Evolution of the structure of ferredoxin based on living relics of primitive amino acid sequences.
Paleogenetic study of ferredoxin structure, reconstructing evolution from amino acid sequence
GENETIC CODE↗
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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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3D reconstruction methods of coronal structures by radio observations
The ability to carry out the three dimensional (3D) reconstruction of structures in the solar corona would represent a major advance in the study of the physical properties in active regions and in flares. Methods which allow a geometric reconstruction of quasistationary coronal structures (for example active region loops) or dynamic structures (for example flaring loops) are described: stereoscopy of multi-day imaging observations by the VLA (Very Large Array); tomography of optically thin emission (in radio or soft x-rays); multifrequency band imaging by the VLA; and tracing of magnetic field lines by propagating electron beams.
Aschwanden, Markus J.↗
Measurement of electronic structure and surface reconstruction in the superionic Cu 2-x Te
Recently, layered copper chalcogenides Cu 2 X family (X=S, Se, Te) has attracted tremendous research interests due to their high thermoelectric performance, which is partly due to the superionic behavior of mobile Cu ions, making these compounds "phonon liquids."Here, we systematically investigate the electronic structure and its temperature evolution of the less studied single crystal Cu 2-x Te by the combination of angle resolved photoemission spectroscopy (ARPES) and scanning tunneling microscope/spectroscopy (STM/STS) experiments. While the band structure of the Cu 2-x Te shows agreement with the calculations, we clearly observe a 2×2 surface reconstruction from both our low temperature ARPES and STM/STS experiments which survives up to room temperature. Interestingly, our low temperature STM experiments further reveal multiple types of reconstruction patterns, which suggests the origin of the surface reconstruction being the distributed deficiency of liquidlike Cu ions. Our findings reveal the electronic structure and impurity level of Cu 2 Te, which provides knowledge about its thermoelectric properties from the electronic degree of freedom.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Reconstructing the spatial structure of quantum correlations in materials
Quantum correlations are a fundamental property of quantum many-body states. Yet they remain experimentally elusive, hindering certification of genuine quantum behavior, especially in quantum materials. Here we show that the momentum-dependent dynamical susceptibility measured via inelastic neutron scattering enables the systematic reconstruction of a general family of quantum correlation functions, which express the degree of quantum coherence in the fluctuations of two spins at an arbitrary mutual distance. Using neutron scattering data for the compound KCuF 3 —a system of weakly coupled S = 1 / 2 Heisenberg chains—and numerically exact quantum Monte Carlo data, we show that quantum correlations possess a radically different spatial structure with respect to conventional correlations. Indeed, they exhibit a different emergent length scale—the quantum coherence length—which is finite at any finite temperature (including when long-range magnetic order develops). Moreover, we show theoretically that coupled Heisenberg spin chains exhibit a form of quantum monogamy, with a trade-off between quantum correlations along and transverse to the spin chains. These results highlight real-space quantum correlators as an informative, model-independent means of probing the underlying quantum state of real quantum materials. Published by the American Physical Society 2024
36 MATERIALS SCIENCE↗
Evaluation of Electron Tomography Capabilities for Shale Imaging
Despite the advantageous resolution of electron tomography (ET), reconstruction of three-dimensional (3D) images from multiple two-dimensional (2D) projections presents several challenges, including small signal-to-noise ratios, and a limited projection range. This study evaluates the capabilities of ET for thin sections of shale, a complex nanoporous medium. A numerical phantom with 1.24 nm pixel size is constructed based on the tomographic reconstruction of a Barnett shale. A dataset of 2D projection images is numerically generated from the 3D phantom and studied over a range of conditions. First, common reconstruction techniques are used to reconstruct the shale structure. The reconstruction uncertainty is quantified by comparing overall values of storage and transport metrics, as well as the misclassification of pore voxels compared to the phantom. We then select the most robust reconstruction technique and we vary the acquisition conditions to quantify the effect of artifacts. We find a strong agreement for large pores over the different acquisition workflows, while a wider variability exists for nanometer-scale features. Furthermore, the limited projection range and reconstruction are identified as the main experimental bottlenecks, thereby suggesting that sample thinning, advanced holders, and advanced reconstruction algorithms offer opportunities for improvement.
3D scanning transmission electron microscopy↗
Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts
Abstract Predicting the quaternary structure of protein complex is an important problem. Inter‐chain residue‐residue contact prediction can provide useful information to guide the ab initio reconstruction of quaternary structures. However, few methods have been developed to build quaternary structures from predicted inter‐chain contacts. Here, we develop the first method based on gradient descent optimization (GD) to build quaternary structures of protein dimers utilizing inter‐chain contacts as distance restraints. We evaluate GD on several datasets of homodimers and heterodimers using true/predicted contacts and monomer structures as input. GD consistently performs better than both simulated annealing and Markov Chain Monte Carlo simulation. Starting from an arbitrarily quaternary structure randomly initialized from the tertiary structures of protein chains and using true inter‐chain contacts as input, GD can reconstruct high‐quality structural models for homodimers and heterodimers with average TM‐score ranging from 0.92 to 0.99 and average interface root mean square distance from 0.72 Å to 1.64 Å. On a dataset of 115 homodimers, using predicted inter‐chain contacts as restraints, the average TM‐score of the structural models built by GD is 0.76. For 46% of the homodimers, high‐quality structural models with TM‐score ≥ 0.9 are reconstructed from predicted contacts. There is a strong correlation between the quality of the reconstructed models and the precision and recall of predicted contacts. Only a moderate precision or recall of inter‐chain contact prediction is needed to build good structural models for most homodimers. Moreover, GD improves the quality of quaternary structures predicted by AlphaFold2 on a Critical Assessment of Techniques for Protein Structure Prediction–Critical Assessments of Predictions of Interactions dataset.
59 BASIC BIOLOGICAL SCIENCES↗
Constructing the Coronal Magnetic Field: by Correlating Parameterized Magnetic Field Lines with Observed Coronal Plasma Structures
The reconstruction of the coronal magnetic field is carried out using a perturbation procedure. A set of magnetic field lines generated from magnetogram data is parameterized and then deformed by varying the parameterized values. The coronal fluxtubes associated with this field are adjusted until the correlation between the field lines and the observed coronal loops is maximized. A mathematical formulation is described which ensures (1) that the normal component of the photospheric field remains unchanged, (2) that the field is given in the entire corona, (3) that the field remains divergence free, and (4) that electrical currents are introduced into the field. It is demonstrated that a simple radial parameterization of a potential field, comprising a radial stretching of the field, can provide a match for a simple bipolar active region, AR 7999, which crossed the central meridian on 1996 Nov 26. At a coronal height of 30 km, the resulting magnetic field is a non-force free magnetic field with the maximum Lorentz force being on the order of 2.6 x 10(exp -9) dyn resulting from an electric current density of $0.13 mu A/ sq m. This scheme is an important tool in generating a magnetic field solution consistent with the coronal flux tube observations and the observed photospheric magnetic field.
Gary, G. A.↗
Interface Reconstruction from Ruddlesden–Popper Structures Impacts Stability in Lead Halide Perovskite Solar Cells
The impact of the bulky-cation-modified interfaces on halide perovskite solar cell stability is underexplored. Here, in this work, the thermal instability of the bulky-cation interface layers used in the state-of-the-art solar cells is demonstrated. X-ray photoelectron spectroscopy and synchrotron-based grazing-incidence X-ray scattering measurements reveal significant changes in the chemical composition and structure at the surface of these films that occur under thermal stress. The changes impact charge-carrier dynamics and device operation, as shown in transient photoluminescence, excitation correlation spectroscopy, and solar cells. The type of cation used for surface treatment affects the extent of these changes, where long carbon chains provide more stable interfaces. These results highlight that prolonged annealing of the treated interfaces is critical to enable reliable reporting of performances and to drive the selection of different bulky cations.
36 MATERIALS SCIENCE↗
CryoTransformer: a transformer model for picking protein particles from Cryo-EM micrographs
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of large protein complexes. Picking single protein particles from cryo-EM micrographs (images) is a crucial step in reconstructing protein structures from them. However, the widely used template-based particle picking process requires some manual particle picking and is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) can potentially automate particle picking, the current AI methods pick particles with low precision or low recall. The erroneously picked particles can severely reduce the quality of reconstructed protein structures, especially for the micrographs with low signal-to-noise-ratio (SNR).
59 BASIC BIOLOGICAL SCIENCES↗
Mechanism of structural colors in binary mixtures of nanoparticle-based supraballs
Inspired by structural colors in avian species, various synthetic strategies have been developed to produce noniridescent, saturated colors using nanoparticle assemblies. Nanoparticle mixtures varying in particle chemistry and size have additional emergent properties that affect the color produced. For complex multicomponent systems, understanding the assembled structure and a robust optical modeling tool can empower scientists to identify structure-color relationships and fabricate designer materials with tailored color. Here, we demonstrate how we can reconstruct the assembled structure from small-angle scattering measurements using the computational reverse-engineering analysis for scattering experiments method and use the reconstructed structure in finite-difference time-domain calculations to predict color. We successfully, quantitatively predict experimentally observed color in mixtures containing strongly absorbing nanoparticles and demonstrate the influence of a single layer of segregated nanoparticles on color produced. The versatile computational approach that we present is useful for engineering synthetic materials with desired colors without laborious trial-and-error experiments.
36 MATERIALS SCIENCE↗
Nanotomography for Quantitative 3D Particle Reconstruction
Particulates are ubiquitous across fuel cycle operations and carry critical information about particle formation, processing, and potential proliferation-related activities. Traditional analytical techniques, including micro-Raman spectroscopy and standard electron microscopy, are often limited in spatial resolution or dimensionality, particularly when used to examine metallic or submicron-scale features. Understanding particle morphology, phase distribution, and internal porosity is essential for constraining formation conditions, thermodynamic environments, and material transport behavior. In this report, we demonstrate the application of plasma focused ion beam nanotomography to reconstruct micron-scale particulates at nanoscale resolution. Using high-resolution backscattered electron imaging and Avizo software, we obtained 3D reconstructions that enabled quantitative analysis of particle morphology, phase composition, and internal voids. Representative examples include a Ta particle with a large central void and a composite particle with embedded tetrahedral crystalline structures. These reconstructions reveal structural and compositional details that are inaccessible through conventional 2D imaging. The results demonstrate that nanotomography provides both qualitative and quantitative insights into particle formation and behavior. Using nanotomography, porosity and phase distributions can be quantified to inform models of particle density, transport, and solidification conditions. Beyond technical insights, the workflow developed here establishes a transferable capability for analyzing heterogeneous particles and has potential applications in bulk materials studies via x-ray computed tomography or other volumetric imaging modalities. Ongoing efforts are focused on optimizing the workflow to process multiple particles simultaneously, increasing throughput and statistical robustness. Overall, this work illustrates the power of nanotomography as a tool for connecting particulate morphology to formation mechanisms, composition, and transport, thereby strengthening analytical capabilities for nuclear forensics, fuel cycle analysis, and related scientific investigations.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Three-Dimensional Reconstruction of Defects and Structures in Additively Manufactured Parts with Automated Serial Sectioning
Metal additive manufacturing (AM) processes have been demonstrated to be effective at reducing costs and lead times associated with complex components for space flight applications. Laser powderbed fusion (L-PBF) is a commonly used AM technology due to the ability to produce complex parts with fine feature resolution in a wide variety of alloys and applications. L-PBF, like many other manufacturing processes, can produce minor flaws in parts when in nominal operation as well as process-escape defects when process abnormalities occur. The effects of the flaws and methods of detecting the flaws are a subject of interest to understand the difficulties in detecting these flaws with current technology and how much risk the flaws or defects pose to potential flight parts. Using a RoboMet.3D automated serial sectioning system, seeded defects as well as minor process flaws can be imaged and reconstructed in three dimensions to compare to non-destructive evaluation (NDE) techniques, such as x-ray computed tomography (CT), neutron CT, and in-situ monitoring. The RoboMet automates the metallography process by automatically grinding, polishing, and imaging samples in a single system and providing the control data for NDE comparisons to know the real size of defects built into coupons. These comparisons provide an understanding behind the technological limitations of the NDE techniques for different alloys. The same serial sectioning methods have also been utilized to characterize the surfaces of parts to reconstruct the surfaces and take measurements of internal features not easily examined with non-destructive methods. Using the RoboMet, fine lattice structures built with L-PBF have been characterized to determine the actual thicknesses of struts and density of the lattice structures. These structures have been used as finer build supports for the L-PBF process, designs for fine catalysts, and other design considerations for small components. The RoboMet data helps to inform the modeling and design efforts around these fine components.
additive manufacturing↗
Reconstruction of Cloud Vertical Structure With a Generative Adversarial Network
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Jussi Leinonen↗
Comprehensive characterization of the structure of Zr-based metallic glasses
Structure of metallic glasses fascinates as the generic amorphous structural template for ubiquitous systems. Its specification necessitates determination of the complete hierarchical structure, starting from short-range-order (SRO) → medium-range-order (MRO) → bulk structure and free volume (FV) distribution. This link has largely remained elusive since previous investigations adopted one-technique-at-a-time approach, focusing on limited aspects of any one domain. Reconstruction of structure from experimental data inversion is non-unique for many of these techniques. As a result, complete and precise structural understanding of glass has not emerged yet. In this work, we demonstrate the first experimental pathway for reconstruction of the integrated structure, for and glasses. Our strategy engages diverse (×7) multi-scale techniques [XAFS, 3D-APT, ABED/NBED, FEM, XRD, PAS, FHREM] on the same glass. This strategy complemented mutual limitations of techniques and corroborated common parameters to generate complete, self-consistent and precise parameters. Further, MRO domain size and inter-void separation were correlated to identify the presence of FV at MRO boundaries. This enabled the first experimental reconstruction of hierarchical subset: SRO → MRO → FV → bulk structure. The first ever image of intermediate region between MRO domains emerged from this link. We clarify that determination of all subsets is not our objective; the essence and novelty of this work lies in directing the pathway towards finite solution, in the most logical and unambiguous way.
36 MATERIALS SCIENCE↗
Structure and energetics of the elbows in the Au(111) herringbone reconstruction
We study the structure of the threading edge dislocations, or “elbows,” which are an essential component of the well-known herringbone reconstruction of the (111) surface of Au. Previous work had shown that these dislocations can be stabilized by long-range elastic relaxations into the bulk. However, the validity of the harmonic spring model that had been used to estimate the energies of the dislocations is uncertain. To enable a more refined model of the dislocation energetics, we have imaged the atomic structure of these dislocations using scanning tunneling microscopy. We find that the harmonic spring model does not adequately reproduce the observed structure. We are able to reproduce the structure, however, with a two-dimensional Frenkel-Kontorova (FK) model that uses a pairwise Morse potential to describe the interactions between the top layer Au atoms on a rigid substrate. The parameters of the potential were obtained by fitting the energy of uniaxially compressed phases, or “stripes”, computed with density functional theory, as a function of surface Au density. Within this model, the formation of the threading dislocations remains unfavorable. However, the large forces on the substrate atoms near the threading-dislocation cores, render the assumption of a completely rigid substrate questionable. Indeed, if the FK parameters are modified to account for the relaxation of just one more atomic layer, threading dislocations can, in principle, become favorable, even without bulk elastic relaxations. Additional evidence for a small elbow energy is that our computed change in the Au(111) surface stress tensor caused by the (√ 3 × 22) reconstruction is considerably smaller than previous estimates.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
LoTToR: An Algorithm for Missing-Wedge Correction of the Low-Tilt Tomographic 3D Reconstruction of a Single-Molecule Structure (LoTToR) v1.0
The low-tilt tomographic reconstruction (LoTToR) method is a post-processing method to correct the missing-wedge artifact, which contains a model-free iteration process under a set of constraints in real and reciprocal spaces. A proof of concept is conducted by using the LoTToR on a phantom, i.e., a simulated 3D reconstruction from a low-tilt series of images, including that within a tilt range of ±15°. The method is validated by using both negative-staining (NS) and cryo-electron tomography (cryo-ET) experimental data. A significantly reduced missing-wedge artifact verifies the capability of LoTToR, suggesting a new tool to support the future study of macromolecular dynamics, fluctuation and chemical activity from the viewpoint of single-molecule 3D structure determination. Moreover, the software can be used for hospital computer tomography (CT) to reduce the radiation damage to patients without reducing the CT image quality.
Ren, Gang↗
Shape and Stress Sensing of Multilayered Composite and Sandwich Structures Using an Inverse Finite Element Method
The marked increase in the use of composite and sandwich material systems in aerospace, civil, and marine structures leads to the need for integrated Structural Health Management systems. A key capability to enable such systems is the real-time reconstruction of structural deformations, stresses, and failure criteria that are inferred from in-situ, discrete-location strain measurements. This technology is commonly referred to as shape- and stress-sensing. Presented herein is a computationally efficient shape- and stress-sensing methodology that is ideally suited for applications to laminated composite and sandwich structures. The new approach employs the inverse Finite Element Method (iFEM) as a general framework and the Refined Zigzag Theory (RZT) as the underlying plate theory. A three-node inverse plate finite element is formulated. The element formulation enables robust and efficient modeling of plate structures instrumented with strain sensors that have arbitrary positions. The methodology leads to a set of linear algebraic equations that are solved efficiently for the unknown nodal displacements. These displacements are then used at the finite element level to compute full-field strains, stresses, and failure criteria that are in turn used to assess structural integrity. Numerical results for multilayered, highly heterogeneous laminates demonstrate the unique capability of this new formulation for shape- and stress-sensing.
Cerracchio, Priscilla↗
A large expert-curated cryo-EM image dataset for machine learning protein particle picking
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of biological macromolecular complexes. Picking single-protein particles from cryo-EM micrographs is a crucial step in reconstructing protein structures. However, the widely used template-based particle picking process is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) based particle picking can potentially automate the process, its development is hindered by lack of large, high-quality labelled training data. To address this bottleneck, we present CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for protein particle picking and analysis. It consists of labelled cryo-EM micrographs (images) of 34 representative protein datasets selected from the Electron Microscopy Public Image Archive (EMPIAR). The dataset is 2.6 terabytes and includes 9,893 high-resolution micrographs with labelled protein particle coordinates. The labelling process was rigorously validated through 2D particle class validation and 3D density map validation with the gold standard. The dataset is expected to greatly facilitate the development of both AI and classical methods for automated cryo-EM protein particle picking.
42 ENGINEERING↗