Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “FRAGMENTATION”

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 1,387 records · Page 77
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

BLINK enables ultrafast tandem mass spectrometry cosine similarity scoring

Metabolomics has a long history of using cosine similarity to match experimental tandem mass spectra to databases for compound identification. Here we introduce the Blur-and-Link (BLINK) approach for scoring cosine similarity. By bypassing fragment alignment and simultaneously scoring all pairs of spectra using sparse matrix operations, BLINK is over 3000 times faster than MatchMS, a widely used loop-based alignment and scoring implementation. Using a similarity cutoff of 0.7, BLINK and MatchMS had practically equivalent identification agreement, and greater than 99% of their scores and matching ion counts were identical. This performance improvement can enable calculations to be performed that would typically be limited by time and available computational resources.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Targeting Aspergillus allergen oryzin with a chemical probe at atomic precision

We report the molecular basis of Aspergillus fumigatus oryzin, allergen Asp f 13, or alkaline proteinase ALP1, containing the sequence motif His–Asp–Ser of the subtilisin family, structure, and function at atomic detail. Given the resolution of the data (1.06 Å), we use fragment molecular replacement with ideal polyalanine α-helices to determine the first crystal structure of oryzin. We probe the catalytic serine through formation of an irreversible bond to a small molecule compound, specifically labeling it, describing the amino acid residues performing the catalytic function. Defined by a self-processed pro-peptide, the active site architecture shapes up pocket-like subsites that bind to and unveil the S1′–S4′ substrate binding preferences. We use molecular modeling to dock a model of the pro-peptide in the S1–S4 region and to dock collagen along the active site cleft. Opposite to the face harboring the catalytic serine, the enzyme binds to a calcium ion in a binding site created by backbone flipping. We use thermal unfolding to show that this metal ion provides structural stability. With no known host inhibitor identified thus far, this structure may hasten the progress of developing new therapeutic agents for diseases caused by pathogenic fungi.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Evaluation of the interfacial bonding strength between hafnia and silica layers deposited by electron-beam evaporation

Factors contributing to the mechanical strength of multilayer optical coatings involving alternating layers of electron-beam evaporated hafnia and silica is investigated. It is observed that upon rupture resulting from nanosecond laser damage, fragments consisting of layer pairs are produced. These pairs are formed as a result of a strong asymmetry in adhesion strength between interfaces, leading to preferential delamination at interfaces where silica is deposited on hafnia, and not the reverse, despite the fact that both interface types consist of the same pair of materials. The observed disparity in adhesion strength was further studied using nanomechanical scratch tests, revealing loads at which fracture occurs, and fracture morphology, both of which are highly dependent on deposition order. Based on these measurements, along with the morphological analysis of the nanostructure of the coatings, we conclude that the surface microstructure in each coating layer affects its adhesion strength with the succeeding layer. The findings outlined here are particularly relevant to the production of large aperture, high-performance optics designed for use in next-generation lasers.

adhesion strength↗
DOE OSTI2020

Structure and function of a malaria transmission blocking vaccine targeting Pfs230 and Pfs230-Pfs48/45 proteins

Proteins Pfs230 and Pfs48/45 are Plasmodium falciparum transmission-blocking (TB) vaccine candidates that form a membrane-bound protein complex on gametes. The biological role of Pfs230 or the Pfs230-Pfs48/45 complex remains poorly understood. Here, we present the crystal structure of recombinant Pfs230 domain 1 (Pfs230D1M), a 6-cysteine domain, in complex with the Fab fragment of a TB monoclonal antibody (mAb) 4F12. We observed the arrangement of Pfs230 on the surface of macrogametes differed from that on microgametes, and that Pfs230, with no known membrane anchor, may exist on the membrane surface in the absence of Pfs48/45. 4F12 appears to sterically interfere with Pfs230 function. Combining mAbs against different epitopes of Pfs230D1 or of Pfs230D1 and Pfs48/45, significantly increased TB activity. These studies elucidate a mechanism of action of the Pfs230D1 vaccine, model the functional activity induced by a polyclonal antibody response and support the development of TB vaccines targeting Pfs230D1 and Pfs230D1-Pfs48/45.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Structure of phospholipase Cε reveals an integrated RA1 domain and previously unidentified regulatory elements

Phospholipase Cε (PLCε) generates lipid-derived second messengers at the plasma and perinuclear membranes in the cardiovascular system. It is activated in response to a wide variety of signals, such as those conveyed by Rap1A and Ras, through a mechanism that involves its C-terminal Ras association (RA) domains (RA1 and RA2). However, the complexity and size of PLCε has hindered its structural and functional analysis. Herein, we report the 2.7 Å crystal structure of the minimal fragment of PLCε that retains basal activity. This structure includes the RA1 domain, which forms extensive interactions with other core domains. A conserved amphipathic helix in the autoregulatory X–Y linker of PLCε is also revealed, which we show modulates activity in vitro and in cells. The studies provide the structural framework for the core of this critical cardiovascular enzyme that will allow for a better understanding of its regulation and roles in disease.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

In vivo pharmacokinetic enhancement of monomeric Fc and monovalent bispecific designs through structural guidance

In a biologic therapeutic landscape that requires versatility in targeting specificity, valency and half-life modulation, the monomeric Fc fusion platform holds exciting potential for the creation of a class of monovalent protein therapeutics that includes fusion proteins and bispecific targeting molecules. Here we report a structure-guided approach to engineer monomeric Fc molecules to adapt multiple versions of half-life extension modifications. Co-crystal structures of these monomeric Fc variants with Fc neonatal receptor (FcRn) shed light into the binding interactions that could serve as a guide for engineering the half-life of antibody Fc fragments. These engineered monomeric Fc molecules also enabled the generation of a novel monovalent bispecific molecular design, which translated the FcRn binding enhancement to improvement of in vivo serum half-life.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Split selectable marker systems utilizing inteins facilitate gene stacking in plants

The ability to stack multiple genes in plants is of great importance in the development of crops with desirable traits but can be challenging due to limited selectable marker options. Here we establish split selectable marker systems using protein splicing elements called “inteins” for Agrobacterium-mediated co-transformation in plants. First, we show that such a split selectable marker system can be used effectively in plants to reconstitute a visible marker, RUBY, from two non-functional fragments through tobacco leaf infiltration. Next, to determine the general applicability of our split selectable marker systems, we demonstrate the utility of these systems in the model plants Arabidopsis and poplar by successfully stacking two reporters eYGFPuv and RUBY, using split Kanamycin or Hygromycin resistance markers. In conclusion, this method enables robust plant co-transformation, providing a valuable tool for the simultaneous insertion of multiple genes into both herbaceous and woody plants efficiently.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The co-crystal structure of Cbl-b and a small-molecule inhibitor reveals the mechanism of Cbl-b inhibition

Cbl-b is a RING-type E3 ubiquitin ligase that is expressed in several immune cell lineages, where it negatively regulates the activity of immune cells. Cbl-b has specifically been identified as an attractive target for cancer immunotherapy due to its role in promoting an immunosuppressive tumor environment. A Cbl-b inhibitor, Nx-1607, is currently in phase I clinical trials for advanced solid tumor malignancies. Using a suite of biophysical and cellular assays, we confirm potent binding of C7683 (an analogue of Nx-1607) to the full-length Cbl-b and its N-terminal fragment containing the TKBD-LHR-RING domains. To further elucidate its mechanism of inhibition, we determined the co-crystal structure of Cbl-b with C7683, revealing the compound’s interaction with both the TKBD and LHR, but not the RING domain. Here, we provide structural insights into a novel mechanism of Cbl-b inhibition by a small-molecule inhibitor that locks the protein in an inactive conformation by acting as an intramolecular glue.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A ligand discovery toolbox for the WWE domain family of human E3 ligases

The WWE domain is a relatively under-researched domain found in twelve human proteins and characterized by a conserved tryptophan-tryptophan-glutamate (WWE) sequence motif. Six of these WWE domain-containing proteins also contain domains with E3 ubiquitin ligase activity. The general recognition of poly-ADP-ribosylated substrates by WWE domains suggests a potential avenue for development of Proteolysis-Targeting Chimeras (PROTACs). Here, we present novel crystal structures of the HUWE1, TRIP12, and DTX1 WWE domains in complex with PAR building blocks and their analogs, thus enabling a comprehensive analysis of the PAR binding site structural diversity. Furthermore, we introduce a versatile toolbox of biophysical and biochemical assays for the discovery and characterization of novel WWE domain binders, including fluorescence polarization-based PAR binding and displacement assays, 15 N-NMR-based binding affinity assays and 19 F-NMR-based competition assays. Through these assays, we have characterized the binding of monomeric iso -ADP-ribose ( iso -ADPr) and its nucleotide analogs with the aforementioned WWE proteins. Finally, we have utilized the assay toolbox to screen a small molecule fragment library leading to the successful discovery of novel ligands targeting the HUWE1 WWE domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

LipidOz enables automated elucidation of lipid carbon–carbon double bond positions from ozone-induced dissociation mass spectrometry data

Lipids play essential roles in many biological processes and disease pathology, but unambiguous identification of lipids is complicated by the presence of multiple isomeric species differing by fatty acyl chain length, stereospecifically numbered (sn) position, and position/stereochemistry of double bonds. Conventional liquid chromatography-mass spectrometry (LC-MS/MS) analyses enable the determination of fatty acyl chain lengths (and in some cases sn position) and number of double bonds, but not carbon-carbon double bond positions. Ozone-induced dissociation (OzID) is a gas-phase oxidation reaction that produces characteristic fragments from lipids containing double bonds. OzID can be incorporated into ion mobility spectrometry (IMS)-MS instruments for the structural characterization of lipids, including additional isomer separation and confident assignment of double bond positions. The complexity and repetitive nature of OzID data analysis and lack of software tool support have limited the application of OzID for routine lipidomics studies. Here, we present an open-source Python tool, LipidOz, for the automated determination of lipid double bond positions from OzID-IMS-MS data, which employs a combination of traditional automation and deep learning approaches. Our results demonstrate the ability of LipidOz to robustly assign double bond positions for lipid standard mixtures and complex lipid extracts, enabling practical application of OzID for future lipidomics.

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

Transient pattern formation in an active matter contact poisoning model

Abstract One of the most notable features in repulsive particle based active matter systems is motility-induced-phase separation (MIPS) where a dense, often crystalline phase and low density fluid coexist. Most active matter studies involve time-dependent activity; however, there are many active systems where individual particles transition from living or moving to dead or nonmotile due to lack of fuel, infection, or poisoning. Here we consider an active matter particle system at densities where MIPS does not occur. When we add a small number of infected particles that can poison other particles, rendering them nonmotile, we find a rich variety of time dependent pattern formation, including MIPS, a wetting phase, and a fragmented state formed when mobile particles plow through a nonmotile packing. We map the patterns as a function of time scaled by epidemic duration, and show that the pattern formation is robust for a wide range of poisoning rates and activity levels. We also show that pattern formation does not occur in a random death model, but requires the promotion of nucleation by contact poisoning. Our results should be relevant to biological and active matter systems where there is some form of poisoning, death, or transition to nonmotility.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Extreme shear-deformation-induced modification of defect structures and hierarchical microstructure in an Al–Si alloy

Abstract Extreme shear deformation is used for several material processing methods and is unavoidable in many engineering applications in which two surfaces are in relative motion against each other while in physical contact. The mechanistic understanding of the microstructural evolution of multi-phase metallic alloys under extreme shear deformation is still in its infancy. Here, we highlight the influence of shear deformation on the microstructural hierarchy and mechanical properties of a binary as-cast Al-4 at.% Si alloy. Shear-deformation-induced grain refinement, multiscale fragmentation of the eutectic Si-lamellae, and metastable solute saturated phases with distinctive defect structures led to a two-fold increase in the flow stresses determined by micropillar compression testing. These results highlight that shear deformation can achieve non-equilibrium microstructures with enhanced mechanical properties in Al–Si alloys. The experimental and computational insights obtained here are especially crucial for developing predictive models for microstructural evolution of metals under extreme shear deformation.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Dendritic deformation modes in additive manufacturing revealed by operando x-ray diffraction

Abstract Dynamic solidification behavior during metal additive manufacturing directly influences the as-built microstructure, defects, and mechanical properties of printed parts. How the formation of these features is driven by temperature variation (e.g., thermal gradient magnitude and solidification front velocity) has been studied extensively in metal additive manufacturing, with synchrotron x-ray imaging becoming a critical tool to monitor these processes. Here, we extend these efforts to monitoring full thermomechanical deformation during solidification through the use of operando x-ray diffraction during laser melting. With operando diffraction, we analyze thermomechanical deformation modes such as torsion, bending, fragmentation, assimilation, oscillation, and interdendritic growth. Understanding such phenomena can aid the optimization of printing strategies to obtain specific microstructural features, including localized misorientations, dislocation substructure, and grain boundary character. The interpretation of operando diffraction results is supported by post-mortem electron backscatter diffraction analyses.

Dass, Adrita (ORCID:000000019100635X)↗
DOE OSTI2025

Alteration history of aluminum-rich rocks at Jezero crater, Mars

Aluminum-rich clay minerals are detected across the ancient surface of Mars and record intervals of intense alteration by liquid water. On Earth, these clay minerals can form from hydrothermal alteration or rainfall-driven chemical weathering over thousands to millions of years, but how they formed on Mars remains a mystery. The Perseverance rover discovered light-toned, cobble-sized, aluminum-rich (30-45 wt% Al 2 O 3 ) “float” rocks (rock fragments), with some exhibiting spectral signatures of kaolinite, an aluminum-rich clay mineral. These rocks now enable an investigation into the ancient kaolinite-bearing terrains of Mars. To interpret their formation, we use data from the SuperCam and Mastcam-Z instruments onboard the rover to compare the chemistry and reflectance spectra of the float rocks with deeply weathered paleosols and hydrothermal kaolin deposits from Earth’s geological record. Aluminum and titanium enrichments coupled with depletion of iron and magnesium are unlike hydrothermal deposits and instead comparable to bleached horizons of paleosols that formed under high rainfall during past greenhouse climates on Earth. These rocks therefore likely represent some of the wettest intervals of Mars’ history.

58 GEOSCIENCES↗
DOE OSTI2025

Catalytic deconstruction of organic additive-containing plastics

Plastics waste ends up in landfills, oceans, and incinerators, posing major environmental and human health threats. Catalytic deconstruction is emerging as a key technological solution to handle complex plastics and has successfully converted virgin polymers into various products. Here, we investigate the resilience of chemical deconstruction technologies to organic additives, which are ubiquitous in plastics. We study catalyst-additive interactions experimentally and via first-principles calculations for plastics additives representative of entire classes. We reveal two deactivation mechanisms and demonstrate that many recently developed catalysts are inadequate for polyolefin conversion due to poisoning caused by the strong adsorption of most additives or their small fragments. Furthermore, we also identify conditions and catalysts that can circumvent the challenge of deconstruction in the presence of additives challenge.

10 SYNTHETIC FUELS↗
DOE OSTI2025

Next-generation electronics by co-design with chalcogenide materials

As Moore’s law approaches its limits, chalcogenides offer a promising route to next-generation computing and sensing, thanks to their topological, magnetoelectric, excitonic, and spintronic properties. Yet the same traits that make them appealing, e.g., exotic properties at monolayer thickness, clean van der Waals interfaces, and strong many-body effects, also heighten sensitivity to fabrication, hindering translation into scalable devices. Progress is further constrained by fragmented knowledge across synthesis, processing, and integration, and by the lack of systematic links between fabrication parameters and performance metrics. This Perspective examines key obstacles in controlling chalcogenide heterostructures and stresses the need for an integrated co-design framework, uniting materials growth, processing, and device architecture to accelerate practical technologies.

36 MATERIALS SCIENCE↗
DOE OSTI2026

An end-to-end workflow for executing a classically bootstrapped variational quantum algorithm on an academic quantum computer

Academic quantum computing platforms often face unique challenges in executing quantum workloads due to fragmented software environments and limited engineering support. Unlike commercial ecosystems, academic devices typically evolve without full-stack integration in mind, making it difficult to run complex applications—such as variational quantum algorithms (VQA)—reliably and efficiently. Issues such as incompatible software layers and lack of automated job management significantly increase the overhead of theory-experiment collaboration. To address these challenges, we develop a modular, end-to-end workflow that decouples application-layer code from low-level hardware control, automates circuit submission and result collection, and supports fine-grained circuit-level job scheduling and recovery. The architecture employs a dual-end application programming interface (API) design, enabling robust operation across unstable or resource-constrained hardware backends. For practical use, the framework is lightweight and user-friendly, allowing rapid prototyping of full-stack workflows using basic Python tools. We validate this workflow on a high-fidelity trapped-ion quantum computer by demonstrating a variational quantum eigensolver (VQE) experiment with a classically bootstrapped ansatz initialization technique. The system successfully executed over 60,000 circuits across multiple molecular test cases with minimal human intervention, highlighting the framework’s effectiveness in enabling reproducible, resilient quantum experimentation in academic settings.

Clifford↗
DOE OSTI2020

A new non-diffusional gas bubble production route in used nuclear fuel: Implications for fission gas release, cladding corrosion, and next generation fuel design

The relationship between noble metal phase particles and fission gas bubble production in used nuclear fuel is described. The majority of Te atoms within noble metal phase undergo radioactive decay to form stable Xe within a few hours after particle formation. This results in the production of clusters of Xe atoms contained within the solid metal matrix exhibiting an equivalent gas bubble pressure approaching 1 GPa. These high pressure bubbles are stabilized by the UO2 within the bulk of the fuel. However, when these bubbles form near the fuel / cladding interface, in combination with local and temporal damage caused by fission recoil, they are capable of overcoming the fracture strength of the UO2 and rupturing catastrophically. The force of the resulting bubble rupture is sufficient to eject noble metal phase particles several microns into the cladding. This proposed mechanism explains the observance of noble metal phase in cladding and is consistent with a host of morphological features found near the fuel / cladding interface.

Schwantes, Jon M.↗