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At least 1,045 records · Page 58

Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids

Premise Recent advances in generating large‐scale phylogenies enable broad‐scale estimation of species diversification. These now common approaches typically are characterized by (1) incomplete species coverage without explicit sampling methodologies and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. We used empirical examples to examine the effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionary biologists based on those results. Methods We used a supermatrix for rosids and one well‐sampled subclade (Cucurbitaceae) as empirical case studies. We compared results using these large phylogenies with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA and BAMM) and semiparametric (DR). Results We found that the impact of sampling on diversification estimates was idiosyncratic and often strong. Compared to full empirical sampling, representative and random sampling schemes either depressed or inflated speciation rates, depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa. Conclusions We suggest caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees and in the use of summary backbone trees and other data sets with high representative bias, and we stress the importance of explicit sampling methodologies in macroevolutionary studies.

59 BASIC BIOLOGICAL SCIENCES↗

Multifidelity Information Fusion with Machine Learning: A Case Study of Dopant Formation Energies in Hafnia

Cost versus accuracy trade-offs are frequently encountered in materials science and engineering, where a particular property of interest can be measured/computed at different levels of accuracy or fidelity. Naturally, the most accurate measurement is also the most resource and time intensive, while the inexpensive quicker alternatives tend to be noisy. In such situations, a number of machine learning (ML) based multifidelity information fusion (MFIF) strategies can be employed to fuse information accessible from varying sources of fidelity and make predictions at the highest level of accuracy. In this work, we perform a comparative study on traditionally employed single-fidelity and three MFIF strategies, namely, (1) Δ-learning, (2) low-fidelity as a feature, and (3) multifidelity cokriging (CK) to compare their relative prediction accuracies and efficiencies for accelerated property predictions and high throughput chemical space explorations. We perform our analysis using a dopant formation energy data set for hafnia, which is a well-known high- k material and is being extensively studied for its promising ferroelectric, piezoelectric, and pyroelectric properties. We use a dopant formation energy data set of 42 dopants in hafnia—each studied in six different hafnia phases—computed at two levels of fidelities to find merits and limitations of these ML strategies. The findings of this work indicate that the MFIF based learning schemes outperform the traditional SF machine learning methods, such as Gaussian process regression and CK provides an accurate, inexpensive and flexible alternative to other MFIF strategies. While the results presented here are for the case study of hafnia, they are expected to be general. Furthermore, materials discovery problems that involve huge chemical space explorations can be studied efficiently (or even made feasible in some situations) through a combination of a large number of low-fidelity and a few high-fidelity measurements/computations, in conjunction with the CK approach.

36 MATERIALS SCIENCE↗

Methods of improving spatial resolution for IR spectroscopy in atmospheric-pressure plasma systems

High-temperature, atmospheric pressure plasma systems operated in molecular gases present complex diagnostic challenges. Infrared spectroscopy has been used to make measurements of the absorbance spectrum of complex molecular gas mixtures and thereby calculate the concentrations and species temperatures in these systems. For atmospheric-pressure systems, high spatial gradients arise and high spatial-resolution measurements are thus desirable. Some systems have achieved increased spatial resolution by reducing the beam diameter. However, this increase in spatial resolution comes at the expense of the optical throughput. Here we propose modifying a commercial Fourier Transform, Infrared spectrometer system with a set of simple optical elements. This design allows for scannable, high spatial resolution absorbance spectrum measurements of a complex molecular gas mix. We analyze the signal-to-noise ratio for this design and compare it with the diameter reduction method. For sufficiently low plasma radiation levels, this design improves the signal-to-noise ratio relative to reducing the beam diameter size while transmitting nearly all of the beam power. Furthermore, whether this design can achieve the desired sub-mm spatial resolution depends on the radiating area of the infrared light source in the spectrometer.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Pseudo-fragment approach for extended systems derived from linear-scaling DFT

We present a computational approach which is tailored for reducing the complexity of the description of extended systems at the density functional theory level. We define a recipe for generating a set of localized basis functions which arc optimized either for the accurate description of pristine, bulk-like Wannier functions, or for the in situ treatment of deformations induced by defective constituents such as boundaries or impurities. Our method enables one to identify the regions of an extended system which require dedicated optimization of the Kohn-Sham degrees of freedom, and provides the user with a reliable estimation of the errors-if any-induced by the locality of the approach. Such a method facilitates on the one hand an effective reduction of the computational degrees of freedom needed to simulate systems at the nanoscale, while in turn providing a description that can be straightforwardly put in relation to effective models, like tight binding Hamiltonians. In conclusion, we present our methodology with SiC nanotube-like cages as a test bed. Nonetheless, the wavelet-based method employed in this paper makes possible calculation of systems with different dimensionalities, including slabs and fully periodic systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A consistent approach for the development of a comprehensive data base of time-dependent parameters for concrete engineered barriers

This paper presents a consistent approach for the development of a comprehensive data base of time-dependent hydraulic and transport parameters for concrete engineered barriers of the future Dessel near surface repository for low level waste. The parameter derivation is based on integration of selected data obtained through an extensive literature review, data from experimental studies on cementitious materials specific for the Dessel repository and numerical modelling using physically-based models of water and mass transport. Best estimate parameter values for assessment calculations are derived, together with source and expert range and their probability density function wherever the data was sufficient. We further discuss a numerical method for up-scaling laboratory derived parameter values to the repository scale; the resulting large-scale effective parameters are commensurate with numerical grids used in models for radionuclide migration. To accommodate different levels of conservatism in the various assessment calculations defined by ONDRAF/NIRAS, several sets of parameter values have been derived based on assumptions that introduce different degrees of conservatism. For pertinent parameters, the time evolution of such properties due to the long-term concrete degradation is also addressed. The implementation of the consistent approach is demonstrated by considering the pore water diffusion coefficient as an example. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

SU-E-I-77: A Noise Reduction Technique for Energy-Resolved Photon-Counting Detectors

Purpose: Finding the optimal energy threshold setting for an energy-resolved photon-counting detector has an important impact on the maximization of contrast-to-noise-ratio (CNR). We introduce a noise reduction method to enhance CNR by reducing the noise in each energy bin without altering the average gray levels in the projection and image domains. Methods: We simulated a four bin energy-resolved photon-counting detector based on Si with a 10 mm depth of interaction. TASMIP algorithm was used to simulate a spectrum of 65 kVp with 2.7 mm Al filter. A 13 mm PMMA phantom with hydroxyapatite and iodine at different concentrations (100, 200 and 300 mg/ml for HA, and 2, 4, and 8 mg/ml for Iodine) was used. Projection-based and Image-based energy weighting methods were used to generate weighted images. A reference low noise image was used for noise reduction purposes. A Gaussian-like weighting function which computes the similarity between pixels of interest was calculated from the reference image and implemented on a pixel by pixel basis for the noisy images. Results: CNR improvement compared to different methods (Charge-Integrated, Photon-Counting and Energy-Weighting) and after noise reduction was highly task-dependent. The CNR improvement with respect to the Charge-Integrated CNR for hydroxyapatite and iodine were 1.8 and 1.5, respectively. In each of the energy bins, the noise was reduced by approximately factor of two without altering their respective average gray levels. Conclusion: The proposed noise reduction technique for energy-resolved photon-counting detectors can significantly reduce image noise. This technique can be used as a compliment to the current energy-weighting methods in CNR optimization.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Technical Note: Improvements in GEANT4 energy-loss model and the effect on low-energy electron transport in liquid water

Purpose: The GEANT4-DNA physics models are upgraded by a more accurate set of electron cross sections for ionization and excitation in liquid water. The impact of the new developments on low-energy electron transport simulations by the GEANT4 Monte Carlo toolkit is examined for improving its performance in dosimetry applications at the subcellular and nanometer level. Methods: The authors provide an algorithm for an improved implementation of the Emfietzoglou model dielectric response function of liquid water used in the GEANT4-DNA existing model. The algorithm redistributes the imaginary part of the dielectric function to ensure a physically motivated behavior at the binding energies, while retaining all the advantages of the original formulation, e.g., the analytic properties and the fulfillment of the f-sum-rule. In addition, refinements in the exchange and perturbation corrections to the Born approximation used in the GEANT4-DNA existing model are also made. Results: The new ionization and excitation cross sections are significantly different from those of the GEANT4-DNA existing model. In particular, excitations are strongly enhanced relative to ionizations, resulting in higher W-values and less diffusive dose-point-kernels at sub-keV electron energies. Conclusions: An improved energy-loss model for the excitation and ionization of liquid water by low-energy electrons has been implemented in GEANT4-DNA. The suspiciously low W-values and the unphysical long tail in the dose-point-kernel have been corrected owing to a different partitioning of the dielectric function.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Comparing Regional Energy Consumption for Direct Drone and Truck Deliveries

Drone delivery, once thought of as fictitious, is becoming a reality with the efforts of both forward-looking enterprises and supportive government policies. This emerging mode of e-commerce delivery raises many concerns. One important concern is the energy efficiency of direct delivery drones compared with conventional delivery trucks at a regional systems level. Here, in this study, we develop and apply methods to quantify the regional energy impacts of drone delivery, then we assess these impacts and compare them with the impacts of truck delivery. To study this problem, we develop an optimization model that determines an optimal set of fulfillment centers (FCs) with variable service capacities that allow drones to make direct e-commerce deliveries. We adopt two drone delivery energy estimation models from the literature and use them as inputs to demonstrate the potential range of energy needs. We also develop another optimization model to account for the energy consumption of diesel trucks (DTs) and battery electric vehicles (BEVs). We test the models using validated simulation data for the Chicago metropolitan area in the U.S. to quantify the energy implications of these three delivery modes. For drone delivery, we further extend our analyses by considering the impact of wind speed and flight patterns. Our results show that direct delivery drones require 15.8% more energy than BEVs on an average windy day, and they need 15% more energy than DTs on a very windy day. We provide essential parameter values for reproducibility and list relevant open problems.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Atomic Decay Data for Modeling K Lines of Iron Peak and Light Odd-Z Elements*

Complete data sets of level energies, transition wavelengths, A-values, radiative and Auger widths and fluorescence yields for K-vacancy levels of the F, Na, P, Cl, K, Sc, Ti, V, Cr, Mn, Co, Cu and Zn isonuclear sequences have been computed by a Hartree-Fock method that includes relativistic corrections as implemented in Cowan's atomic structure computer suite. The atomic parameters for more than 3 million fine-structure K lines have been determined. Ions with electron number N greater than 9 are treated for the first time, and detailed comparisons with available measurements and theoretical data for ions with N less than or equal to 9 are carried out in order to estimate reliable accuracy ratings.

modeling K lines↗

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation

ABSTRACT Multiple molecular assays now enable high-throughput profiling of the ecology, metabolic capacity, and activity of the human microbiome. However, to date, analyses of such multi-omic data typically focus on statistical associations, often ignoring extensive prior knowledge of the mechanisms linking these various facets of the microbiome. Here, we introduce a comprehensive framework to systematically link variation in metabolomic data with community composition by utilizing taxonomic, genomic, and metabolic information. Specifically, we integrate available and inferred genomic data, metabolic network modeling, and a method for predicting community-wide metabolite turnover to estimate the biosynthetic and degradation potential of a given community. Our framework then compares variation in predicted metabolic potential with variation in measured metabolites’ abundances to evaluate whether community composition can explain observed shifts in the community metabolome, and to identify key taxa and genes contributing to the shifts. Focusing on two independent vaginal microbiome data sets, each pairing 16S community profiling with large-scale metabolomics, we demonstrate that our framework successfully recapitulates observed variation in 37% of metabolites. Well-predicted metabolite variation tends to result from disease-associated metabolism. We further identify several disease-enriched species that contribute significantly to these predictions. Interestingly, our analysis also detects metabolites for which the predicted variation negatively correlates with the measured variation, suggesting environmental control points of community metabolism. Applying this framework to gut microbiome data sets reveals similar trends, including prediction of bile acid metabolite shifts. This framework is an important first step toward a system-level multi-omic integration and an improved mechanistic understanding of the microbiome activity and dynamics in health and disease. IMPORTANCE Studies characterizing both the taxonomic composition and metabolic profile of various microbial communities are becoming increasingly common, yet new computational methods are needed to integrate and interpret these data in terms of known biological mechanisms. Here, we introduce an analytical framework to link species composition and metabolite measurements, using a simple model to predict the effects of community ecology on metabolite concentrations and evaluating whether these predictions agree with measured metabolomic profiles. We find that a surprisingly large proportion of metabolite variation in the vaginal microbiome can be predicted based on species composition (including dramatic shifts associated with disease), identify putative mechanisms underlying these predictions, and evaluate the roles of individual bacterial species and genes. Analysis of gut microbiome data using this framework recovers similar community metabolic trends. This framework lays the foundation for model-based multi-omic integrative studies, ultimately improving our understanding of microbial community metabolism.

Noecker, Cecilia↗

A Method of Estimating Low Turbulence Levels in Near Real Time Using Laser Anemometry

Laser anemometry was used to make two independent measurements of the flow velocity by capturing individual Doppler signals with high-speed digitizing boards. The two independent measurements were cross-correlated to reduce the contribution of photo detector shot noise on the frequency determination and subsequently on the turbulence estimate. In addition, criteria were developed to eliminate "bad" Doppler bursts from the data set, which then allowed reasonable low turbulence estimates to be made. The laser anemometer measurements were obtained at the inlet of an annular cascade and at the exit of a flow calibration nozzle and were compared with hot-wire data.

Goldman, Louis J.↗

Ultra-fast computation of electronic spectra for large systems by tight-binding based simplified Tamm-Dancoff approximation (sTDA-xTB)

The computational bottleneck of the extremely fast simplified Tamm-Dancoff approximated (sTDA) time-dependent density functional theory procedure [S. Grimme, J. Chem. Phys. 138, 244104 (2013)] for the computation of electronic spectra for large systems is the determination of the ground state Kohn-Sham orbitals and eigenvalues. This limits such treatments to single structures with a few hundred atoms and hence, e.g., sampling along molecular dynamics trajectories for flexible systems or the calculation of chromophore aggregates is often not possible. The aim of this work is to solve this problem by a specifically designed semi-empirical tight binding (TB) procedure similar to the well established self-consistent-charge density functional TB scheme. The new special purpose method provides orbitals and orbital energies of hybrid density functional character for a subsequent and basically unmodified sTDA procedure. Compared to many previous semi-empirical excited state methods, an advantage of the ansatz is that a general eigenvalue problem in a non-orthogonal, extended atomic orbital basis is solved and therefore correct occupied/virtual orbital energy splittings as well as Rydberg levels are obtained. A key idea for the success of the new model is that the determination of atomic charges (describing an effective electron-electron interaction) and the one-particle spectrum is decoupled and treated by two differently parametrized Hamiltonians/basis sets. The three-diagonalization-step composite procedure can routinely compute broad range electronic spectra (0-8 eV) within minutes of computation time for systems composed of 500-1000 atoms with an accuracy typical of standard time-dependent density functional theory (0.3-0.5 eV average error). An easily extendable parametrization based on coupled-cluster and density functional computed reference data for the elements H–Zn including transition metals is described. The accuracy of the method termed sTDA-xTB is first benchmarked for vertical excitation energies of open- and closed-shell systems in comparison to other semi-empirical methods and applied to exemplary problems in electronic spectroscopy. As side products of the development, a robust and efficient valence electron TB method for the accurate determination of atomic charges as well as a more accurate calculation scheme of dipole rotatory strengths within the Tamm-Dancoff approximation is proposed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cislunar Trajectory Design and Maneuver Autonomy for NASA's Moon to Mars Architecture

NASA’s Moon to Mars architecture is an ambitious roadmap of manned cislunar and deep space exploration. The extensive amount of orbital assets required will place a significant burden on ground-based resources, such as communication networks and operations facilities. Spacecraft autonomy is essential for maintaining a vast number of complex missions beyond Earth orbit. To achieve full autonomy, spacecraft must be able to employ methods of robust maneuver design without an explicit dependence on commands sent from the ground. This level of autonomy is needed not only for stationkeeping, but also for outbound transfers. To address the need of spacecraft maneuver design autonomy, this work investigates the use of neural networks (NNs) in a supervised learning environment. A supervised learning approach for NNs allows for a curated training data set, consisting exclusively of perturbations applied to a desired mission concept of operations (ConOps). The proposed approach allows humans on the ground to design a specific mission ConOps before flight, then employ NNs to fly the mission robustly and autonomously. This investigation numerically tests maneuver autonomy in four highly sensitive regions of flight: orbit raising, translunar injection burns, powered lunar flybys, and invariant manifold insertion burns. These straining cases are contextualized by testing them in a demonstration mission, targeting an Earth-Moon L3 orbit. The study first establishes feasibility by automating impulsive burn maneuvers. However, some guidance algorithms will need more intensive commands, such as inertial pointing and angular rates. To validate this method, NN maneuver autonomy is applied to a finite burn model of the demonstration mission. The use of sequential, mission specific maneuvers provide an appropriate testbed to demonstrate the robustness of a NN trained on feasible perturbed states. Moreover, these scenarios provide preliminary proof-of-concept for fully autonomous missions that execute maneuvers without dependence upon explicit command uplinks. As a result, the technological advancement proposed in this work may significantly ease the strain on ground-based mission operations. This would enable complex and autonomous mission execution in cislunar and deep space regimes, filling a technology gap required to support future manned missions.

NASA↗

A Novel Protection Scheme for Unbalanced Faults in Inverter Dominated Networks: A Computationally Efficient Algorithm for Entry-Level Relays

Microgrids are now a common practice in distribution systems to increase resilience and reliability. However, microgrid protection remains a critical challenge, considering its requirement to operate in both grid connected and islanded, and the variability in fault characteristics under each mode of operation. This paper presents unbalanced power (S unb ) based fault detection algorithm, which considers local voltage and current unbalances to determine faults in the system. S unb is a computationally efficient fault detection algorithm that is suitable for implementation in the programmable logic of entry level protective relays. In addition, the difference in current and voltage unbalance (D n ) is used to determine the fault type. The proposed method demonstrates high sensitivity and selectivity for line-to-ground (LG), line-to-line (LL), and double line-to-ground (LLG) faults, representing the most common faults in distribution systems. It also allows relay coordination with upstream and downstream protection devices in both island and grid connected operation, while preserving grading margins. The same pickup and time multiplier settings of a particular relay for both modes of operation eliminates the need for adaptive settings, which rely on communication networks. Validation was performed with a hardware-in-the-loop (HIL) setup using Typhoon HIL real time simulator interfaced with three entry-level, SEL 751 relays. Results confirmed the algorithm’s ability to discriminate fault conditions, and determine the fault type under both operating modes, maintain fast detection times, and ensure proper protection coordination.

fault classification↗

Rovibrationally resolved Rayleigh and Raman scattering cross sections for molecular hydrogen

Accurate Rayleigh and Raman scattering cross sections, tensor components, depolarization ratios, and reversal coefficients for all rovibrational transitions within the X1Σg+ ground electronic state of H2 have been calculated. Raman spectra have been generated using these data. A method for calculating Raman scattering cross sections is formulated that is valid below the ionization threshold and in the region containing resonances, which explicitly accounts for all bound and dissociative vibrational levels of the bound intermediate electronic states and approximately accounts for the ionization continuum. A representative set of cross sections is presented for incident photon energies below 15 eV and compared with existing results in the literature where possible. Convergence of our results with an increasing number of bound intermediate electronic states is demonstrated. The accuracy of the Placzek–Teller approximation is discussed. The effect of accounting for the intermediate ionization continuum is investigated. Local thermal equilibrium cross sections are calculated for Rayleigh and Raman scattering. This work represents the most accurate and complete treatment of Raman scattering for molecular hydrogen to date. A total of 9582 Rayleigh and Raman scattering cross sections have been generated and are openly available on Zenodo under an open-source Creative Commons Attribution license at https://zenodo.org/doi/10.5281/zenodo.13441471.

74 ATOMIC AND MOLECULAR PHYSICS↗

Two-Level Adaptive Algebraic Multigrid for a Sequence of Problems with Slowly Varying Random Coefficients [Adaptive Algebraic Multigrid for Sequence of Problems with Slowly Varying Random Coefficients]

Our paper proposes an adaptive strategy for reusing a previously constructed coarse space by algebraic multigrid to construct a two-level solver for a problem with nearby characteristics. Furthermore, a main target application is the solution of the linear problems that appear throughout a sequence of Markov chain Monte Carlo simulations of subsurface flow with uncertain permeability field. We demonstrate the efficacy of the method with extensive set of numerical experiments.

97 MATHEMATICS AND COMPUTING↗

Simulating stochastic and additively manufactured foams at large strains and high strain rates (Progress Summary)

Understanding the mechanical response of polymer foams is essential in developing system material models and in designing replacements for legacy pads and cushions. Simulations can help elucidate structure-property relationships and compare local stress distributions to understand aging behavior and improve designs. In many applications, these materials experience significant loadings and computations need the capability to reproduce those conditions. We are applying are previously developed material point method (MPM) simulation capability to understand the aging properties of loaded direct ink write resins. Significant particle loading of a stiffer material in siloxane networks exhibit different compression set behavior than unloaded specimens. We are applying our computational mechanics capabilities to understand this difference at the continuum level. Figure 1 highlights preliminary results, depicting renderings of an unloaded DIW filament alongside one containing a 20% volume loading of spherical particles. Also, the stress distribution of a neat filament at 20% compression is shown. We are planning to study this behavior for a range of loading fractions, particle sizes, and material stiffness ratios. We will explore the sensitivity of the stress response to these variables which could inform aging models of these materials.

36 MATERIALS SCIENCE↗

A technique for rapid source apportionment applied to ambient organic aerosol measurements from a thermal desorption aerosol gas chromatograph (TAG)

Here, we present a rapid method for apportioning the sources of atmospheric organic aerosol composition measured by gas chromatography–mass spectrometry methods. Here, we specifically apply this new analysis method to data acquired on a thermal desorption aerosol gas chromatograph (TAG) system. Gas chromatograms are divided by retention time into evenly spaced bins, within which the mass spectra are summed. A previous chromatogram binning method was introduced for the purpose of chromatogram structure deconvolution (e.g., major compound classes) (Zhang et al., 2014). Here we extend the method development for the specific purpose of determining aerosol samples' sources. Chromatogram bins are arranged into an input data matrix for positive matrix factorization (PMF), where the sample number is the row dimension and the mass-spectra-resolved eluting time intervals (bins) are the column dimension. Then two-dimensional PMF can effectively do three-dimensional factorization on the three-dimensional TAG mass spectra data. The retention time shift of the chromatogram is corrected by applying the median values of the different peaks' shifts. Bin width affects chemical resolution but does not affect PMF retrieval of the sources' time variations for low-factor solutions. A bin width smaller than the maximum retention shift among all samples requires retention time shift correction. A six-factor PMF comparison among aerosol mass spectrometry (AMS), TAG binning, and conventional TAG compound integration methods shows that the TAG binning method performs similarly to the integration method. However, the new binning method incorporates the entirety of the data set and requires significantly less pre-processing of the data than conventional single compound identification and integration. In addition, while a fraction of the most oxygenated aerosol does not elute through an underivatized TAG analysis, the TAG binning method does have the ability to achieve molecular level resolution on other bulk aerosol components commonly observed by the AMS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗