Herschel observations in the ultracompact HII region Mon R2: Water in dense photon-dominated regions (PDRs)

Context. Monoceros R2, at a distance of 830 pc, is the only ultracompact Hii region (UC H_(II)) where the photon-dominated region (PDR) between the ionized gas and the molecular cloud can be resolved with Herschel. Therefore, it is an excellent laboratory to study the chemistry in extreme PDRs (G_0 > 10^5 in units of Habing field, n > 10^6 cm^9−3)). Aims. Our ultimate goal is to probe the physical and chemical conditions in the PDR around the UC H_(II) Mon R2. Methods. HIFI observations of the abundant compounds ^(13)CO, C^(18)O, o-H_2^(18)O, HCO^+, CS, CH, and NH have been used to derive the physical and chemical conditions in the PDR, in particular the water abundance. The modeling of the lines has been done with the Meudon PDR code and the non-local radiative transfer model described by Cernicharo et al. Results. The ^(13)CO, C^(18)O, o-H^(18)_2O, HCO^+ and CS observations are well described assuming that the emission is coming from a dense (n = 5 × 10^6 cm^(−3), N(H_2) > 10^(22) cm^(−2)) layer of molecular gas around the H_(II) region. Based on our o-H^(18)_2O observations, we estimate an o-H_2O abundance of ≈2 × 10^(−8). This is the average ortho-water abundance in the PDR. Additional H^(18)_2O and/or water lines are required to derive the water abundance profile. A lower density envelope (n ~ 10^5 cm^(−3), N(H_2) = 2−5 × 10^(22) 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 ^(13)CO and HCO^+ line profiles are consistent with an expansion of the molecular gas with a velocity law, v_e = 0.5 × (r/R_(out))^(−1) km s^(−1), although the expansion velocity is poorly constrained by the observations presented here. Conclusions. We determine an ortho-water abundance of ≈2 × 10^(−8) in Mon R2. Because shocks are unimportant in this region and our estimate is based on H^(18)_2O observations that avoids opacity problems, this is probably the most accurate estimate of the water abundance in PDRs thus far

Detection of CO+ in the nucleus of M82

We present the detection of the reactive ion CO+ towards the prototypical starburst galaxy M82. This is the first secure detection of this short-lived ion in an external galaxy. Values of [CO+]/[HCO+]>0.04 are measured across the inner 650pc of the nuclear disk of M82. Such high values of the [CO+]/[HCO+] ratio had only been previously measured towards the atomic peak in the reflection nebula NGC7023. This detection corroborates that the molecular gas reservoir in the M82 disk is heavily affected by the UV radiation from the recently formed stars. Comparing the column densities measured in M82 with those found in prototypical Galactic photon-dominated regions (PDRs), we need \~20 clouds along the line of sight to explain our observations. We have completed our model of the molecular gas chemistry in the M82 nucleus. Our PDR chemical model successfully explains the [CO+]/[HCO+] ratios measured in the M~82 nucleus but fails by one order of magnitude to explain the large measured CO+ column densities (~1--4x10^{13} cm^{-2}). We explore possible routes to reconcile the chemical model and the observations.Comment: 12 pages, 2 figure

Protostellar clusters in intermediate-mass (IM) star forming regions

The transition between the low density groups of T Tauri stars and the high density clusters around massive stars occurs in the intermediate-mass (IM) range (M$_*$$\sim$2--8 M$_\odot$). High spatial resolution studies of IM young stellar objects (YSO) can provide important clues to understand the clustering in massive star forming regions. Aims: Our aim is to search for clustering in IM Class 0 protostars. The high spatial resolution and sensitivity provided by the new A configuration of the Plateau de Bure Interferometer (PdBI) allow us to study the clustering in these nearby objects. Methods: We have imaged three IM Class 0 protostars (Serpens-FIRS 1, IC 1396 N, CB 3) in the continuum at 3.3 and 1.3mm using the PdBI. The sources have been selected with different luminosity to investigate the dependence of the clustering process on the luminosity of the source. Results: Only one millimeter (mm) source is detected towards the low luminosity source Serpens--FIRS 1. Towards CB 3 and IC1396 N, we detect two compact sources separated by $\sim$0.05 pc. The 1.3mm image of IC 1396 N, which provides the highest spatial resolution, reveal that one of these cores is splitted in, at least, three individual sources.Comment: 4 pages, 3 figures, accepted for publication in Astronomy and Astrophysics Letters (Special Feature IRAM/PdB

Automation on the generation of genome scale metabolic models

Background: Nowadays, the reconstruction of genome scale metabolic models is a non-automatized and interactive process based on decision taking. This lengthy process usually requires a full year of one person's work in order to satisfactory collect, analyze and validate the list of all metabolic reactions present in a specific organism. In order to write this list, one manually has to go through a huge amount of genomic, metabolomic and physiological information. Currently, there is no optimal algorithm that allows one to automatically go through all this information and generate the models taking into account probabilistic criteria of unicity and completeness that a biologist would consider. Results: This work presents the automation of a methodology for the reconstruction of genome scale metabolic models for any organism. The methodology that follows is the automatized version of the steps implemented manually for the reconstruction of the genome scale metabolic model of a photosynthetic organism, {\it Synechocystis sp. PCC6803}. The steps for the reconstruction are implemented in a computational platform (COPABI) that generates the models from the probabilistic algorithms that have been developed. Conclusions: For validation of the developed algorithm robustness, the metabolic models of several organisms generated by the platform have been studied together with published models that have been manually curated. Network properties of the models like connectivity and average shortest mean path of the different models have been compared and analyzed.Comment: 24 pages, 2 figures, 2 table

ISO observations toward the reflection nebula NGC 7023: A nonequilibrium ortho- to para-H2 ratio

We have observed the S(0), S(1), S(2), S(3), S(4) and S(5) rotational lines of molecular hydrogen (H2) towards the peak of the photodissociation region (PDR) associated with the reflection nebula NGC 7023. The observed H2 line ratios show that they arise in warm gas with kinetic temperatures ~300 - 700 K. However, the data cannot be fitted by an ortho- to para- (OTP) ratio of 3. An OTP ratio in the range ~1.5 - 2 is necessary to explain our observations. This is the first detection of a non-equilibrium OTP ratio measured from the H2 pure-rotational lines in a PDR. The existence of a dynamical PDR is discussed as the most likely explanation for this low OTP ratio.Comment: 4 pages, 3 figure

The IC1396N proto-cluster at a scale of 250 AU

We investigate the mm-morphology of IC1396N with unprecedented spatial resolution to analyze its dust and molecular gas properties, and draw comparisons with objects of similar mass. We have carried out sensitive observations in the most extended configurations of the IRAM Plateau de Bure interferometer, to map the thermal dust emission at 3.3 and 1.3mm, and the emission from the $J$=13$_k\to12_k$ hyperfine transitions of methyl cyanide (CH$_3$CN). We unveil the existence of a sub-cluster of hot cores in IC1396N, distributed in a direction perpendicular to the emanating outflow. The cores are embedded in a common envelope of extended and diffuse dust emission. We find striking differences in the dust properties of the cores ($\beta\simeq$ 0) and the surrounding envelope ($\beta\simeq$ 1), very likely testifying to differences in the formation and processing of dust material. The CH$_3$CN emission peaks towards the most massive hot core and is marginally extended in the outflow direction

Physical structure of the photodissociation regions in NGC 7023: Observations of gas and dust emission with <i>Herschel</i>

The determination of the physical conditions in molecular clouds is a key step towards our understanding of their formation and evolution of associated star formation. We investigate the density, temperature, and column density of both dust and gas in the photodissociation regions (PDRs) located at the interface between the atomic and cold molecular gas of the NGC 7023 reflection nebula. We study how young stars affect the gas and dust in their environment. Our approach combining both dust and gas delivers strong constraints on the physical conditions of the PDRs. We find dense and warm molecular gas of high column density in the PDRs