Ionization potentials in the limit of large atomic number

By extrapolating the energies of non-relativistic atoms and their ions with up to 3000 electrons within Kohn-Sham density functional theory, we find that the ionization potential remains finite and increases across a row, even as $Z\rightarrow\infty$. The local density approximation becomes chemically accurate (and possibly exact) in some cases. Extended Thomas-Fermi theory matches the shell-average of both the ionization potential and density change. Exact results are given in the limit of weak electron-electron repulsion.Comment: 4 pages, 5 figure

Genetic analysis of safflower domestication.

BackgroundSafflower (Carthamus tinctorius L.) is an oilseed crop in the Compositae (a.k.a. Asteraceae) that is valued for its oils rich in unsaturated fatty acids. Here, we present an analysis of the genetic architecture of safflower domestication and compare our findings to those from sunflower (Helianthus annuus L.), an independently domesticated oilseed crop within the same family.We mapped quantitative trait loci (QTL) underlying 24 domestication-related traits in progeny from a cross between safflower and its wild progenitor, Carthamus palaestinus Eig. Also, we compared QTL positions in safflower against those that have been previously identified in cultivated x wild sunflower crosses to identify instances of colocalization.ResultsWe mapped 61 QTL, the vast majority of which (59) exhibited minor or moderate phenotypic effects. The two large-effect QTL corresponded to one each for flower color and leaf spininess. A total of 14 safflower QTL colocalized with previously reported sunflower QTL for the same traits. Of these, QTL for three traits (days to flower, achene length, and number of selfed seed) had cultivar alleles that conferred effects in the same direction in both species.ConclusionsAs has been observed in sunflower, and unlike many other crops, our results suggest that the genetics of safflower domestication is quite complex. Moreover, our comparative mapping results indicate that safflower and sunflower exhibit numerous instances of QTL colocalization, suggesting that parallel trait transitions during domestication may have been driven, at least in part, by parallel genotypic evolution at some of the same underlying genes

DNA sequence diversity and the origin of cultivated safflower (Carthamus tinctorius L.; Asteraceae)

<p>Abstract</p> <p>Background</p> <p>Safflower (<it>Carthamus tinctorius </it>L.) is a diploid oilseed crop whose origin is largely unknown. Safflower is widely believed to have been domesticated over 4,000 years ago somewhere in the Fertile Crescent. Previous hypotheses regarding the origin of safflower have focused primarily on two other species from sect. <it>Carthamus </it>– <it>C. oxyacanthus </it>and <it>C. palaestinus </it>– as the most likely progenitors, although some attention has been paid to a third species (<it>C. persicus</it>) as a possible candidate. Here, we describe the results of a phylogenetic analysis of the entire section using data from seven nuclear genes.</p> <p>Results</p> <p>Single gene phylogenetic analyses indicated some reticulation or incomplete lineage sorting. However, the analysis of the combined dataset revealed a close relationship between safflower and <it>C. palaestinus</it>. In contrast, <it>C. oxyacanthus </it>and <it>C. persicus </it>appear to be more distantly related to safflower.</p> <p>Conclusion</p> <p>Based on our results, we conclude that safflower is most likely derived from the wild species <it>Carthamus palaestinus</it>. As expected, safflower exhibits somewhat reduced nucleotide diversity as compared to its progenitor, consistent with the occurrence of a population genetic bottleneck during domestication. The results of this research set the stage for an investigation of the genetics of safflower domestication.</p

Generalized gradient approximation for solids and their surfaces

Successful modern generalized gradient approximations (GGA) are biased toward atomic energies. Restoration of the first-principles gradient expansion for the exchange energy over a wide range of density gradients eliminates this bias. We introduce PBEsol, a revised Perdew-Burke-Ernzerhof GGA that improves equilibrium properties for many densely-packed solids and their surfaces.Comment: 4pages, 2figures,2table

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Genetic map file of consensus genotypes for each contig

Sequence validation of candidates for selectively important genes in sunflower

Analyses aimed at identifying genes that have been targeted by past selection provide a powerful means for investigating the molecular basis of adaptive differentiation. In the case of crop plants, such studies have the potential to not only shed light on important evolutionary processes, but also to identify genes of agronomic interest. In this study, we test for evidence of positive selection at the DNA sequence level in a set of candidate genes previously identified in a genome-wide scan for genotypic evidence of selection during the evolution of cultivated sunflower. In the majority of cases, we were able to confirm the effects of selection in shaping diversity at these loci. Notably, the genes that were found to be under selection via our sequence-based analyses were devoid of variation in the cultivated sunflower gene pool. This result confirms a possible strategy for streamlining the search for adaptively-important loci process by pre-screening the derived population to identify the strongest candidates before sequencing them in the ancestral population

Exact condition on the Kohn-Sham kinetic energy, and modern parametrization of the Thomas-Fermi density

We study the asymptotic expansion of the neutral-atom energy as the atomic number Z goes to infinity, presenting a new method to extract the coefficients from oscillating numerical data. We find that recovery of the correct expansion is an exact condition on the Kohn-Sham kinetic energy that is important for the accuracy of approximate kinetic energy functionals for atoms, molecules and solids, when evaluated on a Kohn-Sham density. For example, this determines the small gradient limit of any generalized gradient approximation, and conflicts somewhat with the standard gradient expansion. Tests are performed on atoms, molecules, and jellium clusters. We also give a modern, highly accurate parametrization of the Thomas-Fermi density of neutral atoms.Comment: 10 pages, 9 figures, submitted at JC

Relevance of the slowly-varying electron gas to atoms, molecules, and solids

Under a certain scaling, the electron densities of finite systems become both large and slowly-varying, so that the gradient expansions of the density functionals for the Kohn-Sham kinetic and exchange energies become asymptotically exact to order $\nabla^2$. Neutral atoms of large $Z$ scale similarly, but a cusp correction at the nucleus requires generalizing the gradient expansion for exchange, producing the wrong gradient coefficient in the slowly-varying limit. Meta-generalized gradient approximations (meta-GGA's) recover both the slowly-varying and large-$Z$ limits. GGA correlation energies of large-Z atoms are found to be accurate.Comment: 5 pages, 4 figures, submitted at PR

Biogeographic analysis of the Tortugas Ecological Reserve: Examining the refuge effect following reserve establishment

Almost 120 days at sea aboard three NOAA research vessels and one fishing vessel over the past three years have supported biogeographic characterization of Tortugas Ecological Reserve (TER). This work initiated measurement of post-implementation effects of TER as a refuge for exploited species. In Tortugas South, seafloor transect surveys were conducted using divers, towed operated vehicles (TOV), remotely operated vehicles (ROV), various sonar platforms, and the Deepworker manned submersible. ARGOS drifter releases, satellite imagery, ichthyoplankton surveys, sea surface temperature, and diver census were combined to elucidate potential dispersal of fish spawning in this environment. Surveys are being compiled into a GIS to allow resource managers to gauge benthic resource status and distribution. Drifter studies have determined that within the ~ 30 days of larval life stage for fishes spawning at Tortugas South, larvae could reach as far downstream as Tampa Bay on the west Florida coast and Cape Canaveral on the east coast. Together with actual fish surveys and water mass delineation, this work demonstrates that the refuge status of this area endows it with tremendous downstream spillover and larval export potential for Florida reef habitats and promotes the maintenance of their fish communities. In Tortugas North, 30 randomly selected, permanent stations were established. Five stations were assigned to each of the following six areas: within Dry Tortugas National Park, falling north of the prevailing currents (Park North); within Dry Tortugas National Park, falling south of the prevailing currents (Park South); within the Ecological Reserve falling north of the prevailing currents (Reserve North); within the Ecological Reserve falling south of the prevailing currents (Reserve South); within areas immediately adjacent to these two strata, falling north of the prevailing currents (Out North); and within areas immediately adjacent to these two strata, falling south of the prevailing currents (Out South). Intensive characterization of these sites was conducted using multiple sonar techniques, TOV, ROV, diver-based digital video collection, diver-based fish census, towed fish capture, sediment particle-size, benthic chlorophyll analyses, and stable isotope analyses of primary producers, fish, and, shellfish. In order to complement and extend information from studies focused on the coral reef, we have targeted the ecotone between the reef and adjacent, non-reef habitats as these areas are well-known in ecology for indicating changes in trophic relationships at the ecosystem scale. Such trophic changes are hypothesized to occur as top-down control of the system grows with protection of piscivorous fishes. Preliminary isotope data, in conjunction with our prior results from the west Florida shelf, suggest that the shallow water benthic habitats surrounding the coral reefs of TER will prove to be the source of a significant amount of the primary production ultimately fueling fish production throughout TER and downstream throughout the range of larval fish dispersal. Therefore, the status and influence of the previously neglected, non-reef habitat within the refuge (comprising ~70% of TER) appears to be intimately tied to the health of the coral reef community proper. These data, collected in a biogeographic context, employing an integrated Before-After Control Impact design at multiple spatial scales, leave us poised to document and quantify the postimplementation effects of TER. Combined with the work at Tortugas South, this project represents a multi-disciplinary effort of sometimes disparate disciplines (fishery oceanography, benthic ecology, food web analysis, remote sensing/geography/landscape ecology, and resource management) and approaches (physical, biological, ecological). We expect the continuation of this effort to yield critical information for the management of TER and the evaluation of protected areas as a refuge for exploited species. (PDF contains 32 pages.