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