Self-consistent DFT+U method for real-space time-dependent density functional theory calculations

We implemented various DFT+U schemes, including the ACBN0 self-consistent density-functional version of the DFT+U method [Phys. Rev. X 5, 011006 (2015)] within the massively parallel real-space time-dependent density functional theory (TDDFT) code Octopus. We further extended the method to the case of the calculation of response functions with real-time TDDFT+U and to the description of non-collinear spin systems. The implementation is tested by investigating the ground-state and optical properties of various transition metal oxides, bulk topological insulators, and molecules. Our results are found to be in good agreement with previously published results for both the electronic band structure and structural properties. The self consistent calculated values of U and J are also in good agreement with the values commonly used in the literature. We found that the time-dependent extension of the self-consistent DFT+U method yields improved optical properties when compared to the empirical TDDFT+U scheme. This work thus opens a different theoretical framework to address the non equilibrium properties of correlated systems

Ants mediate the structure of phytotelm communities in an ant-garden bromeliad

The main theories explaining the biological diversity of rain forests often confer a limited understanding of the contribution of interspecific interactions to the observed patterns. We show how two-species mutualisms can affect much larger segments of the invertebrate community in tropical rain forests. Aechmea mertensii (Bromeliaceae) is both a phytotelm (plant-held water) and an ant-garden epiphyte. We studied the influence of its associated ant species (Pachycondyla goeldii and Camponotus femoratus) on the physical characteristics of the plants, and, subsequently, on the diversity of the invertebrate communities that inhabit their tanks. As dispersal agents for the bromeliads, P. goeldii and C. femoratus influence the shape and size of the bromeliad by determining the location of the seedling, from exposed to partially shaded areas. By coexisting on a local scale, the two ant species generate a gradient of habitat conditions in terms of available resources (space and food) for aquatic invertebrates, the diversity of the invertebrate communities increasing with greater volumes of water and fine detritus. Two-species mutualisms are widespread in nature, but their influence on the diversity of entire communities remains largely unexplored. Because macroinvertebrates constitute an important part of animal production in all ecosystem types, further investigations should address the functional implications of such indirect effects

Photoionization and transient Wannier-Stark ladder in silicon: First-principles simulations versus Keldysh theory

Nonlinear photoionization of dielectrics and semiconductors is widely treated in the framework of the Keldysh theory whose validity is limited to photon energies that are small compared to the band gap and relatively low laser intensities. The time-dependent density functional theory (TDDFT) simulations, which are free of these limitations, enable one to gain insight into nonequilibrium dynamics of the electronic structure. Here we apply TDDFT to investigate the photoionization of silicon crystal by ultrashort laser pulses in a wide range of laser wavelengths and intensities and compare the results with predictions of the Keldysh theory. Photoionization rates derived from the simulations considerably exceed the data obtained with the Keldysh theory within the validity range of the latter. Possible reasons for the discrepancy are discussed and we provide fundamental data on the photoionization rates beyond the limits of the Keldysh theory. By investigating the features of the Stark shift as a function of photon energy and laser field strength, a manifestation of the transient Wannier-Stark ladder states is revealed, which become blurred with increasing laser field strength. Finally, it is shown that the TDDFT simulations can potentially provide reliable data on the electron damping time that is of high importance for large-scale modeling

Invasive North American bullfrogs transmit lethal fungus Batrachochytrium dendrobatidis infections to native amphibian host species

Invasive species can be a threat to native species in several ways, including transmitting lethal infections caused by the parasites they carry. However, invasive species may also be plagued by novel and lethal infections they acquire when invading, making inferences regarding the ability of an invasive host to vector disease difficult from field observations of infection and disease. This is the case for the pathogenic fungus Batrachochytrium dendrobatidis (Bd) in Europe and one invasive host species, the North American bullfrog Lithobates catesbeianus, hypothesized to be responsible for vectoring lethal infection to European native amphibians. We tested this hypothesis experimentally using the alpine newt Ichthyosaura alpestris as our model native host. Our results show that infected bullfrog tadpoles are effective vectors of Bd. Native adult newts co-housed with experimentally infected bullfrog tadpoles became Bd infected (molecular and histological tests). Moreover, the exposed adult newts suffered mortality while the majority of infected bullfrog tadpoles survived until metamorphosis. Invasive species can be a threat to native species in several ways, including transmitting lethal infections caused by the parasites they carry. However, invasive species may also be plagued by novel and lethal infections they acquire when invading, making inferences regarding the ability of an invasive host to vector disease difficult from field observations of infection and disease. This is the case for the pathogenic fungus Batrachochytrium dendrobatidis (Bd) in Europe and one invasive host species, the North American bullfrog Lithobates catesbeianus, hypothesized to be responsible for vectoring lethal infection to European native amphibians. We tested this hypothesis experimentally using the alpine newt Ichthyosaura alpestris as our model native host. Our results show that infected bullfrog tadpoles are effective vectors of Bd. Native adult newts co-housed with experimentally infected bullfrog tadpoles became Bd infected (molecular and histological tests). Moreover, the exposed adult newts suffered mortality while the majority of infected bullfrog tadpoles survived until metamorphosis. These results cannot resolve the historical role of alien species in establishing the distribution of Bd across Europe or other regions in the world where this species was introduced, but they show its potential role as a Bd reservoir capable of transmitting lethal infections to native amphibians. Finally, our results also suggest that the removal of infected bullfrogs from aquatic environments may serve to reduce the availability of Bd in European amphibian communities, offering another justification for bullfrog eradication programmes that are currently underway or may be considere

Detection of Invasive Mosquito Vectors Using Environmental DNA (eDNA) from Water Samples.

Repeated introductions and spread of invasive mosquito species (IMS) have been recorded on a large scale these last decades worldwide. In this context, members of the mosquito genus Aedes can present serious risks to public health as they have or may develop vector competence for various viral diseases. While the Tiger mosquito (Aedes albopictus) is a well-known vector for e.g. dengue and chikungunya viruses, the Asian bush mosquito (Ae. j. japonicus) and Ae. koreicus have shown vector competence in the field and the laboratory for a number of viruses including dengue, West Nile fever and Japanese encephalitis. Early detection and identification is therefore crucial for successful eradication or control strategies. Traditional specific identification and monitoring of different and/or cryptic life stages of the invasive Aedes species based on morphological grounds may lead to misidentifications, and are problematic when extensive surveillance is needed. In this study, we developed, tested and applied an environmental DNA (eDNA) approach for the detection of three IMS, based on water samples collected in the field in several European countries. We compared real-time quantitative PCR (qPCR) assays specific for these three species and an eDNA metabarcoding approach with traditional sampling, and discussed the advantages and limitations of these methods. Detection probabilities for eDNA-based approaches were in most of the specific comparisons higher than for traditional survey and the results were congruent between both molecular methods, confirming the reliability and efficiency of alternative eDNA-based techniques for the early and unambiguous detection and surveillance of invasive mosquito vectors. The ease of water sampling procedures in the eDNA approach tested here allows the development of large-scale monitoring and surveillance programs of IMS, especially using citizen science projects

High-harmonic generation in liquids with few-cycle pulses: effect of laser-pulse duration on the cut-off energy

High-harmonic generation (HHG) in liquids is opening new opportunities for attosecond light sources and attosecond time-resolved studies of dynamics in the liquid phase. In gas-phase HHG, few-cycle pulses are routinely used to create isolated attosecond pulses and to extend the cut-off energy. Here, we study the properties of HHG in liquids, including water and several alcohols, by continuously tuning the pulse duration of a mid-infrared driver from the multi- to the sub-two-cycle regime. Similar to the gas phase, we observe the transition from discrete odd-order harmonics to continuous extreme-ultraviolet emission. However, the cut-off energy is shown to be entirely independent of the pulse duration. This observation is confirmed by ab-initio simulations of HHG in large clusters. Our results support the notion that the cut-off energy is a fundamental property of the liquid, independent of the driving-pulse properties. Combined with the recently reported wavelength-independence of the cutoff, these results confirm the direct sensitivity of HHG to the mean-free paths of slow electrons in liquids. Our results additionally imply that few-cycle mid-infrared laser pulses are suitable drivers for generating isolated attosecond pulses from liquids

Trees as Islands: Canopy Ant Species Richness Increases with the Size of Liana-Free Trees in a Neotropical Forest

The physical characteristics of habitats shape local community structure; a classic example is the positive relationship between the size of insular habitats and species richness. Despite the high density and proximity of tree crowns in forests, trees are insular habitats for some taxa. Specifically, crown isolation (i.e. crown shyness) prevents the movement of small cursorial animals among trees. Here, we tested the hypothesis that the species richness of ants (Sa) in individual, isolated trees embedded within tropical forest canopies increases with tree size. We predicted that this pattern disappears when trees are connected by lianas (woody vines) or when strong interactions among ant species determine tree occupancy. We surveyed the resident ants of 213 tree crowns in lowland tropical forest of Panama. On average, 9.2 (range = 2–20) ant species occupied a single tree crown. Average (± SE) Sa was ca 25% higher in trees with lianas (10.2 ± 0.26) than trees lacking lianas (8.0 ± 0.51). Sa increased with tree size in liana‐free trees (Sa = 10.99A0.256), but not in trees with lianas. Ant species composition also differed between trees with and without lianas. Specifically, ant species with solitary foragers occurred more frequently in trees with lianas. The mosaic‐like pattern of species co‐occurrence observed in other arboreal ant communities was not found in this forest. Collectively, the results of this study indicate that lianas play an important role in shaping the local community structure of arboreal ants by overcoming the insular nature of tree crowns

Ultrafast Light-Induced Lifshitz Transition

Fermi surface is at the heart of our understanding of metals and strongly correlated many-body systems. An abrupt change in the Fermi surface topology, also called Lifshitz transition, can lead to the emergence of fascinating phenomena like colossal magnetoresistance and superconductivity. While Lifshitz transitions have been demonstrated for a broad range of materials and using different types of static external perturbations such as strain, doping, pressure and temperature, a non-equilibrium route toward ultrafast and transient modification of the Fermi surface topology has not been experimentally demonstrated. Combining time-resolved multidimensional photoemission spectroscopy with state-of-the-art TDDFT+U simulations, we introduce a scheme for driving an ultrafast Lifshitz transition in the correlated Weyl semimetal Td-MoTe2. We demonstrate that this non-equilibrium topological electronic transition finds its microscopic origin in the dynamical modification of the effective electronic correlations. These results shed light on a novel ultrafast and all-optical scheme for controlling the Fermi surface topology in correlated quantum materials

Detection of Mitochondrial COII DNA Sequences in Ant Guts as a Method for Assessing Termite Predation by Ants

Termites and ants contribute more to animal biomass in tropical rain forests than any other single group and perform vital ecosystem functions. Although ants prey on termites, at the community level the linkage between these groups is poorly understood. Thus, assessing the distribution and specificity of ant termitophagy is of considerable interest.We describe an approach for quantifying ant-termite food webs by sequencing termite DNA (cytochrome c oxidase subunit II, COII) from ant guts and apply this to a soil-dwelling ant community from tropical rain forest in Gabon. We extracted DNA from 215 ants from 15 species. Of these, 17.2% of individuals had termite DNA in their guts, with BLAST analysis confirming the identity of 34.1% of these termites to family level or better. Although ant species varied in detection of termite DNA, ranging from 63% (5/7; Camponotus sp. 1) to 0% (0/7; Ponera sp. 1), there was no evidence (with small sample sizes) for heterogeneity in termite consumption across ant taxa, and no evidence for species-specific ant-termite predation. In all three ant species with identifiable termite DNA in multiple individuals, multiple termite species were represented. Furthermore, the two termite species that were detected on multiple occasions in ant guts were in both cases found in multiple ant species, suggesting that anttermite food webs are not strongly compartmentalised. However, two ant species were found to consume only Anoplotermes-group termites, indicating possible predatory specialisation at a higher taxonomic level. Using a laboratory feeding test, we were able to detect termite COII sequences in ant guts up to 2 h after feeding, indicating that our method only detects recent feeding events. Our data provide tentative support for the hypothesis that unspecialised termite predation by ants is widespread and highlight the use of molecular approaches for future studies of ant-termite food webs