Potential transferability and the Knowledgebase of Interatomic Models

Empirical (fitted) interatomic potentials are widely used to predict the response of materials and structures in atomistic simulations. The ability of a potential to predict behavior that it was not fitted to reproduce is referred to as its “transferability.” Despite the importance of the notion of transferability in selecting an empirical potential for a specific application, it has not yet been rigorously addressed by the materials simulation community. This is now possible due to the forthcoming Knowledgebase of Interatomic Models (https://openkim.org) which promises to serve as an abundant source of predictions of potentials and the corresponding first principles and experimental data for various material properties. Making use of this novel data resource in a cumulative manner, we compare representations of atomic environments as well as nonparametric supervised learning algorithms which can be used to systematically define and predict the transferability of empirical potentials

Ensuring reliability, reproducibility and transferability in atomistic simulations: The knowledgebase of interatomic models (https://openkim.org)

Atomistic simulations using empirical interatomic potentials play a key role in realistic scientific and industrial applications. This discussion describes an NSF-funded effort to develop an open-source online tool for promoting the use and reliability of interatomic models. The Knowledgebase of Interatomic Models (https://openkim.org) allows users to compare model predictions with reference data, to generate new predictions by uploading simulation test codes, and to download models conforming to an application programming interface (API) standard that has been developed in collaboration with the atomistic simulation community. An overview will be given of the KIM project and its main components which include the KIM API, the KIM data structure for representing arbitrary material properties, the KIM processing pipeline, and the KIM visualization framework

Knowledgebase of Interatomic Models application programming interface as a standard for molecular simulations

Nanoscale modeling of materials often involves the use of molecular simulations or multiscale methods. These approaches frequently use empirical (fitted) interatomic potentials to represent the response of the material. As part of the open Knowledgebase of Interatomic Models (KIM) project (https://openkim.org), an application programming interface (API) for interatomic potentials has been developed in consultation with key members of the materials simulation community. The KIM API is beginning to emerge as a standard for atomistic simulations of materials. This API makes it possible for any KIM-compliant (KIM API conforming) simulation code (“Simulator”) to seamlessly use any KIM-compliant potential (“Model”) obtained from https://openkim.org. The KIM API is also necessary for the KIM Processing Pipeline in https://openkim.org to automatically compute the predictions of stored Models for a variety of material properties by linking them to computer programs called “Tests” that perform these calculations. The KIM API is lightweight and efficient, supports physical unit conversion, a variety of common neighbor list and boundary conditions used in atomistic simulations, and provides multilanguage support for C++, C, Fortran 2003, Fortran 90/95, and Fortran 77, allowing Simulators and Models written in any of these languages to work together

Meningkatkan Kemampuan Bahasa Inggris Siswa Melalui Model Pembelajaran Kooperatif Tipe Think Pair and Share (TPS) Berbasis Karya Sastra pada Sekolah Menengah Pertama di Kota Makassar

Ringkasan: Kurikulum Tingkat Satuan Pendidikan (KTSP) dalam pelaksanaannya lebih cenderung kepada pendekatan Manajemen Berbasis Sekolah (MBS) atau desentralisasi; guru mengembangkan KTSP dan silabusnya berdasarkan kerangka dasar kurikulum dan standar kompetensi lulusan dari Standar Nasional Pendidikan. Bahasa Inggris untuk satuan tingkat pendidikan menengah termasuk mata pelajaran wajib yang harus diajarkan kepada para siswa di SMP. Apakah pembelajaran bahasa Inggris menggunakan kooperatif learning, Tipe Think Pair ami Share (TPS) berbasis karya sastra dapat meningkatkan kemampuan bahasa Inggris siswa? Penelitian ini bertujuan untuk mengetahui apakah pembelajaran bahasa Inggris menggunakan kooperatif learning. Tipe. Think Pair and Share (TPS) berbasis karya sastra dapat meningkatkan kemampuan bahasa Inggris siswa. Penelitian Hasil penelitian menunjukkan bahwa pembelajaran bahasa Inggris pada Sekolah Menengah Pertama pada SMP Negeri 36 Makassar menggunakan model pembelajaran kooperatif learning, Tipe Think Pair and Share f TPS) berbasis karya sastra dapat meningkatkan kemampuan bahasa Inggris siswa

The only African wild tobacco, Nicotiana africana: Alkaloid content and the effect of herbivory

Herbivory in some Nicotiana species is known to induce alkaloid production. This study examined herbivore-induced defenses in the nornicotine-rich African tobacco N. africana, the only Nicotiana species indigenous to Africa. We tested the predictions that: 1) N. africana will have high constitutive levels of leaf, flower and nectar alkaloids; 2) leaf herbivory by the African bollworm Helicoverpa armigera will induce increased alkaloid levels in leaves, flowers and nectar; and 3) increased alkaloid concentrations in herbivore-damaged plants will negatively affect larval growth. We grew N. africana in large pots in a greenhouse and exposed flowering plants to densities of one, three and six fourth-instar larvae of H. armigera, for four days. Leaves, flowers and nectar were analyzed for nicotine, nornicotine and anabasine. The principal leaf alkaloid was nornicotine (mean: 28 µg/g dry mass) followed by anabasine (4.9 µg/g) and nicotine (0.6 µg/g). Nornicotine was found in low quantities in the flowers, but no nicotine or anabasine were recorded. The nectar contained none of the alkaloids measured. Larval growth was reduced when leaves of flowering plants were exposed to six larvae. As predicted by the optimal defense theory, herbivory had a localized effect and caused an increase in nornicotine concentrations in both undamaged top leaves of herbivore damaged plants and herbivore damaged leaves exposed to one and three larvae. The nicotine concentration increased in damaged compared to undamaged middle leaves. The nornicotine concentration was lower in damaged leaves of plants exposed to six compared to three larvae, suggesting that N. africana rather invests in new growth as opposed to protecting older leaves under severe attack. The results indicate that the nornicotine-rich N. africana will be unattractive to herbivores and more so when damaged, but that potential pollinators will be unaffected because the nectar remains alkaloid-free even after herbivory

Revisiting the species list of freshwater fish in Israel based on DNA barcoding

Abstract Israel's region forms a continental bridge; hence, the freshwater fish fauna in Israel consists of unique populations of species that originated from Africa, Asia, or Europe and are often endemic or at the edge of their distribution range. Worldwide, fish biodiversity suffers significantly from pressures and disturbances of freshwater habitats, especially in arid regions, such as in parts of Israel. Biodiversity conservation requires efficient tools for monitoring changes in populations. DNA barcoding, by complementing and enhancing species identification, provides such monitoring tools. In this study, over 200 specimens representing over 28 species were DNA barcoded and together with previously available records, a DNA barcoding database for freshwater fish of Israel was established. Of the 71 distinct barcodes generated, 37% were new, attesting to the uniqueness of fish populations in Israel. For most species, morphological and molecular species identifications agreed. However, discrepancies were found for five genera. Based on DNA barcoding, we propose Acanthobrama telavivensis as a junior synonym for Acanthobrama lissneri. In Garra spp., we propose splitting Garra nana into two species and assigning Garra rufa in the region to Garra jordanica, or possibly to two species. Israeli Pseudophoxinus kervillei is not the same species as in Syria and Lebanon. However, Pseudophoxinus syriacus might not be endangered since it is genetically very similar to Pseudophoxinus drusensis. In Israel, instead of five reported Oxynoemacheilus species, combining DNA barcoding with morphology suggests only three. Genetic and geographic separation suggested that Aphanius mento is likely a species complex. The study provides a thorough barcoding database, suggests significant species reconsiderations in the region, and highlights the Sea of Galilee and the Beit She'an valley streams as biodiversity “hotspots.” This study will therefore promote further studying of the fish species in the region and their ecology, as well as the monitoring and conservation of freshwater fish biodiversity in Israel and the region

Establishing and using a genetic database for resolving identification of fish species in the Sea of Galilee, Israel.

Freshwaters are a very valuable resource in arid areas, such as Mediterranean countries. Freshwater systems are vulnerable ecological habitats, significantly disturbed globally and especially in arid areas. The Sea of Galilee is the largest surface freshwater body in the Middle East. It is an isolated habitat supporting unique fish populations, including endemic species and populations on the edge of their distribution range. Using the Sea of Galilee for water supply, fishing and recreation has been placing pressure on these fish populations. Therefore, efficient monitoring and effective actions can make a difference in the conservation of these unique fish populations. To set a baseline and develop molecular tools to do so, in this study, DNA barcoding was used to establish a database of molecular species identification based on sequences of Cytochrome C Oxidase subunit I gene. DNA barcodes for 22 species were obtained and deposited in Barcode of Life Database. Among these, 12 barcodes for 10 species were new to the database and different from those already there. Barcode sequences were queried against the database and similar barcodes from the same and closely related species were obtained. Disagreements between morphological and molecular species identification were identified for five species, which were further studied by phylogenetic and genetic distances analyses. These analyses suggested the Sea of Galilee contained hybrid fish of some species and other species for which the species definition should be reconsidered. Notably, the cyprinid fish defined as Garra rufa, should be considered as Garra jordanica. Taken together, along with data supporting reconsideration of species definition, this study sets the basis for further using molecular tools for monitoring fish populations, understanding their ecology, and effectively managing their conservation in this unique and important habitat and in the region