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At least 145 records · Page 8

Field validation of an actuated convergent-beam acoustic Doppler profiler for high resolution flow mapping

Abstract Energetic river and tidal flow environments feature complex hydrodynamic conditions. Conventional acoustic Doppler profiling instrumentation typically requires assumptions of flow homogeneity over the spatial scales of the divergent beam separation. This removes the ability to measure spatio-temporal variability within the flow. However, velocity variability within these spatial scales is often important in the design of structures and devices exposed to such flow, informing dynamic and peak hydrodynamic load predictions. The research presented outlines the development and testing of a flow measurement instrument consisting of multiple spatially-separated single beam acoustic Doppler profilers converging on a remote focal point, the location of which can be programmatically adjusted through actuation. This increases the spatial resolution at which remote field measurements can be made in energetic flow environments. Field testing of the instrument was conducted in a tidal channel at Sequim Bay Inlet, WA, USA. Results are compared with independent reference measurements made by a co-located, motion-corrected acoustic Doppler velocimeter. This comparison, across tidal velocities of 0.4–0.7 m s −1 , showed a mean velocity error of 0.5%–13.2% across nine sample locations within a 3.00 m × 2.25 m plane. To the authors’ knowledge, this is the first publication of flow velocity results from non-intrusive acoustic measurements at an off-axis, focal point location that features 3D positional control.

13 HYDRO ENERGY↗

Analyzing line-of-sight selection biases in galaxy-scale strong lensing with external convergence and shear

The upcoming Vera Rubin Observatory Legacy Survey of Space and Time (LSST) will dramatically increase the number of strong gravitational lensing systems, requiring precise modeling of line-of-sight (LOS) effects to mitigate biases in lensing observations and cosmological inferences. We develop a method to construct joint distributions of external convergence (κ ext ) and shear (γ ext ) for strong lensing LOS by aggregating large-scale structure simulations with high-resolution halo renderings and non-linear correction. Our approach captures both smooth background matter and perturbations from halos, enabling accurate modeling of LOS effects. Here, we apply non-linear LOS corrections to κ ext and γ ext that address the non-additive lensing effects caused by objects along the LOS in strong lensing. We find that, with a minimum image separation of 1.0'', non-linear LOS correction due to the presence of a dominant deflector slightly increases the ratio of quadruple to double lenses; this non-linear LOS correction also introduces systematic biases of ∼ 0.1% for galaxy-AGN lens in the inferred Hubble constant (H 0 ) if not accounted for. We also observe a 0.66% bias for galaxy-galaxy lenses on H 0 , and even larger biases 1.02% for galaxy-AGN systems if LOS effects are not accounted for. These results highlight the importance of LOS for precision cosmology. The publicly available code and datasets provide tools for incorporating LOS effects in future analyses.

Hubble constant↗

Domestication in dry-cured meat Penicillium fungi: Convergent specific phenotypes and horizontal gene transfers without strong genetic subdivision

Some fungi have been domesticated for food production, with genetic differentiation between populations from food and wild environments, and food populations often acquiring beneficial traits through horizontal gene transfers (HGTs). Studying their adaptation to human-made substrates is of fundamental and applied importance for understanding adaptation processes and for further strain improvement. We studied here the population structures and phenotypes of two distantly related Penicillium species used for dry-cured meat production, P. nalgiovense, the most common species in the dry-cured meat food industry, and P. salamii, used locally by farms. Both species displayed low genetic diversity, lacking differentiation between strains isolated from dry-cured meat and those from other environments. Nevertheless, the strains collected from dry-cured meat within each species displayed slower proteolysis and lipolysis than their wild conspecifics, and those of P. nalgiovense were whiter. Phenotypically, the non-dry-cured meat strains were more similar to their sister species than to their conspecific dry-cured meat strains, indicating an evolution of specific phenotypes in dry-cured meat strains. A comparison of available Penicillium genomes from various environments revealed HGTs, particularly between P. nalgiovense and P. salamii (representing almost 1.5 Mb of cumulative length). HGTs additionally involved P. biforme, also found in dry-cured meat products. We further detected positive selection based on amino acid changes. Our findings suggest that selection by humans has shaped the P. salamii and P. nalgiovense populations used for dry-cured meat production, which constitutes domestication. Several genetic and phenotypic changes were similar in P. salamii, P. nalgiovense and P. biforme, indicating convergent adaptation to the same human-made environment. Our findings have implications for fundamental knowledge on adaptation and for the food industry: the discovery of different phenotypes and of two mating types paves the way for strain improvement by conventional breeding, to elucidate the genomic bases of beneficial phenotypes and to generate diversity.

60 APPLIED LIFE SCIENCES↗

A posteriori superlinear convergence bounds for block conjugate gradient

In this paper, we extend to the block case the a posteriori bound showing superlinear convergence of the conjugate gradient method developed by van der Vorst and Vuik in [J. Comput. Applied Math., 48 (1993), pp. 327–341]. That is, we obtain similar bounds but now for the block conjugate gradient method. We also present a series of computational experiments, illustrating the validity of the bound developed here as well as the bound by Simoncini and Szyld from [SIAM Review, 47 (2005), pp. 247–272] using angles between subspaces. Using these bounds, we make some observations on the onset of superlinearity and how this onset depends on the eigenvalue distribution and the block size.

97 MATHEMATICS AND COMPUTING↗

Data for publication Wan et al. (2020, JAMES), Improving time-step convergence in an atmosphere model with simplified physics: the impacts of closure assumption and process coupling

This dataset contains simple condensation mdoel output and CAM4 model output that were used to produce figures in the following paper: Wan, H., Woodward, C. S., Zhang, S., Vogl, C. J., Stinis, P., Gardner, D. J., Rasch, P. J., Zeng, X., Larson, V. E., and Singh, B. (2020): Improving time-step convergence in an atmosphere model with simplified physics: the impacts of closure assumption and process coupling, Journal of Advances in Modeling Earth Systems, https://doi.org/10.1029/2019MS001982

54 ENVIRONMENTAL SCIENCES↗

Position Operators in Terms of Converging Finite-Dimensional Matrices and Their Intertwining with Geometry, Transport, and Gauge

The position operator 𝑟̂ appears as 𝑖∂ 𝑝 in wave mechanics, while its matrix form (e.g., under a Bloch basis) is well known diverging in diagonals, causing difficulties in basis transformation, observable yielding, etc. We aim to find a convergent r-matrix (CRM) to improve the existing divergent r-matrix (DRM), and investigate its influence at both the conceptual and the application levels. A key modification is increasing the familiar substitution of 𝑟̂ by 𝑖∂ 𝑝 to 𝑖∑ 𝑗 ∂ 𝑘 𝑗 , namely the N-th Weyl algebra. Resolving the divergence makes r-matrix rigorously defined, and we are able to show r-matrix is distinct from a spin matrix in terms of its defining principles, transformation behavior, and the observable it yields. Conceptually, the CRM fills the logical gap between the r-matrix and the Berry connection (this unremarked vagueness has caused the diagonal divergence). In application, we focus on transport, and discover that the Hermitian matrix is not identical with the associative Hermitian operator, i.e., 𝑟 𝑚,𝑛 = 𝑟$^∗_{𝑛,𝑚}$ ⇎ 𝑟̂ = 𝑟̂ † , which subtly affects the celebrated Berry curvature formula for adiabatic current. We also discuss how such a non-representation CRM can contribute to building a unified transport theory.

Weyl algebras↗

Superconducting Quantum Metamaterials from Convergence of Soft and Hard Condensed Matter Science

Superconducting quantum metamaterials are expected to exhibit a variety of novel properties, but have been a major challenge to prepare as a result of the lack of appropriate synthetic routes to high-quality materials. Here, the discovery of synthesis routes to block copolymer (BCP) self-assembly-directed niobium nitrides and carbonitrides is described. The resulting materials exhibit unusual structure retention even at temperatures as high as 1000 °C and resulting critical temperature, T c , values comparable to their bulk analogues. Applying the concepts of soft matter self-assembly, it is demonstrated that a series of four different BCP-directed mesostructured superconductors are accessible from a single triblock terpolymer. Resulting materials display a mesostructure-dependent T c without substantial variation of the XRDmeasured lattice parameters. Lastly, field-dependent magnetization measurements of a sample with double-gyroid morphology show abrupt jumps comparable in overall behavior to flux avalanches. Results suggest a fruitful convergence of soft and hard condensed matter science.

36 MATERIALS SCIENCE↗

A convergent genus expansion for the plateau

We conjecture a formula for the spectral form factor of a double-scaled matrix integral in the limit of large time, large density of states, and fixed temperature. The formula has a genus expansion with a nonzero radius of convergence. To understand the origin of this series, we compare to the semiclassical theory of “encounters” in periodic orbits. In Jackiw-Teitelboim (JT) gravity, encounters correspond to portions of the moduli space integral that mutually cancel (in the orientable case) but individually grow at low energies. At genus one we show how the full moduli space integral resolves the low energy region and gives a finite nonzero answer.

2D Gravity↗

Convergence of Hyperbolic Neural Networks Under Riemannian Stochastic Gradient Descent

Abstract We prove, under mild conditions, the convergence of a Riemannian gradient descent method for a hyperbolic neural network regression model, both in batch gradient descent and stochastic gradient descent. We also discuss a Riemannian version of the Adam algorithm. We show numerical simulations of these algorithms on various benchmarks.

Whiting, Wes (ORCID:0000000247505060)↗

On the use of a multigrid-reduction-in-time algorithm for multiscale convergence of turbulence simulations

Simulations of turbulent flow present challenges in terms of accuracy and affordability on modern highly-parallel computer architectures. A multigrid-reduction-in-time algorithm is used to provide a framework for separately evolving different scales of turbulence and for parallelizing the temporal domain, thereby increasing the concurrency. It is hypothesized that the space–time locality of the small scales of turbulence can be used to circumvent difficulties in applying temporal multigrid to flows dominated by inertial physics. For algorithms that fall well short of spectral accuracy (fourth-order is used in this work) attention must be paid to the accuracy of features on scales transferred between multigrid levels. Numerical experiments were performed using implicit large-eddy simulation. Results from applying the approach to an infinite-Reynolds number Taylor–Green flow and a double-shear flow at a Reynolds number of 11650 provide strong evidence that the approach has merit. The multigrid-reduction-in-time framework can be used to parallelize the temporal domain of a high-Reynolds-number turbulent flow and permit independent convergence of different scales. Establishing this foundation allows for future research in reducing the wall-clock time to solve turbulent flows while retaining the same accuracy as sequential solvers. In conclusion, current performance results from parallelizing the temporal domain are not competitive with those from sequential-in-time methods.

97 MATHEMATICS AND COMPUTING↗

Convergent reductive evolution and host adaptation in Mycoavidus bacterial endosymbionts of Mortierellaceae fungi

Intimate associations between fungi and intracellular bacterial endosymbionts are becoming increasingly well understood. Phylogenetic analyses demonstrate that bacterial endosymbionts of Mucoromycota fungi are related either to free-living Burkholderia or Mollicutes species. The so-called Burkholderia-related endosymbionts or BRE comprise Mycoavidus, Mycetohabitans and Candidatus Glomeribacter gigasporarum. These endosymbionts are marked by genome contraction thought to be associated with intracellular selection. However, the conclusions drawn thus far are based on a very small subset of endosymbiont genomes, and the mechanisms leading to genome streamlining are not well understood. The purpose of this study was to better understand how intracellular existence shapes Mycoavidus and BRE functionally at the genome level. To this end we generated and analyzed 14 novel draft genomes for Mycoavidus living within the hyphae of Mortierellomycotina fungi. We found that our novel Mycoavidus genomes were significantly reduced compared to free-living Burkholderiales relatives. Using a genome-scale phylogenetic approach including the novel and available existing genomes of Mycoavidus, we show that the genus is an assemblage composed of two independently derived lineages including three well supported clades of Mycoavidus. Using a comparative genomic approach, we shed light on the functional implications of genome reduction, documenting shared and unique gene loss patterns between the three Mycoavidus clades. We found that many endosymbiont isolates demonstrate patterns of vertical transmission and host-specificity, but others are present in phylogenetically disparate hosts. We discuss how reductive evolution and host specificity reflect convergent adaptation to the intrahyphal selective landscape, and commonalities of eukaryotic endosymbiont genome evolution.

59 BASIC BIOLOGICAL SCIENCES↗

Evaluation of accuracy and convergence of numerical coupling approaches for poroelasticity benchmark problems

Accurate modeling of subsurface flow and transport processes is vital as the prevalence of subsurface activities such as carbon sequestration, geothermal recovery, and nuclear waste disposal increases. Computational modeling of these problems leverages poroelasticity theory, which describes coupled fluid flow and mechanical deformation. Although fully coupled monolithic schemes are accurate for coupled problems, they can demand significant computational resources for large problems. In this work, a fixed stress scheme is implemented into the Sandia Sierra Multiphysics toolkit. Two implementation methods, along with the fully coupled method, are verified with one-dimensional (1D) Terzaghi, 2D Mandel, and 3D Cryer sphere benchmark problems. The impact of a range of material parameters and convergence tolerances on numerical accuracy and efficiency was evaluated. Overall the fixed stress schemes achieved acceptable numerical accuracy and efficiency compared to the fully coupled scheme. However, the accuracy of the fixed stress scheme tends to decrease with low permeable cases, requiring the finer tolerance to achieve a desired numerical accuracy. For the fully coupled scheme, high numerical accuracy was observed in most of cases except a low permeability case where an order of magnitude finer tolerance was required for accurate results. Finally, a two-layer Terzaghi problem and an injection–production well system were used to demonstrate the applicability of findings from the benchmark problems for more realistic conditions over a range of permeability. Simulation results suggest that the fixed stress scheme provides accurate solutions for all cases considered with the proper adjustment of the tolerance. Furthermore, this work clearly demonstrates the robustness of the fixed stress scheme for coupled poroelastic problems, while a cautious selection of numerical tolerance may be required under certain conditions with low permeable materials.

58 GEOSCIENCES↗

Adaptive Activation Functions Accelerate Convergence in Deep and Physics-informed Neural Networks

We employ adaptive activation functions for regression in deep and physics-informed neural networks (PINNs) to approximate smooth and discontinuous functions as well as solutions of linear and nonlinear partial differential equations. In particular, we solve the nonlinear Klein-Gordon equation, which has smooth solutions, the nonlinear Burgers equation, which can admit high gradient solutions, and the Helmholtz equation. We introduce a scalable hyper-parameter in the activation function, which can be optimized to achieve best performance of the network as it changes dynamically the topology of the loss function involved in the optimization process. The adaptive activation function has better learning capabilities than the traditional one (fixed activation) as it improves greatly the convergence rate, especially at early training, as well as the solution accuracy. To better understand the learning process, we plot the neural network solution in the frequency domain to examine how the network captures successively different frequency bands present in the solution. We consider both forward problems, where the approximate solutions are obtained, as well as inverse problems, where parameters involved in the governing equation are identified. Our simulation results show that the proposed method is a very simple and effective approach to increase the efficiency, robustness and accuracy of the neural network approximation of nonlinear functions as well as solutions of partial differential equations, especially for forward problems. We theoretically prove that in the proposed method, gradient descent algorithms are not attracted to suboptimal critical points or local minima.

machine leaning, Bad minima, Inverse problems, Phy↗

Phylogenomics reveals convergent evolution of red-violet coloration in land plants and the origins of the anthocyanin biosynthetic pathway

The flavonoids, one of the largest classes of plant secondary metabolites, are found in lineages that span the land plant phylogeny and play important roles in stress responses and as pigments. Perhaps the most well-studied flavonoids are the anthocyanins that have human health benefits and help plants attract pollinators, regulate hormone production, and confer resistance to abiotic and biotic stresses. The canonical biochemical pathway responsible for the production of these pigments is well-characterized for flowering plants yet its conservation across deep divergences in land plants remains debated and poorly understood. Many early land plants such as mosses, liverworts, and ferns produce flavonoid pigments, but their biosynthetic origins and homologies to the anthocyanin pathway remain uncertain. We conducted phylogenetic analyses using full genome sequences representing nearly all major green plant lineages to reconstruct the evolutionary history of the anthocyanin biosynthetic pathway then test the hypothesis that genes in this pathway are present in early land plants. We found that the entire pathway was not intact until the most recent common ancestor of seed plants and that orthologs of many downstream enzymes are absent from seedless plants including mosses, liverworts, and ferns. Our results also highlight the utility of phylogenetic inference, as compared to pairwise sequence similarity, in orthology assessment within large gene families that have complex duplication-loss histories. Here, we suggest that the production of red-violet flavonoid pigments widespread in seedless plants, including the 3-deoxyanthocyanins, requires the activity of novel, as-yet discovered enzymes, and represents convergent evolution of red-violet coloration across land plants.

59 BASIC BIOLOGICAL SCIENCES↗

Convergent Concordant Mode Approach for Molecular Vibrations: CMA-2

The concordant mode approach (CMA) is a promising new scheme for dramatically increasing the system size and level of theory achievable in quantum chemical computations of molecular vibrational frequencies. Here, we achieve advances in the CMA hierarchy by computations targeting CCSD(T)/cc-pVTZ (coupled cluster singles and doubles with perturbative triples using a correlation-consistent polarized-valence triple-ζ basis set) benchmarks within the G2 molecular test set, executing a statistical analysis for 1501 frequencies from 111 compounds and then separately solving the refractory case of pyridine. First, MP2/cc-pVTZ (second-order Møller–Plesset perturbation theory with the same basis set) proves to be an excellent and preferred choice for generating the underlying (Level B) normal modes of the CMA scheme. Utilizing this Level B within the CMA-0A method reproduces the 1501 benchmark frequencies with a mean absolute error (MAE) of only 0.11 cm –1 and an attendant standard deviation of 0.49 cm –1 . Second, a convergent CMA-2 method is constituted that allows efficient computation of higher level (Level A) frequencies to any reasonable accuracy threshold by using only Hartree–Fock (HF) and MP2 or density functional theory (DFT) data to generate ξ parameters, which select the sparse off-diagonal force field elements for explicit evaluation at Level A. When Level B = MP2/cc-pVTZ, a cutoff of ξ = 0.02 provides an average maximum absolute error per molecule of only 0.17 cm –1 by incurring merely a 33% increase in average cost over CMA-0A. This CMA-2 method also eradicates the 4 problematic CMA-0A outliers of pyridine with even less effort (ξ = 0.04, 22% increase). Finally, the newly developed CMA procedures are shown to be highly successful when applied to 1-(1H-pyrrol-3-yl)ethanol, a new test molecule with diverse types of vibration.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Water Dielectric Function at Finite Wavelength and the Convergence of Its Large Wavelength Limit (Static Dielectric) by Fluctuation Formulas

Here we provide a general analysis of the longitudinal dielectric function ε l (k) via fluctuation formulas at finite wavelength k, including the static dielectric constant ε w = ε l (k → 0), and analyze the different sources of errors, deriving explicit formulas. Simulations with the SPC/E water model show that the convergence of fluctuation formulas to compute the static dielectric constant is slow and requires long simulations. The analysis of ε l (k) allows us to identify the long- and short-wavelength limits and provide a precise determination of the location of the poles as well as the zeros in the complex plane, which determine the short-distance form of the electrostatic (Coulomb) interaction among charged particles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Non-Adiabatic Excited State Molecular Dynamics Methodologies: comparison and convergence

Direct atomistic simulation of nonadiabatic molecular dynamics is a challenging goal that allows important insights into fundamental physical phenomena. A variety of frameworks, ranging from fully quantum treatment of nuclei to semiclassical and mixed quantum–classical approaches, were developed. These algorithms are then coupled to specific electronic structure techniques. Such diversity and lack of standardized implementation make it difficult to compare the performance of different methodologies when treating realistic systems. Here, we compare three popular methods for large chromophores: Ehrenfest, surface hopping, and multiconfigurational Ehrenfest with ab initio multiple cloning (MCE-AIMC). These approaches are implemented in the NEXMD software, which features a common computational chemistry model. The resulting comparisons reveal the method performance for population relaxation and coherent vibronic dynamics. Finally, we study the numerical convergence of MCE-AIMC algorithms by considering the number of trajectories, cloning thresholds, and Gaussian wavepacket width. Our results provide helpful reference data for selecting an optimal methodology for simulating excited-state molecular dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Activity Convergence between Continuous- and Pulsed-Deposition NiFe Hydroxide Anodes in Liquid Alkaline Electrolyzers

Improving the activity of anodes for the alkaline oxygen evolution reaction (OER) is of interest because of the importance of the reaction in electrochemical technology. There is an abundance of studies which confirm that NiFe hydroxide, often prepared by electrodeposition, is the most active catalyst for the alkaline OER. This relatively high level of confidence in the optimal OER catalyst chemistry suggests that exploration of methods which improve on features besides the chemistry of the films, such as their microstructure, could access new heights of activity. In this study, the possible benefits of pulsed current deposition relative to the conventional continuous current approach to the deposition of NiFe hydroxides were investigated. Pulsed deposition densified the film surfaces by preventing metal ion depletion at the electrode surface during film formation. The Fe content, redox reversibility, and OER activity were higher for the pulsed deposition films relative to their continuous deposition counterparts. Though pulsed deposition imparted a higher OER performance of the films compared to continuous deposition at the three-electrode level, this improved performance was not retained during electrolyzer operation. Rather, a convergence of the cell performance is seen irrespective of the deposition approach. This phenomenon was attributed to the way electrolyzer conditionsrelatively high temperature, base concentration, and current densitycan drive alternate mechanisms for observed performance.

08 HYDROGEN↗