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DOE OSTI2021

IMITATION SWITCH is required for normal chromatin structure and gene repression in PRC2 target domains

Significance Polycomb Repressive Complex 2 (PRC2) methylates histones to regulate multicellular development, maintenance of stem cell identity, X-chromosome inactivation, and other important processes. Given these essential roles, there is significant interest in identifying components that function with PRC2 to establish and maintain transcriptionally repressive heterochromatin. Here we document an unexpected new role for a well-studied and conserved chromatin remodeling factor, ISWI. We found that the Neurospora ISWI homolog is required for normal facultative heterochromatin structure and gene repression at PRC2 target regions, and we defined requirements for ATP-dependent catalytic activity and accessory regulatory proteins. These findings provide mechanistic insights into the formation and function of facultative heterochromatin in a model eukaryote.

Kamei, Masayuki↗

DOE OSTI2020

A numerical-homogenization based phase-field fracture modeling of linear elastic heterogeneous porous media

Most porous media, such as geomaterials and biomaterials are highly heterogeneous in nature, and they contain large variations of microscopic pore structures, such as pore sizes, pore distribution, and pore shapes. The oscillation of microscopic structures is a substantial challenge in theoretical characterization and is usually ignored in continuous modeling. However, mechanical behavior of porous media such as deformation and failure, are essentially impacted by the microscopic heterogeneity which needs to be considered in modeling a porous media. Here, this research proposes a numerical modeling framework with a capability to investigate the effect of microscopic heterogeneity on the macroscopic fracture behavior in porous media by using a numerical homogenization technique, combined with the phase-field fracture modeling method. This numerical modeling strategy computes a homogenized elasticity tensor based on microscopic heterogeneous pore structures heterogenous porous domain by solving boundary value problems at microscopic domain. The strain energy and subsequent propagation of macroscopic fractures will be updated using homogenized stiffness information. Using this numerical scheme, the microscopic pore structure’s impact on the fracture behavior through the homogenized elastic tensor will be taken into account. This multiscale technique is benchmarked against classical problems. Finally, the results highlight the importance of the underlying pore structure and reveal that both fracture strength and propagation path can be influenced by the microscopic heterogeneity.

36 MATERIALS SCIENCE↗

DOE OSTI2021

X-ray Nanoimaging of Crystal Defects in Single Grains of Solid-State Electrolyte Li 7–3x Al x La 3 Zr 2 O 12

All-solid-state lithium batteries promise significant improvements in energy density and safety over traditional liquid electrolyte batteries. The Al-doped Li 7 La 3 Zr 2 O 12 (LLZO) solid-state electrolyte shows excellent potential given its high ionic conductivity and good thermal, chemical, and electrochemical stability. Nevertheless, further improvements on electrochemical and mechanical properties of LLZO call for an in-depth understanding of its local microstructure. Here, we employ Bragg coherent diffractive imaging to investigate the atomic displacements inside single grains of LLZO with various Al-doping concentrations, resulting in cubic, tetragonal, and cubic-tetragonal mixed structures. We observe coexisting domains of different crystallographic orientations in the tetragonal structure. We further show that Al doping leads to crystal defects such as dislocations and phase boundaries in the mixed- and cubic-phase grain. This study addresses the effect of Al doping on the nanoscale structure within individual grains of LLZO, which is informative for the future development of solid-state batteries.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2021

Strain-Induced Atomic-Scale Building Blocks for Ferromagnetism in Epitaxial LaCoO 3

The origin of strain-induced ferromagnetism, which is robust regardless of the type and degree of strain in LaCoO 3 (LCO) thin films, is enigmatic despite intensive research efforts over the past decade. Here, by combining scanning transmission electron microscopy with ab initio density functional theory plus U calculations, we report that the ferromagnetism does not emerge directly from the strain itself but rather from the creation of compressed structural units within ferroelastically formed twin-wall domains. Here, the compressed structural units are magnetically active with the rocksalt-type high-spin/low-spin order. Our study highlights that the ferroelastic nature of ferromagnetic structural units is important for understanding the intriguing ferromagnetic properties in LCO thin films.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Piezoelectric domain walls in van der Waals antiferroelectric CuInP2Se6

Polar van der Waals chalcogenophosphates exhibit unique properties, such as negative electrostriction and multi-well ferrielectricity, and enable combining dielectric and 2D electronic materials. Using low temperature piezoresponse force microscopy, we revealed coexistence of piezoelectric and non-piezoelectric phases in CuInP2Se6, forming unusual domain walls with enhanced piezoelectric response. From systematic imaging experiments we have inferred the formation of a partially polarized antiferroelectric state, with inclusions of structurally distinct ferrielectric domains enclosed by the corresponding phase boundaries. The assignment is strongly supported by optical spectroscopies and density-functional-theory calculations. Enhanced piezoresponse at the ferrielectric/antiferroelectric phase boundary and the ability to manipulate this entity with electric field on the nanoscale expand the existing phenomenology of functional domain walls. At the same time, phase-coexistence in chalcogenophosphates may lead to rational strategies for incorporation of ferroic functionality into van der Waals heterostructures, with stronger resilience toward detrimental size-effects.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Giant piezoelectricity in oxide thin films with nanopillar structure

High-performance piezoelectric materials are critical components for electromechanical sensors and actuators. For more than 60 years, the main strategy for obtaining large piezoelectric response has been to construct multiphase boundaries, where nanoscale domains with local structural and polar heterogeneity are formed, by tuning complex chemical compositions. We used a different strategy to emulate such local heterogeneity by forming nanopillar regions in perovskite oxide thin films. We obtained a giant effective piezoelectric coefficient d 33 , f * of ~1098 picometers per volt with a high Curie temperature of ~450°C. Our lead-free composition of sodium-deficient sodium niobate contains only three elements (Na, Nb, and O). The formation of local heterogeneity with nanopillars in the perovskite structure could be the basis for a general approach to designing and optimizing various functional materials.

Science & Technology - Other Topics↗

DOE OSTI2022

Direct visualization and control of antiferromagnetic domains and spin reorientation in a parent cuprate

Here, we report magnetic optical second-harmonic generation (SHG) polarimetry and imaging on Sr 2 Cu 3 O 4 Cl 2 , which allows direct visualization of the mesoscopic antiferromagnetic (AFM) structure of a parent cuprate. Temperature- and magnetic-field-dependent SHG reveals large domains with 90° relative orientations that are stabilized by a combination of uniaxial magnetic anisotropy and the Earth's magnetic field. Below a temperature T R ~ 97 K, we observe an unusual 90° spin reorientation transition, possibly driven by competing magnetic anisotropies of the two copper sublattices, which swaps the AFM domain states while preserving the domain structure. This allows deterministic switching of the AFM states by thermal or laser heating. Near T R , the domain walls become exceptionally responsive to an applied magnetic field, with the Earth's field sufficient to completely expel them from the crystal. Our findings unlock opportunities to study the mesoscopic AFM behavior of parent cuprates and explore their potential for AFM technologies.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Asymmetric Character of the Ferroelectric Phase Transition and Charged Domain Walls in a Hybrid Improper Ferroelectric

Abstract In improper ferroelectrics, the spontaneous ordering is typically driven by a structural distortion or a magnetic spin alignment. The induced electric polarization is only a secondary effect. This dependence is a rich source for unusual phenomena and ferroelectric domain configurations for proper, polarization‐driven ferroelectrics. This study focuses on the polar domain structure and the hysteretic behavior at the ferroelectric phase transition in Ca 3 Mn 1.9 Ti 0.1 O 7 as a representative of the recently discovered hybrid improper ferroelectric class of multiferroics. Combining optical second harmonic generation and Raman spectroscopy gives access to the spontaneous structural distortion and the resulting improper electric polarization. This study shows that hybrid improper ferroelectrics contrast proper and improper ferroelectrics in several ways. Most intriguingly, adjacent ferroelectric domains favor head‐to‐head and tail‐to‐tail domain walls over charge‐neutral configurations. Furthermore, the phase transition occurs in an asymmetric fashion. The regime of phase coexistence of the nonpolar and polar phases shows a clear and abrupt upper temperature limit. In contrast, the coexistence toward low temperatures is best described as a fade‐out process, where 100‐nm‐sized islands of the nonpolar phase expand deep into the polar phase.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Cesium exhibits different mesoscale segregation and ion pairing than lithium, sodium, or potassium in concentrated alkaline aqueous nitrite solutions

Understanding ion pairing in concentrated alkaline electrolytes facilitates the prediction and control of chemical processes in nuclear waste. While sodium is the dominant alkali metal in such systems, cesium often exhibits distinct bulk behavior relative to lighter alkali cations. Aqueous mixtures of cesium hydroxide and sodium nitrite were compared to alkali hydroxide analogs using small-angle x-ray scattering, revealing that cesium disrupts the sodium nitrite electrolyte structure, forming cesium-rich domains. This mesoscale segregation contrasts with the near-ideal mixing observed in other mixed hydroxide–nitrite systems. Raman spectroscopy indicates cesium–nitrite ion pairing, evidenced by vibrational shifts distinct from those associated with sodium. Multinuclear magnetic resonance spectroscopy further supports cesium–nitrite and cesium–hydroxide association, revealing a distinct local environment for nitrite in cesium-containing solutions. Together, these findings show that cesium promotes a unique solution structure dominated by specific ion pairing within segregated domains. This structural organization may influence radical generation pathways in high-ionic-strength alkaline media relevant to nuclear waste processing and management.

Nienhuis, Emily T. [Pacific Northwest National Lab↗

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 OSTI2023

Directional effects of antiferromagnetic ordering on the electronic structure in NdSb

The recent discovery of unconventional surface-state pairs, which give rise to Fermi arcs and spin textures, in antiferromagnetically ordered NdBi raised the interest in rare-earth monopnictides. Several scenarios of antiferromagnetic (AFM) order have been suggested to explain the origin of these states with some of them being consistent with the presence of nontrivial topologies. Here, in this paper, we use angle-resolved photoemission spectroscopy (ARPES) and density-functional-theory (DFT) calculations to investigate the electronic structure of NdSb. We found the presence of distinct domains that have different electronic structures at the surface. These domains correspond to different orientations of magnetic moments in the AFM state with respect to the surface. We demonstrated remarkable agreement between DFT calculations and ARPES that capture all essential changes in the band structure caused by the transition to a magnetically ordered state.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Joint Matrix Completion and Compressed Sensing for State Estimation in Low-observable Distribution System

Limited measurement availability at the distribution grid presents challenges for state estimation and situational awareness. This paper combines the advantages of two sparsity-based state estimation approaches (matrix completion and compressive sensing) that have been proposed recently to address the challenge of unobservability. The proposed approach exploits both the low rank structure and a suitable transform domain representation to leverage the correlation structure of the spatio-temporal data matrix while incorporating the powerflow constraints of the distribution grid. Simulations are carried out on three phase unbalanced IEEE 37 test system to verify the effectiveness of the proposed approach. The performance results reveal - (1) the superiority over traditional matrix completion and (2) very low state estimation errors for high compression ratios representing very low observability.

Dahale, Shweta↗

DOE OSTI2025

N-terminal domain swapping: A new paradigm for spermidine/spermine N -acetyltransferase (SSAT) protein structures?

Enterococcus faecalis is a multi-drug-resistant human pathogen that is found in a variety of environments and is challenging to treat. Under stress conditions, some bacteria regulate intracellular polyamine concentrations via polyamine acetyltransferases to reduce their toxicity. The E. faecalis genome encodes two polyamine acetyltransferases: PmvE and BltD. Both of these proteins belong to the Gcn5-related N-acetyltransferase (GNAT) superfamily. It is unclear why there are two enzymes with similar substrate specificities in this organism. To better understand the structure/function relationship of the E. faecalis BltD enzyme, we determined its crystal structure and performed additional assays to explore its oligomeric state and enzymatic activity. The goal was to determine whether there were structural or catalytic differences between this enzyme and other polyamine acetyltransferases that could explain this redundancy and be exploited for future development of targeted inhibitors for this important human pathogen. We found the BltD enzyme was structurally unique due to its N-terminal domain swapped dimer. However, this enzyme adopts a catalytically active monomer rather than dimer in solution. This indicates the crystal structure we obtained may represent a state that forms at high protein and salt concentrations and at low pH used during crystallization. The BltD dimer found in the crystal may represent a unique view of how an inhibitory peptide or molecule could be designed to occupy its active site. Additionally, this structure shows the extensive flexibility of the N-terminal portion of the E. faecalis BltD enzyme.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Integrated structural model of the palladin–actin complex using XL ‐ MS , docking, NMR , and SAXS

Abstract Palladin is an actin‐binding protein that accelerates actin polymerization and is linked to the metastasis of several types of cancer. Previously, three lysine residues in an immunoglobulin‐like domain of palladin have been identified as essential for actin binding. However, it is still unknown where palladin binds to F‐actin. Evidence that palladin binds to the sides of actin filaments to facilitate branching is supported by our previous study showing that palladin was able to compensate for Arp2/3 in the formation of Listeria actin comet tails. Here, we used chemical crosslinking to covalently link palladin and F‐actin residues based on spatial proximity. Samples were then enzymatically digested, separated by liquid chromatography, and analyzed by tandem mass spectrometry. Peptides containing the crosslinks and specific residues involved were then identified for input to the HADDOCK docking server to model the most likely binding conformation. Small‐angle x‐ray scattering was used to provide further insight into palladin flexibility and the binding interface, and NMR spectra identified potential interactions between palladin's Ig domains. Our final structural model of the F‐actin:palladin complex revealed how palladin interacts with and stabilizes F‐actin at the interface between two actin monomers. Three actin residues that were identified in this study also appear commonly in the actin‐binding interface with other proteins such as myotilin, myosin, and tropomodulin. An accurate structural representation of the complex between palladin and actin extends our understanding of palladin's role in promoting cancer metastasis through the regulation of actin dynamics.

Sargent, Rachel [Department of Chemistry and Bioch↗

DOE OSTI2026

Deterministic Fabrication of Large-Area, High-Crystallinity Oxide Moiré Superlattices

Oxide twistronics extends moiré engineering beyond van der Waals materials, offering a promising platform for accessing emergent interfacial phenomena arising from the strong coupling of lattice, charge, and orbital degrees of freedom in complex oxides. However, deterministic fabrication of high-crystallinity oxide moiré superlattices over large lateral dimensions remains challenging due to the three-dimensional bonding network of oxides. Here, we demonstrate a scalable, generalized fabrication strategy that enables the formation of high-crystallinity oxide moiré superlattices with clean, chemically bonded interfaces and precisely controlled twist angles down to nominal values of 0.1°, achieving subdegree twist-angle accuracy across large contiguous lateral dimensions approaching the millimeter scale. Using NaNbO3 as a model system, we show that the resulting interlayer coupling drives pronounced structural reconstruction that modifies both the phase structure and ferroelectric domain configuration. Synchrotron-based X-ray 3D reciprocal space mapping reveals the emergence of a single-phase state in twisted bilayers, in contrast to the mixed-phase structure observed in single-layer membranes prior to twist assembly. The structural signatures are further consistent with gradual lattice rotation distributed along the thickness direction that may accommodate interfacial shear strain, distinct from reconstruction observed in van der Waals moiré systems which primarily occurs through in-plane stacking rearrangement. This collective lattice response is correlated with twist-dependent nanoscale electromechanical modulations observed by piezoresponse force microscopy. These results establish a scalable materials platform for oxide twistronics and support the implementation of twist-engineered functionalities in practical, macroscale device architectures.

Ghanbari, Reza [North Carolina State University (N↗

DOE OSTI2023

Evolution of the Cellulose Microfibril through Gamma-Valerolactone-Assisted Co-Solvent and Enzymatic Hydrolysis

Biomass recalcitrance during deconstruction remains a key bottleneck to affordable biomass processing technologies. A clear connection between the cell wall structure and biomass deconstruction is necessary to understand how lignocellulosic material is broken down to valuable monomeric components. Here, we monitor changes in the cellulose microfibril domains of poplar, sorghum, and switchgrass throughout gamma-valerolactone (GVL)–water co-solvent pretreatment and enzymatic hydrolysis using solid-state 13 C cross-polarization magic angle spinning nuclear magnetic resonance spectroscopy (CP/MAS 13 C-NMR) and wide-angle X-ray scattering (WAXS). Spectral fitting of NMR peaks corresponding to different cellulose microenvironments at the C 4 carbon center suggests that a mildly acidic GVL–water co-solvent pretreatment of poplar leads to nearly full removal of xylan–cellulose linkages, which primes the cellulose for enzymatic attack. The spectral fitting also suggests that the pretreatment causes significant depletion of the inaccessible fibril surface domains with an increase in more thermally stable crystalline resonances (I β ). WAXS confirmed a decrease in the lattice spacing between (200) crystalline planes with increasing co-solvent pretreatment severity. These results are interpreted as an opening of bound microfibril surfaces previously inaccessible to the co-solvent system, which leaves behind a more thermally stable, crystalline domain that is potentially prone to relaxation and recrystallization. Full conversion of residual GVL-pretreated biomass was achieved after the GVL co-solvent pretreatment at 140 °C using a commercial enzyme cocktail, CTec2, which contains different cellulases and other enzymes. Spectral fitting of enzymatically hydrolyzed samples by a single engineered cellulase, CelR, suggests that the residual cellulose recalcitrance is mainly due to the inability of CelR to digest the I β crystalline domain present in pretreated samples. This work helps to provide new information regarding the structure of the cell wall and recalcitrance throughout GVL–water mild acidolysis and CelR enzymatic biomass deconstruction by tracking the evolution of structural domains within the cellulose microfibril. This work further directs recommendations for improving the conversion and sugar yields in future studies. Finally, our findings inform inquiry into larger questions of cellulose recalcitrance through GVL pretreatment and CelR enzymatic hydrolysis and give insight into subsequent required steps for full cellulose conversion with attention to the most recalcitrant cellulose structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Computing diffraction patterns of microstructures from phase-field simulations

The diffraction pattern of a material contains information not only on the crystal structures of its constituting phases, but also on its mesoscale spatial distributions of phases, grains, and ferroelastic, ferroelectric, and ferromagnetic domains. While diffraction patterns from experiments such as X-ray diffraction are presented in the reciprocal or Fourier space, mesoscale microstructure models such as the phase-field method naturally produce real-space images of spatial distribution of chemical composition, structural, and ferroic domains. Although one could rather readily compute the Fourier amplitudes of chemical and structural domain distributions generated by mesoscale simulations, they only contain information about the length scale and alignment of the real-space chemical and structure domains. Therefore, a direct comparison between diffraction experiments and mesoscale microstructure simulations is not possible. Here, we develop a theoretical approach to directly compute the crystal diffraction patterns of microstructures predicted by phase-field simulations. In particular, we consider five representative examples of microstructure patterns involving purely compositional domains, a single pair of tetragonal twin structures, multiple twin variants in a hexagonal system, ferroelectric polar vortices, and polycrystalline grains. The results are compared with previous experimental observations as well as X-ray diffraction experiments performed in the present study. Furthermore, the theoretical framework allows one to directly connect material microstructures and diffraction patterns predicted from phase-field simulations and the corresponding diffraction patterns from experiments, and thus providing guidance to experimental diffraction characterization and interpretation of microstructures.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Structure-based discovery of potent WD repeat domain 5 inhibitors that demonstrate efficacy and safety in preclinical animal models

WD repeat domain 5 (WDR5) is a core scaffolding component of many multiprotein complexes that perform a variety of critical chromatin-centric processes in the nucleus. WDR5 is a component of the mixed lineage leukemia MLL/SET complex and localizes MYC to chromatin at tumor-critical target genes. As a part of these complexes, WDR5 plays a role in sustaining oncogenesis in a variety of human cancers that are often associated with poor prognoses. Thus, WDR5 has been recognized as an attractive therapeutic target for treating both solid and hematological tumors. Previously, small-molecule inhibitors of the WDR5-interaction (WIN) site and WDR5 degraders have demonstrated robust in vitro cellular efficacy in cancer cell lines and established the therapeutic potential of WDR5. However, these agents have not demonstrated significant in vivo efficacy at pharmacologically relevant doses by oral administration in animal disease models. We have discovered WDR5 WIN-site inhibitors that feature bicyclic heteroaryl P 7 units through structure-based design and address the limitations of our previous series of small-molecule inhibitors. Importantly, our lead compounds exhibit enhanced on-target potency, excellent oral pharmacokinetic (PK) profiles, and potent dose-dependent in vivo efficacy in a mouse MV4:11 subcutaneous xenograft model by oral dosing. Furthermore, these in vivo probes show excellent tolerability under a repeated high-dose regimen in rodents to demonstrate the safety of the WDR5 WIN-site inhibition mechanism. Collectively, our results provide strong support for WDR5 WIN-site inhibitors to be utilized as potential anticancer therapeutics.

60 APPLIED LIFE SCIENCES↗