Parameterizations of Chromospheric Condensations in dG and dMe Model Flare Atmospheres

The origin of the near-ultraviolet and optical continuum radiation in flares is critical for understanding particle acceleration and impulsive heating in stellar atmospheres. Radiative-hydrodynamic simulations in 1D have shown that high energy deposition rates from electron beams produce two flaring layers at T~10^4 K that develop in the chromosphere: a cooling condensation (downflowing compression) and heated non-moving (stationary) flare layers just below the condensation. These atmospheres reproduce several observed phenomena in flare spectra, such as the red wing asymmetry of the emission lines in solar flares and a small Balmer jump ratio in M dwarf flares. The high beam flux simulations are computationally expensive in 1D, and the (human) timescales for completing NLTE models with adaptive grids in 3D will likely be unwieldy for a time to come. We have developed a prescription for predicting the approximate evolved states, continuum optical depth, and the emergent continuum flux spectra of radiative-hydrodynamic model flare atmospheres. These approximate prescriptions are based on an important atmospheric parameter: the column mass (m_ref) at which hydrogen becomes nearly completely ionized at the depths that are approximately in steady state with the electron beam heating. Using this new modeling approach, we find that high energy flux density (>F11) electron beams are needed to reproduce the brightest observed continuum intensity in IRIS data of the 2014-Mar-29 X1 solar flare and that variation in m_ref from 0.001 to 0.02 g/cm2 reproduces most of the observed range of the optical continuum flux ratios at the peaks of M dwarf flares.Comment: 29 pages, 9 figures, accepted for publication in the Astrophysical Journa

Bioinformatics for High-throughput Virus Detection and Discovery

Pathogen detection is a challenging problem given that any given specimen may contain one or more of many different microbes. Additionally, a specimen may contain microbes that have yet to be discovered. Traditional diagnostics are ill-equipped to address these challenges because they are focused on the detection of a single agent or panel of agents. I have developed three innovative computational approaches for analyzing high-throughput genomic assays capable of detecting many microbes in a parallel and unbiased fashion. The first is a metagenomic sequence analysis pipeline that was initially applied to 12 pediatric diarrhea specimens in order to give the first ever look at the diarrhea virome. Metagenomic sequencing and subsequent analysis revealed a spectrum of viruses in these specimens including known and highly divergent viruses. This metagenomic survey serves as a basis for future investigations about the possible role of these viruses in disease. The second tool I developed is a novel algorithm for diagnostic microarray analysis called VIPR: Viral Identification with a PRobabilistic algorithm). The main advantage of VIPR relative to other published methods for diagnostic microarray analysis is that it relies on a training set of empirical hybridizations of known viruses to guide future predictions. VIPR uses a Bayesian statistical framework in order to accomplish this. A set of hemorrhagic fever viruses and their relatives were hybridized to a total of 110 microarrays in order to test the performance of VIPR. VIPR achieved an accuracy of 94% and outperformed existing approaches for this dataset. The third tool I developed for pathogen detection is called VIPR HMM. VIPR HMM expands upon VIPR\u27s previous implementation by incorporating a hidden Markov model: HMM) in order to detect recombinant viruses. VIPR HMM correctly identified 95% of inter-species breakpoints for a set of recombinant alphaviruses and flaviviruses Mass sequencing and diagnostic microarrays require robust computational tools in order to make predictions regarding the presence of microbes in specimens of interest. High-throughput diagnostic assays coupled with powerful analysis tools have the potential to increase the efficacy with which we detect pathogens and treat disease as these technologies play more prominent roles in clinical laboratories

A Unified Computational Model for Solar and Stellar Flares

We present a unified computational framework which can be used to describe impulsive flares on the Sun and on dMe stars. The models assume that the flare impulsive phase is caused by a beam of charged particles that is accelerated in the corona and propagates downward depositing energy and momentum along the way. This rapidly heats the lower stellar atmosphere causing it to explosively expand and dramatically brighten. Our models consist of flux tubes that extend from the sub-photosphere into the corona. We simulate how flare-accelerated charged particles propagate down one-dimensional flux tubes and heat the stellar atmosphere using the Fokker-Planck kinetic theory. Detailed radiative transfer is included so that model predictions can be directly compared with observations. The flux of flare-accelerated particles drives return currents which additionally heat the stellar atmosphere. These effects are also included in our models. We examine the impact of the flare-accelerated particle beams on model solar and dMe stellar atmospheres and perform parameter studies varying the injected particle energy spectra. We find the atmospheric response is strongly dependent on the accelerated particle cutoff energy and spectral index.Comment: Accepted for publication by the Astrophysical Journa

Modeling Mg II h, k and Triplet Lines at Solar Flare Ribbons

Observations from the \textit{Interface Region Imaging Spectrograph} (\textsl{IRIS}) often reveal significantly broadened and non-reversed profiles of the Mg II h, k and triplet lines at flare ribbons. To understand the formation of these optically thick Mg II lines, we perform plane parallel radiative hydrodynamics modeling with the RADYN code, and then recalculate the Mg II line profiles from RADYN atmosphere snapshots using the radiative transfer code RH. We find that the current RH code significantly underestimates the Mg II h \& k Stark widths. By implementing semi-classical perturbation approximation results of quadratic Stark broadening from the STARK-B database in the RH code, the Stark broadenings are found to be one order of magnitude larger than those calculated from the current RH code. However, the improved Stark widths are still too small, and another factor of 30 has to be multiplied to reproduce the significantly broadened lines and adjacent continuum seen in observations. Non-thermal electrons, magnetic fields, three-dimensional effects or electron density effect may account for this factor. Without modifying the RADYN atmosphere, we have also reproduced non-reversed Mg II h \& k profiles, which appear when the electron beam energy flux is decreasing. These profiles are formed at an electron density of $\sim 8\times10^{14}\ \mathrm{cm}^{-3}$ and a temperature of $\sim1.4\times10^4$ K, where the source function slightly deviates from the Planck function. Our investigation also demonstrates that at flare ribbons the triplet lines are formed in the upper chromosphere, close to the formation heights of the h \& k lines

Salvaging the Speaker Clause: The Constitutional Case Against Nonmember Speakers of the House

As the Founding generation understood the word, “Speaker” meant an elected member of the House. Yet modern representatives nominate non-House-members for the speakership—and many argue the practice is constitutional. To correct this constitutional drift, this Article closely analyzes the text of the Speaker Clause, the structure of the Constitution, and 700 years of history and tradition to show that the Constitution requires the Speaker of the House to be a member of the House. It also considers the practicalities of correcting this drift. If, as this Article argues, the Constitution bars nonmembers from the speakership, who can enforce that rule, especially if Congress itself is the one violating it? Though the Speaker Clause likely is not justiciable, Congress has an independent duty—equally important to that of the judiciary—to uphold the Constitution. This Article’s conclusion is significant. It clarifies the procedure and rationale involved in choosing a Speaker of the House. And by excluding nonmembers as candidates for the speakership, this Article’s conclusion promises to make future speakership negotiations and votes smoother, eliminating one avenue for meaningless protest votes

Hydrogen Balmer Line Broadening in Solar and Stellar Flares

The broadening of the hydrogen lines during flares is thought to result from increased charge (electron, proton) density in the flare chromosphere. However, disagreements between theory and modeling prescriptions have precluded an accurate diagnostic of the degree of ionization and compression resulting from flare heating in the chromosphere. To resolve this issue, we have incorporated the unified theory of electric pressure broadening of the hydrogen lines into the non-LTE radiative transfer code RH. This broadening prescription produces a much more realistic spectrum of the quiescent, A0 star Vega compared to the analytic approximations used as a damping parameter in the Voigt profiles. We test recent radiative-hydrodynamic (RHD) simulations of the atmospheric response to high nonthermal electron beam fluxes with the new broadening prescription and find that the Balmer lines are over-broadened at the densest times in the simulations. Adding many simultaneously heated and cooling model loops as a "multithread" model improves the agreement with the observations. We revisit the three-component phenomenological flare model of the YZ CMi Megaflare using recent and new RHD models. The evolution of the broadening, line flux ratios, and continuum flux ratios are well-reproduced by a multithread model with high-flux nonthermal electron beam heating, an extended decay phase model, and a "hot spot" atmosphere heated by an ultrarelativistic electron beam with reasonable filling factors: 0.1%, 1%, and 0.1% of the visible stellar hemisphere, respectively. The new modeling motivates future work to understand the origin of the extended gradual phase emission.Comment: 31 pages, 13 figures, 2 tables, accepted for publication in the Astrophysical Journa

Suppression of Hydrogen Emission in an X-Class White-Light Solar Flare

We present unique NUV observations of a well-observed X-class flare from NOAA 12087 obtained at Ond\v{r}ejov Observatory. The flare shows a strong white-light continuum but no detectable emission in the higher Balmer and Lyman lines. RHESSI and Fermi observations indicate an extremely hard X-ray spectrum and gamma-ray emission. We use the RADYN radiative hydrodynamic code to perform two type of simulations. One where an energy of 3 x 10^11 erg/cm^2/s is deposited by an electron beam with a spectral index of ~3 and a second where the same energy is applied directly to the photosphere. The combination of observations and simulations allow us to conclude that the white-light emission and the suppression or complete lack of hydrogen emission lines is best explained by a model where the dominant energy deposition layer is located in the lower layers of the solar atmosphere rather than the chromosphere.Comment: 13 page

Can Proton Beam Heating Flare Models Explain Sunquakes?

SDO/HMI observations reveal a class of solar flares with substantial energy and momentum impacts in the photosphere, concurrent with white-light emission and helioseismic responses, known as sunquakes. Previous radiative hydrodynamic modeling has demonstrated the challenges of explaining sunquakes in the framework of the standard flare model of `electron beam' heating. One of the possibilities to explain the sunquakes and other signatures of the photospheric impact is to consider additional heating mechanisms involved in solar flares, for example, via flare-accelerated protons. In this work, we analyze a set of single-loop RADYN+FP simulations where the atmosphere is heated by non-thermal power-law-distributed proton beams which can penetrate deeper than the electron beams into the low atmospheric layers. Using the output of the RADYN models, we calculate synthetic Fe I 6173 A line Stokes profiles and from those the line-of-sight (LOS) observables of the SDO/HMI instrument, as well as the 3D helioseismic response and compare them with the corresponding observational characteristics. These initial results show that the models with proton beam heating can produce the enhancement of the HMI continuum observable and explain qualitatively generation of sunquakes. The continuum observable enhancement is evident in all models but is more prominent in ones with $E_{c}\geq$500 keV. In contrast, the models with $E_{c}\leq$100 keV provide a stronger sunquake-like helioseismic impact according to the 3D acoustic modeling, suggesting that low-energy (deka- and hecto-keV) protons have an important role in the generation of sunquakes.Comment: 20 pages, 10 figures, 2 table