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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection

Generating top-down tandem mass spectra (MS/MS) for complex mixtures of proteoforms has become possible through improvements in fractionation, on-line separation, dissociation, and mass analysis. The algorithms to match tandem mass spectra to sequences have undergone a parallel evolution, with both spectral alignment and peak matching being paired with diverse methods for scoring proteoform-spectral matches (PrSMs). This study assesses state-of-the-art algorithms for top-down identification through three distinct challenges. The first is identifying a large yield of PrSMs while controlling false discovery rate (FDR) in identifying thousands of proteoforms from complex cell lysates via four software workflows: ProSight Proteome Discoverer, TopPIC, Informed Proteomics, and pTop. The second is the deconvolution of data from both Thermo Orbitrap-class and Bruker maXis Q-TOF instruments to produce consistent precursor charge and mass determinations while generating fragment mass lists to optimize identification. The third attempts to detect diverse post-translational modifications (PTMs) in proteoforms from cow milk and human ovarian tissue. The data demonstrate that existing software suites produce admirable sensitivity, in some cases identifying a third of collected tandem mass spectra with FDR controlled below 2%; the overlap in these PrSMs, however, illustrates real value in searching data with multiple search engines. Differences among identification workflows seem to result from each search algorithm incorporating its own deconvolution algorithm. By transmitting deconvolution data from multiple deconvolution routes (Thermo Xtract, Bruker Auto MSn, Mascot Distiller, TopFD, and FLASHDeconv) to the downstream TopPIC search algorithm, we were able to detect common causes of deconvolution disagreement. The detection of PTMs was very inconsistent among search algorithms, with some workflows suggesting as little as 1% of PrSMs from cow’s milk were singly-phosphorylated while other workflows found that 18% of PrSMs were singly-phosphorylated. Taken together, these results make a strong argument for top-down researchers to adopt a standard practice of analyzing each MS/MS experiment with at least two different search engines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Overlap-Driven Splitting of Triplet Pairs in Singlet Fission

Here, we analyze correlated-triplet-pair (TT) singlet-fission intermediates toward two-triplet separation (T...T) using spin-state-averaged density matrix renormalization group electronic-structure calculations. Specifically, we compare the triplet–triplet exchange (J) for tetracene dimers, bipentacene, a subunit of the benzodithiophene–thiophene dioxide polymer, and a carotenoid (neurosporene). Exchange-split energy gaps of J and 3J separate a singlet from a triplet and a singlet from a quintet, respectively. We draw two new insights: (a) the canonical tetracene singlet-fission unit cell supports precisely three low-lying TT intermediates with order-of-magnitude differences in J, and (b) the separable TT intermediate in carotenoids emanates from a pair of excitations to the second triplet state. Therefore, unlike with tetracenes, carotenoid fission requires above-gap excitations. In all cases, the distinguishability of the molecular triplets—that is, the extent of orbital overlap—determines the splitting within the spin manifold of TT states. Consequently, J represents a spectroscopic observable that distnguishes the resemblance between TT intermediates and the T...T product.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Explainable machine learning for incipient anomaly detection in compact molten salt heat exchanger with overlapping feature distributions

High-temperature molten salt-cooled reactors (MSCRs) are a promising next-generation nuclear technology option, offering efficient power conversion and inherent safety features. However, the reliability of these systems depends on the robust operation of heat exchangers (HXs), which are susceptible to failure due to temperature gradients and channel plugging caused by fluid freezing. Conventional monitoring methods, relying on inlet and outlet measurements, lack the spatial resolution needed to detect early-stage faults. We propose a novel design of a compact salt-to-salt matrix-type HX design consisting of interleaved arrays of parallel tubes, with integrated synthetic fiber optic distributed temperature sensing (DTS) to enable localized detection of incipient faults. To evaluate performance of this design, we generate high-fidelity synthetic data using heat transfer computational modeling to simulate channel plugging, and introduce sensor noise for realistic modeling of measurements. The dataset comprises of 97% normal operation and 3% anomaly cases, with each anomaly class representing 1% of the data. These early anomalies result in overlapping temperature profiles between normal and faulty channels, producing a non-separable dataset that challenges traditional classification techniques. We benchmark eight supervised machine learning (ML) models and demonstrate that XGBoost achieves the highest performance. To improve transparency, we develop an explainability framework combining Shapley values and partially ordered sets (POSETs) to quantify and structurally analyze feature importance. This approach identifies both dominant predictors and ambiguous feature relationships, enhancing trust and interpretability. Our results highlight the potential of combining DTS and explainable ML with intelligent feature selection to improve predictive maintenance and ensure operational resilience in advanced nuclear systems.

Prantikos, Konstantinos [Argonne National Laborato↗
DOE OSTI2023

Genetics of varicose veins reveals polygenic architecture and genetic overlap with arterial and venous disease

Varicose veins represent a common cause of cardiovascular morbidity, with limited available medical therapies. Although varicose veins are heritable and epidemiologic studies have identified several candidate varicose vein risk factors, the molecular and genetic basis remains uncertain. Here we analyzed the contribution of common genetic variants to varicose veins using data from the Veterans Affairs Million Veteran Program and four other large biobanks. Among 49,765 individuals with varicose veins and 1,334,301 disease-free controls, we identified 139 risk loci. We identified genetic overlap between varicose veins, other vascular diseases and dozens of anthropometric factors. Using Mendelian randomization, we prioritized therapeutic targets via integration of proteomic and transcriptomic data. Finally, topological enrichment analyses confirmed the biologic roles of endothelial shear flow disruption, inflammation, vascular remodeling and angiogenesis. Further, these findings may facilitate future efforts to develop nonsurgical therapies for varicose veins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Penetration through slots in cylindrical cavities with cavity modes overlapping with the first slot resonance

In this work, we analyze the coupling into a slotted cylindrical cavity operating at fundamental cavity modal frequencies overlapping with the slot’s first resonance frequency through an unmatched formulation that accounts for the slot’s absorption and radiation processes. The model is validated through full-wave simulations and experimental data. We then couple the unmatched formulation to a perturbation theory model to investigate an absorber within the cavity to reduce the interior field strength, also validated with full-wave simulations and experiments. These models are pivotal to understanding the physical processes involved in the electromagnetic penetration through slots, and may constitute design tools to mitigate electromagnetic interference effects within cavities.

42 ENGINEERING↗
DOE OSTI2023

Characterizing the intracluster light over the redshift range 0.2 < z < 0.8 in the DES-ACT overlap

ABSTRACT We characterize the properties and evolution of bright central galaxies (BCGs) and the surrounding intracluster light (ICL) in galaxy clusters identified in the Dark Energy Survey and Atacama Cosmology Telescope Survey (DES-ACT) overlapping regions, covering the redshift range 0.20 < z < 0.80. Over this redshift range, we measure no change in the ICL’s stellar content (between 50 and 300 kpc) in clusters with log10(M200m,SZ/M⊙) >14.4. We also measure the stellar mass–halo mass (SMHM) relation for the BCG+ICL system and find that the slope, β, which characterizes the dependence of M200m,SZ on the BCG+ICL stellar mass, increases with radius. The outskirts are more strongly correlated with the halo than the core, which supports that the BCG+ICL system follows a two-phase growth, where recent growth (z < 2) occurs beyond the BCG’s core. Additionally, we compare our observed SMHM relation results to the IllustrisTNG300-1 cosmological hydrodynamic simulations and find moderate qualitative agreement in the amount of diffuse light. However, the SMHM relation’s slope is steeper in TNG300-1 and the intrinsic scatter is lower, likely from the absence of projection effects in TNG300-1. Additionally, we find that the ICL exhibits a colour gradient such that the outskirts are bluer than the core. Moreover, for the lower halo mass clusters (log10(M200m,SZ/M⊙) < 14.59), we detect a modest change in the colour gradient’s slope with lookback time, which combined with the absence of stellar mass growth may suggest that lower mass clusters have been involved in growth via tidal stripping more recently than their higher mass counterparts.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Prolonging genetic circuit stability through adaptive evolution of overlapping genes

Abstract The development of synthetic biological circuits that maintain functionality over application-relevant time scales remains a significant challenge. Here, we employed synthetic overlapping sequences in which one gene is encoded or ‘entangled’ entirely within an alternative reading frame of another gene. In this design, the toxin-encoding relE was entangled within ilvA, which encodes threonine deaminase, an enzyme essential for isoleucine biosynthesis. A functional entanglement construct was obtained upon modification of the ribosome-binding site of the internal relE gene. Using this optimized design, we found that the selection pressure to maintain functional IlvA stabilized the production of burdensome RelE for >130 generations, which compares favorably with the most stable kill-switch circuits developed to date. This stabilizing effect was achieved through a complete alteration of the allowable landscape of mutations such that mutations inactivating the entangled genes were disfavored. Instead, the majority of lineages accumulated mutations within the regulatory region of ilvA. By reducing baseline relE expression, these more ‘benign’ mutations lowered circuit burden, which suppressed the accumulation of relE-inactivating mutations, thereby prolonging kill-switch function. Overall, this work demonstrates the utility of sequence entanglement paired with an adaptive laboratory evolution campaign to increase the evolutionary stability of burdensome synthetic circuits.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Ab initio single-neutron spectroscopic overlaps in lithium isotopes

We calculate single-neutron spectroscopic overlaps for lithium isotopes in the framework of the ab initio symmetry-adapted no-core shell model. We report the associated neutron-nucleus asymptotic normalization coefficients (ANCs) and spectroscopic factors (SFs) that are important ingredients in many reaction cross-section calculations. While spectroscopic factors have been traditionally extracted from experimental cross sections, their sensitivity on the type of reactions, the energy, and the underlying models point to the need for determining SFs from first-principle structure considerations. As illustrative examples, we present 6 Li + n, 7 Li ⁢+ n, and 8 Li ⁢+ n, and we show that the results are in a good agreement with those of other ab initio methods, where available, including the quantum Monte Carlo approach. Here, we compare ANCs and SFs to available experimentally deduced values, with a view toward expanding this study to heavier nuclei and to extracting intercluster effective interactions for input into analyses of existing and future experimental data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Reduction of spectroscopic overlap across the Z = 8 shell in neutron-rich nuclei

The recent discovery and spectroscopic measurements of 27 O and 28 O suggests the disappearance of the N = 20 shell structure in these neutron-rich oxygen isotopes. We measured one- and two-proton removal cross sections from 27 F and 29 N, respectively, extracting spectroscopic factors and comparing them to shell model overlap functions coupled with eikonal reaction model calculations. The invariant mass technique was used to reconstruct the two-body ( 24 O + n) and three-body ( 24 O + 2n) decay energies from knockout reactions of 27 F (106.2 MeV/u) and 29 Ne (112.8 MeV/u) beams impinging on a 9 Be target. The one-proton removal from 27 F strongly populated the ground state of 26 O and the extracted cross section of $3.4^{+0.3}_{-1.5}$ mb agrees with eikonal model calculations that are normalized by the shell model spectroscopic factors and account for the systematic reduction factor observed for single nucleon removal reactions within the models used. For the two-proton removal reaction from 29 Ne an upper limit of 0.08 mb was extracted for populating states in 27 O decaying though the ground state of 26 O. The measured upper limit for the population of the ground state of 26 O in the two-proton removal reaction from 29 Ne indicates a significant difference in the underlying nuclear structure of 27 F and 29 Ne.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Arabidopsis stromal carbonic anhydrases exhibit non–overlapping roles in photosynthetic efficiency and development

Carbonic anhydrases (CAs) are ubiquitous enzymes that accelerate the reversible conversion of CO 2 to HCO 3 – . The Arabidopsis genome encodes members of the α-, β- and γ-CA families, and it has been hypothesized that βCA activity has a role in photosynthesis. In this work, we tested this hypothesis by characterizing the two plastidial βCAs, βCA1 and βCA5, in physiological conditions of growth. We conclusively established that both proteins are localized in the chloroplast stroma and that the loss of βCA5 induced the expression of βCA1, supporting the existence of regulatory mechanisms to control the expression of stromal βCAs. We also established that βCA1 and βCA5 have markedly different enzymatic kinetics and physiological relevance. Specifically, we found that βCA5 had a first-order rate constant ~10-fold lower than βCA1, and that the loss of βCA5 is detrimental to growth and could be rescued by high CO 2 . Furthermore, we established that, while a βCA1 mutation showed near wild-type growth and no significant impact on photosynthetic efficiency, the loss of βCA5 markedly disrupted photosynthetic efficiency and light-harvesting capacity at ambient CO 2 . Therefore, we conclude that in physiological autotrophic growth, the loss of the more highly expressed βCA1 does not compensate for the loss of a less active βCA5, which in turn is involved in growth and photosynthesis at ambient CO 2 levels. These results lend support to the hypothesis that, in Arabidopsis,βCAs have non-overlapping roles in photosynthesis and identify a critical activity of stromal βCA5 and a dispensable role for βCA1.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Gene Tuples ArraNGed in overLapping Elements

GENTANGLE is a high performance containerized pipeline for the computational design of two overlapping genes translated in different reading frames of the genome that can be used to design and test gene entanglements for new microbial engineering projects using arbitrary sets of user specified gene pairs.

Leonard, SeanP↗
DOE OSTI2024

Efficient general method for numerically modeling laser pulse propagation, overlap, and lifetime effects in amplifiers

An efficient numerical time-dependent general method is developed to address incoherent pulse overlap and lifetime effects in laser amplifiers. The alternating propagation-population laser energetics method (APPLE) has been validated against a semi-discrete coupled rate equation numerical method (SDRE) and analytic formalisms in bounding cases. APPLE is based on decoupled rates applied to a time-dependent framework where both space-time-dependent populations and pulse energetics are consistently updated in each time step. A significant advantage of APPLE lies in its conceptual simplicity, ease of implementation, and relatively small computational cost. SDRE tracks the populations through coupled rates and uses the method of lines to discretize the hyperbolic partial differential transport equations allowing for use of ordinary differential equation solvers. With reasonably sized mesh, we report both energetic and power pulse shape relative differences on the order of one percent between the models over a large range of initial conditions.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Controlled Growth of Ta Oxide With Reactive Sputtering for Overlap Josephson Junction Application

Josephson junctions $\($JJs$\)$ are indispensable elements for superconducting quantum electronics. There is a growing need to develop processes for high quality JJs. Here we explore the growth of Ta oxide as a dielectric barrier for Metal-Oxide-Metal overlap JJ implementations. We study films of Ta oxides prepared with reactive magnetron sputtering. TaOx is grown on silicon and Ta films with varying RF power and oxygen concentrations. Tuning these parameters allows us to control the rate of deposition as well as composition of polycrystalline Ta oxides needed to meet our dielectric requirements for Josephson Junctions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

SDSS-V Algorithms: Fast, Collision-free Trajectory Planning for Heavily Overlapping Robotic Fiber Positioners

Robotic fiber positioner (RFP) arrays are becoming heavily adopted in wide-field massively multiplexed spectroscopic survey instruments. RFP arrays decrease nightly operational overheads through rapid reconfiguration between fields and exposures. In comparison to similar instruments, SDSS-V has selected a very dense RFP packing scheme where any point in a field is typically accessible to three or more robots. This design provides flexibility in target assignment. However, the task of collisionless trajectory planning is especially challenging. We present two multiagent distributed control strategies that are highly efficient and computationally inexpensive for determining collision-free paths for RFPs in heavily overlapping workspaces. We demonstrate that a reconfiguration path between two arbitrary robot configurations can be efficiently found if a “folded” state, in which all robot arms are retracted and aligned in a lattice-like orientation, is inserted between the initial and final states. Although developed for SDSS-V, the approach we describe is generic and thus applicable to a wide range of RFP designs and layouts. Robotic fiber positioner technology continues to advance rapidly, and in the near future ultra-densely packed RFP designs may be feasible. Our algorithms are especially capable in routing paths in very crowded environments, where we see efficient results even in regimes significantly more crowded than the SDSS-V RFP design.

42 ENGINEERING↗