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Steven Gordon

Ohio Supercomputer Center

Stellar Astronomy and Astrophysics

Massively Parallel Graph Analytics

(jrn)
Jul 2014 - Aug 2016

2018

Brooks, M. (2018): Factors controlling the seasonal distribution of pelagic Sargassum, Marine Ecology Progress Series (in revision)
Colburn, T., S. L. Seyler, and O. Beckstein (2018): Sampling the conformational transition of a membrane protein with implicit and explicit solvent dynamic importance sampling, (in preparation)
Seyler, S. L., C. E. Seyler, and O. Beckstein (2018): Fluctuating hydrodynamics beyond Navier-Stokes: a numerical model for simulating dense fluids at the nanoscale, (in preparation)
Mansbach, R., and A. Ferguson (2018): A Minimal Patchy Particle Model for a Family of Self-assembling π-conjugated Optoelectronic Peptides, (to be submitted)
Cook, S. Lippmann, T.C., and Irish, J.D. (2018): Modeling nonlinear tidal evolution in an energetic estuary, Ocean Modeling (in review)
Teich, E. G., G. van Anders, and S. C. Glotzer (2018): Identity crisis in alchemical space drives the entropic colloidal glass transition, (in review)
Kurchin, R. C. (2018): Structural and Chemical Features Giving Rise to Defect Tolerance of Binary Semiconductors, Chemistry of Materials (under revision)
Totorica, S. R., F. Fiuza, and T. Abel (2018): A new method for analyzing and visualizing plasma simulations using a phase-space tessellation, Physics of Plasmas (submitted)
Hime, P. M., A. R. Lemmon, E. M. Lemmon, E. S. Prendini, C. J. Raxworthy, J. M. Brown, R. C. Thomson, M. Kortyna, P. L. V. Peloso, B. P. Noonan, J. S. Keogh, S. C. Donnellan, R. A. Pyron, J. D. Kratovil, K. Kunte, S. Das, N. Gaitonde, S. Ron, J. Labisko, R. L. Mueller, D. M. Green, and D. W. Weisrock (2018): Genomic perspectives on the amphibian tree of life, (in preparation)
Butsky, I. and Quinn, T. (2018): The Role of Cosmic Ray Transport in Shaping the Simulated Circumgalactic Medium, The Astrophysical Journal (submitted)
Amir Barati Farimani, Evan N. Feinberg, and Vijay S. Pande (2018): Binding Pathway of Opiates to μ Opioid Receptors Revealed by Unsupervised Machine Learning, (submitted)
Evan N. Feinberg, Debnil Sur, Brooke E. Husic, Doris Mai, Yang Li, Jianyi Yang, Bharath Ramsundar, and Vijay S. Pande (2018): Spatial Graph Convolutions for Drug Discovery, (submitted)
Evan N. Feinberg, Amir Barati Farimani, Rajendra Uprety, Amanda Hunkele, Gavril W. Pasternak, Susruta Majumdar, and Vijay S. Pande (2018): Machine Learning Harnesses Molecular Dynamics to Discover New μ Opioid Chemotypes, (submitted)
Jones, Alexandra L. (2018): Alexandraljones/Mcbrat3D: Initial Public Release, Zenodo
Andrew C. Kirby, Arash Hassanzadeh, Dimitri J. Mavriplis, and Jonathan W. Naughton (2018): Wind Turbine Wake Dynamics Analysis Using a High-Fidelity Simulation Framework with Blade-Resolved Turbine Models, American Institute of Aeronautics and Astronautics, 2018 Wind Energy Symposium, Kissimmee, Florida, U.S.A.
Andrew C. Kirby, Zhi Yang, Dimitri J. Mavriplis, Earl P. Duque, and Brad J. Whitlock (2018): Visualization and Data Analytics Challenges of Large-Scale High-Fidelity Numerical Simulations of Wind Energy Applications, American Institute of Aeronautics and Astronautics, 2018 AIAA Aerospace Sciences Meeting, Kissimmee, Florida, U.S.A.
Michael P. Howard, Athanassios Z. Panagiotopoulos, and Arash Nikoubashman (2018): Efficient Mesoscale Hydrodynamics: Multiparticle Collision Dynamics with Massively Parallel GPU Acceleration, Computer Physics Communications, Elsevier BV, Vol 230, pp10-20
Evan N. Feinberg, Vijay S. Pande, Amir Barati Farimani, and Carlos X. Hernandez (2018): Kinetic Machine Learning Unravels Ligand-Directed Conformational Change of μ Opioid Receptor, Biophysical Journal, Elsevier BV, Vol 114, Num 3, pp56a
Foster, L.M. and Maxwell, R.M. (2018): Using sensitivity analysis and model resolution to scale effective hydraulic conductivity and Manning's n parameters in a mountain headwater catchment, Hydrologic Processes (in review)
Justin A. Drake and B. Montgomery Pettitt (2018): Thermodynamics of Conformational Transitions in a Disordered Protein Backbone Model, Biophysical Journal, Elsevier BV, Vol 114, Num 12, pp2799-2810
Matthew S. Clement, Nathan A. Kaib, Sean N. Raymond, and Kevin J. Walsh (2018): Mars' Growth Stunted by an Early Giant Planet Instability, Icarus, Elsevier BV, Vol 311, Num 33, pp340-356
Foster, L.M., Williams, K.H., and Maxwell, R.M. (2018): When Does Uncertainty Matter While Modeling Climate Change in Mountain Headwaters? Contrasting model resolution and complexity under a changing climate in an alpine catchment, Geophysical Research Letters (submitted)
Jon Calhoun, Franck Cappello, Luke N. Olson, Marc Snir, and William D. Gropp (2018): Exploring the Feasibility of Lossy Compression for PDE Simulations, The International Journal of High Performance Computing Applications, SAGE Publications, pp109434201876203
Alexandra L. Jones and Larry Di Girolamo (2018): Design and Verification of a New Monochromatic Thermal Emission Component for the I3RC Community Monte Carlo Model, Journal of the Atmospheric Sciences, American Meteorological Society, Vol 75, Num 3, pp885-906

2017

Richers, Sherwood, Nagakura, Hiroki, Ott, Christian, Dolence, Joshua, Sumiyoshi, Kohsuke, and Yamada, Shoichi (2017): A Detailed Comparison of Multi-Dimensional Boltzmann Neutrino Transport Methods in Core-Collapse Supernovae (dataset), Zenodo
Andrew C. Kirby, Michael Brazell, Zhi Yang, Rajib Roy, Behzad Reza Ahrabi, Dimitri Mavriplis, Jay Sitaraman, and Michael K. Stoellinger (2017): Wind Farm Simulations Using an Overset Hp-Adaptive Approach with Blade-Resolved Turbine Models, American Institute of Aeronautics and Astronautics, 23rd AIAA Computational Fluid Dynamics Conference, Denver, Colorado, U.S.A.
Michael J. Brazell, Andrew C. Kirby, and Dimitri Mavriplis (2017): A High-Order Discontinuous-Galerkin Octree-Based AMR Solver for Overset Simulations, American Institute of Aeronautics and Astronautics, 23rd AIAA Computational Fluid Dynamics Conference, Denver, Colorado, U.S.A.
Hime, Paul Michael (2017): Genomic Perspectives on Amphibian Evolution across Multiple Phylogenetic Scales, Theses and Dissertations--Biology, University of Kentucky Libraries, Num 45
Jon Calhoun, Marc Snir, Luke N. Olson, and William D. Gropp (2017): Towards a More Complete Understanding of SDC Propagation, ACM Press, Proceedings of the 26th International Symposium on High-Performance Parallel and Distributed Computing (HPDC '17), pp131, Washington, D.C., U.S.A.
S. R. Totorica, T. Abel, and F. Fiuza (2017): Particle Acceleration in Laser-Driven Magnetic Reconnection, Physics of Plasmas, AIP Publishing, Vol 24, Num 4, pp041408
Shu-Ching Ou, Justin A. Drake, and B. Montgomery Pettitt (2017): Nonpolar Solvation Free Energy from Proximal Distribution Functions, The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 121, Num 15, pp3555--3564
Katharine J. Cahill, Scott Lathrop, and Steven Gordon (2017): Building a Community of Practice to Prepare the HPC Workforce, Procedia Computer Science (17th annual International Conference on Computational Science, ICCS 2017), Elsevier BV, Vol 108, pp2131--2140, Zürich, Switzerland
Larissa J. Reames (2017): Diurnal Variations in Severe Weather Forecast Parameters of Rapid Update Cycle-2 Tornado Proximity Environments, Weather and Forecasting, American Meteorological Society, Vol 32, Num 2, pp743--761
George M. Slota, Kamesh Madduri, and Sivasankaran Rajamanickam (2017): Distributed Graph Layout for Scalable Small-world Network Analysis, (submitted)

2016

N. V. Pogorelov and M. C. Bedford and I. A. Kryukov and G. P. Zank (2016): Pickup Ion Effect of the Solar Wind Interaction with the Local Interstellar Medium, Journal of Physics: Conference Series, IOP Publishing Ltd, Vol 767, Num 1, pp012020
Justin A. Drake, Robert C. Harris, and B. Montgomery Pettitt (2016): Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility, Biophysical Journal, Elsevier BV, Vol 111, Num 4, pp756--767
Joshua S. Méndez Harper, and Josef Dufek (2016): The Effects of Granular Dynamics on the Triboelectric Charging of Volcanic ash: Experiments and Numerical Simulations, presented at the 2016 Electrostatics Joint Conference, West Lafayette, Indiana, U.S.A.
Samuel R. Totorica, Tom Abel, and Frederico Fiuza (2016): Nonthermal Electron Energization from Magnetic Reconnection in Laser-Driven Plasmas, Phys. Rev. Lett., American Physical Society (APS), Vol 116, Num 9, pp095003
Alexandra L. Jones (2016): Development of an Accurate 3D Monte Carlo Broadband Atmospheric Radiative Transfer Model, Ph.D. Dissertation, University of Illinois
Edwin R. Mathews, Kan Wang, Meng Wang, and Eric J. Jumper (2016): LES of an Aero-Optical Turret Flow at High Reynolds Number, American Institute of Aeronautics and Astronautics (AIAA), 54th AIAA Aerospace Sciences Meeting, San Diego, California, U.S.A.
Ariana Minot, Yue M. Lu, and Na Li (2016): A Distributed Gauss-Newton Method for Power System State Estimation, IEEE Transactions on Power Systems, Institute of Electrical & Electronics Engineers (IEEE), Vol 31, Num 5, pp3804-3815
Ariana Minot, Yue M. Lu, and Na Li (2016): A Parallel Primal-Dual Interior-Point Method for DC Optimal Power Flow, IEEE, 2016 Power Systems Computation Conference (PSCC), pp1-7, Genoa, Italy

2015

Jon Calhoun, Marc Snir, Luke Olson, and Maria Garzaran (2015): Understanding the Propagation of Error Due to a Silent Data Corruption in a Sparse Matrix Vector Multiply, IEEE, 2015 IEEE International Conference on Cluster Computing, pp541-542, Chicago, Illinois, U.S.A.
Sherwood Richers and Daniel Kasen and Evan O’Connor and Rodrigo Fernández and Christian D. Ott (2015): Monte Carlo Neutrino Transport through Remnant Disks from Neutron Star Mergers, The Astrophysical Journal, The American Astronomical Society, Vol 813, Num 1, pp38
J. Calhoun, L. Olson, M. Snir, and W.D. Gropp (2015): Towards a More Fault Resilient Multigrid Solver, Society for Computer Simulation International, Proceedings of the High Performance Computing Symposium (HPC '15), pp1-8, Alexandria, Virginia, U.S.A.
Edwin R. Mathews, Kan Wang, Meng Wang, and Eric J. Jumper (2015): Numerical Investigation of Aero-Optical Distortions Over a Hemisphere-on-Cylinder Turret with Gaps, American Institute of Aeronautics and Astronautics (AIAA), 46th AIAA Plasmadynamics and Lasers Conference, Dallas, Texas, U.S.A.
Sara I. L. Kokkila Schumacher, Edward G. Hohenstein, Robert M. Parrish, Lee-Ping Wang, and Todd J. Martínez (2015): Tensor Hypercontraction Second-Order Møller–Plesset Perturbation Theory: Grid Optimization and Reaction Energies, J. Chem. Theory Comput., American Chemical Society (ACS), Vol 11, Num 7, pp3042--3052
Ariana Minot, and Na Li (2015): A Fully Distributed State Estimation Using Matrix Splitting Methods, Institute of Electrical & Electronics Engineers (IEEE), 2015 American Control Conference (ACC), pp2488-2493, Chicago, Illinois, U.S.A.
Varvara E. Zemskova, Brian L. White, and Alberto Scotti (2015): Available Potential Energy and the General Circulation: Partitioning Wind, Buoyancy Forcing, and Diapycnal Mixing, J. Phys. Oceanogr., American Meteorological Society, Vol 45, Num 6, pp1510--1531
George M. Slota, and Kamesh Madduri (2015): Parallel Color-Coding, Parallel Computing, Elsevier BV, Vol 47, pp51--69
George M. Slota, Sivasankaran Rajamanickam, and Kamesh Madduri (2015): High-Performance Graph Analytics on Manycore Processors, Institute of Electrical & Electronics Engineers (IEEE), 2015 IEEE International Parallel and Distributed Processing Symposium, pp17-27, Hyderabad, India
George M. Slota, Sivasankaran Rajamanickam, and Kamesh Madduri (2015): Supercomputing for Web Graph Analytics, (submitted)

2014

Jon Calhoun, Luke Olson, and Marc Snir (2014): FlipIt: An LLVM Based Fault Injector for HPC, Springer Science + Business Media, Lecture Notes in Computer Science, pp547--558
Kris Beckwith, Seth Veitzer, Stephen F. McCormick, John W. Ruge, Luke N. Olson, and Jon C. Calhoun (2014): Fully-Implicit Ultrascale Physics Solvers and Application to Ion Source Modelling, Institute of Electrical & Electronics Engineers (IEEE), 2014 IEEE 41st International Conference on Plasma Sciences (ICOPS) held with 2014 IEEE International Conference on High-Power Particle Beams (BEAMS), pp1-8, Washington, D.C., U.S.A.

2012

N. V. Pogorelov, S. N. Borovikov, M. C. Bedford, J. Heerikhuisen, T. K. Kim, I. A. Kryukov, and G. P. Zank (2012): Modeling Solar Wind Flow with the Multi-Scale Fluid-Kinetic Simulation Suite, Astronomical Society of the Pacific, 7th Annual International Conference on Numerical Modeling of Space Plasma Flows (ASTRONUM2012), Vol 474, pp165, Big Island, Hawai'i, U.S.A.

2017

Iryna Butsky (2017): The Role of Cosmic Rays in Isolated Disk Galaxies, 2017 Blue Waters Annual Report, pp262-263
Maureen Brooks (2017): Modeling nonlinear physical-biological interactions: Eddies and Sargassum in the North Atlantic, 2017 Blue Waters Annual Report, pp260-261
Elizabeth Agee (2017): Resolving plant functional biodiversity to quantify forest drought resistance in the Amazon, 2017 Blue Waters Annual Report, pp258-259
Jon Calhoun (2017): Analyzing The Propagation of Soft-Error Corruption in HPC Applications, 2017 Blue Waters Annual Report, pp264-265
Paul Hime (2017): Genomic Perspectives on The Amphibian Tree of Life, 2017 Blue Waters Annual Report, pp268-269
Alexandra Jones (2017): High Accuracy Radiative Transfer in Cloudy Atmospheres, 2017 Blue Waters Annual Report, pp272-273
Andrew Kirby (2017): High Fidelity Blade-Resolved Wind Farm Simulations, 2017 Blue Waters Annual Report, pp274-275
Sara Kokkila Schumacher (2017): Reducing The Computational Cost of Coupled Clustery Theory, 2017 Blue Waters Annual Report, pp276-277
Larissa Reames (2017): Simulated effects of urban environments on the dynamics of a supercell thunderstorm, 2017 Blue Waters Annual Report, pp278-279
Erin Teich (2017): Glassy Dynamics and Identity Crises in Hard-Particle Systems, 2017 Blue Waters Annual Report, pp286-287
Samuel Totorica (2017): Magnetic reconnection in laser-driven plasmas: from astrophysics to the laboratory in silico, 2017 Blue Waters Annual Report, pp288-289
Michael Howard (2017): Multiscale simulations of complex fluid rheology, 2017 Blue Waters Annual Report, pp270-271
Ronald Stenz (2017): The Impacts of Hydrometeor Centrifuging on Tornado Dynamics, 2017 Blue Waters Annual Report, pp284-285

2016

Maureen Brooks (2016): Modeling nonlinear physical-biological interactions: Sargassum in the North Atlantic, 2016 Blue Waters Annual Report, pp260-261
Jon Calhoun (2016): Improving Checkpoint Restart with Lossy Compression, 2016 Blue Waters Annual Report, pp264-265
Justin Drake (2016): Solvation Thermodynamics of The Protein Backbone: Implications for Collapse and Aggregation, 2016 Blue Waters Annual Report, pp266-267
Alexandra Jones (2016): High Accuracy Radiative Transfer in Cloudy Atmospheres, 2016 Blue Waters Annual Report, pp278-279
Joshua Mendez (2016): The Triboelectric Charging of Volcanic Materials, 2016 Blue Waters Annual Report, pp268-269
Ariana Minot (2016): Distributed Algorithms for Power System Monitoring and Control, 2016 Blue Waters Annual Report, pp270-271
Larissa Reames (2016): Sensitivity of Simulated Urban-Atmosphere Interactions in Oklahoma City to Urban Parameterization, 2016 Blue Waters Annual Report, pp284-285
George Slota (2016): Processing Trillion Edge Graphs in Distributed Memory, 2016 Blue Waters Annual Report, pp282-283
Samuel Totorica (2016): Particle Acceleration in Laser-Driven Magnetic Reconection, 2016 Blue Waters Annual Report, pp272-273
Sara Kokkila Schumacher (2016): Reducing The Computational Cost of Coupled Clustery Theory, 2016 Blue Waters Annual Report, pp274-275
Edwin Mathews (2016): Large-Eddy Simulations of Aero-Optic Distortions, 2016 Blue Waters Annual Report, pp262-263
Barbara Zemskova: Ocean Energetics and Convection
Blue Waters Symposium 2017, May 18, 2017

Justin Drake and B.M. Pettitt: The Protein Backbone: How Structural and Thermodynamic Properties Scale With Chain Length


21st Annual Structural Biology Symposium; Galveston, Texas, U.S.A., Apr 23, 2016

Justin Drake and B.M. Pettitt: The Protein Backbone: How Structural and Thermodynamic Properties Scale with The Length of a Model, Disordered Polypeptide


251st American Chemical Society National Meeting and Exposition; San Diego, California, U.S.A., Mar 15, 2016

Maureen T. Brooks: Linking Satellite Observations with Coupled Bio-physical Models of Sargassum


2016 Ocean Sciences Meeting; New Orleans, Louisiana, U.S.A., Feb 23, 2016

Edwin Mathews, K. Wang, M. Wang, and E. J. Jumper: LES Prediction and Analysis of the Aero-optical Environment Around a 3-D Turret


68th Annual Meeting of the American Physical Society (APS) Division of Fluid Dynamics; Boston, Massachusetts, U.S.A., Nov 22, 2015

George Slota: Parallel Graph Algorithms on Modern Systems


29th IEEE International Parallel and Distributed Processing Symposium (IPDPS15); Hyderabad, India, May 26, 2015

Edwin Mathews: High-Fidelity Computation of Aero Optics


Blue Waters Symposium 2015, May 11, 2015

Matthew Clayton Bedford: A Multi-ion Model of the Heliosphere with Secondary Charge Exchange


American Geophysical Union (AGU) Fall 2014 Meeting; San Francisco, California, U.S.A., Dec 15, 2014

UIUC’s Supercomputer Has a Projected $1B Impact On Illinois’ Economy


May 12, 2017

Nestled on the outskirts of the University of Illinois at Urbana-Champaign campus — at the corner of Oak Street and St. Mary’s Road — is Blue Waters, a supercomputer that was first instituted as a result of a 2007 National Science Foundation grant and an initial $60 million investment from the State of Illinois. A report released this past week on the economic impact of this supercomputer — on the UIUC campus, its five surrounding counties, as well as nationwide spillover effects — puts a whole new meaning to the term “return on investment.”


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Blue Waters Graduate Fellow: Erin Teich


Sep 22, 2016

Very generally, what we study in our labs is a process called self-assembly. And this is relevant for a lot of different processes, but it turns out that material on a variety of scales basically self-organizes. This allows for the creation of materials by basically harnessing the urge that things have on certain temperature and energy scales in order to self-organize. They do that because they want to minimize their free energy. For the Blue Waters Fellowship, I'll be looking at disordered materials via simulation. There are materials called glasses, which is just like everyday glass, and amazingly enough, they are still not well understood. Physicists have been studying glass for decades and decades, and really centuries if you think about it, and physical properties of glasses still aren't well understood; like how glasses form, and whether or not that's a phase transition. So with the Blue Waters Fellowship, I'll be simulating glass formation in colloidal systems on the microscale, and trying to uncover, if possible, some of the reasons why glass formation happens in those types of systems.


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Blue Waters Graduate Fellow: Ronald Stenz


Oct 13, 2016

For my research, I am trying to determine the impacts that precipitation centrifuging has on tornado dynamics. I have always been fascinated with severe weather and tornadoes, which inspired me to study atmospheric sciences. I am studying this particular topic because in numerical simulations of tornadoes, an unrealistic rain blob appears in the core of simulated tornadoes. My goal is to make these simulations more realistic with a centrifuging algorithm, and to determine the resulting effect on tornado dynamics. Since gathering accurate and dense observations around a tornado is incredibly difficult and dangerous, numerical modeling is a major tool used to understand tornadoes. For my research I use a model called CM1 to numerically simulate tornadoes so we can study how they form, what environments they form in, and what factors lead to intensification or weakening of tornadoes.


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Blue Waters Graduate Fellow: Andrew Kirby


Dec 13, 2016

I am studying Mechanical Engineering at the University of Wyoming. I research numerical methods for computational fluid dynamics (CFD). My research is in the field of CFD. Specifically, I develop numerical solvers for the Navier-Stokes equations which govern fluid dynamics. I apply these methods that I develop to applications in wind energy and aerospace. We hope to simulate entire wind farm systems to determine properties such as power and thrust of the wind turbines and how their interactions interplay with each other. CFD also allows you to visualize your results. It gives a nice feedback loop on seeing you results (that are usually really cool to look at too). Lately, I have been really interested in the high performance computing aspect as well. I really enjoy trying to write really fast and efficient code that runs on the largest supercomputers in the world.


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Blue Waters Graduate Fellow: Paul Hime


Sep 27, 2016

advances in genome sequencing technologies have opened up exciting new avenues for phylogeneticists to survey broad swaths of the genome and to untangle some of the difficult branches in the Tree of Life. This new flood of genetic data itself is necessary, but not sufficient, to answer some of the most thorny evolutionary questions. As the amount of data available to evolutionary biologists has expanded, so too have the computational challenges to appropriately modeling DNA evolution between organisms. My doctoral research in the Weisrock Lab at University of Kentucky uses new computational and statistical approaches to reconstruct evolutionary relationships. I utilize amphibians (frogs, salamanders, and caecilians) as a model system in which to explore these exciting questions. Access to extremely powerful supercomputing resources is vital to this research, and the Blue Waters Fellowship through the NCSA provides unprecedented opportunities to advance this work. ... the NSF-funded Blue Waters supercomputer will allow me to probe aspects of phylogenetics which have previously been inaccessible due to computational constraints.


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Ten PhD students from across the country selected as Blue Waters Graduate Fellows


Apr 19, 2016

Ten outstanding computational science PhD students from across the country have been selected to receive Blue Waters Graduate Fellowships for 2016-2017. The fellowship program, now in its third year, provides substantial support and the opportunity to leverage the petascale power of National Center for Supercomputing Applications (NCSA) at the University of Illinois’s Blue Waters supercomputer to advance their research. The awards are made to outstanding PhD graduate students who have decided to incorporate high performance computing and data analysis into their research.


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Six PhD students from across the country selected as Blue Waters Graduate Fellows


Apr 28, 2014

Six outstanding computational science PhD students from across the country have been selected to receive the first Blue Waters Graduate Fellowships, which provide graduate students in diverse fields with substantial support and the opportunity to leverage the petascale power of NCSA’s Blue Waters supercomputer to advance their research. Over three years this fellowship program will award more than $1 million and nearly 30 million integer-core hours to support graduate research.


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Blue Waters Graduate Fellow: Sean Seyler


Dec 7, 2016

Proteins, such as membrane transporters or enzymes, are much like nanomachines that undergo structural changes—conformational transitions—between multiple states in order to perform chemical or mechanical work. These transitions are rare events that, due to the equilibrium sampling problem, are difficult to reproduce in equilibrium molecular dynamics (MD) simulation. The paradigm for studying these processes is the so-called structure-function connection; in principle, one should be able to infer a protein's function (its dynamical structural changes) given information about its structure (its 3D "shape" and amino acid sequence). Given the enormous computational difficulty of simulating highly complex, heterogeneous biomacromolecules on sufficiently long time scale, the majority of my research is focused on the development of computational methods and software tools that can help to more effectively sample and quantify protein conformational motions and transitions.


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Blue Waters Graduate Fellow: Elizabeth Agee


Oct 3, 2016

My research is focused on the interactions between forest ecosystems and hydrology. Over 50% of global evapotranspiration comes from forested ecosystems, so this represents a significant pathway for understanding global water and energy cycling. The question that drives my research is how these pathways will respond to climate change. Using Blue Waters, I will explore how tree species in the Amazon rainforest use water in different ways and how those differences influence community resilience to drought events. It is my hope that this work will improve the representation of tropical forests in the current suite of land surface models and provide mechanistic insights into forest community dynamics.


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Blue Waters Graduate Fellow: Sherwood Richers


Oct 31, 2016

My primary interest in neutrino transport has a couple of objectives. Let's look at core-collapse supernovae first. The big problem in this field is that observers watch stars explode on a daily basis, but when we put the most complete set of physics possible in the largest simulations running on supercomputers (like Blue Waters), they don't consistently explode. Something is missing, and that something might be a proper treatment of neutrino transport. The equations describing neutrino transport are notoriously difficult to simulate, so they have to be heavily approximated, but I am trying to remove as much of the approximation as I can.


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Blue Waters Graduate Fellow: Iryna Butsky


Sep 19, 2016

I really enjoyed my research on galactic magnetic fields, and I wanted to pursue it further. I'm very interested in studying the contribution of cosmic rays to the turbulent dynamo which amplifies galactic magnetic fields. Cosmic rays are tricky to model in galaxy simulations and have thus oftentimes been ignored. However, they could be key to the explanation of the strength of observed field strengths.


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Blue Waters Graduate Fellow: Michael Howard


Oct 7, 2016

The goals of my research are two-fold: (1) to develop massively parallel software for doing simulations of multiphase/complex fluids, and (2) to use this software to study enhanced oil recovery. I first plan to implement a developed algorithm for doing these types of simulations (multiparticle collision dynamics—MPCD) on GPUs. GPU acceleration will allow us to study problems at realistic length and time scales. To date, there has only been limited public availability of these types of codes, and so I plan to release the software open-source. I will then apply my software to study the initial stages of enhanced oil recovery—the process by which additional oil is extracted from geological formations.


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Four additional students named Blue Waters Graduate Fellows


Jul 7, 2014

Four additional computational science PhD students have been selected to receive Blue Waters Graduate Fellowships, which provide graduate students in diverse fields with substantial support and the opportunity to leverage the petascale power of NCSA’s Blue Waters supercomputer to advance their research. Six graduate fellows were named earlier this spring. Because of the large number of qualified applicants, NCSA sought and was awarded additional fellowship funding from the National Science Foundation, enabling the Blue Waters project to support a total of 10 graduate fellows.


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Six PhD students from across the country selected as Blue Waters Graduate Fellows


May 4, 2015

Six outstanding computational science PhD students from across the country have been selected to receive Blue Waters Graduate Fellowships for 2015-2016. The fellowship program, now in its second year, provides graduate students in diverse fields with substantial support and the opportunity to leverage the petascale power of NCSA’s Blue Waters supercomputer to advance their research.


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How layout of urban areas affect supercell thunderstorms


Sep 30, 2016

Many things go into consideration when planning a city layout, roads, transportation needs, location relative to natural features. However, one thing has not previously been considered is the shape of the city and how that shape affects the severity of natural disasters, such as extreme thunderstorms or tornadoes. With the help of Blue Waters at the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign, Larissa Reames, a Ph.D student at the University of Oklahoma and a 2015-2016 NCSA Blue Waters Graduate Fellow, is undertaking exciting meteorology research on the effects of supercell thunderstorms and how the specific layout of a city can affect a storm’s impact.


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Blue Waters pushes magnetic reconnection research


Dec 6, 2016

Magnetic reconnection is the scientific process in which oppositely aligned magnetic field lines in a plasma break and form new connections. The newly connected magnetic fields are bent and have a tension that can accelerate the plasma like a slingshot. This process is still not well-understood, but base knowledge is the energy released from the magnetic field accelerates the particles in the plasma during reconnection. Plasma jets, and more generally, plasma, is an important subject in high-energy-density laboratory astrophysics. "Plasma is the most abundant form of ordinary (non-dark) matter in the universe, so understanding plasmas is necessary for understanding systems in astrophysics," said Sam Totorica, NCSA Blue Waters Graduate Fellow from Stanford University.


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Extreme-scale Graph Analysis on Blue Waters


Aug 27, 2016

In this video from the 2016 Blue Waters Symposium, George Slota from Pennsylvania State University presents: Extreme-scale Graph Analysis on Blue Waters.


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NCSA releases 2017 Blue Waters Project Annual Report Detailing Innovative Research and Scientific Breakthroughs


Sep 1, 2017

The National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign released today the 2017 Blue Waters Project Annual Report. For the project’s fourth annual report, research teams were invited to present highlights from their research that leveraged Blue Waters, the National Science Foundation’s (NSF) most powerful system for sustained computation and data analysis. Spanning economics to engineering, geoscience to space science, Blue Waters has accelerated research and impact across an enormous range of science and engineering disciplines throughout its more than 4-year history covered by the report series. This year is no different.


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University of Oklahoma astrophysics team explains Mars’ stunted growth


May 4, 2018

A University of Oklahoma astrophysics team explains why the growth of Mars was stunted by an orbital instability among the outer solar system’s giant planets in a new study on the evolution of the young solar system. The OU study builds on the widely-accepted Nice Model, which invokes a planetary instability to explain many peculiar observed aspects of the outer solar system. An OU model used computer simulations to show how planet accretion (growth) is halted by the outer solar system instability. Without it, Mars possibly could have become a larger, habitable planet like Earth. “This study offers a simple and more elegant solution for why Mars is small, barren and uninhabitable,” said Matthew S. Clement, OU graduate student in the Homer L. Dodge Department of Physics and Astronomy, OU College of Arts and Sciences.


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The Giant Planets in the Solar System Stunted the Growth of Mars


May 10, 2018

For centuries, astronomers and scientists have sought to understand how our Solar System came to be. Since that time, two theories have become commonly-accepted that explain how it formed and evolved over time. These are the Nebular Hypothesis and the Nice Model, respectively. Whereas the former contends that the Sun and planets formed from a large cloud of dust and gas, the latter maintains the giant planets have migrated since their formation. This is what has led to the Solar System as we know it today. However, an enduring mystery about these theories is how Mars came to be the way it is. Why, for example, is it significantly smaller than Earth and inhospitable to life as we know it when all indications show that it should be comparable in size? According to a new study by an international team of scientists, the migration of the giant planets could have been what made the difference. As Matt Clement, a graduate student in the HL Dodge Department of Physics and Astronomy at the University of Oklahoma and the lead author on the paper, explained to Universe Today via email: “In the model, the giant planets (Jupiter, Saturn, Uranus and Neptune) originally formed much closer to the Sun. In order to reach their current orbital locations, the entire solar system undergoes a period of orbital instability. During this unstable period, the size and the shape of the giant planet’s orbits change rapidly.” For the sake of their study, which was recently published in the scientific journal Icarus under the title “Mars Growth Stunted by an Early Giant Planet Instability“, the team expanded on the Nice Model. Through a series of dynamical simulations, they attempted to show how, during the early Solar System, the growth of Mars was halted thanks to the orbital instabilities of the giant planets.


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