Refit to numerically problematic UMIST reaction rate coefficients

Aims. Chemical databases such as the UMIST Database for Astrochemistry (UDFA) are indispensable in the numerical modeling of astrochemical networks. Several of the listed reactions in the UDFA have properties that are problematic in numerical computations: Some are parametrized in a way that leads to extremely divergent behavior for low kinetic temperatures. Other reactions possess multiple entries that are each valid in a different temperature regime, but have no smooth transition when switching from one to another. Numerically, this introduces many difficulties.We present corrected parametrizations for these sets of reactions in the UDFA06 database. Methods. From the tabulated parametrization in UDFA, we created artificial data points and used a Levenberg-Marquardt algorithm to find a set of improved fit parameters without divergent behavior for low temperatures. For reactions with multiple entries in the database that each possess a different temperature regime, we present one joint parametrization that is designed to be valid over the whole cumulative temperature range of all individual reactions. Results. We show that it is possible to parametrize numerically problematic reactions from UDFA in a form that avoids low temperature divergence. Additionally, we demonstrate that it is possible to give a collective parametrization for reaction rate coefficients of reactions with multiple entries in UDFA. We present these new fitted values in tabulated form.Comment: accepted by A&

Carbon Fractionation in PDRs

We upgraded the chemical network from the UMIST Database for Astrochemistry 2006 to include isotopes such as ^{13}C and ^{18}O. This includes all corresponding isotopologues, their chemical reactions and the properly scaled reaction rate coefficients. We study the fractionation behavior of astrochemically relevant species over a wide range of model parameters, relevant for modelling of photo-dissociation regions (PDRs). We separately analyze the fractionation of the local abundances, fractionation of the total column densities, and fractionation visible in the emission line ratios. We find that strong C^+ fractionation is possible in cool C^+ gas. Optical thickness as well as excitation effects produce intensity ratios between 40 and 400. The fractionation of CO in PDRs is significantly different from the diffuse interstellar medium. PDR model results never show a fractionation ratio of the CO column density larger than the elemental ratio. Isotope-selective photo-dissociation is always dominated by the isotope-selective chemistry in dense PDR gas. The fractionation of C, CH, CH^+, and HCO^+ is studied in detail, showing that the fractionation of C, CH and CH^+ is dominated by the fractionation of their parental species. The light hydrides chemically derive from C^+, and, consequently, their fractionation state is coupled to that of C^+. The fractionation of C is a mixed case depending on whether formation from CO or HCO^+ dominates. Ratios of the emission lines of [C II], [C I], ^{13}CO, and H^{13}CO^+ provide individual diagnostics to the fractionation status of C^+, C, and CO.Comment: to be published in A&

Metallicity Effects in PDRs

Almost all properties of a photodissociation region (PDR) depend on its metallicity. The heating and cooling efficiencies that determine the temperature of the gas and dust, the dust composition, as well as the elemental abundances that influence the chemical structure of the PDR are just three examples that demonstrate the importance of metallicity effects in PDRs. PDRs are often associated with sites of star formation. If we want to understand the star formation history of our own Galaxy and of distant low-metallicity objects we need to understanding how metallicity acts on PDR physics and chemistry.Comment: 7 pages, 5 figures, to appear in proceedings of "Far-Infrared and Submillimeter Emission of the Interstellar Medium", EAS Publication Series, Bad Honnef, November 2007, Eds. C. Kramer, S. Aalto, R. Simo

Modelling clumpy PDRs in 3D - Understanding the Orion Bar stratification

Context. Models of photon-dominated regions (PDRs) still fail to fully reproduce some of the observed properties, in particular the combination of the intensities of different PDR cooling lines together with the chemical stratification, as observed e.g. for the Orion Bar PDR. Aims. We aim to construct a numerical PDR model, KOSMA-\tau 3D, to simulate full spectral cubes of line emission from arbitrary PDRs in three dimensions (3D). The model is to reproduce the intensity of the main cooling lines from the Orion Bar PDR and the observed layered structure of the different transitions. Methods. We build up a 3D compound, made of voxels ("3D pixels") that contain a discrete mass distribution of spherical "clumpy" structures, approximating the fractal ISM. To analyse each individual clump the new code is combined with the KOSMA-\tau PDR model. Probabilistic algorithms are used to calculate the local FUV flux for each voxel as well as the voxel-averaged line emissivities and optical depths, based on the properties of the individual clumps. Finally, the computation of the radiative transfer through the compound provides full spectral cubes. To test the new model we try to simulate the structure of the Orion Bar PDR and compare the results to observations from HIFI/Herschel and from the Caltech Submillimetre Observatory (CSO). In this context new Herschel data from the HEXOS guaranteed-time key program is presented. Results. Our model is able to reproduce the line integrated intensities within a factor 2.5 and the observed stratification pattern within 0.016 pc for the [Cii] 158 \mu m and different 12/13 CO and HCO+ transitions, based on the representation of the Orion Bar PDR by a clumpy edge-on cavity wall. In the cavity wall, a large fraction of the total mass needs to be contained in clumps. The mass of the interclump medium is constrained by the FUV penetration. Furthermore, ...Comment: Major changes compared to v1. Also several references have been adde

Modeling and Analysis Generic Interface for eXternal numerical codes (MAGIX)

The modeling and analysis generic interface for external numerical codes (MAGIX) is a model optimizer developed under the framework of the coherent set of astrophysical tools for spectroscopy (CATS) project. The MAGIX package provides a framework of an easy interface between existing codes and an iterating engine that attempts to minimize deviations of the model results from available observational data, constraining the values of the model parameters and providing corresponding error estimates. Many models (and, in principle, not only astrophysical models) can be plugged into MAGIX to explore their parameter space and find the set of parameter values that best fits observational/experimental data. MAGIX complies with the data structures and reduction tools of ALMA (Atacama Large Millimeter Array), but can be used with other astronomical and with non-astronomical data.Comment: 12 pages, 15 figures, 2 tables, paper is also available at http://www.aanda.org/articles/aa/pdf/forth/aa20063-12.pd

Study of Photon Dominated Regions in Cepheus B

Aim: The aim of the paper is to understand the emission from the photon dominated regions in Cepheus B, estimate the column densities of neutral carbon in bulk of the gas in Cepheus B and to derive constraints on the factors which determine the abundance of neutral carbon relative to CO. Methods: This paper presents 15'x15' fully sampled maps of CI at 492 GHz and 12CO 4-3 observed with KOSMA at 1' resolution. The new observations have been combined with the FCRAO 12CO 1-0, IRAM-30m 13CO 2-1 and C18O 1-0 data, and far-infrared continuum data from HIRES/IRAS. The KOSMA-tau spherical PDR model has been used to understand the CI and CO emission from the PDRs in Cepheus B and to explain the observed variation of the relative abundances of both C^0 and CO. Results: The emission from the PDR associated with Cepheus B is primarily at V_LSR between -14 and -11 km s^-1. We estimate about 23% of the observed CII emission from the molecular hotspot is due to the ionized gas in the HII region. Over bulk of the material the C^0 column density does not change significantly, (2.0+-1.4)x10^17 cm^-2, although the CO column density changes by an order of magnitude. The observed \cbyco abundance ratio varies between 0.06 and 4 in Cepheus B. We find an anti-correlation of the observed C/CO abundance ratio with the observed hydrogen column density, which holds even when all previous observations providing C/CO ratios are included. Here we show that this observed variation of C/CO abundance with total column density can be explained only by clumpy PDRs consisting of an ensemble of clumps. At high H2 column densities high mass clumps, which exhibit low C/CO abundance, dominate, while at low column densities, low mass clumps with high C/CO abundance dominate.Comment: 12 pages, 10 figures, Accepted for publication in A&

Diagnostics of the Molecular Component of PDRs with Mechanical Heating

Context. Multitransition CO observations of galaxy centers have revealed that significant fractions of the dense circumnuclear gas have high kinetic temperatures, which are hard to explain by pure photon excitation, but may be caused by dissipation of turbulent energy. Aims. We aim to determine to what extent mechanical heating should be taken into account while modelling PDRs. To this end, the effect of dissipated turbulence on the thermal and chemical properties of PDRs is explored. Methods. Clouds are modelled as 1D semi-infinite slabs whose thermal and chemical equilibrium is solved for using the Leiden PDR-XDR code. Results. In a steady-state treatment, mechanical heating seems to play an important role in determining the kinetic temperature of the gas in molecular clouds. Particularly in high-energy environments such as starburst galaxies and galaxy centers, model gas temperatures are underestimated by at least a factor of two if mechanical heating is ignored. The models also show that CO, HCN and H2 O column densities increase as a function of mechanical heating. The HNC/HCN integrated column density ratio shows a decrease by a factor of at least two in high density regions with n \sim 105 cm-3, whereas that of HCN/HCO+ shows a strong dependence on mechanical heating for this same density range, with boosts of up to three orders of magnitude. Conclusions. The effects of mechanical heating cannot be ignored in studies of the molecular gas excitation whenever the ratio of the star formation rate to the gas density is close to, or exceeds, 7 \times 10-6 M yr-1 cm4.5 . If mechanical heating is not included, predicted column densities are underestimated, sometimes even by a few orders of magnitude. As a lower bound to its importance, we determined that it has non-negligible effects already when mechanical heating is as little as 1% of the UV heating in a PDR.Comment: 26 pages, 14 figures in the text and 13 figures as supplementary material. Accepted for publication in A&

The Photon Dominated Region in the IC 348 molecular cloud

In this paper we discuss the physical conditions of clumpy nature in the IC 348 molecular cloud. We combine new observations of fully sampled maps in [C I] at 492 GHz and 12CO 4--3, taken with the KOSMA 3 m telescope at about 1' resolution, with FCRAO data of 12CO 1--0, 13CO 1--0 and far-infrared continuum data observed by HIRES/IRAS. To derive the physical parameters of the region we analyze the three different line ratios. A first rough estimate of abundance is obtained from an LTE analysis. To understand the [C I] and CO emission from the PDRs in IC 348, we use a clumpy PDR model. With an ensemble of identical clumps, we constrain the total mass from the observed absolute intensities. Then we apply a more realistic clump distribution model with a power law index of 1.8 for clump-mass spectrum and a power law index of 2.3 for mass-size relation. We provide detailed fits to observations at seven representative positions in the cloud, revealing clump densities between 4 10$^{4}$ cm$^{-3}$ and 4 10$^{5}$ cm$^{-3}$ and C/CO column density ratios between 0.02 and 0.26. The derived FUV flux from the model fit is consistent with the field calculated from FIR continuum data, varying between 2 and 100 Draine units across the cloud. We find that both an ensemble of identical clumps and an ensemble with a power law clump mass distribution produce line intensities which are in good agreement (within a factor ~ 2) with the observed intensities. The models confirm the anti-correlation between the C/CO abundance ratio and the hydrogen column density found in many regions.Comment: 11 pages, 8 figures, accepted by A&

A clumpy-cloud PDR model of the global far-infrared line emission of the Milky Way

The fractal structure of the interstellar medium suggests that the interaction of UV radiation with the ISM as described in the context of photon-dominated regions (PDR) dominates most of the physical and chemical conditions, and hence the far-infrared and submm emission from the ISM in the Milky Way. We investigate to what extent the Galactic FIR line emission of the important species CO, C, C+, and O, as observed by the Cosmic Background Explorer (COBE) satellite can be modeled in the framework of a clumpy, UV-penetrated cloud scenario. The far-infrared line emission of the Milky Way is modeled as the emission from an ensemble of clumps with a power law clump mass spectrum and mass-size relation with power-law indices consistent with the observed ISM structure. The individual clump line intensities are calculated using the KOSMA-tau PDR-model for spherical clumps. The model parameters for the cylindrically symmetric Galactic distribution of the mass density and volume filling factor are determined by the observed radial distributions. A constant FUV intensity, in which the clumps are embedded, is assumed. We show that this scenario can explain, without any further assumptions and within a factor of about 2, the absolute FIR-line intensities and their distribution with Galactic longitude as observed by COBE.Comment: 14 pages, 13 figures, accepted by A&A at the 7th of July, 200

Photon Dominated Regions in NGC 3603

Aims: We aim at deriving the excitation conditions of the interstellar gas as well as the local FUV intensities in the molecular cloud surrounding NGC 3603 to get a coherent picture of how the gas is energized by the central stars. Methods: The NANTEN2-4m submillimeter antenna is used to map the [CI] 1-0, 2-1 and CO 4-3, 7-6 lines in a 2' x 2' region around the young OB cluster NGC 3603 YC. These data are combined with C18O 2-1 data, HIRES-processed IRAS 60 and 100 micron maps of the FIR continuum, and Spitzer/IRAC maps. Results: The NANTEN2 observations show the presence of two molecular clumps located south-east and south-west of the cluster and confirm the overall structure already found by previous CS and C18O observations. We find a slight position offset of the peak intensity of CO and [CI], and the atomic carbon appears to be further extended compared to the molecular material. We used the HIRES far-infrared dust data to derive a map of the FUV field heating the dust. We constrain the FUV field to values of \chi = 3 - 6 \times 10^3 in units of the Draine field across the clouds. Approximately 0.2 to 0.3 % of the total FUV energy is re-emitted in the [CII] 158 {\mu}m cooling line observed by ISO. Applying LTE and escape probability calculations, we derive temperatures (TMM1 = 43 K, TMM2 = 47 K), column densities (N(MM1) = 0.9 \times 10^22 cm^-2, N(MM2) = 2.5 \times 10^22 cm^-2) and densities (n(MM1) = 3 \times 10^3 cm^-3, n(MM2) = 10^3 -10^4 cm^-3) for the two observed molecular clumps MM1 and MM2. Conclusions: The cluster is strongly interacting with the ambient molecular cloud, governing its structure and physical conditions. A stability analysis shows the existence of gravitationally collapsing gas clumps which should lead to star formation. Embedded IR sources have already been observed in the outskirts of the molecular cloud and seem to support our conclusions.Comment: 13 pages, 10 figures, accepted for publication by A&