Chemical Modelling of Young Stellar Objects, I. Method and Benchmarks

Upcoming facilities such as the Herschel Space Observatory or ALMA will deliver a wealth of molecular line observations of young stellar objects (YSOs). Based on line fluxes, chemical abundances can then be estimated by radiative transfer calculations. To derive physical properties from abundances, the chemical network needs to be modeled and fitted to the observations. This modeling process is however computationally exceedingly demanding, particularly if in addition to density and temperature, far UV (FUV) irradiation, X-rays, and multi-dimensional geometry have to be considered. We develop a fast tool, suitable for various applications of chemical modeling in YSOs. A grid of the chemical composition of the gas having a density, temperature, FUV irradiation and X-ray flux is pre-calculated as a function of time. A specific interpolation approach is developed to reduce the database to a feasible size. Published models of AFGL 2591 are used to verify the accuracy of the method. A second benchmark test is carried out for FUV sensitive molecules. The novel method for chemical modeling is more than 250,000 times faster than direct modeling and agrees within a mean factor of 1.35. The tool is distributed for public use. In the course of devloping the method, the chemical evolution is explored: We find that X-ray chemistry in envelopes of YSOs can be reproduced by means of an enhanced cosmic-ray ionization rate. We further find that the abundance of CH+ in low-density gas with high ionization can be enhanced by the recombination of doubly ionized carbon (C++) and suggest a new value for the initial abundance of the main sulphur carrier in the hot-core.Comment: Accepted by ApJS. 24 pages, 15 figures. A version with higher resolution images is available from http://www.astro.phys.ethz.ch/staff/simonbr/papgridI.pdf . Online data available at http://www.astro.phys.ethz.ch/chemgrid.html . Second paper of this series of papers available at arXiv:0906.058

Professional, easy to use and robust bioinformatic tools

To make use of Big Data software tools and computer analytics are essential. However, academic software has a bad reputation: hard to read, even harder to understand and impossible to maintain. In addition, it often does not scale up, so when faced with data sets that are increasing rapidly in size and ..

On the effectiveness of run-time checks

Run-time checks are often assumed to be a cost-effective way of improving the dependability of software components, by checking required properties of their outputs and flagging an output as incorrect if it fails the check. However, evaluating how effective they are going to be in a future application is difficult, since the effectiveness of a check depends on the unknown faults of the program to which it is applied. A programming contest, providing thousands of programs written to the same specifications, gives us the opportunity to systematically test run-time checks to observe statistics of their effects on actual programs. In these examples, run-time checks turn out to be most effective for unreliable programs. For more reliable programs, the benefit is relatively low as compared to the gain that can be achieved by other (more expensive) measures, most notably multiple-version diversity

Accounting for Intellectual Property: inconsistencies and challenges

The recognition of the rights attached to some forms of intellectual property is a contested domain in legal frameworks, such as the Trade Related Aspects of Intellectual Property Rights Agreement. The same can be said of economic frameworks, such as accounting which attempt to recognise and value intellectual property for the purposes of providing information for decision making. In this paper we explore the discourse of accounting in the recognition of intellectual property as an asset according to the new International Accounting Standards. We then contrast the legal and accounting discourses in which intellectual property rights are acknowledged, concluding that these discourses are not necessarily aligned. The effects and implications of the development of a global regime for accounting for intangibles may eventually harmonise the accounting treatment for intellectual property but does not resolve the contentious issue of the inconsistencies in the recognition of intellectual property rights under different frameworks and the implications for economic decision making

Evidence of environmental strains on charge injection in silole based organic light emitting diodes

Using d. functional theory (DFT) computations, the authors demonstrated a substantial skeletal relaxation when the structure of 2,5-bis-[4-anthracene-9-yl-phenyl]-1,1-dimethyl-3,4-diphenyl-silole (BAS) is optimized in the gas-phase comparing with the mol. structure detd. from monocrystal x-ray diffraction. The origin of such a relaxation is explained by a strong environmental strains induced by the presence of anthracene entities. Also, the estn. of the frontier orbital levels showed that this structural relaxation affects mainly the LUMO that is lowered of 190 meV in the gas phase. To check if these theor. findings would be confirmed for thin films of BAS, the authors turned to UV photoemission spectroscopy and/or inverse photoemission spectroscopy and electrooptical measurements. The study of the c.d. or voltage and luminance or voltage characteristics of an ITO/PEDOT/BAS/Au device clearly demonstrated a very unusual temp.-dependent behavior. Using a thermally assisted tunnel transfer model, this behavior likely originated from the variation of the electronic affinity of the silole deriv. with the temp. The thermal agitation relaxes the mol. strains in thin films as it is shown when passing from the cryst. to the gas phase. The relaxation of the intramol. thus induces an increase of the electronic affinity and, as a consequence, the more efficient electron injection in org. light-emitting diodes

Entanglement of a qubit with a single oscillator mode

We solve a model of a qubit strongly coupled to a massive environmental oscillator mode where the qubit backaction is treated exactly. Using a Ginzburg-Landau formalism, we derive an effective action for this well known localization transition. An entangled state emerges as an instanton in the collective qubit-environment degree of freedom and the resulting model is shown to be formally equivalent to a Fluctuating Gap Model (FGM) of a disordered Peierls chain. Below the transition, spectral weight is transferred to an exponentially small energy scale leaving the qubit coherent but damped. Unlike the spin-boson model, coherent and effectively localized behaviors may coexist.Comment: 4 pages, 1 figure; added calculation of entanglement entrop

Magnetic excitations in the low-temperature ferroelectric phase of multiferroic YMn2O5 using inelastic neutron scattering

We studied magnetic excitations in a low-temperature ferroelectric phase of the multiferroic YMn2O5 using inelastic neutron scattering (INS). We identify low-energy magnon modes and establish a correspondence between the magnon peaks observed by INS and electromagnon peaks observed in optical absorption [1]. Furthermore, we explain the microscopic mechanism, which results in the lowest-energy electromagnon peak, by comparing the inelastic neutron spectral weight with the polarization in the commensurate ferroelectric phase.Comment: 4 pages, 4 figure

Ga and Gß Proteins Regulate the Cyclic AMP Pathway That Is Required for Development and Pathogenicity of the Phytopathogen Mycosphaerella graminicola

We identified and functionally characterized genes encoding three G alpha proteins and one G beta protein in the dimorphic fungal wheat pathogen Mycosphaerella graminicola, which we designated MgGpa1, MgGpa2, MgGpa3, and MgGpb1, respectively. Sequence comparisons and phylogenetic analyses showed that MgGPA1 and MgGPA3 are most related to the mammalian G alpha(i) and G alpha(s) families, respectively, whereas MgGPA2 is not related to either of these families. On potato dextrose agar (PDA) and in yeast glucose broth (YGB), MgGpa1 mutants produced significantly longer spores than those of the wild type (WT), and these developed into unique fluffy mycelia in the latter medium, indicating that this gene negatively controls filamentation. MgGpa3 mutants showed more pronounced yeast-like growth accompanied with hampered filamentation and secreted a dark-brown pigment into YGB. Germ tubes emerging from spores of MgGpb1 mutants were wavy on water agar and showed a nested type of growth on PDA that was due to hampered filamentation, numerous cell fusions, and increased anastomosis. Intracellular cyclic AMP (cAMP) levels of MgGpb1 and MgGpa3 mutants were decreased, indicating that both genes positively regulate the cAMP pathway, which was confirmed because the WT phenotype was restored by adding cAMP to these mutant cultures. The cAMP levels in MgGpa1 mutants and the WT were not significantly different, suggesting that this gene might be dispensable for cAMP regulation. In planta assays showed that mutants of MgGpa1, MgGpa3, and MgGpb1 are strongly reduced in pathogenicity. We concluded that the heterotrimeric G proteins encoded by MgGpa3 and MgGpb1 regulate the cAMP pathway that is required for development and pathogenicity in M. graminicola

Superfluid-insulator transition of the Josephson junction array model with commensurate frustration

We have studied the rationally frustrated Josephson-junction array model in the square lattice through Monte Carlo simulations of $(2+1)$D XY-model. For frustration $f=1/4$, the model at zero temperature shows a continuous superfluid-insulator transition. From the measurement of the correlation function and the superfluid stiffness, we obtain the dynamical critical exponent $z=1.0$ and the correlation length critical exponent $\nu=0.4 \pm 0.05$. While the dynamical critical exponent is the same as that for cases $f=0$, 1/2, and 1/3, the correlation length critical exponent is surprisingly quite different. When $f=1/5$, we have the nature of a first-order transition.Comment: RevTex 4, to appear in PR