Atomic and Molecular Data for Optical Stellar Spectroscopy

High-precision spectroscopy of large stellar samples plays a crucial role for several topical issues in astrophysics. Examples include studying the chemical structure and evolution of the Milky Way galaxy, tracing the origin of chemical elements, and characterizing planetary host stars. Data are accumulating from instruments that obtain high-quality spectra of stars in the ultraviolet, optical and infrared wavelength regions on a routine basis. These instruments are located at ground-based 2- to 10-m class telescopes around the world, in addition to the spectrographs with unique capabilities available at the Hubble Space Telescope. The interpretation of these spectra requires high-quality transition data for numerous species, in particular neutral and singly ionized atoms, and di- or triatomic molecules. We rely heavily on the continuous efforts of laboratory astrophysics groups that produce and improve the relevant experimental and theoretical atomic and molecular data. The compilation of the best available data is facilitated by databases and electronic infrastructures such as the NIST Atomic Spectra Database, the VALD database, or the Virtual Atomic and Molecular Data Centre (VAMDC). We illustrate the current status of atomic data for optical stellar spectra with the example of the Gaia-ESO Public Spectroscopic Survey. Data sources for 35 chemical elements were reviewed in an effort to construct a line list for a homogeneous abundance analysis of up to 100000 stars.Comment: Published 30 April 2015 in Physica Script

Uncertainty Estimates for Theoretical Atomic and Molecular Data

Sources of uncertainty are reviewed for calculated atomic and molecular data that are important for plasma modeling: atomic and molecular structure and cross sections for electron-atom, electron-molecule, and heavy particle collisions. We concentrate on model uncertainties due to approximations to the fundamental many-body quantum mechanical equations and we aim to provide guidelines to estimate uncertainties as a routine part of computations of data for structure and scattering.Comment: 65 pages, 18 Figures, 3 Tables. J. Phys. D: Appl. Phys. Final accepted versio

Koopmans-compliant functionals and their performance against reference molecular data

Koopmans-compliant functionals emerge naturally from extending the constraint of piecewise linearity of the total energy as a function of the number of electrons to each fractional orbital occupation. When applied to approximate density-functional theory, these corrections give rise to orbital-density-dependent functionals and potentials. We show that the simplest implementations of Koopmans' compliance provide accurate estimates for the quasiparticle excitations and leave the total energy functional almost or exactly intact, i.e., they describe correctly electron removals or additions, but do not necessarily alter the electronic charge density distribution within the system. Additional functionals can then be constructed that modify the potential energy surface, including e.g. Perdew-Zunger corrections. These functionals become exactly one-electron self-interaction free and, as all Koopmans-compliant functionals, are approximately many-electron self-interaction free. We discuss in detail these different formulations, and provide extensive benchmarks for the 55 molecules in the reference G2-1 set, using Koopmans-compliant functionals constructed from local-density or generalized-gradient approximations. In all cases we find excellent performance in the electronic properties, comparable or improved with respect to that of many-body perturbation theories, such as G$_0$W$_0$ and self-consistent GW, at a fraction of the cost and in a variational framework that also delivers energy derivatives. Structural properties and atomization energies preserve or slightly improve the accuracy of the underlying density-functional approximations (Note: Supplemental Material is included in the source)

Incorporating molecular data in fungal systematics: a guide for aspiring researchers

The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching changes as disciplines in the wake of continual improvement in DNA sequencing technology. A taxonomic study that draws from molecular data involves a long series of steps, ranging from taxon sampling through the various laboratory procedures and data analysis to the publication process. All steps are important and influence the results and the way they are perceived by the scientific community. The present paper provides a reflective overview of all major steps in such a project with the purpose to assist research students about to begin their first study using DNA-based methods. We also take the opportunity to discuss the role of taxonomy in biology and the life sciences in general in the light of molecular data. While the best way to learn molecular methods is to work side by side with someone experienced, we hope that the present paper will serve to lower the learning threshold for the reader.Comment: Submitted to Current Research in Environmental and Applied Mycology - comments most welcom

Accounting for molecular stochasticity in systematic revisions: species limits and phylogeny of Paroaria

Different frameworks have been proposed for using molecular data in systematic revisions, but there is ongoing debate on their applicability, merits and shortcomings. In this paper we examine the fit between morphological and molecular data in the systematic revision of Paroaria, a group of conspicuous songbirds endemic to South America. We delimited species based on examination of > 600 specimens, and developed distance-gap, and distance- and character-based coalescent simulations to test species limits with molecular data. The morphological and molecular data collected were then analyzed using parsimony, maximum likelihood, and Bayesian phylogenetics. The simulations were better at evaluating the new species limits than using genetic distances. Species diversity within Paroaria had been underestimated by 60%, and the revised genus comprises eight species. Phylogenetic analyses consistently recovered a congruent topology for the most recently derived species in the genus, but the most basal divergences were not resolved with these data. The systematic and phylogenetic hypotheses developed here are relevant to both setting conservation priorities and understanding the biogeography of South America. 
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Atomic and Molecular Data for Stellar Physics: Former Successes and Future Challenges

This review highlights current (and future) hot topics in astrophysics where atomic or molecular input data are (or will be) essential, with special emphasis on topics relating to nucleosynthesis and cosmochemistry. We first discuss issues (like the abundances of oxygen and iron in the Sun, and that of lithium in post-AGB stars) where the use of poor-quality atomic or molecular data have led to spurious astrophysical puzzles which sparked fancy astrophysical models or theories. We then address issues where the advent of new instruments (like the ultraviolet high-resolution spectrographs--GHRS onboard HST, Keck-HRS or VLT-UVES--or future infrared satellites) calls for new and accurate atomic or molecular data.Comment: 20 pages, 12 figures, to appear in Physica Scripta, Topical Issue (Proceedings of the 35th EGAS conference -- European Group for Atomic Spectroscopy