Large-eddy simulation of saltation over a gaussian dune

International audienceThe aim of this study is to develop a numerical method to simulate the turbulent boundary flow with solidparticle movement over a complex terrain. Large-eddy simulation (LES) is used to compute the flow fieldwith an immersed boundary method, which is imposed by direct forcing as suggested by Lunquist [1].Solid particles are taken into account through a Lagrangian approach. The entrainment model is appliedto initialize the particle movement while particle/soil interaction is accounted for by the rebound model.A canonical simulation case of a turbulent boundary layer flow over a Gaussian dune is performed toverify the accuracy of the immersed boundary method coupled with LES. Recirculation region characteristics,fluid velocity profiles as well as particle concentrations at different streamwise positions arepresented. Good agreement between experimental data and simulated results demonstrates the abilityof the improved solver, which will be applied to the simulation of turbulent boundary layer flow over adeformable sand dune.L'objectif de cette étude est de développer une méthode numérique pour simuler des écoulements tur-bulents sur des terrains complexes. La simulation des grandes échelles (SGE) est utilisée pour calculer l'écoulement du fluide. Cette méthode est couplée avec une méthode de frontière immergée, qui utilise un forçage direct selon une méthode proposée par Lunquist [1]. Les particules solides sont suivies par une approche lagrangienne. Un modèle d'envol est appliqué pour initialiser le mouvement des particules solides tandis que les interactions entre les particules et le sol sont prises en compte par un modèle de rebond. Un cas canonique d'écoulement turbulent sur une colline gaussienne est utilisé pour valider la méthode de frontière immergée couplée avec la SGE. Les caractéristiques de la zone de recirculation ainsi que des profils de vitesse du fluide et de concentration des particules sont presentés. Le bon accord entre les résultats de la simulation et les donnés expérimentales démontre la fiabilité de cette méthode améliorée, qui sera ensuite appliquée pour des cas de simulation d'écoulement turbulent sur une dune déformable

Flow structure transition in thermal vibrational convection

This study investigates the effect of vibration on the flow structure transitions in thermal vibrational convection (TVC) systems, which occur when a fluid layer with a temperature gradient is excited by vibration. Direct numerical simulations of TVC in a two-dimensional enclosed square box were performed over a range of dimensionless vibration amplitudes $0.001 \le a \le 0.3$ and angular frequencies $10^{2} \le \omega \le 10^{7}$, with a fixed Prandtl number of 4.38. The flow visualisation shows the transition behaviour of flow structure upon the varying frequency, characterising three distinct regimes, which are the periodic-circulation regime, columnar regime and columnar-broken regime. Different statistical properties are distinguished from the temperature and velocity fluctuations at the boundary layer and mid-height. Upon transition into the columnar regime, columnar thermal coherent structures are formed, in contrast to the periodic oscillating circulation. These columns are contributed by merging of thermal plumes near the boundary layer, and the resultant thermal updrafts remain at almost fixed lateral position, leading to a decrease in fluctuations. We further find that the critical point of this transition can be described nicely by the vibrational Rayleigh number $Ra_\mathrm{vib}$. As the frequency continues to increase, entering the so-called columnar-broken regime, the columnar structures are broken, and eventually the flow state becomes a large-scale circulation, characterised by a sudden increase in fluctuations. Finally, a phase diagram is constructed to summarise the flow structure transition over a wide range of vibration amplitude and frequency parameters.Comment: 14 pages, 9 figure

Computable features required to evaluate the efficacy of drugs and a universal algorithm to find optimally effective drug in a drug complex

Background The H1N1 pandemic in 2009 and the H5N1 pandemic in 2005 demonstrated that the drugs approved to treat influenza A viruses have low efficacy. This provided a stimulus for new studies of influenza A viruses in the context of the methods used in drug design developed over the past 100 years. Finding new universal drugs is the ultimate goal but its long time horizon is incompatible with emergency situations created by reoccurring influenza outbreaks. Therefore, we propose a computer-aided method for finding efficacious drugs and drug complexes based on the use of the DrugBank database. Methods (1) We start by assembling a panel of target proteins. (2) We then assemble a panel of drugs. (3) This is followed by a selection of benchmark binding pockets based on the panel of target proteins and the panel of drugs. (4) We generate a set of computational features, which measure the efficacy of a drug. (5) We propose a universal program to search for drugs and drug complexes. (6) A case study we report here illustrates how to use this universal program for finding an optimal drug and a drug complex for a given target. (7) Validation of the Azirchromycin and Aspirin complex is provided mathematically. (8) Finally, we propose a simple strategy to validate our computational prediction that the Azirchromycin and Aspirin complex should prove clinically effective. Result A set of computable features are mined and then based on these features, a universal program for finding the potential drug &drug complexes is proposed. Using this universal program, the Azirchromycin and Aspirin complex is selected and its efficacy is predicted mathematically. For clinical validation of this finding, future work is still required

Facile and Scalable Preparation of Graphene Oxide-Based Magnetic Hybrids for Fast and Highly Efficient Removal of Organic Dyes

This study reports the facile preparation and the dye removal efficiency of nanohybrids composed of graphene oxide (GO) and Fe[subscript 3]O[subscript 4] nanoparticles with various geometrical structures. In comparison to previously reported GO/Fe[subscript 3]O[subscript 4] composites prepared through the one-pot, in situ deposition of Fe[subscript 3]O[subscript 4] nanoparticles, the GO/Fe[subscript 3]O[subscript 4] nanohybrids reported here were obtained by taking advantage of the physical affinities between sulfonated GO and Fe[subscript 3]O[subscript 4] nanoparticles, which allows tuning the dimensions and geometries of Fe3O4 nanoparticles in order to decrease their contact area with GO, while still maintaining the magnetic properties of the nanohybrids for easy separation and adsorbent recycling. Both the as-prepared and regenerated nanohybrids demonstrate a nearly 100% removal rate for methylene blue and an impressively high removal rate for Rhodamine B. This study provides new insights into the facile and controllable industrial scale fabrication of safe and highly efficient GO-based adsorbents for dye or other organic pollutants in a wide range of environmental-related applications

Carbon in Chinese grasslands : meta-analysis and theory of grazing effects

Unidad de excelencia María de Maeztu CEX2019-000940-MGlobally, livestock grazing is an important management factor influencing soil degradation, soil health and carbon (C) stocks of grassland ecosystems. However, the effects of grassland types, grazing intensity and grazing duration on C stocks are unclear across large geographic scales. To provide a more comprehensive assessment of how grazing drives ecosystem C stocks in grasslands, we compiled and analyzed data from 306 studies featuring four grassland types across China: desert steppes, typical steppes, meadow steppes and alpine steppes. Light grazing was the best management practice for desert steppes (< 2 sheep ha−1) and typical steppes (3 to 4 sheep ha−1), whereas medium grazing pressure was optimal for meadow steppes (5 to 6 sheep ha−1) and alpine steppes (7 to 8 sheep ha−1) leading to the highest ecosystem C stocks under grazing. Plant biomass (desert steppes) and soil C stocks (meadow steppes) increased under light or medium grazing, confirming the 'intermediate disturbance hypothesis'. Heavy grazing decreased all C stocks regardless of grassland ecosystem types, approximately 1.4 Mg ha−1 per year for the whole ecosystem. The regrowth and regeneration of grasslands in response to grazing intensity (i.e., grazing optimization) depended on grassland types and grazing duration. In conclusion, grassland grazing is a double-edged sword. On the one hand, proper management (light or medium grazing) can maintain and even increase C stocks above- and belowground, and increase the harvested livestock products from grasslands. On the other hand, human-induced overgrazing can lead to rapid degradation of vegetation and soils, resulting in significant carbon loss and requiring long-term recovery. Grazing regimes (i.e., intensity and duration applied) must consider specific grassland characteristics to ensure stable productivity rates and optimal impacts on ecosystem C stocks

What makes efficient circularly polarised luminescence in the condensed phase: aggregation-induced circular dichroism and light emission

In this contribution, we conceptually present a new avenue to construction of molecular functional materials with high performance of circularly polarised luminescence (CPL) in the condensed phase. A molecule (1) containing luminogenic silole and chiral sugar moieties was synthesized and thoroughly characterized. In a solution of 1, no circular dichroism (CD) and fluorescence emission are observed, but upon molecular aggregation, both the CD and fluorescence are simultaneously turned on, showing aggregation-induced CD (AICD) and emission (AIE) effects. The AICD effect is supported by the fact that the molecules readily assemble into right-handed helical nanoribbons and superhelical ropes when aggregated. The AIE effect boosts the fluorescence quantum efficiency (ΦF) by 136 fold (ΦF, ∼0.6% in the solution versus ∼81.3% in the solid state), which surmounts the serious limitations of aggregation-caused quenching effect encountered by conventional luminescent materials. Time-resolved fluorescence study and theoretical calculation from first principles conclude that restriction of the low-frequency intramolecular motions is responsible for the AIE effect. The helical assemblies of 1 prefer to emit right-handed circularly polarised light and display large CPL dissymmetry factors (gem), whose absolute values are in the range of 0.08–0.32 and are two orders of magnitude higher than those of commonly reported organic materials. We demonstrate for the first time the use of a Teflon-based microfluidic technique for fabrication of the fluorescent pattern. This shows the highest gem of −0.32 possibly due to the enhanced assembling order in the confined microchannel environment. The CPL performance was preserved after more than half year storage under ambient conditions, revealing the excellent spectral stability. Computational simulation was performed to interpret how the molecules in the aggregates interact with each other at the molecular level. Our designed molecule represents the desired molecular functional material for generating efficient CPL in the solid state, and the current study shows the best results among the reported organic conjugated molecular systems in terms of emission efficiency, dissymmetry factor, and spectral stability

Approach to Higher Wheat Yield in the Huang-Huai Plain: Improving Post-anthesis Productivity to Increase Harvest Index

Both increased harvest index (HI) and increased dry matter (DM) are beneficial to yield; however, little is known about the priority of each under different yield levels. This paper aims to determine whether HI or DM is more important and identify the physiological attributes that act as indicators of increased yield. Two field experiments involving different cultivation patterns and water-nitrogen modes, respectively, were carried out from 2013 to 2016 in Huang-Huai Plain, China. Plant DM, leaf area index (LAI), and radiation interception (RI) were measured. Increased yield under low yield levels &lt;7500 kg ha-1 was attributed to an increase in both total DM and HI, while increases under higher yield levels &gt;7500 kg ha-1 were largely dependent on an increase in HI. Under high yield levels, HI showed a significant negative correlation with total DM and a parabolic relationship with net accumulation of DM during filling. Higher net accumulation of DM during filling helped slow down the decrease in HI, thereby maintaining a high value. Moreover, net DM accumulation during filling was positively correlated with yield, while post-anthesis accumulation showed a significant linear relationship with leaf area potential (LAP, R2 = 0.404–0.526) and radiation interception potential (RIP, R2 = 0.452–0.576) during grain filling. These findings suggest that the increase in LAP and RIP caused an increase in net DM accumulation after anthesis. Under DM levels &gt;13,000 kg ha-1 at anthesis, maintaining higher LAI and RI in lower layers during grain formation contributed to higher yield. Furthermore, the ratio of upper- to lower-layer RI showed a second-order curve with yield during filling, with an increase in the optimal range with grain development. Pre-anthesis translocation amount, translocation ratios and contribution ratios also showed second-order curves under high yield levels, with optimal values of 3000–4500 kg ha-1, 25–35, and 30–50%, respectively. These results confirm the importance of HI in improving the yield, thereby providing a theoretical basis for wheat production in the Huang-Huai Plain

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe