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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Mitigation of DESI fiber assignment incompleteness effect on two-point clustering with small angular scale truncated estimators

We present a method to mitigate the effects of fiber assignment incompleteness in two-point power spectrum and correlation function measurements from galaxy spectroscopic surveys, by truncating small angular scales from estimators. We derive the corresponding modified correlation function and power spectrum windows to account for the small angular scale truncation in the theory prediction. We validate this approach on simulations reproducing the Dark Energy Spectroscopic Instrument (DESI) Data Release 1 (DR1) with and without fiber assignment. We show that we recover unbiased cosmological constraints using small angular scale truncated estimators from simulations with fiber assignment incompleteness, with respect to standard estimators from complete simulations. Additionally, we present an approach to remove the sensitivity of the fits to high k modes in the theoretical power spectrum, by applying a transformation to the data vector and window matrix. We find that our method efficiently mitigates the effect of fiber assignment incompleteness in two-point correlation function and power spectrum measurements, at low computational cost and with little statistical loss.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Modeling suggests SARS-CoV-2 rebound after nirmatrelvir-ritonavir treatment is driven by target cell preservation coupled with incomplete viral clearance

In a subset of SARS-CoV-2-infected individuals treated with the antiviral nirmatrelvir-ritonavir, the virus rebounds following treatment. The mechanisms driving this rebound are not well understood. We used a mathematical model to describe the longitudinal viral load dynamics of 51 individuals treated with nirmatrelvir-ritonavir, 20 of whom rebounded. Target cell preservation, either by a robust innate immune response or initiation of N-R near the time of symptom onset, coupled with incomplete viral clearance, appears to be the main factor leading to viral rebound. Moreover, the occurrence of viral rebound is likely influenced by the time of treatment initiation relative to the progression of the infection, with earlier treatments leading to a higher chance of rebound. A comparison with an untreated cohort suggests that early treatments with nirmatrelvir-ritonavir may be associated with a delay in the onset of an adaptive immune response. Nevertheless, our model demonstrates that extending the course of nirmatrelvir-ritonavir treatment to a 10-day regimen may greatly diminish the chance of rebound in people with mild-to-moderate COVID-19 and who are at high risk of progression to severe disease. Altogether, our results suggest that in some individuals, a standard 5-day course of nirmatrelvir-ritonavir starting around the time of symptom onset may not completely eliminate the virus. Thus, after treatment ends, the virus can rebound if an effective adaptive immune response has not fully developed. These findings on the role of target cell preservation and incomplete viral clearance also offer a possible explanation for viral rebounds following other antiviral treatments for SARS-CoV-2.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Characterization of DESI fiber assignment incompleteness effect on 2-point clustering and mitigation methods for DR1 analysis

We present an in-depth analysis of the fiber assignment incompleteness in the Dark Energy Spectroscopic Instrument (DESI) Data Release 1 (DR1). This incompleteness is caused by the restricted mobility of the robotic fiber positioner in the DESI focal plane, which limits the number of galaxies that can be observed at the same time, especially at small angular separations. As a result, the observed clustering amplitude is suppressed in a scale-dependent manner, which, if not addressed, can severely impact the inference of cosmological parameters. We discuss the methods adopted for simulating fiber assignment on mocks and data. In particular, we introduce the fast fiber assignment (FFA) emulator, which was employed to obtain the power spectrum covariance adopted for the DR1 full-shape analysis. We present the mitigation techniques, organised in two classes: measurement stage and model stage. We then use high fidelity mocks as a reference to quantify both the accuracy of the FFA emulator and the effectiveness of the different measurement-stage mitigation techniques. This complements the studies conducted in a parallel paper for the model-stage techniques, namely the θ-cut approach. We find that pairwise inverse probability (PIP) weights with angular upweighting recover the “true” clustering in all the cases considered, in both Fourier and configuration space. Notably, we present the first ever power spectrum measurement with PIP weights from real data.

cosmological simulations↗
DOE OSTI2025

Characterization of DESI fiber assignment incompleteness effect on 2-point clustering and mitigation methods for DR1 analysis

We present an in-depth analysis of the fiber assignment incompleteness in the Dark EnergySpectroscopic Instrument (DESI) Data Release 1 (DR1). This incompleteness is caused by therestricted mobility of the robotic fiber positioner in the DESI focal plane, which limits thenumber of galaxies that can be observed at the same time, especially at small angular separations.As a result, the observed clustering amplitude is suppressed in a scale-dependent manner, which,if not addressed, can severely impact the inference of cosmological parameters. We discuss themethods adopted for simulating fiber assignment on mocks and data. In particular, we introducethe fast fiber assignment (FFA) emulator, which was employed to obtain the power spectrumcovariance adopted for the DR1 full-shape analysis. We present the mitigation techniques,organised in two classes: measurement stage and model stage. We then use high fidelity mocks as areference to quantify both the accuracy of the FFA emulator and the effectiveness of the differentmeasurement-stage mitigation techniques. This complements the studies conducted in a parallelpaper for the model-stage techniques, namely the θ-cut approach. We find that pairwiseinverse probability (PIP) weights with angular upweighting recover the “true” clustering in allthe cases considered, in both Fourier and configuration space. Notably, we present the first everpower spectrum measurement with PIP weights from real data.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

A two-level GPU-accelerated incomplete LU preconditioner for general sparse linear systems

This paper presents a parallel preconditioning approach based on incomplete LU (ILU) factorizations in the framework of Domain Decomposition (DD) for general sparse linear systems. We focus on distributed memory parallel architectures, specifically, those that are equipped with graphic processing units (GPUs). In addition to block-Jacobi, we present general purpose two-level ILU Schur complement-based approaches, where different strategies are presented to solve the coarse-level reduced system. These strategies are combined with modified ILU methods in the construction of the coarse-level operator, in order to effectively remove smooth errors by targeting an algebraically smooth vector. We leverage available GPU-based sparse matrix kernels to accelerate the setup and the solve phases of the proposed ILU preconditioner. We evaluate the efficiency of the proposed methods as a smoother for algebraic multigrid (AMG) and as a preconditioner for Krylov subspace methods on challenging anisotropic diffusion problems and a collection of general sparse matrices.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Sempervirens: A Fast Reconstruction Algorithm for Noisy and Incomplete Binary Matrix Representations of Trees

Applications such as reconstructing cell lineage trees (represented as phylogenetic trees) from single-cell sequencing data require reconstructing a {0,1}-matrix that has many errors and missing entries. We introduce Sempervirens, a very fast matrix reconstruction algorithm for noisy and incomplete matrix representations of phylogenetic trees. Sempervirens uses an iterative maximum-likelihood approach to determine the topology tree represented by the corrupted data. We show that Sempervirens is at least three orders of magnitude faster than other methods on thousand by thousand matrices, with the speed gap widening with larger matrices. We also show that Sempervirens matches state-of-the-art methods in reconstruction accuracy. The speed of Sempervirens enables it to be tractably applied to reconstructing much larger matrices than those that other methods can reconstruct. In addition to experimental results, we justify the algorithm with a mathematical treatment of its subprocedures.

algorithms↗
DOE OSTI2026

Flavor as an Incomplete Structure: Conceptual Questions and the Role of DUNE

Flavor remains one of the most successful yet least understood structures of the Standard Model. The discovery of the Higgs boson completed the electroweak account of mass generation, but did not explain the origin of fermion families, mass hierarchies, or mixing patterns. In this sense, flavor can be regarded as an empirically successful but conceptually incomplete structure. Neutrinos occupy a particularly sensitive place within this problem: their masses are tiny, their mixing is large, and their mass-generation mechanism may differ from that of charged fermions. In this article, we discuss flavor as an open conceptual problem and argue that DUNE, as a phased program spanning precision oscillation measurements and sensitivity to BSM and dark-sector phenomena, provides a powerful framework for testing the self-consistency and possible limits of the present three-flavor description. In particular, the complementarity between the long-baseline program and the Phase I near-detector complex, together with the DUNE-PRISM strategy for controlling interaction-model systematics and enabling data-driven near-to-far predictions, makes DUNE especially well-suited to search for small, correlated departures from the minimal flavor framework.

Montanari, Claudio S. [Fermilab; INFN, Pavia] (ORC↗
DOE OSTI2025

Solving high-dimensional inverse problems using amortized likelihood-free inference with noisy and incomplete data

Here, we present a likelihood-free probabilistic inversion method based on normalizing flows for high-dimensional inverse problems. The proposed method is composed of two complementary networks: a summary network for data compression and an inference network for parameter estimation. The summary network encodes raw observations into a fixed-size vector of summary features, while the inference network generates samples of the approximate posterior distribution of the model parameters based on these summary features. The posterior samples are produced in a deep generative fashion by sampling from a latent Gaussian distribution and passing these samples through an invertible transformation. We construct this invertible transformation by sequentially alternating conditional invertible neural network and conditional neural spline flow layers. The summary and inference networks are trained simultaneously. We apply the proposed method to an inversion problem in groundwater hydrology to estimate the posterior distribution of the log-conductivity field conditioned on spatially sparse time-series observations of the system’s hydraulic head responses. The conductivity field is represented with 706 degrees of freedom in the considered problem. Comparison with the likelihood-based iterative ensemble smoother PEST-IES method demonstrates that the proposed method accurately estimates the parameter posterior distribution and the observations’ predictive posterior distribution at a fraction of the inference time of PEST-IES.

conditional invertible neural network↗
DOE OSTI2024

Removing Basis Set Incompleteness Error in Finite-Temperature Electronic Structure Calculations: Two-Electron Systems

We investigate the basis-set-size dependence for quantities related to interacting electrons in the canonical ensemble. Calculations are performed using exact diagonalization (finite temperature full configuration interaction method) on two-electron model systems–the uniform electron gas (UEG) and the helium atom. Our data reproduce previous observations of a competition for how the internal energy converges between the ground-state correlation energy and the high-temperature kinetic energy. We explore how this can be related to component parts of the internal energy including kinetic, exchange, and correlation energies and show there is surprising nuance in how this can be broken down into mostly monotonically converging quantities. We also show that separation of the free energy into a free energy with/without correlation allows for monotonic convergence with basis set size due to the variational principle. We find that the free energy convergence matches the previously observed convergence properties of the internal energy. We discuss the free energy divergence that happens when converging a finite basis analytical hydrogen atom to the complete basis set limit and compare this to the energies of a helium atom in a large periodic box. Reducing the box size, we saw convergence trends for the helium atom that were similar to the UEG.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Learning of networked spreading models from noisy and incomplete data

Recent years have seen a lot of progress in algorithms for learning parameters of spreading dynamics from both full and partial data. Some of the remaining challenges include model selection under the scenarios of unknown network structure, noisy data, missing observations in time, as well as an efficient incorporation of prior information to minimize the number of samples required for an accurate learning. Here, in this work, we introduce a universal learning method based on a scalable dynamic message-passing technique that addresses these challenges often encountered in real data. The algorithm leverages available prior knowledge on the model and on the data, and reconstructs both network structure and parameters of a spreading model. We show that a linear computational complexity of the method with the key model parameters makes the algorithm scalable to large network instances.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Metabolomics of related C3 and C4 Flaveria species indicate differences in the operation of photorespiration under fluctuating light

C 3 photosynthesis can be complemented with a C 4 carbon concentrating mechanism (CCM) to minimize photorespiratory losses. C 4 photosynthesis is often more efficient than C 3 under steady-state conditions. However, the C 4 CCM depends on inter-cellular metabolite concentration gradients, which must increase following increases in light intensity and could decrease rates of C 4 photosynthesis under fluctuating light. Additionally, incomplete flux through photorespiration could prove beneficial to C 4 assimilation during light induction of the CCM. Here, we compare metabolic profiles in the closely related C 3 Flaveria robusta and C 4 Flaveria bidentis during a light transient from low to high light to determine if these non-steady state accumulation patterns provide insight to the induction of the metabolite gradients needed to drive C 4 intermediate transport and if there is incomplete cycling of photorespiratory intermediates. In these C 3 and C 4 species, metabolite steady-state pool sizes suggest that C 4 transport acids maintain concentration gradients across the bundle sheath and mesophyll cell types under these light fluctuations. However, there was incomplete flux through photorespiration in the C 4 F. bidentis, which could reduce photorespiratory CO 2 loss via glycine decarboxylation and help maintain higher rates of assimilation during following induction periods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Optimal invariant sets for atomistic machine learning

The representation of atomic configurations for machine learning models has led to numerous sets of descriptors. However, many descriptor sets are incomplete and/or functionally dependent. Incomplete sets cannot faithfully represent atomic environments. Yet complete constructions often suffer from a high degree of functional dependence, where some descriptors are functions of others. These redundant descriptors do not improve discrimination between atomic environments. We employ pattern recognition techniques to remove dependent descriptors to produce the smallest possible set that satisfies completeness. We apply this in two ways: First, we refine an existing description, the atomic cluster expansion. Second, we augment an incomplete construction, yielding a new message-passing neural network architecture that can recognize up to 5-body patterns. This architecture shows strong accuracy on state-of-the-art benchmarks while retaining low computational cost. Our results demonstrate the utility of this strategy to optimize descriptor sets across a range of descriptors and application datasets.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Complex Phase Transitions of Fully Rigid Sphere–Rod Amphiphiles Induced by Solvent Polarity in Dilute Solutions

Here we report complex macrophase and microphase transitions of rigid amphiphiles with spherical Keggin molecular clusters as the solvophilic block and rod-like rigid oligofluorene (OF) as the solvophobic block in mixed solvents of water and polar organic solvent. By properly adjusting the solvent polarity, the amphiphiles are found to respond accordingly by self-assembling into multilayered incomplete onion-like structures (10–25 vol % THF), single-layered vesicular structures (60 vol % THF), and an unexpected macrophase separation in the middle (40–50 vol % THF), which is due to the anomalous trends in Keggin solubility as a result of the nature of TBA + counterions. The rigidity of the OF block prevents the amphiphile from assembling by following the rule of packing parameters; instead, interdigitation among different rods leads to the formation of the solvophobic domain to achieve self-assembly. The incomplete onion structures are controlled by the interdigitation of rigid rods for the number of layers and the electrostatic interaction among Keggin head groups for the interlayer distance. When the degree of interdigitation becomes lower, the self-assembly process shows a trend that can be explained by the traditional rule of packing parameter. This study demonstrates the formation of different self-assembled structures by rigid amphiphiles and their transitions induced by solvent composition. The self-assembly (microphase separation) of rigid amphiphiles in a dilute solution could indeed represent a broad area containing complicated, uncharted rules.

36 MATERIALS SCIENCE↗
DOE OSTI2026

RuKY Catalyst‐Packed Permeation Membrane for Quantitative Ammonia and d3‐Ammonia Dehydrogenation to Ultrapure Hydrogen

Ammonia is a promising carbon-free hydrogen carrier, but incomplete ammonia dehydrogenation (cracking) generates atmospheric emissions of NO x , a potent greenhouse gas. Additionally, incomplete cracking of ammonia leads to regulatory challenges in nuclear and fusion power, where tritiated ammonia (NT 3 ) emissions are strictly controlled. Therefore, we report the use of low-temperature ammonia dehydrogenation catalysts (3%Ru/1%Y/12%K/Al 2 O 3 ) in a palladium alloy H 2 permeation membrane for quantitative conversion of ammonia into hydrogen and nitrogen at industry-relevant conditions. This catalytic membrane reactor system achieved an astonishing effluent concentration of <1 ppm at 450°C under a 100% NH 3 stream, which is far beyond the 99.6% conversion target required for the adoption of ammonia as a vehicle fuel. The low-temperature ammonia dehydrogenation catalyst was tested in a packed bed reactor with NH 3 and ND 3 to both elucidate the reaction mechanism and to quantify the kinetic isotope effect of the membrane reactor. The rate-limiting step at temperatures relevant to the palladium membrane are isotope independent, indicating that the isotopologue content will not modify the desired reaction kinetics. By reducing emissions to below-trace levels with no additional separation, this work provides a path to greatly simplified and miniaturized ammonia cracking processes.

ammonia decomposition↗
DOE OSTI2025

Structural and functional analyses of SARS-CoV-2 Nsp3 and its specific interactions with the 5’ UTR of the viral genome

ABSTRACT Non-structural protein 3 (Nsp3) is the largest open reading frame encoded in the SARS-CoV-2 genome, essential for the formation of double-membrane vesicles (DMV) wherein viral RNA replication occurs. We conducted an extensive structure-function analysis of Nsp3 and determined the crystal structures of the ubiquitin-like 1 (Ubl1), nucleic acid binding (NAB), β-coronavirus-specific marker (βSM) domains, and a sub-region of the Y domain of this protein. We show that the Ubl1, ADP-ribose phosphatase (ADRP), human SARS Unique (HSUD), NAB, and Y domains of Nsp3 bind the 5’ UTR of the viral genome and that the Ubl1 and Y domains possess affinity for recognition of this region, suggesting high specificity. The Ubl1-Nucleocapsid (N) protein complex binds the 5’ UTR with greater affinity than the individual proteins alone. Our results suggest that multiple domains of Nsp3, particularly Ubl1 and Y, shepherd the 5’ UTR of the viral genome during translocation through the DMV membrane, priming the Ubl1 domain to load the genome onto N protein. IMPORTANCE The largest protein encoded by the SARS-CoV-2 genome is Nsp3. In infected cells, this multi-domain protein forms a pore structure in the virus-induced double-membrane vesicles (DMV). We have incomplete data on Nsp3 molecular structure, and here, we describe crystal structures for multiple domains of Nsp3. It is thought that newly replicated viral RNA transits through the DMV pore; however, we possess incomplete data on which regions of Nsp3 actually interact with RNA. Here, we present data showing that five domains of Nsp3 interact with the 5’ UTR of the SARS-CoV-2 RNA, including the Y domain for which no function has ever been discovered. These data suggest that the pore structure plays an active role in recognizing the terminal end of the genome, transiting and loading the viral RNA onto the cytoplasmic nucleocapsid protein. These data help expand our knowledge of Nsp3 structure and function and the SARS-CoV-2 replication cycle.

Microbiology↗
DOE OSTI2024

Monsoonal MCS Initiation, Rainfall, and Diurnal Gravity Waves over the Bay of Bengal: Observation and a Linear Model

Abstract Previous observational studies have indicated that mesoscale convective systems (MCSs) contribute the majority of precipitation over the Bay of Bengal (BoB) during the summer monsoon season, yet their initiation and propagation remain incompletely understood. To fill this knowledge gap, we conducted a comprehensive study using a combination of 20-yr satellite observations, MCS tracking, reanalysis data, and a theoretical linear model. Satellite observations reveal clear diurnal propagation signals of MCS initiation frequency and rainfall from the west coast of the BoB toward the central BoB, with the MCS rainfall propagating slightly slower than the MCS initiation frequency. Global reanalysis data indicate a strong association between the offshore-propagating MCS initiation frequency/rainfall and diurnal low-level wind perturbations, implying the potential role of gravity waves. To verify the hypothesis, we developed a 2D linear model that can be driven by realistic meteorological fields from reanalysis. The linear model realistically reproduces the characteristics of offshore-propagating diurnal wind perturbations. The wind perturbations, as well as the offshore propagation signals of MCS initiation frequency and rainfall, are associated with diurnal gravity waves emitted from the coastal regions, which in turn are caused by the diurnal land–sea thermal contrast. The ambient wind speed and vertical wind shear play crucial roles in modulating the timing, propagation, and amplitude of diurnal gravity waves. Using the linear model and satellite observations, we further show that the stronger monsoonal flows lead to faster offshore propagation of diurnal gravity waves, which subsequently control the offshore propagation signals of MCS initiation and rainfall. Significance Statement Rainfall over the Bay of Bengal (BoB) is primarily contributed by large and organized rainfall systems in the summer monsoon season. During this season, these systems are commonly observed over the east coast of India around midnight, the western BoB in the morning, and the central BoB in the afternoon. This eastward rainfall propagation is confirmed by observations, reanalysis data, and a theoretical model to have a strong association with atmospheric diurnal gravity waves. These waves are caused by land–sea thermal contrast and can trigger rainfall systems over the offshore regions. We also found that the diurnal gravity waves, as well as their triggered rainfall systems, can be greatly modulated by the large-scale monsoonal flows. All the above findings improve our understanding of diurnal rainfall cycle over the BoB and may contribute to the future improvement of rainfall forecast over the region.

Meteorology & Atmospheric Sciences↗