Estimation and reduction of the uncertainties in chemical models: Application to hot core chemistry

It is not common to consider the role of uncertainties in the rate coefficients used in interstellar gas-phase chemical models. In this paper, we report a new method to determine both the uncertainties in calculated molecular abundances and their sensitivities to underlying uncertainties in the kinetic data utilized. The method is used in hot core models to determine if previous analyses of the age and the applicable cosmic-ray ionization rate are valid. We conclude that for young hot cores ($\le 10^4$ yr), the modeling uncertainties related to rate coefficients are reasonable so that comparisons with observations make sense. On the contrary, the modeling of older hot cores is characterized by strong uncertainties for some of the important species. In both cases, it is crucial to take into account these uncertainties to draw conclusions from the comparison of observations with chemical models.Comment: Accepted for publication in A&

Arcsecond resolution images of the chemical structure of the low-mass protostar IRAS 16293-2422

It remains a key challenge to establish the molecular content of different components of low-mass protostars, like their envelopes and disks, and how this depends on the evolutionary stage and/or environment of the young stars. Observations at submillimeter wavelengths provide a direct possibility to study the chemical composition of low-mass protostars through transitions probing temperatures up to a few hundred K in the gas surrounding these sources. This paper presents a large molecular line survey of the deeply embedded protostellar binary IRAS 16293-2422 from the Submillimeter Array (SMA) - including images of individual lines down to approximately 1.5-3" (190-380 AU) resolution. More than 500 individual transitions are identified related to 54 molecular species (including isotopologues) probing temperatures up to about 550 K. Strong chemical differences are found between the two components in the protostellar system with a separation between, in particular, the sulfur- and nitrogen-bearing species and oxygen-bearing complex organics. The action of protostellar outflow on the ambient envelope material is seen in images of CO and SiO and appear to influence a number of other species, including (deuterated) water, HDO. The effects of cold gas-phase chemistry is directly imaged through maps of CO, N2D+ and DCO+, showing enhancements of first DCO+ and subsequently N2D+ in the outer envelope where CO freezes-out on dust grains.Comment: Accepted for publication in A&A, 30 pages, 22 figure

Observations of gas flows inside a protoplanetary gap

Gaseous giant planet formation is thought to occur in the first few million years following stellar birth. Models predict that giant planet formation carves a deep gap in the dust component (shallower in the gas). Infrared observations of the disk around the young star HD142527, at ~140pc, found an inner disk ~10AU in radius, surrounded by a particularly large gap, with a disrupted outer disk beyond 140AU, indicative of a perturbing planetary-mass body at ~90 AU. From radio observations, the bulk mass is molecular and lies in the outer disk, whose continuum emission has a horseshoe morphology. The vigorous stellar accretion rate would deplete the inner disk in less than a year, so in order to sustain the observed accretion, matter must flow from the outer-disk into the cavity and cross the gap. In dynamical models, the putative protoplanets channel outer-disk material into gap-crossing bridges that feed stellar accretion through the inner disk. Here we report observations with the Atacama Large Millimetre Array (ALMA) that reveal diffuse CO gas inside the gap, with denser HCO+ gas along gap-crossing filaments, and that confirm the horseshoe morphology of the outer disk. The estimated flow rate of the gas is in the range 7E-9 to 2E-7 Msun/yr, which is sufficient to maintain accretion onto the star at the present rate

The solar type protostar IRAS16293-2422: new constraints on the physical structure

Context: The low mass protostar IRAS16293-2422 is a prototype Class 0 source with respect to the studies of the chemical structure during the initial phases of life of Solar type stars. Aims: In order to derive an accurate chemical structure, a precise determination of the source physical structure is required. The scope of the present work is the derivation of the structure of IRAS16293-2422. Methods: We have re-analyzed all available continuum data (single dish and interferometric, from millimeter to MIR) to derive accurate density and dust temperature profiles. Using ISO observations of water, we have also reconstructed the gas temperature profile. Results: Our analysis shows that the envelope surrounding IRAS16293-2422 is well described by the Shu "inside-out" collapsing envelope model or a single power-law density profile with index equal to 1.8. In contrast to some previous studies, our analysis does not show evidence of a large (>/- 800 AU in diameter) cavity. Conclusions: Although IRAS16293-2422 is a multiple system composed by two or three objects, our reconstruction will be useful to derive the chemical structure of the large cold envelope surrounding these objects and the warm component, treated here as a single source, from single-dish observations of molecular emission

Probing MHD Shocks with high-J CO observations: W28F

Context. Observing supernova remnants (SNRs) and modelling the shocks they are associated with is the best way to quantify the energy SNRs re-distribute back into the Interstellar Medium (ISM). Aims. We present comparisons of shock models with CO observations in the F knot of the W28 supernova remnant. These comparisons constitute a valuable tool to constrain both the shock characteristics and pre-shock conditions. Methods. New CO observations from the shocked regions with the APEX and SOFIA telescopes are presented and combined. The integrated intensities are compared to the outputs of a grid of models, which were combined from an MHD shock code that calculates the dynamical and chemical structure of these regions, and a radiative transfer module based on the 'large velocity gradient' (LVG) approximation. Results. We base our modelling method on the higher J CO transitions, which unambiguously trace the passage of a shock wave. We provide fits for the blue- and red-lobe components of the observed shocks. We find that only stationary, C-type shock models can reproduce the observed levels of CO emission. Our best models are found for a pre-shock density of 104 cm-3, with the magnetic field strength varying between 45 and 100 {\mu}G, and a higher shock velocity for the so-called blue shock (\sim25 km s-1) than for the red one (\sim20 km s-1). Our models also satisfactorily account for the pure rotational H2 emission that is observed with Spitzer.Comment: 8 pages, 6 figures, 1 table, accepted for A&A SOFIA/GREAT Special Issu

Receptor activity-modifying protein dependent and independent activation mechanisms in the coupling of calcitonin gene-related peptide and adrenomedullin receptors to Gs

Calcitonin gene-related peptide (CGRP) or adrenomedullin (AM) receptors are heteromers of the calcitonin receptor-like receptor (CLR), a class B G protein-coupled receptor, and one of three receptor activity-modifying proteins (RAMPs). How CGRP and AM activate CLR and how this process is modulated by RAMPs is unclear. We have defined how CGRP and AM induce Gs-coupling in CLR-RAMP heteromers by measuring the effect of targeted mutagenesis in the CLR transmembrane domain on cAMP production, modeling the active state conformations of CGRP and AM receptors in complex with the Gs C-terminus and conducting molecular dynamics simulations in an explicitly hydrated lipidic bilayer. The largest effects on receptor signaling were seen with H295A5.40b, I298A5.43b, L302A5.47b, N305A5.50b, L345A6.49b and E348A6.52b, F349A6.53b and H374A7.47b (class B numbering in superscript). Many of these residues are likely to form part of a group in close proximity to the peptide binding site and link to a network of hydrophilic and hydrophobic residues, which undergo rearrangements to facilitate Gs binding. Residues closer to the extracellular loops displayed more pronounced RAMP or ligand-dependent effects. Mutation of H3747.47b to alanine increased AM potency 100-fold in the CGRP receptor. The molecular dynamics simulation showed that TM5 and TM6 pivoted around TM3. The data suggest that hydrophobic interactions are more important for CLR activation than other class B GPCRs, providing new insights into the mechanisms of activation of this class of receptor. Furthermore the data may aid in the understanding of how RAMPs modulate the signaling of other class B GPCRs

The first ALMA view of IRAS 16293-2422: Direct detection of infall onto source B and high-resolution kinematics of source A

Aims: We focus on the kinematical properties of a proto-binary to study the infall and rotation of gas towards its two protostellar components. Methods: We present ALMA Science Verification observations with high-spectral resolution of IRAS 16293-2422 at 220.2 GHz. The wealth of molecular lines in this source and the very high spectral resolution offered by ALMA allow us to study the gas kinematics with unprecedented detail. Results: We present the first detection of an inverse P-Cygni profile towards source B in the three brightest lines. The line profiles are fitted with a simple two-layer model to derive an infall rate of 4.5x10^-5 Msun/yr. This infall detection would rule-out the previously suggested possibility that source B is a T Tauri star. A position velocity diagram for source A shows evidence for rotation with an axis close to the line-of-sight.Comment: Accepted by A&A Letters. 4 pages, 3 figures, 3 appendices (one for Tables, one for additional figures). This second version includes small language modifications and changes to keep the letter within the 4 page limi

Gender relations and couple negotiations of British men's food practice changes after prostate cancer.

Nutrition plays an important role in the health of men diagnosed with prostate cancer and dietary interventions can therefore be a significant part of prostate cancer survivorship supportive care. Family food provision, however, involves complex social interactions, which shape how men engage with their diets and dietary interventions. The role that gender plays in shaping prostate cancer couples' food practices and men's diets after a prostate cancer diagnosis is thought to be important but is little understood. This study explored couples' accounts of nutrition information seeking and diet change to gain a better understanding of how gender relations shaped men's food practices after prostate cancer diagnosis. Qualitative health interviews with men and their partners were conducted and analysed using interpretive descriptive methods. Findings demonstrated how couples navigated food change journeys that involved seeking information, deciding what changes were warranted and implementing and regulating diet changes. Two overarching themes that illustrated couples' food negotiations were called 'Seeking information and deciding on food changes' and 'Monitoring food changes'. Additional sub-themes described who led food changes, women's filtering of information, and moderation or 'treats'. Throughout these food change journeys interactions between men and women were at play, demonstrating how gender relations and dynamics acted to shape couples food negotiations and men's food practices. Findings reveal that attention to gender relations and the men's family food dynamics should inform diet interventions for men with prostate cancer in order to improve uptake

Genetically encoded photocross-linkers determine the biological binding site of exendin-4 peptide in the N-terminal domain of the intact human glucagon-like peptide-1 receptor (GLP-1R)

The glucagon-like peptide-1 receptor (GLP-1R) is a key therapeutic target in the management of type II diabetes mellitus, with actions including regulation of insulin biosynthesis and secretion, promotion of satiety, and preservation of β-cell mass. Like most class B G protein-coupled receptors (GPCRs), there is limited knowledge linking biological activity of the GLP-1R with the molecular structure of an intact, full-length, and functional receptor·ligand complex. In this study, we have utilized genetic code expansion to site-specifically incorporate the photoactive amino acid p-azido-l-phenylalanine (azF) into N-terminal residues of a full-length functional human GLP-1R in mammalian cells. UV-mediated photolysis of azF was then carried out to induce targeted photocross-linking to determine the proximity of the azido group in the mutant receptor with the peptide exendin-4. Cross-linking data were compared directly with the crystal structure of the isolated N-terminal extracellular domain of the GLP-1R in complex with exendin(9–39), revealing both similarities as well as distinct differences in the mode of interaction. Generation of a molecular model to accommodate the photocross-linking constraints highlights the potential influence of environmental conditions on the conformation of the receptor·peptide complex, including folding dynamics of the peptide and formation of dimeric and higher order oligomeric receptor multimers. These data demonstrate that crystal structures of isolated receptor regions may not give a complete reflection of peptide/receptor interactions and should be combined with additional experimental constraints to reveal peptide/receptor interactions occurring in the dynamic, native, and full-length receptor state