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Large inner dust gaps in transition disks are frequently posited as evidence of giant planets sculpting gas and dust in the disk, or the opening of a gap by photoevaporative winds. Although the former hypothesis is strongly supported by the observations of planets and deep depletions in gas within the gap some disks, many T Tauri stars hosting transition disks accrete at rates typical for an undepleted disk, raising the question of how gap opening occurs in these objects. We thus present an analysis of the structure of the transition disk around the T Tauri star DM Tau, which is strongly accreting ($\sim 10^{-8.3}~\mathrm{M}_\odot~ \mathrm{yr}^{-1}$) and turbulent ($\alpha=0.078 \pm 0.02$). Using the DALI thermochemical code, we fit disk models to simultaneously reproduce the accretion rate, high level of turbulence, the gas traced by ALMA band 6 observations of $^{12}$CO, $^{13}$CO, and C$^{18}$O J=2--1 lines, and the observed dust emission from the mm continuum and spectral energy distribution. We find a shallow depletion in gas surface density of $\sim 10$ relative to the outer disk and a gas rich inner disk is consistent with the observations. The planet mass of $, Comment: Accepted for publication in the Astronomical Journal. 36 pages, 28 figures

This work presents ground-based spectrally-resolved water emission at R = 30000-100000 over infrared wavelengths covered by JWST (2.9-12.8 $\mu$m). Two new surveys with iSHELL and VISIR are combined with previous spectra from CRIRES and TEXES to cover parts of multiple ro-vibrational and rotational bands observable within telluric transmission bands, for a total of $\approx160$ spectra and 85 disks (30 of which are JWST targets in Cycle 1). The general expectation of a range of regions and excitation conditions traced by infrared water spectra is for the first time supported by the combined kinematics and excitation as spectrally resolved at multiple wavelengths. The main findings from this analysis are: 1) water lines are progressively narrower from the ro-vibrational bands at 2-9 $\mu$m to the rotational lines at 12 $\mu$m, and partly match a broad (BC) and narrow (NC) emission components, respectively, as extracted from ro-vibrational CO spectra; 2) rotation diagrams of resolved water lines from upper level energies of 4000-9500 K show vertical spread and curvatures indicative of optically thick emission ($\approx 10^{18}$ cm$^{-2}$) from a range of excitation temperatures ($\approx 800$-1100 K); 3) the new 5 $\mu$m spectra demonstrate that slab model fits to the rotational lines at $> 10$ $\mu$m strongly over-predict the ro-vibrational emission bands at $< 9$ $\mu$m, implying non-LTE vibrational excitation. We discuss these findings in the context of emission from a disk surface and a molecular inner disk wind, and provide a list of guidelines to support the analysis of spectrally-unresolved JWST spectra., Comment: Accepted for publication on AJ

A large fraction of observed protoplanetary disks in nearby Star-Forming Regions (SFRs) are fainter than expected in CO isotopologue emission. Disks not detected in 13CO line emission are also faint and often unresolved in the continuum emission at an angular resolution of around 0.2 arcseconds. Focusing on the Lupus SFR, the aim of this work is to investigate whether the population of CO-faint disks comprises radially extended and low mass disks - as commonly assumed so far - or if it is of intrinsically radially compact disks, an interpretation that we propose in this paper. The latter scenario was already proposed for individual sources or small samples of disks, while this work targets a large population of disks in a single SFR for which statistical arguments can be made. A new grid of physical-chemical models of compact disks has been run with DALI in order to cover a region of the parameter space that had not been explored before with this code. Such models have been compared with 12CO and 13CO ALMA observations of faint disks in Lupus. Disks that are not detected in 13CO emission and with faint or undetected 12CO emission are consistent with compact disk models. For radially compact disk, the emission of CO isotopologues is mostly optically thick and it scales with the surface area: i.e., it is fainter for smaller objects. The fraction of compact disks is potentially between roughly 50% and 60% of the entire Lupus sample. Deeper observations of 12CO and 13CO at a moderate angular resolution will allow us to distinguish whether faint disks are intrinsically compact, or if they are extended but faint, without the need of resolving them. If the fainter end of the disk population observed by ALMA disk surveys is consistent with such objects being very compact, this will either create a tension with viscous spreading or require MHD winds or external processes to truncate the disks., Comment: 10 pages, 3 main figures, 3 appendix figures. Accepted to A&A

Recent ALMA surveys of protoplanetary disks have shown that for most disks the extent of the gas emission is greater than the extent of the thermal emission of the millimeter-sized dust. Both line optical depth and the combined effect of radially dependent grain growth and radial drift may contribute to this observed effect. For a sample of 10 disks from the Lupus survey we investigate how well dust-based models without radial dust evolution reproduce the observed 12CO outer radius, and determine whether radial dust evolution is required to match the observed gas-dust size difference. We used the thermochemical code DALI to obtain 12CO synthetic emission maps and measure gas and dust outer radii (Rco, Rmm) using the same methods as applied to the observations, which were compared to observations on a source-by-source basis. For 5 disks we find that the observed gas-dust size difference is larger than the gas-dust size difference due to optical depth, indicating that we need both dust evolution and optical depth effects to explain the observed gas-dust size difference. For the other 5 disks the observed gas-dust size difference can be explained using only line optical depth effects. We also identify 6 disks not included in our initial sample but part of a survey of the same star-forming region that show significant 12CO emission beyond 4 x Rmm. These disks, for which no Rco is available, likely have gas-dust size differences greater than 4 and are difficult to explain without substantial dust evolution. Our results suggest that radial drift and grain growth are common features among both bright and fain disks. The effects of radial drift and grain growth can be observed in disks where the dust and gas radii are significantly different, while more detailed models and deeper observations are needed to see this effect in disks with smaller differences., Comment: 17 pages, 11 figures, accepted in A&A

The combination of high-resolution and sensitivity offered by ALMA is revolutionizing our understanding of protoplanetary discs, as their bulk gas and dust distributions can be studied independently. In this paper we present resolved ALMA observations of the continuum emission (λ = 1.3 mm) and CO isotopologues (12CO, 13CO, C18O, J = 2 - 1) integrated intensity from the disc around the nearby (d = 162 pc), intermediate-mass (M_{\star }=1.67 M_{\odot }) pre-main-sequence star CQ Tau. The data show an inner depression in continuum and in both 13CO and C18O emission. We employ a thermo-chemical model of the disc reproducing both continuum and gas radial intensity profiles, together with the disc spectral energy distribution. The models show that a gas inner cavity with size between 15 and 25 au is needed to reproduce the data with a density depletion factor between ~10-1 and ~10-3. The radial profile of the distinct cavity in the dust continuum is described by a Gaussian ring centred at R_dust=53 au and with a width of σ =13 au. Three-dimensional gas and dust numerical simulations of a disc with an embedded planet at a separation from the central star of {~ }20 au and with a mass of {~ } 6 - 9 M_Jup reproduce qualitatively the gas and dust profiles of the CQ Tau disc. However, a one-planet model appears not to be able to reproduce the dust Gaussian density profile predicted using the thermo-chemical modeling.

Hydrogen deuteride (HD) rotational line emission can provide reliable protoplanetary disk gas mass measurements, but it is difficult to observe and detections have been limited to three T-Tauri disks. No new data have been available since the \emph{Herschel} Space Observatory mission ended in 2013. We set out to obtain new disk gas mass constraints by analysing upper limits on HD 1-0 emission in \emph{Herschel}/PACS archival data from the DIGIT key programme. With a focus on the Herbig Ae/Be disks, whose stars are more luminous than T Tauris, we determine upper limits for HD in data previosly analysed for its line detections. Their significance is studied with a grid of models run with the DALI physical-chemical code, customised to include deuterium chemistry. Nearly all the disks are constrained to $M_{\rm gas}\leq0.1\,$M$_{\odot}$, ruling out global gravitational instability. A strong constraint is obtained for the HD 163296 disk mass, $M_{\rm gas} \leq 0.067\,$M$_{\odot}$, implying $\Delta_{\rm g/d}\leq100$. This HD-based mass limit is towards the low end of CO-based mass estimates for the disk, highlighting the large uncertainty in using only CO and suggesting that gas-phase CO depletion in HD 163296 is at most a factor of a few. The $M_{\rm gas}$ limits for HD 163296 and HD 100546, both bright disks with massive candidate protoplanetary systems, suggest disk-to-planet mass conversion efficiencies of $M_{\rm p}/(M_{\rm gas} + M_{\rm p})\approx10$ to $40\,$% for present-day values. Near-future observations with SOFIA/HIRMES will be able to detect HD in the brightest Herbig~Ae/Be disks within $150\,$pc with $\approx10\,$h integration time., Comment: Accepted for publication in A&A

[abridged]CO rovibrational lines are efficient probes of warm molecular gas and can give unique insights into the inner 10 AU of proto-planetary disks. Recent studies have found a relation between the ratio of lines originating from the second and first vibrationally excited state, denoted as $v2/v1$, and the emitting radius of CO. In disks around Herbig Ae stars the vibrational excitation is low when CO lines come from close to the star, and high when lines only probe gas at large radii (more than 5 AU). We aim to find explanations for the observed trends between CO vibrational ratio, emitting radii, and NIR excess, and identify their implications in terms of the physical and chemical structure of inner disks around Herbig stars. Slab models and full disk thermo chemical models are calculated. Simulated observations from the models are directly compared to the data. Broad CO lines with low vibrational ratios are best explained by a warm (400-1300 K) inner disk surface with gas-to-dust ratios below 1000; no CO is detected within/at the inner dust rim, due to dissociation at high temperatures. In contrast, explaining the narrow lines with high vibrational ratios requires an inner cavity of a least 5 AU in both dust and gas, followed by a cool (100-300 K) molecular gas reservoir with gas-to-dust ratios greater than 10000 at the cavity wall. In all cases the CO gas must be close to thermalization with the dust. The high gas-to-dust ratios needed to explain high $v2/v1$ in narrow CO lines for a subset of group I disks can naturally be interpreted as due to the dust traps that have been proposed to explain millimeter dust cavities. The broad lines seen in most group II objects indicate a very flat disk in addition to inner disk substructures within 10 AU that can be related to the substructures recently observed with ALMA., Comment: 17 pages, 16 figures, accepted by A&A

Outflows driven by large-scale magnetic fields likely play an important role in the evolution and dispersal of protoplanetary disks, and in setting the conditions for planet formation. We extend our 2-D axisymmetric non-ideal MHD model of these outflows by incorporating radiative transfer and simplified thermochemistry, with the twin aims of exploring how heating influences wind launching, and illustrating how such models can be tested through observations of diagnostic spectral lines. Our model disks launch magnetocentrifugal outflows primarily through magnetic tension forces, so the mass-loss rate increases only moderately when thermochemical effects are switched on. For typical field strengths, thermochemical and irradiation heating are more important than magnetic dissipation. We furthermore find that the entrained vertical magnetic flux diffuses out of the disk on secular timescales as a result of non-ideal MHD. Through post-processing line radiative transfer, we demonstrate that spectral line intensities and moment-1 maps of atomic oxygen, the HCN molecule, and other species show potentially observable differences between a model with a magnetically driven outflow and one with a weaker, photoevaporative outflow. In particular, the line shapes and velocity asymmetries in the moment-1 maps could enable the identification of outflows emanating from the disk surface., Comment: 35 pages, 20 figures, accepted for publication in ApJ

High resolution ALMA observations of protoplanetary disks have revealed that many, if not all primordial disks consist of ring-like dust structures. The origin of these dust rings remains unclear, but a common explanation is the presence of planetary companions that have cleared gaps along their orbit and trapped the dust at the gap edge. A signature of this scenario is a decrease of gas density inside these gaps. In recent work, Isella et al. 2016 derived drops in gas density consistent with Saturn-mass planets inside the gaps in the HD163296 disk through spatially resolved CO isotopologue observations. However, as CO abundance and temperature depends on a large range of factors, the interpretation of CO emission is non-trivial. We use the physical-chemical code DALI to show that the gas temperature increases inside dust density gaps, implying that any gaps in the gas, if present, would have to be much deeper, consistent with planet masses higher than a Jupiter mass. Furthermore, we show that a model with increased grain growth at certain radii, as expected at a snowline, can reproduce the dust rings in HD163296 equally well without the need for companions. This scenario can explain both younger and older disks with observed gaps, as gaps have been seen in systems as young, Accepted by ApJL

Transition disks with large dust cavities around young stars are promising targets for studying planet formation. Previous studies have revealed the presence of gas cavities inside the dust cavities hinting at recently formed, giant planets. However, many of these studies are biased towards the brightest disks in the nearby star forming regions, and it is not possible to derive reliable statistics that can be compared with exoplanet populations. We present the analysis of 11 transition disks with large cavities (>20 AU radius) from a complete disk survey of the Lupus star forming region, using ALMA Band 7 observations at 0.3" (22-30 AU radius) resolution of the 345 GHz continuum, 13CO and C18O 3-2 observations and the Spectral Energy Distribution of each source. Gas and dust surface density profiles are derived using the physical-chemical modeling code DALI. This is the first study of transition disks of large cavities within a complete disk survey within a star forming region. The dust cavity sizes range from 20-90 AU radius and in three cases, a gas cavity is resolved as well. The deep drops in gas density and large dust cavity sizes are consistent with clearing by giant planets. The fraction of transition disks with large cavities in Lupus is ~11%, which is inconsistent with exoplanet population studies of giant planets at wide orbits. Furthermore, we present a hypothesis of an evolutionary path for large massive disks evolving into transition disks with large cavities., 29 pages, 15 figures, Accepted by ApJ

Bright ring-like structure emission of the CN molecule has been observed in protoplanetary disks. We investigate whether such structures are due to the morphology of the disk itself or if they are instead an intrinsic feature of CN emission. With the intention of using CN as a diagnostic, we also address to which physical and chemical parameters CN is most sensitive. A set of disk models were run for different stellar spectra, masses, and physical structures via the 2D thermochemical code DALI. An updated chemical network that accounts for the most relevant CN reactions was adopted. Ring-shaped emission is found to be a common feature of all adopted models; the highest abundance is found in the upper outer regions of the disk, and the column density peaks at 30-100 AU for T Tauri stars with standard accretion rates. Higher mass disks generally show brighter CN. Higher UV fields, such as those appropriate for T Tauri stars with high accretion rates or for Herbig Ae stars or for higher disk flaring, generally result in brighter and larger rings. These trends are due to the main formation paths of CN, which all start with vibrationally excited H2* molecules, that are produced through far ultraviolet (FUV) pumping of H2. The model results compare well with observed disk-integrated CN fluxes and the observed location of the CN ring for the TW Hya disk. CN rings are produced naturally in protoplanetary disks and do not require a specific underlying disk structure such as a dust cavity or gap. The strong link between FUV flux and CN emission can provide critical information regarding the vertical structure of the disk and the distribution of dust grains which affects the UV penetration, and could help to break some degeneracies in the SED fitting. In contrast with C2H or c-C3H2, the CN flux is not very sensitive to carbon and oxygen depletion., Comment: New version of paper, correcting too high H2 excitation rates and consequently too high CN column densities. Qualitative conclusions of the paper remain unchanged. Quantitatively, the CN column densities are an order of magnitude lower whereas fluxes decrease by a factor of 3-4. Rings are larger by up to a factor of 2. 13 pages, 19 figures, accepted for publication in A&A

The oxygen-bearing molecular ions OH+, H2O+, and H3O+ are key species that probe the ionization rate of (partially) molecular gas that is ionized by X-rays and cosmic rays permeating the interstellar medium. We report Herschel far-infrared and submillimeter spectroscopic observations of OH+ in Mrk 231, showing both ground-state P-Cygni profiles, and excited line profiles with blueshifted absorption wings extending up to ~1000 km s^{-1}. In addition, OH+ probes an excited component peaking at central velocities, likely arising from the torus probed by the OH centimeter-wave megamaser. Four lines of H2O+ are also detected at systemic velocities, but H3O+ is undetected. Based on our earlier OH studies, we estimate an abundance ratio of OH/OH+~5-10 for the outflowing components and ~20 for the torus, and an OH+ abundance relative to H nuclei of ~>10^{-7}. We also find high OH+/H2O+ and OH+/H3O+ ratios, both are ~>4 in the torus and ~>10-20 in the outflowing gas components. Chemical models indicate that these high OH+ abundances relative to OH, H2O+, and H3O+ are characteristic of gas with a high ionization rate per unit density, ��/n_H~(1-5)x10^{-17} cm^3 s^{-1} and ~(1-2)x10^{-16} cm^3 s^{-1} for the above components, respectively, and an ionization rate of ��~(0.5-2)x10^{-12} s^{-1}. X-rays appear to be unable to explain the inferred ionization rate, and thus we suggest that low-energy (10-400 MeV) cosmic-rays are primarily responsible for the ionization with \dot{M}_{CR}~0.01 M_{sun} yr^{-1} and \dot{E}_{CR}~10^{44} erg s^{-1}, the latter corresponding to 1% of the AGN luminosity and similar to the energetics of the molecular outflow. We suggest that cosmic-rays accelerated in the forward shock associated with the molecular outflow are responsible for the ionization, as they diffuse through the outflowing molecular phase downstream., 25 pages, 11 figures

This work aims to understand which midplane conditions are probed by the DCO$^+$ emission in the disk around the Herbig Ae star HD 169142. We explore the sensitivity of the DCO$^+$ formation pathways to the gas temperature and the CO abundance. The DCO$^+$ $J$=3-2 transition was observed with ALMA at a spatial resolution of 0.3". The HD 169142 DCO$^+$ radial intensity profile reveals a warm, inner component at radii 120 AU. The warm deuterium fractionation pathway is implemented as a constant DCO$^+$ abundance of 2.0$\times$10$^{-12}$ between 30-70 K. The DCO$^+$ emission probes a reservoir of cold material in the HD 169142 outer disk that is not revealed by the millimeter continuum, the SED, nor the emission from the 12CO, 13CO, or C18O $J$=2-1 lines., Accepted to Astronomy & Astrophysics

Aims: The two stable isotopes of nitrogen, 14N and 15N, exhibit a range of abundance ratios both inside and outside the solar system. The elemental ratio in the solar neighborhood is 440. Recent ALMA observations showed HCN/HC15N ratios from 83 to 156 in six T Tauri and Herbig disks and a CN/C15 N ratio of 323 +/- 30 in one T Tauri star. We aim to determine the dominant mechanism responsible for these enhancements of 15N: low-temperature exchange reactions or isotope-selective photodissociation of N2. Methods: Using the thermochemical code DALI, we model the nitrogen isotope chemistry in circumstellar disks with a 2D axisymmetric geometry. Our chemical network is the first to include both fractionation mechanisms for nitrogen. The model produces abundance profiles and isotope ratios for several key N-bearing species. We study how these isotope ratios depend on various disk parameters. Results: The formation of CN and HCN is closely coupled to the vibrational excitation of H2 in the UV-irradiated surface layers of the disk. Isotope fractionation is completely dominated by isotope-selective photodissociation of N2. The column density ratio of HCN over HC15N in the disk's inner 100 au does not depend strongly on the disk mass, the flaring angle or the stellar spectrum, but it is sensitive to the grain size distribution. For larger grains, self-shielding of N2 becomes more important relative to dust extinction, leading to stronger isotope fractionation. Between disk radii of ~50 and 200 au, the models predict HCN/HC15N and CN/C15N abundance ratios consistent with observations of disks and comets. The HCN/HC15N and CN/C15N column density ratios in the models are a factor of 2-3 higher than those inferred from the ALMA observations., Accepted by A&A; 17 pages, 17 figures; note added in proof

Protoplanetary discs around brown dwarfs and very low mass stars offer some of the best prospects for forming Earth-sized planets in their habitable zones. To this end, we study the nature of the disc around the very low mass star V410 X-ray 1, whose SED is indicative of an optically thick and very truncated dust disc, with our modelling suggesting an outer radius of only 0.6 au. We investigate two scenarios that could lead to such a truncation, and find that the observed SED is compatible with both. The first scenario involves the truncation of both the dust and gas in the disc, perhaps due to a previous dynamical interaction or the presence of an undetected companion. The second scenario involves the fact that a radial location of 0.6 au is close to the expected location of the H$_2$O snowline in the disc. As such, a combination of efficient dust growth, radial migration, and subsequent fragmentation within the snowline leads to an optically thick inner dust disc and larger, optically thin outer dust disc. We find that a firm measurement of the CO $J=2$--1 line flux would enable us to distinguish between these two scenarios, by enabling a measurement of the radial extent of gas in the disc. Many models we consider contain at least several Earth-masses of dust interior to 0.6 au, suggesting that V410 X-ray 1 could be a precursor to a system with tightly-packed inner planets, such as TRAPPIST-1., Comment: 10 pages, 8 figures, accepted for publication in MNRAS

ALMA observations of protoplanetary disks confirm earlier indications that there is a clear difference between the dust and gas radial extents. The origin of this difference is still debated, with both radial drift of the dust and optical depth effects suggested in the literature. In this work, the feedback of realistic dust particle distributions onto the gas chemistry and molecular emissivity is investigated, with a particular focus on CO isotopologues. The radial dust grain size distribution is determined using dust evolution models that include growth, fragmentation and radial drift. A new version of the code DALI is used to take into account how dust surface area and density influence the disk thermal structure, molecular abundances and excitation. The difference of dust and gas radial sizes is largely due to differences in the optical depth of CO lines and millimeter continuum, without the need to invoke radial drift. The effect of radial drift is primarily visible in the sharp outer edge of the continuum intensity profile. The gas outer radius probed by $^{12}$CO emission can easily differ by a factor of $\sim 2$ between the models for a turbulent $\alpha$ ranging between typical values. Grain growth and settling concur in thermally decoupling the gas and dust components, due to the low collision rate with large grains. As a result, the gas can be much colder than the dust at intermediate heights, reducing the CO excitation and emission, especially for low turbulence values. Also, due to disk mid-plane shadowing, a second CO thermal desorption (rather than photodesorption) front can occur in the warmer outer mid-plane disk. The models are compared to ALMA observations of HD 163296 as a test case. In order to reproduce the observed CO snowline of the system, a binding energy for CO typical of ice mixtures needs to be used rather than the lower pure CO value., Comment: 26 pages, 25 figures, accepted for publication in A&A, abstract shortened to fit arXiv requirements

Protoplanetary disks around young stars are the sites of planet formation. While the dust mass can be estimated using standard methods, determining the gas mass - and thus the amount of material available to form giant planets - has proven to be very difficult. Hydrogen deuteride (HD) is a promising alternative to the commonly-used gas mass tracer, CO. We aim to examine the robustness of HD as tracer of the disk gas mass, specifically the effect of gas mass on the HD FIR emission and its sensitivity to the vertical structure. Deuterium chemistry reactions relevant for HD were implemented in the thermochemical code DALI and models were run for a range of disk masses and vertical structures. The HD J=1-0 line intensity depends directly on the gas mass through a sublinear power law relation with a slope of ~0.8. Assuming no prior knowledge about the vertical structure of a disk and using only the HD 1-0 flux, gas masses can be estimated to within a factor of 2 for low mass disks (M$_{\rm disk} < 10^{-3}$ M$_\odot$). For more massive disks, this uncertainty increases to more than an order of magnitude. Adding the HD 2-1 line or independent information about the vertical structure can reduce this uncertainty to a factor of ~3 for all disk masses. For TW Hya, using the radial and vertical structure from Kama et al. 2016b the observations constrain the gas mass to $6\cdot10^{-3}$ M$_\odot$ < M$_{\rm disk} < 9\cdot10^{-3}$ M$_\odot$. Future observations require a 5$��$ sensitivity of $1.8\cdot10^{-20}$ W m$^{-2}$ ($2.5\cdot10^{-20}$ W m$^{-2}$) and a spectral resolving power R > 300 (1000) to detect HD 1-0 (HD 2-1) for all disk masses above $10^{-5}$ M$_\odot$ with a line-to-continuum ratio > 0.01. These results show that HD can be used as an independent gas mass tracer with a relatively low uncertainty and should be considered as an important science goal for future FIR missions., 18 pages, 13 figures, accepted in A&A

The protoplanetary system HD 169142 is one of the few cases where a potential candidate protoplanet has been recently detected via direct imaging. To study the interaction between the protoplanet and the disk itself observations of the gas and dust surface density structure are needed. This paper reports new ALMA observations of the dust continuum at 1.3\,mm, $^{12}$CO, $^{13}$CO and C$^{18}$O $J=2-1$ emission from the system HD 169142 at angular resolution of $\sim 0".18 - 0".28$ ($\sim 20\,$au$ - 33\,$au). The dust continuum emission reveals a double-ring structure with an inner ring between $0".17-0".28$ ($\sim 20 - 35\,$au) and an outer ring between $0".48-0".64$ ($\sim 56 - 83\,$au). The size and position of the inner ring is in good agreement with previous polarimetric observations in the near-infrared and is consistent with dust trapping by a massive planet. No dust emission is detected inside the inner dust cavity ($R \lesssim 20\,$au) or within the dust gap ($\sim 35 - 56\,$au). In contrast, the channel maps of the $J=2-1$ line of the three CO isotopologues reveal the presence of gas inside the dust cavity and dust gap. The gaseous disk is also much larger than the compact dust emission extending to $\sim 1'.5$ ($\sim 180\,$au) in radius. This difference and the sharp drop of the continuum emission at large radii point to radial drift of large dust grains ($>$ \micron-size). Using the thermo-chemical disk code \textsc{dali}, the continuum and the CO isotopologues emission are modelled to quantitatively measure the gas and dust surface densities. The resulting gas surface density is reduced by a factor of $\sim 30-40$ inward of the dust gap. The gas and dust distribution hint at the presence of multiple planets shaping the disk structure via dynamical clearing (dust cavity and gap) and dust trapping (double ring dust distribution)., Accepted for publication in A&A

We performed very deep searches for 2 ground-state water transitions in 13 protoplanetary disks with the HIFI instrument on-board the Herschel Space Observatory, with integration times up to 12 hours per line. Two other water transitions that sample warmer gas were also searched for with shallower integrations. The detection rate is low, and the upper limits provided by the observations are generally much lower than predictions of thermo-chemical models with canonical inputs. One ground-state transition is newly detected in the stacked spectrum of AA Tau, DM Tau, LkCa 15, and MWC 480. We run a grid of models to show that the abundance of gas-phase oxygen needs to be reduced by a factor of at least ~100 to be consistent with the observational upper limits (and positive detections) if a dust-to-gas mass ratio of 0.01 were to be assumed. As a continuation of previous ideas, we propose that the underlying reason for the depletion of oxygen (hence the low detection rate) is the freeze-out of volatiles such as water and CO onto dust grains followed by grain growth and settling/migration, which permanently removes these gas-phase molecules from the emissive upper layers of the outer disk. Such depletion of volatiles is likely ubiquitous among different disks, though not necessarily to the same degree. The volatiles might be returned back to the gas phase in the inner disk (within about 15 AU), which is consistent with current constraints. Comparison with studies on disk dispersal due to photoevaporation indicates that the timescale for volatile depletion is shorter than that of photoevaporation., Comment: Accepted for publication in ApJ

[Abridged] The infrared ro-vibrational emission lines from organic molecules in the inner regions of protoplanetary disks are unique probes of the physical and chemical structure of planet forming regions and the processes that shape them. The non-LTE excitation effects of carbon dioxide (CO2) are studied in a full disk model to evaluate: (i) what the emitting regions of the different CO2 ro-vibrational bands are; (ii) how the CO2 abundance can be best traced using CO2 ro-vibrational lines using future JWST data and; (iii) what the excitation and abundances tell us about the inner disk physics and chemistry. CO2 is a major ice component and its abundance can potentially test models with migrating icy pebbles across the iceline. A full non-LTE CO2 excitation model has been built. The characteristics of the model are tested using non-LTE slab models. Subsequently the CO2 line formation has been modelled using a two-dimensional disk model representative of T-Tauri disks. The CO2 gas that emits in the 15 $\mu$m and 4.5 $\mu$m regions of the spectrum is not in LTE and arises in the upper layers of disks, pumped by infrared radiation. The v$_2$ 15 $\mu$m feature is dominated by optically thick emission for most of the models that fit the observations and increases linearly with source luminosity. Its narrowness compared with that of other molecules stems from a combination of the low rotational excitation temperature (~250 K) and the inherently narrower feature for CO2. The inferred CO2 abundances derived for observed disks are more than two orders of magnitude lower than those in interstellar ices (~10$^5$), similar to earlier LTE disk estimates. Line-to-continuum ratios are low, of order a few %, thus high signal-to-noise (S/N > 300) observations are needed for individual line detections. Prospects of accurate abundance retreival with JWST-MIRI and JWST-NIRSpec are discussed., Comment: 18 pages, 16 figures, 7 appendix figures. Accepted for publication in A&A

The extent of the gas in protoplanetary disks is observed to be universally larger than the extent of the dust. This is often attributed to radial drift and grain growth of the mm grains, but line optical depth produces a similar observational signature. We investigate in what parts of the disk structure parameter space dust evolution and line optical depth are the dominant drivers of the observed gas and dust size difference. Using the thermochemical model DALI with dust evolution included we ran a grid of models aimed at reproducing the observed gas and dust size dichotomy. The relation between R_dust and dust evolution is non-monotonic and depends on the disk structure. R_gas is directly related to the radius where the CO column density drops below 10^15 cm^-2 and CO becomes photodissociated. R_gas is not affected by dust evolution but scales with the total CO content of the disk. R_gas/R_dust > 4 is a clear sign for dust evolution and radial drift in disks, but these cases are rare in current observations. For disks with a smaller R_gas/R_dust, identifying dust evolution from R_gas/R_dust requires modelling the disk structure including the total CO content. To minimize the uncertainties due to observational factors requires FWHM_beam < 1x the characteristic radius and a peak SNR > 10 on the 12CO emission moment zero map. For the dust outer radius to enclose most of the disk mass, it should be defined using a high fraction (90-95%) of the total flux. For the gas, any radius enclosing > 60% of the 12CO flux will contain most of the disk mass. To distinguish radial drift and grain growth from line optical depth effects based on size ratios requires disks to be observed at high enough angular resolution and the disk structure should to be modelled to account for the total CO content of the disk., 18 pages, 27 figures, accepted in A&A

Transitional disks around young stars are promising candidates to look for recently formed, embedded planets. Planet-disk interaction models predict that planets clear a gap in the gas while trapping dust at larger radii. Other physical mechanisms could be responsible for cavities as well. Previous observations have revealed that gas is still present inside these cavities, but the spatial distribution of this gas remains uncertain. We present high spatial resolution observations with the Atacama Large Millimeter/submillimeter Array (ALMA) of 13CO and C18O lines of four well-studied transitional disks. The observations are used to set constraints on the gas surface density, specifically cavity size and density drop inside the cavity. The physical-chemical model DALI is used to analyze the gas images of SR21, HD135344B, DoAr44 and IRS48. The main parameters of interest are the size, depth and shape of the gas cavity. CO isotope-selective photodissociation is included to properly constrain the surface density in the outer disk from C18O emission. The gas cavities are up to 3 times smaller than those of the dust in all four disks. Model fits indicate that the surface density inside the gas cavities decreases by a factor of 100-10000 compared with the surface density profile derived from the outer disk. A comparison with an analytical model of gap depths by planet-disk interaction shows that the disk viscosities are likely low, with a, Accepted by A&A; version after language-editing

Despite intensive studies of protoplanetary disks, there is still no reliable way to determine their total mass and their surface density distribution, quantities that are crucial for describing both the structure and the evolution of disks up to the formation of planets. The goal of this work is to use less abundant CO isotopologues, whose detection is routine for ALMA, to infer the gas mass of disks. Isotope-selective effects need to be taken into account in the analysis, because they can significantly modify CO isotopologues line intensities. CO isotope-selective photodissociation has been implemented in the physical-chemical code DALI and 800 disk models have been run for a range of disk and stellar parameters. Dust and gas temperature structures have been computed self-consistently, together with a chemical calculation of the main species. Both disk structure and stellar parameters have been investigated. Total fluxes have been ray-traced for different CO isotopologues and for various transitions for different inclinations. A combination of 13CO and C18O total intensities allows inference of the total disk mass, although with non-negligible uncertainties. These can be overcome by employing spatially resolved observations, i.e. the disk's radial extent and inclination. Comparison with parametric models shows differences at the factor of a few level, especially for extremely low and high disk masses. Finally, total line intensities for different CO isotopologue and for various low-J transitions are provided and are fitted to simple formulae. The effects of a lower gas-phase carbon abundance and different gas/dust ratios are investigated as well, and comparison with other tracers is made. Disk masses can be determined within a factor of a few by comparing CO isotopologue lines observations with the simulated line fluxes, modulo the uncertainties in the volatile elemental abundances., Comment: 20 pages, 15 figures, A&A accepted

The composition of planetary solids and gases is largely rooted in the processing of volatile elements in protoplanetary disks. To shed light on the key processes, we carry out a comparative analysis of the gas-phase carbon abundance in two systems with a similar age and disk mass, but different central stars: HD 100546 and TW Hya. We combine our recent detections of C$^{0}$ in these disks with observations of other carbon reservoirs (CO, C$^{+}$, C$_{2}$H) and gas mass and warm gas tracers (HD, O$^{0}$), as well as spatially resolved ALMA observations and the spectral energy distribution. The disks are modelled with the DALI 2D physical-chemical code. Stellar abundances for HD 100546 are derived from archival spectra. Upper limits on HD emission from HD 100546 place an upper limit on the total disk mass of $\leq0.1\,M_{\odot}$. The gas-phase carbon abundance in the atmosphere of this warm Herbig disk is at most moderately depleted compared to the interstellar medium, with [C]/[H]$_{\rm gas}=(0.1-1.5)\times 10^{-4}$. HD 100546 itself is a $\lambda\,$Bo\"{o}tis star, with solar abundances of C and O but a strong depletion of rock-forming elements. In the gas of the T Tauri disk TW Hya, both C and O are strongly underabundant, with [C]/[H]$_{\rm gas}=(0.2-5.0)\times 10^{-6}$ and C/O${>}1$. We discuss evidence that the gas-phase C and O abundances are high in the warm inner regions of both disks. Our analytical model, including vertical mixing and a grain size distribution, reproduces the observed [C]/[H]$_{\rm gas}$ in the outer disk of TW Hya and allows to make predictions for other systems., Comment: Accepted for publication in A&A

The gas temperature structure of protoplanetary disks is a key ingredient for interpreting various disk observations and for quantifying the subsequent evolution of these systems. The comparison of low- and mid-$J$ CO rotational lines is a powerful tool to assess the temperature gradient in the warm molecular layer of disks. Spectrally resolved high-$J$ ($J_{\rm u} > 14$) CO lines probe intermediate distances and heights from the star that are not sampled by (sub-)millimeter CO spectroscopy. This paper presents new {\it Herschel}/HIFI and archival PACS observations of $^{12}$CO, $^{13}$CO and \cii \ emission in 4 Herbig AeBe (HD 100546, HD 97048, IRS 48, HD 163296) and 3 T Tauri (AS 205, S CrA, TW Hya) disks. In the case of the T Tauri systems AS 205 and S CrA, the CO emission has a single-peaked profile, likely due to a slow wind. For all other systems, the {\it Herschel} CO spectra are consistent with pure disk emission and the spectrally-resolved lines (HIFI) and the CO rotational ladder (PACS) are analyzed simultaneously assuming power-law temperature and column density profiles, using the velocity profile to locate the emission in the disk. The temperature profile varies substantially from disk to disk. In particular, $T_{\rm gas}$ in the disk surface layers can differ by up to an order of magnitude among the 4 Herbig AeBe systems with HD 100546 being the hottest and HD 163296 the coldest disk of the sample. Clear evidence of a warm disk layer where $T_{\rm gas} > T_{\rm dust}$ is found in all the Herbig Ae disks. The observed CO fluxes and line profiles are compared to predictions of physical-chemical models. The primary parameters affecting the disk temperature structure are the flaring angle, the gas-to-dust mass ratio the scale height and the dust settling., Accepted for publication in A&A

Molecules containing one or a few hydrogen atoms and a heavier atom (hydrides) have been predicted to trace FUV radiation. In some chemical models, FUV emission by the central object or protostar of a star forming region greatly enhances some of the hydride abundances. Two massive regions, W3 IRS5 and AFGL 2591, have been observed in hydride lines by HIFI onboard the {\it Herschel Space Observatory}. We use published results as well as new observations of CH$^+$ towards W3 IRS5. Molecular column densities are derived from ground state absorption lines, radiative transfer modeling or rotational diagrams. Models assuming no internal FUV are compared with two-dimensional models including FUV irradiation of outflow walls. We confirm that the effect of FUV is clearly noticeable and greatly improves the fit. The most sensitive molecules to FUV irradiation are CH$^+$ and OH$^+$, enhanced in abundance by many orders of magnitude. Modeling in addition also full line radiative transfer, Bruderer et al (2010b) achieve good agreement of a two-dimensional FUV model with observations of CH$^+$ in AFGL 2591. It is concluded that CH$^+$ and OH$^+$ are good FUV tracers in star-forming regions., EAS Publications Series, 5th Zermatt conference on Conditions and impact of star formation: New results with Herschel and beyond (invited), submitted

The paper presents new high angular resolution ALMA 1.3 mm dust continuum observations of the protoplanetary system AS 209 in the Ophiuchus star forming region. The dust continuum emission is characterized by a main central core and two prominent rings at $r = 75\,$au and $r = 130\,$au intervaled by two gaps at at $r = 62\,$au and $r = 103\,$au. The two gaps have different widths and depths, with the inner one being narrower and shallower. We determined the surface density of the millimeter dust grains using the 3D radiative transfer disk code \textsc{dali}. According to our fiducial model the inner gap is partially filled with millimeter grains while the outer gap is largely devoid of dust. The inferred surface density is compared to 3D hydrodynamical simulations (FARGO-3D) of planet-disk interaction. The outer dust gap is consistent with the presence of a giant planet ($M_{\rm planet} \sim 0.8\,M_{\rm Staturn}$); the planet is responsible for the gap opening and for the pile-up of dust at the outer edge of the planet orbit. The simulations also show that the same planet can give origin to the inner gap at $r = 62\,$au. The relative position of the two dust gaps is close to the 2:1 resonance and we have investigated the possibility of a second planet inside the inner gap. The resulting surface density (including location, width and depth of the two dust gaps) are in agreement with the observations. The properties of the inner gap pose a strong constraint to the mass of the inner planet ($M_{\rm planet} < 0.1\,M_{\rm J}$). In both scenarios (single or pair of planets), the hydrodynamical simulations suggest a very low disk viscosity ($��< 10^{-4}$). Given the young age of the system (0.5 - 1 Myr), this result implies that the formation of giant planets occurs on a timescale of $\lesssim$ 1\,Myr., Accepted by A&A

Observations of CO+ suggest column densities on the order 10^12 cm^-2 that can not be reproduced by many chemical models. CO+ is more likely to be destroyed than excited in collisions with hydrogen. An anomalous excitation mechanism may thus have to be considered when interpreting CO^+ observations. Chemical models are used to perform a parameter study of CO^+ abundances. Line fluxes are calculated for N(CO+)=10^12 cm^-2 and different gas densities and temperatures using a non-LTE escape probability method. The chemical formation and destruction rates are considered explicitly in the detailed balance equations of the radiative transfer. In addition, the rotational levels of CO+ are assumed to be excited upon chemical formation according to a formation temperature. It is found, that chemical models are generally able to produce high fractional CO+ abundances (x(CO+) =10^-10). In a far-ultraviolet (FUV) dominated environment, however, high abundances of CO+ are only produced in regions with a Habing field G0 > 100 and T(kin) > 600 K, posing a strong constraint on the gas temperature. For gas densities >10^6 cm^-3 and temperatures > 600 K, the combination of chemical and radiative transfer analysis shows little effect on intensities of CO+ lines with upper levels N_up 10^6 cm ^ -3. The Herschel Space Observatory is able to reveal such effects in the terahertz wavelength regime. Ideal objects to observe are protoplanetary disks with densities 10^6 cm^-3. It is finally suggested that the CO+ chemistry may be well understood and that the abundances observed so far can be explained with a high enough gas temperature and a proper geometry., 9 pages, 7 figures

(Abridged*) Models of the young solar nebula assume a hot initial disk with most volatiles are in the gas phase. The question remains whether an actively accreting disk is warm enough to have gas-phase water up to 50 AU radius. No detailed studies have yet been performed on the extent of snowlines in an embedded accreting disk (Stage 0). Quantify the location of gas-phase volatiles in embedded actively accreting disk system. Two-dimensional physical and radiative transfer models have been used to calculate the temperature structure of embedded protostellar systems. Gas and ice abundances of H$_2$O, CO$_2$, and CO are calculated using the density-dependent thermal desorption formulation. The midplane water snowline increases from 3 to 55 AU for accretion rates through the disk onto the star between $10^{-9}$-$10^{-4} \ M_{\odot} \ {\rm yr^{-1}}$. CO$_2$ can remain in the solid phase within the disk for $\dot{M} \leq 10^{-5} \ M_{\odot} \ {\rm yr^{-1}}$ down to $\sim 20$ AU. Most of the CO is in the gas phase within an actively accreting disk independent of disk properties and accretion rate. The predicted optically thin water isotopolog emission is consistent with the detected H$_2^{18}$O emission toward the Stage 0 embedded young stellar objects, originating from both the disk and the warm inner envelope (hot core). An accreting embedded disk can only account for water emission arising from $R < 50$ AU, however, and the extent rapidly decreases for low accretion rates. Thus, the radial extent of the emission can be measured with ALMA observations and compared to this limit. Volatiles sublimate out to 50 AU in young disks and can reset the chemical content inherited from the envelope in periods of high accretion rates. A hot young solar nebula out to 30 AU can only have occurred during the deeply embedded Stage 0, not during the T-Tauri phase of our early solar system., 15 pages, 10 figures, accepted for publication in A&A

Due to instrumental limitations and a lack of disk detections, the structure between the envelope and the rotationally supported disk has been poorly studied. This is now possible with ALMA through observations of CO isotopologs and tracers of freezeout. Class 0 sources are ideal for such studies given their almost intact envelope and young disk. The structure of the disk-envelope interface of the prototypical Class 0 source, VLA1623A which has a confirmed Keplerian disk, is constrained from ALMA observations of DCO+ 3-2 and C18O 2-1. The physical structure of VLA1623 is obtained from the large-scale SED and continuum radiative transfer. An analytic model using a simple network coupled with radial density and temperature profiles is used as input for a 2D line radiative transfer calculation for comparison with the ALMA Cycle 0 12m array and Cycle 2 ACA observations of VLA1623. DCO+ emission shows a clumpy structure bordering VLA1623A's Keplerian disk, suggesting a cold ring-like structure at the disk-envelope interface. The radial position of the observed DCO+ peak is reproduced in our model only if the region's temperature is between 11-16K, lower than expected from models constrained by continuum and SED. Altering the density has little effect on the DCO+ position, but increased density is needed to reproduce the disk traced in C18O. The DCO+ emission around VLA1623A is the product of shadowing of the envelope by the disk. Disk-shadowing causes a drop in the gas temperature outside of the disk on >200AU scales, encouraging deuterated molecule production. This indicates that the physical structure of the disk-envelope interface differs from the rest of the envelope, highlighting the drastic impact that the disk has on the envelope and temperature structure. The results presented here show that DCO+ is an excellent cold temperature tracer., Accepted for publication in Astronomy & Astrophysics, 16 pages with appendices, 17 figures and 3 tables

We utilize magnetohydrodynamic (MHD) simulations to develop a numerical model for GMC-GMC collisions between nearly magnetically critical clouds. The goal is to determine if, and under what circumstances, cloud collisions can cause pre-existing magnetically subcritical clumps to become supercritical and undergo gravitational collapse. We first develop and implement new photodissociation region (PDR) based heating and cooling functions that span the atomic to molecular transition, creating a multiphase ISM and allowing modeling of non-equilibrium temperature structures. Then in 2D and with ideal MHD, we explore a wide parameter space of magnetic field strength, magnetic field geometry, collision velocity, and impact parameter, and compare isolated versus colliding clouds. We find factors of ~2-3 increase in mean clump density from typical collisions, with strong dependence on collision velocity and magnetic field strength, but ultimately limited by flux-freezing in 2D geometries. For geometries enabling flow along magnetic field lines, greater degrees of collapse are seen. We discuss observational diagnostics of cloud collisions, focussing on 13CO(J=2-1), 13CO(J=3-2), and 12CO(J=8-7) integrated intensity maps and spectra, which we synthesize from our simulation outputs. We find the ratio of J=8-7 to lower-J emission is a powerful diagnostic probe of GMC collisions., Comment: 22 pages, 23 figures. Accepted for publication in ApJ

Abridged: Recent simulations have explored different ways to form accretion disks around low-mass stars. We aim to present observables to differentiate a rotationally supported disk from an infalling rotating envelope toward deeply embedded young stellar objects and infer their masses and sizes. Two 3D magnetohydrodynamics (MHD) formation simulations and 2D semi-analytical model are studied. The dust temperature structure is determined through continuum radiative transfer RADMC3D modelling. A simple temperature dependent CO abundance structure is adopted and synthetic spectrally resolved submm rotational molecular lines up to $J_{\rm u} = 10$ are simulated. All models predict similar compact components in continuum if observed at the spatial resolutions of 0.5-1$"$ (70-140 AU) typical of the observations to date. A spatial resolution of $\sim$14 AU and high dynamic range ($> 1000$) are required to differentiate between RSD and pseudo-disk in the continuum. The peak-position velocity diagrams indicate that the pseudo-disk shows a flatter velocity profile with radius than an RSD. On larger-scales, the CO isotopolog single-dish line profiles are similar and are narrower than the observed line widths of low-$J$ lines, indicating significant turbulence in the large-scale envelopes. However a forming RSD can provide the observed line widths of high-$J$ lines. Thus, either RSDs are common or a higher level of turbulence ($b \sim 0.8 \ {\rm km \ s^{-1}}$ ) is required in the inner envelope compared with the outer part. Multiple spatially and spectrally resolved molecular line observations are needed. The continuum data give a better estimate on disk masses whereas the disk sizes can be estimated from the spatially resolved molecular lines observations. The general observable trends are similar between the 2D semi-analytical models and 3D MHD RSD simulations., 16 pages, 14 figures, accepted for publication, A&A

We present multi-epoch high-spectral resolution observations with VLT/CRIRES of the OH doublet $^2\Pi_{3/2}$ P4.5 (1+,1-) (2.934 $\mu$m) towards the protoplanetary disk around HD 100546. The OH doublet is detected at all epochs and is spectrally resolved while nearby H$_2$O lines remains undetected. The OH line velocity profile is different in the three datasets: in the first epoch (April 2012, PA=26$^{\circ}$) the OH lines are symmetric and line broadening is consistent with the gas being in Keplerian rotation around the star. No OH emission is detected within a radius of 8-11 au from the star: the line emitting region is similar in size and extent to that of the CO ro-vibrational lines. In the other two epochs (March 2013 and April 2014, PA=90$^{\circ}$ and 10$^{\circ}$, respectively) the OH lines appear asymmetric and fainter compared to April 2012. We investigate the origin of these line asymmetries which were taken by previous authors as evidence for tidal interaction between an (unseen) massive planet and the disk. We show that the observed asymmetries can be fully explained by a misalignment of the slit of order 0\farcs04-0\farcs20 with respect to the stellar position. The disk is spatially resolved and the slit misalignment is likely caused by the extended dust emission which is brighter than the stellar photosphere at near-infrared wavelengths which is the wavelength used for the pointing. This can cause the photo-center of HD 100546 to be mis-aligned with the stellar position at near-infrared wavelengths., Comment: Accepted for publication in ApJ

(Abridged) Organic molecules are important constituents of protoplanetary disks. Their ro-vibrational lines observed in the near- and mid-infrared are commonly detected toward T Tauri disks. These lines are the only way to probe the chemistry in the inner few au where terrestrial planets form. To understand this chemistry, accurate molecular abundances have to be determined. This is complicated by excitation effects. Most analyses so far have made the assumption of local thermal equilibrium (LTE). Starting from estimates for the collisional rate coefficients of HCN, non-LTE slab models of the HCN emission were calculated to study the importance of different excitation mechanisms. Using a new radiative transfer model, the HCN emission from a full two-dimensional disk was then modeled to study the effect of the non-LTE excitation, together with the line formation. We ran models tailored to the T Tauri disk AS 205 (N) where HCN lines in both the 3 {\mu}m and 14 {\mu}m bands have been observed by VLT-CRIRES and the Spitzer Space Telescope. Reproducing the observed 3 {\mu}m / 14 {\mu}m flux ratios requires very high densities and kinetic temperatures ($n > 10^{14}$ cm$^{-3}$ and $T > 750$ K), if only collisional excitation is accounted for. Radiative pumping can, however, excite the lines easily out to considerable radii $\sim$ 10 au. Consequently, abundances derived from LTE and non-LTE models do not differ by more than a factor of about 3. Models with both a strongly enhanced abundance within $\sim$ 1 au (jump abundance) and constant abundance can reproduce the current observations, but future observations with the MIRI instrument on JWST and METIS on the E-ELT can easily distinguish between the scenarios and test chemical models. Depending on the scenario, ALMA can detect rotational lines within vibrationally excited levels., Comment: Accepted for publication in A&A, 20 pages, 18 figures

We report ALMA Cycle 2 observations of 230 GHz (1.3 mm) dust continuum emission, and $^{12}$CO, $^{13}$CO, and C$^{18}$O J = 2-1 line emission, from the Upper Scorpius transitional disk [PZ99] J160421.7-213028, with an angular resolution of ~0".25 (35 AU). Armed with these data and existing H-band scattered light observations, we measure the size and depth of the disk's central cavity, and the sharpness of its outer edge, in three components: sub-$\mu$m-sized "small" dust traced by scattered light, millimeter-sized "big" dust traced by the millimeter continuum, and gas traced by line emission. Both dust populations feature a cavity of radius $\sim$70 AU that is depleted by factors of at least 1000 relative to the dust density just outside. The millimeter continuum data are well explained by a cavity with a sharp edge. Scattered light observations can be fitted with a cavity in small dust that has either a sharp edge at 60 AU, or an edge that transitions smoothly over an annular width of 10 AU near 60 AU. In gas, the data are consistent with a cavity that is smaller, about 15 AU in radius, and whose surface density at 15 AU is $10^{3\pm1}$ times smaller than the surface density at 70 AU; the gas density grades smoothly between these two radii. The CO isotopologue observations rule out a sharp drop in gas surface density at 30 AU or a double-drop model as found by previous modeling. Future observations are needed to assess the nature of these gas and dust cavities, e.g., whether they are opened by multiple as-yet-unseen planets or photoevaporation., Comment: 34 pages (single column), 13 figures, ApJ in press

One of the methods for deriving disk masses relies on direct observations of the gas, whose bulk mass is in the outer cold ($T\lesssim30$K) regions. This zone can be well traced by rotational lines of less abundant CO isotopologues, that probe the gas down to the midplane. The total CO gas mass is then obtained with the isotopologue ratios taken to be constant at the elemental isotope values found in the local ISM. This approach is however imprecise, because isotope selective processes are ignored. The aim of this work is an isotopologue selective treatment of CO isotopologues, in order to obtain a more accurate determination of disk masses. The isotope-selective photodissociation, the main process controlling the abundances of CO isotopologues in the CO-emissive layer, is properly treated for the first time in a full disk model (DALI, Bruderer et al. 2012; Bruderer 2013). The chemistry, thermal balance, line and continuum radiative transfer are all considered together with a chemical network that treats $^{13}$CO, C$^{18}$O, C$^{17}$O, isotopes of all included atoms, and molecules, as independent species. Isotope selective processes lead to regions in the disk where the isotopologues abundance ratios are considerably different from the elemental ratio. The results of this work show that considering CO isotopologue ratios as constants can lead to an underestimate of disk masses by up to almost two orders of magnitude if grains have grown to larger sizes. This may explain observed discrepancies in mass determinations from different tracers. The dependence of the various isotopologues emission on stellar and disk parameters is investigated. Including CO isotope selective processes is crucial to determine the gas mass of the disk accurately (through ALMA observations) and thus to provide the amount of gas which may eventually form planets or change the dynamics of forming planetary systems., Accepted for publication in A&A, 16 pages, 10 figures, 4 tables

(Abridged) We study the response of the gas to energetic processes associated with high-mass star formation and compare it with studies on low- and intermediate-mass young stellar objects (YSOs) using the same methods. The far-IR line emission and absorption of CO, H$_2$O, OH, and [OI] reveals the excitation and the relative contribution of different species to the gas cooling budget. Herschel-PACS spectra covering 55-190 um are analyzed for ten high-mass star forming regions of various luminosities and evolutionary stages at spatial scales of ~10^4 AU. Radiative transfer models are used to determine the contribution of the envelope to the far-IR CO emission. The close environments of high-mass YSOs show strong far-IR emission from molecules, atoms, and ions. Water is detected in all 10 objects even up to high excitation lines. CO lines from J=14-13 up to typically 29-28 show a single temperature component, Trot~300 K. Typical H$_2$O temperatures are Trot~250 K, while OH has Trot~80 K. Far-IR line cooling is dominated by CO (~75 %) and to a smaller extent by OI (~20 %), which increases for the most evolved sources. H$_2$O is less important as a coolant for high-mass sources because many lines are in absorption. Emission from the envelope is responsible for ~45-85 % of the total CO luminosity in high-mass sources compared with only ~10 % for low-mass YSOs. The highest-J lines originate most likely from shocks, based on the strong correlation of CO and H$_2$O with physical parameters of the sources from low- to high-masses. Excitation of warm CO is very similar for all mass regimes, whereas H$_2$O temperatures are ~100 K higher for high-mass sources than the low-mass YSOs. Molecular cooling is ~4 times more important than cooling by [OI]. The total far-IR line luminosity is about 10$^{-3}$ and 10$^{-5}$ times lower than the dust luminosity for the low- and high-mass YSOs., Comment: 23 pages, 19 figures, 6 Tables. Accepted to Astronomy and Astrophysics

Protostars interact with their surroundings through jets and winds impacting on the envelope and creating shocks, but the nature of these shocks is still poorly understood. Our aim is to survey far-infrared molecular line emission from a uniform and significant sample of deeply-embedded low-mass young stellar objects in order to characterize shocks and the possible role of ultraviolet radiation in the immediate protostellar environment. Herschel/PACS spectral maps of 22 objects in the Perseus molecular cloud were obtained as part of the `William Herschel Line Legacy' survey. Line emission from H$_\mathrm{2}$O, CO, and OH is tested against shock models from the literature. Observed line ratios are remarkably similar and do not show variations with source physical parameters. Observations show good agreement with the shock models when line ratios of the same species are compared. Ratios of various H$_\mathrm{2}$O lines provide a particularly good diagnostic of pre-shock gas densities, $n_\mathrm{H}\sim10^{5}$ cm$^{-3}$, in agreement with typical densities obtained from observations of the post-shock gas. The corresponding shock velocities, obtained from comparison with CO line ratios, are above 20 km\,s$^{-1}$. However, the observations consistently show one-to-two orders of magnitude lower H$_\mathrm{2}$O-to-CO and H$_\mathrm{2}$O-to-OH line ratios than predicted by the existing shock models. The overestimated model H$_\mathrm{2}$O fluxes are most likely caused by an overabundance of H$_\mathrm{2}$O in the models since the excitation is well-reproduced. Illumination of the shocked material by ultraviolet photons produced either in the star-disk system or, more locally, in the shock, would decrease the H$_\mathrm{2}$O abundances and reconcile the models with observations. Detections of hot H$_\mathrm{2}$O and strong OH lines support this scenario., Comment: 28 pages, 12 figures, accepted to Astronomy & Astrophysics

(Abridged) Disks are observed around pre-main sequence stars, but how and when they form is still heavily debated. While disks around young stellar objects have been identified through thermal dust emission, spatially and spectrally resolved molecular line observations are needed to determine their nature. We present subarcsecond observations of dust and gas toward four Class I low-mass young stellar objects in Taurus. The 13CO and C18O J=2-1 transitions at 220 GHz were observed with the Plateau de Bure Interferometer at a spatial resolution of ~0.8'' and analyzed using uv-space position velocity diagrams to determine the nature of their observed velocity radient. Rotationally supported disks (RSDs) are detected around 3 of the 4 Class I sources studied. The derived masses identify them as Stage I objects; i.e., their stellar mass is higher than their envelope and disk masses. The outer radii of the Keplerian disks toward our sample of Class I sources are 100 AU around these sources are dominated by infalling motion (v propto r^-1). A large-scale envelope model is required to estimate the basic parameters of the flattened structure from spatially resolved continuum data. Similarities and differences between the gas and dust disk are discussed. Combined with literature data, the sizes of the RSDs around Class I objects are best described with evolutionary models with an initial rotation of 10^-14 Hz and slow sound speeds. Based on the comparison of gas and dust disk masses, little CO is frozen out within 100 AU in these disks. RSDs with radii up to 100 AU are present around Class I embedded objects. Larger surveys of both Class 0 and I objects are needed to determine whether most disks form late or early in the embedded phase., Comment: Accepted for publication in A&A, 22 pages with appendix; 13 figures

(Abridged) Transition disks are recognized by the absence of emission of small dust grains inside a radius of up to several 10s of AUs. Due to the lack of angular resolution and sensitivity, the gas content of such dust holes has not yet been determined, but is of importance to constrain the mechanism leading to the dust holes. Transition disks are thought to currently undergo the process of dispersal, setting an end to the giant planet formation process. We present new high-resolution observations with the Atacama Large Millimeter/ submillimeter Array (ALMA) of gas lines towards the transition disk Oph IRS 48 previously shown to host a large dust trap. ALMA has detected the $J=6-5$ line of $^{12}$CO and C$^{17}$O around 690 GHz (434 $\mu$m) at a resolution of $\sim$0.25$''$ corresponding to $\sim$30 AU (FWHM). The observed gas lines are used to set constraints on the gas surface density profile. New models of the physical-chemical structure of gas and dust in Oph IRS 48 are developed to reproduce the CO line emission together with the spectral energy distribution (SED) and the VLT-VISIR 18.7 $\mu$m dust continuum images. Integrated intensity cuts and the total spectrum from models having different trial gas surface density profiles are compared to observations. Using the derived surface density profiles, predictions for other CO isotopologues are made, which can be tested by future ALMA observations of the object. The derived gas surface density profile points to the clearing of the cavity by one or more massive planet/companion rather than just photoevaporation or grain-growth., Comment: Accepted by A&A, 17 pages, 15 figures

There is growing observational evidence that disk evolution is stellar-mass dependent. Here, we show that these dependencies extend to the atomic and molecular content of disk atmospheres. We analyze a unique dataset of high-resolution Spitzer/IRS spectra from 8 very low-mass star and brown dwarf disks. We report the first detections of Ne+, H2, CO2, and tentative detections of H2O toward these faint and low-mass disks. Two of our [NeII] 12.81 micron emission lines likely trace the hot (>5,000 K) disk surface irradiated by X-ray photons from the central stellar/sub-stellar object. The H2 S(2) and S(1) fluxes are consistent with arising below the fully or partially ionized surface traced by the [NeII] emission, in gas at about 600 K. We confirm the higher C2H2/HCN flux and column density ratio in brown dwarf disks previously noted from low-resolution IRS spectra. Our high-resolution spectra also show that the HCN/H2O fluxes of brown dwarf disks are on average higher than those of T Tauri disks. Our LTE modeling hints that this difference extends to column density ratios if H2O lines trace warm > 600 K disk gas. These trends suggest that the inner regions of brown dwarf disks have a lower O/C ratio than those of T Tauri disks which may result from a more efficient formation of non-migrating icy planetesimals. A O/C=1, as inferred from our analysis, would have profound implications on the bulk composition of rocky planets that can form around very low-mass stars and brown dwarfs., Accepted to ApJ

(Abridged) Planet formation is closely related to the structure and dispersal of protoplanetary disks. A certain class of disks, called transition disks, exhibit cavities in dust images at scales of up to a few 10s of AU. The formation mechanism of the cavities is still unclear. The gas content of such cavities can be spatially resolved for the first time using the Atacama Large Millimeter/submillimeter Array (ALMA). We have developed a new series of models to simulate the physical conditions and chemical abundances of the gas in cavities to address the question whether the gas is primarily atomic or molecular inside the dust free cavities exposed to intense UV radiation. Molecular/atomic line emission by carbon monoxide (CO), its isotopologues (13CO, C18O, C17O, and 13C18O) and related species ([CI], [CII], and [OI]) is predicted for comparison with ALMA and the Herschel Space Observatory. The gas can remain in molecular form down to very low amounts of gas in the cavity. Shielding of the stellar radiation by a dusty inner disk (pre-transition disk) allows CO to survive down to lower gas masses in the cavity. The main parameter for the CO emission from cavity is the gas mass. Other parameters such as the outer disk mass, bolometric luminosity, shape of the stellar spectrum or PAH abundance are less important. Since the CO pure rotational lines readily become optically thick, the CO isotopologues need to be observed in order to quantitatively determine the amount of gas in the cavity. A wide range of gas masses in the cavity of transition disks (~4 orders of magnitude) can be probed using combined observations of CO isotopologue lines with ALMA. Measuring the gas mass in the cavity will ultimately help to distinguish between different cavity formation theories., Accepted by A&A, 21 pages, 20 figures

The cosmic abundance of hydrides depends critically on high-energy UV, X-ray, and particle irradiation. Here we study hydrides in star-forming regions where irradiation by the young stellar object can be substantial, and density and temperature can be much enhanced over interstellar values. Lines of OH, CH, NH, and SH and their ions OH+, CH+, NH+, SH+, H2O+, and H3O+ were observed in star-forming regions by the HIFI spectrometer onboard the Herschel Space Observatory. Molecular column densities are derived from observed ground-state lines, models, or rotational diagrams. We report here on two prototypical high-mass regions, AFGL 2591 and W3 IRS5, and compare them to chemical calculations by making assumptions on the high-energy irradiation. A model assuming no ionizing protostellar emission is compared with (i) a model assuming strong protostellar X-ray emission and (ii) a two-dimensional (2D) model including emission in the far UV (FUV, 6–13.6 eV), irradiating the outflow walls that separate the outflowing gas and infalling envelope material. We confirm that the effect of FUV in two-dimensional models with enlarged irradiated surfaces is clearly noticeable. A molecule that is very sensitive to FUV irradiation is CH+, enhanced in abundance by more than 5 orders of magnitude. The HIFI observations of CH+ lines agree with the two-dimensional FUV model by Bruderer et al., which computes abundances, non-LTE excitation, and line radiative transfer.20 It is concluded that CH+ is a good FUV tracer in star-forming regions. The effect of potential X-ray irradiation is not excluded but cannot be demonstrated by the present data., The Journal of Physical Chemistry A, 117 (39), ISSN:1089-5639, ISSN:1520-5215

The statistics of discovered exoplanets suggest that planets form efficiently. However, there are fundamental unsolved problems, such as excessive inward drift of particles in protoplanetary disks during planet formation. Recent theories invoke dust traps to overcome this problem. We report the detection of a dust trap in the disk around the star Oph IRS 48 using observations from the Atacama Large Millimeter/submillimeter Array (ALMA). The 0.44-millimeter-wavelength continuum map shows high-contrast crescent-shaped emission on one side of the star originating from millimeter-sized grains, whereas both the mid-infrared image (micrometer-sized dust) and the gas traced by the carbon monoxide 6-5 rotational line suggest rings centered on the star. The difference in distribution of big grains versus small grains/gas can be modeled with a vortex-shaped dust trap triggered by a companion., 25 pages, 7 figures (accepted version prior to language editing)

OH is a key species in the water chemistry of star-forming regions, because its presence is tightly related to the formation and destruction of water. This paper presents OH observations from 23 low- and intermediate-mass young stellar objects obtained with the PACS integral field spectrometer on-board Herschel in the context of the Water In Star-forming Regions with Herschel (WISH) key program. Most low-mass sources have compact OH emission (< 5000 AU scale), whereas the OH lines in most intermediate-mass sources are extended over the whole PACS detector field-of-view (> 20000 AU). The strength of the OH emission is correlated with various source properties such as the bolometric luminosity and the envelope mass, but also with the OI and H2O emission. Rotational diagrams for sources with many OH lines show that the level populations of OH can be approximated by a Boltzmann distribution with an excitation temperature at around 70 K. Radiative transfer models of spherically symmetric envelopes cannot reproduce the OH emission fluxes nor their broad line widths, strongly suggesting an outflow origin. Slab excitation models indicate that the observed excitation temperature can either be reached if the OH molecules are exposed to a strong far-infrared continuum radiation field or if the gas temperature and density are sufficiently high. Using realistic source parameters and radiation fields, it is shown for the case of Ser SMM1 that radiative pumping plays an important role in transitions arising from upper level energies higher than 300 K. The compact emission in the low-mass sources and the required presence of a strong radiation field and/or a high density to excite the OH molecules points towards an origin in shocks in the inner envelope close to the protostar., Accepted for publication in Astronomy and Astrophysics. Abstract abridged

Abridged abstract: For stars to form, material must fall inwards from core scales through the envelope towards the central protostar. The velocity profile around protostars is poorly constrained. 6 Class 0 protostars and one Class I protostars observed with HIFI on board Herschel as part of the "Water in star-forming regions with Herschel" (WISH) survey show infall signatures in water line observations. We use 1-D non-LTE RATRAN radiative transfer models of the observed water lines to constrain the infall velocity and chemistry in the protostellar envelopes of these sources. We assume a free-fall velocity profile and, having found the best fit, vary the radii over which infall takes place. In the well-studied Class 0 protostar NGC1333-IRAS4A we find that infall takes place over the whole envelope to which our observations are sensitive (r>~1000 AU). For 4 sources infall takes place on core to envelope scales (i.e. ~10000-3000 AU). In 2 sources the inverse P-Cygni profiles seen in the ground-state lines are more likely due to larger-scale motions or foreground clouds. Models including a simple consideration of the chemistry are consistent with the observations, while using step abundance profiles are not. The non-detection of excited water in the inner envelope in 6/7 protostars is further evidence that water must be heavily depleted from the gas-phase at these radii. Infall in four of the sources is supersonic and infall in all sources must take place at the outer edge of the envelope, which may be evidence that collapse is global or outside-in rather than inside-out. The mass infall rate in IRAS4A is large (>~10^-4 msol\yr), higher than the mass outflow rate and expected mass accretion rates onto the star, suggesting that any flattened disk-like structure on small scales will be gravitationally unstable, potentially leading to rotational fragmentation and/or episodic accretion., 20 pages, 22 figures, 5 tables. Accepted to Astronomy & Astrophysics

Stars may be assembled in large growth spurts, however the evidence for this hypothesis is circumstantial. Directly studying the accretion at the earliest phases of stellar growth is challenging because young stars are deeply embedded in optically thick envelopes, which have spectral energy distributions that peak in the far-IR, where observations are difficult. In this paper, we consider the feasibility of detecting accretion outbursts from these younger stars by investigating the timescales for how the protostellar envelope responds to changes in the emission properties of the central source. The envelope heats up in response to an outburst, brightening at all wavelengths and with the emission peak moving to shorter wavelengths. The timescale for this change depends on the time for dust grains to heat and re-emit photons and the time required for the energy to escape the inner, optically-thick portion of the envelope. We find that the dust response time is much shorter than the photon propagation time and thus the timescale over which the emission varies is set by time delays imposed by geometry. These times are hours to days near the peak of the spectral energy distribution and weeks to months in the sub-mm. The ideal location to quickly detect continuum variability is therefore in the mid- to far-IR, near the peak of the spectral energy distribution, where the change in emission amplitude is largest. Searching for variability in sub-mm continuum emission is also feasible, though with a longer time separation and a weaker relationship between the amount of detected emission amplitude and change in central source luminosity. Such observations would constrain accretion histories of protostars and would help to trace the disk/envelope instabilities that lead to stellar growth., Comment: 25 pages, 6 figures, accepted for publication in the Astrophysical Journal

Context: Rotationally supported disks are critical in the star formation process. The questions of when do they form and what factors influence or hinder their formation have been studied but are largely unanswered. Observations of early stage YSOs are needed to probe disk formation. Aims: VLA1623 is a triple non-coeval protostellar system, with a weak magnetic field perpendicular to the outflow, whose Class 0 component, VLA1623A, shows a disk-like structure in continuum with signatures of rotation in line emission. We aim to determine whether this structure is in part or in whole a rotationally supported disk, i.e. a Keplerian disk, and what are its characteristics. Methods: ALMA Cycle 0 Early Science 1.3 mm continuum and C$^{18}$O (2-1) observations in the extended configuration are presented here and used to perform an analysis of the disk-like structure using PV diagrams and thin disk modelling with the addition of foreground absorption. Results: The PV diagrams of the C$^{18}$O line emission suggest the presence of a rotationally supported component with a radius of at least 50 AU. Kinematical modelling of the line emission shows that the disk out to 180 AU is actually rotationally supported, with the rotation being well described by Keplerian rotation out to at least 150 AU, and the central source mass to be $\sim$0.2 M$_{sun}$ for an inclination of 55$^{\circ}$. Pure infall and conserved angular momentum rotation models are excluded. Conclusions: VLA1623A, a very young Class 0 source, presents a disk with an outer radius $R_{\rm out}$ = 180 AU with a Keplerian velocity structure out to at least 150 AU. The weak magnetic fields and recent fragmentation in this region of rho Ophiuchus may have played a lead role in the formation of the disk., Accepted for publication in A&A, 17 pages with appendices, 14 figures, 4 tables

Using the Herschel Space Observatory's Heterodyne Instrument for the Far-Infrared (HIFI), we have observed para-chloronium (H2Cl+) toward six sources in the Galaxy. We detected interstellar chloronium absorption in foreground molecular clouds along the sight-lines to the bright submillimeter continuum sources Sgr A (+50 km/s cloud) and W31C. Both the para-H2-35Cl+ and para-H2-37Cl+ isotopologues were detected, through observations of their 1(11)-0(00) transitions at rest frequencies of 485.42 and 484.23 GHz, respectively. For an assumed ortho-to-para ratio of 3, the observed optical depths imply that chloronium accounts for ~ 4 - 12% of chlorine nuclei in the gas phase. We detected interstellar chloronium emission from two sources in the Orion Molecular Cloud 1: the Orion Bar photodissociation region and the Orion South condensation. For an assumed ortho-to-para ratio of 3 for chloronium, the observed emission line fluxes imply total beam-averaged column densities of ~ 2.0E+13 cm-2 and ~ 1.2E+13 cm-2, respectively, for chloronium in these two sources. We obtained upper limits on the para-H2-35Cl+ line strengths toward H2 Peak 1 in the Orion Molecular cloud and toward the massive young star AFGL 2591. The chloronium abundances inferred in this study are typically at least a factor ~10 larger than the predictions of steady-state theoretical models for the chemistry of interstellar molecules containing chlorine. Several explanations for this discrepancy were investigated, but none has proven satisfactory, and thus the large observed abundances of chloronium remain puzzling., Accepted for publication in the Astrophysical Journal

International audience; We report observations of three rotational transitions of molecular oxygen (O2) in emission from the H2 Peak 1 position of vibrationally excited molecular hydrogen in Orion. We observed the 487 GHz, 774 GHz, and 1121 GHz lines using the Heterodyne Instrument for the Far Infrared on the Herschel Space Observatory, having velocities of 11 km s-1 to 12 km s-1 and widths of 3 km s-1. The beam-averaged column density is N(O2) = 6.5 × 1016 cm-2, and assuming that the source has an equal beam-filling factor for all transitions (beam widths 44, 28, and 19''), the relative line intensities imply a kinetic temperature between 65 K and 120 K. The fractional abundance of O2 relative to H2 is (0.3-7.3) × 10-6. The unusual velocity suggests an association with a ~5'' diameter source, denoted Peak A, the Western Clump, or MF4. The mass of this source is ~10 M sun and the dust temperature is >=150 K. Our preferred explanation of the enhanced O2 abundance is that dust grains in this region are sufficiently warm (T >= 100 K) to desorb water ice and thus keep a significant fraction of elemental oxygen in the gas phase, with a significant fraction as O2. For this small source, the line ratios require a temperature >=180 K. The inferred O2 column density sime5 × 1018 cm-2 can be produced in Peak A, having N(H2) ~= 4 × 1024 cm-2. An alternative mechanism is a low-velocity (10-15 km s-1) C-shock, which can produce N(O2) up to 1017 cm-2. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.