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At least 415 records · Page 23

Structural basis for cloverleaf RNA-initiated viral genome replication

The genomes of positive-strand RNA viruses serve as a template for both protein translation and genome replication. In enteroviruses, a cloverleaf RNA structure at the 5' end of the genome functions as a switch to transition from viral translation to replication by interacting with host poly(C)-binding protein 2 (PCBP2) and the viral 3CD pro protein. We determined the structures of cloverleaf RNA from coxsackievirus and poliovirus. Cloverleaf RNA folds into an H-type four-way junction and is stabilized by a unique adenosine-cytidine-uridine (A•C-U) base triple involving the conserved pyrimidine mismatch region. The two PCBP2 binding sites are spatially proximal and are located on the opposite end from the 3CD pro binding site on cloverleaf. We determined that the A•C-U base triple restricts the flexibility of the cloverleaf stem–loops resulting in partial occlusion of the PCBP2 binding site, and elimination of the A•C-U base triple increases the binding affinity of PCBP2 to the cloverleaf RNA. Based on the cloverleaf structures and biophysical assays, we propose a new mechanistic model by which enteroviruses use the cloverleaf structure as a molecular switch to transition from viral protein translation to genome replication.

59 BASIC BIOLOGICAL SCIENCES↗

Investigation of SF6 Alternatives in Spark Gap Switches for GWP Reduction

This primary purpose of this project was to evaluate alternative gas mixtures to sulfur hexafluoride (SF6) developed for high voltage power delivery applications for use in high voltage spark gap switches. These SF6 alternatives lower global warming potential emissions and enable improvements to the pressure-voltage design space. A combined experimental, computational, and theoretical study was used to quantify the impact of persistent breakdown products on the breakdown distribution of SF6-replacement gas mixtures. Viable SF6 replacements suitable for use in spark gap switches were studied to enable performance and agility improvements for next-generation pulsed power research relevant to national security missions. Experimental campaign included establishing parameters of switch gases as function of concentration. Various concentrations and pressures were tested for trends in breakdown voltage, repeatability, and durability, and breakdown constituents. A zero-dimensional plasma global model was used to simulate the plasma arc decay and recombination process in spark-gap switches relevant to the Z machine. Finally, a complete and consistent set of electron-neutral collision cross-sections for the novel insulating gas C4F7N is reported.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Two TonB-dependent transporters in Methylosinus trichosporium OB3b are responsible for uptake of different forms of methanobactin and are involved in the canonical ‘copper switch’

Copper is an important component of methanotrophic physiology as it controls the expression and activity of alternative forms of methane monooxygenase (MMO). To collect copper, some methanotrophs secrete a chalkophore or copper-binding compound called methanobactin (MB). MB is a ribosomally synthesized post-translationally modified polypeptide (RiPP) that, after binding copper, is collected by MbnT, a TonB-dependent transporter (TBDT). Structurally different forms of MB have been characterized, and here we show that different forms of MB are collected by specific TBDTs. Further, we report that in the model methanotroph, Methylosinus trichosporium OB3b, expression of the TBDT required for uptake of a different MB made by Methylocystis sp. strain SB2 (MB-SB2), is induced in the presence of MB-SB2, suggesting that methanotrophs have developed specific machinery and regulatory systems to actively take up MB from other methanotrophs for copper collection. Moreover, the canonical “copper-switch” in Ms. trichosporium OB3b that controls expression of alternative MMOs is apparent if one of the two TBDTs required for MB-OB3b and MB-SB2 uptake is knocked out, but is disrupted if both TBDTs are knocked out. Furthermore, these data indicate that MB uptake, including the uptake of exogenous MB, plays an important role in the copper switch in M. trichosporium OB3b and thus overall activity. Based on these data, we propose a revised model for the “copper-switch” in this methanotroph that involves MB uptake.

54 ENVIRONMENTAL SCIENCES↗

Hybrid model to evaluate the frequency-dependent leakage inductance of partially-filled transformers

The leakage inductance of a transformer designed for a power electronic converter can drop significantly as the switching frequency is increased due to skin and proximity effects. Although the magnetic image method-based double-2-D model can predict the low-frequency leakage inductance of a partially-filled transformer with sufficient accuracy, it is inherently a frequency-independent model. While Dowell’s 1-D model uses frequency-dependent relations to account for both skin and proximity effects, its accuracy is severely affected by the assumed winding geometry. In this paper, a semianalytical hybrid model is proposed that uses superposition to combine a modified Dowell’s model with the double-2-D model to predict the true leakage inductance of partially-filled transformers at any given frequency. All three conductor types—round, foil, and litz wire—are modeled and analyzed. The quasi-2-D model is further investigated on a variable inductance transformer (VIT) whose winding geometry can be modified mechanically to vary its leakage inductance. With less than 5 % error throughout, the semi-analytically evaluated leakage inductances are in excellent agreement with the finite element method (FEM) simulated and experimentally measured leakage inductances.

24 POWER TRANSMISSION AND DISTRIBUTION↗

A system for the simulation and evaluation of satellite communication networks

With the emergence of a new era in satellite communications brought about by NASA's thrust into the Ka band with multibeam and onboard processing technologies, new and innovative techniques for evaluating these concepts and systems are required. To this end, NASA, in conjunction with its extensive program for advanced communications technology development, has undertaken to develop a concept for the simulation and evaluation of a complete communications network. Incorporated in this network will be proof of concept models of the latest technologies proposed for future satellite communications systems. These include low noise receivers, matrix switches, baseband processors, and solid state and tube type high power amplifiers. To accomplish this, numerous supporting technologies must be added to those aforementioned proof of concept models. These include controllers for synchronization, order wire, and resource allocation, gain compensation, signal leveling, power augmentation, and rain fade and range delay simulation. Taken together, these will be assembled to comprise a system capable of addressing numerous design and performance questions. The simulation and evaluation system as planned will be modular in design and implementation, capable of modification and updating to track and evaluate a continuum emerging concepts and technologies.

Bagwell, J. W.↗

Why it is Unfortunate that Linear Machine Learning “Works” so well in Electromechanical Switching of Ferroelectric Thin Films

Machine learning (ML) is relied on for materials spectroscopy. It is challenging to make ML models fail because statistical correlations can mimic the physics without causality. Here, using a benchmark band-excitation piezoresponse force microscopy polarization spectroscopy (BEPS) dataset the pitfalls of the so-called “better”, “faster”, and “less-biased” ML of electromechanical switching are demonstrated and overcome. Using a toy and real experimental dataset, it is demonstrated how linear nontemporal ML methods result in physically reasonable embedding (eigenvalues) while producing nonsensical eigenvectors and generated spectra, promoting misleading interpretations. A new method of unsupervised multimodal hyperspectral analysis of BEPS is demonstrated using long-short-term memory (LSTM) β-variational autoencoders (β-VAEs) . By including LSTM neurons, the ordinal nature of ferroelectric switching is considered. Further, to improve the interpretability of the latent space, a variational Kullback–Leibler-divergency regularization is imposed . Finally, regularization scheduling of β as a disentanglement metric is leveraged to reduce user bias. Combining these experiment-inspired modifications enables the automated detection of ferroelectric switching mechanisms, including a complex two-step, three-state one. Ultimately, this work provides a robust ML method for the rapid discovery of electromechanical switching mechanisms in ferroelectrics and is applicable to other multimodal hyperspectral materials spectroscopies.

36 MATERIALS SCIENCE↗

Transverse Mode Dynamics of VCSELs Undergoing Current Modulation

Transverse mode dynamics of a 20-micron-diameter vertical-cavity surface-emitting laser (VCSEL) undergoing gain switching by deep current modulation is studied numerically. The direct current (dc) level is set slightly below threshold and is modulated by a large alternating current (ac). The resulting optical pulse train and transverse-mode patterns are obtained numerically. The ac frequency is varied from 2.5 GHz to 10 GHz, and the ac amplitude is varied from one-half to four times that of the dc level. At high modulation frequencies, a regular pulse train is not generated unless the ac amplitude is large enough. At all modulation frequencies, the transverse spatial profile switches from single-mode to multiple-mode pattern as the ac pumping level is increased. Optical pulse widths vary in the range 5-30 ps. with the pulse width decreasing when either the frequency is increased or the ac amplitude is decreased. The numerical modeling uses an approximation form of the semiconductor Maxwell-Bloch equations. Temporal evolution of the spatial profiles of the laser (and of carrier density) is determined without any assumptions about the type or number of modes. Keywords: VCSELs, current modulation, gain switching, transverse mode dynamics, computational modeling

Goorjian, Peter M.↗

V-HAMSTeR v1.0.0

V-HAMSTeR is a bioinformatics software tool designed to predict the hosts of viruses directly from genomic sequences. It can be used by researchers to predict animal, prokaryotic, plant, protist or fungal viral hosts including viruses that may be fragmented or discovered in environmental metagenomic datasets. Features & Uses: The software employs a novel dual-stream deep learning architecture that dynamically fuses implicit sequence embeddings from a genomic foundation model with 13 explicit, handcrafted biological features (e.g., coding density and strand switch rates). To ensure maximum reliability, V=HAMSTeR deploys a 5-fold deep ensemble calibrated via Joint Temperature Scaling, providing users with statistically rigorous confidence probabilities. It also features an automated sequence chunking and mean-pooling module to seamlessly process variable-length contigs. Advantages Over Similar Technologies: Existing tools (e.g., IPEV, RNAVirHost) typically rely on either basic k-mers or isolated neural networks. V-HAMSTeR's hybrid architecture captures both broad genomic context and specific biological motifs that standalone foundation models often miss. Furthermore, unlike competitor tools that struggle with incomplete data or exhibit extreme overconfidence, V-HAMSTeR is explicitly benchmarked and mathematically calibrated for fragmented assemblies (1kb–10kb). This makes it uniquely robust, accurate, and trustworthy for the messy reality of real-world environmental viromics.

Grigson, Susie [Lawrence Berkeley National Laborat↗

Non-linear MHD modelling of edge localized modes suppression by resonant magnetic perturbations in ITER

Edge localized modes (ELMs) suppression by resonant magnetic perturbations (RMPs) was studied with the non-linear magneto-hydro-dynamic (MHD) code JOREK for the ITER H-mode scenarios at 15 MA, 12.5 MA, 10 MA/5.3 T. In this study, the main aim was to demonstrate that ELMs can be suppressed by RMPs while the divertor 3D footprints of heat and particle fluxes remain within divertor material limits. The unstable peeling–ballooning modes responsible for ELMs without RMPs were modelled first for each scenario using numerically accessible parameters for ITER. Then the stabilization of ELMs by RMPs was modelled with the same parameters. RMP spectra, optimized by the linear MHD MARS-F code, with main toroidal harmonics N = 2, N = 3, N = 4 have been used as boundary conditions of the computational domain of JOREK, including realistic RMP coils, main plasma, scrape off layer (SOL) divertor and realistic first wall. The model includes all relevant plasma flows: toroidal rotation, two fluid diamagnetic effects and neoclassical poloidal friction. With RMPs, the main toroidal harmonic and the non-linearly coupled harmonics remain dominant at the plasma edge, producing saturated modes and a continuous MHD turbulent transport thereby avoiding ELM crashes in all scenarios considered here. The threshold for ELM suppression was found at a maximum RMP coils current of 45 kAt–60 kAt compared to the coils maximum capability of 90 kAt. In the high beta poloidal steady-state 10 MA/5.3 T scenario, a rotating QH-mode without ELMs was observed even without RMPs. In this scenario with RMPs N = 3, N = 4 at 20 kAt maximum current in RMP coils, similar QH-mode behaviour was observed however with dominant edge harmonic corresponding to the main toroidal number of RMPs. The present MHD modelling was limited in time by few tens of ms after RMPs were switched on until the magnetic energy of the modes saturates. As a consequence the thermal energy was still evolving on this time scale, far from the ITER confinement time scale and hence only the form of 3D footprints on the divertor targets can be indicated within this set-up. Also note, that the divertor physics was missing in this model, so realistic values of fluxes are out of reach in this modelling. However the stationary 3D divertor and particle fluxes could be simply extrapolated from these results to the stationary situation considering that a large power fraction should be radiated in the core and SOL and only about 50 MW power is going to the divertor, which is an arbitrary, but reasonable number used here. The 3D footprints with RMPs show the characteristic splitting with the main RMP toroidal symmetry. The maximum radial extension of the footprints typically was ~20 cm in inner divertor and ~40 cm in outer divertor with stationary heat fluxes decreasing further out from the initial strike point from ~5 MW m ₋2 to ~1 MW m ₋2 assuming a total power in the divertor and walls is 50 MW. The heat fluxes remain within the divertor target and baffle areas, however with rather small margin in the outer divertor which could be an issue for the first wall especially in transient regimes when part of the plasma thermal energy is released due to switching on the RMP coils. This fact should be considered when RMPs are applied with a more favorable application before or soon after the L–H transition, although optimization is required to avoid increasing the L–H power threshold with RMPs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Reformulating a Gurson-based dynamic damage model and demonstrating improved predictive power and numerical robustness

The original Tepla (TEnsile PLAsticity) ductile damage model, based on the Gurson yield surface, has long been used to model damage evolution and material failure under dynamic loading. Unfortunately, Tepla suffered from mesh sensitivity, numerical instability, and limited predictive capability. Here, we theoretically reformulate Tepla to address these issues. We especially focus on the prediction of porosity, which is the key state variable used for modeling ductile damage, as compared to more easily measured surface velocities, which are at best an indirect measure of damage. Key model changes include separating the viscosity during volumetric void growth from underlying shear strength behavior and switching to an iterative bisection solver. The new Tepla is then calibrated on incipient spall experiments on half-hard copper and tantalum, which demonstrate its ability to simultaneously fit the model to recovered porosity distributions and measured surface velocities, a stringent test. Improved numerical behavior, such as greatly reduced mesh sensitivity, is also shown in those simulations. Finally, the new Tepla model is applied to several high-explosive loaded, sweeping wave experiments, showing the ability of the model to predict behavior on tests with significantly different loading conditions and histories than the calibration data.

36 MATERIALS SCIENCE↗

A system for the simulation and evaluation of satellite communication networks

With the emergence of a new era in satellite communications, brought about by NASA's thrust into the Ka band with multibeam and onboard processing technologies, new and innovative techniques for evaluating these concepts and systems are required. To this end, NASA, in conjunction with its extensive program for advanced communications technology development, has undertaken to develop a concept for the simulation and evaluation of a complete communications network. Incorporated in this network will be proof-of-concept models of the latest technologies proposed for future satellite communications systems. These include low noise receivers, matrix switches, baseband processors, and solid state and tube type high power amplifiers. To accomplish this, numerous supporting technologies must be added to those aforementioned proof-of-concept models. These include controllers for synchronization, order wire, resource allocation, gain compensation, signal leveling, power augmentation, and rain fade and range delay simulation. Taken together, these will be assembled to comprise a system capable of addressing numerous design and performance questions. The simulation and evaluation system, as planned, will be modular in design and implementation, capable of modification and updating to track and evaluate a continuum of emerging concepts and technologies. Previously announced in STAR as N84-13400

Bagwell, J. W.↗

Modeling Space Radiation with Radiomimetic Agent Bleomycin

Space radiation consists of proton and helium from solar particle events (SPE) and high energy heavy ions from galactic cosmic ray (GCR). This mixture of radiation with particles at different energy levels has different effects on biological systems. Currently, majority studies of radiation effects on human were based on single-source radiation due to the limitation of available method to model effects of space radiation on living organisms. While NASA Space Radiation Laboratory is working on advanced switches to make it possible to have a mixed field radiation with particles of different energies, the radiation source will be limited. Development of an easily available experimental model for studying effects of mixed field radiation could greatly speed up our progress in our understanding the molecular mechanisms of damage and responses from exposure to space radiation, and facilitate the discovery of protection and countermeasures against space radiation, which is critical for the mission to Mars. Bleomycin, a radiomimetic agent, has been widely used to study radiation induced DNA damage and cellular responses. Previously, bleomycin was often compared to low low Linear Energy Transfer (LET) gamma radiation without defined characteristics. Our recent work demonstrated that bleomycin could induce complex clustered DNA damage in human fibroblasts that is similar to DNA damage induced by high LET radiation. These type of DNA damage is difficult to repair and can be visualized by gamma-H2Ax staining weeks after the initial insult. The survival ratio between early and late plating of human fibroblasts after bleomycin treatment is between low LET and high LET radiation. Our results suggest that bleomycin induces DNA damage and other cellular stresses resembling those resulted from mixed field radiation with both low and high LET particles. We hypothesize that bleomycin could be used to mimic space radiation in biological systems. Potential advantages and limitations of using bleomycin to treat biological specimen as an easily available model to study effects of space radiation on biological systems and to develop countermeasures for space radiation associated risks will be discussed.

Lu, Tao↗

Convolution Neural Network for Fault Identification in Distribution Feeder with High Penetration Solar PV

Identification and zonal classification of the faults is a decisive factor in the relay’s decision to trip or not. Different types of fault like three-phase, line-to-line-to-ground and single-line-to-ground can occur at various locations in the feeder. These faults are seen as the variation in the instantaneous values of three-phase voltages and currents, i.e., waveforms, that are measured at the relay location. The objective of this work is to develop a machine learning model that can identify a fault and classify it to various protection zones based on measured waveforms. In this work, a data-driven relay based on Convolutional Neural Network (CNN) is proposed for fault identification in distribution feeders with high penetration solar PV. The proposed CNN model takes local current and voltage waveforms as input and classify it into fault, no-fault or a capacitor switching. Further, the CNN also attempts to identify fault zones based on the images of waveforms. The overall testing accuracy of the trained model exceeds 95%.

Ramesh, Meghana↗

Modeling and ZVS Operation of the Isolated Modular Multilevel DC–DC Converter With a Unified Trapezoidal Wave Modulation

Here, this article introduces a unified trapezoidal wave (UTW) modulation scheme for the isolated modular multilevel dc–dc (IM2dc) converter, which consolidates multiple existing modulation strategies for the IM2dc converter, including the quasi-square wave (QSW) modulation, trapezoidal wave modulation, and sinusoidal wave modulation, into a unified framework. Furthermore, this article introduces the harmonic state-space (HSS) equations to model the IM2dc converter based on the UTW modulation method. The HSS model operates in the frequency domain, enabling it to circumvent the complexities associated with time-domain analysis and seamlessly integrate with the UTW modulation. This article proceeds to analyze the real and reactive power transfer characteristics of the IM2dc converter, as well as the power factor, considering the influence of multiple modulation parameters. Subsequently, it delves into the examination of zero voltage switching (ZVS) conditions for the IM2dc converter based on the UTW modulation and the HSS model. The complete ZVS boundaries of the IM2dc converter, taking various voltage ratios into account, are derived. This article also illustrates the effects of including harmonic orders in the modeling process, modulation parameters, and internal harmonic ripples on the ZVS boundaries. Finally, experimental validation of the analyses is conducted on a down-scaled prototype.

42 ENGINEERING↗

Metallofullerene photoswitches driven by photoinduced fullerene-to-metal electron transfer

We report on the discovery and detailed exploration of the unconventional photo-switching mechanism in metallofullerenes, in which the energy of the photon absorbed by the carbon cage π-system is transformed to mechanical motion of the endohedral cluster accompanied by accumulation of spin density on the metal atoms. Comprehensive photophysical and electron paramagnetic resonance (EPR) studies augmented by theoretical modelling are performed to address the phenomenon of the light-induced photo-switching and triplet state spin dynamics in a series of Y x Sc 3-x N@C 80 (x = 0–3) nitride clusterfullerenes. Variable temperature and time-resolved photoluminescence studies revealed a strong dependence of their photophysical properties on the number of Sc atoms in the cluster. All molecules in the series exhibit temperature-dependent luminescence assigned to the near-infrared thermally-activated delayed fluorescence (TADF) and phosphorescence. The emission wavelengths and Stokes shift increase systematically with the number of Sc atoms in the endohedral cluster, whereas the triplet state lifetime and S 1 –T 1 gap decrease in this row. For Sc 3 N@C 80 , we also applied photoelectron spectroscopy to obtain the triplet state energy as well as the electron affinity. Spin distribution and dynamics in the triplet states are then studied by light-induced pulsed EPR and ENDOR spectroscopies. The spin–lattice relaxation times and triplet state lifetimes are determined from the temporal evolution of the electron spin echo after the laser pulse. Well resolved ENDOR spectra of triplets with a rich structure caused by the hyperfine and quadrupolar interactions with 14 N, 45 Sc, and 89 Y nuclear spins are obtained. The systematic increase of the metal contribution to the triplet spin density from Y 3 N to Sc 3 N found in the ENDOR study points to a substantial fullerene-to-metal charge transfer in the excited state. These experimental results are rationalized with the help of ground-state and time-dependent DFT calculations, which revealed a substantial variation of the endohedral cluster position in the photoexcited states driven by the predisposition of Sc atoms to maximize their spin population.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Eucalyptus grandis MYB‐Like and RAN‐Like Zinc Finger Proteins Display Dual Roles in Regulating Plant Immunity and Symbiosis Pathways

Plant roots live in constant contact with diverse microbes in the soil. Plant fitness, therefore, relies on signaling pathways that mount an effective immune response against pathogens while fostering mutualistic symbioses. Plant pathways, and specifically immune genes that may act as "switches," discriminating between pathogenic or mutualistic fungi, remain largely unknown. Using Eucalyptus grandis as a model system, we investigate alterations to the root transcriptomic landscape during pre-symbiosis with either the pathogen Armillaria luteobubalina or the mutualistic fungus Pisolithus microcarpus. Comparative analyses identified three strongly counter-regulated genes that may act as immune switches to accommodate or to repress fungal colonization. We characterized two of these, a MYB-like and RAN-like zinc finger protein, using a transgenic approach and demonstrated that they have bifunctional roles in the regulation of cell death and a hypersensitive-like response, depending on the lifestyle of the associated fungus. Using co-expression network analysis, we identified hypothetical pathways correlated to these genes. We functionally validated these predictions using plants with transgenic roots with increased or decreased transcription of these genes, thereby showing the power of co-expression networks as an a priori approach to identify key immune response pathways in plants. Overall, our results demonstrate that prior to physical contact with microbes, MYB-like and RAN-like zinc finger proteins are key regulators of plant immune signaling that respond to fungal signals and enable or repress symbiotic establishment.

mycorrhizal fungi↗

Baseband processor development for the Advanced Communications Satellite Program

An onboard-baseband-processor concept for a satellite-switched time-division-multiple-access (SS-TDMA) communication system was developed for NASA Lewis Research Center. The baseband processor routes and controls traffic on an individual message basis while providing significant advantages in improved link margins and system flexibility. Key technology developments required to prove the flight readiness of the baseband-processor design are being verified in a baseband-processor proof-of-concept model. These technology developments include serial MSK modems, Clos-type baseband routing switch, a single-chip CMOS maximum-likelihood convolutional decoder, and custom LSL implementation of high-speed, low-power ECL building blocks.

Moat, D.↗

Dopant Optimization of Donors in Semiconductor Opening Switches to Eliminate Prepulse

Semiconductor opening switches are solid-state devices capable of delivering nanosecond, hundreds of kilovolts pulses by interrupting kiloamps of current. The interruption of the current occurs in a moderately doped p-region when a high electric field region (HFR) is formed. The HFR occurs because the reverse pumping current cannot be supported by the saturation velocity and majority carrier concentration of the doping level. However, the donor profile also significantly affects the pulse performance. A secondary prepulse occurs if a secondary HFR is formed at the interface of the background n-doping and N+ doping (X n ) . By moving the location of X n deeper into the diode, the effect of the prepulse is reduced. This article investigates the effect of the donor doping profile on the performance metrics of semiconductor opening switches through technology computer-aided design (TCAD) simulations and experimental results. Through a SILVACO TCAD optimization, we designed a P + /p/n - base/n/N + where the intersection of the moderate p-region and intrinsic n-base region (X p ) is at 160 μm and X n is at 220 μm. This profile is fabricated via silicon epitaxy. Experimentally, it is shown that a deep X n (220 μm) compared with a shallow X n (300 μm) reduces the rise time by >5× . In addition, the magnitude of current density during interruption affects the prepulse foot and pulse shape. At lower current densities without the graded donor profile, high peak voltages are not achieved. Comparing the experimental results to the TCAD simulations shows that the model is predictive under high-current densities in the semiconductor opening switch (SOS) regime.

nanosecond pulse power↗