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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 361 records · Page 20

Semi-supervised Machine Learning Enables the Robust Detection of Multireference Character at Low Cost

Multireference (MR) diagnostics are common tools for identifying strongly correlated electronic structure that makes single-reference (SR) methods (e.g., density functional theory or DFT) insufficient for accurate property prediction. However, MR diagnostics typically require computationally demanding correlated wave function theory (WFT) calculations, and diagnostics often disagree or fail to predict MR effects on properties. To overcome these challenges, we introduce a semi-supervised machine learning (ML) approach with virtual adversarial training (VAT) of an MR classifier using 15 WFT and DFT MR diagnostics as inputs. In semi-supervised learning, only the most extreme SR or MR points are labeled, and the remaining point labels are learned. The resulting VAT model outperforms the alternatives, as quantified by the distinct property distributions of SR- and MR-classified molecules. Additionally, to reduce the cost of generating inputs to the VAT model, we leverage the VAT model’s robustness to noisy inputs by replacing WFT MR diagnostics with regression predictions in an MR decision engine workflow that preserves excellent performance. We demonstrate the transferability of our approach to larger molecules and those with distinct chemical composition from the training set. This MR decision engine demonstrates promise as a low-cost, high-accuracy approach to the automatic detection of strong correlation for predictive high-throughput screening.

36 MATERIALS SCIENCE↗

Control over Conformational Landscapes of Polypeptoids by Monomer Sequence Patterning

The ability to program chain conformation and structure through control over the monomer sequence of synthetic polymers has broad implications for next-generation material design. While related problems of protein-folding and de novo design have generated accurate predictions of 3D folded chain structures, generalization to synthetic polymers remains intractable due to the requirement of large structural databases and the intrinsically disordered nature of polymer building blocks. In this work, polypeptoids, a class of peptidomimetic synthetic polymers, are utilized to build a general workflow for the study of relationships between monomer sequence and dynamic 3D chain structure in solution. Furthermore, this work demonstrates how control over the monomer sequence can alter the conformational landscape of synthetic polymers to deviate dramatically from classical chain statistics. Specifically, the distribution of end-to-end distances, as measured by double electron-electron resonance spectroscopy in dilute solvent, is systematically skewed towards shorter distances with an increasing number of hydrophobes and further refined by hydrophobe arrangement in amphiphilic polypeptoid chains.

36 MATERIALS SCIENCE↗

FELIX-2.0: New version of the finite element solver for the time dependent generator coordinate method with the Gaussian overlap approximation

The time-dependent generator coordinate method (TDGCM) is a powerful method to study the largeamplitude collective motion of quantum many-body systems such as atomic nuclei. Under the GaussianOverlap Approximation (GOA), the TDGCM leads to a local, time-dependent Schrödinger equation in amulti-dimensional collective space. In this paper, we present the version 2.0 of the code FELIX that solvesthe collective Schrödinger equation in a finite element basis. This new version features: (i) the ability tosolve a generalized TDGCM+GOA equation with a metric term in the collective Hamiltonian, (ii) supportfor new kinds of finite elements and different types of quadrature to compute the discretized Hamiltonianand overlap matrices, (iii) the possibility to leverage the spectral element scheme, (iv) an explicit Krylovapproximation of the time propagator for time integration instead of the implicit Crank–Nicolson methodimplemented in the first version, (v) an entirely redesigned workflow. We benchmark this release on ananalytic problem as well as on realistic two-dimensional calculations of the low-energy fission of240Puand256Fm. Low to moderate numerical precision calculations are most efficiently performed with simplexelements with a degree 2 polynomial basis. Higher precision calculations should instead use the spectralelement method with a degree 4 polynomial basis. We emphasize that in a realistic calculation of fissionmass distributions of240Pu, FELIX-2.0 is about 20 times faster than its previous release (within a numericalprecision of a few percents).

Regnier, D.↗

Biofoundries: Principles, Tools, and Applications

This chapter aims to provide a broad overview of biofoundries and introduces the principles, concepts, and case studies. We first outline the underlying principles of the Design-Build-Test-Learn (DBTL) framework and the role of automation, digital integration, and standardization. The chapter then explores core biofoundry technologies including robotic liquid handlers, high-throughput analytical instruments, and digital infrastructure for data management and workflow scheduling. Case studies spanning DNA assembly, protein engineering, metabolic engineering, and mammalian cell culture demonstrate the practical applications of the biofoundries. Economic and societal impacts are assessed alongside current limitations. We discuss the emerging trends including artificial intelligence integration and cloud-based distributed facilities to highlight its potential for biotechnology and the bioeconomy.

Singh, Nilmani↗

Optimizing the Weather Research and Forecasting Model with OpenMP Offload and Codee

Currently, the Weather Research and Forecasting model (WRF) utilizes shared memory (OpenMP) and distributed memory (MPI) parallelisms. To take advantage of GPU resources on the Perlmutter supercomputer at NERSC, we port parts of the computationally expensive routine Fast Spectral Bin Microphysics (FSBM) to NVIDIA GPUs using OpenMP device offloading directives. To facilitate this process, we explore a workflow for optimization which uses both runtime profilers and a static code inspection tool Codee to refactor the subroutine. We observe an 2.24x overall speedup for the CONUS-12km storm test case.

Wichitrnithed, Chayanon (Namo) [Odin Institute]↗

ESAC v1: Enhanced AI-Powered Chatbot for EQ-SANS Experiment Automation Improvements and Updates

ESAC (EQ-SANS Assisting Chatbot) is an advanced AI-powered application designed to streamline the workflow of neutron scattering experiments at the Spallation Neutron Source (SNS). This report documents the significant advancements in ESAC v1, which include the integration of a combined In-Context Learning (ICL) + Retrieval-Augmented Generation (RAG) capability, a robust integrated development environment, and standalone executable distribution. These enhancements address the limitations of the original version, making ESAC v1 a transformative tool for researchers. The report also discusses the technical challenges encountered during development and their resolution, highlighting the impact of these improvements on the neutron scattering research community.

36 MATERIALS SCIENCE↗

Global transpiration data from sap flow measurements: the SAPFLUXNET database

Plant transpiration links physiological responses of vegetation to water supply and demand with hydrological, energy, and carbon budgets at the land–atmosphere interface. However, despite being the main land evaporative flux at the global scale, transpiration and its response to environmental drivers are currently not well constrained by observations. Here we introduce the first global compilation of whole-plant transpiration data from sap flow measurements (SAPFLUXNET, https://sapfluxnet.creaf.cat/, last access: 8 June 2021). We harmonized and quality-controlled individual datasets supplied by contributors worldwide in a semi-automatic data workflow implemented in the R programming language. Datasets include sub-daily time series of sap flow and hydrometeorological drivers for one or more growing seasons, as well as metadata on the stand characteristics, plant attributes, and technical details of the measurements. SAPFLUXNET contains 202 globally distributed datasets with sap flow time series for 2714 plants, mostly trees, of 174 species. SAPFLUXNET has a broad bioclimatic coverage, with woodland/shrubland and temperate forest biomes especially well represented (80 % of the datasets). The measurements cover a wide variety of stand structural characteristics and plant sizes. The datasets encompass the period between 1995 and 2018, with 50 % of the datasets being at least 3 years long. Accompanying radiation and vapour pressure deficit data are available for most of the datasets, while on-site soil water content is available for 56 % of the datasets. Many datasets contain data for species that make up 90 % or more of the total stand basal area, allowing the estimation of stand transpiration in diverse ecological settings. SAPFLUXNET adds to existing plant trait datasets, ecosystem flux networks, and remote sensing products to help increase our understanding of plant water use, plant responses to drought, and ecohydrological processes. SAPFLUXNET version 0.1.5 is freely available from the Zenodo repository (https://doi.org/10.5281/zenodo.3971689; Poyatos et al., 2020a). The “sapfluxnetr” R package – designed to access, visualize, and process SAPFLUXNET data – is available from CRAN.

58 GEOSCIENCES↗

Oncentra brachytherapy planning system

In modern cancer management, treatment planning has progressed as a contemporary tool with all the advances in computing power in recent years. One of the advanced planning tools uses 3-dimensional (3D) data sets for accurate dose distributions in patient prescription. Among these planning processes, brachytherapy has been a very important part of a successful cancer management program, offering clinical benefits with specific or combined treatments with external beam therapy. In this chapter, we mainly discussed the Elekta Oncentra planning system, which is the main treatment planning tool for high-dose rate (HDR) modality in our facility and in many other facilities in the United States. HDR is a technically advanced form of brachytherapy; a high-intensity radiation source (3.6 mm in length) is delivered with step motor in submillimeter precision under computer guidance directly into the tumor areas while minimizing injury to surrounding normal healthy tissue. Oncentra planning is the key component to generate a deliverable brachytherapy procedure, which is executed on the microSelectron V3 remote afterloader treatment system. Creating a highly conformal plan can be a time-consuming task. The development of Oncentra software (version 4.5.3) offers a variety of useful tools that facilitate many of the clinical challenging tasks for planning, such as contouring and image reconstruction, as well as rapid planning calculations with dose and dose volume histogram analysis. Oncentra Brachy module creates workflow and optimizes the planning accuracy for wide varieties of clinical HDR treatments, such as skin, gynecologic (GYN), breast, prostate, and many other applications. The treatment file can also be transferred to the afterloader control station for speedy delivery. The design concept, calculation algorithms, and optimization modules presented some key characteristics to plan and treat the patients effectively and accurately. The dose distribution and accuracy of several clinical sample cases were discussed to illustrate the effectiveness and clinical efficacy. The American Association of Physicists in Medicine brachytherapy reports of TG-43 and TG-186 were also described and compared in evaluations of fundamental calculation methodologies.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay

Abstract Motivation The forskolin-induced swelling (FIS) assay has become the preferential assay to predict the efficacy of approved and investigational CFTR-modulating drugs for individuals with cystic fibrosis (CF). Currently, no standardized quantification method of FIS data exists thereby hampering inter-laboratory reproducibility. Results We developed a complete open-source workflow for standardized high-content analysis of CFTR function measurements in intestinal organoids using raw microscopy images as input. The workflow includes tools for (i) file and metadata handling; (ii) image quantification and (iii) statistical analysis. Our workflow reproduced results generated by published proprietary analysis protocols and enables standardized CFTR function measurements in CF organoids. Availability and implementation All workflow components are open-source and freely available: the htmrenamer R package for file handling https://github.com/hmbotelho/htmrenamer; CellProfiler and ImageJ analysis scripts/pipelines https://github.com/hmbotelho/FIS_image_analysis; the Organoid Analyst application for statistical analysis https://github.com/hmbotelho/organoid_analyst; detailed usage instructions and a demonstration dataset https://github.com/hmbotelho/FIS_analysis. Distributed under GPL v3.0. Supplementary information Supplementary data are available at Bioinformatics online.

Hagemeijer, Marne C.↗

Control and Information Systems for the National Ignition Facility

Orchestration of every National Ignition Facility (NIF) shot cycle is managed by the Integrated Computer Control System (ICCS), which uses a scalable software architecture running code on more than 1950 front-end processors, embedded controllers, and supervisory servers. The ICCS operates laser and industrial control hardware containing 66 000 control and monitor points to ensure that all of NIF’s laser beams arrive at the target within 30 ps of each other and are aligned to a pointing accuracy of less than 50 μm root-mean-square, while ensuring that a host of diagnostic instruments record data in a few billionths of a second. NIF’s automated control subsystems are built from a common object-oriented software framework that distributes the software across the computer network and achieves interoperation between different software languages and target architectures. A large suite of business and scientific software tools supports experimental planning, experimental setup, facility configuration, and post-shot analysis. Standard business services using open-source software, commercial workflow tools, and database and messaging technologies have been developed. An information technology infrastructure consisting of servers, network devices, and storage provides the foundation for these systems. Thus, this work is an overview of the control and information systems used to support a wide variety of experiments during the National Ignition Campaign.

42 ENGINEERING↗

Apollo: Democratizing genome annotation

Genome annotation is the process of identifying the location and function of a genome's encoded features. Improving the biological accuracy of annotation is a complex and iterative process requiring researchers to review and incorporate multiple sources of information such as transcriptome alignments, predictive models based on sequence profiles, and comparisons to features found in related organisms. Because rapidly decreasing costs are enabling an ever-growing number of scientists to incorporate sequencing as a routine laboratory technique, there is widespread demand for tools that can assist in the deliberative analytical review of genomic information. To this end, we present Apollo, an open source software package that enables researchers to efficiently inspect and refine the precise structure and role of genomic features in a graphical browser-based platform. Some of Apollo's newer user interface features include support for real-time collaboration, allowing distributed users to simultaneously edit the same encoded features while also instantly seeing the updates made by other researchers on the same region in a manner similar to Google Docs. Its technical architecture enables Apollo to be integrated into multiple existing genomic analysis pipelines and heterogeneous laboratory workflow platforms. Finally, we consider the implications that Apollo and related applications may have on how the results of genome research are published and made accessible.

59 BASIC BIOLOGICAL SCIENCES↗

PanDA: Production and Distributed Analysis System

The Production and Distributed Analysis (PanDA) system is a data-driven workload management system engineered to operate at the LHC data processing scale. The PanDA system provides a solution for scientific experiments to fully leverage their distributed heterogeneous resources, showcasing scalability, usability, flexibility, and robustness. The system has successfully proven itself through nearly two decades of steady operation in the ATLAS experiment, addressing the intricate requirements such as diverse resources distributed worldwide at about 200 sites, thousands of scientists analyzing the data remotely, the volume of processed data beyond the exabyte scale, dozens of scientific applications to support, and data processing over several billion hours of computing usage per year. PanDA’s flexibility and scalability make it suitable for the High Energy Physics community and wider science domains at the Exascale. Beyond High Energy Physics, PanDA’s relevance extends to other big data sciences, as evidenced by its adoption in the Vera C. Rubin Observatory and the sPHENIX experiment. As the significance of advanced workflows continues to grow, PanDA has transformed into a comprehensive ecosystem, effectively tackling challenges associated with emerging workflows and evolving computing technologies. The paper discusses PanDA’s prominent role in the scientific landscape, detailing its architecture, functionality, deployment strategies, project management approaches, results, and evolution into an ecosystem.

97 MATHEMATICS AND COMPUTING↗

Dose Summation Strategies for External Beam Radiation Therapy and Brachytherapy in Gynecologic Malignancy: A Review from the NRG Oncology and NCTN Medical Physics Subcommittees

Definitive, nonsurgical management of gynecologic malignancies involves external beam radiation therapy (EBRT) and/or brachytherapy (BT). Summation of the cumulative dose is critical to assess the total biologic effective dose to targets and organs at risk. Cumulative dose calculation from EBRT and BT can be performed with or without image registration (IR) and biologic dose summation. Among these dose summation strategies, linear addition of dose-volume histogram (DVH) parameters without IR is the global standard for composite dose reporting. This approach stems from an era without image guidance and simple external beam and brachytherapy treatment approaches. With technological advances, EBRT and high-dose-rate BT have evolved to allow for volume-based treatment planning and delivery. Modern conformal therapeutic radiation involves volumetric or intensity modulated EBRT, capable of simultaneously treating multiple targets at different specified dose levels. Therefore, given the complexity of modern radiation treatment, the linear addition of DVH parameters from EBRT and high-dose-rate BT is challenging to represent the combined dose distribution. Deformable image registration (DIR) between EBRT and image guided brachytherapy (IGBT) data sets may provide a more nuanced calculation of multimodal dose accumulation. However, DIR is still nascent in this regard, and needs further development for accuracy and efficiency for clinical use. Biologic dose summation can combine physical dose maps from EBRT and each IGBT fraction, thereby generating a composite DVH from the biologic effective dose. However, accurate radiobiologic parameters are tissue-dependent and not well characterized. A combination of voxel-based DIR and biologic weighted dose maps may be the best approximation of dose accumulation but remains invalidated. The purpose of this report is to review dose summation strategies for EBRT and BT, including conventional equivalent dose in 2-Gy fractions dose summation without image registration, physical dose summation using 3-dimensional rigid IR and DIR, and biologic dose summation. We also provide general clinical workflows for IGBT with a focus on cervical cancer.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

A Cellular Automaton Simulation for Predicting Phase Evolution in Solid-State Reactions

New computational tools for solid-state synthesis recipe design are needed in order to accelerate the experimental realization of novel functional materials proposed by high-throughput materials discovery workflows. This work contributes a cellular automaton simulation framework for predicting the time-dependent evolution of intermediate and product phases during solid-state reactions as a function of precursor choice and amount, reaction atmosphere, and heating profile. The simulation captures the effects of reactant particle spatial distribution, particle melting, and reaction atmosphere. Reaction rates based on rudimentary kinetics are estimated using density functional theory data from the Materials Project and machine learning estimators for the melting point and the vibrational entropy component of the Gibbs free energy. The resulting simulation framework allows for the prediction of the likely outcome of a reaction recipe before any experiments are performed. We analyze five experimental solid-state recipes for BaTiO 3 , CaZrN 2 , and YMnO 3 found in the literature to illustrate the performance of the model in capturing reaction selectivity and reaction pathways as a function of temperature and precursor choice. This simulation framework offers an easier way to optimize existing recipes, aid in the identification of intermediates, and design effective recipes for yet unrealized inorganic solids in silico .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Streaming Readout and Remote Compute

Streaming Readout Data Acquisition systems coupled with distributed resources spread over vast geographic distances present new challenges to the next generation of experiments. High bandwidth modern network connectivity opens the possibility to utilize large, general-use, HTC systems that are not necessarily located close to the experiment. Near real-time response rates and workflow colocation can provide high reliability solutions to ensure efficient use of beam time. This talk will focus on a few technologies currently being developed at Jefferson Lab and in collaboration with ESnet to support fully streaming DAQ systems.

Lawrence, David↗

SBbadger: biochemical reaction networks with definable degree distributions

Abstract Motivation An essential step in developing computational tools for the inference, optimization and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks. General strategies for the assembly of benchmark models include collection from the literature, creation via subnetwork extraction and de novo generation. However, with respect to biochemical reaction networks, these approaches and their associated tools are either poorly suited to generate models that reflect the wide range of properties found in natural biochemical networks or to do so in numbers that enable rigorous statistical analysis. Results In this work, we present SBbadger, a python-based software tool for the generation of synthetic biochemical reaction or metabolic networks with user-defined degree distributions, multiple available kinetic formalisms and a host of other definable properties. SBbadger thus enables the creation of benchmark model sets that reflect properties of biological systems and generate the kinetics and model structures typically targeted by computational analysis and inference software. Here, we detail the computational and algorithmic workflow of SBbadger, demonstrate its performance under various settings, provide sample outputs and compare it to currently available biochemical reaction network generation software. Availability and implementation SBbadger is implemented in Python and is freely available at https://github.com/sys-bio/SBbadger and via PyPI at https://pypi.org/project/SBbadger/. Documentation can be found at https://SBbadger.readthedocs.io. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Probabilistic Deliverability Assessment of Distributed Energy Resources via Scenario-Based AC Optimal Power Flow

As electric grids decarbonize and distributed energy resources (DERs) become increasingly prevalent, interconnection assessments must evolve to reflect operational variability and control flexibility. This paper highlights key modeling limitations observed in practice and reviews approaches for modeling uncertainty. It then introduces a Probabilistic Deliverability Assessment (PDA) framework designed to complement and extend existing procedures. The framework integrates scenario-based AC optimal power flow (AC OPF), corrective dispatch, and optional multi-temporal constraints. Together, these form a structured methodology for quantifying DER utilization, deliverability, and reliability under uncertainty in load, generation, and topology. Outputs include interpretable metrics with confidence intervals that inform siting decisions and evaluate compliance with reliability thresholds across sampled operating conditions. A case study on Puerto Rico’s publicly available bulk power system model demonstrates the framework’s application using minimal input data, consistent with current interconnection practice. Across staged fossil generation retirements, the PDA identifies high-value DER sites and regions requiring additional reactive power support. Results are presented through mean dispatch signals, reliability metrics, and geospatial visualizations, demonstrating how the framework provides transparent, data-driven siting recommendations. The framework’s modular design supports incremental adoption within existing workflows, encouraging broader use of AC OPF in interconnection and planning contexts.

14 SOLAR ENERGY↗

A High-Throughput Computing Infrastructure to Generate Custom, Open Community Geothermal Datasets

The most significant challenge facing geothermal research, development, and deployment is a lack of comprehensive datasets describing the geological and economical properties of North America. Automated knowledge base construction, the process of designing algorithms to analyze text and images to programmatically build new datasets, is one possible solution to this problem. The xDD library of full-text scientific articles (https://xdd.wisc.edu) is one of the largest collections of open and controlled-access scientific documents available for knowledge base construction in the world, but it has been underutilized by experts in geothermal research. The xDD development team attributed the lack of engagement by software developers and geothermal researchers to two perceived shortcomings of the system. First, the workflow for obtaining data from xDD for local development and testing of data mining applications was unnecessarily abstruse and required significant manual intervention by xDD systems administrators. Second, although xDD already held articles from a broad cross-section of scientific literature with an emphasis on the geosciences, it did not have an explicit set of geothermal research documents that could serve as the nucleus of a geothermal data mining application. To address these issues, the Automated Data Extraction PlaTform (ADEPT) was proposed to extend the data distribution capabilities of the xDD system. The ADEPT extension added the following four key features to xDD: 1) integration of National Geothermal Data System (NGDS) documents into the xDD library to provide an explicitly geothermally-themed collection; 2) improved RESTful (i.e., https-protocol driven) web services for external partners to access xDD data for machine learning application development; 3) a web platform for end-users and xDD administrators to coordinate the development of data mining applications from the initial step of browsing available documents to the final stage of deploying a production-quality machine learning application on high-throughput computing infrastructure; and 4) the development of demonstration data mining applications to illustrate the new workflow to potential collaborators. A total of 21,674 geothermal documents from NGDS were fully ingested into the xDD library and the associated metadata is publicly available through the xDD web services; furthermore, the ADEPT web platform is now publicly accessible and fully live at https://xdd.wisc.edu/adept/.

15 GEOTHERMAL ENERGY↗