Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “dimer”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Field-induced partial disorder in a Shastry-Sutherland lattice

Abstract A 2-Q antiferromagnetic order of the ferromagnetic dimers was found below T N = 2.9 K in the Shastry-Sutherland lattice BaNd 2 ZnS 5 by single crystal neutron diffraction. The magnetic order can be understood by the orthogonal arrangement of local Ising Nd spins, identified by polarized neutrons. A field was applied along [1 -1 0] to probe the observed metamagnetic transition in the magnetization measurement. The field decouples two magnetic sublattices corresponding to the propagation vectors q 1 = (½, ½, 0) and q 2 = (−½, ½, 0), respectively. Each sublattice shows a “stripe” order with a Néel-type arrangement in each single layer. The “stripe” order with q 1 remains nearly intact up to 6 T, while the other one with q 2 is suppressed at a critical field H c ~1.7 T, indicating a partial disorder. The H c varies with temperature and is manifested in the H - T phase diagram constructed by measuring the magnetization in BaNd 2 ZnS 5 .

36 MATERIALS SCIENCE↗
DOE OSTI2024

Catalytic carbon–carbon bond cleavage in lignin via manganese–zirconium-mediated autoxidation

Abstract Efforts to produce aromatic monomers through catalytic lignin depolymerization have historically focused on aryl–ether bond cleavage. A large fraction of aromatic monomers in lignin, however, are linked by various carbon–carbon (C–C) bonds that are more challenging to cleave and limit the yields of aromatic monomers from lignin depolymerization. Here, we report a catalytic autoxidation method to cleave C–C bonds in lignin-derived dimers and oligomers from pine and poplar. The method uses manganese and zirconium salts as catalysts in acetic acid and produces aromatic carboxylic acids as primary products. The mixtures of the oxygenated monomers are efficiently converted to cis,cis -muconic acid in an engineered strain of Pseudomonas putida KT2440 that conducts aromatic O -demethylation reactions at the 4-position. This work demonstrates that autoxidation of lignin with Mn and Zr offers a catalytic strategy to increase the yield of valuable aromatic monomers from lignin.

09 BIOMASS FUELS↗
DOE OSTI2024

A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria

Abstract Heme has a critical role in the chemical framework of the cell as an essential protein cofactor and signaling molecule that controls diverse processes and molecular interactions. Using a phylogenomics-based approach and complementary structural techniques, we identify a family of dimeric hemoproteins comprising a domain of unknown function DUF2470. The heme iron is axially coordinated by two zinc-bound histidine residues, forming a distinct two-fold symmetric zinc-histidine-iron-histidine-zinc site. Together with structure-guided in vitro and in vivo experiments, we further demonstrate the existence of a functional link between heme binding by Dri1 (Domain related to iron 1, formerly ssr1698) and post-translational regulation of succinate dehydrogenase in the cyanobacterium Synechocystis , suggesting an iron-dependent regulatory link between photosynthesis and respiration. Given the ubiquity of proteins containing homologous domains and connections to heme metabolism across eukaryotes and prokaryotes, we propose that DRI (Domain Related to Iron; formerly DUF2470) functions at the molecular level as a heme-dependent regulatory domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structure of HIV-1 RRE stem-loop II identifies two conformational states of the high-affinity Rev binding site

During HIV infection, specific RNA-protein interaction between the Rev response element (RRE) and viral Rev protein is required for nuclear export of intron-containing viral mRNA transcripts. Rev initially binds the high-affinity site in stem-loop II, which promotes oligomerization of additional Rev proteins on RRE. Here, we present the crystal structure of RRE stem-loop II in distinct closed and open conformations. The high-affinity Rev-binding site is located within the three-way junction rather than the predicted stem IIB. The closed and open conformers differ in their non-canonical interactions within the three-way junction, and only the open conformation has the widened major groove conducive to initial Rev interaction. Rev binding assays show that RRE stem-loop II has high- and low-affinity binding sites, each of which binds a Rev dimer. We propose a binding model, wherein Rev-binding sites on RRE are sequentially created through structural rearrangements induced by Rev-RRE interactions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

The structural basis for 2′−5′/3′−5′-cGAMP synthesis by cGAS

Abstract cGAS activates innate immune responses against cytosolic double-stranded DNA. Here, by determining crystal structures of cGAS at various reaction stages, we report a unifying catalytic mechanism. apo-cGAS assumes an array of inactive conformations and binds NTPs nonproductively. Dimerization-coupled double-stranded DNA-binding then affixes the active site into a rigid lock for productive metal•substrate binding. A web-like network of protein•NTP, intra-NTP, and inter-NTP interactions ensures the stepwise synthesis of 2′−5′/3′−5′-linked cGAMP while discriminating against noncognate NTPs and off-pathway intermediates. One divalent metal is sufficient for productive substrate binding, and capturing the second divalent metal is tightly coupled to nucleotide and linkage specificities, a process which manganese is preferred over magnesium by 100-fold. Additionally, we elucidate how mouse cGAS achieves more stringent NTP and linkage specificities than human cGAS. Together, our results reveal that an adaptable, yet precise lock-and-key-like mechanism underpins cGAS catalysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Assembly of respiratory syncytial virus matrix protein lattice and its coordination with fusion glycoprotein trimers

Respiratory syncytial virus (RSV) is an enveloped, filamentous, negative-strand RNA virus that causes significant respiratory illness worldwide. RSV vaccines are available, however there is still significant need for research to support the development of vaccines and therapeutics against RSV and related Mononegavirales viruses. Individual virions vary in size, with an average diameter of ~130 nm and ranging from ~500 nm to over 10 µm in length. Though the general arrangement of structural proteins in virions is known, we use cryo-electron tomography and sub-tomogram averaging to determine the molecular organization of RSV structural proteins. We show that the peripheral membrane-associated RSV matrix (M) protein is arranged in a packed helical-like lattice of M-dimers. We report that RSV F glycoprotein is frequently observed as pairs of trimers oriented in an anti-parallel conformation to support potential interactions between trimers. Our sub-tomogram averages indicate the positioning of F-trimer pairs is correlated with the underlying M lattice. These results provide insight into RSV virion organization and may aid in the development of RSV vaccines and anti-viral targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Vacancy-induced suppression of charge density wave order and its impact on magnetic order in kagome antiferromagnet FeGe

Two-dimensional (2D) kagome lattice metals are interesting because their corner sharing triangle structure enables a wide array of electronic and magnetic phenomena. Recently, post-growth annealing is shown to both suppress charge density wave (CDW) order and establish long-range CDW with the ability to cycle between states repeatedly in the kagome antiferromagnet FeGe. Here we perform transport, neutron scattering, scanning transmission electron microscopy (STEM), and muon spin rotation (μSR) experiments to unveil the microscopic mechanism of the annealing process and its impact on magneto-transport, CDW, and magnetism in FeGe. Annealing at 560 °C creates uniformly distributed Ge vacancies, preventing the formation of Ge-Ge dimers and thus CDW, while 320 °C annealing concentrates vacancies into stoichiometric FeGe regions with long-range CDW. The presence of CDW order greatly affects the anomalous Hall effect, incommensurate magnetic order, and spin-lattice coupling in FeGe, placing FeGe as the only kagome lattice material with tunable CDW and magnetic order.

critical phenomena↗
DOE OSTI2025

Frustrated charge density wave and quasi-long-range bond-orientational order in the magnetic kagome FeGe

The intrinsic frustrated nature of a kagome lattice is amenable to the realization of exotic phases of matter, such as quantum spin liquids or spin ices, and the multiple-q charge density waves (CDW) in the kagome metals. Despite intense efforts to understand the mechanism driving the electronic modulations, its origin is still unknown and obscured by competing interactions and intertwined orders. Here, we identify a dimerization-driven 2D hexagonal charge-diffuse precursor in the antiferromagnetic kagome metal FeGe and demonstrate that the fraction of dimerized/undimerized states is the relevant order parameter of the multiple-q CDW of a continuous phase transition. The pretransitional charge fluctuations with propagation vector q = q M at T CDW < T < T*(125 K) are anisotropic, hence holding a quasi-long-range bond-orientational order. The broken translational symmetry emerges from the anisotropic diffuse precursor, akin to the Ising scenario of antiferromagnetic triangular lattices. The temperature and momentum dependence of the critical scattering show parallels to the stacked hexatic B-phases reported in liquid crystals and transient states of CDWs and highlight the key role of the topological defect-mediated melting of the CDW in FeGe.

Subires, D. [Donostia International Physics Center↗
DOE OSTI2025

Decoupled few-femtosecond phase transitions in vanadium dioxide

Abstract The nature of the insulator-to-metal phase transition in vanadium dioxide (VO 2 ) is one of the longest-standing problems in condensed-matter physics. Ultrafast spectroscopy has long promised to determine whether the transition is primarily driven by the electronic or structural degree of freedom, but measurements to date have been stymied by their sensitivity to only one of these components and/or their limited temporal resolution. Here we use ultra-broadband few-femtosecond pump-probe spectroscopy to resolve the electronic and structural phase transitions in VO 2 at their fundamental time scales. Our experiments show that the system transforms into a bad-metallic phase within 10 fs after photoexcitation, but requires another 100 fs to complete the transition, during which we observe electronic oscillations and a partial re-opening of the bandgap, signalling a transient semi-metallic state. Comparisons with tensor-network simulations and density-functional theory calculations show these features result from an unexpectedly fast structural transition, in which the vanadium dimers separate and untwist with two different timescales. Our results resolve the structural and electronic nature of the light-induced phase transition in VO 2 and establish ultra-broadband few-femtosecond spectroscopy as a powerful tool for studying quantum materials out of equilibrium.

Science & Technology - Other Topics↗
DOE OSTI2025

Pressure tuning of competing interactions on a honeycomb lattice

Exchange interactions are mediated via orbital overlaps across chemical bonds. Thus, modifying the bond angles by physical pressure or strain can tune the relative strength of competing interactions. Here we present a remarkable case of such tuning between the Heisenberg (J) and Kitaev (K) exchange, which respectively establish magnetically ordered and spin liquid phases on a honeycomb lattice. We observe a rapid suppression of the Néel temperature (T N ) with pressure in Ag 3 LiRh 2 O 6 , a spin-1/2 honeycomb lattice with both J and K couplings. Using a combined analysis of x-ray data and first-principles calculations, we find that pressure modifies the bond angles in a way that increases the ∣K/J∣ ratio and thereby suppresses T N . Consistent with this picture, we observe a spontaneous onset of muon spin relaxation (μSR) oscillations below T N at low pressure, whereas in the high pressure phase, oscillations appear only when T < T N /2. Unlike other candidate Kitaev materials, Ag 3 LiRh 2 O 6 is tuned toward a quantum critical point by pressure while avoiding a structural dimerization in the relevant pressure range.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Photolytic activation of Ni (II) X 2 L explains how Ni-mediated cross coupling begins

Nickel photocatalysis has recently become vital to organic synthesis, but how the Ni (II) X 2 L pre-catalyst (X = Cl, Br; L = bidentate ligand) becomes activated to Ni (I) XL has remained puzzling and is typically addressed on a case-by-case basis. Here, we reveal a general mechanism where light induces photolysis of the Ni (II) -X bond, either via direct excitation or triplet energy transfer. Photolysis produces Ni (I) XL and a halogen radical, X*. Subsequent hydrogen atom abstraction, often from the solvent, produces a C(sp 3 ) radical, R*, that recombines with Ni (I) to form organonickel(II) complexes, Ni (II) XRL. Rather than acting as a loss pathway, Ni (II) XRL behaves as a light-activated reservoir of Ni (I) via photolysis of the Ni (II) -C bond. These results explain the role of the solvent in protecting the catalyst from off-cycle dimerization, demonstrate that two photons are often required to drive the reaction, and show how tuning the ligand can control the concentration of active Ni (I) species.

08 HYDROGEN↗
DOE OSTI2025

Extending quantum-mechanical benchmark accuracy to biological ligand-pocket interactions

Predicting the binding affinity of ligands to protein pockets is key in the drug design pipeline. The flexibility of ligand-pocket motifs arises from a range of attractive and repulsive electronic interactions during binding. Accurately accounting for all interactions requires robust quantum-mechanical (QM) benchmarks, which are scarce for ligand-pocket systems. Additionally, disagreement between “gold standard” Coupled Cluster (CC) and Quantum Monte Carlo (QMC) methods casts doubt on many benchmarks for larger non-covalent systems. We introduce the “QUantum Interacting Dimer” (QUID) benchmark framework containing 170 non-covalent (non-)equilibrium systems modeling chemically and structurally diverse ligand-pocket motifs. Symmetry-adapted perturbation theory shows that QUID broadly covers non-covalent binding motifs and energetic contributions. Robust binding energies are obtained using complementary CC and QMC methods, achieving agreement of 0.5 kcal/mol. The benchmark data analysis reveals that several dispersion-inclusive density functional approximations provide accurate energy predictions, though their atomic van der Waals forces differ in magnitude and orientation. Contrarily, semiempirical methods and empirical force fields require improvements in capturing non-covalent interactions (NCIs) for out-of-equilibrium geometries. The wide span of NCIs, highly accurate interaction energies, and analysis of molecular properties take QUID beyond the “gold standard” for QM benchmarks of ligand-protein systems.

Puleva, Mirela [University of Luxembourg, Luxembou↗
DOE OSTI2026

Insights into the mechanisms of NH3 inhibition on Cu-CHA SCR catalysts

This work elucidates the atomic-scale mechanism behind ammonia (NH3) inhibition during the selective catalytic reduction (SCR) of NO? on Cu-CHA catalysts, a key issue limiting low-temperature emission control. Using SCR kinetic analysis, operando electron paramagnetic resonance (EPR) spectroscopy, and density functional theory (DFT), we demonstrate that NH3 inhibition primarily slows the oxidation half-cycle (OHC), while the reduction half-cycle (RHC) remains unaffected. DFT simulations reveal that excess NH3 substantially increases the diffusion barrier for CuI ions, hindering formation of essential CuII-oxo dimer intermediates and thus suppressing OHC kinetics. Operando EPR studies confirm that this inhibition strongly depends on operating temperature and catalyst Cu loading. Our findings highlight strategies to counteract NH3 inhibition, including optimizing Cu loading, precisely managing NH3:NO feed ratios, and enhancing CuI ion mobility through tailored catalyst design and operational adjustments, thereby advancing the efficiency of emission control technologies in automotive applications.

Deka, Dhruba Jyoti↗
DOE OSTI2026

Revealing ultrafast proton-transfer-mediated autoionization as a source of low-energy electrons in hydrogen-bonded systems

Ionizing radiation can trigger ultrafast proton transfer, a central mechanism in many chemical and biological functions, that in turn can enable or suppress electron relaxation processes and consequently cause abrupt changes in the reaction pathway. This study combines theory and experiment to probe ultrafast relaxation and dissociation in water dimers following inner- and outer-valence photoionization. By tracking electron and nuclear motion simultaneously, we reveal competing fragmentation pathways that produce low-energy electrons, which are key agents in radiation-induced chemistry, including DNA damage. While low-energy electrons are known to arise via intermolecular Coulombic decay, here we identify a faster relaxation mechanism gated by proton transfer following inner-valence ionization, which we call proton-transfer-mediated autoionization. Occurring within 10 femtoseconds, this process alters fragmentation outcomes, yielding either D 3 O + + OD + or D 2 O + + D 2 O + , depending on the interplay of proton migration and hydrogen back-transfer. Our findings underscore the intricate coupling between electronic and nuclear dynamics in hydrogen-bonded systems and establish proton-transfer-mediated autoionization as a significant pathway for low-energy electron generation.

Atomic and molecular interactions with photons↗
DOE OSTI2023

Structural and biochemical insight into a modular β-1,4-galactan synthase in plants

Rhamnogalacturonan I (RGI) is a structurally complex pectic polysaccharide with a backbone of alternating rhamnose and galacturonic acid residues substituted with arabinan and galactan side chains. Galactan synthase 1 (GalS1) transfers galactose and arabinose to either extend or cap the ..beta..-1,4-galactan side chains of RGI, respectively. Here we report the structure of GalS1 from Populus trichocarpa, showing a modular protein consisting of an N-terminal domain that represents the founding member of a new family of carbohydrate-binding module, CBM95, and a C-terminal glycosyltransferase family 92 (GT92) catalytic domain that adopts a GT-A fold. GalS1 exists as a dimer in vitro, with stem domains interacting across the chains in a 'handshake' orientation that is essential for maintaining stability and activity. In addition to understanding the enzymatic mechanism of GalS1, here we gained insight into the donor and acceptor substrate binding sites using deep evolutionary analysis, molecular simulations and biochemical studies. Combining all the results, a mechanism for GalS1 catalysis and a new model for pectic galactan side-chain addition are proposed.

09 BIOMASS FUELS↗
DOE OSTI2021

Ferromagnetism out of charge fluctuation of strongly correlated electrons in κ -(BEDT-TTF) 2 Hg(SCN) 2 Br

We perform magnetic susceptibility and magnetic torque measurements on the organic κ-(BEDT-TTF) 2 Hg(SCN) 2 Br, which is recently suggested to host an exotic quantum dipole-liquid in its low-temperature insulating phase. Below the metal-insulator (MI) transition temperature, the magnetic susceptibility follows a Curie–Weiss law with a positive Curie–Weiss temperature, and a particular M∝ $\sqrt{H}$ curve is observed. The emergent ferromagnetically interacting spins amount to about 1/6 of the full spin moment of localized charges. Taking account of the possible inhomogeneous quasi-charge-order that forms a dipole-liquid, we construct a model of antiferromagnetically interacting spin chains in two adjacent charge-ordered domains, which are coupled via fluctuating charges on a Mott-dimer at the boundary. We find that the charge fluctuations can draw a weak ferromagnetic moment out of the spin singlet domains.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Understanding temperature-dependent SU(3) spin dynamics in the S = 1 antiferromagnet Ba 2 FeSi 2 O 7

Quantum magnets admit more than one classical limit and N-level systems with strong single-ion anisotropy are expected to be described by a classical approximation based on SU(N) coherent states. Here we test this hypothesis by modeling finite temperature inelastic neutron scattering (INS) data of the effective spin-one antiferromagnet Ba 2 FeSi 2 O 7 . The measured dynamic structure factor is calculated with a generalized Landau-Lifshitz dynamics for SU(3) spins. Unlike the traditional classical limit based on SU(2) coherent states, the results obtained with classical SU(3) spins are in good agreement with the measured temperature dependent spectrum. The SU(3) approach developed here provides a general framework to understand the broad class of materials comprising weakly coupled antiferromagnetic dimers, trimers, or tetramers, and magnets with strong single-ion anisotropy.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Triple tandem trimer immunogens for HIV-1 and influenza nucleic acid-based vaccines

Recombinant native-like HIV-1 envelope glycoprotein (Env) trimers are used in candidate vaccines aimed at inducing broadly neutralizing antibodies. While state-of-the-art SOSIP or single-chain Env designs can be expressed as native-like trimers, undesired monomers, dimers and malformed trimers that elicit non-neutralizing antibodies are also formed, implying that these designs could benefit from further modifications for gene-based vaccination approaches. Here, we describe the triple tandem trimer (TTT) design, in which three Env protomers are genetically linked in a single open reading frame and express as native-like trimers. Viral vectored Env TTT induced similar neutralization titers but with a higher proportion of trimer-specific responses. The TTT design was also applied to generate influenza hemagglutinin (HA) trimers without the need for trimerization domains. Additionally, we used TTT to generate well-folded chimeric Env and HA trimers that harbor protomers from three different strains. In summary, the TTT design is a useful platform for the design of HIV-1 Env and influenza HA immunogens for a multitude of vaccination strategies.

60 APPLIED LIFE SCIENCES↗