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Results for “activation function”

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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

A pathogenic role for histone H3 copper reductase activity in a yeast model of Friedreich’s ataxia

Disruptions to iron-sulfur (Fe-S) clusters, essential cofactors for a broad range of proteins, cause widespread cellular defects resulting in human disease. A source of damage to Fe-S clusters is cuprous (Cu 1+ ) ions. Since histone H3 enzymatically produces Cu 1+ for copper-dependent functions, we asked whether this activity could become detrimental to Fe-S clusters. Here, we report that histone H3–mediated Cu 1+ toxicity is a major determinant of cellular functional pool of Fe-S clusters. Inadequate Fe-S cluster supply, due to diminished assembly as occurs in Friedreich’s ataxia or defective distribution, causes severe metabolic and growth defects in Saccharomyces cerevisiae. Decreasing Cu 1+ abundance, through attenuation of histone cupric reductase activity or depletion of total cellular copper, restored Fe-S cluster–dependent metabolism and growth. Our findings reveal an interplay between chromatin and mitochondria in Fe-S cluster homeostasis and a potential pathogenic role for histone enzyme activity and Cu 1+ in diseases with Fe-S cluster dysfunction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Lewis Acid Site Engineering in Chromite Spinels Orchestrated Surface Reconstruction and Surpasses RuO 2 in Oxygen Evolution

Atomic-scale engineering of chromite spinels featuring redox-active tetrahedral A-sites and strong Cr–O covalency offers a promising route to superior platinum-group-metal-free oxygen evolution reaction (OER) catalysts. However, comprehensive studies addressing how cation substitution influences surface chemistry and governs OER activity and durability in chromite spinels remain limited. Here, in this work, a systematic investigation of the multicationic chromite series Ni x Fe y Cr 3−x−y O 4 is presented, identifying composition-dependent Lewis acidity as a descriptor of superior OER performance. It is further demonstrated that tuning surface acidity directly controls dynamic reconstruction processes and lattice-oxygen participation during spinel-based electrocatalysis. Following activation, the optimized Ni 0.8 Fe 0.3 Cr 1.9 O 4 catalyst delivers a current density of 10 mA cm −2 at an overpotential of 235 mV, surpassing RuO 2 , with excellent long-term stability. Integrating microscopic and spectroscopic analysis with operando impedance spectroscopy, it shows that activation generates an oxyhydroxide overlayer and reveals a previously unrecognized link between surface Lewis acidity and the growth kinetics and activity of these shells. Density functional theory calculations indicate that Fe incorporation at octahedral sites raises the O 2p-band center and lowers oxygen-vacancy formation energy, promoting lattice-oxygen activation and triggering reconstruction, yielding enhanced OER. This work integrates cation-driven surface-acidity modulation, acidity-governed reconstruction, and OER activity enhancement into a unified predictive framework for designing earth-abundant spinel-based catalysts.

operando impedance spectroscopy↗
DOE OSTI2025

Plant-microbial interplay for organic nitrogen mediated by functional specificity of root compartments

The organic form of nitrogen (N) is a critical intermediate in mutualistic and competitive root-microbial interactions, mediated by extracellular enzymes. Visualization of the hotspots of organic N and proteolytic activity might be valuable for revealing root functional specificity in N acquisition and transformation at the level of individual roots and compartments. For the first time, we used time-lapse amino-mapping and zymography to co-localize and map the spatial distribution of amino-N and leucine aminopeptidase (LAP) activity in the soil and different root parts of maize (Zea mays L.). Amino-N distribution was mainly associated with seminal roots and root tips, where it overlapped with LAP activity hotspots. In the lateral roots and bulk soil, however, LAP activity was decoupled from amino-N. Distinct functional traits revealed themselves as the highest amino-N content and LAP activity in seminal root tips and as the largest relative extent of the rhizosphere in lateral root tips. Co-localized amino-N and LAP activities highlighted different nutrient acquisition strategies mediated by root-microbe interactions, depending on the root compartment. Seminal roots and their tips appeared to adopt mutualistic strategies, potentially attracting root-associated microorganisms through releasing oligo- and polypeptides. In contrast, lateral roots, with amino-N detected only at their tips, demonstrated stronger N competition, relying on the enzyme activity of the rhizosphere microbial community for N acquisition. These insights emphasized the role of root functional specialization in shaping plant-microbe interactions, offering pathways to enhance nutrient use efficiency.

Maize (Zea mays L.)↗
DOE OSTI2022

Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition

Protein phosphatase 2A (PP2A) holoenzymes target broad substrates by recognizing short motifs via regulatory subunits. PP2A methylesterase 1 (PME-1) is a cancer-promoting enzyme and undergoes methylesterase activation upon binding to the PP2A core enzyme. Here, we showed that PME-1 readily demethylates different families of PP2A holoenzymes and blocks substrate recognition in vitro. The high-resolution cryoelectron microscopy structure of a PP2A-B56 holoenzyme–PME-1 complex reveals that PME-1 disordered regions, including a substrate-mimicking motif, tether to the B56 regulatory subunit at remote sites. They occupy the holoenzyme substrate-binding groove and allow large structural shifts in both holoenzyme and PME-1 to enable multipartite contacts at structured cores to activate the methylesterase. B56 interface mutations selectively block PME-1 activity toward PP2A-B56 holoenzymes and affect the methylation of a fraction of total cellular PP2A. The B56 interface mutations allow us to uncover B56-specific PME-1 functions in p53 signaling. Our studies reveal multiple mechanisms of PME-1 in suppressing holoenzyme functions and versatile PME-1 activities derived from coupling substrate-mimicking motifs to dynamic structured cores.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Endothelial cells control vascular smooth muscle cell cholesterol levels by regulating 24-dehydrocholesterol reductase expression

Highlights: • Suspended endothelial and vascular smooth muscle cells organize to form spherical vascular organoids in hanging drops. • Vascular smooth muscle cells downregulate the expression of metabolism regulating genes in presence of endothelial cells. • Endothelial cells decrease the levels of 24-dehydrocholesterol reductase and cholesterol in vascular smooth muscle cells. • Diminished cholesterol biosynthesis inhibits vascular smooth muscle cell activity. Communication of vascular cells is essential for the control of organotypic functions of blood vessels. In this context, vascular endothelial cells (EC) act as potent regulators of vascular smooth muscle cell (VSMC) functions such as contraction and relaxation. However, the impact of ECs on the gene expression pattern of VSMCs is largely unknown. Here, we investigated changes of the VSMC transcriptome by utilizing 3D human vascular organoids organized as a core of VSMCs enclosed by a monolayer of ECs. Microarray-based analyses indicated that interaction with ECs for 48 h down-regulates expression of genes in VSMCs controlling rate-limiting steps of the cholesterol biosynthesis such as HMGCR, HMGCS1, DHCR24 and DHCR7. Protein analyses revealed a decrease in the abundance of DHCR24 (24-dehydrocholesterol reductase) and lower cholesterol levels in VSMCs co-cultured with ECs. On the functional level, the blockade of the DHCR24 activity impaired adhesion, migration and proliferation of VSMCs. Collectively, these findings indicate that ECs have the capacity to instruct VSMCs to shut down the expression of DHCR24 thereby limiting their cholesterol biosynthesis, which may support their functional steady state.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Coupled Cluster Downfolding Theory: towards universal many-body algorithms for dimensionality reduction of composite quantum systems in chemistry and materials science

Abstract The recently introduced coupled cluster (CC) downfolding techniques for reducing the dimensionality of quantum many-body problems recast the CC formalism in the form of the renormalization procedure allowing, for the construction of effective (or downfolded) Hamiltonians in small-dimensionality sub-space, usually identified with the so-called active space, of the entire Hilbert space. The resulting downfolded Hamiltonians integrate out the external (out-of-active-space) Fermionic degrees of freedom from the internal (in-the-active-space) parameters of the wave function, which can be determined as components of the eigenvectors of the downfolded Hamiltonians in the active space. This paper will discuss the extension of non-Hermitian (associated with standard CC formulations) and Hermitian (associated with the unitary CC approaches) downfolding formulations to composite quantum systems commonly encountered in materials science and chemistry. The non-Hermitian formulation can provide a platform for developing local CC approaches, while the Hermitian one can serve as an ideal foundation for developing various quantum computing applications based on the limited quantum resources. We also discuss the algorithm for extracting the semi-analytical form of the inter-electron interactions in the active spaces.

Bauman, Nicholas P.↗
DOE OSTI2021

Active magnetic regenerative cooling with smaller magnets

Magnetocaloric heat pumping near room temperature, a.k.a. magnetic cooling, relies on the active regenerator cycle to achieve functional temperature spans and realize economic and societal benefits promised by this emerging solid-state cooling technology. The cycle itself depends upon synchronizing oscillating flow of a heat transfer fluid through a solid porous active material matrix, or the refrigerant, with periods when the refrigerant is in the highest available (field-on) and in nearly zero (field-off) magnetic fields to accomplish heat transfer. With this in mind, in this work we analyze varying flow and magnetic field wave forms and the timing between when the fluid is pumped and when the magnetic field is turned on and off. We demonstrate that the volume and the cost of permanent magnet generating the field changes can be cut nearly in half with little to no effect on the device temperature span and cooling power normalized by the refrigerant mass.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Structural coordination between active sites of a CRISPR reverse transcriptase-integrase complex

CRISPR-Cas systems provide adaptive immunity in bacteria and archaea, beginning with integration of foreign sequences into the host CRISPR genomic locus and followed by transcription and maturation of CRISPR RNAs (crRNAs). In some CRISPR systems, a reverse transcriptase (RT) fusion to the Cas1 integrase and Cas6 maturase creates a single protein that enables concerted sequence integration and crRNA production. To elucidate how the RT-integrase organizes distinct enzymatic activities, we present the cryo-EM structure of a Cas6-RT-Cas1—Cas2 CRISPR integrase complex. The structure reveals a heterohexamer in which the RT directly contacts the integrase and maturase domains, suggesting functional coordination between all three active sites. Together with biochemical experiments, our data support a model of sequential enzymatic activities that enable CRISPR sequence acquisition from RNA and DNA substrates. These findings highlight an expanded capacity of some CRISPR systems to acquire diverse sequences that direct CRISPR-mediated interference.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Design of supported organocatalysts from a biomass-derived difuran compound and catalytic assessment for lactose hydrolysis

The engineered structures and active sites of enzyme catalysts give rise to high catalytic activity and selectivity toward desired reactions. We have employed a biomass-derived difuran compound to append N-substituted maleimides with amino acid (glutamic acid) substitution by Diels–Alder reaction to mimic the chemical functional groups that comprise the active site channels in enzyme catalysts. The difunctionality of the biomass-derived difuran allows production of Diels–Alder adducts by appending two amino acid moieties to form a difunctional organocatalyst. The catalytic activity of the organocatalyst can be improved by immobilizing the organocatalyst on solid supporting materials. Accordingly, the structures of these immobilized organocatalysts can be engineered to mimic enzymatic active sites and to control the interaction between reactants, products, and transition states of catalytic reactions. Lactose hydrolysis was carried out to provide an example of industrial application of this approach to design and fabricate new supported organocatalysts as artificial enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

TRISO Fuel’s Safety Functions, Contributions to Reactor Safety, and Necessary Safety Limits

Safety functions are the actions, passive or active, that structures, systems, and components of nuclear facility that contribute to the safety of the workers, the public, or the environment. Well-defined safety functions are the foundation of a solid safety case for a reactor. For reactors that use TRISO-coated particles, the TRISO fuel plays an important part of the safety case because of its ability to contain radionuclides in the fuel itself. This ability enables the use of a functional containment strategy for the reactor where radionuclide retention is the primary safety function supported by the safety functions of controlling reactivity control and controlling heat rejection. This paper establishes at a deeper level the role that TRISO fuel plays in each of these safety functions and associated quality assurance and testing requirements for TRISO particle manufacturing to ensure these safety functions. Safety limits necessary to protect these safety functions include: operational limits, time at temperature limits, and fission gas release activity limits. In conclusion, this approach demonstrates the role that specific aspects of TRISO fuel play in protecting the safety of workers, the public, and the environment.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

A data driven approach for cross-slip modelling in continuum dislocation dynamics

Cross-slip is a thermally activated process by which screw dislocation changes its glide plane to another slip plane sharing the same Burgers vector. The rate at which this process happens is determined by a Boltzmann type expression that is a function of the screw segment length and the stress acting on the dislocation. In continuum dislocation dynamics (CDD), the information regarding the length of the screw dislocation segment and local stress state on dislocations are lost due to the coarse-grained representation of the density. Here, in this work, a data driven approach to characterize the lost information by analyzing the discrete dislocation configurations is proposed to enable cross-slip modeling in the CDD framework in terms of the coarse-grained dislocation density and stress fields. The analysis showed that the screw segment length follows an exponential distribution, and the stress fluctuations, defined as the difference between the stress on the dislocations and the mean field stress in CDD, follows a Lorentzian distribution. A novel approach for cross slip implementation in CDD employing the screw segment length and stress fluctuation statistics was proposed and rigorously tested by comparing the CDD cross-slip rates with discrete dislocation dynamics (DDD) rates. This approach has been applied in conjunction with three cross-slip models used in DDD simulations differing mainly in the functional form of cross slip activation energy. It was found that different cross-slip activation energy formulations yielded different cross-slip rates, yet the effect on mechanical stress-strain response and dislocation density evolution was minimal for the [001] type loading.

42 ENGINEERING↗
DOE OSTI2021

Dynamically Tunable Terahertz Emission Enabled by Anomalous Optical Phonon Responses in Lead Telluride

Lead telluride (PbTe), a narrow bandgap semiconductor commonly used in infrared detectors, exhibits anomalous vibrational and structural properties, making it appealing for thermoelectrics. Despite significant fundamental interest in the microscopic origins of its unusual vibrational properties, the optical functionalities stemming from phonons and electron–phonon coupling in PbTe have not been closely investigated. This work reports measurements of terahertz (THz) radiation from a PbTe single crystal following ultrafast optical excitation and investigates IR-active phonon responses as a function of excitation fluence and temperature. We uncover a spectrally tunable THz emission peak enabled by an epsilon-near-zero response of the coupled plasmon–longitudinal optical phonon mode that can be dynamically shifted via tuning photocarrier density. Spectral tunability (Δω/ω = 25%) is significant and beyond what has been achieved by any other THz emitter. In addition, the emitted THz fields reveal signatures of a zone center transverse optical phonon anomaly and unveil a new mode at 0.3 THz that diminishes in amplitude under increasing photocarrier density. Temperature-dependent measurements suggest that the transverse-like modes at 1 and 1.5 THz are possibly of different origins. These results indicate that the unusual phononic properties in PbTe are tunable via photoexcitation and enable new optical functionalities in THz applications, such as spectrally tunable emitters and all-optical modulators.

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

Kinetic modeling of microbial growth, enzyme activity, and gene deletions: An integrated model of β-glucosidase function in Cellvibrio japonicus

Understanding the complex growth and metabolic dynamics in microorganisms requires advanced kinetic models containing both metabolic reactions and enzymatic regulation to predict phenotypic behaviors under different conditions and perturbations. Most current kinetic models lack gene expression dynamics and are separately calibrated to distinct media, which consequently makes them unable to account for genetic perturbations or multiple substrates. This challenge limits our ability to gain a comprehensive understanding of microbial processes towards advanced metabolic optimizations that are desired for many biotechnology applications. Here, we present an integrated computational and experimental approach for the development and optimization of mechanistic kinetic models for microbial growth and metabolic and enzymatic dynamics. Our approach integrates growth dynamics, gene expression, protein secretion, and gene-deletion phenotypes. We applied this methodology to build a dynamic model of the growth kinetics in batch culture of the bacterium Cellvibrio japonicus grown using either cellobiose or glucose media. The model parameters were inferred from an experimental data set using an evolutionary computation method. The resulting model was able to explain the growth dynamics of C. japonicus using either cellobiose or glucose media and was also able to accurately predict the metabolite concentrations in the wild-type strain as well as in β-glucosidase gene deletion mutant strains. We validated the model by correctly predicting the non-diauxic growth and metabolite consumptions of the wild-type strain in a mixed medium containing both cellobiose and glucose, made further predictions of mutant strains growth phenotypes when using cellobiose and glucose media, and demonstrated the utility of the model for designing industrially-useful strains. Importantly, the model is able to explain the role of the different β-glucosidases and their behavior under genetic perturbations. Here, this integrated approach can be extended to other metabolic pathways to produce mechanistic models for the comprehensive understanding of enzymatic functions in multiple substrates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Single-cell stable isotope probing in microbial ecology

Abstract Environmental and host-associated microbiomes are typically diverse assemblages of organisms performing myriad activities and engaging in a network of interactions that play out in spatially structured contexts. As the sum of these activities and interactions give rise to overall microbiome function, with important consequences for environmental processes and human health, elucidating specific microbial activities within complex communities is a pressing challenge. Single-cell stable isotope probing (SC-SIP) encompasses multiple techniques that typically utilize Raman microspectroscopy or nanoscale secondary ion mass spectrometry (NanoSIMS) to enable spatially resolved tracking of isotope tracers in cells, cellular components, and metabolites. SC-SIP techniques are uniquely suited for illuminating single-cell activities in microbial communities and for testing hypotheses about cellular functions generated for example from meta-omics datasets. Here, we illustrate the insights enabled by SC-SIP techniques by reviewing selected applications in microbiology and offer a perspective on their potential for future research.

Alcolombri, Uria (ORCID:0000000335615091)↗
DOE OSTI2025

A Change in C–H Activation Mechanism: Experimental and Computational Investigations of Rh-Catalyzed Disubstituted Benzene Functionalization

We report the ethenylation of 1,3- and 1,2-disubstituted benzenes using [(η 2 -C 2 H 4 ) 2 Rh(μ-OAc)] 2 as a catalyst precursor and Cu(OPiv) 2 as the oxidant. The regioselectivity of alkenylation for 1,3-disubstituted benzenes produces 3,5-disubstituted styrene products, while the alkenylation of 1,2-disubstituted benzenes produces 3,4- disubstituted styrene products. The rate of alkenylation is influenced by steric and electronic factors based on the substituents of the benzene unit. In all cases, 1,2-disubstituted benzenes react faster than 1,3-disubstituted benzenes, with a rate difference that is from 2 times up to >70 times more rapid for 1,2-disubstituted substrates. This is likely due to the difference in the number of accessible C−H bonds based on the steric protection of C−H bonds adjacent to functionality. Furthermore, the rate of alkenylation is influenced by the arene substituent electronics. The rates of alkenylation for 1,2-disubstituted benzenes follow the trend OMe > Me > CF 3 > Cl, while for 1,3-disubstituted benzenes the trend is CF 3 > Cl > Me > OMe. Using quantum mechanics DFT calculations, we found that the C−H activation step can occur by two different mechanisms. The electronic properties of substituents on the arene ring change the preferred C−H bond-breaking mechanism for 1,2-disubstituted and 1,3-disubstituted benzenes.

Aromatic compounds↗
DOE OSTI2022

Bibliometric review and recent advances in total scattering pair distribution function analysis: 21 years in retrospect

Global research activities have been driven by the quest to develop and characterize novel materials for technological advancements. The total scattering pair distribution function (TSPDF) is a powerful and versatile characterization technique for examining the structural details of diverse complex materials including liquid, amorphous, disordered crystalline, and nanostructured materials. Thus, it is critical to keep track of research progress, identify research gaps, and future research directions of the application of the TSPDF technique in materials development and discovery. In this work, a bibliometric analysis of literature regarding the TSPDF technique between 2000 and 2021 was conducted using datasets retrieved from the Web of Science database. The research trends based on publication outputs, research subject distribution, co-authorships among institutions, countries/regions, co-citation of referenced sources, and keyword co-occurrence are evaluated and discussed herein. The impact of the TSPDF technique is projected to increase due to its importance in probing emerging functional materials, and the advances in specialized facilities and instrumentation among the scientific communities engaged with it. Finally, current and emerging research hotspots related to TSPDF technique such as catalysis, computer modeling and simulation, pharmaceutics, machine learning, hydrogen storage, battery materials, and layered structured materials are also identified and discussed.

36 MATERIALS SCIENCE↗