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DOE OSTI2023

Evaluating Software Tools for Lipid Identification from Ion Mobility Spectrometry–Mass Spectrometry Lipidomics Data

The unambiguous identification of lipids is a critical component of lipidomics studies and greatly impacts the interpretation and significance of analyses as well as the ultimate biological understandings derived from measurements. The level of structural detail that is available for lipid identifications is largely determined by the analytical platform being used. Mass spectrometry (MS) coupled with liquid chromatography (LC) is the predominant combination of analytical techniques used for lipidomics studies, and these methods can provide fairly detailed lipid identification. More recently, ion mobility spectrometry (IMS) has begun to see greater adoption in lipidomics studies thanks to the additional dimension of separation that it provides and the added structural information that can support lipid identification. At present, relatively few software tools are available for IMS-MS lipidomics data analysis, which reflects the still limited adoption of IMS as well as the limited software support. This fact is even more pronounced for isomer identifications, such as the determination of double bond positions or integration with MS-based imaging. In this review, we survey the landscape of software tools that are available for the analysis of IMS-MS-based lipidomics data and we evaluate lipid identifications produced by these tools using open-access data sourced from the peer-reviewed lipidomics literature.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2013

Multiphysics Application Coupling Toolkit

This particular consortium implementation of the software integration infrastructure will, in large part, refactor portions of the Rocstar multiphysics infrastructure. Development of this infrastructure originated at the University of Illinois DOE ASCI Center for Simulation of Advanced Rockets (CSAR) to support the center's massively parallel multiphysics simulation application, Rocstar, and has continued at IllinoisRocstar, a small company formed near the end of the University-based program. IllinoisRocstar is now licensing these new developments as free, open source, in hopes to help improve their own and others' access to infrastructure which can be readily utilized in developing coupled or composite software systems; with particular attention to more rapid production and utilization of multiphysics applications in the HPC environment. There are two major pieces to the consortium implementation, the Application Component Toolkit (ACT), and the Multiphysics Application Coupling Toolkit (MPACT). The current development focus is the ACT, which is (will be) the substrate for MPACT. The ACT itself is built up from the components described in the technical approach. In particular, the ACT has the following major components: 1.The Component Object Manager (COM): The COM package provides encapsulation of user applications, and their data. COM also provides the inter-component function call mechanism. 2.The System Integration Manager (SIM): The SIM package provides constructs and mechanisms for orchestrating composite systems of multiply integrated pieces.

Campbell, MichaelT.↗

DOE OSTI2013

Multiphysics Application Coupling Toolkit

Campbell, Michael T.↗

DOE OSTI2017

Integrating Visualization Applications, such as ParaView, into HEP Software Frameworks for In-situ Event Displays

ParaView is a high performance visualization application not widely used in High Energy Physics (HEP). It is a long standing open source project led by Kitware and involves several Department of Energy (DOE) and Department of Defense (DOD) laboratories. Futhermore, it has been adopted by many DOE supercomputing centers and other sites. ParaView is unique in speed and efficiency by using state-of-the-art techniques developed by the academic visualization community that are often not found in applications written by the HEP community. In-situ visualization of events, where event details are visualized during processing/analysis, is a common task for experiment software frameworks. Kitware supplies Catalyst, a library that enables scientific software to serve visualization objects to client ParaView viewers yielding a real-time event display. Connecting ParaView to the Fermilab art framework will be described and the capabilities it brings discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

bifacial_radiance: a python package for modeling bifacial solar photovoltaic systems

bifacial_radiance is a national-laboratory-developed, community-supported, open-source toolkit that provides a set of functions and classes for simulating the performance of bifacial photovoltaic (PV) systems. (Bifacial PV modules collect light on the front as well as the rear side.) bifacial_radiance automates calculations of PV system layout and performance to use along with the popular ray-tracing software tool RADIANCE (Ward, 1994). Specific algorithms include design and layout of PV modules, reflective ground surfaces, shading obstructions, and irradiance calculations throughout the system, among others. bifacial_radiance is an important component of a growing ecosystem of open-source tools for solar energy (William F Holmgren et al., 2018).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

OpenSAMPL: An Open Source Library for Timing and Synchronization Measurements and Analytics

Today's power grid operators are implementing timing and synchronization solutions that provide resilience to Global Navigation Satellite System (GNSS) vulnerabilities. These vendor-specific solutions often come with additional software applications that are designed to monitor that vendor's synchronization performance data. However, resilient timing architectures often resulting in multi-vendor solutions, including approaches that blend terrestrial clocks with space-based subscription services. In such an environment, collecting, analyzing, and visualizing data from a variety of sources within a single platform was heretofore not possible. To address this need, the US Department of Energy's Center for Alternative Synchronization and Timing (CAST) developed OpenSAMPL, the Open Synchronized Analytics and Monitoring Platform, an open-source Python framework for processing, loading, and observing clock measurement data from distributed devices. OpenSAMPL enables the ingestion of diverse clock-probe sources into a scalable time-series database and applies robust analytics. OpenSAMPL currently supports two vendor data pipelines, and will be extended to more in the near future, enabling seamless monitoring of a variety of timing and synchronization devices in a common environment.

Grant, Josh [ORNL] (ORCID:0000000163475060)↗

DOE OSTI2022

Data on Cu- and Ni-Si-Mn-rich solute clustering in a neutron irradiated austenitic stainless steel

The data presented in this article is supplementary to the research article “Phase instabilities in austenitic steels during particle bombardment at high and low dose rates” (Levine et al.). Needle-shaped samples were prepared with focused ion beam milling from a 304L stainless steel that was irradiated with fast neutrons (E 0.1 MeV) in the BOR-60 reactor at 318 °C to 47.5 dpa. Atom probe tomography (APT) experiments in voltage mode were then conducted on a Cameca LEAP 5000X HR. Atom position, range, and mass spectrum files after reconstruction with Cameca’s IVAS software are included. Cu- and Ni-Si-Mn-rich solute nanoclusters were identified and analyzed using the Open Source Characterization of APT Reconstructions (OSCAR) program. Python code for OSCAR, information on the program’s underlying algorithm, and sample output files are provided. A proximity histogram of a Ni-Si-Mn-rich cluster and a 1D density/solute concentration profile of a Cu-rich cluster are given to demonstrate OSCAR’s analytical functionalities. The provided APT dataset is valuable for benchmarking phase instabilities in neutron-irradiated austenitic stainless steels that occur at high doses. The OSCAR program can be reused to process other APT data sets where solute nanoclustering is of interest.

42 ENGINEERING↗

DOE OSTI2023

LipidOz enables automated elucidation of lipid carbon–carbon double bond positions from ozone-induced dissociation mass spectrometry data

Lipids play essential roles in many biological processes and disease pathology, but unambiguous identification of lipids is complicated by the presence of multiple isomeric species differing by fatty acyl chain length, stereospecifically numbered (sn) position, and position/stereochemistry of double bonds. Conventional liquid chromatography-mass spectrometry (LC-MS/MS) analyses enable the determination of fatty acyl chain lengths (and in some cases sn position) and number of double bonds, but not carbon-carbon double bond positions. Ozone-induced dissociation (OzID) is a gas-phase oxidation reaction that produces characteristic fragments from lipids containing double bonds. OzID can be incorporated into ion mobility spectrometry (IMS)-MS instruments for the structural characterization of lipids, including additional isomer separation and confident assignment of double bond positions. The complexity and repetitive nature of OzID data analysis and lack of software tool support have limited the application of OzID for routine lipidomics studies. Here, we present an open-source Python tool, LipidOz, for the automated determination of lipid double bond positions from OzID-IMS-MS data, which employs a combination of traditional automation and deep learning approaches. Our results demonstrate the ability of LipidOz to robustly assign double bond positions for lipid standard mixtures and complex lipid extracts, enabling practical application of OzID for future lipidomics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Improvements to PVWatts for Fixed and One-Axis Tracking Systems

This work presents improvements to the widely used NREL PVWatts photovoltaic system energy model to improve modeling accuracy for typical fixed and one axis system designs. The aim is to calculate losses in the PV system assuming typical modern system design practices, while maintaining simplicity by keeping the required set of input parameters small. These improvements allow users to more credibly and quickly evaluate competing system designs in early stage feasibility. Common submodels for module cover, spectral, snow, tracker, transformer, plant controller, and self-shading losses, in addition to a bifacial gain option, are incorporated into the PVWatts model, and are shown to improve PVWatts' system performance prediction capabilities without major impact to ease of use. We anticipate including these improvements in a future release of NREL's open source PVWatts code, and some of the features may become available in the System Advisor Model (SAM) desktop software as well as the popular PVWatts web application.

14 SOLAR ENERGY↗

DOE OSTI2018

Simple utility for creat1n1 and signing SSL certificates.

Generally, for encrypted communication to occur, a root trust must be established (usually In the form of a certificate authority) and used to sign communlcatln1 component's certificates that are used to perform encryption. This process ls rather Involved In a number of manual steps with arcane command syntax. Certlpy wraps the standard Python PyOpenSSL library to simplify the calls to create the above mentioned PKI (public key infrastructure) with both a command line and programming Interface. Certlpy was orlglnally created to automate and manage PKI within the open source JupyterHub project so that It could be deployed safely In Uvennore Computing. JupyterHub Is a collection of software components enabling Interactive python notebooks and reproducible science. To ensure secure communication throuahout, Certlpy signs and Issues certs to each component: enabling encryption and authentication (SSL).

Mendoza, Thomas↗

DOE OSTI2023

pnnl/projection_ntk

This is a repository for work conducted in our research paper we would like to make open source. The main features are that we forked another open source library and added functionality that enabled us to compute neural-kernel objects using random vector projection software for both computer vision and large language text models. The new features are specifically code that enables the calculation of objects we define and refer to as the projection pseudo neural tangent kernel and the projection trace neural tangent kernel; both of which are approximations of the empirical neural tangent kernel. The software that computes the projections themselves are not part of the invention, but are necessarily tied to our software and licensed via MIT license, and BSD 2 license.

Georgiev, Kristian↗

DOE OSTI2026

Vegetation classification map and covariates associated with NEON AOP survey, East River, CO 2018

This package includes geospatial data layers developed to investigate how environmental gradients—specifically topography and near-surface soil properties—drive the spatial arrangement of dominant plant communities in mountainous watersheds. The geospatial products, which support the analysis of these ecological relationships, are derived from airborne hyperspectral and LiDAR datasets acquired by the National Ecological Observatory Network (NEON) Airborne Observation Platform (AOP), in conjunction with an extensive ground field campaign conducted in summer 2018. This work is part of the DOE Watershed Function Science Focus Area (SFA) and features geospatial datasets developed based on observations and ground data collected at East River, Colorado, in collaboration with the National Ecological Observatory Network (NEON) Airborne Observation Platform (AOP) survey in June 2018. Classification Map: - Classification Map (PNG, GeoTIFF): Derived from hyperspectral and LiDAR airborne data using a machine learning approach. - Class Code Mapper (CSV): Associates pixel values with corresponding vegetation/non-vegetation classes. - Classification Reference Data (CSV): Reference data used in the machine learning procedure. LiDAR-Derived Products: - Topographical Metrics (GeoTIFFs): Elevation, slope, curvature, TWI, TPI, solar insolation, and canopy height model (CHM), smoothed with a 5x5 pixel window. Vegetation Indices: - GeoTIFFs of NDVI, NDNI, NDWI: Vegetation indices derived from hyperspectral data. Urban Masks: - Urban Mask (GeoTIFF): Applied to the mapping to convert bare soil classes to urban classes. Software Compatibility: GeoTIFFs: Can be visualized with GIS software or libraries that support GeoTIFF images. CSV Files: Can be opened with any software that handles comma-separated values. The FLMD file provides details and links to the source datasets used to derive the products. The manuscript (in the Method session) provides details on how each product was derived. 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. Update on 2026-03-25: Since the original dataset publication date of 02/28/2020, this package has a new classification map derived by an improved methodology. This update also includes additional ground data that improved the representation of some of the communities. See the methods for further details on what has changed between versions.

2018 NEON and 2025 CHESS Campaigns↗

DOE OSTI2022

Prototyping a self-learning digital twin platform for personalized treatment in melanoma patients (Final Report)

We completed all the Milestones and disseminated results at the 2021 Computational Approaches for Cancer Workshop (CAFCW21) at the SuperComputing21 conference. As part of Milestone 1, we developed and implemented a prototype digital twin of metastatic melanoma patients, performed quality checks on the code and released it as open source. The work has directly driven major grant proposals by the team on computational digital twins and supporting software infrastructure, including a successful fellowship application by the PI. Work was lead by Paul Macklin (Contact PI, Indiana University), in collaboration with Ilya Shmulevich (PI, Institute for Systems Biology), Tina Hernandez-Boussard (PI, Stanford Univ.), Jeffrey Bryan (Co-I, University of Missouri), Snigdhansu Chatterjee (Co-I, University of Minnesota), and Mohammad Fallahi-Sichani (Co-I, U. of Virginia). Postdoctoral student Heber L. Rocha (Macklin lab, IU) performed intensive computational work, in collaboration with Senior Research Scientist Boris Aguilar (Shmulevich lab, ISB).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Simulations of Quantum Circuits with Approximate Noise using qsim and Cirq

We introduce multinode quantum trajectory simulations with qsim, an open source high performance simulator of quantum circuits. qsim can be used as a backend of Cirq, a Python software library for writing quantum circuits. We present a novel delayed inner product algorithm for quantum trajectories which can result in an order of magnitude speedup for low noise simulation. We also provide tools to use this framework in Google Cloud Platform, with high performance virtual machines in a single mode or multinode setting. Multinode configurations are well suited to simulate noisy quantum circuits with quantum trajectories. Finally, we introduce an approximate noise model for Google's experimental quantum computing platform and compare the results of noisy simulations with experiments for several quantum algorithms on Google's Quantum Computing Service.

Isakov, Sergei V.↗

DOE OSTI2022

pvlib python 2022 Update

Summary of updates to pvlib-python in the time since the 2019 PVPMC workshop, covering pvlib versions 0.7.0 to 0.9.2.

MATHEMATICS AND COMPUTING,SOLAR ENERGY↗

DOE OSTI2024

Initial Development of Fusion Magnet Simulation Capabilities for Performance and Safety Evaluation Using the MOOSE Framework

Fusion energy holds the promise of being a transformative technology as a carbon-neutral, sustainable source of energy. Whole device modeling and the development of fusion digital twins will be increasingly important for emerging fusion device concepts at both national laboratories and within the commercial fusion industry. However, meeting the challenge of whole device modeling of fusion energy devices requires robust, multiphysics, multiscale modeling and simulation technologies capable of running on large-scale supercomputers. Detailed analysis of individual systems at-scale is also required to ensure safe and efficient operation as well as provide the safety basis for future device designs and licensing activities. In a tokamak, toroidal and poloidal magnets confine and shape the fusion plasma to promote the fusion reaction. High plasma temperatures and high magnetic field requirements in modern design concepts (leading to high amounts of energy stored within each magnet) impose electrical, thermal, and mechanical loads on the magnet components, which in turn impacts the safety considerations of the magnet and their supporting systems. Idaho National Laboratory (INL) has a history of working in this space, including development and benchmarking of the Magnetic System Circuitry Analysis Program (MSCAP) and Magnet Arcing (MAGARC) codes to study magnet quench events; notably, MAGARC was used to study quenching during the ITER Engineering Design Activity. However, these legacy codes and capabilities are not parallel and scalable, and new tools are required for future advances in this area, which leads to the INL-developed Multiphysics Object-Oriented Simulation Environment (MOOSE) framework. Developed originally for fission reactor systems under United States Department of Energy, Office of Nuclear Energy modeling and simulation programs, the MOOSE framework has been well-suited to multiscale, multiphysics modeling and simulation needs for nuclear systems. The framework is open-source, well-tested, under continuous development and deployment, and developed to a Nuclear Quality Assurance, Level 1 software quality standard. MOOSE has also been used in the fusion space previously in several projects: INL’s Tritium Migration Analysis Program, Version 8 (TMAP8) for tritium migration, UK Atomic Energy Authority’s A Unified Resource for OpenMC (fusion) Reactor Applications (AURORA) code for fusion thermo-mechanical and neutronics analysis, and Argonne National Laboratory’s Cardinal for high-fidelity computational fluid dynamics and neutronics. However, to model superconducting magnets, several MOOSE enhancements are required: additions to the current MOOSE electromagnetic capabilities, new material libraries for superconductors of interest (such as YBCO), as well as fusion-specific models for thermo-mechanics. This talk will discuss initial development activities to build these capabilities in MOOSE, focusing on initial validation and benchmarking activities. Proposed coupling workflows and future work to support the simulation of fusion magnets and magnet structural assemblies for performance and safety evaluation in MOOSE will also be discussed.

70 - PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Dynamic Building Load Control to Facilitate High Penetration of Solar Photovoltaic Generation (Final Technical Report)

Solar photovoltaic (PV) resources are the most common form of distributed generation in residential and commercial customer premises within electric distribution networks. A higher penetration of PV generation in distribution circuits will impose challenges on maintaining service voltages within the range of industry standards, power quality, and power flow. Buildings consume 74% of the electricity produced in the United States, and a significant portion of the building load is dispatchable, making them responsive to electrical grid needs. Oak Ridge National Laboratory—in collaboration with Southern Company; the University of Tennessee, Knoxville; and the Georgia Institute of Technology—is examining the PV integration issues in distribution-level electrical grids and developing integrated demand-side control and communication systems to enable responsive loads. The proposed responsive loads mechanism performs renewable generation following to increase the penetration of solar PV within each feeder. The specific objectives of this project are to (1) examine distribution-level PV integration scenarios to understand requirements, (2) undertake an end-to-end simulation-based design of a distributed control strategy of loads geographically near the PV generation asset to minimize the effect on the distribution feeder, (3) deploy and demonstrate the control technology developed in partnership with utilities, and (4) perform a scalability analysis at the utility scale. This 3-year integrated project aims to develop, demonstrate, and validate demand-side control technology to enable increased the penetration of renewables while mitigating challenges that arise due to their intermittency. Activities in Budget Period (BP) 1 focused on a literature review and the formal design of a control system for integrating local distribution with generation and loads. The team used modeling and simulation to evaluate the impact of varying buildings loads, variable PV generation, and power flow dynamics on the distribution circuit. The dynamic models developed in BP 1 were used in BP 2 to develop a model-based control design and a test bed. The test bed has enabled the simulation-based testing and comparison of different control designs and formulations applied to different configurations of the distribution grid, PVs, and building loads. The control approaches developed in BP 2 were implemented in BP 3 in the form of hardware deployed at the Central Baptist Church (CBC) in Knoxville, Tennessee, for testing and evaluation. The outcome of this project was the development and demonstration of open-source, low-cost, low-touch sensing and control retrofits to distributed PV generation and building loads that, in a coordinated fashion, provide the load-shaping response needed to integrate high levels of renewable penetration. This research addresses the target metrics by dynamically controlling a load with solar generation variability to minimize the extent of two-way power flow, enhance reliability, facilitate high PV penetration (>100% of peak load in a line segment), and generate scalable software and hardware solutions adaptable to any penetration levels. The research and development activities are focused and designed to be impactful within the relevant 2020 targets time frame.An accurate open-source integration simulation framework for end-to-end control design was developed and deployed at the CBC facility for testing and evaluation. This final report provides a detailed review of the technical results achieved during this 3-year integrated project. A novel spectral analysis of PV data is demonstrated to derive the requirements of the control design. A detailed simulation-based analysis of PV integration at increasing penetration levels is presented using 1 year of PV data to demonstrate the impact on the distribution circuits. Two different control strategies were developed and demonstrated via simulation to track variable PV generation with adaptive load dispatch. The report concludes with a summary of accomplishments and recommendations for a path forward.

14 SOLAR ENERGY↗

DOE OSTI2022

Hybrid Solid Oxide Fuel Cell/Gas Turbine Model Development for Electric Aviation

A thermodynamic model was developed and validated to analyze a high-performance solid oxide fuel cell and gas turbine (SOFC-GT) hybrid power system for electric aviation. This study used a process simulation software package (ProMax) to study the role of SOFC design and operation on the feasibility and performance of the hybrid system. Standard modules, including compressor, turbine, heat exchanger, reforming reactor, and combustor were used from the ProMax tool suite while a custom module was created to simulate the SOFC stack. The model used an SOFC test data set as an input. Additional SOFC stack performance effects, such as pressure, temperature, and utilization of air and fuel, were added from open source data. System performance predictors were SOFC specific power, fuel-to-electricity conversion efficiency, and hybrid system efficiency. Using these input data and predictors, a static thermodynamic performance model was created that can be modified for different system configurations and operating conditions. Prior to creating the final aircraft performance model, initial demonstration models were developed to validate output results. We used the NASA SOFC model as a benchmark, which was created with their Numerical Propulsion System Simulator (NPSS) software framework. Our output results matched within 1% of both the NASA model and open source SOFC performance data. With confidence gained in the accuracy of this model, a 1-MW SOFC-GT hybrid power system was constructed for an aircraft propulsion concept. Overall hybrid system efficiencies of > 75% FTE were observed during standard 36,000 feet cruise flight conditions.

30 DIRECT ENERGY CONVERSION↗