Temporal evolution of magnetic molecular shocks II. Analytics of the steady state and semi-analytical construction of intermediate ages

In the first paper of this series (Paper I) we computed time dependent simulations of multifluid shocks with chemistry and a transverse magnetic field frozen in the ions, using an adaptive moving grid. In this paper, we present new analytical results on steady-state molecular shocks. Relationships between density and pressure in the neutral fluid are derived for the cold magnetic precursor, hot magnetic precursor, adiabatic shock front, and the following cooling layer. The compression ratio and temperature behind a fully dissociative adiabatic shock is also derived. To prove that these results may even hold for intermediate ages, we design a test to locally characterise the validity of the steady state equations in a time-dependent shock simulation. Applying this tool to the results of Paper I, we show that most of these shocks (all the stable ones) are indeed in a quasi-steady state at all times, i.e. : a given snapshot is composed of one or more truncated steady shock. Finally, we use this property to produce a construction method of any intermediate time of low velocity shocks (u < 20 km/s) with only a steady-state code. In particular, this method allows one to predict the occurrence of steady CJ-type shocks more accurately than previously proposed criteria.Comment: A&A in pres

A map of OMC-1 in CO 9-8

The distribution of 12C16O J=9-8 (1.037 THz) emission has been mapped in OMC-1 at 35 points with 84" resolution. This is the first map of this source in this transition and only the second velocity-resolved ground-based observation of a line in the terahertz frequency band. There is emission present at all points in the map, a region roughly 4' by 6' in size, with peak antenna temperature dropping only near the edges. Away from the Orion KL outflow, the velocity structure suggests that most of the emission comes from the OMC-1 photon-dominated region, with a typical linewidthof 3-6 km/s. Large velocity gradient modeling of the emission in J=9-8 and six lower transitions suggests that the lines originate in regions with temperatures around 120 K and densities of at least 10^(3.5) cm^(-3) near theta^(1) C Ori and at the Orion Bar, and from 70 K gas at around 10^(4) cm^(-3) southeast and west of the bar. These observations are among the first made with the 0.8 m Smithsonian Astrophysical Observatory Receiver Lab Telescope, a new instrument designed to observe at frequencies above 1 THz from an extremely high and dry site in northern Chile.Comment: Minor changes to references, text to match ApJ versio

The Molecular Condensations Ahead of Herbig-Haro Objects. III. Radiative and dynamical perturbations of the HH 2 condensation

We have carried out an extensive observational study (from BIMA data) and made a preliminary theoretical investigation of the molecular gas around HH2. The molecular maps show a very complex morphological, kinematical and chemical structure. The overall main conclusion of this work confirms the findings of Paper I and II, by demonstrating that in addition to the strong photochemical effects caused by penetration of the UV photons from HH2 into molecular cloud, a range of complex radiative and dynamical interactions occur. Thus, despite the apparent `quiescent' nature of the molecular cloud ahead of HH2, the kinematical properties observed within the field of view suggest that it is possibly being driven out by powerful winds from the VLA 1 protostar.Comment: 20 pages. Accepted for publication to Astronomy & Astrophysic

Infrared Studies of Molecular Shocks in the Supernova Remnant HB21: I. Thermal Admixture of Shocked H_2 Gas in the North

We present near- and mid-infrared observations on the shock-cloud interaction region in the northern part of the supernova remnant HB21, performed with the InfraRed Camera (IRC) aboard AKARI satellite and the Wide InfraRed Camera (WIRC) at the Palomar 5 m telescope. The IRC 7 um (S7), 11 um (S11), and 15 um (L15) band images and the WIRC H2 v = 1 -> 0 S(1) 2.12 um image show similar shock-cloud interaction features. We chose three representative regions, and analyzed their IRC emissions through comparison with H2 line emissions of several shock models. The IRC colors are well explained by the thermal admixture model of H2 gas--whose infinitesimal H2 column density has a power-law relation with the temperature T, dN ~ T^-b dT--with n(H2) ~ 10^3 cm^-3, b ~ 3, and N(H2 ;T > 100K) ~ 3x10^20 cm^-2. The derived b value may be understood by a bow shock picture, whose shape is cycloidal (cuspy) rather than paraboloidal. However, this picture raises another issue that the bow shocks must reside within ~0.01 pc size-scale, smaller than the theoretically expected. Instead, we conjectured a shocked clumpy interstellar medium picture, which may avoid the sizescale issue while explaining the similar model parameters. The observed H2 v = 1 -> 0 S(1) intensities are a factor of ~17 - 33 greater than the prediction from the power-law admixture model. This excess may be attributed to either an extra component of hot H2 gas or to the effects of collisions with hydrogen atoms, omitted in our power-law admixture model, both of which would increase the population in the v = 1 level of H2.Comment: 14 pages, 9 figures, ApJ accepted, higher resolution @ http://astro.snu.ac.kr/~jhshinn/ms.pd

Modelling Herschel observations of hot molecular gas emission from embedded low-mass protostars

Aims. Young stars interact vigorously with their surroundings, as evident from the highly rotationally excited CO (up to Eup=4000 K) and H2O emission (up to 600 K) detected by the Herschel Space Observatory in embedded low-mass protostars. Our aim is to construct a model that reproduces the observations quantitatively, to investigate the origin of the emission, and to use the lines as probes of the various heating mechanisms. Methods. The model consists of a spherical envelope with a bipolar outflow cavity. Three heating mechanisms are considered: passive heating by the protostellar luminosity, UV irradiation of the outflow cavity walls, and C-type shocks along the cavity walls. Line fluxes are calculated for CO and H2O and compared to Herschel data and complementary ground-based data for the protostars NGC1333 IRAS2A, HH 46 and DK Cha. The three sources are selected to span a range of evolutionary phases and physical characteristics. Results. The passively heated gas in the envelope accounts for 3-10% of the CO luminosity summed over all rotational lines up to J=40-39; it is best probed by low-J CO isotopologue lines such as C18O 2-1 and 3-2. The UV-heated gas and the C-type shocks, probed by 12CO 10-9 and higher-J lines, contribute 20-80% each. The model fits show a tentative evolutionary trend: the CO emission is dominated by shocks in the youngest source and by UV-heated gas in the oldest one. This trend is mainly driven by the lower envelope density in more evolved sources. The total H2O line luminosity in all cases is dominated by shocks (>99%). The exact percentages for both species are uncertain by at least a factor of 2 due to uncertainties in the gas temperature as function of the incident UV flux. However, on a qualitative level, both UV-heated gas and C-type shocks are needed to reproduce the emission in far-infrared rotational lines of CO and H2O.Comment: 15 pages (+4 pages appendix), 20 figures, accepted by A&

Functional Group and Substructure Searching as a Tool in Metabolomics

BACKGROUND: A direct link between the names and structures of compounds and the functional groups contained within them is important, not only because biochemists frequently rely on literature that uses a free-text format to describe functional groups, but also because metabolic models depend upon the connections between enzymes and substrates being known and appropriately stored in databases. METHODOLOGY: We have developed a database named "Biochemical Substructure Search Catalogue" (BiSSCat), which contains 489 functional groups, >200,000 compounds and >1,000,000 different computationally constructed substructures, to allow identification of chemical compounds of biological interest. CONCLUSIONS: This database and its associated web-based search program (http://bisscat.org/) can be used to find compounds containing selected combinations of substructures and functional groups. It can be used to determine possible additional substrates for known enzymes and for putative enzymes found in genome projects. Its applications to enzyme inhibitor design are also discussed

Semantic Similarity for Automatic Classification of Chemical Compounds

With the increasing amount of data made available in the chemical field, there is a strong need for systems capable of comparing and classifying chemical compounds in an efficient and effective way. The best approaches existing today are based on the structure-activity relationship premise, which states that biological activity of a molecule is strongly related to its structural or physicochemical properties. This work presents a novel approach to the automatic classification of chemical compounds by integrating semantic similarity with existing structural comparison methods. Our approach was assessed based on the Matthews Correlation Coefficient for the prediction, and achieved values of 0.810 when used as a prediction of blood-brain barrier permeability, 0.694 for P-glycoprotein substrate, and 0.673 for estrogen receptor binding activity. These results expose a significant improvement over the currently existing methods, whose best performances were 0.628, 0.591, and 0.647 respectively. It was demonstrated that the integration of semantic similarity is a feasible and effective way to improve existing chemical compound classification systems. Among other possible uses, this tool helps the study of the evolution of metabolic pathways, the study of the correlation of metabolic networks with properties of those networks, or the improvement of ontologies that represent chemical information

APEX-CHAMP+ high-J CO observations of low-mass young stellar objects: I. The HH 46 envelope and outflow

AIMS Our aim is to characterize the size, mass, density and temperature profiles of the protostellar envelope of HH~46 IRS 1 and its surrounding cloud material as well as the effect the outflow has on its environment.METHODS The CHAMP+ and LABOCA arrays on the APEX telescope, combined with lower frequency line receivers, are used to obtain a large continuum map and smaller heterodyne maps in various isotopologues of CO and HCO+. The high-J lines of CO (6--5 and 7--6) and its isotopologues together with [C I] 2--1, observed with CHAMP+, are used to probe the warm molecular gas in the inner few hundred AU and in the outflowing gas. The data are interpreted with continuum and line radiative transfer models. RESULTS Broad outflow wings are seen in CO low- and high-J lines at several positions, constraining the gas temperatures to a constant value of ~100 K along the red outflow axis and to ~60 K for the blue outflow. The derived outflow mass is of order 0.4--0.8 M_sol, significantly higher than previously found. The bulk of the strong high-J CO line emission has a surprisingly narrow width, however, even at outflow positions. These lines cannot be fit by a passively heated model of the HH 46 IRS envelope. We propose that it originates from photon heating of the outflow cavity walls by ultraviolet photons originating in outflow shocks and the accretion disk boundary layers. At the position of the bow shock itself, the UV photons are energetic enough to dissociate CO. The envelope mass of ~5 M_sol is strongly concentrated towards HH 46 IRS with a density power law of -1.8.Comment: accepted by A&

Scleroderma and related disorders: 223. Long Term Outcome in a Contemporary Systemic Sclerosis Cohort

Background: We have previously compared outcome in two groups of systemic sclerosis (SSc) patients with disease onset a decade apart and we reported data on 5 year survival and cumulative incidence of organ disease in a contemporary SSc cohort. The present study examines longer term outcome in an additional cohort of SSc followed for 10 years. Methods: We have examined patients with disease onset between years 1995 and 1999 allowing for at least 10 years of follow-up in a group that has characteristics representative for the patients we see in contemporary clinical practice. Results: Of the 398 patients included in the study, 252 (63.3%) had limited cutaneous (lc) SSc and 146 (36.7%) had diffuse cutaneous (dc) SSc. The proportion of male patients was higher among the dcSSc group (17.1% v 9.9%, p = 0.037) while the mean age of onset was significantly higher among lcSSc patients (50 ± 13 v 46 ± 13 years ± SD, p = 0.003). During a 10 year follow-up from disease onset, 45% of the dcSSc and 21% of the lcSSc subjects developed clinically significant pulmonary fibrosis, p < 0.001. Among them approximately half reached the endpoint within the first 3 years (23% of dcSSc and 10% of lcSSc) and over three quarters within the first 5 years (34% and 16% respectively). There was a similar incidence of pulmonary hypertension (PH) in the two subsets with a steady rate of increase over time. At 10 years 13% of dcSSc and 15% of lcSSc subjects had developed PH (p=0.558), with the earliest cases observed within the first 2 years of disease. Comparison between subjects who developed PH in the first and second 5 years from disease onset demonstrated no difference in demographic or clinical characteristics, but 5-year survival from PH onset was better among those who developed this complication later in their disease (49% v 24%), with a strong trend towards statistical significance (p = 0.058). Incidence of SSc renal crisis (SRC) was significantly higher among the dcSSc patients (12% v 4% in lcSSc, p = 0.002). As previously observed, the rate of development of SRC was highest in the first 3 years of disease- 10% in dcSSc and 3% in lcSSc. All incidences of clinically important cardiac disease developed in the first 5 years from disease onset (7% in dcSSc v 1% in lcSSc, p < 0.001) and remained unchanged at 10 years. As expected, 10-year survival among lcSSc subjects was significantly higher (81%) compared to that of dcSSc patients (70%, p = 0.006). Interestingly, although over the first 5 years the death rate was much higher in the dcSSc cohort (16% v 6% in lcSSc), over the following years it became very similar for both subsets (14% and 13% between years 5 and 10, and 18% and 17% between years 10 and 15 for dcSSc and lcSSc respectively). Conclusions: Even though dcSSc patients have higher incidence for most organ complications compared to lcSSc subjects, the worse survival among them is mainly due to higher early mortality rate. Mortality rate after first 5 years of disease becomes comparable in the two disease subsets. Disclosure statement: The authors have declared no conflicts of interes

Energy Resolution Performance of the CMS Electromagnetic Calorimeter

The energy resolution performance of the CMS lead tungstate crystal electromagnetic calorimeter is presented. Measurements were made with an electron beam using a fully equipped supermodule of the calorimeter barrel. Results are given both for electrons incident on the centre of crystals and for electrons distributed uniformly over the calorimeter surface. The electron energy is reconstructed in matrices of 3 times 3 or 5 times 5 crystals centred on the crystal containing the maximum energy. Corrections for variations in the shower containment are applied in the case of uniform incidence. The resolution measured is consistent with the design goals