A Navier Stokes Phase Field Crystal Model for Colloidal Suspensions

We develop a fully continuous model for colloidal suspensions with hydrodynamic interactions. The Navier Stokes Phase Field Crystal (NS-PFC) model combines ideas of dynamic density functional theory with particulate flow approaches and is derived in detail and related to other dynamic density functional theory approaches with hydrodynamic interactions. The derived system is numerically solved using adaptive finite elements and used to analyse colloidal crystallization in flowing environments demonstrating a strong coupling in both directions between the crystal shape and the flow field. We further validate the model against other computational approaches for particulate flow systems for various colloidal sedimentation problems

From Molecular Descriptors to Intrinsic Fish Toxicity of Chemicals:An Alternative Approach to Chemical Prioritization

The European and U.S. chemical agencies have listed approximately 800k chemicals about which knowledge of potential risks to human health and the environment is lacking. Filling these data gaps experimentally is impossible, so in silico approaches and prediction are essential. Many existing models are however limited by assumptions (e.g., linearity and continuity) and small training sets. In this study, we present a supervised direct classification model that connects molecular descriptors to toxicity. Categories can be driven by either data (using k-means clustering) or defined by regulation. This was tested via 907 experimentally defined 96 h LC50 values for acute fish toxicity. Our classification model explained ≈90% of the variance in our data for the training set and ≈80% for the test set. This strategy gave a 5-fold decrease in the frequency of incorrect categorization compared to a quantitative structure-activity relationship (QSAR) regression model. Our model was subsequently employed to predict the toxicity categories of ≈32k chemicals. A comparison between the model-based applicability domain (AD) and the training set AD was performed, suggesting that the training set-based AD is a more adequate way to avoid extrapolation when using such models. The better performance of our direct classification model compared to that of QSAR methods makes this approach a viable tool for assessing the hazards and risks of chemicals

Electronic tuneability of a structurally rigid surface intermetallic and Kondo lattice: CePt5_5 / Pt(111)

We present an extensive study of structure, composition, electronic and magnetic properties of Ce--Pt surface intermetallic phases on Pt(111) as a function of their thickness. The sequence of structural phases appearing in low energy electron diffraction (LEED) may invariably be attributed to a single underlying intermetallic atomic lattice. Findings from both microscopic and spectroscopic methods, respectively, prove compatible with CePt$_5$ formation when their characteristic probing depth is adequately taken into account. The intermetallic film thickness serves as an effective tuning parameter which brings about characteristic variations of the Cerium valence and related properties. Soft x-ray absorption (XAS) and magnetic circular dichroism (XMCD) prove well suited to trace the changing Ce valence and to assess relevant aspects of Kondo physics in the CePt$_5$ surface intermetallic. We find characteristic Kondo scales of the order of 10$^2$ K and evidence for considerable magnetic Kondo screening of the local Ce $4f$ moments. CePt$_5$/Pt(111) and related systems therefore appear to be promising candidates for further studies of low-dimensional Kondo lattices at surfaces.Comment: 14 pages, 11 figure

Organic contaminants in bio-based fertilizer treated soil:Target and suspect screening approaches

Using bio-based fertilizer (BBF) in agricultural soil can reduce the dependency on chemical fertilizer and increase sustainability by recycling nutrient-rich side-streams. However, organic contaminants in BBFs may lead to residues in the treated soil. This study assessed the presence of organic contaminants in BBF treated soils, which is essential for evaluating sustainability/risks of BBF use. Soil samples from two field studies amended with 15 BBFs from various sources (agricultural, poultry, veterinary, and sludge) were analyzed. A combination of QuEChERS-based extraction, liquid chromatography quadrupole time of flight mass spectrometry-based (LC-QTOF-MS) quantitative analysis, and an advanced, automated data interpretation workflow was optimized to extract and analyze organic contaminants in BBF-treated agricultural soil. The comprehensive screening of organic contaminants was performed using target analysis and suspect screening. Of the 35 target contaminants, only three contaminants were detected in the BBF-treated soil with concentrations ranging from 0.4 ng g -1 to 28.7 ng g -1; out of these three detected contaminants, two were also present in the control soil sample. Suspect screening using patRoon (an R-based open-source software platform) workflows and the NORMAN Priority List resulted in tentative identification of 20 compounds (at level 2 and level 3 confidence level), primarily pharmaceuticals and industrial chemicals, with only one overlapping compound in two experimental sites. The contamination profiles of the soil treated with BBFs sourced from veterinary and sludge were similar, with common pharmaceutical features identified. The suspect screening results suggest that the contaminants found in BBF-treated soil might come from alternative sources other than BBFs

Quality Control During Aminoacyl-tRNA Synthesis

The fidelity of translation is determined at two major points: the accuracy of aminoacyl-tRNA selection by the ribosomes and synthesis of cognate amino acid/tRNA pairs by aminoacyl-tRNA synthetases (aaRSs) in the course of the aminoacylation reaction. The most important point in aminoacylation is the accurate recognition of cognate substrates coupled with discrimination of non-cognates. While this is generally accomplished by a single enzyme, we have recently found that discrimination against lysine analogues requires the existence of two unrelated lysyl-tRNA synthetases. For other amino acids, initial recognition is not sufficiently accurate with errors being corrected by an intrinsic editing activity. Recent studies indicate how editing prevents the misinterpretation of phenylalanine as tyrosine in the genetic code and have shown the importance of this process in vivo . More recent studies indicate that while these editing reactions are critical in the cytoplasm, some are absent from mitochondria suggesting that the overall idelity of protein synthesis might be reduced in this compartment

Simultaneous detection of pesticides and pharmaceuticals in three types of bio-based fertilizers by an improved QuEChERS method coupled with UHPLC-q-ToF-MS/MS

Bio-based fertilizers (BBFs) have the potential to contain both pesticides and pharmaceutical residues, which may pose a threat to soils, crops, and human health. However, no analytical screening method is available currently to simultaneously analyze a wide range of contaminants in the complex origin-dependent matrices of BBFs. To fill this gap, our study tested and improved an original QuEChERS method (OQM) for simultaneously analyzing 78 pesticides and 18 pharmaceuticals in BBFs of animal, plant, and ashed sewage sludge origin. In spiked recovery experiments, 34-58 pharmaceuticals and pesticides were well recovered (recovery of 70-120%) via OQM at spiking concentrations levels of 10 ng/g and 50 ng/g in these three different types of BBFs. To improve the extraction efficiency further, ultrasonication and end-over-end rotation were added based on OQM, resulting in the improved QuEChERS method (IQM) that could recover 57-79 pesticides and pharmaceuticals, in the range of 70-120%. The detection limits of this method were of 0.16-4.32/0.48-12.97 ng/g, 0.03-11.02/0.10-33.06 ng/g, and 0.06-5.18/0.18-15.54 ng/g for animal, plant, and ash-based BBF, respectively. Finally, the IQM was employed to screen 15 BBF samples of various origins. 15 BBFs contained at least one pesticide or pharmaceutical with ibuprofen being frequently detected in at concentration levels of 4.1-181 ng/g. No compounds were detected in ash-based BBFs

Convergence of simple adaptive Galerkin schemes based on h − h/2 error estimators

We discuss several adaptive mesh-refinement strategies based on (h − h/2)-error estimation. This class of adaptivemethods is particularly popular in practise since it is problem independent and requires virtually no implementational overhead. We prove that, under the saturation assumption, these adaptive algorithms are convergent. Our framework applies not only to finite element methods, but also yields a first convergence proof for adaptive boundary element schemes. For a finite element model problem, we extend the proposed adaptive scheme and prove convergence even if the saturation assumption fails to hold in general

Long-term variations in Iceland–Scotland overflow strength during the Holocene

The overflow of deep water from the Nordic seas into the North Atlantic plays a critical role in global ocean circulation and climate. Approximately half of this overflow occurs via the Iceland–Scotland (I–S) overflow, yet the history of its strength throughout the Holocene (~ 0–11 700 yr ago, ka) is poorly constrained, with previous studies presenting apparently contradictory evidence regarding its long-term variability. Here, we provide a comprehensive reconstruction of I–S overflow strength throughout the Holocene using sediment grain size data from a depth transect of 13 cores from the Iceland Basin. Our data are consistent with the hypothesis that the main axis of the I–S overflow on the Iceland slope was shallower during the early Holocene, deepening to its present depth by ~ 7 ka. Our results also reveal weaker I–S overflow during the early and late Holocene, with maximum overflow strength occurring at ~ 7 ka, the time of a regional climate thermal maximum. Climate model simulations suggest a shoaling of deep convection in the Nordic seas during the early and late Holocene, consistent with our evidence for weaker I–S overflow during these intervals. Whereas the reduction in I–S overflow strength during the early Holocene likely resulted from melting remnant glacial ice sheets, the decline throughout the last 7000 yr was caused by an orbitally induced increase in the amount of Arctic sea ice entering the Nordic seas. Although the flux of Arctic sea ice to the Nordic seas is expected to decrease throughout the next century, model simulations predict that under high emissions scenarios, competing effects, such as warmer sea surface temperatures in the Nordic seas, will result in reduced deep convection, likely driving a weaker I–S overflow

Mechanical oscillations of magnetic strips under the influence of external field

This is the final version of the article. Available from EDP Sciences via the DOI in this record.JEMS 2012 – Joint European Magnetic SymposiaBy application of a magnetic field on an amorphous metallic strip, the orientation of magnetization of Weiss domains can be changed. When the strip changes its length, this effect is called magnetostriction. We simulate this effect using a finite element method. In particular we calculate the change of the mechanical resonance frequency of a magnetic platelet as a function of the applied field. This gives a quantitative model of the influence of the applied magnetic field on the effective Young's Modulus of the material. © 2013 Owned by the authors, published by EDP Sciences

Simultaneous quantification of 12 different nucleotides and nucleosides released from renal epithelium and in human urine samples using ion-pair reversed-phase HPLC

Nucleotides and nucleosides are not only involved in cellular metabolism but also act extracellularly via P1 and P2 receptors, to elicit a wide variety of physiological and pathophysiological responses through paracrine and autocrine signalling pathways. For the first time, we have used an ion-pair reversed-phase high-performance liquid chromatography ultraviolet (UV)-coupled method to rapidly and simultaneously quantify 12 different nucleotides and nucleosides (adenosine triphosphate, adenosine diphosphate, adenosine monophosphate, adenosine, uridine triphosphate, uridine diphosphate, uridine monophosphate, uridine, guanosine triphosphate, guanosine diphosphate, guanosine monophosphate, guanosine): (1) released from a mouse renal cell line (M1 cortical collecting duct) and (2) in human biological samples (i.e., urine). To facilitate analysis of urine samples, a solid-phase extraction step was incorporated (overall recovery rate ? 98 %). All samples were analyzed following injection (100 ?l) into a Synergi Polar-RP 80 Å (250 × 4.6 mm) reversed-phase column with a particle size of 10 ?m, protected with a guard column. A gradient elution profile was run with a mobile phase (phosphate buffer plus ion-pairing agent tetrabutylammonium hydrogen sulfate; pH 6) in 2-30 % acetonitrile (v/v) for 35 min (including equilibration time) at 1 ml min(-1) flow rate. Eluted compounds were detected by UV absorbance at 254 nm and quantified using standard curves for nucleotide and nucleoside mixtures of known concentration. Following validation (specificity, linearity, limits of detection and quantitation, system precision, accuracy, and intermediate precision parameters), this protocol was successfully and reproducibly used to quantify picomolar to nanomolar concentrations of nucleosides and nucleotides in isotonic and hypotonic cell buffers that transiently bathed M1 cells, and urine samples from normal subjects and overactive bladder patients