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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Identification of small-molecule protein–protein interaction inhibitors for NKG2D

NKG2D (natural-killer group 2, member D) is a homodimeric transmembrane receptor that plays an important role in NK, γδ + , and CD8 + T cell-mediated immune responses to environmental stressors such as viral or bacterial infections and oxidative stress. However, aberrant NKG2D signaling has also been associated with chronic inflammatory and autoimmune diseases, and as such NKG2D is thought to be an attractive target for immune intervention. Here, in this study, we describe a comprehensive small-molecule hit identification strategy and two distinct series of protein–protein interaction inhibitors of NKG2D. Although the hits are chemically distinct, they share a unique allosteric mechanism of disrupting ligand binding by accessing a cryptic pocket and causing the two monomers of the NKG2D dimer to open apart and twist relative to one another. Leveraging a suite of biochemical and cell-based assays coupled with structure-based drug design, we established tractable structure–activity relationships with one of the chemical series and successfully improved both the potency and physicochemical properties. Together, we demonstrate that it is possible, albeit challenging, to disrupt the interaction between NKG2D and multiple protein ligands with a single molecule through allosteric modulation of the NKG2D receptor dimer/ligand interface.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Structural and Functional Characterization of DUF1471 Domains of Salmonella Proteins SrfN, YdgH/SssB, and YahO

Bacterial species in the Enterobacteriaceae typically contain multiple paralogues of a small domain of unknown function (DUF1471) from a family of conserved proteins also known as YhcN or BhsA/McbA. Proteins containing DUF1471 may have a single or three copies of this domain. Representatives of this family have been demonstrated to play roles in several cellular processes including stress response, biofilm formation, and pathogenesis. We have conducted NMR and X-ray crystallographic studies of four DUF1471 domains from Salmonella representing three different paralogous DUF1471 subfamilies: SrfN, YahO, and SssB/YdgH (two of its three DUF1471 domains: the N-terminal domain I (residues 21–91), and the C-terminal domain III (residues 244–314)). Notably, SrfN has been shown to have a role in intracellular infection by Salmonella Typhimurium. These domains share less than 35% pairwise sequence identity. Structures of all four domains show a mixed a+b fold that is most similar to that of bacterial lipoprotein RcsF. However, all four DUF1471 sequences lack the redox sensitive cysteine residues essential for RcsF activity in a phospho-relay pathway, suggesting that DUF1471 domains perform a different function(s). SrfN forms a dimer in contrast to YahO and SssB domains I and III, which are monomers in solution. A putative binding site for oxyanions such as phosphate and sulfate was identified in SrfN, and an interaction between the SrfN dimer and sulfated polysaccharides was demonstrated, suggesting a direct role for this DUF1471 domain at the host-pathogen interface.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2010

Versatile modes of peptide recognition by the AAA+ adaptor protein SspB

Energy-dependent proteases often rely on adaptor proteins to modulate substrate recognition. The SspB adaptor binds peptide sequences in the stress-response regulator RseA and in ssrA-tagged proteins and delivers these molecules to the AAA+ ClpXP protease for degradation. The structure of SspB bound to an ssrA peptide is known. Here, we report the crystal structure of a complex between SspB and its recognition peptide in RseA. Notably, the RseA sequence is positioned in the peptide-binding groove of SspB in a direction opposite to the ssrA peptide, the two peptides share only one common interaction with the adaptor, and the RseA interaction site is substantially larger than the overlapping ssrA site. This marked diversity in SspB recognition of different target proteins indicates that it is capable of highly flexible and dynamic substrate delivery.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Predicting sedimentary bedrock subsurface weathering fronts and weathering rates: Dataset

Although bedrock weathering strongly influences water quality and global carbon and nitrogen budgets, the weathering depths and rates within subsurface are not well understood nor predictable. Determination of both porewater chemistry and subsurface water flow are needed in order to develop more complete understanding and obtain weathering rates. In a long-term field study, we applied a multiphase approach along a mountainous watershed hillslope transect underlain by marine shale. Here we report three findings. First, the deepest extent of the water table determines the weathering front, and the range of annually water table oscillations determines the thickness of the weathering zone. Below the lowest water table, permanently water-saturated bedrock remains reducing, preventing deeper pyrite oxidation. Secondly, carbonate minerals and potentially rock organic matter share the same weathering front depth with pyrite, contrary to models where weathering fronts are stratified. Thirdly, the measurements-based weathering rates from subsurface shale are high, amounting to base cation exports of about 70 kmolc ha−1 y−1, yet consistent with weathering of marine shale. Finally, by integrating geochemical and hydrological data we present a new conceptual model that can be applied in other settings to predict weathering and water quality responses to climate change.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1999

System Identification for Integrated Aircraft Development and Flight Testing [l'Identification Des Systemes Pour le Developpement Integre des Aeronefs et les Essais en Vol]

Over the last decades flight vehicles such as aircraft and helicopters entering service and requiring increased operational effectiveness have with few exceptions experienced prolonged flight test development to achieve full certification. In many cases the original requirements had later to be reduced to enable release to service. The impact on the customer, and manufacturer has been considerable leading to increased costs and or reduced operational capabilities. These costly experiences are largely a result of the flight vehicle not behaving as modelled and designed. The evaluation of flight test data can be used as a tool for validating windtunnel results and mathematical models describing the flight dynamical behaviour. In this sense the uncertainty of important aerodynamic stability and control parameters can be reduced and the confidence of aircraft mathematical models improved. An additional important factor comes from the implementation of active control systems offering the promise of significantly increased flight vehicle performance and operational capability. This approach extends the traditional trade-offs between aerodynamics, structures and propulsion systems to include full- time, full-authority fly-by-wire/light systems. It is imperative that the aerodynamic stability and control parameters of such integrated flight and propulsion control systems have to turn out inflight as predicted, since inherent stability margins will be lower and the flight control system must correct these deficiencies to provide flight critical redundancy and safety. With the methodology of system identification from flight tests it is possible to sense the control inputs and the flight vehicle reactions Such as accelerations, rates and attitudes. The mathematical model, e.g. the model structure and parameters, has to be determined from the relationship of the measured control inputs and the system's responses. The aim of this symposium was to review the present state of the art of flight vehicle system and parameter identification techniques, and to provide a critical appraisal of current methods developed and applied to flight test data in a number of NATO nations. Particular emphasis was placed on practical aspects and lessons learned in order to generate information useful to the flight test community in industry and government agencies. The technical papers share invaluable experience and emphasize the advances of flight vehicle system identification over the last years to the point where confidence and robustness level is now reasonably high. The symposium covered overviews of identification methodologies, flight test techniques, recent aircraft and helicopter application programs, and a session of short papers covering up-to-the-minute flight test results. A final discussion included prepared comments from experts and concluded with key issues learned in the application of system identification and future research needs. The essential benefits to NATO nations can be condensed as follows: More accurate mathematical models for high bandwidth flight control systems, Improved assessment and evaluation of flying qualities, High fidelity mathematical models for flight vehicle development and mission training simulators, and generally, Reduced flight test time and costs.

Advisory Group for Aerospace Research and Developm↗
DOE OSTI2020

A Cation-Tethered Flowable Polymeric Interface for Enabling Stable Deposition of Metallic Lithium

A fundamental challenge, shared across many energy storage devices, is the complexity of electrochemistry at the electrode–electrolyte interfaces that impacts the Coulombic efficiency, operational rate capability, and lifetime. Specifically, in energy-dense lithium metal batteries, the charging/discharging process results in structural heterogeneities of the metal anode, leading to battery failure by short-circuit and capacity fade. In this work, we take advantage of organic cations with lower reduction potential than lithium to build an electrically responsive polymer interface that not only adapts to morphological perturbations during electrodeposition and stripping but also modulates the lithium ion migration pathways to eliminate surface roughening. As a result, we find that this concept can enable prolonging the long-term cycling of a high-voltage lithium metal battery by at least twofold compared to bare lithium metal.

25 ENERGY STORAGE↗
DOE OSTI2019

Predicting sedimentary bedrock subsurface weathering fronts and weathering rates

Although bedrock weathering strongly influences water quality and global carbon and nitrogen budgets, the weathering depths and rates within subsurface are not well understood nor predictable. Determination of both porewater chemistry and subsurface water flow are needed in order to develop more complete understanding and obtain weathering rates. In a long-term field study, we applied a multiphase approach along a mountainous watershed hillslope transect underlain by marine shale. Here we report three findings. First, the deepest extent of the water table determines the weathering front, and the range of annually water table oscillations determines the thickness of the weathering zone. Below the lowest water table, permanently water-saturated bedrock remains reducing, preventing deeper pyrite oxidation. Secondly, carbonate minerals and potentially rock organic matter share the same weathering front depth with pyrite, contrary to models where weathering fronts are stratified. Thirdly, the measurements-based weathering rates from subsurface shale are high, amounting to base cation exports of about 70 kmol c ha -1 y -1 , yet consistent with weathering of marine shale. Finally, by integrating geochemical and hydrological data we present a new conceptual model that can be applied in other settings to predict weathering and water quality responses to climate change.

58 GEOSCIENCES↗
DOE OSTI2019

Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1

U6 snRNA undergoes post-transcriptional 3' end modification prior to incorporation into the active site of spliceosomes. The responsible exoribonuclease is Usb1, which removes nucleotides from the 3' end of U6 and, in humans, leaves a 2',3' cyclic phosphate that is recognized by the Lsm2–8 complex. Saccharomycescerevisiae Usb1 has additional 2',3' cyclic phosphodiesterase (CPDase) activity, which converts the cyclic phosphate into a 3' phosphate group. Here we investigate the molecular basis for the evolution of Usb1 CPDase activity. We examine the structure and function of Usb1 from Kluyveromyces marxianus, which shares 25 and 19% sequence identity to the S. cerevisiae and Homo sapiens orthologs of Usb1, respectively. We show that K. marxianus Usb1 enzyme has CPDase activity and determined its structure, free and bound to the substrate analog uridine 5'-monophosphate. We find that the origin of CPDase activity is related to a loop structure that is conserved in yeast and forms a distinct penultimate (n – 1) nucleotide binding site. These data provide structural and mechanistic insight into the evolutionary divergence of Usb1 catalysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Evaluation of Dry Sorbent Injection Technology for Pre-Combustion CO{sub 2} Capture

This document summarizes the work performed on Cooperative Agreement DE-FE0000465, “Evaluation of Dry Sorbent Technology for Pre-Combustion CO{sub 2} Capture,” during the period of performance of January 1, 2010 through September 30, 2013. This project involves the development of a novel technology that combines a dry sorbent-based carbon capture process with the water-gas-shift reaction for separating CO{sub 2} from syngas. The project objectives were to model, develop, synthesize and screen sorbents for CO{sub 2} capture from gasified coal streams. The project was funded by the DOE National Energy Technology Laboratory with URS as the prime contractor. Illinois Clean Coal Institute and The University of Illinois Urbana-Champaign were project co-funders. The objectives of this project were to identify and evaluate sorbent materials and concepts that were suitable for capturing carbon dioxide (CO{sub 2}) from warm/hot water-gas-shift (WGS) systems under conditions that minimize energy penalties and provide continuous gas flow to advanced synthesis gas combustion and processing systems. Objectives included identifying and evaluating sorbents that efficiently capture CO{sub 2} from a gas stream containing CO{sub 2}, carbon monoxide (CO), and hydrogen (H{sub 2}) at temperatures as high as 650 °C and pressures of 400-600 psi. After capturing the CO{sub 2}, the sorbents would ideally be regenerated using steam, or other condensable purge vapors. Results from the adsorption and regeneration testing were used to determine an optimal design scheme for a sorbent enhanced water gas shift (SEWGS) process and evaluate the technical and economic viability of the dry sorbent approach for CO{sub 2} capture. Project work included computational modeling, which was performed to identify key sorbent properties for the SEWGS process. Thermodynamic modeling was used to identify optimal physical properties for sorbents and helped down-select from the universe of possible sorbent materials to seven that were deemed thermodynamically viable for the process. Molecular modeling was used to guide sorbent synthesis through first principles simulations of adsorption and regeneration. Molecular dynamics simulations also modeled the impact of gas phase impurities common in gasified coal streams (e.g., H{sub 2}S) on the adsorption process. The role of inert dopants added for mechanical durability to active sorbent materials was also investigated through molecular simulations. Process simulations were conducted throughout the project to help determine the overall feasibility of the process and to help guide laboratory operating conditions. A large component of the program was the development of sorbent synthesis methods. Three different approaches were used: mechanical alloying (MA), flame spray pyrolysis (FSP), and ultrasonic spray pyrolysis (USP). Sorbents were characterized by a host of analytical techniques and screened for SEWGS performance using a thermogravimetric analyzer (TGA). A feedback loop from screening efforts to sorbent synthesis was established and used throughout the project lifetime. High temperature, high pressure reactor (HTPR) systems were constructed to test the sorbents at conditions mimicking the SEWGS process as identified through process modeling. These experiments were conducted at the laboratory scale to examine sorbents for their CO{sub 2} capacity, conversion of CO to CO{sub 2}, and impacts of adsorption and regeneration conditions, and syngas composition (including impurities and H2O:CO ratio). Results from the HTPR testing showed sorbents with as high as 0.4 g{sub CO{sub 2}}/g{sub sorbent} capacity with the ability to initially shift the WGS completely towards CO{sub 2}/H{sub 2}. A longer term experiment with a simple syngas matrix and N{sub 2}/steam regeneration stream showed a USP sorbent to be stable through 50 adsorption-regeneration cycles, though the sorbent tested had a somewhat diminished initial capacity. The program culminated in a technoeconomic assessment in which two different approaches were taken; one approach was intended to be technically conservative while the second required several key engineering challenges to be met in order to succeed. The project team is confident that, with the proper support, those challenges could be met. The second approach relies on a slipstream of H{sub 2} from the shifted syngas and O{sub 2} from an air separation unit (ASU) to be combusted in the presence of the sorbent for regeneration; termed a regenerating boiler. The approach also makes use of the heat of adsorption to generate >400 MW of turbine quality steam; total plant gross energy output as high as 1 GW was estimated for an IGCC with an initial gross energy output of 737 MW, without any additional coal usage. The regenerating boiler concept could benefit further from additional heat integration, but the results of this effort show a COE of $97.50 per MWh for a rational combination of operating parameters and sorbent lifetime as well as conservative estimates for steam turbines, gas turbine, and ASU. If the COE of CO{sub 2} transmission, storage and monitoring ($5.60 / MWh) is added to the base case for an IGCC ($81.30 / MWh for Case 5 from the DOE Bituminous Coal Report), the cost of CO{sub 2} capture for the regenerating boiler was only $10.60 / MWh; other regenerating boiler cases are as low $6.90 / MWh. The project met all agreed upon milestones and was completed within budget, more than 25% cost share provided by the project team. Results from the program showed that the SEWGS process has great promise, and with further study and evaluation could become a component of a comprehensive carbon capture program. SEWGS requires a paradigm shift in the traditional approach to carbon capture because the regenerating boiler concept is not a ‘back-end’ solution to CO{sub 2} mitigation. Rather, it is an integral part of the plant operations and is responsible for generating more electricity than the IGCC itself. Schemes could be envisioned where the H{sub 2} production is used exclusively to regenerate the sorbent, with any excess sold as a commodity, and the heat of adsorption serving as the primary driver for power generation. Further work with sorbent evaluation, process modeling and heat integration, and scale-up would be needed to more fully vet SEWGS, but the culmination of this program indicates that additional study is warranted.

20 FOSSIL-FUELED POWER PLANTS↗
NASA NTRS1976

Nocturnal lowering of thresholds for sweating and vasodilation

The effect of the time of day on the relation of the heat-dissipating responses (sweating and vasodilation) to esophageal and mean skin temperatures was investigated. These parameters were measured in six subjects exercised at 60-70% of maximal aerobic power in a 25 deg C ambient. Results indicate that a circadian rhythm in the thresholds for sweating and vasodilation can account for much of the rhythm of internal body temperature. The circadian rhythm in the operation of the thermoregulatory system seems to be expressed through a reference point shared by vasomotor and sudomotor controls.

Wenger, C. B.↗
NASA NTRS2009

Cassini/Huygens Probe Entry, Descent, and Landing (EDL) at Titan Independent Technical Assessment

Starting in January 2004, the NESC has received several communications from knowledgeable technical experts at NASA expressing shared concerns (mainly at the Langley Research Center (LaRC) and Ames Research Center (ARC)) about Huygens mission success. It was suggested that NASA become more technically involved directly in the analysis of Huygens' entry, descent and landing (EDL) focusing on the parachute deployment trigger performance and the resultant effects on the operation of the parachute system, and the determination of the radiative heating environment at Titan by ESA and the corresponding thermal protection system (TPS) response. A NESC Team was formed and tasked to provide an independent assessment of these concerns. The results of that assessment are documented in this report.

Powell, Richard W.↗
DOE OSTI2010

System and method for programmable bank selection for banked memory subsystems

A programmable memory system and method for enabling one or more processor devices access to shared memory in a computing environment, the shared memory including one or more memory storage structures having addressable locations for storing data. The system comprises: one or more first logic devices associated with a respective one or more processor devices, each first logic device for receiving physical memory address signals and programmable for generating a respective memory storage structure select signal upon receipt of pre-determined address bit values at selected physical memory address bit locations; and, a second logic device responsive to each of the respective select signal for generating an address signal used for selecting a memory storage structure for processor access. The system thus enables each processor device of a computing environment memory storage access distributed across the one or more memory storage structures.

Blumrich, Matthias A↗
DOE OSTI2022

A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses

Background: In this comparative study we evaluate the performance of four software tools: DNAstar-D (DESeq2), DNAstar-E (edgeR), CLC Genomics and Partek Flow for identification of differentially expressed genes (DEGs) using a transcriptome of E. coli. The RNA-seq data are from the effect of below-background radiation 5.5 nGy total dose (0.2nGy/hr) on E. coli grown shielded from natural radiation 655 m below ground in a pre-World War II steel vault. The gene expression response to three supplemented sources of radiation designed to mimic natural background, 1952 – 5720 nGy in total dose (71–208 nGy/hr), are compared to this “radiation-deprived” treatment. In addition, RNA-seq data of Caenorhabditis elegans nematode from similar radiation treatments was analyzed by three of the software packages. Results: In E. coli, the four software programs identified one of the supplementary sources of radiation (KCl) to evoke about 5 times more transcribed genes than the minus-radiation treatment (69–114 differentially expressed genes, DEGs), and so the rest of the analyses used this KCl vs “Minus” comparison. After imposing a 30-read minimum cutoff, one of the DNAStar options shared two of the three steps (mapping, normalization, and statistic) with Partek Flow (they both used median of ratios to normalize and the DESeq2 statistical package), and these two programs identified the highest number of DEGs in common with each other (53). In contrast, when the programs used different approaches in each of the three steps, between 31 and 40 DEGs were found in common. Regarding the extent of expression differences, three of the four programs gave high fold-change results (15–178 fold), but one (DNAstar’s DESeq2) resulted in more conservative fold-changes (1.5–3.5). In a parallel study comparing three qPCR commercial validation software programs, these programs also gave variable results as to which genes were significantly regulated. Similarly, the C. elegans analysis showed exaggerated fold-changes in CLC and DNAstar’s edgeR while DNAstar-D was more conservative. Conclusions: Regarding the extent of expression (fold-change), and considering the subtlety of the very low level radiation treatments, in E. coli three of the four programs gave what we consider exaggerated fold-change results (15 – 178 fold), but one (DNAstar’s DESeq2) gave more realistic fold-changes (1.5–3.5). When RT-qPCR validation comparisons to transcriptome results were carried out, they supported the more conservative DNAstar-D’s expression results. When another model organism’s (nematode) response to these radiation differences was similarly analyzed, DNAstar-D also resulted in the most conservative expression patterns. Therefore, we would propose DESeq2 (“DNAstar-D”) as an appropriate software tool for differential gene expression studies for treatments expected to give subtle transcriptome responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Roles of ATR1 paralogs YMR279c and YOR378w in boron stress tolerance

Highlights: {yields} ATR1 paralog YMR279c plays role in boron detoxification. {yields} YMR279c overexpression lowers cytoplasmic boron levels. {yields} ATR1 paralog YOR378w has no roles in boron stress response. -- Abstract: Boron is a necessary nutrient for plants and animals, however excess of it causes toxicity. Previously, Atr1 and Arabidopsis Bor1 homolog were identified as the boron efflux pump in yeast, which lower the cytosolic boron concentration and help cells to survive in the presence of toxic amount of boron. In this study, we analyzed ATR1 paralogs, YMR279c and YOR378w, to understand whether they participate in boron stress tolerance in yeast. Even though these genes share homology with ATR1, neither their deletion rendered cells boron sensitive nor their expression was significantly upregulated by boron treatment. However, expression of YMR279, but not YOR378w, from the constitutive GAPDH promoter on a high copy plasmid provided remarkable boron resistance by decreasing intracellular boron levels. Thus our results suggest the presence of a third boron exporter, YMR279c, which functions similar to ATR1 and provides boron resistance in yeast.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

In the Face of Cybersecurity: How the Common Information Model Can Be Used

Efforts are underway to combine smart grid information, devices, networking, and emergency response information to create messages that are not dependent on specific standards development organizations (SDOs). This supports a future-proof approach of allowing changes in the canonical data models (CDMs) going forward without having to perform forklift replacements of solutions that use the messages. This also allows end users (electric utilities) to upgrade individual components of a larger system while keeping the message payload definitions intact. The goal is to enable public and private information sharing securely in a standards-based approach that can be integrated into existing operations. We provide an example architecture that could benefit from this multi-SDO, secure message approach. This article also describes how to improve message security

capability maturity model↗
DOE OSTI2020

Phase 1 NuScale SMR FOAK Nuclear Demonstration Readiness Project (Final Scientific/Technical Report)

The overarching objective of the Phase 1 NuScale SMR First-of-a-Kind (FOAK) Nuclear Demonstration Readiness Project was to enhance competitiveness of the U.S. nuclear industry by enabling timely deployment of the NuScale small modular reactor (SMR). The scope of this Phase 1 project continued to advance the licensing and design maturity, particularly in those areas related to supporting customer readiness, supply chain integration, cost competitiveness, and cost confidence. This investment provided by the Government has accelerated development of these designs and technologies so that the existing domestic fleet of nuclear power plants remains viable and the most mature in the nuclear industry. The intent is to have the new, advanced U.S. designs be deployed as early 2026, and be globally competitive. As a part of the First-of-a-Kind Nuclear Demonstration Readiness Project, NuScale has been developing an advanced reactor design, leading the path for other development projects or complex technology advancements for existing plants that have significant technical and licensing risk. The NuScale Power team (NuScale) is advancing licensing, engineering, supply chain development, testing, and other required activities to enhance the innovation and competitiveness of the U.S. nuclear industry by enabling timely deployment of the NuScale SMR. Specifically, NuScale is performing the following activities in Phase 1. Fully supporting the NRC review of the NuScale DCA to ensure approval of a final safety evaluation report by the end of 2020. Improving plant cost confidence and cost competitiveness through design and supply chain advancement, incorporation of constructability best practices, and margin recovery to increase plant power output. Accelerating design maturity, technology development, and operational program readiness to support a customer commitment for plant deployment. The Department of Energy (DOE) Office of Scientific and Technical Information (OSTI), a unit of the Office of Science, fulfills agency-wide responsibilities to collect, preserve, and disseminate both unclassified and classified scientific and technical information (STI) emanating from DOE-funded research and development (R&D) activities at DOE national laboratories and facilities and at universities and other institutions nationwide. This scientific and technical report provides summaries of the analyses and research that was performed by NuScale under this project that achieves the objective of disseminating information to the nuclear industry to ensure the innovations realized are shared for the benefit of the industry at large.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗