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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Multilayered regulation by RNA thermometers enables precise control of Cas9 expression in E. coli

Cas9-based genome editing technologies can rapidly generate mutations to probe a diverse array of mutant genotypes. However, aberrant Cas9 nuclease translation and activity can occur despite the use of inducible promoters to control expression, leading to extensive cell death. This background killing caused by promoter leakiness severely limits the application of Cas9 for generating mutant libraries because of the potential for population skew. We demonstrate the utility of temperature sensitive RNA elements as a layer of post-transcriptional regulation to reduce the impact of promoter leak. We observe significant temperature-dependent increases in cell survival when certain RNA thermometers (RNATs) are placed upstream of the cas9 coding sequence. We also show that the most highly repressing RNAT, hsp17rep, significantly reduces population skew with a library of characterized guide RNAs in Escherichia coli. This strategy should be applicable to all bacterial Cas9-based methods and technologies.

Kammerdiener, Elise K. [Oak Ridge National Laborat↗
DOE OSTI2020

Accurate and complete genomes from metagenomes

Genomes are an integral component of the biological information about an organism; thus, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures, and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs); but gaps, local assembly errors, chimeras, and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and, in some cases, achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of about 7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. The analysis of cumulative GC skew identified potential misassemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Electronic scattering off a magnetic hopfion

We study scattering of itinerant electrons off a magnetic hopfion in a three-dimensional metallic magnet described by a magnetization vector S(r). A hopfion is a confined topological soliton of S(r) characterized by an emergent magnetic field Bγ(r)≡ε αβγ S∙(∇ α S×∇ β S)/4≠0 with vanishing average value [B(r)]=0. We evaluate the scattering amplitude in the opposite limits of large and small hopfion radius R using the eikonal and Born approximations, respectively. In both limits, we find that the scattering cross section contains a skew-scattering component giving rise to the Hall effect within a hopfion plane. That conclusion contests the popular notion that the Hall effect in noncollinear magnetic structures necessarily implies [B(r)]≠0. In the limit of small hopfion radius pR<<1, we expand the Born series in powers of momentum p and identify different expansion terms corresponding to the hopfion anisotropy, toroidal moment, and skew scattering.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Calculating n-point charge correlations in evolving systems

Background: In dynamic systems such as heavy-ion collisions, charge susceptibilities and local charge correlations change with time. These changes are accompanied by nonlocal correlations, which spread diffusively with time and are constrained by local charge conservation. Such correlations have been measured at the Relativistic Heavy-Ion Collider (RHIC) and have been linked to the chemical evolution of the matter and possible phase separation or critical phenomena. The evolution of such correlations has been modeled for two-point correlators superimposed onto hydrodynamics, but not for three- or four-point correlators. These higher-order correlators represent an essential basis for calculating the kurtosis and skewness of charge distributions measured at RHIC. For short-range correlations, such as those between charges on the same particle, and the associated charge-balance correlations a theoretical formalism was lacking for handling higher-order correlations. In particular, one needed to understand how higher-order charge fluctuations was split onto lower numbers of particles. For example, correlations of order three have contributions with charge all on one particle, split onto two particle, or split onto three. By assuming local chemical equilibrium of short-range correlations, the sources of the various correlators were found to be uniquely determined. The relevant theoretical foundation is presented here, including a diagrammatic technique to correctly account for all the possible terms to higher-order correlations. Here, we found a consistent theoretical treatment and its applicability, viability, and tractability are discussed. The formalism derived here enables realistic and quantitative modeling of the three- and four-point charge correlations necessary for understanding measurements of the kurtosis and skewness of charge distributions at RHIC. These observables have been promoted as signals of phase transitions or measures of chemical evolution.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Empirical radius formulas for canonical neutron stars from bidirectionally selecting features of equations of state in extended Bayesian analyses of observational data

Significant advancement in Bayesian inference of nuclear equation of state (EOS) from gravitational wave and x-ray observations of neutron stars (NSs) has been made by the nuclear astrophysics community especially since GW170817. By extending the traditional Bayesian analysis which normally ends at presenting the marginalized posterior probability distribution functions (PDFs) of individual EOS parameters and their correlations (or sometimes only the Pearson correlation coefficients which are only reliably useful when the variables are linearly correlated while they are actually often not), we search for a data-driven and robust empirical formula for the radius 𝑅 1.4 of canonical NSs in terms of the characteristic EOS parameters (features). We also identify the single most important but currently poorly known EOS parameter for determining the 𝑅 1.4 . Using three regression-model-building methodologies: bidirectional stepwise feature selection, least absolute shrinkage selection operator (LASSO) regression, and neural network regression on a large set of posterior EOSs and the corresponding 𝑅 1.4 values inferred from earlier comprehensive Bayesian analyses of NS observational data, we systematically and rigorously develop the most probable 𝑅 1.4 formulas with varying statistical accuracy and technical complexity. Here, the most important EOS parameters for determining 𝑅 1.4 are found consistently in each of the feature selection processes to be (in order of decreasing importance): curvature 𝐾 sym , slope 𝐿, skewness 𝐽 sym of nuclear symmetry energy, skewness 𝐽 0 , incompressibility 𝐾 0 of symmetric nuclear matter, and the magnitude 𝐸 sym ⁡(𝜌 0 ) of symmetry energy at the saturation density 𝜌 0 of nuclear matter.

Bayesian methods↗
DOE OSTI2024

Spatial imaging of proton via leading-twist nonskewed GPDs with basis light-front quantization

The internal image of the proton is unveiled by examining the generalized parton distributions (GPDs) at zero skewness, within the basis light-front quantized environment. Several distributions emerge when a quark is sampled with different currents depending upon the helicity arrangements of the active quark and the proton target. We investigate six of the eight leading-twist proton GPDs of the valence quarks, the helicity conserving distributions ( H , E , H ˜ ) and the helicity nonconserving ( H T , E T , H ˜ T ) distributions at skewness set to zero ( ζ = 0 ). We consider purely transverse momentum transfer and, hence, obtain results describe only the proton’s two-dimensional structure in the transverse plane. We present the Mellin moments of these distribution functions, where the first moment produces a form factor and the second Mellin moments help extract the information on partonic contributions to the hadronic angular momentum. We compare our results for the Mellin moments with those from lattice QCD and other approaches where available. We also present the GPDs in transverse position space. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2024

Generalized parton distributions from lattice QCD with asymmetric momentum transfer: Axial-vector case

Recently, we made significant advancements in improving the computational efficiency of lattice QCD calculations for generalized parton distributions (GPDs). This progress was achieved by adopting calculations of matrix elements in asymmetric frames, deviating from the computationally-expensive symmetric frame typically used, and allowing freedom in the choice for the distribution of the momentum transfer between the initial and final states. A crucial aspect of this approach involves the adoption of a Lorentz covariant parametrization for the matrix elements, introducing Lorentz-invariant amplitudes. This approach also allows us to propose an alternative definition of quasi-GPDs, ensuring frame independence and potentially reduce power corrections in matching to light cone GPDs. In our previous work, we presented lattice QCD results for twist-2 unpolarized GPDs ( H and E ) of quarks obtained from calculations performed in asymmetric frames at zero skewness. Building upon this work, we now introduce a novel Lorentz covariant parametrization for the axial-vector matrix elements. We employ this parametrization to compute the axial-vector GPD H ˜ at zero skewness, using an N f = 2 + 1 + 1 ensemble of twisted mass fermions with clover improvement. The light-quark masses employed in our calculations correspond to a pion mass of approximately 260 MeV. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Systematic improvement of x -dependent unpolarized nucleon generalized parton distributions in lattice-QCD calculation

We present a first study of the effects of renormalization-group resummation (RGR) and leading-renormalon resummation (LRR) on the systematic errors of the unpolarized isovector nucleon generalized parton distribution in the framework of large-momentum effective theory. This work is done using lattice gauge ensembles generated by the MILC Collaboration, consisting of 2 + 1 + 1 flavors of highly improved staggered quarks with a physical pion mass at lattice spacing a ≈ 0.09 fm and a box width L ≈ 5.76 fm . We present results for the nucleon H and E generalized parton distributions (GPDs) with average boost momentum P z ≈ 2 GeV at momentum transfers Q 2 = [ 0 , 0.97 ] GeV 2 at skewness ξ = 0 as well as Q 2 ∈ 0.23 GeV 2 at ξ = 0.1 , renormalized in the modified minimal subtraction ( MS ¯ ) scheme at scale μ = 2.0 GeV , with two- and one-loop matching, respectively. We demonstrate that the simultaneous application of RGR and LRR significantly reduces the systematic errors in renormalized matrix elements and distributions for both the zero and nonzero skewness GPDs, and that it is necessary to include both RGR and LRR at higher orders in the matching and renormalization processes. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2024

Impact of the newly revised gravitational redshift of x-ray burster GS 1826-24 on the equation of state of supradense neutron-rich matter

Thanks to the recent advancement in producing rare isotopes and measuring their masses with unprecedented precision, the updated nuclear masses around the waiting-point nucleus 64 Ge in the rapid-proton capture process have led to a significant revision of the surface gravitational redshift of the neutron star (NS) in GS 1826-24 by refitting its x-ray burst light curve using Modules for Experiments in Stellar Astrophysics (MESA). The resulting NS compactness ξ is between 0.183 and 0.259 at 95% confidence level, and its upper boundary is significantly smaller than the maximum ξ previously known. Incorporating these new data within a comprehensive Bayesian statistical framework, we investigate its impact on the Equation of State (EOS) of supradense neutron-rich matter and the required spin frequency for GW190814’s minor m 2 with mass 2.59 ± 0.05⁢M ⊙ to be a rotationally stable pulsar. We found that the EOS of high-density symmetric nuclear matter (SNM) has to be softened significantly while the symmetry energy at supersaturation densities stiffened compared to our prior knowledge from earlier analyses using data from both astrophysical observations and terrestrial nuclear experiments. In particular, the skewness J 0 characterizing the stiffness of high-density symmetric nuclear matter (SNM) decreases significantly, while the slope L, curvature K sym , and skewness Jsym of nuclear symmetry energy all increase appreciably compared to their fiducial values. Here, we also found that the most probable spin rate for the m 2 to be a stable pulsar is very close to its mass-shedding limit once the revised redshift data from GS 1826-24 is considered, making the m 2 unlikely the most massive NS observed so far.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Bayesian inference of fine features of the nuclear equation of state from future neutron star radius measurements to 0.1 km accuracy

To more precisely constrain the equation of state (EOS) of supradense neutron-rich nuclear matter, future high-precision x-ray and gravitational wave observatories are proposed to measure the radii of neutron stars (NSs) with an accuracy better than about 0.1 km. However, it remains unclear what particular aspects (other than the stiffness generally spoken of in the literature) of the EOS and to what precision they will be better constrained. In this work, within a Bayesian framework using a metamodel EOS for NSs, we infer the posterior probability distribution functions (PDFs) of incompressibility K 0 and skewness J 0 of symmetric nuclear matter (SNM) as well as the slope L, curvature K sym , and skewness J sym characterizing the density dependence of nuclear symmetry energy E sym ⁡(ρ), respectively, from mean values of NS radii consistent with existing observations and an expected accuracy Δ⁢R ranging from about 1.0 to 0.1 km. Here, we found that (1) the Δ⁢R has little effect on inferring the stiffness of SNM at suprasaturation densities, (2) smaller Δ⁢R reveals more accurately not only the PDFs but also pairwise correlations among parameters characterizing high-density E sym ⁡(ρ), (3) a double-peak feature of the PDF(K sym ) corresponding to the strong K sym – J sym and K sym – L anticorrelations is revealed when Δ⁢R is less than about 0.2 km, and the locations of the two peaks are sensitive to the maximum value of J sym reflecting the stiffness of E sym ⁡(ρ) above about 3 times the saturation density ρ 0 of SNM, and (4) the high-precision radius measurement for canonical NSs is more useful than that for massive ones for constraining the EOS of nucleonic matter around (2–3)⁢ρ 0 .

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Clustering High-dimensional Toxicogenomics Data with Rare Signals

Toxicogenomics studies the gene and protein activities to drug treatments or toxic exposures. As the drugs and genes are numerous, toxicogenomics data are naturally high dimensional, with dimension sizes up to millions. In addition, the distribution of toxicogenomics data is oftentimes skewed, and they contain rare but important signals representing a cell or organism’s response to toxicity. The combination of high dimension and extremely skewed distribution of toxicogenomics data makes clustering analysis extremely challenging.We present our study of clustering toxicogenomics data using classical approaches such as principal component analysis as well as deep learning approaches such as auto-encoders. Our experiments show that these approaches fail to preserve rare signals and produce high-quality clusters. We then explore augmenting matrix factorization with deep learning techniques such as attention mechanism to produce latent representations for clustering. Our technique is able to better preserve rare signals after dimensionality reduction than prior approaches. Furthermore, we combine our augmented matrix factorization with a mechanism similar to autoencoder to balance separable clusters and low regeneration errors. Our experiments demonstrate better clustering with our proposed approach.

Cong, Guojing↗
DOE OSTI2021

Improved Prediction of Cold-Air Pools in the Weather Research and Forecasting Model Using a Truly Horizontal Diffusion Scheme for Potential Temperature

The terrain-following vertical coordinate system used by many atmospheric models, including the Weather Research and Forecasting (WRF) Model, is prone to errors in regions of complex terrain. These errors stem, in part, from the calculation of horizontal gradients within the diffusion term of the momentum or scalar evolution equations. In WRF, such gradients can be calculated along coordinate surfaces, or using metric terms that help account for grid skewness. However, neither of these options ensures a truly horizontal gradient calculation, especially if a grid cell is skewed enough that the heights of the neighboring grid points used in the calculation fall outside the vertical range of the cell. In this work, an improved scheme that uses Taylor series approximations to vertically interpolate variables to the level necessary for a truly horizontal gradient calculation is implemented in WRF for the diffusion of potential temperature. The scheme is validated using an atmosphere-at-rest configuration, in which spurious flows develop only as a result of numerical errors and can thus be used as a proxy for model performance. Following validation, the method is applied to the simulation of cold-air pools (CAPs), which occur in regions of complex terrain and are characterized by strong near-surface temperature gradients. Using the truly horizontal scheme, idealized simulations demonstrate reduced numerical mixing in a quiescent CAP, and a realistic case study in the Columbia River basin shows a reduction in positive wind speed bias by up to roughly 20% compared to observations from the Second Wind Forecast Improvement Project.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Third-Order Resonance Compensation at the FNAL Recycler Ring

The Recycler Ring (RR) at the Fermilab Accelerator Complex performs slip-stacking on 8 GeV protons, doubling the beam intensity delivered to the Main Injector (MI). At MI, the beam is accelerated to 120 GeV and delivered to the high energy neutrino experiments. Femilab’s Proton Improvement Plan II (PIP-II) will require the Recycler to store 50% more beam. Simulations have shown that the space charge tune shift at this new intensity will lead to the excitation of multiple resonance lines. Specifically, this study looks at normal sextupole lines 3 Q_{x}=76 and Q_{x}+2Q_{y}=74, plus skew sextupole lines 3 Q_{y}=73 and 2 Q_{x}+Q_{y}=75. Dedicated normal and skew sextupoles have been installed in order to compensate for these resonance lines. By measuring and calculating the Resonance Driving Terms (RDT), this study shows how each of the resonance lines can be compensated independently. Furthermore, this study shows and discusses initial investigations into compensating multiple lines simultaneously.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

Simultaneous Compensation of Third-Order Resonances at the FNAL Recycler Ring

Third-order resonance lines will have a detrimental effect on the high-intensity operation of the Recycler Ring (RR), under the current Proton Improvement Plan (PIP-II) for the Fermilab Accelerator Complex. Increasing intensity will increase space charge effects, leading to the excitation of normal and skew sextupole lines. Dedicated normal and skew sextupoles have been installed in order to mitigate the effect of these resonance lines. By measuring the response matrix of the third-order Resonance Driving Terms (RDTs) to the currents of these dedicated elements, this study shows how several resonance lines can be compensated simultaneously. Resonance compensation is experimentally verified through loss maps and emittance growth measurements using the Ion Profile Monitor (IPM) system in the Recycler.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

Residential Solar-Adopter Income and Demographic Trends: 2023 Update [Slides]

The report describes income, demographic, and other socio-economic trends among U.S. residential rooftop solar adopters. The report is based on address-level data for roughly 3.4 million residential rooftop solar systems installed through 2022, representing 86% of all U.S. systems. With its unique size, geographic scope, and level of detail, this report is intended to serve as a foundational reference document for policy-makers, industry stakeholders, and researchers. Key findings include the following: (1) Median solar adopter income was about $\$117$k/year in 2022, compared to a U.S. median of about $\$69$k/year for all households and $\$86$k/year for all owner-occupied households; (2) The degree of income skew varies significantly across all states, but all exhibit some positive income skew relative to all households in the state, with median solar-adopter incomes ranging from 108-180% of the respective state-median income for all households; (3) Roughly 45% of solar adopters in 2022 had incomes below 120% of their area median income (AMI), a threshold sometimes used to define “low-and-moderate income” (or LMI), while 23% were below 80% of AMI, often used to define “low-income”; (4) Solar adoption continues to shift toward less affluent households, with the median current income of solar adopters dropping from $\$140$k for households that installed systems in 2010 to $\$117$k in 2022; (5) PV systems installed in 2022 by households earning less than $50k had a median size of 6.1 kW, 34% were third-party owned, and 5% included battery storage, compared to corresponding values of 7.6%, 17%, and 15% for households earning more than 200 dollars k; and (6) Compared to all households in their respective state, solar adopters tend to be negligibly more rural; have higher home values; and are more likely to be college educated, identify as non-Hispanic white, live outside a disadvantaged community (DAC), be middle-aged, work in a business or financial occupation, and own a single-family home In conjunction with the report, Berkeley Lab has published an updated accompanying set of online data visualizations that allow users to further explore the underlying data. Berkeley Lab is also offering related analytical support to states, local agencies, and other organizations on issues related to solar adoption among low-to-moderate income households.

14 SOLAR ENERGY↗
DOE OSTI2024

Reconstruction of the 4D beam matrix

The widely used transverse parameters characterizing particle beams are the Twiss parameters. These parameters can be measured experimentally but they do not fully characterize the beam since they do not account for possible correlations in particle distribution between two transverse coordinates. These correlations may occur due to uncompensated magnetic field at the cathode or misalignment of focusing quadrupoles in the transport beamline. We test a novel diagnostic for diagnosing full 4D beam matrix which may be used to identify such imperfections. The diagnostic is based on transporting the beam through the beamline which includes a quadrupole and a skew quadrupole magnets and measuring the resulting 2D beam distribution at the screen downstream. Such a measurement can be viewed as measuring a 2D projection of the 4D distribution. Different settings of the quads provide measurements of different slices of the phase space. The reconstruction of the original beam matrix from a number of measurements is done using machine learning algorithm, which provides a fast and reliable way of reconstruction for an arbitrary configuration of the scanning beamline. In August 2024, we set up the diagnostic beamline to perform a quadrupole scan of the beam. The setup includes a skew quadrupole, a regular quadrupole, and a screen. The images on the screen were post-processed to remove experimental artifacts and enhance contrast by eliminating background noise outside the core of the distribution=. The rms parameters of the distribution were then calculated and used as inputs for the reconstruction algorithm. This algorithm attempts to determine the initial beam matrix that produces expected images on the screen closely matching the observed images across all quadrupole settings. The algorithm found a solution in which the expected rms parameters closely align with the observations. Validation of the results is planned for FY25.

43 PARTICLE ACCELERATORS↗
DOE OSTI2026

Estimation of the Required Dipole Corrector Magnetic Field for PIP-II Injection Based on Beam Studies

The Fermilab Booster will accept a 600 µs beam pulse from the new superconducting Linac for PIP-II operations. The Booster is a rapid-cycling synchrotron that uses a resonant magnet circuit ramping at 15 Hz. For PIP-II, the cycle rate will increase to 20 Hz, and the injection pulse length will expand from 40 µs to 600 µs due to the lower output current from the new Linac. Because the Booste main bending field follows a sinusoidal waveform, the magnetic field is not constant during the extended injection window. The longer pulse length and higher repetition rate modify the beam orbit and can lead to increased beam losses. The Booster contains 48 dipole-corrector packages distributed across its 24 periods. Each package includes horizontal and vertical dipoles, quadrupole, sextupole, skew-quadrupole, and skew-sextupole elements. By driving the dipole correctors with an appropriately shaped sinusoidal waveform during injection, we can compensate the changing main field and create an effectively flat bending field—referred to as flat injection. Over the past several years, machine studies have been performed to characterize the required correction fields and to determine the corresponding power-supply specifications needed for PIP-II operation. In this presentation, we will summarize the study results and discuss the estimated magnetic field requirements and power supply parameters for achieving flat injection in the Booster.

Seiya, K. [Fermilab] (ORCID:0000000250576943)↗
DOE OSTI2023

A Tale of Two Disks: Mapping the Milky Way with the Final Data Release of APOGEE

We present new maps of the Milky Way disk showing the distribution of metallicity ([Fe/H]), α-element abundances ([Mg/Fe]), and stellar age, using a sample of 66,496 red giant stars from the final data release (DR17) of the Apache Point Observatory Galactic Evolution Experiment survey. We measure radial and vertical gradients, quantify the distribution functions for age and metallicity, and explore chemical clock relations across the Milky Way for the low-α disk, high-α disk, and total population independently. The low-α disk exhibits a negative radial metallicity gradient of -0.06 ± 0.001 dex kpc -1 , which flattens with distance from the midplane. The high-α disk shows a flat radial gradient in metallicity and age across nearly all locations of the disk. The age and metallicity distribution functions shift from negatively skewed in the inner Galaxy to positively skewed at large radius. Significant bimodality in the [Mg/Fe]–[Fe/H] plane and in the [Mg/Fe]–age relation persist across the entire disk. The age estimates have typical uncertainties of ~0.15 in log(age) and may be subject to additional systematic errors, which impose limitations on conclusions drawn from this sample. Nevertheless, these results act as critical constraints on galactic evolution models, constraining which physical processes played a dominant role in the formation of the Milky Way disk. We discuss how radial migration predicts many of the observed trends near the solar neighborhood and in the outer disk, but an additional more dramatic evolution history, such as the multi-infall model or a merger event, is needed to explain the chemical and age bimodality elsewhere in the Galaxy.

79 ASTRONOMY AND ASTROPHYSICS↗