Collisions of electrons with interstellar grains

We have computed cross-sections for elastic and inelastic scattering of electrons on small grains at low-collision energies. Significant differences are again found between the results obtained in the presence and the absence of a ‘permanent’ grain dipole moment. In addition to spherical grains, scattering on ellipsoidal grains is investigated. We conclude that the rate of electron attachment to interstellar grains may be substantially lower in regions of molecular clouds from which the radiation field is excluded, and where the grains are less likely to possess a dipole moment

Shocks in dense clouds. IV. Effects of grain-grain processing on molecular line emission

Grain-grain processing has been shown to be an indispensable ingredient of shock modelling in high density environments. For densities higher than \sim10^5 cm-3, shattering becomes a self-enhanced process that imposes severe chemical and dynamical consequences on the shock characteristics. Shattering is accompanied by the vaporization of grains, which can directly release SiO to the gas phase. Given that SiO rotational line radiation is used as a major tracer of shocks in dense clouds, it is crucial to understand the influence of vaporization on SiO line emission. We have developed a recipe for implementing the effects of shattering and vaporization into a 2-fluid shock model, resulting in a reduction of computation time by a factor \sim100 compared to a multi-fluid modelling approach. This implementation was combined with an LVG-based modelling of molecular line radiation transport. Using this model we calculated grids of shock models to explore the consequences of different dust-processing scenarios. Grain-grain processing is shown to have a strong influence on C-type shocks for a broad range of magnetic fields: they become hotter and thinner. The reduction in column density of shocked gas lowers the intensity of molecular lines, at the same time as higher peak temperatures increase the intensity of highly excited transitions compared to shocks without grain-grain processing. For OH the net effect is an increase in line intensities, while for CO and H2O it is the contrary. The intensity of H2 emission is decreased in low transitions and increased for highly excited lines. For all molecules, the highly excited lines become sensitive to the value of the magnetic field. Although vaporization increases the intensity of SiO rotational lines, this effect is weakened by the reduced shock width. The release of SiO early in the hot shock changes the excitation characteristics of SiO radiation.Comment: Published in Astronomy and Astrophysics (2013). 26 pages, 16 figures, 14 table

Multifluid, Magnetohydrodynamic Shock Waves with Grain Dynamics II. Dust and the Critical Speed for C Shocks

This is the second in a series of papers on the effects of dust on multifluid, MHD shock waves in weakly ionized molecular gas. We investigate the influence of dust on the critical shock speed, v_crit, above which C shocks cease to exist. Chernoff showed that v_crit cannot exceed the grain magnetosound speed, v_gms, if dust grains are dynamically well coupled to the magnetic field. We present numerical simulations of steady shocks where the grains may be well- or poorly coupled to the field. We use a time-dependent, multifluid MHD code that models the plasma as a system of interacting fluids: neutral particles, ions, electrons, and various ``dust fluids'' comprised of grains with different sizes and charges. Our simulations include grain inertia and grain charge fluctuations but to highlight the essential physics we assume adiabatic flow, single-size grains, and neglect the effects of chemistry. We show that the existence of a phase speed v_phi does not necessarily mean that C shocks will form for all shock speeds v_s less than v_phi. When the grains are weakly coupled to the field, steady, adiabatic shocks resemble shocks with no dust: the transition to J type flow occurs at v_crit = 2.76 v_nA, where v_nA is the neutral Alfven speed, and steady shocks with v_s > 2.76 v_nA are J shocks with magnetic precursors in the ion-electron fluid. When the grains are strongly coupled to the field, v_crit = min(2.76 v_nA, v_gms). Shocks with v_crit < v_s < v_gms have magnetic precursors in the ion-electron-dust fluid. Shocks with v_s > v_gms have no magnetic precursor in any fluid. We present time-dependent calculations to study the formation of steady multifluid shocks. The dynamics differ qualitatively depending on whether or not the grains and field are well coupled.Comment: 43 pages with 17 figures, aastex, accepted by The Astrophysical Journa

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

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

Combining algorithms to predict bacterial protein sub-cellular location: Parallel versus concurrent implementations

We describe a novel and potentially important tool for candidate subunit vaccine selection through in silico reverse-vaccinology. A set of Bayesian networks able to make individual predictions for specific subcellular locations is implemented in three pipelines with different architectures: a parallel implementation with a confidence level-based decision engine and two serial implementations with a hierarchical decision structure, one initially rooted by prediction between membrane types and another rooted by soluble versus membrane prediction. The parallel pipeline outperformed the serial pipeline, but took twice as long to execute. The soluble-rooted serial pipeline outperformed the membrane-rooted predictor. Assessment using genomic test sets was more equivocal, as many more predictions are made by the parallel pipeline, yet the serial pipeline identifies 22 more of the 74 proteins of known location

Toward bacterial protein sub-cellular location prediction: single-class discrimminant models for all gram- and gram+ compartments

Based on Bayesian Networks, methods were created that address protein sequence-based bacterial subcellular location prediction. Distinct predictive algorithms for the eight bacterial subcellular locations were created. Several variant methods were explored. These variations included differences in the number of residues considered within the query sequence - which ranged from the N-terminal 10 residues to the whole sequence - and residue representation - which took the form of amino acid composition, percentage amino acid composition, or normalised amino acid composition. The accuracies of the best performing networks were then compared to PSORTB. All individual location methods outperform PSORTB except for the Gram+ cytoplasmic protein predictor, for which accuracies were essentially equal, and for outer membrane protein prediction, where PSORTB outperforms the binary predictor. The method described here is an important new approach to method development for subcellular location prediction. It is also a new, potentially valuable tool for candidate subunit vaccine selection

Multi-class subcellular location prediction for bacterial proteins

Two algorithms, based on Bayesian Networks (BNs), for bacterial subcellular location prediction, are explored in this paper: one predicts all locations for Gram+ bacteria and the other all locations for Gram- bacteria. Methods were evaluated using different numbers of residues (from the N-terminal 10 residues to the whole sequence) and residue representation (amino acid-composition, percentage amino acid-composition or normalised amino acid-composition). The accuracy of the best resulting BN was compared to PSORTB. The accuracy of this multi-location BN was roughly comparable to PSORTB; the difference in predictions is low, often less than 2%. The BN method thus represents both an important new avenue of methodological development for subcellular location prediction and a potentially value new tool of true utilitarian value for candidate subunit vaccine selection

The Structure, Kinematics and Physical Properties of the Molecular Gas in the Starburst Nucleus of NGC 253

We present 5.2" x 2.6" resolution interferometry of CO J=1-0 emission from the starburst galaxy NGC 253. The high spatial resolution of these new data, in combination with recent high resolution maps of 13CO, HCN and near-infrared emission, allow us for the first time to link unambiguously the gas properties in the central starburst of NGC 253 with its bar dynamics. We confirm that the star formation results from bar-driven gas flows as seen in "twin peaks" galaxies. Two distinct kinematic features are evident from the CO map and position-velocity diagram: a group of clouds rotating as a solid body about the kinematic center of the galaxy, and a more extended gas component associated with the near-infrared bar. We model the line intensities of CO, HCN and 13CO to infer the physical conditions of the gas in the nucleus of NGC 253. The results indicate increased volume densities around the radio nucleus in a twin-peaks morphology. Compared with the CO kinematics, the gas densities appear highest near the radius of a likely inner Linblad resonance, and slightly lead the bar minor axis. This result is similar to observations of the face-on, twin-peaks galaxy NGC 6951, and is consistent with models of starburst generation due to gas inflow along a bar.Comment: To appear in the ApJ, 28 pages, 12 figure file

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