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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Structure and flexibility of the yeast NuA4 histone acetyltransferase complex

The NuA4 protein complex acetylates histones H4 and H2A to activate both transcription and DNA repair. We report the 3.1-Å resolution cryo-electron microscopy structure of the central hub of NuA4, which flexibly tethers the histone acetyltransferase (HAT) and Trimer Independent of NuA4 involved in Transcription Interactions with Nucleosomes (TINTIN) modules. The hub contains the large Tra1 subunit and a core that includes Swc4, Arp4, Act1, Eaf1, and the C-terminal region of Epl1. Eaf1 stands out as the primary scaffolding factor that interacts with the Tra1, Swc4, and Epl1 subunits and contributes the conserved HSA helix to the Arp module. Using nucleosome-binding assays, we find that the HAT module, which is anchored to the core through Epl1, recognizes H3K4me3 nucleosomes with hyperacetylated H3 tails, while the TINTIN module, anchored to the core via Eaf1, recognizes nucleosomes that have hyperacetylated H2A and H4 tails. Together with the known interaction of Tra1 with site-specific transcription factors, our data suggest a model in which Tra1 recruits NuA4 to specific genomic sites then allowing the flexible HAT and TINTIN modules to select nearby nucleosomes for acetylation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif

The hallmark of the eukaryotic cell is the complex endomembrane system that compartmentalizes cellular functions. Transport into and out of the nucleus occurs through the nuclear pore complex (NPC). The heptameric Nup84 or Y complex is an essential scaffolding component of the NPC. Here we report two nanobody-bound structures: the full-length Nup84-Nup133 C-terminal domain complex and the Nup133 N-terminal domain, both from S. cerevisiae. Together with previously published structures, this work enables the structural description of the entire 575 kDa Y complex from one species. The structure of Nup84-Nup133CTD details the high flexibility of this dimeric unit of the Y complex. Further, the Nup133NTD contains a structurally conserved amphipathic lipid packing sensor motif, confirmed by liposome interaction studies. The presented structures reveal important details about the function of the Y complex that affect our understanding of NPC structure and assembly.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structure of an anti-PEG antibody reveals an open ring that captures highly flexible PEG polymers

Polyethylene glycol (PEG) is a polymer routinely used to modify biologics and nanoparticles to prolong blood circulation and reduce immunogenicity of the underlying therapeutic. However, several PEGylated therapeutics induce the development of anti-PEG antibodies (APA), leading to reduced efficacy and increased adverse events. Given the highly flexible structure of PEG, how APA specifically bind PEG remains poorly understood. Here, we report a crystal structure illustrating the structural properties and conformation of the APA 6-3 Fab bound to the backbone of PEG. The structure reveals an open ring-like sub-structure in the Fab paratope, whereby PEG backbone is captured and then stabilized via Van der Waals interactions along the interior and exterior of the ring paratope surface. Our finding illustrates a strategy by which antibodies can bind highly flexible repeated structures that lack fixed conformations, such as polymers. This also substantially advances our understanding of the humoral immune response generated against PEG.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Chain Flexibility and Structure of a Polyimide Copolymer: Revisiting the Freely Rotating Chain Model

Poly(4–4′-oxydiphenylene-pyromellitimide)-based polyimides─trade name Kapton─have wide-ranging engineering applications owing to their thermal and mechanical stability, but little is known about underlying chain-level characteristics. While theoretical models have conceptualized Kapton as inflexible polycyclic rods separated by freely rotating diphenyl ether hinge groups, the model’s core predictions remain untested and subtleties of the relaxation behavior are missed, which atomistic modeling can resolve. To these ends, we examine all-atom Kapton structures in crystalline and glassy amorphous configurations using a DFT-validated class II force field. Constructing amorphous configurations is challenging, as the fused-ring-containing backbone has slow relaxation dynamics and scaling suggestive of entanglements even in oligomers. In conclusion, we find larger backbone rearrangements of the linear polycyclic segments about ether groups that are consistent with the rod-hinge picture on the monomer scale, whereas a ring rotation analysis suggests partially flexible rod-like segments and involves multiple facile rotational relaxation modes.

Liesen, Nicholas T. [Lawrence Livermore National L↗
DOE OSTI2021

Networked HIL Simulation System for Modeling Large-scale Power Systems

This paper presents a networked hardware-in-the-loop (HIL) simulation system for modeling large-scale power systems. Researchers have developed many HIL test systems for power systems in recent years. Those test systems can model both microsecond-level dynamic responses of power electronic systems and millisecond-level transients of transmission and distribution grids. By integrating individual HIL test systems into a network of HIL test systems, we can create large-scale power grid digital twins with flexible structures at required modeling resolution that fits for a wide range of system operating conditions. This will not only significantly reduce the need for field tests when developing new technologies but also greatly shorten the model development cycle. In this paper, we present a networked OPAL-RT based HIL test system for developing transmission-distribution coordinative Volt-VAr regulation technologies as an example to illustrate system setups, communication requirements among different HIL simulation systems, and system connection mechanisms. Impacts of communication delays, information exchange cycles, and computing delays are illustrated. Simulation results show that the performance of a networked HIL test system is satisfactory.

Xie, Fuhong↗
DOE OSTI2023

Metal–Carbodithioate-Based 3D Semiconducting Metal–Organic Framework: Porous Optoelectronic Material for Energy Conversion

Solar energy conversion requires the working compositions to generate photoinduced charges with high potential and the ability to deliver charges to the catalytic sites and/or external electrode. These two properties are typically at odds with each other and call for new molecular materials with sufficient conjugation to improve charge conductivity but not as much conjugation as to overly compromise the optical band gap. In this work, we developed a semiconducting metal-organic framework (MOF) prepared explicitly through metal-carbodithioate"(-CS 2 ) n M" linkage chemistry, entailing augmented metal-linker electronic communication. The stronger ligand field and higher covalent character of metal-carbodithioate linkages-when combined with spirofluorene-derived organic struts and nickel-(II) ion-based nodes-provided a stable, semiconducting 3D-porous MOF, Spiro-CS 2 Ni. This MOF lacks long-range ordering and is defined by a flexible structure with non-aggregated building units, as suggested by reverse Monte Carlo simulations of the pair distribution function obtained from total scattering experiments. The solvent-removed "closed pore"material recorded a Brunauer-Emmett-Teller area of similar to 400m 2 /g, where the "open pore" form possesses90 wt % solvent-accessible porosity. Electrochemical measurements suggest that Spiro-CS 2 Ni possesses a band gap of 1.57 eV(sigma = 10 -7 S/cm at -1.3 V bias potential),which can be further improved by manipulating the d-electron configuration through an axial coordination (ligand/substrate), the latter of which indicates usefulness as an electrocatalyst and/or a photoelectrocatalyst(upon substrate binding). Transient-absorption spectroscopy reveals a long-lived photo-generated charge-transfer state (τ CR = 6.5 mu s) capable of chemical transformation under a biased voltage. Spiro-CS 2 Ni can endure a compelling range of pH(1-12 for weeks) and hours of electrochemical and photoelectrochemical conditions in the presence of water and organic acids. We believe this work provides crucial design principles for low-density, porous,light-energy-conversion materials.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Neutron scattering in photosynthesis research: recent advances and perspectives for testing crop plants

The photosynthetic performance of crop plants under a variety of environmental factors and stress conditions, at the fundamental level, depends largely on the organization and structural flexibility of thylakoid membranes. These highly organized membranes accommodate virtually all protein complexes and additional compounds carrying out the light reactions of photosynthesis. Most regulatory mechanisms fine-tuning the photosynthetic functions affect the organization of thylakoid membranes at different levels of the structural complexity. In order to monitor these reorganizations, non-invasive techniques are of special value. On the mesoscopic scale, small-angle neutron scattering (SANS) has been shown to deliver statistically and spatially averaged information on the periodic organization of the thylakoid membranes in vivo and/or, in isolated thylakoids, under physiologically relevant conditions, without fixation or staining. More importantly, SANS investigations have revealed rapid reversible reorganizations on the timescale of several seconds and minutes. In this paper, we give a short introduction into the basics of SANS technique, advantages and limitations, and briefly overview recent advances and potential applications of this technique in the physiology and biotechnology of crop plants. We also discuss future perspectives of neutron crystallography and different neutron scattering techniques, which are anticipated to become more accessible and of more use in photosynthesis research at new facilities with higher fluxes and innovative instrumentation.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2026

Many roads to the seam: How conformational flexibility drives nonadiabatic relaxation in a prototypical tetrapyrrolic chromophore

Large and structurally flexible chromophores pose challenges for in silico modeling of photodeactivation due to the many vibrational modes that can funnel the system toward energy degeneracy. In this work, we examine how the multiple degrees of freedom in biliverdin, a prototypical tetrapyrrolic chromophore, cooperate to drive access to the S 1 /S 0 intersection seam in vacuo. We begin by mapping the ground-state potential energy surface to identify representative biliverdin conformers relevant to photoexcitation. We then use a CASSCF-based framework to map the excited-state landscape and characterize the intersection seam, identifying distinct conical-intersection types. Finally, we employ ab initio multiple spawning to resolve the dynamical pathways by which the system accesses these regions. DFT potential-energy and free-energy mappings indicate that, although several conformers are relevant, the “locked-helix” ZsZsZs conformer predominates in the ground state. The intersection seam comprises numerous geometrically distinct regions characterized by varying degrees and combinations of dihedral torsion, pyramidalization, and bond-length alternation. Yet only select regions lie within energetic reach, and moderate barriers separate them from the S 1 minimum. Nonadiabatic dynamics combined with multivariate analyses show that, despite extensive mode coupling during deactivation that guides the system toward multiple regions of the seam, a single dihedral torsion, together with bond-length alternation, predominantly drives energy degeneracy. This work offers new insight into biliverdin’s intrinsic photochemical response and underscores a general feature of flexible chromophores: many modes may participate during photorelaxation, but only a limited subset ultimately dictates seam accessibility.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

New layered quaternary Zintl pnictide oxides Ba 2 Zn 2 Pn 2 O ( Pn = Sb, Bi): Discovery, crystal structures, band engineering, and transport properties

Three new heteroanionic oxypnictides, Ba 2 Zn 2 Sb 2 O, Ba 2 Zn 2 Bi 2 O, and the solid solution Ba 2 Zn 2 Sb 2−x Bi x O (x ≈ 1.1–1.6), have been synthesized and structurally characterized. They are isostructural with their Mn-bearing analog, adopting the Ba 2 Mn 2 Sb 2 O-type structure (space group P6 3 /mmc, No. 194), and feature a double-layered 2D $^{2}_{∞}$ [Zn 2 Pn 2 O] 2- substructure (Pn = Sb, Bi, Sb/Bi) composed of corner-sharing, distorted tetrahedral ZnPn 3 O units. Electronic structure calculations reveal a systematic progression from semiconducting Ba 2 Zn 2 Sb 2 O to metallic Ba 2 Zn 2 Bi 2 O as Bi content increases. These trends are corroborated by transport property measurements, with Ba 2 Zn 2 Sb 0.9(1) Bi 1.1 O exhibiting relatively low electrical resistivity, high Hall mobilities of ∼160 cm 2 /V·s, and large Seebeck coefficients from 69 to 132 μV K −1 over the 300–600 K temperature range. Comparison with structurally related Zintl pnictides, such as SrIn 2 As 2 and PrZn 3 As 3 phases, situates Ba 2 Zn 2 Pn 2 O (Pn = Sb, Bi) within a broader family of heteroanionic oxypnictide Zintl compounds, highlighting their structural flexibility and amenability to band engineering. Finally, electronic structure and bonding considerations point to tunable semiconducting behavior and underscore the relevance of these materials for thermoelectric and topological applications.

Band engineering↗
DOE OSTI2024

Factors that Impact the Redox Kinetics Associated with Sr1-xAxFeO3 (A = Ca, Ba) in Air Separations Technologies

Perovskite oxides, including SrFeO3-δ, have garnered significant interest for their impressive oxygen storage thermodynamics and kinetics. While traditional oxygen production is performed through cryogenic separation methods at the industrial scale, oxygen carrier-based separations have offered an attractive alternative at the modular scale. Perovskites are considered ideal oxygen carriers, with their structural flexibility minimizing both the thermodynamic barrier and the structural strain related to the oxygen uptake/release cycle. Our latest work has identified a few major factors that directly impact the oxygen release thermodynamics and kinetics for Sr1-xAxFeO3-δ (A = Ca, Ba) materials including elemental composition, crystallographic symmetry, surface area, and pretreatment conditions. This presentation will discuss these factors using Sr1¬-xCaxFeO3 and Ba1-xSrxFeO3 to illustrate their individual and collective impacts on the design of high-performance oxygen carriers when operating at 300-700 °C. Additionally, we will discuss how each of these factors can be leveraged for the numerous catalytic applications also dependent on the redox properties of mixed metal oxides.

Popczun, Eric↗
DOE OSTI2023

Tuning Active Site Flexibility by Defect Engineering of Graphene Ribbon Edge‐hosted Fe−N 3 Sites

Abstract Nitrogen‐doped, carbon‐supported transition metal catalysts are excellent for several reactions. Structural engineering of M−N x sites to boost catalytic activity is rarely studied. Here, we demonstrate that the structural flexibility of Fe−N 3 site is vital for tuning the electronic structure of Fe atoms and regulating the catalytic transfer hydrogenation (CTH) activity. By introducing carbon defects, we construct Fe−N 3 sites with varying Fe−N bond lengths distinguishable by X‐ray absorption spectroscopy. We investigate the CTH activity by density‐functional theory and microkinetic calculations and reveal that the vertical displacement of the Fe atom out of the plane of the support, induced by the Fe−N 3 distortion, raises the Fe orbital and strengthens binding. We propose that the activity is controlled by the relaxation of the reconstructed site, which is further affected by Fe−N bond length, an excellent activity descriptor. We elucidate the origin of the CTH activity and principles for high‐performing Fe−N−C catalysts by defect engineering.

Yang, Piaoping↗
DOE OSTI2023

Tuning Active Site Flexibility by Defect Engineering of Graphene Ribbon Edge–hosted Fe–N3 Sites

Nitrogen-doped, carbon-supported transition metal catalysts are excellent for several reactions. Structural engineering of metal-Nx sites to boost catalytic activity is rarely studied. Here, we demonstrate that the structural flexibility of Fe-N3 site is vital for tuning the electronic structure of Fe atoms and regulating the catalytic transfer hydrogenation (CTH) activity. By introducing carbon defects, we construct Fe-N3 sites with varying Fe-N bond lengths distinguishable by X-ray absorption spectroscopy. We investigate the CTH activity by density functional theory and microkinetic calculations and reveal that the vertical displacement of the Fe atom out of the plane of the support, induced by the Fe-N3 distortion, raises the Fe [[EQUATION]]orbital and strengthens binding. We propose that the activity is controlled by the relaxation of the reconstructed site, which is further affected by Fe-N bond length, an excellent activity descriptor. Furthermore, we elucidate the origin of the CTH activity and principles for high-performing Fe-N-C catalysts by defect engineering.

09 BIOMASS FUELS↗
DOE OSTI2021

Investigating Single-Molecule Fluorescence Spectral Heterogeneity of Rhodamines Using High-Throughput Single-Molecule Spectroscopy

We experimentally investigated several intra-molecular coordinate and environmental changes as potential causes of single-molecule fluorescence spectral heterogeneities (smFSH). Here, we developed a high-throughput single-molecule spectroscopy technique to analyze more than 5,000 single-molecule emission spectra from each of nine commonly used fluorophores with different structural rigidities deposited on substrates with different polarities. We observed an unexpected high smFSH from structurally rigid Rhodamine B compared with a structurally flexible Cyanine dye - Alexa Fluor 647. Based on experimentally measured smFSH, we ruled out the system’s noise uncertainty, single-molecule spectral diffusion, and environmental polarity as the primary causes of the high smFSH. We found that the rotational flexibility of N, N-dialkylated groups contributed to the smFSH. With the high smFSH observed in structurally more rigid model fluorophores, we speculated that other intra-molecular coordinate and environmental changes might also contribute to the high smFSH in Rhodamines.

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

Guest-Controlled Incommensurate Modulation in a Meta-Rigid Metal–Organic Framework Material

Structural transitions of host systems in response to guest binding dominate many chemical processes. We report an unprecedented type of structural flexibility within a meta-rigid material, MFM-520, which exhibits a reversible periodic-to-aperiodic structural transition resulting from a drastic distortion of a [ZnO 4 N] node controlled by the specific host–guest interactions. The aperiodic crystal structure of MFM-520 has no three-dimensional (3D) lattice periodicity but shows translational symmetry in higher-dimensional (3 + 2)D space. In this work, we have directly visualized the aperiodic state which is induced by incommensurate modulation of the periodic framework of MFM-520·H 2 O upon dehydration to give MFM-520. Filling MFM-520 with CO 2 and SO 2 reveals that, while CO 2 has a minimal structural influence, SO 2 can further modulate the structure incommensurately. MFM-520 shows exceptional selectivity for SO 2 under flue-gas desulfurization conditions, and the facile release of captured SO 2 from MFM-520 enabled the conversion to valuable sulfonamide products. MFM-520 can thus be used as a highly efficient capture and delivery system for SO 2 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗