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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 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Sneaking in SpyCatcher using cell penetrating peptides for in vivo imaging

Abstract In vivo imaging of protein complexes is a powerful method for understanding the underlying biological function of these key biomolecules. Though the engineering of small, high affinity nanobodies have become more prevalent, the off-rates of these tags may result in incomplete or partial labeling of proteins in live cells. The SpyCatcher003 and SpyTag split protein system allow for irreversible, covalent binding to a short target peptide unlike nanobody-affinity based probes. However, delivering these tags into a cell without disrupting its normal function is a key challenge. Cell penetrating peptides (CPPs) are short peptide sequences that facilitate the transduction of otherwise membrane-impermeable ‘cargo’ , such as proteins, into cells. Here we report on our efforts to engineer and characterize CPP-SpyCatcher003 fusions as modular imaging probes. We selected three CPPs, CUPID, Pentratin, and pVEC, to engineer fusion protein probes for superresolution microscopy, with the aim to eliminate prior permeabilization treatments that could introduce imaging artifacts. We find that fusing the CPP sequences to SpyCatcher003 resulted in dimer and multimer formation as determined by size exclusion chromatography, dynamic light scattering, and SDS resistant dimers on SDS-PAGE gels. By isolating and labeling the monomeric forms of the engineered protein, we show these constructs retained their ability to bind SpyTag and all three CPP sequences remain membrane active, as assessed by CD spectroscopy in the presence of SDS detergent. Using fluorescence and super resolution Lattice structured illumination microscopy (Lattice SIM) imaging we show that the CPPs did not enhance uptake of SpyCatcher by E. coli, however with Caulobacter crescentus cells, we show that Penetratin, and to a lesser degree CUPID, does enhance uptake. Our results demonstrate the ability of the CPP-SpyCatcher003 to label targets within living cells, providing the groundwork for using split protein systems for targeted in vivo imaging.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Gapless spin liquid and pair density wave of the Hubbard model on three-leg triangular cylinders

We study the ground state properties of the Hubbard model on three-leg triangular cylinders using large-scale density-matrix renormalization group simulations. At half-filling, we identify an intermediate gapless spin liquid phase, which has one gapless spin mode and algebraic spin–spin correlations but exponential decay scalar chiral–chiral correlations, between a metallic phase at weak coupling and Mott insulating dimer phase at strong interaction. Upon light doping the gapless spin liquid, the system exhibits power-law charge-density-wave (CDW) correlations but short-range single-particle, spin–spin, and chiral–chiral correlations. Similar to CDW correlations, the superconducting correlations also decay in power-law but oscillate in sign as a function of distance, which is consistent with the striped pair-density wave. When further doping the gapless spin liquid phase or doping the dimer order phase, another phase takes over, which has similar CDW correlations but all other correlations decay exponentially.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Reversible to irreversible transitions for ac driven skyrmions on periodic substrates

Abstract Using atomistic simulations, we investigate the dynamical behavior of magnetic skyrmions in dimer and trimer molecular crystal arrangements, as well as bipartite lattices at 3/2 and 5/2 fillings, under ac driving over a square array of anisotropy defects. For low ac amplitudes, at all fillings reversible motion appears in which the skyrmions return to their original positions at the end of each ac drive cycle and the diffusion is zero. We also identify two distinct irreversible regimes. The first is a translating regime in which the skyrmions form channels of flow in opposing directions and translate by one substrate lattice constant per ac drive cycle. The translating state appears in the dimer and trimer arrangements, and produces pronounced peaks in the diffusivity in the direction perpendicular to the external drive. For larger ac amplitudes, we find chaotic irreversible motion in which the skyrmions can randomly exchange places with each other over time, producing long-time diffusive behavior both parallel and perpendicular to the ac driving direction.

36 MATERIALS SCIENCE↗
DOE OSTI2023

The structure of the high-affinity nickel-binding site in the Ni,Zn-HypA•UreE2 complex

Abstract The maturation pathway for the nickel-dependent enzyme urease utilizes the protein UreE as a metallochaperone to supply Ni(II) ions. In Helicobacter pylori urease maturation also requires HypA and HypB, accessory proteins that are commonly associated with hydrogenase maturation. Herein we report on the characterization of a protein complex formed between HypA and the UreE2 dimer. Nuclear magnetic resonance (NMR) coupled with molecular modelling show that the protein complex apo, Zn-HypA•UreE2, forms between the rigorously conserved Met-His-Glu (MHE motif) Ni-binding N-terminal sequence of HypA and the two conserved His102A and His102B located at the dimer interface of UreE2. This complex forms in the absence of Ni(II) and is supported by extensive protein contacts that include the use of the C-terminal sequences of UreE2 to form additional strands of β-sheet with the Ni-binding domain of HypA. The Ni-binding properties of apo, Zn-HypA•UreE2 and the component proteins were investigated by isothermal titration calorimetry using a global fitting strategy that included all of the relevant equilibria, and show that the Ni,Zn-HypA•UreE2 complex contains a single Ni(II)-binding site with a sub-nanomolar KD. The structural features of this novel Ni(II) site were elucidated using proteins produced with specifically deuterated amino acids, protein point mutations, and the analyses of X-ray absorption spectroscopy, hyperfine shifted NMR features, as well as molecular modeling coupled with quantum-mechanical calculations. The results show that the complex contains a six-coordinate, high-spin Ni(II) site with ligands provided by both component proteins.

Zambelli, Barbara (ORCID:0000000238760051)↗
DOE OSTI2023

Structure, substrate binding and activity of a unique AAA+ protein: the BrxL phage restriction factor

Abstract Bacteriophage exclusion (‘BREX’) systems are multi-protein complexes encoded by a variety of bacteria and archaea that restrict phage by an unknown mechanism. One BREX factor, termed BrxL, has been noted to display sequence similarity to various AAA+ protein factors including Lon protease. In this study we describe multiple CryoEM structures of BrxL that demonstrate it to be a chambered, ATP-dependent DNA binding protein. The largest BrxL assemblage corresponds to a dimer of heptamers in the absence of bound DNA, versus a dimer of hexamers when DNA is bound in its central pore. The protein displays DNA-dependent ATPase activity, and ATP binding promotes assembly of the complex on DNA. Point mutations within several regions of the protein-DNA complex alter one or more in vitro behaviors and activities, including ATPase activity and ATP-dependent association with DNA. However, only the disruption of the ATPase active site fully eliminates phage restriction, indicating that other mutations can still complement BrxL function within the context of an otherwise intact BREX system. BrxL displays significant structural homology to MCM subunits (the replicative helicase in archaea and eukaryotes), implying that it and other BREX factors may collaborate to disrupt initiation of phage DNA replication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The crystal structure of bacteriophage λ RexA provides novel insights into the DNA binding properties of Rex-like phage exclusion proteins

Abstract RexA and RexB function as an exclusion system that prevents bacteriophage T4rII mutants from growing on Escherichia coli λ phage lysogens. Recent data established that RexA is a non-specific DNA binding protein that can act independently of RexB to bias the λ bistable switch toward the lytic state, preventing conversion back to lysogeny. The molecular interactions underlying these activities are unknown, owing in part to a dearth of structural information. Here, we present the 2.05-Å crystal structure of the λ RexA dimer, which reveals a two-domain architecture with unexpected structural homology to the recombination-associated protein RdgC. Modelling suggests that our structure adopts a closed conformation and would require significant domain rearrangements to facilitate DNA binding. Mutagenesis coupled with electromobility shift assays, limited proteolysis, and double electron–electron spin resonance spectroscopy support a DNA-dependent conformational change. In vivo phenotypes of RexA mutants suggest that DNA binding is not a strict requirement for phage exclusion but may directly contribute to modulation of the bistable switch. We further demonstrate that RexA homologs from other temperate phages also dimerize and bind DNA in vitro. Collectively, these findings advance our mechanistic understanding of Rex functions and provide new evolutionary insights into different aspects of phage biology.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Essential amino acids in the Plant-Conserved and Class-Specific Regions of cellulose synthases

The Plant-Conserved Region (P-CR) and the Class-Specific Region (CSR) are two plant-unique sequences in the catalytic core of cellulose synthases (CESAs) for which specific functions have not been established. Here, we used site-directed mutagenesis to replace amino acids and motifs within these sequences predicted to be essential for assembly and function of CESAs. We developed an in vivo method to determine the ability of mutated CesA1 transgenes to complement an Arabidopsis (Arabidopsis thaliana) temperature-sensitive root-swelling1 (rsw1) mutant. Replacement of a Cys residue in the CSR, which blocks dimerization in vitro, rendered the AtCesA1 transgene unable to complement the rsw1 mutation. Examination of the CSR sequences from 33 diverse angiosperm species showed domains of high-sequence conservation in a class-specific manner but with variation in the degrees of disorder, indicating a nonredundant role of the CSR structures in different CESA isoform classes. The Cys residue essential for dimerization was not always located in domains of intrinsic disorder. Expression of AtCesA1 transgene constructs, in which Pro417 and Arg453 were substituted for Ala or Lys in the coiled-coil of the P-CR, were also unable to complement the rsw1 mutation. Despite an expected role for Arg457 in trimerization of CESA proteins, AtCesA1 transgenes with Arg457Ala mutations were able to fully restore the wild-type phenotype in rsw1. Our data support that Cys662 within the CSR and Pro417 and Arg453 within the P-CR of Arabidopsis CESA1 are essential residues for functional synthase complex formation, but our data do not support a specific role for Arg457 in trimerization in native CESA complexes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Switching charge states in quasi-2D molecular conductors

Abstract 2D molecular entities build next-generation electronic devices, where abundant elements of organic molecules are attractive due to the modern synthetic and stimuli control through chemical, conformational, and electronic modifications in electronics. Despite its promising potential, the insufficient control over charge states and electronic stabilities must be overcome in molecular electronic devices. Here, we show the reversible switching of modulated charge states in an exfoliatable 2D-layered molecular conductor based on bis(ethylenedithio)tetrathiafulvalene molecular dimers. The multiple stimuli application of cooling rate, current, voltage, and laser irradiation in a concurrent manner facilitates the controllable manipulation of charge crystal, glass, liquid, and metal phases. The four orders of magnitude switching of electric resistance are triggered by stimuli-responsive charge distribution among molecular dimers. The tunable charge transport in 2D molecular conductors reveals the kinetic process of charge configurations under stimuli, promising to add electric functions in molecular circuitry.

Huang, Yulong (ORCID:0000000296160134)↗
DOE OSTI2023

Sphingobium lignivorans sp. nov., isolated from river sediment downstream of a paper mill

Here, a bacterial isolate, B1D3A T , was isolated from river sediment collected from the Hiwassee River near Calhoun, TN, by enrichment culturing with a model 5–5' lignin dimer, dehydrodivanillate, as its sole carbon source. B1D3A T was also shown to utilize several model lignin-derived monomers and dimers as sole carbon sources in a variety of minimal media. Cells were Gram-stain-negative, aerobic, motile, rod-shaped and formed yellow/cream-coloured colonies on rich agar. Optimal growth occurred at 30°C, pH 7–8, and in the absence of NaCl. The major fatty acids of B1D3A T were C 18:1 ω7c and C 17:1 ω6c. The predominant hydroxy fatty acids were C 14: 0 2-OH and C 15:0 2-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine and sphingoglycolipid. B1D3A T contained spermidine as the only major polyamine. The major isoprenoid quinone was Q-10 with minor amounts of Q-9 and Q-11. The genomic DNA G+C content of B1D3A T was 65.6mol%. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 49 core, universal genes defined by Clusters of Orthologous Groups gene families indicated that B1D3A T was a member of the genus Sphingobium. B1D3A T was most closely related to Sphingobium sp. SYK-6, with a 100% 16S rRNA gene sequence similarity. B1D3A T showed 78.1–89.9%average nucleotide identity and 19.5–22.2% digital DNA–DNA hybridization identity with other type strains from the genus Sphingobium. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain B1D3A T should be classified as representing a novel species of the genus Sphingobium, for which the name Sphingobium lignivorans sp. nov. is proposed. The type strain is strain B1D3A T (ATCC TSD-279 T =DSM 111877 T ).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Observation of Unprecedented Fractional Magnetization Plateaus in a New Shastry-Sutherland Ising Compound

Geometrically frustrated magnetic systems, such as those based on the Shastry-Sutherland lattice (SSL), offer a rich playground for exploring unconventional magnetic states. The delicate balance between competing interactions in these systems leads to the emergence of novel phases. We present the characterization of Er 2 ⁢Be 2⁢ GeO 7 , an SSL compound with Er 3+ ions forming orthogonal dimers separated by nonmagnetic layers whose structure is invariant under the 𝑃⁢$\bar{4}21$⁢𝑚 space group. Neutron scattering reveals an antiferromagnetic dimer structure at zero field, typical of Ising spins on that lattice and consistent with the anisotropic magnetization observed. However, magnetization measurements exhibit fractional plateaus at 1/4 and 1/2 of saturation, in contrast to the expected 1/3 plateau of the SSL Ising model. By comparing the energy of candidate states with ground-state lower bounds we show that this behavior requires spatially anisotropic interactions, leading to an anisotropic Shastry-Sutherland Ising model symmetric under the 𝐶⁢𝑚⁢𝑚⁢2 space group. This anisotropy is consistent with the small orthorhombic distortion observed with single-crystal neutron diffraction. The other properties, including thermodynamics, which have been investigated theoretically using tensor networks, point to small residual interactions, potentially due to further couplings and quantum fluctuations. This study highlights Er 2 ⁢Be 2 ⁢GeO 7 as a promising platform for investigating exotic magnetic phenomena.

Yadav, Lalit [Duke University, Durham, NC (United ↗
DOE OSTI2025

Phonon spectrum in the spin-Peierls phase of CuGeO 3

CuGeO 3 has long been studied as a prototypical example of the spin-Peierls transition in a 𝑆 = 1/2 Heisenberg chain. Despite intensive investigation of this quasi-one-dimensional material, systematic measurements and calculations of the phonon excitations in the dimerized phase have not to date been possible, leaving certain aspects of the spin-Peierls phenomenon unresolved. We perform state-of-the-art density functional theory (DFT) calculations to compute the electronic structure and phonon dynamics in the low-temperature dimerized phase. We also perform high-resolution neutron spectroscopy to measure the full phonon spectrum over multiple Brillouin zones. We find excellent agreement between our numerical and experimental results that extend to all measurement temperatures. Notable features of our phonon spectra include a number of steeply dispersive modes, nonmonotonic dispersion features, and specific phonon anticrossings, which we relate to the mode eigenvectors. By calculating the magnetic interactions within DFT and studying the effects of different phonon modes on the superexchange paths, we discuss the possibility of observing spin-phonon hybridization effects in experiments performed both in and out of equilibrium.

density functional theory↗
DOE OSTI2020

Ferrimagnetic 120 ° magnetic structure in Cu 2 OSO 4

We report magnetic properties of a 3d 9 (Cu 2+ ) magnetic insulator Cu 2 OSO 4 measured on both powder and single crystal. The magnetic atoms of this compound form layers whose geometry can be described either as a system of chains coupled through dimers or as a kagome lattice where every third spin is replaced by a dimer. Specific heat and DC susceptibility show a magnetic transition at 20 K, which is also confirmed by neutron scattering. Magnetic entropy extracted from the specific heat data is consistent with an S=1/2 degree of freedom per Cu 2+ , and so is the effective moment extracted from DC susceptibility. The ground state has been identified by means of neutron diffraction on both powder and single crystal and corresponds to an ~120° spin structure in which ferromagnetic intradimer alignment results in a net ferrimagnetic moment. No evidence is found for a change in lattice symmetry down to 2 K. Finally, our results suggest that Cu 2 OSO 4 represents a type of model lattice with frustrated interactions where interplay between magnetic order, thermal and quantum fluctuations can be explored.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Spin-liquid behavior of the three-dimensional magnetic system Ba 3 NiIr 2 O 9 with S = 1

The quantum spin liquid (QSL) is an exotic phase of magnetic materials where the spins continue to fluctuate without any symmetry breaking down to zero temperature. Among the handful reports of QSL with spin S ≥ 1, examples with magnetic ions on a three-dimensional (3D) magnetic lattice are extremely rare since both larger spin and higher dimension tend to suppress quantum fluctuations. In this work, we offer a new strategy to achieve 3D QSL with high spin by utilizing two types of transition metal ions; both are magnetically active but located at crystallographically inequivalent positions. Furthermore, we design a 3D magnetic system Ba 3 NiIr 2 O 9 consisting of interconnected corner-shared NiO 6 octahedra and face-shared Ir 2 O 9 dimer, both having triangular arrangements in a-b plane. X-ray absorption spectroscopy measurements confirm the presence of Ni 2+ (S = 1). Furthermore, our detailed thermodynamic and magnetic measurements reveal that this compound is a realization of gapless QSL state down to at least 100 mK. Ab initio calculations find a strong magnetic exchange between Ir and Ni sublattices and in-plane antiferromagnetic coupling between the dimers, resulting in dynamically fluctuating magnetic moments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Peierls transition, ferroelectricity, and spin-singlet formation in monolayer VOI 2

Using ab initio density functional theory and single-orbital Hubbard model calculations via the density matrix renormalization group method, we systematically studied the monolayer VOI 2 with a 3d 1 electronic configuration. Our phonon calculations indicate that the orthorhombic Pmm2 FE-II phase is the most likely ground state, involving a ferroelectric (FE) distortion along the a axis and V-V dimerization along the b axis. Specifically, the “pseudo Jahn-Teller” effect caused by the coupling between empty V (d xz/yz and d 3z 2 -r 2 ) and O 2p states is proposed as the mechanism that stabilizes the FE distortion from the paraelectric phase. Moreover, the half-filled metallic d xy band displays a Peierls instability along the b axis, inducing a V-V dimerization. Additionally, we found very short-range antiferromagnetic coupling along the V-V chain due to the formation of nearly decoupled spin singlets in the ground state.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

First-principles study of superconductivity in α and β gallium

Elemental gallium can exist in several phases under ambient pressure. The stable α phase has a superconducting transition temperature, T c , of 0.9 K. By contrast, the T c of the metastable β phase is around 6 K. To understand the significant improvement in T c in the β phase, we first calculate the electronic structure, phonon dispersion, and the electron-phonon coupling of gallium in the α and β phases. Next, we solve the Eliashberg equations to obtain the superconducting gaps and the transition temperatures. Additionally, using these results, we relate the increased T c in the β phase to structural differences between the phases that affect the electronic and phonon properties. The structure motif of the α phase is Ga 2 dimers, which form strong covalent bonds leading to bonding and antibonding states that reduce the density of states at the Fermi level. The β-Ga structure consists of arrays of Ga chains that favor strong coupling between the lattice vibrations and the electronic states near the Fermi level. The increased density of states and strong coupling to the phonons for the β-Ga chains compared to the αGa 2 dimers enhance superconductivity in the β-Ga phase.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Doping-driven resistive collapse of the Mott insulator in a minimal model for VO 2

Here we study the resistive collapse of the Mott insulator state in the dimer Hubbard model. This minimal model has been used to describe the physics of VO 2 , and should be relevant to other strongly correlated materials. It incorporates the physics of correlated dimers and the explicit competition between on-site Coulomb repulsion and magnetic exchange interactions. Our results unveil that between the Mott insulator at half filling and the Fermi liquid metal at high doping there is an intermediate bad metallic phase with exotic features such as a pseudogap, orbital selectivity, and a first-order metal-metal transition. The model is solved within dynamical mean field theory by means of quantum Monte Carlo, which provides the numerically exact solution of the model in the limit of large lattice dimensionality. This model can be considered as a minimal one that captures exotic phenomena associated to the physics of a doped Mott insulator, shading light on their basic physical mechanism.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Electronic structure, magnetic properties, and pairing tendencies of the copper-based honeycomb lattice Na 2 Cu 2 TeO 6

Spin-1/2 chains with alternating antiferromagnetic (AFM) and ferromagnetic (FM) couplings have attracted considerable interest due to the topological character of their spin excitations. Here, using density functional theory and density-matrix renormalization-group (DMRG) methods, we have systematically studied the dimerized chain system Na 2 Cu 2 TeO 6 with a d 9 electronic configuration. Near the Fermi level, in the nonmagnetic phase the dominant states are mainly contributed by the Cu 3d x 2 -y 2 orbitals highly hybridized with the O 2p orbitals, leading to an “effective” single-orbital low-energy model. By calculating the relevant hoping amplitudes, we explain the size and sign of the exchange interactions in Na 2 Cu 2 TeO 6 . In addition, a single-orbital Hubbard model is constructed for this dimerized chain system where the quantum fluctuations are taken into account. Both AFM and FM couplings (leading to an ↑|-|↓-|↓-↑| state) along the chain were found in our DMRG and Lanczos calculations, in agreement with density functional theory and neutron-scattering results. The hole pairing binding energy ΔE is predicted to be negative at Hubbard U~ 11eV, suggesting incipient pairing tendencies.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗