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At least 307 records · Page 17

A high-throughput workflow to analyze sequence-conformation relationships and explore hydrophobic patterning in disordered peptoids

Understanding how a macromolecule’s primary sequence governs its conformational landscape is crucial for elucidating its function, yet these design principles are still emerging for macromolecules with intrinsic disorder. Herein, we introduce a high-throughput workflow that implements a practical colorimetric conformational assay, introduces a semi-automated sequencing protocol using matrix-assisted laser desorption/ionization and tandem mass spectrometry (MALDI-MS/MS), and develops a generalizable sequence-structure algorithm. Using a model system of 20mer peptidomimetics containing polar glycine and hydrophobic N-butylglycine residues, we identified nine classifications of conformational disorder and isolated 122 unique sequences across varied compositions and conformations. Conformational distributions of three compositionally identical library sequences were corroborated through atomistic simulations and ion mobility spectrometry coupled with liquid chromatography. A data-driven strategy was developed using existing sequence variables and data-derived “motifs” to inform a machine-learning algorithm toward conformation prediction. Here, this multifaceted approach enhances our understanding of sequence-conformation relationships and offers a powerful tool for accelerating the discovery of materials with conformational control.

data-driven analysis↗

Achieving tissue-level softness on stretchable electronics through a generalizable soft interlayer design

Soft and stretchable electronics have emerged as highly promising tools for biomedical diagnosis and biological studies, as they interface intimately with the human body and other biological systems. Most stretchable electronic materials and devices, however, still have Young’s moduli orders of magnitude higher than soft bio-tissues, which limit their conformability and long-term biocompatibility. Here, we present a design strategy of soft interlayer for allowing the use of existing stretchable materials of relatively high moduli to versatilely realize stretchable devices with ultralow tissue-level moduli. We have demonstrated stretchable transistor arrays and active-matrix circuits with moduli below 10 kPa—over two orders of magnitude lower than the current state of the art. Benefiting from the increased conformability to irregular and dynamic surfaces, the ultrasoft device created with the soft interlayer design realizes electrophysiological recording on an isolated heart with high adaptability, spatial stability, and minimal influence on ventricle pressure. In vivo biocompatibility tests also demonstrate the benefit of suppressing foreign-body responses for long-term implantation. With its general applicability to diverse materials and devices, this soft-interlayer design overcomes the material-level limitation for imparting tissue-level softness to a variety of bioelectronic devices.

42 ENGINEERING↗

Activated KCNQ1 channel promotes fibrogenic response in hereditary gingival fibromatosis via clustering and activation of Ras

Abstract Background and Objective Activated potassium channels were found to be strongly correlated with gingival overgrowth (GO) phenotype as we reviewed syndromic hereditary gingival fibromatosis (HGF). Nevertheless, the functional roles of potassium channels in gingival fibrosis or gingival overgrowth remained uncovered. The aim of the present study was to explore the pathogenic role of aberrantly activated potassium channel in Hereditary Gingival Fibromatosis (HGF). Methods Gingival tissues were collected from 9 HGF patients and 15 normal controls. Expression of KCNQ1 was detected by immunohistochemistry. Gingival fibroblasts were isolated, and outward K + currents were detected by whole‐cell patch‐clamp analysis, transmembrane potential was determined by flow cytometry. Normal human gingival fibroblasts (NHGFs) were transfected with KCNQ1 adenovirus or treated with KCNQ1 selective agonist ML277 and antagonist chromanol 293B. Accumulation of Extracellular Matrix (ECM) was measured by Western blotting and Sircol Soluble Collagen Assay. Content of secreted TGF‐β1 was measured by ELISA. Active RAS pull‐down assay and cell immunofluorescence were utilized to verify RAS activation. Results KCNQ1 was upregulated in gingival tissues derived from HGF patients and HGF gingival fibroblasts presented increased outward K + currents than NHGFs. Overexpression of KCNQ1, or KCNQ1 agonist ML277, promoted fibrotic responses of NHGFs. TGF‐β1 and KCNQ1 channels formed a positive feed‐back loop. ML277 generated lateral clustering and activation of Ras on plasma membrane, followed by augmented MAPK/AP‐1 signaling pathway output. JNK or ERK1/2 inhibitors suppressed ML277‐induced AP‐1 and ECM upregulation. Conclusion Activation of KCNQ1 potassium channel promoted fibrogenic responses in NHGFs via Ras/MAPK/AP‐1 signaling.

Gao, Qian↗

Switching Matrix For Optical Signals

Proposed matrix of electronically controlled shutters switches signals in optical fibers between multiple input and output channels. Size, weight, and power consumption reduced. Device serves as building block for small, low-power, broad-band television- and data-signal-switching systems providing high isolation between nominally disconnected channels.

Grove, Charles H.↗

Isotopic and molecular analyses of hydrocarbons and monocarboxylic acids of the Murchison meteorite

The monocarboxylic acids and hydrocarbons of the Murchison meteorite (CM2) were isolated for isotropic analysis. The nonvolatile hydrocarbons were analyzed as crude methanol and benzene-methanol extracts and also after separation by silica gel chromatography into predominantly aliphatic, aromatic, and polar hydrocarbon fractions. The volatile hydrocarbons were obtained after progressive decomposition of the meteorite matrix by freeze-thaw, hot water, and acid treatment. Molecular analyses of the aromatic hydrocarbons showed them to comprise a complex suite of compounds in which pyrene, fluoranthene, phenanthrene, and acenaphthene were the most abundant components, a result similar to earlier analyses. The polar hydrocarbons also comprise a very complex mixture in which aromatic ketones, nitrogen, and sulfur heterocycles were identified. The monocarboxylic acids, aliphatic, aromatic, and polar hydrocarbons, and the indigenous volatile hydrocarbons were found to be D-rich. The deuterium enrichment observed in these compounds is suggestive. In two separate analyses, the delta-D values of the nonvolatile hydrocarbons were observed to increase in the following order: aliphatic-aromatic-polar. This finding is consistent with an early solar system or parent body conversion of aromatic to aliphatic compounds as well as the suggestion of pyrolytic formation of aromatic from aliphatic compounds.

Krishnamurthy, R. V.↗

First-principles insights into chromium-induced oxide phases in NiO

The high-temperature oxidation of Ni–Cr alloys leads to complex oxide scales comprising Ni(Cr)O solid solutions, NiCr 2 O 4 spinel, and Cr 2 O 3 corundum within the NiO matrix. Understanding the atomic-scale mechanisms of Cr segregation and precipitate formation is crucial for enhancing oxidation resistance. Here, we employ density functional theory calculations to investigate Cr behavior on NiO(100), (110), and (111) surfaces and in the bulk. Our results reveal that isolated Cr atoms preferentially segregate to the surfaces, stabilizing Ni(Cr)O solid solutions via strong Cr–O bonding, whereas Cr pairs and clusters favor subsurface migration and bulk aggregation, promoting nucleation of NiCr 2 O 4 and Cr 2 O 3 phases. These findings elucidate a size-dependent segregation mechanism linking Cr coordination environments to oxide phase evolution. This atomic-scale insight informs strategies to tailor oxide microstructures and enhance the high-temperature oxidation resistance of Ni–Cr alloys.

Chromium Segregation↗

Assessment of Survey Results from Advanced Reactor Industry Domain Experts on Nonlinear Soil-Structure Interaction Analysis Software Verification and Validation

The seismic load case has a significant impact on the design and cost of nuclear power plants. Given the need to substantially reduce cost, advanced reactor designers are looking to leverage numerical tools that enable seismic analysis of an integrated vessel/support/structure/soil system. Modern nonlinear analysis tools provide a solution, capturing dynamic coupling between components (including soil-structure interaction (SSI)) concurrent with nonlinear behavior in one or more parts of the system. Although these methods have a rich history of technical development and implementation, software quality assurance (SQA) following nuclear industry standards remains a significant burden for those wishing to adopt such methods for advanced reactor design and licensing. To reduce the SQA burden, this project will develop the guidance for SQA verification and validation (V&V) of coupled nonlinear SSI analysis tools, to include a test matrix of software features and test problems to support commercial grade dedication (CGD). The guidance is intended to be technology-neutral: supporting designers of all advanced reactors. To maximize the value of the project to reactor designers, the project team performed focused surveys of and interviews with advanced reactor designers. Additionally, the project surveyed members of the broader industry involved in reactor design and licensing. The aggregated industry feedback consists of written survey responses, live polling responses, focused interviews, and informal feedback provided after outreach presentations, collectively referred to as “survey results”. Herein, the survey results are reported, reviewed, and assessed to inform follow-on project activities. The survey results confirmed the familiarity of the industry with the coupled nonlinear SSI analysis. They also affirm the project need based upon the expressed intent to (1) incorporate nonlinear features and (2) pursue the coupled nonlinear SSI analysis to reduce seismic demands and construction costs. All reactor designers indicated their intent to incorporate two or more nonlinear features, and all reactor designer respondents opined that the coupled nonlinear SSI analysis would allow for the optimization of the reactor design and construction. However, the programmatic challenges, whether real or perceived, present a significant barrier to reactor designers. The barrier most commonly identified by the reactor designer population was regulatory risk, with 70% citing this as a reason not to pursue the approach. The perceived regulatory risk identified by the reactor designers underscores the importance of regulator engagement and dialogue in this project. Additionally, half of the reactor designers identified cost and lack of guidance as a deterrent. The survey results also provide insights to tailor specific aspects of the guidance document and test matrix. The project plans to prepare both a formal referenceable guidance document and a collaborative, web-based test matrix and problem set. The project will focus on more complete test problem definitions for the prioritized nonlinear features over shallower problem descriptions for a larger set of features. The nonlinearities prioritized as high based upon survey feedback include fluid-structure interaction and seismic isolation and energy dissipation devices. The nonlinearities prioritized as intermediate include nonlinear geomaterials, nonlinear concrete, nonlinear steel, and interface/contact nonlinearity. Deep embedment and the associated nonlinear phenomena are assigned the lowest priority based upon survey feedback.

42 ENGINEERING↗

Vortex Wake Geometry of a Model Tilt Rotor in Forward Flight

A full-span 0.25-scale V-22 tiltrotor was tested in the NASA Ames 40-by 80-Foot Wind Tunnel in November 2000. The main objective of the test was to acquire a comprehensive database to validate tiltrotor analyses. Figure 1 shows the model installed in the Ames 40- by 80-Foot Wind Tunnel. Rotor and vehicle performance measurements were taken in addition to wing pressures, acoustics, and flow visualization. A dual acoustic traverse system was installed to measure blade-vortex interaction (BVI) noise levels and directivity. Test conditions included hover and forward flight in helicopter mode. Angle-of-attack and thrust sweeps for three tunnel speeds were acquired before model problems caused the premature conclusion of the test. The test will resume in the Ames 80- by 120-Foot Wind Tunnel in late 2001. This paper will focus on the wake geometry measurements that were acquired during the test. The wake geometry measurements were a small subset of a larger matrix of planned measurements designed to study the development and structure of the dual vortex system generated during BVI conditions. The present paper will provide wake geometry data for four test conditions. In addition, the data will be compared with previously acquired wake measurements from an isolated tiltrotor

Wadcock, Alan J.↗

Black Hole Airy Tail

In Jackiw-Teitelboim (JT) gravity, which is dual to a random matrix ensemble, the annealed entropy differs from the quenched entropy at low temperatures and goes negative. However, computing the quenched entropy in JT gravity requires a replica limit that is poorly understood. To circumvent this, we define an intermediate quantity called the semiquenched entropy, which has the positivity properties of the quenched entropy, while requiring a much simpler replica trick. We compute this in JT gravity in different regimes using (i) a bulk calculation involving wormholes corresponding to the Airy limit of the dual matrix integral and (ii) a boundary calculation involving one-eigenvalue instanton saddles proposed by Hernández-Cuenca, demonstrating consistency between these two calculations in their common regime of validity. We also clarify why similar one-eigenvalue instanton saddles cannot be used to compute the quenched entropy due to a breakdown of the saddle-point approximation for the one-eigenvalue instanton in the replica limit. Our results show how to use the gravitational path integral to prove that black holes in JT gravity have isolated ground states and to study their properties.

Gauge-gravity dualities↗

A General Materials Data Science Framework for Quantitative 2D Analysis of Particle Growth from Image Sequences

Abstract Phase transformations are a challenging problem in materials science, which lead to changes in properties and may impact performance of material systems in various applications. We introduce a general framework for the analysis of particle growth kinetics by utilizing concepts from machine learning and graph theory. As a model system, we use image sequences of atomic force microscopy showing the crystallization of an amorphous fluoroelastomer film. To identify crystalline particles in an amorphous matrix and track the temporal evolution of the particle dispersion, we have developed quantitative methods of 2D analysis. 700 image sequences were analyzed using a neural network architecture, achieving 0.97 pixel-wise classification accuracy as a measure of the correctly classified pixels. The growth kinetics of isolated and impinged particles were tracked throughout time using these image sequences. The relationship between image sequences and spatiotemporal graph representations was explored to identify the proximity of crystallites from each other. The framework enables the analysis of all image sequences without the requirement of sampling for specific particles or timesteps for various materials systems.

36 MATERIALS SCIENCE↗

Gaseous NH4Cl revisited - A computational investigation of the potential surface and properties

An investigation of the potential surface and properties of the ground state of gaseous NH4Cl is presented. The calculations, which utilize a good basis set and include investigation of the valence correlation effects, result in a description of gaseous NH4Cl as a weakly bound complex with NH3 and HCl structures essentially equivalent to those of the isolated fragments. The charge distributions within the fragments are modifed in the complex, however, and there is a small amount of charge transfer. The results are in reasonable agreement with estimate of D sub 0, super 0 from high temperature mass spectroscopic investigations and vibrational frequencies from matrix experiments. The equilibrium constant for the reversible reaction NH4Cl yields NH3 + HCl indicates that the homogeneous formation of NH4Cl does not represent a significant chemical sink for HCl in the upper atmosphere

Raffenetti, R. C.↗

Progress in demonstrating the performance of Engineered Barriers for the disposal of HLW and SNF: lab studies and demonstration experiments - 20293

Disposal of high-level radioactive waste (HLW) and spent nuclear fuels (SNF) in a geological disposal facility requires a fundamental understanding of the degradation processes of materials used in its engineered barrier system (EBS) over very long timescales. Beyond the wasteform itself (i.e. the borosilicate glass for HLW or the fuel matrix and cladding for SNF), materials often employed in a disposal concept include metallic containers (typically copper and/or carbon steel) and clay-based buffer materials (typically bentonite). In this paper we explore key developments on the long-term evolution of materials employed for the immobilisation, isolation and containment of HLW and SNF in a geological disposal facility, including nuclear glasses, candidate container materials and clay buffers. Our discussion is based on the latest findings from both experimental studies and in-situ demonstration experiments. We present relevant findings from the long-term evolution of HLW glasses (UK composition), metallic materials for the containment system (envisaged in Switzerland, Sweden, Canada and other countries), and bentonite clays (envisaged in many national disposal programmes). (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Integrated-Optic Oxygen Sensors

Compact optical oxygen sensors with self-calibration capabilities are undergoing development. A sensor of this type features a single-chip, integrated-optic design implemented by photolithographic fabrication of optical waveguides in a photosensitive porous glass. The porosity serves as both a matrix for retention of an oxygen-sensitive fluorescent indicator chemical and a medium for diffusion of oxygen to the chemical from the ambient air to be monitored. Each sensor includes at least one such waveguide exposed to the atmosphere and at least one covered with metal for isolation from the atmosphere. The covered one serves as a reference channel. In operation, the concentration of oxygen is deduced from the intensity and lifetime of the fluorescence in the exposed channel, with the help of calibration data acquired via the reference channel. Because the sensory chemical is placed directly in and throughout the cross section of the light path, approximately 99 percent of the light in the waveguide is available for interaction with the chemical, in contradistinction to only about 1 percent of the light in an optical sensor that utilizes evanescentwave coupling. Hence, a sensor of this type is significantly more sensitive.

Mendoza, Edgar A.↗

Rotor Performance Predictions of a Next Generation Mars Science Helicopter

Since Ingenuity took flight and proved aerial capabilities on Mars, the horizon for rotorcraft on the Red Planet has only expanded. One proposed future Martian rotorcraft is the Mars Science Helicopter (MSH). The MSH is a hexacopter capable of carrying scientific payloads. As a part of its joint development by NASA Ames Research Center (ARC) and the Jet Propulsion Laboratory (JPL), key MSH rotor components will be tested inside the in-development Reduced Atmospheric Pressure Testing Of Rotors (RAPTOR) wind tunnel in the Planetary Aeolian Laboratory (PAL) at NASA ARC. In preparation for the test, the Comprehensive Hierarchical Aeromechanics Rotorcraft Model (CHARM) analysis was utilized to predict the aerodynamic performance for one MSH hexacopter isolated rotor. This paper provides an overview of the planned experiments involving the MSH reference blades, as well as CHARM pretest predictions of rotor performance in hover and forward flight. Additionally, the interference effects of wind tunnel walls on rotor performance will be evaluated to inform the test matrix of the upcoming test in the RAPTOR tunnel.

MHS↗

Evaluating performance and portability of high-level programming models: Julia, Python/Numba, and Kokkos on exascale nodes

We explore the performance and portability of the high-level programming models: the LLVM-based Julia and Python/Numba, and Kokkos on high-performance computing (HPC) nodes: AMD Epyc CPUs and MI250X graphical processing units (GPUs) on Frontier’s test bed Crusher system and Ampere’s Arm-based CPUs and NVIDIA’s A100 GPUs on the Wombat system at the Oak Ridge Leadership Computing Facilities. We compare the default performance of a hand-rolled dense matrix multiplication algorithm on CPUs against vendor-compiled C/OpenMP implementations, and on each GPU against CUDA and HIP. Rather than focusing on the kernel optimization per-se, we select this naive approach to resemble exploratory work in science and as a lower-bound for performance to isolate the effect of each programming model. Julia and Kokkos perform comparably with C/OpenMP on CPUs, while Julia implementations are competitive with CUDA and HIP on GPUs. Performance gaps are identified on NVIDIA A100 GPUs for Julia’s single precision and Kokkos, and for Python/Numba in all scenarios. We also comment on half-precision support, productivity, performance portability metrics, and platform readiness. We expect to contribute to the understanding and direction for high-level, high-productivity languages in HPC as the first-generation exascale systems are deployed.

Godoy, William↗

Laser writing of nitrogen-doped silicon carbide for biological modulation

Conducting or semiconducting materials embedded in insulating polymeric substrates can be useful in biointerface applications; however, attainment of this composite configuration by direct chemical processes is challenging. Laser-assisted synthesis has evolved as a fast and inexpensive technique to prepare various materials, but its utility in the construction of biophysical tools or biomedical devices is less explored. Here, we use laser writing to convert portions of polydimethylsiloxane (PDMS) into nitrogen-doped cubic silicon carbide (3C-SiC). The dense 3C-SiC surface layer is connected to the PDMS matrix via a spongy graphite layer, facilitating electrochemical and photoelectrochemical activity. We demonstrate the fabrication of arbitrary two-dimensional (2D) SiC-based patterns in PDMS and freestanding 3D constructs. To establish the functionality of the laser-produced composite, we apply it as flexible electrodes for pacing isolated hearts and as photoelectrodes for local peroxide delivery to smooth muscle sheets.

59 BASIC BIOLOGICAL SCIENCES↗

The 20 x 20 high speed microwave switches

Tests were conducted at NASA Lewis Research Center to characterize the proof-of-concept matrix switches built under NASA contract by Ford Aerospace and Aeronautics Corporation at Palo Alto, California, and the General Electric Company at Valley Forge, Pennsylvania. The contract requirements and goals are tabulated along with the results of the NASA tests. Characteristics examined are bandwidth, insertion loss, ripple, switching speed, isolation, standing wave ratio (input and output), deviation from linear phase, noise figure, reconfiguration rates, spurious responses, gain compression, and third order intermodulation distortion. A brief description of the testing method and a statistical analysis of the test results for each of the switches are provided.

Saunders, A.↗

Reliable statistics-based detection and investigation of anomalies in a SMART valve system

Reliable anomaly detection and diagnosis are critical for the safe operation of complex engineered systems. This study presents a unified framework that integrates statistical, model-based, and data-driven techniques for anomaly detection and investigation, demonstrated on SMART valve systems in hybrid energy applications. Four detection methods—mean deviation, seasonal extreme studentized deviate, ARIMA forecasting, and matrix profiling—were implemented and compared. Matrix profiling was particularly effective in revealing subtle deviations and hidden relationships among variables. Anomaly investigation was performed by analyzing variable-level and grouped signal profiles, with system topology incorporated to distinguish primary faults from propagated effects. Grouping signals by type enhanced interpretability, enabling accurate localization of anomalies across multi-dimensional datasets. Experimental results confirmed the framework's capability to consistently detect and isolate anomalies while providing actionable insights into system interdependencies. The proposed methodology offers a robust, interpretable, and scalable solution for condition monitoring, with potential applications in safety-critical domains such as nuclear energy, aerospace, and process industries.

ARIMA models↗