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Resolved molecular line observations are essential for gaining insight into the physical and chemical structure of protoplanetary disks, particularly in cold, dense regions where planets form and acquire compositions. However, tracing these regions is challenging because most molecules freeze onto grain surfaces and are not observable in the gas phase. We investigated cold molecular chemistry in the triple stellar T Tauri disk GG Tau A, which harbours a massive gas and dust ring and an outer disk, using ALMA Band 7 observations. We present high angular resolution maps of N2H+ and DCO+ emission, with upper limits reported for H2D+, 13CS, and SO2. The radial intensity profile of N2H+ shows most emission near the ring outer edge, while DCO+ exhibits double peaks, one near the ring inner edge and the other in the outer disk. With complementary observations of lower-lying transitions, we constrained the molecular surface densities and rotation temperatures. We compared the derived quantities with model predictions across different cosmic ray ionization (CRI) rates, carbon-to-oxygen (C/O) ratios, and stellar UV fluxes. Cold molecular chemistry, affecting N2H+, DCO+, and H2D+ abundances, is most sensitive to CRI rates, while stellar UV flux and C/O ratios have minimal impact on these three ions. Our best model requires a low cosmic ray ionization rate of 1e-18 s-1. However, it fails to match the low temperatures derived from N2H+ and DCO+, 12 to 16 K, which are much lower than the CO freezing temperature., Comment: Resubmitted to ApJ. Thanks to the two anonymous referees for their constructive comments

Submillimeter and millimeter wavelengths provide a unique view of the Universe, from the gas and dust that fills and surrounds galaxies to the chromosphere of our own Sun. Current single-dish facilities have presented a tantalising view of the brightest (sub-)mm sources, and interferometers have provided the exquisite resolution necessary to analyse the details in small fields, but there are still many open questions that cannot be answered with current facilities. In this report we summarise the science that is guiding the design of the Atacama Large Aperture Submillimeter Telescope (AtLAST). We demonstrate how tranformational advances in topics including star formation in high redshift galaxies, the diffuse circumgalactic medium, Galactic ecology, cometary compositions and solar flares motivate the need for a 50m, single-dish telescope with a 1-2 degree field of view and a new generation of highly multiplexed continuum and spectral cameras. AtLAST will have the resolution to drastically lower the confusion limit compared to current single-dish facilities, whilst also being able to rapidly map large areas of the sky and detect extended, diffuse structures. Its high sensitivity and large field of view will open up the field of submillimeter transient science by increasing the probability of serendipitous detections. Finally, the science cases listed here motivate the need for a highly flexible operations model capable of short observations of individual targets, large surveys, monitoring programmes, target of opportunity observations and coordinated observations with other observatories. AtLAST aims to be a sustainable, upgradeable, multipurpose facility that will deliver orders of magnitude increases in sensitivity and mapping speeds over current and planned submillimeter observatories., Comment: 47 pages, 12 figures. For further details on AtLAST see https://atlast.uio.no

As we learn more about the multi-scale interstellar medium (ISM) of our Galaxy, we develop a greater understanding for the complex relationships between the large-scale diffuse gas and dust in Giant Molecular Clouds (GMCs), how it moves, how it is affected by the nearby massive stars, and which portions of those GMCs eventually collapse into star forming regions. The complex interactions of those gas, dust and stellar populations form what has come to be known as the ecology of our Galaxy. Because we are deeply embedded in the plane of our Galaxy, it takes up a significant fraction of the sky, with complex dust lanes scattered throughout the optically recognisable bands of the Milky Way. These bands become bright at (sub-)millimetre wavelengths, where we can study dust thermal emission and the chemical and kinematic signatures of the gas. To properly study such large-scale environments, requires deep, large area surveys that are not possible with current facilities. Moreover, where stars form, so too do planetary systems, growing from the dust and gas in circumstellar discs, to planets and planetesimal belts. Understanding the evolution of these belts requires deep imaging capable of studying belts around young stellar objects to Kuiper belt analogues around the nearest stars. Here we present a plan for observing the Galactic Plane and circumstellar environments to quantify the physical structure, the magnetic fields, the dynamics, chemistry, star formation, and planetary system evolution of the galaxy in which we live with AtLAST; a concept for a new, 50m single-dish sub-mm telescope with a large field of view which is the only type of facility that will allow us to observe our Galaxy deeply and widely enough to make a leap forward in our understanding of our local ecology., Comment: 27 pages, submitted to Open Research Europe as part of the AtLAST collection: https://open-research-europe.ec.europa.eu/collections/atlast/about

DQ Tau is a unique young high-eccentricity binary system that exhibits regular magnetic reconnection flares and pulsed accretion near periastron. We conducted NuSTAR, Swift, and Chandra observations during the July 30, 2022 periastron to characterize X-ray, near-ultraviolet (NUV), and optical flaring emissions. Our findings confirm the presence of X-ray super-flares accompanied by substantial NUV and optical flares, consistent with previous discoveries of periastron flares in 2010 and 2021. These observations, supported by new evidence, strongly establish the magnetosphere collision mechanism as the primary driver of magnetic energy release during DQ Tau's periastron flares. The energetics of the observed X-ray super-flares remain consistent across the three periastrons, indicating recurring energy sources during each passage, surpassing the capabilities of single stars. The observed flaring across multiple bands supports the Adams et al. model for magnetosphere interaction in eccentric binaries. Evidence from modeling and past and current observations suggests that both the mm/X-ray periastron flares and tentatively, the magnetic reconnection-related components of the optical/NUV emissions, conform to the classical solar/stellar non-thermal thick-target model, except for the distinctive magnetic energy source. However, our NuSTAR observations suffered from high background levels, hindering the detection of anticipated non-thermal hard X-rays. Furthermore, we report serendipitous discovery of X-ray super-flares occurring away from periastron, potentially associated with interacting magnetospheres. The current study is part of a broader multi-wavelength campaign, which is planned to investigate the influence of DQ Tau's stellar radiation on gas-phase ion chemistry within its circumbinary disk., Comment: 27 pages, 9 figures, 3 tables. Accepted for publication in The Astrophysical Journal, October 18, 2023

Aqueous chemistry within carbonaceous planetesimals is promising for synthesizing prebiotic organic matter essential to all life. Meteorites derived from these planetesimals delivered these life building blocks to the early Earth, potentially facilitating the origins of life. Here, we studied the formation of vitamin B$_3$ as it is an important precursor of the coenzyme NAD(P)(H), which is essential for the metabolism of all life as we know it. We propose a new reaction mechanism based on known experiments in the literature that explains the synthesis of vitamin B$_3$. It combines the sugar precursors glyceraldehyde or dihydroxyacetone with the amino acids aspartic acid or asparagine in aqueous solution without oxygen or other oxidizing agents. We performed thermochemical equilibrium calculations to test the thermodynamic favorability. The predicted vitamin B$_3$ abundances resulting from this new pathway were compared with measured values in asteroids and meteorites. We conclude that competition for reactants and decomposition by hydrolysis are necessary to explain the prebiotic content of meteorites. In sum, our model fits well into the complex network of chemical pathways active in this environment., Comment: Accepted for publication in ChemPlusChem. The authors Klaus Paschek and Mijin Lee contributed equally. 18 pages, 7 figures (all colored). Supporting Information is available at https://doi.org/10.6084/m9.figshare.24326575

The Cryogenic IR echelle Spectrometer (CRIRES) instrument at the Very Large Telescope (VLT) was in operation from 2006 to 2014. Great strides in characterizing the inner regions of protoplanetary disks were made using CRIRES observations in the L- and M-band at this time. The upgraded instrument, CRIRES+, became available in 2021 and covers a larger wavelength range simultaneously. Here we present new CRIRES+ Science Verification data of the binary system S Coronae Australis (S CrA). We aim to characterize the upgraded CRIRES+ instrument for disk studies and provide new insight into the gas in the inner disk of the S CrA N and S systems. We analyze the CRIRES+ data taken in all available L- and M-band settings, providing spectral coverage from 2.9 to 5.5 $\mu$m. We detect emission from $^{12}$CO (v=1-0, v=2-1, and v=3-2), $^{13}$CO (v=1-0), hydrogen recombination lines, OH, and H$_2$O in the S CrA N disk. In the fainter S CrA S system, only the $^{12}$CO v=1-0 and the hydrogen recombination lines are detected. The $^{12}$CO v=1-0 emission in S CrA N and S shows two velocity components, a broad component coming from $\sim$0.1 au in S CrA N and $\sim$0.03 au in S CrA S and a narrow component coming from $\sim$3 au in S CrA N and $\sim$5 au in S CrA S. We fit local thermodynamic equilibrium slab models to the rotation diagrams of the two S CrA N velocity components and find that they have similar column densities ($\sim$1-7$\times$10$^{17}$ cm$^{-2}$), but that the broad component is coming from a hotter and narrower region. Two filter settings, M4211 and M4368, provide sufficient wavelength coverage for characterizing CO and H$_2$O at $\sim$5 $\mu$m, in particular covering low- and high-$J$ lines. CRIRES+ provides spectral coverage and resolution that are crucial complements to low-resolution observations, such as those with JWST, where multiple velocity components cannot be distinguished., Comment: 15 pages, 13 figures, accepted to A&A

In this study, we investigate how physical properties, such as the density and temperature profiles, evolve on core scales through the evolutionary sequence during high-mass star formation ranging from protostars in cold infrared dark clouds to evolved UCHII regions. We observed 11 high-mass star-forming regions with ALMA at 3 mm wavelengths. Based on the 3 mm continuum morphology and recombination line emission, tracing locations with free-free (ff) emission, the fragmented cores analyzed in this study are classified into either dust or dust+ff cores. In addition, we resolve three cometary UCHII regions with extended 3 mm emission that is dominated by free-free emission. The temperature structure and radial profiles (T~r^-q ) are determined by modeling molecular emission of CH3CN and CH313CN with XCLASS and by using the HCN-to- HNC intensity ratio as probes for the gas kinetic temperature. The density profiles (n~r^-p ) are estimated from the 3 mm continuum visibility profiles. The masses M and H2 column densities N(H2) are then calculated from the 3 mm dust continuum emission. Results. We find a large spread in mass and peak H2 column density in the detected sources ranging from 0.1-150 Msun and 10^23 - 10^26 cm-2 , respectively. Including the results of the CORE and CORE-extension studies (Gieser et al. 2021, 2022) to increase the sample size, we find evolutionary trends on core scales for the temperature power-~law index q increasing from 0.1 to 0.7 from infrared dark clouds to UCHII regions, while for the the density power-law index p on core scales, we do not find strong evidence for an evolutionary trend. However, we find that on the larger clump scales throughout these evolutionary phases the density profile flattens from p = 2.2 to p = 1.2. (abridged), Comment: 21 pages, 10 figures, accepted for publication in A&A

Aims. With the large amount of molecular emission data from (sub)millimeter observatories and incoming James Webb Space Telescope infrared spectroscopy, access to fast forward models of the chemical composition of protoplanetary disks is of paramount importance. Methods. We used a thermo-chemical modeling code to generate a diverse population of protoplanetary disk models. We trained a K-nearest neighbors (KNN) regressor to instantly predict the chemistry of other disk models. Results. We show that it is possible to accurately reproduce chemistry using just a small subset of physical conditions, thanks to correlations between the local physical conditions in adopted protoplanetary disk models. We discuss the uncertainties and limitations of this method. Conclusions. The proposed method can be used for Bayesian fitting of the line emission data to retrieve disk properties from observations. We present a pipeline for reproducing the same approach on other disk chemical model sets., Comment: 11 pages, 5 figures

Constraining planet formation based on the atmospheric composition of exoplanets is a fundamental goal of the exoplanet community. Existing studies commonly try to constrain atmospheric abundances, or to analyze what abundance patterns a given description of planet formation predicts. However, there is also a pressing need to develop methodologies that investigate how to transform atmospheric compositions into planetary formation inferences. In this study we summarize the complexities and uncertainties of state-of-the-art planet formation models and how they influence planetary atmospheric compositions. We introduce a methodology that explores the effect of different formation model assumptions when interpreting atmospheric compositions. We apply this framework to the directly imaged planet HR 8799e. Based on its atmospheric composition, this planet may have migrated significantly during its formation. We show that including the chemical evolution of the protoplanetary disk leads to a reduced need for migration. Moreover, we find that pebble accretion can reproduce the planet's composition, but some of our tested setups lead to too low atmospheric metallicities, even when considering that evaporating pebbles may enrich the disk gas. We conclude that the definitive inversion from atmospheric abundances to planet formation for a given planet may be challenging, but a qualitative understanding of the effects of different formation models is possible, opening up pathways for new investigations., Comment: Accepted for publication in ApJ, base formation inversion code is available at: https://gitlab.com/mauricemolli/formation-inversion

The origin of life might be sparked by the polymerization of the first RNA molecules in Darwinian ponds during wet-dry cycles. The key life-building block ribose was found in carbonaceous chondrites. Its exogenous delivery onto the Hadean Earth could be a crucial step toward the emergence of the RNA world. Here, we investigate the formation of ribose through a simplified version of the formose reaction inside carbonaceous chondrite parent bodies. Following up on our previous studies regarding nucleobases with the same coupled physico-chemical model, we calculate the abundance of ribose within planetesimals of different sizes and heating histories. We perform laboratory experiments using catalysts present in carbonaceous chondrites to infer the yield of ribose among all pentoses (5Cs) forming during the formose reaction. These laboratory yields are used to tune our theoretical model that can only predict the total abundance of 5Cs. We found that the calculated abundances of ribose were similar to the ones measured in carbonaceous chondrites. We discuss the possibilities of chemical decomposition and preservation of ribose and derived constraints on time and location in planetesimals. In conclusion, the aqueous formose reaction might produce most of the ribose in carbonaceous chondrites. Together with our previous studies on nucleobases, we found that life-building blocks of the RNA world could be synthesized inside parent bodies and later delivered onto the early Earth., Comment: Published in Life, 24 pages, 8 figures (all colored)

This work is part of a multi-wavelength program to study the effects of X-ray/UV/optical stellar radiation on the chemistry of the circumbinary disk around the young high-eccentricity binary DQ Tau. ALMA observations for near/around December 5, 2021 periastron were postponed due to bad weather, but supporting Swift-XRT-UVOT TOO observations were successful. These Swift observations along with previous X-ray-optical-mm data show that DQ Tau keeps exhibiting powerful flares near periastron, offering a unique laboratory for studies of flare effects on the gas-phase ion chemistry in protoplanetary disks., Comment: 6 pages, 1 figure, 1 table, accepted for publication in RNAAS

Prebiotic molecules, fundamental building blocks for the origin of life, have been found in carbonaceous chondrites. The exogenous delivery of these organic molecules onto the Hadean Earth could have sparked the polymerization of the first RNA molecules in Darwinian ponds during wet-dry cycles. Here, we investigate the formation of the RNA and DNA nucleobases adenine, uracil, cytosine, guanine, and thymine inside parent body planetesimals of carbonaceous chondrites. An up-to-date thermochemical equilibrium model coupled with a 1D thermodynamic planetesimal model is used to calculate the nucleobase concentrations. Different from the previous study (Pearce & Pudritz 2016), we assume initial volatile concentrations more appropriate for the formation zone of carbonaceous chondrite parent bodies. This represents more accurately cosmochemical findings that these bodies have formed inside the inner, $\sim 2\mathrm{-}5\,\mathrm{au}$, warm region of the solar system. Due to these improvements, our model represents the concentrations of adenine and guanine measured in carbonaceous chondrites. Our model did not reproduce per se the measurements of uracil, cytosine, and thymine in these meteorites. This can be explained by transformation reactions between nucleobases and potential decomposition of thymine. The synthesis of prebiotic organic matter in carbonaceous asteroids could be well explained by a combination of i) radiogenic heating, ii) aqueous chemistry involving a few key processes at a specific range of radii inside planetesimals where water can exist in the liquid phase, and iii) a reduced initial volatile content (H$_2$, CO, HCN, CH$_2$O) of the protoplanetary disk material in the parent body region compared to the outer region of comets., Comment: Accepted for publication in The Astrophysical Journal. 30 pages, 9 figures (all colored). Supporting figure sets are available at https://doi.org/10.6084/m9.figshare.21545148

The nature of the gas in CO-rich debris discs remains poorly understood, as it could either be a remnant from the earlier Class II phase or of secondary origin, driven by the destruction of icy planetesimals. The aim of this paper was to elucidate the origin of the gas content in the debris discs via various simple molecules that are often detected in the less-evolved Class II discs. We present millimetre molecular line observations of nine circumstellar discs around A-type stars: four CO-rich debris discs (HD 21997, HD 121617, HD 131488, HD 131835) and five old Herbig Ae protoplanetary discs (HD 139614, HD 141569, HD 142666, HD 145718, HD 100453). The sources were observed with the Atacama Large Millimeter/submillimeter Array (ALMA) in Bands 5 and 6 with 1-2'' resolution. The Herbig Ae discs are detected in the CO isotopologues, CN, HCN, HCO$^+$, C2H, and CS lines. In contrast, only CO isotopologues are detected in the debris discs, showing a similar amount of CO to that found in the Herbig Ae protoplanetary discs. Using chemical and radiative transfer modelling, we show that the abundances of molecules other than CO in debris discs are expected to be very low. We consider multiple sets of initial elemental abundances with various degrees of H2 depletion. We find that the HCO+ lines should be the second brightest after the CO lines and that their intensities strongly depend on the overall CO/H$_2$ ratio of the gas. However, even in the ISM-like scenario, the simulated HCO+ emission remains weak as required by our non-detections., Comment: 15 pages, 9 figures, 7 tables Accepted for publication in MNRAS

The mass of protoplanetary disks is arguably one of their most important quantities shaping their evolution toward planetary systems, but it remains a challenge to determine this quantity. Using the high spatial resolution now available on telescopes such as the Atacama Large Millimeter/submillimeter Array (ALMA), recent studies derived a relation between the disk surface density and the location of the "dust lines". This is a new concept in the field, linking the disk size at different continuum wavelengths with the radial distribution of grain populations of different sizes. We aim to use a dust evolution model to test the dependence of the dust line location on disk gas mass. In particular, we are interested in the reliability of the method for disks showing radial substructures, as recent high-resolution observations revealed. Our models show that the determination of the dust line location is a promising approach to the mass estimate of protoplanetay disks, but the exact relation between the dust line location and disk mass depends on the structure of the particular disk. We calibrated the relation for disks without evidence of radial structures, while for more complex structures we ran a simple dust evolution model. However, this method fails when there is evidence of strong dust traps. It is possible to reveal when dust evolution is dominated by traps, providing the necessary information for when the method should be applied with caution., Comment: 14 pages, 18 figures, accepted by Astronomy & Astrophysics

We report observations of polarized line and continuum emission from the disk of TW~Hya using the Atacama Large Millimeter/submillimeter Array. We target three emission lines, $^{12}$CO (3-2), $^{13}$CO (3-2) and CS (7-6), to search for linear polarization due to the Goldreich-Kylafis effect, while simultaneously tracing the continuum polarization morphology at 332\,GHz (900\,\micron{}), achieving a spatial resolution of 0.5\arcsec{} (30~au). We detect linear polarization in the dust continuum emission; the polarization position angles show an azimuthal morphology, and the median polarization fraction is $\sim$\,0.2\%, comparable to previous, lower frequency observations. Adopting a `shift-and-stack' technique to boost the sensitivity of the data, combined with a linear combination of the $Q$ and $U$ components to account for their azimuthal dependence, we detect weak linear polarization of $^{12}$CO and $^{13}$CO line emission at a $\sim 10\sigma$ and $\sim 5\sigma$ significance, respectively. The polarization was detected in the line wings, reaching a peak polarization fraction of $\sim 5\%$ and $\sim 3\%$ for the two molecules between disk radii of 0.5" and 1". The sign of the polarization was found to flip from the blue-shifted side of the emission to the red-shifted side, suggesting a complex, asymmetric polarization morphology. Polarization is not robustly detected for the CS emission; however, a tentative signal, comparable in morphology to that found for the $^{12}$CO and $^{13}$CO emission, is found at a $\lesssim 3\sigma$ significance. We are able to reconstruct a polarization morphology, consistent with the azimuthally averaged profiles, under the assumption that this is also azimuthally symmetric, which can be compared with future higher-sensitivity observations., Comment: Accepted by ApJ

We present a study of emission lines of small hydrocarbons C$_2$H and $c$-C$_3$H$_2$, and COMs precursors H$_2$CO and CH$_3$OH in order to better understand the possible chemical link between the molecular abundances and UV radiation field in photodissociation regions (PDRs). We study two PDRs around extended and compact HII regions with $G \leq 50$~Habings in the S235 star-forming complex. We find the highest abundances of both hydrocarbons on the edges of molecular clumps, while $c$-C$_3$H$_2$ is also abundant in the low-density expanding PDR around compact HII region S235\,A. We see the highest methanol column density towards the positions with the UV~field $G\approx 20-30$~Habings and explain them by reactive desorption from the dust grains. The $N_{\rm C_2H}/N_{\rm CH_3OH}$ ratio is lower by a factor of few or the order of magnitude in comparison with the Horsehead and Orion Bar PDRs. The ratio is similar to the value observed in hot corinos in the Perseus cloud. We conclude that ion-molecular and grain surface chemical routes rule the molecular abundances in the PDRs, and the PDRs inherit molecular abundances from the previous dark stage of molecular cloud evolution in spite of massive stars already emitting in optics., Comment: accepted by MNRAS

The chemical differentiation of seven COMs in the extended region around Sgr B2 has been observed: CH$_2$OHCHO, CH$_3$OCHO, t-HCOOH, C$_2$H$_5$OH, and CH$_3$NH$_2$ were detected both in the extended region and near the hot cores Sgr B2(N) and Sgr B2(M), while CH$_3$OCH$_3$ and C$_2$H$_5$CN were only detected near the hot cores. The density and temperature in the extended region are relatively low. Different desorption mechanisms have been proposed to explain the observed COMs in cold regions but fail to explain the deficiency of CH$_3$OCH$_3$ and C$_2$H$_5$CN. We explored under what physical conditions the chemical simulations can fit the observations and explain the different spatial distribution of these species. We used the Monte Carlo method to perform a detailed parameter space study. We investigated how different mechanisms affect the results. All gas-grain chemical models based on static physics cannot fit the observations. The results based on evolving physical conditions can fit six COMs when $T\sim30-60$ K, but the best-fit temperature is still higher than the observed dust temperature of 20 K. The best agreement at $T\sim27$ K is achieved by considering a short-duration $\sim 10^2$ yr X-ray burst with $\zeta_{\mathrm{CR}}=1.3\times10^{-13}$ s$^{-1}$ when the temperature is 20 K. The reactive desorption is the key mechanism for producing these COMs and inducing the low abundances of CH$_3$OCH$_3$ and C$_2$H$_5$CN. The evolution of the extended region around Sgr~B2 may have begun with a cold, $T\le10$ K phase followed by a warm-up phase. When its temperature reached $T\sim20$ K, an X-ray flare from Sgr A* with a short duration of no more than 100 years was acquired, affecting strongly the Sgr B2 chemistry. The observed COMs retain their observed abundances only several hundred years after such a flare, which could imply that such short-term X-ray flares occur relatively often.

The widespread rings and gaps seen in the dust continuum in protoplanetary disks are sometimes accompanied by similar substructures seen in molecular line emission. One example is the outer gap at 100 au in AS 209, which shows that the H$_{13}$CO$^+$ and C$_{18}$O emission intensities decrease along with the continuum in the gap, while the DCO$^+$ emission increases inside the gap. We aim to study the behavior of DCO$^+$/H$_{13}$CO$^+$ and DCO$^+$/HCO$^+$ ratios in protoplanetary disk gaps assuming the two scenarios: the gas depletion follows the dust depletion and only the dust is depleted. We first modeled the physical disk structure using the thermo-chemical model ANDES. This 1+1D steady-state disk model calculates the thermal balance of gas and dust and includes the FUV, X-rays, cosmic rays, and other ionization sources together with the reduced chemical network for molecular coolants. Afterward, this physical structure was adopted for calculations of molecular abundances with the extended gas-grain chemical network with deuterium fractionation. Ideal synthetic spectra and 0th-moment maps were produced with LIME. We are able to qualitatively reproduce the increase in the DCO$^+$ intensity and the decrease in the H$_{13}$CO$^+$ and C$_{18}$O intensities inside the disk gap, which is qualitatively similar to what is observed in the outer AS 209 gap. The corresponding disk model assumes that both the gas and dust are depleted in the gap. The model with the gas-rich gap, where only the dust is depleted, produces emission that is too bright in all HCO$^+$ isotopologues and C$_{18}$O. The DCO$^+$/H$_{13}$CO$^+$ line ratio can be used to probe gas depletion in dust continuum gaps outside of the CO snow line. The DCO$^+$/C$_{18}$O line ratio shows a similar, albeit weaker, effect; however, these species can be observed simultaneously with a single ALMA or NOEMA setup., Comment: 12 pages, 7 figures, Accepted for publication in Astronomy and Astrophysics

The feasibility of contemporary gas-grain astrochemical models depends on the availability of accurate kinetics data, in particular, for surface processes. We study the sensitivity of gas-grain chemical models to the energy barrier Ea of the important surface reaction between some of the most abundant species: C and H2 (surface C + surface H2 = surface CH2). We used the gas-grain code ALCHEMIC to model the time-dependent chemical evolution over a 2D grid of densities (nH: 10^{3} - 10^{12}cm^{-3}) and temperatures (T: 10 - 300 K), assuming UV-dark (Av = 20 mag) and partly UV-irradiated (Av = 3 mag) conditions that are typical of the dense interstellar medium. We considered two values for the energy barrier of the surface reaction, Ea = 2500 K (as originally implemented in the networks) and Ea = 0 K (as measured in the laboratory and computed by quantum chemistry simulations). We find that if the C + H2 = CH2 surface reaction is barrierless, a more rapid conversion of the surface carbon atoms into methane ice occurs. Overproduction of the CHn hydrocarbon ices affects the surface formation of more complex hydrocarbons, cyanides and nitriles, and CS-bearing species at low temperatures < 10-15 K. The surface hydrogenation of CO and hence the synthesis of complex (organic) molecules become affected as well. As a result, important species whose abundances may change by more than a factor of two at 1 Myr include atomic carbon, small mono-carbonic (C1) and di-carbonic (C2) hydrocarbons, CO2, CN, HCN, HNC, HNCO, CS, H2CO, H2CS, CH2CO, and CH3OH (in either gas and/or ice). The abundances of key species, CO, H2O, and N2 as well as O, HCO+, N2H+, NH3, NO, and most of the S-bearing molecules, remain almost unaffected. Further accurate laboratory measurements and quantum chemical calculations of the surface reaction barriers will be crucial to improve the accuracy of astrochemical models., Comment: Submitted to Astronomy & Astrophysics (A&A), 9 pages

Luminosity outbursts of the FUOri type stars, which have a magnitude of $\sim100 L_{\odot}$ and last for decades, may affect chemical composition of the surrounding protoplanetary disk. Using astrochemical modeling we analyze the changes induced by the outburst and search for species sensitive to the luminosity rise. Some changes in the disk molecular composition appear not only during the outburst itself but can also retain for decades after the end of the outburst. We analyze main chemical processes responsible for these effects and assess timescales at which chemically inert species return to the pre-outburst abundances., Comment: 2 pages, 2 figures

Protoplanetary disks around young stars are the birth sights of planetary systems like our own. Disks represent the gaseous dusty matter left after the formation of their central stars. The mass and luminosity of the star, initial disk mass and angular momentum, and gas viscosity govern disk evolution and accretion. Protoplanetary disks are the cosmic nurseries where microscopic dust grains grow into pebbles, planetesimals, and planets., Comment: 7 pages, 3 figures, to appear in Europhysics News 51/1

The chemical influence of luminosity outbursts on the environments of young solar-type stars is explored. Species are categorised into several types according to their response to the outburst. The first and second types imply chemical changes only during the outburst (with slightly different behaviours). These response types are mostly observed close to the star and are caused by icy mantle evaporation. However, mantles recover after the outburst almost immediately. A notable exception is benzene ice, which is accumulated on dust surfaces during and after the outburst, so that its abundance exceeds the pre-outburst level by orders of magnitude. The third type of response is mostly seen at the disc periphery and implies alteration of abundances during the outburst and preservation of these `abnormal' abundances for centuries. This behaviour is typical of organic compounds, like HCOOCH$_3$, CH$_3$CN, CH$_2$CO. Their presence in the dark disc regions can be a manifestation of the past outburst. CO and CO$_2$ only trace past outbursts at the remote disc regions. The outburst changes the C/O ratio, but it quickly returns to the pre-outburst value almost everywhere in the disc. An important factor determining the sensitivity of molecular composition to the outburst is the dust size distribution. The duration of the pre-outburst stage and of the outburst itself influence the chemical effects, if the burst duration is shorter than 50 yr and the duration of the quiescent phase between the bursts is shorter than 100 kyr., Comment: Accepted to MNRAS

The formation of planets occurs within protoplanetary disks surrounding young stars, resulting in perturbation of the gas and dust surface densities. Here, we report the first evidence of spatially resolved gas surface density ($\Sigma_{g}$) perturbation towards the AS~209 protoplanetary disk from the optically thin C$^{18}$O ($J=2-1$) emission. The observations were carried out at 1.3~mm with ALMA at a spatial resolution of about 0.3$\arcsec$ $\times$ 0.2$\arcsec$ (corresponding to $\sim$ 38 $\times$ 25 au). The C$^{18}$O emission shows a compact ($\le$60~au), centrally peaked emission and an outer ring peaking at 140~au, consistent with that observed in the continuum emission and, its azimuthally averaged radial intensity profile presents a deficit that is spatially coincident with the previously reported dust map. This deficit can only be reproduced with our physico-thermochemical disk model by lowering $\Sigma_{gas}$ by nearly an order of magnitude in the dust gaps. Another salient result is that contrary to C$^{18}$O, the DCO$^{+}$ ($J=3-2$) emission peaks between the two dust gaps. We infer that the best scenario to explain our observations (C$^{18}$O deficit and DCO$^{+}$ enhancement) is a gas perturbation due to forming-planet(s), that is commensurate with previous continuum observations of the source along with hydrodynamical simulations. Our findings confirm that the previously observed dust gaps are very likely due to perturbation of the gas surface density that is induced by a planet of at least 0.2~M$\rm_{Jupiter}$ in formation. Finally, our observations also show the potential of using CO isotopologues to probe the presence of saturn mass planet(s)., Comment: Accepted for publication by ApJ

The FU Ori-type young stellar objects are characterized by a sudden increase in luminosity by 1$-$2 orders of magnitude, followed by slow return to the pre-outburst state on timescales of $\sim$10$-$100 yr. The outburst strongly affects the entire disk, changing its thermal structure and radiation field. In this paper, using a detailed physical-chemical model we study the impact of the FU Ori outburst on the disk chemical inventory. Our main goal is to identify gas-phase molecular tracers of the outburst activity that could be observed after the outburst with modern telescopes such as ALMA and NOEMA. We find that the majority of molecules experience a considerable increase in the total disk gas-phase abundances due to the outburst, mainly due to the sublimation of their ices. Their return to the pre-outburst chemical state takes different amounts of time, from nearly instantaneous to very long. Among the former ones we identify CO, NH$_3$, C$_2$H$_6$, C$_3$H$_4$, etc. Their abundance evolution tightly follows the luminosity curve. For CO the abundance increase does not exceed an order of magnitude, while for other tracers the abundances increase by 2$-$5 orders of magnitude. Other molecules like H$_2$CO and NH$_2$OH have longer retention timescales, remaining in the gas phase for $\sim10-10^3$ yr after the end of the outburst. Thus H$_2$CO could be used as an indicator of the previous outbursts in the post-outburst FU Ori systems. We investigate the corresponding time-dependent chemistry in detail and present the most favorable transitions and ALMA configurations for future observations., Comment: accepted for publication in ApJ

The formation of asteroids, comets and planets occurs in the interior of protoplanetary disks during the early phase of star formation. Consequently, the chemical composition of the disk might shape the properties of the emerging planetary system. In this context, it is crucial to understand whether and what organic molecules are synthesized in the disk. In this Letter, we report the first detection of formic acid (HCOOH) towards the TW Hydrae protoplanetary disk. The observations of the trans-HCOOH 6$_{(1,6)-5(1,5)}$ transition were carried out at 129~GHz with ALMA. We measured a disk-averaged gas-phase t-HCOOH column density of $\sim$ (2-4)$\times$10$^{12}$~cm$^{-2}$, namely as large as that of methanol. HCOOH is the first organic molecules containing two oxygen atoms detected in a protoplanetary disk, a proof that organic chemistry is very active even though difficult to observe in these objects. Specifically, this simplest acid stands as the basis for synthesis of more complex carboxylic acids used by life on Earth., Comment: 9 pages, 4 figures, 1 table, published online in ApJL on 16th July 2018

Protoplanetary disk mass is a key parameter controlling the process of planetary system formation. CO molecular emission is often used as a tracer of gas mass in the disk. In this study we consider the ability of CO to trace the gas mass over a wide range of disk structural parameters and search for chemical species that could possibly be used as alternative mass tracers to CO. Specifically, we apply detailed astrochemical modeling to a large set of models of protoplanetary disks around low-mass stars, to select molecules with abundances correlated with the disk mass and being relatively insensitive to other disk properties. We do not consider sophisticated dust evolution models, restricting ourselves with the standard astrochemical assumption of $0.1~\mu $m dust. We find that CO is indeed the best molecular tracer for total gas mass, despite the fact that it is not the main carbon carrier, provided reasonable assumptions about CO abundance in the disk are used. Typically, chemical reprocessing lowers the abundance of CO by a factor of 3, compared to the case of photo-dissociation and freeze-out as the only ways of CO depletion. On average only 13% C-atoms reside in gas-phase CO, albeit with variations from 2 to 30%. CO$_2$, H$_2$O and H$_2$CO can potentially serve as alternative mass tracers, the latter two being only applicable if disk structural parameters are known., Comment: Accepted for publication in ApJ

Prior to the origin of simple cellular life, the building blocks of RNA (nucleotides) had to form and polymerize in favourable environments on the early Earth. At this time, meteorites and interplanetary dust particles delivered organics such as nucleobases (the characteristic molecules of nucleotides) to warm little ponds whose wet-dry cycles promoted rapid polymerization. We build a comprehensive numerical model for the evolution of nucleobases in warm little ponds leading to the emergence of the first nucleotides and RNA. We couple Earth's early evolution with complex prebiotic chemistry in these environments. We find that RNA polymers must have emerged very quickly after the deposition of meteorites (< a few years). Their constituent nucleobases were primarily meteoritic in origin and not from interplanetary dust particles. Ponds appeared as continents rose out of the early global ocean but this increasing availability of "targets" for meteorites was offset by declining meteorite bombardment rates. Moreover, the rapid losses of nucleobases to pond seepage during wet periods, and to UV photodissociation during dry periods means that the synthesis of nucleotides and their polymerization into RNA occurred in just one to a few wet-dry cycles. Under these conditions, RNA polymers likely appeared prior to 4.17 billion years ago. Significance: There are two competing hypotheses for the site at which an RNA world emerged: hydrothermal vents in the deep ocean and warm little ponds. Because the former lacks wet and dry cycles, which are well known to promote polymerization (in this case, of nucleotides into RNA), we construct a comprehensive model for the origin of RNA in the latter sites. Our model advances the story and timeline of the RNA world by constraining the source of biomolecules, the environmental conditions, the timescales of reaction, and the emergence of first RNA polymers., Comment: Published in PNAS, 24 pages, 16 figures, 4 tables

We obtain high spatial and spectral resolution images of the CO J=2-1, CN N=2-1 and CS J=5-4 emission with ALMA in Cycle~2. The radial distribution of the turbulent broadening is derived with three approaches: two `direct' and one modelling. The first requires a single transition and derives \Tex{} directly from the line profile, yielding a \vturb{}. The second assumes two different molecules are co-spatial thus their relative linewidths allow for a calculation of \Tkin{} and \vturb{}. Finally we fit a parametric disk model where physical properties of the disk are described by power laws, to compare our `direct' methods with previous values. The two direct methods were limited to the outer $r > 40$~au disk due to beam smear. The direct method found \vturb{} ranging from $\approx$~\vel{130} at 40~au, dropping to $\approx$~\vel{50} in the outer disk, qualitatively recovered with the parametric model fitting. This corresponds to roughly $0.2 - 0.4~c_s$. CN was found to exhibit strong non-LTE effects outside $r \approx 140$~au, so \vturb{} was limited to within this radius. The assumption that CN and CS are co-spatial is consistent with observed linewidths only within $r \lesssim 100$~au, within which \vturb{} was found to drop from \vel{100} ($\approx~0.4~c_s$) to nothing at 100~au. The parametric model yielded a near constant \vel{50} for CS ($0.2 - 0.4~c_s$). We demonstrate that absolute flux calibration is and will be the limiting factor in all studies of turbulence using a single molecule. The magnitude of the dispersion is comparable with or below that predicted by the magneto-rotational instability theory. A more precise comparison would require to reach an absolute calibration precision of order 3\%, or to find a suitable combination of light and heavy molecules which are co-located in the disk., Comment: Accepted by A&A, 30/5/16

EX Lupi-type objects (EXors) form a sub-class of T Tauri stars, defined by sudden sporadic flare-ups of 1-5 magnitudes at optical wavelengths. These eruptions are attributed to enhanced mass accretion from the circumstellar disk to the star, and may constitute important events in shaping the structure of the inner disk and the forming planetary system. Although disk properties must play a fundamental role in driving the outbursts, they are surprisingly poorly known. In order to characterize the dust and gas components of EXor disks, here we report on observations of the $^{12}$CO J=3-2 and 4-3 lines, and the $^{13}$CO 3-2 line in EX Lup, the prototype of the EXor class. We reproduce the observed line fluxes and profiles with a line radiative transfer model, and compare the obtained parameters with corresponding ones of other T Tauri disks., Comment: Accepted for publication in the ApJL. 16 pages in manuscript format, 2 figure, 1 table

We present resolved Plateau de Bure Array observations of DM Tau in lines of HCO+ (3-2), (1-0) and DCO+ (3-2). A power-law fitting approach allowed a derivation of column densities of these two molecules. A chemical inner hole of ~50 AU was found in both HCO+ and DCO+ with DCO+ emission extending to only 450 AU. An isotopic ratio of R_D = N(DCO+) / N(HCO+) was found to range from 0.1 at 50 AU and 0.2 at 450 AU. Chemical modeling allowed an exploration of the sensitivity of these molecular abundances to physical parameters out with temperature, finding that X-rays were the domination ionization source in the HCO+ molecular region and that R_D also is sensitive to the CO depletion. The ionization fraction, assuming a steady state system, was found to be x(e-) ~ 10$^{-7}$. Modeling suggests that HCO+ is the dominant charged molecule in the disk but its contribution to ionization fraction is dwarfed by atmoic ions such as C+, S+ and H+., Comment: 13 pages with 8 figures, to be published in A&A, accepted 29/12/14

The Solar System formed about 4.6 billion years ago from a condensation of matter inside a molecular cloud. Trying to reconstruct what happened is the goal of this chapter. For that, we put together our understanding of Galactic objects that will eventually form new suns and planetary systems, with our knowledge on comets, meteorites and small bodies of the Solar System today. Our specific tool is the molecular deuteration, namely the amount of deuterium with respect to hydrogen in molecules. This is the Ariadne's thread that helps us to find the way out from a labyrinth of possible histories of our Solar System. The chapter reviews the observations and theories of the deuterium fractionation in pre-stellar cores, protostars, protoplanetary disks, comets, interplanetary dust particles and meteorites and links them together trying to build up a coherent picture of the history of the Solar System formation. We emphasise the interdisciplinary nature of the chapter, which gathers together researchers from different communities with the common goal of understanding the Solar System history., Comment: Accepted for publication as a chapter in Protostars and Planets VI, University of Arizona Press (2014), eds. H. Beuther, R. Klessen, C. Dullemond, Th. Henning

Protoplanetary disks composed of dust and gas are ubiquitous around young stars and are commonly recognized as nurseries of planetary systems. Their lifetime, appearance, and structure are determined by an interplay between stellar radiation, gravity, thermal pressure, magnetic field, gas viscosity, turbulence, and rotation. Molecules and dust serve as major heating and cooling agents in disks. Dust grains dominate the disk opacities, reprocess most of the stellar radiation, and shield molecules from ionizing UV/X-ray photons. Disks also dynamically evolve by building up planetary systems which drastically change their gas and dust density structures. Over the past decade significant progress has been achieved in our understanding of disk chemical composition thanks to the upgrade or advent of new millimeter/Infrared facilities (SMA, PdBI, CARMA, Herschel, e-VLA, ALMA). Some major breakthroughs in our comprehension of the disk physics and chemistry have been done since PPV. This review will present and discuss the impact of such improvements on our understanding of the disk physical structure and chemical composition., Comment: 24 pages, 4 figures, 1 table, accepted for publication as a chapter in Protostars and Planets VI, University of Arizona Press (2014), eds. H. Beuther, R. Klessen, C. Dullemond, Th. Henning

This comprehensive review summarizes our current understanding of the evolution of gas, solids and molecular ices in protoplanetary disks. Key findings related to disk physics and chemistry, both observationally and theoretically, are highlighted. We discuss which molecular probes are used to derive gas temperature, density, ionization state, kinematics, deuterium fractionation, and study organic matter in protoplanetary disks., Comment: 83 pages, 8 figures, 5 tables, to be published in a Thematic Issue "Astrochemistry" in Chem. Reviews (December 2013). This document is the unedited Author's version of a Submitted Work that was subsequently accepted for publication in Chemical Reviews, copyright (c) American Chemical Society after peer review

(English) In this lecture I discuss recent progress in the understanding of the chemical evolution of protoplanetary disks that resemble our Solar system during the first ten million years. At the verge of planet formation, strong variations of temperature, density, and radiation intensities in these disks lead to a layered chemical structure. In hot, dilute and heavily irradiated atmosphere only simple radicals, atoms, and atomic ions can survive, formed and destroyed by gas-phase processes. Beneath the atmosphere a partly UV-shielded, warm molecular layer is located, where high-energy radiation drives rich chemistry, both in the gas phase and on dust surfaces. In a cold, dense, dark disk midplane many molecules are frozen out, forming thick icy mantles where surface chemistry is active and where complex (organic) species are synthesized., Comment: 28 pages, 1 figure, 3 tables, written in Russian

We study the content in S-bearing molecules of protoplanetary disks around low-mass stars. We used the new IRAM 30-m receiver EMIR to perform simultaneous observations of the $1_{10}-1_{01}$ line of H$_2$S at 168.8 GHz and $2_{23}-1_{12}$ line of SO at 99.3 GHz. We compared the observational results with predictions coming from the astrochemical code NAUTILUS, which has been adapted to protoplanetary disks. The data were analyzed together with existing CS J=3-2 observations. We fail to detect the SO and H$_2$S lines, although CS is detected in LkCa15, DM\,Tau, and GO\,Tau but not in MWC\,480. However, our new upper limits are significantly better than previous ones and allow us to put some interesting constraints on the sulfur chemistry. Our best modeling of disks is obtained for a C/O ratio of 1.2, starting from initial cloud conditions of H density of $2\times 10^5$ cm$^{-3}$ and age of $10^6$ yr. The results agree with the CS data and are compatible with the SO upper limits, but fail to reproduce the H$_2$S upper limits. The predicted H$_2$S column densities are too high by at least one order of magnitude. H$_2$S may remain locked onto grain surfaces and react with other species, thereby preventing the desorption of H$_2$S.

In this paper we review recent progress in our understanding of the chemical evolution of protoplanetary disks. Current observational constraints and theoretical modeling on the chemical composition of gas and dust in these systems are presented. Strong variations of temperature, density, high-energy radiation intensities in these disks, both radially and vertically, result in a peculiar disk chemical structure, where a variety of processes are active. In hot, dilute and heavily irradiated atmosphere only the most photostable simple radicals and atoms and atomic ions exist, formed by gas-phase processes. Beneath the atmosphere a partly UV-shielded, warm molecular layer is located, where high-energy radiation drives rich ion-molecule and radical-radical chemistry, both in the gas phase and on dust surfaces. In a cold, dense, dark disk midplane many molecules are frozen out, forming thick icy mantles where surface chemistry is active and where complex polyatomic (organic) species are synthesized. Dynamical processes affect disk chemical composition by enriching it in abundances of complex species produced via slow surface processes, which will become detectable with ALMA., Comment: 13 pages, 1 figure, 3 tables, IAU 280 "Molecular Universe" invited paper