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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 1,765 records · Page 98
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Rewiring the specificity of extracytoplasmic function sigma factors

Significance Bacterial phenotypes require the concerted expression of multiple genes, usually coordinated by a transcriptional regulator. Although the functions of many genes in sequenced bacterial genomes can be inferred, the regulatory networks that coordinate their expression are only known in a few model systems. Using a bioinformatic and experimental approach, we solve the DNA-specificity code of extracytoplasmic function sigma factors (ECF σs), a major class of bacterial regulators. We develop and use a high-stringency pipeline to predict the genes regulated by 67% of ECF σs in >10,000 species, providing a comprehensive look at the role of a broadly distributed family of gene regulatory proteins. This conceptual and computational framework is potentially applicable to other bacterial regulators.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

HostSub_GP: Precise Galaxy Background Subtraction in Transient Long-slit Spectroscopy with Gaussian Processes

We present a novel host galaxy subtraction technique in long-slit spectroscopy for extragalactic transients. Unlike classic methods which generally estimate the background using simple interpolation of local galaxy flux in the 2D spectrum, our approach leverages multi-band archival images of the host galaxies to model the background emission from the galaxy in the 2D spectrum. Such imaging encodes the wavelength-dependent galaxy profile along the slit, and is readily accessible through wide-field imaging surveys. We construct a smooth prior for the 2D galaxy profile with a Gaussian process (GP) based on these reference images, and use another GP to model the correlated deviations from the prior in the observed spectrum. This enables accurate inference of the galaxy flux blended with the transient. On synthetic long-slit data of a spiral galaxy extracted from a Multi Unit Spectroscopic Explorer hyper-spectral cube, the GP method remains robust as long as the host galaxy is spatially resolved and consistently outperforms classic methods. We apply the method to archival Keck spectra of two real transients, SN 2019eix and AT 2019qiz, to further demonstrate how the method uniquely recovers weak spectral features amid strong galaxy contamination, enabling refined constraints on the properties of both transients. We have released the software implementation, HostSub_GP, a scalable toolkit that leverages JAX, with an MIT license.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Hybrid simulations of sub-cyclotron compressional and global Alfvén eigenmode stability in spherical tokamaks

A comprehensive numerical study has been conducted in order to investigate the stability of beam-driven, sub-cyclotron-frequency compressional Alfvén eigenmodes (CAEs) and global Alfvén eigenmodes (GAEs) in low-aspect-ratio plasmas for a wide range of beam parameters. The presence of CAEs and GAEs has previously been linked to anomalous electron temperature profile flattening at high beam powers in NSTX experiments, prompting a further examination of the conditions necessary for their excitation. Linear simulations have been performed with the hybrid MHD–kinetic initial value code HYM in order to capture the general Doppler-shifted cyclotron resonance that drives the modes. Additionally, three distinct types of modes were found in the simulations—co-CAEs, cntr-GAEs, and co-GAEs—with differing spectral and stability properties. The simulations revealed that unstable GAEs are more ubiquitous than unstable CAEs, which is consistent with experimental observations, as they are excited at lower beam energies and generally have larger growth rates. Local analytic theory is used to explain key features of the simulation results, including the preferential excitation of different modes based on beam injection geometry and the growth rate dependence on the beam injection velocity, critical velocity, and degree of velocity space anisotropy. The background damping rate is inferred from the simulations and analytically estimated for relevant sources absent from the simulation model, indicating that co-CAEs are closer to marginal stability than modes driven by the cyclotron resonances.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks

Abstract Deciphering the sequence-function relationship encoded in enhancers holds the key to interpreting non-coding variants and understanding mechanisms of transcriptomic variation. Several quantitative models exist for predicting enhancer function and underlying mechanisms; however, there has been no systematic comparison of these models characterizing their relative strengths and shortcomings. Here, we interrogated a rich data set of neuroectodermal enhancers in Drosophila, representing cis- and trans- sources of expression variation, with a suite of biophysical and machine learning models. We performed rigorous comparisons of thermodynamics-based models implementing different mechanisms of activation, repression and cooperativity. Moreover, we developed a convolutional neural network (CNN) model, called CoNSEPT, that learns enhancer ‘grammar’ in an unbiased manner. CoNSEPT is the first general-purpose CNN tool for predicting enhancer function in varying conditions, such as different cell types and experimental conditions, and we show that such complex models can suggest interpretable mechanisms. We found model-based evidence for mechanisms previously established for the studied system, including cooperative activation and short-range repression. The data also favored one hypothesized activation mechanism over another and suggested an intriguing role for a direct, distance-independent repression mechanism. Our modeling shows that while fundamentally different models can yield similar fits to data, they vary in their utility for mechanistic inference. CoNSEPT is freely available at: https://github.com/PayamDiba/CoNSEPT.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Crust Composition and the Shallow Heat Source in KS 1731–260

The presence of a strong shallow heat source of unknown origin in accreting neutron star crusts has been inferred by analyzing x-ray observations of their cooling in quiescence. Here, we model the cooling of KS 1731–260 using realistic crust compositions and nuclear heating and cooling sources from detailed nuclear reaction network calculations. We find that the required strength of the shallow heat source in KS 1731–260 is reduced by more than a factor of 3 compared to previous analysis, a 5⁢𝜎 difference that alleviates the need for exotic solutions. Our analysis also suggests the existence of an impure nuclear pasta layer in the inner crust of KS 1731–260, though future observations will provide more stringent constraints. In addition, we obtain constraints on the dominant surface burning modes of KS 1731–260 over its history.

neutron star cooling↗
DOE OSTI2021

Determining the jet transport coefficient $\hat{q}$ from inclusive hadron suppression measurements using Bayesian parameter estimation

We report a new determination of $\hat{q}$, the jet transport coefficient of the quark-gluon plasma. We use the JETSCAPE framework, which incorporates a novel multistage theoretical approach to in-medium jet evolution and Bayesian inference for parameter extraction. The calculations, based on the Matter and Lbt jet quenching models, are compared to experimental measurements of inclusive hadron suppression in Au + Au collisions at the BNL Relativistic Heavy Ion Collider (RHIC) and Pb + Pb collisions at the CERN Large Hadron Collider (LHC). The correlation of experimental systematic uncertainties is accounted for in the parameter extraction. The functional dependence of $\hat{q}$ on jet energy or virtuality and medium temperature is based on a perturbative picture of in-medium scattering, with components reflecting the different regimes of applicability of Matter and Lbt. In the multistage approach, the switch between Matter and Lbt is governed by a virtuality scale Q 0 . Comparison of the posterior model predictions to the RHIC and LHC hadron suppression data shows reasonable agreement, with moderate tension in limited regions of phase space. The distribution of $\hat{q}/T^3$ extracted from the posterior distributions exhibits weak dependence on jet momentum and medium temperature T, with 90% credible region (CR) depending on the specific choice of model configuration. The choice of Matter + Lbt, with switching at virtuality Q 0 , has 90% CR of $2<\hat{q}/T^3<4$ for p T jet > 40 GeV=c. The value of Q 0 , determined here for the first time, is in the range 2.0-2.7 GeV.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Evolution of in-medium baryon-baryon scattering cross sections and stiffness of dense nuclear matter from Bayesian analyses of FOPI proton-flow excitation functions

Within a Bayesian statistical framework using a Gaussian process (GP) emulator for an isospin-dependent Boltzmann-Uehling-Uhlenbeck (IBUU) transport model simulator of heavy-ion reactions with momentum-independent Skyrme interactions, we infer from the proton directed and elliptical flow in mid-central Au + Au reactions, measured at beam energies from 150 to 1200 MeV/nucleon by the FOPI Collaboration, the posterior probability distribution functions (PDFs) of the in-medium baryon-baryon scattering cross section (BBSCS) modification factor 𝑋 (with respect to their free-space values) and the stiffness parameter 𝐾 of dense nuclear matter. Here, we find that the most probable value of 𝑋 evolves from around 0.7 to 1.0 as the beam energy 𝐸 beam /𝐴 increases. On the other hand, the posterior PDF⁡(𝐾) may have dual peaks having roughly the same height or extended shoulders at high 𝐾 values. More quantitatively, the posterior PDF⁡(𝐾) changes from having a major peak around 220 MeV, characterizing a soft EOS in the reaction at 𝐸 beam /𝐴 = 150 MeV, to one that peaks around 320 MeV, indicating a stiff EOS in the reactions at 𝐸 beam /𝐴 higher than about 600 MeV. The transition from soft to stiff happens in mid-central Au + Au reactions at beam energies around 250 MeV/nucleon in which 𝐾 = 220 MeV and 𝐾 = 320 MeV are approximately equally probable. Altogether, the FOPI proton-flow excitation function data indicate a gradual hardening of hot and dense nuclear matter as its density and temperature increase in reactions with higher beam energies.

nuclear matter↗
DOE OSTI2021

Self-interacting neutrinos: Solution to Hubble tension versus experimental constraints

Exotic self-interactions among the Standard-Model neutrinos have been proposed as a potential reason behind the tension in the expansion rate, H 0 , of the universe inferred from different observations. We constrain this proposal using electroweak precision observables, rare meson decays, and neutrinoless double-β decay. In contrast to previous works, we emphasize the importance of carrying out this study in a framework with full Standard-Model gauge invariance. We implement this first by working with a relevant set of Standard- Model-Effective-Field-Theory operators and subsequently by considering a UV completion in the inverse See-Saw model. We find that the scenario in which all flavors of neutrinos self-interact universally is strongly constrained, disfavoring a potential solution to the H 0 problem in this case. The scenario with self-interactions only among tau neutrinos is the least constrained and can potentially be consistent with a solution to the H 0 problem.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Atacama Cosmology Telescope: Constraints on prerecombination early dark energy

The early dark energy (EDE) scenario aims to increase the value of the Hubble constant (H0) inferred from cosmic microwave background (CMB) data over that found in the standard cosmological model (Λ CDM ), via the introduction of a new form of energy density in the early Universe. The EDE component briefly accelerates cosmic expansion just prior to recombination, which reduces the physical size of the sound horizon imprinted in the CMB. Previous work has found that nonzero EDE is not preferred by Planck CMB power spectrum data alone, which yield a 95% confidence level (C.L.) upper limit f EDE < 0.087 on the maximal fractional contribution of the EDE field to the cosmic energy budget. In this paper, we fit the EDE model to CMB data from the Atacama Cosmology Telescope (ACT) data release 4. We find that a combination of ACT, large-scale Planck TT (similar to WMAP), Planck CMB lensing, and BAO data prefers the existence of EDE at >99.7 % C .L . : f EDE = 0.091$^{+0.020}_{-0.036}$, with H 0 = 70.9$^{+1.0}_{-2.0}$ km/s/Mpc (both 68% C.L.). From a model-selection standpoint, we find that EDE is favored over Λ CDM by these data at roughly 3 σ significance. In contrast, a joint analysis of the full Planck and ACT data yields no evidence for EDE, as previously found for Planck alone. We show that the preference for EDE in ACT alone is driven by its TE and EE power spectrum data. The tight constraint on EDE from Planck alone is driven by its high-ℓ TT power spectrum data. Understanding whether these differing constraints are physical in nature, due to systematics, or simply a rare statistical fluctuation is of high priority. Here, the best-fit EDE models to ACT and Planck exhibit coherent differences across a wide range of multipoles in TE and EE, indicating that a powerful test of this scenario is anticipated with near-future data from ACT and other ground-based experiments.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Photometric redshifts and intrinsic alignments: Degeneracies and biases in the 3 × 2 pt analysis

We present a systematic study of cosmological parameter bias in weak lensing and large-scale structure analyses for upcoming imaging surveys induced by the interplay of intrinsic alignments (IA) and photometric redshift (photo-z) model misspecification error. We first examine the degeneracies between the parameters of the tidal alignment–tidal torquing (TATT) model for IA and of a photo-z model including a mean shift ( Δ z ¯ ) and variance ( σ z ) for each tomographic bin of lenses and sources, under a variety of underlying true IA behaviors. We identify strong degeneracies between: (1) the redshift scaling of the tidal alignment amplitude and the mean shift and variances of source bins, (2) the redshift scaling of the tidal torquing amplitude and the variance of the lowest- z source bin, and (3) the IA source density weighting and the mean shift and variance of several source bins. We then use this information to guide our exploration of the level of cosmological parameter bias which can be induced given incorrect modeling of IA, photo-z, or both. We find that marginalizing over all the parameters of TATT is generally sufficient to preclude cosmological parameter bias in the scenarios we consider. However, this does not necessarily mean that IA and photo-z parameters are themselves unbiased, nor does it mean that the best-fit model is a good fit to the data. We also find scenarios where the inferred parameters produce χ d . o . f . 2 values indicative of a good fit but cosmological parameter bias is significant, particularly when the IA source density weighting parameter is not marginalized over. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Evidence for Suppression of Structure Growth in the Concordance Cosmological Model

We present evidence for a suppressed growth rate of large-scale structure during the dark-energy dominated era. Modeling the growth rate of perturbations with the ``growth index'' γ, we find that current cosmological data strongly prefer a higher growth index than the value γ=0.55 predicted by general relativity in a flat ΛCDM cosmology. Both the cosmic microwave background data from Planck and the large-scale structure data from weak lensing, galaxy clustering, and cosmic velocities separately favor growth suppression. When combined, they yield γ = 0.633$^{+0.025}_{–0.024}$, excluding γ = 0.55 at a statistical significance of 3.7σ. The combination of fσ8 and Planck measurements prefers an even higher growth index of γ = 0.639$^{+0.024}_{–0.025}$, corresponding to a 4.2σ-tension with the concordance model. In Planck data, the suppressed growth rate offsets the preference for nonzero curvature and fits the data equally well as the latter model. Furthermore, a higher γ leads to a higher matter fluctuation amplitude S 8 inferred from galaxy clustering and weak lensing measurements, and a lower S 8 from Planck data, effectively resolving the S 8 tension.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

A Scalable Pipeline for Gigapixel Whole Slide Imaging Analysis on Leadership Class HPC Systems

Whole Slide Imaging (WSI) captures microscopic details of a patient's histopathological features at multiple res-olutions organized across different levels. Images produced by WSI are gigapixel-sized, and saving a single image in memory requires a few gigabytes which is scarce since a complicated model occupies tens of gigabytes. Performing a simple met-ric operation on these large images is also expensive. High-performance computing (HPC) can help us quickly analyze such large images using distributed training of complex deep learning models. One popular approach in analyzing these images is to divide a WSI image into smaller tiles (patches) and then train a simpler model with these reduced-sized but large numbers of patches. However, we need to solve three pre-processing challenges efficiently for pursuing this patch-based approach. 1) Creating small patches from a high-resolution image can result in a high number (hundreds of thousands per image) of patches. Storing and processing these images can be challenging due to a large number of I/O and arithmetic operations. To reduce I/Oand memory accesses, an optimal balance between the size and number of patches must exist to reduce I/O and memory accesses. 2) WSI images may have tiny annotated regions for cancer tissue and a significant portion with normal and fatty tissues; correct patch sampling should avoid dataset imbalance. 3) storing and retrieving many patches to and from disk storage might incur I/O latency while training a deep learning model. An efficient distributed data loader should reduce I/O latency during the training and inference steps. This paper explores these three challenges and provides empirical and algorithmic solutions deployed on the Summit supercomputer hosted at the Oak Ridge Leadership Computing Facility.

Dash, Sajal↗
DOE OSTI2018

Review article: therapeutic bile acids and the risks for hepatotoxicity

Summary Background Bile acids play important roles in cholesterol metabolism and signal through farnesoid X receptor and G protein‐coupled receptors. Given their importance in liver biology, bile acid therapy enables therapeutic applications beyond the treatment of cholestatic liver disease. However, predicting hepatotoxicity of bile acids in humans is obscured due to inconsistent extrapolations of animal data to humans. Aim To review the evidence that could explain discordant bile acids hepatotoxicity observed in humans and animals. Method Literature search was conducted in PubMed using keywords “bile acid,” “transporter,” “hepatotoxicity,” “clinical study,” “animal study,” “species difference,” “mechanism,” “genetic disorder.” Relevant articles were selected for review. Results Clinically significant hepatotoxicity was reported in response to certain bile acids, namely chenodeoxycholic acid, which was given a boxed warning for potential hepatotoxicity. The chemical structure, specifically the number and orientation of hydroxyl groups, significantly affects their hydrophobicity, an important factor in bile acid toxicity. Experimental studies show that hydrophobic bile acids can lead to liver injury through various mechanisms, such as death receptor signalling, mitochondrial dysfunction and inflammation. Although animal studies play a central role in investigating bile acid safety, there are considerable differences in bile acid composition, metabolism and hepatobiliary disposition across species. This does not allow appropriate safety inference, especially for predicting hepatotoxicity in humans. Exploring evidences stemming from inborn errors, genetic models of disease and toxicology studies further improves an understanding of bile acid hepatotoxicity. Conclusion Species differences should be considered in the development of bile acid related therapeutics. Although the mechanism of bile acid hepatotoxicity is still not fully understood, continued mechanistic studies will deepen our understanding.

Ashby, K.↗
DOE OSTI2015

Model-data synthesis for the next generation of forest free-air CO 2 enrichment (FACE) experiments

The first generation of forest free-air CO 2 enrichment (FACE) experiments has successfully provided deeper understanding about how forests respond to an increasing CO 2 concentration in the atmosphere. Located in aggrading stands in the temperate zone, they have provided a strong foundation for testing critical assumptions in terrestrial biosphere models that are being used to project future interactions between forest productivity and the atmosphere, despite the limited inference space of these experiments with regards to the range of global ecosystems. Now, a new generation of FACE experiments in mature forests in different biomes and over a wide range of climate space and biodiversity will significantly expand the inference space. These new experiments are: EucFACE in a mature Eucalyptus stand on highly weathered soil in subtropical Australia; AmazonFACE in a highly diverse, primary rainforest in Brazil; BIFoR-FACE in a 150-yr-old deciduous woodland stand in central England; and SwedFACE proposed in a hemiboreal, Pinus sylvestris stand in Sweden. We now have a unique opportunity to initiate a model–data interaction as an integral part of experimental design and to address a set of cross-site science questions on topics including responses of mature forests; interactions with temperature, water stress, and phosphorus limitation; and the influence of biodiversity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Rates of subcritical cracking and long-term rock erosion

Bedrock fracture is a key element of rock erosion and subsequent surface processes. We test the hypothesis that rock's susceptibility to subcritical cracking, a specific type of fracturing, significantly drives and limits rock erosion. We measured 10 Be-derived erosion rates, compressive strength, and crack characteristics on 20 outcrops of different rock units (quartzite, granite, and two metasandstones) in the northern Blue Ridge Mountains of Virginia (USA). We also measured the subcritical cracking index (n), Charles’s law velocity constant (A), and fracture toughness (K IC ) of samples from four of the same outcrops, representative of each rock type. Erosion rates range from 1.16 ± 0.67 to 32.3 ± 7.8 m/m.y. We find strong correlations—across the four rock units—between average erosion rates and the three subcritical cracking parameters (R 2 > 0.85, p < 0.05), but not compressive strength (R 2 = 0.6; p > 0.1). We also find a correlative relationship between n and outcrop fracture length (R 2 = 0.91; p < 0.05). The latter correlation is consistent with that of published model predictions, further indicating a mechanistic link between subcritical cracking and rock erosion. We infer that subcritical cracking parameters closely tie to erosion rates, because subcritical cracking is the dominant process of mechanical weathering, leading to positive feedbacks relating subcritical cracking rates, crack length, porosity, and water accessibility. Finally, these data are the first that directly test and support the hypothesis that subcritical cracking can set the pace of long-term rock erosion.

58 GEOSCIENCES↗
DOE OSTI2021

Hybrid simulations of sub-cyclotron compressional and global Alfven Eigenmode stability in spherical tokamaks

A comprehensive numerical study has been conducted in order to investigate the stability of beam-driven, sub-cyclotron frequency compressional (CAE) and global (GAE) Alfven Eigenmodes in low aspect ratio plasmas for a wide range of beam parameters. The presence of CAEs and GAEs has previously been linked to anomalous electron temperature profile flattening at high beam power in NSTX experiments, prompting further examination of the conditions for their excitation. Linear simulations are performed with the hybrid MHD-kinetic initial value code HYM in order to capture the general Doppler-shifted cyclotron resonance that drives the modes. Three distinct types of modes are found in simulations -- co-CAEs, cntr-GAEs, and co-GAEs -- with differing spectral and stability properties. The simulations reveal that unstable GAEs are more ubiquitous than unstable CAEs, consistent with experimental observations, as they are excited at lower beam energies and generally have larger growth rates. Local analytic theory is used to explain key features of the simulation results, including the preferential excitation of different modes based on beam injection geometry and the growth rate dependence on the beam injection velocity, critical velocity, and degree of velocity space anisotropy. The background damping rate is inferred from simulations and estimated analytically for relevant sources not present in the simulation model, indicating that co-CAEs are closer to marginal stability than modes driven by the cyclotron resonances.

Compressional Alfven Eigenmodes↗
DOE OSTI2021

PayamDiba/CoNSEPT

Deciphering the sequence-function relationship encoded in enhancers holds the key to interpreting non-coding variants and understanding mechanisms of transcriptomic variation. Several quantitative models exist for predicting enhancer function and underlying mechanisms; however, there has been no systematic comparison of these models characterizing their relative strengths and shortcomings. Here, we interrogated a rich data set of neuroectodermal enhancers in Drosophila, representing cis- and trans- sources of expression variation, with a suite of biophysical and machine learning models. We performed rigorous comparisons of thermodynamics-based models implementing different mechanisms of activation, repression and cooperativity. Moreover, we developed a convolutional neural network (CNN) model, called CoNSEPT, that learns enhancer ‘grammar’ in an unbiased manner. CoNSEPT is the first general-purpose CNN tool for predicting enhancer function in varying conditions, such as different cell types and experimental conditions, and we show that such complex models can suggest interpretable mechanisms. We found model-based evidence for mechanisms previously established for the studied system, including cooperative activation and short-range repression. The data also favored one hypothesized activation mechanism over another and suggested an intriguing role for a direct, distance-independent repression mechanism. Our modeling shows that while fundamentally different models can yield similar fits to data, they vary in their utility for mechanistic inference.

Dibaeinia, Payam↗
DOE OSTI2025

Surface orientation ambiguity for single molecules at dielectric interfaces

Fluorescent molecules emit light in a dipole radiation pattern that can be used to infer their orientation through defocused fluorescence microscopy. Proper measurement of the orientation requires mathematical modeling of the radiation pattern expected for a dipole in the geometry of interest and subsequent comparison against experimental data. We point out an ambiguity in common calculations of these patterns that appears to compromise orientation measurements for molecules that are especially near dielectric surfaces. This results in a rotation of the measured emission dipole toward the surface for near-interface molecules, which can be mistaken for a preferentially horizontal orientation among the emitters. The proper treatment for on-surface emitters requires consideration of finite-sized current elements between two dielectric media, and we show that the theoretical ambiguity can be lifted via finite-element modeling. A prescription is provided for correcting measured orientations at arbitrary interfaces.

Dey, E. [University of Texas, Arlington, TX (Unite↗