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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Tools for genetic engineering and gene expression control in Novosphingobium aromaticivorans and Rhodobacter sphaeroides

ABSTRACT Alphaproteobacteria have a variety of cellular and metabolic features that provide important insights into biological systems and enable biotechnologies. For example, some species are capable of converting plant biomass into valuable biofuels and bioproducts that have the potential to contribute to the sustainable bioeconomy. Among the Alphaproteobacteria, Novosphingobium aromaticivorans , Rhodobacter sphaeroides , and Zymomonas mobilis show promise as organisms that can be engineered to convert extracted plant lignin or sugars into bioproducts and biofuels. Genetic manipulation of these bacteria is needed to introduce engineered pathways and modulate expression of native genes with the goal of enhancing bioproduct output. Although recent work has expanded the genetic toolkit for Z. mobilis , N. aromaticivorans and R. sphaeroides still need facile, reliable approaches to deliver genetic payloads to the genome and to control gene expression. Here, we expand the platform of genetic tools for N. aromaticivorans and R. sphaeroides to address these issues. We demonstrate that Tn 7 transposition is an effective approach for introducing engineered DNA into the chromosome of N. aromaticivorans and R. sphaeroides . We screen a synthetic promoter library to identify isopropyl β-D-1-thiogalactopyranoside-inducible promoters with regulated activity in both organisms (up to ~15-fold induction in N. aromaticivorans and ~5-fold induction in R. sphaeroides ). Combining Tn 7 integration with promoters from our library, we establish CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) interference systems for N. aromaticivorans and R. sphaeroides (up to ~10-fold knockdown in N. aromaticivorans and R. sphaeroides ) that can target essential genes and modulate engineered pathways. We anticipate that these systems will greatly facilitate both genetic engineering and gene function discovery efforts in these species and other Alphaproteobacteria. IMPORTANCE It is important to increase our understanding of the microbial world to improve health, agriculture, the environment, and biotechnology. For example, building a sustainable bioeconomy depends on the efficient conversion of plant material to valuable biofuels and bioproducts by microbes. One limitation in this conversion process is that microbes with otherwise promising properties for conversion are challenging to genetically engineer. Here we report genetic tools for Novosphingobium aromaticivorans and Rhodobacter sphaeroides that add to the burgeoning set of tools available for genome engineering and gene expression in Alphaproteobacteria. Our approaches allow straightforward insertion of engineered pathways into the N. aromaticivorans or R. sphaeroides genome and control of gene expression by inducing genes with synthetic promoters or repressing genes using CRISPR interference. These tools can be used in future work to gain additional insight into these and other Alphaproteobacteria and to aid in optimizing yield of biofuels and bioproducts.

Hall, Ashley N.↗
DOE OSTI2021

Simple, Secure, Internet Delivery of MOOSE-based Applications

Application packaging and distribution are the final steps for delivering software to end-users; both are frequently neglected when creating scientific software. Commercial businesses rely on electronic distribution systems that have rendered disk drives obsolete. Still, national laboratories continue to rely heavily on removable media to distribute and limit access to controlled applications. With increasing concerns of unauthorized copying of sensitive applications, a modern distribution system that utilizes cryptographically secure communication and authentication protocols has been developed. This new distribution system will secure the chain of custody for nuclear software while simultaneously simplifying access to these tools. This report summarizes four primary advancements made toward the secure distribution of Nuclear Energy Advanced Modeling and Simulation (NEAMS)-developed, Multiphysics Object Oriented Simulation Environment (MOOSE)-based applications: application installation, package distribution, automated package building, and distribution of documentation. NEAMS is currently developing more than ten separate applications based on the open-source MOOSE Framework. Distribution of these applications has primarily been accomplished by distributing source code, with end-users compiling the applications themselves. This work created a mechanism where MOOSE applications can be installed in a similar way to any other software. This allows both administrators and end-users simplified access to runnable executables. With this new installation capability, it was then possible to rethink distribution. A new, secure capability for delivering MOOSE-based applications over the internet has been created. This system requires unique cryptographic tokens for authentication, greatly securing the custody chain for software. Once granted access, installation of any NEAMS code can be accomplished with these terminal commands: "conda install ncrc" "ncrc install ncrc-bison." After these two commands (and authenticating) the BISON application will be securely down- loaded from Idaho National Laboratory (INL)’s servers, installed, and ready to use. To enable this new distribution capability to be successful, the open-source Continuous Integration, Verification, Enhancement, and Testing (CIVET) Continuous Integration (CI) capability was augmented to add Continuous Delivery (CD). CD enables the automated building and packaging of MOOSE-based applications as they are modified by development teams, ensuring that our customers can obtain up-to-date versions of the software at any time. The need for instruction on how to use these applications was addressed through modifications to the MOOSE documentation system. The MooseDocs capability, which enables robust documentation of MOOSE-based applications, has been extended to allow both for the installation of documentation and the packaging of documentation with installed applications. Together, these enhancements form the core of a new, secure distribution mechanism for nuclear simulation tools. In concert with the Nuclear Computational Resource Center (NCRC), NEAMS- developed applications will now be straightforward to obtain securely.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

srlife: A Fast Tool for High Temperature Receiver Design and Analysis

This report describes a tool for estimating the structural service life of tubular, panel solar receivers operating at high temperatures. A complete version of the tool is available as open source software at https://github.com/Argonne-National-Laboratory/srlife and can be installed through the PyPi (https://pypi.org) package manager. Given the basic receiver geometry and the thermal loads on the receiver, the tool provides 1D, 2D, or 3D thermal and structural (single tube and simplified system) analysis and creep-fatigue service life prediction for six metallic alloys – 316H, 800H, Alloy 617, Alloy 740H, and Alloy 230. With the exception of Alloy 230 where the material data is preliminary, the software included a detailed set of models for the materials, well-supported by high temperature experimental test data. The tool is designed for easy integration with a software stack, including solar field and thermohydraulic simulations, for optimizing receiver designs to meet service life and economic targets. The report describes several heuristics that can be applied in srlife to reduce the analysis time by several orders of magnitude but with fairly accurate life estimation when compared with full analysis. The report provides several examples demonstrating the utility of srlife in receiver design. Finally, the report discusses high temperature tests on Alloy 282, collected as part of this project, used to develop and support the material model for that alloy.

47 OTHER INSTRUMENTATION↗
DOE OSTI2018

LncRNA cancer susceptibility candidate 15 accelerates the breast cancer cells progression via miR-153–3p/KLF5 positive feedback loop

Highlights: • CASC15 expression level was aberrantly high-expressed in breast cancer tissue specimens and cells. • Loss-of-functional experiments showed that knockdown of CASC15 suppressed the malignant behaviors of breast cancer cells. • CASC15 functioned as ceRNA of miR-153–3p, besides, miR-153–3p targeted the 3‘-UTR of KLF5 mRNA. • KLF5 binds with the promoter region of CASC15 and activates the transcription. Emerging literature have illustrated the vital regulatory roles of long noncoding RNAs (lncRNAs) on the breast cancer tumorigenesis. Although series of researches have been proceeded on the pathogenesis, there are still much of unsolved mysteries worth investigating. This study uncovered that CASC15 expression level was aberrantly high-expressed in breast cancer tissue specimens and cells. Functionally, the loss-of-functional experiments showed that knockdown of CASC15 suppressed the malignant behaviors of breast cancer cells, such as proliferation, invasion and tumor growth in vitro and vivo. Mechanically, we confirmed that CASC15 functioned as a competing endogenous RNA (ceRNA) of miR-153–3p, besides, miR-153–3p targeted the 3‘-UTR of KLF5 mRNA utilizing the bioinformatics online tools, luciferase reporter assay and RNA immunoprecipitation. Interestingly, we confirmed that the transcription factor KLF5 binds with the promoter region of CASC15 and activates the transcription. In conclusion, we validated the positive feedback loop of KLF5/CASC15/miR-153–3p/KLF5 in the acceleration of breast cancer malignant behaviors and tumorigenesis, suggesting the important biologic roles of CASC15 on the breast cancer tumorigenesis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Structure-Guided Development of a Potent and Selective Non-covalent Active-Site Inhibitor of USP7

Deubiquitinating enzymes (DUBs) have garnered significant attention as drug targets in the last 5–10 years. The excitement stems in large part from the powerful ability of DUB inhibitors to promote degradation of oncogenic proteins, especially proteins that are challenging to directly target but which are stabilized by DUB family members. Highly optimized and well-characterized DUB inhibitors have thus become highly sought after tools. Most reported DUB inhibitors, however, are polypharmacological agents possessing weak (micromolar) potency toward their primary target, limiting their utility in target validation and mechanism studies. Due to a lack of high-resolution DUB∙small-molecule ligand complex structures, no structure-guided optimization efforts have been reported for a mammalian DUB. In this paper, we report a small-molecule∙ubiquitin-specific protease (USP) family DUB co-structure and rapid design of potent and selective inhibitors of USP7 guided by the structure. Interestingly, the compounds are non-covalent active-site inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Integrating diagnostics and model-based optimization

Energy Management and Information Systems are a family of analytics technologies that include energy information systems, fault detection and diagnostics (FDD), and automated system optimization tools. Such systems have the potential to enable buildings to meet energy management goals of reducing total energy consumption and cost. Most current market offerings use data-driven and rule-based analytics. However, the use of physics-based models in the analytics offers potential improvements by providing an accurate estimation of outputs based on representation of the physical principles governing the building system behaviors. This also permits the use of design stage models to inform commissioning and operation. This paper describes the development and testing of a hybrid data-driven and physics model-based operational tool for energy efficiency in central cooling plants. The tool offers FDD functionality, setpoint optimization, and visualization of key performance parameters. It was demonstrated at a university campus in the mixed-humid ASHRAE Climate Zone 4A. Key performance metrics that were analyzed include plant electricity use reduction, plant model calibration, and system economics. Annual simulations indicate the tool can provide electricity savings of greater than 10% for approximately six months of the year, mainly during the winter season when wet bulb temperatures are low, though only 1.38% savings for the entire year. Additionally, over a 4-day period in April, recommended optimal setpoints were implemented, resulting in 17% savings versus metered baseline consumption. With respect to model calibration, the difference between model-predicted and measured parameters was less than 10% for 90% of data points acquired for three of six chillers, and for each ten cooling towers. Finally, the tool users reported that satisfaction with the capabilities was equal to or better than that with the preexisting BAS system.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2017

Peripheral Blood Biomarkers Associated With Toxicity and Treatment Characteristics After 131 I- Metaiodobenzylguanidine Therapy in Patients With Neuroblastoma

We report few tools exist to predict clinical outcomes after radiopharmaceutical therapy. Our goal was to identify associations between blood-based biomarkers of radiation effect and clinical outcomes after 131 I-metaiodobenzylguanidine ( 131 I-MIBG) therapy in patients with neuroblastoma. We conducted a prospective, single-center cohort study in children with advanced neuroblastoma treated with 131 I-MIBG as monotherapy or in combination with systemic putative radiation sensitizers. We collected serial peripheral blood samples after 131 I-MIBG infusions and quantified a panel of protein and messenger RNA markers. We plotted relative change from baseline to assess degree of modulation over time and then evaluated association of marker modulation with toxicity and response endpoints. The cohort included 40 patients (30 male/10 female; median age 7 years). We observed significant modulation of the majority of markers between baseline and hour 72 after 131 I-MIBG. Greater fold increase of plasma FLT3 ligand was associated with subsequent grade 4 neutropenia (P=.039). Modulation of peripheral blood BCLXL and DDB2 was associated with grade 3+ nonhematologic toxicity (P=.043 and .048, respectively). No markers were associated with tumor response. Greater plasma FLT3 ligand, BCLXL, and BCL2 modulation was observed in patients receiving 131 I-MIBG in combination with radiation sensitizers. Among 9 patients who received 2 courses, the degree of modulation in serum amylase was significantly lower after the second course (P=.012). Peripheral blood biomarkers relevant to radiation exposure are significantly modulated during the acute period after 131 I-MIBG. The degree of modulation of a subset of these markers is associated with toxicity and receipt of concomitant radiation sensitizers.

131I-MIBG↗
DOE OSTI2025

A Markov chain Monte Carlo (MCMC) Bayesian inference approach to analyze apparent activation barriers and reaction orders from microreactor data

Statistical analysis of steady-state catalytic kinetic data is often limited by data sparsity due to the slow pace at which the data is collected. Data sparsity and limitations in statistical analysis make it difficult to differentiate between mechanistic models and catalytic sites. A Bayesian inference tool is reported for catalysis researchers to estimate error in the determination of reaction orders from steady state microreactor data. The benefits of a Bayesian inference approach are discussed, as an alternative to the more common frequentist approach. The approach incorporates prior knowledge of the system and the data collected to form an error estimate on reaction orders. We investigated the effects of three distinct data treatments—individual fitting of trials, pooled analysis, and constrained regression methods—on the precision and uncertainty of reaction order determinations. To assess the robustness of our findings, we conducted sensitivity analyses to evaluate the influence of Bayesian parameters on uncertainty estimation. Additionally, we utilized synthetic data to illustrate how data quality impacts the precision of uncertainty assessments. We show Bayesian analysis can obtain a more precise estimation of error with a sparse data set than a frequentist analysis. Finally, this work provides strong evidence that the adoption of Bayesian analysis of kinetic data may help researchers make more precise arguments as to the strength of their evidence for a particular mechanistic hypothesis, or in comparing across different catalysts.

42 ENGINEERING↗
DOE OSTI2018

Deconvolution of octahedral Pt 3 Ni nanoparticle growth pathway from in situ characterizations

Understanding the growth pathway of faceted alloy nanoparticles at the atomic level is crucial to morphology control and property tuning. Yet, it remains a challenge due to complexity of the growth process and technical limits of modern characterization tools. We report a combinational use of multiple cutting-edge in situ techniques to study the growth process of octahedral Pt3Ni nanoparticles, which reveal the particle growth and facet formation mechanisms. Our studies confirm the formation of octahedral Pt 3 Ni initiates from Pt nuclei generation, which is followed by continuous Pt reduction that simultaneously catalyzes Ni reduction, resulting in mixed alloy formation with moderate elemental segregation. Furthermore, carbon monoxide molecules serve as a facet formation modulator and induce Ni segregation to the surface, which inhibits the (111) facet growth and causes the particle shape to evolve from a spherical cluster to an octahedron as the (001) facet continues to grow.

36 MATERIALS SCIENCE↗
DOE OSTI2024

3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties

Abstract Motivation BISCAP is a state-of-the-art tool for automatically characterizing biofilm images obtained from Optical Coherence Tomography. Limited availability of other software tools is reported in the field. BISCAP’s first version processes 2D images only. Processing 3D images is a problem of greater scientific relevance since it deals with the entire structure of biofilms instead of their 2D slices. Results Building on the image-processing principles and algorithms proposed earlier for 2D images, these were adapted to the 3D case, and a more general implementation of BISCAP was developed. The primary goal concerns the extension of the initial methodology to incorporate the depth axis in 3D images; multiple improvements were also made to boost computational performance. The calculation of structural properties and visual outputs was extended to offer new insights into the 3D structure of biofilms. BISCAP was tested using 3D images of biofilms with different morphologies, consistently delivering accurate characterizations of 3D structures in a few minutes using standard laptop machines. Low user dependency is required for image analysis. Availability and implementation BISCAP is available from https://github.com/diogonarciso/BISCAP. All images used in the tutorials and the validation examples are available from https://web.fe.up.pt/∼fgm/biscap3d.

Narciso, Diogo A. C. (ORCID:0000000227767477)↗
DOE OSTI2016

Voltage Support Study of Smart PV Inverters on a High-Photovoltaic Penetration Utility Distribution Feeder

This paper reports on tools and methodologies developed to study the impact of adding rooftop photovoltaic (PV) systems, with and without the ability to provide voltage support, on the voltage profile of distribution feeders. Simulation results are provided from a study of a specific utility feeder. The simulation model of the utility distribution feeder was built in OpenDSS and verified by comparing the simulated voltages to field measurements. First, we set all PV systems to operate at unity power factor and analyzed the impact on feeder voltages. Then we conducted multiple simulations with voltage support activated for all the smart PV inverters. These included different constant power factor settings and volt/VAR controls.

14 SOLAR ENERGY↗
DOE OSTI2016

SU-C-BRB-05: Determining the Adequacy of Auto-Contouring Via Probabilistic Assessment of Ensuing Treatment Plan Metrics in Comparison with Manual Contours

Purpose: To determine if auto-contour and manual-contour—based plans differ when evaluated with respect to probabilistic coverage metrics and biological model endpoints for prostate IMRT. Methods: Manual and auto-contours were created for 149 CT image sets acquired from 16 unique prostate patients. A single physician manually contoured all images. Auto-contouring was completed utilizing Pinnacle’s Smart Probabilistic Image Contouring Engine (SPICE). For each CT, three different 78 Gy/39 fraction 7-beam IMRT plans are created; PD with drawn ROIs, PAS with auto-contoured ROIs, and PM with auto-contoured OARs with the manually drawn target. For each plan, 1000 virtual treatment simulations with different sampled systematic errors for each simulation and a different sampled random error for each fraction were performed using our in-house GPU-accelerated robustness analyzer tool which reports the statistical probability of achieving dose-volume metrics, NTCP, TCP, and the probability of achieving the optimization criteria for both auto-contoured (AS) and manually drawn (D) ROIs. Metrics are reported for all possible cross-evaluation pairs of ROI types (AS,D) and planning scenarios (PD,PAS,PM). Bhattacharyya coefficient (BC) is calculated to measure the PDF similarities for the dose-volume metric, NTCP, TCP, and objectives with respect to the manually drawn contour evaluated on base plan (D-PD). Results: We observe high BC values (BC≥0.94) for all OAR objectives. BC values of max dose objective on CTV also signify high resemblance (BC≥0.93) between the distributions. On the other hand, BC values for CTV’s D95 and Dmin objectives are small for AS-PM, AS-PD. NTCP distributions are similar across all evaluation pairs, while TCP distributions of AS-PM, AS-PD sustain variations up to %6 compared to other evaluated pairs. Conclusion: No significant probabilistic differences are observed in the metrics when auto-contoured OARs are used. The prostate auto-contour needs improvement to achieve clinically equivalent plans.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

MO-FG-CAMPUS-TeP1-01: An Efficient Method of 3D Patient Dose Reconstruction Based On EPID Measurements for Pre-Treatment Patient Specific QA

Purpose: To demonstrate an efficient and clinically relevant patient specific QA method by reconstructing 3D patient dose from 2D EPID images for IMRT plans. Also to determine the usefulness of 2D QA metrics when assessing 3D patient dose deviations. Methods: Using the method developed by King et al (Med Phys 39(5),2839–2847), EPID images of IMRT fields were acquired in air and converted to dose at 10 cm depth (SAD setup) in a flat virtual water phantom. Each EPID measured dose map was then divided by the corresponding treatment planning system (TPS) dose map calculated with an identical setup, to derive a 2D “error matrix”. For each field, the error matrix was used to adjust the doses along the respective ray lines in the original patient 3D dose. All field doses were combined to derive a reconstructed 3D patient dose for quantitative analysis. A software tool was developed to efficiently implement the entire process and was tested with a variety of IMRT plans for 2D (virtual flat phantom) and 3D (in-patient) QA analysis. Results: The method was tested on 60 IMRT plans. The mean (± standard deviation) 2D gamma (2%,2mm) pass rate (2D-GPR) was 97.4±3.0% and the mean 2D gamma index (2D-GI) was 0.35±0.06. The 3D PTV mean dose deviation was 1.8±0.8%. The analysis showed very weak correlations between both the 2D-GPR and 2D-GI when compared with PTV mean dose deviations (R2=0.3561 and 0.3632 respectively). Conclusion: Our method efficiently calculates 3D patient dose from 2D EPID images, utilising all of the advantages of an EPID-based dosimetry system. In this study, the 2D QA metrics did not predict the 3D patient dose deviation. This tool allows reporting of the 3D volumetric dose parameters thus providing more clinically relevant patient specific QA.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

GeoRePORT Case Studies - Coso, WSMR, Dixie Valley, and Chena Hot Springs

The Geothermal Resource Portfolio Optimization and Reporting Technique (GeoRePORT) was developed with funding from the U.S. Department of Energy Geothermal Technologies Office to assist in identifying and pursuing long-term investment strategies through the development of a resource reporting protocol. GeoRePORT provides scientists and nonscientists a comprehensive and quantitative means of reporting: (1) features intrinsic to geothermal sites (project grade) and (2) maturity of the development (project readiness). Because geothermal feasibility is not determined by any single factor (e.g., temperature, permeability, permitting), a site?s project grade and readiness are evaluated on 12 attributes pertaining to geological, technical, or socio-economic feasibility. In this paper, we present case studies showing how GeoRePORT can be used to compare geological, technical, and socio-economic attributes between geothermal systems. The consistent and objective assessment protocols used in GeoRePORT allow for comparison of project attributes across unique locations and geological settings. GeoRePORT case studies presented here outline the geological, socio-economic, and technical features of four individual geothermal sites: Coso, Chena, Dixie Valley, and White Sands Missile Range. The case studies illustrate the usefulness of GeoRePORT in evaluating project risk and return, identifying gaps in reported data, evaluating R&D impact, and gathering insights on successes and failures as applicable to future projects.

15 GEOTHERMAL ENERGY↗
DOE OSTI2020

NuMI Beam Muon Monitor Data Analysis and Simulation for Improved Beam Monitoring

The NuMI muon monitors (MMs) are a very important diagnostic tool for monitoring the stability of the neutrino beam used by the NOvA experiment at Fermilab. The goal of our study is to maintain the quality of the MM signal and to establish the correlations between the neutrino and muon beam profile. This study could also inform the LBNF decision on the beam diagnostic tools. We report on the progress of beam scan data analysis (beam position, spot size, and magnetic horn current scan) and comparison with the simulation outcomes.

43 PARTICLE ACCELERATORS↗
DOE OSTI2014

Technology Readiness Levels for Advanced Nuclear Fuels and Materials Development

The Technology Readiness Level (TRL) process is used to quantitatively assess the maturity of a given technology. The TRL process has been developed and successfully used by the Department of Defense (DOD) for development and deployment of new technology and systems for defense applications. In addition, NASA has also successfully used the TRL process to develop and deploy new systems for space applications. Advanced nuclear fuels and materials development is a critical technology needed for closing the nuclear fuel cycle. Because the deployment of a new nuclear fuel forms requires a lengthy and expensive research, development, and demonstration program, applying the TRL concept to the advanced fuel development program is very useful as a management and tracking tool. This report provides definition of the technology readiness level assessment process as defined for use in assessing nuclear fuel technology development for the Advanced Fuel Campaign (AFC).

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2016

High-Throughput Method for Strontium Isotope Analysis by Multi-Collector-Inductively Coupled Plasma-Mass Spectrometer

This technical report presents the details of the Sr column configuration and the high-throughput Sr separation protocol. Data showing the performance of the method as well as the best practices for optimizing Sr isotope analysis by MC-ICP-MS is presented. Lastly, this report offers tools for data handling and data reduction of Sr isotope results from the Thermo Scientific Neptune software to assist in data quality assurance, which help avoid issues of data glut associated with high sample throughput rapid analysis.

47 OTHER INSTRUMENTATION↗