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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 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Magic-angle semimetals

Abstract Breakthroughs in two-dimensional van der Waals heterostructures have revealed that twisting creates a moiré pattern that quenches the kinetic energy of electrons, allowing for exotic many-body states. We show that cold atomic, trapped ion, and metamaterial systems can emulate the effects of a twist in many models from one to three dimensions. Further, we demonstrate at larger angles (and argue at smaller angles) that by considering incommensurate effects, the magic-angle effect becomes a single-particle quantum phase transition (including in a model for twisted bilayer graphene in the chiral limit). We call these models “magic-angle semimetals”. Each contains nodes in the band structure and an incommensurate modulation. At magic-angle criticality, we report a nonanalytic density of states, flat bands, multifractal wave functions that Anderson delocalize in momentum space, and an essentially divergent effective interaction scale. As a particular example, we discuss how to observe this effect in an ultracold Fermi gas.

Materials Science↗
DOE OSTI2021

Precursor of pair-density wave in doping Kitaev spin liquid on the honeycomb lattice

Abstract We study the effects of doping the Kitaev model on the honeycomb lattice where the spins interact via the bond-directional interaction J K , which is known to have a quantum spin liquid as its exact ground state. The effect of hole doping is studied within the t - J K model on a three-leg cylinder using density-matrix renormalization group. Upon light doping, we find that the ground state of the system has a dominant quasi-long-range charge-density-wave correlations but short-range single-particle correlations. In the pairing channel, the even-parity superconducting correlation is dominant with d -wave-like symmetry, which oscillates in sign as a function of separation with a period equal to that of the spin-density wave and two times the charge-density wave. Although these correlations fall rapidly (possibly exponentially) at long distances, this is never-the-less the example where a pair-density wave is the leading instability in the pairing channel on the honeycomb lattice.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Correlation-driven electron-hole asymmetry in graphene field effect devices

Electron-hole asymmetry is a fundamental property in solids that can determine the nature of quantum phase transitions and the regime of operation for devices. The observation of electron-hole asymmetry in graphene and recently in twisted graphene and moiré heterostructures has spurred interest into whether it stems from single-particle effects or from correlations, which are core to the emergence of intriguing phases in moiré systems. Here, we report an effective way to access electron-hole asymmetry in 2D materials by directly measuring the quasiparticle self-energy in graphene/Boron Nitride field-effect devices. As the chemical potential moves from the hole to the electron-doped side, we see an increased strength of electronic correlations manifested by an increase in the band velocity and inverse quasiparticle lifetime. These results suggest that electronic correlations intrinsically drive the electron-hole asymmetry in graphene and by leveraging this asymmetry can provide alternative avenues to generate exotic phases in twisted moiré heterostructures.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Vertex dominated superconductivity in intercalated FeSe

Bulk FeSe becomes superconducting below 9 K, but the critical temperature (T c ) is enhanced almost universally by a factor of ~4–5 when it is intercalated with alkali elements. How intercalation modifies the structure is known from in-situ X-ray and neutron scattering techniques, but why T c changes so dramatically is not known. Here we show that there is one-to-one correspondence between the enhancement in magnetic instabilities at certain q vectors and superconducting pairing vertex, even while the nuclear spin relaxation rate 1/(T 1 T) may not reflect this enhancement. Intercalation modifies electronic screening both in the plane and also between layers. We disentangle quantitatively how superconducting pairing vertex gains from each such changes in electronic screening. Intercalated FeSe provides an archetypal example of superconductivity where information derived from the single-particle electronic structure appears to be insufficient to account for the origins of superconductivity, even when they are computed including correlation effects. We show that the five-fold enhancement in T c on intercalation is not sensitive to the exact position of the d xy at Γ point, as long as it stays close to E F . Finally, we show that intercalation also significantly softens the collective charge excitations, suggesting the electron-phonon interaction could play some role in intercalated FeSe.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution

Single-particle cryogenic electron microscopy (cryo-EM) has become a standard technique for determining protein structures at atomic resolution1,2,3. However, cryo-EM studies of protein-free RNA are in their early days. The Tetrahymena thermophila group I self-splicing intron was the first ribozyme to be discovered and has been a prominent model system for the study of RNA catalysis and structure–function relationships4, but its full structure remains unknown. Here we report cryo-EM structures of the full-length Tetrahymena ribozyme in substrate-free and bound states at a resolution of 3.1 Å. Additionally, newly resolved peripheral regions form two coaxially stacked helices; these are interconnected by two kissing loop pseudoknots that wrap around the catalytic core and include two previously unforeseen (to our knowledge) tertiary interactions. The global architecture is nearly identical in both states; only the internal guide sequence and guanosine binding site undergo a large conformational change and a localized shift, respectively, upon binding of RNA substrates. These results provide a long-sought structural view of a paradigmatic RNA enzyme and signal a new era for the cryo-EM-based study of structure–function relationships in ribozymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Cryo-EM structures of PP2A:B55–FAM122A and PP2A:B55–ARPP19

Progression through the cell cycle is controlled by regulated and abrupt changes in phosphorylation. Mitotic entry is initiated by increased phosphorylation of mitotic proteins, a process driven by kinases, whereas mitotic exit is achieved by counteracting dephosphorylation, a process driven by phosphatases, especially PP2A:B55. Although the role of kinases in mitotic entry is well established, recent data have shown that mitosis is only successfully initiated when the counterbalancing phosphatases are also inhibited. Inhibition of PP2A:B55 is achieved by the intrinsically disordered proteins ARPP19 and FAM122A. Despite their critical roles in mitosis, the mechanisms by which they achieve PP2A:B55 inhibition is unknown. Here, we report the single-particle cryo-electron microscopy structures of PP2A:B55 bound to phosphorylated ARPP19 and FAM122A. Consistent with our complementary NMR spectroscopy studies, both intrinsically disordered proteins bind PP2A:B55, but do so in highly distinct manners, leveraging multiple distinct binding sites on B55. Our extensive structural, biophysical and biochemical data explain how substrates and inhibitors are recruited to PP2A:B55 and provide a molecular roadmap for the development of therapeutic interventions for PP2A:B55-related diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural basis for intermodular communication in assembly-line polyketide biosynthesis

Assembly-line polyketide synthases (PKSs) are modular multi-enzyme systems with considerable potential for genetic reprogramming. Understanding how they selectively transport biosynthetic intermediates along a defined sequence of active sites could be harnessed to rationally alter PKS product structures. Here, to investigate functional interactions between PKS catalytic and substrate acyl carrier protein (ACP) domains, we employed a bifunctional reagent to crosslink transient domain–domain interfaces of a prototypical assembly line, the 6-deoxyerythronolide B synthase, and resolved their structures by single-particle cryogenic electron microscopy (cryo-EM). Together with statistical per-particle image analysis of cryo-EM data, we uncovered interactions between ketosynthase (KS) and ACP domains that discriminate between intra-modular and inter-modular communication while reinforcing the relevance of conformational asymmetry during the catalytic cycle. Our findings provide a foundation for the structure-based design of hybrid PKSs comprising biosynthetic modules from different naturally occurring assembly lines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Improvement of cryo-EM maps by density modification

A density-modification procedure for improving maps from single-particle electron cryogenic microscopy (cryo-EM) is presented here. The theoretical basis of the method is identical to that of maximum-likelihood density modification, previously used to improve maps from macromolecular X-ray crystallography. Key differences from applications in crystallography are that the errors in Fourier coefficients are largely in the phases in crystallography but in both phases and amplitudes in cryo-EM, and that half-maps with independent errors are available in cryo-EM. These differences lead to a distinct approach for combination of information from starting maps with information obtained in the density-modification process. The density-modification procedure was applied to a set of 104 datasets and improved map-model correlation and increased the visibility of details in many of the maps. The procedure requires two unmasked half-maps and a sequence file or other source of information on the volume of the macromolecule that has been imaged.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Molecular organization of the E. coli cellulose synthase macrocomplex

Cellulose is frequently found in communities of sessile bacteria called biofilms. Escherichia coli and other enterobacteriaceae modify cellulose with phosphoethanolamine (pEtN) to promote host tissue adhesion. The E. coli pEtN cellulose biosynthesis machinery contains the catalytic BcsA–B complex that synthesizes and secretes cellulose, in addition to five other subunits. The membrane-anchored periplasmic BcsG subunit catalyzes pEtN modification. Here we present the structure of the roughly 1 MDa E. coli Bcs complex, consisting of one BcsA enzyme associated with six copies of BcsB, determined by single-particle cryo-electron microscopy. BcsB homo-oligomerizes primarily through interactions between its carbohydrate-binding domains as well as intermolecular beta-sheet formation. The BcsB hexamer creates a half spiral whose open side accommodates two BcsG subunits, directly adjacent to BcsA’s periplasmic channel exit. The cytosolic BcsE and BcsQ subunits associate with BcsA’s regulatory PilZ domain. As a result, the macrocomplex is a fascinating example of cellulose synthase specification.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures

The advent of single-particle cryo-electron microscopy (cryo-EM) has brought forth a new era of structural biology, enabling the routine determination of large biological molecules and their complexes at atomic resolution. The high-resolution structures of biological macromolecules and their complexes significantly expedite biomedical research and drug discovery. However, automatically and accurately building atomic models from high-resolution cryo-EM density maps is still time-consuming and challenging when template-based models are unavailable. Artificial intelligence (AI) methods such as deep learning trained on limited amount of labeled cryo-EM density maps generate inaccurate atomic models. To address this issue, we created a dataset called Cryo2StructData consisting of 7,600 preprocessed cryo-EM density maps whose voxels are labelled according to their corresponding known atomic structures for training and testing AI methods to build atomic models from cryo-EM density maps. Cryo2StructData is larger than existing, publicly available datasets for training AI methods to build atomic protein structures from cryo-EM density maps. We trained and tested deep learning models on Cryo2StructData to validate its quality showing that it is ready for being used to train and test AI methods for building atomic models.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Energy landscapes from cryo-EM snapshots: a benchmarking study

Abstract Biomolecules undergo continuous conformational motions, a subset of which are functionally relevant. Understanding, and ultimately controlling biomolecular function are predicated on the ability to map continuous conformational motions, and identify the functionally relevant conformational trajectories. For equilibrium and near-equilibrium processes, function proceeds along minimum-energy pathways on one or more energy landscapes, because higher-energy conformations are only weakly occupied. With the growing interest in identifying functional trajectories, the need for reliable mapping of energy landscapes has become paramount. In response, various data-analytical tools for determining structural variability are emerging. A key question concerns the veracity with which each data-analytical tool can extract functionally relevant conformational trajectories from a collection of single-particle cryo-EM snapshots. Using synthetic data as an independently known ground truth, we benchmark the ability of four leading algorithms to determine biomolecular energy landscapes and identify the functionally relevant conformational paths on these landscapes. Such benchmarking is essential for systematic progress toward atomic-level movies of continuous biomolecular function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A substrate-induced gating mechanism is conserved among Gram-positive IgA1 metalloproteases

The mucosal adaptive immune response is dependent on the production of IgA antibodies and particularly IgA1, yet opportunistic bacteria have evolved mechanisms to specifically block this response by producing IgA1 proteases (IgA1Ps). Our lab was the first to describe the structures of a metal-dependent IgA1P (metallo-IgA1P) produced from Gram-positive Streptococcus pneumoniae both in the absence and presence of its IgA1 substrate through cryo-EM single particle reconstructions. This prior study revealed an active-site gating mechanism reliant on substrate-induced conformational changes to the enzyme that begged the question of whether such a mechanism is conserved among the wider Gram-positive metallo-IgA1P subfamily of virulence factors. Here, we used cryo-EM to characterize the metallo-IgA1P of a more distantly related family member from Gemella haemolysans, an emerging opportunistic pathogen implicated in meningitis, endocarditis, and more recently bacteremia in the elderly. While the substrate-free structures of these two metallo-IgA1Ps exhibit differences in the relative starting positions of the domain responsible for gating substrate, the enzymes have similar domain orientations when bound to IgA1. Together with biochemical studies that indicate these metallo-IgA1Ps have similar binding affinities and activities, these data indicate that metallo-IgA1P binding requires the specific IgA1 substrate to open the enzymes for access to their active site and thus, largely conform to an “induced fit” model.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Development of an ultrahigh affinity, trimeric ACE2 biologic as a universal SARS-CoV-2 antagonist

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, utilizes membrane-bound, angiotensin-converting enzyme II (ACE2) for internalization and infection. We describe the development of a biologic that takes advantage of the proximity of the N-terminus of bound ACE2 to the three-fold symmetry axis of the spike protein to create an ultrapotent, trivalent ACE2 entry antagonist. Distinct disulfide bonds were added to enhance serum stability and a single point mutation was introduced to eliminate enzymatic activity. Through surface plasmon resonance, pseudovirus neutralization assays, and single-particle cryo-electron microscopy, we show this antagonist binds to and inhibits SARS-CoV-2 variants. We further show the antagonist binds to and inhibits a 2003 SARS-CoV-1 strain. Collectively, structural insight has allowed us to design a universal trivalent antagonist against all variants of SARS-CoV-2 tested, suggesting it will be active against the emergence of future mutants.

Gonzales, Juliet (ORCID:0000000327219566)↗
DOE OSTI2024

Mechanistic insights into a heterobifunctional degrader-induced PTPN2/N1 complex

PTPN2 (protein tyrosine phosphatase non-receptor type 2, or TC-PTP) and PTPN1 are attractive immuno-oncology targets, with the deletion of Ptpn1 and Ptpn2 improving response to immunotherapy in disease models. Targeted protein degradation has emerged as a promising approach to drug challenging targets including phosphatases. We developed potent PTPN2/N1 dual heterobifunctional degraders (Cmpd-1 and Cmpd-2) which facilitate efficient complex assembly with E3 ubiquitin ligase CRL4 CRBN , and mediate potent PTPN2/N1 degradation in cells and mice. To provide mechanistic insights into the cooperative complex formation introduced by degraders, we employed a combination of structural approaches. Our crystal structure reveals how PTPN2 is recognized by the tri-substituted thiophene moiety of the degrader. We further determined a high-resolution structure of DDB1-CRBN/Cmpd-1/PTPN2 using single-particle cryo-electron microscopy (cryo-EM). This structure reveals that the degrader induces proximity between CRBN and PTPN2, albeit the large conformational heterogeneity of this ternary complex. The molecular dynamic (MD)-simulations constructed based on the cryo-EM structure exhibited a large rigid body movement of PTPN2 and illustrated the dynamic interactions between PTPN2 and CRBN. Together, our study demonstrates the development of PTPN2/N1 heterobifunctional degraders with potential applications in cancer immunotherapy. Furthermore, the developed structural workflow could help to understand the dynamic nature of degrader-induced cooperative ternary complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Long-lived period-doubled edge modes of interacting and disorder-free Floquet spin chains

Floquet spin chains have been a venue for understanding topological states of matter that are qualitatively different from their static counterparts by, for example, hosting π edge modes that show stable period-doubled dynamics. However the stability of these edge modes to interactions has traditionally required the system to be many-body localized in order to suppress heating. In contrast, here we show that even in the absence of disorder, and in the presence of bulk heating, π edge modes are long lived. Their lifetime is extracted from exact diagonalization and is found to be non-perturbative in the interaction strength. A tunneling estimate for the lifetime is obtained by mapping the stroboscopic time-evolution to dynamics of a single particle in Krylov subspace. In this subspace, the π edge mode manifests as the quasi-stable edge mode of an inhomogeneous Su-Schrieffer-Heeger model whose dimerization vanishes in the bulk of the Krylov chain.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Dynamics of molecular associates in methanol/water mixtures

The dynamics of molecular associates in a methanol/water mixture was investigated using quasielastic neutron scattering. By measuring the signal from four methanol/water samples differing only by their isotopic composition, the relative motion of the water to methanol molecules, i.e. their mutual dynamics, was determined at the nanoscale. The thus obtained nanoscopic mutual diffusion coefficient signals a significantly slower process than the single particle diffusion of either methanol or water in the system as well as their macroscopic mutual diffusion. The data do not provide any indication of microsegregation in this preeminent alcohol/water mixture; however, they do indicate the existence of long lived but dynamic molecular associates of water and methanol molecules. Our analysis of the structural relaxation shows that the lifetime of molecular association through hydrogen bonding determines the fact that viscosity of the mixtures at intermediate concentrations is higher than that of both pure components.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Gas-phase oxidation and nanoparticle formation in multi-element laser ablation plumes

The evolution from gas-phase oxidation to nanoparticle and agglomerate formation was studied in nanosecond laser-produced plasmas of a multi-principal element alloy target in air. Here gas-phase oxidation of plasma species was monitored in situ via optical emission spectroscopy, while a custom-built single particle mass spectrometer was used to measure size and compositions of agglomerated nanoparticles formed in laser ablation plumes. Ex situ analysis employing transmission electron microscopy was used to study nanoparticle morphology, crystal structure, and element distribution at the nanoscale. Emission spectra indicate that gas-phase oxidation of elements in the alloy target are formed at varying times during plume evolution, and mass spectrometry results indicate fractal agglomerates contain all principal alloying elements and their oxides. Finally, electron microscopy characterization illustrates that these agglomerates consist of multiple material types: sub-10 nm diameter amorphous, multi-element nanoparticles, ≈10–30 nm diameter Ti-rich crystalline oxide nanoparticles, and ejected base material. Results highlight that the multi-component target composition impacts molecular formation in the gas phase and the morphology, composition, and structure of nanoparticles and agglomerates formed.

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

Expanding the color palette of bicolor-emitting nanocrystals

Owing to their bright and tunable luminescence spectra, nanocrystals appear as a unique playground for light source design. Displays and lighting require white light sources that combine several narrow lines. As Kasha's rule prevents the emission of hot carriers, blends of multiple nanocrystal populations are currently the obvious strategy for broad-band source design. However, a few reports suggest that bicolor emission can also be obtained from a single particle even under weak excitation if a careful design of the exciton scattering mechanism sufficiently slows down its relaxation pathways. A key challenge remains to maintain quantum confinement for color tunability in the same structure, while simultaneously achieving a large size to leverage the critical, slower exciton diffusion or relaxation down to the ground state. In this work, we demonstrate that 2D nanoplatelets offer an original opportunity for the design of confined and large heterostructures. We demonstrate that bicolor emission is not limited to green–red pair and show that blue–yellow and purple–green emissions can be obtained from CdSe/CdTe/CdSe core/crown/crown and CdSe/CdS core/crown heterostructures, respectively.

77 NANOSCIENCE AND NANOTECHNOLOGY↗