Tiago Pereira

• McKevitt, James; Matthews, Sarah; Brooks, David H.; Shimizu, Toshifumi; Tei, Akiko & Ugarte-Urra, Ignacio [Show all 22 contributors for this article] (2026). Pre-flare and active region plasma flows and structure seen by the short wavelength camera on SOLAR-C/EUVST. Publications of the Astronomical Society of Japan (PASJ). ISSN 0004-6264. 78(4), p. 1524–1545. doi: 10.1093/pasj/psag078. Full text in Research Archive Show summary

  The mechanisms triggering solar flares and driving coronal heating occur across wide temperature ranges on small spatial scales and short timescales, making them difficult to observe with current instrumentation. The upcoming SOLAR-C mission, launching in the late 2020s, will provide unprecedented plasma diagnostic capability with its high-throughput extreme-ultraviolet (EUV) spectroscopic telescope (EUVST), capable of 0.2 arcsec/pix spatial sampling (⁠~0.4 arcsec resolution), continuous temperature coverage from 0.02 to 15 MK, and exposure times down to 0.5 s. We present forward modelling of the spectrograph’s short wavelength camera (170.0–212.3 Å; SOLAR-C/EUVST-SW) and its response to log T ~ 6.2 coronal plasma in a three-dimensional MHD-simulated pre-flare active region. We compare this performance to that of the previous-generation EUV Imaging Spectrometer (EIS) on Hinode (SOLAR-B). Our results demonstrate that SOLAR-C/EUVST can distinguish individual flux tubes in simulated active region loops, which Hinode/EIS cannot resolve. In simulated pre-flare plasma, SOLAR-C/EUVST captures sharp velocity gradients between adjacent upflowing and downflowing plasma which Hinode/EIS is unable to resolve. Doppler velocity measurement accuracy will reach better than 1 km/s in active regions. We show that this next-generation spectrograph can be expected to directly observe processes potentially related to flare triggering, such as plasma flows from low-altitude reconnection linked to emerging flux, and determine whether active region loops consist of a small number of strands or the hundreds predicted by magnetic reconnection-induced nanoflare heating models.

• Chaurasiya, Ravi; Pereira, Tiago & Bayanna, Ankala Raja (2026). Multi-thermal dynamics and transverse oscillations of solar spicules revealed by coordinated SST, IRIS, and SDO observations. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 712. doi: 10.1051/0004-6361/202660406. Full text in Research Archive Show summary

  Context. Solar spicules are highly dynamic chromospheric jets that play an important role in the mass and energy balance of the solar atmosphere, even though their connection to the transition region and corona remains unclear. Aims. We investigated the dynamical and multi-thermal properties of spicules, their connection to higher atmospheric layers, and their transverse oscillations and associated energy flux. Methods. We analyzed coordinated high-resolution observations from the Swedish 1-m Solar Telescope in Hα, the Interface Region Imaging Spectrograph in Si IV 1400 Å, and the Solar Dynamics Observatory/Atmospheric Imaging Assembly coronal channels. Space-time diagrams, spectral analysis, and wavelet techniques were used to study temporal evolution, Doppler velocities, and oscillatory properties. Transverse displacements of spicules were tracked to estimate wave properties and energy flux. Results. Space-time analysis reveals a clear correspondence between chromospheric spicules and coronal emission in AIA 171 Å, evolving coherently with spicule extension. Doppler velocities from Hα and Si IV show opposite signs, indicating multi-thermal plasma flows. Wavelet analysis reveals frequently dominant ~3-minute oscillations, along with high-frequency transverse oscillations (65–270 s) with velocity amplitudes of 3.3–9.9 km s−1 and a mean energy flux of (2.14 ± 0.78) × 103 W m−2. Conclusions. These results demonstrate that spicules are multi-thermal dynamic structures connected to the transition region and corona and that transverse waves carry substantial energy, highlighting their role in coronal heating.

• Shields, Joshua V.; Kerzendorf, Wolfgang; Smith, Isaac G.; Pereira, Tiago; Vogl, Christian & Groneck, Ryan [Show all 10 contributors for this article] (2025). Introducing STARDIS: An Open and Modular Stellar Spectral Synthesis Code. The Astrophysical Journal (ApJ). ISSN 0004-637X. 990(1). doi: 10.3847/1538-4357/adee11. Full text in Research Archive Show summary

  We introduce a new 1D stellar spectral synthesis Python code called stardis . stardis is a modular, open-source radiative transfer code that is capable of spectral synthesis from near-UV to IR for FGK stars. We describe the structure, inputs, features, underlying physics, and assumptions of stardis , as well as the radiative transfer scheme implemented. To validate our code, we show spectral comparisons between stardis and korg with the same input atmospheric structure models, and we also compare qualitatively to phoenix for solar models. We find that stardis generally agrees with korg for solar models on the few-percent level or better, though the codes can diverge in the UV, with more extreme differences in cooler stars. stardis can be found at https://github.com/tardis-sn/stardis , and documentation can be found at https://tardis-sn.github.io/stardis/ .

• Mathur, Harsh; Joshi, Jayant; Moe, Thore Espedal; Pereira, Tiago & Nagaraju, K. (2025). The Hα Line as a Probe of Chromospheric Magnetic Fields. Astrophysical Journal Letters. ISSN 2041-8205. 987(2). doi: 10.3847/2041-8213/ade8ea. Full text in Research Archive Show summary

  We explore the diagnostic potential of the H α line for probing the chromospheric magnetic field using a realistic 3D radiative magnetohydrodynamic (rMHD) model. The Stokes profiles of the H α line are synthesized through full 3D radiative transfer under the field-free approximation, alongside the Ca ii 8542 Å and Fe i 6173 Å lines for comparison. The line-of-sight (LOS) magnetic fields are inferred using the weak-field approximation for the H α and Ca ii 8542 Å lines, while the Fe i 6173 Å line is analyzed through Milne-Eddington inversion techniques. The comparison between the inferred LOS magnetic field maps and the magnetic fields in the rMHD model revealed that the H α line core primarily probes the chromospheric magnetic field at log τ 500 = −5.7, which corresponds to higher layers than the Ca ii 8542 Å line core, which is most sensitive to conditions at log τ 500 = −5.1. On average, the Stokes V profiles of the H α line core form 500 km higher than those of the Ca ii 8542 Å line core. The H α polarization signals persist after adding noise, and with noise at the level of 10 −3 I c , most simulated magnetic structures remain visible. These findings suggest that spectropolarimetric observations of the H α line can provide complementary insights into the stratification of the magnetic field at higher altitudes, especially when recorded simultaneously with widely used chromospheric diagnostics such as the Ca ii 8542 Å line.

• Udnæs, Elias R. & Pereira, Tiago (2025). Characteristics of acoustic-wave heating in simulations of the quiet Sun chromosphere. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 699. doi: 10.1051/0004-6361/202453028. Full text in Research Archive Show summary

  Understanding energy transfer through the chromosphere is paramount to solving the coronal heating problem. We investigated the energy dissipation of acoustic waves in the chromosphere of the quiet Sun using 3D radiative magnetohydrodynamic (rMHD) simulations. We analysed the characteristics of acoustic-wave heating and its dependence on height and magnetic field configuration. We find the typical heights where acoustic waves steepen into shocks and the frequencies and wavenumbers that most efficiently dissipate wave energy through this steepening. We combined a comprehensive large-scale analysis, spanning the entirety of the simulations for several solar hours, with a detailed view of an individual shock. We find that the flux of propagating acoustic waves correlates closely with viscous dissipation in the chromosphere above the temperature minimum. Acoustic waves with frequencies close to the acoustic cut-off frequency can efficiently heat the quiet Sun chromosphere at the plasma- β  = 1 interface and play an important role in the chromospheric energy balance.

• Krikova, Kilian & Pereira, Tiago (2025). Small-scale energetic phenomena in Hϵ: Ellerman bombs, UV bursts, and small flares. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 695. doi: 10.1051/0004-6361/202453118. Full text in Research Archive Show summary

  Aims. We investigated the potential of using Hε to diagnose small-scale energetic phenomena such as Ellerman bombs, UV bursts, and small-scale flares. Our focus is to understand the formation of the line and how to use its properties to get insight into the dynamics of small-scale energetic phenomena. Methods. We carried out a forward modeling study, combining simulations and detailed radiative transfer calculations. The 3D radiative magnetohydrodynamic simulations were run with the Bifrost code and included energetic phenomena. We employed a Markovian framework to study the Hε multilevel source function, used relative contribution functions to identify its formation regions, and correlated the properties of synthetic spectra with atmospheric parameters. Results. Ellerman bombs are predominantly optically thick in Hε, appearing as well-defined structures. UV bursts and small flares are partially optically thin and give rise to diffuse structures. The Hε line serves as a good velocity diagnostic for small-scale heating events in the lower chromosphere. However, its emission strength is a poor indicator of temperature, and its line width offers limited utility due to the interplay of various broadening mechanisms. Compared to Hα, Hε exhibits greater sensitivity to phenomena such as Ellerman bombs, as its line core experiences higher extinction than the Hα wing. Conclusions. Hε is a valuable tool for studying small-scale energetic phenomena in the lower chromosphere. It provides more reliable estimates of velocities than those extracted from wing emission in Hα or Hβ. Maps of Hε emission show more abundant energetic events than the Hα counterpart. Our findings highlight Hε’s potential to advance our understanding of dynamic processes in the solar atmosphere.

• Chaurasiya, Ravi; Bayanna, A. Raja; Louis, R.E.; Pereira, Tiago & Mathew, S.K. (2024). On the Response of the Transition Region and the Corona to Rapid Excursions in the Chromosphere. The Astrophysical Journal (ApJ). ISSN 0004-637X. 970(2). doi: 10.3847/1538-4357/ad50d5. Full text in Research Archive Show summary

  Spicules are the thin hair/grass-like structures that are prominently observed at the chromospheric solar limb. It is believed that fibrils and rapid blueshifted and redshifted excursions (RBEs and RREs; collectively referred to as REs) correspond to on-disk counterparts of type I spicules and type II spicules, respectively. Our investigation focuses on observing the response of these REs alongside similar spectral features in the chromosphere, transition region (TR), and corona, utilizing space–time plots derived from coordinated observations from the Swedish 1 m Solar Telescope/Hα, Interface Region Imaging Spectrograph (IRIS), and Solar Dynamics Observatory. Our analysis reveals upflowing REs, promptly reaching temperatures characteristic of the TR and corona, indicating a multithermal nature. Similarly, downflowing features exhibiting similar spectral signatures over the disk display plasma motion from the corona to chromospheric temperatures, demonstrating a multithermal nature. In addition to distinct upflows and downflows, we observe sequential upflow and downflow along the same path, depicting a distinctive parabolic trajectory in space–time plots of observations sampling TR and various coronal passbands. Similar to isolated upflows and downflows, these REs also exhibit a multithermal nature throughout their trajectory. Furthermore, our results reveal a more intricate motion of the REs in which both upflow and downflow coexist at the same spatial location. On a different note, our analysis, utilizing coordinated IRIS spectral observations, shows spatiotemporal redshifts/downflows in both the TR and chromosphere, suggesting that at least subsets of the strong redshifts/downflows observed in TR temperature spectra result from the return from the upper atmosphere flow of plasma in the form of bundles of spicules or features exhibiting similar spectra.

• Moe, Thore Espedal; Pereira, Tiago; Voort, Luc Rouppe van der; Carlsson, Mats; Hansteen, Viggo Haraldson & Calvo, Flavio [Show all 7 contributors for this article] (2024). Comparative clustering analysis of Ca II 854.2 nm spectral profiles from simulations and observations. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 682. doi: 10.1051/0004-6361/202347328. Full text in Research Archive Show summary

  Context. Synthetic spectra from 3D models of the solar atmosphere have become increasingly successful at reproducing observations, but there are still some outstanding discrepancies for chromospheric spectral lines, such as Ca II and Mg II , particularly regarding the width of the line cores. It has been demonstrated that using sufficiently high spatial resolution in the simulations significantly diminishes the differences in width between the mean spectra in observations and simulations, but a detailed investigation into how this impacts subgroups of individual profiles is currently lacking. Aims. We compare and contrast the typical shapes of synthetic Ca II 854.2 nm spectra found in Bifrost simulations having different magnetic activity with the spectral shapes found in a quiet-Sun observation from the Swedish 1-m Solar Telescope (SST). Methods. We used clustering techniques to extract the typical Ca II 854.2 nm profile shapes synthesized from Bifrost simulations with varying amounts of magnetic activity. We degraded the synthetic profiles to observational conditions and repeated the clustering, and we compared our synthetic results with actual observations. Subsequently, we examined the atmospheric structures in our models for some select sets of clusters, with the intention of uncovering why they do or do not resemble actual observations. Results. While the mean spectra for our high resolution simulations compare reasonably well with the observations, we find that there are considerable differences between the clusters of observed and synthetic intensity profiles, even after the synthetic profiles have been degraded to match observational conditions. The typical absorption profiles from the simulations are both narrower and display a steeper transition from the inner wings to the line core. Furthermore, even in our most quiescent simulation, we find a far larger fraction of profiles with local emission around the core, or other exotic profile shapes, than in the quiet-Sun observations. Looking into the atmospheric structure for a selected set of synthetic clusters, we find distinct differences in the temperature stratification for the clusters most and least similar to the observations. The narrow and steep profiles are associated with either weak gradients in temperature or temperatures rising to a local maximum in the line wing forming region before sinking to a minimum in the line core forming region. The profiles that display less steep transitions show extended temperature gradients that are steeper in the range−3 ≲ log τ 5000 ≲ −1.

• Krikova, Kilian & Pereira, Tiago (2024). A Markovian description of the multi-level source function and its application to the Lyman series in the Sun. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 689. doi: 10.1051/0004-6361/202450506. Full text in Research Archive Show summary

  Aims. We introduce a new method to calculate and interpret indirect transition rates populating atomic levels using Markov chain theory. Indirect transition rates are essential to evaluate interlocking in a multi-level source function, which quantifies all the processes that add and remove photons from a spectral line. A better understanding of the multi-level source function is central to interpret optically thick spectral line formation in stellar atmospheres, especially outside local thermodynamical equilibrium (LTE). Methods. We compute the level populations from a hydrogen model atom in statistical equilibrium, using the solar FALC model, a 1D static atmosphere. From the transition rates, we reconstruct the multi-level source function using our new method and compare it with existing methods to build the source function. We focus on the Lyman series lines and analyze the different contributions to the source functions and synthetic spectra. Results. Absorbing Markov chains can represent the level-ratio solution of the statistical equilibrium equation and can therefore be used to calculate the indirect transition rates between the upper and lower levels of an atomic transition. Our description of the multi-level source function allows a more physical interpretation of its individual terms, particularly a quantitative view of interlocking. For the Lyman lines in the FALC atmosphere, we find that interlocking becomes increasingly important with order in the series, with Ly-α showing very little, but Ly-β nearly 50% and Ly-γ about 60% contribution coming from interlocking. In some cases, this view seems opposed to the conventional wisdom that these lines are mostly scattering, and we discuss the reasons why. Conclusions. Our formalism to describe the multi-level source function is general and can provide more physical insight into the processes that set the line source function in a multi-level atom. The effects of interlocking for lines formed in the solar chromosphere can be more important than previously thought, and our method provides the basis for further exploration.

• Krikova, Kilian; Pereira, Tiago & Voort, Luc Rouppe van der (2023). Formation of Hϵ in the solar atmosphere. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 677. doi: 10.1051/0004-6361/202346796. Full text in Research Archive Show summary

  Context. In the solar spectrum, the Balmer series line H ε is a weak blend on the wing of Ca  II H. Recent high-resolution H ε spectroheliograms reveal a reversed granulation pattern and in some cases, even unique structures. It is apparent that H ε could potentially be a useful diagnostic tool for the lower solar atmosphere. Aims. Our aim is to understand how H ε is formed in the quiet Sun. In particular, we consider the particular physical mechanism that sets its source function and extinction, how it is formed in different solar structures, and why it is sometimes observed in emission. Methods. We used a 3D radiative magnetohydrodynamic (MHD) simulation that accounts for non-equilibrium hydrogen ionization, run with the Bifrost code. To synthesize H ε and Ca  II H spectra, we made use of the RH code, which was modified to take into account the non-equilibrium hydrogen ionization. To determine the dominant terms in the H ε source function, we adopted a multi-level description of the source function. Making use of the synthetic spectra and simulation, we studied the contribution function to the relative line absorption or emission and compared it with atmospheric quantities at different locations. Results. Our multi-level source function description suggests that the H ε source function is dominated by interlocking, with the dominant interlocking transition being through the ground level, populating the upper level of H ε via the Lyman series. This makes the H ε source function partly sensitive to temperature. The H ε extinction is set by Lyman- α . In some cases, this temperature dependence gives rise to H ε emission, indicating heating. The typical absorption profiles show reversed granulation and the H ε line core reflects mostly the Ca  II H background radiation. Conclusions. Synthetic H ε spectra can reproduce quiet Sun observations quite well. High-resolution observations reveal that H ε is not just a weak absorption line. Regions with H ε in emission are especially interesting to detect small-scale heating events in the lower solar atmosphere, such as Ellerman bombs. Thus, H ε can be an important new diagnostic tool for studies of heating in the solar atmosphere, augmenting the diagnostic potential of Ca  II H when observed simultaneously.

• Udnæs, Elias Roland & Pereira, Tiago (2023). Irregular grids for 3D NLTE radiative transfer in stellar atmospheres. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 675. doi: 10.1051/0004-6361/202346760. Full text in Research Archive Show summary

  Context . Three-dimensional non-local thermodynamical equilibrium (NLTE) radiative transfer calculations are a fundamental tool for a detailed spectral analysis in stellar atmospheres, but require vast amounts of computer power. This prevents their broader application. Aims . We undertake a first exploration of the use of 3D irregular grids in stellar atmospheres. In particular, we aim to test whether irregular grids can be used to speed up the 3D NLTE problem, in the same way as depth optimisation can lead to faster running times in 1D. Methods . We created irregular grids based on 3D Voronoi diagrams, sampling different distributions from a 3D radiation-magnetohydrodynamic Bifrost simulation. We developed a method for solving radiation on the 3D irregular grid and implemented a simple NLTE solver using Λ-iteration and statistical equilibrium. We applied this to a simplified hydrogen-like atom and studied the convergence properties and accuracy of the irregular grid methods. For reference, we compared them to a standard short-characteristics solver on a regular grid. Results . We find that our method for radiation in irregular grids gives similar results to those from regular grids, and that it is possible to obtain nearly the same results with about ten times fewer points in the irregular grid for the continuum intensity in local thermo-dynamical equilibrium. We find that the irregular grid can give good results for the NLTE problem, but it takes four times longer per iteration than the regular grid, and it converges in about the same number of iterations. This makes it particularly inefficient. Our formulation therefore does not lead to an improvement. We also find that the design of the irregular grid is crucial for accurate results, and find it non-trivial to design an irregular grid that can work well across a wide range of heights.

• Moe, Thore Espedal; Pereira, Tiago; Calvo, Flavio & Leenaarts, Jorrit (2023). Shape-based clustering of synthetic Stokes profiles using k-means and k-Shape. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 675. doi: 10.1051/0004-6361/202346724. Full text in Research Archive Show summary

  Context. The shapes of Stokes profiles contain a great deal of information about the atmospheric conditions that produced them. However, a variety of different atmospheric structures can produce very similar profiles. Thus, it is important for a proper interpretation of the observations to have a good understanding of how the shapes of Stokes profiles depend on the underlying atmosphere. An excellent tool in this regard is forward modeling, namely, computing and studying synthetic spectra from realistic simulations of the solar atmosphere. Modern simulations routinely produce several hundred thousand spectral profiles per snapshot. With such numbers, it becomes necessary to use automated procedures in order to organize the profiles according to their shape. Here, we illustrate the use of two complementary methods, k -means and k -Shape, to cluster similarly shaped profiles and demonstrate how the resulting clusters can be combined with knowledge of the simulation’s atmosphere to interpret spectral shapes. Aims. We aim to showcase the use of clustering analysis for forward modeling. In particular, we wish to introduce the k -Shape clustering method to the solar physics community as a complement to the well-known k -means method. Methods. We generated synthetic Stokes profiles for the Ca  II 854.2 nm line using the Multi3D code from a Bifrost simulation snapshot. We then applied the k -means and k -Shape clustering techniques to group the profiles together according to their shape and investigated the within-group correlations of temperature, line-of-sight velocity, and line-of-sight magnetic field strengths. Results. We show and compare the classes of profile shapes we retrieved from applying both k -means and k -Shape to our synthetic intensity spectra. We then show the structure of the underlying atmosphere for two particular classes of profile shapes retrieved by the clustering and demonstrate how this leads to an interpretation for the formation of those profile shapes. We applied both methods to the subset of our profiles containing the strongest Stokes V signals and we demonstrate how k -Shape can be qualitatively better than k -means at retrieving complex profile shapes when using a small number of clusters.

• Moe, Thore Espedal; Pereira, Tiago & Carlsson, Mats (2022). Effects of spatial resolution on inferences of atmospheric quantities from simulations. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 662. doi: 10.1051/0004-6361/202243192. Full text in Research Archive Show summary

  Context. Small-scale processes are thought to be important for the dynamics of the solar atmosphere. While numerical resolution fundamentally limits their inclusion in magnetohydronamic (MHD) simulations, real observations at the same nominal resolution should still contain imprints of subresolution effects. This means that the synthetic observables from a simulation of a given resolution might not be directly comparable to real observables at the same resolution. It is thus of interest to investigate how inferences based on synthetic spectra from simulations with different numerical resolutions compare, and whether these differences persist after the spectra have been spatially degraded to a common resolution Aims. We aim to compare synthetic spectra obtained from realistic 3D radiative magnetohydrodynamic (rMHD) simulations run at different numerical resolutions from the same initial atmosphere, using very simple methods for inferring line-of-sight velocities and magnetic fields. Additionally we examine how the differing spatial resolution impacts the results retrieved from the STiC inversion code. Methods. We used the RH 1.5D code to synthesize the photospheric Fe  I 617.33 line in local thermodynamic equilibrium (LTE), and the chromospheric Ca  II 854.209 line in non-LTE from three MHD simulation snapshots of differing spatial resolution. The simulations were produced by the Bifrost code, using horizontal grid spacing of 6 km, 12 km, and 23 km, respectively. They were started from the exact same atmosphere, and the snapshots were taken after the same exact elapsed time. The spectra obtained from the high-resolution snapshots were spatially degraded to match the lowest resolution. Simple methods, such as the center-of-gravity approach and the weak field approximation, were then used to estimate line-of-sight velocities and magnetic fields for the three cases after degradation. Finally, the spectra were input into the STiC inversion code and the retrieved line-of-sight velocities and magnetic field strengths, as well as the temperatures, from the inversions were compared. Results. We find that while the simple inferences for all three simulations reveal the same large-scale tendencies, the higher resolutions yield more fine-grained structures and more extreme line-of-sight velocities and magnetic fields in concentrated spots even after spatial smearing. We also see indications that the imprints of subresolution effects on the degraded spectra result in systematic errors in the inversions, and that these errors increase with the amount of subresolution effects included. Fortunately, however, we find that successively including more subresolution yields smaller additional effects; that is to say, there is a clear trend of diminishing importance for progressively finer subresolution effects.

• Chappell, Bruce Arnold & Pereira, Tiago (2022). SunnyNet: A neural network approach to 3D non-LTE radiative transfer. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 658. doi: 10.1051/0004-6361/202142625. Full text in Research Archive Show summary

  Context. Computing spectra from 3D simulations of stellar atmospheres when allowing for departures from local thermodynamic equilibrium (non-LTE) is computationally very intensive. Aims. We develop a machine learning based method to speed up 3D non-LTE radiative transfer calculations in optically thick stellar atmospheres. Methods. Making use of a variety of 3D simulations of the solar atmosphere, we trained a convolutional neural network, SunnyNet, to learn the translation from LTE to non-LTE atomic populations. Non-LTE populations computed with an existing 3D code were considered as the true values. The network was then used to predict non-LTE populations for other 3D simulations, and synthetic spectra were computed from its predicted non-LTE populations. We used a six-level model atom of hydrogen and H α spectra as test cases. Results. SunnyNet gives reasonable predictions for non-LTE populations with a dramatic speedup of about 10 5 times when running on a single GPU and compared to existing codes. When using different snapshots of the same simulation for training and testing, SunnyNet’s predictions are within 20–40% of the true values for most points, which results in average differences of a few percent in H α spectra. Predicted H α intensity maps agree very well with existing codes. Most importantly, they show the telltale signs of 3D radiative transfer in the morphology of chromospheric fibrils. The results are not as reliable when the training and testing are done with different families of simulations. SunnyNet is open source and publicly available.

• Schmit, Don; Martinez-Sykora, Juan; Pereira, Tiago & Ramos, Andrés Asensio (2021). Probing Uncertainties in Diagnostics of a Synthetic Chromosphere. The Astrophysical Journal (ApJ). ISSN 0004-637X. 913(1). doi: 10.3847/1538-4357/abf4d2. Full text in Research Archive
• Haberreiter, Margit; Criscuoli, Serena; Rempel, M. & Pereira, Tiago (2021). Solar atmosphere radiative transfer model comparison based on 3D MHD simulations. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 653. doi: 10.1051/0004-6361/202039237. Full text in Research Archive Show summary

  Context. The reconstruction of the solar spectral irradiance (SSI) on various time scales is essential for the understanding of the Earth’s climate response to the SSI variability. Aims. The driver of the SSI variability is understood to be the intensity contrast of magnetic features present on the Sun with respect to the largely non-magnetic quiet Sun. However, different spectral synthesis codes lead to diverging projections of SSI variability. In this study we compare three different radiative transfer codes and carry out a detailed analysis of their performance. Methods. We perform the spectral synthesis at the continuum wavelength of 665 nm with the Code for Solar Irradiance, and the Rybicki-Hummer, and Max Planck University of Chicago Radiative MHD codes for three 3D MHD simulations snapshots, a non-magnetic case, and MHD simulations with 100 G, and 200 G magnetic field strength. Results. We determine the intensity distributions, the intensity differences and ratios for the spectral synthesis codes. We identify that the largest discrepancies originate in the intergranular lanes where the most field concentration occurs. Conclusions. Overall, the applied radiative transfer codes give consistent intensity distributions. Also, the intensity variation as a function of magnetic field strength for the particular 100 G and 200 G snapshots agree within the 2–3% range.

• Criscuoli, Serena; Rempel, Matthias; Haberreiter, Margit; Pereira, Tiago Mendes Domingos; Uitenbroek, Han & Fabbian, Damian (2020). Comparing Radiative Transfer Codes and Opacity Samplings for Solar Irradiance Reconstructions. Solar Physics. ISSN 0038-0938. 295(3). doi: 10.1007/s11207-020-01614-2. Full text in Research Archive
• Barnes, Will T.; Bobra, Monica G; Christe, Steven D; Freij, N.; Hayes, Laura A. & Ireland, Jack [Show all 34 contributors for this article] (2020). The SunPy Project: Open Source Development and Status of the Version 1.0 Core Package. The Astrophysical Journal (ApJ). ISSN 0004-637X. 890(1). doi: 10.3847/1538-4357/ab4f7a. Full text in Research Archive Show summary

  The goal of the SunPy project is to facilitate and promote the use and development of community-led, free, and open source data analysis software for solar physics based on the scientific Python environment. The project achieves this goal by developing and maintaining the sunpy core package and supporting an ecosystem of affiliated packages. This paper describes the first official stable release (version 1.0) of the core package, as well as the project organization and infrastructure. This paper concludes with a discussion of the future of the SunPy project.

• Bobra, Monica G; Mumford, Stuart J; Hewett, Russell J; Christe, Steven D; Reardon, Kevin P. & Savage, Sabrina L. [Show all 10 contributors for this article] (2020). A Survey of Computational Tools in Solar Physics. Solar Physics. ISSN 0038-0938. 295(4). doi: 10.1007/s11207-020-01622-2. Full text in Research Archive Show summary

  The SunPy Project developed a 13-question survey to understand the software and hardware usage of the solar-physics community. Of the solar-physics community, 364 members across 35 countries responded to our survey. We found that 99±0.5% of respondents use software in their research and 66% use the Python scientific-software stack. Students are twice as likely as faculty, staff scientists, and researchers to use Python rather than Interactive Data Language (IDL). In this respect, the astrophysics and solar-physics communities differ widely: 78% of solar-physics faculty, staff scientists, and researchers in our sample uses IDL, compared with 44% of astrophysics faculty and scientists sampled by Momcheva and Tollerud (2015). 63±4% of respondents have not taken any computer-science courses at an undergraduate or graduate level. We also found that most respondents use consumer hardware to run software for solar-physics research. Although 82% of respondents work with data from space-based or ground-based missions, some of which (e.g. the Solar Dynamics Observatory and Daniel K. Inouye Solar Telescope) produce terabytes of data a day, 14% use a regional or national cluster, 5% use a commercial cloud provider, and 29% use exclusively a laptop or desktop. Finally, we found that 73±4% of respondents cite scientific software in their research, although only 42±3% do so routinely.

• Voort, Luc Rouppe van der; Pontieu, Bart Walter De; Carlsson, Mats; Rodriguez, Jaime de la Cruz; Bose, Souvik & Chintzoglou, Georgios [Show all 33 contributors for this article] (2020). High-resolution observations of the solar photosphere, chromosphere, and transition region: A database of coordinated IRIS and SST observations. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 641. doi: 10.1051/0004-6361/202038732. Full text in Research Archive Show summary

  NASA’s Interface Region Imaging Spectrograph (IRIS) provides high-resolution observations of the solar atmosphere through ultraviolet spectroscopy and imaging. Since the launch of IRIS in June 2013, we have conducted systematic observation campaigns in coordination with the Swedish 1 m Solar Telescope (SST) on La Palma. The SST provides complementary high-resolution observations of the photosphere and chromosphere. The SST observations include spectropolarimetric imaging in photospheric Fe  I lines and spectrally resolved imaging in the chromospheric Ca  II 8542 Å, H α , and Ca  II K lines. We present a database of co-aligned IRIS and SST datasets that is open for analysis to the scientific community. The database covers a variety of targets including active regions, sunspots, plages, the quiet Sun, and coronal holes.

• Bose, Souvik; Henriques, Vasco Manuel de Jorge; Voort, Luc Rouppe van der & Pereira, Tiago Mendes Domingos (2019). Semi-empirical model atmospheres for the chromosphere of the sunspot penumbra and umbral flashes. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 627. doi: 10.1051/0004-6361/201935289. Full text in Research Archive Show summary

  Context: The solar chromosphere and the lower transition region are believed to play a crucial role in the heating of the solar corona. Models that describe the chromosphere (and the lower transition region), accounting for its highly dynamic and structured character are, so far, found to be lacking. This is partly due to the breakdown of complete frequency redistribution (CRD) in the chromospheric layers and also because of the difficulty in obtaining complete sets of observations that adequately constrain the solar atmosphere at all relevant heights. Aims: We aim to obtain semi-empirical model atmospheres that reproduce the features of the Mg II h&k line profiles that sample the middle chromosphere with focus on a sunspot. Methods: We used spectropolarimetric observations of the Ca II 8542 Å spectra obtained with the Swedish 1 m Solar Telescope and used NICOLE inversions to obtain semi-empirical model atmospheres for different features in and around a sunspot. These were used to synthesize Mg II h&k spectra using the RH1.5D code, which we compared with observations taken with the Interface Region Imaging Spectrograph (IRIS). Results: Comparison of the synthetic profiles with IRIS observations reveals that there are several areas, especially in the penumbra of the sunspot, where most of the observed Mg II h&k profiles are very well reproduced. In addition, we find that supersonic hot down-flows, present in our collection of models in the umbra, lead to synthetic profiles that agree well with the IRIS Mg II h&k profiles, with the exception of the line core. Conclusions: We put forward and make available four semi-empirical model atmospheres. Two for the penumbra, reflecting the range of temperatures obtained for the chromosphere, one for umbral flashes, and a model representative of the quiet surroundings of a sunspot.

• Hansteen, Viggo; Ortiz, Ada; Archontis, Vasilis; Carlsson, Mats; Pereira, Tiago Mendes Domingos & Bjørgen, Johan Pires (2019). Ellerman bombs and UV bursts: transient events in chromospheric current sheets. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 626. doi: 10.1051/0004-6361/201935376. Full text in Research Archive Show summary

  Context: Ellerman bombs (EBs), observed in the photospheric wings of the Hα line, and UV bursts, observed in the transition region Si IV line, are both brightenings related to flux emergence regions and specifically to magnetic flux of opposite polarity that meet in the photosphere. These two reconnection-related phenomena, nominally formed far apart, occasionally occur in the same location and at the same time, thus challenging our understanding of reconnection and heating of the lower solar atmosphere. Aims: We consider the formation of an active region, including long fibrils and hot and dense coronal plasma. The emergence of a untwisted magnetic flux sheet, injected 2.5 Mm below the photosphere, is studied as it pierces the photosphere and interacts with the preexisting ambient field. Specifically, we aim to study whether EBs and UV bursts are generated as a result of such flux emergence and examine their physical relationship. Methods: The Bifrost radiative magnetohydrodynamics code was used to model flux emerging into a model atmosphere that contained a fairly strong ambient field, constraining the emerging field to a limited volume wherein multiple reconnection events occur as the field breaks through the photosphere and expands into the outer atmosphere. Synthetic spectra of the different reconnection events were computed using the 1.5D RH code and the fully 3D MULTI3D code. Results: The formation of UV bursts and EBs at intensities and with line profiles that are highly reminiscent of observed spectra are understood to be a result of the reconnection of emerging flux with itself in a long-lasting current sheet that extends over several scale heights through the chromosphere. Synthetic spectra in the Hα and Si IV 139.376 nm lines both show characteristics that are typical of the observations. These synthetic diagnostics suggest that there are no compelling reasons to assume that UV bursts occur in the photosphere. Instead, EBs and UV bursts are occasionally formed at opposite ends of a long current sheet that resides in an extended bubble of cool gas.

• Al-Janabi, Khalid; Antolin, Patrick; Baker, Deborah; Rubio, Luis R. Bellot; Bradley, Louisa & Brooks, David H. [Show all 35 contributors for this article] (2019). Achievements of Hinode in the first eleven years. Publications of the Astronomical Society of Japan (PASJ). ISSN 0004-6264. 71:R1(5), p. 1–118. doi: 10.1093/pasj/psz084. Full text in Research Archive Show summary

  Hinode is Japan’s third solar mission following Hinotori (1981–1982) and Yohkoh (1991–2001): it was launched on 2006 September 22 and is in operation currently. Hinode carries three instruments: the Solar Optical Telescope, the X-Ray Telescope, and the EUV Imaging Spectrometer. These instruments were built under international collaboration with the National Aeronautics and Space Administration and the UK Science and Technology Facilities Council, and its operation has been contributed to by the European Space Agency and the Norwegian Space Center. After describing the satellite operations and giving a performance evaluation of the three instruments, reviews are presented on major scientific discoveries by Hinode in the first eleven years (one solar cycle long) of its operation. This review article concludes with future prospects for solar physics research based on the achievements of Hinode.

• Chintzoglou, G.; Pontieu, Bart Walter De; Martinez-Sykora, Juan; Pereira, Tiago Mendes Domingos; Vourlidas, A. & Beltran, Samuel Tun (2018). Bridging the gap: Capturing the Lyα Counterpart of a Type-II Spicule and its Heating Evolution with VAULT2.0 and IRIS Observations. The Astrophysical Journal (ApJ). ISSN 0004-637X. 857(1). doi: 10.3847/1538-4357/aab607. Full text in Research Archive Show summary

  We present results from an observing campaign in support of the VAULT2.0 sounding rocket launch on 2014 September 30. VAULT2.0 is a Lyα (1216 Å) spectroheliograph capable of providing spectroheliograms at high cadence. Lyα observations are highly complementary to the IRIS observations of the upper chromosphere and the low transition region (TR) but have previously been unavailable. The VAULT2.0 data provide new constraints on upper-chromospheric conditions for numerical models. The observing campaign was closely coordinated with the IRIS mission. Taking advantage of this simultaneous multi-wavelength coverage of target AR 12172 and by using state-of-the-art radiative-MHD simulations of spicules, we investigate in detail a type-II spicule associated with a fast (300 km s−1) network jet recorded in the campaign observations. Our analysis suggests that spicular material exists suspended high in the atmosphere but at lower temperatures (seen in Lyα) until it is heated and becomes visible in TR temperatures as a network jet. The heating begins lower in the spicule and propagates upwards as a rapidly propagating thermal front. The front is then observed as fast, plane-of-the-sky motion typical of a network jet, but contained inside the pre-existing spicule. This work supports the idea that the high speeds reported in network jets should not be taken as real mass upflows but only as apparent speeds of a rapidly propagating heating front along the pre-existing spicule.

• Pereira, Tiago Mendes Domingos; Voort, Luc Rouppe van der; Hansteen, Viggo & Pontieu, Bart Walter De (2018). Chromospheric counterparts of solar transition region unresolved fine structure loops. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 611. doi: 10.1051/0004-6361/201832762. Full text in Research Archive Show summary

  Low-lying loops have been discovered at the solar limb in transition region temperatures by the Interface Region Imaging Spectrograph (IRIS). They do not appear to reach coronal temperatures, and it has been suggested that they are the long-predicted unresolved fine structures (UFS). These loops are dynamic and believed to be visible during both heating and cooling phases. Making use of coordinated observations between IRIS and the Swedish 1-m Solar Telescope, we study how these loops impact the solar chromosphere. We show for the first time that there is indeed a chromospheric signal of these loops, seen mostly in the form of strong Doppler shifts and a conspicuous lack of chromospheric heating. In addition, we find that several instances have a inverse Y-shaped jet just above the loop, suggesting that magnetic reconnection is driving these events. Our observations add several puzzling details to the current knowledge of these newly discovered structures; this new information must be considered in theoretical models. © 2018 ESO

• Antolin, Patrick; Schmit, D.; Pereira, Tiago Mendes Domingos; Pontieu, Bart Walter De & Moortel, I. De (2018). Transverse Wave Induced Kelvin-Helmholtz Rolls in Spicules. The Astrophysical Journal (ApJ). ISSN 0004-637X. 856(1). doi: 10.3847/1538-4357/aab34f. Full text in Research Archive Show summary

  In addition to their jet-like dynamic behavior, spicules usually exhibit strong transverse speeds, multi-stranded structure, and heating from chromospheric to transition region temperatures. In this work we first analyze Hinode and IRIS observations of spicules and find different behaviors in terms of their Doppler velocity evolution and collective motion of their sub-structure. Some have a Doppler shift sign change that is rather fixed along the spicule axis, and lack coherence in the oscillatory motion of strand-like structure, matching rotation models, or long-wavelength torsional Alfvén waves. Others exhibit a Doppler shift sign change at maximum displacement and coherent motion of their strands, suggesting a collective magnetohydrodynamic (MHD) wave. By comparing with an idealized 3D MHD simulation combined with radiative transfer modeling, we analyze the role of transverse MHD waves and associated instabilities in spicule-like features. We find that transverse wave induced Kelvin–Helmholtz (TWIKH) rolls lead to coherence of strand-like structure in imaging and spectral maps, as seen in some observations. The rapid transverse dynamics and the density and temperature gradients at the spicule boundary lead to ring-shaped Mg ii k and Ca ii H source functions in the transverse cross-section, potentially allowing IRIS to capture the Kelvin–Helmholtz instability dynamics. Twists and currents propagate along the spicule at Alfvénic speeds, and the temperature variations within TWIKH rolls, produce the sudden appearance/disappearance of strands seen in Doppler velocity and in Ca ii H intensity. However, only a mild intensity increase in higher-temperature lines is obtained, suggesting there is an additional heating mechanism at work in spicules.

• Pereira, Tiago Mendes Domingos (2018). The dynamic chromosphere: Pushing the boundaries of observations and models. Advances in Space Research. ISSN 0273-1177. p. 1–9. doi: 10.1016/j.asr.2018.09.030. Full text in Research Archive
• Polito, V.; Testa, Paola; Allred, J.; Pontieu, Bart Walter De; Carlsson, Mats & Pereira, Tiago Mendes Domingos [Show all 8 contributors for this article] (2018). Investigating the Response of Loop Plasma to Nanoflare Heating Using RADYN Simulations. The Astrophysical Journal (ApJ). ISSN 0004-637X. 856(2). doi: 10.3847/1538-4357/aab49e. Full text in Research Archive Show summary

  We present the results of 1D hydrodynamic simulations of coronal loops that are subject to nanoflares, caused by either in situ thermal heating or nonthermal electron (NTE) beams. The synthesized intensity and Doppler shifts can be directly compared with Interface Region Imaging Spectrograph (IRIS) and Atmospheric Imaging Assembly (AIA) observations of rapid variability in the transition region (TR) of coronal loops, associated with transient coronal heating. We find that NTEs with high enough low-energy cutoff (${E}_{{\rm{C}}}$) deposit energy in the lower TR and chromosphere, causing blueshifts (up to ~20 km s−1) in the IRIS Si iv lines, which thermal conduction cannot reproduce. The ${E}_{{\rm{C}}}$ threshold value for the blueshifts depends on the total energy of the events (≈5 keV for 1024 erg, up to 15 keV for 1025 erg). The observed footpoint emission intensity and flows, combined with the simulations, can provide constraints on both the energy of the heating event and ${E}_{{\rm{C}}}$. The response of the loop plasma to nanoflares depends crucially on the electron density: significant Si iv intensity enhancements and flows are observed only for initially low-density loops (<109 cm−3). This provides a possible explanation of the relative scarcity of observations of significant moss variability. While the TR response to single heating episodes can be clearly observed, the predicted coronal emission (AIA 94 Å) for single strands is below current detectability and can only be observed when several strands are heated closely in time. Finally, we show that the analysis of the IRIS Mg ii chromospheric lines can help further constrain the properties of the heating mechanisms.

• Voort, Luc Rouppe van der; Pontieu, Bart Walter De; Scharmer, G. B.; Rodriguez, Jaime de la Cruz; Martinez-Sykora, Juan & Nobrega-Siverio, Daniel [Show all 12 contributors for this article] (2017). Intermittent Reconnection and Plasmoids in UV Bursts in the Low Solar Atmosphere. Astrophysical Journal Letters. ISSN 2041-8205. 851(1). doi: 10.3847/2041-8213/aa99dd. Full text in Research Archive Show summary

  Magnetic reconnection is thought to drive a wide variety of dynamic phenomena in the solar atmosphere. Yet, the detailed physical mechanisms driving reconnection are difficult to discern in the remote sensing observations that are used to study the solar atmosphere. In this Letter, we exploit the high-resolution instruments Interface Region Imaging Spectrograph and the new CHROMIS Fabry–Pérot instrument at the Swedish 1-m Solar Telescope (SST) to identify the intermittency of magnetic reconnection and its association with the formation of plasmoids in so-called UV bursts in the low solar atmosphere. The Si iv 1403 Å UV burst spectra from the transition region show evidence of highly broadened line profiles with often non-Gaussian and triangular shapes, in addition to signatures of bidirectional flows. Such profiles had previously been linked, in idealized numerical simulations, to magnetic reconnection driven by the plasmoid instability. Simultaneous CHROMIS images in the chromospheric Ca ii K 3934 Å line now provide compelling evidence for the presence of plasmoids by revealing highly dynamic and rapidly moving brightenings that are smaller than 0farcs2 and that evolve on timescales of the order of seconds. Our interpretation of the observations is supported by detailed comparisons with synthetic observables from advanced numerical simulations of magnetic reconnection and associated plasmoids in the chromosphere. Our results highlight how subarcsecond imaging spectroscopy sensitive to a wide range of temperatures combined with advanced numerical simulations that are realistic enough to compare with observations can directly reveal the small-scale physical processes that drive the wide range of phenomena in the solar atmosphere. © 2017. The American Astronomical Society. All rights reserved.

• Lind, K.; Amarsi, A. M.; Asplund, M.; Barklem, P. S.; Bautista, M. & Bergemann, M. [Show all 10 contributors for this article] (2017). Non-LTE line formation of Fe in late-type stars – IV. Modelling of the solar centre-to-limb variation in 3D. Monthly notices of the Royal Astronomical Society. ISSN 0035-8711. 468(4), p. 4311–4322. doi: 10.1093/mnras/stx673. Full text in Research Archive Show summary

  Our ability to model the shapes and strengths of iron lines in the solar spectrum is a critical test of the accuracy of the solar iron abundance, which sets the absolute zero-point of all stellar metallicities. We use an extensive 463-level Fe atom with new photoionization cross-sections for Fe i and quantum mechanical calculations of collisional excitation and charge transfer with neutral hydrogen; the latter effectively remove a free parameter that has hampered all previous line formation studies of Fe in non-local thermodynamic equilibrium (NLTE). For the first time, we use realistic 3D NLTE calculations of Fe for a quantitative comparison to solar observations. We confront our theoretical line profiles with observations taken at different viewing angles across the solar disc with the Swedish 1-m Solar Telescope. We find that 3D modelling well reproduces the observed centre-to-limb behaviour of spectral lines overall, but highlight aspects that may require further work, especially cross-sections for inelastic collisions with electrons. Our inferred solar iron abundance is log (εFe) = 7.48 ± 0.04 dex. © 2017 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society

• Martinez-Sykora, Juan; Pontieu, Bart Walter De; Hansteen, Viggo; Voort, Luc Rouppe van der; Carlsson, Mats & Pereira, Tiago Mendes Domingos (2017). On the generation of solar spicules and Alfvenic waves. Science. ISSN 0036-8075. 356(6344), p. 1269–1272. doi: 10.1126/science.aah5412. Full text in Research Archive Show summary

  In the lower solar atmosphere, the chromosphere is permeated by jets known as spicules, in which plasma is propelled at speeds of 50 to 150 kilometers per second into the corona. The origin of the spicules is poorly understood, although they are expected to play a role in heating the million-degree corona and are associated with Alfvénic waves that help drive the solar wind. We compare magnetohydrodynamic simulations of spicules with observations from the Interface Region Imaging Spectrograph and the Swedish 1-m Solar Telescope. Spicules are shown to occur when magnetic tension is amplified and transported upward through interactions between ions and neutrals or ambipolar diffusion. The tension is impulsively released to drive flows, heat plasma (through ambipolar diffusion), and generate Alfvénic waves. This is the author’s version of the work. It is posted here by permission of the AAAS for personal use, not for redistribution. The definitive version was published in Science on 23 Jun 2017, DOI: 10.1126/science.aah5412

• Hansteen, Viggo; Archontis, Vasilis; Pereira, Tiago Mendes Domingos; Carlsson, Mats; Voort, Luc Rouppe van der & Leenaarts, Jorrit (2017). Bombs and Flares at the Surface and Lower Atmosphere of the Sun. The Astrophysical Journal (ApJ). ISSN 0004-637X. 839(1). doi: 10.3847/1538-4357/aa6844. Full text in Research Archive Show summary

  A spectacular manifestation of solar activity is the appearance of transient brightenings in the far wings of the Hα line, known as Ellerman bombs (EBs). Recent observations obtained by the Interface Region Imaging Spectrograph have revealed another type of plasma "bombs" (UV bursts) with high temperatures of perhaps up to 8 × 104 K within the cooler lower solar atmosphere. Realistic numerical modeling showing such events is needed to explain their nature. Here, we report on 3D radiative magnetohydrodynamic simulations of magnetic flux emergence in the solar atmosphere. We find that ubiquitous reconnection between emerging bipolar magnetic fields can trigger EBs in the photosphere, UV bursts in the mid/low chromosphere and small (nano-/micro-) flares (106 K) in the upper chromosphere. These results provide new insights into the emergence and build up of the coronal magnetic field and the dynamics and heating of the solar surface and lower atmosphere. © 2017. The American Astronomical Society. All rights reserved.

• Pereira, Tiago Mendes Domingos; Rouppe, Van Der Voort Luc & Carlsson, Mats (2016). The Appearance of Spicules in High Resolution Observations of Ca II H and Hα. The Astrophysical Journal (ApJ). ISSN 0004-637X. 824(2). doi: 10.3847/0004-637X/824/2/65. Full text in Research Archive Show summary

  Solar spicules are chromospheric fibrils that appear everywhere on the Sun, yet their origin is not understood. Using high resolution observations of spicules obtained with the Swedish 1 m Solar Telescope, we aim to understand how spicules appear in filtergrams and Dopplergrams, how they compare in Ca ii H and Hα filtergrams, and what can make them appear and disappear. We find that spicules display a rich and detailed spatial structure, and show a distribution of transverse velocities that, when aligned with the line of sight, can make them appear at different Hα wing positions. They become more abundant at positions closer to the line core, reflecting a distribution of Doppler shifts and widths. In Hα width maps they stand out as bright features both on disk and off limb, reflecting their large Doppler motions and possibly higher temperatures than in the typical Hα formation region. Spicule lifetimes measured from narrowband images at only a few positions will be an underestimate because Doppler shifts can make them disappear prematurely from such images; for such cases, width maps are a more robust tool. In Hα and Ca ii H filtergrams, off-limb spicules essentially have the same properties, appearance, and evolution. We find that the sudden appearance of spicules can be explained by Doppler shifts from their transverse motions, and does not require other convoluted explanations. Reproduced with permission from the Astrophysical Journal. © IOP Publishing

• Pereira, Tiago Mendes Domingos; Carlsson, Mats; Pontieu, Bart Walter De & Hansteen, Viggo (2015). THE FORMATION of IRIS DIAGNOSTICS. IV. the Mg ii TRIPLET LINES AS A NEW DIAGNOSTIC FOR LOWER CHROMOSPHERIC HEATING. The Astrophysical Journal (ApJ). ISSN 0004-637X. 806(1). doi: 10.1088/0004-637X/806/1/14. Full text in Research Archive Show summary

  A triplet of subordinate lines of Mg ii exists in the region around the h&k lines. In solar spectra these lines are seen mostly in absorption, but in some cases can become emission lines. The aim of this work is to study the formation of this triplet, and investigate any diagnostic value they can bring. Using 3D radiative magnetohydrodynamic simulations of quiet Sun and flaring flux emergence, we synthesize spectra and investigate how spectral features respond to the underlying atmosphere. Reproduced with permission from the Astrophysical Journal. © IOP Publishing

• Antolin, Patrick; Vissers, Gregal Joan Maria; Pereira, Tiago Mendes Domingos; Rouppe, Van Der Voort Luc & Scullion, Eamon (2015). THE MULTI-THERMAL and MULTI-STRANDED NATURE of CORONAL RAIN. The Astrophysical Journal (ApJ). ISSN 0004-637X. 806(1). doi: 10.1088/0004-637X/806/1/81. Full text in Research Archive Show summary

  We analyze coordinated observations of coronal rain in loops, spanning chromospheric, transition region (TR), and coronal temperatures with sub-arcsecond spatial resolution. Coronal rain is found to be a highly multithermal phenomenon with a high degree of co-spatiality in the multi-wavelength emission. EUV darkening and quasi-periodic intensity variations are found to be strongly correlated with coronal rain showers. Progressive cooling of coronal rain is observed, leading to a height dependence of the emission. A fast-slow two-step catastrophic cooling progression is found, which may reflect the transition to optically thick plasma states. The intermittent and clumpy appearance of coronal rain at coronal heights becomes more continuous and persistent at chromospheric heights just before impact, mainly due to a funnel effect from the observed expansion of the magnetic field. [...] Reproduced with permission from the Astrophysical Journal. © IOP Publishing

• Skogsrud, Håkon; Rouppe, Van Der Voort Luc; Pontieu, Bart Walter De & Pereira, Tiago Mendes Domingos (2015). ON THE TEMPORAL EVOLUTION OF SPICULES OBSERVED WITH IRIS, SDO, AND HINODE. The Astrophysical Journal (ApJ). ISSN 0004-637X. 806(2). doi: 10.1088/0004-637X/806/2/170. Full text in Research Archive Show summary

  Spicules are ubiquitous, fast moving jets observed off-limb in chromospheric spectral lines. Combining the recently launched Interface Region Imaging Spectrograph with the Solar Dynamics Observatory and Hinode, we have a unique opportunity to study spicules simultaneously in multiple passbands and from a seeing free environment. This makes it possible to study their thermal evolution over a large range of temperatures. A recent study showed that spicules appear in several chromospheric and transition region spectral lines, suggesting that spicules continue their evolution in hotter passbands after they fade from Ca ii H. In this follow-up paper, we answer some of the questions that were raised in the introductory study. In addition, we study spicules off-limb in C ii 1330 Å for the first time. We find that Ca ii H spicules are more similar to Mg ii 2976 Å spicules than initially reported. For a sample of 54 spicules, we find that 44% of Si iv 1400 Å spicules are brighter toward the top; 56% of the spicules show an increase in Si iv emission when the Ca ii H component fades. We find several examples of spicules that fade from passbands other than Ca ii H, and we observe that if a spicule fades from a passband, it also generally fades from the passbands with lower formation temperatures. We discuss what these new, multi-spectral results mean for the classification of type I and II spicules. Reproduced with permission from the Astrophysical Journal. © IOP Publishing

• Pereira, Tiago Mendes Domingos & Uitenbroek, Han (2015). RH 1.5D: A massively parallel code for multi-level radiative transfer with partial frequency redistribution and Zeeman polarisation. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 574. doi: 10.1051/0004-6361/201424785. Full text in Research Archive Show summary

  The emergence of three-dimensional magneto-hydrodynamic simulations of stellar atmospheres has sparked a need for efficient radiative transfer codes to calculate detailed synthetic spectra. We present RH 1.5D, a massively parallel code based on the RH code and capable of performing Zeeman polarised multi-level non-local thermodynamical equilibrium calculations with partial frequency redistribution for an arbitrary amount of chemical species. The code calculates spectra from 3D, 2D or 1D atmospheric models on a column-by-column basis (or 1.5D). While the 1.5D approximation breaks down in the cores of very strong lines in an inhomogeneous environment, it is nevertheless suitable for a large range of scenarios and allows for faster convergence with finer control over the iteration of each simulation column. The code scales well to at least tens of thousands of CPU cores, and is publicly available. In the present work we briefly describe its inner workings, strategies for convergence optimisation, its parallelism, and some possible applications. Reproduced with permission from Astronomy & Astrophysics, © ESO

• Pontieu, Bart Walter De; McIntosh, Scott; Martinez-Sykora, Juan; Peter, Hardi & Pereira, Tiago Mendes Domingos (2015). Why is non-thermal line broadening of spectral lines in the lower transition region of the sun independent of spatial resolution? Astrophysical Journal Letters. ISSN 2041-8205. 799(1). doi: 10.1088/2041-8205/799/1/L12. Full text in Research Archive Show summary

  Spectral observations of the solar transition region (TR) and corona show broadening of spectral lines beyond what is expected from thermal and instrumental broadening. The remaining non-thermal broadening is significant (5–30 km s−1) and correlated with intensity. Here we study spectra of the TR Si iv 1403 Å line obtained at high resolution with the Interface Region Imaging Spectrograph (IRIS). We find that the large improvement in spatial resolution (0farcs33) of IRIS compared to previous spectrographs (2'') does not resolve the non-thermal line broadening which, in most regions, remains at pre-IRIS levels of about 20 km s−1. This invariance to spatial resolution indicates that the processes behind the broadening occur along the line-of-sight (LOS) and/or on spatial scales (perpendicular to the LOS) smaller than 250 km. Both effects appear to play a role. Comparison with IRIS chromospheric observations shows that, in regions where the LOS is more parallel to the field, magneto-acoustic shocks driven from below impact the TR and can lead to significant non-thermal line broadening. This scenario is supported by MHD simulations. While these do not show enough non-thermal line broadening, they do reproduce the long-known puzzling correlation between non-thermal line broadening and intensity. This correlation is caused by the shocks, but only if non-equilibrium ionization is taken into account. In regions where the LOS is more perpendicular to the field, the prevalence of small-scale twist is likely to play a significant role in explaining the invariance and correlation with intensity. © American Astronomical Society. All rights reserved.

• Rouppe, Van Der Voort Luc; Pontieu, Bart Walter De; Pereira, Tiago Mendes Domingos; Carlsson, Mats & Hansteen, Viggo (2015). Heating signatures in the disk counterparts of solar spicules in interface region imaging spectrograph observations. Astrophysical Journal Letters. ISSN 2041-8205. 799(1). doi: 10.1088/2041-8205/799/1/L3. Full text in Research Archive Show summary

  We use coordinated observations with the Interface Region Imaging Spectrograph (IRIS) and the Swedish 1 m Solar Telescope to identify the disk counterpart of type II spicules in upper-chromospheric and transition region (TR) diagnostics. These disk counterparts were earlier identified through short-lived asymmetries in chromospheric spectral lines: rapid blue- or red-shifted excursions (RBEs or RREs). We find clear signatures of RBEs and RREs in Mg II h & k, often with excursions of the central h3 and k3 absorption features in concert with asymmetries in co-temporal and co-spatial Hα spectral profiles. We find spectral signatures for RBEs and RREs in C II 1335 and 1336 Å and Si IV 1394 and 1403 Å spectral lines and interpret this as a sign that type II spicules are heated to at least TR temperatures, supporting other recent work. These C II and Si IV spectral signals are weaker for a smaller network region than for more extended network regions in our data. A number of bright features around extended network regions observed in IRIS slit-jaw imagery SJI 1330 and 1400, recently identified as network jets, can be clearly connected to Hα RBEs and/or RREs in our coordinated data. We speculate that at least part of the diffuse halo around network regions in the IRIS SJI 1330 and 1400 images can be attributed to type II spicules with insufficient opacity in the C II and Si IV lines to stand out as single features in these passbands. © American Astronomical Society. All rights reserved.

• Martinez-Sykora, Juan; Rouppe, Van Der Voort Luc; Carlsson, Mats; Pontieu, Bart Walter De; Pereira, Tiago Mendes Domingos & Boerner, P. [Show all 21 contributors for this article] (2015). Internetwork Chromospheric Bright Grains Observed with IRIS and SST. The Astrophysical Journal (ApJ). ISSN 0004-637X. 803(1). doi: 10.1088/0004-637X/803/1/44. Full text in Research Archive Show summary

  The Interface Region Imaging Spectrograph (IRIS) reveals small-scale rapid brightenings in the form of bright grains all over coronal holes and the quiet Sun. These bright grains are seen with the IRIS 1330, 1400, and 2796 Å slit-jaw filters. We combine coordinated observations with IRIS and from the ground with the Swedish 1 m Solar Telescope (SST) which allows us to have chromospheric (Ca ii 8542 Å, Ca ii H 3968 Å, Hα, and Mg ii k 2796 Å) and transition region (C ii 1334 Å, Si iv 1403 Å) spectral imaging, and single-wavelength Stokes maps in Fe i 6302 Å at high spatial 0."33, temporal, and spectral resolution. We conclude that the IRIS slit-jaw grains are the counterpart of so-called acoustic grains, i.e., resulting from chromospheric acoustic waves in a non-magnetic environment. We compare slit-jaw images (SJIs) with spectra from the IRIS spectrograph. We conclude that the grain intensity in the 2796 Å slit-jaw filter comes from both the Mg ii k core and wings. The signal in the C ii and Si iv lines is too weak to explain the presence of grains in the 1300 and 1400 Å SJIs and we conclude that the grain signal in these passbands comes mostly from the continuum. Although weak, the characteristic shock signatures of acoustic grains can often be detected in IRIS C ii spectra. For some grains, a spectral signature can be found in IRIS Si iv. This suggests that upward propagating acoustic waves sometimes reach all the way up to the transition region. Reproduced with permission from the Astrophysical Journal. © IOP Publishing

• Rathore, Bhavna; Pereira, Tiago Mendes Domingos; Carlsson, Mats & Pontieu, Bart Walter De (2015). The Formation of IRIS Diagnostics. VIII. IRIS Observations in the C II 133.5 nm Multiplet. The Astrophysical Journal (ApJ). ISSN 0004-637X. 814(1). doi: 10.1088/0004-637X/814/1/70. Full text in Research Archive Show summary

  The C ii 133.5 nm multiplet has been observed by NASA's Interface Region Imaging Spectrograph (IRIS) in unprecedented spatial resolution. The aims of this work are to characterize these new observations of the C ii lines, place them in context with previous work, and to identify any additional value the C ii lines bring when compared with other spectral lines. We make use of wide, long exposure IRIS rasters covering the quiet Sun and an active region. Line properties such as velocity shift and width are extracted from individual spectra and analyzed. The lines have a variety of shapes (mostly single-peak or double-peak), are strongest in active regions and weaker in the quiet Sun. The ratio between the 133.4 and 133.5 nm components is always less than 1.8, indicating that their radiation is optically thick in all locations. Maps of the C ii line widths are a powerful new diagnostic of chromospheric structures, and their line shifts are a robust velocity diagnostic. Compared with earlier quiet Sun observations, we find similar absolute intensities and mean line widths, but smaller redshifts; this difference can perhaps be attributed to differences in spectral resolution and spatial coverage. The C ii intensity maps are somewhat similar to those of transition region lines, but also share some features with chromospheric maps such as those from the Mg ii k line, indicating that they are formed between the upper chromosphere and transition region. C ii intensity, width, and velocity maps can therefore be used to gather additional information about the upper chromosphere. Reproduced with permission from the Astrophysical Journal. © IOP Publishing

• Pereira, Tiago Mendes Domingos; Pontieu, Bart Walter De; Carlsson, Mats; Hansteen, Viggo; Tarbell, T.D. & Lemen, J. [Show all 20 contributors for this article] (2014). An interface region imaging spectrograph first view on solar spicules. Astrophysical Journal Letters. ISSN 2041-8205. 792(1). doi: 10.1088/2041-8205/792/1/L15. Full text in Research Archive Show summary

  Solar spicules have eluded modelers and observers for decades. Since the discovery of the more energetic type II, spicules have become a heated topic but their contribution to the energy balance of the low solar atmosphere remains unknown. Here we give a first glimpse of what quiet-Sun spicules look like when observed with NASA's recently launched Interface Region Imaging Spectrograph (IRIS). Using IRIS spectra and filtergrams that sample the chromosphere and transition region, we compare the properties and evolution of spicules as observed in a coordinated campaign with Hinode and the Atmospheric Imaging Assembly. Our IRIS observations allow us to follow the thermal evolution of type II spicules and finally confirm that the fading of Ca II H spicules appears to be caused by rapid heating to higher temperatures. The IRIS spicules do not fade but continue evolving, reaching higher and falling back down after 500-800 s. Ca II H type II spicules are thus the initial stages of violent and hotter events that mostly remain invisible in Ca II H filtergrams. These events have very different properties from type I spicules, which show lower velocities and no fading from chromospheric passbands. The IRIS spectra of spicules show the same signature as their proposed disk counterparts, reinforcing earlier work. Spectroheliograms from spectral rasters also confirm that quiet-Sun spicules originate in bushes from the magnetic network. Our results suggest that type II spicules are indeed the site of vigorous heating (to at least transition region temperatures) along extensive parts of the upward moving spicular plasma. © American Astronomical Society. All rights reserved.

• Pontieu, Bart Walter De; Title, A. M.; Lemen, J. R.; Kushner, G. D.; Akin, D. J. & Allard, B. [Show all 88 contributors for this article] (2014). The Interface Region Imaging Spectrograph (IRIS). Solar Physics. ISSN 0038-0938. 289(7), p. 2733–2779. doi: 10.1007/s11207-014-0485-y. Full text in Research Archive
• Hansteen, Viggo; Pontieu, Bart Walter De; Carlsson, Mats; Lemen, James R.; Title, Alan M. & Boerner, Paul F.X. [Show all 21 contributors for this article] (2014). The unresolved fine structure resolved: IRIS observations of the solar transition region. Science. ISSN 0036-8075. 346(6207). doi: 10.1126/science.1255757. Full text in Research Archive
• Pontieu, Bart Walter De; Rouppe, Van Der Voort Luc; McIntosh, S.W.; Pereira, Tiago Mendes Domingos; Carlsson, Mats & Hansteen, Viggo [Show all 24 contributors for this article] (2014). On the prevalence of small-scale twist in the solar chromosphere and transition region. Science. ISSN 0036-8075. 346(6207). doi: 10.1126/science.1255732. Full text in Research Archive
• Pereira, Tiago Mendes Domingos; Leenaarts, Jorrit; Pontieu, Bart Walter De; Carlsson, Mats & Uitenbroek, Han (2013). THE FORMATION OF IRIS DIAGNOSTICS. III. NEAR-ULTRAVIOLET SPECTRA AND IMAGES. The Astrophysical Journal (ApJ). ISSN 0004-637X. 778(2). doi: 10.1088/0004-637X/778/2/143. Full text in Research Archive Show summary

  The Mg II h&k lines are the prime chromospheric diagnostics of NASA's Interface Region Imaging Spectrograph (IRIS). In the previous papers of this series, we used a realistic three-dimensional radiative magnetohydrodynamics model to calculate the h&k lines in detail and investigated how their spectral features relate to the underlying atmosphere. In this work, we employ the same approach to investigate how the h&k diagnostics fare when taking into account the finite resolution of IRIS and different noise levels. In addition, we investigate the diagnostic potential of several other photospheric lines and near-continuum regions present in the near-ultraviolet (NUV) window of IRIS and study the formation of the NUV slit-jaw images. We find that the instrumental resolution of IRIS has a small effect on the quality of the h&k diagnostics; the relations between the spectral features and atmospheric properties are mostly unchanged. The peak separation is the most affected diagnostic, but mainly due to limitations of the simulation. The effects of noise start to be noticeable at a signal-to-noise ratio (S/N) of 20, but we show that with noise filtering one can obtain reliable diagnostics at least down to a S/N of 5. The many photospheric lines present in the NUV window provide velocity information for at least eight distinct photospheric heights. Using line-free regions in the h&k far wings, we derive good estimates of photospheric temperature for at least three heights. Both of these diagnostics, in particular the latter, can be obtained even at S/Ns as low as 5. Reproduced with permission from the Astrophysical Journal. © IOP Publishing

• Pereira, Tiago Mendes Domingos; Pontieu, Bart De & Carlsson, Mats (2013). THE EFFECTS OF SPATIO-TEMPORAL RESOLUTION ON DEDUCED SPICULE PROPERTIES. The Astrophysical Journal (ApJ). ISSN 0004-637X. 764(1). doi: 10.1088/0004-637X/764/1/69. Full text in Research Archive Show summary

  Spicules have been observed on the Sun for more than a century, typically in chromospheric lines such as Hα and Ca II H. Recent work has shown that so-called "type II" spicules may have a role in providing mass to the corona and the solar wind. In chromospheric filtergrams these spicules are not seen to fall back down, and they are shorter lived and more dynamic than the spicules that have been classically reported in ground-based observations. Observations of type II spicules with Hinode show fundamentally different properties from what was previously measured. In earlier work we showed that these dynamic type II spicules are the most common type, a view that was not properly identified by early observations. The aim of this work is to investigate the effects of spatio-temporal resolution in the classical spicule measurements. Making use of Hinode data degraded to match the observing conditions of older ground-based studies, we measure the properties of spicules with a semi-automated algorithm. These results are then compared to measurements using the original Hinode data. We find that degrading the data has a significant effect on the measured properties of spicules. Most importantly, the results from the degraded data agree well with older studies (e.g., mean spicule duration more than 5 minutes, and upward apparent velocities of about 25 km s–1). These results illustrate how the combination of spicule superposition, low spatial resolution and cadence affect the measured properties of spicules, and that previous measurements can be misleading. Reproduced with permission from the Astrophysical Journal. © IOP Publishing

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• Pereira, Tiago (2026). 22. juli - Reiseradioen - NRK Radio. [Radio]. NRK. Full text in Research Archive Show summary

  Reiseradioen gir deg sommerfølelsen. I dag skal vi slå av en prat med Harald Stanghelle, som for tiden er på Orknøyene. Reporter Even Lusæter er i Honningsvåg og vi får en stemningsrapport derfra i dag.

• Pereira, Tiago (2026). Dagsnytt 18 - TV - NRK TV. [TV]. NRK. Full text in Research Archive Show summary

  Dagsnytt 18 er NRK nyheters daglige aktualitets- og debattprogram. Programledere er Sigrid Sollund og Espen Aas.

• Udnæs, Elias Roland & Pereira, Tiago (2025). Using extensive NLTE spectral analyses in time and space to estimate chromospheric heating. Full text in Research Archive Show summary

  The solar chromosphere is a thin layer situated between the photosphere and the corona, that is intimately tied to both the solar wind and heating of the corona. Therefore, understanding the energy transfer through the solar chromosphere is a prerequisite to solving long-standing problems in solar physics. Our work combines a comprehensive large-scale analysis of two 3D rMHD simulations, spanning the entirety of the simulations for several solar hours to study the energy dissipation in the solar chromosphere. In particular, we focus on the dissipation of acoustic wave energy through the chromosphere. We found a close correlation between viscous dissipation and the decrease of acoustic wave energy in quiet Sun regions, and calculated the frequencies and scales where acoustic wave energy dissipates. We also performed extensive NLTE calculations from hundreds of snapshots of the two simulations to do spectral analyses in time and space of the Ca II H&K, Ca II 8542 Å, and Mg II h&k lines. Our approach involved unsupervised machine learning techniques to estimate energy dissipation by using information from the chromospheric spectral lines. For quiet Sun chromospheric conditions, we were able to estimate chromospheric heating from the spectral data, where we saw that spatial and temporal information gave important context to decipher heating processes. The spectral signatures that reveal chromospheric heating can be used to estimate energy dissipation from observations.

• Pereira, Tiago (2024). Machine learning on observations and simulations. Full text in Research Archive
• Pereira, Tiago (2024). SOLAR-C EUVST Status Report on Modelling. Full text in Research Archive
• Pereira, Tiago (2024). Machine learning on observations and simulations. Full text in Research Archive
• Pereira, Tiago (2024). Solar Astrophysics. Full text in Research Archive
• Pereira, Tiago (2024). Testing inversions at high spatial resolution: the case of Ca II 854.2 nm. Full text in Research Archive
• Pereira, Tiago & Martinez-Sykora, Juan (2024). MUSE synthesis tools. Full text in Research Archive
• Pereira, Tiago (2023). 3D NLTE radiative transfer in stellar atmospheres. Full text in Research Archive
• Pereira, Tiago (2023). Fast 3D non-LTE spectral synthesis with neural networks. Full text in Research Archive
• Pereira, Tiago (2023). Uncovering chromospheric secrets with forward modelling. Full text in Research Archive
• Pereira, Tiago (2023). Hva stjernene er lagd av. Astronomi. ISSN 0802-7587. p. 10–16. Full text in Research Archive
• Krikova, Kilian; Pereira, Tiago; Voort, Luc Rouppe van der & Carlsson, Mats (2022). Diagnostic potential of Hε for small-scale energetic phenomena. Full text in Research Archive
• Pereira, Tiago (2022). Speeding up 3D non-LTE spectral synthesis with neural networks. Full text in Research Archive
• Pereira, Tiago (2022). Speeding up 3D non-LTE spectral synthesis with neural networks. Full text in Research Archive
• Moe, Thore Espedal; Pereira, Tiago & Carlsson, Mats (2022). Effects of spatial resolution on inferences of atmospheric quantities from simulations. Full text in Research Archive
• Moe, Thore Espedal; Pereira, Tiago & Carlsson, Mats (2022). Effects of spatial resolution on inferences of atmospheric quantities from simulations. Full text in Research Archive
• Pereira, Tiago (2021). Solas hete hemmeligheter. Astronomi. ISSN 0802-7587. p. 28–29. Full text in Research Archive
• Pereira, Tiago & Chappell, Bruce (2021). A Neural Network Approach to
 3D NLTE Radiative Transfer. Full text in Research Archive
• Moe, Thore Espedal; Pereira, Tiago & Carlsson, Mats (2021). Effects of spatial resolution on Stokes profiles. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2018). From Big to Small: a Trip Across the Universe. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2018). Thermal coupling through the atmosphere. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2018). Chasing the elusive 1% of solar light. Full text in Research Archive
• Pereira, Tiago Mendes Domingos & Pontieu, Bart Walter De (2016). Planning coordinated observations with IRIS, IRIS7 Weihai. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2016). An Introduction to Python for Scientists. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2016). Evolving views of solar spicules. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2016). Introduction to IRIS data analysis and coordinated observations. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2016). Introduction to IRIS data analysis, IRIS7 Weihai. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2016). Solar spicules: the finest chromospheric structure? Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2015). In search of the lost triplet. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2015). Using IRIS to trace the flow of energy in the solar chromosphere. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2015). The Role of Spicules. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2015). Introduction to IRIS data analysis and CRISPEX. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2015). Introduction to IRIS data analysis. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2015). Fibrils, spicules, and the solar chromospheric puzzle. Full text in Research Archive
• Pereira, Tiago Mendes Domingos; Carlsson, Mats; Pontieu, Bart Walter De & Hansteen, Viggo (2015). The Mg II lines as a diagnostic for heating in the lower chromosphere. Full text in Research Archive
• Pereira, Tiago Mendes Domingos & Rouppe, Van Der Voort Luc (2015). Beyond spicule dynamics: spicule and fibril spectroscopy at high spatial and temporal resolution. Full text in Research Archive
• Pereira, Tiago Mendes Domingos & Rouppe, Van Der Voort Luc (2015). Clashing views of spicules and fibrils. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2015). Towards a deeper understanding of solar spectra through forward modelling. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2014). Lifting the veil on the solar chromosphere. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2014). An IRIS look at spicules. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2014). NAOJ IRIS mini-workshop. Full text in Research Archive
• Kato, Yoshiaki; Pontieu, Bart Walter De; Martinez-Sykora, J.; Hansteen, Viggo; Pereira, Tiago Mendes Domingos & Leenaarts, Jorritt [Show all 7 contributors for this article] (2014). Measuring energy flux of magneto-acoustic wave in the magnetic elements by using IRIS. Full text in Research Archive Show summary

  NASA's Interface Region Imaging Spectrograph (IRIS) has opened a new window to explore the chromospheric/coronal waves that potentially energize the solar atmosphere. By using an imaging spectrograph covering the Si IV and Mg II h&k lines as well as a slit-jaw imager centered at Si IV and Mg II k onboard IRIS, we can determine the nature of propagating magneto-acoustic waves just below and in the transition region. In this study, we compute the vertically emergent intensity of the Si IV and Mg II h&k lines from a time series of snapshots of a magnetic element in a two-dimensional Radiative MHD simulation from the Bifrost code. We investigate the synthetic line profiles to detect the slow magneto-acoustic body wave (slow mode) which becomes a slow shock at the lower chromosphere in the magnetic element. We find that the Doppler shift of the line core gives the velocity amplitude of the longitudinal magneto-acoustic body wave. The contribution function of the line core indicates that the formation of Mg II h&k lines is associated with the propagating shocks and therefore the time evolution of the line core intensity represents the propagating shocks projected on the optical surface. We will report on measurement of the energy flux of slow modes in the magnetic elements by using IRIS observations.

• Pereira, Tiago Mendes Domingos (2014). Introduction to IRIS data analysis. Full text in Research Archive
• Pereira, Tiago Mendes Domingos; Carlsson, Mats & Pontieu, Bart Walter De (2014). The evolution of type II spicules as seen by IRIS. Full text in Research Archive
• Pereira, Tiago Mendes Domingos; Carlsson, Mats & Pontieu, Bart Walter De (2013). An IRIS look at spicules. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2013). The multispectral Sun. Full text in Research Archive
• Pereira, Tiago Mendes Domingos (2013). Mg II h&k line formation and diagnostics. Full text in Research Archive
• Pereira, Tiago Mendes Domingos; Leenarts, Jorrit; Carlsson, Mats; Pontieu, Bart Walter De & Uitenbroek, Han (2013). Physical information from the NUV window of IRIS. Full text in Research Archive
• Carlsson, Mats; Hansteen, Viggo; Pereira, Tiago Mendes Domingos; Leenaarts, Jorrit; Gudiksen, Boris Vilhelm & Pontieu, Bart Walter De (2013). First Comparison between IRIS Data and Numerical Models. Full text in Research Archive
• Krikova, Kilian; Pereira, Tiago & Voort, Luc Rouppe van der (2025). Small-scale energetic phenomena in Hε: line formation and diagnostic potential. Universitetet i Oslo. Full text in Research Archive Show summary

  This dissertation focuses on forward modeling, using state-of-theart 3D radiative magnetohydrodynamic simulations combined with modern non-LTE radiative transfer codes to synthesize spectral lines and analyze their formation. The focus lies on investigating the formation and diagnostic potential of the hydrogen Balmer line Hε in the solar atmosphere, particularly in the context of small-scale energetic phenomena such as Ellerman bombs, UV bursts, and smallscale flares. A deeper understanding of the formation of Hε will help to understand a newly identified phenomenon called quiet Sun Ellerman bombs. Additionally, a modern, in-depth study of the formation of Hε has not yet been performed. By combining state-of-the-art Bifrost 3D radiative magnetohydrodynamic simulations, representing quiet Sun conditions and reproducing small-scale energetic phenomena in combination with the RH1.5D and MULTI3D radiative transfer codes, synthetic spectra were generated to investigate the response of Hε under various solar conditions. We address three core research questions, explored in three papers: 1. How is the Hε spectral line formed under quiet Sun conditions and for different solar features? 2. How can the multi-level source function be calculated, and what role does interlocking play in the line source function? 3. How does Hε respond to small-scale energetic events, such as Ellerman bombs, UV bursts, and small-scale flares? Answering these questions will assist the solar physics community to interpret Hε observations, and also clarify line formation in multi-level atoms, particularly through a deeper understanding of the multi-level source function. Our findings demonstrate that Hε, despite being an unobtrusive spectral line in the solar spectrum, can serve as a valuable diagnostic tool for analyzing and, more importantly, detecting small-scale energetic phenomena. In particular, Hε’s pronounced sensitivity to temperature enhancements in the lower solar atmosphere makes it exceptionally wellsuited for detecting weak heating events in quiet Sun regions, such as quiet Sun Ellerman bombs. This work also underscores the advantages of Hε over other Balmer series lines, such as Hα, in identifying weak energetic events. Unlike Hα or Hβ the line core of Hε is largely unaffected by the solar chromosphere, making it a promising candidate for measuring velocities in the lower chromosphere near the temperature minimum. This dissertation contributes to the field of solar physics by improving the understanding of hydrogen line formation in the solar atmosphere and validating the potential of Hε for upcoming solar missions, such as the Daniel K. Inouye Solar Telescope or the planned European Solar Telescope. Additionally, it provides a detailed investigation of the multi-level source function, a subject rarely addressed in the literature, which will support the interpretation of non-LTE line formation in both solar and stellar atmospheres. The findings especially contribute to the interpretation of high-resolution Hε observations, advancing the exploration of the Sun’s dynamic magnetic processes, and enabling further investigations of a new phenomenon called quiet Sun Ellerman bombs.

• Moe, Thore Espedal; Pereira, Tiago & Carlsson, Mats (2023). Line formation in the magnetized solar chromosphere. Universitetet i Oslo. Full text in Research Archive Show summary

  The theme of this thesis has been the use of forward modeling to study the formation of spectral lines in the solar atmosphere, with a particular focus on the chromospheric Ca II 854.2 nm line which is important for magnetic field diagnostics. Starting from state-of-the-art numerical simulations, modern radiative transfer codes have been used to calculate synthetic spectra, including the effects of Zeeman polarization. Combining the physical state of the model atmospheres with the resulting synthetic spectra has allowed us to investigate how these correlate, thereby guiding the interpretation of real observations. We have used simulations of differing resolutions to estimate the effect of spatially unresolved processes on inferences of atmospheric quantities from spectra. Furthermore, we have examined the use of clustering techniques to classify the shapes of the spectral profiles generated from simulations, and studied how these shapes correlate with the simulations’ atmospheric structure. We have also employed these clustering methods to characterize, contrast and compare the spectra from simulations with the spectra from real observations.

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