phd-dissertation.bib

@inproceedings{dkist,
  title={DKIST: observing the sun at high resolution},
  author={Tritschler, A and Rimmele, TR and Berukoff, S and Casini, R and Craig, SC and Elmore, DF and Hubbard, RP and Kuhn, JR and Lin, H and McMullin, JP and others},
  booktitle={18th Cambridge Workshop on Cool Stars, Stellar Systems, and the Sun},
  volume={18},
  pages={933--944},
  year={2015}
}

@book{leveque2002,
  title={Finite Volume Methods for Hyperbolic Problems},
  author={LeVeque, R.J. and J, L.R. and Crighton, D.G.},
  isbn={9780521009249},
  lccn={2001052642},
  series={Cambridge Texts in Applied Mathematics},
  url={https://books.google.com/books?id=QazcnD7GUoUC},
  year={2002},
  publisher={Cambridge University Press}
}

@article{vonneumann1950,
author = {CHARNEY, J. G. and FJÖRTOFT, R. and Von NEUMANN, J.},
title = {Numerical Integration of the Barotropic Vorticity Equation},
journal = {Tellus},
volume = {2},
number = {4},
pages = {237-254},
doi = {10.1111/j.2153-3490.1950.tb00336.x},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.2153-3490.1950.tb00336.x},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.2153-3490.1950.tb00336.x},
abstract = {Abstract A method is given for the numerical solution of the barotropic vorticity equation over a limited area of the earth's surface. The lack of a natural boundary calls for an investigation of the appropriate boundary conditions. These are determined by a heuristic argument and are shown to be sufficient in a special case. Approximate conditions necessary to insure the mathematical stability of the difference equation are derived. The results of a series of four 24-hour forecasts computed from actual data at the 500 mb level are presented, together with an interpretation and analysis. An attempt is made to determine the causes of the forecast errors. These are ascribed partly to the use of too large a space increment and partly to the effects of baroclinicity. The rôle of the latter is investigated in some detail by means of a simple baroclinic model.},,
year = {1950}
}

@article{vanleer1979,
title = "Towards the ultimate conservative difference scheme. V. A second-order sequel to Godunov's method",
journal = "Journal of Computational Physics",
volume = "32",
number = "1",
pages = "101 - 136",
year = "1979",
issn = "0021-9991",
doi = "https://doi.org/10.1016/0021-9991(79)90145-1",
url = "http://www.sciencedirect.com/science/article/pii/0021999179901451",
author = "Bram van Leer"
}

@article{harten1997,
title = "High Resolution Schemes for Hyperbolic Conservation Laws",
journal = "Journal of Computational Physics",
volume = "135",
number = "2",
pages = "260 - 278",
year = "1997",
issn = "0021-9991",
doi = "https://doi.org/10.1006/jcph.1997.5713",
url = "http://www.sciencedirect.com/science/article/pii/S0021999197957132",
author = "Ami Harten"
}

@book{tannehill1997,
  title={Computational Fluid Mechanics and Heat Transfer, Second Edition},
  author={Pletcher, R.H. and Tannehill, J.C. and Anderson, D.},
  isbn={9781560320463},
  lccn={83018614},
  series={Series in Computational and Physical Processes in Mechanics and Thermal Sciences},
  url={https://books.google.com/books?id=ZJPbtHeilCgC},
  year={1997},
  publisher={Taylor \& Francis}
}

@incollection{hirsch2007,
title = "Preface to the second edition",
editor = "Charles Hirsch",
booktitle = "Numerical Computation of Internal and External Flows (Second Edition)",
publisher = "Butterworth-Heinemann",
edition = "Second Edition",
address = "Oxford",
pages = "xv - xvii",
year = "2007",
isbn = "978-0-7506-6594-0",
doi = "https://doi.org/10.1016/B978-075066594-0/50037-0",
url = "http://www.sciencedirect.com/science/article/pii/B9780750665940500370"
}

@ARTICLE{alshidi2019chromo,
       author = {{Al Shidi}, Qusai and {Cohen}, Ofer and {Song}, Paul and {Tu}, Jiannan},
        title = "{Time-Dependent Two-Fluid Magnetohydrodynamic Model and Simulation of the Chromosphere}",
      journal = {arXiv e-prints},
     keywords = {Astrophysics - Solar and Stellar Astrophysics, Physics - Space Physics},
         year = "2019",
        month = "Apr",
          eid = {arXiv:1904.01572},
        pages = {arXiv:1904.01572},
archivePrefix = {arXiv},
       eprint = {1904.01572},
 primaryClass = {astro-ph.SR},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2019arXiv190401572S},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@Misc{alshidi2019,
author =   {Qusai {Al Shidi}},
title =    {{CoMFi - Collisional Multi-Fluid ion code}},
howpublished = {\url{https://github.com/qalshidi/comfi/}},
year = {2019}
}

@ONLINE{hdf5,
    author = {{The HDF Group}},
    title = "{Hierarchical data format version 5}",
    year = {2000-2010},
    url = {http://www.hdfgroup.org/HDF5}
}

@Article{Hunter2007,
  Author    = {Hunter, J. D.},
  Title     = {Matplotlib: A 2D graphics environment},
  Journal   = {Computing In Science \& Engineering},
  Volume    = {9},
  Number    = {3},
  Pages     = {90--95},
  abstract  = {Matplotlib is a 2D graphics package used for Python
  for application development, interactive scripting, and
  publication-quality image generation across user
  interfaces and operating systems.},
  publisher = {IEEE COMPUTER SOC},
  doi       = {10.1109/MCSE.2007.55},
  year      = 2007
}

@article{bhatnagar1954,
  title = {A Model for Collision Processes in Gases. I. Small Amplitude Processes in Charged and Neutral One-Component Systems},
  author = {Bhatnagar, P. L. and Gross, E. P. and Krook, M.},
  journal = {Phys. Rev.},
  volume = {94},
  issue = {3},
  pages = {511--525},
  numpages = {0},
  year = {1954},
  month = {May},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRev.94.511},
  url = {https://link.aps.org/doi/10.1103/PhysRev.94.511}
}

@Book{mandl1988,
 author = {Mandl, F},
 title = {Statistical physics},
 publisher = {Wiley},
 year = {1988},
 address = {Chichester West Sussex New York},
 isbn = {9780471915331}
 }

@Book{lerner2005,
 author = {Lerner, Rita},
 title = {Encyclopedia of physics},
 publisher = {Wiley-VCH},
 year = {2005},
 address = {Weinheim},
 isbn = {978-3527405541}
 }

@article{riley2012,
author = {Riley, Pete},
title = {On the probability of occurrence of extreme space weather events},
journal = {Space Weather},
volume = {10},
number = {2},
pages = {},
keywords = {space weather},
doi = {10.1029/2011SW000734},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2011SW000734},
eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2011SW000734},
abstract = {By virtue of their rarity, extreme space weather events, such as the Carrington event of 1859, are difficult to study, their rates of occurrence are difficult to estimate, and prediction of a specific future event is virtually impossible. Additionally, events may be extreme relative to one parameter but normal relative to others. In this study, we analyze several measures of the severity of space weather events (flare intensity, coronal mass ejection speeds, Dst, and >30 MeV proton fluences as inferred from nitrate records) to estimate the probability of occurrence of extreme events. By showing that the frequency of occurrence scales as an inverse power of the severity of the event, and assuming that this relationship holds at higher magnitudes, we are able to estimate the probability that an event larger than some criteria will occur within a certain interval of time in the future. For example, the probability of another Carrington event (based on Dst < −850 nT) occurring within the next decade is ∼12\%. We also identify and address several limitations with this approach. In particular, we assume time stationarity, and thus, the effects of long-term space climate change are not considered. While this technique cannot be used to predict specific events, it may ultimately be useful for probabilistic forecasting.},
year = "2012"
}
@article{vanleer1974,
title = "Towards the ultimate conservative difference scheme. II. Monotonicity and conservation combined in a second-order scheme",
journal = "Journal of Computational Physics",
volume = "14",
number = "4",
pages = "361 - 370",
year = "1974",
issn = "0021-9991",
doi = "https://doi.org/10.1016/0021-9991(74)90019-9",
url = "http://www.sciencedirect.com/science/article/pii/0021999174900199",
author = "Bram van Leer",
abstract = "Fromm's second-order scheme for integrating the linear convection equation is made monotonic through the inclusion of nonlinear feedback terms. Care is taken to keep the scheme in conservation form. When applied to a quadratic conservation law, the scheme notably yields a monotonic shock profile, with a width of only 112 mesh."
}

@article{vanalbada1982,
    author = {van Albada, T. S.},
    title = "{Dissipationless galaxy formation and the r1/4 law}",
    journal = {Monthly Notices of the Royal Astronomical Society},
    volume = {201},
    number = {4},
    pages = {939-955},
    year = {1982},
    month = {12},
    abstract = "{Results of collision-free N-body simulations of the collapse phase of galaxy formation are presented. A variety of irregular initial conditions produce density distributions that are in very good agreement with the r1/4 law, provided that the collapse factor is large. This agreement holds for a region between radii containing 10 and 99 per cent of the total mass in the r1/4 model and corresponds to a range in surface brightness of 12 mag. The central densities in the equilibrium configurations are up to a factor 1000 larger than the initial densities. The final models have a strongly anisotropic velocity distribution in their envelopes.}",
    issn = {0035-8711},
    doi = {10.1093/mnras/201.4.939},
    url = {https://doi.org/10.1093/mnras/201.4.939},
    eprint = {http://oup.prod.sis.lan/mnras/article-pdf/201/4/939/2974792/mnras201-0939.pdf},
}

@article{Waterson2007,
 author = {Waterson, N. P. and Deconinck, H.},
 title = {Design Principles for Bounded Higher-order Convection Schemes - a Unified Approach},
 journal = {J. Comput. Phys.},
 issue_date = {May, 2007},
 volume = {224},
 number = {1},
 month = may,
 year = {2007},
 issn = {0021-9991},
 pages = {182--207},
 numpages = {26},
 url = {http://dx.doi.org/10.1016/j.jcp.2007.01.021},
 doi = {10.1016/j.jcp.2007.01.021},
 acmid = {1243580},
 publisher = {Academic Press Professional, Inc.},
 address = {San Diego, CA, USA},
 keywords = {Bounded, Convection, Discretization, Flux limiters, Higher-order, Non-linear, Normalized variables, TVD},
} 

@incollection{Banks1973,
title = "CHAPTER 22 - Thermal Processes of the Ionosphere",
editor = "P.M. Banks and G. Kockarts",
booktitle = "Aeronomy",
publisher = "Academic Press",
pages = "238 - 286",
year = "1973",
isbn = "978-0-12-077802-7",
doi = "https://doi.org/10.1016/B978-0-12-077802-7.50014-2",
url = "http://www.sciencedirect.com/science/article/pii/B9780120778027500142",
author = "P.M. Banks and G. Kockarts"
}

@ARTICLE{SolarProbe16,
	   author = {{Fox}, N.~J. and {Velli}, M.~C. and {Bale}, S.~D. and {Decker}, R. and 
	      	{Driesman}, A. and {Howard}, R.~A. and {Kasper}, J.~C. and {Kinnison}, J. and 
			{Kusterer}, M. and {Lario}, D. and {Lockwood}, M.~K. and {McComas}, D.~J. and 
				{Raouafi}, N.~E. and {Szabo}, A.},
	    title = "{The Solar Probe Plus Mission: Humanity's First Visit to Our Star}",
	      journal = {\ssr},
	       keywords = {Solar Probe Plus, SPP, Corona, Heliophysics, NASA mission, Solar wind},
	            year = 2016,
		        month = dec,
			   volume = 204,
			       pages = {7-48},
			             doi = {10.1007/s11214-015-0211-6},
				        adsurl = {http://adsabs.harvard.edu/abs/2016SSRv..204....7F},
					  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@article{Hillier2016,
		author = {{Hillier, A.} and {Takasao, S.} and {Nakamura, N.}},
			title = {The formation and evolution of reconnection-driven, slow-mode shocks in a partially ionised plasma},
				DOI= "10.1051/0004-6361/201628215"
					url= "https://doi.org/10.1051/0004-6361/201628215",
						journal = {A\&A},
							year = 2016,
								volume = 591,
									pages = "A112",
}


@ARTICLE{Pontieu2001,
	  author={B. De Pontieu and P. C. H. Martens and H. S. Hudson},
	    title={Chromospheric Damping of Alfvén Waves},
	      journal={The Astrophysical Journal},
	        volume={558},
		  number={2},
		    pages={859},
		      url={http://stacks.iop.org/0004-637X/558/i=2/a=859},
		        year={2001},
			  abstract={We analytically study the damping of Alfvén mode oscillations in the chromosphere and in coronal loops. In the partially ionized chromosphere the dominant damping process of Alfvén waves is due to collisions between ions and neutrals. We calculate the damping time for Alfvén waves of a given frequency, propagating through model chromospheres of various solar structures such as active region plage, quiet sun, and the penumbra and umbra of sunspots. For a given wave frequency, the maximum damping always occurs at temperature minimum heights and in the coldest structure(s), i.e., the umbra of sunspots. Energy dissipation due to ion-neutral damping of Alfvén waves with an energy flux of 10 7 ergs cm -3s - 1 can play a considerable role in the energy balance of umbrae, quiet sun, and plage for Alfvén wave periods of the order, respectively, 50, 5, and 0.5 s. We also consider Alfvén waves in coronal loops and the leakage of wave energy through the footpoints. We assume a three-layer model of coronal loops with constant Alfvén speed v A (and no damping) in the corona, v A varying exponentially with height in the dissipative chromosphere, and v A again constant in the photosphere at the end of the loop. We find an exact analytical solution in the chromospheric part. Using these solutions, we estimate the leakage of wave energy from the coronal volume through the footpoint regions of the loop and find that the presence of a moderate amount of chromospheric damping can enhance the footpoint leakage. We apply this result to determine the damping time of standing waves in coronal loops. The enhanced footpoint leakage also has implications for theories of coronal heating based on resonant absorption. Finally, we find exact expressions for the damping of Alfvén waves launched in the photosphere and upward propagating through the chromosphere and into the corona. The partially ionized chromosphere presents an effective barrier for upward propagating Alfvén waves with periods less than a few seconds.}
}


@article{Leake2013,
	author = {Leake,James E.  and Lukin,Vyacheslav S.  and Linton,Mark G. },
	title = {Magnetic reconnection in a weakly ionized plasma},
	journal = {Physics of Plasmas},
	volume = {20},
	number = {6},
	pages = {061202},
	year = {2013},
	doi = {10.1063/1.4811140},
	url = {https://doi.org/10.1063/1.4811140},
	eprint = {https://doi.org/10.1063/1.4811140}
}


@article{Wojcik2018,
	author = {Wójcik, D and Murawski, K and Musielak, Z E},
	title = {Acoustic waves in two-fluid solar atmosphere model: cut-off periods, chromospheric cavity, and wave tunnelling},
	journal = {Monthly Notices of the Royal Astronomical Society},
	volume = {481},
	number = {1},
	pages = {262-267},
	year = {2018},
	doi = {10.1093/mnras/sty2306},
	URL = {http://dx.doi.org/10.1093/mnras/sty2306},
	eprint = {/oup/backfile/content_public/journal/mnras/481/1/10.1093_mnras_sty2306/1/sty2306.pdf}
}


@article{Maneva2017,
  author={Yana G. Maneva and Alejandro Alvarez Laguna and Andrea Lani and Stefaan Poedts},
  title={Multi-fluid Modeling of Magnetosonic Wave Propagation in the Solar Chromosphere: Effects of Impact Ionization and Radiative Recombination},
  journal={The Astrophysical Journal},
  volume={836},
  number={2},
  pages={197},
  url={http://stacks.iop.org/0004-637X/836/i=2/a=197},
  year={2017},
  abstract={In order to study chromospheric magnetosonic wave propagation including, for the first time, the effects of ion–neutral interactions in the partially ionized solar chromosphere, we have developed a new multi-fluid computational model accounting for ionization and recombination reactions in gravitationally stratified magnetized collisional media. The two-fluid model used in our 2D numerical simulations treats neutrals as a separate fluid and considers charged species (electrons and ions) within the resistive MHD approach with Coulomb collisions and anisotropic heat flux determined by Braginskiis transport coefficients. The electromagnetic fields are evolved according to the full Maxwell equations and the solenoidality of the magnetic field is enforced with a hyperbolic divergence-cleaning scheme. The initial density and temperature profiles are similar to VAL III chromospheric model in which dynamical, thermal, and chemical equilibrium are considered to ensure comparison to existing MHD models and avoid artificial numerical heating. In this initial setup we include simple homogeneous flux tube magnetic field configuration and an external photospheric velocity driver to simulate the propagation of MHD waves in the partially ionized reactive chromosphere. In particular, we investigate the loss of chemical equilibrium and the plasma heating related to the steepening of fast magnetosonic wave fronts in the gravitationally stratified medium.}
}

@article{Martinez-Sykora2012,
  author={Juan Martinez-Sykora and Bart De Pontieu and Viggo Hansteen},
  title={Two-dimensional Radiative Magnetohydrodynamic Simulations of the Importance of Partial Ionization in the Chromosphere},
  journal={The Astrophysical Journal},
  volume={753},
  number={2},
  pages={161},
  url={http://stacks.iop.org/0004-637X/753/i=2/a=161},
  year={2012},
  abstract={The bulk of the solar chromosphere is weakly ionized and interactions between ionized particles and neutral particles likely have significant consequences for the thermodynamics of the chromospheric plasma. We investigate the importance of introducing neutral particles into the MHD equations using numerical 2.5D radiative MHD simulations obtained with the Bifrost code. The models span the solar atmosphere from the upper layers of the convection zone to the low corona, and solve the full MHD equations with non-gray and non-LTE radiative transfer, and thermal conduction along the magnetic field. The effects of partial ionization are implemented using the generalized Ohm's law, i.e., we consider the effects of the Hall term and ambipolar diffusion in the induction equation. The approximations required in going from three fluids to the generalized Ohm's law are tested in our simulations. The Ohmic diffusion, Hall term, and ambipolar diffusion show strong variations in the chromosphere. These strong variations of the various magnetic diffusivities are absent or significantly underestimated when, as has been common for these types of studies, using the semi-empirical VAL-C model as a basis for estimates. In addition, we find that differences in estimating the magnitude of ambipolar diffusion arise depending on which method is used to calculate the ion-neutral collision frequency. These differences cause uncertainties in the different magnetic diffusivity terms. In the chromosphere, we find that the ambipolar diffusion is of the same order of magnitude or even larger than the numerical diffusion used to stabilize our code. As a consequence, ambipolar diffusion produces a strong impact on the modeled atmosphere. Perhaps more importantly, it suggests that at least in the chromospheric domain, self-consistent simulations of the solar atmosphere driven by magnetoconvection can accurately describe the impact of the dominant form of resistivity, i.e., ambipolar diffusion. This suggests that such simulations may be more realistic in their approach to the lower solar atmosphere (which directly drives the coronal volume) than previously assumed.}
}

@article{Khomenko2017,
  author={Elena Khomenko},
  title={On the effects of ion-neutral interactions in solar plasmas},
  journal={Plasma Physics and Controlled Fusion},
  volume={59},
  number={1},
  pages={014038},
  url={http://stacks.iop.org/0741-3335/59/i=1/a=014038},
  year={2017},
  abstract={Solar photosphere and chromosphere are composed of weakly ionized plasma for which collisional coupling decreases with height. This implies a breakdown of some hypotheses underlying magnetohydrodynamics at low altitudes and gives rise to non-ideal MHD effects such as ambipolar diffusion, Hall effect, etc. Recently, there has been progress in understanding the role of these effects for the dynamics and energetics of the solar atmosphere. There are evidences that phenomena such as wave propagation and damping, magnetic reconnection, formation of stable magnetic field concentrations, magnetic flux emergence, etc can be affected. This paper reviews the current state-of-the-art of multi-fluid MHD modeling of the coupled solar atmosphere.}
}


@article{Leake2012,
  author={James E. Leake and Vyacheslav S. Lukin and Mark G. Linton and Eric T. Meier},
  title={Multi-fluid Simulations of Chromospheric Magnetic Reconnection in a Weakly Ionized Reacting Plasma},
  journal={The Astrophysical Journal},
  volume={760},
  number={2},
  pages={109},
  url={http://stacks.iop.org/0004-637X/760/i=2/a=109},
  year={2012},
  abstract={We present results from the first self-consistent multi-fluid simulations of chromospheric magnetic reconnection in a weakly ionized reacting plasma. We simulate two-dimensional magnetic reconnection in a Harris current sheet with a numerical model which includes ion-neutral scattering collisions, ionization, recombination, optically thin radiative loss, collisional heating, and thermal conduction. In the resulting tearing mode reconnection the neutral and ion fluids become decoupled upstream from the reconnection site, creating an excess of ions in the reconnection region and therefore an ionization imbalance. Ion recombination in the reconnection region, combined with Alfvénic outflows, quickly removes ions from the reconnection site, leading to a fast reconnection rate independent of Lundquist number. In addition to allowing fast reconnection, we find that these non-equilibria partial ionization effects lead to the onset of the nonlinear secondary tearing instability at lower values of the Lundquist number than has been found in fully ionized plasmas. These simulations provide evidence that magnetic reconnection in the chromosphere could be responsible for jet-like transient phenomena such as spicules and chromospheric jets.}
}


@ARTICLE{Tu2013,
  author={Jiannan Tu and Paul Song},
  title={A Study of Alfvén Wave Propagation and Heating the Chromosphere},
  journal={The Astrophysical Journal},
  volume={777},
  number={1},
  pages={53},
  url={http://stacks.iop.org/0004-637X/777/i=1/a=53},
  year={2013},
  abstract={Alfvén wave propagation, reflection, and heating of the chromosphere are studied for a one-dimensional solar atmosphere by self-consistently solving plasma, neutral fluid, and Maxwell's equations with incorporation of the Hall effect and strong electron-neutral, electron-ion, and ion-neutral collisions. We have developed a numerical model based on an implicit backward difference formula of second-order accuracy both in time and space to solve stiff governing equations resulting from strong inter-species collisions. A non-reflecting boundary condition is applied to the top boundary so that the wave reflection within the simulation domain can be unambiguously determined. It is shown that due to the density gradient the Alfvén waves are partially reflected throughout the chromosphere and more strongly at higher altitudes with the strongest reflection at the transition region. The waves are damped in the lower chromosphere dominantly through Joule dissipation, producing heating strong enough to balance the radiative loss for the quiet chromosphere without invoking anomalous processes or turbulences. The heating rates are larger for weaker background magnetic fields below ~500 km with higher-frequency waves subject to heavier damping. There is an upper cutoff frequency, depending on the background magnetic field, above which the waves are completely damped. At the frequencies below which the waves are not strongly damped, the interaction of reflected waves with the upward propagating waves produces power at their double frequencies, which leads to more damping. The wave energy flux transmitted to the corona is one order of magnitude smaller than that of the driving source.}
}

@article{Martinez-Sykora2017,
  author={Juan Martinez-Sykora and Bart De Pontieu and Mats Carlsson and Viggo H. Hansteen and Daniel Nóbrega-Siverio and Boris V.
Gudiksen},
  title={Two-dimensional Radiative Magnetohydrodynamic Simulations of Partial Ionization in the Chromosphere. II. Dynamics and Energetics of the Low Solar Atmosphere},
  journal={The Astrophysical Journal},
  volume={847},
  number={1},
  pages={36},
  url={http://stacks.iop.org/0004-637X/847/i=1/a=36},
  year={2017},
  abstract={We investigate the effects of interactions between ions and neutrals on the chromosphere and overlying corona using 2.5D radiative MHD simulations with the Bifrost code. We have extended the code capabilities implementing ion–neutral interaction effects using the generalized Ohm’s law, i.e., we include the Hall term and the ambipolar diffusion (Pedersen dissipation) in the induction equation. Our models span from the upper convection zone to the corona, with the photosphere, chromosphere, and transition region partially ionized. Our simulations reveal that the interactions between ionized particles and neutral particles have important consequences for the magnetothermodynamics of these modeled layers: (1) ambipolar diffusion increases the temperature in the chromosphere; (2) sporadically the horizontal magnetic field in the photosphere is diffused into the chromosphere, due to the large ambipolar diffusion; (3) ambipolar diffusion concentrates electrical currents, leading to more violent jets and reconnection processes, resulting in (3a) the formation of longer and faster spicules, (3b) heating of plasma during the spicule evolution, and (3c) decoupling of the plasma and magnetic field in spicules. Our results indicate that ambipolar diffusion is a critical ingredient for understanding the magnetothermodynamic properties in the chromosphere and transition region. The numerical simulations have been made publicly available, similar to previous Bifrost simulations. This will allow the community to study realistic numerical simulations with a wider range of magnetic field configurations and physics modules than previously possible.}
}

@ARTICLE{Gudiksen2011,
   author = {{Gudiksen}, B.~V. and {Carlsson}, M. and {Hansteen}, V.~H. and 
	{Hayek}, W. and {Leenaarts}, J. and {Mart{\'{\i}}nez-Sykora}, J.
	},
    title = "{The stellar atmosphere simulation code Bifrost. Code description and validation}",
  journal = {\aap},
archivePrefix = "arXiv",
   eprint = {1105.6306},
 primaryClass = "astro-ph.SR",
 keywords = {magnetohydrodynamics (MHD), radiative transfer, methods: numerical, Sun: atmosphere, stars: atmospheres},
     year = 2011,
    month = jul,
   volume = 531,
      eid = {A154},
    pages = {A154},
      doi = {10.1051/0004-6361/201116520},
   adsurl = {http://adsabs.harvard.edu/abs/2011A%26A...531A.154G},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}


@ARTICLE{BradyArber2016,
  author={C. S. Brady and T. D. Arber},
  title={Simulations of Alfvén and Kink Wave Driving of the Solar Chromosphere: Efficient Heating and Spicule Launching},
  journal={The Astrophysical Journal},
  volume={829},
  number={2},
  pages={80},
  url={http://stacks.iop.org/0004-637X/829/i=2/a=80},
  year={2016},
  abstract={Two of the central problems in our understanding of the solar chromosphere are how the upper chromosphere is heated and what drives spicules. Estimates of the required chromospheric heating, based on radiative and conductive losses, suggest a rate of ∼0.1 erg cm −3 s −1 in the lower chromosphere and drops to ∼10 −3 erg cm −3 s −1 in the upper chromosphere. The chromosphere is also permeated by spicules, higher density plasma from the lower atmosphere propelled upwards at speeds of ∼10–20 km s −1 , for so-called Type I spicules, which reach heights of ∼3000–5000 km above the photosphere. A clearer understanding of chromospheric dynamics, its heating, and the formation of spicules is thus of central importance to solar atmospheric science. For over 30 years it has been proposed that photospheric driving of MHD waves may be responsible for both heating and spicule formation. This paper presents results from a high-resolution MHD treatment of photospheric driven Alfvén and kink waves propagating upwards into an expanding flux tube embedded in a model chromospheric atmosphere. We show that the ponderomotive coupling from Alfvén and kink waves into slow modes generates shocks, which both heat the upper chromosphere and drive spicules. These simulations show that wave driving of the solar chromosphere can give a local heating rate that matches observations and drive spicules consistent with Type I observations all within a single coherent model.}
}

@ARTICLE{Ni2016,
   author = {{Ni}, L. and {Lin}, J. and {Roussev}, I.~I. and {Schmieder}, B.
	},
    title = "{Heating Mechanisms in the Low Solar Atmosphere through Magnetic Reconnection in Current Sheets}",
  journal = {\apj},
archivePrefix = "arXiv",
   eprint = {1611.01746},
 primaryClass = "astro-ph.SR",
 keywords = {magnetic reconnection, magnetohydrodynamics: MHD, shock waves, Sun: chromosphere},
     year = 2016,
    month = dec,
   volume = 832,
      eid = {195},
    pages = {195},
      doi = {10.3847/0004-637X/832/2/195},
   adsurl = {http://adsabs.harvard.edu/abs/2016ApJ...832..195N},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}


@ARTICLE{Nakariakov1999,
   author = {{Nakariakov}, V.~M. and {Ofman}, L. and {Deluca}, E.~E. and 
	{Roberts}, B. and {Davila}, J.~M.},
    title = "{TRACE observation of damped coronal loop oscillations: Implications for coronal heating}",
  journal = {Science},
     year = 1999,
    month = aug,
   volume = 285,
    pages = {862-864},
      doi = {10.1126/science.285.5429.862},
   adsurl = {http://adsabs.harvard.edu/abs/1999Sci...285..862N},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}


@ARTICLE{Aschwanden1999,
   author = {{Aschwanden}, M.~J. and {Fletcher}, L. and {Schrijver}, C.~J. and 
	{Alexander}, D.},
    title = "{Coronal Loop Oscillations Observed with the Transition Region and Coronal Explorer}",
  journal = {\apj},
 keywords = {SUN: CORONA, SUN: FLARES, SUN: OSCILLATIONS, SUN: UV RADIATION, Sun: Corona, Sun: Flares, Sun: Oscillations, Sun: UV Radiation},
     year = 1999,
    month = aug,
   volume = 520,
    pages = {880-894},
      doi = {10.1086/307502},
   adsurl = {http://adsabs.harvard.edu/abs/1999ApJ...520..880A},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@ARTICLE{Ofman2008,
   author = {{Ofman}, L. and {Wang}, T.~J.},
    title = "{Hinode observations of transverse waves with flows in coronal loops}",
  journal = {\aap},
 keywords = {Sun: flares, Sun: corona, Sun: magnetic fields, Sun: oscillations, waves},
     year = 2008,
    month = may,
   volume = 482,
    pages = {L9-L12},
      doi = {10.1051/0004-6361:20079340},
   adsurl = {http://adsabs.harvard.edu/abs/2008A%26A...482L...9O},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}


@ARTICLE{Jess2009,
   author = {{Jess}, D.~B. and {Mathioudakis}, M. and {Erd{\'e}lyi}, R. and 
	{Crockett}, P.~J. and {Keenan}, F.~P. and {Christian}, D.~J.
	},
    title = "{Alfv{\'e}n Waves in the Lower Solar Atmosphere}",
  journal = {Science},
archivePrefix = "arXiv",
   eprint = {0903.3546},
 primaryClass = "astro-ph.SR",
     year = 2009,
    month = mar,
   volume = 323,
    pages = {1582},
      doi = {10.1126/science.1168680},
   adsurl = {http://adsabs.harvard.edu/abs/2009Sci...323.1582J},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}


@ARTICLE{McIntosh2011,
   author = {{McIntosh}, S.~W. and {de Pontieu}, B. and {Carlsson}, M. and 
	{Hansteen}, V. and {Boerner}, P. and {Goossens}, M.},
    title = "{Alfv{\'e}nic waves with sufficient energy to power the quiet solar corona and fast solar wind}",
  journal = {\nat},
     year = 2011,
    month = jul,
   volume = 475,
    pages = {477-480},
      doi = {10.1038/nature10235},
   adsurl = {http://adsabs.harvard.edu/abs/2011Natur.475..477M},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}


@ARTICLE{Mathioudakis2013,
   author = {{Mathioudakis}, M. and {Jess}, D.~B. and {Erd{\'e}lyi}, R.},
    title = "{Alfv{\'e}n Waves in the Solar Atmosphere. From Theory to Observations}",
  journal = {\ssr},
archivePrefix = "arXiv",
   eprint = {1210.3625},
 primaryClass = "astro-ph.SR",
 keywords = {Sun: Alfv{\'e}n waves, Sun: chromosphere, Sun: corona, Sun: spicules, Plasma wave heating},
     year = 2013,
    month = jun,
   volume = 175,
    pages = {1-27},
      doi = {10.1007/s11214-012-9944-7},
   adsurl = {http://adsabs.harvard.edu/abs/2013SSRv..175....1M},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

 	
@article{AvrettLoeser2008,
  author={Eugene H. Avrett and Rudolf Loeser},
  title={Models of the Solar Chromosphere and Transition Region from SUMER and HRTS Observations: Formation of the Extreme-Ultraviolet Spectrum of Hydrogen, Carbon, and Oxygen},
  journal={The Astrophysical Journal Supplement Series},
  volume={175},
  number={1},
  pages={229},
  url={http://stacks.iop.org/0067-0049/175/i=1/a=229},
  year={2008},
  abstract={We present the results of optically thick non-LTE radiative transfer calculations of lines and continua of H, C I-IV, and O I-VI and other elements using a new one-dimensional, time-independent model corresponding to the average quiet-Sun chromosphere and transition region. The model is based principally on the Curdt et al. SUMER atlas of the extreme ultraviolet spectrum. Our model of the chromosphere is a semiempirical one, with the temperature distribution adjusted to obtain optimum agreement between calculated and observed continuum intensities, line intensities, and line profiles. Our model of the transition region is determined theoretically from a balance between ( a ) radiative losses and ( b ) the downward energy flow from the corona due to thermal conduction and particle diffusion, and using boundary conditions at the base of the transition region established at the top of the chromosphere from the semiempirical model. The quiet-Sun model presented here should be considered as a replacement of the earlier model C of Vernazza et al., since our new model is based on an energy-balance transition region, a better underlying photospheric model, a more extensive set of chromospheric observations, and improved calculations. The photospheric structure of the model given here is the same as in Table 3 of Fontenla, Avrett, Thuiller, & Harder. We show comparisons between calculated and observed continua, and between the calculated and observed profiles of all significant lines of H, C I-IV, and O I-VI in the wavelength range 67-173 nm. While some of the calculated lines are not in emission as observed, we find reasonable general agreement, given the uncertainties in atomic rates and cross sections, and we document the sources of the rates and cross sections used in the calculation. We anticipate that future improvements in the atomic data will give improved agreement with the observations.}
}

@ARTICLE{Pontieu2004,
   author = {{De Pontieu}, B. and {Erdelyi}, R. and {De Moortel}, I. and 
	{Metcalf}, T.},
    title = "{Photospheric Oscillations in the Solar Atmosphere: Driving Chromospheric Spicules and Coronal Waves}",
  journal = {AGU Fall Meeting Abstracts},
 keywords = {7507 Chromosphere, 7509 Corona, 7524 Magnetic fields, 7529 Photosphere, 7546 Transition region},
     year = 2004,
    month = dec,
      eid = {SH13A-1142},
    pages = {SH13A-1142},
   adsurl = {http://adsabs.harvard.edu/abs/2004AGUFMSH13A1142D},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}


@Article{Leake2014,
author="Leake, J. E.
and DeVore, C. R.
and Thayer, J. P.
and Burns, A. G.
and Crowley, G.
and Gilbert, H. R.
and Huba, J. D.
and Krall, J.
and Linton, M. G.
and Lukin, V. S.
and Wang, W.",
title="Ionized Plasma and Neutral Gas Coupling in the Sun's Chromosphere and Earth's Ionosphere/Thermosphere",
journal="Space Science Reviews",
year="2014",
month="Nov",
day="01",
volume="184",
number="1",
pages="107--172",
abstract="We review physical processes of ionized plasma and neutral gas coupling in the weakly ionized, stratified, electromagnetically-permeated regions of the Sun's chromosphere and Earth's ionosphere/thermosphere. Using representative models for each environment we derive fundamental descriptions of the coupling of the constituent parts to each other and to the electric and magnetic fields, and we examine the variation in magnetization of the components. Using these descriptions we compare related phenomena in the two environments, and discuss electric currents, energy transfer and dissipation. We present examples of physical processes that occur in both atmospheres, the descriptions of which have previously been conducted in contrasting paradigms, that serve as examples of how the chromospheric and ionospheric communities can further collaborate. We also suggest future collaborative studies that will help improve our understanding of these two different atmospheres, which while sharing many similarities, also exhibit large disparities in key quantities.",
issn="1572-9672",
doi="10.1007/s11214-014-0103-1",
url="https://doi.org/10.1007/s11214-014-0103-1"
}
@ARTICLE{Tu2016,
   author = {{Tu}, J. and {Song}, P.},
    title = "{A two-dimensional global simulation study of inductive-dynamic magnetosphere-ionosphere coupling}",
  journal = {Journal of Geophysical Research (Space Physics)},
 keywords = {magnetosphere-ionosphere coupling, inductive-dynamic simulation, Alfven wave propagation and reflection, self-consistent numerical simulation, dynamics of field-aligned currents, formation of Pedersen currents},
     year = 2016,
    month = dec,
   volume = 121,
   number = A10,
    pages = {11},
      doi = {10.1002/2016JA023393},
   adsurl = {http://adsabs.harvard.edu/abs/2016JGRA..12111861T},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
@article{Song2014,
  author={P. Song and V. M. Vasyliūnas},
  title={Effect of Horizontally Inhomogeneous Heating on Flow and Magnetic Field in the Chromosphere of the Sun},
  journal={The Astrophysical Journal Letters},
  volume={796},
  number={2},
  pages={L23},
  url={http://stacks.iop.org/2041-8205/796/i=2/a=L23},
  year={2014},
  abstract={}
}

@ARTICLE{Song2011,
   author = {{Song}, P. and {Vasyli{\= u}nas}, V.~M.},
    title = "{Heating of the solar atmosphere by strong damping of Alfv{\'e}n waves}",
  journal = {Journal of Geophysical Research (Space Physics)},
 keywords = {Electromagnetics: Wave propagation (2487, 3285, 4275, 4455, 6934), Magnetospheric Physics: Magnetosphere/ionosphere interactions (2431), Magnetospheric Physics: MHD waves and instabilities (2149, 6050, 7836), Solar Physics, Astrophysics, and Astronomy: Chromosphere, Solar Physics, Astrophysics, and Astronomy: Corona},
     year = 2011,
    month = sep,
   volume = 116,
      eid = {A09104},
    pages = {A09104},
      doi = {10.1029/2011JA016679},
   adsurl = {http://adsabs.harvard.edu/abs/2011JGRA..116.9104S},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}


@ARTICLE{Alissandrakis2018,
       author = {{Alissandrakis}, C.~E. and {Vial}, J. -C. and {Koukras}, A. and
        {Buchlin}, E. and {Chane-Yook}, M.},
        title = "{IRIS Observations of Spicules and Structures Near the Solar Limb}",
      journal = {\solphys},
     keywords = {Chromosphere, quiet, Transition region, Spectrum, ultraviolet, Spectral
        line, intensity and diagnostics},
         year = 2018,
        month = Feb,
       volume = {293},
          eid = {20},
        pages = {20},
          doi = {10.1007/s11207-018-1242-4},
       adsurl = {https://ui.adsabs.harvard.edu/#abs/2018SoPh..293...20A},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@ARTICLE{Hasan08,
   author = {{Hasan}, S.~S.},
    title = "{Chromospheric dynamics}",
  journal = {Advances in Space Research},
     year = 2008,
    month = jul,
   volume = 42,
    pages = {86-95},
      doi = {10.1016/j.asr.2007.08.019},
   adsurl = {http://adsabs.harvard.edu/abs/2008AdSpR..42...86H},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
`
@article{Song2017,
title = {A Model of the Solar Chromosphere: Structure and Internal Circulation},
author = {Song, P.},
abstractNote = {A model of the solar chromosphere that consists of two fundamentally different regions, a lower region and an upper region, is proposed. The lower region is covered mostly by weak locally closed magnetic field and small network areas of extremely strong, locally open field. The field in the upper region is relatively uniform and locally open, connecting to the corona. The chromosphere is heated by strong collisional damping of Alfvén waves, which are driven by turbulent motions below the photosphere. The heating rate depends on the field strength, wave power from the photosphere, and altitude in the chromosphere. The waves in the internetwork area are mostly damped in the lower region, supporting radiation in the lower chromosphere. The waves in the network area, carrying more Poynting flux, are only weakly damped in the lower region. They propagate into the upper region. As the thermal pressure decreases with height, the network field expands to form the magnetic canopy where the damping of the waves from the network area supports radiation in the whole upper region. Because of the vertical stratification and horizontally nonuniform distribution of the magnetic field and heating, one circulation cell is formed in each of the upper and lower regions. The two circulation cells distort the magnetic field and reinforce the funnel-canopy-shaped magnetic geometry. The model is based on classical processes and is semi-quantitative. The estimates are constrained according to observational knowledge. No anomalous process is invoked or needed. Overall, the heating mechanism is able to damp 50% of the total wave energy.},
doi = {10.3847/1538-4357/AA85E1},
journal = {Astrophysical Journal},
number = 2,
volume = 846,
place = {United States},
year = {2017},
month = {9}
}

@article{Nishizuka2011,
  author={N. Nishizuka and T. Nakamura and T. Kawate and K. A. P. Singh and K. Shibata},
  title={Statistical Study of Chromospheric Anemone Jets Observed with Hinode/SOT},
  journal={The Astrophysical Journal},
  volume={731},
  number={1},
  pages={43},
  url={http://stacks.iop.org/0004-637X/731/i=1/a=43},
  year={2011},
  abstract={The Solar Optical Telescope on board Hinode has revealed numerous tiny jets in all regions of the chromosphere outside of sunspots. A typical chromospheric anemone jet has a cusp-shaped structure and bright footpoint, similar to the shape of an X-ray anemone jet observed previously with the Soft X-ray Telescope on board Yohkoh . The similarity in the shapes of chromospheric and X-ray anemone jets suggests that chromospheric anemone jets are produced as a result of the magnetic reconnection between a small bipole (perhaps a tiny emerging flux) and a pre-existing uniform magnetic field in the lower chromosphere. We examine various chromospheric anemone jets in the solar active region near the solar limb and study the typical features (e.g., length, width, lifetime, and velocity) of the chromospheric anemone jets. Statistical studies show that chromospheric anemone jets have: (1) a typical length ~1.0-4.0 Mm, (2) a width ~100-400 km, (3) a lifetime ~100-500 s, and (4) a velocity ~5-20 km s –1 . The velocity of the chromospheric anemone jets is comparable to the local Alfvén speed in the lower solar chromosphere (~10 km s –1 ). The histograms of chromospheric anemone jets near the limb and near the disk center show similar averages and shapes of distributions, suggesting that the characteristic behavior of chromospheric anemone jets is independent of whether they are observed on the disk or at the limb. The observed relationship between the velocity and length of chromospheric anemone jets shows that the jets do not follow ballistic motion but are more likely accelerated by some other mechanism. This is consistent with numerical simulations of chromospheric anemone jets.}
}

@article{Shimojo2000,
  author={Masumi Shimojo and Kazunari Shibata},
  title={Physical Parameters of Solar X-Ray Jets},
  journal={The Astrophysical Journal},
  volume={542},
  number={2},
  pages={1100},
  url={http://stacks.iop.org/0004-637X/542/i=2/a=1100},
  year={2000},
  abstract={We derived the physical parameters of X-ray jets and associated flares using the high-resolution data taken with the soft X-ray telescope aboard Yohkoh . We analyzed 16 X-ray jets and found the following properties of the jets and the footpoint flares: (1) the temperatures and density of the jets, respectively, are 3-8 MK (average: 5.6 MK) and 0.7-4.0 × 10 9 cm -3 (average: 1.7 × 10 9 cm -3 ), (2) the temperatures of the jets are similar to those of the footpoint flares, (3) the thermal energies of the jets are 10 27 -10 29 ergs, which is ##IMG## [http://ej.iop.org/images/0004-637X/542/2/1100/img1.gif] {img1.gif} to ##IMG## [http://ej.iop.org/images/0004-637X/542/2/1100/img2.gif] {img2.gif} of those of the footpoint flares, (4) the apparent velocity of the jets is usually slower than the sound speed, and (5) there is a correlation between the temperatures of the jets and the sizes (square root of area) of the footpoint flares. On the basis of these results, we find that the temperatures of a jet and a footpoint flare are determined by the balance between heating flux and conductive flux and that the mass of a jet is comparable to the theoretical value based on the balance between conductive flux and enthalpy flux carried by the evaporation flow. These results suggest that X-ray jets are evaporation flows produced by the reconnection heating.}
}


@article{KuzmaApJ2017,
  author={Błażej Kuźma and Kris Murawski and Pradeep Kayshap and Darek Wójcik and Abhishek Kumar Srivastava and Bhola N. Dwivedi},
  title={Two-fluid Numerical Simulations of Solar Spicules},
  journal={The Astrophysical Journal},
  volume={849},
  number={2},
  pages={78},
  url={http://stacks.iop.org/0004-637X/849/i=2/a=78},
  year={2017},
  abstract={We aim to study the formation and evolution of solar spicules by means of numerical simulations of the solar atmosphere. With the use of newly developed JOANNA code, we numerically solve two-fluid (for ions + electrons and neutrals) equations in 2D Cartesian geometry. We follow the evolution of a spicule triggered by the time-dependent signal in ion and neutral components of gas pressure launched in the upper chromosphere. We use the potential magnetic field, which evolves self-consistently, but mainly plays a passive role in the dynamics. Our numerical results reveal that the signal is steepened into a shock that propagates upward into the corona. The chromospheric cold and dense plasma lags behind this shock and rises into the corona with a mean speed of 20–25 km s −1 . The formed spicule exhibits the upflow/downfall of plasma during its total lifetime of around 3–4 minutes, and it follows the typical characteristics of a classical spicule, which is modeled by magnetohydrodynamics. The simulated spicule consists of a dense and cold core that is dominated by neutrals. The general dynamics of ion and neutral spicules are very similar to each other. Minor differences in those dynamics result in different widths of both spicules with increasing rarefaction of the ion spicule in time.}
}


@article{Sod1978,
title = "A survey of several finite difference methods for systems of nonlinear hyperbolic conservation laws",
journal = "Journal of Computational Physics",
volume = "27",
number = "1",
pages = "1 - 31",
year = "1978",
issn = "0021-9991",
doi = "https://doi.org/10.1016/0021-9991(78)90023-2",
url = "http://www.sciencedirect.com/science/article/pii/0021999178900232",
author = "Gary A Sod",
abstract = "The finite difference methods of Godunov, Hyman, Lax and Wendroff (two-step), MacCormack, Rusanov, the upwind scheme, the hybrid scheme of Harten and Zwas, the antidiffusion method of Boris and Book, the artificial compression method of Harten, and Glimm's method, a random choice method, are discussed. The methods are used to integrate the one-dimensional Eulerian form of the equations of gas dynamics in Cartesian coordinates for an inviscid, nonheat-conducting fluid. The test problem was a typical shock tube problem. The results are compared and demonstrate that Glimm's method has several advantages."
}

@ARTICLE{Soler2013,
   author = {{Soler}, R. and {Carbonell}, M. and {Ballester}, J.~L. and {Terradas}, J.
	},
    title = "{Alfv{\'e}n Waves in a Partially Ionized Two-fluid Plasma}",
  journal = {\apj},
archivePrefix = "arXiv",
   eprint = {1303.4297},
 primaryClass = "astro-ph.SR",
 keywords = {magnetic fields, magnetohydrodynamics: MHD, plasmas, Sun: atmosphere, Sun: oscillations, waves },
     year = 2013,
    month = apr,
   volume = 767,
      eid = {171},
    pages = {171},
      doi = {10.1088/0004-637X/767/2/171},
   adsurl = {http://adsabs.harvard.edu/abs/2013ApJ...767..171S},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@book{baumjohann1997,
  title={Basic Space Plasma Physics},
  author={Baumjohann, W. and Treumann, R.A.},
  isbn={9781860940798},
  lccn={97102954},
  url={https://books.google.com/books?id=bbVACbm9FjYC},
  year={1997},
  publisher={Imperial College Press}
}

@article{Knipp2018,
author = {Knipp, Delores J. and Fraser, Brian J. and Shea, M. A. and Smart, D. F.},
title = {On the Little-Known Consequences of the 4 August 1972 Ultra-Fast Coronal Mass Ejecta: Facts, Commentary, and Call to Action},
journal = {Space Weather},
volume = {16},
number = {11},
pages = {1635-1643},
keywords = {superstorm, grand challenge, interplanetary shock},
doi = {10.1029/2018SW002024},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018SW002024},
eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2018SW002024},
abstract = {Abstract Today the extreme space weather events of early August 1972 are discussed as benchmarks for Sun-Earth transit times of solar ejecta (14.6 hr) and for solar energetic particle fluxes (10 MeV ion flux >70,000 cm−2·s−1·sr−1). Although the magnetic storm index, Dst, dipped to only −125 nT, the magnetopause was observed within 5.2 RE and the plasmapause within 2 RE. Widespread electric- and communication-grid disturbances plagued North America late on 4 August. There was an additional effect, long buried in the Vietnam War archives that add credence to the severity of the storm impact: a nearly instantaneous, unintended detonation of dozens of sea mines south of Hai Phong, North Vietnam on 4 August 1972. The U.S. Navy attributed the dramatic event to magnetic perturbations of solar storms. Herein we discuss how such a finding is broadly consistent with terrestrial effects and technological impacts of the 4 August 1972 event and the propagation of major eruptive activity from the Sun to the Earth. We also provide insight into the solar, geophysical, and military circumstances of this extraordinary situation. In our view this storm deserves a scientific revisit as a grand challenge for the space weather community, as it provides space-age terrestrial observations of what was likely a Carrington-class storm.},
year = {2018}
}

@article{Baker2013,
author = {Baker, D. N. and Li, X. and Pulkkinen, A. and Ngwira, C. M. and Mays, M. L. and Galvin, A. B. and Simunac, K. D. C.},
title = {A major solar eruptive event in July 2012: Defining extreme space weather scenarios},
journal = {Space Weather},
volume = {11},
number = {10},
pages = {585-591},
keywords = {extreme space weather, severe solar storm, worst case geomagnetic event},
doi = {10.1002/swe.20097},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/swe.20097},
eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1002/swe.20097},
abstract = {AbstractA key goal for space weather studies is to define severe and extreme conditions that might plausibly afflict human technology. On 23 July 2012, solar active region 1520 (~141°W heliographic longitude) gave rise to a powerful coronal mass ejection (CME) with an initial speed that was determined to be 2500 ± 500 km/s. The eruption was directed away from Earth toward 125°W longitude. STEREO-A sensors detected the CME arrival only about 19 h later and made in situ measurements of the solar wind and interplanetary magnetic field. In this paper, we address the question of what would have happened if this powerful interplanetary event had been Earthward directed. Using a well-proven geomagnetic storm forecast model, we find that the 23–24 July event would certainly have produced a geomagnetic storm that was comparable to the largest events of the twentieth century (Dst ~ −500 nT). Using plausible assumptions about seasonal and time-of-day orientation of the Earth's magnetic dipole, the most extreme modeled value of storm-time disturbance would have been Dst = −1182 nT. This is considerably larger than estimates for the famous Carrington storm of 1859. This finding has far reaching implications because it demonstrates that extreme space weather conditions such as those during March of 1989 or September of 1859 can happen even during a modest solar activity cycle such as the one presently underway. We argue that this extreme event should immediately be employed by the space weather community to model severe space weather effects on technological systems such as the electric power grid.},
year = {2013}
}

@article{Finlay2010,
    author = {Finlay, C. C. and Langlais, B. and Lowes, F. J. and Mandea, M. and Menvielle, M. and Tøffner-Clausen, L. and Olsen, N. and Tangborn, A. and Wei, Z. and Manoj, C. and Maus, S. and McLean, S. and Thomson, A. W. P. and Hamilton, B. and Beggan, C. D. and Macmillan, S. and Chernova, T. A. and Zvereva, T. I. and Bondar, T. N. and Golovkov, V. P. and Chambodut, A. and Chulliat, A. and Thébault, E. and Hulot, G. and Lühr, H. and Michaelis, I. and Wardinski, I. and Rauberg, J. and Hamoudi, M. and Rother, M. and Lesur, V. and Holme, R. and Sabaka, T. J. and Kuang, W.},
    title = "{International Geomagnetic Reference Field: the eleventh generation}",
    journal = {Geophysical Journal International},
    volume = {183},
    number = {3},
    pages = {1216-1230},
    year = {2010},
    month = {12},
    abstract = {"The eleventh generation of the International Geomagnetic Reference Field (IGRF) was adopted in December 2009 by the International Association of Geomagnetism and Aeronomy Working Group V-MOD. It updates the previous IGRF generation with a definitive main field model for epoch 2005.0, a main field model for epoch 2010.0, and a linear predictive secular variation model for 2010.0–2015.0. In this note the equations defining the IGRF model are provided along with the spherical harmonic coefficients for the eleventh generation. Maps of the magnetic declination, inclination and total intensity for epoch 2010.0 and their predicted rates of change for 2010.0–2015.0 are presented. The recent evolution of the South Atlantic Anomaly and magnetic pole positions are also examined".},
    issn = {0956-540X},
    doi = {10.1111/j.1365-246X.2010.04804.x},
    url = {https://dx.doi.org/10.1111/j.1365-246X.2010.04804.x},
    eprint = {http://oup.prod.sis.lan/gji/article-pdf/183/3/1216/1785065/183-3-1216.pdf},
}

@article{Knipp2019,
author = {Knipp, Delores J.},
title = {Fall 2018 AGU Editors' Highlights: Living Within the Sun's Stormy Atmosphere},
journal = {Space Weather},
volume = {17},
number = {1},
pages = {3-5},
doi = {10.1029/2019SW002154},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019SW002154},
eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2019SW002154},
abstract = {Abstract This article presents highlights in space weather science presented at the American Geophysical Union Literature Review Session at the 2018 Fall AGU.},
year = {2019}
}

@ARTICLE{Langmuir1928,
   author = {{Langmuir}, I.},
    title = "{Oscillations in Ionized Gases}",
  journal = {Proceedings of the National Academy of Science},
     year = 1928,
    month = aug,
   volume = 14,
    pages = {627-637},
      doi = {10.1073/pnas.14.8.627},
   adsurl = {http://adsabs.harvard.edu/abs/1928PNAS...14..627L},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@article{Tonks1967,
author = {Tonks,Lewi},
title = {The Birth of Plasma},
journal = {American Journal of Physics},
volume = {35},
number = {9},
pages = {857-858},
year = {1967},
doi = {10.1119/1.1974266},
URL = { https://doi.org/10.1119/1.1974266 },
eprint = { https://doi.org/10.1119/1.1974266 }
}

@ARTICLE{glm,
   author = {{Dedner}, A. and {Kemm}, F. and {Kr{\"o}ner}, D. and {Munz}, C.-D. and 
	{Schnitzer}, T. and {Wesenberg}, M.},
    title = "{Hyperbolic Divergence Cleaning for the MHD Equations}",
  journal = {Journal of Computational Physics},
     year = 2002,
    month = jan,
   volume = 175,
    pages = {645-673},
      doi = {10.1006/jcph.2001.6961},
   adsurl = {http://adsabs.harvard.edu/abs/2002JCoPh.175..645D},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@ARTICLE{gabriel1976,
   author = {{Gabriel}, A.~H.},
    title = "{A magnetic model of the solar transition region}",
  journal = {Philosophical Transactions of the Royal Society of London Series A},
 keywords = {Atmospheric Models, Chromosphere, Magnetic Field Configurations, Solar Atmosphere, Solar Magnetic Field, Convective Flow, Emission Spectra, Heat Balance, Magnetic Flux, Magnetohydrodynamic Flow, Solar Granulation, Stellar Models, Two Dimensional Models},
     year = 1976,
    month = may,
   volume = 281,
    pages = {339-352},
      doi = {10.1098/rsta.1976.0031},
   adsurl = {http://adsabs.harvard.edu/abs/1976RSPTA.281..339G},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@ARTICLE{Pontieu2007,
   author = {{de Pontieu}, B. and {McIntosh}, S. and {Hansteen}, V.~H. and 
	{Carlsson}, M. and {Schrijver}, C.~J. and {Tarbell}, T.~D. and 
	{Title}, A.~M. and {Shine}, R.~A. and {Suematsu}, Y. and {Tsuneta}, S. and 
	{Katsukawa}, Y. and {Ichimoto}, K. and {Shimizu}, T. and {Nagata}, S.
	},
    title = "{A Tale of Two Spicules: The Impact of Spicules on the Magnetic Chromosphere}",
  journal = {\pasj},
archivePrefix = "arXiv",
   eprint = {0710.2934},
 keywords = {Sun: chromosphere, Sun: transition region},
     year = 2007,
    month = nov,
   volume = 59,
    pages = {S655-S662},
      doi = {10.1093/pasj/59.sp3.S655},
   adsurl = {http://adsabs.harvard.edu/abs/2007PASJ...59S.655D},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@ARTICLE{1dtu,
  author={Jiannan Tu and Paul Song},
  title={A Study of Alfvén Wave Propagation and Heating the Chromosphere},
  journal={The Astrophysical Journal},
  volume={777},
  number={1},
  pages={53},
  url={http://stacks.iop.org/0004-637X/777/i=1/a=53},
  year={2013},
  abstract={Alfvén wave propagation, reflection, and heating of the chromosphere are studied for a one-dimensional solar atmosphere by self-consistently solving plasma, neutral fluid, and Maxwell's equations with incorporation of the Hall effect and strong electron-neutral, electron-ion, and ion-neutral collisions. We have developed a numerical model based on an implicit backward difference formula of second-order accuracy both in time and space to solve stiff governing equations resulting from strong inter-species collisions. A non-reflecting boundary condition is applied to the top boundary so that the wave reflection within the simulation domain can be unambiguously determined. It is shown that due to the density gradient the Alfvén waves are partially reflected throughout the chromosphere and more strongly at higher altitudes with the strongest reflection at the transition region. The waves are damped in the lower chromosphere dominantly through Joule dissipation, producing heating strong enough to balance the radiative loss for the quiet chromosphere without invoking anomalous processes or turbulences. The heating rates are larger for weaker background magnetic fields below ~500 km with higher-frequency waves subject to heavier damping. There is an upper cutoff frequency, depending on the background magnetic field, above which the waves are completely damped. At the frequencies below which the waves are not strongly damped, the interaction of reflected waves with the upward propagating waves produces power at their double frequencies, which leads to more damping. The wave energy flux transmitted to the corona is one order of magnitude smaller than that of the driving source.}
}
 	
@article{Avrett2008,
  author={Eugene H. Avrett and Rudolf Loeser},
  title={Models of the Solar Chromosphere and Transition Region from SUMER and HRTS Observations: Formation of the Extreme-Ultraviolet Spectrum of Hydrogen, Carbon, and Oxygen},
  journal={The Astrophysical Journal Supplement Series},
  volume={175},
  number={1},
  pages={229},
  url={http://stacks.iop.org/0067-0049/175/i=1/a=229},
  year={2008},
  abstract={We present the results of optically thick non-LTE radiative transfer calculations of lines and continua of H, C I-IV, and O I-VI and other elements using a new one-dimensional, time-independent model corresponding to the average quiet-Sun chromosphere and transition region. The model is based principally on the Curdt et al. SUMER atlas of the extreme ultraviolet spectrum. Our model of the chromosphere is a semiempirical one, with the temperature distribution adjusted to obtain optimum agreement between calculated and observed continuum intensities, line intensities, and line profiles. Our model of the transition region is determined theoretically from a balance between ( a ) radiative losses and ( b ) the downward energy flow from the corona due to thermal conduction and particle diffusion, and using boundary conditions at the base of the transition region established at the top of the chromosphere from the semiempirical model. The quiet-Sun model presented here should be considered as a replacement of the earlier model C of Vernazza et al., since our new model is based on an energy-balance transition region, a better underlying photospheric model, a more extensive set of chromospheric observations, and improved calculations. The photospheric structure of the model given here is the same as in Table 3 of Fontenla, Avrett, Thuiller, & Harder. We show comparisons between calculated and observed continua, and between the calculated and observed profiles of all significant lines of H, C I-IV, and O I-VI in the wavelength range 67-173 nm. While some of the calculated lines are not in emission as observed, we find reasonable general agreement, given the uncertainties in atomic rates and cross sections, and we document the sources of the rates and cross sections used in the calculation. We anticipate that future improvements in the atomic data will give improved agreement with the observations.}
}

@article{Song2014,
	doi = {10.1088/2041-8205/796/2/l23},
	url = {https://doi.org/10.1088%2F2041-8205%2F796%2F2%2Fl23},
	year = 2014,
	month = {nov},
	publisher = {{IOP} Publishing},
	volume = {796},
	number = {2},
	pages = {L23},
	author = {P. Song and V. M. Vasyli{\={u}}nas},
	title = {{EFFECT} {OF} {HORIZONTALLY} {INHOMOGENEOUS} {HEATING} {ON} {FLOW} {AND} {MAGNETIC} {FIELD} {IN} {THE} {CHROMOSPHERE} {OF} {THE} {SUN}},
	journal = {The Astrophysical Journal},
	abstract = {The solar chromosphere is heated by damped Alfvén waves propagating upward from the photosphere at a rate that depends on magnetic field strength, producing enhanced heating at low altitudes in the extended weak-field regions (where the additional heating accounts for the radiative losses) between the boundaries of the chromospheric network as well as enhanced heating per particle at higher altitudes in strong magnetic field regions of the network. The resulting inhomogeneous radiation and temperature distribution produces bulk flows, which in turn affect the configuration of the magnetic field. The basic flow pattern is circulation on the spatial scale of a supergranule, with upward flow in the strong-field region; this is a mirror image in the upper chromosphere of photospheric/subphotospheric convection widely associated with the formation of the strong network field. There are significant differences between the neutral and the ionized components of the weakly ionized medium: neutral flow streamlines can form closed cells, whereas plasma is largely constrained to flow along the magnetic field. Stresses associated with this differential flow may explain why the canopy/funnel structures of the network magnetic field have a greater horizontal extent and are relatively more homogeneous at high altitudes than is expected from simple current-free models.}
}

@ARTICLE{Kuzma2017,
   author = {{Ku{\'z}ma}, B. and {Murawski}, K. and {Zaqarashvili}, T.~V. and 
	{Konkol}, P. and {Mignone}, A.},
    title = "{Numerical simulations of solar spicules: Adiabatic and non-adiabatic studies}",
  journal = {\aap},
 keywords = {Sun: activity, magnetohydrodynamics (MHD), methods: numerical, Sun: corona, Sun: transition region},
     year = 2017,
    month = jan,
   volume = 597,
      eid = {A133},
    pages = {A133},
      doi = {10.1051/0004-6361/201628747},
   adsurl = {http://adsabs.harvard.edu/abs/2017A%26A...597A.133K},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@ARTICLE{glm2,
   author = {{Mignone}, A. and {Tzeferacos}, P. and {Bodo}, G.},
    title = "{High-order conservative finite difference GLM-MHD schemes for cell-centered MHD}",
  journal = {Journal of Computational Physics},
archivePrefix = "arXiv",
   eprint = {1001.2832},
 primaryClass = "astro-ph.HE",
     year = 2010,
    month = aug,
   volume = 229,
    pages = {5896-5920},
      doi = {10.1016/j.jcp.2010.04.013},
   adsurl = {http://adsabs.harvard.edu/abs/2010JCoPh.229.5896M},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@inproceedings{Rutten2007,
   author = {{Rutten}, R.~J.},
    title = "{Observing the Solar Chromosphere}",
booktitle = {The Physics of Chromospheric Plasmas},
     year = 2007,
   series = {Astronomical Society of the Pacific Conference Series},
   volume = 368,
   eprint = {astro-ph/0703637},
   editor = {{Heinzel}, P. and {Dorotovi{\v c}}, I. and {Rutten}, R.~J.},
    month = may,
    pages = {Heinzel},
   adsurl = {http://adsabs.harvard.edu/abs/2007ASPC..368...27R},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@article{kurganov,
title = "New High-Resolution Central Schemes for Nonlinear Conservation Laws and Convection–Diffusion Equations",
journal = "Journal of Computational Physics",
volume = "160",
number = "1",
pages = "241 - 282",
year = "2000",
issn = "0021-9991",
doi = "https://doi.org/10.1006/jcph.2000.6459",
url = "http://www.sciencedirect.com/science/article/pii/S0021999100964593",
author = "Alexander Kurganov and Eitan Tadmor",
abstract = "Central schemes may serve as universal finite-difference methods for solving nonlinear convection–diffusion equations in the sense that they are not tied to the specific eigenstructure of the problem, and hence can be implemented in a straightforward manner as black-box solvers for general conservation laws and related equations governing the spontaneous evolution of large gradient phenomena. The first-order Lax–Friedrichs scheme (P. D. Lax, 1954) is the forerunner for such central schemes. The central Nessyahu–Tadmor (NT) scheme (H. Nessyahu and E. Tadmor, 1990) offers higher resolution while retaining the simplicity of the Riemann-solver-free approach. The numerical viscosity present in these central schemes is of order O((Δx)2r/Δt). In the convective regime where Δt∼Δx, the improved resolution of the NT scheme and its generalizations is achieved by lowering the amount of numerical viscosity with increasing r. At the same time, this family of central schemes suffers from excessive numerical viscosity when a sufficiently small time step is enforced, e.g., due to the presence of degenerate diffusion terms. In this paper we introduce a new family of central schemes which retain the simplicity of being independent of the eigenstructure of the problem, yet which enjoy a much smaller numerical viscosity (of the corresponding order O(Δx)2r−1)). In particular, our new central schemes maintain their high-resolution independent of O(1/Δt), and letting Δt ↓ 0, they admit a particularly simple semi-discrete formulation. The main idea behind the construction of these central schemes is the use of more precise information of the local propagation speeds. Beyond these CFL related speeds, no characteristic information is required. As a second ingredient in their construction, these central schemes realize the (nonsmooth part of the) approximate solution in terms of its cell averages integrated over the Riemann fans of varying size. The semi-discrete central scheme is then extended to multidimensional problems, with or without degenerate diffusive terms. Fully discrete versions are obtained with Runge–Kutta solvers. We prove that a scalar version of our high-resolution central scheme is nonoscillatory in the sense of satisfying the total-variation diminishing property in the one-dimensional case and the maximum principle in two-space dimensions. We conclude with a series of numerical examples, considering convex and nonconvex problems with and without degenerate diffusion, and scalar and systems of equations in one- and two-space dimensions. Time evolution is carried out by the third- and fourth-order explicit embedded integration Runge–Kutta methods recently proposed by A. Medovikov (1998). These numerical studies demonstrate the remarkable resolution of our new family of central scheme."
}

@article{roe,
author = { P L Roe },
title = {Characteristic-Based Schemes for the Euler Equations},
journal = {Annual Review of Fluid Mechanics},
volume = {18},
number = {1},
pages = {337-365},
year = {1986},
doi = {10.1146/annurev.fl.18.010186.002005},
URL = { 
        https://doi.org/10.1146/annurev.fl.18.010186.002005   
},
eprint = { 
        https://doi.org/10.1146/annurev.fl.18.010186.002005
    
}
}

@software{arma,
  author = {Conrad Sanderson and Ryan Curtin},
  title = {Armadillo: a template-based C++ library for linear algebra},
  url = {http://arma.sourceforge.net/},
  journal = {Journal of Open Source Software},
  volume = {1},
  pages = {26},
  year = {2016},
  version = {8.400}
}

@software{viennacl,
  author = {Karl {Rupp}, Philippe Tillet, Florian Rudolf, Josef Weinbub, Andreas Morhammer, Tibor Grasser, Ansgar Jüngel, and Siegfried Selberherr},
  title = {ViennaCL - Linear Algebra Library for Multi- and Many-Core Architectures},
  url = {http://viennacl.sourceforge.net/},
  journal = {SIAM Journal on Scientific Computing},
  volume = {38},
  pages = {S412-S439},
  year = {2016},
  version = {1.7.1}
}