| Summary: | 2017 annual report for the Blue Waters Project NSF OCI-0725070 NSF ACI-1238993 2017 Blue Waters Annual Report Table of Contents 18. Dinshaw S. Balsara, Simulating Two-Fluid MHD Turbulence in Star-Forming Molecular Clouds on the Blue Waters System 20. Tiziana Di Matteo, Supermassive Black Holes at the Cosmic Frontier 22. Gilbert Holder, Theoretical Astrophysics and Data Analysis 24. Eliu Huerta, Detection of Gravitational Wave Sources in Dense Stellar Environments 26. Eliu Huerta, Deep Neural Networks to Enable Real-Time Multimessenger Astrophysics 28. Thomas W. Jones, Toward Robust Magnetohydrodynamic Simulations of Galaxy Cluster Formation 30. Eric J. Lentz, Exploring the Nature of Exploding Massive Stars with High Resolution 32. Deborah Levin, Modeling Plasma Flows with Kinetic Approaches using Hybrid CPU-GPU Computing 34. Yi-Hsin Liu, Three-Dimensional Nature of Collisionless Magnetic Reconnection at Earth’s Magnetopause 36. Warren B. Mori, Transformative Petascale Particle-in-Cell Simulations 38. Scott C. Noble, Mini-disk Dynamics about Supermassive Black Holes Binaries 40. Michael L. Norman, Realistic Simulations of the Intergalactic Medium: The Search for Missing Physics 42. Brian W. O’Shea, Simulating Galaxy Formation Across Cosmic Time 44. Christian D. Ott, 3D General-Relativistic Radiation-Hydrodynamic Simulations of Core-Collapse Supernovae 46. Nikolai Pogorelov, Modeling Physical Processes in the Solar Wind and Local Interstellar Medium with a Multiscale Fluid-Kinetic Simulations Suite 48. Thomas Quinn, Unified Modeling of Galaxy Populations in Clusters 50. Vadim Roytershteyn, Kinetic Simulations of Large-Scale Plasma Turbulence 52. Hsi-Yu Schive, GPU-Accelerated Adaptive Mesh Refinement 54. Stuart L. Shapiro, Magnetorotational Collapse of Supermassive Stars: Black Hole Formation, Gravitational Waves, and Jets 56. Alexander Tchekhovskoy, GPU-Accelerated Simulations: Black Holes, Spaghettified Stars, and Tilted Disks 58. Gabor Toth, Advanced Space Weather Modeling 60. Paul R. Woodward, 3D Simulations of i-Process Nucleosynthesis 64. Marin Clark, High-Resolution Digital Surface Models of the 2016 Mw7.8 Kaikoura Earthquake, New Zealand 66. Jennifer Corcoran, Image Processing to Build a Multi-Temporal Vegetation Elevation Model(MTVEM) of the Great Lakes Basin(GLB) 68. Larry Di-Girolamo, The Terra Data Fusion Project 70. Marcelo H. Garcia, Large-Eddy Simulation of Sediment Transport and Hydrodynamics at River Bifurcations: Using a Highly Scalable Spectral Element-Based CFD Solver 72. Ian Howat, The Reference Elevation Model of Antarctica 74. Sonia Lasher-Trapp, Untangling Entrainment and Precipitation in Convective Clouds 76. Lijun Liu, Understanding the 4-D Evolution of the Solid Earth Using Geodynamic Models with Data Assimilation 78. Philip J. Maechling, Physics-Based Modeling of High-Frequency Ground Motions and Probabilistic Seismic Hazard Analysis 80. Paul Morin, Enhanced Digital Elevation Model for the Artic 82. Leigh Orf, Simulating the Most Devastating Tornadoes Embedded Within Supercell Thunderstorms 84. Robert Rauber, Don Wuebbles, High-Resolution Earth System Modeling Using Blue Waters’ Capabilities 86. Jamesina J. Simpson, Location-Specific Space Weather Hazards to Electric Power Grids Calculated on a Global Scale 88. Ryan L. Sriver, Impact of Ocean Coupling on Simulated Tropical Cyclone Activity in the High-Resolution Community Earth System Mode 90. Robert J. Trapp, Petascale Modeling of Convective Storms Under Climate Change and Variability 92. Junshik Um, Impacts of Orientation and Morphology of Small Atmospheric Ice Crystals on in-situ Aircraft Measurements: Scattering Calculations 94. Albert J. Valocchi, Pore-Scale Simulation of Multiphase Flow in Porous Media with Applications to Geological Sequestration of Carbon Dioxide 96. Matthew West, 3D Particle-Resolved Aerosol Model to Quantify and Reduce Uncertainties in Aerosol-Atmosphere Interactions 98. Donald J. Wuebbles, Particulate Matter Prediction and Source Attribution for U.S. Air Quality Management in a Changing World 102. David Ackerman, Exploring Confinement vs. Orientation Effects in Rigid and Semi-Flexible Polymers Using a Massively Parallel Framework 104. Ange-Therese Akono, Multi-Scale and Multi-Physics Modeling of the Strength of Geopolymer Composites 106. Jean Paul Allain, Harnessing Petascale Computing to Explain Fundamental Mechanisms Driving Nanopatterning of Multicomponent Surfaces by Directed Irradiation Synthesis 108. Narayana R. Aluru, Study of DIBs with Functional Channels 110. Jerzy Bernholc, Petaflops Simulation and Design of Nanoscale Materials and Devices 112. Daniel Bodony, Reducing Jet Aircraft Noise 114. David Ceperley, Properties of Dense Hydrogen 116. Huck Beng Chew, Scalable Nanopatterning of Graphene by Hydrogen-Plasma Etching 118. Davide Curreli, hPIC: A Scalable Electrostatic Particle-In-Cell for Plasma-Material Interactions 120. J. P. Draayer, Innovative Ab Initio Symmetry-Adapted No-Core Shell Model for Advancing Fundamental Physics and Astrophysics 122. Lian Duan, DNS of Pressure Fluctuations Induced by Supersonic Turbulent Boundary Layers 124. Said Elghobashi, Dispersion of Fully Resolved Liquid Droplets in Isotropic Turbulent Flow 126. Elif Ertekin, QMCBD: A Living Database to Accelerate Worldwide Development and use of Quantum Monte Carlo Methods 128. Paul Fischer, Numerical Methods and Software for Computational Fluid Dynamics, NEK5000 130. Marcelo H. Garcia, Direct Numerical Simulation of Turbulence and Sediment Transport in Oscillatory Boundary Layer Flows 132. Paolo Gardoni, 3D Probabilistic Physics-Based Seismic Hazard Maps for Regional Risk Analysis 134. Mattia Gazzola, Optimal Bio-Locomotion Strategies in Fluids 136. Kathryn Huff, Coupled Multi-Physics of Advanced Molten Salt Nuclear Reactors 138. Sohrab Ismail-Beigi, Understanding Hydrogen Storage in Metal Organic Frameworks using Massively-Parallel Electronic Structure Calculations 140. Prashant K. Jain, Atomistic Modeling of Transformations in Nanocrystals 142. Eric Johnsen, Numerical Simulations of Collapsing Cavitation Bubbles on Blue Waters 144. Gerhard Klimeck, Leading Future Electronics into the Nano Regime Using Quantum Atomistic Simulations in NEMO5 146. Deborah A. Levin, Kinetic Simulations of Unsteady Shock-Boundary Layer Interactions 148. Paul Mackenzie, High Energy Physics on Blue Waters 150. Burkhard Militzer, First-Principles Computer Simulations of Hydrocarbons Under Fusion Conditions 152. Sarma L. Rani, Direct Numerical Simulations of the Relative Motion of High-Inertia Particles in Isotropic Turbulence 154. Caroline Riedl, Mapping Proton Quark Structure Using Petabytes of COMPASS Data 156. Andre Schleife, Optical Determination of Crystal Phase in Semiconductor Nanocrystals 158. Ahmed Taha, Advanced Digital Technology for Materials and Manufacturing 160. Brian G. Thomas, Transient Multiphase Flow Phenomena and Defect Formation in Steel Continuous Casting 162. Rafael Tinoco Lopez, High Resolution Numerical Simulation of Oscillatory Flow and Sediment Transport through Aquatic Vegetation 164. Lucas K. Wagner, Quantum Monte Carlo Simulations of Magnetism and Models in Condensed Matter 166. P.K. Yeung, Intermittency, Resolution Effects and High Schmidt Number Mixing in Turbulence 170. Donna Cox, CADENS NSF Project: Digital Literacy, Data Visualization, and the Cinematic Presentation of Science 172. William Gropp, Algorithms for Extreme-Scale Systems 174. Levent Gurel, Parallelization of the Multilevel Fast Multipole Algorithm(MLFMA) on Heterogeneous CPU-GPU Architectures 176. Ravishankar K. Iyer, Predicting Performance Degradation and Failure of Applications through System Activity Monitoring 178. Rakesh Nagi, Parallel Algorithms for Solving Large Assignment Problems 180. Luke Olson, Localizing Communication in Sparse Matrix Operations 182. Edgar Solomonik, Performance Evaluation of New Algebraic Algorithms and Libraries 184. Tandy Warnow, Parallel Algorithms for Big Data Phylogenomics, Proteomics, and Metagenomics 186. Tao Xie, Hardware Acceleration of Deep Learning 188. Kevin Olson, A Critical Evaluation of the OP2/OPS Parallel Meshing and Code Generation Software 192. Aleksei Aksimentiev, DNA Origami Membrane Channels 194. Aleksei Aksimentiev, Molecular Mechanism of Nuclear Transports 196. Gregory Bauer, Improving NWChem Scalability Using the DataSpaces Framework 198. Gustavo Caetano-Anolles, How Function Shapes Dynamics in Protein Evolution 200. Isaac Cann, Cellulosome Structure Determination by Atomistic Simulations Combined with Experimental Assays 202. Vincenzo Carnevale, Mechanism of Temperature Sensitivity in TRPV1 Channel 204. Thomas E. Cheatham III, Exploring the Structure and Dynamics of Converged Ensembles of DNA and RNA Through Molecular Dynamics Simulations 206. Christina C.H. Cheng, Structural Basis for Extreme Cold Tolerance in the Eye Lenses of Teleost Fishes 208. Ken A. Dill, Predicting Protein Structures with Physical Petascale Molecular Simulations 210. Ahmed Elbanna, Multiscale Modeling of Biofilm Dynamics in Drinking Water Distribution Systems: Toward Predictive Modeling of Pathogen Outbreaks 212. Peter Freddolino, Comprehensive in silico Mapping of DNA-Binding Protein Affinity Landscapes 214. Sharon Hammes-Schiffer, Non-Born-Oppenheimer Effects Between Electrons and Protons 216. So Hirata, Brueckner-Goldstone Quantum Monte Carlo 218. Peter Kasson, How Membrane Organization Controls Influenza Infections 220. Zaida Luthey-Schulten, A Hybrid Stochastic-Deterministic Simulation Method Enables Fast Simulation of Cellular Processes in Eukaryotes 222. Nancy Makri, Quantum-Classical Path Integral Simulation of Charge Transfer Reactions 224. Arif Masud, Patient-Specific HPC Models and Simulation-Based Imaging for Cardiovascular Surgical Planning 226. James W. Mazzuca, Quantum Effects of Proton Transfer in Biological Systems 228. Mahmoud Moradi, Thermodynamic Characterization of Conformational Landscape in Proton-Coupled Oligopeptide Transporters 230. Vijay Pande, Machine Learning Reveals Ligand-Directed Conformational Change of u Opioid Receptor 232. Benoit Roux, Elucidating the Molecular Mechanism of C-type Inactivation in Potassium Channels 234. Klaus Schulten, Studying Cellular Processes through the Computational Microscope 236. Diwakar Shukla, Understanding the Protein Allostery in Kinanses and GPCRs 238. Ivan Soltesz, Data-Driven, Biologically Constrained Computational Model of the Hippocampal Network at Full Scale 240. Marcos Sotomayor, Stretching the Cadherin Molecular Velcro of Cell-Cell Junctions 242. Ahsok Srinivasan, Simulation of Viral Infection Propagation through Air Travel 244. Brad Sutton, High-Resolution Magnetic Resonance Imaging of Mechanical Properties of the Brain 246. Ilias Tagkopoulos, A Crystal Ball of Bacterial Behavior: from Data to Prediction using Genome-Scale Models 248. Greg A. Voth, Large-Scale Coarse-Grained Molecular Simulations of the Viral Lifecycle of HIV-1 252. Lars Hansen, Yongyang Cai, Policy Responses to Climate Change in a Dynamic Stochastic Economy 254. Wendy K. Tam Cho, Enabling Redistricting Reform: A Computational Study of Zoning Optimization 258. Elizabeth Agee, Resolving Plant Functional Biodiversity to Quantify Forest Drought Resistance in the Amazon 260. Maureen T. Brooks, Modeling Nonlinear Physical-Biological Interactions: Eddies and Sargassum in the North Atlantic 262. Iryna Butsky, The Role of Cosmic Rays in Isolated Disk Galaxies 264. Jon Calhoun, Analyzing the Propagation of Soft Error Corruption in HPC Applications 266. Justin Drake, Toward Developing a Thermodynamic Model of Binding-Induced Conformational Transitions in Short, Disordered Protein Regions 268. Paul Hime, Genomic Perspectives on the Amphibian Tree of Life 270. Michael P. Howard, Multiscale Simulations of Complex Fluid Rheology 272. Alexandra L. Jones, High Accuracy Radiative Transfer in Cloudy Atmospheres 274. Andrew Kirby, High-Fidelity Blade-Resolved Wind Farm Simulations 276. Sara Kokkila Schumacher, Reducing the Computational Cost of Coupled Clustery Theory 278. Larisa Reames, Simulated Effects of Urban Environments on the Dynamics of a Supercell Thunderstorm 280. Sherwood Richers, Monte Carlo Neutrino Closures in 3D GRMHD Simulations of Core-Collapse Supernovae and Neutron Star Mergers 282. Sean L. Seyler, Understanding the Role of Hydrodynamic Fluctuations in Biomacromolecular Dynamics through the Development of Hybrid Atomistic-Continuum Simulation 284. Ronald Stenz, The Impacts of Hydrometeor Centrifuging on Tornado Dynamics 286. Erin Teich, Glassy Dynamics and Identity Crises in Hard-Particle Systems 288. Samuel Totorica, Magnetic Reconnection in Laser-Driven Plasmas: from Astrophysics to the Laboratory in silico 2017 Blue Waters Annual Report Table of Contents 18. Dinshaw S. Balsara, Simulating Two-Fluid MHD Turbulence in Star-Forming Molecular Clouds on the Blue Waters System 20. Tiziana Di Matteo, Supermassive Black Holes at the Cosmic Frontier 22. Gilbert Holder, Theoretical Astrophysics and Data Analysis 24. Eliu Huerta, Detection of Gravitational Wave Sources in Dense Stellar Environments 26. Eliu Huerta, Deep Neural Networks to Enable Real-Time Multimessenger Astrophysics 28. Thomas W. Jones, Toward Robust Magnetohydrodynamic Simulations of Galaxy Cluster Formation 30. Eric J. Lentz, Exploring the Nature of Exploding Massive Stars with High Resolution 32. Deborah Levin, Modeling Plasma Flows with Kinetic Approaches using Hybrid CPU-GPU Computing 34. Yi-Hsin Liu, Three-Dimensional Nature of Collisionless Magnetic Reconnection at Earth’s Magnetopause 36. Warren B. Mori, Transformative Petascale Particle-in-Cell Simulations 38. Scott C. Noble, Mini-disk Dynamics about Supermassive Black Holes Binaries 40. Michael L. Norman, Realistic Simulations of the Intergalactic Medium: The Search for Missing Physics 42. Brian W. O’Shea, Simulating Galaxy Formation Across Cosmic Time 44. Christian D. Ott, 3D General-Relativistic Radiation-Hydrodynamic Simulations of Core-Collapse Supernovae 46. Nikolai Pogorelov, Modeling Physical Processes in the Solar Wind and Local Interstellar Medium with a Multiscale Fluid-Kinetic Simulations Suite 48. Thomas Quinn, Unified Modeling of Galaxy Populations in Clusters 50. Vadim Roytershteyn, Kinetic Simulations of Large-Scale Plasma Turbulence 52. Hsi-Yu Schive, GPU-Accelerated Adaptive Mesh Refinement 54. Stuart L. Shapiro, Magnetorotational Collapse of Supermassive Stars: Black Hole Formation, Gravitational Waves, and Jets 56. Alexander Tchekhovskoy, GPU-Accelerated Simulations: Black Holes, Spaghettified Stars, and Tilted Disks 58. Gabor Toth, Advanced Space Weather Modeling 60. Paul R. Woodward, 3D Simulations of i-Process Nucleosynthesis 64. Marin Clark, High-Resolution Digital Surface Models of the 2016 Mw7.8 Kaikoura Earthquake, New Zealand 66. Jennifer Corcoran, Image Processing to Build a Multi-Temporal Vegetation Elevation Model(MTVEM) of the Great Lakes Basin(GLB) 68. Larry Di-Girolamo, The Terra Data Fusion Project 70. Marcelo H. Garcia, Large-Eddy Simulation of Sediment Transport and Hydrodynamics at River Bifurcations: Using a Highly Scalable Spectral Element-Based CFD Solver 72. Ian Howat, The Reference Elevation Model of Antarctica 74. Sonia Lasher-Trapp, Untangling Entrainment and Precipitation in Convective Clouds 76. Lijun Liu, Understanding the 4-D Evolution of the Solid Earth Using Geodynamic Models with Data Assimilation 78. Philip J. Maechling, Physics-Based Modeling of High-Frequency Ground Motions and Probabilistic Seismic Hazard Analysis 80. Paul Morin, Enhanced Digital Elevation Model for the Artic 82. Leigh Orf, Simulating the Most Devastating Tornadoes Embedded Within Supercell Thunderstorms 84. Robert Rauber, Don Wuebbles, High-Resolution Earth System Modeling Using Blue Waters’ Capabilities 86. Jamesina J. Simpson, Location-Specific Space Weather Hazards to Electric Power Grids Calculated on a Global Scale 88. Ryan L. Sriver, Impact of Ocean Coupling on Simulated Tropical Cyclone Activity in the High-Resolution Community Earth System Mode 90. Robert J. Trapp, Petascale Modeling of Convective Storms Under Climate Change and Variability 92. Junshik Um, Impacts of Orientation and Morphology of Small Atmospheric Ice Crystals on in-situ Aircraft Measurements: Scattering Calculations 94. Albert J. Valocchi, Pore-Scale Simulation of Multiphase Flow in Porous Media with Applications to Geological Sequestration of Carbon Dioxide 96. Matthew West, 3D Particle-Resolved Aerosol Model to Quantify and Reduce Uncertainties in Aerosol-Atmosphere Interactions 98. Donald J. Wuebbles, Particulate Matter Prediction and Source Attribution for U.S. Air Quality Management in a Changing World 102. David Ackerman, Exploring Confinement vs. Orientation Effects in Rigid and Semi-Flexible Polymers Using a Massively Parallel Framework 104. Ange-Therese Akono, Multi-Scale and Multi-Physics Modeling of the Strength of Geopolymer Composites 106. Jean Paul Allain, Harnessing Petascale Computing to Explain Fundamental Mechanisms Driving Nanopatterning of Multicomponent Surfaces by Directed Irradiation Synthesis 108. Narayana R. Aluru, Study of DIBs with Functional Channels 110. Jerzy Bernholc, Petaflops Simulation and Design of Nanoscale Materials and Devices 112. Daniel Bodony, Reducing Jet Aircraft Noise 114. David Ceperley, Properties of Dense Hydrogen 116. Huck Beng Chew, Scalable Nanopatterning of Graphene by Hydrogen-Plasma Etching 118. Davide Curreli, hPIC: A Scalable Electrostatic Particle-In-Cell for Plasma-Material Interactions 120. J. P. Draayer, Innovative Ab Initio Symmetry-Adapted No-Core Shell Model for Advancing Fundamental Physics and Astrophysics 122. Lian Duan, DNS of Pressure Fluctuations Induced by Supersonic Turbulent Boundary Layers 124. Said Elghobashi, Dispersion of Fully Resolved Liquid Droplets in Isotropic Turbulent Flow 126. Elif Ertekin, QMCBD: A Living Database to Accelerate Worldwide Development and use of Quantum Monte Carlo Methods 128. Paul Fischer, Numerical Methods and Software for Computational Fluid Dynamics, NEK5000 130. Marcelo H. Garcia, Direct Numerical Simulation of Turbulence and Sediment Transport in Oscillatory Boundary Layer Flows 132. Paolo Gardoni, 3D Probabilistic Physics-Based Seismic Hazard Maps for Regional Risk Analysis 134. Mattia Gazzola, Optimal Bio-Locomotion Strategies in Fluids 136. Kathryn Huff, Coupled Multi-Physics of Advanced Molten Salt Nuclear Reactors 138. Sohrab Ismail-Beigi, Understanding Hydrogen Storage in Metal Organic Frameworks using Massively-Parallel Electronic Structure Calculations 140. Prashant K. Jain, Atomistic Modeling of Transformations in Nanocrystals 142. Eric Johnsen, Numerical Simulations of Collapsing Cavitation Bubbles on Blue Waters 144. Gerhard Klimeck, Leading Future Electronics into the Nano Regime Using Quantum Atomistic Simulations in NEMO5 146. Deborah A. Levin, Kinetic Simulations of Unsteady Shock-Boundary Layer Interactions 148. Paul Mackenzie, High Energy Physics on Blue Waters 150. Burkhard Militzer, First-Principles Computer Simulations of Hydrocarbons Under Fusion Conditions 152. Sarma L. Rani, Direct Numerical Simulations of the Relative Motion of High-Inertia Particles in Isotropic Turbulence 154. Caroline Riedl, Mapping Proton Quark Structure Using Petabytes of COMPASS Data 156. Andre Schleife, Optical Determination of Crystal Phase in Semiconductor Nanocrystals 158. Ahmed Taha, Advanced Digital Technology for Materials and Manufacturing 160. Brian G. Thomas, Transient Multiphase Flow Phenomena and Defect Formation in Steel Continuous Casting 162. Rafael Tinoco Lopez, High Resolution Numerical Simulation of Oscillatory Flow and Sediment Transport through Aquatic Vegetation 164. Lucas K. Wagner, Quantum Monte Carlo Simulations of Magnetism and Models in Condensed Matter 166. P.K. Yeung, Intermittency, Resolution Effects and High Schmidt Number Mixing in Turbulence 170. Donna Cox, CADENS NSF Project: Digital Literacy, Data Visualization, and the Cinematic Presentation of Science 172. William Gropp, Algorithms for Extreme-Scale Systems 174. Levent Gurel, Parallelization of the Multilevel Fast Multipole Algorithm(MLFMA) on Heterogeneous CPU-GPU Architectures 176. Ravishankar K. Iyer, Predicting Performance Degradation and Failure of Applications through System Activity Monitoring 178. Rakesh Nagi, Parallel Algorithms for Solving Large Assignment Problems 180. Luke Olson, Localizing Communication in Sparse Matrix Operations 182. Edgar Solomonik, Performance Evaluation of New Algebraic Algorithms and Libraries 184. Tandy Warnow, Parallel Algorithms for Big Data Phylogenomics, Proteomics, and Metagenomics 186. Tao Xie, Hardware Acceleration of Deep Learning 188. Kevin Olson, A Critical Evaluation of the OP2/OPS Parallel Meshing and Code Generation Software 192. Aleksei Aksimentiev, DNA Origami Membrane Channels 194. Aleksei Aksimentiev, Molecular Mechanism of Nuclear Transports 196. Gregory Bauer, Improving NWChem Scalability Using the DataSpaces Framework 198. Gustavo Caetano-Anolles, How Function Shapes Dynamics in Protein Evolution 200. Isaac Cann, Cellulosome Structure Determination by Atomistic Simulations Combined with Experimental Assays 202. Vincenzo Carnevale, Mechanism of Temperature Sensitivity in TRPV1 Channel 204. Thomas E. Cheatham III, Exploring the Structure and Dynamics of Converged Ensembles of DNA and RNA Through Molecular Dynamics Simulations 206. Christina C.H. Cheng, Structural Basis for Extreme Cold Tolerance in the Eye Lenses of Teleost Fishes 208. Ken A. Dill, Predicting Protein Structures with Physical Petascale Molecular Simulations 210. Ahmed Elbanna, Multiscale Modeling of Biofilm Dynamics in Drinking Water Distribution Systems: Toward Predictive Modeling of Pathogen Outbreaks 212. Peter Freddolino, Comprehensive in silico Mapping of DNA-Binding Protein Affinity Landscapes 214. Sharon Hammes-Schiffer, Non-Born-Oppenheimer Effects Between Electrons and Protons 216. So Hirata, Brueckner-Goldstone Quantum Monte Carlo 218. Peter Kasson, How Membrane Organization Controls Influenza Infections 220. Zaida Luthey-Schulten, A Hybrid Stochastic-Deterministic Simulation Method Enables Fast Simulation of Cellular Processes in Eukaryotes 222. Nancy Makri, Quantum-Classical Path Integral Simulation of Charge Transfer Reactions 224. Arif Masud, Patient-Specific HPC Models and Simulation-Based Imaging for Cardiovascular Surgical Planning 226. James W. Mazzuca, Quantum Effects of Proton Transfer in Biological Systems 228. Mahmoud Moradi, Thermodynamic Characterization of Conformational Landscape in Proton-Coupled Oligopeptide Transporters 230. Vijay Pande, Machine Learning Reveals Ligand-Directed Conformational Change of u Opioid Receptor 232. Benoit Roux, Elucidating the Molecular Mechanism of C-type Inactivation in Potassium Channels 234. Klaus Schulten, Studying Cellular Processes through the Computational Microscope 236. Diwakar Shukla, Understanding the Protein Allostery in Kinanses and GPCRs 238. Ivan Soltesz, Data-Driven, Biologically Constrained Computational Model of the Hippocampal Network at Full Scale 240. Marcos Sotomayor, Stretching the Cadherin Molecular Velcro of Cell-Cell Junctions 242. Ahsok Srinivasan, Simulation of Viral Infection Propagation through Air Travel 244. Brad Sutton, High-Resolution Magnetic Resonance Imaging of Mechanical Properties of the Brain 246. Ilias Tagkopoulos, A Crystal Ball of Bacterial Behavior: from Data to Prediction using Genome-Scale Models 248. Greg A. Voth, Large-Scale Coarse-Grained Molecular Simulations of the Viral Lifecycle of HIV-1 252. Lars Hansen, Yongyang Cai, Policy Responses to Climate Change in a Dynamic Stochastic Economy 254. Wendy K. Tam Cho, Enabling Redistricting Reform: A Computational Study of Zoning Optimization 258. Elizabeth Agee, Resolving Plant Functional Biodiversity to Quantify Forest Drought Resistance in the Amazon 260. Maureen T. Brooks, Modeling Nonlinear Physical-Biological Interactions: Eddies and Sargassum in the North Atlantic 262. Iryna Butsky, The Role of Cosmic Rays in Isolated Disk Galaxies 264. Jon Calhoun, Analyzing the Propagation of Soft Error Corruption in HPC Applications 266. Justin Drake, Toward Developing a Thermodynamic Model of Binding-Induced Conformational Transitions in Short, Disordered Protein Regions 268. Paul Hime, Genomic Perspectives on the Amphibian Tree of Life 270. Michael P. Howard, Multiscale Simulations of Complex Fluid Rheology 272. Alexandra L. Jones, High Accuracy Radiative Transfer in Cloudy Atmospheres 274. Andrew Kirby, High-Fidelity Blade-Resolved Wind Farm Simulations 276. Sara Kokkila Schumacher, Reducing the Computational Cost of Coupled Clustery Theory 278. Larisa Reames, Simulated Effects of Urban Environments on the Dynamics of a Supercell Thunderstorm 280. Sherwood Richers, Monte Carlo Neutrino Closures in 3D GRMHD Simulations of Core-Collapse Supernovae and Neutron Star Mergers 282. Sean L. Seyler, Understanding the Role of Hydrodynamic Fluctuations in Biomacromolecular Dynamics through the Development of Hybrid Atomistic-Continuum Simulation 284. Ronald Stenz, The Impacts of Hydrometeor Centrifuging on Tornado Dynamics 286. Erin Teich, Glassy Dynamics and Identity Crises in Hard-Particle Systems 288. Samuel Totorica, Magnetic Reconnection in Laser-Driven Plasmas: from Astrophysics to the Laboratory in silico Not Peer Reviewed not peer reviewed Open
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