Collisional excitation of water by hydrogen atoms

We present quantum dynamical calculations that describe the rotational excitation of H$_2$O due to collisions with H atoms. We used a recent, high accuracy potential energy surface, and solved the collisional dynamics with the close-coupling formalism, for total energies up to 12 000 cm$^{-1}$. From these calculations, we obtained collisional rate coefficients for the first 45 energy levels of both ortho- and para-H$_2$O and for temperatures in the range T = 5-1500 K. These rate coefficients are subsequently compared to the values previously published for the H$_2$O / He and H$_2$O / H$_2$ collisional systems. It is shown that no simple relation exists between the three systems and that specific calculations are thus mandatory

Hyperfine collisional excitation of ammonia by molecular hydrogen

Ammonia is one of the most widely observed molecules in space, and many observations are able to resolve the hyperfine structure due to the electric quadrupole moment of the nitrogen nucleus. The observed spectra often display anomalies in the satellite components of the lines, which indicate substantial deviations from the local thermodynamic equilibrium. The interpretation of the spectra thus requires the knowledge of the rate coefficients for the hyperfine excitation of NH$_3$ induced by collisions with H$_2$ molecules, the dominant collider in the cold interstellar medium. In this paper we present the first such calculations using a recoupling approach. The rate coefficients are obtained for all hyperfine levels within rotation-inversion levels up to $j=4$ and temperatures up to 100 K by means of quantum scattering close-coupling calculations on an accurate, five-dimensional, potential energy surface. We show that the rate coefficients depart significantly from those obtained with the statistical approach and that they do not conform to any simple propensity rules. Finally, we perform radiative transfer calculations to illustrate the impact of our new rate coefficients by modelling the hyperfine line intensities of the inversion transition in ground state para-NH$_3$ ($j_k=1_1$) and of the rotational transition $1_0\rightarrow 0_0$ in ortho-NH$_3$

Collisional Excitation and Non-LTE Modeling of Interstellar Chiral Propylene Oxide

The first set of theoretical rotational cross sections for propylene oxide (CH3CHCH2O) colliding with cold He atoms has been obtained at the full quantum level using a high-accuracy potential energy surface. By scaling the collision reduced mass, rotational rate coefficients for collisions with para-H2 are deduced in the temperature range 5-30 K. These collisional coefficients are combined with radiative data in a non-LTE radiative transfer model in order to reproduce observations of propylene oxide made toward the Sagittarius B2(N) molecular cloud with the Green Bank and Parkes radio telescopes. The three detected absorption lines are found to probe the cold (∼10 K) and translucent (nH ∼2000 cm-3) gas in the outer edges of the extended Sgr B2(N) envelope. The derived column density for propylene oxide is Ntot ∼3 x 1012 cm-2, corresponding to a fractional abundance relative to total hydrogen of ∼2.5 x 10-11. The present results are expected to help our understanding of the chemistry of propylene oxide, including a potential enantiomeric excess, in the cold interstellar medium

Collisional Excitation and Non-LTE Modeling of Interstellar Chiral Propylene Oxide

The first set of theoretical rotational cross sections for propylene oxide (CH3CHCH2O) colliding with cold He atoms has been obtained at the full quantum level using a high-accuracy potential energy surface. By scaling the collision reduced mass, rotational rate coefficients for collisions with para-H2 are deduced in the temperature range 5-30 K. These collisional coefficients are combined with radiative data in a non-LTE radiative transfer model in order to reproduce observations of propylene oxide made toward the Sagittarius B2(N) molecular cloud with the Green Bank and Parkes radio telescopes. The three detected absorption lines are found to probe the cold (∼10 K) and translucent (nH ∼2000 cm-3) gas in the outer edges of the extended Sgr B2(N) envelope. The derived column density for propylene oxide is N tot ∼3 x 1012 cm-2, corresponding to a fractional abundance relative to total hydrogen of ∼2.5 x 10-11. The present results are expected to help our understanding of the chemistry of propylene oxide, including a potential enantiomeric excess, in the cold interstellar medium

The Bioperl toolkit: Perl modules for the life sciences

The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort

Molecular excitation in the Interstellar Medium: recent advances in collisional, radiative and chemical processes

We review the different excitation processes in the interstellar mediumComment: Accepted in Chem. Re

BASECOL2023 scientific content

Context. The global context of making numerous data produced by researchers available requires collecting and organising the data, assigning meaningful metadata, and presenting the data in a meaningful and homogeneous way. The BASECOL database, which collects inelastic rate coefficients for application to the interstellar medium and to circumstellar and cometary atmospheres, meets those requirements. Aims. We aim to present the scientific content of the BASECOL2023 edition. Methods. While the previous versions relied on finding rate coefficients in the literature, the current version is populated with published results sent by the producers of data. The paper presents the database, the type of data that can be found, the type of metadata that are used, and the Virtual Atomic and Molecular Data Centre (VAMDC) standards that are used for the metadata. Finally, we present the different datasets species by species. Results. As the BASECOL database, interconnected with the VAMDC e-infrastructure, uses the VAMDC standards, the collisional data can be extracted with tools using VAMDC standards and can be associated with spectroscopic data extracted from other VAMDC connected databases such as the Cologne database for molecular spectroscopy (CDMS), the jet propulsion laboratory molecular spectroscopy database (JPL), and the high-resolution transmission molecular absorption database (HITRAN)