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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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase

ABSTRACT The composition of bacterial transcriptomes is determined by the transcriptional regulatory network (TRN). The TRN regulates the transition from one physiological state to another. Here, we use independent component analysis to monitor the composition of the transcriptome during the transition from the exponential growth phase to the stationary phase. With Escherichia coli K-12 MG1655 as a model strain, we trigger the transition using carbon, nitrogen, and sulfur starvation. We find that (i) the transition to the stationary phase accompanies common transcriptome changes, including increased stringent responses and reduced production of cellular building blocks and energy regardless of the limiting element; (ii) condition-specific changes are strongly associated with transcriptional regulators ( e.g. , Crp, NtrC, CysB, Cbl) responsible for metabolizing the limiting element; and (iii) the shortage of each limiting element differentially affects the production of amino acids and extracellular polymers. This study demonstrates how the combination of genome-scale datasets and new data analytics reveals the fundamental characteristics of a key transition in the life cycle of bacteria. IMPORTANCE Nutrient limitations are critical environmental perturbations in bacterial physiology. Despite its importance, a detailed understanding of how bacterial transcriptomes are adjusted has been limited. By utilizing independent component analysis (ICA) to decompose transcriptome data, this study reveals key regulatory events that enable bacteria to adapt to nutrient limitations. The findings not only highlight common responses, such as the stringent response, but also condition-specific regulatory shifts associated with carbon, nitrogen, and sulfur starvation. The insights gained from this work advance our knowledge of bacterial physiology, gene regulation, and metabolic adaptation.

Lim, Hyun Gyu (ORCID:0000000204692388)↗
DOE OSTI2024

Energy growth in VLVL → VLVL, VLVLh scattering to probe Higgs cubic and HEFT interactions

Abstract We compute the energy scales of perturbative unitarity violation inV L V L →V L V L hprocesses and compare them toV L V L →hhhprocess, whereV L refers to a longitudinal mode ofZorWboson, andhthe Higgs boson. Using these energy scales, we determine which process is more sensitive to potential modifications in the Higgs sector at high-energy colliders. Within the Higgs Effective Field Theory (HEFT), we consider the Higgs cubic coupling and other interactions with and without derivatives. Any HEFT interactions predict the perturbative unitarity violation at a finite scale, and in a generic case, the minimalistic process is 2 → 3 scattering. Our analysis reveals that the energy scales for unitarity violation inV L V L →V L V L handV L V L →hhhprocesses are similar across all scenarios considered. If the backgrounds are similar,V L V L hfinal states are more feasible becauseV L V L hhas higher branching ratios in cleaner decay modes thanhhh. We also investigate HEFT derivative interactions derived from various UV models. In these cases, bothV L V L →V L V L andV L V L →hhprocesses exhibit unitarity violating behavior. We demonstrate that the energy scales for unitarity violation inV L V L final states are comparable to or even lower than those in thehhfinal state.

Physics↗
DOE OSTI2025

Proton spin from small-x with constraints from the valence quark model

We apply the valence quark model [1] to constrain the non-perturbative initial condition for the small-x helicity evolution. The remaining free parameters are constrained by performing a global analysis akin to [2] to the available polarized small-x deep inelastic scattering data. A good description of the world data is obtained with only 8 free parameters. The model parameters are tightly constrained by the data, allowing us to predict the proton polarized structure function $g^p_1$ to be negative at small x. Furthermore, we obtain the small-x quark and gluon spins to give a contribution $\int^{0.1}_{10^{-5}} dx (\frac{1}{2}\Delta\Sigma + \Delta{G}) = 0.63 ± 0.10$ or $1.35 ± 0.16$ (or to the proton spin, depending on the applied running coupling prescription.

Color-class condensate↗
DOE OSTI2020

Structural trends in the dehydrogenation selectivity of palladium alloys

Alloying is well-known to improve the dehydrogenation selectivity of pure metals, but there remains considerable debate about the structural and electronic features of alloy surfaces that give rise to this behavior. To provide molecular-level insights into these effects, a series of Pd intermetallic alloy catalysts with Zn, Ga, In, Fe and Mn promoter elements was synthesized, and the structures were determined using in situ X-ray absorption spectroscopy (XAS) and synchrotron X-ray diffraction (XRD). The alloys all showed propane dehydrogenation turnover rates 5–8 times higher than monometallic Pd and selectivity to propylene of over 90%. Moreover, among the synthesized alloys, Pd 3 M alloy structures were less olefin selective than PdM alloys which were, in turn, almost 100% selective to propylene. This selectivity improvement was interpreted by changes in the DFT-calculated binding energies and activation energies for C–C and C–H bond activation, which are ultimately influenced by perturbation of the most stable adsorption site and changes to the d-band density of states. Furthermore, transition state analysis showed that the C–C bond breaking reactions require 4-fold ensemble sites, which are suggested to be required for non-selective, alkane hydrogenolysis reactions. These sites, which are not present on alloys with PdM structures, could be formed in the Pd 3 M alloy through substitution of one M atom with Pd, and this effect is suggested to be partially responsible for their slightly lower selectivity.

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

Electron transport in a tokamak scrape-off layer: impact of toroidal nonuniformities of divertor targets

An analysis of electron dynamics is carried out in the tokamak scrape-off layer (SOL) region. Small non-axisymmetric perturbations of the divertor target sheath potential affect electron drift orbits in the SOL and may lead to non-ambipolar electron radial transport. The resulting rates of electron convection, diffusion, and mobility are calculated analytically, and the analytic results are compared with direct numerical simulations of electron drift orbits. The proposed mechanism of non-ambipolar electron transport may be relevant to the sustainment of the SOL plasma quasi-neutrality in the ‘heuristic’ model of the SOL width (Eich et al 2011 Phys. Rev. Lett. 107 215001).

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Robustness and Eventual Slow Decay of Bound States of Interacting Microwave Photons in the Google Quantum AI Experiment

Integrable models are characterized by the existence of stable excitations that can propagate indefinitely without decaying. This includes multimagnon bound states in the celebrated 𝑋⁢𝑋⁢𝑍 spin-chain model and its integrable Floquet counterpart. A recent Google Quantum AI experiment [A. Morvan et al., Nature 612, 240 (2022)] realizing the Floquet model has demonstrated the persistence of such collective excitations even when the integrability is broken: this observation is at odds with the expectation of ergodic dynamics in generic nonintegrable systems. Here, we study the spectrum of the model realized in the experiment using exact diagonalization and physical arguments. We find that isolated bands corresponding to the descendants of the exact bound states of the integrable model are clearly observable in the spectrum for a large range of system sizes. However, our numerical analysis of the localization properties of the eigenstates suggests that the bound states become unstable in the thermodynamic limit. A perturbative estimate of the decay rate agrees with the prediction of an eventual instability for large system sizes.

Exact diagonalization↗
DOE OSTI2025

Proton Spin from Small-x With Constraints from the Valence Quark Model

We apply the valence quark model to constrain the non-perturbative initial condition for the small-x helicity evolution. The remaining free parameters are constrained by performing a global analysis to the available polarized small-x deep inelastic scattering data. A good description of the world data is obtained with only 8 free parameters. The model parameters are tightly constrained by the data, allowing us to predict the proton polarized structure-function to be negative at small x. Furthermore, we obtain the small-x quark and gluon spins, depending on the applied running coupling prescription.

Adamiak, Daniel [Thomas Jefferson National Acceler↗
DOE OSTI2023

A Dynamically Distinct Stellar Population in the Leading Arm of the Sagittarius Stream

We present a chemical and dynamical analysis of the leading arm (LA) and trailing arm (TA) of the Sagittarius (Sgr) stream, as well as for the Sgr dwarf galaxy core (SC), using red giant branch, main-sequence, and RR Lyrae stars from large spectroscopic survey data. The different chemical properties among the LA, TA, and SC generally agree with recent studies and can be understood by a radial metallicity gradient established in the progenitor of the Sgr dwarf, followed by preferential stellar stripping from the outer part of the Sgr progenitor. One striking finding is a relatively larger fraction of low-eccentricity stars (e < 0.4) in the LA than in the TA and SC. The TA and SC exhibit very similar distributions. Considering that a tidal tail stripped off from a dwarf galaxy maintains the orbital properties of its progenitor, we expect that the e-distribution of the LA should be similar to that of the TA and SC. Thus, the disparate behavior of the e-distribution of the LA is of particular interest. Following the analysis of Vasiliev et al., we attempt to explain the different e-distribution by introducing a time-dependent perturbation of the Milky Way by the Large Magellanic Cloud's (LMC) gravitational pull, resulting in substantial evolution of the angular momentum of the LA stars to produce the low-e stars. In addition, we confirm from RR Lyrae stars with high eccentricity (e > 0.6) that the TA stars farther away from the SC are also affected by disturbances from the LMC.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Feasibility of an experiment on clumping induced by the Crow instability along a shocked cylinder

The growth of three-dimensional perturbations subject to the Crow instability along a vortex dipole resulting from the passage of a shock wave through a heavy gaseous cylinder is examined numerically. A linear stability analysis is performed based on geometric parameters extracted from two-dimensional simulations to determine the range of unstable wavenumbers, which is found to extend from 0.0 to 1.3 when normalized by the core separation distance. The analysis is then verified by comparison to three-dimensional simulations, which clearly show the development of the instability and the pinch-off of the vortex dipole into isolated vortex rings, which manifest as clumps of the original cylinder material. A scaling law is developed to determine the relevant spatiotemporal scales of the instability development, which is then used to assess the feasibility of a high-energy-density experiment visualizing clump formation. Specifically, a shocked cylinder with an initial diameter of 100 μm consisting of a perturbation of approximate wavelength and amplitude of 600 and 10 μm, respectively, is expected to form clumps resulting from the Crow instability approximately 40 ns after it is shocked, with dynamics which can be readily visualized on the Omega EP laser facility.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations

The soil environment is constantly changing due to shifts in soil moisture, nutrient availability and other conditions. To contend with these changes, soil microorganisms have evolved a variety of ways to adapt to environmental perturbations, including regulation of gene expression. However, it is challenging to untangle the complex phenotypic response of the soil to environmental change, partly due to the absence of predictive modeling frameworks that can mechanistically link molecular-level changes in soil microorganisms to a community’s functional phenotypes (or metaphenome). Towards filling this gap, we performed a combined analysis of metabolic and gene co-expression networks to explore how the soil microbiome responded to changes in soil moisture and nutrient conditions and to determine which genes were expressed under a given condition. Our integrated modeling approach revealed previously unknown, but critically important aspects of the soil microbiomes’ response to environmental perturbations. Incorporation of metabolomic and transcriptomic data into metabolic reaction networks identified condition-specific signature genes that are uniquely associated with dry, wet, and glycine-amended conditions. A subsequent gene co-expression network analysis revealed that drought-associated genes occupied more central positions in a network model of the soil community, compared to the genes associated with wet, and glycine-amended conditions. These results indicate the occurrence of system-wide metabolic coordination when soil microbiomes cope with moisture or nutrient perturbations. Importantly, the approach that we demonstrate here to analyze large-scale multi-omics data from a natural soil environment is applicable to other microbiome systems for which multi-omics data are available.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Sequential discontinuities of Feynman integrals and the monodromy group

We generalize the relation between discontinuities of scattering amplitudes and cut diagrams to cover sequential discontinuities (discontinuities of discontinuities) in arbitrary momentum channels. The new relations are derived using time-ordered perturbation theory, and hold at phase-space points where all cut momentum channels are simultaneously accessible. As part of this analysis, we explain how to compute sequential discontinuities as monodromies and explore the use of the monodromy group in characterizing the analytic properties of Feynman integrals. We carry out a number of cross-checks of our new formulas in polylogarithmic examples, in some cases to all loop orders.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Linear beam stability in periodic focusing systems: Krein signature and band structure

The general question of how a beam becomes unstable has been one of the fundamental research topics among beam and accelerator physicists for several decades. In this study, we revisited the general problem of linear beam stability in periodic focusing systems by applying the concepts of Krein signature and band structure. We numerically calculated the eigenvalues and other associated characteristics of one-period maps, and discussed the stability properties of single-particle motions with skew quadrupoles and envelope perturbations in high-intensity beams on an equal footing. In particular, an application of the Krein theory to envelope instability analysis was newly attempted in this study. Finally, the appearance of instabilities is interpreted as the result of the collision between eigenmodes of opposite Krein signatures and the formation of a band gap.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Scaling functions for eigenstate entanglement crossovers in harmonic lattices

For quantum matter, eigenstate entanglement entropies obey an area law or log-area law at low energies and small subsystem sizes and cross over to volume laws for high energies and large subsystems. This transition is captured by crossover functions, which assume a universal scaling form in quantum critical regimes. We demonstrate this for the harmonic lattice model, which describes quantized lattice vibrations and is a regularization for free scalar field theories, modeling, e.g., spin-0 bosonic particles. In one dimension, the ground-state entanglement obeys a log-area law. For dimensions d ≥ 2, it displays area laws, even at criticality. The distribution of excited-state entanglement entropies is found to be sharply peaked around subsystem entropies of corresponding thermodynamic ensembles in accordance with the eigenstate thermalization hypothesis. Numerically, we determine crossover scaling functions for the quantum critical regime of the model and do a large-deviation analysis. We show how infrared singularities of the system can be handled and how to access the thermodynamic limit using a perturbative trick for the covariance matrix. Eigenstates for quasi-free bosonic systems are not Gaussian. Here, we resolve this problem by considering appropriate squeezed states instead. For these, entanglement entropies can be evaluated efficiently.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Excitation spectra of quantum matter without quasiparticles. I. Sachdev-Ye-Kitaev models

Here, we study the low-frequency spectra of complex Sachdev-Ye-Kitaev models at general densities. The analysis applies also to SU(M) magnets with random exchange at large M. The spectral densities are computed by numerical analysis of the saddle-point equations on the real frequency ω axis at zero temperature T. The asymptotic low-ω behaviors are found to be in excellent agreement with the scaling dimensions of irrelevant operators which perturb the conformally invariant critical states. Of possible experimental interest is our computation of the universal spin spectral weight of the SU(M) magnets at low ω and T; this includes a contribution from the time reparametrization mode, which is the boundary graviton of the holographic dual. This analysis is extended to a random t-J model in the following paper [M. Tikhanovskaya et al., following paper, Phys. Rev. B 103, 075142 (2021)].

36 MATERIALS SCIENCE↗
DOE OSTI2021

Transition of a network of nonlinear interactions into a regime of strong nonlinear fluctuations: A paradigm for the edge localized mode onset

We study how a network of nonlinear oscillators transits into a regime of strong nonlinear fluctuations when perturbed by a triad. In this regime, most of the potential energy contained in the waves is made available to the system through strong nonlinear fluctuations. This analysis is motivated by recent experimental observations [Dominski and Diallo, Plasma Phys. Control. Fusion 62, 095011 (2020)] where it was found that magnetic fluctuations trigger the onset of edge localized modes by suddenly exciting a network of nonlinear interactions. In our study, we consider the simplest system of many harmonic oscillators that are organized in a network of nonlinear triads. We model and simulate the sudden transition of this network of triads into a regime of strong nonlinear fluctuations—reminiscent of the onset of edge localized modes in tokamaks. This transition is triggered by the activation of a nonlinear perturbation. An abrupt rise of the system's disorder (an entropy-like quantity) is measured during the transition. This transition from weak to strong nonlinear fluctuations is even more abrupt when these fluctuations are chaotic, i.e., when the timescale of the nonlinear interaction is comparable to the timescale of the wave oscillations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Hand Calculations for Nuclear Criticality Safety – Primer Revision

The document “ Hand Calculation Methods for Criticality Safety – A Primer, ” was published by the authors (Los Alamos National Laboratory report LA-14244-M) in December 2006 to provide an overview of the most common hand calculation methods used for criticality safety analysis. Hand calculation methods can be used as a starting point for more advanced calculations, and in many circumstances, they can provide sensitivity and perturbation information quicker than using a criticality code, such as KENO or MCNP. This report has been revised to augment existing basis information and example problems for each of the methods discussed: 1-group and modified 1- group diffusion theory, core-density conversions, buckling conversions, limiting surface density method, density analog method, surface density method, and solid angle method. This primer discusses the applicability of the various methods, illustrates how they are used, and provides an interpretation of the example problem results. The example problems provided are simple, practical problems, and the reference data to solve each example problem is provided. This paper will provide an overview of the Primer revision and how it can be useful for new Nuclear Criticality Safety practitioners.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Hand Calculations for Nuclear Criticality Safety — Primer Revision [Abstract]

The document “ Hand Calculation Methods for Criticality Safety –A Primer, ” was published by the authors (Los Alamos National Laboratory report LA-14244-M) in December 2006 to provide an overview of the most common hand calculation methods used for criticality safety analysis. Hand calculation methods can be used as a starting point for more advanced calculations, and in many circumstances, they can provide sensitivity and perturbation information quicker than using a criticality code, such as KENO or MCNP. This report has been revised to augment existing basis information and example problems for each of the methods discussed: 1-group and modified 1-group diffusion theory, core-density conversions, buckling conversions, limiting surface density method, density analog method, surface density method, and solid angle method. This primer discusses the applicability of the various methods, illustrates how they are used, and provides an interpretation of the example problem results. The example problems provided are simple, practical problems, and the reference data to solve each example problem is provided. This paper will provide an overview of the Primer revision and how it can be useful for new Nuclear Criticality Safety practitioners.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2025

A deep generative model for deciphering cellular dynamics and in silico drug discovery in complex diseases

Human diseases are characterized by intricate cellular dynamics. Single-cell transcriptomics provides critical insights, yet a persistent gap remains in computational tools for detailed disease progression analysis and targeted in silico drug interventions. Here we introduce UNAGI, a deep generative neural network tailored to analyse time-series single-cell transcriptomic data. This tool captures the complex cellular dynamics underlying disease progression, enhancing drug perturbation modelling and screening. When applied to a dataset from patients with idiopathic pulmonary fibrosis, UNAGI learns disease-informed cell embeddings that sharpen our understanding of disease progression, leading to the identification of potential therapeutic drug candidates. Validation using proteomics reveals the accuracy of UNAGI’s cellular dynamics analysis, and the use of the fibrotic cocktail-treated human precision-cut lung slices confirms UNAGI’s predictions that nifedipine, an antihypertensive drug, may have anti-fibrotic effects on human tissues. UNAGI’s versatility extends to other diseases, including COVID, demonstrating adaptability and confirming its broader applicability in decoding complex cellular dynamics beyond idiopathic pulmonary fibrosis, amplifying its use in the quest for therapeutic solutions across diverse pathological landscapes.

Neural Network↗