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DOE OSTI2021

DEIMoS: An Open-Source Tool for Processing High-Dimensional Mass Spectrometry Data

We present DEIMoS: Data Extraction for Integrated Multidimensional Spectrometry, a Python application programming interface and command-line tool for high-dimensional mass spectrometry data analysis workflows, offering ease of development and access to efficient algorithmic implementations. Functionality includes feature detection, feature alignment, collision cross section calibration, isotope detection, and MS/MS spectral deconvolution, with the output comprising detected features aligned across study samples and characterized by mass, CCS, tandem mass spectra, and isotopic signature. Notably, DEIMoS operates on N-dimensional data, largely agnostic to acquisition instrumentation: algorithm implementations utilize all dimensions simultaneously to (i) offer greater separation between features, improving detection sensitivity, (ii) increase alignment/feature matching confidence among datasets, and (iii) mitigate convolution artifacts in tandem mass spectra. We demonstrate DEIMoS with LC-IMS-MS/MS data, demonstrating the advantages of a multidimensional approach in each data processing step.

Colby, Sean M↗

DOE OSTI2022

SpecFIDLER User Manual: Software Version 2.4.0

The Spectroscopic Field Instrument for Detection of Low Energy Radiation (SpecFIDLER) allows response teams to detect and quantify plutonium contamination on the ground. Notional scenarios include dispersion from a weapon accident, or the launch failure of a space probe containing a radioisotope thermoelectric generator. Unlike other instruments, the thin-window sodium iodide detector is sensitive to the low-energy gamma rays emitted by plutonium isotopes. The system supports both mobile survey as well as stationary sampling. This manual provides information about installing, maintaining, and troubleshooting the SpecFIDLER. The scope of this document includes the physical hardware, software for data acquisition, and algorithms for data analysis. Recent changes to the software and algorithms aim to streamline the operation of the system.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

SpecFIDLER User Manual (Software V.2.5.0)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

SpecFIDLER User Manual (Software V.2.6.0)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

SpecFIDLER User Manual (Software V.2.3.0)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Complete resolution across the neodymium/samarium isotopic envelope with a liquid sampling‐atmospheric pressure glow discharge — Orbitrap mass spectrometer

Rationale Nd and Sm isotope ratios play an important role in geological dating and as nuclear forensic signatures; however, the overlap of the respective 144, 148, 150 Nd/Sm isobars requires prior separations to be performed before analysis on typical MS platforms. The work presented here overcomes these isobaric interferences using ultrahigh‐mass resolution to alleviate interference without prior chemical separations. Methods A liquid sampling‐atmospheric pressure glow discharge ion source was coupled to a standard, QExactive Focus Orbitrap mass spectrometer, providing a mass resolution of ~80 k. A Spectroswiss FTMS booster X2 data acquisition package was used to collect extended transients, providing much higher mass resolution; ~230 k and ~600 k are employed here for Nd and Sm isotopes. Results While the standard Orbitrap resolution is far greater than typical “atomic” MS platforms, it was insufficient to alleviate all isobars. The use of a resolution of ~230 k resulted in baseline separation across the entire isotopic envelope for both Nd and Sm. Isotope ratios obtained from Nd:Sm mixtures using high‐resolution were equivalent to those found for individual‐element solutions, while isotope ratios obtained at a resolution of ~80 k (standard for the OEM data system) showed large deviations. Conclusions Use of ultrahigh‐resolution is an attractive alternative to extensive chemical separations to alleviate severe isobaric interferences. Sufficient mass resolution greatly reduces/eliminates the need for sample manipulations (separations) before analysis while reducing costs and total analysis times.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

2010-2012 California Household Travel Survey

The 2010-2012 California Household Travel Survey (CHTS) was administered by the California Department of Transportation, which collected demographic and travel behavior characteristics for residents across the entire state. At the time, it was the largest such regional or statewide survey ever conducted in the United States. Detailed travel behavior information was obtained from more than 42,500 households via multiple data-collection methods, including computer-assisted telephone interviewing, online and mail surveys, wearable (7,574 participants) and in-vehicle (2,910 vehicles) global positioning system devices, and on-board diagnostic sensors that gathered data directly from a vehicle's engine. Details of personal travel behavior were gathered within the region of residence, inter-regionally within the state, and in adjoining states and Mexico. The survey sampling plan was designed to ensure an accurate representation of the entire population of the state. The CHTS included additional features, such as vehicle-acquisition decisions, parking choices, work schedules and flexibility, use of toll lanes/priced facilities, and walk and bicycle trips, to support advanced model development.

1Hz data↗

DOE OSTI2025

Bioelectrochemical crossbar architecture screening platform for extracellular electron transfer

Electroactive microbes can serve as living components in bioelectronic devices, where their unique ability to transfer electrons enables applications in sensing, energy conversion, and synthesis, but they remain challenging to engineer because the bioelectrochemical systems (BESs) used for characterization are low throughput. Here, we present a bioelectrochemical crossbar architecture screening platform (BiCASP) that uses stacked and orthogonally arrayed electrodes to enable individual sample selection for characterization in arrayed formats. This device reports on the current generated by electroactive bacteria on the minute timescale, decreasing the time for data acquisition by several orders of magnitude compared to conventional BESs. This device increases the throughput of screening engineered biological components in cells, identifying mutants of the membrane protein wire MtrA in Shewanella oneidensis that retain the ability to support extracellular electron transfer (EET). BiCASP may be integrated with bioelectronics that need directed evolution of electroactive proteins.

Shewanella↗

DOE OSTI2025

Statistically elucidated responses from low-signal contrast mechanisms in ultrafast electron microscopy

The emergence of ultrafast electron microscopy (UEM) has enabled the discovery of strongly correlated dynamic mechanisms, including electron–phonon coupling, structural phase transitions, thermal transport, and electromagnetic deflection. Most UEM systems operate stroboscopically, meaning that the technique is susceptible to artifacts, mistakes, and misinterpretation of the data due to extensive experimental effort. In contrast to the ultrafast designation, data acquisition is extraordinarily slow because the electron beam has significantly reduced signal compared to traditional transmission electron microscopy due to pulsing the electron beam. Consequently, the sample may drift, tilt, or undergo irreversible structural changes that are independent of the time-resolved dynamics throughout the experimental time frame. Furthermore, these datasets require significant user interpretation that can be problematic when proper controls are not implemented thoroughly. Here, we demonstrate a new algorithm designed to separate ultrafast structural dynamics from long-term artifacts using a LiNbO 3 sample experiencing electrically driven surface acoustic wave propagation. Additionally, we provide examples of the impact of user bias when analyzing the data and provide a methodology, which enables the extraction of time-resolved responses when the image signal is extraordinarily low. Overall, the goal of this publication is to provide methods that validate the experimental results and reduce researcher biases during UEM data interpretation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Video-rate Raman-based metabolic imaging by Airy light-sheet illumination and photon-sparse detection

Despite its massive potential, Raman imaging represents just a modest fraction of all research and clinical microscopy to date. This is due to the ultralow Raman scattering cross-sections of most biomolecules that impose low-light or photon-sparse conditions. Bioimaging under such conditions is suboptimal, as it either results in ultralow frame rates or requires increased levels of irradiance. Here, we overcome this tradeoff by introducing Raman imaging that operates at both video rates and 1,000-fold lower irradiance than state-of-the-art methods. To accomplish this, we deployed a judicially designed Airy light-sheet microscope to efficiently image large specimen regions. Further, we implemented subphoton per pixel image acquisition and reconstruction to confront issues arising from photon sparsity at just millisecond integrations. We demonstrate the versatility of our approach by imaging a variety of samples, including the three-dimensional (3D) metabolic activity of single microbial cells and the underlying cell-to-cell variability. To image such small-scale targets, we again harnessed photon sparsity to increase magnification without a field-of-view penalty, thus, overcoming another key limitation in modern light-sheet microscopy.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Dynamic sparse x-ray nanotomography reveals ionomer hydration mechanism in polymer electrolyte fuel-cell catalyst

Tomographic imaging of time-evolving samples is a challenging yet important task for various research fields. At the nanoscale, current approaches face limitations of measurement speed or resolution due to lengthy acquisitions. We developed a dynamic nanotomography technique based on sparse dynamic imaging and 4D tomography modeling. We demonstrated the technique, using ptychographic x-ray computed tomography as its imaging modality, on resolving the in situ hydration process of polymer electrolyte fuel cell (PEFC) catalyst. The technique provides a 40-time increase in temporal resolution compared to conventional approaches, yielding 28 nm half-period spatial and 12 min temporal resolution. The results allow a quantitative characterization of the water intake process inside PEFC catalysts with nanoscale resolution, which is crucial for understanding their electrochemical mechanisms and optimizing their performance. Our technique enables high-speed operando nanotomography studies and paves the way for wider application of dynamic tomography at the nanoscale.

Science & Technology - Other Topics↗

DOE OSTI2021

Data from: "Warming of alpine tundra enhances belowground production and shifts community towards resource acquisition traits"

This archive contains data used to draw conclusions in “Warming of alpine tundra enhances belowground production and shifts community towards resource acquisition traits”, by Yang et al. 2020. Data were collected on Niwot Ridge, in an alpine meadow within the Alpine Treeline Warming Experiment (ATWE) field sites in Colorado, USA. Samples were also processed in the U.S. Geological Survey Forest and Rangeland Ecosystem Science Center, in Boise, Idaho. File formats in this archive include comma-separated values (.csv), portable document format (.pdf), Microsoft Excel (.xlsx), and two types of geospatial files: keyhole markup language (.kml), and ESRI shapefiles (.shp). Leaf scans are .jpg images, and root scans are .tiff/.tif images.The .csv files can be opened using R, Microsoft Excel, or any simple text-editing software such as TextEdit and Notepad. Microsoft Excel files can be opened using Microsoft Excel, and .pdf files can be opened with Adobe Acrobat Reader, Preview, or other compatible programs. Scanned images can be opened using any photo and/or picture viewing software.The .kml file can be opened using Google Earth and Google Maps, and the shapefiles can be opened by any programs compatible with shapefiles, such as the ArcGIS Desktop suite, and QGIS.------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Measures of belowground net primary productivity (BNPP) are required to understand whether aboveground net primary production (ANPP) changes reflect changes in allocation or are indicative of a whole plant NPP response. Plant functional traits provide a key way to scale from the individual plant to the community level, and provide insight into drivers of NPP responses to environmental change. We used infrared heaters to warm an alpine plant community at Niwot Ridge, Colorado, and applied supplemental water to compensate for soil water loss induced by warming. We measured ANPP, BNPP, and leaf and root functional traits across treatments after 5 years of continuous warming. Community-level ANPP and total NPP (ANPP + BNPP) did not respond to heating or watering, but BNPP increased in response to heating. Heating decreased community-level leaf dry matter content and increased total root length, indicating a shift in strategy from resource conservation to acquisition in response to warming.

13C/12C isotope ratio↗

DOE OSTI2021

Wyoming CarbonSAFE: Advancing Commercialization of Low-Carbon Energy Technologies in Fossil-Rich Wyoming

Wyoming’s Powder River Basin (PRB) is the most prolific coal producer and exporter in the United States and the State of Wyoming’s largest oil-producing basin. In addition to being a leading energy producer, the PRB is the site of research programs whose aim is to develop and integrate low-carbon technologies into existing fossil fuel energy industries. Much of the PRB’s low-carbon research is focused around Dry Fork Station (DFS), which is the newest coal-fired power station in the western US. Currently, DFS hosts five carbon capture projects, including pilot-scale capture projects that utilize different capture technologies and a full front-end engineering and design (FEED) study, a commercial CO 2 pipeline for nearby CO 2 -enhanced oil recovery industry, and is also co-located with the Wyoming Integrated Test Center, which is a host facility for unconventional carbon utilization research (i.e. flue gas carbon-to-products innovations). DFS is also the host site for the Wyoming CarbonSAFE project. Wyoming CarbonSAFE, funded by the Department of Energy/National Energy Technology Laboratory, is a multi-phased program (currently in Phase II) whose core objective is developing and validating storage sites within a complex capable of storing 50 million metric tonnes of CO 2 over a 30 year project period using carbon capture, utilization and storage (CCUS). This paper will provide an overview of the project to-date, showing that CarbonSAFE goals are achievable with respect to geologic, environmental, regulatory, CO 2 source and economic conditions, and why the State of Wyoming offers one of the more favorable environments to advance the commercialization studies. In 2019, the project team designed and completed a ~10,000 foot stratigraphic test well just south of DFS. From this well, the team collected over 600 feet of core, fluid samples from target injection zones, and a full petrophysical log suite. In addition, legacy 2D seismic lines were acquired and a 3D seismic survey was acquired in the fall of 2020. The objective of these field activities has been to identify and characterize target storage reservoirs and associated caprock. This complex has several reservoirs that could meet commercial injection goals, and over 4000 feet of associated caprock. Simulations of site performance suggest that stacked injection provides the most effective storage strategy, and would necessitate several sites within the greater complex to meet final project injection goals. Other work within this project includes the development of a business-case around proximal fields with CO 2 -enhanced oil recovery potential and existing tax credits, assessment of regulatory conditions, including pore space ownership and Class VI injection well permitting requirements, implementation of a robust public outreach Electronic copy available at: https://ssrn.com/abstract=3821220 GHGT-15 McLaughlin 2 program, and surface site characterization activities that have focused on environmental factors. In the PRB and at DFS, the State of Wyoming and other entities have made carbon management a priority of its future energy industry by providing a regulatory and business framework that is favorable to advancing these technologies. These endeavors will become more realistic with the successful implementation of Wyoming CarbonSAFE, and its ability to secure and validate commercial-scale CCUS at the center of Wyoming’s premier low-carbon research efforts.

McLaughlin, Fred↗

DOE OSTI2025

Single-shot electro-optic sampling with arbitrary terahertz polarization

With the recent development of diversity electro-optic sampling (DEOS), significant progress has been made in the range of applicability of single-shot EOS measurements, allowing broadband THz waveforms to be captured in a single shot over large temporal windows. In addition to the decrease in acquisition time compared to standard multishot data acquisition, this technique allows measurements on systems far from equilibrium with large shot-to-shot noise or with irreversible or poorly repeatable dynamics. Although DEOS has been demonstrated and verified for linearly polarized THz waveforms, we investigate the effects resulting from the presence of a secondary polarization component. This imposes new challenges for accurate waveform reconstruction, and opens the opportunity to measure out complex polarization states such as arbitrary elliptically polarized THz field. We demonstrate a single-shot diversity-electro-optic-sampling-based approach to capture both x- and y-THz fields simultaneously with a single (110)-cut EO crystal for THz polarimetry and ellipsometry over a wide range of frequencies.

Lenz, Maximilian [University of California, Los An↗

DOE OSTI2025

Utilization of the LS-APGD microplasma/orbitrap-FTMS booster system for detection and isotopic analysis of neodymium nanoparticles

Detection and isotopic analysis of particle populations has seen rapid growth across several application areas, including environmental analysis, nuclear forensics, and food safety. The ability to characterize the particles' unique elemental and isotopic fingerprints could provide information related to formation, processing history, and transport. Regarding nuclear forensics, isotopic analysis of particles derived from diverse materials is often used as a tool to trace the origin and processing history. Mass spectrometric-based techniques currently used for particle population analysis often suffer from limited mass resolution, particularly when dealing with real-world samples that are affected by isobaric and polyatomic interferences from the matrix. To address these analytical challenges, we propose a novel method utilizing the liquid sampling-atmospheric pressure glow discharge (LS-APGD) microplasma ionization source coupled to an ultrahigh resolution Orbitrap mass spectrometer, further enhanced with the FTMS X2T Booster data acquisition and processing unit. The FTMS Booster enables acquisition of extended transient times of up to 3 s, significantly improving mass resolution, thereby reducing or even eliminating the need for prior separation of isobaric or polyatomic interferences. Additionally, the detection of low-abundance isotopes was improved by increasing the signal-to-noise (S/N) ratio. As proof of concept, this study demonstrates the feasibility of the LS-APGD/Orbitrap-FTMS X2T Booster platform for direct analysis using a suspension of well-characterized ∼120 nm neodymium particles. The quality of the isotope ratios values obtained from a few hundred particles were in good agreement with those obtained from homogeneous ionic solutions. These results highlight the potential of the LS-APGD/Orbitrap platform for rapid, accurate, and interference-resilient isotope ratio analysis of particle populations without the need for dissolution and subsequent chemical separations, offering significant advantages for nuclear forensics, safeguards, and environmental applications. The effort here also points to further paths forward, hopefully towards single particle (SP) analysis using microplasma ionization and the ultrahigh resolving power of the Orbitrap mass analyzer.

FTMS X2T booster↗

DOE OSTI2020

Quantification of Uncoupled Spin Domains in Spin-Abundant Disordered Solids

Materials often contain minor heterogeneous phases that are difficult to characterize yet nonetheless significantly influence important properties. Here we describe a solid-state NMR strategy for quantifying minor heterogenous sample regions containing dilute, essentially uncoupled nuclei in materials where the remaining nuclei experience heteronuclear dipolar couplings. NMR signals from the coupled nuclei are dephased while NMR signals from the uncoupled nuclei can be amplified by one or two orders of magnitude using Carr-Meiboom-Purcell-Gill (CPMG) acquisition. The signal amplification by CPMG can be estimated allowing the concentration of the uncoupled spin regions to be determined even when direct observation of the uncoupled spin NMR signal in a single pulse experiment would require an impractically long duration of signal averaging. We use this method to quantify residual graphitic carbon using 13 C CPMG NMR in poly(carbon monofluoride) samples synthesized by direct fluorination of carbon from various sources. Our detection limit for graphitic carbon in these materials is better than 0.05 mol%. The accuracy of the method is discussed and comparisons to other methods are drawn.

36 MATERIALS SCIENCE↗

DOE OSTI2020

XRFtomo

Based on [1], XRFtomo brings together a variety of image processing tools used for preparing, processing and reconstructing 3D renditions of samples imaged using a synchrotron-based x-ray fluorescence (XRF) microprobe or nanoprobe at the Advanced Photon Source (APS). This software bridges the gap between data acquisition and visualization by providing tools to adjust for misalignment in the imaging process and tools for running reconstructions[2], all with the use of a GUI or command line. XRFtomo accepts .h5 files processed through MAPS[3] and it outputs reconstructed cross-sections, projections, sinograms, metadata, and a configuration file with last-used parameters for rapid processing the next time the program is launched. These images serve as inputs for other 3D visualization software for generating volumetric renderings and animations.

Marin, Fabrico↗

DOE OSTI2025

Integration of LIBS with Machine Learning for Real-Time Monitoring of Feedstock in H 2 Gasification Applications

This project, funded by the U.S. Department of Energy (DOE) – Office of Fossil Energy under Award Number DE-FE0032177, aimed to assess the feasibility of an integrated Laser-Induced Breakdown Spectroscopy (LIBS) system with advanced machine learning (ML) models for real-time characterization and potential control of hydrogen gasifiers running on waste materials as feedstocks. This was a multidisciplinary effort that encompassed the acquisition and standardized analysis of individual and blended feedstocks—comprising biomass, coal waste, and plastic waste, followed by the development of a dynamic LIBS bench system for material sample analysis and development of predictive ML models. Comprehensive laboratory testing enabled the creation of a robust elemental dataset that served as the foundation for ML model training. Techniques such as Random Forest, Gradient Boosting, Support Vector Regression, and Neural Networks were employed to predict key feedstock properties, including higher heating value (HHV), moisture content, thermal conductivity, and ash composition with high accuracy. The results were validated against experimental data and demonstrated strong potential for real-time application in gasifier control systems. The project concluded with a study on the integration of the LIBS+ML approach for gasifier control and a techno-economic analysis of the implementation of the approach into hydrogen (H 2 ) gasification systems. Dissemination of results was carried out at a DOE meeting. This work establishes a scalable framework for automated, in-line feedstock quality assessment, offering significant implications for process optimization and emissions reduction in hydrogen production.

01 COAL, LIGNITE, AND PEAT↗