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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Appendix Q: Recommendations for Developing Molecular Assays for Microbial Pathogen Detection Using Modern In Silico Approaches

We describe the use of in silico approaches to improve the process of molecular assay development and reduce time and cost by utilizing available databases of whole genome pathogen sequences combined with modern bioinformatics and physical modeling tools. Well-characterized assays are needed for accurately detecting pathogens in environmental and patient samples and also for evaluation of the efficacy of a medical countermeasure that may be administered to patients. The polymerase chain reaction (PCR) remains the gold standard for pathogen detection due to the simplicity of its instrumentation, low cost of reagents, and outstanding limit of detection (LOD), sensitivity, and specificity. However, creation of such PCR assays often involves iterations of design, preliminary testing, and thorough validation with clinical isolates and testing in relevant matrices, which can be time consuming, costly, and result in suboptimal assays. Since formal validation (e.g., for Emergency Use Authorization [EUA] or Food and Drug Administration [FDA] licensure) of an infectious disease assay can be very expensive and can require extensive time of development, having a well-designed assay up front is a critical first step. Yet, many assays described in the literature utilized limited design capabilities and many initially promising assays fail the validation process, resulting in increased costs and timelines for successful product development. While the computational approaches outlined in this document by no means obviate the need for wet lab testing, they can reduce the amount of effort wasted on empirical optimization and iterative redesigns and also guide validation studies. The proposed computational approaches also result in higher performing assays with better sensitivity, specificity, and lower LOD and reduce the possibility of assay failure due to signature erosion. To provide clarity, an extensive glossary of defined terms is provided.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Probing the nature of dark matter with accreted globular cluster streams

ABSTRACT The steepness of the central density profiles of dark matter (DM) in low-mass galaxy haloes (e.g. dwarf galaxies) is a powerful probe of the nature of DM. We propose a novel scheme to probe the inner profiles of galaxy subhaloes using stellar streams. We show that the present-day morphological and dynamical properties of accreted globular cluster (GC) streams – those produced from tidal stripping of GCs that initially evolved within satellite galaxies and later merged with the Milky Way (MW) – are sensitive to the central DM density profile and mass of their parent satellites. GCs that accrete within cuspy cold dark matter (CDM) subhaloes produce streams that are physically wider and dynamically hotter than streams that accrete inside cored subhaloes. A first comparison of MW streams ‘GD-1’ and ‘Jhelum’ (likely of accreted GC origin) with our simulations indicates a preference for cored subhaloes. If these results hold up in future data, the implication is that either the DM cusps were erased by baryonic feedback, or their subhaloes naturally possessed cored density profiles implying particle physics models beyond CDM. Moreover, accreted GC streams are highly structured and exhibit complex morphological features (e.g. parallel structures and ‘spurs’). This implies that the accretion scenario can naturally explain the recently observed peculiarities in some of the MW streams. We also propose a novel mechanism for forming ‘gaps’ in stellar streams when the remnant of the parent subhalo (which hosted the GC) later passes through the GC stream. This encounter can last a longer time (and have more of an impact) than the random encounters with DM subhaloes previously considered, because the GC stream and its parent subhalo are on similar orbits with small relative velocities. Current and future surveys of the MW halo will uncover numerous faint stellar streams and provide the data needed to substantiate our preliminary tests with this new probe of DM.

(Galaxy:) globular clusters: individual↗
DOE OSTI2021

Transient quasi-periodic oscillations at γ-rays in the TeV blazar PKS 1510-089

ABSTRACT We present periodicity search analyses on the γ-ray light curve of the TeV blazar PKS 1510-089 observed by the Fermi Large Area Telescope. We report the detection of two transient quasi-periodic oscillations: A 3.6-d QPO during the outburst in 2009 that lasted five cycles (MJD 54906–54923); and a periodicity of 92 d spanning over 650 d from 2018 to 2020 (MJD 58200–58850), which lasted for seven cycles. We employed the Lomb–Scargle periodogram, Weighted Wavelet Z-transform, redfit, and the Monte Carlo light-curve simulation techniques to find any periodicity and the corresponding significance. The 3.6-d QPO was detected at a moderate significance of ∼3.5σ, while the detection significance of the 92-d QPO was ∼7.0σ. We explore a few physical models for such transient QPOs including a binary black hole system, precession of the jet, a non-axisymmetric instability rotating around the central black hole near the innermost stable circular orbit, the presence of quasi-equidistant magnetic islands inside the jet, and a geometric model involving a plasma blob moving helically inside a curved jet.

Roy, Abhradeep (ORCID:0000000249984560)↗
DOE OSTI2023

Interpreting Sunyaev–Zel’dovich observations with MillenniumTNG: mass and environment scaling relations

ABSTRACT Sunyaev–Zel’dovich (SZ) measurements can dramatically improve our understanding of the intergalactic medium and the role of feedback processes in galaxy formation, allowing us to calibrate important astrophysical systematics in cosmological constraints from weak lensing galaxy clustering surveys. However, the signal is only measured in a two-dimensional projection, and its correct interpretation relies on understanding the connection between observable quantities and the underlying intrinsic properties of the gas, in addition to the relation between the gas and the underlying matter distribution. One way to address these challenges is through the use of hydrodynamical simulations such as the high-resolution, large-volume MillenniumTNG suite. We find that measurements of the optical depth, τ, and the Compton-y parameter, Y, receive large line-of-sight contributions that can be removed effectively by applying a compensated aperture photometry filter. In contrast with other τ probes (e.g. X-rays and fast radio bursts), the kinematic SZ-inferred τ receives most of its signal from a confined cylindrical region around the halo due to the velocity decorrelation along the line of sight. Additionally, we perform fits to the Y–M and τ–M scaling relations and report best-fitting parameters adopting the smoothly broken power law formalism. We note that subgrid physics modelling can broaden the error bar on these by 30 per cent for intermediate-mass haloes (${\sim }10^{13} \, {\rm M}_{\odot }$). The scatter of the scaling relations can be captured by an intrinsic dependence on concentration and an extrinsic dependence on tidal shear. Finally, we comment on the effect of using galaxies rather than haloes in observations, which can bias the inferred profiles by ∼20 per cent for L* galaxies.

Hadzhiyska, Boryana (ORCID:0000000223123121)↗
DOE OSTI2023

The entropy of galaxy spectra: how much information is encoded?

Abstract The inverse problem of extracting the stellar population content of galaxy spectra is analysed here from a basic standpoint based on information theory. By interpreting spectra as probability distribution functions, we find that galaxy spectra have high entropy, thus leading to a rather low effective information content. The highest variation in entropy is unsurprisingly found in regions that have been well studied for decades with the conventional approach. We target a set of six spectral regions that show the highest variation in entropy – the 4000 Å break being the most informative one. As a test case with real data, we measure the entropy of a set of high-quality spectra from the Sloan Digital Sky Survey, and contrast entropy-based results with the traditional method based on line strengths. The data are classified into star-forming (SF), quiescent (Q), and active galactic nucleus (AGN) galaxies, and show – independently of any physical model – that AGN spectra can be interpreted as a transition between SF and Q galaxies, with SF galaxies featuring a more diverse variation in entropy. The high level of entanglement complicates the determination of population parameters in a robust, unbiased way, and affects traditional methods that compare models with observations, as well as machine learning (especially deep learning) algorithms that rely on the statistical properties of the data to assess the variations among spectra. Entropy provides a new avenue to improve population synthesis models so that they give a more faithful representation of real galaxy spectra.

Ferreras, Ignacio (ORCID:0000000345843127)↗
DOE OSTI2025

Measurement of the liquid argon scintillation pulse shape using differentiable simulation in the coherent CAPTAIN-Mills experiment

The coherent CAPTAIN-Mills (CCM) experiment is a liquid argon (LAr) light collection detector searching for MeV-scale neutrino and beyond Standard Model physics signatures. Two hundred eight-inch photomultiplier tubes instrument the seven-ton fiducial volume with 50% photocathode coverage to detect light produced by charged particles. CCM’s light-based approach reduces requirements of LAr purity, compared to other detection technologies, such that sub-MeV particles can be reliably detected without additional LAr filtration and with 𝒪⁡(1) parts per million of common contaminants. We present a measurement of LAr light production and propagation parameters, with uncertainties, obtained from a sample of MeV-scale electromagnetic events. The optimization of this high-dimensional parameter space was facilitated by a differentiable optical photon Monte Carlo simulation and detailed photomultiplier tube response characterization. This result accurately predicts the timing and spatial distribution of light due to scintillation and Cherenkov emission in the detector. This is the first description of photon propagation in LAr to include several effects, including anomalous dispersion of the index of refraction near the ultraviolet resonance, Mie scattering from impurities, and Cherenkov light production.

Cherenkov detectors↗
DOE OSTI2025

Neutrino Flavor Transformation in Neutron Star Mergers

Here, we present the first numerical relativity simulations including neutrino flavor transformations that could result from flavor instabilities, quantum many-body effects, or potential beyond standard model physics in neutron star mergers. We find that neutrino flavor transformations impact the composition and structure of the remnant, potentially leaving an imprint on the postmerger gravitational-wave signal. They also have a significant impact on the composition and nucleosynthesis yields of the ejecta.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Investigating event-shape methods in the search for the chiral magnetic effect in relativistic heavy ion collisions

The chiral magnetic effect (CME) is a phenomenon in which electric charge is separated by a strong magnetic field from local domains of chirality imbalance and parity violation in quantum chromodynamics. The CME-sensitive observable, the charge-dependent three-point azimuthal correlator Δ⁢𝛾 , is contaminated by a major physics background proportional to the particle's elliptic flow anisotropy 𝑣 2 . Event-shape engineering (ESE) binning events in dynamical fluctuations of 𝑣 2 and event-shape selection (ESS) binning events in statistical fluctuations of 𝑣 2 are two methods to search for the CME by projecting Δ⁢𝛾 to the measured anisotropy 𝑣 2 = 0 intercept. Here, we conduct a systematic study of these two methods using physics models as well as toy model simulations. It is observed that the ESE method fulfills the general premise of measuring the CME but is statistically hungry. It is found that the intercept from the ESS method depends on the details of the event content, such as the mixtures of background-contributing sources, because of statistical fluctuations of intertwining variables used in the method, and is thus not practically useful to measure the CME.

Relativistic heavy-ion collisions↗
DOE OSTI2022

Perturbative Diagonalization for Time-Dependent Strong Interactions

We present a systematic method to implement a perturbative Hamiltonian diagonalization based on the time-dependent Schrieffer-Wolff transformation. Applying our method to strong parametric interactions we show how, even in the dispersive regime, full Rabi model physics is essential to describe the dressed spectrum. Our results unveil several qualitatively different results, including realization of large energy-level shifts, tunable in magnitude and sign with the frequency and amplitude of the pump mediating the parametric interaction. Crucially, Bloch-Siegert shifts, typically thought to be important only in the ultrastrong or deep-strong coupling regimes, can be rendered large even for weak dispersive interactions to realize points of exact cancelation of dressed shifts (“blind spots”) at specific pump frequencies. The framework developed here highlights the rich physics accessible with time-dependent interactions and serves to significantly expand the functionalities for control and readout of strongly interacting quantum systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Primary observables for gauge boson collider signals

In this paper, we determine a basis for the on-shell four-point amplitudes V V V V for Standard Model gauge bosons V = W ± , Z , γ , g . Following previous work, this completes the analysis of three- and four-point amplitudes for the Standard Model and could be used for model-independent searches for beyond the Standard Model physics at colliders. Our results include a Lagrangian parametrization for the “primary” amplitudes, where including additional derivatives leads to the Mandelstam “descendant” amplitudes, and upper bounds on the coupling constants from imposing unitarity. We also perform an estimate for the sensitivity for new Z decays at the High-Luminosity LHC, finding that Z → γ ℓ ¯ ℓ could be searched for, but that other decay modes, like Z → ( γ γ γ , γ g g ) , are too small to be discovered after imposing unitarity constraints. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2021

Thermomagnetic properties of Bi 2 Te 3 single crystal in the temperature range from 55 K to 380 K

Magnetothermoelectric transport provides an understanding of coupled electron-hole-phonon current in topological materials and has applications in energy conversion and cooling. In this paper, we study the Nernst coefficient, the magneto-Seebeck coefficient, and the magnetoresistance of single-crystalline Bi 2 Te 3 under external magnetic field in the range of –3T to 3T and in the temperature range of 55 K to 380 K. Moreau's relation is employed to justify both the overall trend of the Nernst coefficient and the temperature at which this coefficient changes sign. We observe a nonlinear relationship between the Nernst coefficient and the applied magnetic field in the temperature range of 55 K to 255 K. An increase in both the Nernst coefficient and the magneto-Seebeck coefficient is observed as the temperature is reduced which can be attributed to the increased mobility of the carriers at lower temperatures. First-principles density functional theory calculations were carried out to physically model the experimental data including electronic and transport properties. Simulation findings agreed with the experiments and provide a theoretical insight to justify the measurements.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Impact of neutrino flavor conversions on neutron star merger dynamics, ejecta, nucleosynthesis, and multimessenger signals

We present numerical relativity simulations of binary neutron star mergers incorporating neutrino flavor transformations triggered by fast flavor instability, quantum many-body effects, or potential beyond standard model physics. In both long-lived and short-lived remnant scenarios, neutrino flavor conversions modify species-dependent neutrino luminosities and mean energies, and drive the matter towards more neutron rich conditions. They produce up to more neutron rich ejecta and significantly boost the r-process yields, especially in low-density, near-equatorial outflows. We identify regions unstable to fast flavor instabilities and find that these instabilities persist despite flavor conversions. We further test the sensitivity to the equilibration timescale of the flavor conversions, finding that slower flavor conversions can interact with thermodynamic equilibration, and increase the neutron richness of the ejecta. Flavor conversions may also contribute to stronger gravitational wave and neutrino emissions, pointing to a correlation between neutrino transport and merger dynamics. Furthermore, these results highlight the potential impact of flavor conversions while motivating future work to improve on theoretical understanding of flavor instabilities in global simulations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Climate lags and genetics determine phenology in quaking aspen ( Populus tremuloides )

Spatiotemporal patterns of phenology may be affected by mosaics of environmental and genetic variation. Environmental drivers may have temporally lagged impacts, but patterns and mechanisms remain poorly known. Here, we combine multiple genomic, remotely sensed, and physically modeled datasets to determine the spatiotemporal patterns and drivers of canopy phenology in quaking aspen, a widespread clonal dioecious tree species with diploid and triploid cytotypes. We show that over 391 km 2 of southwestern Colorado: greenup date, greendown date, and growing season length vary by weeks and differ across sexes, cytotypes, and genotypes; phenology has high phenotypic plasticity and heritabilities of 31–61% (interquartile range); and snowmelt date, soil moisture, and air temperature predict phenology, at temporal lags of up to 3 yr. Our study shows that lagged environmental effects are needed to explain phenological variation and that the effect of cytotype on phenology is obscured by its correlation with topography. Phenological patterns are consistent with responses to multiyear accumulation of carbon deficit or hydraulic damage.

carbon allocation↗
DOE OSTI2022

A Forward Feedback Control Scheme for a Solar Thermochemical Moving Bed Counter-Current Flow Reactor

Abstract Pelletized thermochemical energy storage media has a potential for long-duration energy storage. Production of solid-state energy storage media can be done within a cavity chemical reactor that captures concentrated solar radiation from a solar thermal field. The temperature stability of a solar reactor is directly influenced by the solar flux intercepted. This paper presents a low-order physical model to simulate the dynamic response of temperature inside a tubular plug-flow reactor prototype. Solid granular particles are fed to the reactor from the top whereas a counter-current flowing gas enters the reactor from the bottom. An in-house code was developed to model transient heat transfer of the reactor wall, gas, and moving particles. The model was preliminarily validated with packed beds for different temperature ranges and two gas flowrates. Dynamic response of the reactor temperature is simulated for different input power and gas/particle flowrates. The results show that the system response can be controlled efficiently by utilizing input power (solar flux) as a control parameter. A conventional proportional integral (PI) controller is designed to control the temperature inside the reactor and to maintain it during the solar flux intermittency. The controller parameters are tuned using the Ziegler–Nichols method to ensure optimal system response. The results show that the feedback control model is successful in tracking different reference reactor temperatures within a reasonable settling time of 30 min and eliminated overshoot. This study can be extended to include a hybrid reactor with a multi-input, multi-output variable system.

Energy & Fuels↗
DOE OSTI2025

One-shot gas detection with transformer paired neural networks in Mako collected longwave infrared hyperspectral imagery

To date, careful data treatment workflows and statistical detectors are used to perform hyperspectral image (HSI) detection of any gas contained in a spectral library, which is often expanded with physics models to incorporate different spectral characteristics. In general, surrounding evidence or known gas-release parameters are used to provide confidence in or confirm detection capability, respectively. This makes quantifying detection performance difficult as it is nearly impossible to develop an absolute ground truth for gas target pixel presence in collected HSI. Consequently, developing and comparing new detection methods, especially machine learning (ML)-based methods, is susceptible to subjectivity in derived detection map quality. Here, in this work, we demonstrate the first use of transformer-based paired neural networks (PNNs) for one-shot gas target detection for multiple gases while providing quantitative classification and detection metrics for their use on labeled data. Terabytes of training data are generated from a database of long-wave infrared HSI obtained from historical Mako sensor campaigns over Los Angeles. By incorporating labels, singular signature representations, and a model development pipeline, we can tune and select PNNs to detect multiple gas targets that are not seen in training on a quantitative basis. We additionally assess our test set detections using interpretability techniques widely employed with ML-based predictors, but less common with detection methods relying on learned latent spaces.

Hyperspectral imaging↗