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+$\newcommand{\saber}{{\small astro}\textsc{Saber}}$</div>
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+<div id="title">
+
+# Cold atomic gas identified by $\ion{H}{i}$ self-absorption
+
+</div>
+<div id="comments">
+
+[![arXiv](https://img.shields.io/badge/arXiv-2310.02077-b31b1b.svg)](https://arxiv.org/abs/2310.02077)<mark>Appeared on: 2023-10-04</mark> -  _41 pages, 28 figures, accepted for publication in A&A_
+
+</div>
+<div id="authors">
+
+<mark>J. Syed</mark>, et al. -- incl., <mark>H. Beuther</mark>
+
+</div>
+<div id="abstract">
+
+**Abstract:** Stars form in the dense interiors of molecular clouds. The dynamics and physical properties of the atomic interstellar medium (ISM) set the conditions under which molecular clouds and eventually stars will form. It is, therefore, critical to investigate the relationship between the atomic and molecular gas phase to understand the global star formation process. Using the high angular resolution data from The $\ion{H}{i}$ /OH/Recombination line survey of the Milky Way (THOR), we aim to constrain the kinematic and physical properties of the cold atomic hydrogen gas phase toward the inner Galactic plane. $\ion{H}{i}$ self-absorption (HISA) has proven to be a viable method to detect cold atomic hydrogen clouds in the Galactic plane. With the help of a newly developed self-absorption extraction routine ( $\saber$ ), we build upon previous case studies to identify $\ion{H}{i}$ self-absorption toward a sample of Giant Molecular Filaments (GMFs). We find the cold atomic gas to be spatially correlated with the molecular gas on a global scale. The column densities of the cold atomic gas traced by HISA are usually of the order of $10^{20}\rm cm^{-2}$ whereas those of molecular hydrogen traced by $\element[][13]{CO}$ are at least an order of magnitude higher. The HISA column densities are attributed to a cold gas component that accounts for a fraction of $\sim$ 5 \% of the total atomic gas budget within the clouds. The HISA column density distributions show pronounced log-normal shapes that are broader than those traced by $\ion{H}{i}$ emission. The cold atomic gas is found to be moderately supersonic with Mach numbers of a $\sim$ few. In contrast, highly supersonic dynamics drive the molecular gas within most filaments. While $\ion{H}{i}$ self-absorption is likely to trace just a small fraction of the total cold neutral medium within a cloud, probing the cold atomic ISM by the means of self-absorption significantly improves our understanding of the dynamical and physical interaction between the atomic and molecular gas phase during cloud formation.
+
+</div>
+
+<div id="div_fig1">
+
+<img src="tmp_2310.02077/./test_extraction_paper_workflow_alt.png" alt="Fig3" width="100%"/>
+
+**Figure 3. -** Baseline extraction workflow of $\saber$ . In each panel, the black mock spectrum represents the observed $\ion${H}{i} emission spectrum, which is the sum of the three gray dashed components,  with self-absorption features (two red dashed components) superposed. The blue spectrum shows the "pure emission" spectrum that is to be recovered by the $\saber$  algorithm. The algorithm is then applied to the observed spectrum using the optimal smoothing parameters $(\lambda_1,\lambda_2)$. Hatched red areas indicate spectral channels that are masked out due to missing signal. _Left panel:_ The $\saber$  baseline (red) after the first major cycle iteration, that is, after the minor cycle smoothing converged given the input mock spectrum (i.e. after Eq. \eqref{equ:least_squ} has been solved for $\mathbf{z}$). _Middle panel:_ The $\saber$  baseline (red) after the last major cycle iteration, that is, after the major cycle smoothing converged and before adding the residual, which is the absolute difference between the first and last major cycle iteration. _Right panel:_ The final $\saber$  baseline (red) after adding the residual. The baseline so obtained reproduces the pure emission spectrum (blue) well. The resulting HISA features expressed as equivalent emission features are shown in green, and show a good match with the the real HISA absorption features. The smaller subpanels in each column show the residual, which is the difference between the red baseline and the blue emission spectrum, with the horizontal dotted red lines marking values of $\pm\sigma_\mathrm{rms}$. (*fig:mock_spectrum*)
+
+</div>
+<div id="div_fig2">
+
+<img src="tmp_2310.02077/./parameter_space_rchi2_paper.png" alt="Fig1" width="100%"/>
+
+**Figure 1. -** Smoothing parameter optimization using gradient descent. The map shows a sampled representation of the underlying $\vec\lambda$ parameter space in terms of the median value of the reduced chi square results. Initial values, tracks, and convergence locations of the $(\lambda_1,\lambda_2)$ parameters during the optimization are represented by black circles, black lines, and white crosses, respectively. The red cross marks the global minimum in the sampled parameter space. Initial locations that start off too far from the global best solution $(\lambda_1=3.5,\lambda_2=0.6)$ might converge to local minima with less accurate fit results. (*fig:parameter_space*)
+
+</div>
+<div id="div_fig3">
+
+<img src="tmp_2310.02077/./test_second_derivative.png" alt="Fig2" width="100%"/>
+
+**Figure 2. -** Second derivative representation as a means to identify self-absorption. _Top panel:_ The black mock spectrum represents the $\ion${H}{i} emission spectrum, with two self-absorption features superposed (red dashed components) and without any observational noise. The green spectrum shows the second derivative of the black mock spectrum, obtained from the finite differences between spectral channels. _Bottom panel:_ The black mock spectrum represents the $\ion${H}{i} emission spectrum, with two self-absorption features superposed (red dashed components) and with added noise that is comparable to the noise of the THOR-$\ion${H}{i} observations (same spectrum as in Fig. \ref{fig:mock_spectrum}). The green spectrum shows the second derivative of the black mock spectrum, obtained from the finite differences between spectral channels. The dashed blue spectrum represents a regularized least squares solution to the $\ion${H}{i} spectrum, which minimizes the second derivative. The corresponding second derivative is shown in blue, which is now less affected by noise fluctuations. (*fig:second_derivative*)
+
+</div><div id="qrcode"><img src=https://api.qrserver.com/v1/create-qr-code/?size=100x100&data="https://arxiv.org/abs/2310.02077"></div>

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docs/_build/html/logs/log-2023-10-04.md

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+# Arxiv on Deck 2: Logs - 2023-10-04
+
+* Arxiv had 72 new papers
+    * 3 with possible author matches
+
+## Sucessful papers
+
+
+|||
+|---:|:---|
+| [![arXiv](https://img.shields.io/badge/arXiv-arXiv:2310.02077-b31b1b.svg)](https://arxiv.org/abs/arXiv:2310.02077) | **Cold atomic gas identified by HI self-absorption. Cold atomic clouds  toward giant molecular filaments**  |
+|| <mark>J. Syed</mark>, et al. -- incl., <mark>H. Beuther</mark> |
+|*Appeared on*| *2023-10-04*|
+|*Comments*| *41 pages, 28 figures, accepted for publication in A&A*|
+|**Abstract**| Stars form in the dense interiors of molecular clouds. The dynamics and physical properties of the atomic interstellar medium (ISM) set the conditions under which molecular clouds and eventually stars will form. It is, therefore, critical to investigate the relationship between the atomic and molecular gas phase to understand the global star formation process. Using the high angular resolution data from The HI/OH/Recombination line survey of the Milky Way (THOR), we aim to constrain the kinematic and physical properties of the cold atomic hydrogen gas phase toward the inner Galactic plane. HI self-absorption (HISA) has proven to be a viable method to detect cold atomic hydrogen clouds in the Galactic plane. With the help of a newly developed self-absorption extraction routine (astroSABER), we build upon previous case studies to identify HI self-absorption toward a sample of Giant Molecular Filaments (GMFs). We find the cold atomic gas to be spatially correlated with the molecular gas on a global scale. The column densities of the cold atomic gas traced by HISA are usually of the order of $10^{20}\rm\,cm^{-2}$ whereas those of molecular hydrogen traced by $\rm^{13}CO$ are at least an order of magnitude higher. The HISA column densities are attributed to a cold gas component that accounts for a fraction of $\sim$5% of the total atomic gas budget within the clouds. The HISA column density distributions show pronounced log-normal shapes that are broader than those traced by HI emission. The cold atomic gas is found to be moderately supersonic with Mach numbers of a $\sim$few. In contrast, highly supersonic dynamics drive the molecular gas within most filaments. |
+
+## Failed papers
+
+### affiliation error: mpia.affiliation_verifications: '69117' keyword not found. 
+
+
+|||
+|---:|:---|
+| [![arXiv](https://img.shields.io/badge/arXiv-arXiv:2310.01725-b31b1b.svg)](https://arxiv.org/abs/arXiv:2310.01725) | **Super-Earth LHS3844b is tidally locked**  |
+|| X. Lyu, et al. -- incl., <mark>L. Kreidberg</mark> |
+|*Appeared on*| *2023-10-04*|
+|*Comments*| *Submitted*|
+|**Abstract**| Short period exoplanets on circular orbits are thought to be tidally locked into synchronous rotation. If tidally locked, these planets must possess permanent day- and nightsides, with extreme irradiation on the dayside and none on the nightside. However, so far the tidal locking hypothesis for exoplanets is supported by little to no empirical evidence. Previous work showed that the super-Earth LHS 3844b likely has no atmosphere, which makes it ideal for constraining the planet's rotation. Here we revisit the Spitzer phase curve of LHS 3844b with a thermal model of an atmosphere-less planet and analyze the impact of non-synchronous rotation, eccentricity, tidal dissipation, and surface composition. Based on the lack of observed strong tidal heating we rule out rapid non-synchronous rotation (including a Mercury-like 3:2 spin-orbit resonance) and constrain the planet's eccentricity to less than 0.001 (more circular than Io's orbit). In addition, LHS 3844b's phase curve implies that the planet either still experiences weak tidal heating via a small-but-nonzero eccentricity (requiring an undetected orbital companion), or that its surface has been darkened by space weathering; of these two scenarios we consider space weathering more likely. Our results thus support the hypothesis that short period rocky exoplanets are tidally locked, and further show that space weathering can significantly modify the surfaces of atmosphere-less exoplanets. |
+|<p style="color:green"> **ERROR** </p>| <p style="color:green">affiliation error: mpia.affiliation_verifications: '69117' keyword not found.</p> |
+
+### latex error list index out of range 
+
+
+|||
+|---:|:---|
+| [![arXiv](https://img.shields.io/badge/arXiv-arXiv:2310.02213-b31b1b.svg)](https://arxiv.org/abs/arXiv:2310.02213) | **Turbulent Structure In Supernova Remnants G46.8-0.3 And G39.2-0.3 From  THOR Polarimetry**  |
+|| R. Shanahan, et al. -- incl., <mark>H. Beuther</mark> |
+|*Appeared on*| *2023-10-04*|
+|*Comments*| *Has been accepted by ApJ for publication. Figures 3 and 4 did do not render well when using an internet browser to view them, but when the pdf file is downloaded these figures look as they should*|
+|**Abstract**| We present the continued analysis of polarization and Faraday rotation for the supernova remnants (SNRs) G46.8-0.3 and G39.2-0.3 in L-band (1-2 GHz) radio continuum in The HI/OH/Recombination line (THOR) survey. In this work, we present our investigation of Faraday depth fluctuations from angular scales comparable to the size of the SNRs down to scales less than our 16" beam (<~0.7 pc) from Faraday dispersion (sigma_phi). From THOR, we find median sigma_phi of 15.9 +/- 3.2 rad m^-2 for G46.8-0.3 and 17.6 +/- 1.6 rad m^-2 for G39.2-0.3. When comparing to polarization at 6cm, we find evidence for sigma_phi >~ 30 rad m^-2 in localized regions where we detect no polarization in THOR. We combine Faraday depth dispersion with the rotation measure (RM) structure function (SF) and find evidence for a break in the SF on scales less than the THOR beam. We estimate the RM SF of the foreground interstellar medium (ISM) using the SF of extra-Galactic radio sources (EGRS) and pulsars to find that the RM fluctuations we measure originate within the SNRs for all but the largest angular scales. |
+|<p style="color:red"> **ERROR** </p>| <p style="color:red">latex error list index out of range</p> |
+