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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences

Abstract RNA-guided nucleases from CRISPR-Cas systems expand opportunities for precise, targeted genome modification. Endogenous CRISPR-Cas systems in many prokaryotes are attractive to circumvent expression, functionality, and unintended activity hurdles posed by heterologous CRISPR-Cas effectors. However, each CRISPR-Cas system recognizes a unique set of protospacer adjacent motifs (PAMs), which requires identification by extensive screening of randomized DNA libraries. This challenge hinders development of endogenous CRISPR-Cas systems, especially those based on multi-protein effectors and in organisms that are slow-growing or have transformation idiosyncrasies. To address this challenge, we present Spacer2PAM, an easy-to-use, easy-to-interpret R package built to predict and guide experimental determination of functional PAM sequences for any CRISPR-Cas system given its corresponding CRISPR array as input. Spacer2PAM can be used in a ‘Quick’ method to generate a single PAM prediction or in a ‘Comprehensive’ method to inform targeted PAM libraries small enough to screen in difficult to transform organisms. We demonstrate Spacer2PAM by predicting PAM sequences for industrially relevant organisms and experimentally identifying seven PAM sequences that mediate interference from the Spacer2PAM-informed PAM library for the type I-B CRISPR-Cas system from Clostridium autoethanogenum. We anticipate that Spacer2PAM will facilitate the use of endogenous CRISPR-Cas systems for industrial biotechnology and synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Discovery of a novel transcriptional regulator of sugar catabolism in archaea

Abstract The haloarchaeon Haloferax volcanii degrades D‐glucose via the semiphosphorylative Entner‐Doudoroff pathway and D‐fructose via a modified Embden‐Meyerhof pathway. Here, we report the identification of GfcR, a novel type of transcriptional regulator that functions as an activator of both D‐glucose and D‐fructose catabolism. We find that in the presence of D‐glucose, GfcR activates gluconate dehydratase, glyceraldehyde‐3‐phosphate dehydrogenase and pyruvate kinase and also acts as activator of the phosphotransferase system and of fructose‐1,6‐bisphosphate aldolase, which are involved in uptake and degradation of D‐fructose. In addition, glyceraldehyde‐3‐phosphate dehydrogenase and pyruvate kinase are activated by GfcR in the presence of D‐fructose and also during growth on D‐galactose and glycerol. Electrophoretic mobility shift assays indicate that GfcR binds directly to promoters of regulated genes. Specific intermediates of the degradation pathways of the three hexoses and of glycerol were identified as inducer molecules of GfcR. GfcR is composed of a phosphoribosyltransferase (PRT) domain with an N‐terminal helix‐turn‐helix motif and thus shows homology to PurR of Gram‐positive bacteria that is involved in the transcriptional regulation of nucleotide biosynthesis. We propose that GfcR of H. volcanii evolved from a PRT‐like enzyme to attain a function as a transcriptional regulator of central sugar catabolic pathways in archaea.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Reversible Switch in Charge Storage Enabled by Selective Ion Transport in Solid Electrolyte Interphase

Solid-electrolyte interphases (SEIs) in advanced rechargeable batteries ensure reversible electrode reactions at extreme potentials beyond the thermodynamic stability limits of electrolytes by insulating electrons while allowing working ions to transport. Such selective ion transport occurs naturally in biological cell membranes as a ubiquitous prerequisite of many life processes and a foundation of biodiversity. In addition, cell membranes can selectively open and close the ion channels in response to external stimuli (e.g., electrical, chemical, mechanical, thermal), giving rise to “gating” mechanisms that help manage intracellular reactions. We wondered whether the chemistry and structure of SEIs can mimic cell membranes, such that ion gating can be replicated. That is, can SEIs realize a reversible switching between two electrochemical behaviors, i.e., the ion intercalation chemistry of batteries and the ion adsorption of capacitors? Herein, we report such SEIs that result in thermally activated selective ion transport. The function of open/close gate switches is governed by the chemical and structural dynamics of SEIs under different thermal conditions, with precise behaviors as conducting and insulating interphases that enable battery and capacitive processes within a finite temperature window. Such an ion gating function is synergistically contributed by Arrhenius-activated ion transport and SEI dissolution/regrowth. Following the understanding of this new mechanism, we then develop an electrochemical method to heal the SEI layer in situ. As a result, the knowledge acquired in this work reveals the possibility of hitherto unknown biomimetic properties of SEIs, which will guide us to leverage such complexities to design better SEIs for future battery chemistries.

25 ENERGY STORAGE↗
DOE OSTI2026

An information-matching approach to optimal experimental design and active learning

The efficacy of mathematical models heavily depends on the quality of the training data, yet collecting sufficient data is often expensive and challenging. Many modeling applications require inferring parameters only as a means to predict other quantities of interest (QoI). Because models often contain many unidentifiable (sloppy) parameters, QoIs often depend on a relatively small number of parameter combinations. Therefore, we introduce an information-matching criterion based on the Fisher information matrix to select the most informative training data from a candidate pool. This method ensures that the selected data contain sufficient information to learn only those parameters that are needed to constrain downstream QoIs. It is formulated as a convex optimization problem, making it scalable to large models and datasets. Here, we demonstrate the effectiveness of this approach across various modeling problems in diverse scientific fields, including power systems and underwater acoustics. Finally, we use information-matching as a query function within an active learning (AL) loop for materials science applications. In all these applications, we find that a relatively small set of optimal training data can provide the necessary information for achieving precise predictions. These results are encouraging for diverse future applications, particularly AL in large machine-learning models.

Materials science↗
DOE OSTI2020

The microbial rare biosphere: current concepts, methods and ecological principles

ABSTRACT Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the ‘rare biosphere’, across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.

Pascoal, Francisco↗
DOE OSTI2025

Activation, Dehydrogenation, and Carbon–Carbon Coupling of Methane by Iridium Cations Studied by Infrared Multiple Photon Dissociation Spectroscopy and Density Functional Theory

Products resulting from the sequential activation of one, two, three, and four methane molecules by atomic iridium cations were characterized by gas-phase infrared multiple photon dissociation spectroscopy and density functional theory (DFT) calculations. Iridium cations were generated using a laser ablation source and reacted with methane in a linear radiofrequency ion trap before mass analysis and spectroscopic interrogation in a Fourier transform ion cyclotron resonance mass spectrometer coupled to the free-electron laser for intracavity experiments (FELICE) beamline. Product ions were irradiated using infrared light over the 250–1500 cm –1 range. Comparisons between the experimental and DFT-calculated spectra enabled structural determination of the products formed. The observed products include HIrCH + , Ir(CH 2 ) 2 + , H s Ir(C 3 H 5 ) + , and Ir(CH 3 ) s (C 3 H 5 ) + , where the subscript s denotes a syn orientation of the two ligands. Furthermore, formation of the latter two products provides evidence for efficient C–H bond activation and subsequent C–C coupling on the atomic iridium cation.

Chemical reactions↗
DOE OSTI2025

Strongly Correlated States of Transition Metal Spin Defects: The Case of an Iron Impurity in Aluminum Nitride

We investigate the electronic properties of an exemplar transition metal impurity in an insulator, with the goal of accurately describing strongly correlated defect states. Here, we consider iron in aluminum nitride, a material of interest for hybrid quantum technologies, and we carry out calculations with quantum embedding methods, density matrix embedding theory (DMET) and quantum defect embedding theory (QDET), and with spin-flip time-dependent density functional theory (TDDFT). We show that both DMET and QDET accurately describe the ground state and low-lying excited states of the defect and that TDDFT yields photoluminescence spectra in agreement with experiments. In addition, we provide a detailed discussion of the convergence of our results as a function of the active space used in the embedding methods, thus defining a protocol to obtain converged data directly comparable with experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Nucleobase-Functionalized Poly(alkylthiophene)s: One-Pot, Sequential Direct Arylation Polymerization and Deprotection, and Surface Modification for Oil–Water Separations

Direct arylation polymerization (DArP) has emerged as an environmentally friendly, atom efficient method of synthesizing a variety of conjugated polymers. In this work, we report a one-pot approach consisting of DArP followed by Boc deprotection to synthesize a functional, surface-active adenine-containing poly(alkylthiophene). Careful control over the polymerization temperature enables the one-pot polymerization and deprotection strategy for synthesis, with quantitative (>99%) Boc deprotection achieved in 24 h. This temperature-controlled synthesis method reduces extra purification and isolation steps, which makes the total synthesis more efficient and practical, and allows higher molecular weight polymer to be made. We quantify the hydrogen bonding ability of the resulting adenine-containing polythiophene, T Ad -tT 4h , by 1 H NMR host–guest titration studies and analyze the results with the Benesi–Hildebrand model, yielding an association constant of 18.7 M –1 between alkylated thymine and T Ad -tT 4h . We demonstrate that T Ad -tT 4h robustly modifies the surface of cellulosic filter paper (CFP), and the modified cellulosic filter paper, CFP-T Ad -tT 4h , is an effective oil–water separatory filter with superhydrophobic properties (water contact angle (CA) ~151°). The utility of hydrogen bonding interactions between adenine and cellulose highlights the importance of side-chain engineering for creating functional materials.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Impact of shading following installation of agrivoltaic systems on eco-physiological and biochemical attributes of “Howes” cranberry in Massachusetts

Agrivoltaic (AV) systems, which integrate solar energy generation with crop production on the same piece of land, offer a sustainable solution for optimizing land-use efficiency. However, the impact of shading induced by solar panels on crop growth, physiology, and metabolic activities of cranberry is not known. Understanding these interactions is essential for assessing the feasibility of AV systems in cranberry production. In this study we evaluated eco-physiological and biochemical crop responses on a commercial ‘Howes’ cranberry bog grown under an agrivoltaics system using different row spacings in the year immediately following installation. Following installation of fixed tilt solar panels at a height of 3.0 m above the plant canopy, four shading treatments were evaluated: an uncovered control area and row spacings of 9.0 m, 7.0 m, and 5.0 m, corresponding to 30%, 35%, and 37% shading respectively. The shading effect was also evaluated at three different fruit developmental stages (green, blush, and full-red stage). Using microclimate sensors installed in the treatment areas, key eco-physiological and biochemical parameters, including leaf gas exchange, chlorophyll, anthocyanin, and antioxidant content, electrolyte leakage, proline and trehalose accumulation, were assessed. While moderate shading (30% and 35%) alleviated environmental stress, as reflected by improved leaf water status and reduced electrolyte leakage, these same treatments suppressed key physiological and metabolic functions, including photosynthetic activity, carbon reserve accumulation, and the biosynthesis of stress-related osmolytes and antioxidant compounds. Under higher shading (37%), these reductions were even more pronounced, indicating a potential threshold beyond which the benefits of shading are outweighed by declines in assimilate production and secondary metabolism. These findings highlight a trade-off between the stress-mitigating benefits of shading and the alterations in key physiological and metabolic processes under agrivoltaic systems. Minimizing these trade-offs by optimizing row spacing in agrivoltaics systems is critical to maintain cranberry physiological status. Since commercial cranberry is grown as a continuous plant canopy (no interrow spaces for equipment travel), damage caused by the installation process likely impacted crop response evaluated in the first year; multi-year studies are needed to fully understand the dynamics of a dual-use system. Notably, this work provides the first direct measurements of proline, trehalose content, and electrolyte leakage in cranberry grown under AV conditions, offering new insight into their physiological adjustments to shading.

14 SOLAR ENERGY↗
DOE OSTI2022

Inverter Reliability Estimation for Advanced Inverter Functionality

In the near future, grid operators are expected to regularly use advanced distributed energy resource (DER) functions, defined in IEEE 1547-2018, to perform a range of grid-support operations. Many of these functions adjust the active and reactive power of the device through commanded or autonomous modes, which will produce new stresses on the grid-interfacing power electronics components, such as DC/AC inverters. In previous work, multiple DER devices were instrumented to evaluate additional component stress under multiple reactive power setpoints. We utilize quasi-static time-series simulations to determine voltage-reactive power mode (volt-var) mission profile of inverters in an active power system. Mission profiles and loss estimates are then combined to estimate the reduction of the useful life of inverters from different reactive power profiles. It was found that the average lifetime reduction was approximately 0.15% for an inverter between standard unity power factor operation and the IEEE 1547 default volt-var curve based on thermal damage due to switching in the power transistors. For an inverter with an expected 20-year lifetime, the 1547 volt-var curve would reduce the expected life of the device by 12 days. This framework for determining an inverter's useful life from experimental and modeling data can be applied to any failure mechanism and advanced inverter operation.

component degradation↗
DOE OSTI2022

Efficient Pd on carbon catalyst for ammonium formate dehydrogenation: Effect of surface oxygen functional groups

Formate solution is one of a kind promising liquid organic hydrogen carrier but suffers from kinetic challenges. This study investigates the kinetics of the surfacefunctionalized Pd on carbon catalysts for formate dehydrogenation and the impact of O-functional groups. Here, the fraction of the distinguished O-functional groups was modulated by the different concentrated HNO 3 solutions treatment or by H 2 reduction. This study shows that the O-functional groups play critical roles in dispersing Pd nanoparticles and decreasing the activation energy for dehydrogenation. Density functional theory (DFT) calculation reveals that most O-functional groups enhance formate adsorption on the Pd active site. However, the existence of C=O groups consumes reducing agents and hinders the formation of metallic Pd. The electron transfer from Pd to oxygen functional groups is unfavorable to dehydrogenation. The as-prepared Pd5/re-ACA (reduced activated carbon washed by acid) exhibited significant activity with a higher turnover frequency of 13,511 h -1 than commercial Pd/C.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Polymer Waste Valorization into Advanced Carbon Nanomaterials for Potential Energy and Environment Applications

The rise in universal population and accompanying demands have directed toward an exponential surge in the generation of polymeric waste. The estimate predicts that world-wide plastic production will rise to ≈590 million metric tons by 2050, whereas 5000 million more tires will be routinely abandoned by 2030. Handling this waste and its detrimental consequences on the Earth's ecosystem and human health presents a significant challenge. Converting the wastes into carbon-based functional materials viz. activated carbon, graphene, and nanotubes is considered the most scientific and adaptable method. Herein, this world provides an overview of the various sources of polymeric wastes, modes of build-up, impact on the environment, and management approaches. Update on advances and novel modifications made in methodologies for converting diverse types of polymeric wastes into carbon nanomaterials over the last 5 years are given. A remarkable focus is made to comprehend the applications of polymeric waste-derived carbon nanomaterials (PWDCNMs) in the CO 2 capture, removal of heavy metal ions, supercapacitor-based energy storage and water splitting with an emphasis on the correlation between PWDCNMs' properties and their performances. In conclusion, this review offers insights into emerging developments in the upcycling of polymeric wastes and their applications in environment and energy.

36 MATERIALS SCIENCE↗
DOE OSTI2023

NMR relaxometry characterization of water adsorption in corn stover anatomical fractions

Nuclear magnetic resonance (NMR) relaxometry is applied to provide direct measurement of water adsorption in anatomical fractions of corn stover. NMR transverse T 2 relaxation time distribution measurements indicate multiple water populations, which vary with anatomical fraction and water adsorption. Measured T 2 data are used to calculate thermodynamic properties of Brunauer-Emmet-Teller adsorption theory using a model to estimate mono and bilayer relaxation. T 2 data are used directly to determine rotational diffusion correlation times indicating adsorption interaction strength. T 1 -T 2 longitudinal-transverse relaxation time correlation measurements quantify differences in the molecular level structural order of the adsorbate surface water as a function of water activity, i.e. relative humidity or water vapor partial pressure. The T 1 /T 2 ratio provides a measure of the surface energy related to the adsorption strength and surface diffusive mobility of the water adsorbate and differentiates the anatomical fractions. Furthermore, the results indicate that direct measurement of NMR relaxation times can be used to characterize corn stover biomass water adsorption, data relevant to processing and handling considerations.

09 BIOMASS FUELS↗
DOE OSTI2022

Accessing subnuclear fluctuations and saturation with multiplicity dependent J/ψ production in p+p and p+Pb collisions

We study the production of J/ψ vector mesons as a function of charged hadron multiplicity in p+p and p+Pb collisions at LHC energies. We employ the color glass condensate framework, using running coupling Balitsky-Kovchegov evolved dipole amplitudes, to compute gluon and cc¯-pair production. We use fragmentation functions to obtain charged hadrons, and explore two different hadronization schemes for the J/ψ: non-relativistic quantum chromodynamics and the improved color evaporation model. In our framework, event-by-event multiplicity fluctuations of both hadrons and J/ψ are driven by geometric and saturation scale normalization fluctuations. Studying the correlation between J/ψ and hadron multiplicity, we show that the characteristic difference between forward and backward rapidity in p+Pb collisions is a result of different degrees of saturation probed at different rapidities. We demonstrate that experimental data on heavy-flavor production as a function of event activity provide stringent constraints on the fluctuating proton structure

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

Unraveling plant phenotype to genotype associations with daily hyperspectral traits in Populus trichocarpa

Hyperspectral remote sensing is a powerful, high-throughput phenotyping tool that quantifies physiologically and structurally relevant wavelengths across diverse genotypes and over varying temporal scales. In this study, we combined tower-based continuous hyperspectral sensing with genome-wide association studies to analyze 1423 wavebands (400-900 nm) and derivative vegetation indices across 505 genotypes and the genetic architecture of hyperspectral phenotypes over time in Populus trichocarpa Torr. & Gray grown under field conditions. Wavelengths related to chlorophyll and carotenoid absorption spectra exhibited the strongest genetic variation resulting in 98 significant SNP associations. Notably, we found substantial overlap in genetic association between the blue and red spectral regions, indicative of carotenoids and chlorophyll, respectively, and identified more than 10 candidate genes associated with chloroplast function, underpinning photosynthetic activity. Furthermore, fluctuations in associations for vegetative indices, such as the chlorophyll:carotenoid index (CCI), across the growing season reveal a temporally dynamic genetic architecture of physiological traits associated with fall senescence of this temperate tree species. Finally, we also observed correlations (spearman rho = 0.3, p < 1x10 −8 ) between individual wavebands or vegetative indices and growth rate, assessed as the relative change of tree height over the growing season. The growth rate prediction was substantially improved by a regularization multivariate model (spearman rho>0.5, p < 1x10 −16 ), reinforcing the value of hyperspectral measurements for predicting traits linked to tree productivity. These findings highlight the potential of high-throughput, rapid, hyperspectral genome wide association studies GWAS to uncover physiologically meaningful genetic variation and offer promising insights for future acceleration for plant breeding.

09 BIOMASS FUELS↗
DOE OSTI2020

Electrocatalytic Hydrogenation of Biomass-Derived Organics: A review

Sustainable energy generation calls for a shift away from centralized, high-temperature, energy-intensive processes to decentralized, low-temperature conversions that can be powered by electricity produced from renewable sources. Electrocatalytic conversion of biomass-derived feedstocks would allow carbon recycling of distributed, energy-poor resources in the absence of sinks and sources of high-grade heat. Selective, efficient electrocatalysts that operate at low temperatures are needed for electrocatalytic hydrogenation (ECH) to upgrade the feedstocks. For effective generation of energy-dense chemicals and fuels, two design criteria must be met: (i) a high H:C ratio via ECH to allow for high-quality fuels and blends, and (ii) a lower O:C ratio in the target molecules via electrochemical decarboxylation/deoxygenation to improve the stability of fuels and chemicals. The goal of this review is to determine whether the following questions have been sufficiently answered in open literature, and if not, what additional information is required: (1) What organic functionalities are accessible for electrocatalytic hydrogenation under a set of reaction conditions? How do substitutions and functionalities impact the activity and selectivity of ECH? (2) What material properties cause an electrocatalyst to be active for ECH? Can general trends in ECH be formulated based on the type of electrocatalyst? (3) What is the impact of reaction (electrolyte concentration, pH, operating potential) and reactor type conditions?

Catalysts, redox reactions, hydrocarbons, Aromatic↗
DOE OSTI2024

Low Field NMR Relaxometry Characterization of Water Adsorption in Corn Stover Anatomical Fractions

Low magnetic field 2 MHz NMR relaxometry is applied to measure water adsorption processes of intact corn stover anatomical fractions. Comparison with high magnetic field 250 MHz relaxometry of milled corn stover fractions as a function of water activity, i.e., relative humidity, provides insight into the microstructural changes of the biomass and varying water molecular dynamics during adsorption. As a result, the data presented establish a basis for low field portable NMR of biomass in situ in field and processing environments.

09 BIOMASS FUELS↗
DOE OSTI2024

Missing microbial eukaryotes and misleading meta-omic conclusions

Meta-omics is commonly used for large-scale analyses of microbial eukaryotes, including species or taxonomic group distribution mapping, gene catalog construction, and inference on the functional roles and activities of microbial eukaryotes in situ. Here, we explore the potential pitfalls of common approaches to taxonomic annotation of protistan meta-omic datasets. We re-analyze three environmental datasets at three levels of taxonomic hierarchy in order to illustrate the crucial importance of database completeness and curation in enabling accurate environmental interpretation. We show that taxonomic membership of sequence clusters estimates community composition more accurately than returning exact sequence labels, and overlap between clusters can address database shortcomings. Clustering approaches can be applied to diverse environments while continuing to exploit the wealth of annotation data collated in databases, and selecting and evaluating these databases is a critical part of correctly annotating protistan taxonomy in environmental datasets. We argue that ongoing curation of genetic resources is crucial in accurately annotating protists in in situ meta-omic datasets. Moreover, we propose that precise taxonomic annotation of meta-omic data is a clustering problem rather than a feasible alignment problem.

59 BASIC BIOLOGICAL SCIENCES↗