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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 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Crystal structures and functional analysis of the ZnF5-WWE1-WWE2 region of PARP13/ZAP define a distinctive mode of engaging poly(ADP-ribose)

PARP13/ZAP (zinc-finger antiviral protein) acts against multiple viruses by promoting degradation of viral mRNA. PARP13 has four N-terminal zinc (Zn) fingers that bind CG-rich nucleotide sequences, a C-terminal ADP ribosyltransferase fold, and a central region with a fifth Zn finger and tandem WWE domains. The central PARP13 region, ZnF5-WWE1-WWE2, is implicated in binding poly(ADP-ribose); however, there are limited insights into its structure and function. We present crystal structures of ZnF5-WWE1-WWE2 from mouse PARP13 in complex with ADP-ribose and in complex with ATP. The crystal structures and binding studies demonstrate that WWE2 interacts with ADP-ribose and ATP, whereas WWE1 does not have a functional binding site. Binding studies with poly(ADP-ribose) ligands indicate that WWE2 serves as an anchor for preferential binding to the terminal end of poly(ADP-ribose) chains. The composite ZnF5-WWE1-WWE2 structure forms an extended surface to engage ADP-ribose chains, representing a distinctive mode of recognition that provides a framework for investigating the impact of poly(ADP-ribose) on PARP13 function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

An electronic microemulsion phase emerging from a quantum crystal-to-liquid transition

Strongly interacting electronic systems often exhibit a complicated phase diagram that results from the competition between different quantum ground states. One feature of these phase diagrams is the emergence of microemulsion phases, where regions of different phases self-organize across multiple length scales. The experimental characterization of these microemulsions can pose considerable challenges, as the long-range Coulomb interaction microscopically mingles with the competing states. Here we observe the signatures of the microemulsion between an electronic Wigner crystal and an electron liquid in a MoSe 2 monolayer using cryogenic reflectance and magneto-optical spectroscopy. We find that the transition into this microemulsion state is marked by anomalies in exciton reflectance, spin susceptibility and umklapp scattering, establishing it as a distinct phase of electronic matter.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Quantification of Dynamic Scattering Effects in Molecular Crystals using Large Angle Rocking Beam Electron Diffraction

Electron crystallography provides a pathway to solve structure of small crystals (< 1um) in size, and thus overcomes difficult synthesis constraints involved in growing large crystals. Generally, electron diffraction data is collected in the form of integrated intensity using continuous rotation or by precession. The measured intensities in 3D are utilized for structure solution. Using this approach, structure solution of difficult crystals, such as small crystals of zeolites, metal-organic frameworks, molecular crystals, and proteins , can be solved by electron diffraction. However, electron structure solutions are regularly reported with higher Rvalues than x-ray or neutron diffraction. While similar structures are found despite the high R-values, the differences in the measure intensity and theory calculated intensity limit information that can be extracted by electron diffraction. Previous work demonstrated that including multiple-scattering effects significantly reduce the R-values . Thus, it is critical to be able to quantify the dynamical diffraction effects in molecular crystals.

Crystallography↗
DOE OSTI2020

The Convolutional Multiple Whole Profile (CMWP) Fitting Method, a Global Optimization Procedure for Microstructure Determination

The analysis of line broadening in X-ray and neutron diffraction patterns using profile functions constructed on the basis of well-established physical principles and TEM observations of lattice defects has proven to be a powerful tool for characterizing microstructures in crystalline materials. These principles are applied in the convolutional multiple-whole-profile (CMWP) procedure to determine dislocation densities, crystallite size, stacking fault and twin boundary densities, and intergranular strains. The different lattice defect contributions to line broadening are separated by considering the hkl dependence of strain anisotropy, planar defect broadening and peak shifts, and the defect dependent profile shapes. The Levenberg–Marquardt (LM) peak fitting procedure can be used successfully to determine crystal defect types and densities as long as the diffraction patterns are relatively simple. However, in more complicated cases like hexagonal materials or multiple-phase patterns, using the LM procedure alone may cause uncertainties. Here, we extended the CMWP procedure by including a Monte Carlo statistical method where the LM and a Monte Carlo algorithm were combined in an alternating manner. The updated CMWP procedure eliminated uncertainties and provided global optimized parameters of the microstructure in good correlation with electron microscopy methods.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Beyond Magic Barrels: Digital manufacturing for crystallization, process development and optimization of explosive materials: Part II Resveratrol Exemplar

This SAND report summarizes work supported by an Engineering Sciences Research Foundation (ESRF) Lab Directed Research and Development (LDRD) project entitled “Beyond Magic Barrels: Digital manufacturing for crystallization, process development and optimization of explosive materials.” This SAND report is written in two parts with Part 1 discusses recrystallization of our explosive exemplar and Part 2 summarizing our work with recrystallization of resveratrol. We have studied resveratrol recrystallization with a multiscale approach combining experiments, modeling and simulation. At the single crystal scale, microscopy experiments illuminate crystal time-dependent growth rates using advanced image analysis. Bench scale experiments were carried out to look at growth of multiple particles in a small reactor creating thousands of particles and analyzing the results with microscopy and μCT. For the modeling we combine kinetic Monte Carlo (kMC) models with subscale information from density functional theory (DFT) or molecular dynamics. This work is discussed in Part 1 and can also be found in a paper from the project discussing a coarse-grained kMC model specifically developed for resveratrol. For well-mixed systems, we have population balance equations (PBE) linked with species mass conservation forming a set of ordinary differential equations that can be solved quickly. For more complicated geometries, such as the vat crystallization used throughout the complex, a coupled computational fluid dynamic (CFD)/PBE method was developed to account for gradients in temperature and concentration and differences in crystallization rates throughout the domain. These simulations are more complex and require high performance computing. We present results for two cases: 5% seed fast cool with parameters fit to the well-mixed case and 5% seed slow cool using the same parameters. We show reasonable agreement with experiments though are particles are significantly larger than the experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Magnetic ground states of honeycomb lattice Wigner crystals

Lattice Wigner crystal states stabilized by long-range Coulomb interactions have recently been realized in two-dimensional moiré materials. We employ large-scale unrestricted Hartree-Fock techniques to unveil the magnetic phase diagrams of honeycomb lattice Wigner crystals. For the three lattice filling factors with the largest charge gaps, $n=2/3,1/2,1/3$, the magnetic phase diagrams contain multiple phases, including ones with non-collinear and non-coplanar spin arrangements. We discuss magnetization evolution with external magnetic field, which has potential as an experimental signature of exotic spin states. Our theoretical results could potentially be validated in moiré materials formed from group VI transition metal dichalcogenide twisted homobilayers.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Effect of Laser Beam Profile on Rotating Lattice Single Crystal Growth in Sb2S3 Model Glass

Laser heating of chalcogenide glasses has successfully produced rotating lattice single crystals through a solid-solid transformation. To better understand the nature of complex, orientation-dependent lattice rotation, we designed heat profiles of the continuous wave laser by beam shaping, fabricated larger Sb2S3 crystal dots in Sb2S3 glass, and investigated the lattice rotation where the crystal could grow in all radial directions under a circular thermal gradient. The results show that the rate of lattice rotation is highly anisotropic and depends on crystallographic direction. The nature of this rotation is the same in crystals of different orientation relative to the surface. The growth directions that align with the slip planes show the highest rate of rotation and the rotation rate gradually decreases away from this direction. Additionally, the presence of multiple growth directions results in a complicated rotation system. We suggest that the growth front influences the density of dislocations introduced during growth under confinement and thus affects the lattice rotation rate in these crystals.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Mapping nanocrystal orientations via scanning Laue diffraction microscopy for multi-peak Bragg coherent diffraction imaging

The recent commissioning of a movable monochromator at the 34-ID-C endstation of the Advanced Photon Source has vastly simplified the collection of Bragg coherent diffraction imaging (BCDI) data from multiple Bragg peaks of sub-micrometre scale samples. Laue patterns arising from the scattering of a polychromatic beam by arbitrarily oriented nanocrystals permit their crystal orientations to be computed, which are then used for locating and collecting several non-co-linear Bragg reflections. The volumetric six-component strain tensor is then constructed by combining the projected displacement fields that are imaged using each of the measured reflections via iterative phase retrieval algorithms. Complications arise when the sample is heterogeneous in composition and/or when multiple grains of a given lattice structure are simultaneously illuminated by the polychromatic beam. Here, a workflow is established for orienting and mapping nanocrystals on a substrate of a different material using scanning Laue diffraction microscopy. The capabilities of the developed algorithms and procedures with both synthetic and experimental data are demonstrated. The robustness is verified by comparing experimental texture maps obtained with Laue diffraction microscopy at the beamline with maps obtained from electron back-scattering diffraction measurements on the same patch of gold nanocrystals. Such tools provide reliable indexing for both isolated and densely distributed nanocrystals, which are challenging to image in three dimensions with other techniques.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies

Vaccination strategies aimed at maturing broadly neutralizing antibodies (bnAbs) from naïve precursors are hindered by unusual features that characterize these Abs, including insertions and deletions (indels). Longitudinal studies of natural HIV infection cases shed light on the complex processes underlying bnAb development and have suggested a role for superinfection as a potential enhancer of neutralization breadth. Here we describe the development of a potent bnAb lineage that was elicited by two founder viruses to inform vaccine design. The V3-glycan targeting bnAb lineage (PC39-1) was isolated from subtype C-infected IAVI Protocol C elite neutralizer, donor PC39, and is defined by the presence of multiple independent insertions in CDRH1 that range from 1-11 amino acids in length. Memory B cell members of this lineage are predominantly atypical in phenotype yet also span the class-switched and antibody-secreting cell compartments. Development of neutralization breadth occurred concomitantly with extensive recombination between founder viruses before each virus separated into two distinct population “arms” that evolved independently to escape the PC39-1 lineage. Ab crystal structures show an extended CDRH1 that can help stabilize the CDRH3. Overall, these findings suggest that early exposure of the humoral system to multiple related Env molecules could promote the induction of bnAbs by focusing Ab responses to conserved epitopes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Combining Laue diffraction with Bragg coherent diffraction imaging at 34-ID-C

Measurement modalities in Bragg coherent diffraction imaging (BCDI) rely on finding a signal from a single nanoscale crystal object which satisfies the Bragg condition among a large number of arbitrarily oriented nanocrystals. However, even when the signal from a single Bragg reflection with ( hkl ) Miller indices is found, the crystallographic axes on the retrieved three-dimensional (3D) image of the crystal remain unknown, and thus localizing in reciprocal space other Bragg reflections becomes time-consuming or requires good knowledge of the orientation of the crystal. Here, the commissioning of a movable double-bounce Si (111) monochromator at the 34-ID-C endstation of the Advanced Photon Source is reported, which aims at delivering multi-reflection BCDI as a standard tool in a single beamline instrument. The new instrument enables, through rapid switching from monochromatic to broadband (pink) beam, the use of Laue diffraction to determine crystal orientation. With a proper orientation matrix determined for the lattice, one can measure coherent diffraction patterns near multiple Bragg peaks, thus providing sufficient information to image the full strain tensor in 3D. The design, concept of operation, the developed procedures for indexing Laue patterns, and automated measuring of Bragg coherent diffraction data from multiple reflections of the same nanocrystal are discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Development of a scalar-based geometric parameterization approach for the crystal structure landscape of dithienylethene-based crystalline solids

Dithienylethenes (DTEs) are a promising class of organic photoswitches that can be used to create crystalline solids with properties controlled by light. However, the ability of DTEs to adopt multiple conformations, only one of which is photoactive, complicates the rational design of these materials. Herein, the synthesis and structural characterization of 19 crystalline solids containing a single DTE molecule are described. A novel D – D analysis of the molecular geometries obtained from rotational potential energy surface calculations and the ensemble of experimental structures were used to construct a crystal landscape for DTE. Of the 19 crystal structures, 17 contained photoinactive DTE rotamers and only 2 were photoactive. These results highlight the challenges associated with the design of these materials. Overall, the D – D analysis described herein provides rapid, effective and intuitive means of linking the molecular structure to photoactivity that could be applied more broadly to afford a general strategy for producing photoactive diarylethene-based crystalline solids.

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

Protein-ligand binding affinity prediction using multi-instance learning with docking structures

Recent advances in 3D structure-based deep learning approaches demonstrate improved accuracy in predicting protein-ligand binding affinity in drug discovery. These methods complement physics-based computational modeling such as molecular docking for virtual high-throughput screening. Despite recent advances and improved predictive performance, most methods in this category primarily rely on utilizing co-crystal complex structures and experimentally measured binding affinities as both input and output data for model training. Nevertheless, co-crystal complex structures are not readily available and the inaccurate predicted structures from molecular docking can degrade the accuracy of the machine learning methods. We introduce a novel structure-based inference method utilizing multiple molecular docking poses for each complex entity. Our proposed method employs multi-instance learning with an attention network to predict binding affinity from a collection of docking poses. We validate our method using multiple datasets, including PDBbind and compounds targeting the main protease of SARS-CoV-2. The results demonstrate that our method leveraging docking poses is competitive with other state-of-the-art inference models that depend on co-crystal structures. This method offers binding affinity prediction without requiring co-crystal structures, thereby increasing its applicability to protein targets lacking such data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Dislocation density-based plasticity model from massive discrete dislocation dynamics database

In this work, we present a dislocation density-based strain hardening model for single crystal copper through a systematic coarse-graining analysis of more than 200 discrete dislocation dynamics (DDD) simulations of plastic deformation under uniaxial tension. The proposed constitutive model has two components: a generalized Taylor relation connecting resolved shear stresses to dislocation densities on individual slip systems, and a generalized Kocks-Mecking model for dislocation multiplication. The DDD data strongly suggests a logarithmic dependence of flow stress on the plastic shear strain rate on each slip system, and, equivalently, an exponential dependence of the plastic shear strain rate on the resolved shear stress. Hence the proposed generalized Taylor relation subsumes the Orowan relation for plastic flow. The DDD data also calls for a correction to the Kocks-Mecking model of dislocation multiplication to account for the increase of dislocation density on slip systems with negligible plastic shear strain rate. This is accomplished by allowing the multiplication rate on each slip system to include contributions from the plastic strain rates of the two coplanar slip systems. The resulting constitutive model successfully captures the strain hardening rate dependence on the loading orientation as predicted by the DDD simulations, which is also consistent with existing experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Optical second harmonic generation in anisotropic multilayers with complete multireflection of linear and nonlinear waves using ♯SHAARP.ml package

Abstract Optical second harmonic generation (SHG) is a nonlinear optical effect widely used for nonlinear optical microscopy and laser frequency conversion. Closed-form analytical solution of the nonlinear optical responses is essential for evaluating materials whose optical properties are unknown a priori. A recent open-source code, ♯SHAARP. si , can provide such closed form solutions for crystals with arbitrary symmetries, orientations, and anisotropic properties at a single interface. However, optical components are often in the form of slabs, thin films on substrates, and multilayer heterostructures with multiple reflections of both the fundamental and up to ten different SHG waves at each interface, adding significant complexity. Many approximations have therefore been employed in the existing analytical approaches, such as slowly varying approximation, weak reflection of the nonlinear polarization, transparent medium, high crystallographic symmetry, Kleinman symmetry, easy crystal orientation along a high-symmetry direction, phase matching conditions and negligible interference among nonlinear waves, which may lead to large errors in the reported material properties. To avoid these approximations, we have developed an open-source package named Second Harmonic Analysis of Anisotropic Rotational Polarimetry in Multilayers (♯SHAARP. ml ). The reliability and accuracy are established by experimentally benchmarking with both the SHG polarimetry and Maker fringes using standard and commonly used nonlinear optical materials as well as twisted 2-dimensional heterostructures.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Space-tiled colloidal crystals from DNA-forced shape-complementary polyhedra pairing

Generating space-filling arrangements of most discrete polyhedra nanostructures of the same shape is not possible. However, if the appropriate individual building blocks are selected (e.g., cubes), or multiple shapes of the appropriate dimensions are matched (e.g., octahedra and tetrahedra) and their pairing interactions are subsequently forced, space-filled architectures may be possible. With flexible molecular ligands (polyethylene glycol–modified DNA), the shape of a polyhedral nanoparticle can be deliberately altered and used to realize geometries that favor space tessellation. In this work, 10 new colloidal crystals were synthesized from DNA-modified nanocrystal building blocks that differed in shapes and sizes, designed to form space-filling architectures with micron-scale dimensions. The insights and capabilities provided by this new strategy substantially expand the scope of colloidal crystals possible and provide an expanded tool kit for researchers interested in designing metamaterials.

Science & Technology - Other Topics↗
DOE OSTI2026

Substrate-Directed Dimensional and Phase Control of Peptide Assemblies on Two-Dimensional van der Waals Materials

Understanding and controlling biomolecular self-assembly on van der Waals (vdW) materials has the potential to advance hybrid bioelectronic devices by enabling precise tuning of the interface and modulation of the resulting electronic properties of the biomolecule-vdW heterostructure. However, how surface properties of vdW materials direct biomolecule assembly remains poorly understood. To fill this knowledge gap, we investigated the assembly of a peptide known to assemble into two-dimensional (2D) crystalline films on MoS 2 on three representative vdW surfaces: WS 2 , MoS 2 , and highly oriented pyrolytic graphite (HOPG). Using in situ atomic force microscopy (AFM), we find that assembly is substrate-dependent, resulting in multilayers on WS 2 , monolayers on MoS 2 , and multiple coexisting phases on HOPG. WS 2 exhibits a higher negative charge, strong long-range electrostatic interactions, and extensive hydration layering that may promote multilayer stacking. In contrast, MoS 2 has stronger short-range interactions with the peptides but much weaker long-range interactions and hydration structure, which may favor monolayer formation. Molecular dynamics simulations predict a corresponding switch from monolayer to multilayer aggregates of the adsorbed monomers, reflected in their relative mobilities. On hydrophobic HOPG, the peptides bind most strongly and remain as monomers with high surface mobility. The peptide dimers comprising the basic unit of the crystals are more compact on HOPG, which has a smaller lattice constant than WS 2 or MoS 2 , suggesting strain contributes to stabilizing multiple phases. Our results provide mechanistic insights into how surface charge and hydration structure, and the lattice structure of the substrates governs peptide assembly on vdW materials, offering a framework to rationally control the 2D peptide-vdW heterostructures.

Molecular dynamics simulations↗
DOE OSTI2025

Orientation-Dependent Nanomechanical Behavior of Pentaerythritol Tetranitrate as Probed by Multiple Nanoindentation Tip Geometries

Nanoindentation can be leveraged to aid in the high fidelity modeling of dislocation mediated plasticity in pentaerythritol tetranitrate (PETN), an anisotropic energetic molecular crystal. Moreover, nanoindentation tip parameters such as tip geometry, size, and degree of acuity can be utilized to target anisotropic behavior. In this work, nanoindentation was conducted across a range of orientations on the (110) face of PETN to characterize resultant yield behavior, mechanical property measurements, and resultant slip behavior and fracture initiation. Three different indentation tips were utilized: a 3-sided pyramidal Berkovich tip, a 4-sided high aspect ratio Knoop tip, and a 90° conical tip. Ultimately, indenter tip radius was documented to impact yield behavior, whereas tip geometry affected larger scale processes such as slip, and tip acuity was the dominating factor that led to fracture. The axisymmetric conical tip, serving as a baseline, showed the least amount of variation in mechanical property measurements but also the largest distribution of maximum shear stress at which initial yielding occurred. Its high degree of acuity, however, was more prone to induce fracture at higher loads. The Knoop tip was shown to be suitable for average measurements, but also for elucidation of certain anisotropic features. A distinctly higher perceived hardness at 45° was measured with the Knoop tip, indicating less dislocation motion in that direction also observed in this work via scanning probe microscopy. Lastly, the commonly used Berkovich tip was a good compromise whereby it provided a representative volume element describing the average behavior of the material. These results can be utilized to target desired anisotropic behavior in a wider range of molecular crystals, as well as to inform theoretical considerations for dislocation mediated plasticity in PETN.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Thermal transport across nanoscale damage profile in sapphire irradiated by swift heavy ions

In this work, we studied the degradation of thermal conductivity in single crystal sapphire (α-Al 2 O 3 ) irradiated by 167 MeV Xe swift heavy ions (SHIs) over the multiple fluences in the range of 10 12 –10 14 ions/cm 2 . Thermal conductivity was measured primarily in the cross-plane direction using a noncontact ultrafast optical pump-probe technique called picosecond time domain thermoreflectance (TDTR). Multiple samples with variable ion fluences allowed us to probe distinct regions resulting from different regimes of microstructure evolution caused by electronic energy loss. By tuning the penetration depth of the thermal waves using different modulation frequencies, two regions with distinct conductivities were identified and the values of which were found to be consistent with phonon-mediated thermal transport models while the microstructure was confirmed by electron microscopy characterization. These damaged regions were determined to be a several micrometer thick ion track region and several tens of nanometer-thick amorphous layer present only above 5.0 × 10 13 ions/cm 2 . These results demonstrate the applicability of TDTR to resolve thermal transport behavior in SHI irradiated oxides having nonhomogeneous damage profile on a nanometer scale. The presented approach facilitates future studies aiming at resolving the impact of distinct damage resulting from electronic and nuclear stopping regimes under irradiation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗