# Andy Nonaka

Andy
Nonaka

Staff Scientist, CCSE Group Lead

I am a Staff Scientist and Group Lead of the Center for Computational Sciences and Engineering (CCSE) at Lawrence Berkeley National Laboratory. I am interested in HPC implementations of multiphysics and multiscale algorithms for PDEs using structured grid, adaptive mesh, particle/grid, and machine learning algorithms.

Visit my website, or the CCSE website to learn more!

## Journal Articles

### 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., October 12, 2023, 159:144107,

### 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, October 2, 2023, 291:108836,

### 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, September 1, 2023, 290:108757,

### J. G. Wang, D. R. Ladiges, I. Srivastava, S. P. Carney, A. J. Nonaka, A. L. Garcia, J. B. Bell, "Steric effects in induced-charge electro-osmosis for strong electric fields", Physical Review Fluids, August 29, 2023, 8:083702,

### I. Srivastava, D. R. Ladiges, A. Nonaka, A. L. Garcia, J. B. Bell, "Staggered Scheme for the Compressible Fluctuating Hydrodynamics of Multispecies Fluid Mixtures", Physical Review E, January 24, 2023, 107:015305, doi: 10.1103/PhysRevE.107.015305

### S. S. Sawant, Z. Yao, R. Jambunathan, A. Nonaka, "Characterization of Transmission Lines in Microelectronic Circuits Using the ARTEMIS Solver", IEEE Journal on Multiscale and Multiphysics Computational Techniques, December 12, 2022, 8:31-39,

### D. Fan, D. E. Willcox, C. DeGrendele, M. Zingale, and A. Nonaka, "Neural Networks for Nuclear Reactions in MAESTROeX", he Astrophysical Journal, November 29, 2022, 940,

### D. R. Ladiges, J. G. Wang, I. Srivastava, S. P. Carney, A. Nonaka, A. L. Garcia, A. Donev, J. B. Bell, "Modeling Electrokinetic Flows with the Discrete Ion Stochastic Continuum Overdamped Solvent Algorithm", Physical Review E, November 19, 2022, 106:035104, doi: 10.1103/PhysRevE.106.035104

### M. Zingale, M. P. Katz, A. Nonaka, and M. Rasmussen, "An Improved Method for Coupling Hydrodynamics with Astrophysical Reaction Networks", Astrophysical Journal, August 25, 2022, 936,

### J. Bell, A. Nonaka, A. L. Garcia, G. Eyink, "Thermal Fluctuations in the Dissipation Range of Homogeneous Isotropic Turbulence", J. Fluid Mech, March 24, 2022, 939,

### 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, January 10, 2022, accepted,

### Daniel R. Ladiges, Sean P. Carney, Andrew Nonaka, Katherine Klymko, Guy C. Moore, Alejandro L. Garcia, Sachin R. Natesh, Aleksandar Donev, John B. Bell, "A Discrete Ion Stochastic Continuum Overdamped Solvent Algorithm for Modeling Electrolytes", Physical Review Fluids, April 1, 2021, 6(4):044309,

### K. Klymko, A. Nonaka, J. B. Bell, S. P. Carney, A. L. Garcia, "Low Mach number fluctuating hydrodynamics model for ionic liquids", Physical Review Fluids, September 8, 2020, 5, doi: https://doi.org/10.1103/PhysRevFluids.5.093701

### D. Fan, A. Nonaka, A.S. Almgren, A. Harpole, M. Zingale, "MAESTROeX: A Massively Parallel Low Mach Number Astrophysical Solver", The Astrophysical Journal, December 19, 2019,

### 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, December 19, 2019,

### 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", August 14, 2019,

### A. Donev, A. J. Nonaka, C. Kim, A. L. Garcia, J. B. Bell, "Fluctuating hydrodynamics of electrolytes at electroneutral scales", August 10, 2019,

### D. R. Ladiges, A. J. Nonaka, J. B. Bell, A. L. Garcia, "On the Suppression and Distortion of Non-Equilibrium Fluctuations by Transpiration", Physics of Fluids, August 10, 2019,

### Weiqun Zhang, Ann Almgren, Vince Beckner, John Bell, Johannes Blashke, Cy Chan, Marcus Day, Brian Friesen, Kevin Gott, Daniel Graves, Max P. Katz, Andrew Myers, Tan Nguyen, Andrew Nonaka, Michele Rosso, Samuel Williams, Michael Zingale, "AMReX: a framework for block-structured adaptive mesh refinement", Journal of Open Source Software, May 2019, doi: 10.21105/joss.01370

### Aleksandar Donev, Alejandro L. Garcia, Jean-Philippe Péraud, Andrew J. Nonaka, John B. Bell, "Fluctuating Hydrodynamics and Debye-Hückel-Onsager Theory for Electrolytes", Current Opinion in Electrochemistry, 2019, 13:1 - 10, doi: https://doi.org/10.1016/j.coelec.2018.09.004

### Changho Kim, Andy Nonaka, John B. Bell, Alejandro L. Garcia, Aleksandar Donev, "Fluctuating hydrodynamics of reactive liquid mixtures", The Journal of Chemical Physics, 2018, 149:084113, doi: 10.1063/1.5043428

### A Nonaka, MS Day, JB Bell, "A conservative, thermodynamically consistent numerical approach for low Mach number combustion. Part I: Single-level integration", Combustion Theory and Modelling, 2018, 22:156--184, doi: 10.1080/13647830.2017.1390610

### Jean-Philippe Peraud, Andrew J. Nonaka, John B. Bell, Aleksandar Donev, Alejandro L. Garcia, "Fluctuation-enhanced electric conductivity in electrolyte solutions", Proceedings of the National Academy of Sciences, 2017, 114:10829--108, doi: 10.1073/pnas.1714464114

### Changho Kim, Andy Nonaka, John B. Bell, Alejandro L. Garcia, Aleksandar Donev, "Stochastic simulation of reaction-diffusion systems: A fluctuating-hydrodynamics approach", The Journal of Chemical Physics, 2017, 146:124110, doi: 10.1063/1.4978775

### AM Jacobs, M Zingale, A Nonaka, AS Almgren, JB Bell, "Low Mach Number Modeling of Convection in Helium Shells on Sub-Chandrasekhar White Dwarfs. II. Bulk Properties of Simple Models", Astrophysical Journal, 2016, 827, doi: 10.3847/0004-637X/827/1/84

### Jean-Philippe Peraud, Andy Nonaka, Anuj Chaudhri, John B. Bell, Aleksandar Donev, Alejandro L. Garcia, "Low Mach number fluctuating hydrodynamics for electrolytes", Phys. Rev. Fluids, 2016, 1:074103, doi: 10.1103/PhysRevFluids.1.074103

### WE Pazner, A Nonaka, JB Bell, MS Day, ML Minion, "A high-order spectral deferred correction strategy for low Mach number flow with complex chemistry", Combustion Theory and Modelling, 2016, 20:521--547, doi: 10.1080/13647830.2016.1150519

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

### 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, 2015,

### 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, 2015,

### 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, 2014, 782:11,

### 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, 2014, 788:115,

### 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., 2014, 9(1),

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

### 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, 2013, 773:137,

### 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, 2013, 764:97,

### 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,

- Download File: wdTurb.pdf (pdf: 4.6 MB)

### A Nonaka, JB Bell, MS Day, C Gilet, AS Almgren, ML Minion, "A deferred correction coupling strategy for low Mach number flow with complex chemistry", Combustion Theory and Modelling, 2012, 16:1053--1088, doi: 10.1080/13647830.2012.701019

- Download File: LMCSDC.pdf (pdf: 601 KB)

### C. M. Malone, A. Nonaka, A. S. Almgren, J. B. Bell, and M. Zingale, "Multidimensional Modeling of Type I X-ray Bursts. I. Two-Dimensional Convection Prior to the Outburst of a pure 4He Accretor", Astrophysical Journal, 728, 118, February 2011,

- Download File: xrb.pdf (pdf: 6.6 MB)

### 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,

- Download File: wdconvect.pdf (pdf: 2.8 MB)

### 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,

- Download File: BDS3d.pdf (pdf: 1 MB)

### 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,

### A. Nonaka, A.S. Almgren, J. B. Bell, M. J. Lijewski, C. M. Malone, and M. Zingale, "MAESTRO: An Adaptive Low Mach Number Hydrodynamics Algorithm for Stellar Flows", Astrophysical Journal Supplement Series, 188, 358-383, June 2010,

- Download File: multilevel.pdf (pdf: 3.8 MB)

### AS Almgren, VE Beckner, JB Bell, MS Day, LH Howell, CC Joggerst, MJ Lijewski, A Nonaka, M Singer, M Zingale, "Castro: A new compressible astrophysical solver. I. Hydrodynamics and self-gravity", Astrophysical Journal, January 2010, 715:1221--1238, doi: 10.1088/0004-637X/715/2/1221

- Download File: castropaper.pdf (pdf: 1.6 MB)

### A. Nonaka, D. Trebotich, G. H. Miller, D. T. Graves, and P. Colella, "A Higher-Order Upwind Method for Viscoelastic Flow", Comm. App. Math. and Comp. Sci., 4(1):57-83, 2009,

- Download File: nonakaetal.pdf (pdf: 709 KB)

### M. Zingale, A. S. Almgren, J. B. Bell, A. Nonaka, and S. E. Woosley, "Low Mach Number Modeling of Type Ia Supernovae. IV. White Dwarf Convection", Astrophysical Journal, 704, 196-210, 2009,

- Download File: LowMach4.pdf (pdf: 1.9 MB)

### A. S. Almgren, J. B. Bell, A. Nonaka, M. Zingale, "A New Low Mach Number Approach in Astrophysics", Computing in Science and Engineering, vol. 11, no. 2, pp. 24-33, March/April, 2009,

### A. S. Almgren, J. B. Bell, A. Nonaka, and M. Zingale, "Low Mach Number Modeling of Type Ia Supernovae. III. Reactions", Astrophysical Journal, 684, 449-470, 2008, LBNL 58673,

- Download File: LowMach3.pdf (pdf: 1.2 MB)

## Conference Papers

### 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, W. Zhang, "Toward resolved simulations of burning fronts in thermonuclear X-ray bursts", Journal of Physics: Conference Series, 2019, 1225,

### 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, July 1, 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, July 1, 2019,

### M Zingale, AS Almgren, MG Barrios Sazo, VE Beckner, JB Bell, B Friesen, AM Jacobs, MP Katz, CM Malone, AJ Nonaka, DE Willcox, W Zhang, "Meeting the Challenges of Modeling Astrophysical Thermonuclear Explosions: Castro, Maestro, and the AMReX Astrophysics Suite", Journal of Physics: Conference Series, 2018, 1031, doi: 10.1088/1742-6596/1031/1/012024

### M. Zingale, A. Jacobs, A. Almgren, J. Bell, A. Nonaka, C. Malone, S. Woosley, "Understanding Ignition in Type Ia Supernovae", 5rd International Colloquium on the Dynamics of Explosions and Reactive Systems, Leeds, UK, August 2, 2015,

### 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, 2012,

### A Nonaka, AS Almgren, JB Bell, H Ma, SE Woosley, M Zingale, "From Convection to Explosion: End-to-End Simulation of Type Ia Supernovae", Proceedings of SciDAC 2011, July 2011,

- Download File: SCIDAC2011.pdf (pdf: 1001 KB)

### A. Almgren, J. Bell, D. Kasen, M. Lijewski, A. Nonaka, P. Nugent, C. Rendleman, R. Thomas, and M. Zingale, "MAESTRO, CASTRO and SEDONA -- Petascale Codes for Astrophysical Applications", Proceedings of SciDAC 2010, Chattanooga, Tennessee, July 2010,

### H. Ma, M. Zingale, S. E. Woosley, A. J. Aspden, J. B. Bell, A. S. Almgren, A. Nonaka, and S. Dong, "Type Ia Supernovae: Advances in Large Scale Simulation", Proceedings of SciDAC 2010, Chattanooga, Tennessee, July 2010,

- Download File: SCIDAC2010.pdf (pdf: 81 KB)

### S.E. Woosley, A.S. Almgren, A.J. Aspden, J.B. Bell, D. Kasen, A.R. Kerstein, H. Ma, A. Nonaka and M. Zingale, "Type Ia Supernovae: Advances in Large Scale Simulation", SciDAC 2009, J. of Physics: Conference Series, 180, July 2009,

### M. Zingale, A. S. Almgren, J. B. Bell, C. M. Malone and A. Nonaka, "Astrophysical Applications of the MAESTRO Code", SciDAC 2008, J. of Physics: Conference Series, 125, Seattle Washington, July 2008,

- Download File: SciDAC08.pdf (pdf: 430 KB)

### A. Nonaka, S. Gulati, D. Trebotich, G. H. Miller, S. J. Muller, and D. Liepmann, "A Computational Model with Experimental Validation for DNA Flow in Microchannels", Technical Proceedings of the 2005 NSTI Nanotechnology Conference and Trade Show,, May 1, 2005,

### Trebotich, D., Colella, P., Miller, G.H., Nonaka, A., Marshall, T., Gulati, S., Liepmann, D., "A Numerical Algorithm for Complex Biological Flow in Irregular Microdevice Geometries", Technical Proceedings of the 2004 Nanotechnology Conference and Trade Show Vol.2 (2004), pp. 470-473, 2004,

- Download File: A235.pdf (pdf: 419 KB)