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DOE OSTI2022

Research Software Engineering at Oak Ridge National Laboratory

Research software engineers (RSE) play a vital role in scientific discoveries worldwide. They lead the core development of the applications, libraries, and tools that enable today’s supercomputers to process the vast volumes of data generated from the world’s most extensive and complicated scientific instruments and facilities. This article describes the mission, culture, and practices of RSE teams at Oak Ridge National Laboratory (ORNL), including their team dynamics and composition, work ethics, standard practices, and ever-evolving skill sets vital to pursuing scientific innovations and implementing novel ideas. We describe the lessons learned from specific activities that contribute to shaping the identity and growth of RSE roles at ORNL. Lastly, we provide our view for the near future on effective strategies for establishing, leading, and nurturing RSE teams and building a thriving community in collaboration with science stakeholders.

42 ENGINEERING↗

DOE OSTI2026

Coupling of high-resolution mass spectrometer and photosynthesis system for comprehensive leaf volatile metabolite profiling

Background Leaf-level biogenic volatile organic compounds (BVOCs) emissions represent a major source of organic gases in the atmosphere, influencing both climate and air quality. These emissions are strongly driven by environmental perturbations, which affect individual plant- to ecosystem-level processes. Uncovering all the BVOCs and understanding how their emissions respond to altered environmental conditions provide critical insights into vegetation-driven changes in atmospheric chemistry. We developed a tandem instrumentation setup that integrates a proton transfer reaction time-of-flight mass spectrometer (PTR-ToF-MS) with parts-per-trillion detection limits and a photosynthetic infrared gas exchange system for the untargeted survey of all the BVOCs. This novel system enables simultaneous, real-time monitoring of BVOC emissions and photosynthetic parameters at the leaf level, offering new opportunities to disentangle the physiological and environmental drivers of VOC release. Furthermore, we established the VOC Analysis and Processing Optimization Resource (VAPOR), an open-access software tool designed for rapid data post-processing and the analysis of the variability of hundreds of BVOCs. We assessed the performance of the tandem system under varying background conditions, using standard gas mixtures and a range of environmental factors. Results Blank emissions were substantially lower for major BVOCs (e.g., isoprene) compared to those observed in plant emissions. Despite this, the observation of background-level VOCs highlights the importance of routinely acquiring and accounting for blank measurements in analyses using the coupled instrumentation. Introduction of known VOC concentrations to the system demonstrated a linear response across different compounds with varying molecular compositions, indicating minimal gas loss regardless of chemical moieties within the coupled instrumentation. We applied the optimized system to investigate the physiological mechanisms driving BVOC emissions across different genotypes of poplar and pennycress. The high mass resolution capabilities of the PTR-ToF-MS, coupled with comprehensive VAPOR-driven data analysis, enabled the identification of several important BVOCs, including methanol and methanethiol; these BVOCs displayed substantial variation across pennycress genotypes and showed concentrations ~ 100–350% higher than the blank. Moreover, isoprene emissions varied significantly among poplar genotypes grown in different potting media. Conclusions Tandem instrumentation offers a powerful tool for profiling volatile molecular markers and elucidating their genetic and environmental underpinnings. This approach enhances our ability to predict BVOC emissions in response to genotype by environmental interactions and contributes to a deeper understanding of vegetation responses to environmental changes.

Biogenic volatile organic compounds↗

DOE OSTI2024

Building a Simplistic Automatic Extruder: Instrument Development Opportunities for the Laboratory

This work presents an automatic extruder as a research experience for undergraduate students. The system offers a user-friendly approach to preparing vesicles, such as liposomes or polymersomes, with a defined size and polydispersity properties crucial for research in biology and macromolecules. It comprises two syringe pumps connected by a membrane filter. The setup is controlled by software. Compared to manual extrusion, this automated system provides advantages, such as precisely controlled variables. The project describes a tool to enhance undergraduate learning in science and engineering laboratories. Building an automatic extruder serves as a simplified model of a complex industrial process. It offers a clear advantage: automating a well-understood manual extrusion process. To make this project accessible, it is broken down into three manageable tasks: software development, hardware assembly, and testing procedures. This breakdown describes the software created, the hardware components used, and the testing procedures conducted for this project. All project data, including software code, testing data, and procedures, are freely available online. This allows undergraduate students to not only begin their own projects but also contribute to this educational instrument’s ongoing development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

SWARM: Reimagining scientific workflow management systems in a distributed world

Modern scientific workflows process massive amounts of data from diverse instruments and sensors, leveraging geographically distributed, heterogeneous compute and storage resources—from leadership-class systems to edge devices—connected by high-performance networks. The diversity of resources introduces challenges in harnessing their full potential, with resilience issues arising across applications, system software, networks, storage, and hardware. Today, workflow management systems (WMS) coordinate the execution of computation and data management tasks across target resources. However, WMS’s centralized nature makes them vulnerable to faults and scalability issues that may result in failures of entire computational campaigns. In conclusion, this paper introduces a novel agentic framework for workflow management, fully distributing and decentralizing the WMS functions and modeling them as swarm intelligence agents infused with advanced artificial intelligence solutions and traditional distributed computing algorithms that can make coordinated decisions in the presence of failures of the underlying cyberinfrastructure.

Swarm intelligence↗

DOE OSTI2020

CBRN Situational Awareness Tools for the Modern Age

CBRN Situational awareness (SA) should be a key operational requirement in the CNI area of discussion, not only for the “boots-on-the-ground” warfighter, but at a strategic level. For example, maneuver plans will need to be developed for contamination avoidance and battlefield survivability. Large datasets from instruments dispersed across the battlefield will thus need to be collected and processed into a holistic assessment of the radiological hazard. From there, hazard maps then must be distributed at the tactical level, all while continuing to effectively engage a peer adversary. This vision represents a network of sensors, software tools, data processing algorithms, communications suites, and common operational picture (COP) platforms working in concert to inform warfighters and command echelons alike of evolving nuclear and radiological hazards. This complex system-of-systems and the ultimate goal of effective engagement in a nuclear or radiological-hazard battlefield can be achieved through pursuit of improvement in collaborative SA tools.

Becker, Eric M.↗

DOE OSTI2021

Community-Driven Methods for Open and Reproducible Software Tools for Analyzing Datasets from Atom Probe Microscopy

Atom probe tomography, and related methods, probe the three-dimensional architecture of a material. The software tools that microscopists use, and how these tools are connected into workflows, makes a substantial contribution to the accuracy and precision of such a material characterization experiment. Typically, we adapt methods from other communities like mathematics, data science, computational geometry, artificial intelligence, or scientific computing. We also realize that improving on research data management is a challenge when it comes to align with the FAIR data stewardship principles. Faced with this global challenge, we are convinced that collaborating is useful. Here, we report the results and challenges with an inter-laboratory call for developing test cases for several types of atom probe software tools. The results support why defining detailed recipes of software workflows and sharing these recipes is necessary and rewarding: Open source tools and (meta)data exchange can help to make our day-to-day data processing tasks become more efficient, the training of new users and knowledge transfer become easier, and assist us with automated quantification of uncertainties to gain access to substantiated results.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Computational tools and algorithms for ion mobility spectrometry-mass spectrometry

Ion mobility spectrometry-mass spectrometry (IMS-MS or IM-MS) is a powerful analytical technique that combines the gas-phase separation capabilities of IM with the identification and quantification capabilities of MS. IM-MS can differentiate molecules with indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, and contaminant ions). The importance of this analytical technique is reflected by a staged increase in the number of applications for molecular characterization across a variety of fields, from different MS-based omics (proteomics, metabolomics, lipidomics, etc.) to the structural characterization of glycans, organic matter, proteins, and macromolecular complexes. With the increasing application of IM-MS there is a pressing need for effective and accessible computational tools. This article presents an overview of the most recent free and open-source software tools specifically tailored for the analysis and interpretation of data derived from IM-MS instrumentation. This review enumerates these tools and outlines their main algorithmic approaches, while highlighting representative applications across different fields. Finally, a discussion of current limitations and expectable improvements is presented.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Hardware-accelerated inference for real-time gravitational-wave astronomy

The field of transient astronomy has seen a revolution with the first gravitational-wave detections and the arrival of multi-messenger observations they enabled. Transformed by the first detection of binary black hole and binary neutron star mergers, computational demands in gravitational-wave astronomy are expected to grow by at least a factor of two over the next five years as the global network of kilometer-scale interferometers are brought to design sensitivity. With the increase in detector sensitivity, real-time delivery of gravitational-wave alerts will become increasingly important as an enabler of multi-messenger followup. In this work, we report a novel implementation and deployment of deep learning inference for real-time gravitational-wave data denoising and astrophysical source identification. This is accomplished using a generic Inference-as-a-Service model that is capable of adapting to the future needs of gravitational-wave data analysis. Overall, our implementation allows seamless incorporation of hardware accelerators and also enables the use of commercial or private (dedicated) as-a-service computing. Based on our results, we propose a paradigm shift in low-latency and offline computing in gravitational-wave astronomy. Such a shift can address key challenges in peak-usage, scalability and reliability, and provide a data analysis platform particularly optimized for deep learning applications. The achieved sub-millisecond scale latency will also be relevant for any machine learning-based real-time control systems that may be invoked in the operation of near-future and next generation ground-based laser interferometers, as well as the front-end collection, distribution and processing of data from such instruments.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

PyTREES

PyTREES (Python tool for Training/Testing Robust Explainable Ensembles on Spectra) is software that implements a data-driven approach to predicting the amount of specific oxides present in materials samples of laser-induced breakdown spectroscopy (LIBS); such as from the ChemCam instrument suite onboard the NASA Curiosity rover. PyTREES is designed to input LIBS data in the format provided by the ChemCam team [1]. PyTREES then applies appropriate pre-processing to this data [2], and implements several regression methods for predicting oxides from spectra. The regression methods include: ensemble methods (random forest, extra trees, and gradient boosting regression) and blended submodels using the “double blending” technique. PyTREES additionally implements methods for quantifying the importance of features in regression model: (1) mean decrease in impurity (MDI) and (2) permutation importance to investigate the wavelengths used by the regression methods. [1] Gasda et al. (2021). Spectrochim Acta B, 181, 106223. [2] Clegg et al. (2017). Spectrochim Acta B , 129, 64–85.

Oyen, Diane↗

DOE OSTI2025

FY25 Mid-Year Report: FNCL Enhancements Implementation

During the first half of FY25 the FNCL team has made consistent progress toward the completion of our project goals. The FNCL prototype panel design has been successfully applied to a fully instrumented 3-panel system which is actively under construction. The FNCL Demonstrator System contains solid scintillators instrumented with SiPMs, which operate on an updated CAEN digitizer, requires no high-voltage, and has a smaller overall footprint. The onboard software will include the LLNL-developed GMM-PSD signal processing. Later this year the system will be experimentally tested alongside the baseline FNCL instrument at LLNLs ISSA facility. In addition to a full systems test, the performance of a DD generator for active interrogation measurements compared to the standard AmLi source will be established for both systems. The data collected at the ISSA facility will be used to experimentally validate the FNCL-Fast Isotopic Fuel Assay’s (FIFA) capability to measure U-235 loading and to predict gadolinium poison content with passive interrogation. The FNCL-FIFA modal was benchmarked with simulation-based data and a user-friendly GUI was added earlier this year. Three separate codes have been submitted to the LLNL ESW system for review prior to their transfers. These include the Predictive Modeling Response toolkit, GMM-PSD firmware beta version, and the FNCL-FIFA analysis package with GUI and user documentation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Enhancing Discoverability and Management of Atmospheric Data at Scale: Solutions from the ARM Data Center

The Atmospheric Radiation Measurement (ARM) is a multi-laboratory and multi-institutional U.S. Department of Energy (DOE) Office of Science National User Facility. The ARM Data Center (ADC), located at Oak Ridge National Laboratory, collects, archives, and shares vast atmospheric data crucial for climate research. The ADC manages over 7 PB of data from 460 instruments worldwide, processing it into more than 11,000 diverse data products using the Network Common Data Form (NetCDF) for machine-independent accessibility. The primary challenge addressed in this paper is the efficient management and distribution of vast and diverse datasets essential for the climate research community, enhancing accessibility through advanced tools like Data Discovery. The ADC has developed advanced infrastructure and software architecture to handle the continuous influx of heterogeneous data to enhance data discoverability, resulting in increased scientific collaboration. In 2023, users from over 34 countries downloaded and utilized ARM data, resulting in 1,455 publications. The ADC’s efforts have significantly improved the discoverability and usability of atmospheric data, fostering extensive scientific research and collaboration. This paper details the solutions implemented by the ADC team for efficient data discovery and distribution, and it demonstrates ARM’s capability of staging processed data for scientific analysis.

Shah, Chirag [ORNL] (ORCID:0000000203145737)↗

DOE OSTI2026

Data & Code from Phoenix CPPP Phase 2 Analysis

This data and code package supports the analysis presented in “Beyond Surface Cooling: Comprehensive Field Assessment of Reflective Pavement Thermal Performance in Phoenix, Arizona” and provides fully reproducible workflows for evaluating the thermal performance of cool pavement treatments in a hot urban environment. The dataset integrates multi-modal field measurements collected across residential and nonresidential settings, including mobile air temperature traverses, stationary air temperature monitoring, residential mean radiant temperature (MRT) measurements, subsurface temperature profiles, and controlled testbed observations. The data package contains raw and processed datasets in comma-separated value (CSV) format, accompanying metadata files describing site characteristics and measurement protocols, and R scripts (.R files) used for data cleaning, time synchronization, spatial and temporal matching, quality control filtering, statistical comparison, and figure generation. All analyses were conducted using R (version ≥ 4.2.0) with commonly available packages (e.g., tidyverse, lubridate, data.table, ggplot2). No proprietary software is required to reproduce results. Field campaigns were designed to quantify the effects of high-reflectance pavement coatings on surface temperature, near-surface air temperature, subsurface heat propagation, and radiative heat exposure. Temporal alignment procedures include standardized timestamp conversion and nearest-neighbor matching of high-frequency sensor measurements to stop-based metadata within defined tolerance windows to ensure comparability across instruments. The workflows generate summary statistics, treatment–control contrasts, depth-dependent thermal gradients, and time-series visualizations used in the associated publication. By integrating mobile, stationary, radiative, and subsurface measurements within a unified and transparent processing framework, this package enables comprehensive evaluation of cool pavement performance across multiple thermal exposure pathways and supports reuse in future urban heat mitigation and climate resilience studies.

AIR TEMPERATURE↗

DOE OSTI2020

Magnetic Microcalorimeter (MMC) Gamma-Ray Detectors with Ultra-High Energy Resolution. Comprehensive Technology Readiness Assessment

Magnetic Microcalorimeter (MMC) gamma ray detectors have demonstrated very high energy resolution of 38 eV FWHM for gamma ray energies below 100 keV. This is an order or magnitude better than conventional HPGe detector and can remove most line-overlap problems in NDA by gamma spectroscopy below ~130 keV. Unlike superconducting transition edge sensors (TESs), MMCs have a reproducible and almost perfectly linear response, which greatly simplifies adding spectra from different detector pixels and reduces systematic errors in quantitative assays. The instrument is currently at TRL-5 but could advance to TRL-6 by improving the signal processing software and using the system for the quantitative analysis of a safeguards sample provided by e.g. the IAEA. Making MMC detectors commercially viable and used more widely then depends on making the technology more reliable, specifically by increasing the device uniformity and yield, and by developing commercial software. This situation is often only half-jokingly referred to as the “valley of death” and could be addressed though the SBIR program. Our collaborators at STAR Cryoelectronics LLC are well qualified to further advance MMC development, and XIA LLC is well-positioned to develop the data acquisition system and write the software for MMC readout. In addition, the advance to TRL-6 would be desirable to increase the visibility and showcase the value of MMC spectrometers, e.g. by placing one of them into the Safeguards Analytical Laboratory (SAL) at the IAEA, whose NDA experts have recently started to show interest in cryogenic detector technology. As a result of this LCP, we also now have an instrument at LLNL that we will use for various applications of MMCs in nuclear safeguards and science. We are confident that as the number of high-profile results increases, so will the interest in and commercial viability of this technology.

42 ENGINEERING↗

DOE OSTI2020

Magnetic Microcalorimeter (MMC) Gamma-Ray Detectors with Ultra-High Energy Resolution. Comprehensive Technology Readiness Assessment

42 ENGINEERING↗

DOE OSTI2024

DENNIS: a design and analysis tool for dynamic material x-ray diffraction experiments

We present DENNIS (Diffraction Experiment desigN and aNalysiS): a graphical software tool useful for the design and analysis of dynamic x-ray diffraction experiments, such as those performed on the Z Pulsed Power Facility, Thor Pulsed Power Generator, and Dynamic Compression Sector (DCS) of the Advanced Photon Source. DENNIS provides rapid powder and single-crystal diffraction pattern predictions and powder diffraction pattern image integration in three-dimensional geometries. Additional features include crystallographic information file reading, image processing, and synthetic diffraction pattern image generation. We overview the software's capabilities, detail the prediction and integration methodologies, and provide example implementations on Z and DCS experiments.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

A data analysis method to rapidly characterize gallium concentration in plutonium matrices using LIBS

The processing of actinide samples is a complex and costly endeavor that requires compositional analysis at various stages. Laser-induced breakdown spectroscopy (LIBS) has been used to analyze actinide-containing samples in many nuclear applications including waste management, fuel processing and forensics. The LIBS spectrum obtained from actinide materials are generally extremely complex, exhibiting many thousands of strong emission lines. This makes it difficult to identify other elements within the sample of interest, given the rich and dominant actinide spectrum. Here, in this article, we describe a recent effort to identify and quantify impurities and alloying constituents in plutonium matrices using a hand-held LIBS instrument that is used to rapidly and efficiently measure an emission spectrum from a material sample. We tabulate the emission line positions and intensities of plutonium. We report the development of machine-learning software that can identify gallium and quantify its concentration in plutonium matrices. This work has the potential to provide a rapid and nearly non-destructive technique that allows more confidence in characterizing the composition of materials that are present within complex actinide associated targets. We describe how our LIBS measurements and data analysis methods have successfully quantified the gallium concentration in a variety of samples.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Operation of the ATLAS trigger system in Run 2

The ATLAS experiment at the Large Hadron Collider employs a two-level trigger system to record data at an average rate of 1 kHz from physics collisions, starting from an initial bunch crossing rate of 40 MHz. During the LHC Run 2 (2015–2018), the ATLAS trigger system operated successfully with excellent performance and flexibility by adapting to the various run conditions encountered and has been vital for the ATLAS Run-2 physics programme. For proton-proton running, approximately 1500 individual event selections were included in a trigger menu which specified the physics signatures and selection algorithms used for the data-taking, and the allocated event rate and bandwidth. The trigger menu must reflect the physics goals for a given data collection period, taking into account the instantaneous luminosity of the LHC and limitations from the ATLAS detector readout, online processing farm, and offline storage. This document discusses the operation of the ATLAS trigger system during the nominal proton-proton data collection in Run 2 with examples of special data-taking runs. Aspects of software validation, evolution of the trigger selection algorithms during Run 2, monitoring of the trigger system and data quality as well as trigger configuration are presented.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

Improved Beam Loss Accounting with Fast Data Acquisition (DAQ) Chassis

Identifying the source of beam loss events in the CE-BAF accelerator can be a challenging task. However, with our new prototype system, this task becomes more effi-cient. The system, developed in the fall of 2022, utilizes a dispersive beam position monitor (BPM) and the exist-ing switched electrode electronics BPM hardware. Previ-ously a commercial off-the-shelf data acquisition (DAQ) system was employed to capture BPM wire signals at a sample rate of 20 kS/s. The fast shutdown signal triggered the system, which disables the beam at the injector. Analysis of beam position and energy variation before a beam loss event was used to determine if the beam loss event was associated with an energy transient. The proto-type system, implemented using National Instruments hardware and LabVIEW® software, relied on a software trigger. Manual post-processing was required to ascertain whether the fault was due to an un-tripped cavity with a gradient or phase transient. This work focuses on deploying a Fast DAQ Chassis to monitor BPM hardware in real time and during beam loss events. This system was originally developed and in-stalled in CEBAF to monitor the time-domain RF control signals in the legacy analog RF systems. This technology was leveraged to also monitor BPM signals. As the new system employs a hardware trigger, developing tools to automatically identify faults linked to energy transients unrelated to cavity faults will be straightforward. This paper will discuss the project's initial updates, underlin-ing the crucial role of each member of our team in this achievement

Tiskumara, J.↗