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At least 235 records · Page 13

Low-order preconditioning of the Stokes equations

A well-known strategy for building effective preconditioners for higher-order discretizations of some PDEs, such as Poisson's equation, is to leverage effective preconditioners for their low-order analogs. In this work, we show that high-quality preconditioners can also be derived for the Taylor–Hood discretization of the Stokes equations in much the same manner. In particular, we investigate the use of geometric multigrid based on the Q 1 iso Q 2 /Q 1 discretization of the Stokes operator as a preconditioner for the Q 2 /Q 1 discretization of the Stokes system. We utilize local Fourier analysis to optimize the damping parameters for Vanka and Braess–Sarazin relaxation schemes and to achieve robust convergence. Furthermore, these results are then verified and compared against the measured multigrid performance. While geometric multigrid can be applied directly to the Q 2 /Q 1 system, our ultimate motivation is to apply algebraic multigrid within solvers for Q 2 /Q 1 systems via the Q 1 iso Q 2 /Q 1 discretization, which will be considered in a companion paper.

97 MATHEMATICS AND COMPUTING↗

Long-term Coarsening and Function-time Evolution of an Initiator Powder

Long-term effectiveness of high-explosive devices necessitates maintaining a level of specific surface area of initiating powder components within specified margins. This ensures that ignition and detonation performance of the powder does not degrade significantly over time. Flow permeametry is a commonly employed surface characterization tool in this context, as embodied in the Fisher sub-sieve surface area (FSSA). Recently we made alterations to the commercial permeametry apparatus that enables accurate in situ measurements of FSSA using only ~ 100 mg samples. In this work we report on a 24-month aging study in such modified sample holders at elevated temperatures of 40 oC and 60 oC. Through a process called time-temperature-superposition (TTS) the resulting isotherms are translated into a single master curve that predicts powder FSSA evolution over decades under ambient temperature conditions. We generate master curves for two different powders, i.e., pure PETN and 1 wt% added TriPEON, and show that the TriPEON-doped powder coarsens at a rate a few times slower than the non-doped powder. Activation barriers computed from the TTS shift factors shed some light on the coarsening mechanisms.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Quantized Grain Boundary States Promote Nanoparticle Alignment During Imperfect Oriented Attachment

Oriented attachment (OA) has become a well-recognized mechanism for the growth of metal, ceramic, and biomineral crystals. While many computational and experimental studies of OA have shown that particles can attach with some misorientation then rotate to remove adjoining grain boundaries, the underlying atomistic pathways for this “Imperfect OA” process remain the subject of debate. In this paper, molecular dynamics and in situ TEM were used to probe the crystallographic evolution of up to 30 gold and copper nanoparticles during aggregation. It was found that Imperfect OA occurs because (1) grain boundaries become quantized when their size is comparable to the separation between constituent dislocations and (2) kinetic barriers associated with the glide of grain boundary dislocations are small. In support of these findings, TEM experiments show the formation of a single crystal aggregate after annealing 9 initially misoriented, agglomerated particles with evidence of dislocation slip and twin formation during particle/grain alignment. These observations motivate future work on assembled nanocrystals with tailored defects and call for a revision of Read-Shockley models for grain boundary energies in nanocrystalline materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sequential Separation of Linear, Mono–, and Di–Branched Hexane Isomers on a Robust Coordination Polymer with Nonbonding Flexibility

Efficient separation of hexane isomers is a crucial process for upgrading gasoline. Herein, the sequential separation of linear, mono-, and di-branched hexane isomers by a robust stacked 1D coordination polymer termed as Mn-dhbq ([Mn(dhbq)(H 2 O) 2 ], H 2 dhbq = 2,5-dihydroxy-1,4-benzoquinone) is reported. The interchain space of the activated polymer is of optimal aperture size (5.58 Å) that could exclude 2,3-dimethylbutane, while the chain structure can discriminate n-hexane with high capacity (1.53 mmol g –1 at 393 K, 6.67 kPa) by high-density open metal sites (5.18 mmol g –1 ). With the temperature- and adsorbate-dependent swelling of interchain spaces, the affinity between 3-methylpentane and Mn-dhbq can be deliberately controlled from sorption to exclusion, and thus a complete separation of ternary mixture can be achieved. Column breakthrough experiments confirm the excellent separation performance of Mn-dhbq. Furthermore, the ultrahigh stability and easy scalability further highlight the application prospect of Mn-dhbq for separation of hexane isomers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Long‐Range Electron Transport Rates Depend on Wire Dimensions in Cytochrome Nanowires

Abstract The ability to redirect electron transport to new reactions in living systems opens possibilities to store energy, generate new products, or probe physiological processes. Recent work by Huang et al. showed that 3D crystals of small tetraheme cytochromes (STC) can transport electrons over nanoscopic to mesoscopic distances by an electron hopping mechanism, making them promising materials for nanowires. However, fluctuations at room temperature may distort the nanostructure, hindering efficient electron transport. Classical molecular dynamics simulations of these fluctuations at the nano‐ and mesoscopic scales allowed us to develop a graph network representation to estimate maximum electron flow that can be driven through STC wires. In longer nanowires, transient structural fluctuations at protein‐protein interfaces tended to obstruct efficient electron transfer, but these blockages are ameliorated in thicker crystals where alternative electron transfer pathways become more efficient. The model implies that more flexible proteinprotein interfaces limit the required minimum diameter to carry currents commensurate with conventional electronics.

Chemistry↗

High-Resolution Momentum Imaging—From Stern’s Molecular Beam Method to the COLTRIMS Reaction Microscope [Book Chapter]

Multi-particle momentum imaging experiments are now capable of providing detailed information on the properties and the dynamics of quantum systems in Atomic, Molecular and Photon (AMO) physics. Historically, Otto Stern can be considered the pioneer of high-resolution momentum measurements of particles moving in a vacuum and he was the first to obtain sub-atomic unit (a.u.) momentum resolution (Schmidt-Böcking et al. in The precision limits in a single-event quantum measurement of electron momentum and position, these proceedings). A major contribution to modern experimental atomic and molecular physics was his so-called molecular beam method, which Stern developed and employed in his experiments. With this method he discovered several fundamental properties of atoms, molecules and nuclei. As corresponding particle detection techniques were lacking during his time, he was only able to observe the averaged footprints of large particle ensembles. Today it is routinely possible to measure the momenta of single particles, because of the tremendous progress in single particle detection and data acquisition electronics. A “state-of-the-art” COLTRIMS reaction microscope can measure, for example, the momenta of several particles ejected in the same quantum process in coincidence with sub-a.u. momentum resolution. Such setups can be used to visualize the dynamics of quantum reactions and image the entangled motion of electrons inside atoms and molecules. This review will briefly summarize Stern’s work and then present in longer detail the historic steps of the development of the COLTRIMS reaction microscope. Furthermore, some benchmark results are shown which initially paved the way for a broad acceptance of the COLTRIMS approach. Finally, a small selection of milestone work is presented which has been performed during the last two decades.

Jahnke, T.↗

A Topological Approach for Motion Track Discrimination

Detecting small targets at range is difficult because there is not enough spatial information present in an image sub-region containing the target to use correlation-based methods to differentiate it from dynamic confusers present in the scene. Moreover, this lack of spatial information also disqualifies the use of most state-of-the-art deep learning image-based classifiers. Here, we use characteristics of target tracks extracted from video sequences as data from which to derive distinguishing topological features that help robustly differentiate targets of interest from confusers. In particular, we calculate persistent homology from time-delayed embeddings of dynamic statistics calculated from motion tracks extracted from a wide field-of-view video stream. In short, we use topological methods to extract features related to target motion dynamics that are useful for classification and disambiguation and show that small targets can be detected at range with high probability.

Emerson, Tegan H.↗

Grassmannians for scattering amplitudes in 4d $\mathcal{N}=4 $ SYM and 3d ABJM

Scattering amplitudes in 4d N=4 super Yang-Mills theory (SYM) can be described by Grassmannian contour integrals whose form depends on whether the external data is encoded in momentum space, twistor space, or momentum twistor space. Here, after a pedagogical review, we present a new, streamlined proof of the equivalence of the three integral formulations. A similar strategy allows us to derive a new Grassmannian integral for 3d N = 6 ABJM theory amplitudes in momentum twistor space: it is a contour integral in an orthogonal Grassmannian with the novel property that the internal metric depends on the external data. The result can be viewed as a central step towards developing an amplituhedron formulation for ABJM amplitudes. Various properties of Grassmannian integrals are examined, including boundary properties, pole structure, and a homological interpretation of the global residue theorems for N = 4 SYM.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The Role of Sexual Dimorphism and Tissue Selection in Ecotoxicological Studies Using the Riparian Spider Tetragnatha elongata

Tetragnathid spiders (Tetragnatha spp.) found in riparian habitats have recently been used as bioindicators of sediment contamination and insect-mediated contaminant flux. We investigated whether sexual dimorphism (size and behavior) influenced the female:male ratio in composite samples, stable isotope ratios (carbon [δ{sup 13}C], nitrogen [δ{sup 15}N]), and Hg concentrations in the southern United States. Additionally, we explored whether biomass for contaminant analysis could be preserved by using the legs of tetragnathids as a surrogate for whole-body δ{sup 13}C and δ{sup 15}N signatures. We found that female tetragnathids were significantly larger than male spiders and represented a larger proportion of spiders collected at all sites. However, despite the difference in size between sexes, no differences in growth dynamics, isotopic signatures (δ{sup 13}C and δ{sup 15}N), or mercury concentrations were observed. It was determined that the leg of a tetragnathid can accurately represent the stable isotope signature of an entire spider.

54 ENVIRONMENTAL SCIENCES↗

Repetitive diacetyl vapor exposure promotes ubiquitin proteasome stress and precedes bronchiolitis obliterans pathology

Bronchiolitis obliterans (BO) is a devastating lung disease seen commonly after lung transplant but also seen following severe respiratory tract infection or chemical inhalation exposure. Diacetyl (DA; 2,3-butanedione), highly reactive alpha-diketone is known to cause BO when inhaled, however, the mechanisms of how inhalation exposure leads to BO development remains poorly understood. In the current work, we combined two clinically relevant models for studying the pathogenesis of DA-induced BO: (1) an in vivo rat model of repetitive DA vapor exposures with recovery and (2) an in vitro model of primary human airway epithelial cells exposed to pure DA vapors. Rats exposed to 5 consecutive days 200 parts-per-million DA 6 hrs per day had worsening survival, persistent hypoxemia, poor weight gain, and histologic evidence of BO 14 days after DA exposure cessation. At the end of exposure, increased expression of the ubiquitin stress protein, ubiquitin-C, accumulated within DA-exposed rat lung homogenates, localized primarily to the airway epithelium, the primary site of BO development, and did not occur in air-exposed controls. Lung proteasome activity increased concurrently after DA exposure. In primary human airway cultures, global proteomics analysis identified 519 significantly modified proteins in DA-exposed samples relative to controls with the ubiquitin proteasome system, endosomal reticulum transport, and the response to unfolded protein pathways being upregulated while cell-cell adhesion and oxidation-reduction pathways being downregulated in DA-exposed samples. Altogether, repetitive DA vapor exposure resulted in abundant protein damage, accumulation of polyubiquinated proteins, and ubiquitin proteasome stress prior to the development of chemical-induced BO pathology.

59 BASIC BIOLOGICAL SCIENCES↗

Intronic and plasmid-derived regions contribute to the large mitochondrial genome sizes of Agaricomycetes

Sizes of mitochondrial genomes vary extensively between fungal species although they typically contain a conserved set of core genes. We have characterised the mitochondrial genome of the conifer root rot pathogen Heterobasidion irregulare and compared the size, gene content and structure of 20 Basidiomycete mitochondrial genomes. The mitochondrial genome of H. irregulare was 114, 193 bp and contained a core set of 15 protein coding genes, two rRNA genes and 26 tRNA genes. In addition, we found six non-conserved open reading frames (ORFs) and four putative plasmid genes clustered in three separate regions together with 24 introns and 14 intronic homing endonuclease genes, unequally spread across seven of the core genes. The size differences among the 20 Basidiomycetes can largely be explained by length variation of intergenic regions and introns. The Agaricomycetes contained the nine largest mitochondrial genomes in the Basidiomycete group and Agaricomycete genomes are significantly (p < 0.001) larger than the other Basidiomycetes. A feature of the Agaricomycete mitochondrial genomes in this study was the simultaneous occurrence of putative plasmid genes and non-conserved ORFs, with Cantharellus cibarius as only exception, where no non-conserved ORF was identified. This indicates a mitochondrial plasmid origin of the non-conserved ORFs or increased mitochondrial genome dynamics of species harbouring mitochondrial plasmids. We hypothesise that two independent factors are the driving forces for large mitochondrial genomes: the homing endonuclease genes in introns and integration of plasmid DNA.

59 BASIC BIOLOGICAL SCIENCES↗

Automated segmentation of porous thermal spray material CT scans with predictive uncertainty estimation

Abstract Thermal sprayed metal coatings are used in many industrial applications, and characterizing the structure and performance of these materials is vital to understanding their behavior in the field. X-ray computed tomography (CT) enables volumetric, nondestructive imaging of these materials, but precise segmentation of this grayscale image data into discrete material phases is necessary to calculate quantities of interest related to material structure. In this work, we present a methodology to automate the CT segmentation process as well as quantify uncertainty in segmentations via deep learning. Neural networks (NNs) have been shown to excel at segmentation tasks; however, memory constraints, class imbalance, and lack of sufficient training data often prohibit their deployment in high resolution volumetric domains. Our 3D convolutional NN implementation mitigates these challenges and accurately segments full resolution CT scans of thermal sprayed materials with maps of uncertainty that conservatively bound the predicted geometry. These bounds are propagated through calculations of material properties such as porosity that may provide an understanding of anticipated behavior in the field.

Martinez, Carianne↗

Determining the roles of the three alcohol dehydrogenases (AdhA, AdhB and AdhE) in Thermoanaerobacter ethanolicus during ethanol formation

Abstract Thermoanaerobacter ethanolicus is a promising candidate for biofuel production due to the broad range of substrates it can utilize and its high ethanol yield compared to other thermophilic bacteria, such as Clostridium thermocellum. Three alcohol dehydrogenases, AdhA, AdhB and AdhE, play key roles in ethanol formation. To study their physiological roles during ethanol formation, we deleted them separately and in combination. Previously, it has been thought that both AdhB and AdhE were bifunctional alcohol dehydrogenases. Here we show that AdhE has primarily acetyl-CoA reduction activity (ALDH) and almost no acetaldehyde reduction (ADH) activity, whereas AdhB has no ALDH activity and but high ADH activity. We found that AdhA and AdhB have similar patterns of activity. Interestingly, although deletion of both adhA and adhB reduced ethanol production, a single deletion of either one actually increased ethanol yields by 60–70%.

Zhou, Jilai↗

Sensitivity of Turbine-Height Wind Speeds to Parameters in the Planetary Boundary-Layer Parametrization Used in the Weather Research and Forecasting Model: Extension to Wintertime Conditions

This work extends the model sensitivity analysis of Yang et al. (Boundary-Layer Meteorology, 2017, Vol. 162, 117-142) to include results for February 2011, in addition to May of the same year. We investigated the sensitivity of simulated hub-height wind speeds to the selection of 26 parameters applied in the Mellor-Yamada-Nakanishi-Niino (MYNN) planetary boundary-layer parameterization in the Weather Research and Forecasting (WRF) model, including parameters used to represent the dissipation of turbulence kinetic energy (TKE), Prandtl number (Pr), and turbulence length scales. Differences in the sensitivity of the ensemble of simulated wind speed to the various parameters can largely be explained by changes in the static stability. The largest monthly differences were found during the day, while the sensitivity to many of the parameters during the night were similar regardless of the month. This finding is consistent with an increased frequency of day-time stable conditions in February compared to May. The spatial variability of the sensitivity to TKE dissipation, Pr, and k can also be attributed to variability in the static stability across the domain at any point in time.

parametrization schemes, Parametric sensitivity, P↗

Comparison of Observations and Predictions of Daytime Planetary-Boundary-Layer Heights and Surface Meteorological Variables in the Columbia River Gorge and Basin During the Second Wind Forecast Improvement Project

The second Wind Forecast Improvement Project (WFIP2) is an 18-month field campaign in the Pacific Northwest U.S.A., whose goal is to improve the accuracy of numerical-weather-prediction forecasts in complex terrain. The WFIP2 campaign involved the deployment of a large suite of in situ and remote sensing instrumentation, including eight 915-MHz wind-profiling radars, and surface meteorological stations. The evolution and annual variability of the daytime convective planetary-boundary-layer (PBL) height is investigated using the wind-profiling radars. Three models with different horizontal grid spacing are evaluated: the Rapid Refresh, the High-Resolution Rapid Refresh, and its nested version. The results are used to assess errors in the prediction of PBL height within the experimental and control versions of the models, with the experimental versions including changes and additions to the model parametrizations developed during the field campaign, and the control version using the parametrizations present in the National Oceanic and Atmospheric Administration/National Centers for Environmental Prediction operational version of the models at the start of the project. Results show that the high-resolution models outperform the low-resolution versions, the experimental versions perform better compared with the control versions, model PBL height estimations are more accurate on cloud-free days, and model estimates of the PBL height growth rate are more accurate than model estimates of the rate of decay. Finally, using surface sensors, we assess surface meteorological variables, finding improved surface irradiance and, to a lesser extent, improved 2-m temperature in the experimental version of the model.

54 ENVIRONMENTAL SCIENCES↗

Characterizing the movements and habitat use of two fish species of concern in a regulated ecosystem

In freshwater ecosystems in the northwest United States, the distribution and movements of fish between their essential habitats are particularly impacted by the presence of hydroelectric dams. Bull Trout Salvelinus confluentus and Westslope Cutthroat Trout Oncorhynchus clarkii var. lewisi are two fish species of concern inhabiting the Pend Oreille River between Idaho and Washington states. The purpose of this study was to identify the behavior and habitat use of Bull Trout and Westslope Cutthroat Trout in the restricted area of the Pend Oreille River, downstream of Albeni Falls Dam (AFD), using a long-term radiotelemetry dataset. Between 2015 and 2018, 24 Bull Trout and 24 Westslope Cutthroat Trout were captured, tagged, and released downstream AFD. Among the fish tagged, 79% (n = 19 of 24) of Bull Trout and 67% (n = 16 of 24) of Westslope Cutthroat Trout were detected during the study period. Our results revealed movements of fish towards tributary confluences mostly in May, June, and July for both species with Bull Trout traveling longer distances than Westslope Cutthroat Trout. Although the sample size was limited, Bull Trout individual movements towards the dam suggested attempts to re-ascend the river, indicating the importance of restoring upstream connectivity.

Garavelli, Lysel↗