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At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

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↗
DOE OSTI2023

Cryo-EM structures reveal native GABA A receptor assemblies and pharmacology

Type A γ-aminobutyric acid receptors (GABA A Rs) are the principal inhibitory receptors in the brain and the target of a wide range of clinical agents, including anaesthetics, sedatives, hypnotics and antidepressants. However, our understanding of GABA A R pharmacology has been hindered by the vast number of pentameric assemblies that can be derived from 19 different subunits and the lack of structural knowledge of clinically relevant receptors. Here, we isolate native murine GABA A R assemblies containing the widely expressed α1 subunit and elucidate their structures in complex with drugs used to treat insomnia (zolpidem (ZOL) and flurazepam) and postpartum depression (the neurosteroid allopregnanolone (APG)). Using cryo-electron microscopy (cryo-EM) analysis and single-molecule photobleaching experiments, we uncover three major structural populations in the brain: the canonical α1β2γ2 receptor containing two α1 subunits, and two assemblies containing one α1 and either an α2 or α3 subunit, in which the single α1-containing receptors feature a more compact arrangement between the transmembrane and extracellular domains. Interestingly, APG is bound at the transmembrane α/β subunit interface, even when not added to the sample, revealing an important role for endogenous neurosteroids in modulating native GABA A Rs. Together with structurally engaged lipids, neurosteroids produce global conformational changes throughout the receptor that modify the ion channel pore and the binding sites for GABA and insomnia medications. Our data reveal the major α1-containing GABA A R assemblies, bound with endogenous neurosteroid, thus defining a structural landscape from which subtype-specific drugs can be developed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Pair distribution function analysis of nano-object assemblies

The atomic pair distribution function (aPDF) analysis technique, also known as the total scattering method, which considers both Bragg and diffuse scattering, has been used extensively to probe local atomic arrangements in crystalline and disordered materials. In contrast, there have been limited applications of the PDF in self-assembled nanomaterials, which represent a class of materials built from nanoscale objects, such as nano-colloids, micelles and proteins. As distinguished from atoms, nano-objects have polydispersity in size and shape, and such form-factor effects complicate the application of PDF analysis to nano-systems. Here, in this paper, the application of the PDF is extended to spherical nano-object assemblies and the formulae for the nano-PDF (nPDF) are derived, showing some differences from the aPDF. By numerical simulations, the properties of the nPDF (peak broadening and pattern profile) are studied systematically as a function of structural features, such as nano-object parameters (size and size polydispersity) and assembly structural features (size, shape, structure type and lattice disorder), and of data processing parameters ( q cut-off and `missing' data in ultra-small-angle regions). The nPDF analysis method is found to provide an effective route to revealing not only nanoscale but also mesoscale structural properties, for example the morphology of a nano-assembly.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

COVID-19 Evidence Accelerator: A parallel analysis to describe the use of Hydroxychloroquine with or without Azithromycin among hospitalized COVID-19 patients

Background: The COVID-19 pandemic remains a significant global threat. However, despite urgent need, there remains uncertainty surrounding best practices for pharmaceutical interventions to treat COVID-19. In particular, conflicting evidence has emerged surrounding the use of hydroxychloroquine and azithromycin, alone or in combination, for COVID-19. The COVID-19 Evidence Accelerator convened by the Reagan-Udall Foundation for the FDA, in collaboration with Friends of Cancer Research, assembled experts from the health systems research, regulatory science, data science, and epidemiology to participate in a large parallel analysis of different data sets to further explore the effectiveness of these treatments. Methods: Electronic health record (EHR) and claims data were extracted from seven separate databases. Parallel analyses were undertaken on data extracted from each source. Each analysis examined time to mortality in hospitalized patients treated with hydroxychloroquine, azithromycin, and the two in combination as compared to patients not treated with either drug. Cox proportional hazards models were used, and propensity score methods were undertaken to adjust for confounding. Frequencies of adverse events in each treatment group were also examined. Results: Neither hydroxychloroquine nor azithromycin, alone or in combination, were significantly associated with time to mortality among hospitalized COVID-19 patients. No treatment groups appeared to have an elevated risk of adverse events. Conclusion: Administration of hydroxychloroquine, azithromycin, and their combination appeared to have no effect on time to mortality in hospitalized COVID-19 patients. Continued research is needed to clarify best practices surrounding treatment of COVID-19.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

TEAMER: Biofouling Analysis for Wave Energy Piston Design - Load Cell Data

Biofouling and corrosion are a major concern for all ocean-deployed components, especially when mechanical motion is involved. Triton has developed the concept of a biofouling mitigation seal as part of the piston sealing assembly for the Triton Wave Energy Converter (TSI-WEC). This mitigation seal has the purpose of preventing the formation of a biofilm on the inside of the piston cylinder. It is hypothesized that the prevention of a biofilm will reduce the amount of macro-biofouling that can occur in the piston assembly. The mitigation seal can also reduce the wear on the main dynamic seal, helping to maintain smooth operation and water-tightness. The cylinder is made from a thermoset composite epoxy, which is resistant to corrosion. However, no studies have researched the material's performance with biofouling. Triton placed two prototype Power Take-Off (PTO) assemblies in a PNNL biofouling tank, one with a biofouling mitigation seal and one without, allowing for an evaluation of seal effectiveness at the prevention of biofouling. In actual WEC operation, wave action would react against the piston, which would drive the linear actuator and electric generator, providing electrical power. In the test setup, this was reversed; a linear actuator was powered to drive the piston in a consistent motion within the cylinder. There are two assemblies: one has a biofouling mitigation seal, the other (control) does not. The following data encompasses a 4 month test period, with load cells being used to monitor piston friction force. Results from this testing will be used to improve seal design and material selection, mitigating risk of premature failure during open water testing and evaluation. This project is part of the TEAMER RFTS 3 (request for technical support) program.

16 TIDAL AND WAVE POWER↗
DOE OSTI2020

30 cm Drop Modeling

This report documents modeling and analysis of the 30 cm cask drop scenario for spent nuclear fuel (SNF) casks. The 30 cm drop is an important hypothetical dynamic loading scenario for SNF because 10 CFR 71.71 defines testing requirements for normal conditions of transport (NCT) of SNF packages, and free drop (of 30 cm for the heaviest packages) tests are required. Other NCT conditions specified in 10 CFR 71.71 include vibration normally incident to transport, and DOE’s multimodal transportation test (MMTT) and related analysis concluded that mechanical shock and vibration incident to transportation is negligible for SNF structural integrity because the loads are so small. The SNF cask 30 cm drop has a lot more potential to cause damage to SNF because the kinetic energy and momentum of the system is stopped abruptly during the cask impact event. Test data and model predictions both agree that the SNF assemblies are subjected to significantly higher loads in a cask drop event than normal transportation shock and vibration, but currently there is no reason to expect gross structural damage of the fuel assembly or widespread SNF cladding failure as a result of a 30 cm cask drop. The ultimate goal of this work is to close the knowledge gap of stress profiles on SNF rods and fuel assembly components during NCT, and this report describes the progress toward reaching that goal as well as a plan for finishing this work over the next year or two. Key remaining tasks include refining the fuel assembly model, calculating a selection of specific fuel assembly cases to populate the damage model, and finally running the damage model to predict the full general response range of 30 cm drop loads on SNF.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Analysis and Grading of the Test Performance of PS Modules for the CMS Phase-2 Outer Tracker Upgrade

The Outer Tracker of the CMS experiment provides information about the trajectory of charged particles produced in proton-proton collisions at the LHC. During the High Luminosity LHC upgrade, scheduled for the late 2020s, the Outer Tracker will be replaced with new modules capable of transmitting data to the L1 Trigger. These modules are being assembled at several facilities around the world, including Fermilab, necessitating coordinated standards of module quality. Here I discuss the development of POTATO (Phase-2 Outer Tracker Analyzer of Test Outputs), a C++ software which provides a standardized procedure for analyzing and grading test results of the Outer Tracker modules. The particular focus of this poster is on the analysis and grading of the PS (pixel-strip) modules in POTATO.

Riggall, Caroline↗
DOE OSTI2024

Analysis and Grading of the Test Performance of PS Modules for the CMS Phase-II Outer Tracker Upgrade

The Outer Tracker detector of the Compact Muon Solenoid (CMS) experiment provides information about the trajectory of charged particles produced in proton-proton collisions at the Large Hadron Collider (LHC). During the High Luminosity LHC upgrade, scheduled for the late 2020s, the Outer Tracker will be replaced with new modules capable of transmitting data to the L1 Trigger. These modules are being assembled at several facilities around the world, including Fermilab, necessitating coordinated standards of module quality. Here I discuss the development of POTATO (Phase-II Outer Tracker Analyzer of Test Outputs), a C++ software which provides a standardized procedure for analyzing and grading test results of the Outer Tracker modules. The particular focus of this paper is on the analysis and grading of the PS (pixel-strip) modules in POTATO.

43 PARTICLE ACCELERATORS↗
DOE OSTI2020

Neutronic Consideration of TREAT Facility Fuel SiC Recladding

The Transient Reactor Test (TREAT) Facility is an air-cooled reactor composed of graphite-urania fuel encapsulated in zirconium alloy canisters and surrounded by ~2 ft (~61 cm) of nuclear grade graphite. The primary role of TREAT is to provide in-pile nuclear-heated safety research via transient testing [1]. Benchmark efforts have demonstrated sensitivity of TREAT neutronics models to graphite cross section data and key neutron poisons found in the fuel assemblies [2]. During fabrication of TREAT fuel assemblies, a small concentration of boron was inadvertently introduced with variable concentration into the aggregate of fuel blocks prepared for TREAT use. The concentration of boron, and its respective uncertainty, represent the most sensitive component in a neutronics study; unfortunately, nothing can be done to reduce or otherwise mitigate its impact. Hydrogen in the fuel blocks reduces the mean free path of the core and its true quantity and uncertainty is approximated. The hydrogen remains from pitch binder used in the fuel fabrication process and was not completely released due to incomplete fuel graphitization. Destructive fuel testing is necessary to quantify the actual hydrogen content and to improve benchmark model quality. A third neutron poison of some significance is the hafnium impurity in the Zircaloy-3 (Zry-3) assembly cladding. The quantity of hafnium is expected to be within nominal manufacturing limits for nuclear grade zircaloy. Recladding the fuel assemblies with material that is less neutron absorbing is expected to benefit reactor neutron economy. Moreover, TREAT’s total transient energy is restricted based on the rate of Zry-3 oxidation in TREAT’s air coolant environment. Hence, cladding with more benign air reaction kinetics could dramatically uprate the facility’s experimental capability. Silicon carbide (SiC) has been proposed as a candidate material for recladding TREAT assemblies, as SiC/SiC demonstrate favorable properties within nuclear environments [3]. The current operational limits of TREAT are restricted by the oxidation of Zry-3. Change of the cladding to SiC could feasibly double the current temperature limitation. Recladding opportunities allow for previously damaged fuel assemblies to be returned to service, as Zry-3 is not commercially available. The initial effort required to consider proceeding with any recladding effort is to neutronically characterize key reactor parameters while replacing Zry-3 with SiC. A characterization summary, with respective results, is provided herein.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Metagenome-assembled genome extraction and analysis from microbiomes using KBase

Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. In order to realize the hope of capturing Earth’s microbial genetic complement and to facilitate the investigation of the functional roles of specific lineages in a given ecosystem, technologies that accelerate the recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high-quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). Overall, these steps take about a day to obtain extracted genomes when starting from smaller environmental shotgun read libraries, or up to about a week from larger libraries. In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAGs, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq and others. While portions of such capabilities are available individually from other resources, the combination of the intuitive usability, data interoperability and integration of tools in a freely available computational resource makes KBase a powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended with additional MAG recovery and analysis tools, via the KBase software development kit (SDK).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Application of a Physics-Informed Convolutional Neural Network for Monitoring the Temperature Fields in High-Temperature Gas Reactors

Here, this work presents current advances in applying a physics-informed convolutional neural network (CNN) to evaluate temperature distributions in advanced reactors. Our goal is to demonstrate that the CNN can reconstruct temperature fields within the solid region of a prismatic fuel assembly in a high-temperature gas reactor (HTGR) with sensor data available in only a few cooling channels. Before that, we showcase the superior performance of the physics-informed CNN in comparison to a purely data-driven multilayer perceptron (MLP), considering a canonical heated channel setup. This analysis shows the advantages of our approach and justifies its choice. The datasets employed here are obtained upon numerical simulations performed with codes under the Nuclear Energy Advanced Modeling and Simulation program. This work is important, as industry experience indicates that the assembly material in HTGR concepts is prone to large thermal-mechanical loads nearing operational limits. This makes it crucial to characterize peak temperatures and their distributions near hot spots. Modern thermocouples are unreliable in these types of harsh environments because of the high neutron fluxes and elevated temperatures involved. The CNN-based field reconstruction represents an attractive solution, enabling sensor arrays in less aggressive locations and augmenting indirect predictions for less accessible regions. The results show that the CNN reduces prediction errors by orders of magnitude in comparison to the MLP, considering the simple yet well-representative heated channel case. In the case of the HTGR fuel assembly, the CNN can successfully reconstruct temperature fields over various cooling regimes. Furthermore, we also explore the algorithm’s ability to detect abnormalities. Interestingly, the CNN proves it has the capacity to detect blockage in one of the noninstrumented cooling channels.

Machine learning↗
DOE OSTI2021

Rossi-alpha Analysis of CURIE Experiment [Slides]

Critical assembly measurement and operations are crucial to the development of benchmark data. Knowledge of the prompt neutron lifetime informs on the state of the system’s neutron spectrum. Rossi-alpha analysis can give us time-dependent information on the system. Teflon was selected, via genetic algorithm, as a moderator to target the URR in uranium for CURIE. Rossi-alpha measurements of the assembly's approach to critical using He-3 detectors estimated the prompt neutron decay constant (α) at delayed critical. α values of several subcritical measurements were then used to predict the α value at delayed critical.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

High-Fidelity CFD Assessments of Flow Resistance in a 61-Pin Wire-Wrapped Assembly with Partially Blocked Channels

The examination of thermal-hydraulic behaviors in wire-wrapped rod bundles continues to be an active area of research. The sodium fast reactor, a prominent candidate in next-generation nuclear designs, utilizes a hexagonal configuration of wire-wrapped fuel pins. Here, the potential for channel blockage within this compact arrangement poses a significant safety challenge, spurring a number of recent experimental and computational investigations to evaluate its impact on flow and heat transfer. The present work aims to benchmark the high-fidelity NekRS computational fluid dynamics (CFD) solver in predicting the pressure drops associated with substantial blockages, using available experimental data as a reference. A 61-pin wire-wrapped fuel assembly with two flow blockage configurations has been simulated and investigated at a range of low to moderate Reynolds numbers (487 ≤ Re ≤ 14 600). The NekRS solver demonstrates an exponential reduction of spatial discretization error with increasing polynomial order. The high level of agreement between the numerical results and measured data confirms the accuracy and consistency of the present numerical approach. This benchmark study establishes the capability of NekRS to perform reliable hydrodynamic simulations for sodium fast reactor applications and supports its use in design, licensing, and safety analyses.

CFD Benchmarking↗
DOE OSTI2024

The SAGA Survey. V. Modeling Satellite Systems around Milky Way–Mass Galaxies with Updated UniverseMachine

Abstract Environment plays a critical role in shaping the assembly of low-mass galaxies. Here, we use the U niverse M achine (UM) galaxy–halo connection framework and Data Release 3 of the Satellites Around Galactic Analogs (SAGA) Survey to place dwarf galaxy star formation and quenching into a cosmological context. UM is a data-driven forward model that flexibly parameterizes galaxy star formation rates (SFRs) using only halo mass and assembly history. We add a new quenching model to UM, tailored for galaxies with m ⋆ ≲ 10 9 M ⊙ , and constrain the model down to m ⋆ ≳ 10 7 M ⊙ using new SAGA observations of 101 satellite systems around Milky Way (MW)–mass hosts and a sample of isolated field galaxies in a similar mass range from the Sloan Digital Sky Survey. The new best-fit model, “UM-SAGA,” reproduces the satellite stellar mass functions, average SFRs, and quenched fractions in SAGA satellites while keeping isolated dwarfs mostly star-forming. The enhanced quenching in satellites relative to isolated field galaxies leads the model to maximally rely on halo assembly to explain the observed environmental quenching. Extrapolating the model down to m ⋆ ∼ 10 6.5 M ⊙ yields a quenched fraction of ≳30% for isolated field galaxies and ≳80% for satellites of MW-mass hosts at this stellar mass. Spectroscopic surveys can soon test this specific prediction to reveal the relative importance of internal feedback, cessation of mass and gas accretion, satellite-specific gas processes, and reionization for the evolution of faint low-mass galaxies.

Wang, Yunchong (ORCID:000000018913626X)↗
DOE OSTI2020

Finding, Organizing, and Preserving Legacy Nuclear Test Monitoring Data—Examples from the Livermore Nevada Network

A challenge for geophysical research is the relatively short time for which continuous digital data have been available. There are many events of research interest where much of the data were collected by analog or temporary digital means. These legacy data require special efforts to find, organize, and preserve for future research. Here, we focus on one type of legacy data, nuclear explosions, and associated events (e.g., collapses, aftershocks) of high interest for nuclear monitoring research and development. For nuclear tests conducted in Nevada, the Lawrence Livermore Nevada Network recorded valuable data on a variety of formats. In this article, we briefly review this network, and describe one set of data that previously was available via CD-ROM by request, and since 2018 has become available through Incorporated Research Institutions for Seismology as assembled dataset 18-001.

58 GEOSCIENCES↗
DOE OSTI2021

JGI QC impact on assembly, binning, phylogenomics, and functional analysis

Background Investigators using metagenomic sequencing to study their microbiomes are often provided data that has been trimmed and decontaminated or do it themselves without knowing the effect these procedures can have on their downstream analyses. Here we evaluated the impact that JGI trimming and decontamination procedures had on assembly and binning metrics, placement of metagenome assembled genomes into species trees, and functional profiles of metagenome-assembled genomes (MAGs) extracted from twenty three complex rhizosphere metagenomes. We also investigated how more aggressive trimming impacts these binning metrics. Results We found that JGI trimmed and decontamination of input reads had some significant impacts in assembly and binning metrics compared to raw reads, and that differences in placement of MAGs in species trees increased with decreasing completeness and contamination thresholds. More aggressive trimming beyond those used by JGI were found to reduce MAG counts. Conclusions Mild trimming and decontamination of metagenomics reads prior to assembly can change an investigator’s answer to the questions, “Who is there and what are they doing? However, mild trimming and decontamination of metagenomic reads with high quality scores is recommended for those who elect to do so.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

HBU R and D Cask Transportation Options - 20436

The TN-32B HBU Demonstration Cask was successfully loaded in November 2017 with 32 high burnup (HBU) fuel assemblies at Dominion's North Anna Nuclear Plant and is collecting thermal data as intended. The first two phases of this very successful project sponsored by DOE and EPRI was designed to collect thermal data of HBU fuel to support extended storage. The next phase of the project requires the cask be licensed for transportation so the cask can be relocated to a site (to be determined by DOE) to facilitate long term monitoring and additional research on the fuel. This is a unique challenge given the constraints that exist for this particular bolted metal cask. The TN-32B cask is a 234,288 lb. (storage configuration) dry storage system that was selected for this project and it was modified to provide thermal data and the ability to collect gas samples after loading. Several major issues must be addressed to obtain the transport license including protecting the seven lid penetrations that were made to allow for the insertion of the thermocouples into the selected fuel assemblies after the cask was loaded. In order to protect the integrity of the research, the payload must remain as is. Therefore, the cask system must be placed into the transportation configuration without rewetting the fuel, replacing the lid and without removing the thermocouple instrumentation that is currently installed. A critical portion of the design and engineering that was performed in the first two phases of the project was to ensure that future transportation of the cask was integrated into the approach. Efforts were made to accommodate requirements such as containment boundary leakage testing, installation of impact limiter brackets and lid bolts suitable for transportation. Due to the science requirements of the project, the fuel selected was intended to yield the highest payload temperatures permitted to provide the greatest value for the researchers. This resulted in higher than usual external dose rates and surface temperatures that warranted performing as much preparatory work prior to cask loading to ensure ALARA and personnel safety to the greatest extent practical rather than working on a loaded cask. In addition to the work performed prior to cask load, there are remaining challenges such as protecting the modified lid, design and fabrication of impact limiters that accommodate the modified cask lid and preserving the thermocouple connections for continued monitoring. The project team is currently performing the necessary calculations, engineering, and design to support the licensing as required by the US NRC. Pre-application meetings have been held to inform the regulator of the planned technical approach to ensure compliance with the applicable regulations. The current plan is to obtain the transportation C of C by the end of 2021. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗