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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.

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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

Structure of yeast Argonaute with guide RNA

The RNA-induced silencing complex, comprising Argonaute and guide RNA, mediates RNA interference. Here we report the 3.2 {angstrom} crystal structure of Kluyveromyces polysporus Argonaute (KpAGO) fortuitously complexed with guide RNA originating from small-RNA duplexes autonomously loaded and processed by recombinant KpAGO. Despite their diverse sequences, guide-RNA nucleotides 1-8 are positioned similarly, with sequence-independent contacts to bases, phosphates and 2{prime}-hydroxyl groups pre-organizing the backbone of nucleotides 2-8 in a near-A-form conformation. Compared with prokaryotic Argonautes, KpAGO has numerous surface-exposed insertion segments, with a cluster of conserved insertions repositioning the N domain to enable full propagation of guide-target pairing. Compared with Argonautes in inactive conformations, KpAGO has a hydrogen-bond network that stabilizes an expanded and repositioned loop, which inserts an invariant glutamate into the catalytic pocket. Mutation analyses and analogies to ribonuclease H indicate that insertion of this glutamate finger completes a universally conserved catalytic tetrad, thereby activating Argonaute for RNA cleavage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Guiding of laser pulses in plasma waveguides created by linearly-polarized femtosecond laser pulses

We experimentally demonstrate that plasma waveguides produced with ultra-short laser pulses (sub-picosecond) in gas jets are capable of guiding high intensity laser pulses. This scheme has the unique ability of guiding a high-intensity laser pulse in a plasma waveguide created by the same laser system in the very simple and stable experimental setup. A hot plasma column was created by a femtosecond class laser that expands into an on-axis parabolic low density profile suitable to act as a waveguide for high intensity laser beams. We have successfully guided ~10 15 W cm -2 laser pulses in a 8 mm long hydrogen plasma waveguide with a 35% guiding efficiency.

42 ENGINEERING↗
DOE OSTI2023

The engineered single guide RNA structure as a biomarker for gene-editing reagent exposure

Abstract CRISPR arrays and CRISPR-associated (Cas) proteins comprise a prevalent adaptive immune system in bacteria and archaea. These systems defend against exogenous parasitic mobile genetic elements. The adaption of single effector CRISPR-Cas systems has massively facilitated gene-editing due to the reprogrammable guide RNA. The guide RNA affords little priming space for conventional PCR-based nucleic acid tests without foreknowledge of the spacer sequence. Further impeding detection of gene-editor exposure, these systems are derived from human microflora and pathogens ( Staphylococcus pyogenes , Streptococcus aureus , etc.) that contaminate human patient samples. The single guide RNA—formed from the CRISPR RNA (crRNA) and transactivating RNA (tracrRNA)—harbors a variable tetraloop sequence between the two RNA segments, complicating PCR assays. Identical single effector Cas proteins are used for gene-editing and naturally by bacteria. Antibodies raised against these Cas proteins are unable to distinguish CRISPR-Cas gene-editors from bacterial contaminant. To overcome the high potential for false positives, we have developed a DNA displacement assay to specifically detect gene-editors. We leveraged the single guide RNA structure as an engineered moiety for gene-editor exposure that does not cross-react with bacterial CRISPRs. Our assay has been validated for five common CRISPR systems and functions in complex sample matrices.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Guiding center equations for ideal magnetohydrodynamic modes

Guiding center simulations are routinely used for the discovery of mode-particle resonances in tokamaks, for both resistive and ideal instabilities and to find modifications of particle distributions caused by a given spectrum of modes, including large scale avalanches during events with a number of large amplitude modes. One of the most fundamental properties of ideal magnetohydrodynamics is the condition that plasma motion cannot change magnetic topology. The conventional representation of ideal magnetohydrodynamic modes by perturbing a toroidal equilibrium field through {delta}B-vector={nabla} Multiplication-Sign ({xi}-vector Multiplication-Sign B-vector), however, perturbs the magnetic topology, introducing extraneous magnetic islands in the field. A proper treatment of an ideal perturbation involves a full Lagrangian displacement of the field due to the perturbation and conserves magnetic topology as it should. In order to examine the effect of ideal magnetohydrodynamic modes on particle trajectories, the guiding center equations should include a correct Lagrangian treatment. Guiding center equations for an ideal displacement {xi}-vector are derived which preserve the magnetic topology and are used to examine mode particle resonances in toroidal confinement devices. These simulations are compared to others which are identical in all respects except that they use the linear representation for the field. Unlike the case for the magnetic field, the use of the linear field perturbation in the guiding center equations does not result in extraneous mode particle resonances.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2013

Monte Carlo implementation of a guiding-center Fokker-Planck kinetic equation

A Monte Carlo method for the collisional guiding-center Fokker-Planck kinetic equation is derived in the five-dimensional guiding-center phase space, where the effects of magnetic drifts due to the background magnetic field nonuniformity are included. It is shown that, in the limit of a homogeneous magnetic field, our guiding-center Monte Carlo collision operator reduces to the guiding-center Monte Carlo Coulomb operator previously derived by Xu and Rosenbluth [Phys. Fluids B 3, 627 (1991)]. Applications of the present work will focus on the collisional transport of energetic ions in complex nonuniform magnetized plasmas in the large mean-free-path (collisionless) limit, where magnetic drifts must be retained.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Focusing electrode and coaxial reflector used for reducing the guiding magnetic field of the Ku-band foilless transit-time oscillator

Based on the theoretical analysis of the intense relativistic electron beam propagation in the coaxial drift-tube, a focusing electrode and a coaxial reflector is proposed to lessen the demand of the coaxial Ku-band foilless transit-time oscillator (TTO) for the guiding magnetic field. Moreover, a Ku-band TTO with the focusing electrode and the coaxial reflector is designed and studied by particle in cell simulation. When the diode voltage is 390 kV, the beam current 7.8 kA, and the guiding magnetic field is only 0.3 T, the device can output 820 MW microwave pulse at 14.25 GHz by means of the simulation. However, for the device without them, the output power is only 320 MW. The primary experiments are also carried out. When the guiding magnetic field is 0.3 T, the output power of the device with the focusing electrode and the coaxial reflector is double that of the one without them. The simulation and experimental results prove that the focusing electrode and the coaxial reflector are effective on reducing the guiding magnetic field of the device.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

Guiding and focusing of fast electron beams produced by ultra-intense laser pulse using a double cone funnel target

A novel double cone funnel target design aiming at efficiently guiding and focusing fast electron beams produced in high intensity (>10{sup 19 }W/cm{sup 2}) laser-solid interactions is investigated via two-dimensional particle-in-cell simulations. The forward-going fast electron beams are shown to be directed and focused to a smaller size in comparison with the incident laser spot size. This plasma funnel attached on the cone target guides and focuses electrons in a manner akin to the control of liquid by a plastic funnel. Such device has the potential to add substantial design flexibility and prevent inefficiencies for important applications such as fast ignition. Two reasons account for the collimation of fast electron beams. First, the sheath electric fields and quasistatic magnetic fields inside the vacuum gap of the double cone provide confinement of the fast electrons in the laser-plasma interaction region. Second, the interface magnetic fields inside the beam collimator further guide and focus the fast electrons during the transport. The application of this technique to cone-guided fast ignition is considered, and it is shown that it can enhance the laser energy deposition in the compressed fuel plasma by a factor of 2 in comparison with the single cone target case.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

Processing system of jaws tomograms for pathology identification and surgical guide modeling

The aim of the study is to create an image processing system, which allows dentists to find pathological resorption and to build surgical guide surface automatically. X-rays images of jaws from cone beam tomography or spiral computed tomography are the initial data for processing. One patient’s examination always includes up to 600 images (or tomograms), that’s why the development of processing system for fast automation search of pathologies is necessary. X-rays images can be useful not for only illness diagnostic but for treatment planning too. We have studied the case of dental implantation – for successful surgical manipulations surgical guides are used. We have created a processing system that automatically builds jaw and teeth boundaries on the x-ray image. After this step, obtained teeth boundaries used for surgical guide surface modeling and jaw boundaries limit the area for further pathologies search. Criterion for the presence of pathological resorption zones inside the limited area is based on statistical investigation. After described actions, it is possible to manufacture surgical guide using 3D printer and apply it in surgical operation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

Preliminary research on overmoded high-power millimeter-wave Cerenkov generator with dual-cavity reflector in low guiding magnetic field

This paper presents preliminary research on a V-band overmoded Cerenkov generator with dual-cavity reflector operating in a low guiding magnetic field. It is found that the fluctuation of the electron envelope in the low guiding magnetic field can be predicted using an equivalent coaxial model of a foilless diode, and a dual-cavity reflector based on the model matching method can provide strong reflection at the front end of the overmoded structures so that any microwave power that leaks into the diode region can be effectively suppressed. Numerical simulations indicate that the control of the beam envelope and the use of the dual-cavity reflector ease generator operation in the low guiding magnetic field. In the experimental research, the fluctuation of the annular electron beam with the outer radius of 7.5 mm measures approximately 0.7 mm, which is in good agreement with the theoretical results. The disturbance caused by power leaking from the overmoded slow wave structure is eliminated by the dual-cavity reflector. With accurate fabrication and assembly processes, an operating frequency of 61.6 GHz is attained by the fifth harmonic heterodyne method, and the output power is measured to be approximately 123 MW by the far-field measurement method at a diode voltage of 445 kV, a beam current of 4.45 kA, and under a guiding magnetic field of 1.45 T. The output mode is measured using an array of neon flash bulbs, and the pulse shortening phenomenon is both observed and analyzed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2018

Electromagnetic fluctuations during guide field reconnection in a laboratory plasma

Electromagnetic fluctuations are studied during magnetic reconnection in a laboratory plasma for a range of guide magnetic fields from nearly zero up to normalized guide fields B g /B up = 1.2. The predominant fluctuations are identified as right-hand polarized whistler modes, which become increasingly organized and less intermittent, and obtain larger amplitude with the increasing guide field. Here, the fluctuation amplitude also increases with the reconnecting magnetic field, implying a relatively constant conversion of upstream magnetic energy to turbulent fluctuations of ≲1% across guide field strengths.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2019

Effects of the guide field on electron distribution functions in the diffusion region of asymmetric reconnection

Crescent electron distribution functions in the electron diffusion region in asymmetric reconnection with a guide field (strength less than 50% of the upstream magnetic field) are investigated by theory and fully kinetic simulations. Electron motion in the electron diffusion region is a combination of meandering across the current sheet and gyration around the guide field. Combining the two canonical momentum conservation laws in a one-dimensional model with the energy conservation law, we derive the shape of crescent electron distribution functions in both velocity planes: perpendicular to the magnetic field and coplanner with the magnetic field. There are two major effects of the guide field on crescent distribution functions: (1) widening the opening angle of the crescent in a reduced distribution function and (2) the linear cut-off of a distribution function nonparallel to the magnetic field. We also discuss a translational mapping (perpendicular to the linear cut-off) of distribution functions between the X-line and another position. In addition, considering the gyration due to the normal magnetic field, we predict the shape of distribution functions in general positions in the electron diffusion region. Finally, the predictions will be useful to identify features of magnetic reconnection in a guide field by satellite observations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Generation of selective single-mode guided waves by d 36 type piezoelectric wafer

In general, mixed modes and dispersion of guided wave occur at any excitation frequency, while single modes are needed for effective nondestructive evaluation of structures. In this work, we present an approach to generate a selective single-mode guided wave in plate-like structures by exploiting the unique directionality of the d 36 type piezoelectric wafer and the symmetry of fundamental guided wave modes. Specifically, we devise a unified fundamental shear horizontal (SH 0 ) wave/fundamental antisymmetric mode (A 0 ) wave directional transducer pair by attaching the d 36 type piezoelectric wafers back to back on the opposite sides of the plate to provide selective, directional single-mode guided waves for actuation and sensing. Originally, the d 36 -type piezoelectric wafer, poled and cut from the lead magnesium niobate-lead titanate crystal, produces a mixture of the in-plane SH 0 (symmetric) mode and out-of-plane A 0 (asymmetric) and S 0 (symmetric) modes. By applying the in-phase or out-of-phase applied electrical field to the coupled d 36 -type piezoelectric wafer pair, our devised approach generates selective single modes, SH 0 or A 0 , respectively, to propagate in the structure. We describe the theoretical development of our approach and conduct both numerical simulations and laboratory experiments for validations.

42 ENGINEERING↗
DOE OSTI2023

Effect of a guide field on the turbulence like properties of magnetic reconnection

The effect of an external guide field on the turbulence-like properties of magnetic reconnection is studied using five different 2.5D kinetic particle-in-cell (PIC) simulations. The magnetic energy spectrum is found to exhibit a slope of approximately −5/3 in the inertial range, independent of the guide field. On the contrary, the electric field spectrum in the inertial range steepens more with the guide field and approaches a slope of −5/3. In addition, spectral analysis of the different terms of the generalized Ohm's law is performed and found to be consistent with PIC simulations of turbulence and MMS observations. Finally, the guide field effect on the energy transfer behavior is examined using the von Kármán–Howarth (vKH) equation based on incompressible Hall-MHD. The general characteristics of the vKH equation with constant rate of energy transfer in the inertial range are consistent in all the simulations. This suggests that the qualitative behavior of energy spectrum and energy transfer in reconnection are similar to that of turbulence, indicating that reconnection fundamentally involves an energy cascade.

Physics↗
DOE OSTI2024

Adiabatic light guide with S-shaped strips

A light guide is an essential part of many scintillator counters and light collection systems. Our main interest is a light guide for a thin, wide scintillator that has high light transmission while converting the area of the light source to the shape of a photo-detector. Here, we propose a variation of the light guide that avoids a 90° twist of the strips, reduces the length of the light pipe, and reduces the complexity of production. Detailed Monte Carlo simulation studies have been performed for a three-strip S-shaped light-guide system.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Quadrupolar density structures in driven magnetic reconnection experiments with a guide field

Magnetic reconnection is a ubiquitous process in plasma physics, driving rapid and energetic events such as coronal mass ejections. Reconnection between magnetic fields with arbitrary shear can be decomposed into an anti-parallel reconnecting component and a non-reconnecting guide-field component, which is parallel to the reconnecting electric field. This guide field modifies the structure of the reconnection layer and the reconnection rate. We present results from experiments on the MAIZE pulsed-power generator (500 kA peak current, 200 ns rise time), which use two exploding wire arrays, tilted in opposite directions, to embed a guide field in the plasma flows with a relative strength b≡B g /B rec =0, 0.4, or 1. The reconnection layers in these experiments have widths that are less than the ion skin depth, d i =c/ω pi , indicating the importance of the Hall term, which generates a distinctive quadrupolar magnetic field structure along the separatrices of the reconnection layer. Using laser imaging interferometry, we observe quadrupolar structures in the line-integrated electron density, consistent with the interaction of the embedded guide field with the quadrupolar Hall field. Our measurements extend over much larger length scales (40d i ) at higher β (∼1) than previous experiments, providing an insight into the global structure of the reconnection layer.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2017

Abnormal blocking of a guided mode propagating in a silicon optical waveguide with periodic tunnel coupling

This paper considers abnormal blocking of a guided mode propagating in a silicon optical waveguide with periodic tunnelling inserts. Using an independent two-dimensional analysis by the method of lines (MoL) and direct simulation by the finite-difference time-domain (FDTD) method, we have identified additional signal blocking bands, unrelated to Bragg conversion to backward guided modes of the parent silicon waveguide. These bands are due to the conversion of the incident wave energy to a leaky quasi-mode of the periodically segmented structure, which subsequently transfers the energy to the ambient medium in the form of radiation modes. A distinctive feature of this phenomenon is resonant coupling of the guided mode of the strip waveguide with its radiation modes, which is due to the weak tunnel coupling with the periodically segmented structure. This structure does not support independent guided propagation, so the energy stored in it is re-emitted to space. The abnormal blocking effect may find application in optical telecommunications elements and in the fabrication of optical sensors. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Guided plasma jets directed onto wet surfaces: angular dependence and control

The optimal use of atmospheric pressure plasma jets (APPJs) for treatment of surfaces—inorganic, organic and liquid—depends on being able to control the flow of plasma-generated reactive species onto the surface. The typical APPJ is a rare gas mixture (RGM) flowed through a tube to which voltage is applied, producing an RGM plasma plume that extends into the ambient air. The RGM plasma plume is guided by a surrounding shroud of air due to the higher electric field required for an ionization wave (IW) to propagate into the air. Additionally, the mixing of the ambient air with the RGM plasma plume then determines the production of reactive oxygen and nitrogen species (RONS). The APPJ is usually oriented perpendicular to the surface being treated. However, the angle of the APPJ with respect to the surface may be a method to control the production of reactive species to the surface due to the change in APPJ propagation properties and the resulting gas dynamics. In this paper, we discuss results from computational and experimental investigations addressing two points—propagation of IWs in APPJs with and without a guiding gas shroud as a function of angle of the APPJ with respect to the surface; and the use of this angle to control plasma activation of thin water layers. We found that APPJs propagating out of the plasma tube into a same-gas environment lack any of the directional properties of shroud-guided jets, and largely follow electric field lines as the angle of the plasma tube is changed. Guided APPJs propagate coaxially with the tube as the angle is changed, and turn perpendicularly towards the surface only a few mm above the surface. The angle of the APPJ produces different gas dynamic distributions, which enable some degree of control over the content of RONS transferred to thin water layers.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Knowledge-guided learning with curated prior genetic biomarkers for robust model interpretation

Abstract Motivation Knowledge-guided learning offers effective and robust model training strategies in data-scarce settings by incorporating established domain knowledge, thereby enhancing generalization, robustness, and interpretability. By contrast, conventional deep learning approaches rely purely on data-driven learning, which can limit robust model interpretability, particularly in high-dimensional settings with limited size samples. In computational biology, knowledge-guided learning has primarily leveraged network- and structural-based knowledge, leading to biologically interpretable representations and enhanced predictive performance compared to conventional approaches. However, curated biomarkers, one of the most accessible forms of biological knowledge, remain largely unexplored within knowledge-guided paradigms. Results In this study, we propose a model-agnostic training paradigm, Biomarker-driven Explainable Prior-guided Learning (BioExPL), that can be applied to any neural networks that incorporates curated prior knowledge. BioExPL enforces neural networks to reflect curated biomarker priors in their latent representations through a novel knowledge-alignment loss. BioExPL consistently demonstrated significantly improved predictive performance and enhanced model interpretability with minimized computational overhead in simulation studies and intensive experiments on multiple cancer datasets. BioExPL not only integrates prior curated knowledge into the model but also accurately identifies unknown associated signals additionally. BioExPL is model-agnostic and domain-independent, enabling its integration into diverse neural network architectures. Availability and implementation The open-source is publicly available at: https://github.com/datax-lab/BioExPL.

Baek, Beomsu [Department of Computer Science, Univ↗