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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Applying the ATOM drug discovery platform to small-molecule antivirals (Annual Report)

The objective of this project is to advance our understanding of the ML approaches needed to find the most potent inhibitor through an AI guided search that simultaneously optimizes for limited off-target safety activity and desirable pharmacokinetics (PK) properties. The methods will be tested for inhibiting SARS-CoV-2 activity through inhibition of the main protease as a demonstration, but the methodology will be developed to apply to any biothreat target using a small-molecule protein binding-based intervention, with limited experimental data. Computational experiments are conducted using our ATOM generative molecular design (GMD) loop software, which is the implementation of our AI/ML drug design pipeline.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Methodology to Generate Decay Gamma Sources for the Second Target Station Full Target Assembly

This report details the specifics of applying the Position-Averaged Method to the target wedges and staves. The methodology used to calculate the decay gamma sources for a single target wedge to the calculation of the Second Target Station (STS) target assembly activation and the resulting decay gamma source terms are detailed in this report. The methodology has been applied to the entire STS target assembly including all of the target wedges, staves, shaft, and drive. The target staves and shaft have been vertically segmented to ensure the decay gamma source gradient is sufficiently captured. MCNP ® Code Version 6.2.0 with the RNUCS patch coupled with CINDER2008 from the AARE V1.0 package are the main tools used to calculate the decay gamma source terms.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Evaluating the Case for Reduced Precious Metal Catalysts in Proton Exchange Membrane Electrolyzers

Proton exchange membrane (PEM) water electrolyzers are a key technology in decarbonizing hydrogen production. Though the market for PEM electrolyzer systems is growing, there are concerns that the cost and availability of precious metal catalysts utilized in today’s commercial systems can limit deployment. Herein, we show that while the availability of Ir should not impede deployment in the near term, the inelasticity of the Ir commodity price is cause for immediate concern. Here we emphasize that diversifying catalyst materials, even with other precious metals, can reduce system costs and mitigate supply chain risk. Furthermore, we analyze the trade-offs between catalyst capital cost and catalyst activity for a range of operating conditions (i.e., capacity factor, electricity price). The framework presented herein is a first step toward establishing performance targets (i.e., activity, stability, material cost) for reduced precious metal and non-precious metal catalysts as a function of PEM electrolyzer operating conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Label-free affinity screening, design and synthesis of inhibitors targeting the Mycobacterium tuberculosis L-alanine dehydrogenase

The ability of Mycobacterium tuberculosis (Mtb) to persist in its host may enable an evolutionary advantage for drug resistant variants to emerge. A potential strategy to prevent persistence and gain drug efficacy is to directly target the activity of enzymes that are crucial for persistence. We present a method for expedited discovery and structure-based design of lead compounds by targeting the hypoxia-associated enzyme L-alanine dehydrogenase (AlaDH). Biochemical and structural analyses of AlaDH confirmed binding of nucleoside derivatives and showed a site adjacent to the nucleoside binding pocket that can confer specificity to putative inhibitors. Using a combination of dye-ligand affinity chromatography, enzyme kinetics and protein crystallographic studies, we show the development and validation of drug prototypes. Crystal structures of AlaDH-inhibitor complexes with variations at the N6 position of the adenyl-moiety of the inhibitor provide insight into the molecular basis for the specificity of these compounds. We describe a drug-designing pipeline that aims to block Mtb to proliferate upon re-oxygenation by specifically blocking NAD accessibility to AlaDH. The collective approach to drug discovery was further evaluated through in silico analyses providing additional insight into an efficient drug development strategy that can be further assessed with the incorporation of in vivo studies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Steady-State Mechanical Analysis for Target Assembly in the Material Plasma Exposure eXperiment Facility

The Material Plasma Exposure eXperiment (MPEX) steady-state linear plasma facility is currently under design at Oak Ridge National Laboratory to expose target specimens to fusion divertor regimes. The neutron-irradiated target is actively cooled and remote handled in the MPEX facility for conducting plasma-material–interaction (PMI) experiments. Here, the steady-state stresses in the target and target assembly system are investigated using two-dimensional (2-D) and three-dimensional (3-D) models to provide expected stresses/strains under the heat loads to which various system components would be exposed during MPEX operation. The calculated temperatures from the 2-D axisymmetric mechanical model were found to be in excellent agreement with those from the full 3-D thermohydraulic model, providing a strong model validation. Numerical simulation results for the steady-state mechanical model indicate nonuniform distributions for the temperature, stress, and deformation within the critical components. For the initial design, the deformation results indicate possible gap openings between contacting surfaces below the plasma-facing materials. To reduce the possibility of interfacial gap opening, the target assembly was slightly changed and evaluated using the 2-D stress model. Numerical simulation results indicate that the interfacial gap openings can be minimized without drastically changing the entire target assembly. The stress-strain conditions for the target will be further used to assess the appropriate operation during MPEX experiments and gain insight into materials science phenomena during PMI.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

New Laboratory and Astrophysical Probes of Physics Beyond the Standard Model (Final Technical Report)

The first of these directions centers on new ideas in dark matter detection. As experimental scrutiny narrows the window for new physics at the weak scale, it has become apparent that the solution to the dark matter mystery may not reside there. Theoretical developments such as the hidden sector/valley paradigm have, at the same time, shown that compelling theories of dark matter reside below the weak scale. Searching for dark matter at lower mass scales requires looking beyond the current paradigm of dark matter direct detection based on nuclear recoils. It is the goal of this project to provide new ideas to guide the experimental program looking for light dark matter. I am actively proposing ideas for detecting dark matter as light as a meV, well beyond the current focus of GeV-TeV scale dark matter. Some of the ideas I have proposed, such as superconducting, superfluid, and polar material targets, are actively being developed into experiments. My group will provide the relevant calculations to determine dark matter reach, providing crucial input to experiment on which targets should be developed. We will also provide an effective field theory framework to understand which types of experiments are most sensitive to each interaction type. The second of these directions is on probes of dark matter substructure as a mean to constrain, or observe, models of dark matter. The standard ΛCDM paradigm assumes that the dark matter density perturbations are adiabatic, scale invariant, and produced during inflation. However, many standard models of dark matter will produce modifications of this prediction, such as axion models with symmetry broken below the inflationary scale. Remarkably, we have limited direct measurements of the dark matter clumpiness at mass scales below dwarf galaxies. This allows for the possibility of observing modifications from vanilla ΛCDM due to particle dynamics. In many cases, simulations of dark matter structure in the presence of non-scale invariant fluctu- ations are understudied or completely lacking. I plan to develop both theoretical predictions for small scale structure in models with additional matter power on small scales, as well as observa- tional probes of small scale halos or clumps. One idea I have been recently focused on is pulsar timing, though my group will pursue a variety of lensing and astrometric probes. Lastly, the most risky direction involves spacetime fluctuations from quantum gravity. I showed that if one assumes that metric fluctuations in the Minkowski vacuum, at a surface separating a region in and out of causal contact (which we call a “horizon”), are determined by standard thermodynamic considerations at horizon, these metric fluctuations are large enough to observe in an interferometer with similar sensitivity to LIGO. In a follow-up paper we showed that these assumption holds for the vacuum in AdS/CFT. In future work, I plan to connect this work to recent soft graviton results, to frame this work in a concrete Randall-Sundrum model, and to work out concrete phenomenological predictions from the model. This work unquestionably takes a less trodden path, and works well as part of a well-rounded portfolio of less and more risky ideas. Particle physics is currently at a juncture which requires bold exploration of qualitatively new directions. This proposal outlines some of my plans over the coming years in these directions, leaving room also for surprises.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

CRISPR-Cas “Non-Target” Sites Inhibit On-Target Cutting Rates

CRISPR-Cas systems have become ubiquitous for genome editing in eukaryotic as well as bacterial systems. Cas9 forms a complex with a guide RNA (gRNA) and searches DNA for a matching sequence (target site) next to a protospacer adjacent motif (PAM). Once found, Cas9 cuts the DNA. Cas9 is revolutionary for the ability to change the RNA sequence and target a new site easily. However, while algorithms have been developed to predict gRNA-specific Cas9 activity, a fundamental biological understanding of gRNA-specific activity is lacking. Here, the number of PAM sites in the genome is effectively a large pool of inhibitory substrates, competing with the target site for the Cas9/gRNA complex. We demonstrate that increasing the number of non-target sites for a given gRNA reduces on-target activity in a dose-dependent manner. Furthermore, we show that the use of Cas9 mutants with increased PAM specificity toward a smaller subset of PAMs (or smaller pool of competitive substrates) improves cutting rates, while increased PAM promiscuity decreases cutting rates. Decreasing the potential search space by increasing PAM specificity provides a path toward improving on-target activity for slower high-fidelity Cas9 variants. Engineering improved PAM specificity to reduce the competitive search space offers an alternative strategy to engineer Cas9 variants with increased specificity and maintained on-target activity.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2024

A combinatorially complete epistatic fitness landscape in an enzyme active site

Protein engineering often targets binding pockets or active sites which are enriched in epistasis—nonadditive interactions between amino acid substitutions—and where the combined effects of multiple single substitutions are difficult to predict. Few existing sequence-fitness datasets capture epistasis at large scale, especially for enzyme catalysis, limiting the development and assessment of model-guided enzyme engineering approaches. We present here a combinatorially complete, 160,000-variant fitness landscape across four residues in the active site of an enzyme. Assaying the native reaction of a thermostable β-subunit of tryptophan synthase (TrpB) in a nonnative environment yielded a landscape characterized by significant epistasis and many local optima. These effects prevent simulated directed evolution approaches from efficiently reaching the global optimum. There is nonetheless wide variability in the effectiveness of different directed evolution approaches, which together provide experimental benchmarks for computational and machine learning workflows. The most-fit TrpB variants contain a substitution that is nearly absent in natural TrpB sequences—a result that conservation-based predictions would not capture. Thus, although fitness prediction using evolutionary data can enrich in more-active variants, these approaches struggle to identify and differentiate among the most-active variants, even for this near-native function. Overall, this work presents a large-scale testing ground for model-guided enzyme engineering and suggests that efficient navigation of epistatic fitness landscapes can be improved by advances in both machine learning and physical modeling.

biocatalysis↗
DOE OSTI2021

Bioorthogonal catalytic patch

The toxicity and complicated administration procedures of transition metal catalysts have hampered the applications of bioorthogonal catalysis in vivo. Here the authors fill the needles of a microneedle array patch with palladium nanoparticles deposited on titanium nanosheets and show that the device, applied locally on the skin of mouse models bearing melanoma, promotes intratumoural conversion of systemically injected caged doxorubicin into the active drug, reducing its toxicity and side effects. Bioorthogonal catalysis mediated by transition metals has inspired a new subfield of artificial chemistry complementary to enzymatic reactions, enabling the selective labelling of biomolecules or in situ synthesis of bioactive agents via non-natural processes. However, the effective deployment of bioorthogonal catalysis in vivo remains challenging, mired by the safety concerns of metal toxicity or complicated procedures to administer catalysts. Here, we describe a bioorthogonal catalytic device comprising a microneedle array patch integrated with Pd nanoparticles deposited on TiO 2 nanosheets. This device is robust and removable, and can mediate the local conversion of caged substrates into their active states in high-level living systems. In particular, we show that such a patch can promote the activation of a prodrug at subcutaneous tumour sites, restoring its parent drug's therapeutic anticancer properties. Finally, this in situ applied device potentiates local treatment efficacy and eliminates off-target prodrug activation and dose-dependent side effects in healthy organs or distant tissues.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Data for "Viral Delivery of Recombinases Activates Heritable Genetic Switches in Plants"

Viral vectors provide an increasingly versatile platform for transformation-free reagent delivery to plants. RNA viral vectors can be used to induce gene silencing, overexpress proteins, or introduce gene editing reagents; however, they are often constrained by carrying capacity or restricted tropism in germline cells. Site-specific recombinases that catalyze precise genetic rearrangements are powerful tools for genome engineering that vary in size and, potentially, efficacy in plants. In this work, we show that viral vectors based on tobacco rattle virus (TRV) deliver and stably express four recombinases ranging in size from ∼0.6 to ∼1.5 kb and achieve simultaneous marker removal and reporter activation through targeted excision in transgenic Nicotiana benthamiana lines. TRV vectors with Cre, FLP, CinH, and Integrase13 efficiently mediated recombination in infected somatic tissue and led to heritable modifications at high frequency. An excision-activated Ruby reporter enabled simple and high-resolution tracing of infected cell lineages without the need for molecular genotyping. Together, our experiments broaden the scope of viral recombinase delivery and offer insights into infection dynamics that may be useful in developing future viral vectors.

gene editing↗
DOE OSTI2025

Viral delivery of recombinases activates heritable genetic switches in plants

Viral vectors provide an increasingly versatile platform for transformation-free reagent delivery to plants. RNA viral vectors can be used to induce gene silencing, overexpress proteins, or introduce gene editing reagents; however, they are often constrained by carrying capacity or restricted tropism in germline cells. Site-specific recombinases that catalyze precise genetic rearrangements are powerful tools for genome engineering that vary in size and, potentially, efficacy in plants. In this work, we show that viral vectors based on tobacco rattle virus (TRV) deliver and stably express four recombinases ranging in size from ~0.6kb to ~1.5kb and achieve simultaneous marker removal and reporter activation through targeted excision in transgenic Nicotiana benthamiana lines. TRV vectors with Cre, FLP, CinH, and Integrase13 efficiently mediated recombination in infected somatic tissue and led to heritable modifications at high frequency. Here, an excision-activated Ruby reporter enabled simple and high-resolution tracing of infected cell lineages without the need for molecular genotyping. Together, our experiments broaden the scope of viral recombinase delivery and offer insights into infection dynamics that may be useful in developing future viral vectors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Characterization of D-T Generator Neutron Flux Spectrum for Cyclic Neutron Activation Analysis Experiments

Improving nuclear data for short-lived fission product yields will further our fundamental understanding of fission, which is needed across various scientific fields and applications. One method of attaining the needed product yield data is through cyclic neutron activation, which allows a target to be irradiated in a neutron environment and then transported for counting of the radionuclides produced, typically via g spectroscopy. Recently, such a system has been constructed and commissioned at Pacific Northwest National Laboratory. Targets are shuttled between the head of a D-T neutron generator and a counting station with a transit time of 2 seconds. As part of the characterization of this system, the neutron flux was studied using two activation targets. The neutron flux from the deuterium-tritium fusion generator was determined to be 9.95(33) x10^8 n/cm2-s with a peak energy of 14.9 MeV and a spread of approximately 4 decades between the epithermal and 14 MeV peak group flux.

cyclic neutron activation, gamma-ray spectroscopy,↗
DOE OSTI2025

Combining MicroED and native mass spectrometry for structural discovery of enzyme–small molecule complexes

With the goal of accelerating the discovery of small molecule–protein complexes, we leverage fast, low-dose, event-based electron counting microcrystal electron diffraction (MicroED) data collection and native mass spectrometry. This approach, which we term electron diffraction with native mass spectrometry (ED-MS), allows assignment of protein target structures bound to ligands with data obtained from crystal slurries soaked with mixtures of known inhibitors and crude biosynthetic reactions. This extends to libraries of printed ligands dispensed directly onto TEM grids for later soaking with microcrystal slurries, and complexes with noncovalent ligands. ED-MS resolves structures of the natural product, epoxide-based cysteine protease inhibitor E-64, and its biosynthetic analogs bound to the model cysteine protease, papain. It further identifies papain binding to its preferred natural products, by showing that two analogs of E-64 outcompete others in binding to papain crystals, and by detecting papain bound to E-64 and an analog from crude biosynthetic reactions, without purification. ED-MS also resolves binding of the CTX-M-14 β-lactamase, a target of active drug development, to the non-β-lactam inhibitor, avibactam, alone or in a cocktail of unrelated compounds. These results illustrate the utility of ED-MS for natural product ligand discovery and for structure-based screening of small molecule binders to macromolecular targets, promising utility for drug discovery.

MicroED↗
DOE OSTI2021

Cross Section Measurements of Photonuclear Reaction Pathways Towards Promising Medical Radioisotopes

Project Objectives: The goal of this project was to generate data relevant to radioisotope production while developing innovative technologies that foster and enhance novel production of radioisotopes, and, also, while providing opportunities for cultivating and training future generations of scientists. This work has provided the foundation for methodologies for determination of photonuclear cross sections over multiple energies in a single irradiation. Simultaneously, the feasibility of electron LINAC production of several in-demand radioisotopes such as 47 Sc, 67 Cu, 77 As, and 186 Re has been demonstrated. To accomplish these objectives a collaboration was formed between two complimentary facilities, the Low Energy Accelerator Facility (LEAF) at Argonne National Laboratory and the High Intensity Gamma-ray Source (HIGS) at Triangular Universities Nuclear Laboratory (TUNL). The involvement of the research group from North Carolina Central University gave students at this Historically Black University experience in forefront nuclear-physics research relevant to addressing a high-priority interdisciplinary issue. Project Description: HIGS provides a nearly monoenergetic gamma-ray beam by intra-cavity Compton backscattering of free-electron photons from electrons circulating in a storage ring. This beam can be collimated to produce a very precise energy beam. If the beam is un-collimated a calculated and precise energy spread of the beam occurs radially. The γ-flux can be evenly distributed over the radial distribution of energy and used to perform activation experiments on concentric ring targets. Thus providing multiple energy ranges in a single irradiation. Each concentric ring target can be counted separately in order to determine activation at the given energy and successively be correlated to the activation cross section. Targets were activated to determine production feasibility using electron beams at LEAF. Potential Impact: The Nuclear Science Advisory Committee recently named production of radioisotopes with electron LINACs as one of the most compelling and largest-impact opportunities for the production of high specific activity radioisotopes. Improving the photonuclear cross sectional data base with experimentally verified results will greatly enhance a researcher’s ability to rationalize electron LINAC production routes towards desired radioisotopes. This work will provide the foundation for methodologies for determination of photonuclear cross sections over multiple energies and multiple targets in a single irradiation. The techniques developed in this project will enable future studies to continue verifying theoretically predicted photonuclear cross section with experimental results. These data will also enable adaptation of models and support more precise theoretical calculation of photonuclear cross sections. This research will involve undergraduates, graduate students, and post-docs to give them a valuable research experience leading towards the next generation of scientists in the field of medical isotopes.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2020

Activity Estimations for HSA Co-60 targets for Cycles 168A, 168B, and 169A Memo

67 HSA cobalt targets have been irradiated in the ATR, starting back on 2/10/15. Individual HSA cobalt targets may have been moved to different positions and irradiated at different times in the ATR. A tool called the Isotope Production and Activation tool (IPA tool) was developed to capture the changes for different irradiation conditions. The IPA tool uses cross section and flux data, cycle history data, and HSA experiment positioning data to estimate a range of specific activities for each of the HSA cobalt targets to generate SCALE/ORIGENS inputs for each target. The IPA tool also post-processes the results for use in tables and figures. The IPA tool derived results that can be independently verified using an acceptable alternative method. The memo contains the specific activity for all 67 HSA cobalt targets.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

acCRISPR: an activity-correction method for improving the accuracy of CRISPR screens

Abstract High throughput CRISPR screens are revolutionizing the way scientists unravel the genetic underpinnings of engineered and evolved phenotypes. One of the critical challenges in accurately assessing screening outcomes is accounting for the variability in sgRNA cutting efficiency. Poorly active guides targeting genes essential to screening conditions obscure the growth defects that are expected from disrupting them. Here, we develop acCRISPR, an end-to-end pipeline that identifies essential genes in pooled CRISPR screens using sgRNA read counts obtained from next-generation sequencing. acCRISPR uses experimentally determined cutting efficiencies for each guide in the library to provide an activity correction to the screening outcomes via calculation of an optimization metric, thus determining the fitness effect of disrupted genes. CRISPR-Cas9 and -Cas12a screens were carried out in the non-conventional oleaginous yeast Yarrowia lipolytica and acCRISPR was used to determine a high-confidence set of essential genes for growth under glucose, a common carbon source used for the industrial production of oleochemicals. acCRISPR was also used in screens quantifying relative cellular fitness under high salt conditions to identify genes that were related to salt tolerance. Collectively, this work presents an experimental-computational framework for CRISPR-based functional genomics studies that may be expanded to other non-conventional organisms of interest.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Factor VIII moiety of recombinant Factor VIII Fc fusion protein impacts Fc effector function and CD16 + NK cell activation

Recombinant Factor VIII-Fc fusion protein (rFVIIIFc) is an enhanced half-life therapeutic protein product used for the management of hemophilia A. Recent studies have demonstrated that rFVIIIFc interacts with Fc gamma receptors (FcγR) resulting in the activation or inhibition of various FcγR-expressing immune cells. We previously demonstrated that rFVIIIFc, unlike recombinant Factor IX-Fc (rFIXFc), activates natural killer (NK) cells via Fc-mediated interactions with FcγRIIIA (CD16). Additionally, we showed that rFVIIIFc activated CD16 + NK cells to lyse a FVIII-specific B cell clone. Here, we used human NK cell lines and primary NK cells enriched from peripheral blood leukocytes to study the role of the FVIII moiety in rFVIIIFc-mediated NK cell activation. Following overnight incubation of NK cells with rFVIIIFc, cellular activation was assessed by measuring secretion of the inflammatory cytokine IFNγ by ELISA or by cellular degranulation. We show that anti-FVIII, anti-Fc, and anti-CD16 all inhibited indicating that these molecules were involved in rFVIIIFc-mediated NK cell activation. To define which domains of FVIII were involved, we used antibodies that are FVIII domain-specific and demonstrated that blocking FVIII C1 or C2 domain-mediated membrane binding potently inhibited rFVIIIFc-mediated CD16 + NK cell activation, while targeting the FVIII heavy chain domains did not. We also show that rFVIIIFc binds CD16 with about five-fold higher affinity than rFIXFc. Based on our results we propose that FVIII light chain-mediated membrane binding results in tethering of the fusion protein to the cell surface, and this, together with increased binding affinity for CD16, allows for Fc-CD16 interactions to proceed, resulting in NK cellular activation. Our working model may explain our previous results where we observed that rFVIIIFc activated NK cells via CD16, whereas rFIXFc did not despite having identical IgG1 Fc domains.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Garcinoic Acid Is a Natural and Selective Agonist of Pregnane X Receptor

Pregnane X receptor (PXR) is a master xenobiotic-sensing transcription factor and a validated target for immune and inflammatory diseases. The identification of chemical probes to investigate the therapeutic relevance of the receptor is still highly desired. In fact, currently available PXR ligands are not highly selective and can exhibit toxicity and/or potential off-target effects. In this study, we have identified garcinoic acid as a selective and efficient PXR agonist. The properties of this natural molecule as a specific PXR agonist were demonstrated by the screening on a panel of nuclear receptors, the assessment of the physical and thermodynamic binding affinity, and the determination of the PXR-garcinoic acid complex crystal structure. Cytotoxicity, transcriptional, and functional properties were investigated in human liver cells, and compound activity and target engagement were confirmed in vivo in mouse liver and gut tissue. In conclusion, garcinoic acid is a selective natural agonist of PXR and a promising lead compound toward the development of new PXR-regulating modulators.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗