Close-coupling calculations of rotational energy transfer in p-H2+HD

We report quantum-mechanical close-coupling calculations for rotational state resolved cross sections for p-H2+HD collisions. The low temperature limit of p-H2+HD is investigated, which is of significant astrophysical interest in regard to the cooling of primordial gas and the interstellar media. Sharp resonances have been reproduced in the cross sections of some transition states at very low kinetic energies, E< 0.00001 eV.Comment: 10 pages, 6 figure

Coral Reefs, Fisheries, and Food Security: Integrated Approaches to Addressing Multiple Challenges in the Coral Triangle

The Coral Triangle is the most biologically and economically valuable marine ecosystem on the planet. Covering just three percent of the globe, the region represents more than half of the world's reefs and boasts 76 percent of its known coral species. Sustaining more than 130 million people who rely directly on the marine ecosystems for their livelihoods and food, the marine habitats of the Coral Triangle contribute billions of dollars each year toward the economies of the region.Although the environmental imperative for preserving this area of incredible value and biodiversity is obvious, the growing pressures and threats from widespread poverty, rapid development, and global demands continue to place enormous strain on the natural marine resources of the Coral Triangle

On the hierarchical classification of G Protein-Coupled Receptors

Motivation: G protein-coupled receptors (GPCRs) play an important role in many physiological systems by transducing an extracellular signal into an intracellular response. Over 50% of all marketed drugs are targeted towards a GPCR. There is considerable interest in developing an algorithm that could effectively predict the function of a GPCR from its primary sequence. Such an algorithm is useful not only in identifying novel GPCR sequences but in characterizing the interrelationships between known GPCRs. Results: An alignment-free approach to GPCR classification has been developed using techniques drawn from data mining and proteochemometrics. A dataset of over 8000 sequences was constructed to train the algorithm. This represents one of the largest GPCR datasets currently available. A predictive algorithm was developed based upon the simplest reasonable numerical representation of the protein's physicochemical properties. A selective top-down approach was developed, which used a hierarchical classifier to assign sequences to subdivisions within the GPCR hierarchy. The predictive performance of the algorithm was assessed against several standard data mining classifiers and further validated against Support Vector Machine-based GPCR prediction servers. The selective top-down approach achieves significantly higher accuracy than standard data mining methods in almost all cases

SiO line emission from C-type shock waves : interstellar jets and outflows

We study the production of SiO in the gas phase of molecular outflows, through the sputtering of Si--bearing material in refractory grain cores, which are taken to be olivine; we calculate also the rotational line spectrum of the SiO. The sputtering is driven by neutral particle impact on charged grains, in steady--state C-type shock waves, at the speed of ambipolar diffusion. The emission of the SiO molecule is calculated by means of an LVG code. A grid of models has been generated. We compare our results with those of an earlier study (Schilke et al. 1997). Improvements in the treatment of the coupling between the charged grains and the neutral fluid lead to narrower shock waves and lower fractions of Si being released into the gas phase. More realistic assumptions concerning the initial fractional abundance of O2 lead to SiO formation being delayed, so that it occurs in the cool, dense postshock flow. Good agreement is obtained with recent observations of SiO line intensities in the L1157 and L1448 molecular outflows. The inferred temperature, opacity, and SiO column density in the emission region differ significantly from those estimated by means of LVG `slab' models. The fractional abundance of SiO is deduced. Observed line profiles are wider than predicted and imply multiple, unresolved shock regions within the beam.Comment: 1 tex doc, 19 figure

State resolved rotational excitation cross sections and rates in H2+H2 collisions

Rotational transitions in molecular hydrogen collisions are computed. The two most recently developed potential energy surfaces for the H2-H2 system are used from the following works: 1) A.I. Boothroyd, P.G. Martin, W.J. Keogh, M.J. Peterson, J. Chem. Phys., 116 (2002) 666, and 2) P. Diep, J.K. Johnson, J. Chem. Phys., 113 (2000) 3480; ibid. 112, 4465. Cross sections for rotational transitions 00->20, 22, 40, 42, 44 and corresponding rate coefficients are calculated using a quantum-mechanical approach. Results are compared for a wide range of kinetic temperatures 300 K < T < 3000 K.Comment: 9 pages, 3 figures, 3 table

H2_2D+^+ line emission in Proto-Planetary Disks

%Context: {Previous studies have indicated that the 372.4 GHz ground transition of ortho-H$_2$D$^+$ might be a powerful probe of Proto-Planetary Disks. The line could be especially suited for study of the disk mid-plane, where the bulk of the mass resides and where planet formation takes place.} %Aims: {Provide detailed theoretical predictions for the line intensity, profile and maps expected for representative disk models.} %Methods: {We determine the physical and chemical structure of the disks from the model developed by Ceccarelli & Dominik (2005). The line emission is computed with the new radiative transfer method developed recently by Elitzur & Asensio Ramos (2006).} %Results: {We present intensity maps convolved with the expected ALMA resolution, which delineate the origin of the H$_2$D$^+$ 372.4 GHz line. In the disk inner regions, the line probes the conditions in the mid-plane out to radial distances of a few tens of AU, where Solar-like planetary systems might form. In the disk outermost regions, the line originates from slightly above the mid-plane. When the disk is spatially resolved, the variation of line profile across the image provides important information about the velocity field. Spectral profiles of the entire disk flux show a double peak shape at most inclination angles.} %Conclusions: {Our study confirms that the 372.4 GHz H$_2$D$^+$ line provides powerful diagnostics of the mid-plane of Proto-Planetary Disks. Current submillimeter telescopes are capable of observing this line, though with some difficulties. The future ALMA interferometer will have the sensitivity to observe and even spatially resolve the H$_2$D$^+$ line emission.}Comment: To appear in A&

The Ratio of Ortho- to Para-H2 in Photodissociation Regions

We discuss the ratio of ortho- to para-H2 in photodissociation regions (PDRs). We draw attention to an apparent confusion in the literature between the ortho-to-para ratio of molecules in FUV-pumped vibrationally excited states, and the H2 ortho-to-para abundance ratio. These ratios are not the same because the process of FUV-pumping of fluorescent H2 emission in PDRs occurs via optically thick absorption lines. Thus, gas with an equilibrium ratio of ortho- to para-H2 equal to 3 will yield FUV-pumped vibrationally excited ortho-to-para ratios smaller than 3, because the ortho-H2 pumping rates are preferentially reduced by optical depth effects. Indeed, if the ortho and para pumping lines are on the ``square root'' part of the curve-of-growth, then the expected ratio of ortho and para vibrational line strengths is the square root of 3, ~ 1.7, close to the typically observed value. Thus, contrary to what has sometimes been stated in the literature, most previous measurements of the ratio of ortho- to para-H2 in vibrationally excited states are entirely consistent with a total ortho-to-para ratio of 3, the equilibrium value for temperatures greater than 200 K. We present an analysis and several detailed models which illustrate the relationship between the total ratios of ortho- to para-H2 and the vibrationally excited ortho-to-para ratios in PDRs. Recent Infrared Space Observatory (ISO) measurements of pure rotational and vibrational H2 emissions from the PDR in the star-forming region S140 provide strong observational support for our conclusions.Comment: 23 pages (including 5 figures), LaTeX, uses aaspp4.sty, accepted for publication in Ap

On the evolution of the molecular line profiles induced by the propagation of C-shock waves

We present the first results of the expected variations of the molecular line emission arising from material recently affected by C-shocks (shock precursors). Our parametric model of the structure of C-shocks has been coupled with a radiative transfer code to calculate the molecular excitation and line profiles of shock tracers such as SiO, and of ion and neutral molecules such as H13CO+ and HN13C, as the shock propagates through the unperturbed medium. Our results show that the SiO emission arising from the early stage of the magnetic precursor typically has very narrow line profiles slightly shifted in velocity with respect to the ambient cloud. This narrow emission is generated in the region where the bulk of the ion fluid has already slipped to larger velocities in the precursor as observed toward the young L1448-mm outflow. This strongly suggests that the detection of narrow SiO emission and of an ion enhancement in young shocks, is produced by the magnetic precursor of C-shocks. In addition, our model shows that the different velocity components observed toward this outflow can be explained by the coexistence of different shocks at different evolutionary stages, within the same beam of the single-dish observations.Comment: 7 pages, 4 figures, accepted for publication in Ap