Publications and theses +++++++++++++++++++++++ A good source of various benchmarks and other tests is A. Hakim's `Simulation Journal `_ and its `github webpage `_. We have also compiled input files for the simulations reported in publications in `this repository `_. Note that this collection is incomplete as not all authors have desposited they input files with us. Doctoral Dissertations ---------------------- - Bradshaw, K. (2024, February 23) "Emitting Wall Boundary Conditions in Continuum Kinetic Simulations: Unlocking the Effects of Energy-Dependent Material Emission on the Plasma Sheath." Ph.D. dissertation, Virginia Polytechnic Institute and State University, 2024. https://vtechworks.lib.vt.edu/handle/10919/118137 - Mandell, N. R. (2021, March 26) "Magnetic Fluctuations in Gyrokinetic Simulations of Scrape-Off Layer Turbulence". Ph.D. dissertation, Princeton University, 2021. `arXiv:2103.16062 `_ - Juno, J. (2020, March 27) "A Deep Dive into the Distribution Function: Understanding Phase Space Dynamics Using Continuum Vlasov-Maxwell Simulations". Ph. D. dissertation, University of Maryland, College Park, 2020. `arXiv:2005.13539 `_ - Bernard, T. N. "Discontinuous Galerkin Modeling of Plasma Turbulence in a Simple Magnetized Torus". Ph. D. dissertation, The University of Texas at Austin, 2019. `PDF `_ - Ng, J. "Fluid closures for the modeling of reconnection and instabilities in magnetotail current sheets". Ph.D. dissertation, Princeton University, 2018. `PDF `_ - Cagas, P. (2018, July 30). "Continuum kinetic simulations of plasma sheaths and instabilities". Ph.D. dissertation, Virginia Polytechnic Institute and State University, 2018. https://vtechworks.lib.vt.edu/handle/10919/84979 - Wang, L. (2014, Aug 30). "Integrating Kinetic Physics in Fluid Models for Magnetic Reconnection". Ph.D. dissertation, University of New Hampshire, 2014. - Shi, E. L. (2017, August 24). "Gyrokinetic Continuum Simulation of Turbulence in Open-Field-Line Plasmas", Ph.D. dissertation, Princeton University, 2017 `arXiv:1708.07283 `_ Algorithms papers ----------------- - Francisquez, M., Mandell, N. R., Hakim, A., Hammett, G. W. (2024) "Conservative discontinuous Galerkin interpolation: sheared boundary conditions" *Compute Physics Communications* **298**, 109109. https://doi.org/10.1016/j.cpc.2024.109109 - Cagas, P and Hakim, A and Srinivasan, B. (2021) "A boundary value “reservoir problem” and boundary conditions for multi-moment multifluid simulations of sheaths." *Physics of Plasmas* **28.1**. https://doi.org/10.1063/5.0024510 - Hakim, A and Juno, J. (2020). "Alias-free, Matrix-free, and Quadrature-free Discontinuous Galerkin Algorithms for (Plasma) Kinetic Equations". *SC20: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis*, IEEE Press. https://doi.org/10.1109/SC41405.2020.00077 - Francisquez, M., Bernard, T. N., Mandell, N. R., Hammett, G. W., Hakim, A. (2020). "Conservative discontinuous Galerkin scheme of a gyro-averaged Dougherty collision operator", *Nuclear Fusion*, **60**, (9). https://doi.org/10.1088%2F1741-4326%2Faba0c9 - Hakim, A., Francisquez, M., Juno, J., & Hammett, G. W. (2020). "Conservative discontinuous Galerkin schemes for nonlinear Dougherty–Fokker–Planck collision operators", *Journal of Plasma Physics*, **86**, (4). https://doi.org/10.1017/S0022377820000586 - Wang, L., Hakim, A., Ng, J., Dong, C., & Germaschewski, K. (2020). "Exact and locally implicit source term solvers for multifluid-Maxwell systems", *Journal of Computational Physics*, **415**, 109510. https://doi.org/10.1016/j.jcp.2020.109510 - Cagas, P., Hakim, A., & Srinivasan, B. (2020). "Plasma-material boundary conditions for discontinuous Galerkin continuum-kinetic simulations, with a focus on secondary electron emission", *Journal of Computational Physics*, **406**, 109215. https://doi.org/10.1016/j.jcp.2019.109215 - Mandell, N. R., Hakim, A., Hammett, G. W., & Francisquez, M. (2020). "Electromagnetic full-f gyrokinetics in the tokamak edge with discontinuous Galerkin methods", *Journal of Plasma Physics*, **86**. https://doi.org/10.1017/S0022377820000070 - Juno, J., Hakim, A., TenBarge, J., Shi, E., & Dorland, W. (2018). "Discontinuous Galerkin algorithms for fully kinetic plasmas", *Journal of Computational Physics*, **353**, 110–147. https://doi.org/10.1016/j.jcp.2017.10.009 - Hakim, A., Hammett, G. W., Shi, E. L. (2014). "On discontinuous Galerkin discretizations of second-order derivatives", `arXiv:1405.5907 `_ Physics papers -------------- - Bradshaw, K., Srinivasan, B. (2024). "Energy-dependent implementation of secondary electron emission models in continuum kinetic sheath simulations", *Plasma Sources Science and Technology* **33**, 035008. https://doi.org/10.1088/1361-6595/ad331c - Liu, Z., White, R., Francisquez, M., Milanese, L. M., Loureiro, N. F. (2024). "A two-dimensional numerical study of ion-acoustic turbulence", *Journal of Plasma Physics* **90**, 965900101. https://doi.org/10.1017/S0022377824000060 - Francisquez, M., Rosen, M. H., Mandell, N. R., Hakim, A., Forest, C. B., Hammett, G. W. (2023). "Towards continuum gyrokinetic study of high-field mirrors" *Physics of Plasmas* **30**, 102504. https://doi.org/10.1063/5.0152440 - Cagas, P., Juno, J., Hakim, A., LaJoie, A., Chu, F., Langendorf, S., Srinivasan, B. (2023). "An investigation of shock formation versus shock mitigation of colliding plasma jets", *Physics of Plasmas*, **30**, 053903. https://doi.org/10.1063/5.0135389. - Skolar, C. R., Bradshaw, K., Juno, J., Srinivasan, B., (2023), "Continuum kinetic investigation of the impact of bias potentials in the current saturation regime on sheath formation", *Physics of Plasmas*, **30**, 012504. https://doi.org/10.1063/5.0134656. - Rodman, J., Cagas, P., Hakim, A., Srinivasan, B. (2022). "A kinetic interpretation of the classical Rayleigh-Taylor instability", *Physical Review E*, `PhysRevE.105.065209 `_. - Francisquez, M., Juno, J., Hakim, A., Hammett, G. W., Ernst, D. R. (2022). "Improved multispecies Dougherty collisions" *Journal of Plasma Physics* 88, 905880303. https://doi.org/10.1017/S0022377822000289 - Bernard, T. N., Halpern, F., Hammett, G. W., Francisquez, M., Mandell, N. R., Juno, J., Hakim, A., Wilkie, G., Guterl, J. (2022). "Kinetic modeling of neutral transport for a continuum gyrokinetic code", *Physics of Plasmas*, **29**, 052501. https://doi.org/10.1063/5.0087131 - Mandell, N. R., Hammett, G. W., Hakim, A., Francisquez, M. (2022). "Reduction of transport due to magnetic shear in gyrokinetic simulations of the scrape-off layer", `arXiv:2112.14220 `_. Under review in Plasma Physics and Controlled Fusion. - Mandell, N. R., Hammett, G. W., Hakim, A., Francisquez, M. (2022). "Turbulent broadening of electron heat-flux width in electromagnetic gyrokinetic simulations of a helical scrape-off layer model", *Physics of Plasmas*, **29**, 042504. https://doi.org/10.1063/5.0082486 - Mathews, A., Mandell, M., Francisquez, M., Hughes, J., Hakim, A. (2021). "Turbulent field fluctuations in gyrokinetic and fluid plasmas", *Physics of Plasmas*, **28**, 112301. https://doi.org/10.1063/5.0066064 - Wang, L., Hakim, A., Srinivasan, B., Juno, J. (2021). "Electron cyclotron drift instability and anomalous transport: two-fluid moment theory and modeling", `arXiv:2107.09874 `_. - Jenab, S. M., Brodin, G., Juno, J., Kourakis, I. (2021). "Ultrafast Electron Holes in Plasma Phase Space Dynamics", *Scientific Reports*, **11**. https://doi.org/10.1038/s41598-021-95652-w - Juno, J., Howes, G. G., TenBarge, J. M., Wilson III, L. B., Spitkovsky, A., Caprioli, D., Klein, K. G., Hakim, A. (2021). "A field-particle correlation analysis of a perpendicular magnetized collisionless shock", *Journal of Plasma Physics*, **87**, (3). https://doi.org/10.1017/S0022377821000623 - Pezzi, O., Liang, H., Juno, J. L., Cassak, P. A., Vásconez, C. L., Sorriso-Valvo, L., Perrone, D., Servidio, S., Roytershteyn, V., TenBarge, J.M., & Matthaeus, W. H. (2021). "Dissipation measures in weakly collisional plasmas", *Monthly Notices of the Royal Astronomical Society*, **505**, (4), Pages 4857–4873. https://doi.org/10.1093/mnras/stab1516 - Ng, J., Hakim, A., Wang, L., & Bhattacharjee, A. (2020). "An improved ten-moment closure for reconnection and instabilities", *Physics of Plasmas*, **27**, 082106. https://doi.org/10.1063/5.0012067 - Juno, J., Swisdak, M. M., TenBarge. J. M., Skoutnev, V., & Hakim, A. (2020). "Noise-induced magnetic field saturation in kinetic simulations", *Journal of Plasma Physics*, **86**, (4). https://doi.org/10.1017/S0022377820000707 - Ng, J., Chen, L.‐J., Hakim, A., & Bhattacharjee, A. (2020). "Reconstruction of electron and ion distribution functions in a magnetotail reconnection diffusion region", *Journal of Geophysical Research: Space Physics*, **125**, e2020JA027879. https://doi.org/10.1029/2020JA027879 - Francisquez, M., Bernard, T. N., Zhu, B., Hakim, A., Rogers, B. N., & Hammett, G. W. (2020). "Fluid and gyrokinetic turbulence in open field-line, helical plasmas", *Physics of Plasmas*, **27**, 082301. https://doi.org/10.1063/5.0005333 - Bernard, T. N., Stoltzfus-Dueck, T., Gentle, K. W., Hakim, A., Hammett, G. W., & Shi, E. L. (2020). "Investigating shear flow through continuum gyrokinetic simulations of limiter biasing in the Texas Helimak", *Physics of Plasmas*, **27**, 062304. https://doi.org/10.1063/5.0003904 - Hakim, A. H., Mandell, N. R., Bernard, T. N., Francisquez, M., Hammett, G. W., & Shi, E. L. "Continuum electromagnetic gyrokinetic simulations of turbulence in the tokamak scrape-off layer and laboratory devices", *Physics of Plasmas*, **27**, 042304. https://doi.org/10.1063/1.5141157 - Pusztai, I., Juno, J., Brandenburg, A., Tenbarge, J. M., Hakim, A., Francisquez, M., & Sundström, A. (2020). "Dynamo in Weakly Collisional Nonmagnetized Plasmas Impeded by Landau Damping of Magnetic Fields", *Physical Review Letters*, **124**, 255102. https://link.aps.org/doi/10.1103/PhysRevLett.124.255102 - TenBarge, J. M., Ng, J., Juno, J., Wang, L., Hakim, A. & Bhattacharjee, A. (2019). "An extended MHD study of the 16 October 2015 MMS diffusion region crossing", *Journal of Geophysical Research: Space Physics*, 124, 8474-8487. https://doi.org/10.1029/2019JA026731 - Ng, J., Hakim, A., Juno, J., & Bhattacharjee, A. (2019). Drift instabilities in thin current sheets using a two‐fluid model with pressure tensor effects. *Journal of Geophysical Research: Space Physics*, 124, 3331-3346. https://doi.org/10.1029/2018JA026313 - Dong, C., Wang, L., Hakim, A., Bhattacharjee, A., Slavin, J. A., DiBraccio, G. A., & Germaschewski, K. (2019). "A Novel Ten-Moment Multifluid Model for Mercury: From the Planetary Conducting Core to the Dynamic Magnetosphere", *Geophysical Review Letters*, 46, 11584-11596. https://doi.org/10.1029/2019GL083180 - Shi, E. L., Hammett, G. W., Stoltzfus-Dueck, T., & Hakim, A. (2019). "Full-f gyrokinetic simulation of turbulence in a helical open-field-line plasma", *Physics of Plasmas*, **26**, 012307. https://doi.org/10.1063/1.5074179 - Bernard, T. N., Shi, E. L., Gentle, K. W., Hakim, A., Hammett, G. W., Stoltzfus-Dueck, T., & Taylor, E. I. (2019). "Gyrokinetic continuum simulations of plasma turbulence in the Texas Helimak", *Physics of Plasmas*, **26**, 042301. https://doi.org/10.1063/1.5085457 - Skoutnev, V., Hakim, A., Juno, J., & TenBarge, J. M. (2019). "Temperature-Dependent Saturation of Weibel-Type Instabilities in Counter-streaming Plasmas", *Astrophysical Journal Letters*, **872**, (2). https://doi.org/10.3847%2F2041-8213%2Fab0556 - Sundström, A., Juno, J., TenBarge, J. M., & Pusztai, I. (2019). "Effect of a weak ion collisionality on the dynamics of kinetic electrostatic shocks", *Journal of Plasma Physics*, **85**. https://doi.org/10.1017/S0022377819000023 - Srinivasan, B. and Hakim, A. (2018). "Role of electron inertia and electron/ion finite Larmor radius effects in low-beta, magneto-Rayleigh-Taylor instability", *Physics of Plasmas*, **25**, 092108. https://doi.org/10.1063/1.5046098 - Ng, J., Hakim, A., & Bhattacharjee, A. (2018). "Using the maximum entropy distribution to describe electrons in reconnecting current sheets", *Physics of Plasmas*, **25**, 082113. https://doi.org/10.1063/1.5041758 - Wang, L., Germaschewski, K., Hakim, A., Dong, C., Raeder, J., & Bhattacharjee, A. (2018). "Electron Physics in 3-D Two-Fluid 10-Moment Modeling of Ganymede's Magnetosphere", *Journal of Geophysical Research: Space Physics*, **41** (A3), 8688–16. https://doi.org/10.1002/2017JA024761 - Pusztai, I., TenBarge, J. M., Csapó, A. N., Juno, J., Hakim, A., Yi, K & Fülöp, T. (2018). "Low Mach-number collisionless electrostatic shocks and associated ion acceleration", *Plasma Physics and Controlled Fusion*, **60** (3), 035004–11. https://doi.org/10.1088/1361-6587/aaa2cc - Shi, E. L., Hammett, G. W., Stolzfus-Dueck, T., Hakim, A. (2017). "Gyrokinetic continuum simulation of turbulence in a straight open-field-line plasma", *Journal of Plasma Physics*, **83**, 1–27. https://doi.org/10.1017/S002237781700037X - Cagas, P., Hakim, A., Scales, W., Srinivasan, B. (2017). "Nonlinear saturation of the Weibel instability", *Physics of Plasmas*, **24** (11), 112116. https://doi.org/10.1063/1.4994682 - Ng, J., Hakim, A., Bhattacharjee, A., Stanier, A., & Daughton, W. (2017). "Simulations of anti-parallel reconnection using a nonlocal heat flux closure", *Physics of Plasmas*, **24** (8), 082112. https://doi.org/10.1063/1.4993195 - Stanier, A., Daughton, W., Simakov, A. N., Chacón, L., Le, A., Karimabadi, H., Ng, J., & Bhattacharjee, A. (2017). "The role of guide field in magnetic reconnection driven by island coalescence", *Physics of Plasmas*, **24**, 022124. https://doi.org/10.1063/1.4976712 - Cagas, P., Hakim, A., Juno, J., Srinivasan, B. (2017). "Continuum kinetic and multi-fluid simulations of classical sheaths", *Physics of Plasmas*, **24** (2), 022118. https://doi.org/10.1063/1.4976544 - Ng, J., Huang, Y.-M., Hakim, A., Bhattacharjee, A., Stanier, A., Daughton, W., Wang, L., & Germaschewski, K. (2015). "The island coalescence problem: Scaling of reconnection in extended fluid models including higher-order moments", *Physics of Plasma*, **22**, 112104. https://doi.org/10.1063/1.4935302 - Stanier, A., Daughton, W., Chacón, L., Karimabadi, H., Ng, J., Huang, Y.-M., Hakim, A., & Bhattacharjee, A. (2015). "Role of Ion Kinetic Physics in the Interaction of Magnetic Flux Ropes", *Physical Review Letters*, **115**, 175004. https://doi.org/10.1103/PhysRevLett.115.175004 - Wang, L., Hakim, A. H., Bhattacharjee, A., & Germaschewski, K. (2015). "Comparison of multi-fluid moment models with particle-in-cell simulations of collisionless magnetic reconnection", *Physics of Plasmas*, **22** (1), 012108. https://doi.org/10.1063/1.4906063