Search NASA⌕ Search

SEARCH · Search NASA

Results for “competition for substrate”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2

Dopant Incorporation Efficiency in CVD Silicon Carbide Epilayers

In order to ensure reproducible and reliable SiC semiconductor device characteristics, controlled dopant incorporation must be accomplished. Some of the many factors which greatly influence dopant incorporation are the site-competition effect, SiC(0001) substrate polarity, substrate temperature, and the dopant-source reactor concentration. In this paper, dopant incorporation is considered and compared for various dopants in the context of dopant incorporation efficiency. By using secondary ion mass spectrometry (SIMS), the relative dopant incorporation efficiencies were calculated by dividing the SIMS determined dopant concentration in the resulting epitaxial layer by the intentional gas phase dopant concentration used during the SiC CVD. Specifically, the relative magnitudes of dopant incorporation efficiencies for nitrogen, phosphorus, and boron in 6H-SiC (0001) Si-face epitaxial layers are compared as a function of the site-competition effect and the dopant-source reactor concentrations. This serves as a first approximation for comparison of the relative 'doping potencies' of some common dopants used in SiC CVD epitaxial growth.

Larkin, D. J.↗

Trophic interactions shape the spatial organization of medium-chain carboxylic acid producing granular biofilm communities

Abstract Granular biofilms producing medium-chain carboxylic acids (MCCA) from carbohydrate-rich industrial feedstocks harbor highly streamlined communities converting sugars to MCCA either directly or via lactic acid as intermediate. We investigated the spatial organization and growth activity patterns of MCCA producing granular biofilms grown on an industrial side stream to test (i) whether key functional guilds (lactic acid producing Olsenella and MCCA producing Oscillospiraceae) stratified in the biofilm based on substrate usage, and (ii) whether spatial patterns of growth activity shaped the unique, lenticular morphology of these biofilms. First, three novel isolates (one Olsenella and two Oscillospiraceae species) representing over half of the granular biofilm community were obtained and used to develop FISH probes, revealing that key functional guilds were not stratified. Instead, the outer 150–500 µm of the granular biofilm consisted of a well-mixed community of Olsenella and Oscillospiraceae, while deeper layers were made up of other bacteria with lower activities. Second, nanoSIMS analysis of 15N incorporation in biofilms grown in normal and lactic acid amended conditions suggested Oscillospiraceae switched from sugars to lactic acid as substrate. This suggests competitive-cooperative interactions may govern the spatial organization of these biofilms, and suggests that optimizing biofilm size may be a suitable process engineering strategy. Third, growth activities were similar in the polar and equatorial biofilm peripheries, leaving the mechanism behind the lenticular biofilm morphology unexplained. Physical processes (e.g., shear hydrodynamics, biofilm life cycles) may have contributed to lenticular biofilm development. Together, this study develops an ecological framework of MCCA-producing granular biofilms that informs bioprocess development.

09 BIOMASS FUELS↗

Solid-phase hetero epitaxial growth of α-phase formamidinium perovskite

Conventional epitaxy of semiconductor films requires a compatible single crystalline substrate and precisely controlled growth conditions, which limit the price competitiveness and versatility of the process. We demonstrate substrate-tolerant nano-heteroepitaxy (NHE) of high-quality formamidinium-lead-tri-iodide (FAPbI 3 ) perovskite films. The layered perovskite templates the solid-state phase conversion of FAPbI 3 from its hexagonal non-perovskite phase to the cubic perovskite polymorph, where the growth kinetics are controlled by a synergistic effect between strain and entropy. The slow heteroepitaxial crystal growth enlarged the perovskite crystals by 10-fold with a reduced defect density and strong preferred orientation. This NHE is readily applicable to various substrates used for devices. The proof-of-concept solar cell and light-emitting diode devices based on the NHE-FAPbI 3 showed efficiencies and stabilities superior to those of devices fabricated without NHE.

36 MATERIALS SCIENCE↗

Metal-Free, Oxidative Condensation of Heteroaryl- and Aryl Carbaldehydes towards Functionalized Carbonitriles

Functionalization of pyridines with the carbonitrile group for advanced cyclization reactions routinely incorporates metals, toxic oxidants, and cyanide reagents, often in linear synthetic sequences. Here, motivated by the strategic need of a heteroaryl carbonitrile synthon for further elaboration, we disclose an efficient, metal-free, one-pot reaction sequence that uses ammonium acetate as the nitrogen source and bis-acetoxyiodobenzene as the oxidant with low loadings. The developed method tolerates a diverse substrate scope including heteroaryl, aryl, and alkyl substrates with similar efficiency and expands the practitioner's reaction. Method development, optimization, substrate scope, preliminary mechanistic observations, competition experiments, and a scale up reaction are delineated herein.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Radio-frequency plasma chemical vapor deposition growth of diamond

Plasma chemical vapor deposition (CVD) at 13.56 MHz has been used to produce diamond particles in two different inductively coupled systems with a mixture of methane and hydrogen. The effect of a diamondlike carbon (DLC) overcoating on silicon, niobium, and stainless-steel substrates has been investigated and in the case of silicon has been found to enhance particle formation as compared to uncoated polished silicon. In addition the use of carbon monoxide in hydrogen has been found to produce well-defined individual faceted particles as well as polycrystalline films on quartz and DLC coated silicon substrates. Plasma CVD is a competitive approach to production of diamond films. It has the advantage over microwave systems of being easily scaled to large volume and high power.

Meyer, Duane E.↗

Conversion of bioprocess ethanol to industrial chemical products - Applications of process models for energy-economic assessments

An assessment approach for accurate evaluation of bioprocesses for large-scale production of industrial chemicals is presented. Detailed energy-economic assessments of a potential esterification process were performed, where ethanol vapor in the presence of water from a bioreactor is catalytically converted to ethyl acetate. Results show that such processes are likely to become more competitive as the cost of substrates decreases relative to petrolium costs. A commercial ASPEN process simulation provided a reasonably consistent comparison with energy economics calculated using JPL developed software. Detailed evaluations of the sensitivity of production cost to material costs and annual production rates are discussed.

Rohatgi, Naresh K.↗

Biogeochemical and plant trait mechanisms drive enhanced methane emissions in response to whole-ecosystem warming

Abstract. Climate warming perturbs ecosystem carbon (C) cycling, causing both positive and negative feedbacks on greenhouse gas emissions. In 2016, we began a tidal marsh field experiment in two vegetation communities to investigate the mechanisms by which whole-ecosystem warming alters C gain, via plant-driven sequestration in soils, and C loss, primarily via methane (CH4) emissions. Here, we report the results from the first 4 years. As expected, warming of 5.1 ∘C more than doubled CH4 emissions in both plant communities. We propose this was caused by a combination of four mechanisms: (i) a decrease in the proportion of CH4 consumed by CH4 oxidation, (ii) more C substrates available for methanogenesis, (iii) reduced competition between methanogens and sulfate-reducing bacteria, and (iv) indirect effects of plant traits. Plots dominated by Spartina patens consistently emitted more CH4 than plots dominated by Schoenoplectus americanus, indicating key differences in the roles these common wetland plants play in affecting anaerobic soil biogeochemistry and suggesting that plant composition can modulate coastal wetland responses to climate change.

54 ENVIRONMENTAL SCIENCES↗

Aqueous buffer solution-induced crystallization competes with enzymatic depolymerization of pre-treated post-consumer poly (ethylene terephthalate) waste

In this paper, the complex relationship between kinetics and substrate morphology during enzymatic depolymerization of melt processed poly(ethylene terephthalate) (PET) is explored and the effects of competing transformations are analyzed. Extruded PET substrates from post-consumer recycled PET (RPET) bottles flakes subjected to enzymatic depolymerization are examined to reveal increases in crystallinity from ~10% post-extrusion to >30% after 3 days of depolymerization as well as increases in glass transition temperature (T g ) from ~66°C to > 80°C. Further investigation into this behavior shows that post-extrusion RPET substrates do not exhibit changes in crystallinity when subjected to dry annealing at 65°C in an oven over 7 days, but they do experience annealing in depolymerization buffer solution with no enzymes at 65°C within 3 days. This difference may be attributed to plasticization of PET in the presence of water, also known as solvent induced crystallization. The impact of this plasticized annealing behavior is demonstrated by subjecting RPET substrates to increasing enzyme-to-substrate loads. As enzyme load increases, overall conversion of substrates increases despite crystallinity also increasing to similar levels regardless of the initial enzyme loading. The competition between depolymerization and crystallization suggests that the rate at which PET substrates are depolymerized at the operational temperature is integral to achieving high conversion to monomeric product. This, in turn, also suggests that savings from lowered enzyme loadings may be more detrimental than helpful in pursuing the most cost-effective recycling systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sulfate adenylyl transferase kinetics and mechanisms of metabolic inhibitors of microbial sulfate respiration

Abstract Sulfate analog oxyanions that function as selective metabolic inhibitors of dissimilatory sulfate reducing microorganisms (SRM) are widely used in ecological studies and industrial applications. As such, it is important to understand the mode of action and mechanisms of tolerance or adaptation to these compounds. Different oxyanions vary widely in their inhibitory potency and mechanism of inhibition, but current evidence suggests that the sulfate adenylyl transferase/ATP sulfurylase (Sat) enzyme is an important target. We heterologously expressed and purified the Sat from the model SRM, Desulfovibrio alaskensis G20. With this enzyme we determined the turnover kinetics (kcat, KM) for alternative substrates (molybdate, selenate, arsenate, monofluorophosphate, and chromate) and inhibition constants (KI) for competitive inhibitors (perchlorate, chlorate, and nitrate). These measurements enable the first quantitative comparisons of these compounds as substrates or inhibitors of a purified Sat from a respiratory sulfate reducer. We compare predicted half-maximal inhibitory concentrations (IC50) based on Sat kinetics with measured IC50 values against D. alaskensis G20 growth and discuss our results in light of known mechanisms of sensitivity or resistance to oxyanions. This analysis helps with the interpretation of recent adaptive laboratory evolution studies and illustrates the value of interpreting gene–microbe–environment interactions through the lens of enzyme kinetics.

Carlson, Hans K. (ORCID:0000000215835313)↗

Controlling Metal–Organic Framework/ZnO Heterostructure Kinetics through Selective Ligand Binding to ZnO Surface Steps

Metal–organic framework (MOF) heterostructures exhibit unique properties beyond those of individual components, but their design requires an understanding of energetic and kinetic controls at MOF–substrate interfaces. Although the structural relationship has been widely used in heterostructure design, it overlooks the interplay between the organic ligand and the substrate which controls the kinetics and energetics of growth of the final structure. In this study, we used zeolitic imidazolate frameworks (ZIF-8) on ZnO as a model system to evaluate this interplay via in situ monitoring and simulations. Our results demonstrate multiple roles of the 2-methyl-imidazole (2-MIM) ligand as “dissolution-promoter”, “step-pinner”, and “terrace-binder” on the ZnO (001) face and “dissolution-promoter” and “terrace-binder” on the ZnO (100) face. Through these multiple face-specific roles, 2-MIM modulates ZnO dissolution kinetics and, hence, the Zn 2+ release rate, tuning local supersaturations that dictating the characteristic ZIF-8 crystallization kinetics on different substrate faces. The critical thickness for transition from 2D to 3D growth is dictated by competition between interfacial and strain energies. The atomic-scale mechanism of the coupled substrate dissolution and MOF growth, mediated by selective linker–substrate binding, furnishes a new synthesis pathway for other complex heterostructures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Pseudouridine synthase 7 is an opportunistic enzyme that binds and modifies substrates with diverse sequences and structures

Pseudouridine (Ψ) is a ubiquitous RNA modification incorporated by pseudouridine synthase (Pus) enzymes into hundreds of noncoding and protein-coding RNA substrates. Here, in this study, we determined the contributions of substrate structure and protein sequence to binding and catalysis by pseudouridine synthase 7 (Pus7), one of the principal messenger RNA (mRNA) modifying enzymes. Pus7 is distinct among the eukaryotic Pus proteins because it modifies a wider variety of substrates and shares limited homology with other Pus family members. We solved the crystal structure of Saccharomyces cerevisiae Pus7, detailing the architecture of the eukaryotic-specific insertions thought to be responsible for the expanded substrate scope of Pus7. Additionally, we identified an insertion domain in the protein that fine-tunes Pus7 activity both in vitro and in cells. These data demonstrate that Pus7 preferentially binds substrates possessing the previously identified UGUAR (R = purine) consensus sequence and that RNA secondary structure is not a strong requirement for Pus7-binding. In contrast, the rate constants and extent of Ψ incorporation are more influenced by RNA structure, with Pus7 modifying UGUAR sequences in less-structured contexts more efficiently both in vitro and in cells. Although less-structured substrates were preferred, Pus7 fully modified every transfer RNA, mRNA, and nonnatural RNA containing the consensus recognition sequence that we tested. Our findings suggest that Pus7 is a promiscuous enzyme and lead us to propose that factors beyond inherent enzyme properties (e.g., enzyme localization, RNA structure, and competition with other RNA-binding proteins) largely dictate Pus7 substrate selection.

59 BASIC BIOLOGICAL SCIENCES↗

Towards chloroplastic nanofactories: formation of proteinaceous scaffolds for metabolic engineering

The evolution of eukaryotic lipid-bound organelles allows for specialized metabolism to occur within spatially distinct metabolic landscapes within the same cell. However, this strategy of compartmentalization is not unique to eukaryotic organisms. Many bacteria, spread across 45 different phyla, contain loci that encode for specialized bacterial microcompartments (BMCs) (Sutter et al., 2021). The formation of a BMC involves self-assembly from three families of shell proteins to form the outer shell membrane, in addition to the encapsulation of an enzymatic core packaged within the lumen of a BMC (Kerfeld et al., 2018). These proteinaceous organelles provide a competitive growth advantage by enabling organisms to process inaccessible substrates by sequestering metabolic intermediates (i.e. aldehydes) that would otherwise be toxic within the cytoplasm. While BMCs perform specific metabolic functions in their native organism, synthetic, empty BMC shells can form without the requirement of native cargo inside (Doron and Kerfeld, 2024). This provides a transferable and tunable platform of protein scaffolding for guiding metabolic engineering within a host organism of choice (Raba and Kerfeld, 2022).

59 BASIC BIOLOGICAL SCIENCES↗

Competition within low-density bacterial populations as an unexpected factor regulating carbon decomposition in bulk soil

Bacterial decomposition of organic matter in soils is generally believed to be mainly controlled by the access bacteria have to organic substrate. The influence of bacterial traits on this control has, however, received little attention. Using the substrate-dependent Monod growth model, we develop a bioreactive transport model to screen the interactive impacts of spatial dispersion and bacterial traits on mineralization. Bacterial traits primarily involved in the bacterial response to the substrate concentration, such as the maximum specific uptake rate and efficiency, the adaptation time of the uptake rate and the initial population density, are considered. We compare the model results with two sets of previously performed cm-scale soil-core experiments in which the mineralization of the pesticide 2,4-D was measured under well-controlled initial distributions and transport conditions. Bacterial dispersion away from the initial substrate location induced a significant increase in 2,4-D mineralization. Additionally, it reveals an increase of specific uptake rates at lower bacterial densities, more than compensating the decrease of specific uptake rates caused by substrate dilution. This regulation of bacterial activities by density, caused by the local depletion of substrate by competing bacteria, becomes dominant for bacteria with an efficient uptake of substrate at low substrate concentrations (a common feature of oligotrophs). Such oligotrophs, commonly found in soils, compete with each other for substrate even at remarkably low population densities. The ratio-dependent Contois growth model, which includes a density regulation in the expression of the uptake efficiency, is more accurate and convenient to calibrate than the substrate-dependent Monod model, at least under these conditions. In view of their strong interactions, bioreactive and transport processes cannot be handled independently but should be integrated, in particular when reactive processes of interest are carried out by oligotrophs.

59 BASIC BIOLOGICAL SCIENCES↗

Catalytic 1,3-Proton Transfer in Alkenes Enabled by Fe=NR Bond Cooperativity: A Strategy for p K a -Dictated Regioselective Transposition of C=C Double Bonds

Transition metal catalyzed alkene double bond transposition usually involves metal hydride intermediates. Despite significant advances in the design of catalysts that dictate product selectivity, control over substrate selectivity is less advanced and transition metal catalysts that selectively transpose double bonds in substrates containing multiple 1-alkene functionalities are rare. Herein, we report that the three-coordinate high spin (S = 2) Fe(II) imido complex [Ph 2 B( t BuIm) 2 Fe=NDipp][K(18-C-6)THF 2 ] (1-K(18-C-6)) catalyzes 1,3-proton transfer from 1-alkene substrates to afford 2-alkene transposition products. Mechanistic investigations involving kinetics, competition, and isotope labeling studies, supported by experimentally calibrated DFT computations, strongly support an unusual nonhydridic mechanism for alkene transposition that is enabled by the cooperative action of the iron center and basic imido ligand. As dictated by the pK a of the allylic protons, this catalyst enables the regioselective transposition of C=C double bonds in substrates containing multiple 1-alkenes. The high spin (S = 2) state of the complex allows a wide scope of functional groups to be tolerated, including those that are typical catalyst poisons, such as amines, N-heterocycles, and phosphines. Furthermore, these results demonstrate a new strategy for metal-catalyzed alkene transposition with predictable substrate regioselectivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Interactions between microbial diversity and substrate chemistry determine the fate of carbon in soil.

Microbial decomposition drives the transformation of plant-derived substrates into microbial products that form stable soil organic matter (SOM). Recent theories have posited that decomposition depends on an interaction between SOM chemistry with microbial diversity and resulting function. Here, we explicitly test these theories by coupling quantitative stable isotope probing and metabolomics to track the fate of 13C enriched substrates that vary in chemical composition as they are assimilated by microbes and transformed into new metabolic products in soil. We found that mycorrhizal-driven differences in forest nutrient economies (e.g., nutrient cycling, microbial competition) led to arbuscular mycorrhizal (AM) soils harboring greater micro8ial diversity than ectomycorrhizal (ECM) soils. When incubated with 13C enriched substrates, substrate type drove shifts in the identity of active decomposers and their metabolic products in the highly diverse AM soils. The decomposition pathways were more static in the less diverse, ECM soil. Importantly, the majority of these shifts were driven by taxa only present in the AM soil suggesting a strong link between microbial identity and specialized function. Collectively, these results highlight an important interaction between ecosystem-level processes and microbial diversity; whereby the identity and function of active decomposers impacts the composition of decomposition products that can form stable SOM.

Raczka, Nanette↗

Competitive Metabolism of Polycyclic Aromatic Hydrocarbons (PAHs): An Assessment Using In Vitro Metabolism and Physiologically Based Pharmacokinetic (PBPK) Modeling

Humans are routinely exposed to complex mixtures such as polycyclic aromatic hydrocarbons (PAHs) rather than to single compounds, as are often assessed for hazards. Cytochrome P450 enzymes (CYPs) metabolize PAHs, and multiple PAHs found in mixtures can compete as substrates for individual CYPs (e.g., CYP1A1, CYP1B1, etc.). The objective of this study was to assess competitive inhibition of metabolism of PAH mixtures in humans and evaluate a key assumption of the Relative Potency Factor approach that common human exposures will not cause interactions among mixture components. To test this objective, we co-incubated binary mixtures of benzo[a]pyrene (BaP) and dibenzo[def,p]chrysene (DBC) in human hepatic microsomes and measured rates of enzymatic BaP and DBC disappearance. We observed competitive inhibition of BaP and DBC metabolism and measured inhibition coefficients (K i ), observing that BaP inhibited DBC metabolism more potently than DBC inhibited BaP metabolism (0.061 vs. 0.44 µM K i , respectively). We developed a physiologically based pharmacokinetic (PBPK) interaction model by integrating PBPK models of DBC and BaP and incorporating measured metabolism inhibition coefficients. The PBPK model predicts significant increases in BaP and DBC concentrations in blood AUCs following high oral doses of PAHs (≥100 mg), five orders of magnitude higher than typical human exposures. We also measured inhibition coefficients of Supermix-10, a mixture of the most abundant PAHs measured at the Portland Harbor Superfund Site, on BaP and DBC metabolism. We observed similar potencies of inhibition coefficients of Supermix-10 compared to BaP and DBC. Overall, results of this study demonstrate that these PAHs compete for the same enzymes and, at high doses, inhibit metabolism and alter internal dosimetry of exposed PAHs. This approach predicts that BaP and DBC exposures required to observe metabolic interaction are much higher than typical human exposures, consistent with assumptions used when applying the Relative Potency Factor approach for PAH mixture risk assessment.

54 ENVIRONMENTAL SCIENCES↗

Small molecule microarray identifies inhibitors of tyrosyl-DNA phosphodiesterase 1 that simultaneously access the catalytic pocket and two substrate binding sites

Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a member of the phospholipase D family of enzymes, which catalyzes the removal of both 3'- and 5'-DNA phosphodiester adducts. Importantly, it is capable of reducing the anticancer effects of type I topoisomerase (TOP1) inhibitors by repairing the stalled covalent complexes of TOP1 with DNA. It achieves this by promoting the hydrolysis of the phosphodiester bond between the Y723 residue of human TOP1 and the 3'-phosphate of its DNA substrate. Blocking TDP1 function is an attractive means of enhancing the efficacy of TOP1 inhibitors and overcoming drug resistance. Previously, we reported the use of an X-ray crystallographic screen of more than 600 fragments to identify small molecule variations on phthalic acid and hydroxyquinoline motifs that bind within the TDP1 catalytic pocket. Yet, the majority of these compounds showed limited (millimolar) TDP1 inhibitory potencies. We now report examining a 21 000-member library of drug-like Small Molecules in Microarray (SMM) format for their ability to bind Alexa Fluor 647 (AF647)-labeled TDP1. The screen identified structurally similar N,2-diphenylimidazo[1,2-a]pyrazin-3-amines as TDP1 binders and catalytic inhibitors. We then explored the core heterocycle skeleton using one-pot Groebke–Blackburn–Bienayme multicomponent reactions and arrived at analogs having higher inhibitory potencies. Solving TDP1 co-crystal structures of a subset of compounds showed their binding at the TDP1 catalytic site, while mimicking substrate interactions. Although our original fragment screen differed significantly from the current microarray protocol, both methods identified ligand–protein interactions containing highly similar elements. Importantly inhibitors identified through the SMM approach show competitive inhibition against TDP1 and access the catalytic phosphate-binding pocket, while simultaneously providing extensions into both the substrate DNA and peptide-binding channels. As such, they represent a platform for further elaboration of trivalent ligands, that could serve as a new genre of potent TDP1 inhibitors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Competitive Adsorption of Ionic Liquids Versus Friction Modifier and Anti-Wear Additive at Solid/Lubricant Interface—Speciation with Vibrational Sum Frequency Generation Spectroscopy

A modern lubricant contains various additives with different functionalities and the interactions or reactions between these additives could induce synergistic or antagonistic effects in tribological performance. In this study, sum frequency generation (SFG) spectroscopy was used to investigate competitive adsorption of lubricant additives at a solid/base oil interface. A silica substrate was used as a model solid surface. The lubricant additives studied here included two oil-soluble ionic liquids (ILs, [N888H][DEHP] and [P8888][DEHP]), an antiwear additive (secondary ZDDP), an organic friction modifier (OFM), and a dispersant (PIBSI). Our results showed that for mixtures of ZDDP and IL in a base oil (PAO4), the silica surface is dominated by the IL molecules. In the cases of base oils containing OFM and IL, the silica/lubricant interface is dominated by OFM over [N888H][DEHP], while it is preferentially occupied by [P8888][DEHP] over OFM. The presence of PIBSI in the mixture of PAO4 and IL leads to the formation of a mixed surface layer at the silica surface with PIBSI as a major component. The SFG results in this investigation provide fundamental insights that are helpful to design the formulation of new lubricant additives of desired properties.

25 ENERGY STORAGE↗