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At least 505 records · Page 28

minervachem

Minervachem is a tool for cheminformatics and machine learning in chemistry. It includes both algorithms from existing literature and algorithms which we have developed. Its features center around two main themes: molecular representations and algorithms, both for molecular machine learning. It provides a scikit-learn transformer interface for molecular featurization and an estimator interface for machine learning algorithms. It also provides visualization tools for explaining machine learning predictions. We aim to continue developing this software to improve its performance and usability and expand its capabilities within the realm of molecular machine learning, cheminformatics, and visualization.

Lubbers, Nicholas↗

pnnl/QASMBench

A low-level OpenQASM benchmark suite for NISQ evaluation and simulation. Please see our paper for details. n this repository you will find a low-level and light-weighted benchmark suite based on IBM OpenQASM language (see spec). It collects commonly seen quantum algorithms and routines from various domains including chemistry, simulation, linear algebra, searching, optimization, arithmetic, machine learning, fault tolerance, cryptography, etc. QASMBench trades-off between generality and usability, covering the number of qubits ranging from 2 to 60K, and the circuit depth from 4 to 12M

Li, Ang↗

Python Robust Phase Estimation (PyRPE)

Robust Phase Estimation (RPE) is a quantum algorithm to determine the relative phases of eigenstates of a unitary operator. This code implements the classical portion of the RPE algorithm, useful both in simulation (e.g., Sandia's pyGSTi or IBM's Qiskit simulators) and on actual quantum hardware (e.g., IBM's Qiskit Quantum Experience). It additionally implements improvements in these dependent software packages, for both required core function of the RPE and improved usability. SAND2020-12547 M 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.

Russo, Antonio↗

BUTTER-Clarifier [SWR-23-61]

This repository contains a python package of neural network interpretability techniques (interpretability) and a keras callback to easily compute and capture data related to these techniques (values metrics) during training. It was developed to be used with NREL's BUTTER Deep Learning Experimental Framework, but does not depend on this framework and may be useful to projects outside of this framework. The vision for this codebase is to collect algorithms for explainable artificial intelligence (XAI) in a single framework that is easy to use, easy to read, and can be expand upon. Here, we package XAI algorithms into a module called "metrics", which are implemented as python functions. The return type of a metric is typically a dictionary holding data of multiple data types, such as real values and numpy matrices. Callbacks and any other connector code is provided as necessary in a separate module to make these metrics more easily usable. This project depends on Tensorflow's Keras API, although it would be nice to try and support multiple backends one day. Related to: https://github.com/NREL/BUTTER-Empirical-Deep-Learning-Experimental-Framework

Perr-Sauer, Jordan↗

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↗

yihuishen/metabolic_flux_regulation

Metabolic efficiency profoundly influences organismal fitness. Heterotrophs, from yeast to mammals, derive usable energy primarily through glycolysis and respiration. While respiration is more energy-efficient, some cells favor glycolysis even when oxygen is available (aerobic glycolysis, Warburg effect). A leading explanation is that glycolysis is more efficient in terms of ATP production per unit mass of protein (i.e. faster). Through quantitative flux analysis and proteomics, we find however that mitochondrial respiration is actually more proteome-efficient than aerobic glycolysis. This is shown across yeasts, T cells, cancer cells, and tissues and tumors in vivo. Instead of aerobic glycolysis being valuable for fast ATP production, it correlates with high glycolytic protein expression, which is valuable for hypoxic growth. Aerobic glycolytic yeasts do not excel at aerobic growth, but outgrow respiratory cells in oxygen limitation. Thus, aerobic glycolysis emerges from cells maintaining a proteome conducive to both aerobic and hypoxic growth.

Shen, Yihui↗

yihuishen/T_cell_MFA

Metabolic efficiency profoundly influences organismal fitness. Heterotrophs, from yeast to mammals, derive usable energy primarily through glycolysis and respiration. While respiration is more energy-efficient, some cells favor glycolysis even when oxygen is available (aerobic glycolysis, Warburg effect). A leading explanation is that glycolysis is more efficient in terms of ATP production per unit mass of protein (i.e. faster). Through quantitative flux analysis and proteomics, we find however that mitochondrial respiration is actually more proteome-efficient than aerobic glycolysis. This is shown across yeasts, T cells, cancer cells, and tissues and tumors in vivo. Instead of aerobic glycolysis being valuable for fast ATP production, it correlates with high glycolytic protein expression, which is valuable for hypoxic growth. Aerobic glycolytic yeasts do not excel at aerobic growth, but outgrow respiratory cells in oxygen limitation. Thus, aerobic glycolysis emerges from cells maintaining a proteome conducive to both aerobic and hypoxic growth.

Shen, Yihui↗

Ascribe XR v0.1.0

Ascribe XR is an immersive visualization software designed for scientists and engineers working with 3D data sets. Its key features include interactive exploration, multi-user collaboration, and flexible data import capabilities, supporting various formats such as meshes, volumes, and terrain maps. The software utilizes Godot, OpenXR and PC-VR technology to provide an immersive experience. Ascribe XR is used for data analysis, visualization, and collaboration in various fields, enabling users to gain deeper insights into complex data sets. Its advantages over similar technologies include its flexibility, customizability, and ease of use. Ascribe XR's interactive and immersive environment facilitates collaboration and accelerates the discovery process. Compared to traditional 2D visualization tools, Ascribe XR offers a more engaging and intuitive experience, allowing users to explore complex data sets in a more natural and interactive way. Its ability to support multi-user collaboration and flexible data import capabilities make it a versatile tool for various applications. Overall, Ascribe XR provides a unique combination of features, usability, and performance, making it an attractive solution for scientists and engineers working with 3D data sets.

Pandolfi, Ronald [Lawrence Berkeley National Labor↗

SEED: Semantic Energy Exploration and Discovery

The Bioenergy Knowledge Discovery Framework (KDF) hosts a vast repository of specialized data, yet traditional keyword-based search methods often struggle to provide direct answers, requiring significant domain expertise and manual effort to filter through raw documents. To overcome these barriers, this software introduces a semantic search engine that enables both specialists and non-specialists to query the KDF using natural language. By shifting from rigid keyword matching to intent-based retrieval, the tool automatically identifies and ranks the most relevant sources within the database. The system functions by processing natural language queries to extract the most pertinent information, delivering an AI-generated plain-language summary alongside exact supporting quotes from retrieved documents. This integrated approach provides users with immediate, evidence-based answers while eliminating the need for exhaustive manual review. By surfacing direct insights and contextual evidence, the software enhances the usability of existing KDF resources and democratizes access to complex bioenergy data. Ultimately, this semantic search solution accelerates the discovery process and supports faster, more informed decision-making across the bioenergy sector.

Pan, Meiyu (Melrose) [Oak Ridge National Laborator↗

Pysl: Least-squares Unfolding With Python

This software simplifies and expands current approaches to the processing of foil- or wire-based neutron spectrometric measurements and spectral unfolding. With a focus on the cleanliness and usability of Python, this package allows a user to quickly process experimental results and compare results from multiple unfolding algorithms.

Boyington, JohnC.↗

Asi Nuclear Energy Sensors Data Portal Chatbot And Data Structuring Tool

The Idaho National Laboratory (INL) is advancing the development of an AI-powered chatbot and data structuring tool specifically designed to accelerate data mining processes for sensor-related information and seamlessly integrate the results into the ASI Sensors Data Portal (https://nes.energy.gov/). By doing so, the software aims to enhance the accessibility, usability, and organization of sensor data for nuclear energy applications. The software initial phase focuses on retrieving comprehensive datasets, prioritizing the past five years of publicly available information from the Office of Scientific and Technical Information (OSTI). These datasets will be meticulously processed to ensure compatibility, employing cleaning and preprocessing steps to eliminate irrelevant, incomplete, or corrupted information, thus establishing a robust foundation for subsequent AI use. The data will serve as the backbone for training an AI model and chatbot, which will act as an interactive tool enabling users to ask complex, context-specific questions and receive accurate, validated answers derived from constrained literature. In parallel, the project incorporates a data structuring process supported by AI to organize sensor information from multiple sources into a standardized format. This structured data will include detailed sensor specifications, such as measurement range, applications, accuracy, and operating conditions, generated and documented with AI. These specifications will be systematically integrated into the sensor portal. To maintain the highest levels of accuracy and relevance, all AI-generated outputs will be reviewed and validated by subject matter experts (SMEs), with additional fields or parameters added as needed. Future stages of the project aim to expand the dataset beyond OSTI to include other sources and potentially incorporate unclassified controlled information (UCI) with restricted access protocols to address security and confidentiality requirements.

Mapes, NormanJ. [Idaho National Laboratory (INL), ↗

A Reverse Logistics Tool For Ev Battery Recycling And Repurposing,

The demand for electric vehicles (EVs) in the United States is projected to rise significantly, with sales expected to reach approximately 4.1 million units by 2030. However, the U.S. remains heavily reliant on imports for the batteries and critical raw materials—such as lithium, cobalt, and nickel—that power these vehicles. As of 2024, around 70% of these imports originate from China. This dependency has become even more precarious following China’s imposition of export restrictions in April 2025, a retaliatory move against U.S. tariffs. These developments highlight the strategic vulnerabilities posed by China’s dominant position in the critical materials market. Compounding the issue, decades of intensive extraction have severely depleted global reserves of critical materials, widening the gap between supply and growing demand. This situation underscores the urgent need for the U.S. and other nations to diversify their sources of critical materials and enhance domestic capabilities to secure these resources—an essential step toward ensuring long-term energy security. At the end of their lifecycle—whether due to the battery’s degradation or the retirement of the vehicle—EV batteries are often improperly disposed of or sent to landfills. However, many of these batteries still retain usable capacity and can follow one of three alternative pathways: (a) Re-used: deployed in another vehicle with a shorter driving range, (b) Re-purposed: utilized act as a backup storage/power for data centers, solar panels, and e-scotters or (c) Recycled: broken down to recover the critical materials. To that end, the proposed tool (REBORN) is designed to optimize the reverse logistics network for battery repurposing and recycling. Its goal is to minimize associated costs while identifying optimal locations for battery collection and processing. Ultimately, REBORN ensures that each battery is used to its fullest potential.

Srinivas, SrikarV. [Idaho National Laboratory (INL↗

Advances in the Application and Utility of Subseasonal-to-Seasonal Predictions

The subseasonal-to-seasonal (S2S) predictive time scale, encompassing lead times ranging from 2 weeks to a season, is at the frontier of forecasting science. Forecasts on this time scale provide opportunities for enhanced application-focused capabilities to complement existing weather and climate services and products. There is, however, a “knowledge–value” gap, where a lack of evidence and awareness of the potential socioeconomic benefits of S2S forecasts limits their wider uptake. To address this gap, here we present the first global community effort at summarizing relevant applications of S2S forecasts to guide further decision-making and support the continued development of S2S forecasts and related services. Focusing on 12 sectoral case studies spanning public health, agriculture, water resource management, renewable energy and utilities, and emergency management and response, we draw on recent advancements to explore their application and utility. These case studies mark a significant step forward in moving from potential to actual S2S forecasting applications. We show that by placing user needs at the forefront of S2S forecast development—demonstrating both skill and utility across sectors—this dialogue can be used to help promote and accelerate the awareness, value, and cogeneration of S2S forecasts. We also highlight that while S2S forecasts are increasingly gaining interest among users, incorporating probabilistic S2S forecasts into existing decision-making operations is not trivial. Nevertheless, S2S forecasting represents a significant opportunity to generate useful, usable, and actionable forecast applications for and with users that will increasingly unlock the potential of this forecasting time scale.

54 ENVIRONMENTAL SCIENCES↗

DAWN: Dashboard for Agricultural Water Use and Nutrient Management—A Predictive Decision Support System to Improve Crop Production in a Changing Climate

Abstract Climate change presents huge challenges to the already-complex decisions faced by U.S. agricultural producers, as seasonal weather patterns increasingly deviate from historical tendencies. Under USDA funding, a transdisciplinary team of researchers, extension experts, educators, and stakeholders is developing a climate decision support Dashboard for Agricultural Water use and Nutrient management (DAWN) to provide Corn Belt farmers with better predictive information. DAWN’s goal is to provide credible, usable information to support decisions by creating infrastructure to make subseasonal-to-seasonal forecasts accessible. DAWN uses an integrated approach to 1) engage stakeholders to coproduce a decision support and information delivery system; 2) build a coupled modeling system to represent and transfer holistic systems knowledge into effective tools; 3) produce reliable forecasts to help stakeholders optimize crop productivity and environmental quality; and 4) integrate research and extension into experiential, transdisciplinary education. This article presents DAWN’s framework for integrating climate–agriculture research, extension, and education to bridge science and service. We also present key challenges to the creation and delivery of decision support, specifically in infrastructure development, coproduction and trust building with stakeholders, product design, effective communication, and moving tools toward use.

Meteorology & Atmospheric Sciences↗

Phoenix Dust Storm (PHX-DUST) Scale: A Cooperatively Developed Dust Storm Scale for Phoenix, Arizona

Using extensive localized meteorological and air quality data for central Arizona from 2010 to 2023, we create a postevent dust storm scale for use by the primary stakeholders in central Arizona for the Phoenix metropolitan area called the Phoenix Dust Storm (PHX-DUST) scale. To ensure usability across a wide spectrum of users, a core concept was to “keep it simple.” The PHX-DUST scale is based on (i) maximum dust concentration for particulate matter (PM10) across the network in micrograms per cubic meter which determines category, e.g., “category 5 (the highest observed category)” and category 4; (ii) the number of network monitors achieving dust concentrations above a threshold of 500 μg m−3 (categorized as “widespread” or “isolated,” as measures of spatial extent); (iii) a duration parameter (which determines “long duration” or “short duration”); and (iv) a measure of wind speed over the affected area (maximum wind gust recorded over the network, which may not be the maximum wind of the storm). Using this index for the 189 dust storms impacting the Phoenix metropolitan area for the period 2010–23, the most severe dust storm occurred on 5 July 2011 and is classified as a “Category 5, Widespread, Long-Duration High-Gust” event. This initial attempt at defining the PHX-DUST scale holds valuable applications for research, education, and applied analyses. It demonstrates that a consortium of interested groups can effectively work to create products benefiting the weather community and general public. Here, the PHX-DUST scale can also serve as a foundational framework for application in other regions where dust storms pose a threat to the well-being of populations, infrastructure, and ecosystems.

Atmosphere↗

Race conditions and data partitioning: risks posed by common errors to reproducible parallel simulations

When parallel algorithms for simulation were introduced in the 1970s, their development and use interested only experts in parallel computation. This circumstance changed as multi-core processors became commonplace, putting a parallel computer into the hands of every modeler. A natural outcome is growing interest in parallel simulation among persons not intimately familiar with parallel computing. At the same time, parallel simulation tools continue to be developed with the implicit assumption that the modeler is knowledgeable about parallel programming. The unintended consequence is a rapidly growing number of users of parallel simulation tools that are unlikely to recognize when the interaction of race conditions, partitioning strategies, and simultaneous action in their simulation models make results non-reproducible, thereby calling into question the validity of conclusions drawn from the simulation data. Here, we illustrate the potential dangers of exposing parallel algorithms to users who are not experts in parallel computation with example models constructed using existing parallel simulation tools. By doing so, we hope to refocus tool developers on usability, even if this new focus incurs loss of some performance.

97 MATHEMATICS AND COMPUTING↗

Semi-Automatic Geographic Information System Framework for Creating Photo-Realistic Digital Twin Cities to Support Autonomous Driving Research

Digital twin cities are frequently used in vehicle and traffic simulations to render realistic on-road driving scenarios under various traffic and environmental conditions. These digital twins provide a high-fidelity replica of the physical world (e.g., buildings, roads, infrastructures, traffic) to create three-dimensional (3D) virtual-physical environments to support various emerging vehicle and transportation technologies such as connected and automated vehicles. These virtual environments provide a cost-effective digital proving ground to evaluate, validate, and test emerging technologies that include control algorithms, localization, perception, and sensors. Replicating a real-world traffic scenario in a digital twin using a traditional 3D modeling approach is a time-consuming and labor-intensive effort. Here this paper presents a semi-automated spatial framework to construct realistic 3D digital twin cities to support autonomous driving research using readily available geographic information system (GIS) data and 3D prefabricated (prefab) models. We start with a comprehensive review of geospatial data sources of essential digital entities required in a 3D digital twin city and present an integrated GIS-3D modeling pipeline using customized QGIS/GDAL and Blender scripting in Python. The pipeline outputs are realistic 3D digital twin cities compatible with common vehicle simulation software, such as CARLA and IPG CarMaker. The paper closes with a showcase to demonstrate the quality and usability of a digital twin city created to replicate the Shallowford Road corridor in Chattanooga in both Unity and Unreal engine-based virtual environment. The generated digital twin city can be applied to a hardware-in-the-loop simulation environment with an actual testing vehicle to facilitate autonomous driving research.

33 ADVANCED PROPULSION SYSTEMS↗