Modelling the sulphur chemistry evolution in Orion KL

We study the sulphur chemistry evolution in the Orion KL along the gas and grain phases of the cloud. We investigate the processes that dominate the sulphur chemistry and to determine how physical and chemical parameters, such as the final star mass and the initial elemental abundances, influence the evolution of the hot core and of the surrounding outflows and shocked gas (the plateau). We independently modelled the chemistry evolution of both components using the time-dependent gas-grain model UCL_CHEM and considering two different phase calculations. Phase I starts with the collapsing cloud and the depletion of atoms and molecules onto grain surfaces. Phase II starts when a central protostar is formed and the evaporation from grains takes place. We show how the gas density, the gas depletion efficiency, the initial sulphur abundance, the shocked gas temperature and the different chemical paths on the grains leading to different reservoirs of sulphur on the mantles affect sulphur-bearing molecules at different evolutionary stages. We also compare the predicted column densities with those inferred from observations of the species SO, SO2, CS, OCS, H2S and H2CS. The models that reproduce the observations of the largest number of sulphur-bearing species are those with an initial sulphur abundance of 0.1 times the sulphur solar abundance and a density of at least n_H=5x10^6 cm^-3 in the shocked gas region. We conclude that most of the sulphur atoms were ionised during Phase I, consistent with an inhomogeneous and clumpy region where the UV interstellar radiation penetrates leading to sulphur ionisation. We also conclude that the main sulphur reservoir on the ice mantles was H2S. In addition, we deduce that a chemical transition currently takes place in the shocked gas, where SO and SO2 gas-phase formation reactions change from being dominated by O2 to being dominated by OH.Comment: 14 pages, 28 figures, 6 table

A line confusion-limited millimeter survey of Orion KL. III. Sulfur oxide species

We present a study of the sulfur-bearing species detected in a line confusion-limited survey towards Orion KL performed with the IRAM 30m telescope in the range 80-281 GHz. The study is part of an analysis of the line survey divided into families of molecules. Our aim is to derive accurate physical conditions and molecular abundances in the different components of Orion KL from observed SO and SO2 lines. First we assumed LTE conditions obtain rotational temperatures. We then used a radiative transfer model, assuming either LVG or LTE excitation to derive column densities of these molecules in the different components of Orion KL. We have detected 68 lines of SO, 34SO, 33SO, and S18O and 653 lines of SO2, 34SO2, 33SO2, SO18O and SO2 v2=1. We provide column densities for all of them and also upper limits for the column densities of S17O, 36SO, 34S18O, SO17O and 34SO2 v2=1 and for several undetected sulfur-bearing species. In addition, we present 2'x2' maps around Orion IRc2 of SO2 transitions with energies from 19 to 131 K and also maps with four transitions of SO, 34SO and 34SO2. We observe an elongation of the gas along the NE-SW direction. An unexpected emission peak appears at 20.5 km/s in most lines of SO and SO2. A study of the spatial distribution of this emission feature shows that it is a new component ~5" in diameter, which lies ~4" west of IRc2. We suggest the emission from this feature is related to shocks associated to the BN object. The highest column densities for SO and SO2 are found in the high-velocity plateau (a region dominated by shocks) and in the hot core. These values are up to three orders of magnitude higher than the results for the ridge components. We also find high column densities for their isotopologues in both components. Therefore, we conclude that SO and SO2 are good tracers, not only of regions affected by shocks, but also of regions with warm dense gas.Comment: Paper (ref AA/2013/21285) accepted for publication by A&A. 52 Pages, 26 figures, 13 table

Extended warm gas in Orion KL as probed by methyl cyanide

In order to study the temperature distribution of the extended gas within the Orion Kleinmann-Low nebula, we have mapped the emission by methyl cyanide (CH3CN) in its J=6_K-5_K, J=12_K-11_K, J=13_K-12_K, and J=14_K-13_K transitions at an average angular resolution of ~10 arcsec (22 arcsec for the 6_K-5_K lines), as part of a new 2D line survey of this region using the IRAM 30m telescope. These fully sampled maps show extended emission from warm gas to the northeast of IRc2 and the distinct kinematic signatures of the hot core and compact ridge source components. We have constructed population diagrams for the four sets of K-ladder emission lines at each position in the maps and have derived rotational excitation temperatures and total beam-averaged column densities from the fitted slopes. In addition, we have fitted LVG model spectra to the observations to determine best-fit physical parameters at each map position, yielding the distribution of kinetic temperatures across the region. The resulting temperature maps reveal a region of hot (T > 350 K) material surrounding the northeastern edge of the hot core, whereas the column density distribution is more uniform and peaks near the position of IRc2. We attribute this region of hot gas to shock heating caused by the impact of outflowing material from active star formation in the region, as indicated by the presence of broad CH3CN lines. This scenario is consistent with predictions from C-shock chemical models that suggest that gas-phase methyl cyanide survives in the post-shock gas and can be somewhat enhanced due to sputtering of grain mantles in the passing shock front.Comment: 24 pages, 20 figures, accepted for publication in A&

A combined IRAM and Herschel/HIFI study of cyano(di)acetylene in Orion KL: tentative detection of DC3N

We present a study of cyanoacetylene (HC3N) and cyanodiacetylene (HC5N) in Orion KL, through observations from two line surveys performed with the IRAM 30m telescope and the HIFI instrument on board the Herschel telescope. The frequency ranges covered are 80-280 GHz and 480-1906 GHz. We model the observed lines of HC3N, HC5N, their isotopologues (including DC3N), and vibrational modes, using a non-LTE radiative transfer code. To investigate the chemical origin of HC3N and DC3N in Orion KL, we use a time-dependent chemical model. We detect 40 lines of the ground state of HC3N and 68 lines of its 13C isotopologues. We also detect 297 lines of six vibrational modes of this molecule (nu_7, 2nu_7, 3nu_7, nu_6, nu_5, and nu_6+nu_7) and 35 rotational lines of the ground state of HC5N. We report the first tentative detection of DC3N in a giant molecular cloud with a DC3N/HC3N abundance ratio of 0.015. We provide column densities and isotopic and molecular abundances. We also perform a 2x2" map around Orion IRc2 and we present maps of HC3N lines and maps of lines of the HC3N vibrational modes nu_6 and nu_7. In addition, a comparison of our results for HC3N with those in other clouds allows us to derive correlations between the column density, the FWHM, the mass, and the luminosity of the clouds. The high column densities of HC3N obtained in the hot core, make this molecule an excellent tracer of hot and dense gas. In addition, the large frequency range covered reveals the need to consider a temperature and density gradient in the hot core in order to obtain better line fits. The high D/H ratio (comparable to that obtained in cold clouds) that we derive suggests a deuterium enrichment. Our chemical models indicate that the possible deuterated HC3N present in Orion KL is formed during the gas-phase. This fact provides new hints concerning the processes leading to deuteration.Comment: 50 pages, 33 figures, 13 tables. Accepted for publication in A&

Erratum: Surface chemistry in photodissociation regions (vol 591, A52, 2016)

Laboratory astrophysics and astrochemistr

Parameterizing the interstellar dust temperature

The temperature of interstellar dust particles is of great importance to astronomers. It plays a crucial role in the thermodynamics of interstellar clouds, because of the gas-dust collisional coupling. It is also a key parameter in astrochemical studies that governs the rate at which molecules form on dust. In 3D (magneto)hydrodynamic simulations often a simple expression for the dust temperature is adopted, because of computational constraints, while astrochemical modelers tend to keep the dust temperature constant over a large range of parameter space. Our aim is to provide an easy-to-use parametric expression for the dust temperature as a function of visual extinction ($A_{\rm V}$) and to shed light on the critical dependencies of the dust temperature on the grain composition. We obtain an expression for the dust temperature by semi-analytically solving the dust thermal balance for different types of grains and compare to a collection of recent observational measurements. We also explore the effect of ices on the dust temperature. Our results show that a mixed carbonaceous-silicate type dust with a high carbon volume fraction matches the observations best. We find that ice formation allows the dust to be warmer by up to 15% at high optical depths ($A_{\rm V}> 20$ mag) in the interstellar medium. Our parametric expression for the dust temperature is presented as $T_{\rm d} = \left[ 11 + 5.7\times \tanh\bigl( 0.61 - \log_{10}(A_{\rm V})\bigr) \right] \, \chi_{\rm uv}^{1/5.9}$, where $\chi_{\rm uv}$ is in units of the Draine (1978) UV fieldComment: 16 pages, 17 figures, 4 tables. Accepted for publication in A&A. Version 2: the omission of factor 0.921 in equation 4 is correcte

Bench-to-bedside review : targeting antioxidants to mitochondria in sepsis

Peer reviewedPublisher PD

Linking the dust and chemical evolution: Taurus and Perseus -- New collisional rates for HCN, HNC, and their C, N, and H isotopologues

HCN, HNC, and their isotopologues are ubiquitous molecules that can serve as chemical thermometers and evolutionary tracers to characterize star-forming regions. Despite their importance in carrying information that is vital to studies of the chemistry and evolution of star-forming regions, the collision rates of some of these molecules have not been available for rigorous studies in the past. We perform an up-to-date gas and dust chemical characterization of two different star-forming regions, TMC 1-C and NGC 1333-C7, using new collisional rates of HCN, HNC, and their isotopologues. We investigated the possible effects of the environment and stellar feedback in their chemistry and their evolution. With millimeter observations, we derived their column densities, the C and N isotopic fractions, the isomeric ratios, and the deuterium fractionation. The continuum data at 3 mm and 850 $\mu$m allowed us to compute the emissivity spectral index and look for grain growth as an evolutionary tracer. The H$^{13}$CN/HN$^{13}$C ratio is anticorrelated with the deuterium fraction of HCN, thus it can readily serve as a proxy for the temperature. The spectral index $(\beta\sim 1.34-2.09)$ shows a tentative anticorrelation with the H$^{13}$CN/HN$^{13}$C ratio, suggesting grain growth in the evolved, hotter, and less deuterated sources. Unlike TMC 1-C, the south-to-north gradient in dust temperature and spectral index observed in NGC 1333-C7 suggests feedback from the main NGC 1333 cloud. With this up-to-date characterization of two star-forming regions, we found that the chemistry and the physical properties are tightly related. The dust temperature, deuterium fraction, and the spectral index are complementary evolutionary tracers. The large-scale environmental factors may dominate the chemistry and evolution in clustered star-forming regions.Comment: 25 pages, 20 figure

Herschel Observations of Extraordinary Sources: Analysis of the HIFI 1.2 THz Wide Spectral Survey toward Orion KL. I. Methods

We present a comprehensive analysis of a broadband spectral line survey of the Orion Kleinmann-Low nebula (Orion KL), one of the most chemically rich regions in the Galaxy, using the HIFI instrument on board the Herschel Space Observatory. This survey spans a frequency range from 480 to 1907 GHz at a resolution of 1.1 MHz. These observations thus encompass the largest spectral coverage ever obtained toward this high-mass star-forming region in the submillimeter with high spectral resolution and include frequencies >1 THz, where the Earth's atmosphere prevents observations from the ground. In all, we detect emission from 39 molecules (79 isotopologues). Combining this data set with ground-based millimeter spectroscopy obtained with the IRAM 30 m telescope, we model the molecular emission from the millimeter to the far-IR using the XCLASS program, which assumes local thermodynamic equilibrium (LTE). Several molecules are also modeled with the MADEX non-LTE code. Because of the wide frequency coverage, our models are constrained by transitions over an unprecedented range in excitation energy. A reduced χ^2 analysis indicates that models for most species reproduce the observed emission well. In particular, most complex organics are well fit by LTE implying gas densities are high (>10^6 cm^(–3)) and excitation temperatures and column densities are well constrained. Molecular abundances are computed using H_2 column densities also derived from the HIFI survey. The distribution of rotation temperatures, T_(rot), for molecules detected toward the hot core is significantly wider than the compact ridge, plateau, and extended ridge T_(rot) distributions, indicating the hot core has the most complex thermal structure

Capturing the systemic immune signature of a norovirus infection: an n-of-1 case study within a clinical trial.

BACKGROUND: The infection of a participant with norovirus during the adaptive study of interleukin-2 dose on regulatory T cells in type 1 diabetes (DILT1D) allowed a detailed insight into the cellular and cytokine immune responses to this prevalent gastrointestinal pathogen. METHODS: Serial blood, serum and peripheral blood mononuclear cell (PBMC) samples were collected pre-, and post-development of the infection. To differentiate between the immune response to norovirus and to control for the administration of a single dose of aldesleukin (recombinant interleukin-2, rIL-2) alone, samples from five non-infected participants administered similar doses were analysed in parallel. RESULTS: Norovirus infection was self-limited and resolved within 24 hours, with the subsequent development of anti-norovirus antibodies. Serum pro- and anti-inflammatory cytokine levels, including IL-10, peaked during the symptomatic period of infection, coincident with increased frequencies of monocytes and neutrophils. At the same time, the frequency of regulatory CD4 + T cell (Treg), effector T cell (Teff) CD4 + and CD8 + subsets were dynamically reduced, rebounding to baseline levels or above at the next sampling point 24 hours later.  NK cells and NKT cells transiently increased CD69 expression and classical monocytes expressed increased levels of CD40, HLA-DR and SIGLEC-1, biomarkers of an interferon response. We also observed activation and mobilisation of Teffs, where increased frequencies of CD69 + and Ki-67 + effector memory Teffs were followed by the emergence of memory CD8 + Teff expressing the mucosal tissue homing markers CD103 and β7 integrin. Treg responses were coincident with the innate cell, Teff and cytokine response. Key Treg molecules FOXP3, CTLA-4, and CD25 were upregulated following infection, alongside an increase in frequency of Tregs with the capacity to home to tissues. CONCLUSIONS: The results illustrate the innate, adaptive and counter-regulatory immune responses to norovirus infection. Low-dose IL-2 administration induces many of the Treg responses observed during infection