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

Time-Resolved Exciton Wave Functions from Time-Dependent Density-Functional Theory

Time-dependent density-functional theory (TDDFT) is a computationally efficient first-principles approach for calculating optical spectra in insulators and semiconductors including excitonic effects. We show how exciton wave functions can be obtained from TDDFT via the Kohn–Sham transition density matrix, both in the frequency-dependent linear-response regime and in real-time propagation. The method is illustrated using one-dimensional model solids. In particular, we show that our approach provides insight into the formation and dissociation of excitons in real time. This opens the door to time-resolved studies of exciton dynamics in materials by means of real-time TDDFT

Transition Property for α\alpha-Power Free Languages with α≥2\alpha\geq 2 and k≥3k\geq 3 Letters

In 1985, Restivo and Salemi presented a list of five problems concerning power free languages. Problem $4$ states: Given $\alpha$-power-free words $u$ and $v$, decide whether there is a transition from $u$ to $v$. Problem $5$ states: Given $\alpha$-power-free words $u$ and $v$, find a transition word $w$, if it exists. Let $\Sigma_k$ denote an alphabet with $k$ letters. Let $L_{k,\alpha}$ denote the $\alpha$-power free language over the alphabet $\Sigma_k$, where $\alpha$ is a rational number or a rational "number with $+$". If $\alpha$ is a "number with $+$" then suppose $k\geq 3$ and $\alpha\geq 2$. If $\alpha$ is "only" a number then suppose $k=3$ and $\alpha>2$ or $k>3$ and $\alpha\geq 2$. We show that: If $u\in L_{k,\alpha}$ is a right extendable word in $L_{k,\alpha}$ and $v\in L_{k,\alpha}$ is a left extendable word in $L_{k,\alpha}$ then there is a (transition) word $w$ such that $uwv\in L_{k,\alpha}$. We also show a construction of the word $w$

Repetitions in infinite palindrome-rich words

Rich words are characterized by containing the maximum possible number of distinct palindromes. Several characteristic properties of rich words have been studied; yet the analysis of repetitions in rich words still involves some interesting open problems. We address lower bounds on the repetition threshold of infinite rich words over 2 and 3-letter alphabets, and construct a candidate infinite rich word over the alphabet $\Sigma_2=\{0,1\}$ with a small critical exponent of $2+\sqrt{2}/2$. This represents the first progress on an open problem of Vesti from 2017.Comment: 12 page

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

The biochemical toxin arsenal from ant venoms

© 2016 by the authors; licensee MDPI, Basel, Switzerland. Ants (Formicidae) represent a taxonomically diverse group of hymenopterans with over 13,000 extant species, the majority of which inject or spray secretions from a venom gland. The evolutionary success of ants is mostly due to their unique eusociality that has permitted them to develop complex collaborative strategies, partly involving their venom secretions, to defend their nest against predators, microbial pathogens, ant competitors, and to hunt prey. Activities of ant venom include paralytic, cytolytic, haemolytic, allergenic, pro-inflammatory, insecticidal, antimicrobial, and pain-producing pharmacologic activities, while non-toxic functions include roles in chemical communication involving trail and sex pheromones, deterrents, and aggregators. While these diverse activities in ant venoms have until now been largely understudied due to the small venom yield from ants, modern analytical and venomic techniques are beginning to reveal the diversity of toxin structure and function. As such, ant venoms are distinct from other venomous animals, not only rich in linear, dimeric and disulfide-bonded peptides and bioactive proteins, but also other volatile and non-volatile compounds such as alkaloids and hydrocarbons. The present review details the unique structures and pharmacologies of known ant venom proteinaceous and alkaloidal toxins and their potential as a source of novel bioinsecticides and therapeutic agents

Comparisons of Protein and Peptide Complexity in Poneroid and Formicoid Ant Venoms

© 2016 American Chemical Society. Animal venom peptides are currently being developed as novel drugs and bioinsecticides. Because ants use venoms for defense and predation, venomous ants represent an untapped source of potential bioactive toxins. This study compared the protein and peptide components of the poneroid ants Neoponera commutata, Neoponera apicalis, and Odontomachus hastatus and the formicoid ants Ectatomma tuberculatum, Ectatomma brunneum, and Myrmecia gulosa. 1D and 2D PAGE revealed venom proteins in the mass range 250 kDa. NanoLC-ESI-QTOF MS/MS analysis of tryptic peptides revealed the presence of common venom proteins and also many undescribed proteins. RP-HPLC separation followed by MALDI-TOF MS of the venom peptides also revealed considerable heterogeneity. It was found that the venoms contained between 144 and 1032 peptides with 5-95% of peptides in the ranges 1-4 and 1-8 kDa for poneroid and formicoid ants, respectively. By employing the reducing MALDI matrix 1,5-diaminonapthalene, up to 28 disulfide-bonded peptides were also identified in each of the venoms. In particular, the mass range of peptides from poneroid ants is lower than peptides from other venoms, indicating possible novel structures and pharmacologies. These results indicate that ant venoms represent an enormous, untapped source of novel therapeutic and bioinsecticide leads