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2025

Hannah Klion, Robert Hetland, Jean Sexton, Ann Almgren, Iulian Grindeanu, Kyle Hinson, Vijay Mahadevan REMORA: Regional Modeling of Oceans Refined Adaptively (built on AMReX), Journal of Open Source Software, Submitted.

R. Jambunathan, H. Jones, L. Corrales, H. Klion, M. Rowan, A. Myers, W. Zhang, and J.-L. Vay, Application of mesh refinement to relativistic magnetic reconnection , Physics of Plasmas, 32, 013905, January 2025. [link]

Y. Tang, W. Xu, J. Cao, J. Ma, W. Gao, S. Farrell, B. Erichson, M. W. Mahoney, A. Nonaka, Z. Yao, MatterChat: A Multi-Modal LLM for Material Science, submitted for publication, 2025. [arXiv]

Aaron Lattanzi, Ann Almgren, Eliot Quon, Mahesh Natarajan, Branko Kosovic, Jeffrey Mirocha, Bruce Perry, David Wiersema, Donald Willcox, Xingqiu Yuan, Weiqun Zhang, ERF: Energy Research and Forecasting Model, submitted for publication, 2025. [arXiv]

J. B. Bell, A. Nonaka, and A. L. Garcia, Comment on "Brownian motion of droplets induced by thermal noise", submitted for publication, 2025. [arXiv]

I. Srivastava, A. J. Nonaka, W. Zhang, A. L. Garcia, and J. B. Bell, Molecular Fluctuations Inhibit Intermittency in Compressible Turbulence, submitted for publication, 2025. [arXiv]

Qianqian Su, F. Li, W. An, V. Decyk, Y. Zhao, L. Hildebrand, T.N. Dalichaouch, S. Zhou, P. Alves, A.S. Almgren and W.B. Mori, Mesh refinement in QuickPIC, submitted for publication.

Ana Djurdjevac, Ann Almgren, and John Bell, A Hybrid Algorithm for Systems of Non-interacting Particles, submitted for publication, 2025. [arxiv]

S. S. Sawant, F. Leonard, Z. Yao, A. Nonaka, ELEQTRONeX: A GPU-Accelerated Exascale Framework for Non-Equilibrium Quantum Transport in Nanomaterials, submitted for publication, 2025. [arxiv]

Y. Tang, R. Chen, M. Lou, J. Fan, C. Yu, A. Nonaka, Z. Yao., W. Gao, Optical Neural Engine for Solving Scientific Partial Differential Equations, submitted for publication, 2025. [arxiv]

M. Polimeno, C. Kim, F. Blanchette, I. Srivastava, A. L. Garcia, A. Nonaka, and J. B. Bell, Thermodynamic consistency and fluctuations in mesoscopic stochastic simulations of reactive gas mixtures, submitted for publication, 2025. [arxiv]

J. B. Bell, A. Nonaka, and A. L. Garcia, Spherical and sessile droplet dynamics by fluctuating hydrodynamics, Physics of Fluids, 37, 012024, 2025. [link]

J. M. Monti, I. Srivastava, L. E. Silbert, A. P. Santos, J. B. Lechman, G. S. Grest, Emergence of Intermediate Range Order in Jammed Packings, submitted for publication, 2025. [arxiv]

Bruce J. Palmer, Connah G.M. Johnson, Ann S. Almgren, Andrew T Myers, and William R. Cannon, Three-dimensional modeling of hyphal fusion, branching and nutrient tranport in filamentous fungi, to appear, 2025.

2024

Alejandro L. Garcia, John B. Bell, Andrew Nonaka, Ishan Srivastava, Daniel Ladiges, Changho Kim, An Introduction to Computational Fluctuating Hydrodynamics, 2024. [arxiv]

R. Zgadzaj, J. Welch, Y. Cao, L. D. Amorim, A. Cheng, A. Gaikwad, P. Iapozzutto, P. Kumar, V. N. Litvinenko, I. Petrushina, R. Samulyak, N. Vafaei-Najafabadi, C. Joshi, C. Zhang, M. Babzien, M. Fedurin, R. Kupfer, K. Kusche, M. A. Palmer, I. V. Pogorelsky, M. N. Polyanskiy, C. Swinson, and M. C. Downer, Plasma electron acceleration driven by a long-wave-infrared laser, Nat Commun 15, 4037 (2024). [doi].

Andrew Myers, Weiqun Zhang, Ann Almgren, Thierry Antoun, John Bell, Axel Huebl and Alexander Sinn, AMReX and pyAMReX: Looking Beyond ECP, International Journal of High Performance Computing Applications , August 2024, [doi]

P. Kumar, M. Hoffmann, A. Nonaka, S. Salahuddin, and Z. Yao 3D ferroelectric phase field simulations of polycrystalline multi-phase hafnia and zirconia based ultra-thin films, Advanced Electronic Materials, 2400085, 2024. [link]

A.M. Lattanzi, W.D. Fullmer, A. Myers, J. Musser, Towards polydisperse flows with MFIX-Exa, ASME. J. Fluids Eng, 23 January 2024. [doi].

Lois Curfman McInnes, Michael Heroux, David E. Bernholdt, Anshu Dubey, Elsa Gonsiorowski, Rinku Gupta, Osni Marques, J. David Moulton, Hai Ah Nam, Boyana Norris, Elaine M. Raybourn, Jim Willenbring, Ann Almgren, Ross Bartlett, Kita Cranfill, Stephen Fickas, Don Frederick, William Godoy, Patricia Grubel, Rebecca Hartman-Baker, Axel Huebl, Rose Lynch, Addi Maiviya Thakur, Reed Milewicz, Mark C. Miller, Miranda Mundt, Erik Palmer, Suzanne Parete-Koon, Megan Phinney, Katherine Riley, David M. Rogers, Ben Sims, Deborah Stevens, Gregory R. Watson, A cast of thousands: How the IDEAS Productivity project has advanced software productivity and sustainability, Computing in Science and Engineering, 2024. [ieee] [arxiv]

I. Barrio Sanchez, A. S. Almgren, J. B. Bell, M.T. Henry de Frahan, W. Zhang, A New Re-redistribution Scheme for Weighted State Redistribution with Adaptive Mesh Refinement, J. Comp. Phys., Volume 504, 1 May 2024. [arxiv], [doi]

J. L. Loffeld, A. J. Nonaka, D. R. Reynolds, D. J. Gardner, and C. S. Woodward, Performance of explicit and IMEX MRI multirate methods on complex reactive flow problems within modern parallel adaptive structured grid frameworks, International Journal of High Performance Computing Applications, 10943420241227914, 2024. [link]

Marc T. Henry de Frahan, Lucas Esclapez, Jon Rood, Nicholas Wimer, Paul Mullowney, Bruce A. Perry, Landon Owen, Hariswaran Sitaraman, Shashank Yellapantula, Malik Hassanaly, Mohammad J. Rahimi, Michael Martin, Olga Doronina, Sreejith Nadakkal Appukuttan, Martin Rieth, Wenjun Ge, Ramanan Sankaran, Ann Almgren, Weiqun Zhang, John B. Bell, Ray Grout, Marc S. Day, Jacqueline H. Chen, The Pele Simulation Suite for Reacting Flows at Exascale, SIAM Proceedings Series on Parallel Processing for Scientific Computing, 2024. [link]

Ashesh Sharma, Michael J. Brazell, Ganesh Vijayakumar, Shreyas Ananthan, Lawrence Cheung, Nathaniel deVelder, Marc T. Henry de Frahan, Neil Matula, Paul Mullowney, Jon Rood, Philp Sakievich, Ann Almgren, Paul S. Crozier, Michael A. Sprague, ExaWind: Open-Source CFD for Hybrid-RANS/LES Geometry-Resolved Wind Turbine Simulations in Atmospheric Flows, Wind Energy, 23 January 2024. [doi]

2023

J. M. Monti, I. Srivastava, L. E. Silbert, J. B. Lechman, G. S. Grest, Fractal Dimensions of Jammed Packings with Power-Law Particle Size Distributions in Two and Three Dimensions, Phys. Rev. E, 108, L042902, 2023. [link]

L. Esclapez, M. Day, J. Bell, A. Felden, C. Gilet, R. Grout, M. Henry de Frahan, E. Motheau, A. Nonaka, L. Owen, B. Perry, J. Rood, N. Wimer, and W. Zhang, PeleLMeX: an AMR Low Mach Number Reactive Flow Simulation Code without level sub-cycling, Journal of Open Source Software, 8, 2023. [link]

A. J. Peterson, D. Willcox, and P. Moesta, Code generation for AMReX with applications to numerical relativity, Classical and Quantum Gravity, 8, 245013, 2023. [link]

J. Galen Wang, Daniel R. Ladiges, Ishan Srivastava, Sean P. Carney, Andy J. Nonaka, Alejandro L. Garcia, John B. Bell, Steric effects in induced-charge electro-osmosis for strong electric fields, Physical Review Fluids, 8, 083702, 2023. [arxiv] [doi]

H. Klion, R. Jambunathan, M. E. Rowan, E. Yang, D. Willcox, J.-L. Vay, R. Lehe, A. Myers, A. Huebl, W. Zhang, Particle-in-Cell Simulations of Relativistic Magnetic Reconnection with Advanced Maxwell Solver Algorithms, The Astrophysical Journal, 925, 1, 2023. [arxiv] [doi]

Bryn Barker, John Bell and Alejandro Garcia, Fluctuating Hydrodynamics and the Rayleigh-Plateau Instability, PNAS, 120(30), July 2023. [arxiv] [doi]

R. Jambunathan, Z. Yao, R. Lombardini, A. Rodriguez, and A. Nonaka, Two-Fluid Physical Modeling of Superconducting Resonators in the ARTEMIS Framework, Computer Physics Communications, 291, 2023. [arxiv] [doi]

Bruce J. Palmer, Ann S. Almgren, Connah G.M. Johnson, Andrew T Myers, and William R. Cannon, BMX: Biological Modelling and interface eXchange, Nature Scientific Reports, 13, July 2023. [doi]

Ann Almgren, Aaron Lattanzi, Riyaz Haque, Pankaj Jha, Branko Kosovic, Jeffrey Mirocha, Bruce Perry, Eliot Quon, Michael Sanders, David Wiersema, Donald Willcox, Xingqiu Yuan, Weiqun Zhang, ERF: Energy Research and Forecasting, Journal of Open Source Software, 8(87), 5202, 2023. [doi]

Roberto Porcu, Jordan Musser, Ann S. Almgren, John B. Bell, William D. Fullmer, Deepak Rangarajan, MFIX-Exa: CFD-DEM simulations of thermodynamics and chemical reactions in multiphase flows, Chemical Engineering Science, 273, 118614, 2023. [doi]

E. Mercado, H. T. Jung, C. Kim, A. L. Garcia, A. J. Nonaka, and J. B. Bell, Surface Coverage Dynamics for Reversible Dissociative Adsorption on Finite Linear Lattices, J. Chem. Phys., 159, 2023. [doi] [arxiv]

F. Baras, Alejandro L. Garcia, and M. Malek Mansour, Validity of path thermodynamic description of reactive systems: Microscopic simulations, Phys. Rev. E 107, 014106, 2023. [doi]

Yadong Zeng, Han Liu, Qiang Gao, Ann Almgren, Amneet Pal Singh Bhalla, Lian Shen, A consistent adaptive level set framework for incompressible two-phase flows with high density ratios and high Reynolds numbers, J. Comp. Phys., vol. 478, 2023.

P. Kumar, A. Nonaka, R. Jambunathan, G. Pahwa, S. Salahuddin, and Z. Yao, FerroX: A GPU-accelerated, 3D Phase-Field Simulation Framework for Modeling Ferroelectric Devices, Computer Physics Communications, 108757, 2023 [link]

I. Srivastava, D. R. Ladiges, A. Nonaka, A. L. Garcia, J. B. Bell, A Staggered Scheme for the Compressible Fluctuating Hydrodynamics of Multispecies Fluid Mixtures, Physical Review E, 107, 015305, 2023. [arxiv] [doi]

2022

Z. Chang, L. Fang, V. Fedorov, S. Ghimire, C. Heide, N. Ishii, J. Itatani, C. Joshi, Y. Kobayashi, P. Kumar, A. Marra , S. Mirov, I. Petrushina, M. Polyanskiy, D. A. Reis, S. Tochitsky, S. Vasilyev, L. Wang, Y. Wu, and F. Zhou, Intense infrared lasers for strong-field science, Advances in Optics and Photonics 2022. [link]

S. T. Sewell, P. Kumar, and K. Hara, Effects of the wavelength of the plasma waves on cross-field electron transport in partially magnetized plasmas, IEEE Transactions on Plasma Science, vol. 50, no. 10, pp. 3498-3506 2022. [link]

K. Yu, P. Kumar, S. Yuan, A. Cheng, and R. Samulyak, SPACE: 3D parallel solvers for Vlasov-Maxwell and Vlasov-Poisson equations for relativistic plasmas with atomic transformations, Computer Physics Communications 277 (2022) 108396 2022. [link]

A. Castillo, P. Kumar, C. Limbach, and K. Hara, Mutually Guided Light and Particle Beam Propagation, Scientific Reports volume 12, Article number: 4810 2022. [link]

D. R. Ladiges, J. G. Wang, I. Srivastava, S. P. Carney, A. Nonaka, A. L. Garcia, A. Donev and J. B. Bell, Modeling Electrokinetic Flows with the Discrete Ion Stochastic Continuum Overdamped Solvent Algorithm, Physical Review E, 106, 035104, 2022. [doi]

Solene Chabanier, J.D. Emberson, Zarija Lukic, Jesus Pulido, Salman Habib, Esteban Rangel, Jean Sexton, Nicholas Frontiere, Michael Buehlmann, Modeling the Lyman-alpha forest with Eulerian and SPH hydrodynamical methods, MNRAS, 518, 3, January 2023. [arxiv] [doi]

Luca Fedeli, Axel Huebl, France Boillod-Cerneux, Thomas Clark, Kevin Gott, Conrad Hillairet, Stephan Jaure, Adrien Leblanc, Rémi Lehe, Andrew Myers, Christelle Piechurski, Mitsuhisa Sato, Neil Zaïm, Weiqun Zhang, Jean-Luc Vay, Henri Vincenti, Pushing the frontier in the design of laser-based electron accelerators with groundbreaking mesh-refined particle-in-cell simulations on exascale-class supercomputers, SC '22: Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, November 2022, Article No.: 3, Pages 1–12 [doi]

J. M. Monti, J. T. Clemmer, I. Srivastava, L. E. Silbert, G. S. Grest, J. B. Lechman, Large-Scale Frictionless Jamming with Power-Law Particle Size Distributions, Physical Review E, 106, 034901, 2022. [doi]

S. Sawant, Z. Yao, R. Jambunathan, and A. Nonaka, Characterization of Transmission Lines in Microelectronics Circuits using the ARTEMIS Solver, IEEE J. on Multiscale and Multiphysics Comp. Tech., 8, 2022. [link]

D. Fan, D. E. Willcox, C. DeGrendele, M. Zingale, and A. Nonaka, Neural Networks for Nuclear Reactions in MAESTROeX, The Astrophysical Journal, 940, 2, 2022. [link]

M. Zingale, M. P. Katz, A. Nonaka, and M. Rasmussen, An Improved Method for Coupling Hydrodynamics with Astrophysical Reaction Networks, The Astrophysical Journal, 936, 6, 2022. [link]

A. P. Santos, I. Srivastava, L. E. Silbert, J. B. Lechman and G. S. Grest, Fluctuations and Power-Law Scaling of Dry, Frictionless Granular Rheology Near the Hard-Particle Limit, Physical Review Fluids, 7, 084303, 2022. [doi]

Jon Rood, Marc Henry de Frahan, Marc Day, Hariswaran Sitaraman, Shashank Yellapantula, Bruce Perry, Ray Grout, Ann Almgren, Weiqun Zhang, John B. Bell, Jacqueline Chen, PeleC: An Adaptive Mesh Refinement Solver for Compressible Reacting Flows, International Journal of High Performance Computing Applications, 2022. [doi]

Soumya Dutta, Terece Turton, David Rogers, Jordan M. Musser, James Ahrens, Ann S. Almgren, In Situ Feature Analysis for Large-Scale Multiphase Flow Simulations,, Journal of Computational Science, 2022.

Mu-Hua Chien, Olivier M. Pauluis, Ann S. Almgren, Hurricane-like Vortices in Conditionally Unstable Moist Convection, Journal of Advances in Modeling Earth Systems, 2022. [ESSOAr]

A. Giuliani, A.S. Almgren, J.B. Bell, M.J. Berger, M.T. Henry de Frahan, D. Rangarajan, Weighted State Redistribution Algorithms for Embedded Boundary Methods, J. Comp. Phys., Vol 464, Sept. 2022.

John Bell, Andrew Nonaka, Alejandro L. Garcia, Gregory Eyink, Thermal Fluctuations in the Dissipation Range of Homogeneous Isotropic Turbulence, J. Fluid Mech., 939, 2022. [link]

Severin Diederichs, Carlo Benedetti, Axel Huebl, Remi Lehe, Andrew Myers, Alexander Sinn, Jean-Luc Vay, Weiqun Zhang, Maxence Thevenet, HiPACE++: a portable, 3D quasi-static Particle-in-Cell code, Computer Physics Communications, 278, 108421, 2022. [link][arXiv]

Malte Buschmann, Joshua W foster, Anson Hook, Adam Peterson, Don E Willcox, Weiqun Zhang, Benjamn R Safdi, Dark Matter from Axion Strings with Adaptive Mesh Refinement, Nature Communications, 13, 1049, 2022. [doi][arXiv]

Mahesh Natarajan, Ray Grout, Weiqun Zhang, Marcus Day, A Moving Embedded Boundary Approach for the Compresible Navier-Stokes Equations in a Block-Structured Adaptive Refinement Framework, J. Comp. Phys., 465, 2022. [doi][arXiv]

V. Gulizzi, A. S. Almgren, John B. Bell "A coupled discontinuous Galerkin-Finite Volume framework for solving gas dynamics over embedded geometries", J. Comp. Phys., 450, 2022. [arxiv]

2021

J. Mueller, J. Park, R.Sahu, C. Varadharajan, B. Arora, B. Faybishenko, D. Agarwal, Surrogate Optimization of Deep Neural Networks for Groundwater Predictions, J. Global Optimization, 81, 2021. [springer].

Sherwood Richers, Donald Willcox, Nicole Ford, Neutrino Fast Flavor Instability in Three Dimensions, Physical Review D, 104, 103023, 2021. [doi]

Robin J Dolleman, Debadi Chakraborty, Daniel R Ladiges, Herre SJ van der Zant, John E Sader, and Peter G Steeneken, Squeeze-film effect on atomically thin resonators in the high-pressure limit, Nano Letters, 2021. [doi]

Andrew Myers, Ann Almgren, Diana Almorim, John Bell, Luca Fedeli, Lixin Ge, Kevin Gott, David Grote, Mark Hogan, Axel Huebl, Revathi Jambunathan, Remi Lehe, Cho Ng, Michael Rowan, Olga Shapoval, Maxence Thevenet, Jean-Luc Vay, Henri Vincenti, Eloise Yang, Neil Zaim, Weiqun Zhang, Yin Zhao, Edoardo Zoni, Porting WarpX to GPU-accelerated platforms, Parallel Computing, 2021.

I. Srivastava, L. E. Silbert, J. B. Lechman and G. S. Grest, Flow and Arrest in Stressed Granular Materials, Soft Matter, 2022. [doi]

I. Srivastava, S. A. Roberts, J. T. Clemmer, L. E. Silbert, J. B. Lechman, G. S. Grest, Jamming of Bidisperse Frictional Spheres, Physical Review Research, 3(3), L032042, 2021. [doi]

J. T. Clemmer, I. Srivastava, G. S. Grest, J. B. Lechman, Shear is Not Always Simple: Rate-Dependent Effects of Loading Geometry on Granular Rheology, Physical Review Letters, 127, 268003, 2021. [doi]

Jean Sexton, Zarija Lukic, Ann Almgren, Chris Daley, Brian Friesen, Andrew Myers, and Weiqun Zhang, Nyx: A Massively Parallel AMR Code for Computational Cosmology, Journal of Open Source Software, 6(63), 3068, 2021. [doi]

L. Fedeli, A. Sainte-Marie, N. Zaim, M. Thevenet, J. L. Vay, A. Myers, F. Quere, and H. Vincenti, Probing strong-field QED with Doppler-boosted petawatt-class lasers, accepted by Physical Review Letters, May 10, 2021, [PRL]

D. R. Ladiges, S. P. Carney, A. Nonaka, K. Kymko, G. C. Moore, A. L. Garcia, S. R. Natesh, A. Donev and J. B. Bell, A Discrete Ion Stochastic Continuum Overdamped Solvent Algorithm for Modeling Electrolytes, Physical Review Fluids, 6(4), 044309, 2021. [arxiv]

J. G. Wang and R. N. Zia, Vitrification is a spontaneous non-equilibrium transition driven by osmotic pressure, Journal of Physics: Condensed Matter, 33, 184002, 2021. [doi]

William D. Fullmer, Roberto Porcu, Jordan Musser, Ann S. Almgren, Ishan Srivastava, The divergence of nearby trajectories in soft-sphere DEM Particuology, 63, 1, 2022. [doi]

Weiqun Zhang, Andrew Myers, Kevin Gott, Ann Almgren and John Bell, AMReX: Block-Structured Adaptive Mesh Refinement for Multiphysics Applications, International Journal of High Performance Computing Applications, 35(6):508-526, 2021. [IJHPCA] [doi]

A. Harpole, N. M. Ford, K. Eiden, M. Zingale, D. E. Willcox, Y. Cavecchi, and M. P. Katz, Dynamics of Laterally Propagating Flames in X-Ray Bursts. II. Realistic Burning and Rotation, The Astrophysical Journal, 912 36, 2021. [doi]

Z. Yao, R. Jambunathan, Y. Zeng, and A. Nonaka, A Massively Parallel Time-Domain Coupled Electrodynamics-Micromagnetics Solver, International Journal of High Performance Computing Applications, 10943420211057906, 2021. [link]

Sherwood Richers, Don E. Willcox, Nicole M. Ford, Andrew Myers, Particle-in-cell Simulation of the Neutrino Fast Flavor Instability, Physical Review D, 103, 083013, 2021. [doi]

J-L Vay, Ann Almgren, LD Amorim, John Bell, L Fedeli, L Ge, K Gott, DP Grote, M Hogan, A Huebl, R Jambunathan, R Lehe, A Myers, C Ng, M Rowan, O Shapoval, M Thevenet, H Vincenti, E Yang, N Zaim, W Zhang, Y Zhao and E Zoni Modeling of a chain of three plasma accelerator stages with the WarpX electromagnetic PIC code on GPUs, Physics of Plasmas, 28(2), 2021. [doi]

I. Srivastava, L. E. Silbert, G. S. Grest, J. B. Lechman Viscometric Flow of Dense Granular Materials under Controlled Pressure and Shear Stress, Journal of Fluid Mechanics, 907(A18) 1, 2021. [doi]

Brandon Runnels, Vinamra Agrawal, Weiqun Zhang and Ann Almgren, Massively parallel finite difference elasticity using a block-structured adaptive mesh refinement with a geometric multigrid solver, J. Comp. Phys., 427, 2021. [doi] [arxiv].

L. Esclapez, F. Collin-Bastiani, E. Riber and B. Cuenot, "A statistical model to predict ignition probability", Combustion and Flame, 2021. [arxiv] [doi]

R. Jambunathan and D. Levin, "Kinetic, 3-D, PIC-DSMC Simulations of Ion Thruster Plumes and the Backflow Region" IEEE Transactions on Plasma Science, June 2020. [doi]

R. Jambunathan and D. Levin, "A self-consistent open boundary condition for fully-kinetic plasma thruster simulations", IEEE Transactions on Plasma Science, March 2020. [doi]

Jordan Musser, Ann S Almgren, William D Fullmer, Oscar Antepara, John B Bell, Johannes Blaschke,Kevin Gott, Andrew Myers, Roberto Porcu, Deepak Rangarajan, Michele Rosso, Weiqun Zhang, and Madhava Syamlal, MFIX:Exa: A Path Towards Exascale CFD-DEM Simulations, International Journal of High Performance Computing Applications, April 16, 2021.

E. Motheau and J. Wakefield, On the numerical accuracy in finite-volume methods to accurately capture turbulence in compressible flows, Int. J. Numer. Methods Fluids, 2021. [doi]

2020

Max P. Katz, Ann S. Almgren, Maria Barrios Sazo, Kiran Eiden, Kevin Gott, Alice Harpole, Jean M. Sexton, Don E. Willcox, Weiqun Zhang, and Michael Zingale, Preparing nuclear astrophysics for exascale, SC20: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, p. 1, 2020

Ann Almgren, Maria Barrios Sazo, John Bell, Alice Harpole, Max Katz, Jean Sexton, Donald Willcox, Weiqun Zhang, and Michael Zingale, CASTRO: A Massively Parallel Compressible Astrophysics Simulation Code, Journal of Open Source Software, 5, 54, 2513, 2020

Luigi Delle Site, Matej Praprotnik, John B. Bell and Rupert Klein, Particle-Continuum Coupling and its Scaling Regimes: Theory and Applications, Advanced Theory and Simulations, Vol. 3, No. 5, 1900232, 2020. [doi]

Y. Zhao, R. Lehe, A. Myers, M. Thevenet, A. Huebl, C. B. Schroeder, and J.-L. Vay, Modeling of emittance growth due to Coulomb collisions in plasma-based accelerators, Physics of Plasmas, October, 2020. [doi]

J-L Vay, Ann Almgren, LD Amorim, John Bell, L Ge, K Gott, DP Grote, M Hogan, A Huebl, R Jambunathan, R Lehe, A Myers, C Ng, J Park, M Rowan, O Shapoval, M Thevenet, W Zhang, Y Zhao, and E Zoni Toward the modeling of chains of plasma accelerator stages with WarpX, Journal of Physics: Conference Series, 1596, 1, 012059, 2020

A. Biswas, J. Ahrens, S. Dutta, A. Almgren, J. Musser, and T. Turton, Feature Analysis, Tracking, and Data Reduction: An Application to Multiphase Reactor Simulation MFiX-Exa for In-Situ Use Case, Computing in Science & Engineering, doi: 10.1109/MCSE.2020.3016927, 2020. [doi]

Yellapantula, S., Henry de Frahan, M., King, R., Day, M., and Grout. R., Machine Learning of Combustion LES Models from Reacting Direct Numerical Simulation in Data Analysis for Direct Numerical Simulations of Turbulent Combustion pp. 273-292, Sprint, Cham [doi]

D. Dalakoti, A. Wehrfritz, B. Savard, M. Day, J. Bell, and E. Hawkes, An a priori evaluation of a principal component and artificial neural network based combustion model in diesel engine conditions, Proc. Combust. Inst., 38, 1961-1969, 2021.

D. Dalakoti, B. Savard, E. R. Hawkes, A. Wehrfritz, H. Wang, M. Day, and J. Bell, Direct numerical simulation of a spatially developing n-dodecane jet flame under Spray A thermochemical conditions: Flame structure and stabilisation mechanism, Combust. Flame, 217:57-76, 2020.

K. Klymko, S. P. Carney, A. Nonaka, A. L. Garcia, and J. B. Bell, A Low Mach Number Fluctuating Hydrodynamics Model For Ionic Liquids, Phys. Rev. Fluids, 5, 9, 2020. [arxiv]

E. Motheau and J. Wakefield, "Investigation of finite-volume methods to capture shocks and turbulence spectra in compressible flows", Commun. in Appl. Math. and Comput. Sci, 15-1 (2020), 1--36. [arxiv]

V. Gulizzi, I. Benedetti, A. Milazzo "A high-resolution layer-wise discontinuous Galerkin formulation for multilayered composite plates", Composite Structures, 242, June 2020. [doi]

Leen Alawieh, Jonathan Goodman, John B. Bell, Iterative construction of Gaussian process surrogate models for Bayesian inference, Journal of Statistical Planning and Inference, 207, July 2020. [doi]

Nicholas Z. Liu, Daniel R. Ladiges, Jason Nassios, and John E. Sader, Acoustic flows in a slightly rarefied gas, Physical Review Fluids, 5(4), 043401, 2019. [doi]

F. Alexander, A. Almgren, J. Bell, A. Bhattacharjee, J. Chen, P. Colella, D. Daniel, J. DeSlippe, L. Diachin, E. Draeger, A. Dubey, T. Dunning, T. Evans, I. Foster, M. Francois, T. Germann, M. Gordon, S. Habib, M. Halappanavar, S. Hamilton, W. Hart, Z. Huang, A. Hungerford, D. Kasen, P. Kent, T. Kolev, D. Kothe, A. Kronfeld, Y. Luo, P. Mackenzie, D. McCallen, B. Messer, S. Mniszewski, C. Oehmen, A. Perazzo, D. Perez, D. Richard, W. Rider, R. Rieben, K. Roche, A. Siegel, M. Sprague, C. Steefel, R. Stevens, M. Syamlal, M. Taylor, J. Turner, J.-L. Vay, A. Voter, T. Windus and K. Yelick, Exascale applications: skin in the game, Phil. Trans. R. Soc. A, 2020. [doi].

W. Langhans, J. Mueller and W.D. Collins, Optimization of the Eddy-Diffusivity/Mass-Flux shallow cumulus and boundary-layer parametrization using surrogate models Journal of Advances in Modeling Earth Systems (JAMES), 11, 2, Feb. 2019. [doi]

Deepak K. Dalakoti, Alex Krisman, Bruno Savard, Armin Wehrfritz, Haiou Wang, Marc S. Day, John B. Bell, and Evatt R Hawkes Structure and propagation of two-dimensional, partially premixed, laminar flames in diesel engine conditions, Proc. Combust. Inst 37 (2) 2018. [doi]

2019

M. T. Henry de Frahan, S. Yellapantula, R. King, M. S. Day, R. W. Grout, Deep learning for presumed probability density function models Combustion and Flame 208, 2019. [doi]

D. Dasgupta, W. Sun, M. Day, A. Aspden and T. Lieuwen, Analysis of chemical pathways for n-dodecane/air turbulent premixed flames, Combustion and Flame 207, p. 36-50, 2019. [doi]

J. Mueller, An algorithmic framework for the optimization of computationally expensive bi-fidelity black-box problems, INFOR: Information Systems and Operational Research., 2019. [link].

J. Mueller and M. Day, Surrogate Optimization of Computationally Expensive Black-box Problems with Hidden Constraints INFORMS Journal on Computing, 31(4) 633, 2019. [doi]

Yong Shi, Daniel. R. Ladiges, and John E. Sader, Origin of spurious oscillations in lattice Boltzmann simulations of oscillatory noncontinuum gas flows, Physical Review E, 100(5), 053317, 2019. [doi]

D. Fan, A. Nonaka, A. S. Almgren, D. E. Willcox, A. Harpole, and M. Zingale, MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver Journal of Open Source Software, 4, 44, 1757, 2019. [link]

D. Fan, A. Nonaka, A. S. Almgren, A. Harpole, and M. Zingale, MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver Astrophysical Journal, 887, 2, 2019. [link]

M. Zingale, M. P. Katz, J. B. Bell, M. L. Minion, A. J. Nonaka, W. Zhang, Improved Coupling of Hydrodynamics and Nuclear Reactions via Spectral Deferred Corrections, Astrophysical Journal, 886, 2, 2019 [arxiv]

Muhammad Nufail Farooqi, Tan Nguyen, Weiqun Zhang, Ann Almgren, John Shalf, and Didem Unat, Asynchronous AMR on Multi-GPUs, ISC High Performance conference: REFAC'19, 2019.

Knut Sverdrup, Ann S. Almgren, and Nikolaos Nikiforakis, An embedded boundary approach for efficient simulations of viscoplastic fluids in three dimensions, Physics of Fluids, 2019 [doi].

W. Zhang, A. Almgren, V. Beckner, J. Bell, J. Blaschke, C Chan, M. Day, B. Friesen, K. Gott, D. Graves, M. Katz, A. Myers T. Nguyen, A. Nonaka, M. Rosso, S. Williams and M. Zingale, AMReX: a framework for block-structured adaptive mesh refinement, Journal of Open Source Software, 4(37), 1370, 2019. [doi]

J. M. Epstein, K. Klymko, and K. K. Mandadapu, Statistical mechanics of transport processes in active fluids. II. Equations of hydrodynamics for active Brownian particles, J. Chem. Phys., 150, 164111, 2019. [doi]

L. Esclapez, V. Ricchiuti, J. B. Bell, and M. S. Day, A spectral deferred correction strategy for low Mach number flows subject to electric fields Combustion Theory and Modelling, 2019, [link], [arXiv].

A. Harpole, D. Fan, M. P. Katz, A. J. Nonaka, D. E. Willcox, and M. Zingale, Modelling low Mach number stellar hydrodynamics with MAESTROeX proceedings of Astronum 2019, Paris, July 1-5, 2019.

M. Zingale, A. S. Almgren, M. Barrios Sazo, J. B. Bell, K. Eiden, A. Harpole, M. P. Katz, A. J. Nonaka, D. E. Willcox, and W. Zhang, The Castro AMR Simulation Code: Current and Future Developments proceedings of Astronum 2019, Paris, July 1-5, 2019.

D. R. Ladiges, A. J. Nonaka, J. B. Bell, and A. L. Garcia, On the Suppression and Distortion of Non-Equilibrium Fluctuations by Transpiration, Phys. Fluids, 149, 052002, 2019. [doi]

A. Donev, A. J. Nonaka, C. Kim, A. L. Garcia and J. B. Bell, Fluctuating hydrodynamics of electrolytes at electroneutral scales, Phys. Rev. Fluids. 4, 4, 2019. [link]

M. Zingale, K. Eiden, Y. Cavecchi, A. Harpole, J. B. Bell, M. Chang, I. Hawke, M. P. Katz, C.M. Malone, A. J. Nonaka, D. E. Willcox, and W. Zhang, Toward resolved simulations of burning fronts in thermonuclear X-ray bursts, Journal of Physics: Conference Series, 1225, p, 012005, 2019. [arxiv]

A. J. Aspden, M. S. Day and J. B. Bell, Towards the Distributed Burning Regime in Turbulent Premixed Flames, Journal of Fluid Mechanics 871, pp. 1-21. 2019. [arxiv]

J. Bell, M. Day, J. Goodman, R. Grout and M. Morzfeld, A Bayesian approach to calibrating hydrogen flame kinetics using many experiments and parameters, Combustion and Flame, 205, pp. 305-315, 2019. [arxiv]

M. Emmett, E. Motheau, W. Zhang, M. Minion and J. B. Bell, A Fourth-Order Adaptive Mesh Refinement Algorithm for the Multicomponent, Reacting Compressible Navier-Stokes Equations, Combustion Theory and Modelling, 23:4, 592-625, 2019. [arxiv]

A. Donev, A. L. Garcia, J.-P. Péraud, A. J. Nonaka and J. B. Bell, Fluctuating hydrodynamics and Debye-Hückel-Onsager theory for electrolytes, Current Opinion in Electrochemistry, 13, 2019. [link], [arxiv]

2018

M. N. Farooqi, T. Nguyen, W. Zhang, A. S. Almgren, J. Shalf, and D. Unat, "Phase asynchronous AMR execution for productive andperformant astrophysical flows", Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis, 2018, p. 70

F. P. Hamon, M. S. Day, M. L. Minion, "Concurrent Implicit Spectral Deferred Correction Scheme for Low-Mach Number Combustion with Detailed Chemistry", Combustion and Flame 2018. [arxiv] [doi]

Knut Sverdrup, Nikolaos Nikiforakis, and Ann S. Almgren, "Highly parallelisable simulations of time-dependent viscoplastic fluid flow simulations with structured adaptive mesh refinement", Physics of Fluids, 30:9, 2018. Named Editor's Pick. [doi]

C. Kim, A. Nonaka, J.B. Bell, A.L. Garcia, and A. Donev, "Fluctuating hydrodynamics of reactive liquid mixtures," J. Chem. Phys. 149, 084113, 2018. [doi] [arxiv]

K.-S. Kim, M.H. Han, C. Kim, Z. Li, G.E. Karniadakis, and E.K. Lee, "Nature of intrinsic uncertainties in equilibrium molecular dynamics estimation of shear viscosity for simple and complex fluids," J. Chem. Phys. 149, 044510, 2018. [doi] [arxiv]

J.-L. Vay, A. Almgren, J. Bell, L. Ge, D. P. Grote, M. Hogan, O. Kononenko, R. Lehe, A. Myers, C. Ng, J. Park, R. Ryne, O. Shapoval, M. Thevenet, W. Zhang "Warp-X: a new exascale computing platform for beam-plasma simulations," Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 2018 [arxiv]

B Loring, A Myers, D Camp, EW Bethel, Python-based in situ analysis and visualization Proceedings of the Workshop on In Situ Infrastructures for Enabling Extreme-Scale Analysis and Visualization - ISAV 18, ACM Press, 2018

E. Motheau, M. Duarte, A. Almgren, J. Bell, "A Hybrid Adaptive Low-Mach-Number/Compressible Method: Euler Equations," Journal of Computational Physics, Volume 372, Pages 1027-1047, 2018. [pdf].

Alan Calder, Platon I. Karpov, Maria Barrios Sazo, Michael Zingale, and Weiqun Zhang Toward simulating Black Widow binaries with CASTRO Journal of Computational Science Education Volume 8, Issue 3, pp. 25-29, 2018

M. Morzfeld, M. Day, R. Grout, G. S. H. Pau, S. Finsterle, J. Bell, "Iterative importance sampling algorithms for parameter estimation problems," SIAM J. Scientific Computing 40 (2) B329-B352, 2018. [arxiv]

A. Donev, C.-Y. Yang, and C. Kim, "Efficient reactive Brownian dynamics," J. Chem. Phys. 148, 034103, 2018. [doi] [arxiv]

K.H. Han, C. Kim, P. Talkner, G.E. Karniadakis, and E.K. Lee, "Molecular hydrodynamics: Vortex formation and sound wave propagation," J. Chem. Phys. 148, 024506, 2018. [doi] [arxiv]

D. J. Gardner, J. E. Guerra, F. P. Hamon, D. R. Reynolds, P. A. Ullrich, C. S. Woodward, "Implicit-Explicit Runge-Kutta Methods for Non-Hydrostatic Atmospheric Models", Geosci. Model Dev., 11(4), pp 1497-1515, 2018. [pdf]

F. P. Hamon, B. T. Mallison, H. A. Tchelepi, "Implicit Hybrid Upwinding for Two-Phase Flow in Heterogeneous Porous Media with Buoyancy and Capillarity", Comput. Methods in Appl. Mech. Eng., 331, pp 701-727, 2018. [link]

A. Nonaka, M. S. Day, and J. B. Bell, "A conservative, thermodynamically consistent numerical approach for low Mach number combustion. I. Single-level integration," Combust. Theor. Model., vol. 22, no. 1, pp. 156-184, 2018. [link]

M. Zingale, A. S. Almgren, M. G. Barrios Sazo, V. E. Beckner, J. B. Bell, B. Friesen, A. M. Jacobs, M. P. Katz, C. M. Malone, A. J. Nonaka, D. E. Willcox, and W. Zhang, "Meeting the Challenges of Modeling Astrophysical Thermonuclear Explosions: Castro, Maestro, and the AMReX Astrophysics Suite", J. Phys.: Conf. Ser. 1031, 2018. [arxiv] [iop]

2017

B. Choi, K.H. Han, C. Kim, P. Talkner, A. Kidera, and E.K. Lee, "Nature of self-diffusion in two-dimensional fluids," New J. Phys. 19, 123038, 2017. [doi] [arxiv]

E. Lovegrove, S.E. Woosley, and W. Zhang, "Very Low-energy Supernovae: Light Curves and Spectra of Shock Breakout", Astrophysical Journal, 845, 103, 2017. [arxiv]

B. Bastem, D. Unat, W. Zhang, A. Almgren, and J. Shalf, "Overlapping Data Transfers with Computation on GPU with Tiles", 2017 46th International Conference on Parallel Processing (ICPP), pp. 171-180 [link]

J-P. Péraud, A. Nonaka, J. B. Bell, A. Donev, and A. L. Garcia, "Fluctuation-enhanced electric conductivity in electrolyte solutions", P. Natl. Acad. Sci. USA, 114, 41, 2017. [link]

Muhammad Nufail Farooqi, Didem Unat, Tan Nguyen, Weiqun Zhang, Ann Almgren and John Shalf, "Nonintrusive AMR Asynchrony for Communication Optimization," Euro-Par 2017 [pdf]

Emmanuel Motheau, Ann Almgren, John Bell, "Navier-Stokes Characteristic Boundary Conditions Using Ghost Cells," AIAA J., Vol. 55, No. 10 : pp. 3399-3408, 2017 [doi]

C. Kim, A. Nonaka, J. B. Bell, A. L. Garcia, and A. Donev, "Stochastic simulation of reaction-diffusion systems: A fluctuating-hydrodynamics approach," J. Chem. Phys. 146, 124110, 2017. [doi] [arxiv]

D. Dalakoti, E. Hawkes, M. Day and J. Bell, "Direct numerical simulation of two-stage combustion and flame stabilization in diesel engine-relevant conditions" 26th ICDERS, Boston, USA, 2017.

E. Motheau, A. Almgren and J.B. Bell. "Navier-Stokes Characteristic Boundary Conditions Using Ghost Cells", 23rd AIAA Computational Fluid Dynamics, Denver, CO, USA, June 6 2017. [pdf]

E. Motheau, M. Duarte, A. Almgren and J.B. Bell. " A Hybrid Adaptive Low-Mach-Number/Compressible Method for the Euler Equations", 23rd AIAA/CEAS Aeroacoustics Conference, Denver, CO, USA, June 5 2017. [pdf]

J. Mueller and J. Woodbury, "GOSAC: Global Optimization with Surrogate Approximation of Constraints", Journal of Global Optimization. 69(1), pp 117-136, 2017. [link].

J. Mueller, "SOCEMO: Surrogate Optimization of Computationally Expensive Multi-Objective Problems", INFORMS Journal on Computing. 29(4), pp 581-596, 2017. [link].

R.W.Grout, H. Kolla, M.L. Minion and J.B. Bell, "Achieving algorithmic resilience for temporal integration through spectral deferred corrections," Commun. in Appl. Math. and Comput. Sci, 12(1), pp 25-50, 2017. [arxiv].

D. Dasgupta, M. Day, W. Sun and T. Lieuwen, "Effect of turbulence-chemistry interactions on chemical pathways for turbulent hydrogen-air premixed flames," Combust. Flame, 176, pp. 191-201, 2017.

D. Dasgupta, W. Sun, M. Day, T. Lieuwen "Sensitivity of chemical pathways to reaction mechanisms for n-dodecane," 10th U. S. National Combustion Meeting, April, 2017.

D. Dasgupta, W. Sun, M. Day and T. Lieuwen, "Turbulence effects on the chemical pathways for premixed Methane/Air flames," 55th AIAA Aerospace Sciences Meeting, January, 2017. [doi]

A. J. Aspden, J. B. Bell, M. S. Day and F. N. Egolfopoulos, "Turbulence-Flame Interactions in Lean Premixed Dodecane Flames," Proc. Combust. Inst., 36(2), pp. 2005-2016, 2017. [doi]

2016

Cy Chan, John Bachan, Joseph Kenny, Jeremiah Wilke, Vincent Beckner, Ann Almgren and John Bell "Topology-Aware Performance Optimization and Modeling of Adaptive Mesh Refinement Codes for Exascale," COMHPC 2016 - SC16 Workshop on Communication Optimization in High Performance Computing, Salt Lake City, UT, November 18, 2016. [pdf]

T. Nguyen, D. Unat, W. Zhang, A. Almgren, N. Farooqi, J. Shalf, "Perilla: Metadata-based optimizations of an asynchronous runtime for adaptive mesh refinement," SC '16 Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, p. 81, 2016

H. Shan, S. Williams, Y. Zheng, W. Zhang, B. Wang, S. Ethier, Z. Zhao, "Experiences of applying one-sided communication to nearest-neighbor communication," Proceedings of the First Workshop on PGAS Applications, pp 17-24, 2016 [pdf]

J. Peraud, A. Nonaka, A. Chaudhri, J. B. Bell, A. Donev, and A. L. Garcia, "Low Mach Number Fluctuating Hydrodynamics for Electrolytes," Phys. Rev. Fluids, 1, 074103, 2016. [link]

Brian Friesen, Ann Almgren, Zarija Lukic, Gunther Weber, Dmitriy Morozov, Vincent Beckner, Marcus Day, "In situ and in-transit analysis of cosmological simulations," Computational Astrophysics and Cosmology, 3:4, 2016 [pdf]

Wahid Bhimji, Debbie Bard, Melissa Romanus, David Paul, Andrey Ovsyanikov, Brian Friesen, Matt Bryson, Joaquin Correa, Glenn K. Lockwood, Vakho Tsulaia, Suren Byna, Steve Farrell, Doga Gursoy, Chris Daley, Vincent Beckner, Brian van Straalen, Nicholas J. Wright, Katie Antypas, Prabhat, "Accelerating Science with the NERSC Burst Buffer Early User Program," CUG 2016 [pdf]

D. Unat, T. Nguyen, W. Zhang, M. N. Farooqi, B. Bastem, G. Michelogiannakis, A. Almgren, and J. Shalf, "TiDA: High-Level Programming Abstractions for Data Locality Management," High Performance Computing: 31st International Conference, ISC High Performance 2016, Springer, pp 116-135, 2016.

Weiqun Zhang, Ann Almgren, Marcus Day, Tan Nguyen, John Shalf, Didem Unat, "BoxLib with Tiling: An AMR Software Framework," SIAM J. Scientific Computing, 38(5):S156-S172 , 2016 [arxiv]

Max P. Katz, Michale Zingale, Alan C. Calder, F. Douglas Swesty, Ann S. Almgren, Weiqun Zhang, "White Dwarf Mergers on Adaptive Meshes. I. Methodology and Code Verification", Astrophysical Journal, 819, 94, 2016. [arxiv]

W. Pazner, A. Nonaka, J. B. Bell, M. S. Day, and M. L. Minion, "A High-Order Spectral Deferred Correction Strategy for Low Mach Number Flow With Complex Chemistry," Combust. Theor. Model., vol. 20, no. 3, pp. 521-547, 2016. [link]

A. J. Aspden, M. S. Day and J. B. Bell, "Three-Dimensional Direct Numerical Simulation of Turbulent Lean Premixed Methane Combustion with Detailed Kinetics," Combustion and Flame, 166, pp. 266-283, 2016. [DOI]

A.M. Jacobs, M. Zingale, A. Nonaka, A.S. Almgren, J.B. Bell, "Low Mach Number Modeling of Convection in Helium Shells on Sub-Chandrasekhar White Dwarfs II: Bulk Properties of Simple Models," Astrophysical Journal, 827, 84, 2016. [iop].

W. Schmidt, J.F. Engels, J.C. Niemeyer, A.S. Almgren, "Hot and Turbulent Gas in Clusters," Monthly Notices of the Royal Astronomical Society, 459(1), 701-719, 2016 [arxiv].

D. Dasgupta, W. Sun, M. Day and T. Lieuwen, "Investigation of chemical pathways for turbulent Hydrogen-Air premixed flames" AIAA Aerospace Sciences Meeting, San Diego, CA, 2016. [DOI]

J. Mueller, "MISO: Mixed-Integer Surrogate Optimization Framework", Optimization and Engineering, 17:1, 177-203, March 2016. [link].

2015

A. Donini, M.S. Day, R.J.M. Bastiaans, J.A. van Oijen and L.P.H. de Goey, "An a Priori DNS Subgrid Analysis of the Presumed beta-PDF Model," J. Hydrogen Energy, 40(37), pp. 12811-12823, 2015.

Ke-Jung Chen, Alexander Heger, Stan Woosley, Ann Almgren and Daniel J. Whalen, "Pair-Instability Supernovae of Non-Zero Metallicity Stars," Numerical Modeling of Space Plasma Flows, ASTRONUM-2014, 498, 2015. [arxiv].

A. Nonaka, Y. Sun, J. B. Bell, and A. Donev, "Low Mach Number Fluctuating Hydrodynamics of Binary Liquid Mixtures," Comm. App. Math. and Comp. Sci., vol. 10, no. 2, 2015. [pdf].

M. Zingale, A. Jacobs, A. Almgren, J. Bell, A. Nonaka, C. Malone, S. Woosley, "Understanding Ignition in Type Ia Supernovae", 25rd International Colloquium on the Dynamics of Explosions and Reactive Systems, Leeds, UK, August 2-7, 2015.

A. K. Bhattacharjee, K. Balakrishnan, A. L. Garcia, J. B. Bell, and A. Donev, "Fluctuating hydrodynamics of multispecies reactive mixtures," J. Chem. Phys., 142, 224107, 2015 [arxiv].

A. Donev, A. Nonaka, A. K. Bhattacharjee, A. L. Garcia, and J. B. Bell, "Low Mach Number Fluctuating Hydrodynamics of Multispecies Liquid Mixtures," Phys. Fluids, 27, 037103, 2015. [arxiv].

M. Day, S. Tachibana, J. Bell, M. Lijewski, V. Beckner and R. Cheng, "A combined computational and experimental characterization of lean premixed turbulent low swirl laboratory flames. II. Hydrogen flames.", Combustion and Flame, 162(5), pp. 2148-2165, 2015. [CNF].

Zarija Lukic, Casey Stark, Peter Nugent, Martin White, Avery Meiksin, Ann Almgren, "The Lyman-alpha forest in optically-thin hydrodynamical simulations," Monthly Notices of the Royal Astronomical Society, 446, 3697-3724, 2015. [arxiv].

W. Schmidt, J. Schulz, L. Iapichino, A.S. Almgren, " Influence of adaptive mesh refinement and the hydro solver on shear-induced mass stripping in a minor merger scenario," Astronomy and Computing, 9, 49-64, March 2015 [arxiv].

A. Amato, M. Day, R. K. Cheng, J. Bell, D. Dasgupta, T. Lieuwen, "Topology and Burning Rates of Turbulent, Lean, H2-Air Flames", Combustion and Flame 162, pp. 4553-4565, 2015 [DOI].

M. Zingale, C. M. Malone, A. Nonaka, A. S. Almgren, and J. B. Bell, "Comparisons of Two- and Three-Dimensional Convection in Type I X-ray Bursts," Astrophysical Journal, 807, 60, 2015. [arxiv].

M. Duarte, A.S. Almgren, and J.B. Bell, "A Low Mach Number Model for Moist Atmospheric Flows," Journal of the Atmospheric Sciences, 72(4), pp. 1605-1620, 2015 [arxiv].

M. Minion, R. Speck, M. Bolten, M. Emmett, and D. Ruprecht "Interweaving PFASST and parallel multigrid", SIAM J. Scientific Computing, 37(5), pp. S244-S263, 2015.

R. Speck, D. Ruprecht, M. Minion, and R. Krause, "Inexact Spectral Deferred Corrections", Domain Decomposition Methods in Science and Engineering XXII, 104, pp. 127--133, 2015.

J.C. Dolence, A. Burrows, and W. Zhang, "Two-Dimensional Core-Collapse Supernova Models with Multi-Dimensional Transport," Astrophysical Journal, 800, 10, 2015. [arxiv].

Didem Unat, Cy Chan, Weiqun Zhang, Samuel Williams, John Bachan, John Bell, and John Shalf "ExaSAT: An Exascale Co-Design Tool for Performance Modeling," International Journal of High Performance Computing Applications (IJHPCA), February 2015, doi: 10.1177/1094342014568690

2014

A. Amato, M. Day, R. K. Cheng, J. Bell, T. Lieuwen, "Leading Edge Statistics of Turbulent, Lean, H2-Air Flames," Proc. Combust. Inst. 35, pp. 1313-1320, 2014. [PCI].

M. Duarte, and M. Emmett "High order schemes based on operator splitting and deferred corrections for stiff time dependent PDEs", https://hal.archives-ouvertes.fr/hal-01016684, 2014.

R. Speck, D. Ruprecht, M. Emmett, M. Bolten, and R. Krause "A space-time parallel solver for the three-dimensional heat equation", Parallel Computing: Accelerating Computational Science and Engineering (CSE), 25, pp. 263--272. IOS Press. 2014.

J. Mueller, R. Paudel, N. Mahowald, C. Shoemaker, "CH4 Parameter Estimation in CLM4.5bgc Using Surrogate Global Optimization", Geoscientific Model Development, 8:141-207, 2015 [pdf].

Antonio Valles and Weiqun Zhang, "Optimizing For Reacting Navier-Stokes Equations" in "High Performance Parallelism Pearls: Multicore And Many-Core Programming Approaches", James Reinder and Jim Jeffers (Eds.), Morgan Kaufmann, 2014. [link]

A.J. Aspden, M. S. Day, and J. B. Bell, "Turbulence-Chemistry Interaction in Lean Premixed Hydrogen Combustion," Proc. Combust. Inst. 35(2), pp. 1321-1329, 2014 [PCI].

Anuj Chaudhri, John Bell, Alejandro Garcia and Aleksandar Donev "Modeling Multi-Phase Flow using Fluctuating Hydrodynamics", Phys. Rev. E, 90(3), 033014, 2014. [arxiv].

M. Cai, A. Nonaka, B. E. Griffith, J. B. Bell, and A. Donev, "Efficient Variable-Coefficient Finite-Volume Stokes Solvers," Commun. Comput. Phys., 16, 1263-1297, 2014. [link]

Ann Almgren, John Bell, Andy Nonaka and Michael Zingale, "Low Mach Number Modeling of Stratified Flows," Finite Volumes for Complex Applications VII -- Methods and Theoretical Aspects, Springer Proceedings in Mathematics and Statistics, eds. J. Fuhrmann, M. Ohlberger, C. Rohde, Berlin, June 2014. [link]

A. Dubey, A. Almgren, J. Bell, M. Berzins, S. Brandt, G. Bryan, P. Colella, D. Graves, M. Lijewski, F. Loffler, B. O'Shea, E. Schnetter, B. Van Straalen, K. Weide "A Survey of High Level Frameworks in Block-Structured Adaptive Mesh Refinement Packages", Journal of Parallel and Distributed Computing, 74, pp. 3217-3227, 2014 [arxiv] [doi].

H. Braun, W. Schmidt, J.C. Niemeyer, A.S. Almgren, "Large-eddy simulations of isolated disk galaxies with thermal and turbulent feedback," Monthly Notices of the Royal Astronomical Society, 442, pp. 3407-3426, 2014.

A. Donev, A. Nonaka, Y. Sun, T. Fai, A. Garcia and J. Bell, "Low Mach Number Fluctuating Hydrodynamics of Diffusively Mixing Fluids" Comm. App. Math. and Comp. Sci., vol. 9, no. 1, 2014. [pdf]

C. M. Malone, M. Zingale, A. Nonaka, A. S. Almgren, and J. B. Bell, "Multidimensional Modeling of Type I X-ray Bursts. II. Two-Dimensional Convection in a Mixed H/He Accretor", Astrophysical Journal, 788, 115, 2014. [arxiv]

W. Schmidt, A.S. Almgren, H. Braun, J.F. Engels, J.C. Niemeyer, R.R. Mekuria, A.J. Aspden, J.B. Bell, "Cosmological Fluid Mechanics with Adaptively Refined Large Eddy Simulations," Monthly Notices of the Royal Astronomical Society, 440, pp. 3051-3077, 2014. [arxiv]

K. Balakrishnan, A. Garcia, A. Donev, and J. Bell, "Fluctuating hydrodynamics of multispecies nonreactive mixtures" Physical Review E, vol. 89, No. 1, January 2014. [pdf]

C. M. Malone, A. Nonaka, S. E. Woosley, A. S. Almgren, J. B. Bell, S. Dong, and M. Zingale, "The Deflagration Stage of Chandrasekhar Mass Models for Type Ia Supernovae: I. Early Evolution", Astrophysical Journal, 782, 11, 2014. [iop]

Samuel Williams, Mike Lijewski, Ann Almgren, Brian Van Straalen, Erin Carson, Nicholas Knight, and James Demmel, "s-Step Krylov Subspace Methods as Bottom Solvers for Geometric Multigrid", Proceedings of the 28th IEEE International Parallel & Distributed Processing Symposium, May 2014.

Ke-Jung Chen, Alexander Heger, Stan Woosley, Ann Almgren, and Daniel Whalen, "Pair Instability Supernovae of Very Massive Population III Stars" Astrophysical Journal, 792, 44, 2014. [arxiv].

Ke-Jung Chen, Alexander Heger, S.E. Woosley, Ann S. Almgren, and Daniel J. Whalen, "Two-Dimensional Simulations of Pulsational Pair-Instability Supernova", Astrophysical Journal, 792, 28, 2014. [arxiv].

Ke-Jung Chen, Alexander Heger, S.E. Woosley, Ann Almgren, and Daniel J. Whalen, and Jarrett L. Johnson, "The General Relativistic Instability Supernova of a Supermassive Population III Star", Astrophysical Journal, 790, 162, 2014.

M. Duarte, A.S. Almgren, K. Balakrishnan, J.B. Bell, D.M. Romps, "A Numerical Study of Methods for Moist Atmospheric Flows: Compressible Equations," Monthly Weather Review, 142, pp. 4269--4283, 2014 [arxiv].

M. Emmett, W. Zhang, J.B. Bell, "High-Order Algorithms for Compressible Reacting Flow with Complex Chemistry", Combustion Theory and Modelling, pp. 361-387, May 2014 [doi] [arxiv].

R. Speck, D. Ruprecht, M. Emmett, M. Minion, M. Bolten, and R. Krause "A multi-level spectral deferred correction method", BIT Numerical Mathematics, 2014 [arxiv].

S. Descombes, M. Duarte, T. Dumont, F. Laurent, V. Louvet, and M. Massot, "Analysis of operator splitting in the non-asymptotic regime for nonlinear reaction-diffusion equations. Application to the dynamics of premixed flames", SIAM J. Num. Anal., 52, 1311-1334, 2014. [arxiv].

M. Emmett and M. Minion "Efficient implementation of a multi-level parallel in time algorithm", Proceedings of the 21st International Conference on Domain Decomposition Methods, DD21, , 98, 359-366, 2014.

2013

J. B. Bell, M. S. Day and M. J. Lijewski, "Simulation of Nitrogen Emissions in a Premixed Hydrogen Flame Stabilized on a Low Swirl Burner", Proceedings of the Combustion Institute, Proceedings of the Combustion Institute, 34(1), pp. 1173-1182, 2013. [pdf]

Ke-Jung Chen, Alexander Heger, and Ann S. Almgren, "Numerical Approaches for Multidimensional Simulations of Stellar Explosions", Astronomy and Computing, 3-4, pp. 70-78, Nov.-Dec. 2013. [doi]

Didem Unat, Cy Chan, Weiqun Zhang, John Bell, and John Shalf, Tiling as a Durable Abstraction for Parallelism and Data Locality, WOLFHPC 2013 - SC13 Workshop on Domain-Specific Languages and High-Level Frameworks for High-Performance Computing, 2013.

Cy Chan, Joseph Kenny, Gilbert Hendry, Didem Unat, Vincent Beckner, John Bell and John Shalf, An AMR Computation and Communication Dependency and Analysis Methodology, IA^3 2013 - SC13 Workshop on Irregular Applications: Architectures and Algorithms, 2013. [arxiv]

K. Chen, A. Heger, S. Woosley, A. Almgren, and W. Zhang, "The Most Powerful Stellar Explosion", Bulletin of the American Physical Society, 2013, vol. 58, no. 4.

Cy Chan, Didem Unat, Michael Lijewski, Weiqun Zhang, John Bell, and John Shalf, "Software Design Space Exploration for Exascale Combustion Co-design", International Supercomputing Conference 2013, Lecture Notes in Computer Science, vol. 7905, 2013, pp 196-212.

C. Gilet, A.S. Almgren, J.B. Bell, A. Nonaka, S.E. Woosley and M. Zingale, "Low-Mach Number Modeling of Core Convection in Massive Stars", Astrophysical Journal, 773, 137, 2013. [pdf]

Haitao Ma, Stan Woosley, Chris Malone, Ann Almgren, and J.B. Bell, "Carbon Deflagration in Type Ia Supernovae: I. Centrally Ignited Models", Astrophysical Journal, 771, 58, 2013.

M. Zingale, A. Nonaka, A. S. Almgren, J. B. Bell, C. Malone, and R. Orvedahl, "Low Mach Number Modeling of Convection in Helium Shells on Sub-Chandrasekhar White Dwarfs. I. Methodology", Astrophysical Journal, 764, 97, 2013. [pdf]

Weiqun Zhang, L. Howell, A. Almgren, A. Burrows, J. Dolence, J. Bell, "CASTRO: A New Compressible Astrophysical Solver. III. Multigroup Radiation Hydrodynamics", Astrophysical Journal Supplement Series, 204, 7, 2013. [pdf]

A.S. Almgren, A.J. Aspden, J. B. Bell, and M. L. Minion, "On the Use of Higher-Order Projection Methods for Incompressible Turbulent Flow", SIAM J. Sci. Comput., 35, 1, B25-B42, 2013. [pdf]

A. S. Almgren, J. B. Bell, M.J. Lijewski, Z. Lukic, E. Van Andel, "Nyx: A Massively Parallel AMR Code for Computational Cosmology" Astrophysical Journal, 765, 39, 2013. [pdf]

2012

Ke-Jung Chen, Alexander Heger and Ann Almgren, "Conservative Initial Mapping for Multidimensional Simulations of Stellar Explosions", Journal of Physics: Conference Series, 402, Conf. 1, 2012.

R. Speck, D. Ruprecht, R. Krause, M. Emmett, M. Minion, M. Winkel, and P. Gibbon, "A massively space-time parallel N-body solver", Proceedings of the International Conference on High Performance Computing, SC'12, 92:1-11, 2012.

R. Speck, D. Ruprecht, R. Krause, M. Emmett, M. Minion, M. Winkel, and P. Gibbon, "Integrating an N-body problem with SDC and PFASST", Proceedings of the 21st International Conference on Domain Decomposition Methods, DD21, 2012.

F. Balboa Usabiaga, J. Bell, R. Delgado-Buscalioni, A. Donev, T. Fai, B. Griffith, C. Peskin, "Staggered Schemes for Fluctuating Hydodynamics", Multiscale Modeling and Simulation, 10, 4, 1360-1408, 2012. [pdf]

K. Balakrishnan, J.B. Bell, A. Donev, and A. Garcia, "Fluctuating Hydrodynamics and Direct Simulation Monte Carlo", 28th International Symposium on Rarefied Gas Dynamics , AIP Conf. Proc. 1501 , 695-704, 2012. [pdf]

A. Nonaka, J. B. Bell, M. S. Day, C. Gilet, A. S. Almgren, and M. L. Minion, "A Deferred Correction Coupling Strategy for Low Mach Number Flow with Complex Chemistry", Combustion Theory and Modelling, 16(6), pp. 1053-1088, 2012. [pdf]

R. Sisneros, C. Malone, A. Nonaka, and S. Woosley, "Investigation of Turbulence in the Early Stages of a High Resolution Supernova Simulation", Proceedings of the Supercomputing 2012 Conference. [pdf]

R. Tiron, A.S. Almgren, R. Camassa, "Shear instability of internal solitary waves in Euler fluids with thin pycnoclines", Journal of Fluid Mechanics, 710, pp. 324-361, 2012.

S. Williams, D. Kalamkar, A. Singh, A. Deshpande, B. Van Straalen, M. Smelyanskiy, A. Almgren, P. Dubey, J. Shalf, L. Oliker, "Optimization of Geometric Multigrid for Emerging Multi- and Manycore Processors", Proceedings of the Supercomputing 2012 Conference, 2012.

Samuel Williams, Dhiraj D. Kalamkar, Amik Singh, Anand M. Deshpande, Brian Van Straalen, Mikhail Smelyanskiy, Ann Almgren, Pradeep Dubey, John Shalf, Leonid Oliker, "Implementation and Optimization of miniGMG - a Compact Geometric Multigrid Benchmark", LBNL 6676E, December 2012.

A. Nonaka, A. J. Aspden, M. Zingale, A. S. Almgren, J. B. Bell, and S. E. Woosley, "High-Resolution Simulations of Convection Preceding Ignition in Type Ia Supernovae Using Adaptive Mesh Refinement", Astrophysical Journal, 745, 73, 2012. [pdf] [arxiv]

J. Nordhaus, T.D. Brandt, A. Burrows, A. Almgren, "The Hydrodynamic Origin of Neutron Star Kicks", Monthly Notices of the Royal Astronomical Society, 423, Issue 2, June 2012.

K. Balakrishnan, A. L. Kuhl, J. B. Bell and V. E. Beckner, "An Empirical Model for the Ignition of Explosively Dispersed Aluminum Particle Clouds", Shock Waves, 22, 591, 2012. [pdf]

G. S. H. Pau, J. B. Bell, A. S. Almgren, K. M. Fagnan and M. J. Lijewski, "An Adaptive Mesh Refinement Algorithm for Compressible Two-Phase Flow In Porous Media", Computational Geosciences, 16, 577-592, 2012. [pdf]

M. Day, S. Tachibana, J. Bell, M. Lijewski, V. Beckner and R. Cheng, "A combined computational and experimental characterization of lean premixed turbulent low swirl laboratory flames. I. Methane flames.", Combustion and Flame, 159(1), 275-290, 2012. [pdf]

2011

K.M. Fagnan, M.J. Lijewski, G.Pau, N.J. Wright, "Acceleration of porous media simulations on the Cray XE6 platform", Proceedings of CUG2011, Fairbanks, Alaska, 2011.

Emmanouela Rantsiou, Adam Burrows, Jason Nordhaus, Ann Almgren, "Induced Rotation in Three-Dimensional Simulations of Core-Collapse Supernovae: Implications for Pulsar Spins," Astrophysical Journal, 732, 57, 2011. [arxiv].

Adam Burrows, Jason Nordhaus, Ann Almgren, John Bell, "The potential role of spatial dimension in the neutrino-driving mechanism of core-collapse supernova explosions,", Comp. Phys. Comm., 182, Issue 9, pp. 1764-1766, 2011.

A. Garcia, A. Donev, J.B. Bell, and B. Alder, "Hydrodynamic fluctuations in a particle-continuum hybrid for complex fluids", 27th International Symposium on Rarefied Gas Dynamics , AIP Conf. Proc. 1333 , 551-556, 2011. [pdf]

K. Balakrishnan, A. L. Kuhl, J. B. Bell and V. E. Beckner, "An Empirical Model for the Ignition of Aluminum Particle Clouds Behind Blast Waves", 23rd International Colloquium on the Dynamics of Explosions and Reactive Systems, Irvine, CA, July 24-29, 2011. [pdf]

K. Balakrishnan, A. L. Kuhl, J. B. Bell and V. E. Beckner, "Ignition of Aluminum Particle Clouds Behind Reflected Shock Waves", 23rd International Colloquium on the Dynamics of Explosions and Reactive Systems, Irvine, CA, July 24-29, 2011. [pdf]

A. L. Kuhl, J. B. Bell, V. E. Beckner and K. Balakrishnan, "Spherical Combustion Clouds in Explosions", 23rd International Colloquium on the Dynamics of Explosions and Reactive Systems, Irvine, CA, July 24-29, 2011. [pdf]

A. Nonaka, A. S. Almgren, J. B. Bell, H. Ma, S. E. Woosley, and M. Zingale, "From Convection to Explosion: End-to-End Simulation of Type Ia Supernovae," Proceedings of SciDAC 2011, Denver, Colorado, July 2011. [pdf] [arxiv]

K. Balakrishnan, J. B. Bell, A. L. Kuhl and W. M. Howard, "Riemann Solver for the Nigmatulin Model of Two-Phase Flow", 17th Biennial International Conference of the APS Topical Group on Shock Compression of Condensed Matter, Chicago, IL, June 26-July 1, 2011.

W. Zhang, L. Howell, A. Almgren, A. Burrows, and J. Bell "CASTRO: A New Compressible Astrophysical Solver. II. Gray Radiation Hydrodynamics", Astrophysical Journal Supplement Series, 196, 20, 2011 [pdf]

A. Donev, A. de la Fuente, J. B. Bell, and A. L. Garcia, "Enhancement of Diffusive Transport by Nonequilibrium Thermal Fluctuations", JSTAT, Vol. 2011, P06014, (2011). [pdf]

A. Donev, A. de la Fuente, J. B. Bell, and A. L. Garcia, "Diffusive Transport by Thermal Velocity Fluctuations", Phys. Rev. Lett., Vol. 106, No. 20, page 204501, 2011. [pdf]

A. J. Aspden, J. B. Bell, S. Dong, and S. E. Woosley, "Burning Thermals in Type Ia Supernovae", Astrophysical Journal, 738, pp. 94-107, 2011. [ApJ] [pdf]

M. Zingale, A. Nonaka, A. S. Almgren, J. B. Bell, C. M. Malone, and S. E. Woosley, "The Convective Phase Preceding Type Ia Supernovae", Astrophysical Journal, 740, 8, (2011). [pdf]

A. Nonaka, S. May, A. S. Almgren, and J. B. Bell, "A Three-Dimensional, Unsplit Godunov Method for Scalar Conservation Laws", SIAM J. Sci. Comput., vol. 33, no. 4, 2011. [pdf]

S. May, A. Nonaka, A. S. Almgren, and J. B. Bell, "An Unsplit, Higher-Order Godunov Method Using Quadratic Reconstruction for Advection in Two Dimensions", Comm. App. Math. and Comp. Sci., vol. 6, no. 1, 2011. [pdf]

R.J.M. Bastiaans and M. Day, "Analysis of subgrid scale phenomena of premixed turbulent combustion of methane and hydrogen in comparable regimes",, Center for Turbulence Research, Annual Research Briefs, 2012.

A. Donini, R.J.M. Bastiaans, J.A. van Oijen, M.S. Day and L.P.H. de Goey, "A Priori Assessment of the Potential of Flamelet Generated Manifolds to Model Lean Turbulent Premixed Hydrogen Combustion," In: Kuerten H., Geurts B., Armenio V., Froehlich J. (eds) Direct and Large-Eddy Simulation VIII. ERCOFTAC Series, vol 15, Springer, Dordrecht, 2011 [doi]