Author name code: cally
ADS astronomy entries on 2022-09-14
author:"Cally, Paul S." 
------------------------------------------------------------------------  

Title: On the fragility of Alfvén waves in a stratified atmosphere
Authors: Cally, Paul S.
Bibcode: 2022MNRAS.510.1093C
Altcode: 2021MNRAS.tmp.3141C; 2021arXiv211113435C
  Complete asymptotic expansions are developed for slow, Alfvén, and
  fast magnetohydrodynamic waves at the base of an isothermal 3D plane
  stratified atmosphere. Together with existing convergent Frobenius
  series solutions about z = ∞, matchings are numerically calculated
  that illuminate the fates of slow and Alfvén waves injected from
  below. An Alfvén wave in a two-dimensional model is 2.5D in the sense
  that the wave propagates in the plane of the magnetic field but its
  polarization is normal to it in an ignorable horizontal direction, and
  the wave remains an Alfvén wave throughout. The rotation of the plane
  of wave propagation away from the vertical plane of the magnetic field
  pushes the plasma displacement vector away from horizontal, thereby
  coupling it to stratification. It is shown that potent slow-Alfvén
  coupling occurs in such 3D models. It is found that about 50 per cent
  of direction-averaged Alfvén wave flux generated in the low atmosphere
  at frequencies comparable to or greater than the acoustic cut-off can
  reach the top as Alfvén flux for small magnetic field inclinations
  θ, and this increases to 80 per cent or more with increasing θ. On
  the other hand, direction-averaged slow waves can be 40 per cent
  effective in converting to Alfvén waves at small inclination, but
  this reduces sharply with increasing θ and wave frequency. Together
  with previously explored fast-slow and fast-Alfvén couplings, this
  provides valuable insights into which injected transverse waves can
  reach the upper atmosphere as Alfvén waves, with implications for
  solar and stellar coronal heating and solar/stellar wind acceleration.

Title: Benchmarking hall-induced magnetoacoustic to Alfvén mode
    conversion in the solar chromosphere
Authors: Raboonik, Abbas; Cally, Paul S.
Bibcode: 2021MNRAS.507.2671R
Altcode: 2021MNRAS.tmp.2106R
  A 2.5D numerical model of magnetoacoustic-Alfvén linear mode
  conversions in the partially ionized low solar atmosphere induced
  by the Hall effect is surveyed, varying magnetic field strength and
  inclination, and wave frequency and horizontal wavenumber. It is
  found that only the magnetic component of wave energy is subject to
  Hall-mediated conversions to Alfvén wave-energy via a process of
  polarization rotation. This strongly boosts direct mode conversion
  between slow magnetoacoustic and Alfvén waves in the quiet low
  chromosphere, even at mHz frequencies. However, fast waves there,
  which are predominantly acoustic in nature, are only subject to
  Hall-induced conversion via an indirect two-step process: (i) a
  geometry-induced fast-slow transformation near the Alfvén-acoustic
  equipartition height z<SUB>eq</SUB>; and (ii) Hall-rotation of the
  fast wave in z &gt; z<SUB>eq</SUB>. Thus, for the two-stage process to
  yield upgoing Alfvén waves, z<SUB>eq</SUB> must lie below or within
  the Hall-effective window 0 ≲ z ≲ 700 km. Magnetic field strengths
  over 100 G are required to achieve this. Since the potency of this
  Hall effect varies inversely with the field strength but directly
  with the wave frequency, only frequencies above about 100 mHz are
  significantly affected by the two-stage process. Increasing magnetic
  field inclination θ generally strengthens the Hall convertibility,
  but the horizontal wavenumber k<SUB>x</SUB> has little effect. The
  direct and indirect Hall mechanisms both have implications for the
  ability of MHD waves excited at the photosphere to reach the upper
  chromosphere, and by implication the corona.

Title: Benchmarking Hall-Induced Magnetoacoustic to Alfvén Mode
    Conversion in the Solar Chromosphere
Authors: Raboonik, Abbas; Cally, Paul
Bibcode: 2021arXiv210802396R
Altcode:
  A 2.5D numerical model of magnetoacoustic-Alfvén linear mode
  conversions in the partially ionised low solar atmosphere induced
  by the Hall effect is surveyed, varying magnetic field strength and
  inclination, and wave frequency and horizontal wave number. It is
  found that only the magnetic component of wave energy is subject to
  Hall-mediated conversions to Alfvén wave-energy via a process of
  polarisation rotation. This strongly boosts direct mode conversion
  between slow magneto\-acoustic and Alfvén waves in the quiet low
  chromosphere, even at mHz frequencies. However, fast waves there, which
  are predominantly acoustic in nature, are only subject to Hall- induced
  conversion via an indirect two-step process: (i) a geometry-induced
  fast-slow transformation near the Alfvén-acoustic equipartition height
  $z_{\rm eq}$; and (ii) Hall-rotation of the fast wave in $z&gt;z_{\rm
  eq}$. Thus, for the two-stage process to yield upgoing Alfvén waves,
  $z_{\rm eq}$ must lie below or within the Hall-effective window
  $0\lesssim z\lesssim700$ km. Magnetic field strengths over 100 G are
  required to achieve this. Since the potency of this Hall effect varies
  inversely with the field strength but directly with the wave frequency,
  only frequencies above about 100 mHz are significantly affected by
  the two-stage process. Increasing magnetic field inclination $\theta$
  generally strengthens the Hall convertibility, but the horizontal
  wavenumber $k_x$ has little effect. The direct and indirect Hall
  mechanisms both have implications for the ability of MHD waves excited
  at the photosphere to reach the upper chromosphere, and by implication
  the corona.

Title: Second bounces of seismic signals from sunquakes: modelling
    and data
Authors: Donea, A.; Cally, P.
Bibcode: 2021AAS...23811318D
Altcode:
  The 6 September 2017 X9.3 solar flare produced interesting magnetic
  field transients and a few seismic sources generating visible acoustic
  ripples in the quiet magnetic bay of the hosting active region.Zharkov
  et al (2020) for the first time presented observations of the second
  bounce of acoustic waves generated in the solar photosphere by one of
  the seismic sources. In this work we model the second skips using the
  ray-theory and simple models of magnetic fields of a sunspot. We want
  to understand how various parametrisations related to the local magnetic
  field, source locations and source movements can influence the behaviour
  of the first and second skips in time-distance plots. This work will
  help us to understand why the majority of sunquakes do not present
  second bounces; it may give us clues on how to look at observations
  in search for ripples and will help with backtracking information on
  seismic sources.

Title: Conversion and Smoothing of MHD Shocks in Atmospheres with
    Open and Closed Magnetic Field and Neutral Points
Authors: Pennicott, Jamon D.; Cally, Paul S.
Bibcode: 2021SoPh..296...97P
Altcode: 2021arXiv210502329P
  Planar acoustically dominated magnetohydrodynamic waves are initiated
  at the high-β base of a simulated 2D isothermal stratified atmosphere
  with potential magnetic field exhibiting both open and closed field
  regions as well as neutral points. They shock on their way upward toward
  the Alfvén-acoustic equipartition surface a =c , where a and c are
  the Alfvén and sound speeds, respectively. Expanding on recent 1.5D
  findings that such shocks mode-convert to fast shocks and slow smoothed
  waves on passing through a =c , we explore the implications for these
  more complex magnetic geometries. It is found that the 1.5D behaviour
  carries over to the more complex case, with the fast shocks strongly
  attracted to neutral points, which are disrupted producing extensive
  fine structure. It is also observed that shocks moving in the opposite
  direction, from a &gt;c to a &lt;c , split into fast and slow components
  too, and that again it is the slow component that is smoothed.

Title: Chromospheric Heating by Magnetohydrodynamic Waves and
    Instabilities
Authors: Srivastava, A. K.; Ballester, J. L.; Cally, P. S.; Carlsson,
   M.; Goossens, M.; Jess, D. B.; Khomenko, E.; Mathioudakis, M.;
   Murawski, K.; Zaqarashvili, T. V.
Bibcode: 2021JGRA..12629097S
Altcode: 2021arXiv210402010S
  The importance of the chromosphere in the mass and energy transport
  within the solar atmosphere is now widely recognized. This review
  discusses the physics of magnetohydrodynamic waves and instabilities
  in large-scale chromospheric structures as well as in magnetic flux
  tubes. We highlight a number of key observational aspects that have
  helped our understanding of the role of the solar chromosphere
  in various dynamic processes and wave phenomena, and the heating
  scenario of the solar chromosphere is also discussed. The review
  focuses on the physics of waves and invokes the basics of plasma
  instabilities in the context of this important layer of the solar
  atmosphere. Potential implications, future trends and outstanding
  questions are also delineated.

Title: Study of Acoustic Halos in NOAA Active Region 12683
Authors: Tripathy, S. C.; Jain, K.; Kholikov, S.; Hill, F.; Cally, P.
Bibcode: 2020ASSP...57..121T
Altcode:
  We characterize the spatio-temporal power distribution around the
  active region 12683 as a function of height in the solar atmosphere,
  wave frequencies, magnetic field strength and inclination of the
  magnetic field.

Title: An introductory guide to fluid models with anisotropic
    temperatures. Part 1. CGL description and collisionless fluid
    hierarchy
Authors: Hunana, P.; Tenerani, A.; Zank, G. P.; Khomenko, E.;
   Goldstein, M. L.; Webb, G. M.; Cally, P. S.; Collados, M.; Velli,
   M.; Adhikari, L.
Bibcode: 2019JPlPh..85f2002H
Altcode: 2019arXiv190109354H
  We present a detailed guide to advanced collisionless fluid models
  that incorporate kinetic effects into the fluid framework, and that are
  much closer to the collisionless kinetic description than traditional
  magnetohydrodynamics. Such fluid models are directly applicable to
  modelling the turbulent evolution of a vast array of astrophysical
  plasmas, such as the solar corona and the solar wind, the interstellar
  medium, as well as accretion disks and galaxy clusters. The text
  can be viewed as a detailed guide to Landau fluid models and it is
  divided into two parts. Part 1 is dedicated to fluid models that
  are obtained by closing the fluid hierarchy with simple (non-Landau
  fluid) closures. Part 2 is dedicated to Landau fluid closures. Here
  in Part 1, we discuss the fluid model of Chew-Goldberger-Low (CGL)
  in great detail, together with fluid models that contain dispersive
  effects introduced by the Hall term and by the finite Larmor radius
  corrections to the pressure tensor. We consider dispersive effects
  introduced by the non-gyrotropic heat flux vectors. We investigate
  the parallel and oblique firehose instability, and show that the
  non-gyrotropic heat flux strongly influences the maximum growth rate of
  these instabilities. Furthermore, we discuss fluid models that contain
  evolution equations for the gyrotropic heat flux fluctuations and that
  are closed at the fourth-moment level by prescribing a specific form
  for the distribution function. For the bi-Maxwellian distribution,
  such a closure is known as the `normal' closure. We also discuss a
  fluid closure for the bi-kappa distribution. Finally, by considering
  one-dimensional Maxwellian fluid closures at higher-order moments,
  we show that such fluid models are always unstable. The last possible
  non Landau fluid closure is therefore the `normal' closure, and beyond
  the fourth-order moment, Landau fluid closures are required.

Title: An introductory guide to fluid models with anisotropic
    temperatures. Part 2. Kinetic theory, Padé approximants and Landau
    fluid closures
Authors: Hunana, P.; Tenerani, A.; Zank, G. P.; Goldstein, M. L.;
   Webb, G. M.; Khomenko, E.; Collados, M.; Cally, P. S.; Adhikari, L.;
   Velli, M.
Bibcode: 2019JPlPh..85f2003H
Altcode: 2019arXiv190109360H
  In Part 2 of our guide to collisionless fluid models, we concentrate
  on Landau fluid closures. These closures were pioneered by Hammett
  and Perkins and allow for the rigorous incorporation of collisionless
  Landau damping into a fluid framework. It is Landau damping that sharply
  separates traditional fluid models and collisionless kinetic theory,
  and is the main reason why the usual fluid models do not converge to the
  kinetic description, even in the long-wavelength low-frequency limit. We
  start with a brief introduction to kinetic theory, where we discuss in
  detail the plasma dispersion function Z(ζ), and the associated plasma
  response function R(ζ)=1+ζZ(ζ)=-Z^' }(ζ)/2. We then consider a
  one-dimensional (1-D) (electrostatic) geometry and make a significant
  effort to map all possible Landau fluid closures that can be constructed
  at the fourth-order moment level. These closures for parallel moments
  have general validity from the largest astrophysical scales down to
  the Debye length, and we verify their validity by considering examples
  of the (proton and electron) Landau damping of the ion-acoustic mode,
  and the electron Landau damping of the Langmuir mode. We proceed by
  considering 1-D closures at higher-order moments than the fourth order,
  and as was concluded in Part 1, this is not possible without Landau
  fluid closures. We show that it is possible to reproduce linear
  Landau damping in the fluid framework to any desired precision,
  thus showing the convergence of the fluid and collisionless kinetic
  descriptions. We then consider a 3-D (electromagnetic) geometry in the
  gyrotropic (long-wavelength low-frequency) limit and map all closures
  that are available at the fourth-order moment level. In appendix Ae
  provide comprehensive tables with Padé approximants of R(ζ) up to
  the eighth-pole order, with many given in an analytic form.

Title: Fast-to-Alfvén Mode Conversion and Ambipolar Heating in
    Structured Media. I. Simplified Cold Plasma Model
Authors: Cally, Paul S.; Khomenko, Elena
Bibcode: 2019ApJ...885...58C
Altcode:
  Linear fast magnetoacoustic waves are introduced into a cold
  stratified plasma model made up of a doubly periodic ensemble of
  straight diminished-Alfvén-speed tubes. Coupling between fast and
  Alfvén waves is produced by stratification and the tube structures,
  and scattering is strong for wavelengths comparable to the inter-tube
  separation. Ambipolar diffusion is found to be enhanced by the
  structuring and is potentially significant at high frequencies. The
  production of kink waves is discussed and modeled. It is found that
  the tube structure significantly alters the wave energy reaching the
  corona and the form that it takes, even for moderate fast-slow tube
  contrast, with Alfvén waves becoming prominent.

Title: Hall-coupling of Slow and Alfvén Waves at Low Frequencies
    in the Lower Solar Atmosphere
Authors: Raboonik, Abbas; Cally, Paul S.
Bibcode: 2019SoPh..294..147R
Altcode:
  The Hall effect due to weak ionization in the lower solar atmosphere
  is shown to produce significant coupling between slow magneto-acoustic
  and Alfvén waves, especially in highly inclined magnetic fields,
  and even at low frequencies (≈5 mHz and above). Based on the exact
  magneto-acoustic linear wave solutions in a 2D isothermal model
  atmosphere, a perturbation approach is used to calculate the coupling
  to Alfvén waves polarized in the third dimension. First, a fast
  wave is injected at the bottom and is partially and often strongly
  reflected/converted to a down-going slow wave at the Alfvén-acoustic
  equipartition height, depending on magnetic field inclination,
  frequency, and wave number. This slow wave then couples strongly to
  the down-going Alfvén wave via the Hall effect for realistic Hall
  parameters. The coupling is strongest for horizontal wavenumbers
  oriented opposite to the field inclination, and magnetic fields around
  100 G, for which large values of the Hall parameter are co-spatial
  with the region where slow and Alfvén waves have almost identical
  wave forms. Second, a slow wave is injected at the bottom, and found
  to couple even more strongly to up-going Alfvén waves in certain
  regions of the wavenumber-frequency plane where acoustic-gravity waves
  are evanescent. These results contrast with those for Hall-mediated
  fast-Alfvén coupling, which occurs higher in the atmosphere and is
  evident only at much higher frequencies.

Title: Fast-to-Alfvén Mode Conversion and Ambipolar Heating in
    Structured Media. II. Numerical Simulation
Authors: Khomenko, Elena; Cally, Paul S.
Bibcode: 2019ApJ...883..179K
Altcode:
  This paper studies the effectiveness of production of Alfvén waves
  in the solar atmosphere through the processes of mode conversion,
  taking into account several new effects that have not been considered
  before. We perform simulations of wave propagation and conversion from
  the photosphere to the corona. Both magnetic field and plasma parameters
  are structured in the form of small-scale flux tubes with characteristic
  scale significantly below the wavelength of the waves. The waves are
  allowed to dissipate through the ambipolar diffusion (AD) mechanism. We
  use an analytical magneto-static equilibrium model, which provides
  the AD coefficient values at the lower end of what is expected for
  the quiet solar regions. This work extends the simplified study of
  mode conversion by Cally and Cally &amp; Khomenko to the case of warm,
  partially ionized, and structured plasma. We conclude that interaction
  of waves with the flux tube ensemble produces a discrete spectrum of
  high-order harmonics. The scattering is a linear process: however,
  the nonlinear effects have considerable influence upon the amplitudes
  of the harmonics. The magnetic Poynting flux reaching the corona is
  enhanced by about 35% and the reflection of waves at the transition
  region is decreased by about 50% when the flux tubes structure is
  present, relative to the horizontally homogeneous case. The energy
  flux of Alfvén waves exceeds that of acoustic waves at coronal
  heights. Ambipolar diffusion decreases the magnetic Poynting flux in
  the corona because the fast waves entering the transformation region
  at chromospheric heights are degraded and have lower amplitudes. The
  effect of the enhancement of Alfvén wave production due to interaction
  with flux tubes is independent of the numerical resolution, while the
  effect of the AD is resolution-dependent and is not converged at the
  10 km resolution of our best simulations.

Title: Smoothing of MHD Shocks in Mode Conversion
Authors: Pennicott, Jamon D.; Cally, Paul S.
Bibcode: 2019ApJ...881L..21P
Altcode: 2019arXiv190710954P
  Shock waves are simulated passing through the Alfvén-acoustic
  equipartition layer in a stratified isothermal magneto-atmosphere. The
  recent ray-theoretic calculations of Núñez predicted smoothing of the
  shock through this layer, causing both the fast and slow components to
  emerge as continuous waves. However, it is found that the partial mode
  conversion expected from linear theory for oblique incidence of the
  shock on the magnetic field is accompanied by a smoothing of the slow
  shock only, while the fast shock persists. Explanations are presented
  based on magnetohydrodynamic mode conversion and shock theory.

Title: Fast-to-Alfvén Mode Conversion Mediated by Hall
    Current. II. Application to the Solar Atmosphere
Authors: González-Morales, P. A.; Khomenko, E.; Cally, P. S.
Bibcode: 2019ApJ...870...94G
Altcode: 2018arXiv181106565G
  Coupling between fast magnetoacoustic and Alfvén waves can be observed
  in fully ionized plasmas mediated by stratification and 3D geometrical
  effects. In Paper I, Cally &amp; Khomenko have shown that in a weakly
  ionized plasma, such as the solar photosphere and chromosphere, the
  Hall current introduces a new coupling mechanism. The present study
  extends the results from Paper I to the case of warm plasma. We report
  on numerical experiments where mode transformation is studied using
  quasi-realistic stratification in thermodynamic parameters resembling
  the solar atmosphere. This redresses the limitation of the cold plasma
  approximation assumed in Paper I, in particular allowing the complete
  process of coupling between fast and slow magnetoacoustic modes and
  subsequent coupling of the fast mode to the Alfvén mode through
  the Hall current. Our results confirm the efficacy of the mechanism
  proposed in Paper I for the solar case. We observe that the efficiency
  of the transformation is a sensitive function of the angle between
  the wave propagation direction and the magnetic field, and of the
  wave frequency. The efficiency increases when the field direction and
  the wave direction are aligned for increasing wave frequencies. After
  scaling our results to typical solar values, the maximum amplitude of
  the transformed Alfvén waves, for a frequency of 1 Hz, corresponds
  to an energy flux (measured above the height of peak Hall coupling)
  of ∼10<SUP>3</SUP> W m<SUP>-2</SUP>, based on an amplitude of 500
  m s<SUP>-1</SUP> at β = 1, which is sufficient to play a major role
  in both quiet and active region coronal heating.

Title: Investigation of Acoustic Halos using Multi-Height SDO
    Observations
Authors: Tripathy, S. C.; Jain, Kiran; Kholikov, S.; Burtseva, O.;
   Hill, F.; Cally, P.
Bibcode: 2018csc..confE.130T
Altcode:
  The interpretation of acoustic waves surrounding active regions has
  been a challenging task since the influence of magnetic field on the
  incident waves is not fully understood. As a result, structure and
  dynamics of active regions beneath the surface show significant
  uncertainties. Recent numerical simulations and helioseismic
  measurements in active regions have demonstrated that the key to the
  understanding of these complex processes requires a synergy between
  models and helioseismic inferences from observations. In this context,
  using data from Helioseismic Magnetic Imager and Atmospheric Imaging
  Assembly instruments on board the Solar Dynamics Observatory, we
  characterize the spatio-temporal power distribution around active
  regions as a function of the height in the solar atmosphere. We
  find power enhancements (acoustic halos) occur above the acoustic
  cutoff frequency and extends up to 10 mHz in HMI Doppler and AIA
  170 nm observations and are strong functions of magnetic field and
  their inclination angle. We also examine the relative phases and
  cross-coherence spectra and find different wave characteristics at
  different heights.

Title: Probing sunspots with two-skip time-distance helioseismology
Authors: Duvall, Thomas L., Jr.; Cally, Paul S.; Przybylski, Damien;
   Nagashima, Kaori; Gizon, Laurent
Bibcode: 2018A&A...613A..73D
Altcode: 2018arXiv180601032D
  Context. Previous helioseismology of sunspots has been sensitive to
  both the structural and magnetic aspects of sunspot structure. <BR />
  Aims: We aim to develop a technique that is insensitive to the magnetic
  component so the two aspects can be more readily separated. <BR />
  Methods: We study waves reflected almost vertically from the underside
  of a sunspot. Time-distance helioseismology was used to measure travel
  times for the waves. Ray theory and a detailed sunspot model were used
  to calculate travel times for comparison. <BR /> Results: It is shown
  that these large distance waves are insensitive to the magnetic field
  in the sunspot. The largest travel time differences for any solar
  phenomena are observed. <BR /> Conclusions: With sufficient modeling
  effort, these should lead to better understanding of sunspot structure.

Title: Fast-to-Alfvén Mode Conversion in the Presence of Ambipolar
    Diffusion
Authors: Cally, Paul S.; Khomenko, Elena
Bibcode: 2018ApJ...856...20C
Altcode:
  It is known that fast magnetohydrodynamic waves partially convert to
  upward and/or downward propagating Alfvén waves in a stratified
  atmosphere where Alfvén speed increases with height. This
  happens around the fast wave reflection height, where the fast
  wave’s horizontal phase speed equals the Alfvén speed (in a
  low-β plasma). Typically, this takes place in the mid to upper
  solar chromosphere for low-frequency waves in the few-millihertz
  band. However, this region is weakly ionized and thus susceptible to
  nonideal MHD processes. In this article, we explore how ambipolar
  diffusion in a zero-β plasma affects fast waves injected from
  below. Classical ambipolar diffusion is far too weak to have any
  significant influence at these low frequencies, but if enhanced
  by turbulence (in the quiet-Sun chromosphere but not in sunspot
  umbrae) or the production of sufficiently small-scale structure,
  can substantially absorb waves for turbulent ambipolar Reynolds
  numbers of around 20 or less. In that case, it is found that the mode
  conversion process is not qualitatively altered from the ideal case,
  though conversion to Alfvén waves is reduced because the fast wave
  flux reaching the conversion region is degraded. It is also found
  that any upward propagating Alfvén waves generated in this process
  are almost immune to further ambipolar attenuation, thereby reducing
  local ambipolar heating compared to cases without mode conversion. In
  that sense, mode conversion provides a form of “Alfvén cooling.”

Title: Role of Interaction between Magnetic Rossby Waves and
    Tachocline Differential Rotation in Producing Solar Seasons
Authors: Dikpati, Mausumi; McIntosh, Scott W.; Bothun, Gregory; Cally,
   Paul S.; Ghosh, Siddhartha S.; Gilman, Peter A.; Umurhan, Orkan M.
Bibcode: 2018ApJ...853..144D
Altcode:
  We present a nonlinear magnetohydrodynamic shallow-water model
  for the solar tachocline (MHD-SWT) that generates quasi-periodic
  tachocline nonlinear oscillations (TNOs) that can be identified with
  the recently discovered solar “seasons.” We discuss the properties
  of the hydrodynamic and magnetohydrodynamic Rossby waves that interact
  with the differential rotation and toroidal fields to sustain these
  oscillations, which occur due to back-and-forth energy exchanges among
  potential, kinetic, and magnetic energies. We perform model simulations
  for a few years, for selected example cases, in both hydrodynamic and
  magnetohydrodynamic regimes and show that the TNOs are robust features
  of the MHD-SWT model, occurring with periods of 2-20 months. We find
  that in certain cases multiple unstable shallow-water modes govern
  the dynamics, and TNO periods vary with time. In hydrodynamically
  governed TNOs, the energy exchange mechanism is simple, occurring
  between the Rossby waves and differential rotation. But in MHD cases,
  energy exchange becomes much more complex, involving energy flow among
  six energy reservoirs by means of eight different energy conversion
  processes. For toroidal magnetic bands of 5 and 35 kG peak amplitudes,
  both placed at 45° latitude and oppositely directed in north and south
  hemispheres, we show that the energy transfers responsible for TNO, as
  well as westward phase propagation, are evident in synoptic maps of the
  flow, magnetic field, and tachocline top-surface deformations. Nonlinear
  mode-mode interaction is particularly dramatic in the strong-field
  case. We also find that the TNO period increases with a decrease in
  rotation rate, implying that the younger Sun had more frequent seasons.

Title: Sensitivity of coronal loop sausage mode frequencies and
decay rates to radial and longitudinal density inhomogeneities:
    a spectral approach
Authors: Cally, Paul S.; Xiong, Ming
Bibcode: 2018JPhA...51b5501C
Altcode: 2017arXiv171100256C
  Fast sausage modes in solar magnetic coronal loops are only fully
  contained in unrealistically short dense loops. Otherwise they are
  leaky, losing energy to their surrounds as outgoing waves. This
  causes any oscillation to decay exponentially in time. Simultaneous
  observations of both period and decay rate therefore reveal the
  eigenfrequency of the observed mode, and potentially insight into the
  tubes’ nonuniform internal structure. In this article, a global
  spectral description of the oscillations is presented that results
  in an implicit matrix eigenvalue equation where the eigenvalues are
  associated predominantly with the diagonal terms of the matrix. The
  off-diagonal terms vanish identically if the tube is uniform. A
  linearized perturbation approach, applied with respect to a uniform
  reference model, is developed that makes the eigenvalues explicit. The
  implicit eigenvalue problem is easily solved numerically though,
  and it is shown that knowledge of the real and imaginary parts of the
  eigenfrequency is sufficient to determine the width and density contrast
  of a boundary layer over which the tubes’ enhanced internal densities
  drop to ambient values. Linearized density kernels are developed that
  show sensitivity only to the extreme outside of the loops for radial
  fundamental modes, especially for small density enhancements, with no
  sensitivity to the core. Higher radial harmonics do show some internal
  sensitivity, but these will be more difficult to observe. Only kink
  modes are sensitive to the tube centres. Variation in internal and
  external Alfvén speed along the loop is shown to have little effect
  on the fundamental dimensionless eigenfrequency, though the associated
  eigenfunction becomes more compact at the loop apex as stratification
  increases, or may even displace from the apex.

Title: A study of acoustic halos in active region NOAA 11330 using
    multi-height SDO observations
Authors: Tripathy, S. C.; Jain, K.; Kholikov, S.; Hill, F.; Rajaguru,
   S. P.; Cally, P. S.
Bibcode: 2018AdSpR..61..691T
Altcode: 2017arXiv171101259T
  We analyze data from the Helioseismic Magnetic Imager (HMI) and the
  Atmospheric Imaging Assembly (AIA) instruments on board the Solar
  Dynamics Observatory (SDO) to characterize the spatio-temporal acoustic
  power distribution in active regions as a function of the height in
  the solar atmosphere. For this, we use Doppler velocity and continuum
  intensity observed using the magnetically sensitive line at 6173 Å
  as well as intensity at 1600 Å and 1700 Å. We focus on the power
  enhancements seen around AR 11330 as a function of wave frequency,
  magnetic field strength, field inclination and observation height. We
  find that acoustic halos occur above the acoustic cutoff frequency and
  extends up to 10 mHz in HMI Doppler and AIA 1700 Å observations. Halos
  are also found to be strong functions of magnetic field and their
  inclination angle. We further calculate and examine the spatially
  averaged relative phases and cross-coherence spectra and find different
  wave characteristics at different heights.

Title: The Origin of the "Seasons" in Space Weather
Authors: Dikpati, Mausumi; Cally, Paul S.; McIntosh, Scott W.;
   Heifetz, Eyal
Bibcode: 2017NatSR...714750D
Altcode:
  Powerful `space weather' events caused by solar activity pose
  serious risks to human health, safety, economic activity and national
  security. Spikes in deaths due to heart attacks, strokes and other
  diseases occurred during prolonged power outages. Currently it is
  hard to prepare for and mitigate the impact of space weather because
  it is impossible to forecast the solar eruptions that can cause these
  terrestrial events until they are seen on the Sun. However, as recently
  reported in Nature, eruptive events like coronal mass ejections and
  solar flares, are organized into quasi-periodic "seasons", which
  include enhanced bursts of eruptions for several months, followed by
  quiet periods. We explored the dynamics of sunspot-producing magnetic
  fields and discovered for the first time that bursty and quiet
  seasons, manifested in surface magnetic structures, can be caused by
  quasi-periodic energy-exchange among magnetic fields, Rossby waves
  and differential rotation of the solar interior shear-layer (called
  tachocline). Our results for the first time provide a quantitative
  physical mechanism for forecasting the strength and duration of
  bursty seasons several months in advance, which can greatly enhance
  our ability to warn humans about dangerous solar bursts and prevent
  damage to satellites and power stations from space weather events.

Title: Alfvén waves in the structured solar corona
Authors: Cally, Paul S.
Bibcode: 2017MNRAS.466..413C
Altcode: 2016arXiv161202064C
  A simple model of a periodic ensemble of closely packed flux tubes,
  sitting atop a vertically stratified layer, reveals that an incident
  fast wave from below preferentially converts almost immediately to
  Alfvén waves in the flux tubes, with kink waves restricted to at most
  a very few Fourier modes. This suggests that observations of coronal
  kink modes in such structured systems may greatly underestimate the net
  wave-energy flux being transported into and through the corona, much
  of which may reside in harder-to-observe Alfvén waves. The processes
  of mode conversion/resonant absorption and Alfvén phase mixing are
  implicated. It is suggested that the Sun's internal p-mode field -
  the 5-min oscillations - may contribute substantially to the process
  by supplying incident fast waves in the chromosphere that scatter and
  mode-convert in the tube ensemble.

Title: Current State of Seismic Emission Associated with Solar Flares
Authors: Besliu-Ionescu, D.; Donea, A.; Cally, P.
Bibcode: 2017SunGe..12...59B
Altcode:
  Certain solar flares are followed by photospheric seismic emission,
  also known as sunquakes. Sunquakes were predicted more than 40 years
  ago, but observed for the first time 20 years ago. A valid scenario
  that would fit all discoveries made so far is still missing. This paper
  summarises the current state of the literature concerning sunquakes. It
  describes all published reports of known seismic sources to date and
  presents possible triggering mechanisms.

Title: Helioseismology with Solar Orbiter
Authors: Löptien, Björn; Birch, Aaron C.; Gizon, Laurent; Schou,
   Jesper; Appourchaux, Thierry; Blanco Rodríguez, Julián; Cally,
   Paul S.; Dominguez-Tagle, Carlos; Gandorfer, Achim; Hill, Frank;
   Hirzberger, Johann; Scherrer, Philip H.; Solanki, Sami K.
Bibcode: 2017hdsi.book..257L
Altcode:
  No abstract at ADS

Title: Magnetoseismology of Active Regions using Multi-wavelength
    Observations from SDO
Authors: Tripathy Sushanta C.; Jain, Kiran; Kholikov, Shukur; Hill,
   Frank; Cally, Paul S.
Bibcode: 2016usc..confE..85T
Altcode:
  The structure and dynamics of active regions beneath the surface show
  significant uncertainties due to our limited understanding of the
  wave interaction with magnetic field. Recent numerical simulations
  further demonstrate that the atmosphere above the photospheric
  levels also modifies the seismic observables at the surface. Thus
  the key to improve helioseismic interpretation beneath the active
  regions requires a synergy between models and helioseismic inferences
  from observations. In this context, using data from Helioseismic
  Magnetic Imager and Atmospheric Imaging Assembly onboard Solar
  Dynamics Observatory, we characterize the spatio-temporal power
  distribution in and around active regions. Specifically, we focus on
  the power enhancements seen around active regions as a function of wave
  frequencies, strength, inclination of magnetic field and observation
  height as well as the relative phases of the observables and their
  cross-coherence functions. It is expected that these effects will help
  us to comprehend the interaction of acoustic waves with fast and slow
  MHD waves in the solar photosphere.

Title: Magnetoseismology of Active Regions using Multi-wavelength
    Observations from GONG and SDO
Authors: Tripathy, Sushanta; Jain, Kiran; Kholikov, Shukur; Hill,
   Frank; Cally, Paul
Bibcode: 2016SPD....47.0721T
Altcode:
  The structure and dynamics of active regions beneath the surface show
  significant uncertainties due to our limited understanding of the wave
  interaction with magnetic field. Recent numerical simulations further
  demonstrate that the atmosphere above the photospheric levels also
  modifies the seismic observables at the surface. Thus the key to improve
  helioseismic interpretation beneath the active regions requires a
  synergy between models and helioseismic inferences from observations. In
  this context, using data from Global Oscillation Network Group and from
  Helioseismic Magnetic Imager and Atmospheric Imaging Assembly onboard
  Solar Dynamics Observatory, we characterize the spatio-temporal power
  distribution in and around active regions. Specifically, we focus on
  the power enhancements seen around active regions as a function of wave
  frequencies, strength, inclination of magnetic field and observation
  height as well as the relative phases of the observables and their
  cross-coherence functions. It is expected that these effects will help
  us to comprehend the interaction of acoustic waves with magnetic field
  in the solar photosphere.

Title: Seismology and the Wounded Sun
Authors: Cally, Paul
Bibcode: 2016SPD....47.0704C
Altcode:
  Active regions provide an opening in the Sun's surface that allow
  seismic waves to penetrate the overlying atmosphere. Some proportion
  then return due to reflection, with implications for "internal"
  seismology. This is illustrated using simulations with particular
  reference to "travel times" and acoustic halos.

Title: Amplitudes of MHD Waves in Sunspots
Authors: Norton, Aimee Ann; Cally, Paul; Baldner, Charles; Kleint,
   Lucia; Tarbell, Theodore D.; De Pontieu, Bart; Scherrer, Philip H.;
   Rajaguru, Paul
Bibcode: 2016SPD....47.1009N
Altcode:
  The conversion of p-modes into MHD waves by strong magnetic fields
  occurs mainly in the sub-photospheric layers. The photospheric
  signatures of MHD waves are weak due to low amplitudes at the beta=1
  equipartion level where mode-conversion occurs. We report on small
  amplitude oscillations observed in the photosphere with Hinode SOT/SP
  in which we analyze time series for sunspots ARs 12186 (11.10.2014)
  and 12434 (17.10.2015). No significant magnetic field oscillations
  are recovered in the umbra or penumbra in the ME inversion. However,
  periodicities in the inclination angle are found at the umbral/penumbral
  boundary with 5 minute periods. Upward propagating waves are indicated
  in the intensity signals correlated between HMI and AIA at different
  heights. We compare SP results with the oscillations observed in HMI
  data. Simultaneous IRIS data shows transition region brightening above
  the umbral core.

Title: Division E Commission 10: Solar Activity
Authors: Schrijver, Carolus J.; Fletcher, Lyndsay; van Driel-Gesztelyi,
   Lidia; Asai, Ayumi; Cally, Paul S.; Charbonneau, Paul; Gibson, Sarah
   E.; Gomez, Daniel; Hasan, Siraj S.; Veronig, Astrid M.; Yan, Yihua
Bibcode: 2016IAUTA..29..245S
Altcode: 2015arXiv151003348S
  After more than half a century of community support related to the
  science of ``solar activity'', IAU's Commission 10 was formally
  discontinued in 2015, to be succeeded by C.E2 with the same area
  of responsibility. On this occasion, we look back at the growth of
  the scientific disciplines involved around the world over almost a
  full century. Solar activity and fields of research looking into the
  related physics of the heliosphere continue to be vibrant and growing,
  with currently over 2,000 refereed publications appearing per year from
  over 4,000 unique authors, publishing in dozens of distinct journals
  and meeting in dozens of workshops and conferences each year. The
  size of the rapidly growing community and of the observational and
  computational data volumes, along with the multitude of connections
  into other branches of astrophysics, pose significant challenges;
  aspects of these challenges are beginning to be addressed through,
  among others, the development of new systems of literature reviews,
  machine-searchable archives for data and publications, and virtual
  observatories. As customary in these reports, we highlight some
  of the research topics that have seen particular interest over the
  most recent triennium, specifically active-region magnetic fields,
  coronal thermal structure, coronal seismology, flares and eruptions,
  and the variability of solar activity on long time scales. We close
  with a collection of developments, discoveries, and surprises that
  illustrate the range and dynamics of the discipline.

Title: On mode conversion, reflection, and transmission of
    magnetoacoustic waves from above in an isothermal stratified
    atmosphere
Authors: Hansen, Shelley C.; Cally, Paul S.; Donea, Alina-C.
Bibcode: 2016MNRAS.456.1826H
Altcode: 2015arXiv151107364H
  We use the exact solutions for magnetoacoustic waves in a
  two-dimensional (2D) isothermal atmosphere with uniform inclined
  magnetic field to calculate the wave reflection, transmission, and
  conversion of slow and fast waves incident from above (z = ∞). This is
  relevant to the question of whether waves excited by flares in the solar
  atmosphere can penetrate the Alfvén/acoustic equipartition layer (which
  we identify as the canopy) to reach the photosphere with sufficient
  energy to create sunquakes. It is found that slow waves above the
  acoustic cutoff frequency efficiently penetrate (transmit) as acoustic
  (fast) waves if directed at a small attack angle to the magnetic field,
  with the rest converting to magnetic (slow) waves, in accord with
  Generalized Ray Theory. This may help explain the compact nature of
  seismic sources of sunquakes identified using seismic holography. The
  incident slow waves can also efficiently transmit at low frequency
  in inclined field due to the reduction in acoustic cutoff frequency
  (ramp effect). Incident fast (magnetic) `waves' from infinity with
  specified non-zero horizontal wavenumber are necessarily evanescent,
  but can carry energy to the equipartition level by tunnelling. It is
  found that this can then efficiently convert to acoustic (fast) energy
  that can again reach the photosphere as a travelling wave. Overall,
  there appear to be ample avenues for substantial compressive wave
  energy to penetrate the canopy and impact the photosphere.

Title: Erratum: Erratum to: Multiple Scattering of Seismic Waves
    from Ensembles of Upwardly Lossy Thin Flux Tubes
Authors: Hanson, Chris S.; Cally, Paul S.
Bibcode: 2016SoPh..291..727H
Altcode: 2016SoPh..tmp....7H
  No abstract at ADS

Title: p-Mode Interaction with Sunspots
Authors: Cally, P. S.; Moradi, H.; Rajaguru, S. P.
Bibcode: 2016GMS...216..489C
Altcode:
  This chapter brings together two of the prominent features of our star
  the Sun: its well-developed p-mode spectrum of global oscillations
  excited by near-surface convection, and its magnetic activity famously
  represented by sunspots. Modern developments in observations of p-mode
  and sunspot magnetic field interactions have helped bridge the gap
  between theory and observations: both the oscillations within a sunspot
  and in the immediate surroundings of the sunspot appear to be due to
  magnetohydrodynamics waves driven by p-modes with characteristic spatial
  patterns of frequencies intimately related to magnetic inclination
  and the height variation of the plasma p = 1 layer. The chapter makes
  the case that the behavior of waves in sunspots is dominated by four
  processes: the ramp effect; fast-to-slow mode conversion; fast-wave
  reflection; and fast-to-Alfvén mode conversion. The chapter then
  discusses some of the major developments in helioseismic forward and
  inverse modeling that have occurred over the last decade.

Title: 3D Simulations of Realistic Power Halos in Magnetohydrostatic
Sunspot Atmospheres: Linking Theory and Observation
Authors: Rijs, Carlos; Rajaguru, S. P.; Przybylski, Damien; Moradi,
   Hamed; Cally, Paul S.; Shelyag, Sergiy
Bibcode: 2016ApJ...817...45R
Altcode: 2015arXiv151201297R
  The well-observed acoustic halo is an enhancement in time-averaged
  Doppler velocity and intensity power with respect to quiet-Sun
  values that is prominent for the weak and highly inclined field
  around the penumbra of sunspots and active regions. We perform 3D
  linear wave modeling with realistic distributed acoustic sources in
  a magnetohydrostatic sunspot atmosphere and compare the resultant
  simulation enhancements with multiheight SDO observations of the
  phenomenon. We find that simulated halos are in good qualitative
  agreement with observations. We also provide further proof that the
  underlying process responsible for the halo is the refraction and
  return of fast magnetic waves that have undergone mode conversion at
  the critical a = c atmospheric layer. In addition, we also find strong
  evidence that fast Alfvén mode conversion plays a significant role
  in the structure of the halo, taking energy away from photospheric and
  chromospheric heights in the form of field-aligned Alfvén waves. This
  conversion process may explain the observed “dual-ring” halo
  structure at higher (&gt;8 mHz) frequencies.

Title: Helioseismology with Solar Orbiter
Authors: Löptien, Björn; Birch, Aaron C.; Gizon, Laurent; Schou,
   Jesper; Appourchaux, Thierry; Blanco Rodríguez, Julián; Cally,
   Paul S.; Dominguez-Tagle, Carlos; Gandorfer, Achim; Hill, Frank;
   Hirzberger, Johann; Scherrer, Philip H.; Solanki, Sami K.
Bibcode: 2015SSRv..196..251L
Altcode: 2014arXiv1406.5435L; 2014SSRv..tmp...31L
  The Solar Orbiter mission, to be launched in July 2017, will
  carry a suite of remote sensing and in-situ instruments, including
  the Polarimetric and Helioseismic Imager (PHI). PHI will deliver
  high-cadence images of the Sun in intensity and Doppler velocity
  suitable for carrying out novel helioseismic studies. The orbit of
  the Solar Orbiter spacecraft will reach a solar latitude of up to
  21<SUP>∘</SUP> (up to 34<SUP>∘</SUP> by the end of the extended
  mission) and thus will enable the first local helioseismology studies of
  the polar regions. Here we consider an array of science objectives to be
  addressed by helioseismology within the baseline telemetry allocation
  (51 Gbit per orbit, current baseline) and within the science observing
  windows (baseline 3×10 days per orbit). A particularly important
  objective is the measurement of large-scale flows at high latitudes
  (rotation and meridional flow), which are largely unknown but play an
  important role in flux transport dynamos. For both helioseismology
  and feature tracking methods convection is a source of noise in
  the measurement of longitudinally averaged large-scale flows, which
  decreases as T <SUP>-1/2</SUP> where T is the total duration of the
  observations. Therefore, the detection of small amplitude signals (e.g.,
  meridional circulation, flows in the deep solar interior) requires long
  observation times. As an example, one hundred days of observations at
  lower spatial resolution would provide a noise level of about three m/s
  on the meridional flow at 80<SUP>∘</SUP> latitude. Longer time-series
  are also needed to study temporal variations with the solar cycle. The
  full range of Earth-Sun-spacecraft angles provided by the orbit will
  enable helioseismology from two vantage points by combining PHI with
  another instrument: stereoscopic helioseismology will allow the study
  of the deep solar interior and a better understanding of the physics
  of solar oscillations in both quiet Sun and sunspots. We have used a
  model of the PHI instrument to study its performance for helioseismology
  applications. As input we used a 6 hr time-series of realistic solar
  magneto-convection simulation (Stagger code) and the SPINOR radiative
  transfer code to synthesize the observables. The simulated power
  spectra of solar oscillations show that the instrument is suitable for
  helioseismology. In particular, the specified point spread function,
  image jitter, and photon noise are no obstacle to a successful mission.

Title: Fast-to-Alfvén Mode Conversion Mediated by the Hall
    Current. I. Cold Plasma Model
Authors: Cally, Paul S.; Khomenko, Elena
Bibcode: 2015ApJ...814..106C
Altcode: 2015arXiv151003927C
  The photospheric temperature minimum in the Sun and solar-like
  stars is very weakly ionized, with an ionization fraction f as
  low as 10<SUP>-4</SUP>. In galactic star-forming regions, f can be
  10<SUP>-10</SUP> or lower. Under these circumstances, the Hall current
  can couple low-frequency Alfvén and magnetoacoustic waves via the
  dimensionless Hall parameter ɛ =ω /{{{Ω }}}<SUB>{{i</SUB>}}f,
  where ω is the wave frequency and {{{Ω }}}<SUB>{{i</SUB>}} is the
  mean ion gyrofrequency. This is analyzed in the context of a cold
  (zero-β) plasma and in less detail for a warm plasma. It is found
  that Hall coupling preferentially occurs where the wavevector is nearly
  field-aligned. In these circumstances, Hall coupling in theory produces
  a continual oscillation between fast and Alfvén modes as the wave
  passes through the weakly ionized region. At low frequencies (mHz),
  characteristic of solar and stellar normal modes, ɛ is probably too
  small for more than a fraction of one oscillation to occur. On the
  other hand, the effect may be significant at the far higher frequencies
  (Hz) associated with magnetic reconnection events. In another context,
  characteristic parameters for star-forming gas clouds suggest that
  {O}(1) or more full oscillations may occur in one cloud crossing. This
  mechanism is not expected to be effective in sunspots, due to their high
  ion gyrofrequencies and Alfvén speeds, since the net effect depends
  inversely on both and therefore inverse quadratically on field strength.

Title: Spectropolarimetrically Accurate Magnetohydrostatic Sunspot
    Model for Forward Modeling in Helioseismology
Authors: Przybylski, D.; Shelyag, S.; Cally, P. S.
Bibcode: 2015ApJ...807...20P
Altcode: 2015arXiv150402189P
  We present a technique to construct a spectropolarimetrically
  accurate magnetohydrostatic model of a large-scale solar magnetic
  field concentration, mimicking a sunspot. Using the constructed model
  we perform a simulation of acoustic wave propagation, conversion,
  and absorption in the solar interior and photosphere with the sunspot
  embedded into it. With the 6173 Å magnetically sensitive photospheric
  absorption line of neutral iron, we calculate observable quantities
  such as continuum intensities, Doppler velocities, as well as the full
  Stokes vector for the simulation at various positions at the solar disk,
  and analyze the influence of non-locality of radiative transport in
  the solar photosphere on helioseismic measurements. Bisector shapes
  were used to perform multi-height observations. The differences
  in acoustic power at different heights within the line formation
  region at different positions at the solar disk were simulated
  and characterized. An increase in acoustic power in the simulated
  observations of the sunspot umbra away from the solar disk center was
  confirmed as the slow magnetoacoustic wave.

Title: Multiple Scattering of Seismic Waves from Ensembles of Upwardly
    Lossy Thin Flux Tubes
Authors: Hanson, Chris S.; Cally, Paul S.
Bibcode: 2015SoPh..290.1889H
Altcode: 2015SoPh..tmp...86H; 2015arXiv150607638H
  Our previous semi-analytic treatment of f - and p -mode multiple
  scattering from ensembles of thin flux tubes (Hanson and Cally,
  Astrophys. J.781, 125, 2014a; 791, 129, 2014b) is extended by
  allowing both sausage and kink waves to freely escape at the top of
  the model using a radiative boundary condition there. As expected,
  this additional avenue of escape, supplementing downward loss into the
  deep solar interior, results in substantially greater absorption of
  incident f - and p -modes. However, less intuitively, it also yields
  mildly to substantially smaller phase shifts in waves emerging from
  the ensemble. This may have implications for the interpretation of
  seismic data for solar plage regions, and in particular their small
  measured phase shifts.

Title: Directional time-distance probing of model sunspot atmospheres
Authors: Moradi, H.; Cally, P. S.; Przybylski, D.; Shelyag, S.
Bibcode: 2015MNRAS.449.3074M
Altcode: 2015arXiv150304270M
  A crucial feature not widely accounted for in local helioseismology is
  that surface magnetic regions actually open a window from the interior
  into the solar atmosphere, and that the seismic waves leak through this
  window, reflect high in the atmosphere, and then re-enter the interior
  to rejoin the seismic wave field normally confined there. In a series
  of recent numerical studies using translation invariant atmospheres,
  we utilized a `directional time-distance helioseismology' measurement
  scheme to study the implications of the returning fast and Alfvén waves
  higher up in the solar atmosphere on the seismology at the photosphere
  (Cally &amp; Moradi 2013; Moradi &amp; Cally 2014). In this study,
  we extend our directional time-distance analysis to more realistic
  sunspot-like atmospheres to better understand the direct effects
  of the magnetic field on helioseismic travel-time measurements
  in sunspots. In line with our previous findings, we uncover a
  distinct frequency-dependent directional behaviour in the travel-time
  measurements, consistent with the signatures of magnetohydrodynamic
  mode conversion. We found this to be the case regardless of the sunspot
  field strength or depth of its Wilson depression. We also isolated and
  analysed the direct contribution from purely thermal perturbations
  to the measured travel times, finding that waves propagating in the
  umbra are much more sensitive to the underlying thermal effects of
  the sunspot.

Title: MHD Wave Refraction and the Acoustic Halo Effect around Solar
Active Regions: A 3D Study
Authors: Rijs, Carlos; Moradi, Hamed; Przybylski, Damien; Cally,
   Paul S.
Bibcode: 2015ApJ...801...27R
Altcode: 2015arXiv150101074R
  An enhancement in high-frequency acoustic power is commonly observed
  in the solar photosphere and chromosphere surrounding magnetic active
  regions. We perform three-dimensional linear forward wave modeling
  with a simple wavelet pulse acoustic source to ascertain whether the
  formation of the acoustic halo is caused by MHD mode conversion through
  regions of moderate and inclined magnetic fields. This conversion
  type is most efficient when high frequency waves from below intersect
  magnetic field lines at a large angle. We find a strong relationship
  between halo formation and the equipartition surface at which the
  Alfvén speed a matches the sound speed c, lending support to the
  theory that photospheric and chromospheric halo enhancement is due
  to the creation and subsequent reflection of magnetically dominated
  fast waves from essentially acoustic waves as they cross a = c. In
  simulations where we have capped a such that waves are not permitted
  to refract after reaching the a = c height, halos are non-existent,
  which suggests that the power enhancement is wholly dependent on
  returning fast waves. We also reproduce some of the observed halo
  properties, such as a dual 6 and 8 mHz enhancement structure and a
  spatial spreading of the halo with height.

Title: Time-Distance Seismology and the Solar Transition Region
Authors: Hansen, Shelley C.; Cally, Paul S.
Bibcode: 2014SoPh..289.4425H
Altcode: 2014SoPh..tmp..128H
  Time-Distance `travel time' perturbations (as inferred from wave
  phase) are calculated relative to the quiet-Sun as a function of wave
  orientation and field inclination in a uniform inclined magnetic
  field. Modelling indicates that the chromosphere-corona Transition
  Region (TR) profoundly alters travel times at inclinations from the
  vertical θ for which the ramp-reduced acoustic cutoff frequency
  ω<SUB>c</SUB>cosθ is similar to the wave frequency ω. At smaller
  inclinations phase shifts are much smaller as the waves are largely
  reflected before reaching the TR. At larger inclinations, the shifts
  resume their quiet-Sun values, although with some resonant oscillatory
  behaviour. Changing the height of the TR in the model atmosphere has
  some effect, but the thickness and temperature jump do not change
  the results substantially. There is a strong correspondence between
  travel-time shifts and the Alfvén flux that emerges at the top of the
  modelled region as a result of fast/Alfvén mode conversion. We confirm
  that the TR transmission coefficient for Alfvén waves generated by
  mode conversion in the chromosphere is far larger (typically 30 %
  or more) than for Alfvén waves injected from the photosphere.

Title: The Scattering of f- and p-modes from Ensembles of Thin
Magnetic Flux Tubes: An Analytical Approach
Authors: Hanson, Chris S.; Cally, Paul S.
Bibcode: 2014ApJ...791..129H
Altcode: 2014arXiv1407.0780H
  Motivated by the observational results of Braun, we extend the model
  of Hanson &amp; Cally to address the effect of multiple scattering of
  f and p modes by an ensemble of thin vertical magnetic flux tubes in
  the surface layers of the Sun. As in the observational Hankel analysis,
  we measure the scatter and phase shift from an incident cylindrical wave
  in a coordinate system roughly centered in the core of the ensemble. It
  is demonstrated that although thin flux tubes are unable to interact
  with high-order fluting modes individually, they can indirectly absorb
  energy from these waves through the scatters of kink and sausage
  components. It is also shown how the distribution of absorption and
  phase shift across the azimuthal order m depends strongly on the tube
  position as well as on the individual tube characteristics. This is
  the first analytical study into an ensembles multiple-scattering regime
  that is embedded within a stratified atmosphere.

Title: An Analytical Approach to Scattering Regimes Between Thin
    Magnetic Flux Tubes Within an Ensemble
Authors: Hanson, Chris S; Cally, Paul S
Bibcode: 2014AAS...22411204H
Altcode:
  Motivated by the inability to directly observe the small scale structure
  of solar magnetic features. We present an analytical method to model
  the multiple scattering regime within ensembles of random thin magnetic
  flux tubes, embedded in a stratified medium. Results demonstrate that
  the near-field interactions play an important role in the resultant
  scattered wave field. As such the ensemble no longer behaves as a
  bunch of individual tubes, rather as a larger collective. It is also
  shown that the scattering between azimuth orders (m) is as significant
  as scattering between p-modes. We present a comparison between this
  analytical model and observations, as well as recent numerical studies.

Title: An Analytical Approach to Scattering between Two thin Magnetic
    Flux Tubes in a Stratified Atmosphere
Authors: Hanson, Chris S.; Cally, Paul S.
Bibcode: 2014ApJ...781..125H
Altcode: 2014arXiv1401.0027H
  We expand on recent studies to analytically model the behavior of
  two thin flux tubes interacting through the near- and acoustic
  far-field. The multiple scattering that occurs between the pair
  alters the absorption and phase of the outgoing wave when compared
  to non-interacting tubes. We have included both the sausage and kink
  scatter produced by the pair. It is shown that the sausage mode's
  contribution to the scattered wave field is significant, and plays an
  equally important role in the multiple scattering regime. A disparity
  between recent numerical results and analytical studies, in particular
  the lack of symmetry between the two kink modes, is addressed. This
  symmetry break is found to be caused by an incorrect solution for the
  near-field modes.

Title: Sensitivity of Helioseismic Travel Times to the Imposition
    of a Lorentz Force Limiter in Computational Helioseismology
Authors: Moradi, Hamed; Cally, Paul S.
Bibcode: 2014ApJ...782L..26M
Altcode: 2014arXiv1401.5518M
  The rapid exponential increase in the Alfvén wave speed with height
  above the solar surface presents a serious challenge to physical
  modeling of the effects of magnetic fields on solar oscillations,
  as it introduces a significant Courant-Friedrichs-Lewy time-step
  constraint for explicit numerical codes. A common approach adopted in
  computational helioseismology, where long simulations in excess of
  10 hr (hundreds of wave periods) are often required, is to cap the
  Alfvén wave speed by artificially modifying the momentum equation
  when the ratio between the Lorentz and hydrodynamic forces becomes
  too large. However, recent studies have demonstrated that the Alfvén
  wave speed plays a critical role in the MHD mode conversion process,
  particularly in determining the reflection height of the upwardly
  propagating helioseismic fast wave. Using numerical simulations of
  helioseismic wave propagation in constant inclined (relative to the
  vertical) magnetic fields we demonstrate that the imposition of such
  artificial limiters significantly affects time-distance travel times
  unless the Alfvén wave-speed cap is chosen comfortably in excess of
  the horizontal phase speeds under investigation.

Title: Helioseismic Implications of Mode Conversion
Authors: Moradi, H.; Cally, P. S.
Bibcode: 2013ASPC..478..263M
Altcode:
  The Sun leaks waves through its active regions. The leakage of acoustic
  waves into the atmosphere through these ‘magnetoacoustic portals’
  is well known, but magnetic (fast) waves also enter the atmosphere
  there. Fast waves ultimately reflect because of the increase in Alfvén
  speed with height, but when they do so they can partially convert to
  Alfvén waves. The weakened fast waves then re-enter the interior, to
  rejoin the seismic p-mode field. But how has the Alfvénic loss they
  suffered affected the seismology? We present results from simulations
  that compare Alfvénic losses with travel-time shifts, and draw
  general conclusions about the role of active region atmospheres in
  local helioseismology.

Title: Seismology of the wounded Sun
Authors: Cally, Paul S.; Moradi, Hamed
Bibcode: 2013MNRAS.435.2589C
Altcode: 2013MNRAS.tmp.2129C; 2013arXiv1308.1184C
  Active regions are open wounds in the Sun's surface. Seismic
  oscillations from the interior pass through them into the atmosphere,
  changing their nature in the process to fast and slow magneto-acoustic
  waves. The fast waves then partially reflect and partially mode convert
  to upgoing and downgoing Alfvén waves. The reflected fast and downgoing
  Alfvén waves then re-enter the interior through the active regions that
  spawned them, infecting the surface seismology with signatures of the
  atmosphere. Using numerical simulations of waves in uniform magnetic
  fields, we calculate the upward acoustic and Alfvénic losses in the
  atmosphere as functions of field inclination and wave orientation as
  well as the time-distance `travel time' perturbations, and show that
  they are related. Travel time perturbations relative to quiet Sun
  can exceed 40 s in 1 kG magnetic field. It is concluded that active
  region seismology is indeed significantly infected by waves leaving
  and re-entering the interior through magnetic wounds, with differing
  travel times depending on the orientation of the wave vector relative
  to the magnetic field. This presages a new directional-time-distance
  seismology.

Title: Alfvén Waves in Simulations of Solar Photospheric Vortices
Authors: Shelyag, S.; Cally, P. S.; Reid, A.; Mathioudakis, M.
Bibcode: 2013ApJ...776L...4S
Altcode: 2013arXiv1309.2019S
  Using advanced numerical magneto-hydrodynamic simulations of the
  magnetized solar photosphere, including non-gray radiative transport and
  a non-ideal equation of state, we analyze plasma motions in photospheric
  magnetic vortices. We demonstrate that apparent vortex-like motions in
  photospheric magnetic field concentrations do not exhibit "tornado"-like
  behavior or a "bath-tub" effect. While at each time instance the
  velocity field lines in the upper layers of the solar photosphere show
  swirls, the test particles moving with the time-dependent velocity
  field do not demonstrate such structures. Instead, they move in a
  wave-like fashion with rapidly changing and oscillating velocity field,
  determined mainly by magnetic tension in the magnetized intergranular
  downflows. Using time-distance diagrams, we identify horizontal
  motions in the magnetic flux tubes as torsional Alfvén perturbations
  propagating along the nearly vertical magnetic field lines with local
  Alfvén speed.

Title: PREFACE:  Eclipse on the Coral Sea: Cycle 24 Ascending
Authors: Cally, Paul; Erdélyi, Robert; Norton
Bibcode: 2013JPhCS.440a1001C
Altcode:
  A total solar eclipse is the most spectacular and awe-inspiring
  astronomical phenomenon most people will ever see in their
  lifetimes. Even hardened solar scientists draw inspiration from it. The
  eclipse with 2 minutes totality in the early morning of 14 November 2012
  (local time) drew over 120 solar researchers (and untold thousands of
  the general public) to the small and picturesque resort town of Palm
  Cove just north of Cairns in tropical north Queensland, Australia,
  and they were rewarded when the clouds parted just before totality
  to reveal a stunning solar display. <P />Eclipse photograph <P />The
  eclipse was also the catalyst for an unusually broad and exciting
  conference held in Palm Cove over the week 12--16 November. Eclipse on
  the Coral Sea: Cycle 24 Ascending served as GONG 2012, LWS/SDO-5, and
  SOHO 27, indicating how widely it drew on the various sub-communities
  within solar physics. Indeed, as we neared the end of the ascending
  phase of the peculiar Solar Cycle 24, it was the perfect time to
  bring the whole community together to discuss our Sun's errant recent
  behaviour, especially as Cycle 24 is the first to be fully observed by
  the Solar Dynamics Observatory (SDO). The whole-Sun perspective was a
  driving theme of the conference, with the cycle probed from interior
  (helioseismology), to atmosphere (the various lines observed by the
  Atmospheric Imaging Assemble (AIA) aboard SDO, the several instruments
  on Hinode, and other modern observatories), and beyond (CMEs etc). The
  quality of the presentations was exceptional, and the many speakers
  are to be commended for pitching their talks to the broad community
  present. <P />These proceedings draw from the invited and contributed
  oral presentations and the posters exhibited in Palm Cove. They give an
  (incomplete) snapshot of the meeting, illustrating its broad vistas. The
  published contributions are organized along the lines of the conference
  sessions, as set out in the Contents, leading off with a provocative
  view of Cycle 24 thus far from Sarbani Basu. Other invited papers
  presented here include an appreciation of Hinode's view of solar
  activity as the cycle rises by Toshifumi Shimizu; a first taxonomy of
  magnetic tornadoes and chromospheric swirls by Sven Wedemeyer {\it et
  al}; an analysis of Hinode/EIS observations of transient heating events;
  a timely re-examination of solar dynamo theory by Paul Charbonneau;
  an exciting teaser for the solar potential of the Murchison Widefield
  Array now operating in Western Australia by Steven Tingay {\it et al};
  an overview and critique of the state of nonlinear force-free magnetic
  field extrapolation theory and practice by Mike Wheatland and Stuart
  Gilchrist; and a masterful review of atmospheric MHD wave coupling to
  the Sun's internal p-mode oscillations by Elena Khomenko and Irantzu
  Calvo Santamaria. The many contributed papers published here are no less
  exciting. <P />All papers have been refereed to a high standard. The
  editors thank all the referees, drawn both from conference attendees
  and the wider community, who have taken their tasks very seriously and
  provided very detailed and helpful reports. Nearly all contributions
  have been substantially improved by the process. We must also thank
  our financial sponsors. Both the Global Oscillations Network Group
  (GONG) and LWS/SDO were generous in their support, as were the School
  of Mathematical Sciences and the Monash Centre for Astrophysics (MoCA)
  at Monash University, Melbourne, and the Centre for Astronomy at James
  Cook University, Townsville. The Local Organizing Committee and the
  many students who assisted before and during the conference also deserve
  high praise for facilitating such a memorable meeting. <P />Paul Cally,
  Robert Erdélyi and Aimee Norton <P />Conference photograph

Title: Modelling Fast-Alfvén Mode Conversion Using SPARC
Authors: Moradi, H.; Cally, P. S.
Bibcode: 2013JPhCS.440a2047M
Altcode: 2013arXiv1302.6301M
  We successfully utilise the SPARC code to model fast-Alfvén mode
  conversion in the region c<SUB>A</SUB> &gt;&gt; c<SUB>s</SUB> via 3-D
  MHD numerical simulations of helioseismic waves within constant inclined
  magnetic field configurations. This was achieved only after empirically
  modifying the background density and gravitational stratifications in
  the upper layers of our computational box, as opposed to imposing a
  traditional Lorentz Force limiter, to ensure a manageable timestep. We
  found that the latter approach inhibits the fast-Alfvén mode conversion
  process by severely damping the magnetic flux above the surface.

Title: MHD wave propagation in the solar network
Authors: Calvo Santamaria, I.; Khomenko, E.; Cally, P. S.; Collados, M.
Bibcode: 2013hsa7.conf..806C
Altcode:
  Magneto-acoustic and Alfvénic waves are ubiquitous in solar coronal
  loops, possibly being excited by photospheric motions. It is not
  clear, though, how these waves get so high, having obstacles such as
  the acoustic cut-off frequency, reflection and refraction of fast
  MHD waves and also the strongly reflecting transition region. In
  this contribution we report on 2D numerical modelling of waves in
  magnetic arcade structures extending from photospheric layers through
  the transition region to the corona. Waves in the arcade are excited
  by sub-photospheric p-modes. We discuss the behaviour of waves, their
  conversion and propagation properties and possible mechanisms allowing
  their escape through the transition region.

Title: Near- and Far-field Response to Compact Acoustic Sources in
    Stratified Convection Zones
Authors: Cally, Paul S.
Bibcode: 2013ApJ...768...35C
Altcode: 2013arXiv1303.4027C
  The role of the acoustic continuum associated with compact sources
  in the Sun's interior wave field is explored for a simple polytropic
  model. The continuum produces a near-field acoustic structure—the
  so-called acoustic jacket—that cannot be represented by a
  superposition of discrete normal modes. Particular attention is paid
  to monochromatic point sources of various frequency and depth, and
  to the surface velocity power that results, both in the discrete f-
  and p-mode spectrum and in the continuum. It is shown that a major
  effect of the continuum is to heal the surface wave field produced by
  compact sources, and therefore to hide them from view. It is found that
  the continuous spectrum is not a significant contributor to observable
  inter-ridge seismic power.

Title: Alfvén Reflection and Reverberation in the Solar Atmosphere
Authors: Cally, P. S.
Bibcode: 2012SoPh..280...33C
Altcode: 2012SoPh..tmp..157C; 2012arXiv1206.2114C
  Magneto-atmospheres with Alfvén speed [a] that increases monotonically
  with height are often used to model the solar atmosphere, at least out
  to several solar radii. A common example involves a uniform vertical
  or inclined magnetic field in an isothermal atmosphere, for which
  the Alfvén speed is exponential. We address the issue of internal
  reflection in such atmospheres, both for time-harmonic and for transient
  waves. It is found that a mathematical boundary condition may be devised
  that corresponds to perfect absorption at infinity, and, using this,
  that many atmospheres where a(x) is analytic and unbounded present
  no internal reflection of harmonic Alfvén waves. However, except
  for certain special cases, such solutions are accompanied by a wake,
  which may be thought of as a kind of reflection. For the initial-value
  problem where a harmonic source is suddenly switched on (and optionally
  off), there is also an associated transient that normally decays with
  time as O(t^{-1}) or O(t^{-1}\ln t), depending on the phase of the
  driver. Unlike the steady-state harmonic solutions, the transient
  does reflect weakly. Alfvén waves in the solar corona driven by a
  finite-duration train of p-modes are expected to leave such transients.

Title: Web-based Comprehensive Data Archive of Seismically Active
    Solar Flares
Authors: Besliu-Ionescu, Diana; Donea, Alina; Cally, Paul; Lindsey,
   Charles
Bibcode: 2012asst.book...31B
Altcode:
  Some solar flares can release acoustic transients into the solar
  subsurface of the active regions that host them. Most of the acoustic
  power in these transients propagates something like 10-30 Mm beneath
  the photosphere before it is refracted back to the surface, where it
  raises a significant disturbance. In the strongest of these "sunquakes",
  the manifestation of this transient in helio-seismic movies is an
  outwardly expanding surface ripple that becomes conspicuous about
  20 minutes after the impulsive phase of the flare. These "sunquakes"
  offer a powerful diagnostic of wave propagation in the active region
  photosphere and of the structure and dynamics of the subphotosphere. We
  will present here a detailed description of our comprehensive survey
  of the SOHO-MDI database for acoustic signatures from flares and the
  technique used in this process. The results of the survey are presented
  in a database of seismic sources generated by X and M class solar flares
  during 1996-2007. It is based on a table format showing the general
  characteristics of the acoustically active flares, and the times of the
  solar quakes (beginning, maximum and end). The database is linked to
  a composite of images of the seismic sources in different wavelengths.

Title: Benchmarking Fast-to-Alfvén Mode Conversion in a Cold MHD
    Plasma. II. How to Get Alfvén Waves through the Solar Transition
    Region
Authors: Hansen, Shelley C.; Cally, Paul S.
Bibcode: 2012ApJ...751...31H
Altcode: 2012arXiv1203.3822H
  Alfvén waves may be difficult to excite at the photosphere due
  to low-ionization fraction and suffer near-total reflection at the
  transition region (TR). Yet they are ubiquitous in the corona and
  heliosphere. To overcome these difficulties, we show that they may
  instead be generated high in the chromosphere by conversion from
  reflecting fast magnetohydrodynamic waves, and that Alfvénic TR
  reflection is greatly reduced if the fast reflection point is within
  a few scale heights of the TR. The influence of mode conversion on
  the phase of the reflected fast wave is also explored. This phase
  can potentially be misinterpreted as a travel speed perturbation with
  implications for the practical seismic probing of active regions.

Title: Numerical Simulations of Conversion to Alfvén Waves in
    Sunspots
Authors: Khomenko, E.; Cally, P. S.
Bibcode: 2012ApJ...746...68K
Altcode: 2011arXiv1111.2851K
  We study the conversion of fast magnetoacoustic waves to Alfvén waves
  by means of 2.5D numerical simulations in a sunspot-like magnetic
  configuration. A fast, essentially acoustic, wave of a given frequency
  and wave number is generated below the surface and propagates upward
  through the Alfvén/acoustic equipartition layer where it splits
  into upgoing slow (acoustic) and fast (magnetic) waves. The fast wave
  quickly reflects off the steep Alfvén speed gradient, but around and
  above this reflection height it partially converts to Alfvén waves,
  depending on the local relative inclinations of the background magnetic
  field and the wavevector. To measure the efficiency of this conversion
  to Alfvén waves we calculate acoustic and magnetic energy fluxes. The
  particular amplitude and phase relations between the magnetic field
  and velocity oscillations help us to demonstrate that the waves
  produced are indeed Alfvén waves. We find that the conversion to
  Alfvén waves is particularly important for strongly inclined fields
  like those existing in sunspot penumbrae. Equally important is the
  magnetic field orientation with respect to the vertical plane of
  wave propagation, which we refer to as "field azimuth." For a field
  azimuth less than 90° the generated Alfvén waves continue upward, but
  above 90° downgoing Alfvén waves are preferentially produced. This
  yields negative Alfvén energy flux for azimuths between 90° and
  180°. Alfvén energy fluxes may be comparable to or exceed acoustic
  fluxes, depending upon geometry, though computational exigencies limit
  their magnitude in our simulations.

Title: On the Dispersion and Scattering of Magnetohydrodynamic Waves
    by Longitudinally Stratified Flux Tubes
Authors: Andries, J.; Cally, P. S.
Bibcode: 2011ApJ...743..164A
Altcode:
  We provide a fairly general analytic theory for the dispersion and
  scattering of magnetohydrodynamic waves by longitudinally stratified
  flux tubes. The theory provides a common framework for, and synthesis
  of, many previous studies of flux tube oscillations that were
  carried out under various simplifying assumptions. The present theory
  focuses on making only a minimal number of assumptions. As a result
  it thus provides an analytical treatment of several generalizations of
  existing tube oscillation models. The most important practical cases are
  inclusion of plasma pressure and possibly buoyancy effects in models
  of straight non-diverging tubes as applied in coronal seismology, and
  relaxation of the "thin tube" approximation in oscillation models of
  diverging tubes as applied both in the context of p-mode scattering
  and coronal seismology. In particular, it illustrates the unifying
  theoretical framework underlying both the description of waves scattered
  by flux tubes and the dispersion of waves carried along flux tubes.

Title: Mode conversion of radiatively damped magnetogravity waves
    in the solar chromosphere
Authors: Newington, Marie E.; Cally, Paul S.
Bibcode: 2011MNRAS.417.1162N
Altcode: 2011arXiv1107.2208N; 2011MNRAS.tmp.1413N
  Modelling of adiabatic gravity wave propagation in the solar atmosphere
  showed that mode conversion to field guided acoustic waves or Alfvén
  waves was possible in the presence of highly inclined magnetic
  fields. This work aims to extend the previous adiabatic study,
  exploring the consequences of radiative damping on the propagation
  and mode conversion of gravity waves in the solar atmosphere. We
  model gravity waves in a VAL-C atmosphere, subject to a uniform,
  and arbitrarily orientated magnetic field, using the Newton cooling
  approximation for radiatively damped propagation. The results indicate
  that the mode conversion pathways identified in the adiabatic study
  are maintained in the presence of damping. The wave energy fluxes are
  highly sensitive to the form of the height dependence of the radiative
  damping time. While simulations starting from 0.2 Mm result in modest
  flux attenuation compared to the adiabatic results, short damping times
  expected in the low photosphere effectively suppress gravity waves in
  simulations starting at the base of the photosphere. It is difficult
  to reconcile our results and observations of propagating gravity waves
  with significant energy flux at photospheric heights unless they are
  generated in situ.

Title: Benchmarking Fast-to-Alfvén Mode Conversion in a Cold
    Magnetohydrodynamic Plasma
Authors: Cally, Paul S.; Hansen, Shelley C.
Bibcode: 2011ApJ...738..119C
Altcode: 2011arXiv1105.5754C
  Alfvén waves may be generated via mode conversion from fast
  magnetoacoustic waves near their reflection level in the solar
  atmosphere, with implications both for coronal oscillations and for
  active region helioseismology. In active regions this reflection
  typically occurs high enough that the Alfvén speed a greatly
  exceeds the sound speed c, well above the a = c level where the
  fast and slow modes interact. In order to focus on the fundamental
  characteristics of fast/Alfvén conversion, stripped of unnecessary
  detail, it is therefore useful to freeze out the slow mode by adopting
  the gravitationally stratified cold magnetohydrodynamic model c →
  0. This provides a benchmark for fast-to-Alfvén mode conversion in
  more complex atmospheres. Assuming a uniform inclined magnetic field
  and an exponential Alfvén speed profile with density scale height h,
  the Alfvén conversion coefficient depends on three variables only:
  the dimensionless transverse-to-the-stratification wavenumber κ = kh,
  the magnetic field inclination from the stratification direction θ,
  and the polarization angle phi of the wavevector relative to the plane
  containing the stratification and magnetic field directions. We present
  an extensive exploration of mode conversion in this parameter space
  and conclude that near-total conversion to outward-propagating Alfvén
  waves typically occurs for small θ and large phi (80°-90°), though
  it is absent entirely when θ is exactly zero (vertical field). For
  wavenumbers of helioseismic interest, the conversion region is broad
  enough to encompass the whole chromosphere.

Title: Analyses Of Three-dimensional Magnetohydrodynamic Instability
    of Antisolar Latitudinal Differential Rotation in F, G, and K Stars
Authors: Dikpati, Mausumi; Cally, Paul S.
Bibcode: 2011ApJ...739....4D
Altcode: 2011arXiv1107.2434D
  Motivated by observations that only a very few stars have been found
  to have antisolar differential rotation, much weaker in amplitude than
  that of the Sun, we analyze the stability of antisolar and solar-type
  latitudinal differential rotations in the tachoclines of typical F,
  G, and K stars. We employ two three-dimensional thin-shell models,
  one for a Boussinesq but nonhydrostatic system and the other for
  a hydrostatic but non-Boussinesq system. We find that, in general,
  the combination of toroidal field band and differential rotation is
  more unstable, and unstable for lower toroidal fields, for antisolar
  than for solar-type differential rotation. In the antisolar case,
  the instability is always found to weaken the differential rotation,
  even if the primary energy source for the instability is the magnetic
  field. This favors surface antisolar differential rotations in stars
  being weaker than solar types, if the instability in the tachocline
  is felt at the surface of the star. This is most likely to happen in F
  stars, whose convection zones are much thinner than they are in G and
  K stars. This effect could help explain why the antisolar differential
  rotations that have been found are very weak compared with the rotation
  of the Sun.

Title: Resonant Absorption as Mode Conversion? II. Temporal Ray Bundle
Authors: Hanson, Chris S.; Cally, Paul S.
Bibcode: 2011SoPh..269..105H
Altcode: 2010arXiv1011.3808H; 2010SoPh..tmp..250H
  A fast-wave pulse in a simple, cold, inhomogeneous MHD model plasma
  is constructed by Fourier superposition over frequency of harmonic
  waves that are singular at their respective Alfvén resonances. The
  pulse partially reflects before reaching the resonance layer, but also
  partially tunnels through to it to convert to an Alfvén wave. The exact
  absorption/conversion coefficient for the pulse is shown to be given
  precisely by a function of transverse wavenumber tabulated in Paper
  I of this sequence, and to be independent of frequency and pulse width.

Title: Alfvén waves are easy: mode conversion in magnetic regions
Authors: Cally, P. S.
Bibcode: 2011ASInC...2..221C
Altcode:
  Alfvén waves are shown to be readily generated by mode conversion
  from fast MHD waves reflecting off the steep atmospheric Alfvén speed
  gradient in active region atmospheres. A simple analytic description
  of this process in terms of an `interaction integral' indicates that
  it is spread over many vertical scale heights, and indeed fills the
  whole active region chromosphere for waves of moderate helioseismic
  degree ℓ, even up to ℓ=1000 or more. This suggests that active
  region chromospheres are Alfvén wave factories.

Title: Numerical simulations of conversion to Alfvén waves in solar
    active regions
Authors: Khomenko, E.; Cally, P. S.
Bibcode: 2011JPhCS.271a2042K
Altcode: 2010arXiv1009.4575K
  We study the coupling of magneto-acoustic waves to Alvén waves using
  2.5D numerical simulations. In our experiment, a fast magnetoacoustic
  wave of a given frequency and wavenumber is generated below the
  surface. The magnetic field in the domain is assumed homogeneous and
  inclined. The efficiency of the conversion to Alfvén waves near the
  layer of equal acoustic and Alfven speeds is measured calculating
  their energy flux. The particular amplitude and phase relations
  between the oscillations of magnetic field and velocity help us to
  demonstrate that the waves produced after the transformation and
  reaching upper atmosphere are indeed Alfvén waves. We find that
  the conversion from fast magneto-acoustic waves to Alfvén waves is
  particularly important for the inclination θ and azimuth phi angles of
  the magnetic field between 55 and 65 degrees, with the maximum shifted
  to larger inclinations for lower frequency waves. The maximum Alfvén
  flux transmitted to the upper atmosphere is about 2-3 times lower than
  the corresponding acoustic flux.

Title: Solar physics research in Australia
Authors: Cally, P. S.; Wheatland, M. S.; Cairns, I. H.; Melrose, D. B.
Bibcode: 2011ASInC...2..397C
Altcode:
  Australia has a small but world-class solar physics research community,
  with strong international ties, working in areas of particular
  strength defined by the research interests of individuals and small
  groups. Most research occurs at the major universities, and a small
  number of Ph.D. students are trained in the field each year. This paper
  surveys Australia's current contribution to solar physics research,
  and the prospects for future development of the field.

Title: How to turn gravity waves into Alfvén waves and other
    such tricks
Authors: Newington, Marie E.; Cally, Paul S.
Bibcode: 2011JPhCS.271a2037N
Altcode:
  Recent observations of travelling gravity waves at the base of the
  chromosphere suggest an interplay between gravity wave propagation and
  magnetic field. Our aims are: to explain the observation that gravity
  wave flux is suppressed in magnetic regions; to understand why we see
  travelling waves instead of standing waves; and to see if gravity waves
  can undergo mode conversion and couple to Alfvén waves in regions where
  the plasma beta is of order unity. We model gravity waves in a VAL C
  atmosphere, subject to a uniform magnetic field of various orientations,
  considering both adiabatic and radiatively damped propagation. Results
  indicate that in the presence of a magnetic field, the gravity wave can
  propagate as a travelling wave, with the magnetic field orientation
  playing a crucial role in determining the wave character. For
  the majority of magnetic field orientations, the gravity wave is
  reflected at low heights as a slow magneto-acoustic wave, explaining
  the observation of reduced flux in magnetic regions. In a highly
  inclined magnetic field, the gravity wave undergoes mode conversion
  to either field guided acoustic waves or Alfvén waves. The primary
  effect of incorporating radiative damping is a reduction in acoustic
  and magnetic fluxes measured at the top of the integration region. By
  demonstrating the mode conversion of gravity waves to Alfvén waves,
  this work identifies a possible pathway for energy transport from the
  solar surface to the upper atmosphere.

Title: How surface magnetism affects helioseismic waves
Authors: Cally, Paul S.
Bibcode: 2010HiA....15..349C
Altcode:
  It has been known for two decades that sunspots both absorb and advance
  the phase of solar f and p-modes. More recently, Time-Distance and
  other local helioseismic techniques have been used to probe active
  regions by exploring phase shifts which are interpreted as travel-time
  perturbations. Although absorption is an intrinsically magnetic effect,
  phase shifts may be produced by both thermal and magnetic effects
  (and of course flows, though these can be factored out by averaging
  travel times in opposite directions). We will show how these two
  effects alter wave phase, and conclude that phase shifts in umbrae
  are predominantly thermal, whilst those in highly inclined field
  characteristic of penumbrae are essentially magnetic. The two effects
  are generally not additive.

Title: Resonant Absorption as Mode Conversion?
Authors: Cally, P. S.; Andries, J.
Bibcode: 2010SoPh..266...17C
Altcode: 2010arXiv1007.1808C; 2010SoPh..tmp..151C
  Resonant absorption and mode conversion are both extensively studied
  mechanisms for wave "absorption" in solar magnetohydrodynamics
  (MHD). But are they really distinct? We re-examine a well-known simple
  resonant absorption model in a cold MHD plasma that places the resonance
  inside an evanescent region. The normal mode solutions display the
  standard singular resonant features. However, these same normal modes
  may be used to construct a ray bundle which very clearly undergoes
  mode conversion to an Alfvén wave with no singularities. We therefore
  conclude that resonant absorption and mode conversion are in fact the
  same thing, at least for this model problem. The prime distinguishing
  characteristic that determines which of the two descriptions is
  most natural in a given circumstance is whether the converted wave
  can provide a net escape of energy from the conversion/absorption
  region of physical space. If it cannot, it is forced to run away in
  wavenumber space instead, thereby generating the arbitrarily small
  scales in situ that we recognize as fundamental to resonant absorption
  and phase mixing. On the other hand, if the converted wave takes net
  energy away, singularities do not develop, though phase mixing may
  still develop with distance as the wave recedes.

Title: Seismic Discrimination of Thermal and Magnetic Anomalies in
    Sunspot Umbrae
Authors: Lindsey, C.; Cally, P. S.; Rempel, M.
Bibcode: 2010ApJ...719.1144L
Altcode:
  Efforts to model sunspots based on helioseismic signatures need to
  discriminate between the effects of (1) a strong magnetic field that
  introduces time-irreversible, vantage-dependent phase shifts, apparently
  connected to fast- and slow-mode coupling and wave absorption and (2)
  a thermal anomaly that includes cool gas extending an indefinite depth
  beneath the photosphere. Helioseismic observations of sunspots show
  travel times considerably reduced with respect to equivalent quiet-Sun
  signatures. Simulations by Moradi &amp; Cally of waves skipping
  across sunspots with photospheric magnetic fields of order 3 kG show
  travel times that respond strongly to the magnetic field and relatively
  weakly to the thermal anomaly by itself. We note that waves propagating
  vertically in a vertical magnetic field are relatively insensitive to
  the magnetic field, while remaining highly responsive to the attendant
  thermal anomaly. Travel-time measurements for waves with large skip
  distances into the centers of axially symmetric sunspots are therefore
  a crucial resource for discrimination of the thermal anomaly beneath
  sunspot umbrae from the magnetic anomaly. One-dimensional models of
  sunspot umbrae based on compressible-radiative-magnetic-convective
  simulations such as by Rempel et al. can be fashioned to fit
  observed helioseismic travel-time spectra in the centers of sunspot
  umbrae. These models are based on cooling of the upper 2-4 Mm of the
  umbral subphotosphere with no significant anomaly beneath 4.5 Mm. The
  travel-time reductions characteristic of these models are primarily
  a consequence of a Wilson depression resulting from a strong downward
  buoyancy of the cooled umbral medium.

Title: Reflection and conversion of magnetogravity waves in the
solar chromosphere: windows to the upper atmosphere
Authors: Newington, Marie E.; Cally, Paul S.
Bibcode: 2010MNRAS.402..386N
Altcode: 2009arXiv0910.3233N; 2009MNRAS.tmp.1790N
  The detection of upward propagating internal gravity waves at the base
  of the Sun's chromosphere has recently been reported by Straus et al.,
  who postulated that these may efficiently couple to Alfvén waves in
  magnetic regions. This may be important in transporting energy to higher
  levels. Here we explore the propagation, reflection and mode conversion
  of linear gravity waves in a model atmosphere and find that even weak
  magnetic fields usually reflect gravity waves back downwards as slow
  magnetoacoustic waves well before they reach the Alfvén/acoustic
  equipartition height at which mode conversion might occur. However,
  for certain highly inclined magnetic field orientations in which the
  gravity waves manage to penetrate near or through the equipartition
  level, there can be substantial conversion to either or both up-going
  Alfvén and acoustic waves. Wave-energy fluxes comparable to the
  chromospheric radiative losses are expected.

Title: Nonlinear Evolution of Axisymmetric Twisted Flux Tubes in
    the Solar Tachocline
Authors: Hollerbach, R.; Cally, P. S.
Bibcode: 2009SoPh..260..251H
Altcode: 2009arXiv0909.3809H
  We numerically study the evolution of magnetic fields and fluid flows in
  a thin spherical shell. We take the initial field to be a latitudinally
  confined, predominantly toroidal flux tube. For purely toroidal,
  untwisted flux tubes, we recover previously known radial-shredding
  instabilities, and show further that in the nonlinear regime these
  instabilities can very effectively destroy the original field. For
  twisted flux tubes, also including a poloidal component, there are
  several possibilities, including the suppression of the radial-shredding
  instability, but also a more directly induced evolution, brought about
  because twisted flux tubes in general are not equilibrium solutions
  of the governing equations.

Title: Investigating The Role of Strong Magnetic Fields on
    Helioseismic Wave Propagation and the Consequences for Time-Distance
    Helioseismology
Authors: Moradi, H.; Hanasoge, S. M.; Cally, P. S.
Bibcode: 2009ASPC..416..143M
Altcode:
  We investigate the direct contribution of strong, sunspot-like magnetic
  fields to helioseismic wave travel-time shifts via two numerical
  forward models, a 3D ideal MHD solver and MHD ray theory. We confirm
  some existing ideas and bring forth new ones: (i) that the observed
  travel-time shifts in the vicinity of sunspots are largely governed by
  MHD physics, (ii) the travel-time shifts are sensitively dependent on
  frequency and phase speed filter parameters and the background power
  below the p_1 mode, and finally, (iii) despite its seeming limitations,
  MHD ray theory appears to succeed in capturing the essence of the
  travel-time variations as derived from the MHD simulations.

Title: Seismology and the Dynamo: History and Prospects
Authors: Cally, P. S.
Bibcode: 2009ASPC..416....3C
Altcode:
  The rapid "advances" in our knowledge and understanding of solar
  and stellar dynamos that resulted from the development of mean-field
  dynamo theory were sent into even more rapid retreat in the 1980s by
  difficulties in explaining observed features of the solar cycle, and
  especially by the new helioseismically derived differential rotation
  profiles. The climb back out of the mire has been slow and uncertain. A
  promising—but by no means universally accepted—route is afforded
  by the resurrection of Babcock-Leighton (flux transport) models of the
  dynamo, where meridional circulation plays a dominant "conveyor belt"
  role, aided and abetted by other near-surface flow patterns which
  disperse old flux poleward. In this brief overview, we review what
  helioseismology has told us about meridional and near-surface flows,
  and muse on the prospects for improved flow measurements in the future.

Title: Axisymmetric MHD Instabilities in Solar/Stellar Tachoclines
Authors: Dikpati, M.; Cally, P. S.; Gilman, P. A.; Miesch, M. S.
Bibcode: 2009ASPC..416..525D
Altcode:
  We show that banded toroidal fields in the tachoclines of the Sun and
  other stars should be unstable to 3-D axisymmetric overturning modes if
  the peak toroidal field is ∼100 kG or more. This instability should
  fragment and limit the amplitude of toroidal fields in tachoclines.

Title: Magnetic and thermal phase shifts in the local helioseismology
    of sunspots
Authors: Cally, Paul S.
Bibcode: 2009MNRAS.395.1309C
Altcode: 2009arXiv0902.4727C; 2009MNRAS.tmp..493C
  Phase perturbations due to inclined surface magnetic field of active
  region strength are calculated numerically in quiet Sun and simple
  sunspot models in order to estimate and compare the direct and
  indirect (thermal) effects of the fields on helioseismic waves. It
  is found that the largest direct effects occur in highly inclined
  field characteristic of penumbrae, and scale roughly linearly with
  magnetic field strength. The combined effects of sunspot magnetic and
  thermal anomalies typically yield negative travel-time perturbations
  in penumbrae. Travel-time shifts in umbrae depend on details of how the
  thermal and density structure differs from the quiet Sun. The combined
  shifts are generally not well approximated by the sum of the thermal
  and magnetic effects applied separately, except at low field strengths
  of around 1 kG or less, or if the thermal shift is small. A useful
  rule-of-thumb appears to be that travel-time perturbations in umbrae are
  predominantly thermal, whereas in penumbrae they are mostly magnetic.

Title: Multiple Scattering of Waves by a Pair of Gravitationally
    Stratified Flux Tubes
Authors: Hanasoge, Shravan M.; Cally, Paul S.
Bibcode: 2009ApJ...697..651H
Altcode: 2008arXiv0812.1284H
  We study the near-field coupling of a pair of flux tubes embedded in
  a gravitationally stratified environment. The mutual induction of the
  near-field jackets of the two flux tubes can considerably alter the
  scattering properties of the system, resulting in sizable changes in
  the magnitudes of scattering coefficients and bizarre trends in the
  phases. The dominant length scale governing the induction zone turns
  out to be approximately half the horizontal wavelength of the incident
  mode, a result that fits in quite pleasantly with extant theories
  of scattering. Higher-β flux tubes are more strongly coupled than
  weaker ones, a consequence of the greater role that the near-field
  jacket modes play in such tubes. We also comment on the importance
  of incorporating the effects of multiple scattering when studying the
  effects of mode absorption in plage and interpreting related scattering
  measurements. That the near field plays such an important role in
  the scattering process lends encouragement to the eventual goal of
  observationally resolving subwavelength features of flux tubes using
  techniques of helioseismology.

Title: Discriminating Thermal and Magnetic Seismic Anomalies in
    Sunspot Umbrae
Authors: Lindsey, Charles A.; Cally, P. S.
Bibcode: 2009SPD....40.0702L
Altcode:
  Efforts to model sunspots based on helioseismic signatures are
  confronted by the need to discriminate between two significantly
  separate anomalies: (1) a strong magnetic field that introduces
  time-irreversible, vantage-dependent phase shifts apparently connected
  to fast- and slow-mode coupling and wave absorption, and (2) a thermal
  anomaly that includes cool gas extending an unknown depth beneath the
  photosphere. Simulations by Moradi &amp; Cally of waves skipping across
  sunspots with photospheric magnetic fields of order 3 kG show travel
  times that respond strongly to the magnetic field and relatively
  weakly to the thermal anomaly by itself. We understand that waves
  propagating vertically in a vertical magnetic field are insensitive
  to the magnetic field and highly responsive to an attendant thermal
  anomaly. We therefore recognize travel-time measurements for waves with
  large skip distances into the centers of axially symmetric sunspots
  as an important resource for discrimination of the thermal anomaly
  beneath sunspot umbrae. Helioseismic observations of the response of
  sunspot umbrae to low-degree waves impinging into them from beneath
  their photospheres invariably show strongly reduced travel times,
  the reduction increasing sharply with frequency. These profiles
  agree nicely by 1-D simulations of the acoustics of a strong thermal
  deficit in the upper few hundred km beneath the sunspot photosphere
  with no significant anomaly below 2.2 Mm. This thermal structure is
  characteristic of sunspot simulations by Rempel, Schuessler &amp;
  Knoelker. We understand the reduced travel times for these models
  to be substantially the result of a 450-km Wilson depression caused
  by the foregoing thermal deficit. According to this understanding,
  the travel-time reduction due to the Wilson depression significantly
  outweighs the effect of a reduced sound speed in the cool gas.

Title: An Exact Test of Generalised Ray Theory in Local
    Helioseismology
Authors: Hansen, Shelley C.; Cally, Paul S.
Bibcode: 2009SoPh..255..193H
Altcode:
  Generalised ray theory provides a simple description of MHD mode
  transmission and conversion between magnetoacoustic fast and slow waves
  and is directly applicable to solar active regions. Here it is tested
  in a simple two-dimensional, isothermal, gravitationally stratified
  model with inclined magnetic field using previously published exact
  solutions and found to perform very well.

Title: Phase Jumps in Local Helioseismology
Authors: Cally, P. S.
Bibcode: 2009SoPh..254..241C
Altcode:
  Helioseismic rays trapped in a nonmagnetic acoustic cavity suffer
  a +90° phase jump at their lower (Lamb) turning point and −90°
  at the upper (acoustic cutoff) reflection point. That the two cancel
  allows helioseismologists to effectively assume that phase is locally
  continuous along a ray path joining two surface points. However, in
  strong surface magnetic field, as found in sunspots, it is shown - for
  an isothermal model with uniform magnetic field - that the phase jump
  for fast magnetoacoustic rays that penetrate the acoustic/Alfvénic
  equipartition level (c=a) is around −120°. Moreover, there are
  further negative phase jumps on the upgoing and downgoing legs at c=a
  that add to the net phase change. Neglecting these effects can lead to
  a misinterpretation of helioseismic data in terms of travel-time shifts.

Title: An Exact Test of Generalized Ray Theory in Local
    Helioseismology
Authors: Hansen, Shelley C.; Cally, Paul S.
Bibcode: 2009arXiv0902.1581H
Altcode:
  Generalized Ray Theory (GRT) provides a simple description of MHD mode
  transmission and conversion between magnetoacoustic fast and slow waves
  and is directly applicable to solar active regions. Here it is tested
  in a simple two-dimensional, isothermal, gravitationally-stratified
  model with inclined magnetic field using previously published exact
  solutions and found to perform very well.

Title: Axisymmetric MHD Instabilities in Solar/Stellar Tachoclines
Authors: Dikpati, Mausumi; Gilman, Peter A.; Cally, Paul S.; Miesch,
   Mark S.
Bibcode: 2009ApJ...692.1421D
Altcode:
  Extensive studies over the past decade showed that HD and MHD
  nonaxisymmetric instabilities exist in the solar tachocline for
  a wide range of toroidal field profiles, amplitudes, and latitude
  locations. Axisymmetric instabilities (m = 0) do not exist in two
  dimensions, and are excited in quasi-three-dimensional shallow-water
  systems only for very high field strengths (2 mG). We investigate here
  MHD axisymmetric instabilities in a three-dimensional thin-shell model
  of the solar/stellar tachocline, employing a hydrostatic, non-Boussinesq
  system of equations. We deduce a number of general properties of the
  instability by use of an integral theorem, as well as finding detailed
  numerical solutions for unstable modes. Toroidal bands become unstable
  to axisymmetric perturbations for solar-like field strengths (100
  kG). The e-folding time can be months down to a few hours if the field
  strength is 1 mG or higher, which might occur in the solar core, white
  dwarfs, or neutron stars. These instabilities exist without rotation,
  with rotation, and with differential rotation, although both rotation
  and differential rotation have stabilizing effects. Broad toroidal
  fields are stable. The instability for modes with m = 0 is driven from
  the poleward shoulder of banded profiles by a perturbation magnetic
  curvature stress that overcomes the stabilizing Coriolis force. The
  nonaxisymmetric instability tips or deforms a band; with axisymmetric
  instability, the fluid can roll in latitude and radius, and can convert
  bands into tubes stacked in radius. The velocity produced by this
  instability in the case of low-latitude bands crosses the equator,
  and hence can provide a mechanism for interhemispheric coupling.

Title: Numerical Models of Travel-Time Inhomogeneities in Sunspots
Authors: Moradi, H.; Hanasoge, S. M.; Cally, P. S.
Bibcode: 2009ApJ...690L..72M
Altcode: 2008arXiv0808.3628M
  We investigate the direct contribution of strong, sunspot-like magnetic
  fields to helioseismic wave travel-time shifts via two numerical forward
  models, a three-dimensional ideal MHD solver and MHD ray theory. The
  simulated data cubes are analyzed using the traditional time-distance
  center-to-annulus measurement technique. We also isolate and analyze the
  direct contribution from purely thermal perturbations to the observed
  travel-time shifts, confirming some existing ideas and bringing forth
  new ones: (i) that the observed travel-time shifts in the vicinity
  of sunspots are largely governed by MHD physics, (ii) the travel-time
  shifts are sensitively dependent on frequency and phase-speed filter
  parameters and the background power below the p <SUB>1</SUB> ridge,
  and finally, (iii) despite its seeming limitations, ray theory succeeds
  in capturing the essence of the travel-time variations as derived from
  the MHD simulations.

Title: Three-dimensional magneto-shear instabilities in the solar
    tachocline - II. Axisymmetric case
Authors: Cally, Paul S.; Dikpati, Mausumi; Gilman, Peter A.
Bibcode: 2008MNRAS.391..891C
Altcode: 2008MNRAS.tmp.1248C
  A Boussinesq model of the development of non-axisymmetric (in particular
  m = 1) three-dimensional magneto-shear instabilities in the solar
  tachocline was presented in Paper I. However, there it was erroneously
  concluded that the axisymmetric (m = 0) modes are stable, and they were
  not discussed further. Here it is shown that, although m = 0 modes are
  indeed stable for broad magnetic profiles, they are strongly unstable to
  radial shredding (high radial wavenumber) instabilities on the poleward
  shoulders of toroidal magnetic bands at high field strengths (roughly
  40-100kG depending on bandwidth and latitude). These instabilities
  have growth rates comparable to or greater than those for tipping
  instabilities (m = 1) in many cases, but both are strongly stabilized
  by gravitational stratification characteristic of the upper radiative
  core. Weaker fields are m = 0 stable (though weakly m = 1 unstable),
  even in neutral gravitational stratification (convection zone).

Title: Helioseismic analysis of the solar flare-induced sunquake of
    2005 January 15 - II. A magnetoseismic study
Authors: Martínez-Oliveros, J. C.; Donea, A. -C.; Cally, P. S.;
   Moradi, H.
Bibcode: 2008MNRAS.389.1905M
Altcode: 2008arXiv0807.3783M; 2008MNRAS.tmp.1032M; 2008MNRAS.tmp..971M
  On 2005 January 15, the active region AR10720 produced an X1.2 solar
  flare that induced high levels of seismicity in the photospheric
  layers. The seismic source was detected using helioseismic holography
  and analysed in detail in Paper I. Egression power maps at 6 mHz, with a
  2 mHz bandwidth, revealed a compact acoustic source, strongly correlated
  with the footpoints of the coronal loop that hosted the flare. We
  present a magnetosiesmic study of this active region to understand,
  for the first time, the magnetic topological structure of a coronal
  field that hosts an acoustically active solar flare. The accompanying
  analysis attempts to answer questions such as: can the magnetic field
  act as a barrier and prevent seismic waves from spreading away from the
  focus of the sunquake? What is the most efficient magnetic structure
  that would facilitate the development of a strong seismic source in
  the photosphere?

Title: Three-dimensional ray propagation in a toy sunspot
Authors: Moradi, H.; Cally, P. S.
Bibcode: 2008JPhCS.118a2037M
Altcode:
  In time-distance helioseismology wave travel times are measured from
  the cross-correlation between Doppler velocities recorded at any two
  locations on the solar surface. However, one of the main uncertainties
  associated with such measurements is how to interpret observations made
  in regions of strong magnetic field. Isolating the effects of wave
  anisotropies produced by the magnetic field from those thought to be
  associated with temperature and flow perturbations has proved to be
  quite complex and has yet to yield results when extracting acoustic
  travel times from the cross-correlation function. One possible way to
  decouple these effects is by using a three-dimensional toy sunspot with
  a surrounding stratified field-free Model S atmosphere to model the
  magneto-acoustic ray propagation and produce artificial travel time
  perturbation maps that directly account for wave speed anisotropies
  produced by the magnetic field.

Title: Three-Dimensional MHD Wave Propagation and Conversion to
    Alfvén Waves near the Solar Surface. I. Direct Numerical Solution
Authors: Cally, P. S.; Goossens, M.
Bibcode: 2008SoPh..251..251C
Altcode: 2007arXiv0711.0498C
  The efficacy of fast - slow MHD mode conversion in the surface
  layers of sunspots has been demonstrated over recent years
  using a number of modelling techniques, including ray theory,
  perturbation theory, differential eigensystem analysis, and direct
  numerical simulation. These show that significant energy may be
  transferred between the fast and slow modes in the neighbourhood
  of the equipartition layer where the Alfvén and sound speeds
  coincide. However, most of the models so far have been two
  dimensional. In three dimensions the Alfvén wave may couple to the
  magnetoacoustic waves with important implications for energy loss from
  helioseismic modes and for oscillations in the atmosphere above the
  spot. In this paper, we carry out a numerical "scattering experiment,"
  placing an acoustic driver 4 Mm below the solar surface and monitoring
  the acoustic and Alfvénic wave energy flux high in an isothermal
  atmosphere placed above it. These calculations indeed show that energy
  conversion to upward travelling Alfvén waves can be substantial,
  in many cases exceeding loss to slow (acoustic) waves. Typically,
  at penumbral magnetic field strengths, the strongest Alfvén fluxes
  are produced when the field is inclined 30° - 40° from the vertical,
  with the vertical plane of wave propagation offset from the vertical
  plane containing field lines by some 60° - 80°.

Title: Physical Properties of Wave Motion in Inclined Magnetic Fields
    within Sunspot Penumbrae
Authors: Schunker, H.; Braun, D. C.; Lindsey, C.; Cally, P. S.
Bibcode: 2008SoPh..251..341S
Altcode: 2008arXiv0801.4448S; 2008SoPh..tmp...41S
  At the surface of the Sun, acoustic waves appear to be affected by the
  presence of strong magnetic fields in active regions. We explore the
  possibility that the inclined magnetic field in sunspot penumbrae may
  convert primarily vertically-propagating acoustic waves into elliptical
  motion. We use helioseismic holography to measure the modulus and phase
  of the correlation between incoming acoustic waves and the local surface
  motion within two sunspots. These correlations are modeled by assuming
  the surface motion to be elliptical, and we explore the properties
  of the elliptical motion on the magnetic-field inclination. We also
  demonstrate that the phase shift of the outward-propagating waves is
  opposite to the phase shift of the inward-propagating waves in stronger,
  more vertical fields, but similar to the inward phase shifts in weaker,
  more-inclined fields.

Title: A Comparison of the Acoustic Hardness of Acoustically Active
    and Non-Active Solar Flares
Authors: Beşliu-Ionescu, Diana; Donea, Alina; Cally, Paul
Bibcode: 2008AIPC.1043..252B
Altcode:
  Recent corrections to some of the GONG+intensity images of flares allow
  us to image the acoustic power of white light flare signatures. The
  images clearly show compact regions of white light power at 6 mHz,
  which are well correlated spatially with the seismic signatures of the
  flares, when the flare proved to be acoustically active. It has been a
  puzzle why some of the white light flares, mainly very strong flares,
  did not induced any seismic waves into the photosphere. We believe
  that a comparison of the white light spectral hardness of two flares
  (one seismically active and another one seismically quiet) is the clue
  to understand the physics of the sun quakes.

Title: Time - Distance Modelling in a Simulated Sunspot Atmosphere
Authors: Moradi, H.; Cally, P. S.
Bibcode: 2008SoPh..251..309M
Altcode: 2008SoPh..tmp...91M; 2008arXiv0804.2716M
  In time - distance helioseismology, wave travel times are measured
  from the cross-correlation between Doppler velocities recorded at
  any two locations on the solar surface. However, one of the main
  uncertainties associated with such measurements is how to interpret
  observations made in regions of strong magnetic field. Isolating the
  effects of the magnetic field from thermal or sound-speed perturbations
  has proved to be quite complex and has yet to yield reliable results
  when extracting travel times from the cross-correlation function. One
  possible way to decouple these effects is by using a 3D sunspot model
  based on observed surface magnetic-field profiles, with a surrounding
  stratified, quiet-Sun atmosphere to model the magneto-acoustic ray
  propagation, and analyse the resulting ray travel-time perturbations
  that will directly account for wave-speed variations produced by the
  magnetic field. These artificial travel-time perturbation profiles
  provide us with several related but distinct observations: i) that
  strong surface magnetic fields have a dual effect on helioseismic rays
  - increasing their skip distance while at the same time speeding them
  up considerably compared to their quiet-Sun counterparts, ii) there
  is a clear and significant frequency dependence of both skip-distance
  and travel-time perturbations across the simulated sunspot radius,
  iii) the negative sign and magnitude of these perturbations appears
  to be directly related to the sunspot magnetic-field strength and
  inclination, iv) by "switching off" the magnetic field inside the
  sunspot, we are able to completely isolate the thermal component
  of the travel-time perturbations observed, which is seen to be both
  opposite in sign and much smaller in magnitude than those measured
  when the magnetic field is present. These results tend to suggest that
  purely thermal perturbations are unlikely to be the main effect seen in
  travel times through sunspots, and that strong, near-surface magnetic
  fields may be directly and significantly altering the magnitude and
  lateral extent of sound-speed inversions of sunspots made by time -
  distance helioseismology.

Title: Preface
Authors: Gizon, Laurent; Cally, Paul; Leibacher, John
Bibcode: 2008SoPh..251....1G
Altcode: 2008SoPh..tmp..148G
  No abstract at ADS

Title: HXR photospheric footprints
Authors: Martínez-Oliveros, J. C.; Donea, A. -C.; Cally, P. S.
Bibcode: 2008IAUS..247..110M
Altcode: 2007IAUS..247..110M
  We have analysed the 6 mHz egression power signatures of some
  accoustically active X-class solar flares. During the impulsive
  phase these flares produced conspicuous seismic signatures which
  have kernel-like structures, mostly aligned with the neutral line of
  the host active region. The kernel-like structures show the effect
  of constructive interference of the acoustic waves emanating from
  the complex sources, suggesting motion of the acoustic sources. The
  co-aligment between the seismic signatures and the hard X-ray emission
  observed by RHESSI from the footpoints of the coronal loops suggests
  a direct link between relativistic particles accelerated during the
  flare and the hydrodynamic response of the photosphere during flares.

Title: Correlative study of the emission from flares associated with
    Sun quakes
Authors: Martínez-Oliveros, J. C.; Donea, A. -C.; Cally, P. S.
Bibcode: 2008IAUS..247...99M
Altcode: 2007IAUS..247...99M
  Multi-wavelength studies of energetic solar flares with seismic
  emissions have revealed interesting common features that may help us
  to identify the correlations of flare signatures from the inner to
  the outer solar atmosphere and, to develop diagnostic techniques to
  aid in the sun quake detection. In our study, we make use the relation
  between the microwave and the hard X-ray emissions associated with such
  flares to propose a scenario for the ignition of seismic transients
  from flares. We explore the mechanisms of energy transport to the
  photosphere, such us back-warming or direct particle impacts.

Title: Recent Developments in Solar Quakes Studies
Authors: Bešliu-Ionescu, D.; Donea, A. -C.; Cally, P.; Lindsey, C.
Bibcode: 2008ASPC..383..297B
Altcode:
  Observations in hard and soft X-rays, chromospheric lines, and the
  visible continuum, together with helioseismic observations, make
  it possible to model the 3-dimensional profile of a sunquake from
  the corona into the subphotosphere of the active region that hosts
  the flare. Chromospheric line observations show us the part of the
  solar atmosphere where high-energy electrons are thought to cause
  thick-target heating that causes intense white-light emission and
  drives seismic waves into the active region subphotosphere. We have
  made a preliminary analysis of observations for some of the strongest
  acoustically noisy flares, including spectral observations in line
  NaD1 (586.9 nm) and line-center observations in Hα. Hα line-center
  observations will be shown for other sunquakes in Solar Cycle 23. Hinode
  will give us especially high-resolution chromospheric-line observations
  of acoustically active flares in Solar Cycle 24.

Title: Signatures of Seismic Absorption in Magnetic Regions
Authors: Lindsey, C.; Cally, P. S.
Bibcode: 2008ASPC..383..141L
Altcode:
  One of the major developments in local helioseismology of the late
  1980s was the discovery by Braun, Duvall, &amp; LaBonte that magnetic
  regions strongly absorb p modes that the quiet Sun itself efficiently
  reflects. A second major development, in the mid 1990s with the advent
  of the {Solar and Heliospheric Observatory}, was the discovery by
  Duvall et al. that phase travel times for waves propagating into sunspot
  photospheres are significantly longer than for waves propagating away
  from them along identical paths, a phenomenon to which we refer in
  this review as ``the phase asymmetry.'' Theoretical work by Cally et
  al. proposes to explain absorption of p modes by coupling of p modes to
  Alfvén modes. Recent work by Schunker et al. shows compelling evidence
  that this coupling contributes strongly to the phase asymmetry. More
  recent work by Rajaguru et al. suggests that radiative transfer effects
  in magnetic photospheres with upward-propagating waves contribute
  significantly to the phase asymmetry. Both of these contributions
  depend on strong absorption of p modes in magnetic photospheres. We
  will comment on the physics that relates phase shifts that underlie
  phenomena such as the phase asymmetry to irreversible processes such
  as p-mode absorption in magnetic regions. Magnetic contributions to
  the phase asymmetry have significant implications respecting seismic
  diagnostics of flows in active region subphotospheres.

Title: From Gigahertz to Millihertz: A Multiwavelength Study of the
    Acoustically Active 14 August 2004 M7.4 Solar Flare
Authors: Martínez-Oliveros, J. C.; Moradi, H.; Besliu-Ionescu, D.;
   Donea, A. -C.; Cally, P. S.; Lindsey, C.
Bibcode: 2007SoPh..245..121M
Altcode: 2007arXiv0707.2019M
  We carried out an electromagnetic acoustic analysis of the solar
  flare of 14 August 2004 in active region AR10656 from the radio to the
  hard X-ray spectrum. The flare was a GOES soft X-ray class M7.4 and
  produced a detectable sun quake, confirming earlier inferences that
  relatively low energy flares may be able to generate sun quakes. We
  introduce the hypothesis that the seismicity of the active region is
  closely related to the heights of coronal magnetic loops that conduct
  high-energy particles from the flare. In the case of relatively short
  magnetic loops, chromospheric evaporation populates the loop interior
  with ionised gas relatively rapidly, expediting the scattering of
  remaining trapped high-energy electrons into the magnetic loss cone and
  their rapid precipitation into the chromosphere. This increases both
  the intensity and suddenness of the chromospheric heating, satisfying
  the basic conditions for an acoustic emission that penetrates into
  the solar interior.

Title: Chromospheric Line Emission Analysis of the July 16, 2004
    Sun Quake
Authors: Beşliu-Ionescu, Diana; Donea, Alina; Cally, Paul; Lindsey,
   Charles
Bibcode: 2007AIPC..934...38B
Altcode:
  Observations in chromospheric lines and the visible continuum together
  with photospheric helioseismic measurements make possible to image a
  3-dimensional profile of a sun quake in a flaring region. Chromospheric
  line observations show us the part of the solar atmosphere where
  high-energy electrons are thought to cause thick target heating that
  then could also cause intense white-light emission and could drive
  seismic waves into the active region subphotosphere, we present here
  the preliminary results of the sun quake of July 16, 2004.

Title: Modified p-modes in penumbral filaments?
Authors: Bloomfield, D. S.; Solanki, S. K.; Lagg, A.; Borrero, J. M.;
   Cally, P. S.
Bibcode: 2007A&A...469.1155B
Altcode: 2007arXiv0705.0481B
  Aims:The primary objective of this study is to search for and identify
  wave modes within a sunspot penumbra. <BR />Methods: Infrared
  spectropolarimetric time series data are inverted using a model
  comprising two atmospheric components in each spatial pixel. Fourier
  phase difference analysis is performed on the line-of-sight velocities
  retrieved from both components to determine time delays between the
  velocity signals. In addition, the vertical separation between the
  signals in the two components is calculated from the Stokes velocity
  response functions. <BR />Results: The inversion yields two atmospheric
  components, one permeated by a nearly horizontal magnetic field, the
  other with a less-inclined magnetic field. Time delays between the
  oscillations in the two components in the frequency range 2.5-4.5 mHz
  are combined with speeds of atmospheric wave modes to determine wave
  travel distances. These are compared to expected path lengths obtained
  from response functions of the observed spectral lines in the different
  atmospheric components. Fast-mode (i.e., modified p-mode) waves exhibit
  the best agreement with the observations when propagating toward the
  sunspot at an angle ~50° to the vertical.

Title: Surface magnetic field effects in local helioseismology
Authors: Schunker, H.; Braun, D. C.; Cally, P. S.
Bibcode: 2007AN....328..292S
Altcode: 2010arXiv1002.2379S
  Using helioseismic holography strong evidence is presented that
  the phase (or equivalent travel-time) of helioseismic signatures in
  Dopplergrams within sunspots depend upon the line-of-sight angle in
  the plane containing the magnetic field and vertical directions. This
  is shown for the velocity signal in the penumbrae of two sunspots
  at 3, 4 and 5 mHz. Phase-sensitive holography demonstrates that they
  are significantly affected in a strong, moderately inclined magnetic
  field. This research indicates that the effects of the surface magnetic
  field are potentially very significant for local helioseismic analysis
  of active regions.

Title: Magnetoseismic signatures and flow diagnostics beneath
    magnetic regions
Authors: Lindsey, C.; Schunker, H.; Cally, P. S.
Bibcode: 2007AN....328..298L
Altcode:
  % One of the major, important developments in local helioseismology was
  the discovery by Duvall et al. (1996) that the travel times of seismic
  waves into sunspots from the surrounding quiet Sun significantly exceed
  the same in the reverse direction, a behavior they suggested was the
  result of rapid downflows directly beneath the sunspot photosphere. This
  led to the need for rapid near-surface horizontal inflows to replace the
  mass evacuated from the sunspot subphotosphere by such downflows. The
  lack of independent evidence for such inflows led to the suggestion
  that the travel-time asymmetry could be explained by a relative phase
  delay in the response of the sunspot photosphere to incoming waves with
  respect to that of the quiet Sun. In the succeeding ten years major
  progress has been made in our understanding of how magnetic photospheres
  respond to incoming waves, at the instigation of theoretical work by
  Spruit, Cally and Bogdan. This has led to the recognition of inclined
  penumbral magnetic fields as a major avenue for control work on the
  subject of the travel-time asymmetry and its relation to the absorption
  of p-modes by magnetic regions. A major recent development has been
  the discovery by Schunker et al. (2005) that the phase of this response
  in Doppler observations of penumbral photospheres depends strongly on
  the vantage of the Doppler measurements projected into the vertical
  plane of the magnetic field. This discovery heavily reinforces the
  proposition that the travel-time asymmetry is largely the signature of
  the same irreversible damping processes that are responsible for the
  strong absorption of p-modes in magnetic regions. We will elaborate
  on the implications of the foregoing developments respecting the
  diagnostics of subphotospheric flows based on seismic observations in
  which magnetic regions cannot be avoided.

Title: What to look for in the seismology of solar active regions
Authors: Cally, P. S.
Bibcode: 2007AN....328..286C
Altcode:
  Using a newly developed extension of ray theory which accounts for
  mode transmission and conversion between fast and slow magnetoacoustic
  waves, as well as simple wave mechanical calculations, we find that
  strong surface magnetic fields, as may be found in solar and stellar
  active regions, have several related but distinct effects on seismic
  waves: transmission/conversion, shortened travel times, a directional
  filtering of acoustic waves entering the overlying atmosphere, and
  a tendency to more closely align velocities with the field as height
  increases in the atmosphere. Magnetic field inclination is particularly
  relevant to these effects. Here, we briefly review these findings,
  and present some new results on ray travel times and magnetic filtering.

Title: Helioseismic analysis of the solar flare-induced sunquake of
    2005 January 15
Authors: Moradi, H.; Donea, A. -C.; Lindsey, C.; Besliu-Ionescu, D.;
   Cally, P. S.
Bibcode: 2007MNRAS.374.1155M
Altcode: 2007arXiv0704.3472M; 2006MNRAS.tmp.1369M
  We report the discovery of one of the most powerful sunquakes
  detected to date, produced by an X1.2-class solar flare in active
  region AR10720 on 2005 January 15. We used helioseismic holography
  to image the source of seismic waves emitted into the solar interior
  from the site of the flare. Acoustic egression power maps at 3 and 6
  mHz with a 2-mHz bandpass reveal a compact acoustic source strongly
  correlated with impulsive hard X-ray and visible-continuum emission
  along the penumbral neutral line separating the two major opposing
  umbrae in the δ-configuration sunspot that predominates AR10720. At 6
  mHz the seismic source has two components, an intense, compact kernel
  located on the penumbral neutral line of the δ-configuration sunspot
  that predominates AR10720, and a significantly more diffuse signature
  distributed along the neutral line up to ~15 Mm east and ~30 Mm west
  of the kernel. The acoustic emission signatures were directly aligned
  with both hard X-ray and visible continuum emission that emanated
  during the flare. The visible continuum emission is estimated at 2.0
  × 10<SUP>23</SUP> J, approximately 500 times the seismic emission
  of ~4 × 10<SUP>20</SUP> J. The flare of 2005 January 15 exhibits
  the same close spatial alignment between the sources of the seismic
  emission and impulsive visible continuum emission as previous flares,
  reinforcing the hypothesis that the acoustic emission may be driven
  by heating of the low photosphere. However, it is a major exception
  in that there was no signature to indicate the inclusion of protons
  in the particle beams thought to supply the energy radiated by the
  flare. The continued strong coincidence between the sources of seismic
  emission and impulsive visible continuum emission in the case of a
  proton-deficient white-lightflare lends substantial support to the
  `back-warming' hypothesis, that the low photosphere is significantly
  heated by intense Balmer and Paschen continuum-edge radiation from
  the overlying chromosphere in white-light flares.

Title: Study of the Seismically Active Flare of July 16, 2004
Authors: Besliu-Ionescu, D.; Donea, A. C.; Cally, P.; Lindsey, C.
Bibcode: 2007RoAJ...17S..83B
Altcode:
  Sunquakes have proven to be the most powerful events occurring at the
  solar surface. They are triggered by the impulsive flares produced
  in the corona, just above the acoustically active regions. Not
  every impulsive flare produces seismic waves emanating from the
  highly depressed photosphere, just beneath the flare. So far, we
  have identified a few mechanisms which can deliver acoustic energy
  into the photosphere: 1) the back-warming radiation suddenly heating
  the photosphere; 2) a strong shock-like compression wave propagating
  downwards into the chromosphere; 3) relativistic particles delivering
  directly the energy and momentum into the photosphere; and, 4)
  probably the magnetic tension at the feet of the loops. In order to
  discriminate which of these is the most efficient or dominated during a
  particular acoustically active flare, we have analysed the coronal and
  chromospheric emission of the regions just above the seismic source. We
  have performed a multiwavelength analysis of the active region 10649
  that hosted the acoustically active solar flare of July 16, 2004. The
  spatial coincidence between the emissions at different layers of the
  sun, from the photosphere to the corona, suggests that high-energy
  particles travel through the coronal layers from the reconnection
  site, hit the solar chromosphere warming it up, which then, responds
  by sending further into the photosphere enough energy (carried either
  by the shock wave or by the Balmer and Pachen radiation) to produce
  a seismic event.

Title: Global MHD instabilities of the tachocline
Authors: Gilman, Peter A.; Cally, Paul S.
Bibcode: 2007sota.conf..243G
Altcode:
  No abstract at ADS

Title: Chromospheric line emission in seismically active flares
Authors: Beşliu-Ionescu, D.; Donea, A. -C.; Lindsey, C.; Cally, P.;
   Mariş, G.
Bibcode: 2007AdSpR..40.1921B
Altcode:
  Some flares are known to drive seismic transients into the solar
  interior. The effects of these seismic transients are seen in
  helioseismic observations of the Sun's surface thousands of km
  from their sources in the hour succeeding the impulsive phase of
  the flare. Energetic particles impinging from the corona into the
  chromosphere are known to drive strong, downward-propagating shocks in
  active region chromospheres during the impulsive phases of flares. Hα
  observations have served as an important diagnostic of these shocks,
  showing intense emission with characteristic transient redshifts. In
  most flares no detectable transients penetrate beneath the active region
  photosphere. In those that do, there is a strong correlation between
  compact white-light emission and the signature of seismic emission. This
  study introduces the first known Hα observations of acoustically active
  flares, centered in the core of the line. The morphology of line-core
  emission Hα in the impulsive phase of the flare is similar to that
  of co-spatial line-core emission in NaD <SUB>1</SUB>, encompassing
  the site of seismic emission but more extended. The latter shows a
  compact red shift in the region of seismic emission, but a similar
  feature is known to appear in a conjugate magnetic footpoint from
  which no seismic emission emanates. Radiative MHD modelling based
  on the profiles of chromospheric line emission during the impulsive
  phases of flares can contribute significantly to our understanding of
  the mechanics of flare acoustic emission penetrating into the solar
  interior and the conditions under which it occurs.

Title: New Detection of Acoustic Signatures from Solar Flares
Authors: Donea, A. C.; Besliu-Ionescu, D.; Cally, P.; Lindsey, C.
Bibcode: 2006ASPC..354..204D
Altcode:
  With the advancement of local helioseismic techniques such as
  helioseismic holography we have now detected numerous seismic sources
  of varying size and intensity produced by solar flares. We have
  performed a systematic survey of the SOHO-MDI database in search for
  seismic waves from X-class flares produced during 1996 -- 2005. The
  detection of acoustically active flares <P />has opened a new and
  promising connection between helioseismology and flare physics. The
  main question we ask is: why are some large flares acoustically active
  while most are acoustically inactive? <P />We also address questions
  such as: Is photospheric heating by high-energy protons a major factor
  in seismic emission from flares? What is the effect of magnetic fields
  in the acoustics of a flare?

Title: Seismic Emission from A M9.5-Class Solar Flare
Authors: Donea, A. -C.; Besliu-Ionescu, D.; Cally, P. S.; Lindsey,
   C.; Zharkova, V. V.
Bibcode: 2006SoPh..239..113D
Altcode: 2006SoPh..tmp...65D
  Following the discovery of a few significant seismic sources at
  6.0 mHz from the large solar flares of October 28 and 29, 2003, we
  have extended SOHO/MDI helioseismic observations to moderate M-class
  flares. We report the detection of seismic waves emitted from the β
  γ δ active region NOAA 9608 on September 9, 2001. A quite impulsive
  solar flare of type M9.5 occurred from 20:40 to 20:48 UT. We used
  helioseismic holography to image seismic emission from this flare into
  the solar interior and computed time series of egression power maps
  in 2.0 mHz bands centered at 3.0 and 6.0 mHz. The 6.0 mHz images show
  an acoustic source associated with the flare some 30 Mm across in the
  East - West direction and 15 Mm in the North - South direction nestled
  in the southern penumbra of the main sunspot of AR 9608. This coincides
  closely with three white-light flare kernels that appear in the sunspot
  penumbra. The close spatial correspondence between white-light and
  acoustic emission adds considerable weight to the hypothesis that the
  acoustic emission is driven by heating of the lower photosphere. This
  is further supported by a rough hydromechanical model of an acoustic
  transient driven by sudden heating of the low photosphere. Where direct
  heating of the low photosphere by protons or high-energy electrons is
  unrealistic, the strong association between the acoustic source and
  co-spatial continuum emission can be regarded as evidence supporting
  the back-warming hypothesis, in which the low photosphere is heated
  by radiation from the overlying chromosphere. This is to say that a
  seismic source coincident with strong, sudden radiative emission in the
  visible continuum spectrum indicates a photosphere sufficiently heated
  so as to contribute significantly to the continuum emission observed.

Title: The Role of MHD Mode Conversion in Sunspot Seismology
Authors: Crouch, A. P.; Cally, P. S.; Charbonneau, P.; Braun, D. C.;
   Desjardins, M.
Bibcode: 2006ASPC..354..161C
Altcode:
  Sunspots absorb energy from and shift the phase of f and p modes
  incident upon them. Understanding the mechanism causing each of these
  effects is vital to the local helioseismology of sunspots (and magnetic
  flux concentrations in general). Because the beta-equals-unity layer
  typically lies in the near surface layers below the photospheres
  of sunspot umbrae, MHD mode conversion can occur. Mode conversion
  provides a promising absorption mechanism because the slow
  magnetoacoustic-gravity waves and Alfvén waves guide energy along
  the magnetic field away from the acoustic cavity. Our previous mode
  conversion calculations have shown that simple sunspot models with
  non-vertical magnetic fields can produce ample absorption to explain the
  Hankel analysis measurements, along with phase shift predictions that
  agree well with the observations. Those calculations only considered
  the possibility of MHD waves propagating down the magnetic field into
  the interior. In this contribution, we consider a second additional
  possibility -- waves propagating up into the atmosphere overlying
  sunspots.

Title: Behaviour of Acoustic Waves in Sunspots
Authors: Schunker, H.; Braun, D. C.; Cally, P. S.; Lindsey, C.
Bibcode: 2006ASPC..354..244S
Altcode:
  Because helioseismology uses surface signals to calculate subsurface
  characteristics the behaviour of surface acoustic oscillations in
  sunspots is important in interpreting helioseismic results. SOHO-MDI
  Doppler velocity analysis of AR9026 and AR9033 at 3, 4, and 5 mHz,
  using helioseismic holography, show that the amplitude and the phase
  in the correlation of the acoustic ingression with the observed surface
  velocity are found to be sensitive to the relative line-of-sight angle
  in the penumbra of both sunspots. This is consistent with a conversion
  of vertically propagating acoustic waves into magneto-acoustic waves
  with motion described by ellipses.

Title: Magnetohelioseismic Analysis of AR10720 Using Helioseismic
    Holography
Authors: Moradi, H.; Donea, A.; Besliu-Ionescu, D.; Cally, P.; Lindsey,
   C.; Leka, K.
Bibcode: 2006ASPC..354..168M
Altcode:
  We report on the recent discovery of one of the most powerful sunquakes
  detected to date produced by the January 15, 2005 X1.2 solar flare
  in active region 10720. We used helioseismic holography to image the
  acoustic source of the seismic waves produced by the flare. Egression
  power maps at 6 mHz with a 2 mHz bandwidth reveal a strong, compact
  acoustic source correlated with the footpoints of a coronal loop
  that hosted the flare. Using data from various solar observatories,
  we present a comprehensive analysis of the acoustic properties of
  the sunquake and investigate the role played by the configuration of
  the photospehric magnetic field in the production of flare generated
  sunquakes.

Title: Seismic emission from M-class solar flares
Authors: Besliu-Ionescu, D.; Donea, A. -C.; Cally, P.; Lindsey, C.
Bibcode: 2006ESASP.624E..67B
Altcode: 2006soho...18E..67B
  No abstract at ADS

Title: Magnetic field inclination and atmospheric oscillations above
solar active regions: theory
Authors: Cally, P. S.; Schunker, H.
Bibcode: 2006ESASP.624E..64C
Altcode: 2006soho...18E..64C
  No abstract at ADS

Title: Observed and simulated photospheric velocities within inclined
    magnetic fields
Authors: Schunker, H.; Cally, P.
Bibcode: 2006ESASP.624E...5S
Altcode: 2006soho...18E...5S
  No abstract at ADS

Title: Magnetic field inclination and atmospheric oscillations above
    solar active regions
Authors: Schunker, H.; Cally, P. S.
Bibcode: 2006MNRAS.372..551S
Altcode: 2006MNRAS.tmp.1003S
  Recent observational evidence for magnetic field direction effects
  on helioseismic signals in sunspot penumbrae is suggestive of
  magnetohydrodynamic (MHD) mode conversion occurring at lower
  levels. This possibility is explored using wave mechanical and ray
  theory in a model of the Sun's surface layers permeated by uniform
  inclined magnetic field. It is found that fast-to-slow conversion
  near the equipartition depth at which the sound and Alfvén speeds
  coincide can indeed greatly enhance the atmospheric acoustic signal
  at heights observed by Solar and Heliospheric Observatory/Michelson
  Doppler Imager and other helioseismic instruments, but that this effect
  depends crucially on the wave attack angle, i.e. the angle between
  the wavevector and the magnetic field at the conversion/transmission
  depth. A major consequence of this insight is that the magnetic field
  acts as a filter, preferentially allowing through acoustic signal from
  a narrow range of incident directions. This is potentially testable
  by observation.

Title: The acoustically active solar flare of 2005 January 15
Authors: Moradi, H.; Donea, A. -C.; Lindsey, C.; Besliu-Ionescu, D.;
   Cally, P. S.
Bibcode: 2006ESASP.624E..66M
Altcode: 2006soho...18E..66M
  No abstract at ADS

Title: The interaction between acoustic waves and inclined magnetic
    fields near the β~1 layer
Authors: Schunker, H.; Braun, D. C.; Cally, P. S.; Lindsey, C.
Bibcode: 2006IAUJD..17E..16S
Altcode:
  The acoustic showerglass effect may be hindering our helioseismic
  renditions of the solar subsurface. We present the results of near
  -surface wave conversion of acoustic waves in a model polytropic
  atmosphere by a uniform, inclined magnetic field. The upcoming fast,
  acoustic wave undergoes conversion to a slow, magnetic wave at the β
  ~ 1 layer where the sound speed and Alfven speed are comparable. The
  conversion is dependent upon the " attack angle" between the ray path
  and the magnetic field. The angle of the wave vectors at the polytropic
  " surface" is compared to observations of surface velocity vectors in
  sunspot penumbrae. AR9026 and AR9057 both have well- defined, static
  penumbrae and their Doppler velocities are viewed from different
  angles by SOHO-MDI as they cross the solar disk. The phase of the
  correlation between the ingression and surface velocity, determined by
  helioseismic holography, is used to assess the effect the penumbral
  magnetic field has on incoming acoustic waves. The phase is found to
  be dependent upon the line-of-sight of observation indicating that
  this is a surface phenomenon, which could otherwise be interpreted as
  subsurface travel-time perturbations of up to one minute. Furthermore,
  using vector magnetograms from the IVM at the Mees Observatory, the
  phase of the correlation is found to be dependent on the magnetic
  field tilt from vertical, and the dependence is consistent across the
  two sunspots. Comparing the results from the polytropic model with the
  observations show strong support for the near-surface wave conversion
  theory, although many questions still remain.

Title: Dispersion relations, rays and ray splitting in
    magnetohelioseismology
Authors: Cally, P. S.
Bibcode: 2006RSPTA.364..333C
Altcode:
  No abstract at ADS

Title: Seismic Radiation from M-class Solar Flares
Authors: Besliu-Ionescu, Diana; Donea, Alina-C.; Cally, Paul; Lindsey,
   Charles
Bibcode: 2006IAUS..233..385B
Altcode:
  Helioseismic holography is a technique used to image the sources
  of seismic disturbances observed at the solar surface. It has been
  used to detect acoustic emission, known as sun quakes, radiated from
  X-class solar flares. Since the seismic power emitted by the X-class
  flares has proved to be independent of the strength of the flare,
  we have undertaking a systematic search for seismic signatures from
  M-class solar flares, observed by SOHO-MDI.We have detected significant
  acoustic emission from a few M-class solar flares. Preliminary results
  of the survey of M-type solar flares studied so far is available at:
  aira.astro.ro/~deanna/M.html.

Title: Note on the Initial Value Problem for Coronal Loop Kink Waves
Authors: Cally, P. S.
Bibcode: 2006SoPh..233...79C
Altcode:
  Simple fluxtube models of coronal loops have previously been found
  to support leaky oscillations, where energy escapes from the tube
  laterally, thereby damping the mode. Of particular interest is the
  Principal Fast Leaky Kink mode (PFLK), which may be implicated in
  the decay of loop oscillations observed by TRACE. However, recently,
  M.S. Ruderman and B. Roberts, J. Plarma Phys. (in press), claimed
  that the PFLK mode, and many other leaky modes of oscillation, are
  unphysical, based on an initial value calculation. In this note,
  their arguments are shown to be incorrect.

Title: Significant Acoustic Activity in AR10720 on January 15, 2005
Authors: Beşliu-Ionescu, D.; Donea, A. -C.; Cally, P.; Lindsey, C.
Bibcode: 2006RoAJ...16S.203B
Altcode: 2006RoAJS..16..203B
  We report the recent discovery of one of the most acoustically powerful
  flare detected to date produced by the January 2005 2005, X1.2 solar
  flare in AR10720. We used helioseismic holography to image the acoustic
  source of the seismic waves produced by the flare. Egression Power maps
  at 6 mHz show a strong, extended acoustic signature which is the focus
  of the solar quake. At approximately 20 minutes after the appearance
  of the flare signature, we could also see the seismic response of
  the photosphere to the energy deposited by the flare in the form of
  "ripples" on the solar surface.

Title: a Survey of X-Class Solar Flares during 2001 and 2002 IN
    Search for Seismic Radiation
Authors: Besliu-Ionescu, D.; Donea, A. -C.; Cally, P.; Lindsey, C.
Bibcode: 2005ESASP.600E.111B
Altcode: 2005ESPM...11..111B; 2005dysu.confE.111B
  No abstract at ADS

Title: Genetic magnetohelioseismology with Hankel analysis data
Authors: Crouch, A. D.; Cally, P. S.; Charbonneau, P.; Braun, D. C.;
   Desjardins, M.
Bibcode: 2005MNRAS.363.1188C
Altcode: 2005MNRAS.tmp..856C
  Hankel analysis determined that sunspots absorb energy from and
  shift the phase of f- and p-modes incident upon them. One promising
  mechanism that can explain the absorption is partial conversion
  to slow magnetoacoustic-gravity (MAG) waves and Alfvén waves,
  which guide energy along the magnetic field away from the acoustic
  cavity. Our recent mode conversion calculations demonstrated that
  simple sunspot models, which roughly account for the radial variation
  of the magnetic field strength and inclination, can produce ample
  absorption to explain the observations, along with phase shifts that
  agree remarkably well with the Hankel analysis data. In this paper,
  we follow the same approach, but adopt a more realistic model for the
  solar convection zone that includes the thermal perturbation associated
  with a sunspot's magnetic field. Consistent with our earlier findings,
  we show that a moderately inclined, uniform magnetic field exhibits
  significantly enhanced absorption (mode conversion) in comparison
  to a vertical field (depending on the frequency and radial order of
  the mode). A genetic algorithm is employed to adjust the parameters
  that control the radial structure of our sunspot models, in order
  to minimize the discrepancy between the theoretical predictions and
  the Hankel analysis measurements. For models that best fit the phase
  shifts, the agreement with the Hankel analysis data is excellent, and
  the corresponding absorption coefficients are generally in excess of the
  observed levels. On the other hand, for models that best fit the phase
  shift and absorption data simultaneously, the overall agreement is very
  good but the phase shifts agree less well. This is most likely caused
  by the different sizes of the regions responsible for the absorption and
  phase shift. Typically, the field strengths required by such models lie
  in the range 1-3kG, compatible with observations for sunspots and active
  regions. While there remain some uncertainties, our results provide
  further evidence that mode conversion is the predominant mechanism
  responsible for the observed absorption in sunspots; and that field
  inclination away from vertical is a necessary ingredient for any model
  that aims to simultaneously explain the phase shift and absorption data.

Title: Modelling the Interaction of p-modes With Sunspots
Authors: Crouch, A. D.; Cally, P. S.; Charbonneau, P.; Desjardins, M.
Bibcode: 2005AGUSMSP23C..04C
Altcode:
  Sunspots absorb energy from and shift the phase of f- and p-modes
  incident upon them. One promising absorption mechanism is partial
  conversion to slow magnetoacoustic-gravity waves (and Alfvén waves),
  which guide energy along the magnetic field away from the acoustic
  cavity. Recent mode conversion calculations by Cally, Crouch, and
  Braun have shown that simple sunspot models with non-vertical magnetic
  fields can produce ample absorption to explain the observations,
  along with phase shift predictions that agree remarkably well with the
  Hankel analysis data. In this investigation, we further test the mode
  conversion hypothesis. We use a realistic solar model that accounts for
  both the magnetic and thermal influences associated with a sunspot. Our
  model has several adjustable parameters - the field strength and
  inclination can vary (crudely) across the spot. We employ a genetic
  algorithm to adjust these parameters to optimize the agreement between
  the model predictions and the observations. At this stage, our model
  is too simple to perform quantitative forward modelling. However,
  the genetic algorithm allows us to rigorously test the model. We
  will discuss the results of this testing in detail. Broadly speaking,
  our findings are consistent with those of Cally, Crouch, and Braun:
  the predicted phase shifts are in excellent agreement with the
  Hankel analysis data, and the corresponding absorption coefficients
  are generally ample to explain the observations. While there remain
  several uncertainties, our results further verify that mode conversion
  is a significant process in sunspot acoustics.

Title: Towards Assessing, Understanding, and Correcting the Influence
    of Surface Magnetism in Local Helioseismology
Authors: Braun, D. C.; Schunker, H.; Lindsey, C.; Cally, P. S.
Bibcode: 2005AGUSMSP23C..03B
Altcode:
  Efforts to probe subsurface wave-speed variations and mass flows
  near and under solar active regions are complicated and potentially
  compromised by strong phase and amplitude perturbations introduced in
  the photosphere by magnetic fields. Recently it has been shown that
  the phase distortions correlate with surface magnetic field strength
  and may be corrected to image wave-speed variations underlying active
  regions. A strong phase asymmetry between waves arriving into and
  departing from a magnetic region is also shown to produce spurious
  signatures of horizontal outflows below active regions. Further
  evidence of the photospheric origin of these phase distortions, as
  well as a key to their physical origin, is also presented. Using MDI
  observations, from the SOHO spacecraft, we perform ingression control
  correlations in the inclined magnetic fields of sunspot penumbra and
  demonstrate that incoming acoustic waves produce photospheric motion
  that describes an ellipse tilted towards the inclination of the magnetic
  field. A consequence is that the phase of the correlation varies with
  the viewing angle with respect to the field direction. Observations
  of the vector components of the photospheric fields could be used to
  correct these phase perturbations analogous to the procedures already
  developed using line-of-sight magnetograms. A physical understanding
  of surface distortions will come through MHD modeling, including
  simulations of the interaction of acoustic and magneto-acoustic-gravity
  waves with prescribed magnetic and sound-speed perturbations and flows
  (artificial data). The development of appropriate tools for assessing
  and correcting the effects of the surface magnetism will be vital for
  the interpretation of helioseismic data from the upcoming HMI mission
  on SDO. DCB and CL gratefully acknowledge support from the NSF (SAA/AST)
  and NASA (LWS, SR&amp;T).

Title: Local magnetohelioseismology of active regions
Authors: Cally, P. S.
Bibcode: 2005MNRAS.358..353C
Altcode: 2005MNRAS.tmp..156C
  Solar active regions are distinguished by their strong magnetic
  fields. Modern local helioseismology seeks to probe them by observing
  waves which emerge at the solar surface having passed through their
  interiors. We address the question of how an acoustic wave from
  below is partially converted to magnetic waves as it passes through
  a vertical magnetic field layer where the sound and Alfvén speeds
  coincide (the equipartition level), and find that (i) there is no
  associated reflection at this depth, either acoustic or magnetic,
  only transmission and conversion to an ongoing magnetic wave; and (ii)
  conversion in active regions is likely to be strong, though not total,
  at frequencies typically used in local helioseismology, with lower
  frequencies less strongly converted. A simple analytical formula is
  presented for the acoustic-to-magnetic conversion coefficient.

Title: The Local Helioseismology of Inclined Magnetic Fields and
    the Showerglass Effect
Authors: Schunker, H.; Braun, D. C.; Cally, P. S.; Lindsey, C.
Bibcode: 2005ApJ...621L.149S
Altcode:
  We present evidence for the dependence of helioseismic Doppler
  signatures in active regions on the line-of-sight angle in inclined
  magnetic fields. Using data from the Michelson Doppler Imager
  (MDI) on board the Solar and Heliospheric Observatory, we performed
  phase-sensitive holography in the penumbrae of sunspots over the
  course of several days as the spots traversed the solar disk. Control
  correlations, which comprise a correlation of the surface wave amplitude
  with the incoming acoustic wave amplitude from a surrounding region,
  were mapped. There is a direct dependence of control-correlation phase
  signatures on the line-of-sight angle in the plane defined by the
  vertical and magnetic field vectors. The phase shift of waves observed
  along directions close to the orientation of the magnetic field is
  smaller than the phase shift observed when the line of sight is at a
  significant angle with respect to the field orientation. These findings
  have important implications for local helioseismology. The variation
  in phase shift (or the equivalent acoustic travel-time perturbations)
  with line-of-sight direction suggests that a substantial portion of the
  phase shift occurs in the photospheric magnetic field. Observations of
  the vector components of the field may be used to develop a proxy to
  correct these phase perturbations (known as the acoustic showerglass)
  that introduce uncertainties in the signatures of acoustic perturbations
  below the surface.

Title: Mode Conversion of Solar p-Modes in Non-Vertical Magnetic
    Fields
Authors: Crouch, A. D.; Cally, P. S.
Bibcode: 2005SoPh..227....1C
Altcode:
  Sunspots absorb and scatter incident f- and p-modes. Until
  recently, the responsible absorption mechanism was uncertain. The
  most promising explanation appears to be mode conversion to slow
  magnetoacoustic-gravity waves, which carry energy down the magnetic
  field lines into the interior. In vertical magnetic field, mode
  conversion can adequately explain the observed f-mode absorption,
  but is too inefficient to account for the absorption of p-modes. In
  the first paper of the present series we calculated the efficiency
  of fast-to-slow magnetoacoustic-gravity wave conversion in uniform
  non-vertical magnetic fields. We assumed two-dimensional propagation,
  where the Alfvén waves decouple. In comparison to vertical field, it
  was found that mode conversion is significantly enhanced in moderately
  inclined fields, especially at higher frequencies. Using those results,
  Cally, Crouch, and Braun showed that the resultant p-mode absorption
  produced by simple sunspot models with non-vertical magnetic fields is
  ample to explain the observations. In this paper, we further examine
  mode conversion in non-vertical magnetic fields. In particular,
  we consider three-dimensional propagation, where the fast and slow
  magnetoacoustic-gravity waves and the Alfvén waves are coupled. Broadly
  speaking, the p-mode damping rates are not substantially different to
  the two-dimensional case. However, we do find that the Alfvén waves
  can remove similar quantities of energy to the slow MAG waves.

Title: Simultaneous Magnetic Field Time Series in AR10486 and AR10488
    During the Period October 29--31, 2003
Authors: Beşliu, Diana; Donea, Alina-Catalina; Cally, Paul; Maris,
   Georgeta
Bibcode: 2005RoAJ...15...33B
Altcode:
  No abstract at ADS

Title: Observations and Interpretation of Subsurface Magnetic
    Structures
Authors: Cally, P. S.; Crouch, A. D.
Bibcode: 2005HiA....13..435C
Altcode:
  Immediate subsurface local structures - flow magnetic and thermal -
  especially those associated with active regions are of considerable
  interest and are potentially accessible using high l helioseismology. In
  recent years though classical modal seismology has been supplemented
  with new approaches such as time-distance helioseismology and acoustic
  holography. In this talk the various methods and their results
  are briefly reviewed and implications discussed. Of the structure
  types subsurface magnetic fields are the most difficult to identify
  observationally so an overview is also given of how solar oscillations
  are expected to interact with them.

Title: Local Helioseismology of Inclined Magnetic Fields and the
    Showerglass Effect
Authors: Schunker, H.; Braun, D. C.; Lindsey, C.; Cally, P. S.
Bibcode: 2004ESASP.559..227S
Altcode: 2004soho...14..227S
  No abstract at ADS

Title: What can P-Mode Absorption and Phase Shift Data Currently Tell
    us about the Subsurface Structure of Sunspots? Preliminary Results
Authors: Crouch, A. D.; Cally, P. S.
Bibcode: 2004ESASP.559..392C
Altcode: 2004soho...14..392C
  No abstract at ADS

Title: Acoustics of Surface Magnetic Fields
Authors: Cally, P. S.
Bibcode: 2004ESASP.559..213C
Altcode: 2004soho...14..213C
  No abstract at ADS

Title: Linear Analysis and Nonlinear Evolution of Two-Dimensional
    Global Magnetohydrodynamic Instabilities in a Diffusive Tachocline
Authors: Dikpati, Mausumi; Cally, Paul S.; Gilman, Peter A.
Bibcode: 2004ApJ...610..597D
Altcode:
  We develop a more realistic two-dimensional model for global MHD
  instabilities in the solar tachocline, by including diffusion in
  the form of kinetic and magnetic drag (following Newton's cooling
  law formulation). This instability has previously been studied by us
  and others for an idealized tachocline with no kinematic viscosity
  and magnetic diffusivity. Since radial diffusion is more important
  than latitudinal diffusion in the thin solar tachocline, diffusive
  decay of flow and magnetic fields can be considered as proportional
  to those variables. We find that, for solar-like toroidal magnetic
  fields of ~100 kG, instability exists for a wide range of kinetic
  and magnetic drag parameters, providing a mechanism for enhanced
  angular momentum transport in latitudes, which could explain how thin
  the solar tachocline is. From a detailed parameter space survey,
  we set upper limits of 5×10<SUP>11</SUP> and 3×10<SUP>10</SUP>
  cm<SUP>2</SUP> s<SUP>-1</SUP> for kinematic viscosity and magnetic
  diffusivity, respectively, such that this instability occurs in the
  solar tachocline on a timescale shorter than a sunspot cycle. We
  find that magnetic drag has much more influence than kinetic drag
  in damping this instability. This happens because the sink due to
  magnetic drag dissipates perturbation magnetic energy faster than
  the vorticity sink from kinetic drag dissipates perturbation kinetic
  energy. Consequently, in the presence of a large enough magnetic drag,
  the nonsolar-like clamshell pattern, found by Cally to be an inevitable
  final state of a broad profile undergoing an ideal MHD tachocline
  instability, is suppressed, whereas a banded profile still tips with
  no reduction in tip angle. We discuss how tipping may affect various
  surface manifestations of magnetic features, such as the latitudes
  and orientations of bipolar active regions.

Title: Absorption of Waves in Sunspots
Authors: Cally, P. S.
Bibcode: 2004ESASP.547...15C
Altcode: 2004soho...13...15C
  Sunspots absorb and scatter the sun's global modes, the fand
  p-modes. Initial hopes were that this would allow us to probe the
  subsurface structure of spots, as helioseismology has been probing
  the sun on a global scale. However, it has turned out to be more
  difficult than first imagined. At the INTAS Workshop on MHD Waves in
  Mallorca in 2001, I explained the supposed mechanism, coupling to slow
  magnetoacoustic waves, but gave a rather gloomy picture of its ability
  to quantitatively match observations. However, recent advances in
  modelling in CSPA at Monash have for the first time produced results
  which seem to explain much of the data. In this talk, a simple model
  is presented, and its predictions compared with the best available
  observational Hankel data. Discrepancies concerning near-surface
  wave speeds between Hankel and holographic analyses on the one
  hand and time-distance inversions on the other are discussed. It
  is suggested that helioseismic inversions of active regions should
  address magneto-acoustic mode coupling if they are to fully account
  for absorption and wave speed variations.

Title: The Solar Tachocline: Limiting Magneto-Tipping Instabilities
Authors: Cally, P. S.; Dikpati, M.; Gilman, P. A.
Bibcode: 2004IAUS..219..541C
Altcode: 2003IAUS..219E.172C
  Two dimensional magneto-shear instabilities in the solar tachocline
  have been extensively explored in recent years. One of their most
  notable traits over a wide range of shear and magnetic profiles is
  a propensity for the magnetic field to tip substantially from its
  initial axisymmetric configuration with possible implications for
  patterns of flux emergence. However it is found that modifications
  of the standard models to include either kinetic and magnetic drag
  or prograde toroidal velocity jets associated with magnetic bands
  can suppress the instabilities or considerably reduce their nonlinear
  development. In the case of tip reduction by jets for a toroidal field
  of ~100kG in the tachocline (required for sunspots to emerge in sunspot
  latitudes) simulations indicate that jets capable of reducing tipping
  below the limits of detection from sunspot patterns at the surface are
  potentially detectable by helioseismic methods and should be looked
  for. Establishing an upper limit to the jet may result in a lower
  limit for the amount of tipping to be expected.

Title: Mode Conversion of Solar p-Modes In Non-Vertical Magnetic
    Fields
Authors: Crouch, A. D.; Cally, P. S.
Bibcode: 2004ESASP.547...81C
Altcode: 2004soho...13...81C
  Sunspots absorb and scatter incident - and -modes. One suggested
  absorption mechanism is mode conversion to slow magnetoacoustic-gravity
  waves, which carry some of the energy down magnetic field lines
  into the interior, or, less preferentially, up into the overlying
  atmosphere. Assuming uniform vertical magnetic field, this mechanism
  easily explains -mode absorption, but cannot fully account for the
  observed absorption of -modes, especially beyond the first few radial
  orders. Recently, we have calculated the efficiency of mode conversion
  in uniform non-vertical magnetic fields assuming two dimensional
  propagation, where the Alfvén waves decouple. In moderately inclined
  field ( ) at higher frequencies ( ), we found significant absorption
  enhancements - up to an order of magnitude. Using these two dimensional
  calculations, Cally, Crouch, and Braun constructed a simplified model
  for the interaction between a sunspot and its surroundings. They found
  excellent agreement with the observational -mode absorption and phase
  shift data. In this investigation, we determine the efficiency of
  mode conversion in non-vertical magnetic field with three dimensional
  propagation, where fast and slow magnetoacoustic-gravity waves and
  Alfvén waves are all coupled.

Title: Probing sunspot magnetic fields with p-mode absorption and
    phase shift data
Authors: Cally, P. S.; Crouch, A. D.; Braun, D. C.
Bibcode: 2003MNRAS.346..381C
Altcode:
  Long-standing observations of incoming and outgoing f- and p-modes
  in annuli around sunspots reveal that the spots partially absorb
  and substantially shift the phase of waves incident upon them. The
  commonly favoured absorption mechanism is partial conversion to
  slow magneto-acoustic waves that disappear into the solar interior
  channelled by the magnetic field of the sunspot. However, up until
  now, only f-mode absorption could be accounted for quantitatively by
  this means. Based on vertical magnetic field models, the absorption of
  p-modes was insufficient. In this paper, we use the new calculations
  of Crouch &amp; Cally for inclined fields, and a simplified model of
  the interaction between spot interior and exterior. We find excellent
  agreement with phase shift data assuming field angles from the
  vertical in excess of 30° and Alfvén/acoustic equipartition depths
  of around 600-800 km. The absorption of f-modes produced by such
  models is considerably larger than is observed, but consistent with
  numerical simulations. On the other hand, p-mode absorption is generally
  consistent with observed values, up to some moderate frequency dependent
  on radial order. Thereafter, it is too large, assuming absorbing regions
  comparable in size to the inferred phase-shifting region. The excess
  absorption produced by the models is in stark contrast with previous
  calculations based on a vertical magnetic field, and is probably due
  to finite mode lifetimes and excess emission in acoustic glories. The
  excellent agreement of phase shift predictions with observational
  data allows some degree of probing of subsurface field strengths, and
  opens up the possibility of more accurate inversions using improved
  models. Most importantly, though, we have confirmed that slow mode
  conversion is a viable, and indeed the likely, cause of the observed
  absorption and phase shifts.

Title: A comparison between model calculations and observations of
    sunspot oscillations
Authors: Rüedi, I.; Cally, P. S.
Bibcode: 2003A&A...410.1023R
Altcode:
  We investigate the signal which is expected to be produced by magnetic
  field oscillations in sunspots umbrae due to the combination of the
  oscillation model, radiative transfer and observing procedure. For
  this purpose we investigate the signal expected to be produced by
  theoretical models of sunspot oscillations and compare them with the
  signal seen in observed power spectra of sunspot magnetograms. We show
  that the amplitudes of the observed oscillations are compatible with
  the predictions of the theoretical model of magnetoacoustic oscillations
  for the 5-min as well as for the 3-min band. For the particular sunspot
  umbral oscillation models used, our analysis suggests that most of
  the expected observed power in the magnetogram signal oscillations is
  actually due to cross-talk from the temperature and density oscillations
  associated with the magnetoacoustic wave. A detailed modelling of
  the observing procedure turns out to be of central importance for the
  assignment of the observed oscillations to a specific wave type.

Title: Coronal Leaky Tube Waves and Oscillations Observed with Trace
Authors: Cally, P. S.
Bibcode: 2003SoPh..217...95C
Altcode:
  Leaky tube waves are examined in the context of kink oscillations
  in coronal loops, observed in recent years using TRACE. It
  is pointed out that the standard (non-leaky) principal
  kink mode has a leaky bifurcated counterpart with decay time
  τ<SUB>ℓ</SUB>≈4π<SUP>−4</SUP>(L/R)<SUP>2</SUP>P, where
  R and L are the loop radius and length, and P is the oscillation
  period. This is somewhat too long to explain the observed decays,
  except for very short or thick loops, but may be implicated in the
  initial excitation. Higher harmonics decay much more rapidly. The
  external solution takes the form of a wave running nearly parallel to
  the tube, but with a small outward component. In addition, a number of
  other leaky modes are described which decay on timescales of seconds,
  τ<SUB>ℓ</SUB>=Ra<SUB>e</SUB>/a<SUP>2</SUP>, where a and a<SUB>e</SUB>
  are the loop and external Alfvén speeds respectively, and which can
  be identified as being almost radially propagating fast magnetoacoustic
  waves. These are outside the currently observable range, but are likely
  to be important energetically.

Title: Mode Conversion of Solar p Modes in non-Vertical Magnetic
    Fields - i. two-Dimensional Model
Authors: Crouch, A. D.; Cally, P. S.
Bibcode: 2003SoPh..214..201C
Altcode:
  Sunspots absorb incident p modes. The responsible mechanism
  is uncertain. One possibility is mode conversion to slow
  magnetoacoustic-gravity waves. In vertical field mode conversion
  can adequately explain the observed f-mode absorption, but is too
  inefficient to explain the absorption of p modes. In this investigation
  we calculate the efficiency of fast-to-slow magnetoacoustic-gravity wave
  conversion in non-vertical field. We assume two-dimensional propagation
  where the Alfvén waves decouple. It is found that resultant p-mode
  absorption is significantly enhanced for moderate inclinations at
  higher frequencies, whereas for p modes at lower frequencies, and
  the f mode in general, there is no useful enhancement. However, the
  enhancement is insufficient to explain the observed p-mode absorption
  by sunspots. Paper II considers the efficiency of mode conversion in
  non-vertical field with three-dimensional propagation, where fast and
  slow magnetoacoustic-gravity waves and Alfvén waves are coupled.

Title: The Search for a Tipped Toroidal Field
Authors: Norton, A. A.; Gilman, P. A.; Henney, C. J.; Cally, P. S.
Bibcode: 2003SPD....34.1903N
Altcode: 2003BAAS...35..842N
  A magnetic tipping instability of the tachocline toroidal field has
  been predicted (Cally et al., 2003) that could produce a toroidal
  field tipped with respect to the equatorial axis. One result of a
  tipped toroidal band is the eruption of magnetic flux over a range of
  latitudes from the same toroidal ring. The longitudinal dependence
  of this flux emergence would contribute to non-axisymmetry of the
  whole flux emergence pattern by giving it a longitudinal wavenumber
  m=1 dependence. We search for evidence (or lack thereof) of a tipped
  toroidal field for some phases of the solar cycle by examining the
  dominant latitude of emerging flux as a function of longitude. We use
  the existing observational data from Kitt Peak synoptic Carrington
  Rotation magnetograms to identify the location of strong flux,
  independently in each hemisphere, and test whether the location of
  the flux reveals a pattern compatible with the tipping instability m=1.

Title: Three-dimensional magneto-shear instabilities in the solar
    tachocline
Authors: Cally, P. S.
Bibcode: 2003MNRAS.339..957C
Altcode:
  The solar tachocline straddles the base of the convection zone. In the
  radiative part, global scale latitudinal magneto-shear instabilities
  have been thought to be constrained to two dimensions by strongly
  stable stratification, and so two-dimensional (2D) instabilities have
  been examined in great detail recently. However, it is shown here that
  three-dimensional (3D) effects can be important. We generalize the
  linear 2D analysis to 3D in the Boussinesq thin layer approximation
  for models where the magnetic field is wrapped toroidally around the
  Sun, and the equilibrium field and flow are independent of depth. It
  is found that a very rapid `polar kink instability' dominates the
  dynamics of broad magnetic field distributions if the polar Alfvén
  angular speed α<SUB>p</SUB> exceeds the rotational angular velocity
  ω<SUB>p</SUB>, with maximum growth rate (α<SUP>2</SUP><SUB>p</SUB>-
  ω<SUP>2</SUP><SUB>p</SUB>)<SUP>1/2</SUP>. This might typically
  produce an e-folding time as short as a few months. Interestingly,
  the instability only affects the m= 1`tipping modes', twisting
  polar loops towards a vertical orientation. On the other hand,
  for α<SUP>2</SUP><SUB>p</SUB> &lt; ω<SUP>2</SUP><SUB>p</SUB>,
  3D instabilities are restricted to radial length scales in which
  perhaps just a few wavelengths could fit across the tachocline. These
  could supplement, or even dominate, the shallow-water modes examined
  recently by Gilman and Dikpati. An analysis of the role of a large
  Brunt-Väisälä frequency, as found in the radiative part of the
  tachocline, suggests that its main effect is to flatten the motions in
  the instabilities rather than to suppress them. Strong banded magnetic
  profiles are found to be susceptible to an instability similar to but
  distinct from the polar kink.

Title: Clamshell and Tipping Instabilities in a Two-dimensional
    Magnetohydrodynamic Tachocline
Authors: Cally, Paul S.; Dikpati, Mausumi; Gilman, Peter A.
Bibcode: 2003ApJ...582.1190C
Altcode:
  Building on Cally's nonlinear model of two-dimensional MHD tachocline
  instability, we further explore the evolution of a wide variety of
  toroidal field profiles due to this instability. Cally showed in a
  recent study that an initially broad toroidal field opens up into a
  ``clamshell'' pattern because of nonlinear evolution of MHD tachocline
  instability. Various other toroidal field profiles-single toroidal
  bands, double bands, and mixed profiles with a band in addition to
  broad profiles-may also occur in the Sun during various phases of the
  solar cycle. Detailed study of the evolution of banded profiles shows
  no occurrence of clamshell instability, but the bands commonly tip
  relative to the axis of rotation. The higher the latitude location of
  the band, the more it tips. Extreme tipping results when the band is
  at 60° latitude or higher-the magnetic ring hangs from the pole on one
  side of the Sun. For bands of 10° latitude width at sunspot latitudes
  (&lt;=40°), the band tip is within +/-10° about the mean latitude
  of the band. This tipping could either enhance or reduce the observed
  tilt in bipolar active regions. Double bands, or profiles consisting
  of a band and a broad profile, may exist at certain phases of the
  solar cycle. We find that double-band systems with two oppositely
  directed bands separated widely (&gt;15°) in latitude, as well
  as two close bands of same polarities, do not interact in the same
  hemisphere-the higher latitude band tips, while the lower latitude
  band hardly responds. A significant interaction between two individual
  bands in one hemisphere takes place only when the band separation is
  &lt;=15° and the bands are oppositely directed, which is a nonsolar
  case. In this case, the band system either tips or forms the clamshell
  pattern depending on the dominant mode symmetry. We also show that
  a mixed profile with oppositely directed narrow fields close to the
  equator in addition to the broad fields evolve in such a way as to
  oppose the reconnection of the broad fields across the equator, and
  thus inhibiting the clamshell formation, at least at certain phases
  of the solar cycle. Finally, we note that the tipping and clamshell
  instabilities strongly inhibit differential rotation.

Title: Interaction of Solar p-modes with Magnetic Field
Authors: Cally, P. S.
Bibcode: 2003ASPC..305..152C
Altcode: 2003mfob.conf..152C
  No abstract at ADS

Title: Observations and Interpretation of Sub-Surface Structures
Authors: Cally, Paul
Bibcode: 2003IAUJD..12E..43C
Altcode:
  Immediate subsurface local structures - flow magnetic and thermal -
  especially those associated with active regions are of considerable
  interest and are potentially accessible using high l helioseismology. In
  recent years though classical modal seismology has been supplemented
  with new approaches such as time-distance helioseismology and acoustic
  holography. In this talk the various methods and their results
  are briefly reviewed and implications discussed. Of the structure
  types subsurface magnetic fields are the most difficult to identify
  observationally so an overview is also given of how solar oscillations
  are expected to interact with them.

Title: Numerical Solutions of Three-Dimensional Pressure-Bounded
    Magnetohydrostatic Flux Tubes
Authors: Hennig, B. S.; Cally, P. S.
Bibcode: 2001SoPh..201..289H
Altcode:
  We present a three-dimensional technique for the solution of the
  magnetohydrostatic equations when we are modeling structures bounded by
  a current sheet that is free to move to satisfy pressure balance. The
  magnetic field is expressed in terms of Euler potentials and the
  equations are transformed to flux coordinates, greatly simplifying the
  problem of locating the free boundary. Multi-grid techniques are used
  to rapidly solve the resulting nonlinear elliptic partial differential
  equations. The method is tested against Low's (1982) exact solution
  of a bipolar plasma loop. It is shown that fast, accurate solutions
  can be found.

Title: Nonlinear Evolution of 2d Tachocline Instabilities
Authors: Cally, P. S.
Bibcode: 2001SoPh..199..231C
Altcode:
  A spectral method is used to explore the nonlinear evolution
  of known linear instabilities in a 2D differentially rotating
  magneto-hydrodynamic shell, representing the solar tachocline. Several
  simulations are presented, with a range of outcomes for the magnetic
  field configuration. Most spectacularly, the `clam instability', which
  occurs for solar differential rotation and a strong broad toroidal
  magnetic field structure, results in the field tipping over by 90°
  and reconnecting. A common characteristic of all the simulations though
  is that the nonlinear instabilities produce a strong angular momentum
  mixing effect which pushes the rotation towards a solid body form. It
  is argued that this may be the mechanism required by the model of
  Spiegel and Zahn to limit the tachocline's thickness.

Title: Note on an Exact Solution for Magnetoatmospheric Waves
Authors: Cally, P. S.
Bibcode: 2001ApJ...548..473C
Altcode:
  Solutions for magnetoatmospheric waves in an isothermal plane
  stratified atmosphere with uniform vertical magnetic field have
  long been known in terms of Meijer G-functions. It is pointed out
  that they may alternatively be expressed using the more familiar
  hypergeometric <SUB>2</SUB>F<SUB>3</SUB> functions, with significant
  advantages for ease of use and physical interpretation. The nature
  of these solutions in different regions of the frequency-wavenumber
  plane is fully discussed, with particular reference to reflection,
  transmission, and mode conversion. Reflection, transmission, and mode
  conversion coefficients for slow and fast waves incident from below,
  including the effects of tunnelling, are calculated exactly. The exact
  solutions are useful in interpreting observational results and numerical
  simulations of more complex magnetoatmospheric waves.

Title: An Observational Manifestation of Magnetoatmospheric Waves
    in Internetwork Regions of the Chromosphere and Transition Region
Authors: McIntosh, S. W.; Bogdan, T. J.; Cally, P. S.; Carlsson, M.;
   Hansteen, V. H.; Judge, P. G.; Lites, B. W.; Peter, H.; Rosenthal,
   C. S.; Tarbell, T. D.
Bibcode: 2001ApJ...548L.237M
Altcode:
  We discuss an observational signature of magnetoatmospheric waves in
  the chromosphere and transition region away from network magnetic
  fields. We demonstrate that when the observed quantity, line or
  continuum emission, is formed under high-β conditions, where β is
  the ratio of the plasma and magnetic pressures, we see fluctuations in
  intensity and line-of-sight (LOS) Doppler velocity consistent with the
  passage of the magnetoatmospheric waves. Conversely, if the observations
  form under low-β conditions, the intensity fluctuation is suppressed,
  but we retain the LOS Doppler velocity fluctuations. We speculate that
  mode conversion in the β~1 region is responsible for this change in
  the observational manifestation of the magnetoatmospheric waves.

Title: Frequency Dependent Ray Paths in Local Helioseismology
Authors: Barnes, G.; Cally, P. S.
Bibcode: 2001PASA...18..243B
Altcode:
  The surface of the Sun is continually oscillating due to sound waves
  encroaching on it from the interior. Measurements of the surface
  velocity are used to infer some of the properties of the regions
  through which the sound waves have propagated. Traditionally,
  this has been done by using a modal decomposition of the surface
  disturbances. However, the use of ray descriptions, in the form
  of acoustic holography or time-distance helioseismology, provides
  an alternative approach which may reveal more detailed information
  about the properties of local phenomena such as sunspots and active
  regions. Fundamental to any such treatment is determining the correct
  ray paths in a given atmosphere. In the simplest approach, the ray
  paths are constructed to minimise the travel time between two points
  (Fermat's principle). However, such an approach is only valid in the
  high frequency limit, ω≫ω<SUP>c</SUP>, N, where ω<SUP>c</SUP>
  is the acoustic cut-off and N the Brunt-Väisälä frequency. Although
  ω<SUP>c</SUP> is often included in time-distance calculations, and N
  occasionally, the same is not true of acoustic holography. We argue
  that this raises concerns about image sharpness. As illustrations,
  representative ray paths are integrated in a realistic solar model to
  show that the Fermat approximation performs poorly for frequencies of
  helioseismic interest. We also briefly discuss the importance of the
  Brunt-Väisälä frequency to the time-distance diagram.

Title: A Sufficient Condition for Instability in a Sheared
    Incompressible Magnetofluid
Authors: Cally, P. S.
Bibcode: 2000SoPh..194..189C
Altcode:
  It is shown that a sufficient condition for the stability of an
  incompressible sheared gravitationally stratified ideal magnetofluid
  with flow-aligned horizontal magnetic field is that there exists a
  Galilean frame in which the flow is nowhere super-Alfvénic (similarly,
  stability is assured in a compressible shear flow without gravity
  if there exists a frame in which the flow nowhere exceeds the cusp
  speed). Complex eigenvalue bounds are presented for unstable flows. The
  stability condition is applied to the solar tachocline; it suggests
  that any shear instabilities associated with radial gradients in flow
  speed should be stabilized by fields of above about 7 kG.

Title: Mode Mixing by a Shallow Sunspot
Authors: Barnes, G.; Cally, P. S.
Bibcode: 2000SoPh..193..373B
Altcode:
  Sunspots are strong absorbers of f and p modes. A possible
  absorption mechanism is direct conversion to slow magnetoacoustic
  waves. Calculations based on vertical magnetic field models show that
  this works well for f modes, but is inadequate for p modes. Using a very
  simple `shallow spot' model, in which the effects of the magnetic field
  are accounted for solely by a surface condition, we investigate the
  possibility that p modes first scatter into f modes inside the spot,
  which are then more susceptible to conversion to slow modes. We find
  that the coupling between an incident p mode and the internal f mode
  is unlikely to be strong enough to account for the observed absorption,
  but that the incident modes do couple strongly to the acoustic jacket in
  some cases, leading to a region immediately around the sunspot where a
  significant fraction of the surface velocity is due to the jacket modes.

Title: Modelling p-Mode Interaction with a Spreading Sunspot Field
Authors: Cally, P. S.
Bibcode: 2000SoPh..192..395C
Altcode:
  Sunspots absorb and scatter incident p modes. The dominant mechanism
  is still uncertain. One possibility, mode conversion to slow
  magneto-acoustic waves, has been shown to yield results in agreement
  with observations for the f mode only. Absorption of p modes in simple
  vertical magnetic field models is too weak by an order of magnitude or
  more. Here we report on numerical calculations of p modes encountering
  a simple sunspot model with field which spreads with height. It is
  found that p-mode absorption is greatly enhanced by field spread, to
  a level consistent with observations, and it appears that it occurs
  preferentially in the outer regions of the spot, in line with recent
  results from acoustic holography.

Title: The Contribution by Thin Magnetic Flux Tubes to p-Mode
    Line Widths
Authors: Crouch, A. D.; Cally, P. S.
Bibcode: 1999ApJ...521..878C
Altcode:
  The contribution to p-mode line widths from the excitation of tube mode
  oscillations on an individual magnetic fibril is computed. An idealized
  model of the fibril within the photosphere is implemented, consisting
  of a vertical, thin magnetic flux tube embedded in a plane-parallel
  isentropic polytrope of index m. Bogdan et al. considered a similar
  model but imposed a stress-free boundary condition at the top of
  the photosphere, which acts to reflect any upward-propagating tube
  waves completely back down into the tube. The stress-free boundary
  condition neglects a possibly important physical process: the loss of
  energy to the upper solar atmosphere by the excitation of waves in the
  chromosphere and corona. Using simple models of the solar chromosphere
  and corona, we explore the consequences of applying various boundary
  conditions. The resultant upward energy fluxes are not large, but
  surprisingly the more realistic upper boundary conditions lead to a
  significant increase in kink mode flux out the bottom. Nevertheless, the
  sausage mode remains dominant in cases of interest and is essentially
  unaffected by the new boundary conditions. Consequently, the resultant
  total p-mode line width computed here can account for only a few
  percent of the observed line width.

Title: Interaction of P-Modes with Sunspots
Authors: Bogdan, T. J.; Barnes, G. K.; Cally, P. S.; Crouch, A. D.
Bibcode: 1999AAS...194.5607B
Altcode: 1999BAAS...31R.912B
  We report on our ongoing efforts to model the interaction of
  the solar acoustic oscillations with solar surface magnetic flux
  concentrations. The simulation code employs a finite difference
  discretization of the linearized MHD wave equations written in
  conservative form. A staggered grid is used to ensure strict numerical
  conservation, and the time-stepping is based on a Lax-Wendroff-type
  two-step method that yields negligible numerical diffusion. Analysis
  of the results from these computations indicates that a significant
  fraction of the incident acoustic wave flux is converted into MHD waves
  which propagate along the magnetic lines of force. The efficiency
  of this coupling increases as the magnetic flux concentration is
  endowed with a more pronounced penumbra, wherein the magnetic field
  is highly inclined with respect to the local surface gravity. Intense
  small-scale fluid motions accompany this enhancement, particularly in
  the super-penumbral canopy that surrounds the flux concentration. Such
  a wave-coupling process provides an excellent qualitative explanation
  of the observed absorption of solar p-modes by sunspots, and is in
  basic accord with the excess in the penumbral Doppler signal relative
  to that recorded in the sunspot umbra. The versatility of our numerical
  simulations permits a sensible quantitative comparison between the model
  predictions and these observations, opening the potential to diagnose
  certain aspects of the hidden subsurface structure of sunspots. The
  National Center for Atmospheric Research is sponsored by the National
  Science Foundation.

Title: Mode Mixing by a Shallow Sunspot
Authors: Barnes, G.; Cally, P. S.
Bibcode: 1999soho....9E..35B
Altcode:
  In a polytropic atmosphere, the oscillation modes are described by
  well-known special functions. However, the presence of a magnetic
  field inside a sunspot makes the mode structure much more complex,
  so that analytic expressions are not available. Recent observations
  of sunspots suggest that most of the scattering and absorption due
  to the spots occurs in a layer immediately below the surface of the
  sun. We have therefore modelled the acoustic modes inside a sunspot by
  assuming that the effect of the magnetic field is concentrated right
  at the surface. Instead of imposing the conventional upper boundary
  condition, that the divergence of the velocity vanish, we require
  that the horizontal component of the velocity vanish, which allows
  us to write down analytic expressions for the acoustic modes inside
  the spot. This may be justified by arguing that a vertical magnetic
  field will tend to inhibit horizontal fluid motions. In effect, we are
  introducing a purely scattering disk to the surface of the sun. More
  realistic models, in which the disk both scatters and absorbs energy are
  also possible. We consider the scattering of an incident p-mode off our
  "sunspot," matching the pressure and horizontal velocity across the
  boundary. The result is a mixing of the incident mode into outgoing
  external p-modes and internal p-modes, as well as jacket modes both
  inside and outside the spot. We find that the inclusion of the jacket
  modes is crucial to satisfying the matching conditions, and we present
  results indicating the spectrum of outgoing and internal modes that
  are present.

Title: Modelling P-Mode Interaction with a Spreading Sunspot Field
Authors: Cally, Paul; Bogdan, Tom
Bibcode: 1999soho....9E..47C
Altcode:
  Sunspots absorb and scatter incident p-modes. The dominant mechanism
  is still uncertain. One possibility, mode conversion to slow
  magneto-acoustic waves, has been shown to yield results in agreement
  with observations for the f-mode only. Absorption of p-modes in simple
  vertical magnetic field models is too weak by an order of magnitude or
  more. Here we report on numerical calculations of p-modes encountering
  a simple sunspot model with field which spreads with height. It is
  found that interesting interactions take place in the near horizontal
  "canopy" which may greatly enhance absorption. We present a video
  which aids in visualizing the interactions.

Title: Sunspot magnetic oscillations: Comparison between observations
    and models
Authors: Rüedi, I.; Solanki, S. K.; Bogdan, T.; Cally, P.
Bibcode: 1999ASSL..243..337R
Altcode: 1999sopo.conf..337R
  No abstract at ADS

Title: Velocity and Magnetic Field Fluctuations in the Photosphere
    of a Sunspot
Authors: Lites, Bruce W.; Thomas, John H.; Bogdan, Thomas J.; Cally,
   Paul S.
Bibcode: 1998ApJ...497..464L
Altcode:
  We use a data set of exceptionally high quality to measure oscillations
  of Doppler velocity, intensity, and the vector magnetic field at
  photospheric heights in a sunspot. Based on the full Stokes inversion
  of the line profiles of Fe I 630.15 and 630.25 nm, in the sunspot umbra
  we find upper limits of 4 G (root mean square [rms]) for the amplitude
  of 5 minute oscillations in magnetic field strength and 0.09d (rms)
  for the corresponding oscillations of the inclination of the magnetic
  field to the line of sight. Our measured magnitude of the oscillation
  in magnetic field strength is considerably lower than that found in
  1997 by Horn, Staude, &amp; Landgraf. Moreover, we find it likely
  that our measured magnetic field oscillation is at least partly due to
  instrumental and inversion cross talk between the velocity and magnetic
  signals, so that the actual magnetic field strength fluctuations are
  even weaker than 4 G. In support of this we show, on the basis of the
  eigenmodes of oscillation in a theoretical model of the sunspot umbra,
  that magnetic field variations of at most 0.5 G are all that is to
  be expected. The theoretical model also provides an explanation of
  the shift of power peaks in Doppler velocity to the 3 minute band in
  chromospheric umbral oscillations, as a natural consequence of the
  drastic change in character of the eigenmodes of oscillation between
  frequencies of about 4.5 and 5.0 mHz due to increased tunneling through
  the acoustic cutoff-frequency barrier. Using measurements of the
  phase of velocity oscillations above the acoustic cutoff frequency,
  we determine the relative velocity response height in the umbra of
  four different photospheric spectral lines from the phase differences
  between velocities in these lines, assuming that the oscillations
  propagate vertically at the local sound speed. In spacetime maps of
  fluctuations in continuum intensity, Doppler velocity, magnetic field
  strength, and field inclination, we see distinct features that migrate
  radially inward from the inner penumbra all the way to the center of
  the umbra, at speeds of a few tenths of a kilometer per second. These
  moving features are probably a signature of the convective interchange
  of magnetic flux tubes in the sunspot, although we failed to find any
  strong correlation among the features in the different quantities,
  indicating that these features have not been fully resolved.

Title: Simulation of f- and p-Mode Interactions with a Stratified
    Magnetic Field Concentration
Authors: Cally, P. S.; Bogdan, T. J.
Bibcode: 1997ApJ...486L..67C
Altcode:
  The interaction of f- and p-modes with a slab of vertical magnetic
  field of sunspot strength is simulated numerically in two spatial
  dimensions. Both f-modes and p-modes are partially converted to
  slow magnetoatmospheric gravity (MAG) waves within the magnetic slab
  because of the strong gravitational stratification of the plasma along
  the magnetic lines of force. The slow MAG waves propagate away from
  the conversion layer guided by the magnetic field lines, and the
  energy they extract from the incident f- and p-modes results in a
  reduced amplitude for these modes as they exit from the back side of
  the slab. In addition, the incident p-modes are partially mixed into
  f-modes of comparable frequency, and therefore larger spherical harmonic
  degree, when they exit the magnetic flux concentration. These findings
  have important implications for the interpretation of observations
  of p-mode absorption by sunspots, both in terms of the successes and
  failures of this simple numerical simulation viewed in the sunspot
  seismology context.

Title: Waves in magnetized polytropes.
Authors: Bogdan, T. J.; Cally, P. S.
Bibcode: 1997RSPSA.453..943B
Altcode: 1997RSPSA.453..943J
  The authors consider the linear oscillations of a plane-parallel
  semi-infinite electrically conducting atmosphere with a constant
  temperature gradient, subjected to an imposed uniform gravitational
  acceleration and uniform magnetic field. The oscillations are treated
  in the ideal (dissipationless) limit and the uniform gravitational
  acceleration and magnetic field are taken to be co-aligned with the
  prevailing temperature gradient. It is demonstrated that atmospheric
  motions with prescribed horizontal variations of the form exp(ikx),
  with k real, possess both a discrete set of complex eigenfrequencies
  w<SUB>n</SUB>, n=0, 1, 2,..., and a continuous spectrum. These
  two behaviours derive from a particular fourth-order ordinary
  differential equation that arises in the solution of the initial value
  problem via an integral transform and describes the coupled fast-
  and slow-magnetoatmospheric waves. The authors devote considerable
  efforts to document how the discrete spectrum varies in response to
  incremental changes in the horizontal wavenumber k and they compare
  and contrast this behaviour with that found by Lamb for the same
  atmosphere, but with the magnetic field being absent. Implications
  for the helioseismology of sunspots are discussed.

Title: Absorption of p-Modes by Slender Magnetic Flux Tubes and
    p-Mode Lifetimes
Authors: Bogdan, T. J.; Hindman, B. W.; Cally, P. S.; Charbonneau, P.
Bibcode: 1996ApJ...465..406B
Altcode:
  The presence of a fibril magnetic field in the solar envelope not only
  induces shifts in the p-mode resonant frequencies, but also contributes
  to the line width of the modes. The augmentation of the line widths
  results from two related physical processes: the excitation of tube
  mode oscillations on the individual magnetic fibrils and the attendant
  mode mixing between p-modes with identical oscillation frequencies. We
  assay the magnitude of the contribution from the former physical
  process based upon an idealized model consisting of vertical, slender,
  magnetic flux tubes embedded in a plane-parallel isentropic polytrope
  of index m. We restrict our attention to axisymmetric flux tubes
  that are in mechanical and thermal equilibrium with their immediate
  nonmagnetic surroundings. For low p-mode oscillation frequencies,
  ω, this model predicts that the line width, F, varies as <P />Γ
  ∝ fωM<SUP>-½</SUP> ∝fω<SUP>m+2</SUP>, <P />where M the mode
  mass, and f is the magnetic filling factor reckoned at the surface
  of the polytrope. This scaling is in better overall agreement with
  the observations (Γ ∝ ω<SUP>4.2</SUP>) than previous predictions
  based on the excitation and damping of solar p-modes by turbulent
  convection (which yields Γ ∝ γ<SUP>2</SUP> M<SUP>-1</SUP>
  ∝ω<SUP>2m+4</SUP>), or the scattering of p-modes by convective
  eddies (which yields Γ ∝ ω<SUP>(4/3)m+3)</SUP>, and it suggests
  that tube mode excitation on fibril magnetic fields may be a dominant
  and detectable (through its solar cycle variation) component of the
  low-frequency p-mode line widths.

Title: Driven Acoustic Oscillations within a Vertical Magnetic Field
Authors: Hindman, Bradley W.; Zweibel, Ellen G.; Cally, P. S.
Bibcode: 1996ApJ...459..760H
Altcode:
  We examine the effects of a vertical magnetic field on p-mode
  frequencies, line widths, and eigenfunctions. We employ a simple solar
  model consisting of a neutrally stable polytropic interior matched to
  an isothermal chromosphere. The p-modes are produced by a spatially
  distributed driver. The atmosphere is threaded by a constant vertical
  magnetic field. The frequency shifts due to the vertical magnetic
  field are much smaller than the shifts caused by horizontal fields
  of similar strength. A large vertical field of 2000 G produces shifts
  on the order of 1 muHz while a weak field of 50 G produces very small
  shifts of several nanohertz. We find that the frequency shifts decrease
  with increasing frequency and increase with field strength. The shifts
  are positive, except at high frequency and low field strength, where
  small negative shifts are possible. Coupling of the acoustic fast mode
  to escaping slow modes is extremely inefficient. Constant vertical
  magnetic field models are therefore incapable of explaining the high
  level of absorption observed in sunspots and plage The damping due
  to this mode conversion process produces very narrow line widths. For
  a 2000 G field the line widths are several microhertz and for a 50 G
  field the line widths are several nanohertz.

Title: Jacket Modes: Solar Acoustic Oscillations Confined to Regions
    Surrounding Sunspots and Plage
Authors: Bogdan, T. J.; Cally, P. S.
Bibcode: 1995ApJ...453..919B
Altcode:
  It is demonstrated by the application of classical eigenfunction
  expansion techniques that the interaction of an incident solar acoustic
  oscillation, or p-mode, with a scattering obstacle-such as a sunspot
  involves not only the scattering of the incident p-mode into other
  p-modes of like frequency (mode mixing), but also the generation of an
  acoustic halo localized like a "jacket" about the scatterer. This halo
  oscillates at the same frequency as the incident p-mode and is composed
  of a superposition of a continuous spectrum of modes referred to as
  jacket modes. It is pointed out that these jacket modes should appear
  as a broad enhancement to the background power underlying the p-mode
  ridges in κ-ω diagrams for regions in close proximity to sunspots and
  the boundaries of plage The basic results draw upon a remarkable analogy
  between the oscillations of an adiabatically stratified plane-parallel
  polytrope and the wave functions for the hydrogen atom: the laterally
  propagating p-modes that participate in the mode mixing correspond
  to the negative-energy bounds states of the hydrogen atom, while the
  continuous spectrum of jacket modes corresponds to the continuum of
  positive-energy states in which the electron is not bound to the proton.

Title: Coupling of magnetospheric cavity modes to field line
resonances: A study of resonance widths
Authors: Mann, Ian R.; Wright, Andrew N.; Cally, Paul S.
Bibcode: 1995JGR...10019441M
Altcode:
  By using a box model for the magnetosphere and by using a matrix
  eigenvalue method to solve the cold linearized ideal MHD equations,
  we examine the temporal evolution of the irreversible coupling
  between fast magnetospheric cavity modes and field line resonances
  (FLRs). By considering the fast mode frequency to be of the form
  ω<SUB>f</SUB>=ω<SUB>fr</SUB>-iω<SUB>fi</SUB>, and using a Fourier
  transform approach, we have determined the full time-dependent evolution
  of resonance energy widths. We find that at short times the resonances
  are broad, and narrower widths continue to develop in time. Ultimately,
  an asymptotic resonance Alfvén frequency full width at half maximum
  (FWHM) of Δω<SUB>A</SUB>=2ω<SUB>fi</SUB> develops on a timescale of
  τ<SUB>fi</SUB>=ω<SUB>fi</SUB><SUP>-1</SUP>. On timescales longer than
  τ<SUB>fi</SUB>, we find that the resonance perturbations can continue
  to develop even finer scales by phase mixing. Thus, at any time, the
  finest scales within the resonance are governed by the phase mixing
  length L<SUB>ph</SUB>(t)=2π(tdω<SUB>A</SUB>/dx)<SUP>-1</SUP>. The
  combination of these two effects naturally explains the localisation of
  pulsations in L shells observed in data, and the finer perturbation
  scales which may exist within them. <P />During their evolution,
  FLRs may have their finest perturbation scales limited by either
  ionospheric dissipation or by kinetic effects (including the
  breakdown of single fluid MHD). For a continually driven resonance,
  we define an ionospheric limiting timescale τ<SUB>I</SUB> in terms
  of the height-integrated Pedersen conductivity Σ<SUB>P</SUB>,
  and hence derive a limiting ionospheric perturbation scale
  L<SUB>I</SUB>=2π(τ<SUB>I</SUB>dω<SUB>A</SUB>/dx)<SUP>-1</SUP>,
  in agreement with previous steady state analyses. For sufficiently
  high Σ<SUB>P</SUB>, FLR might be able to evolve so that their
  radial scales reach a kinetic scale length L<SUB>k</SUB>. For
  this to occur, we require the pulsations to live for longer than
  τ<SUB>k</SUB>=2π(L<SUB>k</SUB>dω<SUB>A</SUB>/dx)<SUP>-1</SUP>. For
  t&lt;τ<SUB>k</SUB>,τ<SUB>I</SUB>, kinetic effects and ionospheric
  dissipation are not dominant, and the ideal MHD results presented
  here may be expected to model realistically the growth phase of ULF
  pulsations. .

Title: Effects of Weak-to-Moderate Vertical Magnetic Fields on Solar
    f- and p-Modes
Authors: Cally, P. S.
Bibcode: 1995ApJ...451..372C
Altcode:
  Observations indicate that solar p-modes encountering regions of
  enhanced magnetic field such as active region plage are partially
  absorbed. We adopt a simple vertical field model and investigate
  the possibility that the responsible mechanism is slow mode leakage,
  which has been at least partially successful in explaining absorption
  by sunspots. It is found that there are two frequency ranges with
  very different behavior: (1) below the chromospheric acoustic cutoff
  frequency, and (2) above it. In the first case, which includes the 5
  minute band, the f- and p<SUB>1</SUB>-modes would be expected to suffer
  substantial absorption, but p-modes of higher radial order would not
  be damped sufficiently to account for observations. On the other hand,
  in the higher frequency range (≥ 5 mHz), damping lengths of f- and
  P<SUB>1</SUB>-P<SUB>3</SUB> modes are smaller than or comparable to
  typical plage sizes, indicating that substantial absorption should
  occur.

Title: Driven Acoustic Oscillations Within a Vertical Magnetic Field
Authors: Hindman, B. W.; Zweibel, E. G.; Cally, P. S.
Bibcode: 1995ESASP.376b..77H
Altcode: 1995help.confP..77H; 1995soho....2...77H
  Examines the effects of a vertical magnetic field on p-mode frequencies,
  line widths, and eigenfunctions. The authors employ a simple solar
  model consisting of a neutrally stable polytropic interior matched to
  an isothermal chromosphere. The p-modes are produced by a spatially
  distributed driver. The atmosphere is threaded by a constant vertical
  magnetic field. The frequency shifts due to the vertical magnetic
  field are much smaller than the shifts caused by horizontal fields of
  similar strength. A large vertical field of 2000 G produces shifts
  on the order of a μHz while a weak field of 50 G produces very
  small shifts of several nHz. The authors find that the frequency
  shifts decrease with increasing frequency and increase with field
  strength. Coupling of the acoustic fast mode to escaping slow modes
  is extremely inefficient. Constant vertical magnetic field models are
  therefore incapable of explaining the high level of absorption observed
  in sunspots and plages.

Title: Umbral Oscillations in Sunspots: Absorption of p-Modes and
    Active Region Heating by Mode Conversion
Authors: Cally, P. S.; Bogdan, T. J.; Zweibel, E. G.
Bibcode: 1994ApJ...437..505C
Altcode:
  The linear adiabatic oscillations of an infinite, stratified,
  perfectly conducting atmosphere pervaded by a uniform vertical magnetic
  field are computed. The stratification is chosen to approximate the
  conditions appropriate for a sunspot umbra where strong reflection
  of the fast magnetoacoustic-gravity waves from the rapid increase
  of the Alfven speed with height and the sound speed with depth is
  anticipated. Since the umbral oscillations are presumably excited by
  external p-mode forcing, the angular frequency omega is prescribed --
  being set by the p-modes -- and it is required to solve for the allowed
  eigenvalues assumed by the horizontal wavenumber k and the corresponding
  displacement eigenfunctions. We term these allowed solutions pi-modes
  in recognition of the crucial influence of the imposed magnetic
  field and to distinguish them from their p-mode cousins present in
  the surrounding nonmagnetic quiet Sun. The wavenumber eigenvalues are
  complex and are consistent with the spatial decay of the pi-modes inward
  toward the center of the sunspot from the umbral boundary. This spatial
  attenuation is a consequence of the slow magnetoacoustic-gravity waves
  that propagate along the magnetic field lines and extract energy from
  the trapped fast waves through mode coupling in the layers where the
  sound and Alfven speeds are comparable. Through the consideration of
  several ancillary computations we argue that this salient attribute
  of the pi-modes may be essential both in explaining the observed
  absorption of (the forcing) p-modes by sunspots and in providing a
  source of mechanical energy for the overlying active regions. However,
  more realistic calculations are clearly called for before these notions
  may be confirmed.

Title: A Fourier-space description of oscillations in an inhomogeneous
    plasma. Part 1. Continuous Fourier transformation
Authors: Sedláček, Z.; Cally, P. S.
Bibcode: 1994JPlPh..52..245S
Altcode:
  Oscillations in inhomogeneous cold plasmas or inhomogeneous
  magnetofluids are interpreted in terms of the dynamics of their
  spectra in wavenumber space. By Fourier transforming the basic
  integro-differential equation of the problem, a generalized
  wave equation in wavenumber space is derived, thus converting the
  oscillation and phase-mixing processes in the original χ space into
  processes of dispersive propagation and scattering of the spectrum
  in wavenumber space. The Barston singular continuum eigenmodes
  correspond to stationary scattering states of a monochromatic wave in
  wavenumber space, whereas the damping phenomena in χ space correspond
  to transient ‘leaking’ phenomena accompanying scattering and
  dispersive propagation of a wave packet in wavenumber space.

Title: A Fourier-space description of oscillations in an inhomogeneous
    plasma. Part 2. Discrete approach
Authors: Cally, P. S.; Sedláček, Z.
Bibcode: 1994JPlPh..52..265C
Altcode:
  The process of phase mixing in inhomogeneous MHD or cold plasmas
  is interpreted as one of energy propagation in discrete Fourier
  space. Three instructive scenarios are examined: (i) an isolated
  inhomogeneity with zero boundary conditions; (ii) a periodic
  inhomogeneity; and (iii) a monotonic inhomogeneity sandwiched between
  two semi-infinite uniform regions. In each case the coefficients of the
  associated wave equation in Fourier space for an appropriately chosen
  dependent variable are very nearly constant almost everywhere, so the
  propagation is like that of a free unreflected wave. An exception
  may arise in the coupling of the lowest modes, which can be highly
  reflective. It is argued that Fourier space is the simplest and most
  natural context in which to discuss the development of fine-scale
  oscillations.

Title: Modelling magnetoacoustic oscillations in sunspots: a
    progress report
Authors: Charbonneau, P.; Cally, P. S.; Bogdan, T. J.
Bibcode: 1994smf..conf..251C
Altcode:
  No abstract at ADS

Title: Solar p-Modes in a Vertical Magnetic Field: Trapped and Damped
    pi -Modes
Authors: Cally, P. S.; Bogdan, T. J.
Bibcode: 1993ApJ...402..721C
Altcode:
  The study addresses the question of whether the polytropic atmosphere
  with an imposed uniform vertical magnetic field possesses normal
  modes of oscillation despite the potential for the s-modes to drain
  energy from the resonant cavity created by the favorable vertical
  stratification. This question is answered in the affirmative via
  direct numerical construction of these eigenfunctions for the complete
  uniformly magnetized polytrope. The basic equilibrium atmosphere
  is discussed, and the relevant linearized equations and boundary
  conditions are provided. The properties of the trapped pi-modes are
  considered. It is suggested that they play a role in the magnetized
  sunspot atmosphere analogous to that played by the p-modes in the
  unmagnetized surrounding quiet sun. Oscillations in sunspots and sunspot
  seismology are reassessed in light of the discovery of the natural modes
  of oscillation of unbounded atmospheres with vertical magnetic fields.

Title: Steady and Nonsteady Siphon Flow in Hot Coronal Loops
Authors: Robb, T. D.; Cally, P. S.
Bibcode: 1992ApJ...397..329R
Altcode:
  Siphon flow in hot coronal loops is examined, in both its steady
  and dynamic states, in the latter case using a flux-corrected
  transport simulation. We find that such flows are inhibited by (1)
  low heating rates, (2) high pressures, (3) short loop lengths, and
  (4) turbulence. In accordance with expectations, we find that small
  footpoint pressure asymmetries produce steady subsonic flow. However,
  the standard picture that larger values yield standing shocks is
  shown to be valid only for sufficiently high heating, long loops, or
  low pressure. Values of these parameters more characteristic of active
  regions produce instead a quasi-periodic 'surge' flow when the pressure
  asymmetry exceeds a critical value at which the temperature gradient
  at the inflow end reverses sign. These flows are normally subsonic,
  though examples can be found where the surge is supersonic for a part
  of each period. The difficulty of driving substantial siphon flows
  for realistic hot loop models is in accordance with the comparative
  rarity of observations of these flows.

Title: Phase mixing and surface-wave decay in an inhomogeneous plasma
Authors: Cally, P. S.; Sedláček, Z.
Bibcode: 1992JPlPh..48..145C
Altcode:
  The decay rate of an Alfvén or plasma surface wave propagating along
  an inhomogeneous layer of plasma is calculated. The inhomogeneous
  profile is thin and odd, but otherwise arbitrary. The wave's decay
  rate is determined using two fundamentally different methods,
  the integro-differential equation approach of Sedl´ček and the
  Sturm-Liouville expansion technique of Cally, and found by both to
  depend only on the slope of the Alfvén or plasma frequency profile at
  the ‘resonant point’, and not on other details of its shape. The
  result is verified numerically. This problem represents a good example
  with which to compare and contrast the two methods.

Title: Resonant structures within incompressible ideal MHD
Authors: Zorzan, C.; Cally, P. S.
Bibcode: 1992JPlPh..47..321Z
Altcode:
  The resonant characteristics of an incompressible ideal MHD fluid
  are highly structured. To help expose this structure, an equivalent
  electrical analogue of the MHD system is developed. The model, in
  the form of a transmission line, makes it possible to identify a
  number of new and important concepts, one of which is the effective
  impedance. This in turn enables entire regions of MHD fluid to be
  replaced with equivalent impedances. When fully exploited, the model
  also provides a more consistent interpretation of the spectrum of ideal
  MHD. The discrete Alfvén modes are found to be highly degenerate,
  while the transition to a discontinuous profile is accompanied by
  a redistribution of an uncountably infinite number of ‘poles’
  from the continuous spectrum and onto the Alfvén modes. In addition,
  the electrical analogue shows that within a continuously structured
  fluid the characteristic behaviour is not necessarily dominated by the
  ‘surface mode’ alone. This view is also supported by the results of
  a numerical simulation of the linear MHD equations. Depending on the
  initial conditions, the collective behaviour can have any frequency
  within the range spanned by the transition zone. The energy itself
  is monitored using a new pair of energy and flux expressions derived
  from a variational (Lagrangian) description of the MHD system. Again
  the electrical model is used to provide a physical interpretation
  of the individual terms within these expressions. In particular,
  it allows a partition of the total energy into separate kinetic-
  and potential-energy terms.

Title: Phase-mixing and surface waves: a new interpretation
Authors: Cally, P. S.
Bibcode: 1991JPlPh..45..453C
Altcode:
  The classical incompressible MHD or cold plasma phase mixing problem,
  which involves Alfvén or plasma waves in inhornogeneous media,
  is re-examined using a spatial Fourier series rather than the usual
  temporal Fourier or Laplace transform approach. A number of exact and
  near-exact analytic and numerical results are derived which reveal
  an attractive picture of energy cascading to smaller length-scales in
  a manner reminiscent of turbulence. Furthermore, we present a simple
  and unambiguous description of how a surface wave arises in the limit
  in which the inhomogeneity becomes a discontinuity.

Title: Stability, Structure, and Evolution of Cool Loops
Authors: Cally, P. S.; Robb, T. D.
Bibcode: 1991ApJ...372..329C
Altcode:
  The criteria for the existence and stability of cool loops are
  reexamined. It is found that the stability of the loops strongly depends
  on the form of the heating and radiative loss functions and that if the
  Ly-alpha peak which appears in most calculations of the radiative loss
  function is real, cool loops are almost certainly unstable. Removing
  the hydrogen contribution from the recent loss function Q(T) by Cook
  et al. (1989) does not produce the much-used result, Q proportional to
  T-cubed, which is so favorable to cool loop stability. Even using the
  probably unrealistically favorable loss function Q1 of Cook et al. with
  the hydrogen contribution removed, the maximum temperature attainable
  in stable cool loops is a factor of 2-3 too small to account for the
  excess emission observed in lower transition region lines. Dynamical
  simulations of cool loop instabilities reveal that the final state of
  such a model is the hot loop equilibrium.

Title: Why Heating is Not Necessary in the Transition Region or
    Upper Chromosphere (With 3 Figures)
Authors: Cally, P. S.
Bibcode: 1991mcch.conf..103C
Altcode:
  No abstract at ADS

Title: Turbulent Thermal Conduction in the Solar Transition Region
Authors: Cally, P. S.
Bibcode: 1990ApJ...355..693C
Altcode:
  Emission measures E(T) derived from EUV observations of the lower
  solar transition region indicate that there is far more material in
  that temperature range than can be explained within the steady single
  flux-tube scenario if the classical energy transfer and loss mechanisms
  are adopted. This suggests that some mechanism may be operating which
  reduces the temperature gradient. The inclusion of a turbulent thermal
  conductivity kappa(T) = phi rho c(p)ul in a one-dimensional model
  is investigated, where u is the rms microvelocity in one direction,
  l is the mixing length, and phi is a constant of order unity. If it
  is assumed that that l is proportional to T exp-alpha, it is shown
  that near-perfect agreement with the observed emission measures is
  obtained for alpha = 3/2, both as regards the slope d log E/d log T
  equal to about -3 in the LTR, and the upturn at the top of this range.

Title: Force and Energy Balance in the Transition Region Network
Authors: Fiedler, R. A. S.; Cally, P. S.
Bibcode: 1990SoPh..126...69F
Altcode:
  Two-dimensional numerical models of the solar transition region
  are calculated using an inverse coordinates method which attains
  pressure equilibrium between the network magnetic field and the
  external comparatively field-free gas. If A(y, z) is the magnetic
  potential (a scalar in 2D), which is constant on field lines, the
  method involves interchanging dependent and independent variables to
  obtain a quasi-linear PDE for y(A, z), which is solved iteratively. The
  advantage of this approach is that magnetic field lines, including any
  magnetic interface, become coordinate lines, thereby simplifying the
  energy equation and free boundary problem. In order to examine the
  effects of self-consistent geometry on the thermal structure of the
  transition region network, we calculate four models. The energy balance
  includes the effects of radiation, conduction, and enthalpy flux. It
  is confirmed that the lower branch of the emission measure curve cannot
  be explained within the single fluxtube model if the classical Spitzer
  thermal conductivity is used. However, by including a turbulent thermal
  conductivity as proposed by Cally (1990a), transition region models
  are obtained for which the resulting emission measure curves exhibit
  the correct behaviour, including the observed turn-up below about 200
  000 K. In summary, the broad conclusions of previous non-turbulent 2D
  models are confirmed, but most importantly, the turbulent conductivity
  hypothesis tested in 1D by Cally is shown to produce excellent agreement
  with observations in the more realistic geometry.

Title: Magnetohydrodynamic Tube Waves and High Speed Solar Wind
    Streams
Authors: Cally, P. S.
Bibcode: 1987SoPh..108..183C
Altcode:
  It has been widely conjectured that magnetohydrodynamic (MHD) waves
  may provide the extra momentum or energy required to explain the high
  speed solar wind streams that originate in coronal holes. Although the
  magnetic structuring inherent in this problem has been incorporated into
  models of the bulk flow, this is not generally true of the associated
  treatments of wave propagation. In particular, as pointed out by
  Davila (1985), we might generally expect the magnetic geometry to
  substantially modify those waves whose wavelength is comparable to the
  hole width. Using both a geometrical optics and an eigenmode approach,
  Davila addressed the question of wave propagation in a simple uniform
  width flux slab model of a coronal hole and concluded the hole may act
  as a `leaky wave guide', i.e., waves travelling along it may leak into
  the surrounding corona, but

Title: Leaky and Non-Leaky Oscillations in Magnetic Flux Tubes
Authors: Cally, P. S.
Bibcode: 1986SoPh..103..277C
Altcode:
  An extensive analysis, both analytic and numerical, of waves in flux
  tubes imbedded in (possibly) magnetic surroundings is given. It is
  shown that any wave confined to the tube and its neighbourhood can
  be put into one of seven categories. Simple criteria for deciding the
  existence of each type in any particular case are derived. Many other
  (leaky) modes are found which excite waves in the external medium
  and thereby lose energy to the surroundings. A number of asymptotic
  analyses allow much information to be gained about these without the
  need for numerical solution of the complicated equations involved. Three
  particular cases, pertaining to photospheric flux tubes, Hα fibrils,
  and coronal loops, are considered in detail.

Title: Magnetohydrodynamic tube waves - Waves in fibrils
Authors: Cally, P. S.
Bibcode: 1985AuJPh..38..825C
Altcode:
  A discussion of waves in magnetic flux tubes imbedded in magnetic
  unstratified surroundings is given. Seven types of non-leaky wave
  are identified. Many more leaky waves, tube oscillations which
  drive waves in the external medium and thereby lose energy to it,
  are also found. The particular example of longitudinal and transverse
  oscillations in chromospheric fibrils is examined in detail.

Title: Magnetohydrodynamic critical levels and radiative damping
Authors: Cally, P. S.
Bibcode: 1984A&A...136..121C
Altcode:
  The full MHD wave equation for radiatively damped wave propagation in
  a stratified magnetoatmosphere permeated by a horizontal magnetic field
  is derived. In the adiabatic case a discussion of the various types of
  singularity (critical level) is given. For an isothermal atmosphere
  with uniform magnetic field the damped wave equation is solved in
  terms of hypergeometric functions, and it is concluded that for many
  cases of interest the erstwhile discontinuity in the wave energy flux
  is considerably "smoothed out" by the damping. Substantial fluxes
  (≡10<SUP>8</SUP> erg cm<SUP>-2</SUP> s<SUP>-1</SUP>) are found to
  be carried by some modes which, in the absence of critical levels,
  would carry no energy.

Title: Chromospheric and coronal Alfvénic oscillations in
    non-vertical magnetic fields
Authors: Schwartz, S. J.; Cally, P. S.; Bel, N.
Bibcode: 1984SoPh...92...81S
Altcode:
  We generalize previous studies of Alfvénic oscillations in the solar
  atmosphere to geometries in which the background magnetic field is
  not parallel to the gravitational acceleration. A uniform but inclined
  field produces only subtle changes in the mathematics, and virtually
  no changes to the coronal energy flux, over previous vertical field
  studies. We show that simple, two-layer models agree remarkably
  well with more sophisticated, multi-layer calculations. In addition,
  we derive several useful and accurate analytic results with which we
  highlight many features and parameter dependences. We also study a model
  with a spreading field geometry. For low magnetic fields (∼- 10 G)
  the corona still appears WKB to the oscillations and we do not find
  any significant deviations from the uniform field calculations. This
  is not the case for higher magnetic fields in active regions (∼-
  3000 G) where we confirm previous results which suggest an order
  of magnitude increase in the coronal flux. Again, we derive useful
  analytic approximations.

Title: Umbral Oscillations in the Presence of a Spreading Magnetic
    Field
Authors: Cally, P. S.
Bibcode: 1983SoPh...88...77C
Altcode:
  A simple umbral model incorporating spreading magnetic field lines is
  introduced, and the equations governing Magneto-Acoustic-Gravity (MAG)
  and Alfvén modes are derived. In the absence of stratification analytic
  solutions may be found. For the MAG modes, under coronal conditions,
  these consist of a travelling (slow) wave and an evanescent (fast)
  mode, whilst the Alfvén solution may be expressed in terms of a
  Hankel function. These are matched onto numerical solutions in a
  stratified model photosphere-chromosphere, and the vertical energy
  fluxes are calculated. Resonant frequencies are generally found to be
  shifted downwards compared with the vertical field case, though the
  MAG flux is virtually unaltered otherwise; however, the Alfvén flux is
  increased by up to two orders of magnitude. In an unstratified medium,
  the usual formula for the Alfvén flux, F = ϱa «δv<SUP>2</SUP>»,
  is shown to be generally incorrect in the presence of field spread,
  and must be replaced by F = N<SUP>−2/3</SUP>(4π)<SUP>−1</SUP>ϱa
  «δv<SUP>2</SUP>», where N is a spread parameter which usually
  satisfies N ≪ 1.

Title: On photospheric and chromospheric penumbral waves.
Authors: Cally, P. S.; Adam, J. A.
Bibcode: 1983SoPh...85...97C
Altcode:
  The full magnetoatmospheric wave equation is numerically solved for the
  particular penumbral model of Nye and Thomas (1974). For chromospheric
  running penumbral waves it is found that the maximum vertical velocity
  occurs at the base of the Hα region (z ≈ 300 km) much lower than
  previous WKB estimates have suggested. The maximum `vertical' kinetic
  energy occurs at z ≈ - 130 km. Very significant horizontal velocities
  are also found for these waves, and, in the absence of shear flow it
  appears that previous estimates of photospheric vertical velocities
  of order 10<SUP>−1</SUP> km s<SUP>−1</SUP> could be substantial
  underestimates. For the photospheric events of Musman et al. (1976),
  a high vertical velocity maximum is found in the corona, and the
  modes appear highly dispersive for periods ≥ 220 s. The effects of a
  sinusoidal shear flow profile on running penumbral waves are examined,
  and it is found that the eigenvalues (horizontal wavenumber k) are
  changed little, but the eigenmodes become significantly distorted;
  the position of the vertical velocity peak rises compared to the zero
  flow case, and the velocity below that peak drops significantly. This
  effect may well cancel the increased estimates based on zero flow.

Title: Photospheric and Chromospheric Penumbral Waves
Authors: Adam, J. A.; Cally, P. S.
Bibcode: 1983BAAS...15Q.706A
Altcode:
  No abstract at ADS

Title: Complex eigenvalue bounds in magnetoatmospheric shear flow. II
Authors: Cally, P. S.; Adam, J. A.
Bibcode: 1983GApFD..23...57C
Altcode:
  A method discussed in Paper I (Cally, 1983) for determining complex
  eigenvalue bounds for second-order ordinary differential systems
  is applied to an isothermal, perfectly conducting, compressible,
  stratified medium permeated by a horizontal magnetic field and aligned
  shear flow. The magnetic field is chosen such that the Alfvén velocity
  is everywhere constant. For this particular system, the eigenvalue
  bounds obtained are generally tighter than those obtained in Paper I,
  and an additional feature is that the bound on the maximum growth
  rate peaks at a finite value of horizontal wavenumber k, not as k ,
  as is found in Paper I.

Title: Complex eigenvalue bounds in magnetoatmospheric shear flow. I
Authors: Cally, P. S.
Bibcode: 1983GApFD..23...43C
Altcode:
  A general method is presented for deriving complex eigenvalue bounds for
  linear second order systems. It is applied to the problem of stratified
  horizontal magnetohydrodynamic shear flow, and it is found that, if the
  system is convectively stable, the imaginary part of the eigenfrequency
  is bounded by ½ú'0max, where u0 is the flow velocity. In the absence
  of a magnetic field, the classical Miles-Howard-Chimonas result is
  recovered, but with more detail about the growth rates of individual
  modes. These results are shown to hold for free as well as rigid
  boundaries.

Title: The equilibrium statistical mechanics of self-gravitating
    systems
Authors: Cally, P. S.
Bibcode: 1981AuJPh..34..267C
Altcode:
  The investigation of the exact statistical mechanics of self-gravitating
  systems presents certain difficulties, because of the long-range forces
  involved. The reported investigation is concerned with the equilibrium
  structure of a spherically confined system consisting of a large
  number of identical particles. One objective of the investigation
  is to verify that in the large N limit the thermodynamics and the
  distribution functions are as predicted by the continuum theory. This
  is of interest in connection with some doubt which may arise concerning
  the applicability of the conventional thermodynamic ideas to systems
  with long-range forces. The investigation shows that, at least for
  the system in a heat bath, the thermodynamics derived from statistical
  mechanics is equivalent to classical thermodynamics for the spherically
  symmetric self-gravitating system.

Title: Statistical mechanics and the gravothermal catastrophe.
Authors: Cally, P. S.; Monaghan, J. J.
Bibcode: 1981JMP....22..348C
Altcode: 1981JMaPh..22..348C
  Jensen's inequality is applied to the canonical partition function of
  a self-gravitating system to determine the best independent particle
  potential. The inequality allows the stability to be analyzed very
  easily. We recover the results of Lynden-Bell and Wood for the onset of
  an instability in an isothermal sphere in a heat bath. Our eigenvalue
  analysis leads to results very similar to those of Horwitz and Katz,
  but we differ in the description of the l=1 perturbation.

Title: Many body problems in astrophysics
Authors: Cally, Paul Stuart
Bibcode: 1979PhDT.......233C
Altcode:
  No abstract at ADS

