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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,243 records · Page 69
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Large-scale quasi-Newton trust-region methods with low-dimensional linear equality constraints

We propose two limited-memory BFGS (L-BFGS) trust-region methods for large-scale optimization with linear equality constraints. Here, the methods are intended for problems where the number of equality constraints is small. By exploiting the structure of the quasi-Newton compact representation, both proposed methods solve the trust-region subproblems nearly exactly, even for large problems. We derive theoretical global convergence results of the proposed algorithms, and compare their numerical effectiveness and performance on a variety of large-scale problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Additive manufacturing of metal matrix composites

Although Metal matrix composites (MMCs) are superior to most sought-after metallic alloys, their challenging fabricability has limited their widespread use in bulk-form applications. Among the many advanced fabrication techniques, Additive Manufacturing (AM), owing to its unique capabilities to produce near-net shapes, has drawn significant traction in the past two decades, especially for materials that are difficult to process using traditional methods. However, unlike pure metal/alloy systems, MMCs are highly sensitive to the processing conditions prevailing in AM techniques due to factors such as the high melting point of reinforcement particles and the potential for in-situ reactions. Therefore, it may be a while before metal matrix composites are commercially produced via AM. This review will discuss the current state-of-the-art design, fabricability, and performance of various additively manufactured MMCs. A particular focus will be on microstructural evolution and microstructure-property relationships. The most employed AM techniques, such as directed energy deposition, powder bed fusion, binder jetting, sheet lamination, and solid-state friction stir processing, are fundamentally different in terms of thermo-kinetics, forming the perspective for this review. A detailed comparison of microstructural evolution and process parameter optimization, including feedstock preparation methods and the role of machine learning and modeling among the different AM processes, is also presented. Finally, a critical evaluation of emerging AM technologies for MMCs is also provided, highlighting their potential advantages and challenges.

36 - MATERIALS SCIENCE↗
DOE OSTI2025

One Galaxy Sample to Rule Them All: Halo Occupation Distribution Modeling of DES Year 3 Source Galaxies

Abstract For the joint analysis of second-order weak-lensing and galaxy clustering statistics, so-called 3 × 2 analyses, the selection and characterization of optimal galaxy samples is a major area of research. One promising choice is to use the same galaxy sample as lenses and sources, which reduces the systematics parameter space that describes the uncertainties related to galaxy samples. Such a “lens-equal-source” analysis significantly improves the self-calibration of photo- z systematics, leading to improved cosmological constraints. With the aim of enabling a lens-equal-source analysis on small scales, we investigate the halo–galaxy connection of DES Year 3 source galaxies. We develop a technique to construct mock source galaxy populations by matching COSMOS/UltraVISTA photometry to U niverse M achine galaxies. These mocks predict a source halo occupation distribution (HOD) that exhibits significant redshift evolution, nontrivial central incompleteness, and galaxy assembly bias. We produce multiple realizations of mock source galaxies drawn from the U niverse M achine posterior, with added uncertainties in the measured Dark Energy Survey photometry and galaxy shapes. We fit a modified HOD formalism to these realizations to produce priors on the galaxy–halo connection for cosmological analyses. We additionally train an emulator that predicts this HOD to ∼2% accuracy from redshift z = 0.1−1.3 that models the dependence of this HOD on (1) observational uncertainties in galaxy size and photometry and (2) uncertainties in the U niverse M achine predictions.

Salcedo, Andrés N. (ORCID:000000031420527X)↗
DOE OSTI2024

A Gaussian process autoregressive model capturing microstructure evolution paths in a Ni–Mo–Nb alloy

Additive manufacturing is increasingly being employed to produce components of complex geometries in structural alloys because of the expected energy savings associated with the near-net-shape capability and the ability to build in novel internal features that are not possible with many conventional manufacturing approaches. However, because of the extreme thermal conditions encountered, the non-equilibrium microstructures produced during powder bed-based additive manufacturing processes must be subjected to custom post-heat treatment processes to recover the target mechanical properties. Phase-field models and simulation techniques have matured to a state where the microstructure evolution paths, and the morphologies of the resulting precipitate phases can be predicted reasonably accurately, considering alloy-specific thermodynamic and kinetic aspects of the nucleation and growth processes. However, phase-field simulations are computationally intensive, which precludes the ability to apply the simulations directly to the length scale of the entire component. Therefore, it is highly desirable to develop low-computational-cost surrogate models that effectively capture the physics at the microstructural length scale, while facilitating the design of optimized processing conditions resulting in location-specific targeted microstructures at the component scale. The work presented here demonstrates the application of the materials knowledge system framework to develop a surrogate model that effectively captures the microstructural path during annealing of a Ni–Mo–Nb alloy containing different Mo and Nb compositions known to segregate during solidification under additive manufacturing conditions. Specifically, the surrogate model built in this work is based on a Gaussian process autoregressive model informed by statistical representation of simulated microstructures using two-point correlations and dimensionality reduction through principal component analysis. In conclusion, this surrogate model is shown to capture the bifurcation of the microstructural path during precipitation, which yields a microstructure dominated by the $\gamma^{\prime\prime}$ phase at high Nb concentrations and the $\delta$ phase at low Nb concentrations.

36 MATERIALS SCIENCE↗
DOE OSTI2018

A New Design for the Hilumi Radio-Frequency Dipole Bare Cavity

Crabbing cavities are one of the technological landmark that will allow the LHC to optimize its per-formance and maximize its integrated luminosity by allowing a head-on collision between the bunches despite the non-zero crossing angle. A total of 8 crab cavities will be installed in the interaction region of each of the two experiments, ATLAS and CMS. In the last years, the two types of crab cavities were de-signed, built and tested under the US-LARP R&D pro-gram. Horizontal crabbing is obtained with a radio-frequency dipole cavity (RFD) designed by Old Do-minion University (ODU), SLAC and Fermilab (FNAL). In this paper a new mechanical design, that uses passive stiffeners, is presented. This design leads to a decrease of the Lorentz Force Detuning frequency shift, satisfy the requirements on pressure sensitivity, validate the structural integrity and increase the tuner sensitivity and the maximum elastic tuning range. Furthermore, it will be possible to greatly simplify the shape of the magnetic shield and Helium vessel with respect to the current design.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

Regal Beloit Final Technical Report

The original project proposal submitted from NovaTorque Inc (NovaTorque) in 2016 was to improve the existing motor with 95% efficiency by reducing the losses by 21% to achieve 96%. A few months after the proposal was submitted, NovaTorque lost funding and went out of business. The assets of NovaTorque were then acquired by Regal Beloit Corporation (“Regal Beloit” or “Regal”). When the NovaTorque proposal was selected, the project was transferred to Regal Beloit. Once we had production samples from the new Regal production line, they were tested at the Regal Beloit test lab in Wausau, WI. The original NovaTorque motor had an efficiency of 95%, but when the technology was transferred to Regal Beloit, there were multiple manufacturing improvements made, even though the basic electromagnetic design did not change. The test results in Wausau showed that the motors made at the Regal Beloit plant had an efficiency of 96%. Since the goal of the project was to reduce the losses by 21%, a new efficiency target of 96.8% became the project objective. In the first budget period, motors were tested to get the baseline performance. We then used FEA modeling with ANSYS Maxwell to model the existing motor to get correlation between the FEA simulations and the actual test results. Once the model was validated, we evaluated some changes that could be made to the stator to reduce the losses and improve efficiency without changing the rotor or stator housing, keeping the modifications easy to implement. The changes were primarily in the area of making the stator axially shorter and adding Soft Magnetic Composite (SMC) tooth tips. In the second budget period, we proceeded to design and build the new stator that was identified above and identified additional improvements in the process that included a stator machining modification and the use of rectangular wire. When we actually built the motor, the choice of rectangular wire turned out to be a problem. The wire was made by squishing round wire to get the rectangular shape, which caused work hardening, making the wire too stiff to make the desired coils. We shifted to annealed square wire which was better, but we still could not maintain the proper coil envelope. The result was that we had reduced cross section area for stator laminations. We also had to have a radial offset resulting in a radial misalignment between the stator and rotor because of the oversized coils. After the motor was completed, it was shipped to Texas A&M University for testing. With the loss of flux from these issues, the measured motor efficiency was only 96.3%. The primary focus of this motor was to make sure our FEA simulation model predicted the measured losses and overall efficiency, this we moved on to the FEA simulation. The FEA simulations of the motor “as built” with misalignments had good correlation with the test results, so the next step was to use that model to optimize the design of the motor for a final build. This time we considered changes to the stator and rotor and also minor changes to the housing diameter. In the third budget period, we did the detailed design and construction of the final prototypes. The final prototypes had a slight increase in the stator diameter to fit in a standard Regal Beloit housing. We shortened the stator and use more layers of wire in the coils. We also increased the cone angle of the rotor and stator from the original 110 degrees to 130 degrees to get some additional efficiency and optimized the stator cross section. The predicted efficiency from the FEA simulations was 96.9%. When completed, the motors were tested. We were a little short of reaching our target efficiency goal of 96.8%. We were only able to get to 96.7% efficiency. While it may be possible with additional iterations in designs and future builds to gain that additional 0.1%, we believe that we are close to the best we can achieve from a practical viewpoint, and additional iterations would be more work than the potential gains would be worth. No other motor in this class can even reach the 96% that we started with.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2023

Thermal Spray toolpath development for a capped cylinder (“cake pan”) substrate

A near net shape coating is desired to be applied to the outer surface of a capped cylinder (“cake pan”) type substrate using thermal spray technology. A capped cylinder geometry is more complex than simple coupon-level substrate substrates (e.g., flat panels, cylinders) and thus requires a more complex toolpath to deposit a uniform coating. This report documents a practical theoretical approach to calculating relative torch-to-substrate speeds for coating the cylindrical, corner, and cap region of a rotating capped cylinder based on fundamental thermal spray toolpath principles. A preliminary experimental test deposited a thermal spray coating onto a mock substrate using toolpath speeds calculated by the theoretical approach proposed. The mock substrate was metallographically inspected to assess coating uniformity across the cylindrical, corner, and cap region. Inspection of the mock substrate revealed qualitatively uniform coating microstructure and thickness where theoretically predicted, demonstrating the viability of the proposed toolpath method and associated calculations. Pathways forward to optimizing coating uniformity at the cap center are proposed as near term suggested future work.

42 ENGINEERING↗
DOE OSTI2024

Exploring Ecological, Morphological, and Environmental Controls on Coastal Foredune Evolution at Annual Scales Using a Process-Based Model

Coastal communities commonly rely upon foredunes as the first line of defense against sea-level rise and storms, thus requiring management guidance to optimize their protective services. Here, we use the AeoLiS model to simulate wind-driven accretion and wave-driven erosion patterns on foredunes with different morphologies and ecological properties under modern-day conditions. Additional sets of model runs mimic potential future climate changes to inform how both morphological and ecological properties may have differing contributions to net dune changes under evolving environmental forcing. This exploratory study, applied to represent the morphological, environmental, and ecological conditions of the northern Outer Banks, North Carolina, USA, finds that dunes experiencing minimal wave collision have similar net volumetric growth rates regardless of beach morphology, though the location and density of vegetation influence sediment deposition patterns across the dune profile. The model indicates that high-density, uniform planting strategies trap sediment close to the dune toe, whereas low-density plantings may allow for accretion across a broader extent of the dune face. The initial beach and dune shape generally plays a larger role in annual-scale dune evolution than vegetation cover. For steeper beach slopes and/or low dune toe elevations, the model generally predicts wave-driven dune erosion at the annual scale.

Environmental Sciences & Ecology↗
DOE OSTI2024

Axial H-Bonding Solvent Controls Inhomogeneous Spectral Broadening, While Peripheral H-Bonding Solvent Controls Vibronic Broadening: Cresyl Violet in Methanol

The dynamics of the nuclei of both a chromophore and its condensed-phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral line shapes. For the cresyl violet chromophore in methanol, we here analyze and isolate the effect of specific chromophore–solvent interactions on simulated spectral densities, reorganization energies, and linear absorption spectra. Employing both chromophore and its condensed-phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral line shapes. For the cresyl violet chromophore in methanol, we here analyze and isolate the effect of specific chromophore–solvent interactions on simulated spectral densities, reorganization energies, and linear absorption spectra. Employing both force field and ab initio molecular dynamics trajectories along with the inclusion of only certain solvent molecules in the excited-state calculations, we determine that the methanol molecules axial to the chromophore are responsible for the majority of inhomogeneous broadening, with a single methanol molecule that forms an axial hydrogen bond dominating the response. Furthermore, the strong peripheral hydrogen bonds do not contribute to spectral broadening, as they are very stable throughout the dynamics and do not lead to increased energy-gap fluctuations. We also find that treating the strong peripheral hydrogen bonds as molecular mechanical point charges during the molecular dynamics simulation underestimates the vibronic coupling. Including these peripheral hydrogen bonding methanol molecules in the quantum-mechanical region in a geometry optimization increases the vibronic coupling, suggesting that a more advanced treatment of these strongly interacting solvent molecules during the molecular dynamics trajectory may be necessary to capture the full vibronic spectral broadening.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

COMSOL Results for the Nominal Steady-State Operation of the Proposed 95-MW LEU Silicide Core for HFIR Conversion

Engineering design studies are being performed to determine the feasibility of converting the High Flux Isotope Reactor (HFIR) from highly enriched uranium (HEU) to low-enriched uranium (LEU) fuel at Oak Ridge National Laboratory. This activity is sponsored by the Office of Reactor Conversion and Uranium Supply (ORCUS) under the auspices of the US Department of Energy National Nuclear Security Administration’s Office of Material Management and Minimization. HFIR is a very high flux, pressurized, light water–cooled and moderated, flux trap–type research reactor with a core made of involute shaped U 3 O 8 /Al cermet fuel plates and coolant channels. HFIR currently operates at a thermal power of 85 MW and supports key national and international missions in neutron scattering, isotope production, materials/fuels irradiation, neutron activation analysis, gamma irradiation, and neutrino research. Advanced multiphysics computational fluid dynamics models have been developed in the COMSOL Multiphysics software to simulate the steady-state operating conditions for the proposed low-and high-density LEU U 3 Si 2 -Al (uranium silicide dispersion) fuel designs. The COMSOL models for HFIR inner and outer fuel element models incorporate various essential inputs and physics such as spatially dependent nuclear heat deposition, multilayer heat conduction, conjugate heat transfer, turbulent flows (using Reynolds-averaged Navier Stokes turbulence models), structural mechanics (thermal–structural interactions and fuel swelling), and oxide layer build-up. This report presents the best-estimate thermal hydraulics results for the low- and high-density optimized silicide LEU core designs at 95 MW steady-state nominal operation.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2018

Design and convergence analysis of the conforming virtual element method for polyharmonic problems

In the recent years, there has been a tremendous interest to numerical methods that approximate partial differential equations (PDEs) on computational meshes with arbitrarily-shaped polygonal/polyhedral (polytopal, for short) elements. A nonexhaustive list of such methods include the Mimetic Finite Difference method [4, 9, 21, 24, 28, 33, 35, 62, 64–67], the Polygonal Finite Element Method [68, 73, 74], the polygonal Discontinuous Galerkin Finite Element Methods [5, 7, 8, 10, 13–15, 18, 36, 38, 39, 41, 50], the Hybridizable Discontinuous Galerkin and Hybrid High-Order Methods [46–48, 51], the Gradient Discretization method [49, 53, 54], the Finite Volume Method [52], and the BEM-based FEM [71]. An alternative approach that also proved to be very successful is provided by the Virtual Element method (VEM), which was originally proposed in [19] for the numerical treatment of second-order elliptic problems [43, 44], and readily extended to linear and nonlinear elasticity [22, 25, 56], plate bending problems [37], Cahn-Hilliard equation [3], Stokes equations [2], Laplace-Beltrami equation [55], Darcy-Brinkam equation [76], discrete topology optimization problems [6], fracture networks problems [29], eigenvalue problems [59, 75]. The mixed virtual element formulation was proposed in [20, 34]; the nonconforming Virtual element formulations was proposed for second-order elliptic problems in [16], and later extended to general advection-reaction-diffusion problems, Stokes equation, the biharmonic problems, the iegenvalue problem, and the Schrodinger equation in [11, 30, 42, 45, 58, 80]. The p- and hp-version of the VEM were developed in [26, 27] and efficient multigrid methods for the resulting linear system of equations in [12]. A posteriori error estimates can be found in [40].

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Adaptive Data-Driven Deep-Learning Surrogate Model for Frontal Polymerization in Dicyclopentadiene

Frontal polymerization (FP) is a self-sustaining curing process that enables rapid and energy-efficient manufacturing of thermoset polymers and composites. Computational methods conventionally used to simulate the FP process are time-consuming, and repeating simulations are required for sensitivity analysis, uncertainty quantification, or optimization of the manufacturing process. Here, in this work, we develop an adaptive surrogate deep-learning model for FP of dicyclopentadiene (DCPD), which predicts the evolution of temperature and degree of cure orders of magnitude faster than the finite-element method (FEM). The adaptive algorithm provides a strategy to select training samples efficiently and save computational costs by reducing the redundancy of FEM-based training samples. The adaptive algorithm calculates the residual error of the FP governing equations using automatic differentiation of the deep neural network. A probability density function expressed in terms of the residual error is used to select training samples from the Sobol sequence space. The temperature and degree of cure evolution of each training sample are obtained by a 2D FEM simulation. The adaptive method is more efficient and has a better prediction accuracy than the random sampling method. With the well-trained surrogate neural network, the FP characteristics (front speed, shape, and temperature) can be extracted quickly from the predicted temperature and degree-of-cure fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Amplification-free nucleic acid detection with a fluorescence-based waveguide biosensor

Early detection of pathogens using nucleic acids in clinical samples often requires sensitivity at the single-copy level, which currently necessitates time-consuming and expensive nucleic acid amplification. Here, we describe 1) a redesigned flow cell in the shape of a trapezoid-subtracted geometric stadium, and 2) modified experimental procedures that allow for the measurement of sub-attomolar analytes in microliter quantities on a fluorescence-based waveguide biosensor. We verified our instrumental sensitivity with a 200-μL sample of a fluorescent streptavidin conjugate at 100 zM (100 zeptomolar, or 100·10 −21 mol L −1 ) and theoretically explored the applicability of this modified sensing platform in a sandwich immunoassay format using a Langmuir adsorption model. We present assays that demonstrate specific detection of synthetic influenza A DNA (in buffer) and RNA (in saliva) oligonucleotides at the single-copy level (200 μL at 10 zM) using a fluorescent molecular beacon. Lastly, we demonstrate detection of isolated genomic influenza A RNA at a clinically relevant concentration. This work constitutes a sensitivity improvement of over twelve orders of magnitude compared to our previous nucleic acid detection work, illustrating the significant enhancements that can be gained with optimized experimental design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Simulation of the Multi-Wake Evolution of Two Sandia National Labs/National Rotor Testbed Turbines Operating in a Tandem Layout

The future of wind power systems deployment is in the form of wind farms comprised of scores of such large turbines, most likely at offshore locations. Individual turbines have grown in span from a few tens of meters to today’s large turbines with rotor diameters that dwarf even the largest commercial aircraft. These massive dynamical systems present unique challenges at scales unparalleled in prior applications of wind science research. Fundamental to this effort is the understanding of the wind turbine wake and its evolution. Furthermore, the optimization of the entire wind farm depends on the evolution of the wakes of different turbines and their interactions within the wind farm. In this article, we use the capabilities of the Common ODE Framework (CODEF) model for the analysis of the effects of wake–rotor and wake-to-wake interactions between two turbines situated in a tandem layout fully and partially aligned with the incoming wind. These experiments were conducted in the context of a research project supported by the National Rotor Testbed (NRT) program of Sandia National Labs (SNL). Results are presented for a layout which emulates the turbine interspace and relative turbine emplacement found at SNL’s Scaled Wind Technologies Facility (SWiFT), located in Lubbock, Texas. The evolution of the twin-wake interaction generates a very rich series of secondary transitions in the vortex structure of the combined wake. These ultimately affect the wake’s axial velocity patterns, altering the position, number, intensity, and shape of localized velocity-deficit zones in the wake’s cross-section. This complex distribution of axial velocity patterns has the capacity to substantially affect the power output, peak loads, fatigue damage, and aeroelastic stability of turbines located in subsequent rows downstream on the farm.

Baruah, Apurva (ORCID:0000000252354068)↗
DOE OSTI2023

Optimal Frequency-domain Analysis for Spacecraft Time Series: Introducing the Missing-data Multitaper Power Spectrum Estimator

While the Lomb–Scargle periodogram is foundational to astronomy, it has a significant shortcoming: the variance in the estimated power spectrum does not decrease as more data are acquired. Statisticians have a 60 yr history of developing variance-suppressing power spectrum estimators, but most are not used in astronomy because they are formulated for time series with uniform observing cadence and without seasonal or daily gaps. Here we demonstrate how to apply the missing-data multitaper power spectrum estimator to spacecraft data with uniform time intervals between observations but missing data during thruster fires or momentum dumps. The F-test for harmonic components may be applied to multitaper power spectrum estimates to identify statistically significant oscillations that would not rise above a white noise–based false alarm probability. Multitapering improves the dynamic range of the power spectrum estimate and suppresses spectral window artifacts. We show that the multitaper–F-test combination applied to Kepler observations of KIC 6102338 detects differential rotation without requiring iterative sinusoid fitting and subtraction. Significant signals reside at harmonics of both fundamental rotation frequencies and suggest an antisolar rotation profile. Next we use the missing-data multitaper power spectrum estimator to identify the oscillation modes responsible for the complex "scallop-shell" shape of the K2 light curve of EPIC 203354381. We argue that multitaper power spectrum estimators should be used for all time series with regular observing cadence.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Deep Generative Modeling of Periodic Variable Stars Using Physical Parameters

The ability to generate physically plausible ensembles of variable sources is critical to the optimization of time domain survey cadences and the training of classification models on data sets with few to no labels. Traditional data augmentation techniques expand training sets by reenvisioning observed exemplars, seeking to simulate observations of specific training sources under different (exogenous) conditions. Unlike fully theory-driven models, these approaches do not typically allow principled interpolation nor extrapolation. Moreover, the principal drawback of theory-driven models lies in the prohibitive computational cost of simulating source observables from ab initio parameters. In this work, we propose a computationally tractable machine learning approach to generate realistic light curves of periodic variables capable of integrating physical parameters and variability classes as inputs. Our deep generative model, inspired by the transparent latent space generative adversarial networks, uses a variational autoencoder (VAE) architecture with temporal convolutional network layers, trained using the OGLE-III optical light curves and physical characteristics (e.g., effective temperature and absolute magnitude) from Gaia DR2. A test using the temperature–shape relationship of RR Lyrae demonstrates the efficacy of our generative “physics-enhanced latent space VAE” (PELS-VAE) model. Such deep generative models, serving as nonlinear nonparametric emulators, present a novel tool for astronomers to create synthetic time series over arbitrary cadences.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Planck 2018 results

We analyse the Planck full-mission cosmic microwave background (CMB) temperature and E -mode polarization maps to obtain constraints on primordial non-Gaussianity (NG). We compare estimates obtained from separable template-fitting, binned, and optimal modal bispectrum estimators, finding consistent values for the local, equilateral, and orthogonal bispectrum amplitudes. Our combined temperature and polarization analysis produces the following final results: f NL local = -0.9 ± 5.1; f NL equil = -26 ± 47; and f NL ortho = -38 ± 24 (68% CL, statistical). These results include low-multipole (4 ≤ ℓ < 40) polarization data that are not included in our previous analysis. The results also pass an extensive battery of tests (with additional tests regarding foreground residuals compared to 2015), and they are stable with respect to our 2015 measurements (with small fluctuations, at the level of a fraction of a standard deviation, which is consistent with changes in data processing). Polarization-only bispectra display a significant improvement in robustness; they can now be used independently to set primordial NG constraints with a sensitivity comparable to WMAP temperature-based results and they give excellent agreement. In addition to the analysis of the standard local, equilateral, and orthogonal bispectrum shapes, we consider a large number of additional cases, such as scale-dependent feature and resonance bispectra, isocurvature primordial NG, and parity-breaking models, where we also place tight constraints but do not detect any signal. The non-primordial lensing bispectrum is, however, detected with an improved significance compared to 2015, excluding the null hypothesis at 3.5 σ . Beyond estimates of individual shape amplitudes, we also present model-independent reconstructions and analyses of the Planck CMB bispectrum. Our final constraint on the local primordial trispectrum shape is g NL local = (-5.8 ± 6.5) × 10 4 (68% CL, statistical), while constraints for other trispectrum shapes are also determined. Exploiting the tight limits on various bispectrum and trispectrum shapes, we constrain the parameter space of different early-Universe scenarios that generate primordial NG, including general single-field models of inflation, multi-field models (e.g. curvaton models), models of inflation with axion fields producing parity-violation bispectra in the tensor sector, and inflationary models involving vector-like fields with directionally-dependent bispectra. Our results provide a high-precision test for structure-formation scenarios, showing complete agreement with the basic picture of the ΛCDM cosmology regarding the statistics of the initial conditions, with cosmic structures arising from adiabatic, passive, Gaussian, and primordial seed perturbations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit—and revealed many critical ecosystem roles for viruses—microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated short- and long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data (‘enhanced’ viromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using long- and short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in the other assemblies), 30% of which were uniquely assembled through inclusion of long-reads, and 22% of the top 10% most abundant virus populations derived from assembly of long-reads. Viral populations unique to VirION2 assemblies had significantly higher microdiversity means, which may explain why short-read virome approaches failed to capture them. These findings suggest the VirION2 sample prep and workflow can help researchers better investigate the virosphere, even from challenging low-biomass samples. Our new protocols are available to the research community on protocols.io as a ‘living document’ to facilitate dissemination of updates to keep pace with the rapid evolution of long-read sequencing technology.

Long-reads↗