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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Identifying intragenic functional modules of genomic variations associated with cancer phenotypes by learning representation of association networks

Background Genome-wide Association Studies (GWAS) aims to uncover the link between genomic variation and phenotype. They have been actively applied in cancer biology to investigate associations between variations and cancer phenotypes, such as susceptibility to certain types of cancer and predisposed responsiveness to specific treatments. Since GWAS primarily focuses on finding associations between individual genomic variations and cancer phenotypes, there are limitations in understanding the mechanisms by which cancer phenotypes are cooperatively affected by more than one genomic variation. Results This paper proposes a network representation learning approach to learn associations among genomic variations using a prostate cancer cohort. The learned associations are encoded into representations that can be used to identify functional modules of genomic variations within genes associated with early- and late-onset prostate cancer. The proposed method was applied to a prostate cancer cohort provided by the Veterans Administration’s Million Veteran Program to identify candidates for functional modules associated with early-onset prostate cancer. The cohort included 33,159 prostate cancer patients, 3181 early-onset patients, and 29,978 late-onset patients. The reproducibility of the proposed approach clearly showed that the proposed approach can improve the model performance in terms of robustness. Conclusions To our knowledge, this is the first attempt to use a network representation learning approach to learn associations among genomic variations within genes. Associations learned in this way can lead to an understanding of the underlying mechanisms of how genomic variations cooperatively affect each cancer phenotype. This method can reveal unknown knowledge in the field of cancer biology and can be utilized to design more advanced cancer-targeted therapies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Binary Quantum Control Optimization with Uncertain Hamiltonians

Optimizing the controls of quantum systems plays a crucial role in advancing quantum technologies. The time-varying noises in quantum systems and the widespread use of inhomogeneous quantum ensembles raise the need for high-quality quantum controls under uncertainties. In this paper, we consider a stochastic discrete optimization formulation of a discretized binary optimal quantum control problem involving Hamiltonians with predictable uncertainties. We propose a sample-based reformulation that optimizes both risk-neutral and risk-averse measurements of control policies, and solve these with two gradient-based algorithms using sum-up-rounding approaches. Furthermore, we discuss the differentiability of the objective function and prove upper bounds of the gaps between the optimal solutions to binary control problems and their continuous relaxations. We conduct numerical simulations on various sized problem instances based on two applications of quantum pulse optimization; we evaluate different strategies to mitigate the impact of uncertainties in quantum systems. In conclusion, we demonstrate that the controls of our stochastic optimization model achieve significantly higher quality and robustness compared with the controls of a deterministic model.

conditional value-at-risk (CVaR)↗
DOE OSTI2025

Preliminary Results on Bayesian Inverse UQ for OECD/NEA WPNCS Subgroup 14 Benchmark Exercise for Error Recovery and Experimental Coverage

The Organization for Economic Cooperation and Development (OECD) Working Party on Nucelar Criticality Safety (WPNCS) has proposed a benchmark exercise representative of neutronic behavior in criticality experiments. Here, the goal is to develop confidence in data assimilation techniques used to adjust nuclear data. Participants are given synthetic experimental models with associated measured data and asked to estimate the model parameters given the model and measurements as well as provide predictions for separate application models. In this work, we performed data assimilation using Bayesian inverse Uncertainty Quantification (UQ) with machine learning surrogate models to produce posterior parameter distributions for the requested parameters and posterior predictive distributions for the requested responses. Several experimental models are shown to insufficiently inform the posterior parameter distributions for the applications involved. However, given sufficient experimental data, posterior parameter estimates yielded reduced uncertainty in the response predictions of interest while covering the experimental data.

Bayesian Inference↗
DOE OSTI2025

Interferometric focal planes

We propose arrays of integrated interferometers to characterize the mutual intensity on focal planes. While focal coherence measurement does not increase the aperture-limited spatial bandpass, it can increase Shannon information capacity relative to irradiance measurement by increasing the number of degrees of freedom per Nyquist sample. We describe a sampling model for interferometric measurement using arrays of 2-port Mach-Zehnder interferometers and show within this model that interferometric focal planes enable more accurate estimation of prototypical scene parameters.

Brady, David J. (ORCID:0000000156552478)↗
DOE OSTI2023

Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages

Phages are one of the key ecological drivers of microbial community dynamics, function, and evolution. Despite their importance in bacterial ecology and evolutionary processes, phage genes are poorly characterized, hampering their usage in a variety of biotechnological applications. Methods to characterize such genes, even those critical to the phage life cycle, are labor intensive and are generally phage specific. Here, we develop a systematic gene essentiality mapping method scalable to new phage–host combinations that facilitate the identification of nonessential genes. As a proof of concept, we use an arrayed genome-wide CRISPR interference (CRISPRi) assay to map gene essentiality landscape in the canonical coliphages λ and P1. Results from a single panel of CRISPRi probes largely recapitulate the essential gene roster determined from decades of genetic analysis for lambda and provide new insights into essential and nonessential loci in P1. We present evidence of how CRISPRi polarity can lead to false positive gene essentiality assignments and recommend caution towards interpreting CRISPRi data on gene essentiality when applied to less studied phages. Finally, we show that we can engineer phages by inserting DNA barcodes into newly identified inessential regions, which will empower processes of identification, quantification, and tracking of phages in diverse applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Breaking the reproducibility barrier with standardized protocols for plant–microbiome research

Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure, where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.

Novak, Vlastimil↗
DOE OSTI2021

Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO)

Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5,000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a 10-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Recommended reporting items for epidemic forecasting and prediction research: The EPIFORGE 2020 guidelines

Background: The importance of infectious disease epidemic forecasting and prediction research is underscored by decades of communicable disease outbreaks, including COVID-19. Unlike other fields of medical research, such as clinical trials and systematic reviews, no reporting guidelines exist for reporting epidemic forecasting and prediction research despite their utility. We therefore developed the EPIFORGE checklist, a guideline for standardized reporting of epidemic forecasting research. Methods and findings: We developed this checklist using a best-practice process for development of reporting guidelines, involving a Delphi process and broad consultation with an international panel of infectious disease modelers and model end users. The objectives of these guidelines are to improve the consistency, reproducibility, comparability, and quality of epidemic forecasting reporting. The guidelines are not designed to advise scientists on how to perform epidemic forecasting and prediction research, but rather to serve as a standard for reporting critical methodological details of such studies. Conclusions: These guidelines have been submitted to the EQUATOR network, in addition to hosting by other dedicated webpages to facilitate feedback and journal endorsement.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Platelet cloaking of circulating tumour cells in patients with metastatic prostate cancer: Results from ExPeCT, a randomised controlled trial

Background: Circulating tumour cells (CTCs) represent a morphologically distinct subset of cancer cells, which aid the metastatic spread. The ExPeCT trial aimed to examine the effectiveness of a structured exercise programme in modulating levels of CTCs and platelet cloaking in patients with metastatic prostate cancer. Methods: Participants (n = 61) were randomised into either standard care (control) or exercise arms. Whole blood was collected for all participants at baseline (T0), three months (T3) and six months (T6), and analysed for the presence of CTCs, CTC clusters and platelet cloaking. CTC data was correlated with clinico-pathological information. Results: Changes in CTC number were observed within group over time, however no significant difference in CTC number was observed between groups over time. Platelet cloaking was identified in 29.5% of participants. A positive correlation between CTC number and white cell count (WCC) was observed (p = 0.0001), in addition to a positive relationship between CTC clusters and PSA levels (p = 0.0393). Conclusion: The presence of platelet cloaking has been observed in this patient population for the first time, in addition to a significant correlation between CTC number and WCC. Trial registration: ClincalTrials.gov identifier NCT02453139 .

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Water chemistry data and calculations for Fracture Sustainability Tests

Measured cation, anion, and silica are presented as well as calculations evaluating mass balance performed for 4 fracture sustainability tests under EGS conditions: Stripa granite, Metamudstone, Rhyolitic Ashflow Tuff, and Silicified Rhyolitic Tuff. Calculations of charge balance are included for water samples in the 4 tests.

15 GEOTHERMAL ENERGY↗
DOE OSTI2023

Artificial intelligence for materials research at extremes

Abstract Materials development is slow and expensive, taking decades from inception to fielding. For materials research at extremes, the situation is even more demanding, as the desired property combinations such as strength and oxidation resistance can have complex interactions. Here, we explore the role of AI and autonomous experimentation (AE) in the process of understanding and developing materials for extreme and coupled environments. AI is important in understanding materials under extremes due to the highly demanding and unique cases these environments represent. Materials are pushed to their limits in ways that, for example, equilibrium phase diagrams cannot describe. Often, multiple physical phenomena compete to determine the material response. Further, validation is often difficult or impossible. AI can help bridge these gaps, providing heuristic but valuable links between materials properties and performance under extreme conditions. We explore the potential advantages of AE along with decision strategies. In particular, we consider the problem of deciding between low-fidelity, inexpensive experiments and high-fidelity, expensive experiments. The cost of experiments is described in terms of the speed and throughput of automated experiments, contrasted with the human resources needed to execute manual experiments. We also consider the cost and benefits of modeling and simulation to further materials understanding, along with characterization of materials under extreme environments in the AE loop. Graphical abstract AI sequential decision-making methods for materials research: Active learning, which focuses on exploration by sampling uncertain regions, Bayesian and bandit optimization as well as reinforcement learning (RL), which trades off exploration of uncertain regions with exploitation of optimum function value. Bayesian and bandit optimization focus on finding the optimal value of the function at each step or cumulatively over the entire steps, respectively, whereas RL considers cumulative value of the labeling function, where the latter can change depending on the state of the system (blue, orange, or green).

36 MATERIALS SCIENCE↗
DOE OSTI2025

Materials laboratories of the future for alloys, amorphous, and composite materials

In alignment with the Materials Genome Initiative and as the product of a workshop sponsored by the US National Science Foundation, we define a vision for materials laboratories of the future in alloys, amorphous materials, and composite materials; chart a roadmap for realizing this vision; identify technical bottlenecks and barriers to access; and propose pathways to equitable and democratic access to integrated toolsets in a manner that addresses urgent societal needs, accelerates technological innovation, and enhances manufacturing competitiveness. Spanning three important materials classes, this article summarizes the areas of alignment and unifying themes, distinctive needs of different materials research communities, key science drivers that cannot be accomplished within the capabilities of current materials laboratories, and open questions that need further community input. Here, we provide a broader context for the workshop, synopsize the salient findings, outline a shared vision for democratizing access and accelerating materials discovery, highlight some case studies across the three different materials classes, and identify significant issues that need further discussion.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Multiscale approaches for optimizing the impact of strain on Na-ion battery cycle life

Abstract The high costs and geopolitical challenges inherent to the lithium-ion (Li-ion) battery supply chain have driven a rising interest in the development of sodium-ion (Na-ion) batteries as a potential alternative. Unfortunately, the larger ionic radius of Na limits the reversibility of cycling because of the extensive atomic rearrangements that accompany Na-ion insertion, which in turn limit diffusion and charging speed, and lead to rapid degradation of the electrodes. The Center for Strain Optimization for Renewable Energy (STORE) was established to address these challenges and develop new electrode materials for Na-ion cells. This article discusses the current state-of-the-art materials used in Na-ion cells and several directions that STORE believes are critical to understand and control the structural and volumetric changes during the reversible (de)insertion of large cations. Graphical abstract Highlights Understanding the fundamental way materials respond to localized strains at the atomic length-scale is a critical first step in the development of highly reversible, long cycle life, Na-ion insertion hosts. This perspective explores a variety of methods that can be employed to mitigate the detrimental effects of large strain. The insights gained from these investigations should help lay the foundation for the creation of more economical and sustainable batteries that could have immediate impact on global energy infrastructure. Discussion Although there is near universal agreement that electrochemical energy storage must be an integral part of a green-energy future, there is less agreement about how to reduce the cost of energy storage. Replacing high-cost lithium-ion cells with lower-cost sodium-ion batteries is one option frequently considered in future energy models, but the details of what can be achieve with optimized sodium cell performance remains unclear. Here we posit that developing methods to mitigating strain on the electrode particle length scale is a key factor for achieving long-cycle-life sodium-ion batteries. Mitigating strain on the atomic scale suppress electrode-level volume change. Allowing for fast cycling in materials without the problems of electrode cracking or delamination. We further posit that understanding volume change in sodium-ion electrodes at a fundamental level will lead to the designing new sodium-ion electrode materials that will allow for efficient, stable, lower-cost energy storage.

Brady, Michael J.↗
DOE OSTI2023

CCSI Toolset 3.19 Release

CCSI Toolset 3.19 Release Highlights A gradient generation tool was developed to support GENN models in FOQUS. Certain machine learning tools train gradient-enhanced neural network (GENN) models which can be more accurate for complex datasets given a priori knowledge of model derivatives. However, the derivatives must be known beforehand and are not often available for process data. This tool automatically predicts the gradients for a training dataset in a form usable by common GENN trainers, such as Surrogate Modeling Toolbox. Support was added for Surrogate Modeling Toolbox GENN models in FOQUS, including updates to the run methods, node properties, test framework, documentation and optional dependencies list. Users can train/save Surrogate Modeling Toolbox gradient-enhanced neural network (GENN) models with custom objects and produce .pkl files compatible with the Machine Learning/Artificial Intelligence Plugin in FOQUS. A simpler implementation of the ordering algorithm in the Sequential Design of Experiments (SDOE) module was included. The SDOE examples documentation was updated. The Optimality-Based Design of Experiments was updated to improve the error handling when the results are None.

AS↗
DOE OSTI2020

Oral Histories

Index of oral histories in our holdings.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2020

Optimizing an Integrated Renewable-Electrolysis System

Hydrogen is a versatile energy carrier that is used in a wide variety of chemical and industrial processes. Producing hydrogen using electrolysis can enable integration of multiple sectors including electricity, heating, and industrial sectors; however, the cost of producing hydrogen from electrolysis remains a challenge for encouraging greater adoption. With growing amounts of renewable generation on the California grid, there is downward pressure on wholesale electricity prices, particularly during the afternoon from photovoltaics (PV). These lower, or even potentially negative prices, challenge the business cases for new and existing PV plants. In addition, as the grid transitions to less flexible generation, there is greater need for system flexibility. To help improve the economics for both solar PV and hydrogen production using electrolyzers, we explore the benefit of combining PV and electrolysis systems. The optimal breakeven hydrogen production cost for six unique market participation configurations is calculated at six candidate locations where PV is already installed. The six market configurations include islanded, separated, retail, net energy metering (NEM), hybrid retail/wholesale and wholesale. Using the Revenue Operation and Device Optimization Model (RODeO) model, the optimal breakeven hydrogen price over the lifetime of the equipment is calculated. The cost includes production, storage, and compression in preparation for gaseous delivery trucks. Revenue streams include the sale of hydrogen, low carbon fuel standard (LCFS) credits, renewable electricity sold to the grid, and Renewable Energy Credits (REC). The costs included are the electricity costs, capital and fixed operation and maintenance cost (FOM) for the electrolyzer, PV, and storage and compression systems as well as taxes and financing costs. In addition, cost reductions are achieved through retail and wholesale rate optimization, by which electricity is purchased at the lowest price and sold, if possible, at the highest price. For all locations, the breakeven hydrogen production cost results show that, in the order of decreasing cost, the system configurations are islanded (highest), separated, NEM, retail, hybrid retail/wholesale, and wholesale (lowest). The resulting system design balances between the capital and maintenance cost components, the operation costs (i.e., electricity costs) and the additional market revenues. The integration of solar PV and electrolysis is shown to provide a mutually beneficial relationship. For PV, integration with electrolysis offers the potential to hedge against wholesale market price volatility, and integration with electrolysis may offer the potential to defer or avoid transmission investment to deliver power to the point-of-use and instead use it on-site. When compared with SMR without considering any renewable hydrogen premiums, this study finds that PV + Electrolysis systems with current costs are likely not competitive; however, with cost reductions for electrolysis equipment consistent with DOE projections, it was found that systems with wholesale market access would be competitive, largely on account of both low capital costs and low-cost electricity. The electrolysis units can provide greater flexibility than is required based on retail rate optimization, so there is an opportunity for a utility or CAISO to increase system flexibility with PV + Electrolysis systems in return for commensurate compensation. In this way, there are potentially several solutions that fall between the hybrid configuration and the wholesale configuration that could provide sufficient compensation for a PV + Electrolysis unit to compete with SMR while also providing greater flexibility to the grid.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2020

The Project Y Spies [Slides]

A talk on the subject of the various spies that were present at Los Alamos during the Manhattan Project.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2020

Oscar Seborer: Father of the Soviet Atomic Bomb?

Seventy-five years after the end of World War II, atomic spies continue to captivate and revolt the American public. Theodore "Ted" Hall, Klaus Fuchs, and David Greenglass all committed espionage at Los Alamos during the war. It has also been conjectured that there was an unidentified spy known only by the code-name PERSEUS, but there is a growing consensus among scholars that PERSEUS never existed. However, in September 2019, historians Harvey Klehr and John Earl Haynes unmasked a fourth Los Alamos spy code-named GODSEND. His name: Oscar Seborer. When the New York Times reported the story of Seborer's treachery in November 2019, almost nothing was known about his work at the Laboratory. However, recently discovered documents in the National Security Research Center (NSRC) at Los Alamos National Laboratory (LANL) offer some clues as to what GODSEND may have stolen for Stalin.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗