Error estimates for solid-state density-functional theory predictions: an overview by means of the ground-state elemental crystals

Predictions of observable properties by density-functional theory calculations (DFT) are used increasingly often in experimental condensed-matter physics and materials engineering as data. These predictions are used to analyze recent measurements, or to plan future experiments. Increasingly more experimental scientists in these fields therefore face the natural question: what is the expected error for such an ab initio prediction? Information and experience about this question is scattered over two decades of literature. The present review aims to summarize and quantify this implicit knowledge. This leads to a practical protocol that allows any scientist - experimental or theoretical - to determine justifiable error estimates for many basic property predictions, without having to perform additional DFT calculations. A central role is played by a large and diverse test set of crystalline solids, containing all ground-state elemental crystals (except most lanthanides). For several properties of each crystal, the difference between DFT results and experimental values is assessed. We discuss trends in these deviations and review explanations suggested in the literature. A prerequisite for such an error analysis is that different implementations of the same first-principles formalism provide the same predictions. Therefore, the reproducibility of predictions across several mainstream methods and codes is discussed too. A quality factor Delta expresses the spread in predictions from two distinct DFT implementations by a single number. To compare the PAW method to the highly accurate APW+lo approach, a code assessment of VASP and GPAW with respect to WIEN2k yields Delta values of 1.9 and 3.3 meV/atom, respectively. These differences are an order of magnitude smaller than the typical difference with experiment, and therefore predictions by APW+lo and PAW are for practical purposes identical.Comment: 27 pages, 20 figures, supplementary material available (v5 contains updated supplementary material

A demographic model for sex ratio evolution and the effects of sex-biased offspring costs

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ecology and Evolution 6 (2016): 1470–1492, doi:10.1002/ece3.1902.The evolution of the primary sex ratio, the proportion of male births in an individual's offspring production strategy, is a frequency-dependent process that selects against the more common sex. Because reproduction is shaped by the entire life cycle, sex ratio theory would benefit from explicitly two-sex models that include some form of life cycle structure. We present a demographic approach to sex ratio evolution that combines adaptive dynamics with nonlinear matrix population models. We also determine the evolutionary and convergence stability of singular strategies using matrix calculus. These methods allow the incorporation of any population structure, including multiple sexes and stages, into evolutionary projections. Using this framework, we compare how four different interpretations of sex-biased offspring costs affect sex ratio evolution. We find that demographic differences affect evolutionary outcomes and that, contrary to prior belief, sex-biased mortality after parental investment can bias the primary sex ratio (but not the corresponding reproductive value ratio). These results differ qualitatively from the widely held conclusions of previous models that neglect demographic structure.National Science Foundation Graduate Research Grant Number: 1122374; NSF Grant Numbers: DEB1145017, DEB1257545; European Research Council Grant Number: 322989; Woods Hole Oceanographic Institution Academic Programs Offic

Evolving thermal thresholds explain the distribution of temperature sex reversal in an Australian dragon lizard

Aim: Species with temperature-dependent sex determination (TSD) are particularly vulnerable to climate change because a resultant skew in population sex ratio can have severe demographic consequences and increase vulnerability to local extinction. The Australian central bearded dragon (Pogona vitticeps) has a thermosensitive ZZ male/ZW female system of genetic sex determination (GSD). High incubation temperatures cause reversal of the ZZ genotype to a viable female phenotype. Nest temperatures in the wild are predicted to vary on a scale likely to produce heterogeneity in the occurrence of sex reversal, and so we predict that sex reversal will correlate positively with inferred incubation conditions. Location: Mainland Australia. Methods: Wild-caught specimens of P. vitticeps vouchered in museum collections and collected during targeted field trips were genotypically and phenotypically sexed to determine the distribution of sex reversal across the species range. To determine whether environmental conditions or genetic structure can explain this distribution, we infer the incubation conditions experienced by each individual and apply a multi-model inference approach to determine which conditions associate with sex reversal. Further, we conduct reduced representation sequencing on a subset of specimens to characterize the population structure of this broadly distributed species. Results: Here we show that sex reversal in this widespread Australian dragon lizard is spatially restricted to the eastern part of the species range. Neither climatic variables during the inferred incubation period nor geographic population genetic structure explain this disjunct distribution of sex reversal. The main source of genetic variation arose from isolation by distance across the species range. Main conclusions: We propose that local genetic adaptation in the temperature threshold for sex reversal can counteract the sex-reversing influence of high incubation temperatures in P. vitticeps. Our study demonstrates that complex evolutionary processes need to be incorporated into modelling biological responses to future climate scenarios

Erectile dysfunction, physical activity and metabolic syndrome: differences in markers of atherosclerosis

<p>Abstract</p> <p>Background</p> <p>Erectile dysfunction (ED), impaired arterial elasticity, elevated resting heart rate as well as increased levels of oxidized LDL and fibrinogen associate with future cardiovascular events. Physical activity is crucial in the prevention of cardiovascular diseases (CVD), while metabolic syndrome (MetS) comprises an increased risk for CVD events. The aim of this study was to assess whether markers of subclinical atherosclerosis are associated with the presence of ED and MetS, and whether physical activity is protective of ED.</p> <p>Methods</p> <p>57 MetS (51.3 ± 8.0 years) and 48 physically active (PhA) (51.1 ± 8.1 years) subjects participated in the study. ED was assessed by the International Index of Erectile Function (IIEF) questionnaire, arterial elasticity by a radial artery tonometer (HDI/PulseWave™ CR-2000) and circulating oxLDL by a capture ELISA immunoassay. Fibrinogen and lipids were assessed by validated methods. The calculation of mean daily energy expenditure of physical exercise was based on a structured questionnaire.</p> <p>Results</p> <p>ED was more often present among MetS compared to PhA subjects, 63.2% and 27.1%, respectively (p < 0.001). Regular physical exercise at the level of > 400 kcal/day was protective of ED (OR 0.12, 95% CI 0.017-0.778, p = 0.027), whereas increased fibrinogen (OR 4.67, 95% CI 1.171-18.627, p = 0.029) and elevated resting heart rate (OR 1.07, 95% CI 1.003-1.138, p = 0.04) were independently associated with the presence of ED. In addition, large arterial elasticity (ml/mmHgx10) was lower among MetS compared to PhA subjects (16.6 ± 4.0 <it>vs</it>. 19.6 ± 4.2, p < 0.001), as well as among ED compared to non-ED subjects (16.7 ± 4.6 <it>vs</it>. 19.0 ± 3.9, p = 0.008). Fibrinogen and resting heart rate were highest and large arterial elasticity lowest among subjects with both MetS and ED.</p> <p>Conclusions</p> <p>Markers of subclinical atherosclerosis associated with the presence of ED and were most evident among subjects with both MetS and ED. Thus, especially MetS patients presenting with ED should be considered at high risk for CVD events. Physical activity, on its part, seems to be protective of ED.</p> <p>Trial registration</p> <p>ClinicalTrials.gov <a href="http://www.clinicaltrials.gov/ct2/show/NCT01119404">NCT01119404</a></p