Sulfur chemistry: 1D modeling in massive dense cores

The main sulfur-bearing molecules OCS, H2S, SO, SO2, and CS have been observed in four high mass dense cores (W43-MM1, IRAS 18264, IRAS 05358, and IRAS 18162). Our goal is to put some constraints on the relative evolutionary stage of these sources by comparing these observations with time-dependent chemical modeling. We used the chemical model Nahoon, which computes the gas-phase chemistry and gas-grain interactions of depletion and evaporation. Mixing of the different chemical compositions shells in a 1D structure through protostellar envelope has been included since observed lines suggest nonthermal supersonic broadening. Observed radial profiles of the temperature and density are used to compute the chemistry as a function of time. With our model, we underproduce CS by several orders of magnitude compared to the other S-bearing molecules, which seems to contradict observations, although some uncertainties in the CS abundance observed at high temperature remain. The OCS/SO2, SO/SO2, and H2S/SO2 abundance ratios could in theory be used to trace the age of these massive protostars since they show a strong dependence with time, but the sources are too close in age compared to the accuracy of chemical models and observations. Our comparison between observations and modeling may, however, indicate that W43-MM1 could be chemically younger than the three other sources. Turbulent diffusivity through the protostellar envelopes has to be less efficient than 2e14 cm2s-1. Otherwise, it would have smoothed out the abundance profiles, and this would have been observed. The sulfur chemistry depends strongly on the 1D physical conditions. In our case, no conclusion can be given on the relative age of IRAS 18264, IRAS 18162 and IRAS 05358 except that they are very close. W43-MM1 seems younger than the other sources.Comment: Accepted for publication to A&

Chemical sensitivity to the ratio of the cosmic-ray ionization rates of He and H2 in dense clouds

Aim: To determine whether or not gas-phase chemical models with homogeneous and time-independent physical conditions explain the many observed molecular abundances in astrophysical sources, it is crucial to estimate the uncertainties in the calculated abundances and compare them with the observed abundances and their uncertainties. Non linear amplification of the error and bifurcation may limit the applicability of chemical models. Here we study such effects on dense cloud chemistry. Method: Using a previously studied approach to uncertainties based on the representation of rate coefficient errors as log normal distributions, we attempted to apply our approach using as input a variety of different elemental abundances from those studied previously. In this approach, all rate coefficients are varied randomly within their log normal (Gaussian) distribution, and the time-dependent chemistry calculated anew many times so as to obtain good statistics for the uncertainties in the calculated abundances. Results: Starting with so-called ``high-metal'' elemental abundances, we found bimodal rather than Gaussian like distributions for the abundances of many species and traced these strange distributions to an extreme sensitivity of the system to changes in the ratio of the cosmic ray ionization rate zeta\_He for He and that for molecular hydrogen zeta\_H2. The sensitivity can be so extreme as to cause a region of bistability, which was subsequently found to be more extensive for another choice of elemental abundances. To the best of our knowledge, the bistable solutions found in this way are the same as found previously by other authors, but it is best to think of the ratio zeta\_He/zeta\_H2 as a control parameter perpendicular to the ''standard'' control parameter zeta/n\_H.Comment: Accepted for publicatio

Sensitivity analyses of dense cloud chemical models

Because of new telescopes that will dramatically improve our knowledge of the interstellar medium, chemical models will have to be used to simulate the chemistry of many regions with diverse properties. To make these models more robust, it is important to understand their sensitivity to a variety of parameters. In this article, we report a study of the sensitivity of a chemical model of a cold dense core, with homogeneous and time-independent physical conditions, to variations in the following parameters: initial chemical inventory, gas temperature and density, cosmic-ray ionization rate, chemical reaction rate coefficients, and elemental abundances. From the results of the parameter variations, we can quantify the sensitivity of the model to each parameter as a function of time. Our results can be used in principle with observations to constrain some parameters for different cold clouds. We also attempted to use the Monte Carlo approach with all parameters varied collectively. Within the parameter ranges studied, the most critical parameters turn out to be the reaction rate coefficients at times up to 4e5 yr and elemental abundances at later times. At typical times of best agreement with observation, models are sensitive to both of these parameters. The models are less sensitive to other parameters such as the gas density and temperature. The improvement of models will require that the uncertainties in rate coefficients of important reactions be reduced. As the chemistry becomes better understood and more robust, it should be possible to use model sensitivities concerning other parameters, such as the elemental abundances and the cosmic ray ionization rate, to yield detailed information on cloud properties and history. Nevertheless, at the current stage, we cannot determine the best values of all the parameters simultaneously based on purely observational constraints.Comment: Accepted for publication in Astronomy & Astrophysic

Reactions forming C(0,+)n=2,10, Cn=2,4H(0,+) and C3H(0,+) in the gas phase: semi empirical branching ratios

The aim of this paper is to provide a new set of branching ratios for interstellar and planetary chemical networks based on a semi empirical model. We applied, instead of zero order theory (i.e. only the most exoergic decaying channel is considered), a statistical microcanonical model based on the construction of breakdown curves and using experimental high velocity collision branching ratios for their parametriza- tion. We applied the model to ion-molecule, neutral-neutral, and ion-pair reactions implemented in the few popular databases for astrochemistry such as KIDA, OSU and UMIST. We studied the reactions of carbon and hydrocarbon species with electrons, He+, H+, CH+, CH, C, and C+ leading to intermediate complexes of the type Cn=2,10, Cn=2,4 H, C3 H2, C+n=2,10, Cn=2,4 H+, or C3 H+2 . Comparison of predictions with measurements supports the validity of the model. Huge deviations with respect to database values are often obtained. Effects of the new branching ratios in time dependant chemistry for dark clouds and for photodissociation region chemistry with conditions similar to those found in the Horsehead Nebula are discussed

Modulation of triglyceride and cholesterol ester synthesis impairs assembly of infectious hepatitis C virus

In hepatitis C virus infection, replication of the viral genome and virion assembly are linked to cellular metabolic processes. In particular, lipid droplets, which store principally triacylglycerides (TAGs) and cholesterol esters (CEs), have been implicated in production of infectious virus. Here, we examine the effect on productive infection of triacsin C and YIC-C8-434, which inhibit synthesis of TAGs and CEs by targeting long-chain acyl-CoA synthetase and acyl-CoA:cholesterol acyltransferase, respectively. Our results present high resolution data on the acylglycerol and cholesterol ester species that were affected by the compounds. Moreover, triacsin C, which blocks both triglyceride and cholesterol ester synthesis, cleared most of the lipid droplets in cells. By contrast, YIC-C8-434, which only abrogates production of cholesterol esters, induced an increase in size of droplets. Although both compounds slightly reduced viral RNA synthesis, they significantly impaired assembly of infectious virions in infected cells. In the case of triacsin C, reduced stability of the viral core protein, which forms the virion nucleocapsid and is targeted to the surface of lipid droplets, correlated with lower virion assembly. In addition, the virus particles that were released from cells had reduced specific infectivity. YIC-C8-434 did not alter the association of core with lipid droplets but appeared to decrease production of infectious virus particles, suggesting a block in virion assembly. Thus, the compounds have antiviral properties, indicating that targeting synthesis of lipids stored in lipid droplets might be an option for therapeutic intervention in treating chronic hepatitis C virus infection

Sensitive survey for 13CO, CN, H2CO, and SO in the disks of T Tauri and Herbig Ae stars II: Stars in ρ\rho Oph and upper Scorpius

We attempt to determine the molecular composition of disks around young low-mass stars in the $\rho$ Oph region and to compare our results with a similar study performed in the Taurus-Auriga region. We used the IRAM 30 m telescope to perform a sensitive search for CN N=2-1 in 29 T Tauri stars located in the $\rho$ Oph and upper Scorpius regions. $^{13}$CO J=2-1 is observed simultaneously to provide an indication of the level of confusion with the surrounding molecular cloud. The bandpass also contains two transitions of ortho-H$_2$CO, one of SO, and the C$^{17}$O J=2-1 line, which provides complementary information on the nature of the emission. Contamination by molecular cloud in $^{13}$CO and even C$^{17}$O is ubiquitous. The CN detection rate appears to be lower than for the Taurus region, with only four sources being detected (three are attributable to disks). H$_2$CO emission is found more frequently, but appears in general to be due to the surrounding cloud. The weaker emission than in Taurus may suggest that the average disk size in the $\rho$ Oph region is smaller than in the Taurus cloud. Chemical modeling shows that the somewhat higher expected disk temperatures in $\rho$ Oph play a direct role in decreasing the CN abundance. Warmer dust temperatures contribute to convert CN into less volatile forms. In such a young region, CN is no longer a simple, sensitive tracer of disks, and observations with other tracers and at high enough resolution with ALMA are required to probe the gas disk population.Comment: 18 pages, 5 figures, accepted for publication in A&

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&

A sensitivity study of the neutral-neutral reactions C + C3 and C + C5 in cold dense interstellar clouds

Chemical networks used for models of interstellar clouds contain many reactions, some of them with poorly determined rate coefficients and/or products. In this work, we report a method for improving the predictions of molecular abundances using sensitivity methods and ab initio calculations. Based on the chemical network osu.2003, we used two different sensitivity methods to determine the most important reactions as a function of time for models of dense cold clouds. Of these reactions, we concentrated on those between C and C3 and between C and C5, both for their effect on specific important species such as CO and for their general effect on large numbers of species. We then used ab initio and kinetic methods to determine an improved rate coefficient for the former reaction and a new set of products, plus a slightly changed rate coefficient for the latter. Putting our new results in a pseudo-time-dependent model of cold dense clouds, we found that the abundances of many species are altered at early times, based on large changes in the abundances of CO and atomic C. We compared the effect of these new rate coefficients/products on the comparison with observed abundances and found that they shift the best agreement from 3e4 yr to (1-3)e5 yr

CID: Chemistry In Disks VII. First detection of HC3N in protoplanetary disks

Molecular line emission from protoplanetary disks is a powerful tool to constrain their physical and chemical structure. Nevertheless, only a few molecules have been detected in disks so far. We take advantage of the enhanced capabilities of the IRAM 30m telescope by using the new broad band correlator (FTS) to search for so far undetected molecules in the protoplanetary disks surrounding the TTauri stars DM Tau, GO Tau, LkCa 15 and the Herbig Ae star MWC 480. We report the first detection of HC3N at 5 sigma in the GO Tau and MWC 480 disks with the IRAM 30-m, and in the LkCa 15 disk (5 sigma), using the IRAM array, with derived column densities of the order of 10^{12}cm^{-2}. We also obtain stringent upper limits on CCS (N < 1.5 x 10^{12} cm^{-3}). We discuss the observational results by comparing them to column densities derived from existing chemical disk models (computed using the chemical code Nautilus) and based on previous nitrogen and sulfur-bearing molecule observations. The observed column densities of HC3N are typically two orders of magnitude lower than the existing predictions and appear to be lower in the presence of strong UV flux, suggesting that the molecular chemistry is sensitive to the UV penetration through the disk. The CCS upper limits reinforce our model with low elemental abundance of sulfur derived from other sulfur-bearing molecules (CS, H2S and SO).Comment: 8 pages, 4 figures, 3 tables, Accepted for publication in Ap

Molecular Cloud Chemistry and The Importance of Dielectronic Recombination

Dielectronic recombination (DR) of singly charged ions is a reaction pathway that is commonly neglected in chemical models of molecular clouds. In this study we include state-of-the-art DR data for He+, C+, N+, O+, Na+, and Mg+ in chemical models used to simulate dense molecular clouds, protostars, and diffuse molecular clouds. We also update the radiative recombination (RR) rate coefficients for H+, He+, C+, N+, O+, Na+, and Mg+ to the current state-of-the-art values. The new RR data have little effect on the models. However, the inclusion of DR results in significant differences in gas-grain models of dense, cold molecular clouds for the evolution of a number of surface and gas-phase species. We find differences of a factor of 2 in the abundance for 74 of the 655 species at times of 104-106 yr in this model when we include DR. Of these 74 species, 16 have at least a factor of 10 difference in abundance. We find the largest differences for species formed on the surface of dust grains. These differences are due primarily to the addition of C+ DR, which increases the neutral C abundance, thereby enhancing the accretion of C onto dust. These results may be important for the warm-up phase of molecular clouds when surface species are desorbed into the gas phase. We also note that no reliable state-of-the-art RR or DR data exist for Si+, P+, S+, Cl+, and Fe+. Modern calculations for these ions are needed to better constrain molecular cloud models