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At least 1,153 records · Page 64

All sources NASA NTRS DOE OSTI

DOE OSTI2023

Towards deep computer vision for in-line defect detection in polymer electrolyte membrane fuel cell materials

Polymer Electrolyte Membrane (PEM) fuel cells are a promising source of alternative energy. However, their production is limited by a lack of well-established methods for quality control of their constituent materials like the membrane-electrode assembly during roll-to-roll manufacturing. One potential solution is the implementation of deep learning methods to detect unwanted defects through their detection in scanned images. Here we explore the detection of defects like scratches, pinholes, and scuffs in a sample dataset of PEM optical images using two deep learning algorithms: Patch Distribution Modeling (PaDiM) for unsupervised anomaly detection and Faster-RCNN for supervised object detection. Both methods achieve scores on performance metrics (ROC-AUC and PRO-AUC for PaDiM and AP for Faster-RCNN) that are comparable to their scores on benchmark datasets. These methods also have the potential to detect a wider range of defects compared to IR thermography and previous optical inspection methods. Overall, deep learning shows promise at detecting relevant defects of interest and has the potential to achieve real-time defect detection.

30 DIRECT ENERGY CONVERSION↗

DOE OSTI2015

Low-Dose (10-Gy) Total Skin Electron Beam Therapy for Cutaneous T-Cell Lymphoma: An Open Clinical Study and Pooled Data Analysis

Purpose: Cutaneous T-cell lymphomas (CTCLs) are dominated by mycosis fungoides (MF) and Sézary syndrome (SS), and durable disease control is a therapeutic challenge. Standard total skin electron beam therapy (TSEBT) is an effective skin-directed therapy, but the possibility of retreatments is limited to 2 to 3 courses in a lifetime due to skin toxicity. This study aimed to determine the clinical effect of low-dose TSEBT in patients with MF and SS. Methods and Materials: In an open clinical study, 21 patients with MF/SS stages IB to IV were treated with low-dose TSEBT over <2.5 weeks, receiving a total dose of 10 Gy in 10 fractions. Data from 10 of these patients were published previously but were included in the current pooled data analysis. Outcome measures were response rate, duration of response, and toxicity. Results: The overall response rate was 95% with a complete cutaneous response or a very good partial response rate (<1% skin involvement with patches or plaques) documented in 57% of the patients. Median duration of overall cutaneous response was 174 days (5.8 months; range: 60-675 days). TSEBT-related acute adverse events (grade 1 or 2) were observed in 60% of patients. Conclusions: Low-dose (10-Gy) TSEBT offers a high overall response rate and is relatively safe. With this approach, reirradiation at times of relapse or progression is likely to be less toxic than standard dose TSEBT. It remains to be established whether adjuvant and combination treatments can prolong the beneficial effects of low-dose TSEBT.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2021

Key Elements of Auroral Substorm Development and their Relationship to Recent Observations of Detached Sub-Auroral Phenomena Including STEVE-like Emissions

Since Akasofu introduced the concept of the substorm in 1964, numerous refinements have been added to the phenomenological model of how auroral substorms develop. Here, we review several of the most important of these including; polar cap patches, intensifications of the Polar Activated Band (PAB) at the poleward edge of the bulge, the development of new arcs poleward, the generation of auroral streamers, the evolution of streamers into auroral torches and omega bands, the association of streamers with particle injection and BBF activity in the tail, and wedgelet-like magnetic perturbations on the ground. We also review the concept of “contact breakups” which are breakups that appear to be triggered by the arrival of streamer-like forms in the equatorward regions of the oval. Finally, we remind the community that the addition of detached sub-auroral emissions was made to the phenomenological picture of substorm develop in the late 1960s along with the concept of auroral streamers. Newer observations of detached sub-auroral (STEVE-like emissions) from the Viking/UVI and POLAR/VIS imagers are presented which confirm that they are east-west aligned bands of emission that separate away from the equatorward edge of the auroral oval in response to intensifications of the poleward edge of the bulge and subsequent streamer production. We propose a new model for the formation of detached sub-auroral (STEVE-like) emissions in which a non-linear growth of a SAPS-driven instability (e.g. like the shear-flow/ballooning instability) at the plasmapause results in the disruption of the boundary separating hot plasma sheet particle from the cold plasmaspheric plasma. It is proposed that the resulting intermixing of plasma populations leads to both the observed STEVE-like emissions and also provides a source of cold plasma on open drift paths that can feed the long-lived drainage plumes that have recently been discovered.

58 GEOSCIENCES↗

DOE OSTI2025

A conserved chaperone protein is required for the formation of a noncanonical type VI secretion system spike tip complex

Type VI secretion systems (T6SSs) are dynamic protein nanomachines found in Gram-negative bacteria that deliver toxic effector proteins into target cells in a contact-dependent manner. Prior to secretion, many T6SS effector proteins require chaperones and/or accessory proteins for proper loading onto the structural components of the T6SS apparatus. However, despite their established importance, the precise molecular function of several T6SS accessory protein families remains unclear. In this study, we set out to characterize the DUF2169 family of T6SS accessory proteins. Using gene co-occurrence analyses, we find that DUF2169-encoding genes strictly co-occur with genes encoding T6SS spike complexes formed by valine-glycine repeat protein G (VgrG) and DUF4150 domains. Although structurally similar to Pro-Ala-Ala-Arg (PAAR) domains, “PAAR-like” DUF4150 domains lack PAAR motifs and instead contain a conserved PIPY motif, leading us to designate them PIPY domains. Next, we present both genetic and biochemical evidence that PIPY domains require a cognate DUF2169 protein to form a functional T6SS spike complex with VgrG. This contrasts with canonical PAAR proteins, which bind VgrG on their own to form functional spike complexes. By solving the first crystal structure of a DUF2169 protein, we show that this T6SS accessory protein adopts a novel protein fold. Furthermore, biophysical and structural modeling data suggest that DUF2169 contains a dynamic loop that physically interacts with a hydrophobic patch on the surface of its cognate PIPY domain. Based on these findings, we propose a model whereby DUF2169 proteins function as molecular chaperones that maintain VgrG–PIPY spike complexes in a secretion-competent state prior to their export by the T6SS apparatus.

DUF2169↗

DOE OSTI2024

Specific iron binding to natural sphingomyelin membrane induced by non-specific co-solutes

Sphingomyelin (SPM), a crucial phospholipid in the myelin sheath, plays a vital role in insulating nerve fibers. We hypothesize that iron ions selectively bind to the phosphatidylcholine (PC) template within the SPM membrane under near-physiological conditions, resulting in disruptions to membrane organization. These interactions could potentially contribute to the degradation of the myelin sheath, thereby playing a role in the development of neurodegenerative diseases. We utilized synchrotron-based X-ray spectroscopy and diffraction techniques to study the interaction of iron ions with a bovine spinal-cord SPM monolayer (ML) at the liquid-vapor interface under physiological conditions. The SPM ML serves as a model system, representing localized patches of lipids within a more complex membrane structure. The experiments assessed iron binding to the SPM membrane both in the presence of salts and with additional evaluation of the effects of various ion species on membrane behavior. Grazing incidence X-ray diffraction was employed to analyze the impact of iron binding on the structural integrity of the SPM membrane. Furthermore, our results demonstrate that iron ions in dilute solution selectively bind to the PC template of the SPM membrane exclusively at near-physiological salt concentrations (e.g., NaCl, KCl, KI, or CaCl 2 ) and are pH-dependent. In-significant binding was detected in the absence of these salts or at near-neutral pH with salts. The surface adsorption of iron ions is correlated with salt concentration, reaching saturation at physiological levels. In contrast, multivalent ions such as La 3+ and Ca 2+ do not bind to SPM under similar conditions. Notably, iron binding to the SPM membrane disrupts its in-plane organization, suggesting that these interactions may compromise membrane integrity and contribute to myelin sheath damage associated with neurological disorders.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Application of lipid-stabilized liquid-liquid interfaces in 3D printing of biomaterials

Developing strategies to stabilize liquid-liquid interfaces is essential for advancing applications in various biomedical systems. This study introduces a novel biocompatible in situ-forming material in which lipid self-assembly stabilizes water–oil interfaces, enabling controlled structuring of liquids through liquid-in-liquid 3D printing. The stabilization process, driven by the formation of nanostructures at the interface, is thoroughly analyzed through small-angle X-ray scattering (SAXS), rheometry, and microscopy techniques. This material system enables the fabrication of complex 3D constructs, including fibers, substrates, and microneedle patches, which exhibit outstanding mechanical properties and biocompatibility, as confirmed by tensile testing and cell viability tests. Here, by leveraging the unique properties of lipid-stabilized interfaces, this work demonstrates the potential of this approach for diverse biomedical applications such as drug delivery and tissue engineering while establishing a foundation for future advancements in liquid-in-liquid 3D printing technology.

36 MATERIALS SCIENCE↗

DOE OSTI2016

ColDICE: A parallel Vlasov–Poisson solver using moving adaptive simplicial tessellation

Resolving numerically Vlasov–Poisson equations for initially cold systems can be reduced to following the evolution of a three-dimensional sheet evolving in six-dimensional phase-space. We describe a public parallel numerical algorithm consisting in representing the phase-space sheet with a conforming, self-adaptive simplicial tessellation of which the vertices follow the Lagrangian equations of motion. The algorithm is implemented both in six- and four-dimensional phase-space. Refinement of the tessellation mesh is performed using the bisection method and a local representation of the phase-space sheet at second order relying on additional tracers created when needed at runtime. In order to preserve in the best way the Hamiltonian nature of the system, refinement is anisotropic and constrained by measurements of local Poincaré invariants. Resolution of Poisson equation is performed using the fast Fourier method on a regular rectangular grid, similarly to particle in cells codes. To compute the density projected onto this grid, the intersection of the tessellation and the grid is calculated using the method of Franklin and Kankanhalli [65–67] generalised to linear order. As preliminary tests of the code, we study in four dimensional phase-space the evolution of an initially small patch in a chaotic potential and the cosmological collapse of a fluctuation composed of two sinusoidal waves. We also perform a “warm” dark matter simulation in six-dimensional phase-space that we use to check the parallel scaling of the code.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2017

Scientific data interpolation with low dimensional manifold model

Here, we propose to apply a low dimensional manifold model to scientific data interpolation from regular and irregular samplings with a significant amount of missing information. The low dimensionality of the patch manifold for general scientific data sets has been used as a regularizer in a variational formulation. The problem is solved via alternating minimization with respect to the manifold and the data set, and the Laplace–Beltrami operator in the Euler–Lagrange equation is discretized using the weighted graph Laplacian. Various scientific data sets from different fields of study are used to illustrate the performance of the proposed algorithm on data compression and interpolation from both regular and irregular samplings.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

The X-Ray Crystal Structure of the Keratin 1-Keratin 10 Helix 2B Heterodimer Reveals Molecular Surface Properties and Biochemical Insights into Human Skin Disease

Keratins 1 (K1) and 10 (K10) are the primary keratins expressed in differentiated epidermis. Mutations in K1/K10 are associated with human skin diseases. We determined the crystal structure of the complex between the distal (2B) helices of K1 and K10 to better understand how human keratin structure correlates with function. The 3.3 Å resolution structure confirms many features inferred by previous biochemical analyses, but adds unexpected insights. It demonstrates a parallel, coiled-coil heterodimer with a predominantly hydrophobic intermolecular interface; this heterodimer formed a higher order complex with a second K1-K10-2B heterodimer via a Cys401K10 disulfide link, although the bond angle is unanticipated. The molecular surface analysis of K1-K10-2B identified several pockets, one adjacent to the disulfide linkage and conserved in K5-K14. The solvent accessible surface area of the K1-K10 structure is 20–25% hydrophobic. The 2B region contains mixed acidic and basic patches proximally (N-terminal), whereas it is largely acidic distally (C-terminal). Mapping of conserved and nonconserved residues between K1-K10 and K5-K14 onto the structure demonstrated the majority of unique residues align along the outer helical ridge. Finally, the structure permitted a fresh analysis of the deleterious effects caused by K1/K10 missense mutations found in patients with phenotypic skin disease.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Multivalent Interactions by the Set8 Histone Methyltransferase With Its Nucleosome Substrate

Set8 is the only mammalian monomethyltransferase responsible for H4K20me1, a methyl mark critical for genomic integrity of eukaryotic cells. We present here a structural model for how Set8 uses multivalent interactions to bind and methylate the nucleosome based on crystallographic and solution studies of the Set8/nucleosome complex. Here, our studies indicate that Set8 employs its i-SET and c-SET domains to engage nucleosomal DNA 1 to 1.5 turns from the nucleosomal dyad and in doing so, it positions the SET domain for catalysis with H4 Lys20. Surprisingly, we find that a basic N-terminal extension to the SET domain plays an even more prominent role in nucleosome binding, possibly by making an arginine anchor interaction with the nucleosome H2A/H2B acidic patch. We further show that proliferating cell nuclear antigen and the nucleosome compete for binding to Set8 through this basic extension, suggesting a mechanism for how nucleosome binding protects Set8 from proliferating cell nuclear antigen-dependent degradation during the cell cycle.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Why do receptor–ligand bonds in cell adhesion cluster into discrete focal-adhesion sites?

We report that cell adhesion often exhibits the clustering of the receptor–ligand bonds into discrete focal-adhesion sites near the contact edge, thus resembling a rosette shape or a contracting membrane anchored by a small number of peripheral forces. The ligands on the extracellular matrix are immobile, and the receptors in the cell plasma membrane consist of two types: high-affinity integrins (that bond to the substrate ligands and are immobile) and low-affinity integrins (that are mobile and not bonded to the ligands). Thus the adhesion energy density is proportional to the high-affinity integrin density. This paper provides a mechanistic explanation for the clustering/assembling of the receptor–ligand bonds from two main points: (1) the cellular contractile force leads to the density evolution of these two types of integrins, and results into a large high-affinity integrin density near the contact edge and (2) the front of a propagating crack into a decreasing toughness field will be unstable and wavy. From this fracture mechanics perspective, the chemomechanical equilibrium is reached when a small number of patches with large receptor–ligand bond density are anticipated to form at the cell periphery, as opposed to a uniform distribution of bonds on the entire interface. Finally, cohesive fracture simulations show that the de-adhesion force can be significantly enhanced by this nonuniform bond density field, but the de-adhesion force anisotropy due to the substrate elastic anisotropy is significantly reduced.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Optimizing the hypre solver for manycore and GPU architectures

The solution of large-scale combustion problems with codes such as Uintah on modern computer architectures requires the use of multithreading and GPUs to achieve performance. Uintah uses a low-Mach number approximation that requires iteratively solving a large system of linear equations. The Hypre iterative solver has solved such systems in a scalable way for Uintah, but the use of OpenMP with Hypre leads to at least slowdown due to OpenMP overheads. The proposed solution uses the MPI Endpoints within Hypre, where each team of threads acts as a different MPI rank. This approach minimizes OpenMP synchronization overhead and performs as fast or (up to 1.44) faster than Hypre's MPI-only version, and allows the rest of Uintah to be optimized using OpenMP. The profiling of the GPU version of Hypre shows the bottleneck to be the launch overhead of thousands of micro-kernels. The GPU performance was improved by fusing these micro-kernels and was further optimized by using Cuda-aware MPI, resulting in an overall speedup of 1.16—1.44 compared to the baseline GPU implementation. The above optimization strategies were published in the International Conference on Computational Science 2020 [1]. This work extends the previously published research by carrying out the second phase of communication-centered optimizations in Hypre to improve its scalability on large-scale supercomputers. Additionally, this includes an efficient non-blocking inter-thread communication scheme, communication-reducing patch assignment, and expression of logical communication parallelism to a new version of the MPICH library that utilizes the underlying network parallelism [2]. The above optimizations avoid communication bottlenecks previously observed during strong scaling and improve performance by up to 2 on 256 nodes of Intel Knight's Landing processor.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Morphology and crystallographic orientation relationship in isothermally transformed Fe–N austenite

The 225 °C isothermal transformation of a high-nitrogen austenite with Fe–2.71 wt.% N was investigated by means of electron microscopy. It was found that the transformation products were composed of ultrafine α-Fe and γ′-Fe{sub 4}N plus retained austenite γ, which were in two types of morphologies, namely, (i) with the retained austenite patches dispersed among the (α-Fe + γ′-Fe{sub 4}N) packets and (ii) with the ultrafine α-Fe and γ/γ′-Fe{sub 4}N laths interwoven with each other within a single bainitic packet. A cube–cube orientation relationship between the γ (austenite) and γ′-Fe{sub 4}N, and a near Greninger–Troiano (G–T) one between the γ (austenite) and the bainitic α-ferrite were detected. The morphology, orientation relationship and high hardness (> 1000 HV) of the transformation products indicated that the isothermal transformation of the high nitrogen austenite was analogous to a bainitic one. - Highlights: • Isothermal transformation products consisted of nano-sized α-Fe + γ′ + γ (retained). • The hardness of transformation product exceeded 1000 HV. • The α-Fe and γ/γ′-Fe{sub 4}N kept a near G-T OR in the grain interior.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Primal interface debonding formulation for finite strain isotropic plasticity

In this work, a framework is developed for modeling ductile damage of nonlinear materials whose plastic deformation is characterized using rate independent classical plasticity. This method relies on the assumption that the free energy can be decomposed into elastic, plastic and damage parts. A thermodynamically consistent method is derived which satisfies the second law of thermodynamics in the Clausius–Duhem inequality form. The dissipation associated with plasticity takes place in the domain only, while damage dissipation is localized to the interface. The method is developed using Variational Multiscale ideas to obtain definitions of the interface fluxes within a primal formulation analogous to the Discontinuous Galerkin method, which ensures weakly vanishing interface gap prior to reaching a damage initiation criterion. The local nonlinear problem to calculate both plastic deformation gradient and damage variable follows an incremental approach similar to classical plasticity return mapping algorithm. This elastoplastic damage formulation is developed for material undergoing finite strain, and it naturally accommodates a trapezoidal traction separation law (TSL) whose shape can be varied to model either ductile interface behavior or brittle interface behavior. The formulation's performance is assessed through modeling a patch test and a compact tension specimen.

42 ENGINEERING↗

DOE OSTI2022

NaroNet: Discovery of tumor microenvironment elements from highly multiplexed images

Understanding the spatial interactions between the elements of the tumor microenvironment -i.e. tumor cells. fibroblasts, immune cells- and how these interactions relate to the diagnosis or prognosis of a tumor is one of the goals of computational pathology. We present NaroNet, a deep learning framework that models the multi-scale tumor microenvironment from multiplex-stained cancer tissue images and provides patient-level interpretable predictions using a seamless end-to-end learning pipeline. Trained only with multiplex-stained tissue images and their corresponding patient-level clinical labels, NaroNet unsupervisedly learns which cell phenotypes, cell neighborhoods, and neighborhood interactions have the highest influence to predict the correct label. To this end, NaroNet incorporates several novel and state-of-the-art deep learning techniques, such as patch-level contrastive learning, multi-level graph embeddings, a novel max-sum pooling operation, or a metric that quantifies the relevance that each microenvironment element has in the individual predictions. We validate NaroNet using synthetic data simulating multiplex-immunostained images where a patient label is artificially associated to the -adjustable- probabilistic incidence of different microenvironment elements. We then apply our model to two sets of images of human cancer tissues: 336 seven-color multiplex-immunostained images from 12 high-grade endometrial cancer patients; and 382 35-plex mass cytometry images from 215 breast cancer patients. In both synthetic and real datasets, NaroNet provides outstanding predictions of relevant clinical information while associating those predictions to the presence of specific microenvironment elements.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

Reduced repair capacity of a DNA clustered damage site comprised of 8-oxo-7,8-dihydro-2'-deoxyguanosine and 2-deoxyribonolactone results in an increased mutagenic potential of these lesions

A signature of ionizing radiation is the induction of DNA clustered damaged sites. Non-double strand break (DSB) clustered damage has been shown to compromise the base excision repair pathway, extending the lifetimes of the lesions within the cluster, compared to isolated lesions. This increases the likelihood the lesions persist to replication and thus increasing the mutagenic potential of the lesions within the cluster. Lesions formed by ionizing radiation include 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) and 2-deoxyribonolactone (dL). dL poses an additional challenge to the cell as it is not repaired by the short-patch base excision repair pathway. Here we show recalcitrant dL repair is reflected in mutations observed when DNA containing it and a proximal 8-oxodGuo is replicated in Escherichia coli . 8-oxodGuo in close proximity to dL on the opposing DNA strand results in an enhanced frequency of mutation of the lesions within the cluster and a 20 base sequence flanking the clustered damage site in an E. coli based plasmid assay. In vitro repair of a dL lesion is reduced when compared to the repair of an abasic (AP) site and a tetrahydrofuran (THF), and this is due mainly to a reduction in the activity of polymerase β, leading to retarded FEN1 and ligase 1 activities. This study has given insights in to the biological effects of clusters containing dL.

Cunniffe, Siobhan↗

DOE OSTI2014

A Mechanism-based Model for Deformation Twinning in Polycrystalline FCC Steel

Deformation twinning, a common and important plastic deformation mechanism, is the key contributor to the excellent combination of strength and ductility in twinning-induced plasticity (TWIP) steel. In the open literature, a significant amount of research has been reported on the microstructural characteristics of deformation twinning and its influence on the overall deformation behavior of TWIP steel. In this study, we examine the feasibility of a mechanism-based crystal plasticity model in simulating the microstructural level deformation characteristics of TWIP steel. To this end, a model considering both double-slip and double-twin is developed to investigate the stress-strain behavior and local microstructural features related to the formation and growth of micro-twins in low stacking fault energy (SFE) TWIP steel. The twin systems are described as pseudo-slips that can be activated when their resolved shear stress reaches the corresponding critical value. A hardening law that accounts for the interaction among the slip and twin systems is also developed. Numerical simulations for dDifferent mesh sizes and single crystal patch tests under different loading modes are carried out to verify the modeling procedure. Our simulation results reveal that, despite its simple nature, the double-slip/double-twin model can capture the key deformation features of TWIP steel, including twin volume fraction evolution, continuous strain hardening, and the final fracture in the form of strain localization.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2023

Ultra-fast and sensitive magneto-optical hydrogen sensors using a magnetic nano-cap array

Magnetism in curved nano-geometries has opened a new path to design novel characteristics and phenomena that could greatly impact the future fundamental and applied studies of materials. Here, in this report, a hexagonally-packed array of magnetic nano-caps (or nano-patches, NP) exhibiting unique magnetic anisotropy and optimal nanostructure for fast hydrogen kinetics is explored as a sensing element for the spark-free magnetic-circular-dichroism (MCD) H 2 sensor. The MCD H 2 sensor outperforms the state-of-the-art optical sensors reported to date and satisfies the most challenging performance targets imposed by US Department of Energy. In particular, a Pd 67 Co 33 NP sensor exhibits response time of t 90 < 0.9 s, recovery time of t 10 < 9.0 s over the 1-100 mbar H 2 partial pressure range, and limit of detection (LOD) of ~1 ppm. The LOD improves to <700 ppb, when the signal-to-noise ratio is enhanced by stacking three NP arrays. Using a 30-nm TAF (Teflon AF 2400) polymer coating, the sorption kinetics of the Pd 67 Co 33 /TAF sensor are significantly accelerated, with t 90 < 0.4 s and t 10 < 2.8 s over the same pressure range. When the Pd 67 Co 33 /TAF sensor is further coated with a 100-nm poly(methyl methacrylate) (PMMA) layer, a rapid sorption time of t 90 < 0.5 s, LOD < 1 ppm and excellent sensor accuracy (<2.5% full scale) are maintained, while the sensor obtains strong selectivity against interference gases and moisture and a negligible aging effect. The MCD nano-cap sensor platform may have a great impact on the future deployment of H 2 fuel, H 2 environmental monitoring sensors, and fast proton-based magneto-ionic devices.

Fast and sensitive hydrogen sensors↗