Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “structural alignment”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15

Since the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14), AlphaFold2 has become the standard method for protein tertiary structure prediction. One remaining challenge is to further improve its prediction. We developed a new version of the MULTICOM system to sample diverse multiple sequence alignments (MSAs) and structural templates to improve the input for AlphaFold2 to generate structural models. The models are then ranked by both the pairwise model similarity and AlphaFold2 self-reported model quality score. The top ranked models are refined by a novel structure alignment-based refinement method powered by Foldseek. Moreover, for a monomer target that is a subunit of a protein assembly (complex), MULTICOM integrates tertiary and quaternary structure predictions to account for tertiary structural changes induced by protein-protein interaction. The system participated in the tertiary structure prediction in 2022 CASP15 experiment. Our server predictor MULTICOM_refine ranked 3rd among 47 CASP15 server predictors and our human predictor MULTICOM ranked 7th among all 132 human and server predictors. The average GDT-TS score and TM-score of the first structural models that MULTICOM_refine predicted for 94 CASP15 domains are ~0.80 and ~0.92, 9.6% and 8.2% higher than ~0.73 and 0.85 of the standard AlphaFold2 predictor respectively.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Parallel diffusion operator for magnetized plasmas with improved spectral fidelity

Diffusive transport processes in magnetized plasmas are highly anisotropic, with fast parallel transport along the magnetic field lines sometimes faster than perpendicular transport by orders of magnitude. This constitutes a major challenge for describing non-grid-aligned magnetic structures in Eulerian (grid-based) simulations. Here, the present paper describes and validates a new method for parallel diffusion in magnetized plasmas based on the anti-symmetry representation [Halpern and Waltz, Phys. Plasmas 25, 060703 (2018)]. In the anti-symmetry formalism, diffusion manifests as a flow operator involving the logarithmic derivative of the transported quantity. Qualitative plane wave analysis shows that the new operator naturally yields better discrete spectral resolution compared to its conventional counterpart. Numerical simulations comparing the new method against existing finite difference methods are carried out, showing significant improvement. In particular, we find that combining anti-symmetry with finite differences in diagonally staggered grids essentially eliminates the so-called “artificial numerical diffusion” that affects conventional finite difference and finite volume methods.

Anisotropic diffusion↗
DOE OSTI2026

In situ study on radiation response of tungsten manufactured by laser powder bed fusion

Tungsten (W) produced by laser powder bed fusion (LPBF) was examined by in situ Krypton (Kr) ion irradiation at 400 °C up to 2.52 displacements per atom (dpa) to investigate its radiation response. Dislocation loops with identical Burgers vectors form aligned raft structures, inducing significant grain misorientation accumulation. Defect saturation was observed beyond 0.36 dpa, marked by constant loop density and raft spacing. WO 3 nanoparticles are found in the as-printed matrix and served as efficient defect sinks. Dislocation loops were absorbed at the W/WO 3 interface, facilitating defect annihilation and suppressing defect accumulation. In conclusion, these findings highlight the role of LPBF microstructure and oxide interfaces in mediating radiation-induced defect evolution, offering insights for designing radiation tolerant W-based materials.

Defect sink↗
DOE OSTI2021

Solvent Processing and Ionic Liquid-Enabled Long-Range Vertical Ordering in Block Copolymer Films with Enhanced Film Stability

Rapid and reliable processing methods for forming ordered block copolymer (BCP) materials with low defect density in a thin film geometry are required for many nanotechnology applications. Vertically aligned BCP structures, in particular, have applications ranging from nanolithography for electronics and photonics to nanoporous membranes for water remediation and novel batteries for flexible electronics. However, the attainment of nearly complete vertical orientational order of the BCP ordered phase remains challenging. Solvent-based techniques, such as direct immersion annealing (DIA) and solvent vapor annealing (SVA), have immense potential for these applications of BCP films, as it allows for tuning of their thermodynamic, structural, and chain mobility driven kinetic properties. We first demonstrate that DIA, using a judicious choice of binary solvent mixtures along with a relatively hydrophobic ionic liquid (IL), induces the rapid vertical ordering in polystyrene-b-polymethylmethacrylate (PS-PMMA) block copolymer in lamellar films. The IL establishes synergy to the binary solvent mixture of toluene and heptane to 1 create a near-neutral solvent environment for attaining the vertical microstructure of the BCP. Next, we show that IL can suppress the de-wetting of the PS-PMMA films to achieve long-range order using SVA in cylindrical films for long annealing times. Both vertical and horizontal morphology is attained in these films by selecting different solvent environments. Furthermore, attaining enhanced vertical and horizontal BCP structure with long-range defect-free order by tuning solvent quality and using additives like IL can render them useful for many nanotech applications.

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

River Delta Morphotypes Emerge From Multiscale Characterization of Shorelines

Abstract Delta shoreline structure has long been hypothesized to encode information on the relative influence of fluvial, wave, and tidal processes on delta formation and evolution. We introduce here a novel multiscale characterization of shorelines by defining three process‐informed morphological metrics. We show that this characterization yields self‐emerging classes of morphologically similar deltas, that is, delta morphotypes, and also predicts the dominant forcing of each morphotype. Then we show that the dominant forcings inferred from shoreline structure generally align with those estimated via relative sediment fluxes, while positing that misalignments arise from spatiotemporal heterogeneity in deltaic sediment fluxes not captured in their estimates. The proposed framework for shoreline characterization advances our quantitative understanding of how shoreline features reflect delta forcings, and may aid in deciphering paleoclimate from images of ancient deposits and projecting delta morphologic response to changes in sediment fluxes.

Vulis, L.↗
DOE OSTI2026

Self-oscillating synchronematic colloids

Self-oscillators that sustain periodic dynamics under constant input are ubiquitous in natural and engineered systems, where their interactions enable spatiotemporal coordination among many individual units. New forms of organization can emerge when these self-oscillating units are free to move and rotate, coupling their spatial arrangement and alignment with their oscillation frequencies and phases. Here, we report experiments and simulations on populations of Quincke colloids that behave as self-oscillating units with position, orientation, frequency, and phase. Depending on the initial distribution, these active oscillators spontaneously organize into distinct collective states characterized by temporal synchronization and directional alignment, which we term synchronematic order. In fluid-like clusters, this order is short-ranged and decays over a length scale set by the competition between hydrodynamic interactions and athermal noise. In crystalline clusters, these interactions drive flobal synchronization and circular alignment-synchronematic crystals-whose collective frequency increases with cluster size due to non-reciprocal interactions. Our results establish self-oscillating colloids as a model system for active oscillatory matter and reveal fundamental principles by which synchronization, alignment, and structure co-emerge, offering new pathways for designing adaptive, frequency-tunable materials.

colloids↗
DOE OSTI2024

Nuclear magnetic resonance investigation of superconducting and normal state Nb 3 Sn

The superconductor Nb3Sn has important applications for construction of very high-field superconducting magnets. In this work we investigate its microscopic electronic structure with 93 Nb nuclear magnetic resonance (NMR). The high-quality Nb 3 Sn powder sample was studied in both 3.2 T and 7 T magnetic fields in the temperature range from 4 K to 300 K. From measurement of the spectrum and its theoretical analysis, we find evidence for anisotropy despite its cubic crystal structure. Magnetic alignment of the powder grains in the superconducting state was also observed. The Knight shift and spin-lattice relaxation rate, T 1 -1 , were measured and the latter compared with BCS theory for the energy gap Δ(0) = 2.7 ± 0.3k B T c at 3.2 T and Δ(0) = 2.33 ± 0.07 k B T c at 7 T, indicating suppression of the order parameter by magnetic field.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Deployable UHV Pump

This project presents an external motorized actuation system for a deployable ultra-high vacuum (UHV) pump, enabling internal motion without compromising vacuum conditions. All active components remain external due to environmental and space constraints. A motor-driven mechanical feedthrough transfers motion into the pump, supported by a modular, adjustable mounting system that maintains alignment and integrates with existing hardware. CAD modeling and iterative design were used to refine geometry and ensure proper fit. The final design reliably transfers motion while maintaining alignment and structural integrity. Its adjustability improves installation and maintenance, demonstrating a practical solution for actuation in UHV systems.

Remington, Austin [Northern Illinois U.]↗
DOE OSTI2023

Ducted fuel injection system alignment device

An alignment device for a ducted fuel injection system comprising a mounting block removably attachable to a duct of the ducted fuel injection system. The mounting block can include a passageway extending therethrough. The passageway can align with the duct when the mounting block is attached to the duct. The alignment device further comprises an imaging device configured to capture an image viewing through the duct toward an outlet of a fuel injector. A portion of the imaging device can extend in the passageway. The alignment device additionally comprises a centering structure configured to align a portion of the imaging device with a central axis of the duct. The image captured by the imaging device can be configured for use aligning a position of an outlet of a fuel injector with respect to a position of the duct.

Nilsen, Christopher William↗
DOE OSTI2023

Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15

To enhance the AlphaFold-Multimer-based protein complex structure prediction, we developed a quaternary structure prediction system (MULTICOM) to improve the input fed to AlphaFold-Multimer and evaluate and refine its outputs. MULTICOM samples diverse multiple sequence alignments (MSAs) and templates for AlphaFold-Multimer to generate structural predictions by using both traditional sequence alignments and Foldseek-based structure alignments, ranks structural predictions through multiple complementary metrics, and refines the structural predictions via a Foldseek structure alignment-based refinement method. The MULTICOM system with different implementations was blindly tested in the assembly structure prediction in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022 as both server and human predictors. MULTICOM_qa ranked 3 rd among 26 CASP15 server predictors and MULTICOM_human ranked 7 th among 87 CASP15 server and human predictors. The average TM-score of the first predictions submitted by MULTICOM_qa for CASP15 assembly targets is ~0.76, 5.3% higher than ~0.72 of the standard AlphaFold-Multimer. The average TM-score of the best of top 5 predictions submitted by MULTICOM_qa is ~0.80, about 8% higher than ~0.74 of the standard AlphaFold-Multimer. Moreover, the Foldseek Structure Alignment-based Multimer structure Generation (FSAMG) method outperforms the widely used sequence alignment-based multimer structure generation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Embedded 3D printing of isotropically enhanced lattice structure with programmable elasticity via three-dimensional fiber alignment

Engineered composites with fiber orientation in a complete three-dimensional (3D) context are highly desired for maximizing structural performance as they mimic the well-organized fiber arrangement in natural composites. However, most fabrication techniques lack the capability for through-plane (z-axis) alignment, limiting the possibility for structural design and performance optimization. In this study, we present an embedded 3D printing approach that enables complete 3D fiber alignment, including region-specific alignment control along the through-plane direction. Our method utilizes the extrusion and suspension of composite inks within a supporting matrix. By regionally adjusting the ink extrusion rate and nozzle translation rate, we locally manipulated the fiber arrangement within the composite 3D architecture. Here, we demonstrate that the 3D alignment of carbon fibers in a structural composite significantly enhances both mechanical properties and thermal conductivity in the in-plane and through-plane directions. Furthermore, by strategically arranging regional fiber orientations within micro-architected materials, we fabricated metamaterial engineered composites with programmable anisotropy ratio and directional moduli.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Reconfigurable structural color by reversible switching of colloidal discoid liquid crystal alignment

Combining the effects of alternating-current (AC) electric fields and sedimentation reconfigures colloidal discoids between planar and homeotropic orientational alignments, thereby controlling the material’s structural color. Here, we self-assemble micrometer-size polystyrene discoids in an isopropanol-water mixture. After sedimentation, the discoids adopt a homeotropic alignment, with the minor axis perpendicular to the substrate. Adding an AC electric field (1 kHz) of ≥0.50 V switches the discoids to planar alignment—with the minor axis parallel to the substrate—within ∼100 s. Removing the field switches them back to homeotropic alignment within ∼300 s. Kinetic modeling of the field-induced torques yields good agreement with these measurements. The peak wavelength and intensity of the crystal’s diffraction response shift significantly upon reconfiguration; scattering simulation predicts these shifts. The reconfiguration is maintained for at least 10 cycles. This method is a simple, scalable avenue to reconfigure the optical properties of colloidal crystals produced from simple dielectric spheroids.

colloidal crystals↗
DOE OSTI2022

Self-alignment features for III-V ridge process and angled facet die

A method of forming a laser including device is provided that in one embodiment includes providing a laser chip including at least one ridge structure that provides an alignment features. The method further includes bonding a type IV photonics chip to the laser chip, wherein a vertical alignment feature from the type IV photonics chip is inserted in a recess relative to the at least one ridge structure that provides the alignment features of the laser structure.

Barwicz, Tymon↗
DOE OSTI2024

Self-aligned fabrication of vertical, fin-based structures

Modern power devices rely on complex, three-dimensional, vertical designs to increase their power density, ease their thermal management, and improve their reliability. However, fabrication techniques have historically relied on 2D processes for patterning lateral features. This work presents a new technology that uses multiple steps of angled depositions to fabricate self-aligned vertical, fin-based devices that avoid fundamental lithography resolution and alignment limitations. The fabrication flows of two devices, the self-aligned vertical finFET and the high-κ dielectric fin diode, are presented to demonstrate how angled depositions can readily achieve transistors with submicrometer, vertical gates in a source-first process and also create high-aspect ratio GaN fins with a record 70:1 aspect ratio.

Perozek, Joshua (ORCID:0000000251519131)↗
DOE OSTI2021

Range-separated hybrid functionals for mixed dimensional heterojunctions: Application to phthalocyanines/MoS 2

We analyze the electronic structure and level alignment of transition-metal phthalocyanine (MPc) molecules adsorbed on two-dimensional MoS 2 employing density functional theory (DFT) calculations. We develop a procedure for multi-objective optimal tuning of parameters of range-separated hybrid functionals in these mixed-dimensional systems. Using this procedure, which leads to the asymptotically-correct exchange-correlation potential between molecule and two-dimensional material, we obtain electronic structures consistent with experimental photoemission results for both energy level alignment and electronic bandgaps, representing a significant advance compared to standard DFT methods. We elucidate the MoS 2 valence resonance with the transition-metal phthalocyanine non-frontier 3d orbitals and its dependence on the transition metal atomic number. Based on our calculations, we derive parameter-free, model self-energy corrections that quantitatively accounts for the effects of the heterogeneous dielectric environment on the electronic structure of these mixed-dimensional heterojunctions.

2D materials↗
DOE OSTI2023

Relative alignment between magnetic fields and molecular gas structure in molecular clouds

Here, we compare the structure of synthetic dust polarization with synthetic molecular line emission from radiative transfer calculations using a three-dimensional, turbulent collapsing-cloud magnetohydrodynamics simulation. The histogram of relative orientation (HRO) technique and the projected Rayleigh statistic (PRS) are considered. In our trans-Alfvénic (more strongly magnetized) simulation, there is a transition to perpendicular alignment at densities above ~4 × 10 3 cm –3 . This transition is recovered in most of our synthetic observations of optically thin molecular tracers; however, for 12 CO it does not occur and the PRS remains in parallel alignment across the whole observer space. We calculate the physical depth of the optical depth τ = 1 surface and find that for 12 CO it is largely located in front of the cloud mid-plane, suggesting that 12 CO is too optically thick and instead mainly probes low-volume density gas. In our super-Alfvénic simulation, the magnetic field becomes significantly more tangled, and all observed tracers tend towards no preference for perpendicular or parallel alignment. An observable difference in alignment between optically thin and optically thick tracers may indicate the presence of a dynamically important magnetic field, though there is some degeneracy with viewing angle. We convolve our data with a Gaussian beam and compare it with HRO results of the Vela C molecular cloud. We find good agreement between these results and our sub-Alfvénic simulations when viewed with the magnetic field in the plane of the sky (especially when sensitivity limitations are considered), though the observations are also consistent with an intermediately inclined magnetic field.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Core-shell metallic alloy nanopillars-in-dielectric hybrid metamaterials with magneto-plasmonic coupling

Combining plasmonic and magnetic properties, namely magneto-plasmonic coupling, inspires great research interest and the search for magneto-plasmonic nanostructure becomes considerably critical. In this work, we designed a nanopillar-in-matrix structure with core–shell alloyed nanopillars for both BaTiO 3 (BTO)-Au 0.5 Co 0.5 (AuCo) and BTO-Au 0.25 Cu 0.25 Co 0.25 Ni 0.25 (AuCuCoNi) hybrid systems, i.e., ferromagnetic alloy cores (e.g., Co or CoNi) with plasmonic shells (e.g., Au or Au/Cu). These core–shell alloy nanopillars are uniformly embedded into a dielectric BTO matrix to form a vertically aligned nanocomposite (VAN) structure. Both hybrid systems present excellent epitaxial quality and interesting multi-functionality, e.g., high magnetic anisotropy, magneto-optical coupling response, tailorable plasmonic resonance wavelength, tunable hyperbolic properties and strong optical anisotropy. These alloyed nanopillars-in-matrix designs provide enormous potential for complex hybrid material designs with multi-functionality and demonstrate strong interface enabled magneto-plasmonic coupling along with plasmonic and magnetic performance.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Novel vertically aligned nanocomposite of Bi 2 WO 6 -Co 3 O 4 with room-temperature multiferroic and anisotropic optical response

A review of a new vertically aligned nanocomposite (VAN) structure based on two-dimensional (2D) layered oxides has been designed and self-assembled on both LaAlO 3 (001) and SrTiO 3 (001) substrates. The new VAN structure consists of epitaxially grown Co 3 O 4 nanopillars embedded in the Bi 2 WO 6 matrix with a unique 2D layered structure, as evidenced by the microstructural analysis. Physical property measurements show that the new Bi 2 WO 6 -Co 3 O 4 VAN structure exhibits strong ferromagnetic and piezoelectric response at room temperature as well as anisotropic permittivity response. This work demonstrates a new approach in processing multifunctional VANs structure based on the layered oxide systems towards future nonlinear optics, ferromagnets, and multiferroics.

77 NANOSCIENCE AND NANOTECHNOLOGY↗