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Results for “substrate specificity”

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 883 records · Page 49
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Genotype to ecotype in niche environments: adaptation of Arthrobacter to carbon availability and environmental conditions

Niche environmental conditions influence both the structure and function of microbial communities and the cellular function of individual strains. The terrestrial subsurface is a dynamic and diverse environment that exhibits specific biogeochemical conditions associated with depth, resulting in distinct environmental niches. Here, we present the characterization of seven distinct strains belonging to the genus Arthrobacter isolated from varying depths of a single sediment core and associated groundwater from an adjacent well. We characterized genotype and phenotype of each isolate to connect specific cellular functions and metabolisms to ecotype. Arthrobacter isolates from each ecotype demonstrated functional and genomic capacities specific to their biogeochemical conditions of origin, including laboratory-demonstrated characterization of salinity tolerance and optimal pH, and genes for utilization of carbohydrates and other carbon substrates. Analysis of the Arthrobacter pangenome revealed that it is notably open with a volatile accessory genome compared to previous pangenome studies on other genera, suggesting a high potential for adaptability to environmental niches.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Broadband, 920-nm mirror thin film damage competition

This year’s competition proposed to survey the state-of-the-art broadband, near-IR multilayer dielectric (MLD) mirrors designed for ultra-short, pulsed laser applications. The requirements for the coatings were a minimum reflection of 99.5% at 45-degree incidence angle for S-polarization from 830 nm to 1010 nm and group delay dispersion (GDD) < ± 50 fs 2 . The participants in this effort selected the coating materials, coating design, and deposition method. Samples were damage tested at a single testing facility to enable direct comparison among the participants using a 25 ± 5 fs OPCPA laser system operating at 5 Hz. A double blind test assured sample and submitter anonymity. The damage performance results, sample rankings, details of the deposition processes, coating materials and substrate cleaning methods are shared here. We found that multilayer coatings using tantala and/or hafnia as high index materials were top performers within several coating deposition groups. Specifically, dense coatings by ion-beam sputtering (IBS), magnetron sputtering (MS), and electron-beam ion assisted deposition (e-beam IAD) exhibited highest damage initiation onset (LIDT) while e-beam coatings were low performers. In addition, damage growth onset (LDGT) was also examined and the results are reported here for all samples as this performance metric plays an important role in establishing the safe operational conditions for larger aperture, ultrashort pulsed lasers. As a result, not all coating samples in the survey met the GDD requirements stated above and associated measurements are discussed in the context of the present and past competitions focused on similar broadband, near-IR MLD coatings.

42 ENGINEERING↗
NASA NTRS1995

Sinterless Fabrication Of Contact Pads On InP Devices

Research has shown that with proper choice of material, low-resistance contact pads deposited on solar cells and other devices by improved technique that does not involve sintering. Research directed at understanding mechanisms involved in contact-sintering process has resulted in identification of special group of materials that includes phosphides of gold, silver, and nickel; specifically, Au(2)P(3), AgP(2), and Ni(3)P. Incorporation of phosphide interlayer substantially reduces resistivity between gold current-carrying layer and indium phosphide substrate. Further research indicated only very thin interlayer of any of these compounds needed to obtain low contact resistance, without subjecting contact to destructive sintering process.

Weizer, Victor G.↗
NASA NTRS2004

Single Wall Carbon Nanotube-Based Structural Health Sensing Materials

Single wall carbon nanotube (SWCNT)-based materials represent the future aerospace vehicle construction material of choice based primarily on predicted strength-to-weight advantages and inherent multifunctionality. The multifunctionality of SWCNTs arises from the ability of the nanotubes to be either metallic or semi-conducting based on their chirality. Furthermore, simply changing the environment around a SWCNT can change its conducting behavior. This phenomenon is being exploited to create sensors capable of measuring several parameters related to vehicle structural health (i.e. strain, pressure, temperature, etc.) The structural health monitor is constructed using conventional electron-beam lithographic and photolithographic techniques to place specific electrode patterns on a surface. SWCNTs are then deposited between the electrodes using a dielectrophoretic alignment technique. Prototypes have been constructed on both silicon and polyimide substrates, demonstrating that surface-mountable and multifunctional devices based on SWCNTs can be realized.

Watkins, A. Neal↗
DOE OSTI2019

A two-phase substrate model for enzymatic hydrolysis of lignocellulose: application to batch and continuous reactors

Abstract Background Enzymatic hydrolysis continues to have a significant projected production cost for the biological conversion of biomass to fuels and chemicals, motivating research into improved enzyme and reactor technologies in order to reduce enzyme usage and equipment costs. However, technology development is stymied by a lack of accurate and computationally accessible enzymatic-hydrolysis reaction models. Enzymatic deconstruction of cellulosic materials is an exceedingly complex physico-chemical process. Models which elucidate specific mechanisms of deconstruction are often too computationally intensive to be accessible in process or multi-physics simulations, and empirical models are often too inflexible to be effectively applied outside of their batch contexts. In this paper, we employ a phenomenological modeling approach to represent rate slowdown due to substrate structure (implemented as two substrate phases) and feedback inhibition, and apply the model to a continuous reactor system. Results A phenomenological model was developed in order to predict glucose and solids concentrations in batch and continuous enzymatic-hydrolysis reactors from which liquor is continuously removed by ultrafiltration. A series of batch experiments were performed, varying initial conditions (solids, enzyme, and sugar concentrations), and best-fit model parameters were determined using constrained nonlinear least-squares methods. The model achieved a good fit for overall sugar yield and insoluble solids concentration, as well as for the reduced rate of sugar production over time. Additionally, without refitting model coefficients, good quantitative agreement was observed between results from continuous enzymatic-hydrolysis experiments and model predictions. Finally, the sensitivity of the model to its parameters is explored and discussed. Conclusions Although the phenomena represented by the model correspond to behaviors that emerge from clusters of mechanisms, and hence a set of model coefficients are unique to the substrate and the enzyme system, the model is efficient to solve and may be applied to novel reactor schema and implemented in computational fluid dynamics (CFD) simulations. Hence, this modeling approach finds the right balance between model complexity and computational efficiency. These capabilities have broad application to reactor design, scale-up, and process optimization.

09 BIOMASS FUELS↗
DOE OSTI2025

Rapid Screening of Liquid Metal Wetting for a Materials Compatibility Library

Wetting behavior of molten metals on solid substrates is a critical phenomenon influencing numerous industrial applications, including welding, anti-corrosion coatings, and metal additive manufacturing (AM). In particular, molten metal jetting (MMJ), an emerging AM technology, requires that the molten metal remain pinned at the nozzle exit. Thus, each new metal requires a specific nozzle material to ensure consistent droplet ejection and deposition, making it important to rapidly identify the appropriate wetting combinations. However, traditional measurements of wetting angles require expensive equipment and only allow one combination of materials to be investigated at a time which can be time consuming. This work introduces a rapid screening method based on sessile droplet experiments to evaluate wetting profiles across multiple metal–substrate combinations simultaneously. This study investigates the wetting interactions of molten Al alloy (Al4008), Cu, and Sn on various ceramic and metal substrates to identify optimal material combinations for MMJ nozzle designs. Results demonstrate that Al4008 achieves wetting on ceramic substrates such as AlN, TiO 2 , and SiC, with varying mechanisms including chemical reactions and weak surface interactions. Additionally, theoretical predictions regarding miscibility gaps and melting point differences were verified for Cu and Sn on refractory metals like Mo and W. Findings from this study contribute to the establishment of a materials compatibility library, enabling the selection of wetting/non-wetting combinations for stable MMJ operation. This resource not only advances MMJ technologies but also provides valuable insights for broader applications such as welding, coating, and printed electronics.

Materials science↗
DOE OSTI2019

Mixtures of aromatic compounds induce ligninolytic gene expression in the wood-rotting fungus Dichomitus squalens

Heterologous production of fungal ligninolytic cocktails is challenging due to the low yields of catalytically active lignin modifying peroxidases. Production using a natural system, such as a wood-rotting fungus, is a promising alternative if specific or preferential induction of the ligninolytic activities could be achieved. Using transcriptomics, gene expression of the white-rot Dichomitus squalens during growth on mixtures of aromatic compounds, with ring structures representing the two major lignin sub-units, was compared to a wood substrate. Most of the genes encoding lignin modifying enzymes (laccases and peroxidases) categorised as highly or moderately expressed on wood were expressed similarly on aromatic compounds. Higher expression levels of a subset of manganese and versatile peroxidases was observed on di- compared to mono-methoxylated aromatics. The expression of polysaccharide degrading enzymes was lower on aromatic compounds compared to wood, demonstrating that the induction of lignin modifying enzymes became more specific. Finally, this study suggests potential for aromatic waste streams, e.g. from lignocellulose pretreatment, to produce a lignin-specific enzyme cocktail from D. squalens or other white-rot fungi.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

A Single Amino Acid Switch Alters the Isoprene Donor Specificity in Ribosomally Synthesized and Post-Translationally Modified Peptide Prenyltransferases

Mutation at a single amino acid alters the isoprene donor specificity of prenyltransferases involved in the modification of ribosomally synthesized and post-translationally modified peptides (RiPPs). Though most characterized RiPP prenyltransferases carry out the regiospecific transfer of C 5 dimethylallyl donor to the side chain atoms on macrocyclic acceptor substrates, the elucidation of the cyanobactin natural product piricyclamide 70005E1 identifies an O-geranyl modification on Tyr, a reaction with little prior biochemical precedence. Reconstitution and kinetic studies of the presumptive geranyltransferase PirF shows that the enzyme utilizes a C 10 donor, with no C 5 transferase activity. The crystal structure of PirF reveals a single amino acid difference in the vicinity of the isoprene-binding pocket, relative to the C 5 utilizing enzymes. Remarkably, only a single amino acid mutation is necessary to completely switch the donor specificity from a C 5 to a C 10 prenyltransferase, and vice versa. Lastly, we demonstrate that these enzymes may be used for the chemospecific attachment of C 5 or C 10 lipid groups on lanthipeptides, an unrelated class of RiPP natural products. Overall, these studies represent a rare example where prenyl donor specificity can be discretely altered, which expands the arsenal of synthetic biology tools for tuning biological activities of peptide natural products.

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

Plant-specific features of respiratory supercomplex I + III2 from Vigna radiata

Abstract The last steps of cellular respiration—an essential metabolic process in plants—are carried out by mitochondrial oxidative phosphorylation. This process involves a chain of multi-subunit membrane protein complexes (complexes I–V) that form higher-order assemblies called supercomplexes. Although supercomplexes are the most physiologically relevant form of the oxidative phosphorylation complexes, their functions and structures remain mostly unknown. Here we present the cryogenic electron microscopy structure of the supercomplex I + III 2 from Vigna radiata (mung bean). The structure contains the full subunit complement of complex I, including a newly assigned, plant-specific subunit. It also shows differences in the mitochondrial processing peptidase domain of complex III 2 relative to a previously determined supercomplex with complex IV. The supercomplex interface, while reminiscent of that in other organisms, is plant specific, with a major interface involving complex III 2 ’s mitochondrial processing peptidase domain and no participation of complex I’s bridge domain. The complex I structure suggests that the bridge domain sets the angle between the enzyme’s two arms, limiting large-scale conformational changes. Moreover, complex I’s catalytic loops and its response in active-to-deactive assays suggest that, in V. radiata , the resting complex adopts a non-canonical state and can sample deactive- or open-like conformations even in the presence of substrate. This study widens our understanding of the possible conformations and behaviour of complex I and supercomplex I + III 2 . Further studies of complex I and its supercomplexes in diverse organisms are needed to determine the universal and clade-specific mechanisms of respiration.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural basis for SHOC2 modulation of RAS signalling

The RAS–RAF pathway is one of the most commonly dysregulated in human cancers. Despite decades of study, understanding of the molecular mechanisms underlying dimerization and activation of the kinase RAF remains limited. Recent structures of inactive RAF monomer and active RAF dimer bound to 14-3-3 have revealed the mechanisms by which 14-3-3 stabilizes both RAF conformations via specific phosphoserine residues. Prior to RAF dimerization, the protein phosphatase 1 catalytic subunit (PP1C) must dephosphorylate the N-terminal phosphoserine (NTpS) of RAF to relieve inhibition by 14-3-3, although PP1C in isolation lacks intrinsic substrate selectivity. SHOC2 is as an essential scaffolding protein that engages both PP1C and RAS to dephosphorylate RAF NTpS, but the structure of SHOC2 and the architecture of the presumptive SHOC2–PP1C–RAS complex remain unknown. Here we present a cryo-electron microscopy structure of the SHOC2–PP1C–MRAS complex to an overall resolution of 3Å, revealing a tripartite molecular architecture in which a crescent-shaped SHOC2 acts as a cradle and brings together PP1C and MRAS. Our work demonstrates the GTP dependence of multiple RAS isoforms for complex formation, delineates the RAS-isoform preference for complex assembly, and uncovers how the SHOC2 scaffold and RAS collectively drive specificity of PP1C for RAF NTpS. Our data indicate that disease-relevant mutations affect complex assembly, reveal the simultaneous requirement of two RAS molecules for RAF activation, and establish rational avenues for discovery of new classes of inhibitors to target this pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Surface-Synthesized Graphene Nanoribbons for Room Temperature Switching Devices: Substrate Transfer and ex Situ Characterization

Recent progress in the on-surface synthesis of graphene nanoribbons (GNRs) has given access to atomically precise narrow GNRs with tunable electronic band gaps which makes them excellent candidates for room temperature switching devices such as field-effect transistors (FET). However, in spite of their exceptional properties, significant challenges remain for GNR processing and characterization. This contribution addresses some of the most important challenges, including GNR fabrication scalability, substrate transfer, long-term stability under ambient conditions, and ex situ characterization. We focus on 7- and 9-atom-wide armchair graphene nanoribbons (i.e., 7-AGNR and 9-AGNR) grown on 200 nm Au(111)/mica substrates using a high throughput system. Transfer of both 7- and 9-AGNRs from their Au growth substrate onto various target substrates for additional characterization is accomplished utilizing a polymer-free method that avoids residual contamination. This results in a homogeneous GNR film morphology with very few tears and wrinkles, as examined by atomic force microscopy. Raman spectroscopy indicates no significant degradation of GNR quality upon substrate transfer and reveals that GNRs have remarkable stability under ambient conditions over a 24 month period. The transferred GNRs are analyzed using multiwavelength Raman spectroscopy, which provides detailed insight into the wavelength dependence of the width-specific vibrational modes. Finally, we characterize the optical properties of 7- and 9-AGNRs via ultraviolet–visible (UV–vis) spectroscopy.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Inkless, dry printing nanographene via in-Situ Coordinated laser ablation and sintering processes

Printing carbon, such as graphene and other carbon structures, for flexible and printed electronics currently relies on either ink-based printing, laser-induced forward transfer (LIFT), or laser-induced graphitization (LIG) to convert carbon-rich precursor materials, such as polymers, to graphene-like carbon structures. Liquid inks contain toxic solvents, surfactants, and stabilizing additives that degrade electrical conductivity and require high-temperature post-processing. On the other hand, LIG is limited by the substrate. Here, this study introduces an additive manufacturing method for dry-printing carbon nanomaterials, ranging from amorphous carbon to crystalline graphene-like structures, on various substrates. The system utilizes laser ablation of a solid graphite target to create pure carbon nanoparticles in situ and on demand. An inert gas carries the nanoparticles onto the substrate, where they can be deposited either as amorphous structures or laser-sintered in real time to form various graphitic structures. The study of laser processing parameters, specifically fluence and pulse repetition frequency, revealed three unique regimes of nanostructure evolution that influence the morphological and electrical properties of these printed structures. Raman spectroscopy confirmed graphitization with a resistivity slightly higher than that of the bulk graphite target. The conductivity/resistivity could be tuned as a function of sintering laser power. Scanning transmission electron microscopy (STEM) revealed that turbostratic nanographene formed with an interlayer spacing of 0.40 nm. Despite ink-based printing methods, such as screen printing, inkjet printing (IJP), and aerosol jet printing (AJP), this eco-friendly and green manufacturing technique could eliminate toxic chemicals, reduce environmental impact, and enable single-step fabrication of carbon-based devices for applications in wearable sensors, energy storage, flexible electronics, and Internet of Things (IoT) devices.

Additive nanomanufacturing↗
DOE OSTI2020

DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation

DNA methylation maintenance by DNMT1 is an essential process in mammals but molecular mechanisms connecting DNA methylation patterns and enzyme activity remain elusive. Here, we systematically analyzed the specificity of DNMT1, revealing a pronounced influence of the DNA sequences flanking the target CpG site on DNMT1 activity. We determined DNMT1 structures in complex with preferred DNA substrates revealing that DNMT1 employs flanking sequence-dependent base flipping mechanisms, with large structural rearrangements of the DNA correlating with low catalytic activity. Moreover, flanking sequences influence the conformational dynamics of the active site and cofactor binding pocket. Importantly, we show that the flanking sequence preferences of DNMT1 highly correlate with genomic methylation in human and mouse cells, and 5-azacytidine triggered DNA demethylation is more pronounced at CpG sites with flanks disfavored by DNMT1. Overall, our findings uncover the intricate interplay between CpG-flanking sequence, DNMT1-mediated base flipping and the dynamic landscape of DNA methylation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19

The SARS-CoV-2 3CL protease is a critical drug target for small molecule COVID-19 therapy, given its likely druggability and essentiality in the viral maturation and replication cycle. Based on the conservation of 3CL protease substrate binding pockets across coronaviruses and using screening, we identified four structurally distinct lead compounds that inhibit SARS-CoV-2 3CL protease. After evaluation of their binding specificity, cellular antiviral potency, metabolic stability, and water solubility, we prioritized the GC376 scaffold as being optimal for optimization. We identified multiple drug-like compounds with <10nM potency for inhibiting SARS-CoV-2 3CL and the ability to block SARS-CoV-2 replication in human cells, obtained co-crystal structures of the 3CL protease in complex with these compounds, and determined that they have pan-coronavirus activity. We selected one compound, termed coronastat, as an optimized lead and characterized it in pharmacokinetic and safety studies in vivo. Coronastat represents a new candidate for a small molecule protease inhibitor for the treatment of SARS-CoV-2 infection for eliminating pandemics involving coronaviruses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Soil texture and environmental conditions influence the biogeochemical responses of soils to drought and flooding

Abstract Climate change is intensifying the global water cycle, with increased frequency of drought and flood. Water is an important driver of soil carbon dynamics, and it is crucial to understand how moisture disturbances will affect carbon availability and fluxes in soils. Here we investigate the role of water in substrate-microbe connectivity and soil carbon cycling under extreme moisture conditions. We collected soils from Alaska, Florida, and Washington USA, and incubated them under Drought and Flood conditions. Drought had a stronger effect on soil respiration, pore-water carbon, and microbial community composition than flooding. Soil response was not consistent across sites, and was influenced by site-level pedological and environmental factors. Soil texture and porosity can influence microbial access to substrates through the pore network, driving the chemical response. Further, the microbial communities are adapted to the historic stress conditions at their sites and therefore show site-specific responses to drought and flood.

58 GEOSCIENCES↗
DOE OSTI2026

Quantifying the relationship between electric field enhancement and plasmon-driven electron transfer

Plasmonic materials interact strongly with light to create localized, out-of-equilibrium environments with intense electromagnetic fields known as hotspots. After forming, hotspots dissipate energy into their surroundings and can transfer energy and charge carriers to nearby molecules, giving plasmonic materials the potential to drive reactions with sunlight. However, the field needs a better mechanistic understanding of plasmon–molecule interactions and how the local plasmon environment, specifically the electromagnetic field enhancement and spatial distribution of hotspots, impacts the reaction yield. Here, in this work, we mapped plasmon-driven charge transfer across ordered plasmonic substrates using diffraction-limited surface-enhanced Raman spectroscopy (SERS) microscopy to understand the relationship between the average local electric field enhancement and charge transfer reaction yield. We tracked the plasmon-induced electron transfer to buckminsterfullerene (C 60 ) and found that areas with the greatest SERS intensity were not the areas with the greatest ensemble-averaged reduction of C 60 , suggesting that areas with higher electric field enhancement—or “hotter,” more enhancing hotspots—do not improve the charge transfer reaction yield. This work shows that efforts to improve plasmon-driven charge transfer should not merely focus on creating substrates with extremely enhancing regions but also consider how other factors could optimize photoreduction yields.

Koble, MaKenna M. [Univ. of Minnesota, Minneapolis↗
DOE OSTI2023

In vitro maturation of NiSOD reveals a role for cytoplasmic histidine in processing and metalation

The importance of cellular low molecular weight (LMW) ligands in metalloenzyme maturation is largely unexplored. Maturation of NiSOD requires post-translational N-terminal processing of the proenzyme, SodN, by its cognate protease, SodX. Here we provide evidence for the participation of L-histidine in the protease-dependent maturation of Nickel-dependent Superoxide Dismutase (NiSOD) from Streptomyces coelicolor. Furthermore, in vitro studies using purified proteins cloned from S. coelicolor and overexpressed in E. coli support a model where a ternary complex formed between the substrate (SodN), the protease (SodX) and L-Histidine creates a novel Ni-binding site that is capable of the N-terminal processing of SodN and specifically incorporates Ni into the apo-NiSOD product. Thus, L-Histidine serves many of the functions associated with a metallochaperone or, conversely, eliminates the need for a metallochaperone in NiSOD maturation.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2026

Imaging surface topography with coherent x-ray reflectivity: Theory, kinematics, and simulations

A theoretical formalism is described for understanding coherent x-ray reflectivity (CXR) from the surface of a semi-infinite crystal having a variable surface topography, described by the height profile ℎ(𝑥,𝑦). The surface topography is imaged as a complex “effective density,” obtained from the phasing and inversion of the coherent x-ray reflectivity data, measured through a rocking scan centered at a vertical momentum transfer 𝑄$^{0}_{𝑧}$ and a vertical range Δ⁢𝑄 𝑧 . The formalism predicts that the effective density has an amplitude with a maximum located at the surface height for each position within the surface plane. The phase of the effective density has a lateral variation that is controlled by the surface height and a vertical variation that reflects a combination of the interfacial structure and specific choice of measurement conditions. This understanding enables direct observation of nanometer-scale interfacial topography, i.e., ℎ⁡(𝑥,𝑦)⁢𝑐 𝑠 (where 𝑐 𝑠 is the vertical substrate lattice parameter) with Å-scale sensitivity to surface height. Numerical simulations illustrate and confirm the theoretical results. These results show how the interpretation of the interfacial density phase obtained by CXR data inversion (i.e., surface topography with respect to a flat surface) is conceptually similar to that previously known for Bragg coherent diffraction imaging (BCDI) measurements of isolated nanoparticles (i.e., lattice displacements with respect to an ideal crystal lattice). This suggests that CXR can be thought of as a form of dark field imaging with respect to the bright field BCDI approach. An implication of these results is that interfacial imaging may bypass some of the significant challenges associated with BCDI imaging of multiple particles having different orientations.

X-ray imaging↗