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DOE OSTI2019

P-Mart: Interactive Analysis of Ion Abundance Global Proteomics Data

The use of mass-spectrometry-based techniques for global protein profiling of biomedical or environmental experiments has become a major focus in research centered on biomarker discovery; however, one of the most important issues recently highlighted in the new era of omics data generation is the ability to perform analyses in a robust and reproducible manner. This has been hypothesized to be one of the issues hindering the ability of clinical proteomics to successfully identify clinical diagnostic and prognostic biomarkers of disease. P-Mart (https://pmart.labworks.org) is an interactive web-based software environment that enables domain scientists to perform quality-control processing, statistics, and exploration of large-complex proteomics data sets without requiring statistical programming. P-Mart is developed in a manner that allows researchers to perform analyses via a series of modules, explore the results using interactive visualization, and finalize the analyses with a collection of output files documenting all stages of the analysis and a report to allow reproduction of the analysis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Many-Body Adaptive Configuration Interaction Suite (MACIS) v0.1.0

The Many-Body Adaptive Configuration Interaction Suite (MACIS) is a modern C++ software infrastructure for the development of selected-configuration interaction (sCI) methods for the fermionic many-body problem in quantum chemistry and materials science. MACIS provides a high-performance, parallel implementation of the Adaptive Sampling Configuration Interaction (ASCI) method as related solvers such as self-consistent orbital optimization and the evaluation of excited states and spectral functions. Unlike existing sCI software, MACIS is developed as a modular software infrastructure which allows it to exist both as a standalone sCI solver and as a library to integrate into existing many-body codes. This modularity allows MACIS to be quickly extensible, including its integration with other sCI methods and high-performance solvers.

Williams-Young, David↗

DOE OSTI2018

nbodykit: An Open-source, Massively Parallel Toolkit for Large-scale Structure

We present nbodykit, an open-source, massively parallel Python toolkit for analyzing large-scale structure (LSS) data. Using Python bindings of the Message Passing Interface, we provide parallel implementations of many commonly used algorithms in LSS. nbodykit is both an interactive and scalable piece of scientific software, performing well in a supercomputing environment while still taking advantage of the interactive tools provided by the Python ecosystem. Existing functionality includes estimators of the power spectrum, two- and three-point correlation functions, a friends-of-friends grouping algorithm, mock catalog creation via the halo occupation distribution technique, and approximate N-body simulations via the FastPM scheme. The package also provides a set of distributed data containers, insulated from the algorithms themselves, that enables nbodykit to provide a unified treatment of both simulation and observational data sets. nbodykit can be easily deployed in a high-performance computing environment, overcoming some of the traditional difficulties of using Python on supercomputers. We provide performance benchmarks illustrating the scalability of the software. The modular, component-based approach of nbodykit allows researchers to easily build complex applications using its tools. The package is extensively documented at http://nbodykit.readthedocs.io, which also includes an interactive set of example recipes for new users to explore. As open-source software, we hope nbodykit provides a common framework for the community to use and develop in confronting the analysis challenges of future LSS surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

DEEPER: An Intergrated Platform for Deeper Roots

Crops with deeper roots would have multiple benefits, including better drought tolerance, reduced requirement for nitrogen fertilizer, and better sequestration of atmospheric CO 2 . DEEPER is an integrated platform of phenomic, genomic, and in silico technologies to generate maize lines with deeper roots. DEEPER is: LEADER (Leaf Elemental Accumulation from Deep Roots) is a breakthrough technology to nondestructively measure rooting depth by using the plant itself as a sensor. LEADER uses handheld X-ray Fluorescence spectrometry to quantify foliar accumulation of elements that are differentially distributed in the soil profile. LEADER is nondestructive and is orders of magnitude cheaper, faster, and more precise than any competing assay of rooting depth in the field. LEADER is able to distinguish deep-rooted from shallow-rooted maize lines in the field without the need for costly and noisy soil coring. RootRobot/DIRT3D, to automatically phenotype root architecture in any field, combining RootRobot, a mechatronics platform to excavate, clean, section, and image mature root crowns, with DIRT3D, software to quantify architectural traits in 3D. Anatomics, a high-throughput platform to phenotype root anatomy, combining LAT 2.0, a technology for 3D imaging of root anatomy and composition, with RootScan3D, software to automatically extract 3D anatomical and cell wall composition metrics from LAT 2.0 output. Using this platform we discovered two novel root traits, parenchyma cell wall thickness and multiseriate cortical sclerenchyma, that improve rooting depth and drought tolerance in maize and wheat. OpenSimRoot/Deep, software to simulate root interaction with hard subsoils. Using this platform we discovered novel concepts regarding how to increase crop rooting depth by modulating how individual root axes respond to hard soil. DeepGenes, a toolkit of genes, parent lines, and genomic selection strategies to enable breeding hybrids with deeper roots. We discovered 3 novel root genes that increase rooting depth in maize and wheat. DEEPER discovered novel root phenotypes for deeper rooting, and delivered validated ideotypes for deeper-rooted maize; novel technologies to rapidly assess root depth, root architecture and anatomy in field-grown plants; novel software tools for root modeling and 3D image analysis of root architecture and anatomy; and validated genes and genomic selection models to deploy traits for deeper rooting in maize breeding. Each DEEPER technology is transformative in its own right, and exceeds existing technologies. They are mutually synergistic, deployable for field-grown plants, and are ready for application. The phenotyping and modeling technologies are readily applicable to many crops, and genetic leads in maize may have utility in other grasses. Taken as a whole they represent a transformative platform to develop deeper-rooted crops, with greater drought tolerance, reduced fertilizer requirement, and greater carbon sequestration.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

SaS4D Home Team UI (SaS4D-HT-UI) v1.0

The SaS4D Home Team UI (python) is a software to view and interact with different layers of 3D geometries and generate usable MCNP-style input file. It is used by the remote Home Team in providing guidance and building models of environments they have never seen in order to investigate threat object discovered at the Working Point. The UI visualizes a colorized mesh, a semantic labelled mesh, and a semantic labelled probability mesh of the scanned environment as well as individual water-tight material-labeled objects. It allows for manipulation and re-processing of these objects. The UI also contains measurement tools to facilitate better MCNP input file generation in the manipulation workflow. The software is a key component in ensuring the Home Team has prompt awareness of the Working Point.

Chen, Xin↗

DOE OSTI2025

Neutrino interaction vertex reconstruction in DUNE with Pandora deep learning

The Pandora Software Development Kit and algorithm libraries perform reconstruction of neutrino interactions in liquid argon time projection chamber detectors. Pandora is the primary event reconstruction software used at the Deep Underground Neutrino Experiment, which will operate four large-scale liquid argon time projection chambers at the far detector site in South Dakota, producing high-resolution images of charged particles emerging from neutrino interactions. While these high-resolution images provide excellent opportunities for physics, the complex topologies require sophisticated pattern recognition capabilities to interpret signals from the detectors as physically meaningful objects that form the inputs to physics analyses. A critical component is the identification of the neutrino interaction vertex. Subsequent reconstruction algorithms use this location to identify the individual primary particles and ensure they each result in a separate reconstructed particle. A new vertex-finding procedure described in this article integrates a U-ResNet neural network performing hit-level classification into the multi-algorithm approach used by Pandora to identify the neutrino interaction vertex. The machine learning solution is seamlessly integrated into a chain of pattern-recognition algorithms. The technique substantially outperforms the previous BDT-based solution, with a more than 20% increase in the efficiency of sub-1 cm vertex reconstruction across all neutrino flavours.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Aquifer Injection Modeling (AIM) Toolbox User Guide

The Aquifer Injection Modeling Toolbox (“AIM Toolbox”) software was developed by the Pacific Northwest National Laboratory (PNNL) for the U.S. Environmental Protection Agency’s (EPA) to provide a collection of analytical solutions suitable for evaluating the potential extent of the area impacted by subsurface injection operations. Subsurface injection operations are regulated under the EPA’s Underground Injection Control (UIC) program and are typically related to oil/gas development, waste disposal, or subsurface mining or storage. The analytical algorithms provided in the AIM Toolbox each have different approaches/assumptions/focus with respect to the nature and processes in subsurface and the nature of the injection operations. Collectively the set of analysis algorithms provides a broader evaluation of the area that can potentially be impacted by an injection operation. By providing estimates for the injectate plume extent, the software supports technical aspects of planning, evaluation, and overseeing injection activities. That is, the results help assess when further regulatory controls (e.g., monitoring, reporting) may be required and, in the case of disposal into an underground source of drinking water, the extent of the impacted area would require exemption from protection under the Safe Drinking Water Act. The AIM Toolbox software is available as a single-page web application, providing an interface to provide the necessary inputs, and both chart and map panes for visualizing the results. This User Guide describes the AIM Toolbox software, information required, user interactions, and the underlying basis of the calculations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Aquifer Injection Modeling (AIM) Toolbox User Guide

58 GEOSCIENCES↗

DOE OSTI2021

Dynamic Probabilistic Safety Assessment Studies for Advanced Reactor Using RAVEN

Probabilistic Safety Assessment (PSA) is used extensively to evaluate the risks associated with complex engineering systems like Nuclear Power Plants (NPPs). Current PSA models are based on the Event-Tree/Fault-Tree (ET/FT) methodology. ET and FT models are static and are based on Boolean logic approaches. In the past, concerns have been raised in the literature regarding the capability of the traditional static modelling approaches to adequately account for the impact of process, hardware, software, firmware and human interactions on the stochastic system behaviour. To overcome the limitations of the traditional approach to PSA, several dynamic PSA methodologies have been proposed. One of the dynamic PSA methodologies used for dynamic evaluations is Dynamic Event Tree (DET) framework which can be used to assess the impact of the parameter variability and scenario dynamics on the PSA model for the initiating event. The DET framework couples the stochastic model (number of component/trains that start on demand, operator action timing, etc.) with a Thermal-Hydraulic (TH) model of the plant. This paper explores the use of DET along with a case study on advanced reactor. The initiating event selected for the study was Class IV power supply failure event. The TH analysis considering uncertainty in various parameters was performed using RELAP5 and Reactor Analysis and Virtual control ENvironment (RAVEN) tool. Based on the uncertainty analysis, it is concluded that the peak clad temperatures (PCT) are within the limits in all the code runs implying a high-degree of safety margin. However, variation in time to reach the PCT was observed among the code runs and the mean time to reach the PCT was found to be around 8590sec (approximately 2.4 hours). Hence, sufficient time margin is available for human intervention and the operator might have a relatively stress-free state during such an accident scenario. Due to the static nature of the traditional PSA models, the safety margin available was lesser, whereas, with the help of dynamic PSA models, one can demonstrate that the actual available safety margin is more in the present case study and is valuable input from the design point of view.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2016

Real-Time Considerations for Rugged Embedded Systems

This chapter introduces the characterizing aspects of embedded systems, and discusses the specific features that a designer should address to an embedded system “rugged”, i.e., able to operate reliably in harsh environments. The chapter addresses both the hardware and the less obvious software aspect. After presenting a current list of certifications for ruggedization, the chapters present a case study that focuses on the interaction of the hardware and software layers in reactive real-time system. In particular, it shows how the use of fast FPGA prototyping could provide insights on unexpected factors that influence the performance and thus responsiveness to events of a scheduling algorithm for multiprocessor systems that manages both periodic, hard real-time task, and aperiodic tasks. The main lesson is that to make the system “rugged”, a designer should consider these issues by, for example, overprovisioning resources and/or computation capabilities.

FPGA↗

DOE OSTI2026

MCP-eGridGPT (MCP-Enabled Chatbot with Electrical Power System Analysis and Interactive Visualization Tool) [SWR-25-126]

This software is an advanced chatbot system that integrates the Model Context Protocol (MCP) to provide intelligent electrical power system analysis and automated visualization generation. The system enables users to interact with complex electrical engineering tools through natural language, automatically analyzes power system data for voltage violations and grid health assessment, and generates professional interactive HTML dashboards and reports. Key features include dynamic tool discovery from MCP servers, multi-LLM provider support, intelligent data interpretation using large language models, automated chart generation, and a web-based interface for real-time analysis. The software bridges sophisticated electrical engineering analysis with user-friendly interfaces, making power system diagnostics accessible through conversational AI.

Choi, Seong [National Laboratory of the Rockies (N↗

DOE OSTI2021

ARGONNE DISCOVERY CLOUD SDK&CLI

Software development kit and command-line interface to access and interact with the Argonne Discovery Cloud platform. Software code can be used to enable software developers to add their own integrates into their own software.

AVARCA, ANTHONY↗

DOE OSTI2021

Software Verification and Validation Guidelines for Non-Linear Soil-Structure Interaction Analysis

Seismic analysis of structures, systems, and components (SSCs), including the consideration of soil-structure interaction (SSI) effects, is an important and required step in the design and licensing of nuclear power plant SSCs important to safety. Historically, the SSI analysis of nuclear structures has been performed using equivalent linear methods. However, there has been considerable industry investment in alternative seismic design and analysis approaches to reduce the construction cost of new reactors. Toward that goal and in alignment with the Licensing Modernization Project (LMP) framework, the Nuclear Regulatory Commission (US NRC) has proposed a risk-informed, performance-based approach to seismic design that allows inelastic response in those nuclear plant structures not required for confinement. As a complementary effort, reactor designers are exploring nonlinear seismic analysis methods to optimize structural designs and reduce construction costs.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2015

A Software Developer’s Guide to Informal Evaluation of Visual Analytics Environments Using VAST Challenge Information

The VAST Challenge has been a popular venue for academic and industry participants for over ten years. Many participants comment that the majority of their time in preparing VAST Challenge entries is discovering elements in their software environments that need to be redesigned in order to solve the given task. Fortunately, there is no need to wait until the VAST Challenge is announced to test out software systems. The Visual Analytics Benchmark Repository contains all past VAST Challenge tasks, data, solutions and submissions. This paper details the various types of evaluations that may be conducted using the Repository information. In this paper we describe how developers can do informal evaluations of various aspects of their visual analytics environments using VAST Challenge information. Aspects that can be evaluated include the appropriateness of the software for various tasks, the various data types and formats that can be accommodated, the effectiveness and efficiency of the process supported by the software, and the intuitiveness of the visualizations and interactions. Researchers can compare their visualizations and interactions to those submitted to determine novelty. In addition, the paper provides pointers to various guidelines that software teams can use to evaluate the usability of their software. While these evaluations are not a replacement for formal evaluation methods, this information can be extremely useful during the development of visual analytics environments.

evaluation↗

DOE OSTI2016

Systematic network assessment of the carcinogenic activities of cadmium

Cadmium has been defined as type I carcinogen for humans, but the underlying mechanisms of its carcinogenic activity and its influence on protein-protein interactions in cells are not fully elucidated. The aim of the current study was to evaluate, systematically, the carcinogenic activity of cadmium with systems biology approaches. From a literature search of 209 studies that performed with cellular models, 208 proteins influenced by cadmium exposure were identified. All of these were assessed by Western blotting and were recognized as key nodes in network analyses. The protein-protein functional interaction networks were constructed with NetBox software and visualized with Cytoscape software. These cadmium-rewired genes were used to construct a scale-free, highly connected biological protein interaction network with 850 nodes and 8770 edges. Of the network, nine key modules were identified and 60 key signaling pathways, including the estrogen, RAS, PI3K-Akt, NF-κB, HIF-1α, Jak-STAT, and TGF-β signaling pathways, were significantly enriched. With breast cancer, colorectal and prostate cancer cellular models, we validated the key node genes in the network that had been previously reported or inferred form the network by Western blotting methods, including STAT3, JNK, p38, SMAD2/3, P65, AKT1, and HIF-1α. These results suggested the established network was robust and provided a systematic view of the carcinogenic activities of cadmium in human. - Highlights: • A cadmium-influenced network with 850 nodes and 8770 edges was established. • The cadmium-rewired gene network was scale-free and highly connected. • Nine modules were identified, and 60 key signaling pathways related to cadmium-induced carcinogenesis were found. • Key mediators in the network were validated in multiple cellular models.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

KinCat v.1.0

SAND2024-02099O The software is designed to allow researchers to perform kinetic Monte Carlo (KMC) simulations of catalytic reactions on a 2D lattice. The code is written efficiently to run on a variety of shared memory computing architectures (e.g. GPU, multi-core) and to natively express the full complexity of lateral interactions on reaction rates. The software allows researchers to perform KMC simulations of catalytic reactions on a 2D lattice. It uses parallel shared-memory computing architectures to reduce run-times and allows for simultaneous simulation of multiple independent runs. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Najm, Habib↗

DOE OSTI2022

A Case Study of the Glycoside Hydrolase Enzyme Mechanism Using an Automated QM-Cluster Model Building Toolkit

Glycoside hydrolase enzymes are important for hydrolyzing the β-1,4 glycosidic bond in polysaccharides for deconstruction of carbohydrates. The two-step retaining reaction mechanism of Glycoside Hydrolase Family 7 (GH7) was explored with different sized QM-cluster models built by the Residue Interaction Network ResidUe Selector (RINRUS) software using both the wild-type protein and its E217Q mutant. The first step is the glycosylation, in which the acidic residue 217 donates a proton to the glycosidic oxygen leading to bond cleavage. In the subsequent deglycosylation step, one water molecule migrates into the active site and attacks the anomeric carbon. Residue interaction-based QM-cluster models lead to reliable structural and energetic results for proposed glycoside hydrolase mechanisms. The free energies of activation for glycosylation in the largest QM-cluster models were predicted to be 19.5 and 31.4 kcal mol −1 for the wild-type protein and its E217Q mutant, which agree with experimental trends that mutation of the acidic residue Glu217 to Gln will slow down the reaction; and are higher in free energy than the deglycosylation transition states (13.8 and 25.5 kcal mol −1 for the wild-type protein and its mutant, respectively). For the mutated protein, glycosylation led to a low-energy product. This thermodynamic sink may correspond to the intermediate state which was isolated in the X-ray crystal structure. Hence, the glycosylation is validated to be the rate-limiting step in both the wild-type and mutated enzyme.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

A review of microgrid development in the United States – A decade of progress on policies, demonstrations, controls, and software tools

Microgrids have become increasingly popular in the United States. Supported by favorable federal and local policies, microgrid projects can provide greater energy stability and resilience within a project site or community. Here, we review major federal, state, and utility-level policies driving microgrid development in the United States. Representative U.S. demonstration projects are selected and their technical characteristics and non-technical features are introduced. The paper discusses trends in the technology development of microgrid systems as well as microgrid control methods and interactions within the electricity market. Software tools for microgrid design, planning, and performance analysis are illustrated with each tool's core capability. Finally, the paper summarizes the successes and lessons learned during the recent expansion of the U.S. microgrid industry that may serve as a reference for other countries developing their own microgrid industries.

24 POWER TRANSMISSION AND DISTRIBUTION↗