arXiv subjects

Tiago M. D. Pereira

Publications and source records attributed to Tiago M. D. Pereira.

At least 19 recordsLinked to original sources

arXiv2026

Solar Vortices as Conduits for Magnetoacoustic Waves: Multi-Layer Coupling and Their Role in Atmospheric Heating

Vortices are widespread throughout the solar atmosphere and commonly interpreted as channels for Alfvén wave energy transport. However, this interpretation has mostly been inferred from the apparent alignment of rotating plasma structures with the magnetic field, rather than direct evidence of the nature of the waves involved. We present observational and numerical evidence that solar vortices act as coherent waveguides dominated by magnetoacoustic waves in the lower atmosphere, combining high-resolution SST observations and Bifrost simulation data. Using Normalised Mutual Information and Jensen-Shannon Divergence as coupling diagnostics, we provide the first observational identification of a solar vortex footpoint through information-theoretic metrics, locating it in the photospheric region of highest shared information with the chromospheric swirl. Spectral Proper Orthogonal Decomposition separates dominant dynamical patterns, allowing us to identify sausage, kink, and helical wave modes propagating along vortex structures. In the Bifrost simulation, we find no evidence for torsional Alfvén waves supported by vortices below 1 Mm. Instead, the waves supported by vortices are magnetoacoustic, and their energy transport is predominantly compressive in the lower atmosphere, with the magnetic component becoming dominant only at greater heights. Even the compressive wave component alone reaches nanoflare-level magnitudes ($\sim10^{25}$~erg), indicating that vortex-associated compressive perturbations may provide an energetically relevant contribution in regimes where magnetic-energy transport dominates. The recovery of sausage and helical modes in temperature perturbations shows that these modes carry a thermal signature, further supporting their relevance for chromospheric energy transport and localised heating.

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arXiv2026

The umbrella effect: Magnetic canopy topology modulates spatially averaged chromospheric three-minute power

Three-minute ($\sim$5 mHz) oscillations are a prominent signature of wave propagation in the solar chromosphere, but their measured power can vary substantially between full-disc observations and small, high-resolution fields of view. We investigate whether chromospheric magnetic canopy topology, particularly its lateral continuity and areal filling, modulates field-of-view-averaged three-minute power. We analyse H$α$ and Ca II 8542 Å spectral imaging from the Swedish 1-m Solar Telescope, comparing canopy-poor quiet-Sun scenes with canopy-dominated active-region environments, complemented by radiative-MHD Bifrost simulations of canopy-poor and canopy-rich atmospheres. We compute field-of-view-averaged power spectra from fixed-wavelength intensities and bisector-derived velocities in the observations, and from synthetic intensities, velocities, and temperature proxies in the simulations. We also quantify the relation between integrated 3-5 mHz excess power and canopy filling factor, using HMI-based magnetic-field extrapolations for the observations. In both observations and simulations, canopy-poor scenes show clear 3-5 mHz power enhancements, whereas canopy-dominated scenes show strongly reduced measured power. The trend is present in H$α$ and Ca II 8542 Å intensities and is supported by complementary velocity and temperature proxies. Integrated 3-5 mHz excess power decreases with increasing canopy filling factor. We conclude that chromospheric field-of-view-averaged three-minute power is a topology-weighted observable: dense, laterally continuous magnetic canopies can strongly reduce the measured large-scale three-minute signature without requiring the absence of local wave activity. This provides a practical criterion for interpreting chromospheric oscillation power as a proxy for atmospheric wave energy in the Sun and in magnetised cool-star atmospheres.

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arXiv2026

Bifrost spectral inversions, Fast non-LTE solar chromospheric diagnostics from 3D simulations

Modern solar observatories produce vast amounts of detailed spectral data. To infer atmospheric parameters from these data, in particular for the solar chromosphere, requires immense computational resources. This problem is becoming more acute as spatial resolution improves, and faster methods are much needed to make sense of the data. Archive-based inversions provide a cost-effective way to infer atmospheric parameters from solar spectra, and involve building databases of synthetic spectra and atmospheric models. We extend this idea to a $k$-nearest neighbour inversion with non-LTE chromospheric spectra from a three-dimensional radiative-magnetohydrodynamic simulation. Our database consists of 150 million \theline\ line profiles from a magnetically quiet simulation. We validate our method on a different simulation, and then apply the database inversion on high-cadence observations taken with the Swedish 1-m Solar Telescope and find excellent agreement between the observed and fitted spectra for almost the entire field of view. We recover the chromospheric temperature and line-of-sight velocity, and calculate the uncertainty in their inversions. The gas temperature has small uncertainties over a broad range of optical depths, and we recover a physically consistent solution over a broad range of optical depths, even beyond the line sensitivity region. Compared with the traditional inversion method, our approach is four orders of magnitude faster. Limitations and future improvements of the method are discussed.

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arXiv2026

Pre-flare and active region plasma flows and structure seen by the short wavelength camera on SOLAR-C/EUVST

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 0.02-15 MK, and exposure times down to 0.5 seconds. We present forward modelling of the spectrograph's short wavelength camera (170-210 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.

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arXiv2026

Multi-thermal dynamics and transverse oscillations of solar spicules revealed by coordinated SST, IRIS, and SDO observations

% context heading (optional) {Solar spicules are highly dynamic chromospheric jets that play an important role in the mass and energy balance of the solar atmosphere, though their connection to the transition region and corona remains unclear.} % aims heading (mandatory) {We investigate the dynamical and multi-thermal properties of spicules, their connection to higher atmospheric layers, and their transverse oscillations and associated energy flux.} % methods heading (mandatory) {We analyse coordinated high-resolution observations from the Swedish 1-m Solar Telescope (SST) in H$α$, the Interface Region Imaging Spectrograph (IRIS) in \ion{Si}{iv} 1400~Å, and the Solar Dynamics Observatory (SDO)/Atmospheric Imaging Assembly (AIA) coronal channels. Space-time diagrams, spectral analysis, and wavelet techniques are used to study temporal evolution, Doppler velocities, and oscillatory properties. Transverse displacements of spicules are tracked to estimate wave properties and energy flux.} % results heading {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 H$α$ and \ion{Si}{iv} show opposite signs, indicating multi-thermal plasma flows. Wavelet analysis reveals frequently dominant $\sim$3-minute oscillations, along with high-frequency transverse oscillations (65--270~s) with velocity amplitudes of 3.3--9.9~km~s$^{-1}$ and a mean energy flux of $(2.14 \pm 0.78)\times10^{3}$~W~m$^{-2}$.} % conclusions heading (optional) {These results demonstrate that spicules are multithermal, dynamic structures connected to the transition region and corona, and that transverse waves carry substantial energy, highlighting their role in coronal heating.}

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arXiv2026

Spectral signatures of bright grains determine chromospheric heating

Chromospheric heating is an important ingredient in the energy budget of the solar atmosphere, which is challenging to quantify from observations. By using 3D radiative magnetohydrodynamic simulations of the solar atmosphere combined with non-LTE spectral synthesis, we estimated chromospheric heating from synthetic spectra and studied the spectral and temporal signatures of heating events. We performed k-means clustering on the Mg II h, Ca II H, and Ca II 8542 Å lines to identify representative profiles associated with elevated chromospheric heating and studied their atmospheric stratification. We find that locations with the strongest chromospheric heating show spectral signatures with strong emission. Profiles with strong emission in the blue wing of the lines (blue grains) are created by upward-propagating shock waves and have an order of magnitude higher heating in the chromosphere than the ambient heating. Profiles with strong emission in the red wing (red grains) also display heating that is an order of magnitude stronger than the baseline, but these spectra do not show a characteristic atmospheric stratification. Spectra classified as blue grains have a consistent temporal evolution, which is an oscillating sawtooth pattern in the line core and emission in the blue wing. However, spectra classified as red grains did not show a consistent temporal signature: Red wing emission from the simulations can appear spontaneously or be associated with an oscillation. While red and blue grain profiles account for around 3% of our synthetic spectra, they account for more than 12% of the total chromospheric heating in these simulations. By comparing two quiet Sun simulations, we find that the prevalence of bright grains is influenced by the magnetic field configuration, with a unipolar configuration showing fewer bright grains and consequently a lower share of heating from such events.

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arXiv2025

The H$α$ line as a probe of chromospheric magnetic fields

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 (WFA) for theH$α$ 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 tau_500 = -5.7, which corresponds to higher layers than the Ca II 8542 Å line core, which is most sensitive to conditions at log tau_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 Ic, 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.

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arXiv2025

Characteristics of acoustic-wave heating in simulations of the quiet Sun chromosphere

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.

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arXiv2025

Introducing STARDIS: An Open and Modular Stellar Spectral Synthesis Code

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 also compare qualitatively to phoenix for solar models. We find that stardis generally agrees well with korg for solar models on the few percent level or better, that the codes can diverge in the ultraviolet, 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/.

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arXiv2023

Comparative clustering analysis of Ca II 854.2 nm spectral profiles from simulations and observations

We aim to 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). We use clustering techniques to extract the typical Ca II 854.2 nm profile shapes synthesized from Bifrost simulations with varying amounts of magnetic activity. We degrade the synthetic profiles to observational conditions and repeat the clustering, and we compare our synthetic results with actual observations. 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. 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 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 $-3 \lesssim \log τ_{5000} \lesssim -1$.

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arXiv2023

Shape-based clustering of synthetic Stokes profiles using k-means and k-Shape

The shapes of Stokes profiles contain much 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 proper interpretation of 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, i.e. 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. We generate synthetic Stokes profiles for the Ca II 854.2 nm line using the Multi3D code from a Bifrost simulation snapshot. We then apply the k-means and k-Shape clustering techniques to group the profiles together according to their shape. We show and compare the classes of profile shapes we retrieve 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. Furthermore, we apply both methods to the subset of our profiles containing the strongest Stokes V signals, and demonstrate how k-Shape can be qualitatively better than k-means at retrieving complex profile shapes when using a small number of clusters.

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arXiv2023

Irregular grids for 3D NLTE radiative transfer in stellar atmospheres

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 thermodynamical 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.

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arXiv2022

Effects of spatial resolution on inferences of atmospheric quantities from simulations

Small scale processes are thought to be important for the dynamics of the solar atmosphere. While numerical resolution fundamentally limits their inclusion in MHD simulations, real observations at the same nominal resolution should still contain imprints of sub-resolution effects. This means that the synthetic observables from a simulation of 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. We aim to compare synthetic spectra obtained from realistic 3D radiative magnetohydrodynamic (rMHD) simulations run at three 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. 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/magnetic fields in concentrated spots even after spatial smearing. We also see indications that the imprints of sub-resolution effects on the degraded spectra result in systematic errors in the inversions, and that these errors increase with the amount of sub-resolution effects included. Fortunately, however, we find that including successively more sub-resolution yields smaller additional effects; i.e. there is a clear trend of diminishing importance for progressively finer sub-resolution effects.

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arXiv2021

SunnyNet: A neural network approach to 3D non-LTE radiative transfer

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.

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arXiv2020

A Survey of Computational Tools in Solar Physics

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

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arXiv2019

Semi-empirical model atmospheres for the chromosphere of the sunspot penumbra and umbral flashes

Context. The solar chromosphere and the lower transition region is 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 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 use spectropolarimetric observations of the Ca II 8542 A spectra obtained with the Swedish 1-m Solar Telescope (SST) and use NICOLE inversions to obtain semi-empirical model atmospheres for different features in and around a sunspot. These are used to synthesize Mg II h&k spectra using RH1.5D code, which we compare 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 downflows, 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. These are available in electronic as well as in table formats.

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arXiv2018

The dynamic chromosphere: pushing the boundaries of observations and models

The interface between the bright solar surface and the million-degree corona continues to hold the key to many unsolved problems in solar physics. Advances in instrumentation now allow us to observe the dynamic structures of the solar chromosphere down to less than 0.1" with cadences of just a few seconds and in multiple polarisation states. Such observational progress has been matched by the ever-increasing sophistication of numerical models, which have become necessary to interpret the complex observations. With an emphasis on the quiet Sun, I will review recent progress in the observation and modelling of the chromosphere. Models have come a long way from 1D static atmospheres, but their predictions still fail to reproduce several key observed features. Nevertheless, they have given us invaluable insight into the physical processes that energise the atmosphere. With more physics being added to models, the gap between predictions and observations is narrowing. With the next generation of solar observatories just around the corner, the big question is: will they close the gap?

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arXiv2018

Chromospheric counterparts of solar transition region unresolved fine structure loops

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.

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