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[Abridged] Far-infrared observations with Herschel revealed a surprisingly low abundance of cold-water reservoirs in protoplanetary discs. On the other hand, a handful of discs show emission of hot water transitions excited at temperatures above a few hundred Kelvin. In particular, the protoplanetary discs around the Herbig Ae stars HD 100546 and HD 163296 show opposite trends in terms of cold versus hot water emission: in the first case, the ground-state transitions are detected and the high-J lines are undetected, while the trend is opposite in HD 163296. We performed a spectral analysis using the thermo-chemical model DALI. We find that HD 163296 is characterised by a water-rich (abundance $\gtrsim 10^{-5}$) hot inner disc (within the snowline) and a water-poor ($< 10^{-10}$) outer disc: the relative abundance may be due to the thermal desorption of icy grains that have migrated inward. Remarkably, the size of the H$_2$O emitting region corresponds to a narrow dust gap visible in the millimeter continuum at $r=10\,$au with ALMA. The low-J lines detected in HD 100546 instead imply an abundance of a few $10^{-9}$ in the cold outer disc ($> 40$ au). The emitting region of the cold H$_2$O transitions is spatially coincident with that of the H$_2$O ice previously seen in the near-infrared. Notably, millimetre observations with ALMA reveal the presence of a large dust gap between nearly 40 and 150 au, likely opened by a massive embedded protoplanet. In both discs, we find that the warm molecular layer in the outer region (beyond the snow line) is highly depleted of water molecules, implying an oxygen-poor chemical composition of the gas. We speculate that gas-phase oxygen in the outer disc is readily depleted and its distribution in the disc is tightly coupled to the dynamics of the dust grains., Comment: Accepted for publication on A&A

[Abridged] Most disks observed at high angular resolution show substructures. Knowledge about the gas surface density and temperature is essential to understand these. The aim of this work is to constrain the gas temperature and surface density in two transition disks: LkCa15 and HD 169142. We use new ALMA observations of the $^{13}$CO $J=6-5$ transition together with archival $J=2-1$ data of $^{12}$CO, $^{13}$CO and C$^{18}$O to observationally constrain the gas temperature and surface density. Furthermore, we use the thermochemical code DALI to model the temperature and density structure of a typical transition disk. The $6-5/2-1$ line ratio in LkCa15 constrains the gas temperature in the emitting layers inside the dust cavity to be up to 65 K, warmer than in the outer disk at 20-30 K. For the HD 169142, the peak brightness temperature constrains the gas in the dust cavity of HD 169142 to be 170 K, whereas that in the outer disk is only 100 K. Models also show that a more luminous central star, a lower abundance of PAHs and the absence of a dusty inner disk increase the temperature of the emitting layers and hence the line ratio in the gas cavity. The gas column density in the LkCa15 dust cavity drops by a factor >2 compared to the outer disk, with an additional drop of an order of magnitude inside the gas cavity at 10 AU. In the case of HD 169142, the gas column density drops by a factor of 200$-$500 inside the gas cavity, which could be due to a massive companion of several M$_{\mathrm{J}}$. The broad dust-depleted gas region from 10-68 AU for LkCa15 may imply several lower mass planets. This work demonstrates that knowledge of the gas temperature is important to determine the gas surface density and thus whether planets, and if so what kind of planets, are the most likely carving the dust cavities., Comment: Accepted for publication in Astronomy and astrophysics

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

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

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., Comment: 18 pages, 27 figures, accepted 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, \zeta/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 \zeta~(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., Comment: 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 <30 AU and a broad, ring-like structure from ~50-230 AU with a peak at 100 AU just beyond the millimeter grain edge. We modeled DCO$^+$ emission in HD 169142 with a physical disk structure adapted from the literature, and employed a simple deuterium chemical network to investigate the formation of DCO$^+$ through the cold deuterium fractionation pathway via H$_2$D$^+$. Contributions from the warm deuterium fractionation pathway via CH$_2$D$^+$ are approximated using a constant abundance in the intermediate disk layers. Parameterized models show that alterations to the midplane gas temperature and CO abundance of the literature model are both needed to recover the observed DCO$^+$ radial intensity profile. The best-fit model contains a shadowed, cold midplane in the region z/r < 0.1 with an 8 K decrease in gas temperature and a factor of five CO depletion just beyond the millimeter grain edge, and a 2 K decrease in gas temperature for r > 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., Comment: Accepted to Astronomy & Astrophysics

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

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 ($\alpha < 10^{-4}$). 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., Comment: Accepted by A&A

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 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)., Comment: Accepted for publication in A&A

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., Comment: Accepted for publication in A&A

Hydrides are simple compounds containing one or a few hydrogen atoms bonded to a heavier atom. They are fundamental precursor molecules in cosmic chemistry and many hydride ions have become observable in high quality for the first time thanks to the Herschel Space Observatory. Ionized hydrides, such as CH+ and OH+, and also HCO+ that affect the chemistry of molecules such as water, provide complementary information on irradiation by far UV (FUV) or X-rays and gas temperature. The targeted lines of CH+, OH+, H2O+, C+ and CH are detected mostly in blue-shifted absorption. H3O+ and SH+ are detected in emission and only toward some high-mass objects. The observed line parameters and correlations suggest two different origins, related to gas entrained by the outflows and to the circumstellar envelope. The column density ratios of CH+/OH+ are estimated from chemical slab models, assuming that the H2 density is given by the specific density model of each object at the beam radius. For the low-mass YSOs the observed ratio can be reproduced for an FUV flux of 2-400 times the ISRF at the location of the molecules. In two high-mass objects, the UV flux is 20-200 times the ISRF derived from absorption lines, and 300-600 ISRF using emission lines. If the FUV flux required for low-mass objects originates at the central protostar, a substantial FUV luminosity, up to 1.5 L_sun, is required. There is no molecular evidence for X-ray induced chemistry in the low-mass objects on the observed scales of a few 1000 AU. For high-mass regions, the FUV flux required to produce the observed molecular ratios is smaller than the unattenuated flux expected from the central object(s) at the Herschel beam radius. This is consistent with an FUV flux reduced by circumstellar extinction or by bloating of the protostar., Comment: 40 pages, 97 figures, accepted by Astronomy and Astrophysics

The gas-solid budget of carbon in protoplanetary disks is related to the composition of the cores and atmospheres of the planets forming in them. The key gas-phase carbon carriers CO, C$^{0}$ and C$^{+}$ can now be observed in disks. The gas-phase carbon abundance in disks has not yet been well characterized, we aim to obtain new constraints on the [C]/[H] ratio in a sample of disks, and to get an overview of the strength of [CI] and warm CO emission. We carried out a survey of the CO$\,6$--$5$ and [CI]$\,1$--$0$ and $2$--$1$ lines towards $37$ disks with APEX, and supplemented it with [CII] data from the literature. The data are interpreted using a grid of models produced with the DALI code. We also investigate how well the gas-phase carbon abundance can be determined in light of parameter uncertainties. The CO$\,6$--$5$ line is detected in $13$ out of $33$ sources, the [CI]$\,1$--$0$ in $6$ out of $12$, and the [CI]$\,2$--$1$ in $1$ out of $33$. With deep integrations, the first unambiguous detections of [CI]~$1$--$0$ in disks are obtained, in TW~Hya and HD~100546. Gas-phase carbon abundance reductions of a factor $5$--$10$ or more can be identified robustly based on CO and [CI] detections. The atomic carbon detection in TW~Hya confirms a factor $100$ reduction of [C]/[H]$_{\rm gas}$ in that disk, while the data are consistent with an ISM-like carbon abundance for HD~100546. In addition, BP~Tau, T~Cha, HD~139614, HD~141569, and HD~100453 are either carbon-depleted or gas-poor disks. The low [CI]~$2$--$1$ detection rates in the survey mostly reflect insufficient sensitivity to detect T~Tauri disks. The Herbig~Ae/Be disks with CO and [CII] upper limits below the models are debris disk like systems. A roughly order of magnitude increase in sensitivity compared to our survey is required to obtain useful constraints on the gas-phase [C]/[H] ratio in most of the targeted systems., Comment: 8 figures, accepted for publication in A\&A

Emission from high-J CO lines in galaxies has long been proposed as a tracer of X-ray dominated regions (XDRs) produced by AGN. Of particular interest is the question of whether the obscuring torus, which is required by AGN unification models, can be observed via high-J CO cooling lines. Here we report on the analysis of a deep Herschel-PACS observation of an extremely high J CO transition (40-39) in the Seyfert 2 galaxy NGC 1068. The line was not detected, with a derived 3$\sigma$ upper limit of $2 \times 10^{-17}\,\text{W}\,\text{m}^{-2}$. We apply an XDR model in order to investigate whether the upper limit constrains the properties of a molecular torus in NGC 1068. The XDR model predicts the CO Spectral Line Energy Distributions for various gas densities and illuminating X-ray fluxes. In our model, the CO(40-39) upper limit is matched by gas with densities $\sim 10^{6}-10^{7}\,\text{cm}^{-3}$, located at $1.6-5\,\text{pc}$ from the AGN, with column densities of at least $10^{25}\,\text{cm}^{-2}$. At such high column densities, however, dust absorbs most of the CO(40-39) line emission at $\lambda = 65.69\, \mu$m. Therefore, even if NGC 1068 has a molecular torus which radiates in the CO(40-39) line, the dust can attenuate the line emission to below the PACS detection limit. The upper limit is thus consistent with the existence of a molecular torus in NGC 1068. In general, we expect that the CO(40-39) is observable in only a few AGN nuclei (if at all), because of the required high gas column density, and absorption by dust., Comment: 22 pages, accepted for publication in ApJ

Context: High-resolution studies of class 0 protostars represent the key to constraining protostar formation models. VLA16234-2417 represents the prototype of class 0 protostars, and it has been recently identified as a triple non-coeval system. Aim: We aim at deriving the physical properties of the jets in VLA16234-2417 using tracers of shocked gas. Methods: ALMA Cycle 0 Early Science observations of CO(2-1) in the extended configuration are presented in comparison with previous SMA CO(3-2) and Herschel-PACS [OI}] 63 micron observations. Gas morphology and kinematics were analysed to constrain the physical structure and origin of the protostellar outflows. Results: We reveal a collimated jet component associated with the [OI] 63 micron emission at about 8'' (about 960 AU) from source B. This newly detected jet component is inversely oriented with respect to the large-scale outflow driven by source A, and it is aligned with compact and fast jet emission very close to source B (about 0.3'') rather than with the direction perpendicular to the A disk. We also detect a cavity-like structure at low projected velocities, which surrounds the [OI] 63 micron emission and is possibly associated with the outflow driven by source A. Finally, no compact outflow emission is associated with source W. Conclusions: Our high-resolution ALMA observations seem to suggest there is a fast and collimated jet component associated with source B. This scenario would confirm that source B is younger than A, that it is in a very early stage of evolution, and that it drives a faster, more collimated, and more compact jet with respect to the large-scale slower outflow driven by A. However, a different scenario of a precessing jet driven by A cannot be firmly excluded from the present observations., Comment: Accepted for publication in Astronomy & Astrophysics

ALMA observations of a small sample of transitional disks with large dust cavities observed in Cycle 0 and 1 are summarized. The gas and dust surface density structures are inferred from the continuum and 12CO, 13CO and C18O line data using the DALI physical-chemical code. Thanks to its ability to self-shield, CO can survive inside dust cavities in spite of being exposed to intense UV radiation and can thus be used as a probe of the gas structure. Modeling of the existing data shows that gas is present inside the dust cavities in all cases, but at a reduced level compared with the gas surface density profile of the outer disk. The gas density decrease inside the dust cavity radius by factors of up to 10^4 suggests clearing by one or more planetary-mass companions. The accompanying pressure bumps naturally lead to trapping of the mm-sized dust grains observed in the ALMA images., Comment: 4 pages, 2 figures; dd. March 18 2015. To appear in "Revolution in Astronomy with ALMA: the 3rd year", 2015, ed. D. Iono et al. (ASP conference series)

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

We investigate new and archival 3-5 $\mu$m high resolution ($\sim3$ km s$^{-1}$) spectroscopy of molecular gas in the inner disk of the young solar-mass star EX Lupi, taken during and after the strong accretion outburst of 2008. The data were obtained using the CRIRES spectrometer at the ESO Very Large Telescope in 2008 and 2014. In 2008, emission lines from CO, H$_{2}$O, and OH were detected with broad profiles tracing gas near and within the corotation radius (0.02-0.3 AU). In 2014, the spectra display marked differences. The CO lines, while still detected, are much weaker, and the H$_{2}$O and OH lines have disappeared altogether. At 3 $\mu$m a veiled stellar photospheric spectrum is observed. Our analysis finds that the molecular gas mass in the inner disk has decreased by an order of magnitude since the outburst, matching a similar decrease in the accretion rate onto the star. We discuss these findings in the context of a rapid depletion of material accumulated beyond the disk corotation radius during quiescent periods, as proposed by models of episodic accretion in EXor type young stars., Comment: 6 pages, 4 figures, 1 table, accepted for publication in the Astrophysical Journal Letters

In diffuse interstellar clouds the chemistry that leads to the formation of the oxygen bearing ions OH+, H2O+, and H3O+ begins with the ionization of atomic hydrogen by cosmic rays, and continues through subsequent hydrogen abstraction reactions involving H2. Given these reaction pathways, the observed abundances of these molecules are useful in constraining both the total cosmic-ray ionization rate of atomic hydrogen (zeta_H) and molecular hydrogen fraction, f(H2). We present observations targeting transitions of OH+, H2O+, and H3O+ made with the Herschel Space Observatory along 20 Galactic sight lines toward bright submillimeter continuum sources. Both OH+ and H2O+ are detected in absorption in multiple velocity components along every sight line, but H3O+ is only detected along 7 sight lines. From the molecular abundances we compute f(H2) in multiple distinct components along each line of sight, and find a Gaussian distribution with mean and standard deviation 0.042+-0.018. This confirms previous findings that OH+ and H2O+ primarily reside in gas with low H2 fractions. We also infer zeta_H throughout our sample, and find a log-normal distribution with mean log(zeta_H)=-15.75, (zeta_H=1.78x10^-16 s^-1), and standard deviation 0.29 for gas within the Galactic disk, but outside of the Galactic center. This is in good agreement with the mean and distribution of cosmic-ray ionization rates previously inferred from H3+ observations. Ionization rates in the Galactic center tend to be 10--100 times larger than found in the Galactic disk, also in accord with prior studies., Comment: 76 pages, 25 figures, 6 tables; accepted for publication in ApJ

Context: Outflows are an important part of the star formation process as both the result of ongoing active accretion and one of the main sources of mechanical feedback on small scales. Water is the ideal tracer of these effects because it is present in high abundance in various parts of the protostar. Method: We present \textit{Herschel} HIFI spectra of multiple water-transitions towards 29 nearby Class 0/I protostars as part of the WISH Survey. These are decomposed into different Gaussian components, with each related to one of three parts of the protostellar system; quiescent envelope, cavity shock and spot shocks in the jet and at the base of the outflow. We then constrain the excitation conditions present in the two outflow-related components. Results: Water emission is optically thick but effectively thin, with line ratios that do not vary with velocity, in contrast to CO. The physical conditions of the cavity and spot shocks are similar, with post-shock H$_{2}$ densities of order 10$^{5}-$10$^{8}$\,cm$^{-3}$ and H$_{2}$O column densities of order 10$^{16}-$10$^{18}$\,cm$^{-2}$. H$_{2}$O emission originates in compact emitting regions: for the spot shocks these correspond to point sources with radii of order 10-200\,AU, while for the cavity shocks these come from a thin layer along the outflow cavity wall with thickness of order 1-30\,AU. Conclusions: Water emission at the source position traces two distinct kinematic components in the outflow; J shocks at the base of the outflow or in the jet, and C shocks in a thin layer in the cavity wall. Class I sources have similar excitation conditions to Class 0 sources, but generally smaller line-widths and emitting region sizes. We suggest that it is the velocity of the wind driving the outflow, rather than the decrease in envelope density or mass, that is the cause of the decrease in H$_{2}$O intensity between Class 0 and I., Comment: Abstract is abridged. Accepted to Astronomy & Astrophysics. 50 pages (21 excluding appendices), 15 figures and 7 tables in the main paper, 18 figures and 10 tables in the appendices. Table 4 updated to Corrigendum version

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) 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

Herschel/HIFI spectroscopic observations of CO J=10-9, CO J=16-15 and [CII] towards HD 100546 are presented. The objective is to resolve the velocity profile of the lines to address the emitting region of the transitions and directly probe the distribution of warm gas in the disk. The spectra reveal double-peaked CO line profiles centered on the systemic velocity, consistent with a disk origin. The J=16-15 line profile is broader than that of the J=10-9 line, which in turn is broader than those of lower J transitions (6-5, 3-2, observed with APEX), thus showing a clear temperature gradient of the gas with radius. A power-law flat disk model is used to fit the CO line profiles and the CO rotational ladder simultaneously, yielding a temperature of T_0=1100 \pm 350 K (at r_0 = 13 AU) and an index of q=0.85 \pm 0.1 for the temperature radial gradient. This indicates that the gas has a steeper radial temperature gradient than the dust (mean q_{dust} ~ 0.5), providing further proof of the thermal decoupling of gas and dust at the disk heights where the CO lines form. The [CII] line profile shows a strong single-peaked profile red-shifted by 0.5 km s-1 compared to the systemic velocity. We conclude that the bulk of the [CII] emission has a non-disk origin (e.g., remnant envelope or diffuse cloud)., Comment: Accepted for publication in ApJL

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., Comment: 20 pages, 22 figures, 5 tables. Accepted to Astronomy & Astrophysics

(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., Comment: Accepted by A&A, 21 pages, 20 figures

[abridged] We present far-infrared spectroscopic observations of PMS stars taken with Herschel/PACS as part of the DIGIT key project. The sample includes 22 Herbig AeBe and 8 T Tauri sources. Multiple atomic fine structure and molecular lines are detected at the source position: [OI], [CII], CO, OH, H_2O, CH^+. The most common feature is the [OI] 63micron line detected in almost all of the sources followed by OH. In contrast with CO, OH is detected toward both Herbig AeBe groups (flared and non-flared sources). An isothermal LTE slab model fit to the OH lines indicates column densities of 10^13 < N_OH < 10^16 cm^-2, emitting radii 15 < r < 100 AU and excitation temperatures 100 < T_ex < 400 K. The OH emission thus comes from a warm layer in the disk at intermediate stellar distances. Warm H_2O emission is detected through multiple lines toward the T Tauri systems AS 205, DG Tau, S CrA and RNO 90 and three Herbig AeBe systems HD 104237, HD 142527, HD 163296 (through line stacking). Overall, Herbig AeBe sources have higher OH/H_2O abundance ratios across the disk than do T Tauri disks, from near- to far-infrared wavelengths. Far-infrared CH^+ emission is detected toward HD 100546 and HD 97048. The slab model suggests moderate excitation (T_ex ~ 100 K) and compact (r ~ 60 AU) emission in the case of HD 100546. The [CII] emission is spatially extended in all sources where the line is detected. This suggests that not all [CII] emission is associated with the disk and that there is a substantial contribution from diffuse material around the young stars. The flux ratios of the atomic fine structure lines are consistent with a disk origin for the oxygen lines for most of the sources., Comment: Accepted for publication in A&A

Herschel-HIFI spectra of H2O towards low-mass protostars show a distinct velocity component not seen in observations from the ground of CO or other species. The aim is to characterise this component in terms of excitation conditions and physical origin. A velocity component with an offset of ~10 km/s detected in spectra of the H2O 110-101 557 GHz transition towards six low-mass protostars in the 'Water in star-forming regions with Herschel' (WISH) programme is also seen in higher-excited H2O lines. The emission from this component is quantified and excitation conditions are inferred using 1D slab models. Data are compared to observations of hydrides (high-J CO, OH+, CH+, C+, OH) where the same component is uniquely detected. The velocity component is detected in all 6 targeted H2O transitions (Eup~50-250K), and in CO 16-15 towards one source, Ser SMM1. Inferred excitation conditions imply that the emission arises in dense (n~5x10^6-10^8 cm^-3) and hot (T~750K) gas. The H2O and CO column densities are ~10^16 and 10^18 cm^-2, respectively, implying a low H2O abundance of 10^-2 with respect to CO. The high column densities of ions such as OH+ and CH+ (both ~10^13 cm^-2) indicate an origin close to the protostar where the UV field is strong enough that these species are abundant. The estimated radius of the emitting region is 100AU. This component likely arises in dissociative shocks close to the protostar, an interpretation corroborated by a comparison with models of such shocks. Furthermore, one of the sources, IRAS4A, shows temporal variability in the offset component over a period of two years which is expected from shocks in dense media. High-J CO gas detected with Herschel-PACS with Trot~700K is identified as arising in the same component and traces the part of the shock where H2 reforms. Thus, H2O reveals new dynamical components, even on small spatial scales in low-mass protostars., Comment: 13 pages, accepted for publication in A&A

(Abridged) Far-infrared Herschel-PACS spectra of 18 low-mass protostars of various luminosities and evolutionary stages are studied. We quantify their far-infrared line emission and the contribution of different atomic and molecular species to the gas cooling budget during protostellar evolution. We also determine the spatial extent of the emission and investigate the underlying excitation conditions. Most of the protostars in our sample show strong atomic and molecular far-infrared emission. Water is detected in 17 objects, including 5 Class I sources. The high-excitation H2O line at 63.3 micron is detected in 7 sources. CO transitions from J=14-13 up to 49-48 are found and show two distinct temperature components on Boltzmann diagrams with rotational temperatures of ~350 K and ~700 K. H2O has typical excitation temperatures of ~150 K. Emission from both Class 0 and I sources is usually spatially extended along the outflow direction but with a pattern depending on the species and the transition. The H2O line fluxes correlate strongly with those of the high-J CO lines, as well as with the bolometric luminosity and envelope mass. They correlate less strongly with OH and not with [OI] fluxes. The PACS data probe at least two physical components. The H2O and CO emission likely arises in non-dissociative (irradiated) shocks along the outflow walls with a range of pre-shock densities. Some OH is also associated with this component, likely resulting from H2O photodissociation. UV-heated gas contributes only a minor fraction to the CO emission observed by PACS, based on the strong correlation between the shock-dominated CO 24-23 line and the CO 14-13 line. [OI] and some of the OH emission probe dissociative shocks in the inner envelope. The total far-infrared cooling is dominated by H2O and CO, with [OI] increasing for Class I sources., Comment: Accepted for publication in A&A, 48 pages with appendix

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., Comment: Accepted for publication in Astronomy and Astrophysics. Abstract abridged

We report on Herschel/PACS observations of absorption lines of OH+, H2O+ and H3O+ in NGC 4418 and Arp 220. Excited lines of OH+ and H2O+ with E_lower of at least 285 and \sim200 K, respectively, are detected in both sources, indicating radiative pumping and location in the high radiation density environment of the nuclear regions. Abundance ratios OH+/H2O+ of 1-2.5 are estimated in the nuclei of both sources. The inferred OH+ column and abundance relative to H nuclei are (0.5-1)x10^{16} cm-2 and \sim2x10^{-8}, respectively. Additionally, in Arp 220, an extended low excitation component around the nuclear region is found to have OH+/H2O+\sim5-10. H3O+ is detected in both sources with N(H3O+)\sim(0.5-2)x10^{16} cm-2, and in Arp 220 the pure inversion, metastable lines indicate a high rotational temperature of ~500 K, indicative of formation pumping and/or hot gas. Simple chemical models favor an ionization sequence dominated by H+ - O+ - OH+ - H2O+ - H3O+, and we also argue that the H+ production is most likely dominated by X-ray/cosmic ray ionization. The full set of observations and models leads us to propose that the molecular ions arise in a relatively low density (\gtrsim10^4 cm-3) interclump medium, in which case the ionization rate per H nucleus (including secondary ionizations) is zeta>10^{-13} s-1, a lower limit that is severalx10^2 times the highest rate estimates for Galactic regions. In Arp 220, our lower limit for zeta is compatible with estimates for the cosmic ray energy density inferred previously from the supernova rate and synchrotron radio emission, and also with the expected ionization rate produced by X-rays. In NGC 4418, we argue that X-ray ionization due to an AGN is responsible for the molecular ion production., Comment: 24 pages, 13 figures. Accepted for publication in Astronomy & Astrophysics

We present observations of far-infrared (50-200 micron) OH and H2O emission of the disk around the Herbig Ae star HD 163296 obtained with Herschel/PACS in the context of the DIGIT key program. In addition to strong [OI] emission, a number of OH doublets and a few weak highly excited lines of H2O are detected. The presence of warm H2O in this Herbig disk is confirmed by a line stacking analysis, enabled by the full PACS spectral scan, and by lines seen in Spitzer data. The line fluxes are analyzed using an LTE slab model including line opacity. The water column density is 10^14 - 10^15 cm^-2, and the excitation temperature is 200-300 K implying warm gas with a density n > 10^5 cm^-3. For OH we find a column density of 10^14 - 2x10^15 cm^-2 and T_ex ~ 300-500 K. For both species we find an emitting region of r ~ 15-20 AU from the star. We argue that the molecular emission arises from the protoplanetary disk rather than from an outflow. This far-infrared detection of both H2O and OH contrasts with near- and mid-infrared observations, which have generally found a lack of water in the inner disk around Herbig AeBe stars due to strong photodissociation of water. Given the similarity in column density and emitting region, OH and H2O emission seems to arise from an upper layer of the disk atmosphere of HD 163296, probing a new reservoir of water. The slightly lower temperature of H2O compared to OH suggests a vertical stratification of the molecular gas with OH located higher and water deeper in the disk, consistent with thermo-chemical models., Comment: Accepted for publication in A&A

(Abridged) Water is a key tracer of dynamics and chemistry in low-mass protostars, but spectrally resolved observations have so far been limited in sensitivity and angular resolution. In this first systematic survey of spectrally resolved water emission in low-mass protostellar objects, H2O was observed in the ground-state transition at 557 GHz with HIFI on Herschel in 29 embedded Class 0 and I protostars. Complementary far-IR and sub-mm continuum data (including PACS data from our program) are used to constrain the spectral energy distribution of each source. H2O intensities are compared to inferred envelope and outflow properties and CO 3-2 emission. H2O emission is detected in all objects except one. The line profiles are complex and consist of several kinematic components. The profiles are typically dominated by a broad Gaussian emission feature, indicating that the bulk of the water emission arises in outflows, not the quiescent envelope. Several sources show multiple shock components in either emission or absorption, thus constraining the internal geometry of the system. Furthermore, the components include inverse P-Cygni profiles in 7 sources (6 Class 0, 1 Class I) indicative of infalling envelopes, and regular P-Cygni profiles in 4 sources (3 Class I, 1 Class 0) indicative of expanding envelopes. "Bullets" moving at >50 km/s are seen in 4 Class 0 sources; 3 of these are new detections. In the outflow, the H2O/CO abundance ratio as a function of velocity is nearly the same for all sources, increasing from 10^-3 at <5 km/s to >10^-1 at >10 km/s. The H2O abundance in the outer envelope is low, ~10^-10. The different H2O profile components show a clear evolutionary trend: in the Class 0 sources, emission is dominated by outflow components originating inside an infalling envelope. When the infall diminishes during the Class I phase, the outflow weakens and H2O emission disappears., Comment: Accepted for publication in A&A

Models of pure gas-phase chemistry in well-shielded regions of molecular clouds predict relatively high levels of molecular oxygen, O2, and water, H2O. Contrary to expectation, the space missions SWAS and Odin found only very small amounts of water vapour and essentially no O2 in the dense star-forming interstellar medium. Only toward rho Oph A did Odin detect a weak line of O2 at 119 GHz in a beam size of 10 arcmin. A larger telescope aperture such as that of the Herschel Space Observatory is required to resolve the O2 emission and to pinpoint its origin. We use the Heterodyne Instrument for the Far Infrared aboard Herschel to obtain high resolution O2 spectra toward selected positions in rho Oph A. These data are analysed using standard techniques for O2 excitation and compared to recent PDR-like chemical cloud models. The 487.2GHz line was clearly detected toward all three observed positions in rho Oph A. In addition, an oversampled map of the 773.8GHz transition revealed the detection of the line in only half of the observed area. Based on their ratios, the temperature of the O2 emitting gas appears to vary quite substantially, with warm gas (> 50 K) adjacent to a much colder region, where temperatures are below 30 K. The exploited models predict O2 column densities to be sensitive to the prevailing dust temperatures, but rather insensitive to the temperatures of the gas. In agreement with these model, the observationally determined O2 column densities seem not to depend strongly on the derived gas temperatures, but fall into the range N(O2) = (3 to >6)e15/cm^2. Beam averaged O2 abundances are about 5e-8 relative to H2. Combining the HIFI data with earlier Odin observations yields a source size at 119 GHz of about 4 - 5 arcmin, encompassing the entire rho Oph A core., Comment: 10 pages, 8 figures intended for publication in A&A

We present a comparison of archival Spitzer spectra of the strongly variable T Tauri EX Lupi, observed before and during its 2008 outburst. We analyze the mid-infrared emission from gas-phase molecules thought to originate in a circumstellar disk. In quiescence the emission shows a forest of H2O lines, highly excited OH lines, and the Q branches of the organics C2H2, HCN, and CO2, similar to the emission observed toward several T Tauri systems. The outburst emission shows instead remarkable changes: H2O and OH line fluxes increase, new OH, H2, and HI transitions are detected, and organics are no longer seen. We adopt a simple model of a single-temperature slab of gas in local thermal equilibrium, a common approach for molecular analyses of Spitzer spectra, and derive the excitation temperature, column density, and emitting area of H2O and OH. We show how model results strongly depend on the selection of emission lines fitted, and that spectrally-resolved observations are essential for a correct interpretation of the molecular emission from disks, particularly in the case of water. Using H2O lines that can be approximated as thermalized to a single temperature, our results are consistent with a column density decrease in outburst while the emitting area of warm gas increases. A rotation diagram analysis suggests that the OH emission can be explained with two temperature components, which remarkably increase in column density in outburst. The relative change of H2O and OH emission suggests a key role for UV radiation in the disk surface chemistry., Comment: 17 pages, 11 figures, 5 tables, accepted for publication on ApJ

Aims. Young stars interact vigorously with their surroundings, as evident from the highly rotationally excited CO (up to Eup=4000 K) and H2O emission (up to 600 K) detected by the Herschel Space Observatory in embedded low-mass protostars. Our aim is to construct a model that reproduces the observations quantitatively, to investigate the origin of the emission, and to use the lines as probes of the various heating mechanisms. Methods. The model consists of a spherical envelope with a bipolar outflow cavity. Three heating mechanisms are considered: passive heating by the protostellar luminosity, UV irradiation of the outflow cavity walls, and C-type shocks along the cavity walls. Line fluxes are calculated for CO and H2O and compared to Herschel data and complementary ground-based data for the protostars NGC1333 IRAS2A, HH 46 and DK Cha. The three sources are selected to span a range of evolutionary phases and physical characteristics. Results. The passively heated gas in the envelope accounts for 3-10% of the CO luminosity summed over all rotational lines up to J=40-39; it is best probed by low-J CO isotopologue lines such as C18O 2-1 and 3-2. The UV-heated gas and the C-type shocks, probed by 12CO 10-9 and higher-J lines, contribute 20-80% each. The model fits show a tentative evolutionary trend: the CO emission is dominated by shocks in the youngest source and by UV-heated gas in the oldest one. This trend is mainly driven by the lower envelope density in more evolved sources. The total H2O line luminosity in all cases is dominated by shocks (>99%). The exact percentages for both species are uncertain by at least a factor of 2 due to uncertainties in the gas temperature as function of the incident UV flux. However, on a qualitative level, both UV-heated gas and C-type shocks are needed to reproduce the emission in far-infrared rotational lines of CO and H2O., Comment: 15 pages (+4 pages appendix), 20 figures, accepted by A&A

OH is an important molecule in the H2O chemistry and the cooling budget of star-forming regions. The goal of the Herschel key program `Water in Star-forming regions with Herschel' (WISH) is to study H2O and related species during protostellar evolution. Our aim in this letter is to assess the origin of the OH emission from star-forming regions and constrain the properties of the emitting gas. High-resolution observations of the OH 2Pi1/2 J = 3/2-1/2 triplet at 1837.8 GHz (163.1 micron) towards the high-mass star-forming region W3 IRS 5 with the Heterodyne Instrument for the Far-Infrared (HIFI) on Herschel reveal the first hyperfine velocity-resolved OH far-infrared spectrum of a star-forming region. The line profile of the OH emission shows two components: a narrow component (FWHM approx. 4-5 km/s) with partially resolved hyperfine structure resides on top of a broad (FWHM approx. 30 km/s) component. The narrow emission agrees well with results from radiative transfer calculations of a spherical envelope model for W3 IRS 5 with a constant OH abundance of approx. 8e-9. Comparison with H2O yields OH/H2O abundance ratios of around 1e-3 for T > 100 K and around unity for T < 100K, consistent with the current picture of the dense cloud chemistry with freeze-out and photodesorption. The broad component is attributed to outflow emission. An abundance ratio of OH/H2O > 0.028 in the outflow is derived from comparison with results of water line modeling. This ratio can be explained by a fast J-type shock or a slower UV-irradiated C-type shock., Comment: accepted for publication as a letter in Astronomy and Astrophysics

We investigate the physics and chemistry of the gas and dust in dense photon-dominated regions (PDRs), along with their dependence on the illuminating UV field. Using Herschel-HIFI observations, we study the gas energetics in NGC 7023 in relation to the morphology of this nebula. NGC 7023 is the prototype of a PDR illuminated by a B2V star and is one of the key targets of Herschel. Our approach consists in determining the energetics of the region by combining the information carried by the mid-IR spectrum (extinction by classical grains, emission from very small dust particles) with that of the main gas coolant lines. In this letter, we discuss more specifically the intensity and line profile of the 158 micron (1901 GHz) [CII] line measured by HIFI and provide information on the emitting gas. We show that both the [CII] emission and the mid-IR emission from polycyclic aromatic hydrocarbons (PAHs) arise from the regions located in the transition zone between atomic and molecular gas. Using the Meudon PDR code and a simple transfer model, we find good agreement between the calculated and observed [CII] intensities. HIFI observations of NGC 7023 provide the opportunity to constrain the energetics at the surface of PDRs. Future work will include analysis of the main coolant line [OI] and use of a new PDR model that includes PAH-related species., Comment: Accepted for publication in Astronomy and Astrophysics Letters (Herschel HIFI special issue), 5 pages, 5 figures

HERSCHEL-HIFI observations of water from the intermediate mass protostar NGC7129 FIRS 2 provide a powerful diagnostic of the physical conditions in this star formation environment. Six spectral settings, covering four H216O and two H218O lines, were observed and all but one H218O line were detected. The four H2 16 O lines discussed here share a similar morphology: a narrower, \approx 6 km/s, component centered slightly redward of the systemic velocity of NGC7129 FIRS 2 and a much broader, \approx 25 km/s component centered blueward and likely associated with powerful outflows. The narrower components are consistent with emission from water arising in the envelope around the intermediate mass protostar, and the abundance of H2O is constrained to \approx 10-7 for the outer envelope. Additionally, the presence of a narrow self-absorption component for the lowest energy lines is likely due to self-absorption from colder water in the outer envelope. The broader component, where the H2O/CO relative abundance is found to be \approx 0.2, appears to be tracing the same energetic region that produces strong CO emission at high J., Comment: 6 pages, 4 figures, accepted by A&A

Herschel-HIFI observations of high-J lines (up to J_u=10) of 12CO, 13CO and C18O are presented toward three deeply embedded low-mass protostars, NGC 1333 IRAS 2A, IRAS 4A, and IRAS 4B, obtained as part of the Water In Star-forming regions with Herschel (WISH) key program. The spectrally-resolved HIFI data are complemented by ground-based observations of lower-J CO and isotopologue lines. The 12CO 10-9 profiles are dominated by broad (FWHM 25-30 km s^-1) emission. Radiative transfer models are used to constrain the temperature of this shocked gas to 100-200 K. Several CO and 13CO line profiles also reveal a medium-broad component (FWHM 5-10 km s^-1), seen prominently in H2O lines. Column densities for both components are presented, providing a reference for determining abundances of other molecules in the same gas. The narrow C18O 9-8 lines probe the warmer part of the quiescent envelope. Their intensities require a jump in the CO abundance at an evaporation temperature around 25 K, thus providing new direct evidence for a CO ice evaporation zone around low-mass protostars., Comment: 8 pages, 9 figures

Using Herschel's HIFI instrument we have observed [C II] along a cut through S140 and high-J transitions of CO and HCO+ at two positions on the cut, corresponding to the externally irradiated ionization front and the embedded massive star forming core IRS1. The HIFI data were combined with available ground-based observations and modeled using the KOSMA-tau model for photon dominated regions. Here we derive the physical conditions in S140 and in particular the origin of [C II] emission around IRS1. We identify three distinct regions of [C II] emission from the cut, one close to the embedded source IRS1, one associated with the ionization front and one further into the cloud. The line emission can be understood in terms of a clumpy model of photon-dominated regions. At the position of IRS1, we identify at least two distinct components contributing to the [C II] emission, one of them a small, hot component, which can possibly be identified with the irradiated outflow walls. This is consistent with the fact that the [C II] peak at IRS1 coincides with shocked H2 emission at the edges of the outflow cavity. We note that previously available observations of IRS1 can be well reproduced by a single-component KOSMA-tau model. Thus it is HIFI's unprecedented spatial and spectral resolution, as well as its sensitivity which has allowed us to uncover an additional hot gas component in the S140 region., Comment: accepted for publication in Astronomy and Astrophysics (HIFI special issue)

Early results from the Herschel Space Observatory revealed the water cation H2O+ to be an abundant ingredient of the interstellar medium. Here we present new observations of the H2O and H2O+ lines at 1113.3 and 1115.2 GHz using the Herschel Space Observatory toward a sample of high-mass star-forming regions to observationally study the relation between H2O and H2O+ . Nine out of ten sources show absorption from H2O+ in a range of environments: the molecular clumps surrounding the forming and newly formed massive stars, bright high-velocity outflows associated with the massive protostars, and unrelated low-density clouds along the line of sight. Column densities per velocity component of H2 O+ are found in the range of 10^12 to a few 10^13 cm-2 . The highest N(H2O+) column densities are found in the outflows of the sources. The ratios of H2O+/H2O are determined in a range from 0.01 to a few and are found to differ strongly between the observed environments with much lower ratios in the massive (proto)cluster envelopes (0.01-0.1) than in outflows and diffuse clouds. Remarkably, even for source components detected in H2O in emission, H2O+ is still seen in absorption., Comment: 5 pages, 4 figures, accepted for publication as a letter in the A&A Herschel-HIFI special issue

We present Herschel observations of the water molecule in the massive star-forming region W3 IRS5. The o-H17O 110-101, p-H18O 111-000, p-H2O 22 202-111, p-H2O 111-000, o-H2O 221-212, and o-H2O 212-101 lines, covering a frequency range from 552 up to 1669 GHz, have been detected at high spectral resolution with HIFI. The water lines in W3 IRS5 show well-defined high-velocity wings that indicate a clear contribution by outflows. Moreover, the systematically blue-shifted absorption in the H2O lines suggests expansion, presumably driven by the outflow. No infall signatures are detected. The p-H2O 111-000 and o-H2O 212-101 lines show absorption from the cold material (T ~ 10 K) in which the high-mass protostellar envelope is embedded. One-dimensional radiative transfer models are used to estimate water abundances and to further study the kinematics of the region. We show that the emission in the rare isotopologues comes directly from the inner parts of the envelope (T > 100 K) where water ices in the dust mantles evaporate and the gas-phase abundance increases. The resulting jump in the water abundance (with a constant inner abundance of 10^{-4}) is needed to reproduce the o-H17O 110-101 and p-H18O 111-000 spectra in our models. We estimate water abundances of 10^{-8} to 10^{-9} in the outer parts of the envelope (T < 100 K). The possibility of two protostellar objects contributing to the emission is discussed., Comment: Accepted for publication in the A&A HIFI special issue

The Heterodyne Instrument for the Far Infrared (HIFI) onboard the Herschel Space Observatory allows the first observations of light diatomic molecules at high spectral resolution and in multiple transitions. Here, we report deep integrations using HIFI in different lines of hydrides towards the high-mass star forming region AFGL 2591. Detected are CH, CH+, NH, OH+, H2O+, while NH+ and SH+ have not been detected. All molecules except for CH and CH+ are seen in absorption with low excitation temperatures and at velocities different from the systemic velocity of the protostellar envelope. Surprisingly, the CH(JF,P = 3/2_2,- - 1/2_1,+) and CH+(J = 1 - 0, J = 2 - 1) lines are detected in emission at the systemic velocity. We can assign the absorption features to a foreground cloud and an outflow lobe, while the CH and CH+ emission stems from the envelope. The observed abundance and excitation of CH and CH+ can be explained in the scenario of FUV irradiated outflow walls, where a cavity etched out by the outflow allows protostellar FUV photons to irradiate and heat the envelope at larger distances driving the chemical reactions that produce these molecules., Comment: Accepted for publication in Astronomy and Astrophysics (HIFI first results issue)

'Water In Star-forming regions with Herschel' (WISH) is a key programme dedicated to studying the role of water and related species during the star-formation process and constraining the physical and chemical properties of young stellar objects. The Heterodyne Instrument for the Far-Infrared (HIFI) on the Herschel Space Observatory observed three deeply embedded protostars in the low-mass star-forming region NGC1333 in several H2-16O, H2-18O, and CO transitions. Line profiles are resolved for five H16O transitions in each source, revealing them to be surprisingly complex. The line profiles are decomposed into broad (>20 km/s), medium-broad (~5-10 km/s), and narrow (<5 km/s) components. The H2-18O emission is only detected in broad 1_10-1_01 lines (>20 km/s), indicating that its physical origin is the same as for the broad H2-16O component. In one of the sources, IRAS4A, an inverse P Cygni profile is observed, a clear sign of infall in the envelope. From the line profiles alone, it is clear that the bulk of emission arises from shocks, both on small (<1000 AU) and large scales along the outflow cavity walls (~10 000 AU). The H2O line profiles are compared to CO line profiles to constrain the H2O abundance as a function of velocity within these shocked regions. The H2O/CO abundance ratios are measured to be in the range of ~0.1-1, corresponding to H2O abundances of ~10-5-10-4 with respect to H2. Approximately 5-10% of the gas is hot enough for all oxygen to be driven into water in warm post-shock gas, mostly at high velocities., Comment: Accepted for publication in the A&A HIFI special issue

Water in Star-forming regions with Herschel (WISH) is a Herschel Key Program investigating the water chemistry in young stellar objects (YSOs) during protostellar evolution. Hydroxyl (OH) is one of the reactants in the chemical network most closely linked to the formation and destruction of H2O. High-temperature chemistry connects OH and H2O through the OH + H2 <-> H2O + H reactions. Formation of H2O from OH is efficient in the high-temperature regime found in shocks and the innermost part of protostellar envelopes. Moreover, in the presence of UV photons, OH can be produced from the photo-dissociation of H2O. High-resolution spectroscopy of the OH 163.12 micron triplet towards HH 46 and NGC 1333 IRAS 2A was carried out with the Heterodyne Instrument for the Far Infrared (HIFI) on board Herschel. The low- and intermediate-mass YSOs HH 46, TMR 1, IRAS 15398-3359, DK Cha, NGC 7129 FIRS 2, and NGC 1333 IRAS 2A were observed with the Photodetector Array Camera and Spectrometer (PACS) in four transitions of OH and two [OI] lines. The OH transitions at 79, 84, 119, and 163 micron and [OI] emission at 63 and 145 micron were detected with PACS towards the class I low-mass YSOs as well as the intermediate-mass and class I Herbig Ae sources. No OH emission was detected from the class 0 YSO NGC 1333 IRAS 2A, though the 119 micron was detected in absorption. With HIFI, the 163.12 micron was not detected from HH 46 and only tentatively detected from NGC 1333 IRAS 2A. The combination of the PACS and HIFI results for HH 46 constrains the line width (FWHM > 11 km/s) and indicates that the OH emission likely originates from shocked gas. This scenario is supported by trends of the OH flux increasing with the [OI] flux and the bolometric luminosity. Similar OH line ratios for most sources suggest that OH has comparable excitation temperatures despite the different physical properties of the sources., Comment: Accepted for publication in Astronomy and Astrophysics (Herschel special issue)

We performed a sensitive search for the ground-state emission lines of ortho- and para-water vapor in the DM Tau protoplanetary disk using the Herschel/HIFI instrument. No strong lines are detected down to 3sigma levels in 0.5 km/s channels of 4.2 mK for the 1_{10}--1_{01} line and 12.6 mK for the 1_{11}--0_{00} line. We report a very tentative detection, however, of the 1_{10}--1_{01} line in the Wide Band Spectrometer, with a strength of T_{mb}=2.7 mK, a width of 5.6 km/s and an integrated intensity of 16.0 mK km/s. The latter constitutes a 6sigma detection. Regardless of the reality of this tentative detection, model calculations indicate that our sensitive limits on the line strengths preclude efficient desorption of water in the UV illuminated regions of the disk. We hypothesize that more than 95-99% of the water ice is locked up in coagulated grains that have settled to the midplane., Comment: 5 pages, 3 figures. Accepted for publication in the Herschel HIFI special issue of A&A

Mon R2, at a distance of 830 pc, is the only ultracompact HII region (UC HII) where the photon-dominated region (PDR) between the ionized gas and the molecular cloud can be resolved with Herschel. HIFI observations of the abundant compounds 13CO, C18O, o-H2-18O, HCO+, CS, CH, and NH have been used to derive the physical and chemical conditions in the PDR, in particular the water abundance. The 13CO, C18O, o-H2-18O, HCO+ and CS observations are well described assuming that the emission is coming from a dense (n=5E6 cm-3, N(H2)>1E22 cm-2) layer of molecular gas around the UC HII. Based on our o-H2-18O observations, we estimate an o-H2O abundance of ~2E-8. This is the average ortho-water abundance in the PDR. Additional H2-18O and/or water lines are required to derive the water abundance profile. A lower density envelope (n~1E5 cm-3, N(H2)=2-5E22 cm-2) is responsible for the absorption in the NH 1_1-0_2 line. The emission of the CH ground state triplet is coming from both regions with a complex and self-absorbed profile in the main component. The radiative transfer modeling shows that the 13CO and HCO+ line profiles are consistent with an expansion of the molecular gas with a velocity law, v_e =0.5 x (r/Rout)^{-1} km/s, although the expansion velocity is poorly constrained by the observations presented here., Comment: 4 pages, 5 figures

SWAS and Odin provided stringent upper limits on the gas phase water abundance of dark clouds (x(H2O) < 7x10^-9). We investigate the chemistry of water vapor in starless cores beyond the previous upper limits using the highly improved angular resolution and sensitivity of Herschel and measure the abundance of water vapor during evolutionary stages just preceding star formation. High spectral resolution observations of the fundamental ortho water (o-H2O) transition (557 GHz) were carried out with Herschel HIFI toward two starless cores: B68, a Bok globule, and L1544, a prestellar core embedded in the Taurus molecular cloud complex. The rms in the brightness temperature measured for the B68 and L1544 spectra is 2.0 and 2.2 mK, respectively, in a velocity bin of 0.59 km s^-1. The continuum level is 3.5+/-0.2 mK in B68 and 11.4+/-0.4 mK in L1544. No significant feature is detected in B68 and the 3 sigma upper limit is consistent with a column density of o-H2O N(o-H2O) < 2.5x10^13 cm^-2, or a fractional abundance x(o-H2O) < 1.3x10^-9, more than an order of magnitude lower than the SWAS upper limit on this source. The L1544 spectrum shows an absorption feature at a 5 sigma level from which we obtain the first value of the o-H2O column density ever measured in dark clouds: N(o-H2O) = (8+/-4)x10^12 cm^-2. The corresponding fractional abundance is x(o-H2O) ~ 5x10^-9 at radii > 7000 AU and ~2x10^-10 toward the center. The radiative transfer analysis shows that this is consistent with a x(o-H2O) profile peaking at ~10^-8, 0.1 pc away from the core center, where both freeze-out and photodissociation are negligible. Herschel has provided the first measurement of water vapor in dark regions. Prestellar cores such as L1544 (with their high central densities, strong continuum, and large envelopes) are very promising tools to finally shed light on the solid/vapor balance of water in molecular clouds., Comment: Accepted for publication in Astronomy and Astrophysics (HIFI first results issue)