Guided Trace Reading Optimization
Technical presentation for internal and laboratory audience
97 MATHEMATICS AND COMPUTING↗
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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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Spherical fitting for oscilloscope film trace reading
This report describes a spherical fitting algorithm that can be used for estimating the oscilloscope film trace coordinates. This algorithm was adopted from a least square algebraic spherical fitting algorithm developed by the author earlier for photovoltaic velocimetry applications. Preliminary assessment suggests that the algorithm may be used for optimizing the coordinates manually digitized by the user, or may be used as an uncertainty estimator for the user’s film reading uncertainties.
97 MATHEMATICS AND COMPUTING↗
BICEP Array: 150 GHz Detector Module Development
The Background Imaging of Cosmic Extragalactic Polarization (BICEP)/Keck (BK) collaboration is currently leading the quest for the highest-sensitivity measurements of the polarized cosmic microwave background (CMB) anisotropies on a degree scale with a series of cryogenic telescopes, of which BICEP Array (BA) is the latest Stage-3 upgrade with a total of ~ 32,000 detectors. The instrument comprises 4 receivers spanning 30–270 GHz, with the low-frequency 30/40 GHz deployed to the South Pole Station in late 2019. The full complement of receivers is forecast to set the most stringent constraints on the tensor-to-scalar ratio r. Building on these advances, the overarching small-aperture telescope concept is already being used as the reference for further Stage-4 experiment design. This paper describes the development of the BICEP Array 150 GHz detector module and its fabrication requirements, with highlights on the high-density time division multiplexing (TDM) design of the cryogenic circuit boards. The low-impedance wiring required between the detectors and the frst stage of superconducting quantum interference device amplifers is crucial to maintaining a stable bias current on the detectors. Here, a novel multilayer FR4 Printed Circuit Board with superconducting traces, capable of reading out up to 648 detectors, is detailed along with its validation tests. An ultra-high-density TDM detector module concept we developed for a CMB-S4-like experiment that allows up to 1920 detectors to be read out is also presented. TDM has been chosen as the detector readout technology for the Cosmic Microwave Background Stage-4 (CMB-S4) experiment based on its proven low-noise performance, predictable costs, and overall maturity of the architecture. The heritage for TDM is rooted in mm- and sub-mm-wave experiments dating back 20 years and has since evolved to support a multiplexing factor of 64x in Stage-3 experiments.
79 ASTRONOMY AND ASTROPHYSICS↗
Diagnosis of PV Cell Passivation Degradation Resulting from Hot-Humid, High Voltage Potential Aging
Corrosion of the antireflective coating on the cell ("AR c corrosion") was previously observed in studies using hot-humid test conditions with external high voltage (HV) bias. Because AR c corrosion is not well understood, mini-modules (MiMos) were examined in a comparative experiment using PERC and PERT as well as legacy Al-BSF cells. For separate MiMos with the cell circuit electrical at +1500 V, -1500 V, or unbiased "V oc", test conditions in the comparative study included 60degrees C/60% RH for 96 h, as in IEC TS 62804-1; 70degrees C/70%RH for 200 h; and 85degrees C/85% RH for 200 h. Characterizations at each read point included: camera and electroluminescence (EL) imaging, colorimetry, and I-V curve tracing. Characterizations at the final read point included: SunsVoc; spatially mapping external quantum efficiency (EQE); high resolution: photoluminescence (PL), EL, and dark lock-in thermographic (DLIT) imaging. Forensics were performed on extracted cores, including scanning electron microscopy (SEM) with energy-dispersive X-ray spectroscopy (EDS) and scanning Auger microscopy (SAM). Forensics were also conducted on MiMos (stepped HV aging) and full-sized modules (outdoor aging) from previous studies. AR c corrosion was specifically observed for the glass/encapsulant/cell side of +1500 V (HV+) stressed MiMos, where appearance, color, and reflectance were the characteristics most distinguished relative to simultaneously occurring degradation modes. SEM/EDS and SAM identified conversion of silicon nitride to silicon oxide or hydrous silica, preferentially occurring at the edges and tips of the pyramidal textured cell surface.
aging↗
Unraveling trace anomaly of supradense matter via neutron star compactness scaling
The trace anomaly Δ ≡ 1/3 −𝑃/𝜖 =1/3 −𝜙 quantifies the possibly broken conformal symmetry in supradense matter under pressure 𝑃 at energy density 𝜖. Perturbative QCD (pQCD) predicts a vanishing Δ at extremely high energy or baryon densities when the conformal symmetry is realized but its behavior at intermediate densities reachable in neutron stars (NSs) is still very uncertain. The extraction of Δ from NS observations strongly depends on the employed model for nuclear equation of state (EOS). Using the IPAD-TOV method based on an intrinsic and perturbative analysis of the dimensionless (IPAD) Tolman-Oppenheimer-Volkoff (TOV) equations that are further verified numerically by using 10 5 EOSs generated randomly with a metamodel in a very broad EOS parameter space constrained by terrestrial nuclear experiments and astrophysical observations, here we first show that the compactness 𝜉 ≡ 𝐺𝑀 NS /𝑅𝑐 2 ≡ 𝑀 NS /𝑅 of a NS with mass 𝑀 NS and radius 𝑅 scales very accurately with $\bar{Π}$ c ≡ $Π$ c · (1 +18X/25) ≡ X/(1 +3X 2 +4X) · (1 +18X/25) where X ≡ 𝜙 c = 𝑃 c /𝜖 c is the ratio of pressure over energy density at NS centers. The scaling of NS compactness thus enables one to readily read off the central trace anomaly Δ c = 1/3 −X directly from the observational data of either the mass-radius or red-shift measurements. Finally, we then demonstrate indeed that the available NS data themselves from recent X-ray and gravitational wave observations can determine model insensitively the trace anomaly as a function of energy density in NS cores, providing a stringent test of existing NS models and a clear guidance in a new direction for further understanding the nature and EOS of supradense matter.
nuclear astrophysics↗
CMS Storage Performance with RNTuple
CMS is transitioning to use ROOT’s new RNTuple data storage format for the files CMS will write in the HL-LHC era. Based on initial tests, CMS expects faster I/O and smaller files compared to the present TTree storage format. This contribution will show a comprehensive performance comparison between RNTuple and TTree I/O using CMS AOD and MiniAOD data formats as test cases for both simulation and collision data corresponding to similar data taking conditions of LHC Run 3. Quantities such as the resulting file size, the memory usage of the I/O components, and the rate of events being read from a file or written to a file will be measured. CMS’ data processing relies heavily on reading files over the local or wide area networks. The file read patterns are important because the latencies have been seen to influence the total production job times. Therefore a study on the file read patterns will be conducted by recording traces of the offset, size, and timestamp of each read request for both RNTuple and TTree. The behavior of network reads will be mimicked by reading local files where artificial latency will be added to the read requests. The effect of different latency values on the job times will be studied.
Jones, Christopher D. [Fermilab]↗
Reading Error Analysis (REA) Software Version 1
This is training presentation for REA (Reading Error Analysis) software. REA is designed for analyzing UGT scope reading errors and for developing reading points optimization algorithms.
97 MATHEMATICS AND COMPUTING↗
From photosynthetic electron flow to gene regulation: redox signal transduction in cyanobacteria
In cyanobacteria, the free-living ancestors of chloroplasts, photosynthesis simultaneously sustains growth and generates reactive oxygen species (ROS) that damage proteins, lipids, and DNA when light capture outpaces carbon fixation. Maintaining redox balance, therefore, requires cells to read photosynthetic electron flow as a signal that continuously tunes gene expression and protein activity. This review traces how these redox signals are transduced to transcription machinery through three routes: membrane-localized sensors, cytoplasmic redox sensors downstream of photosystem I, and ROS generated when electron sinks are saturated. Membrane-bound histidine kinases (two-component systems) relay the redox state of the plastoquinone pool to control photosystem remodeling, pigment biosynthesis, and circadian timing. Cytoplasmic one-component regulators, by contrast, sense redox directly through thiol-disulfide switches, glutathionylation, iron-sulfur clusters, and metal-catalyzed oxidation to control photosystem-cofactor, electron-carrier, and transition-metal homeostasis. Because many of these regulators persist in algal and plant chloroplasts, cyanobacteria illuminate principles of redox control across photosynthetic eukaryotes. Post-transcriptional and translational control further shapes redox-dependent gene expression programs through transcript stability, ribosome assembly, and translation initiation, extending redox regulation beyond transcription to every step of protein synthesis and even activity modulation. Finally, we connect redox regulation to photosynthetic physiology, stress resilience, and the rational engineering of cyanobacteria for sustainable bioproduction.
59 BASIC BIOLOGICAL SCIENCES↗
Film Grain Simulation for Oscilloscope Trace Image Synthesis
Explore the source record for details and available documents.
99 GENERAL AND MISCELLANEOUS↗
Surface Water Quality Data from Beaver-Impacted Streams; Trail Creek and East River, Colorado 2025
This data package contains surface water chemistry measurements collected in 2025 to evaluate how beaver damming and low-tech process-based stream restoration influence water quality and metal mobility in mountainous headwater systems of the Upper Colorado River Basin. Sampling was conducted at Trail Creek (Taylor Park watershed, Colorado), a tributary undergoing restoration through installation of low-tech process-based structures (i.e., beaver dam analogs), and at off-channel beaver ponds within the East River floodplain (East River watershed, Colorado). Samples were collected along longitudinal transects spanning upstream control reaches, beaver-influenced ponded reaches, and downstream segments. Additional samples were collected from near-surface pore waters within a beaver dam seepage face. The dataset includes concentrations of major and trace elements measured by inductively coupled plasma–mass spectrometry (ICP-MS) and inductively coupled plasma–optical emission spectrometry (ICP-OES), major anions measured by ion chromatography (IC), and dissolved organic carbon (DOC; reported as non-purgeable organic carbon, NPOC). Samples were size-fractionated at 0.45 micrometers (µm), 0.22 µm, and 0.02 µm to distinguish particulate (>0.45 µm), colloidal (0.22–0.02 µm), and dissolved (<0.02 µm) fractions. The data package consists of comma-separated value (.csv) files containing tabulated chemical concentration data, sample metadata (site identifiers, geographic coordinates, sampling dates, fraction type), and quality control flags. All files are provided in open, non-proprietary formats that can be accessed using standard data analysis software such as Microsoft Excel, R, Python, MATLAB, or other programs capable of reading .csv files. Units, detection limits, and analytical methods are documented in accompanying metadata files. The dataset is designed to support analyses of (1) how beaver impoundment and restoration structures alter elemental partitioning and transport, (2) the role of iron and organic carbon in mediating trace metal mobility, and (3) reach-scale changes in water quality across restoration gradients. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. Part of this work was performed at SLAC Accelerator Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-76SF00515.
Anions↗
On reading Youden: Learning about the practice of statistics and applied statistical research from a master applied statistician
From reading William John “Jack” Youden’s books and articles, Youden (1900-1971), an analytical chemist, becomes an applied statistician by the time he joins the National Bureau of Standards (NBS) in 1948. Here, this article traces his transition from chemist to applied statistician and what his body of work mostly at NBS (1948-1965) demonstrates about his practice of statistics and the role that applied statistical research plays in it. There is much we can learn from a master applied statistician.
42 ENGINEERING↗
Discovery of additional ancient genome duplications in yeasts
Whole-genome duplication (WGD) has had profound macroevolutionary impacts on diverse lineages, preceding adaptive radiations in vertebrates, teleost fish, and angiosperms. In contrast to the many known ancient WGDs in animals, and especially plants, we are aware of evidence for only four WGDs in fungi. The oldest of these occurred ∼100 million years ago (mya) and is shared by ∼60 extant Saccharomycetales species, including the baker’s yeast Saccharomyces cerevisiae. Notably, this is the only known ancient WGD event in the yeast subphylum Saccharomycotina. The dearth of ancient WGD events in fungi remains a mystery. Some studies have suggested that fungal lineages that experience chromosome and genome duplication quickly go extinct, leaving no trace in the genomic record, while others contend that the lack of known WGDs is due to an absence of data. Under the second hypothesis, additional sampling and deeper sequencing of fungal genomes should lead to the discovery of more WGD events. Coupling hundreds of recently published genomes from nearly every described Saccharomycotina species, with three additional long-read assemblies, we discovered three novel WGD events. Although the functions of retained duplicate genes originating from these events are broad, they bear similarities to the well-known WGD that occurred in the Saccharomycetales. In conclusion, our results suggest that WGD may be a more common evolutionary force in fungi than previously believed.
convergent evolution↗
Post-DTL Beam Delivery
Ensuring that the beam delivered from the upgraded Front-End (FE) meets the Key Performance Parameters (KPPs) at each user facility is critical to the success of the LANSCE Accelerator Modernization Project (LAMP). For a high-intensity, multi-user facility like LANSCE, compliance with beam loss and radiation thresholds is as important as the charge delivered to each target. While early LAMPF/LANSCE operations relied on iterative tuning to minimize losses from beam halo and tail particles, the new FE may introduce different beam distributions and loss modes—making predictive modeling essential. To manage this, the F2E (Front-End to End) effort is developing detailed particle-tracking models that reflect realistic beamline conditions, including halo formation and expected diagnostic readings. These "snapshot" simulations aim to benchmark live machine performance at a given moment. This will help quantify how beam quality from the new FE will propagate downstream through the facility. Only by validating these models can we confidently assess and mitigate the potential impacts of the LAMP FE on beam delivery. Post-DTL, the beam splits to serve five major user facilities. Historically, low-energy beam transport has been modeled using TRACE, and higher-energy sections with TRANSPORT. These have now been unified into MAD-X format and validated with codes such as Elegant, pyOrbit, XSuite, Impact-Z, and HPSim. The primary focus now is on accurate modeling of full particle distributions (including beam halo) as they traverse the accelerator and beamlines to each experimental station. All models are at various stages of validation with empirical data.
43 PARTICLE ACCELERATORS↗
Strings in irrelevant deformations of AdS 3 /CFT 2
We generalize our recent analysis [1] of probe string dynamics to the case of general single-trace TT¯,JT¯ and TJ¯ deformations. We show that in regions in coupling space where the bulk geometry is smooth, the classical trajectories of such strings are smooth and approach the linear dilaton boundary at either the far past or the far future. These trajectories give rise to quantum scattering states with arbitrarily high energies. When the bulk geometry has closed timelike curves (CTC’s), the trajectories are singular for energies above a critical value E c . This singularity occurs in the region with CTC’s, and the value of E c agrees with that read off from the dual boundary theory for all values of the couplings and charges.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Budding yeasts in the subphylum Saccharomycotina Genome sequencing and assembly
Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available. By extracting mitochondrial reads from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades. Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements. As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.
diversity↗
Microbiomes of frozen blood plasma samples reveal potential pathogens in wild birds and rodents
The lack of genomic data on pathogens from wildlife severely limits our ability to track transmission patterns and trace the origins of an outbreak. There are currently millions of wildlife samples in biobanks around the world, including blood samples. Blood has traditionally been viewed as a sterile environment in healthy individuals, but recent evidence suggests that this is not the case, especially for wild animals. Our goal was to determine whether frozen plasma samples can be surveyed using 16S sequencing to provide information about potential hosts for pathogens for a more complete understanding of disease systems. We sequenced blood plasma from wild North American deer mice ( Peromyscus maniculatus ) and American kestrels ( Falco sparverius ) that were cryogenically stored for 7 and 13 years, respectively, and compared two DNA extraction kits. The kestrel samples contained a very high number of reads that could not be identified to phylum compared to the mouse samples. The two kits differed in the phyla and genera that were detected, and the Zymo kit, which is optimized for plasma and serum, produced more high-quality reads for both kestrel and mouse samples. We identified several pathogenic genera, including Mycoplasma, Escherichia-Shigella , and Bartonella . Sequencing blood samples for pathogens could potentially have broad applications for identifying important reservoir hosts for pathogen transmission and provide a reduced set of species on which to follow up.
59 BASIC BIOLOGICAL SCIENCES↗
Memoirs of Mass Accretion: Probing the Edges of Intracluster Light in Simulated Galaxy Clusters
The diffuse starlight extending throughout massive galaxy clusters, known as intracluster light (ICL), has the potential to be read as a memoir of mass accretion: informative, individual, and yet imperfect. Here, we combine dark-matter-only zoom-in simulations from the Symphony suite with the Nimbus “star-tagging” model of the stellar halo to assess how much information about the mass assembly of an individual galaxy cluster can be gleaned from idealized measurements of ICL outskirts. We show that the edges of a cluster’s stellar profile—the primary (R sp⋆,1 ) and secondary (R sp⋆,2 ) stellar “splashback” radii—are sensitive to both continuous mass accretion histories (MAHs) and discrete merger events, making them potentially powerful probes of a cluster’s past. We find that R sp⋆,1 strongly correlates with the cluster’s mass ∼1 dynamical time ago, while R sp⋆,2 traces more recent MAH to a slightly lesser degree. In combination, these features can further distinguish between clusters that have and have not undergone a major merger within the past dynamical time. We use both to predict realistic cluster MAHs with the MultiCAM framework. These outer ICL features are significantly more sensitive to mass accretion and merger histories than the stellar mass gap and halo concentration, and perform comparably to the commonly used X-ray-based tracer of relaxedness, x off . While our analysis is idealized, the relevant ICL features are potentially detectable in next-generation deep imaging of nearby clusters. This work highlights the promise of ICL measurements and lays the groundwork for more detailed forecasts of their power.
79 ASTRONOMY AND ASTROPHYSICS↗
A Bayesian approach to time-domain photonic Doppler velocimetry analysis
Photonic Doppler velocimetry (PDV) is an established technique for measuring the velocities of fast-moving surfaces in high-energy-density experiments. In the standard approach to PDV analysis, the short-time Fourier transform (STFT) is used to generate a spectrogram from which the velocity history of the target is inferred. The user chooses the form, duration, and separation of the window function. Here, in this study, we present a Bayesian approach to infer the velocity directly from the PDV oscilloscope trace, without using the spectrogram for analysis. This is clearly a difficult inference problem due to the highly periodic nature of the data, but we find that with carefully chosen prior distributions for the model parameters, we can accurately recover the injected velocity from synthetic data. We validate this method using PDV data collected at the STAR two-stage light gas gun at Sandia National Laboratories, recovering shock-front velocities in quartz that are consistent with those inferred using the STFT-based approach and are interpolated across regions of low signal-to-noise data. Although this method does not rely on the same user choices as the STFT, we caution that it can be prone to misspecification if the chosen model is not sufficient to capture the velocity behavior. Analysis using posterior predictive checks can be used to establish whether a better model is required, although more complex models come with additional computational cost, often taking more than several hours to converge when sampling the Bayesian posterior. We, therefore, recommend it be viewed as a complementary method to that of the STFT-based approach.
Allison, James R. [First Light Fusion Ltd., Yarnto↗