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At least 847 records · Page 47
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Decoding Active Sites for Highly Efficient Semihydrogenation of Acetylene in Palladium–Copper Nanoalloys

Accurately decoding the three-dimensional atomic structure of surface active sites is essential yet challenging for a rational catalyst design. Here, we used comprehensive techniques combining the pair distribution function and reverse Monte Carlo simulation to reveal the surficial distribution of Pd active sites and adjacent coordination environment in palladium-copper nanoalloys. After the fine-tuning of the atomic arrangement, excellent catalytic performance with 98% ethylene selectivity at complete acetylene conversion was obtained in the Pd 34 Cu 66 nanocatalysts, outperforming most of the reported advanced catalysts. Further, t he quantitative deciphering shows a large number of active sites with a Pd-Pd coordination number of 3 distributed on the surface of Pd 34 Cu 66 nanoalloys, which play a decisive role in highly efficient semihydrogenation. This finding not only opens the way for guiding the precise design of bimetal nanocatalysts from atomic-level insight but also provides a method to resolve the spatial structure of active sites.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice

Abstract Background Genes with multiple co-active promoters appear common in brain, yet little is known about functional requirements for these potentially redundant genomic regulatory elements. SCN1A, which encodes the Na V 1.1 sodium channel alpha subunit, is one such gene with two co-active promoters. Mutations in SCN1A are associated with epilepsy, including Dravet syndrome (DS). The majority of DS patients harbor coding mutations causing SCN1A haploinsufficiency; however, putative causal non-coding promoter mutations have been identified. Methods To determine the functional role of one of these potentially redundant Scn1a promoters, we focused on the non-coding Scn1a 1b regulatory region, previously described as a non-canonical alternative transcriptional start site. We generated a transgenic mouse line with deletion of the extended evolutionarily conserved 1b non-coding interval and characterized changes in gene and protein expression, and assessed seizure activity and alterations in behavior. Results Mice harboring a deletion of the 1b non-coding interval exhibited surprisingly severe reductions of Scn1a and Na V 1.1 expression throughout the brain. This was accompanied by electroencephalographic and thermal-evoked seizures, and behavioral deficits. Conclusions This work contributes to functional dissection of the regulatory wiring of a major epilepsy risk gene, SCN1A . We identified the 1b region as a critical disease-relevant regulatory element and provide evidence that non-canonical and seemingly redundant promoters can have essential function.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Engineering Surface Oxygenated Functionalities on Commercial Carbon toward Ultrafast Sodium Storage in Ether-Based Electrolytes

The pursuit of a high-capacity anode material has been urgently required for commercializing sodium-ion batteries with a high energy density and an improved working safety. In the absence of thermodynamically stable sodium intercalated compounds with graphite, constructing nanostructures with expanded interlayer distances is still the mainstream option for developing high-performance carbonaceous anodes. In this regard, a surface-functionalized and pore-forming strategy through a facile CO 2 thermal etching route was rationally adopted to engineer negligible oxygenated functionalities on commercial carbon for boosting the sodium storage process. Benefitted from the abundant ionic/electronic pathways and more active reaction sites in the microporous structure with noticeable pseudocapacitive behaviors, the functionalized porous carbon could achieve a highly reversible capacity of 505 mA h g -1 at 50 mA g -1 , an excellent rate performance of 181 mA h g -1 at 16,000 mA g -1 , and an exceptional rate cycle stability of 176 mA h g -1 at 3200 mA g -1 over 1000 cycles. These outstanding electrochemical properties should be ascribed to a synergistic mechanism, fully utilizing the graphitic and amorphous structures for synchronous intercalations of sodium ions and solvated sodium ion compounds, respectively. Finally, the controllable generation and evolution of a robust but thin solid electrolyte interphase film with the emergence of obvious capacitive reactions on the defective surface, favoring the rapid migration of sodium ions and solvated species, also contribute to a remarkable electrochemical performance of this porous carbon black.

25 ENERGY STORAGE↗
DOE OSTI2021

Modeling Activities Related to Waste Form Degradation: Progress Report

This report represents the milestone deliverable M4SF-21SN010309021 “Modeling Activities Related to Waste Form Degradation: Progress Report” that describes the progress of R&D activities of ongoing modeling investigations specifically on nuclear waste glass degradation, Density Functional Theory (DFT) studies on clarkeite structure and stability, and electrochemical modeling of spent nuclear fuel (SNF). These activities are part of the newly-created Waste form Testing, Modeling, and Performance work package at Sandia National Laboratories (SNL). This work package is part of the “Inventory and Waste Form Characteristics and Performance” control account that includes various experimental and modeling activities on nuclear waste degradation conducted at Oak Ridge National Laboratory (ORNL), SNL, Argonne National Laboratory (ANL), and Pacific Northwest National Laboratory (PNNL).

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

A map of the rubisco biochemical landscape

Rubisco is the primary CO 2 -fixing enzyme of the biosphere, yet it has slow kinetics. The roles of evolution and chemical mechanism in constraining its biochemical function remain debated. Engineering efforts aimed at adjusting the biochemical parameters of rubisco have largely failed, although recent results indicate that the functional potential of rubisco has a wider scope than previously known. Here we developed a massively parallel assay, using an engineered Escherichia coli in which enzyme activity is coupled to growth, to systematically map the sequence–function landscape of rubisco. Composite assay of more than 99% of single-amino acid mutants versus CO 2 concentration enabled inference of enzyme velocity and apparent CO 2 affinity parameters for thousands of substitutions. This approach identified many highly conserved positions that tolerate mutation and rare mutations that improve CO 2 affinity. These data indicate that non-trivial biochemical changes are readily accessible and that the functional distance between rubiscos from diverse organisms can be traversed, laying the groundwork for further enzyme engineering efforts.

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

Characterization of Mammalian In Vivo Enhancers Using Mouse Transgenesis and CRISPR Genome Editing [Book Chapter]

Embryonic morphogenesis is strictly dependent on tight spatiotemporal control of developmental gene expression, which is typically achieved through the concerted activity of multiple enhancers driving cell type-specific expression of a target gene. Mammalian genomes are organized in topologically associated domains, providing a preferred environment and framework for interactions between transcriptional enhancers and gene promoters. While epigenomic profiling and three-dimensional chromatin conformation capture have significantly increased the accuracy of identifying enhancers, assessment of subregional enhancer activities via transgenic reporter assays in mice remains the gold standard for assigning enhancer activity in vivo. Once this activity is defined, the ideal method to explore the functional necessity of a transcriptional enhancer and its contribution to target gene dosage and morphological or physiological processes is deletion of the enhancer sequence from the mouse genome. Here we present detailed protocols for efficient introduction of enhancer-reporter transgenes and CRISPR-mediated genomic deletions into the mouse genome, including a step-by-step guide for pronuclear microinjection of fertilized mouse eggs. We provide instructions for the assembly and genomic integration of enhancer-reporter cassettes that have been used for validation of thousands of putative enhancer sequences accessible through the VISTA enhancer browser, including a recently published method for robust site-directed transgenesis at the H11 safe-harbor locus. Together, these methods enable rapid and large-scale assessment of enhancer activities and sequence variants in mice, which is essential to understand mammalian genome function and genetic diseases.

cis-regulatory elements↗
DOE OSTI2020

Structural Insights into the SPRED1-Neurofibromin-KRAS Complex and Disruption of SPRED1-Neurofibromin Interaction by Oncogenic EGFR

Sprouty-related, EVH1 domain-containing (SPRED) proteins negatively regulate RAS/mitogen-activated protein kinase (MAPK) signaling following growth factor stimulation. This inhibition of RAS is thought to occur primarily through SPRED1 binding and recruitment of neurofibromin, a RasGAP, to the plasma membrane. Here, we report the structure of neurofibromin (GTPase-activating protein [GAP]-related domain) complexed with SPRED1 (EVH1 domain) and KRAS. The structure provides insight into how the membrane targeting of neurofibromin by SPRED1 allows simultaneous interaction with activated KRAS. SPRED1 and NF1 loss-of-function mutations occur across multiple cancer types and developmental diseases. Analysis of the neurofibromin-SPRED1 interface provides a rationale for mutations observed in Legius syndrome and suggests why SPRED1 can bind to neurofibromin but no other RasGAPs. We show that oncogenic EGFR(L858R) signaling leads to the phosphorylation of SPRED1 on serine 105, disrupting the SPRED1-neurofibromin complex. The structural, biochemical, and biological results provide new mechanistic insights about how SPRED1 interacts with neurofibromin and regulates active KRAS levels in normal and pathologic conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Solubility Predictions for Hanford Tank Concentrates with HSC - 20459

The commercially available Outotec HSC 9.9.0{sup R} provides excellent predictions for the solubilities of many species for Hanford waste tank concentrates. The HSC solubility predictions with a Harvie activity model agreed well with five boildowns that showed solubility limits for NaNO{sub 3}, NaNO{sub 2}, Na{sub 2}CO{sub 3}, NaF, Na{sub 2}SO{sub 4}, and Na{sub 3}PO{sub 4}. However, the HSC did not predict density and therefore water content very well and therefore we used the measured densities and derived water content from the difference between measured density and assays. Furthermore, we adjusted the HSC enthalpy for the minor species Na{sub 3}PO{sub 4}*NaF double salt in order to fit the five boildowns as well. Previous work has shown that gibbsite becomes and remains supersaturated in all of these boildowns and so there was no alumina precipitation despite supersaturation. Furthermore, an equilibrium model like HSC always shows complete oxidation of any TOC in the presence of nitrate and nitrite. We therefore suppressed the HSC oxidation of acetate and oxalate in order to fit measured acetate and oxalate solubilities as TOC. Space in Hanford waste tanks is very limited and therefore evaporator campaigns continue to recover needed tank space from dilute tank liquids. Prior to each evaporator campaign, a boildown of a sample of tank liquid for each campaign provides a basis for planning by measuring density, water activity, soluble species, and solids precipitation as a function of concentration at 18 deg. C. These boildowns then provide validations and calibrations for the HSC solubility prediction for Hanford wastes. Previous work has shown the solubilities of minor electrolytes in these five boildowns follow rather simple power law solubility products. Hanford's 222-S laboratory has reported each of five boildowns for concentrated liquids from five waste tanks and tank blends. All boildowns eventually showed the precipitation of the dominant electrolyte, NaNO{sub 3}, and overall solution activity largely drives all solubility. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Developing Enzyme Immobilization with Fibrous Membranes: Longevity and Characterization Considerations

Fibrous membranes offer broad opportunities to deploy immobilized enzymes in new reactor and application designs, including multiphase continuous flow-through reactions. Enzyme immobilization is a technology strategy that simplifies the separation of otherwise soluble catalytic proteins from liquid reaction media and imparts stabilization and performance enhancement. Flexible immobilization matrices made from fibers have versatile physical attributes, such as high surface area, light weight, and controllable porosity, which give them membrane-like characteristics, while simultaneously providing good mechanical properties for creating functional filters, sensors, scaffolds, and other interface-active biocatalytic materials. This review examines immobilization strategies for enzymes on fibrous membrane-like polymeric supports involving all three fundamental mechanisms of post-immobilization, incorporation, and coating. Post-immobilization offers an infinite selection of matrix materials, but may encounter loading and durability issues, while incorporation offers longevity but has more limited material options and may present mass transfer obstacles. Coating techniques on fibrous materials at different geometric scales are a growing trend in making membranes that integrate biocatalytic functionality with versatile physical supports. Biocatalytic performance parameters and characterization techniques for immobilized enzymes are described, including several emerging techniques of special relevance for fibrous immobilized enzymes. Diverse application examples from the literature, focusing on fibrous matrices, are summarized, and biocatalyst longevity is emphasized as a critical performance parameter that needs increased attention to advance concepts from lab scale to broader utilization. This consolidation of fabrication, performance measurement, and characterization techniques, with guiding examples highlighted, is intended to inspire future innovations in enzyme immobilization with fibrous membranes and expand their uses in novel reactors and processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Characterization of the polysilicon resistor in silicon strip sensors for ATLAS inner tracker as a function of temperature, pre- and post-irradiation

The high luminosity upgrade of the Large Hadron Collider, foreseen for 2029, requires the replacement of the ATLAS Inner Detector with a new all-silicon Inner Tracker (ITk). The expected ultimate total integrated luminosity of 4000 fb –1 means that the strip part of the ITk detector will be exposed to the total particle fluences and ionizing doses reaching the values of 1.6 · 10 15 1 MeV n eq /cm 2 and 0.66 MGy, respectively, including a safety factor of 1.5. Radiation hard n + -in-p micro-strip sensors were developed by the ATLAS ITk strip collaboration and are produced by Hamamatsu Photonics K.K. The active area of each ITk strip sensor is delimited by the n-implant bias ring, which is connected to each individual n + implant strip by a polysilicon bias resistor. The total resistance of the polysilicon bias resistor should be within a specified range to keep all the strips at the same potential, prevent the signal discharge through the grounded bias ring and avoid the readout noise increase. While the polysilicon is a ubiquitous semiconductor material, the fluence and temperature dependence of its resistance is not easily predictable, especially for the tracking detector with the operational temperature significantly below the values typical for commercial microelectronics. Dependence of the resistance of polysilicon bias resistor on the temperature, as well as on the total delivered fluence and ionizing dose, was studied on the specially-designed test structures called ATLAS Testchips, both before and after their irradiation by protons, neutrons, and gammas to the maximal expected fluence and ionizing dose. The resistance has an atypical negative temperature dependence. It is different from silicon, which shows that the grain boundary has a significant contribution to the resistance. Finally, we discuss the contributions by parameterizing the activation energy of the polysilicon resistance as a function of the temperature for unirradiated and irradiated ATLAS Testchips.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Multiplicity functions of quasars: predictions from the MassiveBlackII simulation

ABSTRACT We examine multiple active galactic nucleus (AGN) systems (triples and quadruples, in particular) in the MassiveBlackII simulation over a redshift range of 0.06 ≲ z ≲ 4. We identify AGN systems (with bolometric luminosity $L_{\mathrm{bol}}\gt 10^{42}~\mathrm{erg\, s}^{-1}$) at different scales (defined by the maximum distance between member AGNs) to determine the AGN multiplicity functions. This is defined as the volume/surface density of AGN systems per unit richness R, the number of AGNs in a system. We find that gravitationally bound multiple AGN systems tend to populate scales of ${\lesssim}0.7~\mathrm{cMpc}\, h^{-1}$; this corresponds to angular separations of ≲100 arcsec and a line-of-sight velocity difference ${\lesssim}200~\mathrm{km\, s}^{-1}$. The simulation contains ∼10 and ∼100 triples/quadruples per deg2 up to depths of DESI (g ≲ 24) and LSST (g ≲ 26) imaging, respectively; at least $20{{\ \rm per\ cent}}$ of these should be detectable in spectroscopic surveys. The simulated quasar ($L_{\mathrm{bol}}\gt 10^{44}~\mathrm{erg\, s}^{-1}$) triples and quadruples predominantly exist at 1.5 ≲ z ≲ 3. Their members have black hole masses $10^{6.5}\lesssim M_{\mathrm{ bh}}\lesssim 10^{9}~\mathrm{M}_{\odot }\, h^{-1}$ and live in separate (one central and multiple satellite) galaxies with stellar masses $10^{10}\lesssim M_{*}\lesssim 10^{12}~\mathrm{M}_{\odot }\, h^{-1}$. They live in the most massive haloes (e.g. ${\sim}10^{13}~\mathrm{M}_{\odot }\, h^{-1}$ at z = 2.5; ${\sim}10^{14}~\mathrm{M}_{\odot }\, h^{-1}$ at z = 1) in the simulation. Their detections provide an exciting prospect for understanding massive black hole growth and their merger rates in galaxies in the era of multimessenger astronomy.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Coupled Experimental–Theoretical Characterization of a Carbon Electrode in Vanadium Redox Flow Batteries using X-ray Absorption Spectroscopy

Vanadium redox flow batteries (VRFBs) have emerged as promising solutions for stationary grid energy storage due to their high efficiency, scalability, safety, near room-temperature operation conditions, and the ability to independently size power and energy capacities. The performance of VRFBs heavily relies on the redox couple reactions of V 2+ /V 3+ and VO 2+ /VO 2 + on carbon electrodes. Therefore, a thorough understanding of the surface functionality of carbon electrodes and their propensity for degradation during electrochemical cycles is crucial for designing VRFBs with extended lifespans. In this study, we present a coupled experimental–theoretical approach based on carbon K edge X-ray absorption spectroscopy (XAS) to characterize carbon electrodes prepared under different conditions and identify relevant functional groups that contribute to unique spectroscopic features. Atomic models were created to represent functional groups, such as hydroxyl, carboxyl, methyl, and aldehyde, bonded to carbon atoms in either sp 2 or sp 3 environments. The interactions between functionalized carbon and various solvated vanadium complexes were modeled using density functional theory. A library of carbon K-edge XAS spectra was generated for distinct carbon atoms in different functional groups, both before and after interacting with solvated vanadium complexes. Here we demonstrate how these simulated spectra can be used to deconvolve ex situ experimental spectra measured from carbon electrodes and to track changes in the electrode composition following immersion in different electrolytes or extended cycling within a functional VRFB. By doing so, we identify the active species present on the carbon electrodes, which play a crucial role in determining their electrochemical performance.

25 ENERGY STORAGE↗
DOE OSTI2024

Ancient Origin of Acetyltransferases Catalyzing O -acetylation of Plant Cell Wall Polysaccharides

Abstract Members of the domain of unknown function 231/trichome birefringence–like (TBL) family have been shown to be O-acetyltransferases catalyzing the acetylation of plant cell wall polysaccharides, including pectins, mannan, xyloglucan and xylan. However, little is known about the origin and evolution of plant cell wall polysaccharide acetyltransferases. Here, we investigated the biochemical functions of TBL homologs from Klebsormidium nitens, a representative of an early divergent class of charophyte green algae that are considered to be the closest living relatives of land plants, and Marchantia polymorpha, a liverwort that is an extant representative of an ancient lineage of land plants. The genomes of K. nitens and Marchantia polymorpha harbor two and six TBL homologs, respectively. Biochemical characterization of their recombinant proteins expressed in human embryonic kidney 293 cells demonstrated that the two K. nitens TBLs exhibited acetyltransferase activities acetylating the pectin homogalacturonan (HG) and hence were named KnPOAT1 and KnPOAT2. Among the six M. polymorpha TBLs, five (MpPOAT1 to 5) possessed acetyltransferase activities toward pectins and the remaining one (MpMOAT1) catalyzed 2-O- and 3-O-acetylation of mannan. While MpPOAT1,2 specifically acetylated HG, MpPOAT3,4,5 could acetylate both HG and rhamnogalacturonan-I. Consistent with the acetyltransferase activities of these TBLs, pectins isolated from K. nitens and both pectins and mannan from M. polymorpha were shown to be acetylated. These findings indicate that the TBL genes were recruited as cell wall polysaccharide O-acetyltransferases as early as in charophyte green algae with activities toward pectins and they underwent expansion and functional diversification to acetylate various cell wall polysaccharides during evolution of land plants.

Cell Biology↗
DOE OSTI2020

Hole–hole Tamm–Dancoff-approximated density functional theory: A highly efficient electronic structure method incorporating dynamic and static correlation

The study of photochemical reaction dynamics requires accurate as well as computationally efficient electronic structure methods for the ground and excited states. While time-dependent density functional theory (TDDFT) is not able to capture static correlation, complete active space self-consistent field methods neglect much of the dynamic correlation. Hence, inexpensive methods that encompass both static and dynamic electron correlation effects are of high interest. Here, we revisit hole–hole Tamm–Dancoff approximated (hh-TDA) density functional theory for this purpose. The hh-TDA method is the hole–hole counterpart to the more established particle–particle TDA (pp-TDA) method, both of which are derived from the particle–particle random phase approximation (pp-RPA). In hh-TDA, the N-electron electronic states are obtained through double annihilations starting from a doubly anionic (N+2 electron) reference state. In this way, hh-TDA treats ground and excited states on equal footing, thus allowing for conical intersections to be correctly described. Furthermore, the treatment of dynamic correlation is introduced through the use of commonly employed density functional approximations to the exchange-correlation potential. Additionally, we show that hh-TDA is a promising candidate to efficiently treat the photochemistry of organic and biochemical systems that involve several low-lying excited states—particularly those with both low-lying ππ* and nπ* states where inclusion of dynamic correlation is essential to describe the relative energetics. In contrast to the existing literature on pp-TDA and pp-RPA, we employ a functional-dependent choice for the response kernel in pp- and hh-TDA, which closely resembles the response kernels occurring in linear response and collinear spin-flip TDDFT.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

How thermal fluctuations influence the function of the FeMo cofactor in nitrogenase enzymes

The catalytic mechanism of N 2 fixation by nitrogenase remains unresolved in how the strong N≡N bond is activated and why the reductive elimination of H 2 is required. Here, we use density functional theory and physiologically relevant thermal simulations to elucidate the mechanism of the complete nitrogenase catalytic cycle. Over the accumulation of four reducing equivalents, we find that protons and electrons transfer to the FeMo cofactor to weaken and break its bridge Fe–S bond, leading to temporary H 2 S formation that exposes the Fe sites to weakly bind N 2 . Remarkably, we find that subsequent H 2 formation is responsible for chemical activation to an N=N double bond accompanied by a low barrier for H 2 release. We emphasize that finite temperature effects smooth out mechanistic differences between DFT functionals observed at 0 K, thus leading to a consistent understanding as to why H formation is an obligatory step in N 2 adsorption and activation.

DFT↗
DOE OSTI2023

Expression and characterization of spore coat Cot$\mathrm{H}$ kinases from the cellulosomes of anaerobic fungi ( Neocallimastigomycetes )

Anaerobic fungi (Neocallimastigomycetes) found in the guts of herbivores are biomass deconstruction specialists with a remarkable ability to extract sugars from recalcitrant plant material. Anaerobic fungi, as well as many species of anaerobic bacteria, deploy multi-enzyme complexes called cellulosomes, which modularly tether together hydrolytic enzymes, to accelerate biomass hydrolysis. While the majority of genomically encoded cellulosomal genes in Neocallimastigomycetes are biomass degrading enzymes, the second largest family of cellulosomal genes encode spore coat CotH domains, whose contribution to fungal cellulosome and/or cellular function is unknown. Structural bioinformatics of CotH proteins from the anaerobic fungus Piromyces finnis shows anaerobic fungal CotH domains conserve key ATP and Mg 2+ binding motifs from bacterial Bacillus CotH proteins known to act as protein kinases. Experimental characterization further demonstrates ATP hydrolysis activity in the presence and absence of substrate from two cellulosomal P. finnis CotH proteins when recombinantly produced in E. coli. These results present foundational evidence for CotH activity in anaerobic fungi and provide a path towards elucidating the functional contribution of this protein family to fungal cellulosome assembly and activity.

59 BASIC BIOLOGICAL SCIENCES↗