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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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DOE OSTI2014

Tombusviruses upregulate phospholipid biosynthesis via interaction between p33 replication protein and yeast lipid sensor proteins during virus replication in yeast

Positive-stranded RNA viruses induce new membranous structures and promote membrane proliferation in infected cells to facilitate viral replication. In this paper, the authors show that a plant-infecting tombusvirus upregulates transcription of phospholipid biosynthesis genes, such as INO1, OPI3 and CHO1, and increases phospholipid levels in yeast model host. This is accomplished by the viral p33 replication protein, which interacts with Opi1p FFAT domain protein and Scs2p VAP protein. Opi1p and Scs2p are phospholipid sensor proteins and they repress the expression of phospholipid genes. Accordingly, deletion of OPI1 transcription repressor in yeast has a stimulatory effect on TBSV RNA accumulation and enhanced tombusvirus replicase activity in an in vitro assay. Altogether, the presented data convincingly demonstrate that de novo lipid biosynthesis is required for optimal TBSV replication. Overall, this work reveals that a (+)RNA virus reprograms the phospholipid biosynthesis pathway in a unique way to facilitate its replication in yeast cells. - Highlights: • Tombusvirus p33 replication protein interacts with FFAT-domain host protein. • Tombusvirus replication leads to upregulation of phospholipids. • Tombusvirus replication depends on de novo lipid synthesis. • Deletion of FFAT-domain host protein enhances TBSV replication. • TBSV rewires host phospholipid synthesis.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Evaluating Energy Savings Measures for Building Retrofits in an Interactive Workshop Environment

As part of the Better Buildings Summit 2025, a workshop was developed to simulate the decision process for implementing a set of energy savings measures on an existing building. As part of the workshop a "game" was created around energy savings strategies, and workshop participants selected renovation cards that provided data around the impacts of that renovation choice. Participants then were able to calculate overall savings and payback from the selected retrofit opportunities. This publication has been produced to package the resources used in the activity in an organized document so that the materials can be distributed and reused more broadly. It provides a comprehensive framework for replicating the workshop, including step-by-step instructions, retrofit "game cards" with data points, and facilitation guidance. By using these materials, readers can conduct their own version of this interactive workshop with stakeholders in their networks, such as building owners, energy managers, or policy makers. The goal is to empower users to simulate the decision-making processes for energy projects, foster collaboration, and drive meaningful discussions around cost-effective retrofit opportunities and goal-oriented outcomes.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2016

Using GIS for Processing, Analysis and Visualization of Hydrological Model Data - 16202

The Applied Research Center at Florida International University (ARC-FIU) is supporting the soil and groundwater remediation efforts of the U.S. Department of Energy's (DOE's) Savannah River Site (SRS) by developing a surface water model to simulate the hydrology and the fate and transport of contaminants and sediment in the Tims Branch watershed. Advances in ArcGIS software through the development of spatial GIS database (geo-database) technology, coupled with the development of data models such as ArcHydro which possesses a spatial relational database management system (RDMS) schema and relationship structure specific to hydrologic systems, provides modelers with tools and applications to assist in the processing, analysis and visualization of flow and contaminant transport data. In addition, the coupling of this type of geo-database structure with a numerical modeling package such as MIKE SHE/MIKE 11 can serve as an efficient tool that significantly reduces the time needed for data preparation. The MIKE modeling system has a geographic information systems (GIS) user interface built into its system that can directly use GIS data for model inputs. GIS-based hydrologic models can provide a spatial element that other hydrologic models lack. GIS is important for processing and analysis of large spatio-temporal datasets derived from multiple sources that are being used for setting up of models, model calibration and simulation of flow and contaminant fate and transport. GIS-based approaches in hydrological modeling can also provide the benefit of combining different layers of geographic data to create new integrated information which can be quite useful for creating dependent or independent hydrological variables. ARC-FIU has developed an ArcGIS geo-database to support the hydrological modeling work being conducted at SRS. The SRS geo-database was developed based on the ArcHydro and ArcGIS Base Map data models with modifications made for project specific input parameters. The significance of this approach was to ensure its replicability for potential application at other DOE sites. The SRS geo-database assists in the storage and management of GIS and time series data being used for hydrological model development at Savannah River Site. Other GIS tools such as ArcGIS Model Builder coupled with Python scripting have enabled the automation of many of the repetitive geo-processing tasks required for pre- and post-processing of the hydrological modeling data. Automation of many of the data processing tasks has facilitated faster and hence more complex analyses of field test data. The toolbox created is also a scalable and reusable application that can be implemented in other watersheds. This paper describes the use of ArcGIS tools for the pre-processing, spatial delineation and analysis of hydrological model data; for automation of repetitive geo-processing tasks; and for visualization of different hydrological components of the Tims Branch watershed. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

Commercial Building Energy Code Field Study: Data Collection Methodology and Protocol

In support of the U.S. Department of Energy’s Commercial Buildings Energy Code Field Study, this data collection methodology and protocol provides guidance on all aspects of undertaking a compliance study, from development of a sampling plan to recruitment to code requirements and compliance checks for each energy code measure specified to be collected. The protocol also includes a data collection form that captures all key information needed for analysis of commercial energy code compliance. This methodology was developed by the Institute for Market Transformation in coordination with Pacific Northwest National Laboratory (PNNL) and the U.S. Department of Energy Building Energy Codes Program with the objective of assisting states, jurisdictions, utilities and others as they seek to measure and demonstrate compliance rates with energy codes in commercial buildings, as well as to target areas for improvement through increased energy code compliance and broader energy-efficiency programs. It is also intended to facilitate a consistent and replicable approach to research studies of this type and establish a transparent data set representing baseline construction practices across the U.S.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2023

Commercial Building Energy Code Field Study: Data Collection Methodology and Protocol

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2026

Evaluation of a Reduced-Order Model for IBR Fault Response Representation via OEM Blackbox Models: Preprint

Driven by the need to capture the electromagnetic transients of transmission lines, inverter switching behavior, and detailed control systems, electromagnetic transient (EMT) studies have become increasingly important in industry, such as IBR interconnection study and fault study. However, original equipment manufacturer (OEM) inverter models typically include extensive parameters and proprietary settings that are unavailable to protection engineers. This paper introduces a data-driven, reduced-order model (ROM) developed as a PSCAD library component for use in EMT-based fault studies. The ROM replicates key OEM model behaviors without requiring detailed knowledge of control design or parameterization. The accompanying Python automation scripts streamline data generation, parameter fitting, and validation. The ROM's performance is demonstrated through comparison with both IEEE 2800-compliant and non-compliant OEM models in a real-world power system. Relay responses show nearly identical results, while simulation runtime is reduced by an average of 32.8\%, highlighting the ROM's practicality for protection engineers.

14 SOLAR ENERGY↗

DOE OSTI2026

Integrative SP3 Workflow for Multi-PTM Proteomics Profiling (TZ-DP0)

The goal of the experiment was to demonstrate that the optimized multiplexed multi-PTM profiling workflow can comprehensively and quantitatively capture dynamic changes in protein abundance, cysteine oxidation, phosphorylation, and acetylation in cytokine-induced inflammatory stress in mouse pancreatic ß-cells. Global proteomic, redox proteomic, phosphoproteomic, and acetylomic were data collected from mouse Beta-TC-6 pancreatic Beta-cells, untreated (mock) and cytokine-treated Beta-cells at 4, 8, and 24 hours with 4 biological replicates. Samples were digested with trypsin and Lys-C, then analyzed by LC-MS/MS. Data were searched with MS-GF+, MASIC, and MaxQuant using PNNL's DMS processing pipeline.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Complementing Dynamical Downscaling With Super‐Resolution Convolutional Neural Networks

Despite advancements in Artificial Intelligence (AI) methods for climate downscaling, significant challenges remain for their practicality in climate research. Current AI-methods exhibit notable limitations, such as limited application in downscaling Global Climate Models (GCMs), and accurately representing extremes. To address these challenges, we implement an AI-based methodology using super-resolution convolutional neural networks (SRCNN), trained and evaluated on 40 years of daily precipitation data from a reanalysis and a high-resolution dynamically downscaled counterpart. The dynamical downscaled simulations, constrained using spectral nudging, enable the replication of historical events at a higher resolution. This allows the SRCNN to emulate dynamical downscaling effectively. Modifications, such as incorporating elevation data and data pre-processing enhances overall model performance, while using exponential and quantile loss functions improve the simulation of extremes. Our findings show SRCNN models efficiently and skillfully downscale precipitation from GCMs. Future work will expand this methodology to downscale additional variables for future climate projections.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Modeling dark- and light-induced crystal structures and single-crystal optical absorption spectra of ruthenium-based complexes that undergo SO 2 -linkage photoisomerization

A family of coordination complexes of the type [Ru(SO 2 )(NH 3 ) 4 X] m+ Y n – (m, n = 1 or 2) exhibit optical switching capabilities in their single-crystal states. This striking effect is caused by the light-induced formation of SO 2 -linkage photoisomers, which are metastable if kept at suitably cool temperatures. We modeled the dark- and light-induced states of these large crystalline complexes via plane-wave (PW)- and molecular-orbital (MO)-based density functional theory (DFT) and time-dependent DFT in order to calculate their structural and optical properties; the calculated results are compared with experimental data. We show that the PW-DFT-based periodic models replicate the structural properties of these complexes more effectively than the MO-DFT-based molecular-fragment models, observing only small deviations in key bond lengths relative to the experimentally derived crystal structures. The periodic models were also found to more effectively simulate trends seen in experimental optical absorption spectra, with optical absorbance and coverage of the visible region increasing with the formation of the photoinduced geometries. The contribution of the metastable photoisomeric species more heavily focuses on the lower-energy end of the spectra. Spectra generated from the molecular-fragment models are limited by the geometry of the fragment used and the number of excited-state roots considered in those calculations. In general, periodic models outperform the molecular-fragment models owing to their ability to better appreciate the periodic phenomena that are present in these crystalline materials as opposed to MO approaches, which are finite methods. We thus demonstrate that PW-DFT-based periodic models should be considered as a more than viable method for simulating the optical and electronic properties of these single-crystal optical switches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Data compression and covariance matrix inspection: Cosmic shear

Covariance matrices are among the most difficult pieces of end-to-end cosmological analyses. In principle, for two-point functions, each component involves a four-point function, and the resulting covariance often has hundreds of thousands of elements. We investigate various compression mechanisms capable of vastly reducing the size of the covariance matrix in the context of cosmic shear statistics. This helps identify which of its parts are most crucial to parameter estimation. We start with simple compression methods, by isolating and “removing” 200 modes associated with the lowest eigenvalues, then those with the lowest signal-to-noise ratio, before moving on to more sophisticated schemes like compression at the tomographic level and, finally, with the massively optimized parameter estimation and data compression (MOPED). We find that, while most of these approaches prove useful for a few parameters of interest, like Ω m , the simplest yield a loss of constraining power on the intrinsic alignment (IA) parameters as well as S 8 . For the case considered—cosmic shear from the first year of data from the Dark Energy Survey—only MOPED was able to replicate the original constraints in the 16-parameter space. Finally, we apply a tolerance test to the elements of the compressed covariance matrix obtained with MOPED and confirm that the IA parameter A IA is the most susceptible to inaccuracies in the covariance matrix.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2019

Development of Simplified Model Test Methods for Creep-Fatigue Evaluation

The Simplified Model Test (SMT) approach is an alternative creep-fatigue evaluation method that no longer requires the use of the damage interaction diagram, or D-diagram. The reason is that the combined effects of creep and fatigue are accounted for in the test data by means of a SMT specimen that is designed to replicate or bound the stress and strain redistribution that occurs in actual components when loaded in the creep regime. However, creep-fatigue experiments on SMT key feature articles are specialized and difficult to perform by the general research community. In this paper, two innovative SMT based creep-fatigue experimental methods are developed and implemented. These newly-developed SMT test methods have resolved all the critical challenges in the SMT key feature article testing and enable the potential of further development of the SMT based creep-fatigue evaluation method into a standard testing method. Scoping test results on Alloy 617 and SS 316H using the newly developed SMT methods are summarized and discussed. The concepts of the SMT methodology for creep-fatigue evaluation are explained.

Wang, Yanli↗

DOE OSTI2021

Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism

Abstract Background Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2671 families with autism (discovery cohort of 516 families, replication cohort of 2155 families). We focused on DNVs in enhancers with characterized in vivo activity in the brain and identified an excess of DNVs in an enhancer named hs737. Results We adapted the fitDNM statistical model to work in noncoding regions and tested enhancers for excess of DNVs in families with autism. We found only one enhancer (hs737) with nominal significance in the discovery (p = 0.0172), replication (p = 2.5 × 10 −3 ), and combined dataset (p = 1.1 × 10 −4 ). Each individual with a DNV in hs737 had shared phenotypes including being male, intact cognitive function, and hypotonia or motor delay. Our in vitro assessment of the DNVs showed they all reduce enhancer activity in a neuronal cell line. By epigenomic analyses, we found that hs737 is brain-specific and targets the transcription factor gene EBF3 in human fetal brain. EBF3 is genome-wide significant for coding DNVs in NDDs (missense p = 8.12 × 10 −35 , loss-of-function p = 2.26 × 10 −13 ) and is widely expressed in the body. Through characterization of promoters bound by EBF3 in neuronal cells, we saw enrichment for binding to NDD genes (p = 7.43 × 10 −6 , OR = 1.87) involved in gene regulation. Individuals with coding DNVs have greater phenotypic severity (hypotonia, ataxia, and delayed development syndrome [HADDS]) in comparison to individuals with noncoding DNVs that have autism and hypotonia. Conclusions In this study, we identify DNVs in the hs737 enhancer in individuals with autism. Through multiple approaches, we find hs737 targets the gene EBF3 that is genome-wide significant in NDDs. By assessment of noncoding variation and the genes they affect, we are beginning to understand their impact on gene regulatory networks in NDDs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Association of AK4 Protein From Stem Cell–Derived Neurons With Cognitive Reserve

Background and Objectives: Identifying protein targets that provide cognitive reserve is a strategy to prevent and treat Alzheimer disease and Alzheimer disease related dementias (AD/ADRD). Previous studies using bulk human brain tissue reported 12 proteins associated with cognitive reserve. This study examined whether the same proteins from induced neurons (iNs) are associated with cognitive reserve of their human donors. Methods: Here, induced pluripotent stem cell (iPSC) lines were generated from cryopreserved peripheral blood mononuclear cells of older adults who were autopsied as part of the Religious Orders Study or Rush Memory and Aging Project. Neurons were induced from iPSCs using a standard neurogenin2 protocol. Tandem mass tag proteomics analyses were conducted on iNs day 21. Cognitive reserve of their human donors was measured as person-specific slopes of cognitive change not accounted for by common neuropathologies. Results: The 53 human donors died at a mean age of 91 years, all were non-Latino White, and 36 (67.9%) were female. Eighteen were diagnosed with Alzheimer dementia proximate to death, and 34 had pathologic AD diagnosis at autopsy. Approximately 60% of the donors had above-average cognitive reserve such that their cognition declined slower than an average person with comparable burdens of neuropathologies. Eight of the 12 candidate proteins were quantified in iNs proteomics analyses. Higher adenylate kinase 4 (AK4) expression in iNs was associated with lower cognitive reserve, consistent with the previous report for brain AK4 expression. Discussion: By replicating cortical protein associations with cognitive reserve in human iNs, these data provide a valuable molecular readout for studying complex clinical phenotypes such as cognitive reserve in a dish.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Parameter Sensitivity Analysis of the SparTen High Performance Sparse Tensor Decomposition Software (Extended Analysis)

Tensor decomposition models play an increasingly important role in modern data science applications. One problem of particular interest is fitting a low-rank Canonical Polyadic (CP) tensor decomposition model when the tensor has sparse structure and the tensor elements are nonnegative count data. SparTen is a high-performance C++ library which computes a low-rank decomposition using different solvers: a first-order quasi-Newton or a second-order damped Newton method, along with the appropriate choice of runtime parameters. Since default parameters in SparTen are tuned to experimental results in prior published work on a single real-world dataset conducted using MATLAB implementations of these methods, it remains unclear if the parameter defaults in SparTen are appropriate for general tensor data. Furthermore, it is unknown how sensitive algorithm convergence is to changes in the input parameter values. This report addresses these unresolved issues with large-scale experimentation on three benchmark tensor data sets. Experiments were conducted on several different CPU architectures and replicated with many initial states to establish generalized profiles of algorithm convergence behavior.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Identifying a novel pathway for extracellular electron uptake in Methanosarcina barkeri using shotgun

The overarching goal of this project was to identify the genetic and/or enzymatic basis for extracellular electron uptake in Methanosarcina barkeri—an organism we previously characterized to be capable of this process using poised potential electrodes and a range of electrochemical techniques. In our first aim, we will utilized proteomic techniques that labels extracellular proteins with free amine groups with biotin and perform a selective purification of these proteins from the rest of the proteome. These were identified using mass spectrometry, providing us insight into the identity of the cell surface proteins, including redox active proteins present during extracellular electron uptake. We will also used an isobaric tagging technique (iTRAQ labeling) of proteomes from different experiment conditions to look at differential proteins expression and better understand the total pathway involved in extracellular electron uptake coupled to methanogenesis. In our final aim, we will investigated the electrochemical nature of electron uptake in co-cultures, compared to our pure culture data sets. We predict the process of electron uptake from electrodes replicates what goes on in nature when these organisms for co-cultures with electrogenic microbes such as Geobacter, and to test this hypothesis we have begun to probe co-cultures electrochemically during direct interspecies electron transfer. Our final aim took much longer than expected due to challenges replicating co-cultures between Geobacter metallireducens and Methanosarcina barkeri. We found the major problem with this work was the inability of the M. barkeri strain we used (and we tried strains from three different labs) to successfully grow on acetate in the absence of hydrogen. As such, we began to use the strain Methanosarcina acetivorans—another close relative that specializes on acetate growth. We are currently in the process of comparing electrochemical observations of this microorganism between pure and co-culture experiments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Corn Stover Removal Responses on Soil Test P and K Levels in Coastal Plain Ultisols

Corn (Zea mays L.) stover is used as a biofuel feedstock in the U.S. Selection of stover harvest rates for soils is problematic, however, because excessive stover removal may have consequences on plant available P and K concentrations. Our objective was to quantify stover harvest impacts on topsoil P and K contents in the southeastern U.S. Coastal Plain Ultisols. Five stover harvest rates (0, 25, 50, 75 and 100% by wt) were removed for five years from replicated plots. Grain and stover mass with P and K concentration data were used to calculate nutrient removal. Mehlich 1 (M1)-extractable P and K concentrations were used to monitor changes within the soils. Grain alone removed 13–15 kg ha –1 P and 15–18 kg ha –1 K each year, resulting in a cumulative removal of 70 and 85 kg ha –1 or 77 and 37% of the P and K fertilizer application, respectively. Harvesting stover increased nutrient removal such that when combined with grain removed, a cumulative total of 95% of the applied P and 126% of fertilizer K were taken away. This caused M1 P and K levels to decline significantly in the first year and even with annual fertilization to remain relatively static thereafter. For these Ultisols, we conclude that P and K fertilizer recommendations should be fine-tuned for P and K removed with grain and stover harvesting and that stover harvest of >50% by weight will significantly decrease soil test M1 P and K contents.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Data-Informed Synthetic Networks of Water Distribution Systems for Resilience Analysis in Puerto Rico

The increasing potential of infrastructure disruptions calls for high-quality infrastructure models to be used in resilience analysis and decision making. Unfortunately, many utilities and communities do not have access to accurate and detailed models due to a lack of data and resources. Furthermore, security restrictions on sharing infrastructure models present roadblocks to research, analysis, and decision making. Recent advances in the development of synthetic water distribution models provide a potential solution to this problem. There is an opportunity to improve these methods by leveraging incomplete pipe datasets to aid synthetic network generation. To address this gap, we developed a methodology for synthetic network generation that incorporates partial pipe data using a modification of the minimum cost flow algorithm for network generation and pipe sizing. This methodology demonstrates how partial pipe data can be leveraged to improve site-specific synthetic network generation. For the study area of Mayagüez, Puerto Rico, a synthetic model generated using 50% of real pipe data matches the pressure of the validation system with an average error of 23.5 m of head, which improves upon the average error of 31.6 m of head produced by a synthetic model generated using no data of the real pipes. Additionally, synthetic networks are shown to replicate the pressure response under a disruption scenario of the validation network, suggesting potential use in resilience analysis.

resilience analysis↗

DOE OSTI2020

Multiplexed binary assembly and quantitative tracking of bacterial populations

Compositions and methods for tracking combinations of mutations in populations by coupling DNA assembly and paired-end sequencing technology with high-throughput sequencing. This allows for an unlimited number of mutation sites in a population of microorganisms to be identified, and allows sites to be sequenced across several replicates. Unique identifiers (DNA barcodes) can be used to measure fitness data by sequencing of the barcodes multiplexed with the mutation sites with high-throughput short sequencing read technology, allowing selections to be rapidly performed on populations of known combinatorial genotypes.

59 BASIC BIOLOGICAL SCIENCES↗