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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

PeakQC: A Software Tool for Omics-Agnostic Automated Quality Control of Mass Spectrometry Data

Mass spectrometry is broadly employed to study complex molecular mechanisms in various biological and environmental fields, enabling 'omics' research such as proteomics, metabolomics, and lipidomics. As study cohorts grow larger and more complex with dozens to hundreds of samples, the need for robust quality control (QC) measures through automated software tools becomes paramount to ensure the integrity, high quality, and validity of scientific conclusions from downstream analyses and minimize the waste of resources. Since existing QC tools are mostly dedicated to proteomics, automated solutions supporting metabolomics are needed. To address this need, we developed the software PeakQC, a tool for automated QC of MS data that is independent of omics molecular types (i.e., omics-agnostic). It allows automated extraction and inspection of peak metrics of precursor ions (e.g., errors in mass, retention time, arrival time) and supports various instrumentations and acquisition types, from infusion experiments or using liquid chromatography and/or ion mobility spectrometry front-end separations and with/without fragmentation spectra from data-dependent or independent acquisition analyses. Diagnostic plots for fragmentation spectra are also generated. Here, in this paper, we describe and illustrate PeakQC’s functionalities using different representative data sets, demonstrating its utility as a valuable tool for enhancing the quality and reliability of omics mass spectrometry analyses.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Genetic variation associated with adult migration timing in lineages of Steelhead and Chinook Salmon in the Columbia River

Abstract With the discovery of a major effect region (GREB1L, ROCK1) for adult migration timing in genomes of both Chinook Salmon and Steelhead, several subsequent studies have investigated the effect size and distribution of early and late migration alleles among populations in the Columbia River. Here, we synthesize the results of these studies for the major lineages of Chinook Salmon and Steelhead that include highly distinct groups in the interior Columbia River that exhibit atypical life histories from most coastal lineage populations of these two species. Whole‐genome studies with high marker density have provided extensive insight into SNPs most associated with adult migration timing, and suites of markers for each species have been genotyped in large numbers of individuals to further validate phenotypic effects. For Steelhead, the largest phenotypic effect sizes have been observed in the coastal lineage (36% of variation for passage timing at Bonneville Dam; 43% of variation for tributary arrival timing) compared to the inland lineage (7.5% of variation for passage timing at Bonneville Dam; 8.4% of variation for tributary arrival timing) that overwinter in freshwater prior to spawning. For Chinook Salmon, large effect sizes have been observed in all three lineages for multiple adult migration phenotypes (Coastal lineage: percentage of variation of 27.9% for passage timing at Bonneville Dam, 28.7% for arrival timing for spawning; Interior ocean type: percentage of variation of 47.6% for passage timing at Bonneville Dam, 39.6% for tributary arrival timing, 77.9% for arrival timing for spawning; Interior stream type: percentage of variation of 35.3% for passage at Bonneville Dam, 9.8% for tributary arrival timing, 4.7% for arrival timing for spawning). Together, these results have extended our understanding of genetic variation associated with life history diversity in distinct populations of the Columbia River, however, much research remains necessary to determine the causal mechanism for this major effect region on migration timing in these species.

Narum, Shawn R.↗
DOE OSTI2022

Jet timing

The measurement of the arrival time of a particle, such as a lepton, a photon, or a pion, reaching the detector provides valuable information. A similar measurement for a hadronic final state, however, is much more challenging as one has to extract the relevant information from a collection of particles. In this paper, we explore various possibilities in defining the time of a jet through the measurable arrival times of the jet constituents. We find that a definition of jet time based on a transverse momentum weighted sum of the times of the constituents has the best performance. For prompt jets, the performance depends on the jet trajectory. For delayed jets, the performance depends on the trajectory of the jet, the trajectory of the mother particle, and the location of the displaced vertex. Compared to the next-best-performing jet time definition, the transverse momentum weighted sum has roughly a factor of ten times better jet time resolution. We give a detailed discussion of the relevant effects and characterize the full geometrical dependence of the performance. These results highlight the critical importance of using a proper definition of jet time with its corresponding detector-dependent calibration and the exciting possibility of deepening our understanding of jets in the time domain.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Shock and contact interaction with a simple cubic array of particles

Shock-particle interaction is a fundamental pillar of multiphase compressible flows that has been studied at length for many decades. However, little attention has been paid to the interaction of particles with a contact interface that follows a shock in shock tube experiments and applications relating to blast waves. Presently, the phenomenon is studied at the microscale via particle resolved simulations of shock contact systems interacting with a structured array of particles as well as isolated particles. Simulations are conducted at particle volume fractions of 0%, 5%, 10%, 20%, and 40% at three contact Mach numbers. Additionally, the diaphragm position is varied, which controls the timing of the shock arrival time in relation to the contact arrival time. The modification to the drag on these stationary particles by the contact is analyzed and compared to the compressible Maxey–Riley–Gatignol model, which is adequate for the single particle cases but does not account for fluid mediated particle–particle interactions.

Mechanics↗
DOE OSTI2023

A Catalog of Temporally Localized Systematic Deviations in Global Body Wave Travel-Time Measurements

Accurate measurements of the arrival times of seismic waves are crucial for seismological analyses such as robust locations of earthquakes, characterization of seismic sources, and high-fidelity imaging of the Earth’s interior. However, these travel-time measurements can sometimes be contaminated by timing errors at the stations which record this data. In this study, we apply a classical approach, based on identifying time-dependence in measured body wave arrival times, to identify these timing errors in a dataset on the order of 107 individual measurements. We find timing deviations at a subset of the stations in our dataset and document the temporal location, extent, and severity of these errors, finding errors at 83 stations, and impacting ~100,000 measurements. This catalog of deviations may enable future investigators to obtain a more accurate dataset through the implementation of quality control measures to eliminate the contaminated data we have identified.

58 GEOSCIENCES↗
DOE OSTI2025

Self-Supervised T-GCN for Detection of Disturbance and Propagation in Power Grid

Urban power systems increasingly rely on dense sensing to monitor grid reliability, yet disturbance labels are scarce and events are rare. We present a self-supervised spatio-temporal method that detects, localizes, and characterizes grid frequency disturbances across urban areas using only unlabeled data. Our approach trains a tiny Temporal Graph Convolutional Network (T-GCN) to forecast per-site frequency residuals (deviation from 60 Hz). The sensor graph is constructed directly from signals using pre-event Pearson correlation with a cross-correlation lag penalty without geocoding. At inference, node-level anomalies are the model's forecast errors; region-level alarms arise from connected components of high-score nodes. We estimate disturbance propagation by computing per-node arrival times (first persistent exceedance), then fit a planar or time-of-arrival model to obtain direction, speed, and an epicenter proxy. With only three real events collected at decisecond resolution across U.S. cities, we evaluate the T-GCN and report time-to-detect, footprint size, and propagation consistency. We further show that short-window embeddings from the T-GCN's hidden states enable few-shot event-vs-background recognition via a simple prototypical classifier. Despite minimal data and no labels, our system yields fast, spatially coherent detection and interpretable propagation maps, offering a practical, lightweight pathway to city-scale grid resilience analytics.

Niu, Haoran [ORNL] (ORCID:0000000155228297)↗
DOE OSTI2024

Inferring the Focal Depths of Small Earthquakes in Southern California Using Physics-Based Waveform Features

Determining the depths of small crustal earthquakes is challenging in many regions of the world, because most seismic networks are too sparse to resolve trade-offs between depth and origin time with conventional arrival-time methods. Precise and accurate depth estimation is important, because it can help seismologists discriminate between earthquakes and explosions, which is relevant to monitoring nuclear test ban treaties and producing earthquake catalogs that are uncontaminated by mining blasts. Here, we examine the depth sensitivity of several physics-based waveform features for ~8000 earthquakes in southern California that have well-resolved depths from arrival-time inversion. We focus on small earthquakes (2 < M L < 4) recorded at local distances (<150 km), for which depth estimation is especially challenging. We find that differential magnitudes (M w /M L –M c ) are positively correlated with focal depth, implying that coda wave excitation decreases with focal depth. We analyze a simple proxy for relative frequency content, Φ≡log 10 (M 0 )+3log 10 (f c ), and find that source spectra are preferentially enriched in high frequencies, or “blue-shifted,” as focal depth increases. Here, we also find that two spectral amplitude ratios Rg 0.5–2 Hz/Sg 0.5–8 Hz and Pg/Sg at 3–8 Hz decrease as focal depth increases. Using multilinear regression with these features as predictor variables, we develop models that can explain 11%–59% of the variance in depths within 10 subregions and 25% of the depth variance across southern California as a whole. We suggest that incorporating these features into a machine learning workflow could help resolve focal depths in regions that are poorly instrumented and lack large databases of well-located events. Some of the waveform features we evaluate in this study have previously been used as source discriminants, and our results imply that their effectiveness in discrimination is partially because explosions generally occur at shallower depths than earthquakes.

58 GEOSCIENCES↗
DOE OSTI2021

Investigation of a digitizer for the plastic scintillation detectors of time-of-flight mass measurements

A CAEN DT5742 digitizer has been investigated to process the fast signals from the photomultiplier tubes of the time-of-flight detectors for fast ion beams. A test setup consisting of two plastic scintillation detectors and a pulsed laser source provided signals which were recorded by the digitizer and systematically analyzed with different algorithms to derive the amplitude, rise time and arrival time of the detection signal. To obtain the best amplitude and time resolutions, various optimization techniques including peak fitting and signal smoothing, interpolation improvement, and time-walk correction by amplitude and rise time have been performed and compared in detail. Here we compared the time resolutions obtained by three digital algorithms of leading-edge, zero-crossing constant-fraction (ZC-CFD) and direct constant-fraction discriminations. Finally, we found that the best time-of-flight resolution between two PMTs can be achieved as 12 ps by the method using sample minimum for peak location and using the time-walk-resistant ZC-CFD with 4-point interpolation for timing.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Overview of the front-end electronics of CMS HGCal - including readout and powering

The end-cap calorimeters of CMS will be upgraded to a single High Granularity Calorimeter (HG-Cal) for the HL-LHC, including both silicon sensors and scintillator tiles with on-tile SiPMs as active elements. The readout of the active elements is performed by an ASIC (HGCROC in 130 nm CMOS technology) that measures the amplitude and arrival time of the signals. The amplitude is measured over a large dynamic range to allow calibration with single particles and the measurement of TeV showers. The time of arrival of high-energy showers will be measured with a precision of around 30 ps. A second pair of “concentrator” ASICs - ECON-T and ECON-D - takes the data from the HGCROC channels and packages them for transmission via optical links to the off-detector electronics. The ECON-T transmits trigger data at 40 MHz, to form part of the level-1 trigger. The ECON-D transmits concentrated data packets at up to 1 MHz, upon reception of a level-1 trigger signal. In addition to these ASICs, HGCal will use modified versions of common HL-LHC electronics developments, for the power chain and the optical control and readout. The dense nature of the HGCal provides additional challenges for the electronic boards and cabling. In this proceedings the overall HGCal front electronics scheme, including the latest performance of the HGCROC and ECON ASICs is presented.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Utah FORGE - Development of a Reservoir Seismic Velocity Model and Seismic Resolution Study

This is data from and a final report on the development of a 3D velocity model for the larger FORGE area and on the seismic resolution in the stimulated fracture volume at the bottom of well 16A-32. The velocity model was developed using RMS velocities of the seismic reflection survey and seismic velocity logs from borehole measurements as an input model. To improve the accuracy of the model in the shallow subsurface, travel times phase arrivals of the direct propagating P-waves were determined from the seismic reflection data, using PhaseNet, a deep-neural-network-based seismic arrival time picking method. The travel times were subsequently inverted using the input velocity model. The seismic resolution study used borehole and surface seismic sensors as well as the seismicity observed during the April 2022 stimulation experiment to estimate the seismic resolution in the activated fracture reservoir. The data contain a 3D P- and S-wave velocity model for the larger FORGE area.

15 GEOTHERMAL ENERGY↗
DOE OSTI2024

Quantum Random Walk Simulator Using Ultrafast Optical Switches

Quantum random walk processes have many intriguing applications in high energy physics including the simulation of parton shower evolution. We will present the design and initial results of a fiber loop time-bin quantum walk architecture using the hardware platform already in operation at the Fermilab Quantum Network in which the state of the photon is defined by its time-of-arrival. The fiber loop consists of an unbalanced Mach-Zehnder interferometer implemented using an ultrafast electro-optical switch. The input switch controls the photon path within the interferometer, while the output switch will direct the photon back into the interferometer or to single photon detectors to measure the probability distribution of arrival times. Depending on which path the photon takes each pass through the loop, its wave function will interfere on these optical switches similar to quantum interference on a beam splitter. This work is an important step towards utilizing real-world advantages of quantum information protocols to solve problems in high energy physics.

Cameron, Andrew [Fermilab]↗
DOE OSTI2025

Characterization of Gas-Phase Native(-like) Proteins Using Structures for Lossless Ion Manipulations

High-resolution mobility-based ion separations in Structures for Lossless Ion Manipulations (SLIM) have been useful for ion mobility separations for a variety of molecular classes in the gas phase. Here, in this study, we present multipass SLIM separations for gas-phase proteins in their near-native state exhibiting charge-state-dependent arrival time distributions using carbonic anhydrase (29 kDa), alcohol dehydrogenase (148 kDa), and apo-transferrin (79 kDa). The experimental CCS values were obtained from calibration curves for the arrival times of Agilent Tune Mix ions. For multipass separations, the ATDs were converted to CCS values by deconvoluting the multipass arrival times into accurate single-pass values amenable to the single-pass calibration curves. Mass spectra of carbonic anhydrase (CA) showed three different charge states (z = 9+ to 11+). Their corresponding mobility peaks were baseline-separated by using 8-m single-pass separations. When compared to the corresponding drift tube ion mobility (DTIMS) measurements, the CCS values obtained from DTIMS and SLIM were in agreement within experimental error. Single-pass analysis of alcohol dehydrogenase (ADH) exhibits three predominant charge states (z = 23+ to 25+) with mobility overlap between adjacent charge states. The mobility peak resolution for ADH improved with multipass separations (up to 24-m path length). In addition, CCS distributions obtained for charge states z = 16+ to 18+ of apo-transferrin reveal a transition from a compact unimodal form (z = 18+ and 19+) to broader multimodal CCS distributions for z = 16+. For apo-transferrin, 40-m multipass separations were performed allowing for complete isolation of the selected mobility range corresponding to z = 17+, leading to selective isolation of a narrow arrival time window. The extended mobility separations provided minimal alterations to the structure of the proteins, and the experimentally derived CCS values showed minimal change as a function of the separation time or number of passes. Mobility-based ion separations for native-like proteins, using SLIM, open opportunities for native-IMS applications as well as other manipulations enabled by SLIM-like mobility-selective isolation and collection.

charge state distribution↗
DOE OSTI2024

Detecting dark matter substructures on small scales with fast radio bursts

The matter power spectrum is only weakly constrained on subgalactic scales, while physics beyond the Standard Model can leave unique imprints, especially on sub-parsec scales. We propose measuring the arrival-time difference of fast radio bursts (FRBs) along two adjacent sightlines as a new probe to dark matter substructures on scales down to ∼ 1 AU . We discuss two observational scenarios in which it may be possible to place interesting constraints on such models through the monitoring of repeating FRB sources: (i) By sending radio receivers to space to form a baseline of tens of AU or more and measuring the temporal variation of the arrival-time difference between receivers. (ii) By measuring the temporal variation of the arrival-time difference between two lensed images of one strongly lensed repeater. In both scenarios, obtaining interesting constraints requires correlating the voltage time series to measure the radio signal arrival time to sub-nanosecond precision. We find that two radio dishes separated by 20 AU may be sensitive to the enhancement of small-scale structures at ∼ 10 - 8 M ⊙ masses in the QCD axion dark matter scenario, or from an early epoch of matter domination with a reheating temperature up to 60 MeV. Other dark matter models, such as those composed of ∼ 10 - 13 M ⊙ primordial black holes produced during inflation, would also be probed by this method. We further show that a strong lensing situation of multiple images provides an equivalent ∼ 2000 AU ( σ v / 10 3 km s - 1 ) ( δ t / 10 yr ) baseline, for a typical velocity of dark matter substructures σ v and an observational time span δ . This is much more sensitive, but with the uncertainty that intervening decoherence from the interstellar medium may degrade the timing precision, and that spatial variation in the FRB emission spot may result in confounding signals. We show that the lensing magnifications of Type Ia supernovae constrain a similar quantity to such FRB timing, with present limits being equivalent to ruling out the same parameter space that would be probed by a 0.14 AU baseline.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Denoising Seismograms in the Time Domain Using a Deep Learning Model

Deep learning has emerged as a transformative tool for enhancing the extraction of reliable information from seismograms, addressing the increasing demand for precise and efficient seismic data analysis. We introduce an innovative encoder–decoder deep learning model, named WaveDenoiser, designed for noise reduction in the time domain, thereby eliminating the need for spectrogram computations that have been used for existing deep learning tools and significantly improving processing speed. Utilizing the benchmark dataset that is Stanford Earthquake Dataset, we developed three models of varying sizes: base, medium, and large. Notably, the large (referred to as WaveDenoiser) model demonstrated superior performance, achieving a median signal‐to‐noise ratio improvement of 8.8 dB on in‐distribution unseen data (in the same geographic region) and 7.7 dB on out‐distribution unseen data (in a new geographic region), outpacing both the base and medium models. Further evaluation of the WaveDenoiser model revealed a reduction in median arrival‐time errors by 0.02 s for P waves and 0.01 s for S waves when processing waveforms prior to phase picking using PhaseNet on in‐distribution unseen data. When tested on out‐distribution unseen data, the model also effectively reduced the P‐wave median arrival‐time error by 0.02 and 0.01 s in median arrival‐time error for S waves. Importantly, the application of WaveDenoiser resulted in a significant reduction of phase picking outliers by 1.1% to 3.6% for both P and S waves. In addition, we achieved over five times acceleration in processing speed compared with the seisBench implementation of DeepDenoiser. Our findings underscore the potential of WaveDenoiser as a powerful tool for improving seismic data analysis and processing efficiency.

P-waves↗
DOE OSTI2025

Divide and conquer: separating the two probabilities in seismic phase picking

There are two fundamental probabilities in the seismic phase picking process—the probability of the existence of a seismic phase (detection probability) and the probability associated with the phase arrival time estimation (timing probability). The nearly ubiquitous approach in developing deep learning phase picking models is to use a kernel, such as a truncated Gaussian, to mask the labelled phase arrival time and train a segmentation model. Once a model is trained, the times of the peaks in the output are taken as phase arrival times (picks), and the height of the peaks are taken as ‘probability’ of the picks. Here, we show that this ‘probability’ represents neither the detection nor the timing probability because this approach forces the output to follow the shape of the kernel. We introduce an approach using two models to estimate these two distinct probabilities. We use a binary classifier with a calibrated confidence to address the detection probability and a multiclass classifier to obtain a probability mass function to address the timing probability. This new approach can make the deep learning-based phase picking process more interpretable and provide options to logically control seismic monitoring workflows.

58 GEOSCIENCES↗
DOE OSTI2024

The Value of Hyperparameter Optimization in Phase-Picking Neural Networks

The effectiveness of neural networks for picking seismic phase arrival times has been demonstrated through several case studies, and seismic monitoring programs are starting to adopt the technology into their workflows. However, published models were designed and trained using rather arbitrary choices of hyperparameters, limiting their performance. In this study, we use phase picks from both routine and template-matching analyses from multiple regions (Ridgecrest, California; Kilauea, Hawaii; Yellowstone, Wyoming–Montana–Idaho) to test a hyperparameter optimization scheme for phase-picking neural networks and to evaluate their performance. We show that a published model, namely PhaseNet (Zhu and Beroza, 2019), can be simplified and improved with reasonable effort and there are preferred choices of hyperparameters that increase the performance. We also show that models optimized based on the arrival times reported in routine event catalogs consistently perform well when picking arrival times of smaller events, which is crucial for many tasks from microseismicity to explosion monitoring.

58 GEOSCIENCES↗
DOE OSTI2022

Monitoring Fracture Saturation With Internal Seismic Sources and Twin Neural Networks

Seismic coda-wave analysis is a well-developed method for detecting subtle physical changes in complex media by measuring arrival times in the late-arriving energy from multiply scattered or reflected waves. However, a challenge arises when multiply scattered waves are not sufficiently separated in time from the direct arrivals to provide a clear coda wave train. Additional complications for monitoring changes in fracture systems arise when the signals originate from unsynchronized internal sources, such as natural or induced seismicity, from acoustic emission, or from transportable intra-fracture sources (chattering dust), that generate uncontrolled signals that vary in arrival time, amplitude and frequency content. Here, we use a twin neural network (TNN also known as a Siamese neural network) for dimensionality reduction to analyze signals from chattering dust to classify the fluid saturation state of a synthetic fracture system. The TNN with shared weights generates a low-dimensional representation of the data input by minimizing contrastive loss, serving as the input to a multiclass classifier that accurately classifies whether multiple fractures in a fracture system are fully saturated or partially saturated, or whether a change in saturation has occurred in different fractures in the system. Furthermore, these results show that information buried in unresolved codas from uncontrolled sources can be extracted using machine learning to monitor the evolution of fracture systems caused by physical and chemical processes even when the scattered and direct wave fields overlap.

58 GEOSCIENCES↗
DOE OSTI2022

Data for Monitoring Fracture Saturation with Internal Transportable Seismic Sources and Twin Neural Networks

Seismic coda-wave analysis is a well-developed method for detecting subtle physical changes in complex media by measuring arrival times in the late-arriving energy from multiply-scattered or reflected waves. However, a challenge arises when multiply-scattered waves are not sufficiently separated in time from the direct arrivals to provide a clear coda wave train. Additional complications for monitoring changes in fracture systems arise when the signals originate from unsynchronized internal sources, such as natural induced seismicity, from acoustic emission, or from transportable intra-fracture sources (chattering dust), that generate uncontrolled signals that vary in arrival time, amplitude and frequency content. Here, we use a twin neural network (also known as a Siamese neural network) for dimensionality reduction to analyze signals from chattering dust to classify the fluid saturation state of a synthetic fracture system. The twin neural network with shared weights generates a low-dimensional representation of the data input by minimizing contrastive loss, serving as the input to a multiclass classifier that accurately classifies whether multiple fractures in a fracture system are fully saturated or partially saturated, or whether a change in saturation has occurred in different fractures in the system. These results show that information buried in unresolved codas from uncontrolled sources can be extracted using machine learning to monitor the evolution of fracture systems caused by physical and chemical processes even when the scattered and direct wave fields overlap.

58 GEOSCIENCES↗