Insightful classification of crystal structures using deep learning

Computational methods that automatically extract knowledge from data are critical for enabling data-driven materials science. A reliable identification of lattice symmetry is a crucial first step for materials characterization and analytics. Current methods require a user-specified threshold, and are unable to detect average symmetries for defective structures. Here, we propose a machine-learning-based approach to automatically classify structures by crystal symmetry. First, we represent crystals by calculating a diffraction image, then construct a deep-learning neural-network model for classification. Our approach is able to correctly classify a dataset comprising more than 100 000 simulated crystal structures, including heavily defective ones. The internal operations of the neural network are unraveled through attentive response maps, demonstrating that it uses the same landmarks a materials scientist would use, although never explicitly instructed to do so. Our study paves the way for crystal-structure recognition of - possibly noisy and incomplete - three-dimensional structural data in big-data materials science.Comment: Nature Communications, in press (2018

Surface-induced crystallization in supercooled tetrahedral liquids

Freezing is a fundamental physical phenomenon that has been studied over many decades; yet the role played by surfaces in determining nucleation has remained elusive. Here we report direct computational evidence of surface induced nucleation in supercooled systems with a negative slope of their melting line (dP/dT < 0). This unexpected result is related to the density decrease occurring upon crystallization, and to surface tension facilitating the initial nucleus formation. Our findings support the hypothesis of surface induced crystallization of ice in the atmosphere, and provide insight, at the atomistic level, into nucleation mechanisms of widely used semiconductors.Comment: 5 pages, 4 figure

Exchange Splitting and Charge Carrier Spin Polarization in EuO

High quality thin films of the ferromagnetic semiconductor EuO have been prepared and were studied using a new form of spin-resolved spectroscopy. We observed large changes in the electronic structure across the Curie and metal-insulator transition temperature. We found that these are caused by the exchange splitting of the conduction band in the ferromagnetic state, which is as large as 0.6 eV. We also present strong evidence that the bottom of the conduction band consists mainly of majority spins. This implies that doped charge carriers in EuO are practically fully spin polarized.Comment: 4 pages, 5 figure

High-resolution resonant inelastic soft X-ray scattering as a probe of the crystal electrical field in lanthanides demonstrated for the case of CeRh2Si2

The magnetic properties of rare earth compounds are usually well captured by assuming a fully localized f shell and only considering the Hund's rule ground state multiplet split by a crystal electrical field (CEF). Currently, the standard technique for probing CEF excitations in lanthanides is inelastic neutron scattering. Here we show that with the recent leap in energy resolution, resonant inelastic soft X-ray scattering has become a serious alternative for looking at CEF excitations with some distinct advantages compared to INS. As an example we study the CEF scheme in CeRh2Si2, a system that has been intensely studied for more than two decades now but for which no consensus has been reached yet as to its CEF scheme. We used two new features that have only become available very recently in RIXS, high energy resolution of about 30 meV as well as polarization analysis in the scattered beam, to find a unique CEF description for CeRh2Si2. The result agrees well with previous INS and magnetic susceptibility measurements. Due to its strong resonant character, RIXS is applicable to very small samples, presents very high cross sections for all lanthanides, and further benefits from the very weak coupling to phonon excitation. The rapid progress in energy resolution of RIXS spectrometers is making this technique increasingly attractive for the investigation of the CEF scheme in lanthanides

Local structure of liquid carbon controls diamond nucleation

Diamonds melt at temperatures above 4000 K. There are no measurements of the steady-state rate of the reverse process: diamond nucleation from the melt, because experiments are difficult at these extreme temperatures and pressures. Using numerical simulations, we estimate the diamond nucleation rate and find that it increases by many orders of magnitude when the pressure is increased at constant supersaturation. The reason is that an increase in pressure changes the local coordination of carbon atoms from three-fold to four-fold. It turns out to be much easier to nucleate diamond in a four-fold coordinated liquid than in a liquid with three-fold coordination, because in the latter case the free-energy cost to create a diamond-liquid interface is higher. We speculate that this mechanism for nucleation control is relevant for crystallization in many network-forming liquids. On the basis of our calculations, we conclude that homogeneous diamond nucleation is likely in carbon-rich stars and unlikely in gaseous planets

Origin of interface magnetism in BiMnO3/SrTiO3 and LaAlO3/SrTiO3 heterostructures

Possible ferromagnetism induced in otherwise non-magnetic materials has been motivating intense research in complex oxide heterostructures. Here we show that a confined magnetism is realized at the interface between SrTiO3 and two insulating polar oxides, BiMnO3 and LaAlO3. By using polarization dependent x-ray absorption spectroscopy, we find that in both cases the magnetic order is stabilized by a negative exchange interaction between the electrons transferred to the interface and local magnetic moments. These local magnetic moments are associated to Ti3+ ions at the interface itself for LaAlO3/SrTiO3 and to Mn3+ ions in the overlayer for BiMnO3/SrTiO3. In LaAlO3/SrTiO3 the induced magnetic moments are quenched by annealing in oxygen, suggesting a decisive role of oxygen vacancies in the stabilization of interfacial magnetism.Comment: 5 pages, 4 figure

Estudo da variabilidade entomopatogênicos nematóides populações (Heterorhabditidae) da Argentina

Entomopathogenic nematodes (EPN) belonging to the Heterorhabditidae family are lethal parasites of soil-dwelling insects. Two species were reported in Argentina: Heterorhabditis argentinensis and Heterorhabditis bacteriophora characterized mainly by morphometric features. In this work a comparative and phylogenetic study between five Heterorhabditis populations from Argentina was conducted to analyze the variability between strains and to evaluate the taxonomic position of Heterorhabditis argentinensis. The PCA analyses of morphometric characters separated the larger juvenile, female and male H. argentinensis from H. bacteriophora populations. The juvenile (IJs) stage provided the clearest separation of Heterorhabditis populations presenting the least variability between strains. The variable L and MBW were highly related to H. argentinensis IJs. Three groups were separated by this stage considering PC1 and PC2: one formed by H. bacteriophora OLI, RIV and RN strains, (isolates from Córdoba and Río Negro province), one for H. bacteriophora VELI strain (Buenos Aires province) and one for H. argentinensis (Santa Fe province). Heterorhabditis bacteriophora VELI and H. argentinensis isolated from regions with more rainfalls and humidity presented larger values for morphometric features. Molecular analyses showed the Argentinian populations (H. bacteriophora VELI strain and H. argentinensis), forming a same clade, with six other H. bacteriophora populations (not from Argentina) with a genetic similarity between them of 99%. Heterorhabditis argentinensis presented one unique nucleotide that was not present in any of the other species of the clade. Considering the results of this study H. argentinensis would be conspecific to H. bacteriophora, constituting a strain with a great morphometric variation where the host and climatic conditions could have influenced on the measurements.Nematóides entomopatogênicos (EPN) pertencentes á família Heterorhabditidae são parasitas letais de insetos que vivem no solo. Duas espécies foram relatados na Argentina: Heterorhabditis argentinensis e Heterorhabditis bacteriophora, caracterizada principalmente por características morfométricas. Neste trabalho um estudo comparativo e filogenética entre cinco populações do Heterorhabditis da Argentina foi conduzido para analisar a variabilidade entre as linhagens e avaliar a posição taxonômica das Heterorhabditis argentinensis. Características morfométricas de Heterorhabditis bacteriophora VELI e H. argentinensis isoladas de regiões com mais chuvas e umidade apresentaram dimensões maiores. Analisa o PCA de personagens morfométricas separou a maior juvenil, feminino e masculino H. argentinensis de H. bacteriophora populações. A fase juvenil (JIs) fornece a mais clara separação de populações Heterorhabditis apresentando a menor variação entre as cepas. A L variável e MBW foram altamente relacionada com H. argentinensis JIs. Três grupos foram separados por esta fase considerando PC1 e PC2: um formado por H. bacteriophora OLI, RIV e estirpes RN, (isolados de Córdoba e província de Rio Negro), um para a estirpe H. bacteriophora VELI (província de Buenos Aires) e um para H. argentinensis (província de Santa Fe). Heterorhabditis bacteriophora VELI e H. argentinensis isolado a partir de regiões com mais chuvas e umidade apresentaram maiores valores para as características morfométricas. A análise molecular mostrou as populações da Argentina (estirpe H. bacteriophora VELI e H. argentinensis), formando um mesmo subtipo, com seis outras populações H. bacteriophora (não da Argentina), com uma similaridade genética entre eles de 99%. Heterorhabditis argentinensis apresentado um único nucleótido que não estava presente em nenhum dos outros espécies do clado. Considerando os resultados deste estudo H. argentinensis seria conspecific a H. bacteriophora, constituindo uma estirpe com uma grande variação morfométrica onde o anfitrião e as condições climáticas podem ter influenciado nas medições.Centro de Estudios Parasitológicos y de Vectore

(Meta-)stability and Core–Shell Dynamics of Gold Nanoclusters at Finite Temperature

Gold nanoclusters have been the focus of numerous computational studies, but an atomistic understanding of their structural and dynamical properties at finite temperature is far from satisfactory. To address this deficiency, we investigate gold nanoclusters via ab initio molecular dynamics, in a range of sizes where a core–shell morphology is observed. We analyze their structure and dynamics using state-of-the-art techniques, including unsupervised machine-learning nonlinear dimensionality reduction (sketch-map) for describing the similarities and differences among the range of sampled configurations. In the examined temperature range between 300 and 600 K, we find that whereas the gold nanoclusters exhibit continuous structural rearrangement, they are not amorphous. Instead, they clearly show persistent motifs: a cationic core of 1–5 atoms is loosely bound to a shell which typically displays a substructure resulting from the competition between locally spherical versus planar fragments. Besides illuminating the properties of core–shell gold nanoclusters, the present study proposes a set of useful tools for understanding their nature in operando

Estudo da variabilidade entomopatogênicos nematóides populações (Heterorhabditidae) da Argentina

Entomopathogenic nematodes (EPN) belonging to the Heterorhabditidae family are lethal parasites of soil-dwelling insects. Two species were reported in Argentina: Heterorhabditis argentinensis and Heterorhabditis bacteriophora characterized mainly by morphometric features. In this work a comparative and phylogenetic study between five Heterorhabditis populations from Argentina was conducted to analyze the variability between strains and to evaluate the taxonomic position of Heterorhabditis argentinensis. The PCA analyses of morphometric characters separated the larger juvenile, female and male H. argentinensis from H. bacteriophora populations. The juvenile (IJs) stage provided the clearest separation of Heterorhabditis populations presenting the least variability between strains. The variable L and MBW were highly related to H. argentinensis IJs. Three groups were separated by this stage considering PC1 and PC2: one formed by H. bacteriophora OLI, RIV and RN strains, (isolates from Córdoba and Río Negro province), one for H. bacteriophora VELI strain (Buenos Aires province) and one for H. argentinensis (Santa Fe province). Heterorhabditis bacteriophora VELI and H. argentinensis isolated from regions with more rainfalls and humidity presented larger values for morphometric features. Molecular analyses showed the Argentinian populations (H. bacteriophora VELI strain and H. argentinensis), forming a same clade, with six other H. bacteriophora populations (not from Argentina) with a genetic similarity between them of 99%. Heterorhabditis argentinensis presented one unique nucleotide that was not present in any of the other species of the clade. Considering the results of this study H. argentinensis would be conspecific to H. bacteriophora, constituting a strain with a great morphometric variation where the host and climatic conditions could have influenced on the measurements.Nematóides entomopatogênicos (EPN) pertencentes á família Heterorhabditidae são parasitas letais de insetos que vivem no solo. Duas espécies foram relatados na Argentina: Heterorhabditis argentinensis e Heterorhabditis bacteriophora, caracterizada principalmente por características morfométricas. Neste trabalho um estudo comparativo e filogenética entre cinco populações do Heterorhabditis da Argentina foi conduzido para analisar a variabilidade entre as linhagens e avaliar a posição taxonômica das Heterorhabditis argentinensis. Características morfométricas de Heterorhabditis bacteriophora VELI e H. argentinensis isoladas de regiões com mais chuvas e umidade apresentaram dimensões maiores. Analisa o PCA de personagens morfométricas separou a maior juvenil, feminino e masculino H. argentinensis de H. bacteriophora populações. A fase juvenil (JIs) fornece a mais clara separação de populações Heterorhabditis apresentando a menor variação entre as cepas. A L variável e MBW foram altamente relacionada com H. argentinensis JIs. Três grupos foram separados por esta fase considerando PC1 e PC2: um formado por H. bacteriophora OLI, RIV e estirpes RN, (isolados de Córdoba e província de Rio Negro), um para a estirpe H. bacteriophora VELI (província de Buenos Aires) e um para H. argentinensis (província de Santa Fe). Heterorhabditis bacteriophora VELI e H. argentinensis isolado a partir de regiões com mais chuvas e umidade apresentaram maiores valores para as características morfométricas. A análise molecular mostrou as populações da Argentina (estirpe H. bacteriophora VELI e H. argentinensis), formando um mesmo subtipo, com seis outras populações H. bacteriophora (não da Argentina), com uma similaridade genética entre eles de 99%. Heterorhabditis argentinensis apresentado um único nucleótido que não estava presente em nenhum dos outros espécies do clado. Considerando os resultados deste estudo H. argentinensis seria conspecific a H. bacteriophora, constituindo uma estirpe com uma grande variação morfométrica onde o anfitrião e as condições climáticas podem ter influenciado nas medições.Centro de Estudios Parasitológicos y de Vectore

Effects of Fetal Bovine Serum deprivation in cell cultures on the production of Anticarsia gemmatalis Multinucleopolyhedrovirus

<p>Abstract</p> <p>Background</p> <p><it>Anticarsia gemmatalis </it>is a pest in South America's soybean crops, which could be controlled by the Multinucleopolyhedrovirus of <it>A. gemmatalis </it>(AgMNPV). Currently, its commercial production is based on infected larvae. However, the possibility of using modified baculoviruses in Integrated Pest Management programs has stimulated an interest to develop alternative multiplication processes. This study evaluated the AgMNPV production in UFL-Ag-286 cells previously deprived Fetal Bovine Serum.</p> <p>Results</p> <p>Culture media containing 1% FBS during the previous 48 hours achieved a synchronized condition where 90% of cells were found in G₀/G₁stage, showing the presence of non-filamentous actin. All characteristics were estimated from cellular viability tests, cell actin detection trials and flow cytometer cell cycle analysis. AgMNPV production was tested by transcript studies and budded viruses (BVs) and occlusion bodies (OBs) yield quantitation. Results showed that the productivity in FBS deprived cells was 9.8 times more in BVs and 3.8 times more in OBs with respect to non-treated cells.</p> <p>Conclusions</p> <p>UFL-Ag-286 cells previously deprived in FBS shown to be a better host for AgMNPV propagation, increasing the useful for both <it>in vitro </it>bioinsecticide production and applications such as recombinant protein expression or gene delivery.</p