and J. C. P. Hemmings (2017), Climate change impacts on southern Ross Sea phytoplankton composition, productivity, and export. J. Geophys. Res. Oceans, 122, 2339–2359, doi:10.1002/2016JC012514.
  10. Kaufman, D.E. (2017). Using high-resolution glider data and biogeochemical modeling to investigate phytoplankton variability in the Ross Sea. Doctoral thesis. Virginia Institute of Marine Science, College of William and Mary.
  11. M. Motta and S. Zhang, Computation of Ground-State Properties in Molecular Systems: Back-Propagation with Auxiliary-Field Quantum Monte Carlo. J. Chem. Theory Comput., 2017, 13 (11), pp 5367–5378. doi: 10.1021/acs.jctc.7b00730.
  12. Mario Motta, David M. Ceperley, Garnet Kin-Lic Chan, John A. Gomez, Emanuel Gull, Sheng Guo, Carlos A. Jiménez-Hoyos, Tran Nguyen Lan, Jia Li, Fengjie Ma, Andrew J. Millis, Nikolay V. Prokof’ev, Ushnish Ray, Gustavo E. Scuseria, Sandro Sorella, Edwin M. Stoudenmire, Qiming Sun, Igor S. Tupitsyn, Steven R. White, Dominika Zgid, and Shiwei Zhang (Simons Collaboration on the Many-Electron Problem).  Towards the Solution of the Many-Electron Problem in Real Materials: Equation of State of the Hydrogen Chain with State-of-the-Art Many-Body Methods. Phys. Rev. X 7, 031059 (2017).
  13. Peter Rosenberg, Hao Shi, and Shiwei Zhang, Ultracold Atoms in a Square Lattice with Spin-Orbit Coupling: Charge Order, Superfluidity, and Topological Signatures. Phys. Rev. Lett. 119, 265301 (2017).
  14. Ettore Vitai, Hao Shi, Mingpu Qin, and Shiwei Zhang. Response Functions for the Two-Dimensional Ultracold Fermi Gas: Dynamical BCS Theory and Beyond.  J Low Temp Phys (2017) 189: 312. https://doi.org/10.1007/s10909-017-1805-z

  15. T. J. Huffman, C. Hendriks, E. J. Walter, Joonseok Yoon, Honglyoul Ju, R. Smith, G. L. Carr, H. Krakauer, and M. M. Qazilbash. Insulating phases of vanadium dioxide are Mott-Hubbard insulators. Phys. Rev. B 95, 075125 (2017).
  16. Fengjie Ma, Shiwei Zhang, and Henry Krakauer. Auxiliary-field quantum Monte Carlo calculations with multiple-projector pseudopotentials. Phys. Rev. B 95, 165103 (2017).
  17. Priest, G.R., Witter, R.C., Zhang, Y., Goldfinger, C., and Wang, K. (2017) New constraints on coseismic slip during southern Cascadia subduction zone earthquakes over the past 4600 years implied by tsunami deposits and marine turbidites, Natural Hazards. DOI: 10.1007/s11069-017-2864-9
  18. Yu, H-S., Zhang, Y., Yu, J.C.S., Terng, C., Sun, W., Ye, F., Wang, H.V., Wang, Z., and Huang, H. (2017) Simulating multi-scale oceanic processes around Taiwan on unstructured grids, Ocean Modelling, 112, 72-93. http://dx.doi.org/10.1016/j.ocemod.2017.09.007
  19. Peter Rosenberg, Hao Shi, Shiwei Zhang, Accurate computations of Rashba spin-orbit coupling in interacting systems: From the Fermi gas to real materials, Journal of Physics and Chemistry of Solidsin press, https://doi.org/10.1016/j.jpcs.2017.12.026
  20. Irby, I.D., M.A.M. Friedrichs, F. Da and K. Hinson, 2017. The competing impacts of climate change and nutrient reductions on dissolved oxygen in Chesapeake Bay. Biogeosciences Discussions, in review. doi: 10.5194/bg-2017-416.
  21. ​​Luettich, R.A., L.D. Wright, C.R. Nichols, R. Baltes, M.A.M. Friedrichs, A. Kurapov, A.J. van der Westhuysen, K. Fennel and E. Howlett, 2017. A U.S Integrated Ocean Observing System Coastal and Ocean Modeling Testbed to improve understanding and operational forecasts of extreme events and chronic environmental conditions, https://doi.org/10.1029/2017EO078243
  22. Moriarty, Julia M. (2017). The Role of Seabed Resuspension on Oxygen and Nutrient Dynamics in Coastal Systems: A Numerical Modeling Study. Ph.D. Dissertation submitted to the Virginia Institute of Marine Science, the College of William & Mary.
  23. Mingpu Qin, Hao Shi, and Shiwei Zhang, Numerical results on the short-range spin correlation functions in the ground state of the two-dimensional Hubbard model. Phys Rev B 96, 075156 (2017) https://doi.org/10.1103/PhysRevB.96.075156
  24. Ettore Vitali, Hao Shi, Mingpu Qin, and Shiwei Zhang, Visualizing the BEC-BCS crossover in a two-dimensional Fermi gas: Pairing gaps and dynamical response functions from ab initio computations. Phys Rev A 96, 061601(R) (2017). https://doi.org/10.1103/PhysRevA.96.061601
  25. Bo-Xiao Zheng, Chia-Min Chung, Philippe Corboz, Georg Ehlers, Ming-Pu Qin, Reinhard M. Noack, Hao Shi, Steven R. White, Shiwei Zhang, Garnet Kin-Lic Chan, Stripe order in the underdoped region of the two-dimensional Hubbard model. Science,  Vol. 358, Issue 6367, pp. 1155-1160 (2017). https://doi.org/10.1126/science.aam7127
  26. Santos, B.S. 2017. Integrating Empirical Data and Ocean Drift Models to Better Understand Sea Turtle Strandings in Virginia. Master's thesis. Virginia Institute of Marine Science, College of William and Mary.
2016

  1. Zhang, Y., Ye, F., Stanev, E.V., Grashorn, S. (2016). Seamless cross-scale modeling with SCHISM, Ocean Modelling, 102, 64-81. doi:10.1016/j.ocemod.2016.05.002
  2. Zhang, Y., Priest, G.R., Allan, J., Stimely, L. (in press) Benchmarking an unstructured-grid model for tsunami current modeling, Pure and Applied Geophysics.
  3. Zhang, Y., Stanev, E.V. and S. Grashorn (2016) Unstructured-grid model for the North Sea and Baltic Sea: validation against observations, Ocean Modelling, 97, 91-108.
  4. Najjar, R., P. Sedwick, M. Mulholland, M.A.M. Friedrichs, A. Thompson, D. Martins, P. Bernhardi, M. Herrmann, L. Price, B. Sohst, C. Sookhdeo, P. St-Laurent, B. Widner. Deposition of atmospheric nitrogen to coastal ecosystems (DANCE): A study in seasonally oligotrophic waters off the eastern U.S. AGU-ASLO-TOS Ocean Sciences Meeting, New Orleans LA, February 2016.
  5. M. A. Mohr, Quantitative Analysis of Periodic Breathing and Very Long Apnea in Preterm Infants, dissertation, 2015.
  6. Karen Fairchild, Mary Mohr, Alix Paget-Brown, Christa Tabacaru, Douglas Lake, John Delos, Joseph Randall Moorman, John Kattwinkel. Clinical associations of immature breathing in preterm infants: part 1-central apnea. Pediatric Research 80, 21-27 (9th March 2016) doi:10.1038/pr.2016.43
  7. Manisha Patel, Mary Mohr, Douglas Lake, John Delos, J. Randall Moorman, Robert A. Sinkin, John Kattwinkel, Karen Fairchild. Clinical associations with immature breathing in preterm infants: part 2-periodic breathing. Pediatric Research 80, 28-34 (22nd March 2016) doi:10.1038/pr.2016.58
  8. Plante, M.; Richter, A.W.; Throckmorton, N.A. The Zero Lower Bound and Endogenous Uncertainty. Economic Journal, forthcoming. Author's version.
  9. Tan, J.A., Rose, J.T., Cassidy, J.P., Rohatgi, S.K. and Wustholz, K.L. Dispersive Electron-Transfer Kinetics of Rhodamines on TiO2: Impact of Structure and Driving Force on Single-Molecule Photophysics. J. Phys. Chem. C. 2016, 120 (37), 20710 - 20720.
  10. Ye, F., Zhang, Y., Friedrichs, M., Wang, H.V., Irby, I., Shen, J., and Z. Wang (2016) A 3D, cross-scale, baroclinic model with implicit vertical transport for the Upper Chesapeake Bay and its tributaries, Ocean Modelling, vol. 107, 82-96. 10.1016/j.ocemod.2016.10.004.
  11. Mingpu Qin, Hao Shi, and Shiwei Zhang, Coupling quantum Monte Carlo and independent-particle calculations: Self-consistent constraint for the sign problem based on the density or the density matrix. Phys Rev B 94, 235119 (2016) https://doi.org/10.1103/PhysRevB.94.235119
  12. E. Vitali, H. Shi, M. Qin, and S. Zhang, Computation of dynamical correlation functions for many-fermion systems with auxiliary-field quantum Monte Carlo. Phys Rev B 94, 085140 (2016) https://doi.org/10.1103/PhysRevB.94.085140
  13. Mingpu Qin, Hao Shi, and Shiwei Zhang, Benchmark study of the two-dimensional Hubbard model with auxiliary-field quantum Monte Carlo method. Phys Rev B 94, 085103 (2016) https://doi.org/10.1103/PhysRevB.94.085103
2015
  1. Purwanto, W.; Zhang, S.; Krakauer, H. An Auxiliary-Field Quantum Monte Carlo Study of the Chromium Dimer. J. Chem. Phys. 2015, 142 (6), 064302.
  2. M. Komelj and H. Krakauer. Electron-phonon coupling and exchange-correlation effects in superconducting H3S under high pressure. Phys. Rev. B. 92 (20), 205125 (2015). DOI:10.1103/PhysRevB.92.205125, November 2015.
  3. Moriarty, J.M., Harris, C.K., and Hadfield, M. G. (2015).  Event-to-seasonal sediment dispersal on the Waipaoa River Shelf, New Zealand: A numerical modeling studyContinental Shelf Research, 10:108-123. DOI:10.1016/j.csr.2015.10.005.
  4. Saporito, Salvatore and David Van Riper. Do Irregularly Shaped School Attendance Zones Contribute to Racial Segregation or Integration? Social Currents, doi:10.1177/2329496515604637, September 2015.
  5. F. Ma, W. Purwanto, S. Zhang, and H. Krakauer. Quantum Monte Carlo Calculations in Solids with Downfolded Hamiltonians. Phys. Rev. Lett. 2015, 114 (22), 226401, doi:10.1103/PhysRevLett.114.226401, June 2015.
  6. G. Casale, V. De Nitto-Persone, and E. Smirni. QRF: an Optimization-Based Framework for Evaluating Complex Stochastic Networks. ACM TOMACS. Author's version.
  7. P. Rosenberg, S. Chiesa and S. Zhang. FFLO order in ultra-cold atoms in three-dimensional optical lattices. J. Phys.: Condens. Matter 27 225601, doi:10.1088/0953-8984/27/22/225601, June 2015.
  8. J. P. F. LeBlanc, Andrey E. Antipov, Federico Becca, Ireneusz W. Bulik, Garnet Kin-Lic Chan, Chia-Min Chung,Youjin Deng, Michel Ferrero, Thomas M. Henderson, Carlos A. Jiménez-Hoyos, E. Kozik, Xuan-Wen Liu, Andrew J. Millis, N. V. Prokof’ev, Mingpu Qin, Gustavo E. Scuseria, Hao Shi, B. V. Svistunov, Luca F. Tocchio, I. S. Tupitsyn, Steven R. White, Shiwei Zhang, Bo-Xiao Zheng, Zhenyue Zhu, and Emanuel Gull (Simons Collaboration on the Many-Electron Problem). Solutions of the Two-Dimensional Hubbard Model: Benchmarks and Results from a Wide Range of Numerical Algorithms. Physical Review X 5, 041041 (2015).  https://doi.org/10.1103/PhysRevX.5.041041