Research:Publications and Reports

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Following is a list of publications that were produced using ARCC resources, as reported by the project's Principal Investigator.

Publications produced using ARCC resources

Project: EvolvingAI

  • Clune J, Mouret J-B, Lipson H (2013) The evolutionary origins of modularity. Proceedings of the Royal Society B. 280: 20122863.
  • Huizinga J, Mouret J-B, Clune J (2014) Evolving neural networks that are both modular and regular: HyperNEAT plus the Connection Cost Technique. Proceedings of the Genetic and Evolutionary Computation Conference.
  • Nguyen A, Yosinski J, Bengio Y, Dosovitskiy A, Clune J (2016) Plug & Play Generative Networks: Conditional Iterative Generation of Images in Latent Space. arXiv 1612.00005.
  • Stanton C, Clune J (2016) Curiosity Search: Producing generalists by encouraging individuals to continually explore and acquire skills throughout their lifetime. PLoS ONE 11(9): e0162235.
  • Nguyen A, Yosinski J, Clune J (2016) Understanding Innovation Engines: Automated creativity and improved stochastic optimization via Deep Learning. Evolutionary Computation.
  • Nguyen A, Dosovitskiy A, Yosinski J, Brox T, Clune J (2016) Synthesizing the preferred inputs for neurons in neural networks via deep generator networks. Advances in Neural Information Processing Systems (NIPS)
  • Norouzzadeh M, Clune J (2016) Neuromodulation improves the evolution of forward models. Proceedings of the Genetic and Evolutionary Computation Conference. Roby Velez, Jeff Clune (2016) Identifying core functional networks and functional modules within artificial neural networks via subsets regression. Proceedings of the Genetic and Evolutionary Computation Conference.
  • Mengistu H, Lehman J, Clune J (2016) Evolvability Search: Directly selecting for evolvability in order to study and produce it. Proceedings of the Genetic and Evolutionary Computation Conference.
  • Huizinga J, Mouret JB, Clune J (2016) Does aligning phenotypic and genotypic modularity improve the evolution of neural networks? Proceedings of the Genetic and Evolutionary Computation Conference.
  • Nguyen A, Yosinski J, Clune J (2016) Multifaceted Feature Visualization: Uncovering the different types of features learned by each neuron in deep neural networks. Visualization for Deep Learning workshop. International Conference on Machine Learning.
  • Mengistu H, Huizinga J, Mouret JB, Clune J (2016) The evolutionary origins of hierarchy.

Project: stochasticaquiferinv

  • Dongdong Wang§, Ye Zhang, Subsurface Data Integration and Stochastic Inversion Assessing Aquifer Parameter and Boundary Condition Uncertainty, Journal of Hydrology, in revision
  • Jianying Jiao§, Ye Zhang, Julian Zhu, Direct Hydraulic Characterization for diverse soil types under Infiltration and Evaporation, Transport in Porous Media, accepted for publication.
  • Jianying Jiao§, Ye Zhang (2016) Direct Method of Hydraulic Conductivity Structure Identification for Subsurface Transport Modeling, Journal of Hydrologic Engineering , 10.1061/(ASCE)HE.1943-5584.0001410, 04016033.

Project: geologiccarbonseq

  • Minh Nguyen§, Ye Zhang, Jun Li, Xiaochun Li, Bing Bai, Haiqing Wu, Ning Wei, Philip Stauffer (2017) A Geostatistical Study in Support of CO2 Storage in Deep Saline Aquifers of the Shenhua CCS Project, Energy Procedia.

In Review:

  • Mingkan Zhang§, Ye Zhang, Peter Lichtner, Effect of Multiscale Permeability Heterogeneity on Developing Convective Mixing in Geological Carbon Sequestration, International Journal of Greenhouse Gas Control.
  • Minh C. Nguyen1*, Ye Zhang1, Philip H. Stauffer2 (2017) Object-based Modeling and Sensitivity Analysis in Support of CO2 Storage in Deep Saline Aquifers at the Shenhua site, Ordos basin, China , IJGHGC.

Project: elecdisp

  • Robert Godby, Tara Righetti, Kipp Coddington, Dalia Patino-Echeverri and Temple Stoellinger, “The role of energy models: characterizing the uncertainty of the future electricity system to design more efficient and effective laws and regulations,”, George Washington Journal of Energy & Environmental Law, in press.
  • Robert Godby and Roger Coupal, “The Potential Impact of Rate-based or Mass-based Rules on Coal-Producing States under the Clean Power Plan,” with Roger Coupal, Electricity Journal, Vol. 29:6, July 2016.
  • Robert Godby and Roger Coupal, “A Comparison of Clean Power Plan Forecasts for Wyoming: the Importance of Implementation and Modeling Assumptions,” with Roger Coupal, Electricity Journal, Vol. 29:1, February 2016, pp. 53-62.
  • Greg Torell, “Essays on Electricity Modeling, Transmission Congestion and Carbon Policy,” Ph.D. Dissertation, Department of Economics and Finance, University of Wyoming, July, 2016.
  • Robert Godby, Roger Coupal and David Taylor, “An Assessment of Wyoming's Competitiveness to attract new Wind Development, and the Potential impacts such development may bring the State", prepared for the Wyoming Business Council and Carbon County Economic Development Corp (Wyoming), September 2016.

Project: qdots

  • Choi, J. K., Tohgha, U., Pap, L., Elliott, K, W., Leonard, B. M., Kubelka, J., Dzyuba, S. V., Varga, K., and Balaz, M. (2016) “Ligand-induced inversion of chirality in CdSe and CdS quantum dots without changing the stereochemistry of the capping ligand.” ACS Nano 10, 3809-3815

Project: twpm

  • Wood, Aaron D., Charles F. Mason, and David Finnoff, “OPEC, the Seven Sisters, and Oil Market Dominance: An Evolutionary Game Theory and Agent-Based Modeling Approach,” Journal of Economic Behavior and Organization, 2016 v. 132 (Part B), pp. 66-78

Project: HOD

  • S. Eftekharzadeh, A. D. Myers, J. F. Hennawi, S. G. Djorgovski, G. T. Richards, A. A. Mahabal, M. J. Graham (2017) "Clustering on very small scales from a large sample of confirmed quasar pairs: Does quasar clustering track from Mpc to kpc scales?"

Project: Chemcal

  • Bradley M Schmidt, Jeramie J. Adams, Suman Debnath, Navamoney Arulsamy, and Dean M Roddick: "Catalytic Ethylene dimerization by (PP)PtMe(C2H4)+ Complexes: Phosphine Steric and Electronic Effects"

Project: simturtle

  • Poster presentation at PICES 2016 (North Pacific Marine Science Organization), November 2-13, San Diego, USA “Project Sim Turtle: novel approaches for understanding biophysical interactions in the mesoscale”, by Cheryl S. Harrison, Nathan Putman, Jessica Y. Luo, Qingfeng Li, Mathew Long

Project: preamble

In Review:

  • Juliano, T. W., T. R. Parish, D. A. Rahn, and D. Leon, 2017: An Atmospheric Hydraulic Jump in the Santa Barbara Channel, J. Applied Meteor. Clim.

Project: pecan

  • Parish, T. R., R. D. Clark, 2017: On the Initiation of the 20 June 2015 Great Plains Low-Level Jet. J. Applied Meteor. Clim., (conditionally accepted).

Project: wcl

  • Rebecca Pauly - M.S. Department of Atmospheric Science, December 2015. Thesis title: An Evaluation of PBL Parameterizations Utilizing Compact Airborne Raman Lidar Data

Project: Coalgasif

  • J. Cai, S. Roy, M.F. Modest, A comparison of specularly reflective boundary conditions and rotationally invariant formulations for Discrete Ordinate Methods in axisymmetric geometries, J. Quant. Spectrosc. Radiat. Transfer., 182, 75-86, 2016

Project: qco

  • Moorhouse, Williford, Double Covers of Symplectic Dual Polar Space Graphs, Discrete Mathematics 339 (2016) p. 571-588. Moorhouse, Sun, Williford, The Eigenvalues of the graphs D(4,q). accepted to Journal of Combinatorial Theory, Series B.

Project: rd-hea

  • Gaurav Arora and Dilpuneet S. Aidhy, (2017) "Segregation and binding energetics at grain boundaries in fluorite oxides"

Project: turbulencemodeling

  • Mokhtarpoor R., Heinz S. and Stoellinger M. (2016), “Dynamic Unified RANS-LES Simulations of High Reynolds Number Separated Flows”, Phys. Fluids 28, 095101/1-36. Roy R., and Stoellinger M. (2017), “Large Eddy Simulation of Wind Flow Over Complex Terrain: The Bolund Hill Case”, AIAA Aviation 2017, Grapevine, TX, AIAA Paper 17-1160.
  • Han Y., and Stoellinger M. (2017), “Large eddy simulation of atmospheric boundary layer flows over complex terrain with varying stability conditions”, AIAA Aviation 2017, Grapevine, TX, AIAA Paper 17-1161.
  • Mokhtarpoor R., Heinz S., Stoellinger M., and Balakumar P. (2017), “Dynamic Large Eddy Simulation: Analysis of Stability and Realizability”, AIAA Aviation 2017, Grapevine, TX, AIAA Paper 17-0992.
  • Mokhtarpoor R., Heinz S., and Stoellinger M. (2017), “LES and Hybrid RANS-LES of High Reynolds Number Separated Flows”, AIAA Aviation 2017, Grapevine, TX, AIAA Paper 17-0994.
  • Han Y., Stoellinger M., and Naughton J. (2016), “Large eddy simulation for atmospheric boundary layer flow over flat and complex terrains”, J. Phys.: Conf. Ser. 753 03204.
  • Ashton N. and Stoellinger M. (2016), "Computation of Turbulent Flow in a Rotating Pipe using the Elliptic Blending Reynolds Stress Model", 46th AIAA Fluid Dynamics Conference, AIAA AVIATION Forum, (AIAA 2016-3943).

Project: inbrev

  • Chhatre, VE and Emerson KJE (2017) StrAuto: Automation and Parallelization of STRUCTURE Analysis.

Project: f3dt

  • Subsurface fault geometries in Southern California illuminated through Full-3D Seismic Waveform Tomography (F3DT), En-Jui Lee and Po Chen, Tectonophysics, DOI: 10.1016/j.tecto.2017.03.005, 2017.
  • Improved Basin Structures in Southern California Obtained Through Full-3D Seismic Waveform Tomography (F3DT), En-Jui Lee and Po Chen, Seismological Research Letters, Volume 87, Number 4, July/August, 2016.
  • Reducing Disk Storage of Full-3D Seismic Waveform Tomography (F3DT) Through Lossy Online Compression, Peter Lindstrom, Po Chen, En-Jui Lee, Computers and Geosciences (2016), pp. 45-54.
  • pSIN: a scalable, Parallel algorithm for Seismic INterferometry of large-N ambientnoise data, Po Chen, Nicholas J. Taylor, Ken G. Dueker, Ian S. Keifer, Andra K. Wilson, Casey L. McGuffy, Christopher G. Novitsky, Alec J. Spears, W. Steven Holbrook, Computers and Geosciences (2016), pp. 88-95.

Project: rotarywingcfd

  • (InPreparation)MichaelJ.Brazell, AndrewC.Kirby, DimitriJMavriplis. ”Ahigh-orderdiscontinuousGalerkin octree-based AMR solver for overset simulations,” 2017 AIAA Aviation Forum, Denver, CO., June 2017.
  • (In Preparation) Andrew C. Kirby, Michael J. Brazell, Rajib Roy, Behzad Ahrabi, Dimitri J Mavriplis, Michael Stoellinger, Jay Sitaraman. ”Wind Farm Simulations Using an Overset hp-Adaptive Approach with Blade-Resolved Turbine Models,” 2017 AIAA Aviation Forum, Denver, CO., June 2017.
  • Donya Ramezanian and Dimitri J. Mavriplis. ”An Order N log 2(N) Parallel Solver for Time Spectral Problems”, 55th AIAA Aerospace Sciences Meeting, AIAA SciTech Forum, (AIAA 2017-1219).
  • Dimitri J. Mavriplis, Enrico Fabiano, and Evan Anderson. ”Recent Advances in High-Fidelity Multidisciplinary Adjoint-Based Optimization with the NSU3D Flow Solver Framework”, 55th AIAA Aerospace Sciences Meeting, AIAA SciTech Forum, (AIAA 2017-1669).
  • Behzad Reza Ahrabi and Dimitri J. Mavriplis. ”Scalable Solution Strategies for Stabilized FiniteElementFlowSolversonUnstructuredMeshes”, 55thAIAAAerospaceSciencesMeeting, AIAASciTech Forum, (AIAA 2017-0517).
  • Shervin Sammak, Arash G. Nouri, Michael J. Brazell, Dimitri J. Mavriplis, and Peyman Givi. ”Discontinuous Galerkin-Monte Carlo Solver for Large Eddy Simulation of Compressible Turbulent Flows”, 55th AIAA Aerospace Sciences Meeting, AIAA SciTech Forum, (AIAA 2017-0982).
  • Dimitri Mavriplis, Evan Anderson, Ray S. Fertig, and Mark Garnich. ”Development of a High-Fidelity Time-Dependent Aero-Structural Capability for Analysis and Design”, 57th AIAA/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials Conference, AIAA SciTech Forum, (AIAA 2016-1175).
  • Enrico Fabiano and Dimitri J. Mavriplis. ”Adjoint-Based Aerodynamic Design On Unstructured Meshes”, 54th AIAA Aerospace Sciences Meeting, AIAA SciTech Forum, (AIAA 2016-1295).
  • Michael J. Brazell, Jay Sitaraman, Dimitri J. Mavriplis. An overset mesh approach for 3D mixed element high order discretizations. Journal of Computational Physics. Vol. 322, 33-51, 2016, Elsevier.
  • Asitav Mishra, Dimitri Mavriplis, and Jay Sitaraman. Time-Dependent Aeroelastic AdjointBased Aerodynamic Shape Optimization of Helicopter Rotors in Forward Flight. AIAA Journal, December 2016, Vol. 54, No. 12 : pp. 3813-3827.
  • Michael J. Brazell, Andrew Kirby, Jayanarayanan Sitaraman, and Dimitri J. Mavriplis. ”A Multi-Solver Overset Mesh Approach for 3D Mixed Element Variable Order Discretizations”, 54th AIAA Aerospace Sciences Meeting, AIAA SciTech Forum, (AIAA 2016-2053).
  • Andrew C. Kirby, Michael J. Brazell, Jay Sitaraman, Dimitri J. Mavriplis. ”An Overset Adaptive High-Order Approach for Blade-Resolved Wind Energy Applications,” Paper presented at AHS Forum 72, West Palm Beach FL, May 2016.
  • Enrico Fabiano and Dimitri J. Mavriplis. ”Adjoint-based Aeroacoustic Design-Optimization of Flexible Rotors in Forward Flight,” Paper presented at AHS Forum 72, West Palm Beach FL, May 2016. Alfred Gessow Forum Best Paper Award

Project: euo

  • Vitaly Proshchenko and Yuri Dahnovsky, Weak d 0 ferromagnetism: Zn vacancy condensation in ZnS nanocrystals, J. Phys.: Condens. Matter 29, 025803 (20017).
  • Andrew J. Yost, Artem Pimachev, Chun-Chih Ho, Seth B. Darling, Leeyih Wang, Wei-Fang Su, Yuri Dahnovsky, and TeYu Chien, Coexistence of Two Electronic Nano-Phases on a CH3NH3PbI3−xClx Surface Observed in STM Measurements, ACS Appl. Mater. Interfaces, 2016, 8 (42), pp 29110–29116.
  • A. Pimachev, U. Poudyal, V. Proshchenko, W. Wang and Yu. Dahnovsky, Large enhancement in photocurrent by Mn doping in CdSe/ZTO quantum dot sensitized solar cells, Phys. Chem. Chem. Phys., 18, 26771-26776, (2016) DOI: 10.1039/c6cp04263e.
  • G. Rimal, A. K. Pimachev, A. J. Yost, U. Poudyal, S. Maloney, W. Wang, TeYu Chien, Yu. Dahnovsky, and J. Tang, Giant photocurrent enhancement by transition metal doping in quantum dot sensitized solar cells, Appl. Phys. Lett. 119, 103901 (2016).
  • F. V. Kusmartsev, V. D. Krevchik, M. B. Semenov, D. O. Filatov, A. M. Shorokhov, A. A. Bukharev, Yu. I. Dahnonovsky, A. V. Nikolaev, N. A. Pyataev, R. B. Zaitsev, P. V. Krevcjk, I. A Egorov, K. Yamamoto, A. K. Aringazin, Phonon assisted resonant tunneling and its phonon control. JETP Lett. 104 (6), 392-397 (2016) (Russ. JETP Lett., 104, 406-412 (2016)).
  • Vitaly Proshchenko, Anri Karanovich, and Yuri Dahnovsky, Surface-Bulk Model for d0 Ferromagnetism in ZnS Quantum Dots, J. Phys. Chem. C, 120, 11253-11261 (2016).
  • Vitaly Proshchenko , Sabit Horoz , Jinke Tang , and Yuri Dahnovsky, Room temperature d0 ferromagnetism in ZnS nanocrystals, Journal of Applied Physics 119 , 223901 (2016)

Project: solvatedaminoacids

  • Chi, H., Welch, W. R. W., Kubelka, J. and Keiderling, T. A. (2013) "Insight into the packing pattern of 2 fibrils. A model study of glutamic acid rich oligomers with 13C isotopic edited vibrational spectroscopy." Biomacromolecules, 14, 3880-3891.
  • Welch, W. R. W., Keiderling, T. A. and Kubelka, J. (2013) "Structural analyses of experimental 13C edited amide I' IR and VCD for peptide -sheet aggregates and fibrils using DFT-based spectral simulations." J. Phys. Chem. B., 117, 10359-10369.
  • Welch, W. R. W., Kubelka, J. and Keiderling, T. A. (2013) "Infrared, VCD and Raman spectral simulations for -sheet structures with various isotopic labels, inter-strand and stacking arrangements using Density Functional Theory." J. Phys. Chem. B., 117, 10343-10358.
  • Welch, W. R. W. and Kubelka, J. (2012) “DFT-Based Simulations of Amide I ' IR Spectra of a small protein in solution using empirical electrostatic map with a continuum solvent model.” J. Phys. Chem. B 116, 10739-10747

Project: brqtl

  • Brock MT, Lucas LK, Anderson NA, Rubin MJ, Markelz RJC, Covington MF et al (2016). Genetic architecture, biochemical underpinnings and ecological impact of floral UV patterning. Molecular Ecology 25(5): 1122-1140.
  • Yarkhunova Y, Edwards CE, Ewers BE, Baker RL, Aston TL, McClung CR et al (2016). Selection during crop diversification involves correlated evolution of the circadian clock and ecophysiological traits in Brassica rapa. New Phytologist 210(1): 133-144.

In Review:

  • Baker, RL, WF Leong, MT Brock, M Rubin, N An, S Welch, and C Weinig. In revision. Leveraging Bayesian inference and high-throughput remote sensing indices for quantitative genetic analyses of Function-Valued Traits. Theoretical and Applied Genetics.
  • Brock MT, RL Winkelman, MJ Rubin, CE Edwards, BE Ewers, and C Weinig. Accepted pending revisions. Floral allocation currencies are affected by distinct environmental stresses, show whorl × environment interactions, and exhibit whorl-specific QTL. Heredity.
  • Rubin M, MT Brock, A Davis, Z German, M Knapp, S Welch, S Harmer, J Maloof, S Davis, and C Weinig. In revision. Circadian rhythms vary over the growing season and correlate with fitness components. Molecular Ecology.

In Prep:

  • Baker, RL, WF Leong, N An, S Welch, and C Weinig. In prep. Predicting developmental phenotypes based on genotypes: A Bayesian function-valued trait approach to phenotypic plasticity in Brassica rapa leaves. For Genetics.
  • Hubbard C, MT Brock, L van Diepen, L Maignien, and C weinig. In prep. The circadian clock influences rhizosphere community structure and function. For ISME Journal.

Project: Inversion

  • Pafeng, J., S. Mallick, and H. Sharma, 2017, Prestack waveform inversion of three-dimensional seismic data—an example from the Rock Springs Uplift, Wyoming, USA, Geophysics, 82, B1-B12, doi: 10.1190/Geo2016-0079.1.
  • Mallick, S., D. Mukherjee, L. Shafer, and E. Campbell-Stone, 2017, Azimuthal anisotropy analysis of P-wave seismic data and estimation of the orientation of the in situ stress fields – an example from the Rock-Springs uplift, Wyoming, USA: Geophysics, 82, no. 2, B63-B77.
  • Sharma, H., S. Mallick, S. Verma, and E. Campbell, 2017, Azimuthal anisotropy analysis of multiazimuth P-wave seismic data—an example from the Rock-Springs uplift, Wyoming, USA, First draft prepared for submission to Geophysics.

In Review:

  • Sharma, H., S. Mallick, S. Verma, and E. Campbell, 2017, Azimuthal anisotropy analysis to estimate the in-situ stress orientation and the relative fracture density- a real data example, SEG Technical Program Expanded Abstracts.
  • Ayani, M., S. Mallick, J. Hunziker, and L. MacGragor, 2017, Inversion of frequency domain marine controlled-source electromagnetic data using genetic algorithm, SEG Technical Program Expanded Abstracts.
  • Jia, L., and S. Mallick, 2017, Finite Element Reverse Time Prestack Depth Migration – Concerns and Discussions, SEG Technical Program Expanded Abstracts.
  • Jia, L. and S. Mallick, 2017, A new imaging condition for the reverse time prestack depth migration, SEG Technical Program Expanded Abstracts.
  • Jia, L., S. Mallick, W. S. Holbrook, and W. Fortin, 2017, Joint prestack waveform inversion and acoustic reverse time migration, SEG Technical Program Expanded Abstracts.

Project: lessf

  • Reza Mokhtarpoor, Stefan Heinz and Michael Stoellinger,“Dynamic unified RANS-LES simulations of high Reynolds number separated flows”, Phys.Fluids 28, 095101, 2016.
  • R. Mokhtarpoor, S. Heinz and M. K. Stoellinger, Dynamic Unified RANS-LES Simulations of Periodic Hill Flow at High Reynolds Number. TSFP-10, Chicago, IL, USA, TSFP Paper 2017-xx-x, 1-6.
  • R. Mokhtarpoor, S. Heinz and M. K. Stoellinger, Realizability and Stability Analysis of Dynamic LES. TSFP-10, Chicago, IL, USA, TSFP Paper 2017-P-xx, 1-6.
  • R. Mokhtarpoor, S. Heinz, M. Stoellinger and P. Balakumar, “Dynamic Large Eddy Simulation: Analysis of Stability and Realizability”. AIAA SciTech 2017, Grapevine, TX, AIAA Paper 17-0992.
  • R. Mokhtarpoor, S. Heinz and M. Stoellinger, “LES and Hybrid RANS-LES of High Reynolds Number Separated Flows”. AIAA SciTech 2017, Grapevine, TX, AIAA Paper 17-0994.