QuantumATK: an integrated platform of electronic and atomic-scale modelling tools.

QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been previously presented, the purpose of this paper is to give a general overview of the platform. The QuantumATK simulation engines enable electronic-structure calculations using density functional theory or tight-binding model Hamiltonians, and also offers bonded or reactive empirical force fields in many different parametrizations. Density functional theory is implemented using either a plane-wave basis or expansion of electronic states in a linear combination of atomic orbitals. The platform includes a long list of advanced modules, including Green's-function methods for electron transport simulations and surface calculations, first-principles electron-phonon and electron-photon couplings, simulation of atomic-scale heat transport, ion dynamics, spintronics, optical properties of materials, static polarization, and more. Seamless integration of the different simulation engines into a common platform allows for easy combination of different simulation methods into complex workflows. Besides giving a general overview and presenting a number of implementation details not previously published, we also present four different application examples. These are calculations of the phonon-limited mobility of Cu, Ag and Au, electron transport in a gated 2D device, multi-model simulation of lithium ion drift through a battery cathode in an external electric field, and electronic-structure calculations of the composition-dependent band gap of SiGe alloys.

Prediction of deoxynivalenol toxicokinetics in humans by in vitro-to-in vivo extrapolation and allometric scaling of in vivo animal data.

Deoxynivalenol (DON) is the most prevalent mycotoxin in cereals worldwide. It can cause adverse health effects in humans and animals, and maximum levels in food and feed have been implemented by food authorities based on risk assessments derived from estimated intake levels. The lack of human toxicokinetic data such as absorption, distribution, and elimination characteristics hinders the direct calculation of DON plasma levels and exposure. In the present study, we have, therefore, used in vitro-to-in vivo extrapolation of depletion constants in hepatic microsomes from different species and allometric scaling of reported in vivo animal parameters to predict the plasma clearance [0.24 L/(h × kg)] and volume of distribution (1.24 L/kg) for DON in humans. In addition, we have performed a toxicokinetic study with oral and intravenous administration of DON in pigs to establish benchmark parameters for the in vitro extrapolation approach. The determined human toxicokinetic parameters were then used to calculate the bioavailability (50-90%), maximum concentration, and total exposure in plasma, and urinary concentrations under consideration of typical DON levels in grain-based food products. The results were compared to data from biomonitoring studies in human populations.

Effects and biotransformation of the mycotoxin deoxynivalenol in growing pigs fed with naturally contaminated pelleted grains with and without the addition of Coriobacteriaceum DSM 11798.

Deoxynivalenol (DON) is one of the most prevalent Fusarium mycotoxins in grain and can cause economic losses in pig farming due to reduced feed consumption and lower weight gains. Biodetoxification of mycotoxins using bacterial strains has been a focus of research for many years. However, only a few in vivo studies have been conducted on the effectiveness of microbial detoxification of fusariotoxins. This study was therefore aimed at investigating the effect of a feed additive containing the bacterial strain Coriobacteriaceum DSM 11798 (the active ingredient in Biomin® BBSH 797) on growth performance and blood parameters, as well as uptake and metabolism of DON, in growing pigs. Forty-eight crossbred (Landrace-Yorkshire/Duroc-Duroc) weaning pigs were fed with pelleted feed made from naturally contaminated oats, with DON at four concentration levels: (1) control diet (DON < 0.2 mg kg-1), (2) low-contaminated diet (DON = 0.92 mg kg-1), (3) medium-contaminated diet (DON = 2.2 mg kg-1) and (4) high-contaminated diet (DON = 5.0 mg kg-1) and equivalent diets containing DSM 11798 as feed additive. During the first 7 days of exposure, pigs in the highest-dose group showed a 20-28% reduction in feed intake and a 24-34% reduction in weight gain compared with pigs in the control and low-dose groups. These differences were levelled out by study completion. Towards the end of the experiment, dose-dependent reductions in serum albumin, globulin and total serum protein were noted in the groups fed with DON-contaminated feed compared with the controls. The addition of DSM 11798 had no effect on the DON-related clinical effects or on the plasma concentrations of DON. The ineffectiveness of the feed additive in the present study could be a consequence of its use in pelleted feed, which might have hindered its rapid release, accessibility or detoxification efficiency in the pig's gastrointestinal tract.

Skeletal muscle O-GlcNAc transferase is important for muscle energy homeostasis and whole-body insulin sensitivity.

OBJECTIVE: Given that cellular O-GlcNAcylation levels are thought to be real-time measures of cellular nutrient status and dysregulated O-GlcNAc signaling is associated with insulin resistance, we evaluated the role of O-GlcNAc transferase (OGT), the enzyme that mediates O-GlcNAcylation, in skeletal muscle. METHODS: We assessed O-GlcNAcylation levels in skeletal muscle from obese, type 2 diabetic people, and we characterized muscle-specific OGT knockout (mKO) mice in metabolic cages and measured energy expenditure and substrate utilization pattern using indirect calorimetry. Whole body insulin sensitivity was assessed using the hyperinsulinemic euglycemic clamp technique and tissue-specific glucose uptake was subsequently evaluated. Tissues were used for histology, qPCR, Western blot, co-immunoprecipitation, and chromatin immunoprecipitation analyses. RESULTS: We found elevated levels of O-GlcNAc-modified proteins in obese, type 2 diabetic people compared with well-matched obese and lean controls. Muscle-specific OGT knockout mice were lean, and whole body energy expenditure and insulin sensitivity were increased in these mice, consistent with enhanced glucose uptake and elevated glycolytic enzyme activities in skeletal muscle. Moreover, enhanced glucose uptake was also observed in white adipose tissue that was browner than that of WT mice. Interestingly, mKO mice had elevated mRNA levels of Il15 in skeletal muscle and increased circulating IL-15 levels. We found that OGT in muscle mediates transcriptional repression of Il15 by O-GlcNAcylating Enhancer of Zeste Homolog 2 (EZH2). CONCLUSIONS: Elevated muscle O-GlcNAc levels paralleled insulin resistance and type 2 diabetes in humans. Moreover, OGT-mediated signaling is necessary for proper skeletal muscle metabolism and whole-body energy homeostasis, and our data highlight O-GlcNAcylation as a potential target for ameliorating metabolic disorders.

Tuning the activity of Pt alloy electrocatalysts by means of the lanthanide contraction.

The high platinum loadings required to compensate for the slow kinetics of the oxygen reduction reaction (ORR) impede the widespread uptake of low-temperature fuel cells in automotive vehicles. We have studied the ORR on eight platinum (Pt)-lanthanide and Pt-alkaline earth electrodes, Pt5M, where M is lanthanum, cerium, samarium, gadolinium, terbium, dysprosium, thulium, or calcium. The materials are among the most active polycrystalline Pt-based catalysts reported, presenting activity enhancement by a factor of 3 to 6 over Pt. The active phase consists of a Pt overlayer formed by acid leaching. The ORR activity versus the bulk lattice parameter follows a high peaked "volcano" relation. We demonstrate how the lanthanide contraction can be used to control strain effects and tune the activity, stability, and reactivity of these materials.

Correlation between diffusion barriers and alloying energy in binary alloys.

In this paper, we explore the notion that a negative alloying energy may act as a descriptor for long term stability of Pt-alloys as cathode catalysts in low temperature fuel cells. Using density functional theory calculations, we show that there is a correlation between the alloying energy of an alloy, and the diffusion barriers of the minority component. Alloys with a negative alloying energy may show improved long term stability, despite the fact that there is typically a greater thermodynamic driving force towards dissolution of the solute metal over alloying. In addition to Pt, we find that this trend also appears to hold for alloys based on Al and Pd.