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At least 1,135 records · Page 63

Dissecting ion-specific dielectric spectra of sodium-halide solutions into solvation water and ionic contributions

Using extensive equilibrium molecular dynamics simulations we determine the dielectric spectra of aqueous solutions of NaF, NaCl, NaBr, and NaI. The ion-specific and concentration-dependent shifts of the static dielectric constants and the dielectric relaxation times match experimental results very well, which serves as a validation of the classical and non-polarizable ionic force fields used. The purely ionic contribution to the dielectric response is negligible, but determines the conductivity of the salt solutions. The ion-water cross correlation contribution is negative and reduces the total dielectric response by about 5%-10% for 1 M solutions. The dominating water dielectric response is decomposed into different water solvation shells and ion-pair configurations, by this the spectral blue shift and the dielectric decrement of salt solutions with increasing salt concentration is demonstrated to be primarily caused by first-solvation shell water. With rising salt concentration the simulated spectra show more pronounced deviations from a single-Debye form and can be well described by a Cole-Cole fit, in quantitative agreement with experiments. Our spectral decomposition into ionic and different water solvation shell contributions does not render the individual contributions more Debye-like, this suggests the non-Debye-like character of the dielectric spectra of salt solutions not to be due to the superposition of different elementary relaxation processes with different relaxation times. Rather, the non-Debye-like character is likely to be an inherent spectral signature of solvation water around ions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Genetic correlations between switchgrass performance in sward conditions and surrogate measures

Switchgrass (Panicum virgatum L.) breeders use spaced-seedling plots for evaluations of biomass yield, but prior studies are ambiguous about the relationship between performance in spaced plots and commercial seeded sward performance. This study used a split-plot incomplete block design to evaluate 52 half-sib switchgrass families across two years to determine the correlations among four different plot types (including seeded swards) and four individual plant traits. Plots (1.62 m 2 ) that contained 3, 6, and 18 plants had mean yields of 5.92, 8.04, and 11.06 Mg ha –1 , respectively, while seeded-sward plots had a mean of 5.37 Mg ha –1 . In a mixed-model analysis including family-, year-, and plot-type interactions with a spatial-spline correction, the largest proportion of family variance was accounted for by the main family effect (48%), while the plot type-by-family effect was only 17% of family variance. These results indicate that spaced-plant plots are reasonable surrogates for biomass performance in sward conditions. Yield reliability was 0.50 across all plot types with a mean of 0.46 for individual plot types. Surrogates for sward yield varied due to genetic background of the families. Yield of families derived from the Liberty cultivar (n = 32) had genetic correlations with winter survivorship scores (0.66). Diverse lowland ecotype families (n = 20) had genetic correlations with plant height and heading date. This study highlighted a major difference in performance among the plot types, specifically that seeded swards have depressed yield due to high plant density. This should encourage further research for the mechanism behind this difference in performance.

59 BASIC BIOLOGICAL SCIENCES↗

Atmospheric circulation of hot jupiters: dayside-nightside temperature differences. II. Comparison with observations

The full-phase infrared light curves of low-eccentricity hot Jupiters show a trend of increasing fractional dayside–nightside brightness temperature difference with increasing incident stellar flux, both averaged across the infrared and in each individual wavelength band. The analytic theory of Komacek and Showman shows that this trend is due to the decreasing ability with increasing incident stellar flux of waves to propagate from day to night and erase temperature differences. Here, we compare the predictions of this theory with observations, showing that it explains well the shape of the trend of increasing dayside–nightside temperature difference with increasing equilibrium temperature. Applied to individual planets, the theory matches well with observations at high equilibrium temperatures but, for a fixed photosphere pressure of 100 mbar, systematically underpredicts the dayside–nightside brightness temperature differences at equilibrium temperatures less than 2000 K. We interpret this as being due to the effects of a process that moves the infrared photospheres of these cooler hot Jupiters to lower pressures. We also utilize general circulation modeling with double-gray radiative transfer to explore how the circulation changes with equilibrium temperature and drag strengths. As expected from our theory, the dayside–nightside temperature differences from our numerical simulations increase with increasing incident stellar flux and drag strengths. We calculate model phase curves using our general circulation models, from which we compare the broadband infrared offset from the substellar point and dayside–nightside brightness temperature differences against observations, finding that strong drag or additional effects (e.g., clouds and/or supersolar metallicities) are necessary to explain many observed phase curves.

79 ASTRONOMY AND ASTROPHYSICS↗

Calibration Inter-Comparison of MODIS and VIIRS Reflective Solar Bands Using Lunar Observations

Multispectral band observations from Terra and Aqua MODIS, launched in December 1999 and May 2002, respectively, and from SNPP and NOAA-20 VIIRS, launched in November 2011 and October 2017, respectively, have continuously enabled a broad range of applications and studies of the Earth system and its changes via a set of geophysical and environmental parameters. The quality of MODIS and VIIRS science and environmental data products relies strongly on the calibration accuracy and stability of individual sensors, as well as their calibration consistency, especially for the data products generated using observations from sensors across different platforms. Both MODIS and VIIRS instruments carry a similar set of on-board calibrators for their on-orbit calibration. Besides, lunar observations are regularly scheduled and implemented in support of their reflective solar bands (RSB) calibration, especially their long-term stability monitoring. In this paper, we provide an overview of MODIS and VIIRS solar and lunar calibration methodologies applied for the RSB on-orbit calibration, and describe the approach developed for their calibration inter-comparisons using lunar observations, including corrections for the effects caused by differences in the relative spectral response and adopted solar spectra between individual sensors. The MODIS and VIIRS calibration inter-comparison results derived from their regularly scheduled lunar observations are presented and discussed, including associated uncertainties and a comparison with those derived using the Earth-view targets. Also discussed are remaining challenges in lunar calibration and inter-comparison for the Earth-observing sensors, as well as on-going efforts for future improvements.

Multispectral band↗

Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites

Termites are important contributors to carbon and nitrogen cycling in tropical ecosystems. Higher termites digest lignocellulose in various stages of humification with the help of an entirely prokaryotic microbiota housed in their compartmented intestinal tract. Previous studies revealed fundamental differences in community structure between compartments, but the functional roles of individual lineages in symbiotic digestion are mostly unknown. Furthermore, we conducted a highly resolved analysis of the gut microbiota in six species of higher termites that feed on plant material at different levels of humification. Combining amplicon sequencing and metagenomics, we assessed similarities in community structure and functional potential between the major hindgut compartments (P1, P3, and P4). Cluster analysis of the relative abundances of orthologous gene clusters (COGs) revealed high similarities among woodand litter-feeding termites and strong differences to humivorous species. However, abundance estimates of bacterial phyla based on 16S rRNA genes greatly differed from those based on protein-coding genes. In conclusion, the community structure and functional potential of the microbiota in individual gut compartments are clearly driven by the digestive strategy of the host. The metagenomics libraries obtained in this study provide the basis for future studies that elucidate the fundamental differences in the symbiont-mediated breakdown of lignocellulose and humus by termites of different feeding groups. Furthermore, the high proportion of uncultured bacterial lineages in all samples calls for a reference-independent approach for the correct taxonomic assignment of protein-coding genes.

59 BASIC BIOLOGICAL SCIENCES↗

Root and xylem anatomy varies with root length, root order, soil depth and environment in intermediate wheatgrass (Kernza®) and alfalfa

Abstract Background and Aims Deep roots (i.e. >1 m depth) are important for crops to access water when the topsoil is dry. Root anatomy and hydraulic conductance play important roles in the uptake of soil water, particularly water located deep in the soil. We investigated whether root and xylem anatomy vary as a function of root type, order and length, or with soil depth in roots of two deep-rooted perennial crops: intermediate wheatgrass [Thinopyrum intermedium (Kernza®)] and alfalfa (Medicago sativa). We linked the expression of these anatomical traits to the plants’ capacity to take up water from deep soil layers. Methods Using laser ablation tomography, we compared the roots of the two crops for cortical area, number and size of metaxylem vessels, and their estimated root axial hydraulic conductance (ERAHCe). The deepest roots investigated were located at soil depths of 2.25 and at 3.5 m in the field and in rhizoboxes, respectively. Anatomical differences were characterized along 1-m-long individual roots, among root types and orders, as well as between environmental conditions. Key Results For both crops, a decrease in the number and diameter, or both, of metaxylem vessels along individual root segments and with soil depth in the field resulted in a decrease in ERAHCe. Alfalfa, with a greater number of metaxylem vessels per root throughout the soil profile and, on average, a 4-fold greater ERAHCe, took up more water from the deep soil layers than intermediate wheatgrass. Root anatomical traits were significantly different across root types, classes and growth conditions. Conclusions Root anatomical traits are important tools for the selection of crops with enhanced exploitation of deep soil water. The development and breeding of perennial crops for improved subsoil exploitation will be aided by greater understanding of root phenotypes linked to deep root growth and activity.

Plant Sciences↗

Reductive Elimination From Tetra‐Alkyl Cuprates [Me n Cu(CF 3 ) 4− n ] − ( n =0–4): Beyond Simple Oxidation States

Abstract In recent years, the electronic structures of organocuprates in general and the complex [Cu(CF 3 ) 4 ] − in particular have attracted significant interest. A possible key indicator in this context is the reactivity of these species. Nonetheless, this aspect has received only limited attention. Here, we systematically study the series of tetra‐alkyl cuprates [Me n Cu(CF 3 ) 4− n ] − and their unimolecular reactivity in the gas phase, which includes concerted formal reductive eliminations as well as radical losses. Through computational studies, we characterize the electronic structures of the complexes and show how these are connected to their reactivity. We find that all [Me n Cu(CF 3 ) 4− n ] − ions feature inverted ligand fields and that the distinct reactivity patterns of the individual complexes arise from the interplay of different effects.

Zimmer, Bastian↗

Integrative teaching of metabolic modeling and flux analysis with interactive python modules

Abstract The modeling of rates of biochemical reactions—fluxes—in metabolic networks is widely used for both basic biological research and biotechnological applications. A number of different modeling methods have been developed to estimate and predict fluxes, including kinetic and constraint‐based (Metabolic Flux Analysis and flux balance analysis) approaches. Although different resources exist for teaching these methods individually, to‐date no resources have been developed to teach these approaches in an integrative way that equips learners with an understanding of each modeling paradigm, how they relate to one another, and the information that can be gleaned from each. We have developed a series of modeling simulations in Python to teach kinetic modeling, metabolic control analysis, 13C‐metabolic flux analysis, and flux balance analysis. These simulations are presented in a series of interactive notebooks with guided lesson plans and associated lecture notes. Learners assimilate key principles using models of simple metabolic networks by running simulations, generating and using data, and making and validating predictions about the effects of modifying model parameters. We used these simulations as the hands‐on computer laboratory component of a four‐day metabolic modeling workshop and participant survey results showed improvements in learners' self‐assessed competence and confidence in understanding and applying metabolic modeling techniques after having attended the workshop. The resources provided can be incorporated in their entirety or individually into courses and workshops on bioengineering and metabolic modeling at the undergraduate, graduate, or postgraduate level.

Kaste, Joshua A. M.↗

XScan: An Integrated Tool for Understanding Open Source Community-Based Scientific Code

Many scientific communities have adopted community-based models that integrate multiple components to simulate whole system dynamics. The community software projects’ complexity, stems from the integration of multiple individual software components that were developed under different application requirements and various machine architectures, has become a challenge for effective software system understanding and continuous software development. The paper presents an integrated software toolkit called X-ray Software Scanner (in abbreviation, XScan) for a better understanding of large-scale community-based scientific codes. Our software tool provides support to quickly summarize the overall information of scientific codes, including the number of lines of code, programming languages, external library dependencies, as well as architecture-dependent parallel software features. The XScan toolkit also realizes a static software analysis component to collect detailed structural information and provides an interactive visualization and analysis of the functions. We use a large-scale community-based Earth System Model to demonstrate the workflow, functions and visualization of the toolkit. We also discuss the application of advanced graph analytics techniques to assist software modular design and component refactoring.

Zheng, Weijian↗

Inclusion Capture Probability Prediction Model for Bubble Floatation in Turbulent Steel Flow

The turbulent flow around bubbles is simulated for the fixed turbulent kinetic energy. Inclusion motion through the flow field is studied by considering the stochastic effect of turbulence to calculate the capture probability of inclusions with different sizes to a fixed-size individual bubble according to the redefinition. Using the cubic spline interpolation, the capture probability is predicted as functions of the bubble size, inclusion size and turbulent kinetic energy.

36 MATERIALS SCIENCE↗

Correlations among void shape distributions, dynamic damage mode, and loading kinetics [Correlations among spall void shape distributions, damage mode and shock loading kinetics]

Here, three-dimensional x-ray tomography (XRT) provides a nondestructive technique to characterize the size, shape, and location of damage in dynamically loaded metals. A shape-fitting method comprising the inertia tensors of individual damage sites was applied to study differences of spall damage development in face-centered-cubic (FCC) and hexagonal-closed-packed (HCP) multicrystals and for a suite of experiments on high-purity copper to examine the influence of loading kinetics on the spall damage process. Applying a volume-weighted average to the best-fit ellipsoidal aspect-ratios allows a quantitative assessment for determining the extent of damage coalescence present in a shocked metal. It was found that incipient transgranular HCP spall damage nucleates in a lenticular shape and is heavily oriented along particular crystallographic slip directions. In polycrystalline materials, shape distributions indicate that a decrease in the tensile loading rate leads to a transition to coalesced damage dominance and that the plastic processes driving void growth are time dependent.

36 MATERIALS SCIENCE↗

Comparative modelling of the coupled thermal–hydraulic-mechanical (THM) processes in a heated bentonite pellet column with hydration

For the deep geological disposal of high-level radioactive waste in argillaceous rocks, the heat production of the waste is an important driver for thermal–hydraulic-mechanical (THM)-coupled processes. These THM processes influence the properties and conditions of the near field that in many repository designs contains bentonite as a clay buffer. One task in the DECOVALEX-2015 (DEvelopment of COupled models and their VALidation against Experiments) project was the modelling of a heated bentonite column (Villar et al. in Long-term THM tests reports: THM cells for the HE-E test: update of results until February 2014. Deliverable-no: D2.2-7.3. CIEMAT Technical Report IEMAT/DMA/2G210/03/2014, 2014) in preparation for the in situ heater experiment HE-E at the underground rock laboratory Mont Terri. DECOVALEX is an international cooperative project that focuses on the development and validation of mathematical models for simulating such coupled processes associated with disposal in deep geological repositories. Eight modelling teams developed their own THM-coupled models for the bentonite column experiment, using six different simulation codes. Each of the teams individually calibrated the THM parameters for the bentonite material. The eight resulting parameter sets agree well and allow a satisfactory reproduction of the TH measurements by all models. The modelling results for the evolution of temperature and relative humidity over time at three sensors in the bentonite column are in good agreement between the teams and with the measured data. Also, changes of the temperature due to modifications of the insulation and the adjustment of the heating power during the course of the experiment are well reproduced. The models were thus able to reproduce the main physical processes of the experiment, both for vapour-dominated diffusion during the heating phase and combined liquid and vapour transport during a subsequent heating and hydration phase. Lastly, based on the parameter sets, the teams predict a penetration of the water infiltration front in the 48-cm column filled with bentonite pellets to a depth between 25 and 35 cm over the 15,000 h (i.e. over 20 months) of the hydration phase of the experiment.

58 GEOSCIENCES↗

Hydrogen Bonding Stiffens Peptide Amphiphile Supramolecular Filaments by Aza-Glycine Residues

Peptide amphiphiles (PAs) are a class of molecules comprised of short amino acid sequences conjugated to hydrophobic moieties that may exhibit self-assembly in water into supramolecular structures. Here, we investigate here how mechanical properties of hydrogels formed by PA supramolecular nanofibers are affected by hydrogen bond densities within their internal structure by substituting glycine for aza-glycine (azaG) residues. We found that increasing the number of PA molecules that contain azaG up to 5 mol% in PA supramolecular nanofibers increases their persistence length fivefold and decreases their diffusion coefficients as measured by fluorescence recovery after photobleaching. When these PAs are used to create hydrogels, their bulk storage modulus (G') was found to increase as azaG PA content in the supramolecular assemblies increases up to a value of 10 mol% and beyond this value a decrease was observed, likely due to diminished levels of nanofiber entanglement in the hydrogels as a direct result of increased supramolecular rigidity. Interestingly, we found that the bioactivity of the scaffolds toward dopaminergic neurons derived from induced pluripotent stem cells can be enhanced directly by persistence length independently of storage modulus. We hypothesize that this is due to interactions between the cells and the extracellular environment across different size scales: from filopodia adhering to individual nanofiber bundles to cell adhesion sites that interact with the hydrogel as a bulk substrate. Fine tuning of hydrogen bond density in self-assembling peptide biomaterials such as PAs provides an approach to control nanoscale stiffness as part of an overall strategy to optimize bioactivity in these supramolecular systems. supramolecular biomaterials.

36 MATERIALS SCIENCE↗

Sectoral and growth rate control on elemental uptake by individual calcite crystals

Heterogeneous distribution of trace elements (impurities) within individual calcite crystals is a phenomenon commonly observed in natural and laboratory systems. Changes in thermodynamic intensive parameters (mostly chemical potential and temperature) cannot always explain the inhomogeneous impurity patterns in calcite crystals and it has been suggested that growth rate and crystallographic orientation may exert strong effects on elemental incorporation into calcite. In addition, there are a number of experimental studies on micro-scale element (E) distribution between non-equivalent pairs of calcite vicinal faces (known as sectoral zoning); however, the variability of partition coefficients (e.g., K E = (E/Ca) calcite /(E/Ca) fluid ) within individual crystals remains undetermined. In this study, we have extended the work on elemental distribution between crystal sectors to evaluation of partition coefficients of trace and minor elements (Li, B, Mg, and Sr) in calcite crystal faces (10–14) and (01-12), whose growth rates were assessed. Growth entrapment model (GEM) and lattice strain theory were applied to explain K E heterogeneity by varying near-surface diffusivity of Mg and Sr and by varying surface enrichment factor for Li, B, Mg, and Sr. Decoupling of sectoral and growth rate effects reveals that sectoral zoning plays a key role in elemental distribution. More specifically, K Li and K B vary by more than one order of magnitude and K Mg varies by a factor of two within individual crystal faces. Strontium sectoral distribution is different from those of Li, B, and Mg and K Sr varies by up to a factor of two. Finally, these behaviors likely reflect different mechanisms of incorporation of Li, B, Mg, and Sr into calcite.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

GMRES with embedded ensemble propagation for the efficient solution of parametric linear systems in uncertainty quantification of computational models

In a previous work, embedded ensemble propagation was proposed to improve the efficiency of sampling-based uncertainty quantification methods of computational models on emerging computational architectures. It consists of simultaneously evaluating the model for a subset of samples together, instead of evaluating them individually. A first approach introduced to solve parametric linear systems with ensemble propagation is ensemble reduction. In Krylov methods for example, this reduction consists in coupling the samples together using an inner product that sums the sample contributions. Ensemble reduction has the advantages of being able to use optimized implementations of BLAS functions and having a stopping criterion which involves only one scalar. However, the reduction potentially decreases the rate of convergence due to the gathering of the spectra of the samples. In this paper, we investigate a second approach: ensemble propagation without ensemble reduction in the case of GMRES. This second approach solves each sample simultaneously but independently to improve the convergence compared to ensemble reduction. This raises two new issues which are solved in this paper: the fact that optimized implementations of BLAS functions cannot be used anymore and that ensemble divergence, whereby individual samples within an ensemble must follow different code execution paths, can occur. We tackle those issues by implementing a high-performing ensemble GEMV and by using masks. The proposed ensemble GEMV leads to a similar cost per GMRES iteration for both approaches, i.e. with and without reduction. For illustration, we study the performances of the new linear solver in the context of a mesh tying problem. Furthermore, this example demonstrates improved ensemble propagation speed-up without reduction.

BLAS↗

Calculating elements of matrix functions using divided differences

In this work, we introduce a method for calculating individual elements of matrix functions. Our technique makes use of a novel series expansion for the action of matrix functions on basis vectors that is memory efficient even for very large matrices. We showcase our approach by calculating the matrix elements of the exponential of a transverse-field Ising model and evaluating quantum transition amplitudes for large many-body Hamiltonians of sizes up to 2 64 x 2 64 on a single workstation. We also discuss the application of the method to matrix inverses. We relate and compare our method to the state-of-the-art and demonstrate its advantages. We also discuss practical applications of our method.

97 MATHEMATICS AND COMPUTING↗