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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 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Resilient Hydrogels from the Nanoscale to the Macroscale

Biological systems illustrate how a material composed of fragile molecular components can collectively be highly resilient. While the average protein, cell, or even tissue may not last more than a few weeks, many animals and plants live for more than a century. Continual component regeneration and multiple systems to resist mechanical and chemical damage together make this longetivity possible. This project sought to develop biomimetic methods to enable a specific type of material, a hydrogel, to resist damage across multiple scales using distinct, modular damage protection mechanisms. Because hydrogels share many features with biological tissues, they are an ideal substrate for exploring biomimetic strategies for designing resilience and self-repair. We specifically focused in this study on DNA-crosslinked hydrogels, which contain DNA strands that can serve as material to link it together or to control its current state or properties. We investigated how new tools from dynamic DNA nanotechnology could make it possible to actively recover from damage by continually growing and forming a materials shape, or by identifying damage and directing an adaptive response to that damage involving chemical synthesis to reconstruct a structure. We developed embedded molecular sensors able to detect and strain of the gel before damage occurred and react to counteract damage. We also developed methods to continually create shapes and patterns using chemical processes that will allow those patterns to reform when they are damaged. The ability to design resilient materials capable of self-repair has important implications for materials engineering. Instead of designing a material to withstand the worst stresses it may encounter, we could instead design a material to survive under average conditions, but self-repair or reconfigure to resist impending damage. Resilient, self-repairing hydrogels will also have diverse applications such as sensors or actuators.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Substrate multiplexed protein engineering facilitates promiscuous biocatalytic synthesis

Enzymes with high activity are readily produced through protein engineering, but intentionally and efficiently engineering enzymes for an expanded substrate scope is a contemporary challenge. One approach to address this challenge is Substrate Multiplexed Screening (SUMS), where enzyme activity is measured on competing substrates. SUMS has long been used to rigorously quantitate native enzyme specificity, primarily for in vivo settings. SUMS has more recently found sporadic use as a protein engineering approach but has not been widely adopted by the field, despite its potential utility. Here, we develop principles of how to design and interpret SUMS assays to guide protein engineering. This rich information enables improving activity with multiple substrates simultaneously, identifies enzyme variants with altered scope, and indicates potential mutational hot-spots as sites for further engineering. These advances leverage common laboratory equipment and represent a highly accessible and customizable method for enzyme engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

INBOUND APPOINTEE PUBLICATION Importance of Substrate-Particle Repulsion for Protein-Templated Assembly of Metal Nanoparticles

We study the protein-directed assembly of colloidal gold nanoparticles on de novo designed protein nanofiber templates. Using sequential assembly on glass substrates, we attach of positively-charged gold nanoparticles to protein nanofibers engineered to have a high density of negatively-charged surface residues. Using a combination of electron and optical microscopy, we measure the density of particle attachment and characterize binding specificity. By varying nanoparticle size and pH of the solution, we explore the importance of charge-dependent particle-fiber and particle-substrate interactions. We find an inverse correlation between particle size and attachment density to the protein nanofibers, attributed to the balance between size-dependent electrostatic particle-fiber attraction and particle-substrate repulsion. We show pH-dependent particle attachment density and binding specificity in relation to the protonation fraction of each assembly layer. Finally, we employ hyperspectral scattering microscopy to draw conclusions about particle density and interparticle spacings of optically-observable particle assemblies.

Guye, Kathryn N.↗
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

Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi

Colletotrichum fungi infect a wide diversity of monocot and dicot hosts, causing diseases on almost all economically important plants worldwide. Colletotrichum is also a suitable model for studying gene family evolution on a fine scale to uncover events in the genome associated with biological changes. Here we present the genome sequences of 30 Colletotrichum species covering the diversity within the genus. Evolutionary analyses revealed that the Colletotrichum ancestor diverged in the late Cretaceous in parallel with the diversification of flowering plants. We provide evidence of independent host jumps from dicots to monocots during the evolution of Colletotrichum, coinciding with a progressive shrinking of the plant cell wall degradative arsenal and expansions in lineage-specific gene families. Comparative transcriptomics of 4 species adapted to different hosts revealed similarity in gene content but high diversity in the modulation of their transcription profiles on different plant substrates. Combining genomics and transcriptomics, we identified a set of core genes such as specific transcription factors, putatively involved in plant cell wall degradation. These results indicate that the ancestral Colletotrichum were associated with dicot plants and certain branches progressively adapted to different monocot hosts, reshaping the gene content and its regulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Optical and photoelectric properties of surface barrier diodes based on n- Hg3In2Te6 crystals

The high radiation resistance of Hg3In2Te6 (MIT) single crystals to large doses of ionizing radiation makes devices quite attractive. Such a feature of the crystal structure has not only important advantages, but also causes serious technological difficulties in doping and controlling the specific resistance within the required limits and type of conductivity of single crystals. These technological difficulties create serious problems when creating structures with a potential barrier, especially with a p-n junction. At the moment, there are no publications on the creation of a p-n junction based on MIT. The only alternative is to create a potential barrier such as a Schottky diode or a metal-dielectric-semiconductor structure. This limits the use of MIT to produce, for example, rectifier diodes that can operate at relatively high reverse bias voltages. The typical resistivity of single crystals of MIT of n-type conductivity, which are used for the manufacture of diodes and photodiodes, is approximately equal to ρ≈103-104 Ω×cm. Such a specific resistance leads to a relatively large resistance of the neutral part of the single crystal, which in turn limits the direct currents of the rectifier diodes and significantly limits an important parameter of photodiodes - the dynamic range of the watt-ampere characteristic. This problem arises from the relatively high series resistance of the substrate. For rectifier diodes, this relatively large series resistance leads to a significant forward bias voltage drop, which reduces both the rectification factor and the amount of rectified current. We have already created diodes and photodiodes on Cr/MIT/Cr single crystals with a specific resistance of ρ≈103-104 Ω×cm. The diodes had relatively small dark currents but had the disadvantage of a relatively large specific resistance of the substrate, which we have already discussed above [1,2,3].

Sklyarchuk, V.↗
DOE OSTI2020

A Low-Cost Iron-Based Current Collector for Alkaline Battery Electrodes

The use of three-dimensional porous nickel foam as the current collector of the nickel hydroxide electrode adds significantly to the cost of the nickel-based alkaline rechargeable batteries. Although iron is considerably less expensive than nickel, iron corrodes at the operating potential of the nickel hydroxide electrode. We have found that a 70–100 nm thick thermal coating of cobalt ferrite spinel protects the iron from corrosion. Such a coated iron substrate was found to be stable against corrosion even when polarized anodically at 10 mA cm -2 in 30% potassium hydroxide electrolyte for 1000 h. While the thermal coating of cobalt ferrite protected iron against corrosion, incorporation of lithium ions into the coating was found to enhance the electrical conductivity of the coating. XPS and EXAFS studies confirmed that the enhanced conductivity resulted from an increase in the population of Co 3+ in the ferrite spinel lattice. An inexpensive iron (steel) substrate protected by such a coating when used as a nickel hydroxide battery electrode exhibited a specific capacity of 0.25 Ah g -1 at C/5 discharge rate, comparable to a nickel hydroxide electrode based on a relatively expensive nickel foam substrate. The steel-based electrode also exhibited no noticeable degradation over 150 cycles at C/2 rate. This demonstration of a robust and economical steel substrate presents a unique opportunity for reducing the cost of the nickel hydroxide battery electrode in alkaline batteries

25 ENERGY STORAGE↗
DOE OSTI2022

Structures of Fission Yeast Inositol Pyrophosphate Kinase Asp1 in Ligand-Free, Substrate-Bound, and Product-Bound States

Expression of the fission yeast Schizosaccharomyces pombe phosphate regulon is sensitive to the intracellular level of the inositol pyrophosphate signaling molecule 1,5-IP 8 . IP 8 dynamics are determined by Asp1, a bifunctional enzyme consisting of an N-terminal kinase domain and a C-terminal pyrophosphatase domain that catalyze IP 8 synthesis and catabolism, respectively. Here, we report structures of the Asp1 kinase domain, crystallized with two protomers in the asymmetric unit, one of which was complexed with ligands (ADPNP, ADP, or ATP; Mg 2+ or Mn 2+ ; IP 6 , 5-IP 7 , or 1,5-IP 8 ) and the other which was ligand-free. The ligand-free enzyme adopts an “open” conformation that allows ingress of substrates and egress of products. ADPNP, ADP, and ATP and associated metal ions occupy a deep phospho-donor pocket in the active site. IP 6 or 5-IP 7 engagement above the nucleotide favors adoption of a “closed” conformation, in which surface protein segments undergo movement and a disordered-to-ordered transition to form an inositol polyphosphate-binding site. In a structure mimetic of the kinase Michaelis complex, the anionic 5-IP 7 phosphates are encaged by an ensemble of nine cationic amino acids: Lys43, Arg223, Lys224, Lys260, Arg274, Arg285, Lys290, Arg293, and Lys341. Alanine mutagenesis of amino acids that contact the adenosine nucleoside of the ATP donor underscored the contributions of Asp258 interaction with the ribose 3'-OH and of Glu248 with adenine-N 6 . Changing Glu248 to Gln elicited a gain of function whereby the kinase became adept at using GTP as phosphate donor. Wild-type Asp1 kinase can utilize N 6 -benzyl-ATP as phosphate donor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A minimal motif for sequence recognition by mitochondrial transcription factor A (TFAM)

Abstract Mitochondrial transcription factor A (TFAM) plays a critical role in mitochondrial transcription initiation and mitochondrial DNA (mtDNA) packaging. Both functions require DNA binding, but in one case TFAM must recognize a specific promoter sequence, while packaging requires coating of mtDNA by association with non sequence-specific regions. The mechanisms by which TFAM achieves both sequence-specific and non sequence-specific recognition have not yet been determined. Existing crystal structures of TFAM bound to DNA allowed us to identify two guanine-specific interactions that are established between TFAM and the bound DNA. These interactions are observed when TFAM is bound to both specific promoter sequences and non-sequence specific DNA. These interactions are established with two guanine bases separated by 10 random nucleotides (GN10G). Our biochemical results demonstrate that the GN10G consensus is essential for transcriptional initiation and contributes to facilitating TFAM binding to DNA substrates. Furthermore, we report a crystal structure of TFAM in complex with a non sequence-specific sequence containing a GN10G consensus. The structure reveals a unique arrangement in which TFAM bridges two DNA substrates while maintaining the GN10G interactions. We propose that the GN10G consensus is key to facilitate the interaction of TFAM with DNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Phonon spectra of a two-dimensional solid dusty plasma modified by two-dimensional periodic substrates

Here, phonon spectra of a two-dimensional (2D) solid dusty plasma modulated by 2D square and triangular periodic substrates are investigated using Langevin dynamical simulations. The commensurability ratio, i.e., the ratio of the number of particles to the number of potential well minima, is set to 1 or 2. The resulting phonon spectra show that propagation of waves is always suppressed due to the confinement of particles by the applied 2D periodic substrates. For a commensurability ratio of 1, the spectra indicate that all particles mainly oscillate at one specific frequency, corresponding to the harmonic oscillation frequency of one single particle inside one potential well. At a commensurability ratio of 2, the substrate allows two particles to sit inside the bottom of each potential well, and the resulting longitudinal and transverse spectra exhibit four branches in total. We find that the two moderate branches come from the harmonic oscillations of one single particle and two combined particles in the potential well. The other two branches correspond to the relative motion of the two-body structure in each potential well in the radial and azimuthal directions. The difference in the spectra between the square and triangular substrates is attributed to the anisotropy of the substrates and the resulting alignment directions of the two-body structure in each potential well.

36 MATERIALS SCIENCE↗
DOE OSTI2024

High-Efficiency and Low-Carbon Energy Storage and Power Generation System for Electric Aviation

This report summarizes the work performed by University of California San Diego (UCSD) – Honeywell Aerospace (Honeywell) team for the U.S. Department of Energy/Advanced Research Projects Agency-Energy (DOE/ARPA-E) under Phase 1 (April 2021 – October 2023) project, Cooperative Agreement DE-AR0001347 entitled “High-Efficiency and Low-Carbon Energy Storage and Power Generation System for Electric Aviation”. The main objective of this project is to develop and demonstrate an energy storage and power generation (ESPG) system operating on bio liquid natural gas (LNG) for electric aviation applications. The ESPG system concept in this project is a fuel cell, battery, and gas turbine hybrid system that incorporates an innovative solid oxide fuel cell (SOFC) technology. This SOFC technology has two main novel elements: (i) a lightweight and compact stack architecture that consists of cells and cell modules in electrical parallel and series connections (the module design) and (ii) exceptionally high performance, direct methane thin-film cells on porous substrate made by sputtering deposition process. This fuel cell has the specific power and volumetric power density suitable for electric aviation applications. Based on the current status of the SOFC technology, the Phase 1 work focused on the following activities: (i) ESPG System Modeling – to design and optimize an aircraft SOFC-based ESPG system concept that met the performance, weight and cost targets; (ii) Cell Material Development and Scaleup – to demonstrate scalability of the sputtering process for manufacture of thin-film SOFC cells of practical sizes, confirm the exceptional performance of sputtered cells, improve cell stability and durability for operation with hydrogen and methane fuel, and develop a suitable electrically conducting porous substrate to replace the current non-conducting ceramic substrate; (iii) Stack Development – to design and manufacture stack components for the stack architecture, evaluate and select a suitable sealant, and build and operate multi-cell stacks to demonstrate stack operation, and (iv) Technology to Market – to develop business models and commercialization plans, conduct various market and technology analysis and estimate SOFC and ESPG system costs.

25 ENERGY STORAGE↗
DOE OSTI2021

Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease

Abstract Long interspersed nuclear element-1 (L1) is an autonomous non-LTR retrotransposon comprising ∼20% of the human genome. L1 self-propagation causes genomic instability and is strongly associated with aging, cancer and other diseases. The endonuclease domain of L1’s ORFp2 protein (L1-EN) initiates de novo L1 integration by nicking the consensus sequence 5′-TTTTT/AA-3′. In contrast, related nucleases including structurally conserved apurinic/apyrimidinic endonuclease 1 (APE1) are non-sequence specific. To investigate mechanisms underlying sequence recognition and catalysis by L1-EN, we solved crystal structures of L1-EN complexed with DNA substrates. This showed that conformational properties of the preferred sequence drive L1-EN’s sequence-specificity and catalysis. Unlike APE1, L1-EN does not bend the DNA helix, but rather causes ‘compression’ near the cleavage site. This provides multiple advantages for L1-EN’s role in retrotransposition including facilitating use of the nicked poly-T DNA strand as a primer for reverse transcription. We also observed two alternative conformations of the scissile bond phosphate, which allowed us to model distinct conformations for a nucleophilic attack and a transition state that are likely applicable to the entire family of nucleases. This work adds to our mechanistic understanding of L1-EN and related nucleases and should facilitate development of L1-EN inhibitors as potential anticancer and antiaging therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Synthesizing Carbon‐Supported, High‐Loading, Ultra‐Small Pt 3 Ni Nanoparticles via Tuning the Surface Electrostatic Effect

Carbon‐supported nanoparticles (NPs) are widely used as catalysts in fuel cells and electrolyzers. While it is well known that NPs with smaller size and higher loading often lead to better catalytic activity, they remain challenging to synthesize due to the weak control over the surface properties of the support. Herein, a facile approach to synthesize carbon‐supported, high‐loading, and ultra‐small Pt 3 Ni NPs via applying thermal shock on strongly interacted carbon support with metal salt is reported. Specifically, sodium citrate is introduced into the precursor solution and substrate mixture, which induces strong electrostatic effect between metal salts and carbon particles that markedly improves precursor anchoring and dispersion, thereby achieving high particle loading as well as small size and distribution. As a proof‐of‐concept, the synthesis of Pt 3 Ni NPs supported on carbon black with particle size of 1.56 ± 0.36 nm at 30 wt% loading and 1.66 ± 0.56 nm at 40 wt% loading is reported, where the sizes are among the smallest while the loadings are among the highest in the literature. This approach can be readily extended to many compositions and substrates, with tunable particle size and loading, thereby substantially expanding the synthesis space for NP catalysts in various electrochemical applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Fundamentals of Au(111) Surface Dynamics: Coarsening of Two-Dimensional Au Islands

Au(111) surfaces play a central role in many applications, yet studies of fundamental aspects of their dynamics are limited. Thus, using scanning tunneling microscopy (STM) at 300 K, we analyze the coarsening of first-layer 2D Au islands directly on the Au(111) substrate and also of second-layer 2D Au islands. Specifically, we monitor the decay of Au first-layer islands with areas of about 100–500 nm 2 in the vicinity of larger islands or extended step edges over a period of approximately 40 h, the relevant time scale for this process. Experimentally observed behavior is captured by analytical theory for terrace-diffusion-limited decay incorporating DFT results for the Au terrace diffusion barrier and the adatom formation energy.Lastly, experimental observations of second-layer island decay are also compared with appropriate analytical theory and stochastic simulations, thereby determining the effective Ehrlich–Schwoebel barrier for Au on Au(111).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Flux-Closure Domain Structures in Ferroelectric K 0.5 Na 0.5 NbO 3 Thin Films

Topological domain structures in ferroelectric materials have garnered increasing attention due to their intriguing physical properties and promising applications. While most existing topological structures in ferroelectric perovskite oxides originate from tetragonal or rhombohedral bulk phases, much less is understood about their counterparts in orthorhombic ferroelectrics. Here, in this work, we employ ferroelectric K 0.5 Na 0.5 NbO 3 (KNN) thin films as a model system and leverage phase-field simulations to theoretically predict the static structures and dynamic behaviors of three types of flux-closure domain configurations: in-plane (Type-I), out-of-plane (Type-II), and superdomain (Type-III) flux-closure structures. We systematically investigate the effects of finite size, misfit strains, and electrical boundary conditions on the formation and switching of these topological structures. For the Type-I structure, size reduction or small misfit strain facilitates a transition of the flux-closure pattern to polar vortices. Type-II structures emerge under open-circuit electrical boundary conditions of the film, forming at the junctions of specific domain walls with the film surface or the film–substrate interface. The formation mechanisms of these two flux-closure structures are rationalized from an energy perspective. We demonstrated switching capabilities of Type-II and Type-III structures by obtaining polarization–electric field hysteresis loops. Our simulations also reveal a reversible electric-field-induced transition between the orthorhombic and rhombohedral ferroelectric phases with a checkerboard domain pattern, during which the integrity of the flux-closure structure is preserved. These findings provide theoretical insights and practical guidance for identifying and manipulating topological structures in low-symmetry ferroelectrics, paving the way for developing energy-efficient microelectronic devices based on topological structures.

P-E loop↗
DOE OSTI2021

Mapping the catalytic conformations of an assembly-line polyketide synthase module

Assembly-line polyketide synthases, such as the 6-deoxyerythronolide B synthase (DEBS), are large enzyme factories prized for their ability to produce specific and complex polyketide products. By channeling protein-tethered substrates across multiple active sites in a defined linear sequence, these enzymes facilitate programmed small-molecule syntheses that could theoretically be harnessed to access countless polyketide product structures. Additionally, using cryogenic electron microscopy to study DEBS module 1, we present a structural model describing this substrate-channeling phenomenon. Our 3.2- to 4.3-angstrom-resolution structures of the intact module reveal key domain-domain interfaces and highlight an unexpected module asymmetry. We also present the structure of a product-bound module that shines light on a recently described “turnstile” mechanism for transient gating of active sites along the assembly line.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Nanopore Activity Assays for Detection of Biomarker Protease Activity: Design and Testing of Substrates for Both Nanopore Sequencing and PCR-Based Detection Methods

The work performed in this project has demonstrated the ability to construct proteolytic enzyme substrates that are PCR and sequencing-readable reporter molecules. Specifically, the goal was to detect those reporter molecules via PCR and Oxford Nanopore Technologies MinION sequencing methods following exposure to the biomarker protease thrombin. The assay development focused on binding the constructed peptide-oligonucleotide chimera to immobilized streptavidin. The action of thrombin on the peptide portion of the molecule released the oligonucleotide for detection. Detection of protease activity was demonstrated in a concentration-dependent manner using MALDI-MS, RT-PCR and DNA sequencing. Additional steps to remove background release of reporter molecules during the assay was used to improve the difference in detected oligonucleotide reporter following protease activity. Additional steps in assay development will be to (1) test the assay in an appropriate matrix, (2) investigate detection using additional DNA sequencing platforms and (3) demonstrate multiplexed detection of multiple protease markers in a single reaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Mutations in the proximal binding site and F-loop of AdeJ confer resistance to efflux pump inhibitors

Multidrug efflux is one of the major mechanisms of antibiotic resistance in gram-negative bacteria. Inhibitors of efflux pumps potentiate the activities of antibiotics, and their discovery could lead to new therapeutic options. The AdeIJK pump in Acinetobacter baumannii is a promising target for efflux pump inhibitors (EPIs) due to its high clinical importance and conservation, and several classes of EPIs targeting this and other A. baumannii efflux transporters have been recently reported. However, the mechanisms of action of these EPIs and their resistance liability remain underexplored. Here, we analyzed the impact of site-specific substitutions in the substrate/EPI translocation path of the inner membrane transporter AdeJ on efflux of substrate antibiotics and fluorescent probes and activities of substituted 4,6-diaminoquinoline EPIs. We found that substitutions in amino acid residues located in the entrance cleft (R701) and the flexible loop (E675) of AdeJ lead to resistance specifically against biphenyl-substituted EPIs, whereas the substitution of F178 in the distal binding pocket increased AdeJ sensitivity to certain naphthyl- and biphenyl-substituted EPIs. No major differences in docking scores and poses of substrates and EPIs were observed between the wild type and corresponding AdeJ variants for any of the mutations considered. This study concludes that substrates and EPIs bound along the translocation path of AdeJ participate in its conformational transitions and can either increase or decrease the rate of transport and therefore the efficiency of EPIs.

Acinetobacter↗