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Results for “electronic structure regulation”

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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Structural basis of chromatin regulation by histone variant H2A.Z

Abstract The importance of histone variant H2A.Z in transcription regulation has been well established, yet its mechanism-of-action remains enigmatic. Conflicting evidence exists in support of both an activating and a repressive role of H2A.Z in transcription. Here we report cryo-electron microscopy (cryo-EM) structures of nucleosomes and chromatin fibers containing H2A.Z and those containing canonical H2A. The structures show that H2A.Z incorporation results in substantial structural changes in both nucleosome and chromatin fiber. While H2A.Z increases the mobility of DNA terminus in nucleosomes, it simultaneously enables nucleosome arrays to form a more regular and condensed chromatin fiber. We also demonstrated that H2A.Z’s ability to enhance nucleosomal DNA mobility is largely attributed to its characteristic shorter C-terminus. Our study provides the structural basis for H2A.Z-mediated chromatin regulation, showing that the increase flexibility of the DNA termini in H2A.Z nucleosomes is central to its dual-functions in chromatin regulation and in transcription.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural basis of RNA conformational switching in the transcriptional regulator 7SK RNP

7SK non-coding RNA (7SK) negatively regulates RNA polymerase II (RNA Pol II) elongation by inhibiting positive transcription elongation factor b (P-TEFb), and its ribonucleoprotein complex (RNP) is hijacked by HIV-1 for viral transcription and replication. Methylphosphate capping enzyme (MePCE) and La-related protein 7 (Larp7) constitutively associate with 7SK to form a core RNP, while P-TEFb and other proteins dynamically assemble to form different complexes. Here, we present the cryo-EM structures of 7SK core RNP formed with two 7SK conformations, circular and linear, and uncover a common RNA-dependent MePCE-Larp7 complex. Further, together with NMR, biochemical, and cellular data, these structures reveal the mechanism of MePCE catalytic inactivation in the core RNP, unexpected interactions between Larp7 and RNA that facilitate a role as an RNP chaperone, and that MePCE-7SK-Larp7 core RNP serves as a scaffold for switching between different 7SK conformations essential for RNP assembly and regulation of P-TEFb sequestration and release.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Regulation of Energy and Mass Transport in a Hydrogen-Bonded Framework for Visible-Light-Driven CO2 Reduction in Water

Photoenzymatic reduction of CO2 to formate is a promising strategy for carbon valorization, yet its efficiency is still limited by inefficient energy and mass transport. Here, we design a series of isostructural hydrogen-bonded organic frameworks (HOFs) that establish confinement effects to promote photocatalytic NADH regeneration and the subsequent NADH-dependent enzymatic CO2-to-formate reduction. We demonstrate that spatial confinement within the framework channels localizes exciton migration to nanoscale domains and promotes interfacial dissociation. Additionally, Rh-induced electronic-structure modulation enables ultrafast electron transfer, while the intrinsic hydrogen-bond network furnishes directional proton conduction to NAD+. These synergistic regulations afford a photocatalytic NADH regeneration efficiency of 99.8% with a record apparent quantum efficiency of 32.8%, and drive formate production at a rate of 3020 μmol g-1 h-1 with 100% selectivity─the highest rate reported to date for all light-driven systems in water. The HOF-based catalyst retains 86.3% of its initial activity over five cycles, highlighting its robustness. This work offers mechanistic insight into how microenvironment engineering within HOF architectures regulates energy and mass transport in photoenzymatic catalysis, paving the way for the rational design of advanced hybrid catalytic systems.

Xu, Jiaxing↗
DOE OSTI2026

Spatiotemporal structure of edge harmonic oscillation and its role in ELM-free QH-mode at KSTAR

In Quiescent H-mode (QH-mode), edge-localized modes (ELMs) are naturally replaced by a low-n edge harmonic oscillation (EHO), yet the self-regulating transport mechanism driven by the EHO remains insufficiently understood. Using high-spatiotemporal-resolution imaging diagnostics on KSTAR—electron cyclotron emission imaging and broadband electron cyclotron emission—we resolve the eigenmode structure of the EHO and elucidate its regulatory role in edge transport. The EHO is localized within the pedestal near the maximum pressure gradient, propagates in the ion-diamagnetic direction, and its radial envelope expands with increasing shear, suggesting that rotational shear is closely associated with the structural evolution of the EHO. Information-theoretic Transfer Entropy analysis identifies a distinct ‘dual-stabilization’ regulatory interaction pattern: the EHO is associated with enhanced outward energy transport to limit the pressure gradient, while the background shear flow is associated with preferential regulatory influence on the EHO saturation amplitude and energy flux. These results demonstrate that the QH-mode pedestal is sustained by a shear-associated regulation mechanism, where the coupling between rotational shear and mode structure appears closely linked to the sustained ELM-free state.

ECEI↗
DOE OSTI2022

Mass spectrometry-based technologies for probing the 3D world of plant proteins

Abstract Over the past two decades, mass spectrometric (MS)-based proteomics technologies have facilitated the study of signaling pathways throughout biology. Nowhere is this needed more than in plants, where an evolutionary history of genome duplications has resulted in large gene families involved in posttranslational modifications and regulatory pathways. For example, at least 5% of the Arabidopsis thaliana genome (ca. 1,200 genes) encodes protein kinases and protein phosphatases that regulate nearly all aspects of plant growth and development. MS-based technologies that quantify covalent changes in the side-chain of amino acids are critically important, but they only address one piece of the puzzle. A more crucially important mechanistic question is how noncovalent interactions—which are more difficult to study—dynamically regulate the proteome’s 3D structure. The advent of improvements in protein 3D technologies such as cryo-electron microscopy, nuclear magnetic resonance, and X-ray crystallography has allowed considerable progress to be made at this level, but these methods are typically limited to analyzing proteins, which can be expressed and purified in milligram quantities. Newly emerging MS-based technologies have recently been developed for studying the 3D structure of proteins. Importantly, these methods do not require protein samples to be purified and require smaller amounts of sample, opening the wider proteome for structural analysis in complex mixtures, crude lysates, and even in intact cells. These MS-based methods include covalent labeling, crosslinking, thermal proteome profiling, and limited proteolysis, all of which can be leveraged by established MS workflows, as well as newly emerging methods capable of analyzing intact macromolecules and the complexes they form. In this review, we discuss these recent innovations in MS-based “structural” proteomics to provide readers with an understanding of the opportunities they offer and the remaining challenges for understanding the molecular underpinnings of plant structure and function.

Plant Sciences↗
DOE OSTI2026

Function, Structure, and Regulation of Nitrogen Fixation-like Metalloproteins for Nitrogen, Energy, Carbon, and Sulfur Metabolism

Nitrogenases (N 2 ases) and nitrogen fixation-like (NFL) systems play distinct roles in nitrogen, carbon, sulfur, and energy metabolism based on their fundamental differences in structure and metallocofactor identity. As new NFL systems have recently been identified and characterized, striking parallels and differences compared to N 2 ase structure, catalysis, and regulation have emerged. NFL systems use metallocofactors that span from simple [4Fe-4S] clusters to complex clusters akin to FeMo-co, previously only thought to occur in N 2 ase. This review describes the present state of knowledge on the function, structure, catalytic mechanisms, and regulation of NFL systems that perform distinct biological roles across all three domains of life. Recent advancements in N 2 ase spectroscopic techniques for probing metallocofactor structure and electronic states guide current and future work on how each NFL system catalyzes its specific biological reaction(s). Key knowledge gaps and needed areas of research for uncovering the specific metallocofactors and structural motifs that are at the heart of NFL system reaction specificity, along with how these systems are regulated, are discussed.

Bacteria↗
DOE OSTI2024

Engineering Ultrathin Alloy Shell in Au@AuPd Core-Shell Nanoparticles for Efficient Plasmon-Driven Photocatalysis

Bimetallic core-shell nanoparticles (NPs) possessing a synergetic coupling of plasmonic and catalytic metals have emerged as promising prototypes for efficient plasmon-driven photocatalysis. Here, Au@AuPd core-shell NPs composed of Au core NP and ultrathin AuPd shell are introduced to acquire improved light utilization efficiency in photocatalytic selective oxidation. With systematical control of the composition of the ultrathin alloy shell, it reveals that the Au@AuPd core-shell NPs with 10 at% Pd (in the single-atom alloy regime) is an effective nanostructure capable of maximizing the quantum yield of plasmon-induced light absorption and optimizing the surface electronic structure for catalytic reactions. This controlled system provides new insights into shell engineering for enhancing photocatalytic performance via the regulation of energy funneling processes in core-shell nanocatalysts.

36 MATERIALS SCIENCE↗
DOE OSTI2024

SISGR: The regulation of carbon fixation in plant and green algae: Rubisco activase and the origin of heat inactivation of CO 2 assimilation

Rubisco activase (Rca) is a critical AAA+ ATPase protein complex that remodels and promotes the Rubisco enzyme, a key player in photosynthetic performance and carbon fixation. The assembly and function of the Rca protein complex are regulated by a range of factors, including subunit concentration, nucleotide-binding states, thermal conditions, metal-ion coordination, and post-translational modifications, such as phosphorylation. Despite its importance in photosynthesis, the detailed molecular mechanisms underlying the regulation of plant Rca and how it activates Rubisco remain elusive. This project aims to bridge this knowledge gap by integrating sophisticated enzymology tools with single-molecule methods and high-resolution electron microscopy to elucidate the structure and function of plant Rca. Through these multiple approaches, we have systematically investigated how the activity of plant Rca is impacted by various factors, such as phosphorylation and metal-ion coordination. The Rca complex assembly/disassembly dynamics were captured using anti-Brownian electrokinetic (ABEL) trap-based measurements, providing unprecedented insight into its structural flexibility and diverse assembly states. Furthermore, the structural analysis of Rca through electron crystallography and single-particle cryogenic electron microscopy (cryo-EM) reveals novel assembly states of the spinach Rca, providing insight into the mechanistic action for Rubisco remodeling. By combining cutting-edge tools and approaches, this work uncovers critical aspects of Rca’s regulation and assembly, paving the way for a deeper understanding of its role in photosynthetic efficiency and the potential for enhancing carbon fixation in crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Toward Complete Transformation of Sodium Polysulfides by Regulating the Second-Shell Coordinating Environment of Atomically Dispersed Fe

Room temperature sodium-sulfur (RT Na-S) batteries are highly competitive as potential energy storage devices. Nevertheless, their actually achieved reversible capacities are far below the theoretical value due to incomplete transformation of polysulfides. Herein, atomically dispersed Fe-N/S active center by regulating the second-shell coordinating environment of Fe single atom is proposed. The Fe-N4S2 coordination structure with enhanced local electronic concentration around the Fermi level is revealed via synchrotron radiation X-ray absorption spectroscopy (XAS) and theoretical calculations, which can not only significantly promote the transformation kinetics of polysulfides, but induce uniform Na deposition for dendrite-free Na anode. Here as a result, the obtained S cathode delivers a high initial reversible capacity of 1590 mAh g-1, nearly the theoretical value. Here this work opens up a new avenue to facilitate the complete transformation of polysulfides for RT Na-S batteries.

25 ENERGY STORAGE↗
DOE OSTI2023

Silver-carbon interlayers in anode-free solid-state lithium metal batteries: Current development, interfacial issues, and instability challenges

As an interlayer between the anode and the electrolyte of the all-solid-state lithium metal batteries (ASSLMBs), the silver-carbon (Ag-C) nanocomposite has been reported to significantly increase the energy density and cycle rate of solid-state lithium metal batteries. Ag-C interlayers serve as mixed ionic-electronic conductor that conducts both Li+ ions and electrons and lithium storage capacity. Unfortunately, it was unclear how the Ag-C interlayer regulated lithium plating and stripping. Moreover, the structural and chemical instabilities between the interlayer and the electrolyte, within the interlayer, or beneath the interlayer on lithium substrate are likely to cause cell failure. In this review, we discuss interfacial issues and summarize recent progress in solution strategies for ASSLMBs, with a specific focus on the use of a silver-carbon (Ag-C) nanocomposite interlayer in anode-free setups. Based on the Li transport kinetics among the Ag-C interlayers, the interfacial configurations of Ag-C interlayers are classified as either exterior or internal. Furthermore, the review concludes with a discussion of the perspectives and future prospects, allowing for the improvement of interlayer techniques for solid-state batteries.

25 ENERGY STORAGE↗
DOE OSTI2022

Structural basis for inhibition of the Cation-chloride cotransporter $\mathrm{NKCC1}$ by the diuretic drug bumetanide

Cation-chloride cotransporters (CCCs) NKCC1 and NKCC2 catalyze electroneutral symport of 1 Na + , 1K + , and 2 Cl - across cell membranes. NKCC1 mediates trans-epithelial Cl - secretion and regulates excitability of some neurons and NKCC2 is critical to renal salt reabsorption. Both transporters are inhibited by the so-called loop diuretics including bumetanide, and these drugs are a mainstay for treating edema and hypertension. Here, our single-particle electron cryo-microscopy structures supported by functional studies reveal an outward-facing conformation of NKCC1, showing bumetanide wedged into a pocket in the extracellular ion translocation pathway. Based on these and the previously published inward-facing structures, we define the translocation pathway and the conformational changes necessary for ion translocation. We also identify an NKCC1 dimer with separated transmembrane domains and extensive transmembrane and C-terminal domain interactions. We further define an N-terminal phosphoregulatory domain that interacts with the C-terminal domain, suggesting a mechanism whereby (de)phosphorylation regulates NKCC1 by tuning the strength of this domain association.

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

Ionic/electronic conductivity regulation of n-type polyoxadiazole lithium sulfonate conductive polymer binders for high-performance silicon microparticle anodes

Low-cost silicon microparticles (SiMP), as a substitute for nanostructured silicon, easily suffer from cracks and fractured during the electrochemical cycle. A novel n-type conductive polymer binder with excellent electronic and ionic conductivities as well as good adhesion, has been successfully designed and applied for high-performance SiMP anodes in lithium-ion batteries to address this problem. Its unique features are attributed to the strong electron-withdrawing oxadiazole ring structure with sulfonate polar groups. The combination of rigid and flexible components in the polymer ensures its good mechanical strength and ductility, which is beneficial to suppress the expansion and contraction of SiMP s during the charge/discharge process. By fine-tuning the monomer ratio, the conjugation and sulfonation degrees of the polymer can be precisely controlled to regulate its ionic and electronic conductivities, which has been systematically analyzed with the help of an electrochemical test method, filling in the gap on the conductivity measurement of the polymer in the doping state. The experimental results indicate that the cell with the developed n-type polymer binder and SiMP (~0.5 μm) anodes achieves much better cycling performance than traditional non-conductive binders. It has been considered that the initial capacity of the SiMP anode is controlled by the synergetic effect of ionic and electronic conductivity of the binder, and the capacity retention mainly depends on its electronic conductivity when the ionic conductivity is sufficient. Here, it is worth noting that the fundamental research of this work is also applicable to other battery systems using conductive polymers in order to achieve high energy density, broadening their practical applications.

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

Exemption of lattice collapse in Ni–MnO 2 birnessite regulated by the structural water mobility

Lattice collapse and associated mechanical fracture frequently occur in Li-intercalated metal oxide cathodes at the deep charge state upon Li-ion removal, governed by chemical compositions and the resulting electron density of the oxygen atoms. However, similar lattice collapse for metal oxide electrodes in aqueous storage and its mitigation have not been well studied. In this work, we reported the lattice collapse of MnO 2 layered birnessite during the aqueous de-sodiation process at high voltage due to the structural water motion, as evidenced by in situ XRD. Unlike non-aqueous Li-intercalated electrodes, Ni-dopants mitigated the lattice collapse of birnessite at deep charge states. Moreover, density functional theory (DFT) calculations showed that Ni doping induces charge depletion of lattice oxygen due to its higher electronegativity than Mn. This charge reduction, in turn, yields a significant decrease in electrostatic repulsion between the oxygens belonging to lattice and structural water. Classical molecular dynamics simulations based on atomic charges obtained from DFT elucidate that Ni-doping facilitates immobilization of structural water in (Ni)MnO 2 and prevents lattice collapse upon Na-ion removal. (Ni)MnO 2 exempted from lattice collapse shows an improved storage capacity relative to MnO 2 while maintaining similar cycling stability.

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

Toward Complete Transformation of Sodium Polysulfides by Regulating the Second–Shell Coordinating Environment of Atomically Dispersed Fe

Room temperature sodium-sulfur (RT Na-S) batteries are highly competitive as potential energy storage devices. Nevertheless, their actually achieved reversible capacities are far below the theoretical value due to incomplete transformation of polysulfides. Herein, atomically dispersed Fe-N/S active center by regulating the second-shell coordinating environment of Fe single atom is proposed. The Fe–N 4 S 2 coordination structure with enhanced local electronic concentration around the Fermi level is revealed via synchrotron radiation X-ray absorption spectroscopy (XAS) and theoretical calculations, which can not only significantly promote the transformation kinetics of polysulfides, but induce uniform Na deposition for dendrite-free Na anode. As a result, the obtained S cathode delivers a high initial reversible capacity of 1590 mAh g –1 , nearly the theoretical value. Finally, this work opens up a new avenue to facilitate the complete transformation of polysulfides for RT Na-S batteries.

25 ENERGY STORAGE↗
DOE OSTI2025

Structural insights into transcriptional regulation by the helicase RECQL5

Abstract Transcription poses a major challenge for genome stability. The RECQL5 helicase helps safeguard genome integrity and is the only member of the human RecQ helicase family that directly binds to RNA polymerase II (Pol II) and affects its progression. While RECQL5 mitigates transcription stress in cells, the molecular mechanism underlying this phenomenon is unclear. Here, we use cryo-electron microscopy to determine the structures of stalled human Pol II elongation complexes (ECs) bound to RECQL5. Our structures reveal the molecular interactions stabilizing RECQL5 binding to the Pol II EC and highlight its role as a transcriptional roadblock. Additionally, we find that, in its nucleotide-free state, RECQL5 twists the downstream DNA in the EC and, upon nucleotide binding, undergoes a conformational change that allosterically induces Pol II toward a post-translocation state. We propose that this mechanism may help restart Pol II elongation and, therefore, contribute to reducing transcription stress.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Probing the atomically diffuse interfaces in Pd@Pt core-shell nanoparticles in three dimensions

Deciphering the three-dimensional atomic structure of solid-solid interfaces in core-shell nanomaterials is the key to understand their catalytical, optical and electronic properties. Here, we probe the three-dimensional atomic structures of palladium-platinum core-shell nanoparticles at the single-atom level using atomic resolution electron tomography. We quantify the rich structural variety of core-shell nanoparticles with heteroepitaxy in 3D at atomic resolution. Instead of forming an atomically-sharp boundary, the core-shell interface is found to be atomically diffuse with an average thickness of 4.2 Å, irrespective of the particle’s morphology or crystallographic texture. The high concentration of Pd in the diffusive interface is highly related to the free Pd atoms dissolved from the Pd seeds, which is confirmed by atomic images of Pd and Pt single atoms and sub-nanometer clusters using cryogenic electron microscopy. These results advance our understanding of core-shell structures at the fundamental level, providing potential strategies into precise nanomaterial manipulation and chemical property regulation.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Structural analysis of the NifL-NifA complex reveals the molecular basis of anti-activation of nitrogen fixation gene expression in Azotobacter vinelandii

Understanding the molecular basis of regulated nitrogen (N 2 ) fixation is essential for engineering N 2 -fixing bacteria that fulfill the demand of crop plants for fixed nitrogen, reducing our reliance on synthetic nitrogen fertilizers. In Azotobacter vinelandii and many other members of Proteobacteria, the two-component system comprising the anti-activator protein (NifL) and the Nif-specific transcriptional activator (NifA)controls the expression of nif genes, encoding the nitrogen fixation machinery. The NifL-NifA system evolved the ability to integrate several environmental cues, such as oxygen, nitrogen, and carbon availability. The nitrogen fixation machinery is thereby only activated under strictly favorable conditions, enabling diazotrophs to thrive in competitive environments. While genetic and biochemical studies have enlightened our understanding of how NifL represses NifA, the molecular basis of NifA sequestration by NifL depends on structural information on their interaction. Here, we present mechanistic insights into how nitrogen fixation is regulated by combining biochemical and genetic approaches with a low-resolution cryo-electron microscopy (cryo-EM) map of the oxidized NifL-NifA complex. Our findings define the interaction surface between NifL and NifA and reveal how this interaction can be manipulated to generate bacterial strains with increased nitrogen fixation rates able to secrete surplus nitrogen outside the cell, a crucial step in engineering improved nitrogen delivery to crop plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Regulating off-centering distortion maximizes photoluminescence in halide perovskites

Abstract Metal halide perovskites possess unique atomic and electronic configurations that endow them with high defect tolerance and enable high-performance photovoltaics and optoelectronics. Perovskite light-emitting diodes have achieved an external quantum efficiency of over 20%. Despite tremendous progress, fundamental questions remain, such as how structural distortion affects the optical properties. Addressing their relationships is considerably challenging due to the scarcity of effective diagnostic tools during structural and property tuning as well as the limited tunability achievable by conventional methods. Here, using pressure and chemical methods to regulate the metal off-centering distortion, we demonstrate the giant tunability of photoluminescence (PL) in both the intensity (>20 times) and wavelength (>180 nm/GPa) in the highly distorted halide perovskites [CH3NH3GeI3, HC(NH2)2GeI3, and CsGeI3]. Using advanced in situ high-pressure probes and first-principles calculations, we quantitatively reveal a universal relationship whereby regulating the level of off-centering distortion towards 0.2 leads to the best PL performance in the halide perovskites. By applying this principle, intense PL can still be induced by substituting CH3NH3+ with Cs+ to control the distortion in (CH3NH3)1-xCsxGeI3, where the chemical substitution plays a similar role as external pressure. The compression of a fully substituted sample of CsGeI3 further tunes the distortion to the optimal value at 0.7 GPa, which maximizes the emission with a 10-fold enhancement. This work not only demonstrates a quantitative relationship between structural distortion and PL property of the halide perovskites but also illustrates the use of knowledge gained from high-pressure research to achieve the desired properties by ambient methods.

halide perovskites↗