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DOE OSTI2019

Effects of α-tubulin acetylation on microtubule structure and stability

Acetylation of K40 in α-tubulin is the sole posttranslational modification to mark the luminal surface of microtubules. It is still controversial whether its relationship with microtubule stabilization is correlative or causative. We have obtained high-resolution cryo-electron microscopy (cryo-EM) reconstructions of pure samples of αTAT1-acetylated and SIRT2-deacetylated microtubules to visualize the structural consequences of this modification and reveal its potential for influencing the larger assembly properties of microtubules. We modeled the conformational ensembles of the unmodified and acetylated states by using the experimental cryo-EM density as a structural restraint in molecular dynamics simulations. We found that acetylation alters the conformational landscape of the flexible loop that contains αK40. Modification of αK40 reduces the disorder of the loop and restricts the states that it samples. We propose that the change in conformational sampling that we describe, at a location very close to the lateral contacts site, is likely to affect microtubule stability and function.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1991

Infrared spectral studies of asteroids

The research objective was to improve the understanding of the surface mineralogy of asteroids and to link the vast existing body of meteorite geochemical data with specific astronomical objects which may be the targets of future NASA missions. The methodology used is as follow: (1) to use advanced astronomical instrumentation to obtain reflection spectra in the 0.3 to 5.2 micron wavelength range of selected asteroids; (2) to compare the asteroid data with similar data on simulated asteroid regoliths of various compositions to determine the surface mineralogy and meteoritic affinities of asteroid spectral classes and specific asteroids; (3) to integrate the mineralogical information with other astronomical data, orbital dynamics studies, and meteoritic geochemistry data to reconstruct the condensational, thermal, and collisional history of the present asteroids and their parent planetesimals; and (4) to use the information obtained to assist planning of future NASA asteroid missions such as Galileo and CRAF.

Bell, Jeffrey F.↗

NASA NTRS1992

Performance effects resulting from plugged liquid oxygen posts of the Space Shuttle Main Engine Injector

The paper discusses the performance effects resulting from plugged LOX posts of the Space Shuttle Main Engine Injector. The simulation was performed with the REFLEQS 2-D code. Analysis was performed axisymmetrically and injector surface was divided into several regions to account for the mixture ratio variation on the injector surface. The reduction of vaccum specific impulse was approximately 0.01 second per plugged LOX post. This reduction is an order of magnitude higher than the result of Space Shuttle flight reconstruction data. It is presumed that this overprediction is due to the axisymmetric simulation that smears local effects.

Kim, S.↗

NASA NTRS2003

Revisiting the Least-squares Procedure for Gradient Reconstruction on Unstructured Meshes

The accuracy of the least-squares technique for gradient reconstruction on unstructured meshes is examined. While least-squares techniques produce accurate results on arbitrary isotropic unstructured meshes, serious difficulties exist for highly stretched meshes in the presence of surface curvature. In these situations, gradients are typically under-estimated by up to an order of magnitude. For vertex-based discretizations on triangular and quadrilateral meshes, and cell-centered discretizations on quadrilateral meshes, accuracy can be recovered using an inverse distance weighting in the least-squares construction. For cell-centered discretizations on triangles, both the unweighted and weighted least-squares constructions fail to provide suitable gradient estimates for highly stretched curved meshes. Good overall flow solution accuracy can be retained in spite of poor gradient estimates, due to the presence of flow alignment in exactly the same regions where the poor gradient accuracy is observed. However, the use of entropy fixes has the potential for generating large but subtle discretization errors.

Mavriplis, Dimitri J.↗

NASA NTRS2004

Inverse FEM for Full-Field Reconstruction of Elastic Deformations in Shear Deformable Plates and Shells

The inverse problem of real-time reconstruction of full-field structural displacements is addressed through the application of a new variational formulation leading to versatile, robust and computationally efficient inverse shell finite element analysis. Utilizing surface strain measurements from strain sensors mounted on the load-carrying structural components, the methodology enables accurate computations of the three-dimensional displacement field. This high fidelity computational technology is essential for providing feedback to the actuation and control systems of the next generation of aerospace vehicles.

Tessler, Alexander↗

NASA NTRS2007

A Time-Accurate Upwind Unstructured Finite Volume Method for Compressible Flow with Cure of Pathological Behaviors

A time-accurate, upwind, finite volume method for computing compressible flows on unstructured grids is presented. The method is second order accurate in space and time and yields high resolution in the presence of discontinuities. For efficiency, the Roe approximate Riemann solver with an entropy correction is employed. In the basic Euler/Navier-Stokes scheme, many concepts of high order upwind schemes are adopted: the surface flux integrals are carefully treated, a Cauchy-Kowalewski time-stepping scheme is used in the time-marching stage, and a multidimensional limiter is applied in the reconstruction stage. However even with these up-to-date improvements, the basic upwind scheme is still plagued by the so-called "pathological behaviors," e.g., the carbuncle phenomenon, the expansion shock, etc. A solution to these limitations is presented which uses a very simple dissipation model while still preserving second order accuracy. This scheme is referred to as the enhanced time-accurate upwind (ETAU) scheme in this paper. The unstructured grid capability renders flexibility for use in complex geometry; and the present ETAU Euler/Navier-Stokes scheme is capable of handling a broad spectrum of flow regimes from high supersonic to subsonic at very low Mach number, appropriate for both CFD (computational fluid dynamics) and CAA (computational aeroacoustics). Numerous examples are included to demonstrate the robustness of the methods.

Loh, Ching Y.↗

DOE OSTI2016

Three-Dimensional FIB/EBSD Characterization of Irradiated HfAl3-Al Composite

A thermal neutron absorbing material, comprised of 28.4 vol% HfAl3 in an Al matrix, was developed to serve as a conductively cooled thermal neutron filter to enable fast flux materials and fuels testing in a pressurized water reactor. In order to observe the microstructural change of the HfAl3-Al composite due to neutron irradiation, an EBSD-FIB characterization approach is developed and presented in this paper. Using the focused ion beam (FIB), the sample was fabricated to 25µm × 25µm × 20 µm and mounted on the grid. A series of operations were carried out repetitively on the sample top surface to prepare it for scanning electron microscopy (SEM). First, a ~100-nm layer was removed by high voltage FIB milling. Then, several cleaning passes were performed on the newly exposed surface using low voltage FIB milling to improve the SEM image quality. Last, the surface was scanned by Electron Backscattering Diffraction (EBSD) to obtain the two-dimensional image. After 50 to 100 two-dimensional images were collected, the images were stacked to reconstruct a three-dimensional model using DREAM.3D software. Two such reconstructed three-dimensional models were obtained from samples of the original and post-irradiation HfAl3-Al composite respectively, from which the most significant microstructural change caused by neutron irradiation apparently is the size reduction of both HfAl3 and Al grains. The possible reason is the thermal expansion and related thermal strain from the thermal neutron absorption. This technique can be applied to three-dimensional microstructure characterization of irradiated materials.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2021

Earth as a Proxy Exoplanet: Deconstructing and Reconstructing Spectrophotometric Light Curves

Point-source spectrophotometric (single-point) light curves of Earth-like planets contain a surprising amount of information about the spatial features of those worlds. Spatially resolving these light curves is important for assessing time-varying surface features and the existence of an atmosphere, which in turn is critical to life on Earth and significant for determining habitability on exoplanets. Given that Earth is the only celestial body confirmed to harbor life, treating it as a proxy exoplanet by analyzing time-resolved spectral images provides a benchmark in the search for habitable exoplanets. The Earth Polychromatic Imaging Camera (EPIC) on the Deep Space Climate Observatory (DSCOVR) provides such an opportunity, with observations of ∼5000 full-disk sunlit Earth images each year at 10 wavelengths with high temporal frequency. We disk-integrate these spectral images to create single-point light curves and decompose them into principal components (PCs). Using machine-learning techniques to relate the PCs to six preselected spatial features, we find that the first and fourth PCs of the single-point light curves, contributing ∼83.23% of the light-curve variability, contain information about low and high clouds, respectively. Surface information relevant to the contrast between land and ocean reflectance is contained in the second PC, while individual land subtypes are not easily distinguishable (<0.1% total light-curve variation). We build an Earth model by systematically altering the spatial features to derive causal relationships to the PCs. This model can serve as a baseline for analyzing Earth-like exoplanets and guide wavelength selection and sampling strategies for future observations.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2017

Macrophage infiltration regulates the adipose ECM reconstruction and the fibrosis process after fat grafting

Background: Fat grafting experiences a regeneration process from free lipoaspirate to intact adipose tissue. The adipose extracellular matrixes (ECM) provide the structure and biochemical support for surrounding cells; inflammatory cells, like macrophages, regulate the process. Our hypothesis states that transferred fat undergoes ECM remodeling after fat grafting and this process is regulated by macrophage infiltration. Methods: Lipoaspirate was injected subcutaneously into the back of nude mice. The micro-structure of the fat grafts was observed and evaluated using scanning electron microscope (SEM) and collagen I immunohistostaining. The gene transcription level of collagen proteins and the matrix metalloproteinases (MMPs) were assessed by qRT-PCR. Local injection of clodronate-encapsulated liposome was used to evaluate the role of macrophages of fat grafts at different stages in ECM remodeling, depletion of macrophages, at different time points (Week 1 and Week 4). Results: Results from the SEM analysis showed that liposuction caused severe damage to the ECM structure in freshly aspirated adipose tissue. On Day 1 post-transplantation, the surface of adipocytes was covered with platelets and this secreted fibrin network on the fat grafts. An integral adipose structure was already established with an intact ECM at the end of Week 1. The early depletion of macrophages remarkably hindered ECM reconstruction process by down-regulating the expression of collagen proteins and MMPs. Expression of Collagen I was significantly decreased after depletion of macrophages in both gene and protein levels. Results also showed that the depletion of macrophages at the later stage of fat grafting resulted in less fibrosis and capsule formation. Conclusion: Free fat aspirates undergo a prompt ECM reconstruction process and completed in the first week; this process can be initiated with platelets and mainly modulated by inflammatory cells such as macrophages. It was also observed that prolonged macrophage infiltration contributes to fibrosis and capsule formation in fat grafts. - Highlights: • Free fat aspirates undergo a prompt ECM reconstruction process in the first week. • The ECM reconstruction process is initiated with platelets and modulated by macrophages. • Depletion of macrophage in transferred fat resulted in delayed ECM reconstruction.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Imaging the magnetic nanowire cross section and magnetic ordering within a suspended 3D artificial spin-ice

Artificial spin-ice systems are patterned arrays of magnetic nanoislands arranged into frustrated geometries and provide insight into the physics of ordering and emergence. The majority of these systems have been realized in two-dimensions, mainly due to the ease of fabrication, but with recent developments in advanced nanolithography, three-dimensional artificial spin ice (ASI) structures have become possible, providing a new paradigm in their study. Such artificially engineered 3D systems provide new opportunities in realizing tunable ground states, new domain wall topologies, monopole propagation, and advanced device concepts, such as magnetic racetrack memory. Direct imaging of 3DASI structures with magnetic force microscopy has thus far been key to probing the physics of these systems but is limited in both the depth of measurement and resolution, ultimately restricting measurement to the uppermost layers of the system. In this work, a method is developed to fabricate 3DASI lattices over an aperture using two-photon lithography, thermal evaporation, and oxygen plasma exposure, allowing the probe of element-specific structural and magnetic information using soft x-ray microscopy with x-ray magnetic circular dichroism (XMCD) as magnetic contrast. The suspended polymer–permalloy lattices are found to be stable under repeated soft x-ray exposure. Analysis of the x-ray absorption signal allows the complex cross section of the magnetic nanowires to be reconstructed and demonstrates a crescent-shaped geometry. Measurement of the XMCD images after the application of an in-plane field suggests a decrease in magnetic moment on the lattice surface due to oxidation, while a measurable signal is retained on sub-lattices below the surface.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Modeling MTS pyrolysis and SiC deposition kinetics using principal component analysis and neural networks

Accurate chemical kinetics modeling is crucial for improving the efficiency of chemical processing and synthesis of ceramic matrix composites. Detailed kinetic models are computationally expensive due to the large number of transported chemical species, while the simplified physics-based models, such as single-step global mechanisms, are efficient but often overlook key chemical intermediates and pathways. Recent deep learning approaches promise accurate and cost-effective models. Yet, they require additional closures for the transported nonlinear latent variables, complicating integration with existing solvers. In this work, we develop a hybrid linear—nonlinear reduced model for silicon carbide deposition from methyltrichlorosilane precursor by combining principal component analysis (PCA) and autoencoder (AE) neural network (NN) approaches. PCA is used to identify a smaller set of linear transport variables, enabling direct reuse of conventional transport solvers. NNs then reconstruct the full chemical state from these reduced variables. We demonstrate the method on a chemical vapor deposition reactor—comprising a gas-phase pyrolysis plug flow reactor and a heterogeneous surface reactor—over a wide range of temperatures, pressures, and residence times. Our PCA–AE model achieves high accuracy with only five transported scalars, achieving an eightfold cost reduction compared to detailed mechanisms, in both a priori (using data from the test set only) and a posteriori (coupled with a differential equation solver). In conclusion, notable errors arise primarily near training domain boundaries and for long residence times, indicating the need for domain shift indicators and better long-horizon predictions in future reduced chemistry model development.

autoencoder neural networks↗

DOE OSTI2016

Polyhedral 3D structure of human plasma very low density lipoproteins by individual particle cryo-electron tomography

Human VLDLs assembled in the liver and secreted into the circulation supply energy to peripheral tissues. VLDL lipolysis yields atherogenic LDLs and VLDL remnants that strongly correlate with CVD. Although the composition of VLDL particles has been well-characterized, their 3D structure is elusive because of their variations in size, heterogeneity in composition, structural flexibility, and mobility in solution. Here, we employed cryo-electron microscopy and individual-particle electron tomography to study the 3D structure of individual VLDL particles (without averaging) at both below and above their lipid phase transition temperatures. The 3D reconstructions of VLDL and VLDL bound to antibodies revealed an unexpected polyhedral shape, in contrast to the generally accepted model of a spherical emulsion-like particle. The smaller curvature of surface lipids compared with HDL may also reduce surface hydrophobicity, resulting in lower binding affinity to the hydrophobic distal end of the N-terminal β-barrel domain of cholesteryl ester transfer protein (CETP) compared with HDL. The directional binding of CETP to HDL and VLDL may explain the function of CETP in transferring TGs and cholesteryl esters between these particles. This first visualization of the 3D structure of VLDL could improve our understanding of the role of VLDL in atherogenesis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

ACHILLES-GENIE Interface for Neutrino Simulations, ADRIANO2 Tile Prototype for High-Granularity Dual-Readout Calorimetry

ICARUS (Imaging Cosmic And Rare Underground Signals) is a liquid argon time projection chamber (LArTPC) detector that pursues the sterile neutrino, which relies on accurate simulations of neutrino-argon interactions. REDTOP (Rare Eta Decays To Observe new Physics) is a proposed low-energy, high-intensity meson factory designed to explore rare $\eta$/$\eta'$ meson decays and probe physics beyond the Standard Model. As a next-generation experiment, this requires both accurate simulations and innovative detector technologies. This project contributes to both ICARUS, from a simulation perspective, and REDTOP, from both a simulation and detection perspective, through the event generation of lepton-nucleon interactions and the physical enhancement of the calorimeter technology within the REDTOP detector. We developed an interface between ACHILLES (A CHIcago Land Lepton Event Simulator), a theory-driven lepton-level event generator, and GENIE, a robust event generator framework used for neutrino physics. By incorporating the precise theoretical cross-section calculations of ACHILLES into the experimental realism of GENIE, the interface allows for improved accuracy of neutrino-nucleon simulations, which can be adapted for the proton beam specifications of the REDTOP meson factory as well as for the ICARUS experiment. In parallel, we developed an improved prototype for the ADRIANO2 (A Dual Readout Integrally Active Non-segmented Option) dual-readout calorimeter tiles for the REDTOP detector. To improve the efficiency of the lead-glass tiles trapping Cherenkov light for energy reconstruction and particle identification, we optimized the application of a highly reflective coating. Through viscosity and thickness control, masking, and a custom spray technique, we refined the coating process to reduce surface defects and improve light yield. Together, these efforts strengthen the ICARUS neutrino program and REDTOP's capability of detecting rare decay events.

Visser, Erin [Michigan State U.]↗

DOE OSTI2025

Enhancing ICARUS and REDTOP Software and Hardware: Event Generator Interface Development and Calorimeter Tile Prototype

Visser, Erin [Michigan State U.] (ORCID:0009000184↗

DOE OSTI2020

High-speed volumetric imaging of formaldehyde in a lifted turbulent jet flame using an acousto-optic deflector

The development of high-speed volumetric laser-induced fluorescence measurements of formaldehyde (CH 2 O-LIF) using a pulse-burst laser operated at a repetition rate of 100 kHz is presented here. A novel laser scanning system employing an acousto-optic deflector (AOD) enables quasi-4D CH 2 O-LIF imaging at a scan frequency of 10 kHz. The diagnostic capability of time-resolved volumetric imaging is demonstrated in a partially premixed DME/air lifted turbulent jet flame near the flame base. Simultaneous imaging of laser beam profiles is performed to account for the laser pulse energy fluctuation and laser sheet inhomogeneity. With the accurate registration of laser sheet positions, the volumetric reconstruction of CH 2 O-LIF signals is performed within a detection volume of 17.3 × 11.9 × 2.3 mm 3 with an average out-of-plane spatial resolution of 250μm. A surface detection algorithm with adaptive thresholding is used to determine the global maximum intensity gradient by calculating gradient percentiles. The flame topology characteristics are investigated by evaluating the 3D curvatures of CH 2 O surfaces. Curvatures calculated using 2D data systematically underestimate the full 3D curvature due to the lack of out-of-plane information. The inner surfaces near the turbulent fuel jet exhibit higher probabilities of large mean curvature than the outer surfaces. The saddle and cylindrical structures are dominant on both the inner and outer surfaces and the elliptic structures occur with lower probability. The results suggest that the damping of turbulent fluctuations by the temperature increase through the CH 2 O region reduces the curvature, but the local structure topology remains self-similar.

42 ENGINEERING↗

DOE OSTI2024

The use of digital thread for reconstruction of local fiber orientation in a compression molded pin bracket via deep learning

A deep convolutional neural network (DCNN) was used for microstructure reconstruction using artificial intelligence (MR-AI) by predicting local average fiber orientation distributions (FOD) in a 3D prepreg platelet molded composite (PPMC) pin bracket. To train the MR-AI model, surface strain fields from residual stresses simulated in PPMC plates were used as the input to the DCNN. A training dataset included PPMC plates with various degrees of global fiber alignment, based on the information obtained from high-fidelity flow simulation of a pin bracket. Further, the MR-AI model was then deployed to analyze FOD in the 3D pin bracket by conducting thermo-elastic residual stress analysis. Initially, the MR-AI model was established entirely on the synthetic simulation data. Then, a μCT scan of a physically molded pin bracket was used to create a finite element model that provided data for additional validation of the DCNN model. For the μCT scan finite element pin bracket the MR-AI model predicted the distribution of fiber orientation tensor components with MAE of 0.10 indicating a global prediction error of 10%. For the flow simulated pin bracket, the MR-AI model predicted the distribution of fiber orientation tensor components with a global prediction error of 11%. The MR-AI model showed the ability to predict regions of varying alignment in the base and flange of the pin bracket. The proposed MR-AI methodology allows for rapid prediction of FOD in geometrically complex parts and offers a promising path to detecting unique fiber orientation states in molded components.

42 ENGINEERING↗

DOE OSTI2016

Surface energies of elemental crystals

The surface energy is a fundamental property of the different facets of a crystal that is crucial to the understanding of various phenomena like surface segregation, roughening, catalytic activity, and the crystal's equilibrium shape. Such surface phenomena are especially important at the nanoscale, where the large surface area to volume ratios lead to properties that are significantly different from the bulk. Here, we present the largest database of calculated surface energies for elemental crystals to date. This database contains the surface energies of more than 100 polymorphs of about 70 elements, up to a maximum Miller index of two and three for non-cubic and cubic crystals, respectively. Well-known reconstruction schemes are also accounted for. The database is systematically improvable and has been rigorously validated against previous experimental and computational data where available. We will describe the methodology used in constructing the database, and how it can be accessed for further studies and design of materials.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Light-tight Skipper-CCDs for X-Ray Detection in Space

Skipper Charge-Coupled Devices (skipper-CCDs) are pixelated silicon detectors with deep sub-electron resolution. Their radiation hardness and capability to reconstruct energy deposits with unprecedented precision make them a promising technology for space-based X-ray astronomy. In this scenario, optical and near-infrared photons may saturate the sensor, distorting the reconstructed signal. We present a light-tight shield for skipper-CCDs to suppress optical backgrounds while preserving X-ray detection efficiency. We deposited thin aluminum layers on the CCD surface using an e-beam evaporator and evaluated their blinding performance across wavelengths from 650 to 1000 nm using a monochromator, as well as the X-ray transmission using an 55 Fe source. We find that 50 and 100 nm layers provide >99.6% light suppression, with no efficiency loss for 5.9 and 6.4 keV X-rays. In addition, we used Geant4 simulations to extend these results to a broader energy range and quantify the efficiency loss for different aluminum thicknesses. Results show that thin aluminum coatings are an effective, low-cost solution for optical suppression in skipper-CCDs intended for X-ray detection and space instrumentation.

79 ASTRONOMY AND ASTROPHYSICS↗