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PDF File of the 2019 Blue Waters Annual ReportPDF


Title:Blue Waters 2019 Annual Report
Author(s):Blue Waters Project
Contributor(s):Watkins, Catherine; Duensing, Steve; Janeski, Megan; Kramer, William
Subject(s):Blue Waters
High Performance Computing
Abstract:2019 annual report for the Blue Waters Project
Issue Date:2019
Genre:Report (Grant or Annual)
Table of Contents:

14. Dinshaw S. Balsara, Simulating Two-Fluid MHD Turbulence and Dynamos in Star-Forming Molecular Clouds and a New Paradigm for Computational Astrophysics for Spherical Systems 16. Adam Burrows, The Computational Keys to the Supernova Puzzle: How Multiple 3D Radiation/Hydrodynamic Models Can Unlock the Supernova Mystery 18. Manuela Campanelli, Shedding Light on Supermassive Binary Black Hole Mergers 20. Manuela Campanelli, Accretion Dynamics of Supermassive Black Hole Binaries 22. Matias Carrasco Kind, Achieving Probabilistic Classification of Cosmic Web Particles Using Rapidly Generated Training Data: A Method for Classifying Galaxies into Their Cosmic Web Structural Groups Using Supervised Machine Learning 24. Tiziana Di Mattteo, The Epoch of the First Luminous Black Holes: Evolving the Blue Tides Simulation into the First Billion Years of Cosmic History 26. Jerry Draayer, Advancing First-Principle Symmetry-Guided Nuclear Modeling for Studies of Nucleosynthesis and Fundamental Symmetries in Nature 28. Charles F. Gammie, Magnetized Models of Giant Impacts 30. Nickolayk Gnedin, Cosmic Reionization on Computers 32. John Hawley, Elucidating the Alignment Mechanism for Black Hole Accretion Disks Subjected to Lense-Thirring Torques 34. Philip F. Hopkins, Understanding the Origins of the Stars and Galaxies in our Universe 36. Eliu Huerta, Deep Learning at Scale for the Construction of Galaxy Catalogs with the Dark Energy Survey 38. Eliu Huerta, Characterization of Numerical Relativity Waveforms of Eccentric Binary Black Hole Mergers 40. Eiu Huerta, Fusing Numerical Relativity and Deep Learning to Detect Eccentric Binary Black Hole Mergers Using Higher-Order Waveform Multipoles 42. Athol J. Kemball, Data-and Compute-Intensive Challenges for Observational Astronomy in the Great Survey Era 44. Deborah A. Levin, Modal Decompositions of Shock Interactions 46. Deborah A. Levin, Plume Plasma Spacecraft Interactions 48. Yi-Hsin Liu, The Spreading of Three-Dimensional Magnetic Reconnection in Asymmetric Geometry 50. Felipe Menanteau, Assembling a Map of the Universe: Shapes and Mass Distribution for the Dark Energy Survey 52. Philipp Mosta, Petascale Simulations of Binary Neutron Star Mergers 54. Michael L. Norman, Development of a Scalable Gravity Solver for Enzo-E 56. Brian O’Shea, Simulating Galaxy Formation Across Cosmic Time 58. Donald Petravick, Processing Dark Energy Camera Data to Make the World’s Best Map of the Night Sky 60. Nikolai Pogorelov, Coupling the Solar Wind and Local Interstellar Medium in the Era of the New Horizons, Interstellar Boundary Explorer, Parker Solar Probe, Ulysses, and Voyager Spacecraft 62. Jane Pratt, Interior Dynamics of Young Stars Revealed by 3D Hydrodynamic Simulations 64. Thomas Quinn, Modeling of Galaxy Populations 66. Paul Ricker, Effects of Active Galaxy Feedback on the Intracluster Medium 68. Stuart Shapiro, Gravitational and Electromagnetic Signatures from Binary Black Hole-Neutron Star Mergers: A Jet Engine for Short Gamma-Ray Bursts 70. Alexander Tchekhovskoy, Feeding Black Holes: Tilt with a Twist 72. Gabor Toth, Scaling the BATS-R-US MHD Model to Over 100,000 Cores with Efficient Hybrid OpenMP and MPI Parallelization 74. Mathew Turk, Numerical Study on the Fragmentation Condition in a Primordial Accretion Disk 75. Saul A. Teukolsky, Merging Black Holes and Neutron Stars 78. Jennifer Corcoran, Image Processing to Build a Multitemporal Vegetation Elevation Ecosystem Model of the Great Lakes Basin 80. Larry Di Girolamo, Petascale Processing of Satellite Earth Observations 82. Chunyuan Diao, Large-Scale Remote Monitoring of Invasive Species Dynamics Through a Petascale High-Performance Computing System 84. Francina Domiguez, Deforestation of the Amazon Forest: Understanding Hydroclimate Impacts by Tracing the Water that Evaporates from the Forest 86. Patricia M. Gregg, Forecasting Volcanic Unrest and Eruption Potential Using Statistical Data Assimilation 88. Kaiyu Guan, Monitoring Field-Scale Crop Water Use Using a Satellite Data-Driven Mechanistic Modeling Approach 90. Kaiyu Guan, Building an Objective Seasonal Forecasting System for U.S. Corn and Soybean Yields 92. Sonia Lasher-Trapp, Inflow and Outflow from Thunderstorms: Tracking Their Influence on Precipitation and Further Growth 94. Paul Morin, Petascale Polar Topography Production 96. Stephen W. Nesbitt, High-Resolution Numerical Simulations of Convection Initiation over the Sierras de Cordoba Mountains in Argentina 98. Leigh G. Orf, Simulations of Violently Tornadic Supercells and Damaging Thunderstorms 100. Nikolaos Pavlis, Prediction of Geomagnetic Secular Variation with Large-Ensemble Geomagnetic Data Assimilation 102. Nicole Riemer, Machine Learning for Error Quantification in Simulating the Climate Impacts of Atmospheric Aerosols 104. Clay Tabor, Simulating Hydroclimate Change in Southwest North America at 21,000 Years Ago 106. Robert J. Trapp, Implementation and Use of a Global Nonhydrostatic Model for Extended-Range Weather Prediction during the RELAMPAGO Field Campaign 108. John Vidale, Simulating Large California Earthquakes Before They Occur 110. Renata Wentzcovitch Materials Simulations in Geophysics 112. Mathew West, Simulating Aerosol Impacts on Climate, One Particle at a Time: A Regional-Scale, Particle-Resolved Aerosol Model to Quantify and Reduce Uncertainties in Aerosol-Atmosphere Interactions 114. Donald J. Wuebbles, Evolving Air Quality Under the Changing Climate 116. Xiangdong Zhang, Sensitivity of Arctic Sea Ice Thickness Distribution to Sea Ice Internal Dynamics in a Changing Climate 120. Narayana R. Aluru, The Mechanism of Proton Diffusion in ABO3 Perovskite Oxides 122. Narayana R. Aluru, Identification of Amino Acids with Sensitive Nanoporous MoS2: Toward Machine Learning-Based Prediction 124. Narayana R Aluru, Transfer-Learning-Based Course-Graining Method for Simple Fluids: Toward Deep Inverse Liquid-State Theory 126. Guillermo Araya, High-End Visualization of Coherent Structures and Turbulent Events in Wall-Bounded Flows with a Passive Scalar 128. Jerzy Bernholc, Design of Atomically Precise Nanoscale Negative Differential Resistance Devices 130. Daniel Bodony, Using OpenMP Offloading to Run Code on Blue Waters’ GPU Nodes 132. Christoph Brehm, Numerical Investigation of Turbulence Suppression in Rotating Flows 134. Oliver M. F. Browne, An Efficient Method for Hypersonic Laminar-Turbulent Transition Prediction 136. Carlo Pierleoni, Quantum Simulations: Properties of Dense Hydrogen 138. Huck Beng Chew, Role of Interfaces on the Shear Strength and Bending Properties of vander Waals Two-Dimensional Materials 140. Bryan Clark, Atypically Entangled Phases and New Methods for the Quantum Many-Body Problem 142. Lian Duan, Direct Numerical Simulation of Pressure Fluctuations Induced by Supersonic Turbulent Boundary Layers 144. Aida X. El-Khadra, The Anomalous Magnetic Moment of the Muon: An Improved Ab Initio Calculation of the Hadronic Vacuum Polarization Contribution 146. Elif Ertekin, Accelerating Thermoelectric Materials Discovery via Dopability Predictions 148. Jonathan Freund, Machine-Learning Turbulence Models for Simulations of Turbulent Combustion 150. Marcelo Garcia, Turbulence-Resolving Modeling of Oscillatory Boundary Layer Flows 152. Benjamin Hooberman, Machine Learning for Particle Physics: Employing Deep Learning for Particle Identification and Measurement of Colliders 154. Kathryn Huff, Molten-Salt Reactors and Their Fuel Cycles 156. Prashant K. Jain, A Novel Crystal Structure with Spin-Protected Surface Electronic Conduction 158. Eric Johnsen, Inertial Collapse of Individual Bubbles near Solid/Free Boundaries 160. Harley T. Johnson, Electronic Structure of Microscale Dielectric Barrier Discharges 162. Seid Koric, Accelerating Virtual Prototyping and Certification in the Aerospace Industry with Scalable Finite-Element Analysis 164. Jean-Pierre Leburton, Graphene Nanopore Transistor for DNA-Nick Detection 166. Farzad Mashayek, Compressibility Effects on Spatially Developing Plane Free Shear Layer 168. Moshe Matalon, Outwardly Propagating Turbulent Flames 170. Mark Neubauer, Deep Learning for Higgs Boson Identification and Searches for New Physics at the Large Hadron Collider 172. Rajib Rahman, Designing Quantum Logic Gates on Silicon Chips with Large-Scale Multiphysics Simulations 174. Venkat Raman, Simulation of Rotating Detonation Engines 176. Caroline Riedl, Mapping Proton Quark Structure: Looking Inside the Proton-How do Quarks Spin? 178. Andre’ Schleife, Electron Dynamics of Ion-Irradiated Two-Dimensional Materials 180. Andre’ Schleife, Discovery of New Plasmonic Materials via High-Throughput Machine Learning 182. Brian G. Thomas, Turbulent Multiphase Thermal Flow Modeling of Defect Formation Mechanisms and Electromagnetic Force Effects in Continuous Steel Casting 184. Rafael Tinoco Lopez, Investigation of Sediment Transport Through Aquatic Vegetation Using Large-Scale High-Fidelity Turbulence Simulations 186. Kimani Toussaint, Machine Learning-Assisted High-Throughput Computational Design of Solvents for Liquid-Exfoliation 188. Dallas R. Trinkle, High-Throughput Materials Modeling Optimization 190. Lela Vukovic, Detecting Neurotransmitters with DNA-Wrapped Nanotube Sensors 192. Lucas Wagner, Accurate Effective Interactions in Quantum Materials 194. Zhi Jian Wang, Supersonic Jet Noise Prediction Using High-Order Large-Eddy Simulation 196. Bin Xu, Spin Spirals in Multiferroic Bismuth Ferrite and at Metal Surface: From Fully First Principles 198. Zhen Xu, Numerical Simulations of a Collapsing Cavitation Bubble Near an Elastically Deformable Object 200. Yonghua Yan, Numerical Study on Shock Wave-Boundary Layer Interaction and Its Control 202. Jinhui Yan, Free-Surface Flow Modeling of Multiple Tidal Turbines 204. Pui-Kuen Yeung, New Insights on Intermittency and Circulation Statistics Obtained From a Massive Turbulence Simulation Database 206. Yang Zhang, Effects of Surface Defects on Hydrophobicity at Rare-Earth Oxide Interfaces Using Molecular Dynamics Simulations Driven by Ab Initio-Based Deep Neural Network Potentials 208. Phiala Shanahan, Constraining the Properties and Interactions of Dark Matter 212. Donna Cox, Cinematic Scientific Data Visualization for CADENS 214. Iwan Duursma, The Structure and Statistics of Reed-Muller Codes 216. William Gropp, A Parallel Framework for Scaling Phylogeny Estimation Methods to Large Genomic Data Sets 218. William Gropp, Algorithms for Extreme-Scale Systems 220. Ravishankar Iyer, Kaleidoscope: Live Forensics for Large-Scale Data Center Storage Systems 222. Shantenu Jha, Extensible and Scalable Adaptive Sampling to Fold Proteins on Supercomputers 224. Luke Olson, Improved Scalability Through Node-Aware Communicators 226. Luke Olson, Scalable Line and Plane Solvers 228. Marc Snir, Detection of Silent Data Corruptions Using Machine Learning 230. Edgar Solomonik, Pushing the Boundaries of Large-Scale Tensor Computations 232. Tandy Warnow, Algorithms for Large-Scale Evolutionary Tree Construction: Improving Scalability and Accuracy through Divide-and-Conquer 234. Justin Sirigano, HPC Development of Deep Learning Models in Scientific Computing and Finance 235. David Taflin, Optimization of a Field Data Parallel Output Library 238. Aleksei Aksimentiev, Resolving the Structure of Bacteriophage HK97 with Atomistic Resolution 240. Aleksei Aksimentiev, A Nanopore System for Single-Molecule Protein Sequencing 242. Aleksei Aksimentiev, Dynamic Interactions Between Lipid-Tethered DNA and Phospholipid Membranes 244. Rommie Amaro, Influence Virulence and Transmissibility Through the Computational Microscope 246. Rafael C. Bernardi, How Blue Waters Is Aiding the Fight Against Sepsis 248. Gustavo Caetano-Annoles, A Phylogenomic History of Protein Function and Dynamics 250. Colleen E. Clancy, Predicting Drug-Induced Cardiac Arrhythmias Using Atomistic Simulations 252. Julie Dickerson, MRNA Isoform Prediction 254. Ken Dill, Petascale Integrative Approaches to Protein Structure Prediction 256. Andrew Ferguson, Discovery of Slow Kinetic Modes from Molecular Simulation Trajectories 258. Mattia Gazzola, Harnessing Viscous Streaming in Complex Active Systems: Minibots in Fluids 260. Jodi A. Hadden-Perilla, Molecular Dynamics Simulations of HBV Capsid 262. Jodi A. Hadden-Perilla, Molecular Dynamics Simulations of the HBV Capsid as a Drug Target 264. So Hirata, Toward Predictive Computational Design of Precision Molecular Optoelectronics 266. Mathew E. Hudson, Impact of Batch Effect and Study Design Biases on Identification of Genetic Risk Factors in Sequencing Data 268. Tao Jiang, Microscopic Identification of PIP2 Binding Sites on a Ca2+-activated Cl- Channel 270. Fatemah Khalili-Araghi, Paracellular Ion Transport 272. David LeBauer, The TERRA Phenotyping Refence Platform: Open Data and Software for Precision Field Crop Measurement and Analysis 274. Nancy Makri, Quantum-Classical Path Integral Simulation of Proton Translocation in Biological Channels 276. Arif Masud, A New Stabilized Fluid-Structure Interaction Method: Coupled System of Anisotropic Viscoelastic Model for Artery and Non-Newtonian Model for Blood 278. Jeffery S. Moore, Atomic Scale Simulation of Amyloid Beta with Dismantling Peptide-Based Inhibitors 280. Mahmoud Moradi, Transport Mechanism of POT Transporters: Employing Loosely Coupled Molecular Dynamics Simulations to Characterize Protein Structural Dynamics 282. Mahmoud Moradi, Activation Mechanisms of the Mechanosensitive Channel of Large Conductance: Employing Loosely Coupled Molecular Dynamics Simulations to Characterize Protein Structural Dynamics 284. Juan Perilla, Molecular Mechanisms of Infection by Chlamydia 286. Joseph R. Peterson, Calibrating the SimBioSys TumorScope for the Fight on Cancer: A Scenario Analysis Engine for Determining Optimal Therapy Choice 288. Kimberly Prather, Investigating the Climate-Relevant Impacts of Chemical Complexity in Marine Aerosols 290. Benoit Roux, Molecular Dynamics Binding Free Energy Calculations Offer a Window to Understand Protein-Protein Binding Specificity 292. Diwakar Shukla, Molecular Basis of the Nitrate Transport Mechanism in Plants 294. Diwakar Shukla, Simulations Uncover the Mechanism of Serotonin Transport in the Brain 296. Diwakar Shukla, Elucidating the Ligand Selectivity and Activation Mechanisms of Cannabinoid Receptors 298. Ivan Soltesz, Full-Scale Biophysical Modeling of Hippocampal Networks During Spatial Navigation 300. Marcos Sotomayor, Desmosomal Cadherins Beating Under Tension 302. Ashok Srinivasan, Simulation of Viral Infection Propagation During Air Travel 304. Brad Sutton, MRI-Based Biomarkers Through High-Performance Computing 306. Emad Tajkhorshid, Mechanobiology: Using Blue Waters to Decipher the Physical Principles of Protein Mechanics 308. Emad Tajkhorshid, Atomistic Simulations of a Protocell 310. Emad Tajkhorshid, Modeling of a Zika Virus Envelope at Atomic Resolution 312. Gregory Voth, Multiscale Simulations of Complex Self-Assembling Biomolecules: Targeting HIV-1 314. Victor Anisimov, Improving the Agreement of AMBER Simulation of Crystals of Nucleic Acid Bases with Experimental Data 315. Mohammed El-Kebir, Algorithms for Cancer Phylogenetics 316. Taras V. Pogorelov, Amphotericin-Driven Sterol Extraction: Probing the Mechanism 320. Yongyang Cai, Climate Policy in a Dynamic Stochastic Economy 322. J. Stephen Downie, Characterizing Descriptivity in Writing through Text Analysis of Books from the HathiTrust Digital Library 324. Mao Ye, High-Frequency Trading in Nanoseconds: Analysis, Modeling, and Policy Implications 328. Wendy K. Tam Cho, A Massively Parallel Evolutionary Markov Chain Monte Carlo Algorithm for Sampling Spatial State Spaces 332. Eizabeth Agee, The Contributions of Root Systems to Drought Response in the Amazon Rainforest 334. Elaad Applebaum, Star Formation in Dwarf Galaxies: Using Simulations to Identify Key Observables to Test Models 336. Katelyn Barber, Improving Convectively Induced Turbulence Forecast Parameters Through Bulk Numerical Simulations for Aviation Safety 338. Maureen T. Brooks, Modeling Nonlinear Physical-Biological Interactions: Inertia and Sargassum in the North Atlantic 340. Iryna Butsky, Predictions About the Invisible Gas in Galaxy Clusters 342. Robert Cieri, Computational Fluid Dynamics Investigation into Pulmonary Airflow Patterns in Monitor Lizards(Varanidae) 344. Mathew Clement, The Early Instability Scenario for Planet Formation in the Solar System 346. Salme Cook, The Distribution of Shear Stress and Nutrients in a Tidally Energetic Estuary: The Role of Numerical Resolution and Vegetation 348. Andrew Emerick, Exascale Astrophysics with Enzo-E: Development of Physics Modules for Galaxy-Scale and Cosmology Simulations 350. Forrest Glines, Magnetohydrodynamic Simulation: Galaxies 352. Alexander Gurvich, GPU-Accelerated Interstellar Chemistry with WIND: A General Ordinary Differential Equation Solver 254. Jennifer M. Hayes, Using Spectroscopic Data and Molecular Simulations to Estimate Heterogeneous Ensembles: How to Study Complicated, Flexible Proteins When Experimental Data Are Limited 356. Joshua Lansford, Electron Density-Based Machine Learning for Accelerating Quantum Calculations 358. Kara Marsac, Extending the Longevity of Produced Water Disposal Wells: Evaluation Using Reactive Transport Simulation 360. Nicole Rosato, Improved Trumpet Initial Lapse and Shift for Binary Black Hole Simulations 361. Shanna Chu, Understanding the Physical Processes Causing Intermediate-Depth Earthquakes 362. Micheline Soley, Escaping From an Ultracold Inferno: The Ultracold KRb Dimer Reaction 364. Ronald Stenz, The Impacts of Hydrometeor Centrifuging on Tornado Dynamics: Improving the Realism of Tornado Simulations 366. Darius Teo, Unraveling Functional Hole Hopping Pathways in The [Fe4S4]-Containing DNA Primase 368. Walter Torres, The Transport and Dynamics of Wave-Driven Reef Jets Under the Influence of Rotation and Bottom Friction 370. Samuel Whitman, Simulation of Bluff Body Stabilized Flames with PeleC: Adaptively Resolving Turbulence-Combustion Interactions in Real-World Engineering Problems
Peer Reviewed:Not Peer Reviewed
Sponsor:NSF OCI-0725070
NSF ACI-1238993
Date Available in IDEALS:2021-07-08

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