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The precursors to larger, biologically-relevant molecules are detected throughout interstellar space, but determining the presence and properties of these molecules during planet formation requires observations of protoplanetary disks at high angular resolution and sensitivity. Here we present 0.3" observations of HC$_3$N, CH$_3$CN, and $c$-C$_3$H$_2$ in five protoplanetary disks observed as part of the Molecules with ALMA at Planet-forming Scales (MAPS) Large Program. We robustly detect all molecules in four of the disks (GM Aur, AS 209, HD 163296 and MWC 480) with tentative detections of $c$-C$_3$H$_2$ and CH$_3$CN in IM Lup. We observe a range of morphologies -- central peaks, single or double rings -- with no clear correlation in morphology between molecule nor disk. Emission is generally compact and on scales comparable with the millimetre dust continuum. We perform both disk-integrated and radially-resolved rotational diagram analysis to derive column densities and rotational temperatures. The latter reveals 5-10 times more column density in the inner 50-100 au of the disks when compared with the disk-integrated analysis. We demonstrate that CH$_3$CN originates from lower relative heights in the disks when compared with HC$_3$N, in some cases directly tracing the disk midplane. Finally, we find good agreement between the ratio of small to large nitriles in the outer disks and comets. Our results indicate that the protoplanetary disks studied here are host to significant reservoirs of large organic molecules, and that this planet- and comet-building material can be chemically similar to that in our own Solar System. This paper is part of the MAPS special issue of the Astrophysical Journal Supplement Series., Comment: 24 pages, 11 figures, 5 tables. Accepted for publication in ApJSS. Updated to cross-reference other MAPS publications

Sulfur-bearing molecules play an important role in prebiotic chemistry and planet habitability. They are also proposed probes of chemical ages, elemental C/O ratio, and grain chemistry processing. Commonly detected in diverse astrophysical objects, including the Solar System, their distribution and chemistry remain, however, largely unknown in planet-forming disks. We present CS ($2-1$) observations at $\sim0."3$ resolution performed within the ALMA-MAPS Large Program toward the five disks around IM Lup, GM Aur, AS 209, HD 163296, and MWC 480. CS is detected in all five disks, displaying a variety of radial intensity profiles and spatial distributions across the sample, including intriguing apparent azimuthal asymmetries. Transitions of C$_2$S and SO were also serendipitously covered but only upper limits are found. For MWC 480, we present complementary ALMA observations at $\sim0."5$, of CS, $^{13}$CS, C$^{34}$S, H$_2$CS, OCS, and SO$_2$. We find a column density ratio N(H$_{2}$CS)/N(CS)$\sim2/3$, suggesting that a substantial part of the sulfur reservoir in disks is in organic form (i.e., C$_x$H$_y$S$_z$). Using astrochemical disk modeling tuned to MWC 480, we demonstrate that $N$(CS)/$N$(SO) is a promising probe for the elemental C/O ratio. The comparison with the observations provides a super-solar C/O. We also find a depleted gas-phase S/H ratio, suggesting either that part of the sulfur reservoir is locked in solid phase or that it remains in an unidentified gas-phase reservoir. This paper is part of the MAPS special issue of the Astrophysical Journal Supplement., Comment: Accepted for publication in The Astrophysical Journal Supplement (27 pages, 13 figures, 5 tables)

Emission substructures in gas and dust are common in protoplanetary disks. Such substructures can be linked to planet formation or planets themselves. We explore the observed gas substructures in AS 209 using thermochemical modeling with RAC2D and high-spatial resolution data from the Molecules with ALMA at Planet-forming Scales(MAPS) program. The observations of C$^{18}$O J=2-1 emission exhibit a strong depression at 88 au overlapping with the positions of multiple gaps in millimeter dust continuum emission. We find that the observed CO column density is consistent with either gas surface-density perturbations or chemical processing, while C$_2$H column density traces changes in the C/O ratio rather than the H$_2$ gas surface density. However, the presence of a massive planet (> 0.2 M$_{Jup}$) would be required to account for this level of gas depression, which conflicts with constraints set by the dust emission and the pressure profile measured by gas kinematics. Based on our models, we infer that a local decrease of CO abundance is required to explain the observed structure in CO, dominating over a possible gap-carving planet present and its effect on the H$_2$ surface density. This paper is part of the MAPS special issue of the Astrophysical Journal Supplement Series., Comment: 21 pages, 18 figures

Here we present high resolution (15-24 au) observations of CO isotopologue lines from the Molecules with ALMA on Planet-forming Scales (MAPS) ALMA Large Program. Our analysis employs $^{13}$CO and C$^{18}$O ($J$=2-1), (1-0), and C$^{17}$O (1-0) line observations of five protoplanetary disks. We retrieve CO gas density distributions, using three independent methods: (1) a thermo-chemical modeling framework based on the CO data, the broadband spectral energy distribution, and the mm-continuum emission; (2) an empirical temperature distribution based on optically thick CO lines; and (3) a direct fit to the C$^{17}$O hyperfine lines. Results from these methods generally show excellent agreement. The CO gas column density profiles of the five disks show significant variations in the absolute value and the radial shape. Assuming a gas-to-dust mass ratio of 100, all five disks have a global CO-to-H$_2$ abundance of 10-100 times lower than the ISM ratio. The CO gas distributions between 150-400 au match well with models of viscous disks, supporting the long-standing theory. CO gas gaps appear to be correlated with continuum gap locations, but some deep continuum gaps do not have corresponding CO gaps. The relative depths of CO and dust gaps are generally consistent with predictions of planet-disk interactions, but some CO gaps are 5-10 times shallower than predictions based on dust gaps. This paper is part of the MAPS special issue of the Astrophysical Journal Supplement., Comment: This paper is part of the MAPS special issue of the Astrophysical Journal Supplement. 36 pages, 21 figures, accepted for publication in ApJS

Gas mass remains one of the most difficult protoplanetary disk properties to constrain. With much of the protoplanetary disk too cold for the main gas constituent, H2, to emit, alternative tracers such as dust, CO, or the H2 isotopolog HD are used. However, relying on disk mass measurements from any single tracer requires assumptions about the tracer's abundance relative to \hh\ and the disk temperature structure. Using new Atacama Large Millimeter/submillimeter Array (ALMA) observations from the Molecules with ALMA at Planet-forming Scales (MAPS) ALMA Large Program as well as archival ALMA observations, we construct a disk physical/chemical model of the protoplanetary disk GM Aur. Our model is in good agreement with the spatially resolved CO isotopolog emission from eleven rotational transitions with spatial resolution ranging from 0.15'' to 0.46'' (24-73 au at 159 pc) and the spatially unresolved HD J=1-0 detection from Herschel. Our best-fit model favors a cold protoplanetary disk with a total gas mass of approximately 0.2 solar masses, a factor of 10 reduction in CO gas inside roughly 100 au and a factor of 100 reduction outside of 100 au. Despite its large mass, the disk appears to be on the whole gravitationally stable based on the derived Toomre Q parameter. However, the region between 70 and 100 au, corresponding to one of the millimeter dust rings, is close to being unstable based on the calculated Toomre Q of <1.7. This paper is part of the MAPS special issue of the Astrophysical Journal Supplement., Comment: 18 pages, 12 figures

The Molecules with ALMA at Planet-forming Scales (MAPS) Large Program provides a unique opportunity to study the vertical distribution of gas, chemistry, and temperature in the protoplanetary disks around IM Lup, GM Aur, AS 209, HD 163296, and MWC 480. By using the asymmetry of molecular line emission relative to the disk major axis, we infer the emission height ($z$) above the midplane as a function of radius ($r$). Using this method, we measure emitting surfaces for a suite of CO isotopologues, HCN, and C$_2$H. We find that $^{12}$CO emission traces the most elevated regions with $z/r > 0.3$, while emission from the less abundant $^{13}$CO and C$^{18}$O probes deeper into the disk at altitudes of $z/r \lesssim 0.2$. C$_2$H and HCN have lower opacities and SNRs, making surface fitting more difficult, and could only be reliably constrained in AS 209, HD 163296, and MWC 480, with $z/r \lesssim 0.1$, i.e., relatively close to the planet-forming midplanes. We determine peak brightness temperatures of the optically thick CO isotopologues and use these to trace 2D disk temperature structures. Several CO temperature profiles and emission surfaces show dips in temperature or vertical height, some of which are associated with gaps and rings in line and/or continuum emission. These substructures may be due to local changes in CO column density, gas surface density, or gas temperatures, and detailed thermo-chemical models are necessary to better constrain their origins and relate the chemical compositions of elevated disk layers with those of planet-forming material in disk midplanes. This paper is part of the MAPS special issue of the Astrophysical Journal Supplement., Comment: 31 pages, 20 figures, accepted for publication in ApJS, MAPS cross-references updated

The concentric gaps and rings commonly observed in protoplanetary disks in millimeter continuum emission have lent the impression that planet formation generally proceeds within orderly, isolated systems. While deep observations of spatially resolved molecular emission have been comparatively limited, they are increasingly suggesting that some disks interact with their surroundings while planet formation is underway. We present an analysis of complex features identified around GM Aur in $^{12}$CO $J=2-1$ images at a spatial resolution of $\sim40$ au. In addition to a Keplerian disk extending to a radius of $\sim550$ au, the CO emission traces flocculent spiral arms out to radii of $\sim$1200 au, a tail extending $\sim1800$ au southwest of GM Aur, and diffuse structures extending from the north side of the disk up to radii of $\sim1900$ au. The diffuse structures coincide with a "dust ribbon" previously identified in scattered light. The large-scale asymmetric gas features present a striking contrast with the mostly axisymmetric, multi-ringed millimeter continuum tracing the pebble disk. We hypothesize that GM Aur's complex gas structures result from late infall of remnant envelope or cloud material onto the disk. The morphological similarities to the SU Aur and AB Aur systems, which are also located in the L1517 cloud, provide additional support to a scenario in which interactions with the environment are playing a role in regulating the distribution and transport of material in all three of these Class II disk systems. This paper is part of the MAPS special issue of the Astrophysical Journal Supplement., Comment: 34 pages, 21 figures, in press at ApJS, cross-references updated

Constraining the distribution of gas and dust in the inner 20 au of protoplanetary disks is difficult. At the same time, this region is thought to be responsible for most planet formation, especially around the water ice line at 3-10 au. Under the assumption that the gas is in a Keplerian disk, we use the exquisite sensitivity of the Molecules with ALMA at Planet-forming Scales (MAPS) ALMA large program to construct radial surface brightness profiles with a ~3 au effective resolution for the CO isotopologue J=2-1 lines using the line velocity profile. IM Lup reveals a central depression in 13CO and C18O that is ascribed to a pileup of ~500 $M_\oplus$ of dust in the inner 20 au, leading to a gas-to-dust ratio of around <10. This pileup is consistent with efficient drift of grains ($\gtrsim$ 100 $M_\oplus$ Myr$^{-1}$) and a local gas-to-dust ratio that suggests that the streaming instability could be active. The CO isotopologue emission in the GM Aur disk is consistent with a small (~15 au), strongly depleted gas cavity within the ~40 au dust cavity. The radial surface brightness profiles for both the AS 209 and HD 163296 disks show a local minimum and maximum in the C18O emission at the location of a known dust ring (~14 au) and gap (~10 au), respectively. This indicates that the dust ring has a low gas-to-dust ratio ($>$ 10) and that the dust gap is gas-rich enough to have optically thick C18O., Comment: 22 pages, 14 figures, accepted by ApJS. This paper is part of the MAPS special issue of the Astrophysical Journal Supplement. Update with correct references to other MAPS papers

The elemental composition of the gas and dust in a protoplanetary disk influences the compositions of the planets that form in it. We use the Molecules with ALMA at Planet-forming Scales (MAPS) data to constrain the elemental composition of the gas at the locations of potentially forming planets. The elemental abundances are inferred by comparing source-specific gas-grain thermochemical models, with variable C/O ratios and small-grain abundances, from the DALI code with CO and C2H column densities derived from the high-resolution observations of the disks of AS 209, HD 163296, and MWC 480. Elevated C/O ratios (~2.0), even within the CO ice line, are necessary to match the inferred C2H column densities, over most of the pebble disk. Combined with constraints on the CO abundances in these systems, this implies that both the O/H and C/H ratios in the gas are substellar by a factor of 4-10, with the O/H depleted by a factor of 20-50, resulting in the high C/O ratios. This necessitates that even within the CO ice line, most of the volatile carbon and oxygen is still trapped on grains in the midplane. Planets accreting gas in the gaps of the AS 209, HD 163296, and MWC 480 disks will thus acquire very little carbon and oxygen after reaching the pebble isolation mass. In the absence of atmosphere-enriching events, these planets would thus have a strongly substellar O/H and C/H and superstellar C/O atmospheric composition., Comment: 19 pages, 8 figures This paper is part of the MAPS special issue of the Astrophysical Journal Supplement. Updates references for other MAPS papers

We explore the dynamical structure of the protoplanetary disks surrounding HD 163296 and MWC 480 as part of the Molecules with ALMA at Planet Forming Scales (MAPS) large program. Using the $J = 2-1$ transitions of $^{12}$CO, $^{13}$CO and C$^{18}$O imaged at spatial resolutions of $\sim 0.^{\prime \prime}15$ and with a channel spacing of $200$ ${\rm m\,s^{-1}}$, we find perturbations from Keplerian rotation in the projected velocity fields of both disks ($\lesssim\!5\%$ of the local Keplerian velocity), suggestive of large-scale (10s of au in size), coherent flows. By accounting for the azimuthal dependence on the projection of the velocity field, the velocity fields were decomposed into azimuthally averaged orthogonal components, $v_{\phi}$, $v_r$ and $v_z$. Using the optically thick $^{12}$CO emission as a probe of the gas temperature, local variations of $\approx\! 3$ K ($\approx\! 5 \%$ relative changes) were observed and found to be associated with the kinematic substructures. The MWC 480 disk hosts a suite of tightly wound spiral arms. The spirals arms, in conjunction with the highly localized perturbations in the gas velocity structure (kinematic planetary signatures), indicate a giant planet, $\sim\! 1$ $M_{\rm Jup}$, at a radius of $\approx 245$ au. In the disk of HD 163296, the kinematic substructures were consistent with previous studies of Pinte et al. (2018a) and Teague et al. (2018a) advocating for multiple $\sim\! 1$ $M_{\rm Jup}$ planets embedded in the disk. These results demonstrate that molecular line observations that characterize the dynamical structure of disks can be used to search for the signatures of embedded planets. This paper is part of the MAPS special issue of the Astrophysical Journal Supplement., Comment: 32 pages, 21 figures, accepted for publication in ApJS, MAPS cross-references updated

The Molecules with ALMA at Planet-forming Scales (MAPS) Large Program provides a detailed, high resolution (${\sim}$10-20 au) view of molecular line emission in five protoplanetary disks at spatial scales relevant for planet formation. Here, we present a systematic analysis of chemical substructures in 18 molecular lines toward the MAPS sources: IM Lup, GM Aur, AS 209, HD 163296, and MWC 480. We identify more than 200 chemical substructures, which are found at nearly all radii where line emission is detected. A wide diversity of radial morphologies - including rings, gaps, and plateaus - is observed both within each disk and across the MAPS sample. This diversity in line emission profiles is also present in the innermost 50 au. Overall, this suggests that planets form in varied chemical environments both across disks and at different radii within the same disk. Interior to 150 au, the majority of chemical substructures across the MAPS disks are spatially coincident with substructures in the millimeter continuum, indicative of physical and chemical links between the disk midplane and warm, elevated molecular emission layers. Some chemical substructures in the inner disk and most chemical substructures exterior to 150 au cannot be directly linked to dust substructure, however, which indicates that there are also other causes of chemical substructures, such as snowlines, gradients in UV photon fluxes, ionization, and radially-varying elemental ratios. This implies that chemical substructures could be developed into powerful probes of different disk characteristics, in addition to influencing the environments within which planets assemble. This paper is part of the MAPS special issue of the Astrophysical Journal Supplement., Comment: 62 pages, 31 figures, accepted for publication in ApJS, MAPS cross-references updated, corrected Figure 21, updated gas disk sizes (Table 2, Figures 15-16) from associated Erratum

The Molecules with ALMA at Planet-forming Scales large program (MAPS LP) surveyed the chemical structures of five protoplanetary disks across more than 40 different spectral lines at high angular resolution (0.15" and 0.30" beams for Bands 6 and 3, respectively) and sensitivity (spanning 0.3 - 1.3 mJy/beam and 0.4 - 1.9 mJy/beam for Bands 6 and 3, respectively). In this article, we describe our multi-stage workflow -- built around the CASA tclean image deconvolution procedure -- that we used to generate the core data product of the MAPS LP: the position-position-velocity image cubes for each spectral line. Owing to the expansive nature of the survey, we encountered a range of imaging challenges; some are familiar to the sub-mm protoplanetary disk community, like the benefits of using an accurate CLEAN mask, and others less well-known, like the incorrect default flux scaling of the CLEAN residual map first described in Jorsater & van Moorsel 1995 (the "JvM effect"). We distill lessons learned into recommended workflows for synthesizing image cubes of molecular emission. In particular, we describe how to produce image cubes with accurate fluxes via the "JvM correction," a procedure that is generally applicable to any image synthesized via CLEAN deconvolution but is especially critical for low S/N emission. We further explain how we used visibility tapering to promote a common, fiducial beam size and contextualize the interpretation of signal to noise ratio when detecting molecular emission from protoplanetary disks. This paper is part of the MAPS special issue of the Astrophysical Journal Supplement., Comment: ApJS accepted. Part of the MAPS ALMA large program series: http://www.alma-maps.info/. Updated bibliography with MAPS LP arXiv references

To date, at least three comets -- 2I/Borisov, C/2016 R2 (PanSTARRS), and C/2009 P1 (Garradd) -- have been observed to have unusually high CO concentrations compared to water. We attempt to explain these observations by modeling the effect of drifting solid (ice and dust) material on the ice compositions in protoplanetary disks. We find that, independent of the exact disk model parameters, we always obtain a region of enhanced ice-phase CO/H2O that spreads out in radius over time. The inner edge of this feature coincides with the CO snowline. Almost every model achieves at least CO/H2O of unity, and one model reaches a CO/H2O ratio > 10. After running our simulations for 1 Myr, an average of 40% of the disk ice mass contains more CO than H2O ice. In light of this, a population of CO ice enhanced planetesimals are likely to generally form in the outer regions of disks, and we speculate that the aforementioned CO-rich comets may be more common, both in our own Solar System and in extrasolar systems, than previously expected., Comment: 13 pages, 5 figures; accepted for publication in ApJ

Massive star-forming regions exhibit an extremely rich and diverse chemistry, which in principle provides a wealth of molecular probes, as well as laboratories for interstellar prebiotic chemistry. Since the chemical structure of these sources displays substantial spatial variation among species on small scales (${\lesssim}10^4$ au), high angular resolution observations are needed to connect chemical structures to local environments and inform astrochemical models of massive star formation. To address this, we present ALMA 1.3 mm observations toward OB cluster-forming region G10.6-0.4 (hereafter "G10.6") at a resolution of 0.14$^{\prime\prime}$ (700 au). We find highly-structured emission from complex organic molecules (COMs) throughout the central 20,000 au, including two hot molecular cores and several shells or filaments. We present spatially-resolved rotational temperature and column density maps for a large sample of COMs and warm gas tracers. These maps reveal a range of gas substructure in both O- and N-bearing species. We identify several spatial correlations that can be explained by existing models of COM formation, including NH$_2$CHO/HNCO and CH$_3$OCHO/CH$_3$OCH$_3$, but also observe unexpected distributions and correlations which suggest that our current understanding of COM formation is far from complete. Importantly, complex chemistry is observed throughout G10.6, rather than being confined to hot cores. The COM composition appears to be different in the cores compared to the more extended structures, which illustrates the importance of high spatial resolution observations of molecular gas in elucidating the physical and chemical processes associated with massive star formation., Comment: 41 pages, 25 figures, accepted for publication in ApJ

In this era of Gaia and ALMA, dynamical stellar mass measurements provide benchmarks that are independent of observations of stellar characteristics and their uncertainties. These benchmarks can then be used to validate and improve stellar evolutionary models, which can lead to both imprecise and inaccurate mass predictions for pre-main-sequence, low-mass stars. We present the dynamical stellar masses derived from disks around three M-stars (FP Tau, J0432+1827, and J1100-7619) using ALMA observations of $^{12}$CO (J=2--1) and $^{13}$CO (J=2--1) emission. These are the first dynamical stellar mass measurements for J0432+1827 and J1100-7619 and the most precise measurement for FP Tau. Fiducial stellar evolutionary model tracks, which do not include any treatment of magnetic activity, agree with the dynamical measurement of J0432+1827 but underpredict the mass by $\sim$60\% for FP Tau and $\sim$80\% for J1100-7619. Possible explanations for the underpredictions include inaccurate assumptions of stellar effective temperature, undetected binarity for J1100-7619, and that fiducial stellar evolutionary models are not complex enough to represent these stars. In the former case, the stellar effective temperatures would need to be increased by $\sim$40K to $\sim$340K to reconcile the fiducial model predictions with the dynamically-measured masses. In the latter case, we show that the dynamical masses can be reproduced using results from stellar evolutionary models with starspots, which incorporate fractional starspot coverage to represent the manifestation of magnetic activity. Folding in low-mass M-stars from the literature and assuming that the stellar effective temperatures are imprecise but accurate, we find tentative evidence of a relationship between fractional starspot coverage and observed effective temperature for these young, cool stars., Comment: 37 pages (14 pages in the main document, 23 pages in the appendix), 35 figures, 5 tables. Accepted in ApJ (December 2020)

Formaldehyde (H$_2$CO) is an important precursor to organics like methanol (CH$_3$OH). It is important to understand the conditions that produce H$_2$CO and prebiotic molecules during star and planet formation. H$_2$CO possesses both gas-phase and solid-state formation pathways, involving either UV-produced radical precursors or CO ice and cold ($\lesssim 20$ K) dust grains. To understand which pathway dominates, gaseous H$_2$CO's ortho-to-para ratio (OPR) has been used as a probe, with a value of 3 indicating "warm" conditions and $<3$ linked to cold formation in the solid-state. We present spatially resolved ALMA observations of multiple ortho- and para-H$_2$CO transitions in the TW Hya protoplanetary disk to test H$_2$CO formation theories during planet formation. We find disk-averaged rotational temperatures and column densities of $33\pm2$ K, ($1.1\pm0.1)\times10^{12}$ cm$^{-2}$ and $25\pm2$ K, $(4.4\pm0.3)\times10^{11}$ cm$^{-2}$ for ortho- and para-H$_2$CO, respectively, and an OPR of $2.49\pm0.23$. A radially resolved analysis shows that the observed H$_2$CO emits mostly at rotational temperatures of 30-40 K, corresponding to a layer with $z/R\ge0.25$. The OPR is consistent with 3 within 60 au, the extent of the pebble disk, and decreases beyond 60 au to $2.0\pm0.5$. The latter corresponds to a spin temperature of 12 K, well below the rotational temperature. The combination of relatively uniform emitting conditions, a radial gradient in the OPR, and recent laboratory experiments and theory on OPR ratios after sublimation, lead us to speculate that gas-phase formation is responsible for the observed H$_2$CO across the TW Hya disk.

The ionization fraction plays a key role in the physics and chemistry of the neutral interstellar medium, from controlling the coupling of the gas to the magnetic field to allowing fast ion-neutral reactions that drive interstellar chemistry. Most estimations of the ionization fraction have relied on deuterated species such as DCO+, whose detection is limited to dense cores representing an extremely small fraction of the volume of the giant molecular clouds they are part of. As large field-of-view hyperspectral maps become available, new tracers may be found. We search for the best observable tracers of the ionization fraction based on a grid of astrochemical models. We build grids of models that sample randomly a large space of physical conditions (unobservable quantities such as gas density, temperature, etc.) and compute the corresponding observables (line intensities, column densities) and the ionization fraction. We estimate the predictive power of each potential tracer by training a Random Forest model to predict the ionization fraction from that tracer, based on these model grids. In both translucent medium and cold dense medium conditions, several observable tracers with very good predictive power for the ionization fraction are found. Several tracers in cold dense medium conditions are found to be better and more widely applicable than the traditional DCO+/HCO+ ratio. We also provide simpler analytical fits for estimating the ionization fraction from the best tracers, and for estimating the associated uncertainties. We discuss the limitations of the present study and select a few recommended tracers in both types of conditions. The method presented here is very general and can be applied to the measurement of any other quantity of interest (cosmic ray flux, elemental abundances, etc.) from any type of model (PDR models, time-dependent chemical models, etc.). (abridged), Comment: 29 pages, 15 figures. Accepted for publication in A&A

While protoplanetary disks often appear to be compact and well-organized in millimeter continuum emission, CO spectral line observations are increasingly revealing complex behavior at large distances from the host star. We present deep ALMA maps of the $J=2-1$ transition of $^{12}$CO, $^{13}$CO, and C$^{18}$O, as well as the $J=3-2$ transition of DCO$^+$, toward the T Tauri star RU Lup at a resolution of $\sim0.3''$ ($\sim50$ au). The CO isotopologue emission traces four major components of the RU Lup system: a compact Keplerian disk with a radius of $\sim120$ au, a non-Keplerian ``envelope-like'' structure surrounding the disk and extending to $\sim260$ au from the star, at least five blueshifted spiral arms stretching up to 1000 au, and clumps outside the spiral arms located up to 1500 au in projection from RU Lup. We comment on potential explanations for RU Lup's peculiar gas morphology, including gravitational instability, accretion of material onto the disk, or perturbation by another star. RU Lup's extended non-Keplerian CO emission, elevated stellar accretion rate, and unusual photometric variability suggest that it could be a scaled-down Class II analog of the outbursting FU Ori systems., Comment: 32 pages, 13 figures, accepted by ApJ. Typos corrected. Data are available at https://zenodo.org/record/3928862

The volatile contents of protoplanetary disks both set the potential for planetary chemistry and provide valuable probes of defining disk system characteristics such as stellar mass, gas mass, ionization, and temperature structure. Current disk molecular inventories are fragmented, however, giving an incomplete picture: unbiased spectral line surveys are needed to assess the volatile content. We present here an overview of such a survey of the protoplanetary disks around the Herbig Ae star MWC 480 and the T Tauri star LkCa 15 in ALMA Band 7, spanning $\sim$36 GHz from 275--317 GHz and representing an order of magnitude increase in sensitivity over previous single-dish surveys. We detect 14 molecular species (including isotopologues), with 5 species (C$^{34}$S, $^{13}$CS, H$_{2}$CS, DNC, and C$_2$D) detected for the first time in protoplanetary disks. Significant differences are observed in the molecular inventories of MWC~480 and LkCa~15, and we discuss how these results may be interpreted in light of the different physical conditions of these two disk systems., Comment: 20 pages, 11 figures

There is mounting evidence that the composition and structure of planetary systems are intimately linked to their birth environments. During the past decade, several spectral surveys probed the chemistry of the earliest stages of star formation and of late planet-forming disks. However, very little is known about the chemistry of intermediate protostellar stages, i.e. Class I Young Stellar Objects (YSOs), where planet formation may have already begun. We present here the first results of a 3mm spectral survey performed with the IRAM-30m telescope to investigate the chemistry of a sample of seven Class I YSOs located in the Taurus star-forming region. These sources were selected to embrace the wide diversity identified for low-mass protostellar envelope and disk systems. We present detections and upper limits of thirteen small ($N_{\rm atoms}\leq3$) C, N, O, and S carriers - namely CO, HCO$^+$, HCN, HNC, CN, N$_2$H$^+$, C$_2$H, CS, SO, HCS$^+$, C$_2$S, SO$_2$, OCS - and some of their D, $^{13}$C, $^{15}$N, $^{18}$O, $^{17}$O, and $^{34}$S isotopologues. Together, these species provide constraints on gas-phase C/N/O ratios, D- and $^{15}$N-fractionation, source temperature and UV exposure, as well as the overall S-chemistry. We find substantial evidence of chemical differentiation among our source sample, some of which can be traced back to Class I physical parameters, such as the disk-to-envelope mass ratio (proxy for Class I evolutionary stage), the source luminosity, and the UV-field strength. Overall, these first results allow us to start investigating the astrochemistry of Class I objects, however, interferometric observations are needed to differentiate envelope versus disk chemistry., Comment: 27 pages, 17 figures, 4 tables, accepted for publication in ApJ

H$_2$CO is one of the most abundant organic molecules in protoplanetary disks and can serve as a precursor to more complex organic chemistry. We present an ALMA survey of H$_2$CO towards 15 disks covering a range of stellar spectral types, stellar ages, and dust continuum morphologies. H$_2$CO is detected towards 13 disks and tentatively detected towards a 14th. We find both centrally-peaked and centrally-depressed emission morphologies, and half of the disks show ring-like structures at or beyond expected CO snowline locations. Together these morphologies suggest that H$_2$CO in disks is commonly produced through both gas-phase and CO-ice-regulated grain-surface chemistry. We extract disk-averaged and azimuthally-averaged H$_2$CO excitation temperatures and column densities for four disks with multiple H$_2$CO line detections. The temperatures are between 20-50K, with the exception of colder temperatures in the DM Tau disk. These temperatures suggest that H$_2$CO emission in disks is generally emerging from the warm molecular layer, with some contributions from the colder midplane. Applying the same H$_2$CO excitation temperatures to all disks in the survey, we find that H$_2$CO column densities span almost three orders of magnitude ($\sim 5 \times 10^{11} - 5 \times 10^{14} \mathrm{cm}^{-2}$). The column densities appear uncorrelated with disk size and stellar age, but Herbig Ae disks may have less H$_2$CO compared to T Tauri disks, possibly because of less CO freeze-out. More H$_2$CO observations towards Herbig Ae disks are needed to confirm this tentative trend, and to better constrain under which disk conditions H$_2$CO and other oxygen-bearing organics efficiently form during planet formation., Comment: 20 pages, 14 figures, 3 figure sets, 9 tables. Published in ApJ (February 2020)

The composition of a protoplanetary disk is set by a combination of interstellar inheritance and gas and grain surface chemical reactions within the disk. The survival of inherited molecules, as well as the disk in situ chemistry depends on the local temperature, density and irradiation environment, which can change over time due to stellar and disk evolution, as well as transport in the disk. We address one aspect of this coupling between the physical and chemical evolution in disks by following accretion streamlines of gas and small grains in the disk midplane, while simultaneously taking the evolving star into account. This approach is computationally efficient and enables us to take into account changing physical conditions without reducing the chemical network. We find that many species are enhanced in the inner disk midplane in the dynamic model due to inward transport of cosmic-ray driven chemical products, resulting in, e.g., orders-of magnitude hydrocarbon enhancements at 1 au, compared to a static disk. For several other chemical families, there is no difference between the static and dynamic models, indicative of a robust chemical reset, while yet others show differences between static and dynamic models that depend on complex interactions between physics and chemistry during the inward track. The importance of coupling dynamics and chemistry when modeling the chemical evolution of protoplanetary disks is thus depends on what chemistry is of interest., Comment: Accepted for publication in ApJ

Complex nitriles, such as HC3N, and CH3CN, are observed in a wide variety of astrophysical environments, including at relatively high abundances in photon-dominated regions (PDR) and the UV exposed atmospheres of planet-forming disks. The latter have been inferred to be oxygen-poor, suggesting that these observations may be explained by organic chemistry in C-rich environments. In this study we first explore if the PDR complex nitrile observations can be explained by gas-phase PDR chemistry alone if the elemental C/O ratio is elevated. In the case of the Horsehead PDR, we find that gas-phase chemistry with C/O $\gtrsim$ 0.9 can indeed explain the observed nitrile abundances, increasing predicted abundances by several orders of magnitude compared to standard C/O assumptions. We also find that the nitrile abundances are sensitive to the cosmic ray ionization treatment, and provide constraints on the branching ratios between CH3CN and CH3NC productions. In a fiducial disk model, an elevated C/O ratio increases the CH3CN and HC3N productions by more than an order of magnitude, bringing abundance predictions within an order of magnitude to what has been inferred from observations. The C/O ratio appears to be a key variable in predicting and interpreting complex organic molecule abundances in photon-dominated regions across a range of scales., Comment: 15 pages, 7 figures, 2 tables, accepted for publication in ApJ

Snowlines of major volatiles regulate the gas and solid C/N/O ratios in the planet-forming midplanes of protoplanetary disks. Snow surfaces are the 2D extensions of snowlines in the outer disk regions, where radiative heating results in a decreasing temperature with disk height. CO and N$_2$ are two of the most abundant carriers of C, N and O. N$_2$H$^+$ can be used to probe the snow surfaces of both molecules, because it is destroyed by CO and formed from N$_2$. Here we present Atacama Large Millimeter/submillimeter Array (ALMA) observations of N$_2$H$^+$ at 0.2$''$-0.4$''$ resolution in the disks around LkCa 15, GM Aur, DM Tau, V4046 Sgr, AS 209, and IM Lup. We find two distinctive emission morphologies: N$_2$H$^+$ is either present in a bright, narrow ring surrounded by extended tenuous emission, or in a broad ring. These emission patterns can be explained by two different kinds of vertical temperature structures. Bright, narrow N$_2$H$^+$ rings are expected in disks with a thick Vertically Isothermal Region above the Midplane (VIRaM) layer (LkCa 15, GM Aur, DM Tau) where the N$_2$H$^+$ emission peaks between the CO and N$_2$ snowlines. Broad N$_2$H$^+$ rings come from disks with a thin VIRaM layer (V4046 Sgr, AS 209, IM Lup). We use a simple model to extract the first sets of CO and N$_2$ snowline pairs and corresponding freeze-out temperatures towards the disks with a thick VIRaM layer. The results reveal a range of N$_2$ and CO snowline radii towards stars of similar spectral type, demonstrating the need for empirically determined snowlines in disks., Comment: Accepted for publication in ApJ

CO is thought to be the main reservoir of volatile carbon in protoplanetary disks, and thus the primary initial source of carbon in the atmospheres of forming giant planets. However, recent observations of protoplanetary disks point towards low volatile carbon abundances in many systems, including at radii interior to the CO snowline. One potential explanation is that gas phase carbon is chemically reprocessed into less volatile species, which are frozen on dust grain surfaces as ice. This mechanism has the potential to change the primordial C/H ratio in the gas. However, current observations primarily probe the upper layers of the disk. It is not clear if the low volatile carbon abundances extend to the midplane, where planets form. We have run a grid of 198 chemical models, exploring how the chemical reprocessing of CO depends on disk mass, dust grain size distribution, temperature, cosmic ray and X-ray ionization rate, and initial water abundance. Building on our previous work focusing on the warm molecular layer, here we analyze the results for our grid of models in the disk midplane at 12 au. We find that either an ISM level cosmic ray ionization rate or the presence of UV photons due to a low dust surface density are needed to chemically reduce the midplane CO gas abundance by at least an order of magnitude within 1 Myr. In the majority of our models CO does not undergo substantial reprocessing by in situ chemistry and there is little change in the gas phase C/H and C/O ratios over the lifetime of the typical disk. However, in the small sub-set of disks where the disk midplane is subject to a source of ionization or photolysis, the gas phase C/O ratio increases by up to nearly 9 orders of magnitude due to conversion of CO into volatile hydrocarbons., Comment: Accepted for publication in ApJ, 15 pages, 10 figures, 3 tables

Evidence for exocomets, icy bodies in extrasolar planetary systems, has rapidly increased over the past decade. Volatiles are detected through the gas that exocomets release as they collide and grind down within their natal belts, or as they sublimate once scattered inwards to the regions closest to their host star. Most detections are in young, 10 to a few 100 Myr-old systems that are undergoing the final stages of terrestrial planet formation. This opens the exciting possibility to study exocomets at the epoch of volatile delivery to the inner regions of planetary systems. Detection of molecular and atomic gas in exocometary belts allows us to estimate molecular ice abundances and overall elemental abundances, enabling comparison with the Solar Nebula and Solar System comets. At the same time, observing star-grazing exocomets transiting in front of their star (for planetary systems viewed edge-on) and exozodiacal dust in the systems' innermost regions gives unique dynamical insights into the inward scattering process producing delivery to inner rocky planets. The rapid advances of this budding subfield of exoplanetary science will continue in the short term with the upcoming JWST, WFIRST and PLATO missions. In the longer term, the priority should be to explore the full composition of exocomets, including species crucial for delivery and later prebiotic synthesis. Doing so around an increasingly large population of exoplanetary systems is equally important, to enable comparative studies of young exocomets at the epoch of volatile delivery. We identify the proposed LUVOIR and Origins flagship missions as the most promising for a large-scale exploration of exocometary gas, a crucial component of the chemical heritage of young exo-Earths., Comment: White Paper submitted to the US National Academy of Sciences Astro2020 Decadal Survey (8 pages, 3 figures)

The nature and abundance of sulfur chemistry in protoplanetary disks (PPDs) may impact the sulfur inventory on young planets and therefore their habitability. PPDs also present an interesting test bed for sulfur chemistry models, since each disk present a diverse set of environments. In this context, we present new sulfur molecule observations in PPDs, and new S-disk chemistry models. With ALMA we observed the CS 5-4 rotational transition toward five PPDs (DM Tau, DO Tau, CI Tau, LkCa 15, MWC 480), and the CS 6-5 transition toward three PPDs (LkCa 15, MWC 480 and V4046 Sgr). Across this sample, CS displays a range of radial distributions, from centrally peaked, to gaps and rings. We also present the first detection in PPDs of $^{13}$CS 6-5 (LkCa 15 and MWC 480), C$^{34}$S 6-5 (LkCa 15), and H$_2$CS $8_{17}-7_{16}$, $9_{19}-8_{18}$ and $9_{18}-8_{17}$ (MWC 480) transitions. Using LTE models to constrain column densities and excitation temperatures, we find that either $^{13}$C and $^{34}$S are enhanced in CS, or CS is optically thick despite its relatively low brightness temperature. Additional lines and higher spatial resolution observations are needed to distinguish between these scenarios. Assuming CS is optically thin, CS column density model predictions reproduce the observations within a factor of a few for both MWC 480 and LkCa 15. However, the model underpredicts H$_2$CS by 1-2 orders of magnitude. Finally, comparing the H$_2$CS/CS ratio observed toward the MWC~480 disk and toward different ISM sources, we find the closest match with prestellar cores., Comment: 33 pages, 34 figures, accepted for publication in ApJ

Small hydrocarbons are an important organic reservoir in protostellar and protoplanetary environments. Constraints on desorption temperatures and binding energies of such hydrocarbons are needed for accurate predictions of where these molecules exist in the ice vs. gas-phase during the different stages of star and planet formation. Through a series of temperature programmed desorption (TPD) experiments, we constrain the binding energies of 2 and 3-carbon hydrocarbons (C$_{2}$H$_{2}$ - acetylene, C$_{2}$H$_{4}$ - ethylene, C$_{2}$H$_{6}$ - ethane, C$_{3}$H$_{4}$ - propyne, C$_{3}$H$_{6}$ - propene, and C$_{3}$H$_{8}$ - propane) to 2200-4200 K in the case of pure amorphous ices, to 2400-4400 K on compact amorphous H$_{2}$O, and to 2800-4700 K on porous amorphous H$_{2}$O. The 3-carbon hydrocarbon binding energies are always larger than the 2-carbon hydrocarbon binding energies. Within the 2- and 3-carbon hydrocarbon families, the alkynes (i.e., least-saturated) hydrocarbons exhibit the largest binding energies, while the alkane and alkene binding energies are comparable. Binding energies are $\sim$5-20% higher on water ice substrates compared to pure ices, which is a small increase compared to what has been measured for other volatile molecules such as CO and N$_{2}$. Thus in the case of hydrocarbons, H$_{2}$O has a less pronounced effect on sublimation front locations (i.e., snowlines) in protoplanetary disks., Comment: 12 pages, 15 figures. Accepted for publication in The Astrophysical Journal

Water is fundamental to our understanding of the evolution of planetary systems and the delivery of volatiles to the surfaces of potentially habitable planets. Yet, we currently have essentially no facilities capable of observing this key species comprehensively. With this white paper, we argue that we need a relatively large, cold space-based observatory equipped with a high-resolution spectrometer, in the mid- through far-infrared wavelength range (25-600~$\mu$m) in order to answer basic questions about planet formation, such as where the Earth got its water, how giant planets and planetesimals grow, and whether water is generally available to planets forming in the habitable zone of their host stars., Comment: Science white paper submitted to the Astro2020 Decadal Survey

Filaments are a key step on the path that leads from molecular clouds to star formation. However, their characteristics are heavily debated, and the exact processes that lead to their formation and fragmentation into dense cores still remain to be fully understood. We aim at characterising the mass, kinematics, and stability against gravitational collapse of a statistically significant sample of filaments in the Orion B molecular cloud, which is renown for its very low star formation efficiency. We characterise the gas column densities and kinematics over a field of 1.9 deg$^2$, using C$^{18}$O(J=1-0) data from the IRAM-30m large programme ORION-B. Using two different Hessian-based filters, we extract and compare two filamentary networks, each containing over 100 filaments. Independent of the extraction method, the filaments have widths of 0.12$\pm$0.04 pc, and show a wide range of linear (1 - 100 $M_{\odot}$pc$^{-1}$) and volume densities (2.10$^3$ - 2.10$^5$ cm$^{-3}$). Compared to previous studies, the filament population is dominated by low-density, thermally sub-critical structures, suggesting that most of the identified filaments are not collapsing to form stars. In fact, only ~1% of the Orion B cloud mass covered by our observations can be found in super-critical, star-forming filaments, explaining the low star formation efficiency of the region. The velocity profiles observed across the filaments show quiescence in the centre, and coherency in the plane of the sky, despite being mostly supersonic. The filaments in Orion B apparently belong to a continuum which contains a few elements comparable to already studied star-forming filaments as well as many lower-density, gravitationally unbound structures. This comprehensive study of the Orion B filaments shows that the mass fraction in super-critical filaments is a key factor in determining star formation efficiency., Comment: 22 pages, 15 figures. Accepted by A&A

Millimeter observations of CO gas in planetesimal belts show a high detection rate around A stars, but few detections for later type stars. We present the first CO detection in a planetesimal belt around an M star, TWA 7. The optically thin CO (J=3-2) emission is co-located with previously identified dust emission from the belt, and the emission velocity structure is consistent with Keplerian rotation around the central star. The detected CO is not well shielded against photodissociation, and must thus be continuously replenished by gas release from exocomets within the belt. We analyze in detail the process of exocometary gas release and destruction around young M dwarfs and how this process compares to earlier type stars. Taking these differences into account, we find that CO generation through exocometary gas release naturally explains the increasing CO detection rates with stellar luminosity, mostly because the CO production rate from the collisional cascade is directly proportional to stellar luminosity. More luminous stars will therefore on average host more massive (and hence more easily detectable) exocometary CO disks, leading to the higher detection rates observed. The current CO detection rates are consistent with a ubiquitous release of exocometary gas in planetesimal belts, independent of spectral type., Comment: 11 pages, 3 figures; Accepted for publication in AJ

Protoplanetary disks (PPDs) are characterized by different kinds of gas dynamics and chemistry, which are coupled via ionization, heating and cooling processes, as well as advective and turbulent transport. However, directly coupling gas dynamics with time-dependent chemistry is prohibitively computationally expensive when using comprehensive chemical reaction networks. In this paper, we evaluate the utility of a species-based network reduction method in different disk environments to produce small chemical networks that reproduce the abundances of major species found in large gas-phase chemistry networks. We find that the method works very well in disk midplane and surfaces regions, where approximately 20-30 gas phase species, connected by $\sim$50-60 gas phase reactions, are sufficient to reproduce the targeted ionization fraction and chemical abundances. Most species of the reduced networks, including major carriers of oxygen, carbon and nitrogen, also have similar abundances in the reduced and complete network models. Our results may serve as an initial effort for future hydrodynamic/magnetohydrodynamic simulations of PPDs incorporating time-dependent chemistry in appropriate regions. Accurately modeling the abundances of major species at intermediate disk heights, however, will require much more extended network incorporating gas-grain chemistry and are left for future studies., Comment: accepted for publication in ApJ

Methanol (CH$_3$OH) is at the root of organic ice chemistry in protoplanetary disks. However, its weak emission has made detections difficult. To date, gas-phase CH$_3$OH has been detected in only one Class II disk, TW Hya. We use the Atacama Large Millimeter/submillimeter Array (ALMA) to search for a total of four CH$_3$OH emission lines in bands 6 and 7 toward the disk around the young Herbig Ae star HD 163296. The disk-averaged column density of methanol and its related species formaldehyde (H$_2$CO) are estimated assuming optically thin emission in local thermodynamic equilibrium. We compare these results to the gas-phase column densities of the TW Hya disk. No targeted methanol lines were detected individually nor after line stacking. The 3$\sigma$ disk-integrated intensity upper limits are $< 51$ mJy km s$^{-1}$ for the band 6 lines and $< 26$ mJy km s$^{-1}$ for the band 7 lines. The band 7 lines provide the strictest 3$\sigma$ upper limit on disk-averaged column density with $N_{\mathrm{avg}} < 5.0 \times 10^{11}$ cm$^{-2}$. The methanol-to-formaldehyde ratio is CH$_3$OH/H$_2$CO $< 0.24$ in the HD 163296 disk compared to a ratio of $1.27$ in the TW Hya disk. Differences in the stellar irradiation of Herbig disks compared to T Tauri disks likely influence the gaseous methanol and formaldehyde content. Possible reasons for the lower HD 163296 methanol-to-formaldehyde ratio include: a higher than expected gas-phase formation of H$_2$CO in the HD 163296 disk, uncertainties in the grain surface formation efficiency of CH$_3$OH and H$_2$CO, and differences in the disk structure and/or CH$_3$OH and H$_2$CO desorption processes that release the molecules from ice mantles back into the gas phase. These results provide observational evidence that the gas-phase chemical complexity found in disks may be strongly influenced by the spectral type of the host star., Comment: Accepted to Astronomy & Astrophysics, 11 pages, 3 figures

We present an analysis of ALMA 1.25 millimeter continuum observations of spiral structures in three protoplanetary disks from the Disk Substructures at High Angular Resolution Project. The disks around Elias 27, IM Lup, and WaOph 6 were observed at a resolution of $\sim40-60$ mas ($\sim6-7$ au). All three disks feature $m=2$ spiral patterns in conjunction with annular substructures. Gas kinematics established by $^{12}$CO $J=2-1$ observations indicate that the continuum spiral arms are trailing. The arm-interarm intensity contrasts are modest, typically less than 3. The Elias 27 spiral pattern extends throughout much of the disk, and the arms intersect the gap at $R\sim69$ au. The spiral pattern in the IM Lup disk is particularly complex-it extends about halfway radially through the disk, exhibiting pitch angle variations with radius and interarm features that may be part of ring substructures or spiral arm branches. Spiral arms also extend most of the way through the WaOph 6 disk, but the source overall is much more compact than the other two disks. We discuss possible origins for the spiral structures, including gravitational instability and density waves induced by a stellar or planetary companion. Unlike the millimeter continuum counterparts of many of the disks with spiral arms detected in scattered light, these three sources do not feature high-contrast crescent-like asymmetries or large ($R>20$ au) emission cavities. This difference may point to multiple spiral formation mechanisms operating in disks., Comment: 19 pages, 9 figures, minor typos corrected

The Disk Substructures at High Angular Resolution Project used ALMA to map the 1.25 millimeter continuum of protoplanetary disks at a spatial resolution of ~5 au. We present a systematic analysis of annular substructures in the 18 single-disk systems targeted in this survey. No dominant architecture emerges from this sample; instead, remarkably diverse morphologies are observed. Annular substructures can occur at virtually any radius where millimeter continuum emission is detected and range in widths from a few au to tens of au. Intensity ratios between gaps and adjacent rings range from near-unity to just a few percent. In a minority of cases, annular substructures co-exist with other types of substructures, including spiral arms (3/18) and crescent-like azimuthal asymmetries (2/18). No clear trend is observed between the positions of the substructures and stellar host properties. In particular, the absence of an obvious association with stellar host luminosity (and hence the disk thermal structure) suggests that substructures do not occur preferentially near major molecular snowlines. Annular substructures like those observed in DSHARP have long been hypothesized to be due to planet-disk interactions. A few disks exhibit characteristics particularly suggestive of this scenario, including substructures in possible mean-motion resonance and "double gap" features reminiscent of hydrodynamical simulations of multiple gaps opened by a planet in a low-viscosity disk., Comment: 33 pages, 12 figures, captions corrected

We present a detailed analysis of new ALMA observations of the disk around the T-Tauri star HD 143006, which at 46 mas (7.6 au) resolution reveal new substructures in the 1.25 mm continuum emission. The disk resolves into a series of concentric rings and gaps together with a bright arc exterior to the rings that resembles hydrodynamics simulations of a vortex, and a bridge-like feature connecting the two innermost rings. Although our $^{12}$CO observations at similar spatial resolution do not show obvious substructure, they reveal an inner disk depleted of CO emission. From the continuum emission and the CO velocity field we find that the innermost ring has a higher inclination than the outermost rings and the arc. This is evidence for either a small ($\sim8^{\circ}$) or moderate ($\sim41^{\circ}$) misalignment between the inner and outer disk, depending on the specific orientation of the near/far sides of the inner/outer disk. We compare the observed substructures in the ALMA observations with recent scattered light data from VLT/SPHERE of this object. In particular, the location of narrow shadow lanes in the SPHERE image combined with pressure scale height estimates, favor a large misalignment of about $41^{\circ}$. We discuss our findings in the context of a dust-trapping vortex, planet-carved gaps, and a misaligned inner disk due to the presence of an inclined companion to HD 143006., Comment: 15 pages, 8 figures, accepted for publication at ApJ Letters

We introduce the Disk Substructures at High Angular Resolution Project (DSHARP), one of the initial Large Programs conducted with the Atacama Large Millimeter/submillimeter Array (ALMA). The primary goal of DSHARP is to find and characterize substructures in the spatial distributions of solid particles for a sample of 20 nearby protoplanetary disks, using very high resolution (0.035 arcsec, or 5 au FWHM) observations of their 240 GHz (1.25 mm) continuum emission. These data provide a first homogeneous look at the small-scale features in disks that are directly relevant to the planet formation process, quantifying their prevalence, morphologies, spatial scales, spacings, symmetry, and amplitudes, for targets with a variety of disk and stellar host properties. We find that these substructures are ubiquitous in this sample of large, bright disks. They are most frequently manifested as concentric, narrow emission rings and depleted gaps, although large-scale spiral patterns and small arc-shaped azimuthal asymmetries are also present in some cases. These substructures are found at a wide range of disk radii (from a few au to more than 100 au), are usually compact ($<$10 au), and show a wide range of amplitudes (brightness contrasts). Here we discuss the motivation for the project, describe the survey design and the sample properties, detail the observations and data calibration, highlight some basic results, and provide a general overview of the key conclusions that are presented in more detail in a series of accompanying articles. The DSHARP data -- including visibilities, images, calibration scripts, and more -- are released for community use at https://almascience.org/alma-data/lp/DSHARP., Comment: ApJ Letters, in press; some figure resolutions reduced, full-res version at https://www.cfa.harvard.edu/~sandrews/DSHARP_I.pdf ; Data Release at https://almascience.org/alma-data/lp/DSHARP

We present a detailed analysis of the high-angular resolution (0.''037, corresponding to 5 au) observations of the 1.25 mm continuum and $^{12}$CO $2-1$ emission from the disk around the T Tauri star AS 209. AS 209 hosts one of the most unusual disks from the DSHARP sample, the first high angular resolution ALMA survey of disks (Andrews et al. 2018), as nearly all of the emission can be explained with concentric Gaussian rings. In particular, the dust emission consists of a series of narrow and closely spaced rings in the inner $\sim$60 au, two well-separated bright rings in the outer disk, centered at 74 and 120 au, and at least two fainter emission features at 90 and 130 au. We model the visibilities with a parametric representation of the radial surface brightness profile, consisting of a central core and 7 concentric Gaussian rings. Recent hydro-dynamical simulations of low viscosity disks show that super-Earth planets can produce the multiple gaps seen in AS 209 millimeter continuum emission. The $^{12}$CO line emission is centrally peaked and extends out to $\sim$300 au, much farther than the millimeter dust emission. We find axisymmetric, localized deficits of CO emission around four distinct radii, near 45, 75, 120 and 210 au. The outermost gap is located well beyond the edge of the millimeter dust emission, and therefore cannot be due to dust opacity and must be caused by a genuine CO surface density reduction, due either to chemical effects or depletion of the overall gas content., Comment: ApJ Letters, in press

This paper presents a systematic survey of the deuterated and 13C isotopologues of a variety of oxygen-bearing complex organic molecules on Solar System scales toward the protostar IRAS 16293-2422B. We use the data from an unbiased molecular line survey between 329 and 363 GHz from the Atacama Large Millimeter/submillimeter Array (ALMA). The observations probe scales of 60 AU where most of the organic molecules have sublimated off dust grains and are present in the gas-phase. The complex organic molecules can be divided into two groups with one group, the simpler species, showing a D/H ratio of approximately 2% and the other, the more complex species, D/H ratios of 4-8%. This division may reflect the formation time of each species in the ices before or during warm-up/infall of material through the protostellar envelope. No significant differences are seen in the deuteration of different functional groups for individual species, possibly a result of the short time-scale for infall through the innermost warm regions where exchange reactions between different species may be taking place. The species show differences in excitation temperatures between 125 K and 300 K. This likely reflects the binding energies/sublimation temperatures of the individual species, in good agreement to what has previously been found for high-mass sources. For dimethyl ether, the 12C/13C ratio is found to be lower by up to a factor of 2 compared to typical ISM values similar to what has previously been inferred for glycolaldehyde. The results point to the importance of ice surface chemistry for the formation of these complex organic molecules at different stages in the evolution of embedded protostars and demonstrate the use of accurate isotope measurements for understanding the history of individual species., Comment: Accepted for publication in A&A. Abstract abridged

We present a suite of ALMA interferometric molecular line and continuum images that elucidate, on linear size scales of $\sim$30--40 AU, the chemical structure of the nearby, evolved, protoplanetary disk orbiting the close binary system V4046 Sgr. The observations were undertaken in the 1.1--1.4 mm wavelength range (ALMA Bands 6 and 7) with antenna configurations involving maximum baselines of several hundred meters, yielding subarcsecond-resolution images in more than a dozen molecular species and isotopologues. Isotopologues of CO and HCN display centrally peaked morphologies of integrated emission line intensity, whereas the line emission from complex nitrile group molecules (HC$_3$N, CH$_3$CN), deuterated molecules (DCN, DCO$^+$), hydrocarbons (as traced by C$_2$H), and potential CO ice line tracers (N$_2$H$^+$, and H$_2$CO) appears as a sequence of sharp and diffuse rings. The dimensions and morphologies of HC$_3$N and CH$_3$CN emission are suggestive of photodesorption of organic ices from the surfaces of dust grains, while the sequence of increasing radius of peak intensity represented by DCN (smallest), DCO$^+$, N$_2$H$^+$, and H$_2$CO (largest) is qualitatively consistent with the expected decline of midplane gas temperature with increasing disk radius. Empirical modeling indicates that the sharp-edged C$_2$H emission ring lies at relatively deep disk layers, leaving open the question of the origin of C$_2$H abundance enhancements in evolved disks. This study of the "molecular anatomy" of V4046 Sgr should serve as motivation for additional subarcsecond ALMA molecular line imaging surveys of nearby, evolved protoplanetary disks aimed at addressing major uncertainties in protoplanetary disk physical and chemical structure and molecular production pathways., Comment: 32 pages, 10 figures; accepted 26 June 2018 by The Astrophysical Journal

Controlling the contamination of silicon materials by iron, especially dissolved interstitial iron (Fe$_{\mathrm{i}}$), is a longstanding problem with recent developments and several open issues. Among these we have the question whether hydrogen can assist iron diffusion, or if significant amounts of substitutional iron (Fe$_{\mathrm{s}}$) can be created. Using density functional calculations we explore the structure, formation energies, binding energies, migration, and electronic levels of several FeH complexes in Si. We find that a weakly bound Fe$_{\mathrm{i}}$H pair has a migration barrier close to that of isolated Fe$_{\mathrm{i}}$ and a donor level at $E_{\mathrm{v}}+0.5$~eV. Conversely, Fe$_{\mathrm{i}}$H$_{2}(0/+)$ is estimated at $E_{\mathrm{v}}+0.33$~eV. These findings suggest that the hole trap at $E_{\mathrm{v}}+0.32$~eV measured by capacitance measurements should be assigned to Fe$_{\mathrm{i}}$H$_{2}$ . Fe$_{\mathrm{s}}$H-related complexes show only deep acceptor activity and are expected to have little effect on minority carrier life-time in $p$-type Si. The opposite conclusion can be drawn for $n$-type Si. We find that while in H-free material Fe$_{\mathrm{i}}$ defects have lower formation energy than Fe$_{\mathrm{s}}$, in hydrogenated samples Fe$_{\mathrm{s}}$-related defects become considerably more stable. This would explain the observation of an EPR signal attributed to a Fe$_{\mathrm{s}}$H-related complex in hydrogenated Si, which was quenched from above 1000$^{\circ}$C to iced-water temperature.

SPHEREx is a proposed NASA MIDEX mission selected for Phase A study. SPHEREx would carry out the first all-sky spectral survey in the near infrared. At the end of its two-year mission, SPHEREx would obtain 0.75-to-5$\mu$m spectra of every 6.2 arcsec pixel on the sky, with spectral resolution R>35 and a 5-$\sigma$ sensitivity AB$>$19 per spectral/spatial resolution element. More details concerning SPHEREx are available at http://spherex.caltech.edu. The SPHEREx team has proposed three specific science investigations to be carried out with this unique data set: cosmic inflation, interstellar and circumstellar ices, and the extra-galactic background light. Though these three themes are undoubtedly compelling, they are far from exhausting the scientific output of SPHEREx. Indeed, SPHEREx would create a unique all-sky spectral database including spectra of very large numbers of astronomical and solar system targets, including both extended and diffuse sources. These spectra would enable a wide variety of investigations, and the SPHEREx team is dedicated to making the data available to the community to enable these investigations, which we refer to as Legacy Science. To that end, we have sponsored two workshops for the general scientific community to identify the most interesting Legacy Science themes and to ensure that the SPHEREx data products are responsive to their needs. In February of 2016, some 50 scientists from all fields met in Pasadena to develop these themes and to understand their implications for the SPHEREx mission. The 2016 workshop highlighted many synergies between SPHEREx and other contemporaneous astronomical missions, facilities, and databases. Consequently, in January 2018 we convened a second workshop at the Center for Astrophysics in Cambridge to focus specifically on these synergies. This white paper reports on the results of the 2018 SPHEREx workshop., Comment: 50 pages, 24 figures, more details at http://spherex.caltech.edu

Cometary studies suggest that the organic composition of the early Solar Nebula was rich in complex nitrile species such a CH$_3$CN. Recent ALMA detections in protoplanetary disks suggest that these species may be common during planet and comet formation, but connecting gas phase measurements to cometary abundances first requires constraints on formation chemistry and distributions of these species. We present here the detection of seven spatially resolved transitions of CH$_3$CN in the protoplanetary disk around the T-Tauri star TW Hya. Using a rotational diagram analysis we find a disk-averaged column density of N$_T$=1.45$^{+0.19}_{-0.15}\times10^{12}$ cm$^{-2}$ and a rotational temperature of T$_{rot}$=32.7$^{+3.9}_{-3.4}$ K. A radially resolved rotational diagram shows the rotational temperature to be constant across the disk, suggesting that the CH$_3$CN emission originates from a layer at z/r$\sim$0.3. Through comparison of the observations with predictions from a disk chemistry model, we find that grain-surface reactions likely dominate CH$_3$CN formation and that in situ disk chemistry is sufficient to explain the observed CH$_3$CN column density profile without invoking inheritance from the protostellar phase. However, the same model fails to reproduce a Solar System cometary abundance of CH$_3$CN relative to H$_2$O in the midplane, suggesting that either vigorous vertical mixing or some degree of inheritance from interstellar ices occurred in the Solar Nebula., Comment: 15 pages, 12 figures, accepted for publication in ApJ

Resolved observations of millimetre-sized dust, tracing larger planetesimals, have pinpointed the location of 26 Edgeworth-Kuiper belt analogs. We report that a belt's distance $R$ to its host star correlates with the star's luminosity $L_{\star}$, following $R\propto L^{0.19}_{\star}$ with a low intrinsic scatter of $\sim$17%. Remarkably, our Edgeworth-Kuiper belt in the Solar System and the two CO snow lines imaged in protoplanetary disks lie close to this $R$-$L_{\star}$ relation, suggestive of an intrinsic relationship between protoplanetary disk structures and belt locations. To test the effect of bias on the relation, we use a Monte Carlo approach and simulate uncorrelated model populations of belts. We find that observational bias could produce the slope and intercept of the $R$-$L_{\star}$ relation, but is unable to reproduce its low scatter. We then repeat the simulation taking into account the collisional evolution of belts, following the steady state model that fits the belt population as observed through infrared excesses. This significantly improves the fit by lowering the scatter of the simulated $R$-$L_{\star}$ relation; however, this scatter remains only marginally consistent with the one observed. The inability of observational bias and collisional evolution alone to reproduce the tight relationship between belt radius and stellar luminosity could indicate that planetesimal belts form at preferential locations within protoplanetary disks. The similar trend for CO snow line locations would then indicate that the formation of planetesimals and/or planets in the outer regions of planetary systems is linked to the volatility of their building blocks, as postulated by planet formation models., Comment: Accepted for publication in ApJ. 23 pages, 9 figures

Modern radio interferometers enable observations of spectral lines with unprecedented spatial resolution and sensitivity. In spite of these technical advances, many lines of interest are still at best weakly detected and therefore necessitate detection and analysis techniques specialized for the low signal-to-noise ratio (SNR) regime. Matched filters can leverage knowledge of the source structure and kinematics to increase sensitivity of spectral line observations. Application of the filter in the native Fourier domain improves SNR while simultaneously avoiding the computational cost and ambiguities associated with imaging, making matched filtering a fast and robust method for weak spectral line detection. We demonstrate how an approximate matched filter can be constructed from a previously observed line or from a model of the source, and we show how this filter can be used to robustly infer a detection significance for weak spectral lines. When applied to ALMA Cycle 2 observations of CH3OH in the protoplanetary disk around TW Hya, the technique yields a ~53% SNR boost over aperture-based spectral extraction methods, and we show that an even higher boost will be achieved for observations at higher spatial resolution. A Python-based open-source implementation of this technique is available under the MIT license at https://github.com/AstroChem/VISIBLE., Comment: 20 pages, 8 figures, accepted for publication in The Astronomical Journal

Hydroxyapatite (HAp) is an important component of mammal bones and teeth, being widely used in prosthetic implants. Despite the importance of HAp in medicine, several promising applications involving this material e.g. in photo-catalysis), depend on how well we understand its fundamental properties. Among the ones that are either unknown or not known accurately we have the electronic band structure and all that relates to it, including the band gap width. We employ state-of-the-art methodologies, including density hybrid-functional theory and many-body perturbation theory within the GW approximation, to look at the optoelectronic properties of HAp. These methods are also applied to the calculation of defect levels. We find that the use of a mix of (semi-)local and exact exchange in the exchange-correlation functional, brings a drastic improvement to the band structure. Important side-effects include improvements in the description of dielectric and optical properties, not only involving conduction band (excited) states, but also the valence. We find that the highly dispersive conduction band bottom of HAp originates from anti-bonding $\sigma^{*}$ states along the $\cdots\textrm{OH-OH-}\cdots$ infinite chain, suggesting the formation of a conductive 1D-ice phase. The choice of the exchange-correlation treatment to the calculation of defect levels was also investigated by using the OH-vacancy as testing-model. We find that donor and acceptor transitions obtained within semi-local DFT differ from those of hybrid-DFT by almost 2 eV. Such a large discrepancy emphasizes the importance of using a high-quality description of the electron-electron interactions in the calculation of electronic and optical transitions of defects in HAp.

CO is commonly used as a tracer of the total gas mass in both the interstellar medium and in protoplanetary disks. Recently there has been much debate about the utility of CO as a mass tracer in disks. Observations of CO in protoplanetary disks reveal a range of CO abundances, with measurements of low CO to dust mass ratios in numerous systems. One possibility is that carbon is removed from CO via chemistry. However, the full range of physical conditions conducive to this chemical reprocessing is not well understood. We perform a systematic survey of the time dependent chemistry in protoplanetary disks for 198 models with a range of physical conditions. We varying dust grain size distribution, temperature, comic ray and X-ray ionization rate, disk mass, and initial water abundance, detailing what physical conditions are necessary to activate the various CO depletion mechanisms in the warm molecular layer. We focus our analysis on the warm molecular layer in two regions: the outer disk (100 au) well outside the CO snowline and the inner disk (19 au) just inside the midplane CO snow line. After 1 Myr, we find that the majority of models have a CO abundance relative to H$_2$ less than $10^{-4}$ in the outer disk, while an abundance less than $10^{-5}$ requires the presence of cosmic rays. Inside the CO snow line, significant depletion of CO only occurs in models with a high cosmic ray rate. If cosmic rays are not present in young disks it is difficult to chemically remove carbon from CO. Additionally, removing water prior to CO depletion impedes the chemical processing of CO. Chemical processing alone cannot explain current observations of low CO abundances. Other mechanisms must also be involved., Comment: 23 pages, 25 figures, 5 tables, accepted for publication in ApJ

The exocometary origin of CO gas has been confirmed in several extrasolar Kuiper belts, with CO ice abundances consistent with Solar System comets. We here present a molecular survey of the $\beta$ Pictoris belt with the Submillimeter Array (SMA), reporting upper limits for CN, HCN, HCO$^+$, N$_2$H$^+$ and H$_2$CO, as well as for H$_2$S, CH$_3$OH, SiO and DCN from archival ALMA data. Non-detections can be attributed to rapid molecular photodissociation due to the A-star's strong UV flux. CN is the longest-lasting and most easily detectable molecule after CO in this environment. We update our NLTE excitation model to include UV fluorescence, finding it plays a key role in CO and CN excitation, and use it to turn the SMA CN/CO flux ratio constraint into an upper limit of $<2.5$% on the HCN/(CO+CO$_2$) ratio of outgassing rates. This value is consistent with, but at the low end of, the broad range observed in Solar System comets. If sublimation dominates outgassing, then this low value may be caused by decreased outgassing for the less volatile molecule HCN compared to CO. If instead UV photodesorption or collisional vaporization of unbound grains dominates outgassing, then this low ratio of rates would imply a low ice abundance ratio, which would in turn indicate a variation in cometary cyanide abundances across planetary systems. To conclude, we make predictions for future molecular surveys and show that CN and HCN should be readily detectable with ALMA around $\beta$ Pictoris for Solar-System-like exocometary compositions., Comment: Accepted for publication in ApJ. 19 pages, 7 figures

Diffusion of species in icy dust grain mantles is a fundamental process that shapes the chemistry of interstellar regions; yet measurements of diffusion in interstellar ice analogs are scarce. Here we present measurements of CO diffusion into CO$_2$ ice at low temperatures (T=11--23~K) using CO$_2$ longitudinal optical (LO) phonon modes to monitor the level of mixing of initially layered ices. We model the diffusion kinetics using Fick's second law and find the temperature dependent diffusion coefficients are well fit by an Arrhenius equation giving a diffusion barrier of 300 $\pm$ 40 K. The low barrier along with the diffusion kinetics through isotopically labeled layers suggest that CO diffuses through CO$_2$ along pore surfaces rather than through bulk diffusion. In complementary experiments, we measure the desorption energy of CO from CO$_2$ ices deposited at 11-50 K by temperature-programmed desorption (TPD) and find that the desorption barrier ranges from 1240 $\pm$ 90 K to 1410 $\pm$ 70 K depending on the CO$_2$ deposition temperature and resultant ice porosity. The measured CO-CO$_2$ desorption barriers demonstrate that CO binds equally well to CO$_2$ and H$_2$O ices when both are compact. The CO-CO$_2$ diffusion-desorption barrier ratio ranges from 0.21-0.24 dependent on the binding environment during diffusion. The diffusion-desorption ratio is consistent with the above hypothesis that the observed diffusion is a surface process and adds to previous experimental evidence on diffusion in water ice that suggests surface diffusion is important to the mobility of molecules within interstellar ices.

The carbon vacancy in $4H$-SiC is a powerful minority carrier recombination center and a major cause of degradation of SiC-based devices. Despite the extensiveness of the literature regarding the characterization and modeling of the defect, many fundamental questions persist. Among them we have the shaky connection of the EPR data to the electrical measurements, the physical origin of the pseudo-Jahn-Teller (pJT) effect, the reasoning for the observed sub-lattice dependence of the paramagnetic states, and the severe temperature-dependence of some hyperfine signals which cannot be accounted for by a thermally-activated dynamic averaging between equivalent JT-distorted structures. In this work we address these problems by means of semi-local and hybrid density functional calculations. We start by inventorying a total of four vacancy structures. Diamagnetic states have well defined low-energy structures, whereas paramagnetic states display metastability. This rich structural variety is traced back to the filling of electronic states which are shaped by a crystal-field-dependent pJT effect. From calculated minimum energy paths for defect rotation and transformation mechanisms, combined with the calculated formation energies and electrical levels, we arrived at a configuration-coordinate diagram of the defect. The diagram provides us with a detailed first-principles picture of the defect when subject to optical and thermal excitations. The calculated acceptor and donor transitions agree well with Z$_{1/2}$ and EH$_{6/7}$ trap energies, respectively. From comparison of calculated and measured $U$-values, and correlating the site-dependent formation energies with the relative intensity of the DLTS peaks in as-grown material, we assign Z$_{1}$ (EH$_{6}$) and Z$_{2}$ (EH$_{7}$) signals to acceptor (donor) transitions of carbon vacancies located on the $h$ and $k$ sub-lattice sites, respectively., Comment: to appear in Physical Review B