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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 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Instabilities and turbulence in low-$β$ guide field reconnection exhausts with kinetic Riemann simulations

The role of turbulence in low-$β$, guide-field reconnection exhausts is explored in 2D reconnection and 2D and 3D Riemann simulations. The structure of the exhaust and associated turbulence is controlled by a pair of rotational discontinuities (RDs) at the exhaust boundary and a pair of slow shocks (SSs) that are generated by counterstreaming ions beams. In 2D, the exhaust develops large-amplitude striations at the ion Larmor radius scale that are produced by electron-beam-driven ion cyclotron waves. The electron beams driving the instability are injected into the exhaust from one of the RDs. However, in 3D Riemann simulations, the additional dimension (in the out-of-plane direction) results in strong Buneman and electron-electron streaming instabilities at the RD which suppress the electron beam formation and therefore the striations in the exhaust. The strength of the streaming instabilities at the RD is controlled by the ratio of the electron thermal speed to Alfvén speed, with the lower thermal speed being more unstable. In the 3D simulations, an ion-ion streaming instability acts to partially thermalize the counterstreaming ion beams at the SSs. This instability is controlled by the ratio of the sound speed to Alfvén speed and is expected to be stable in the low $β$ solar corona. The results suggest that in a guide field reconnection exhaust with 1 $\gg$ $β >$ $m_e/m_i$, the kinetic-scale turbulence that develops will be too weak to play a significant role in energy conversion and particle acceleration. Therefore, the energy conversion will be mostly controlled by laminar physics or multi-x-line reconnection.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Data-guided Multi-Map variables for ensemble refinement of molecular movies

Driving molecular dynamics simulations with data-guided collective variables offer a promising strategy to recover thermodynamic information from structure-centric experiments. In this study, the three-dimensional electron density of a protein, as it would be determined by cryo-EM or x-ray crystallography, is used to achieve simultaneously free-energy costs of conformational transitions and refined atomic structures. Unlike previous density-driven molecular dynamics methodologies that determine only the best map-model fits, our work employs the recently developed Multi-Map methodology to monitor concerted movements within equilibrium, non-equilibrium, and enhanced sampling simulations. Construction of all-atom ensembles along the chosen values of the Multi-Map variable enables simultaneous estimation of average properties, as well as real-space refinement of the structures contributing to such averages. Using three proteins of increasing size, we demonstrate that biased simulation along the reaction coordinates derived from electron densities can capture conformational transitions between known intermediates. The simulated pathways appear reversible with minimal hysteresis and require only low-resolution density information to guide the transition. The induced transitions also produce estimates for free energy differences that can be directly compared to experimental observables and population distributions. The refined model quality is superior compared to those found in the Protein Data Bank. We find that the best quantitative agreement with experimental free-energy differences is obtained using medium resolution density information coupled to comparatively large structural transitions. Practical considerations for probing the transitions between multiple intermediate density states are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Guiding center and gyrokinetic orbit theory for large electric field gradients and strong shear flows

The guiding center and gyrokinetic theory of magnetized particle motion is extended to the regime of large electric field gradients perpendicular to the magnetic field. A gradient in the electric field directly modifies the oscillation frequency and causes the Larmor orbits to deform from circular to elliptical trajectories. In order to retain a good adiabatic invariant, there can only be strong dependence on a single coordinate at lowest order, so that resonances do not generate chaotic motion that destroys the invariant. When the gradient across magnetic flux surfaces is dominant, the guiding center drift velocity becomes anisotropic in response to external forces and additional curvature drifts must be included. The electric polarization density remains gyrotropic, but both the polarization and magnetization are modified by the change in gyrofrequency. The theory can be applied to shear flows that are even stronger than those observed in the edge transport barrier of a high-performance tokamak (H-mode) pedestal, even if the toroidal field is as small as or even smaller than the poloidal field. Yet, the theory retains a mathematical form that is similar to the standard case and can readily be implemented within existing simulation tools.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Physics guided machine learning using simplified theories

Recent applications of machine learning, in particular deep learning, motivate the need to address the generalizability of the statistical inference approaches in physical sciences. In this Letter, we introduce a modular physics guided machine learning framework to improve the accuracy of such data-driven predictive engines. The chief idea in our approach is to augment the knowledge of the simplified theories with the underlying learning process. To emphasize their physical importance, our architecture consists of adding certain features at intermediate layers rather than in the input layer. To demonstrate our approach, we select a canonical airfoil aerodynamic problem with the enhancement of the potential flow theory. We include the features obtained by a panel method that can be computed efficiently for an unseen configuration in our training procedure. By addressing the generalizability concerns, our results suggest that the proposed feature enhancement approach can be effectively used in many scientific machine learning applications, especially for the systems where we can use a theoretical, empirical, or simplified model to guide the learning module.

42 ENGINEERING↗
DOE OSTI2021

Generation of straight and curved hollow plasma channels by laser-generated nonlinear wakefields and studies of ultra-intense laser pulse guiding

We report on a study of highly controllable, quasi-static hollow plasma channels generated by ion motion following a laser–plasma interaction via numerical simulations. These channels are generated by ion motion in a nonlinear wakefield, which has an asymmetry between focusing and defocusing periods. Such plasma channels, driven by a fs duration, 100 TW level laser pulse, have the capability to guide more powerful laser pulses. Moreover, we show that curved plasma channels can be generated in a transverse density gradient plasma and alloptical guiding of a second, significantly more powerful laser pulse in such a curved plasma channel. This mechanism may be useful for creating plasma optics for multi-stage TeV laser plasma accelerators and compact synchrotron radiation sources.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Toward a machine-guided approach to energetic material discovery

In this article, we trained a machine learning (ML) model to connect microstructural details of an energetic material formulation to its performance for the purpose of guiding the discovery of new explosive formulations. Our hypothesis was that the algorithm would robustly learn the training data and produce an accurate surrogate model. Specifically, the algorithm learned the relationship between details of the void size distribution (VSD), initiating shock pressure, and the energetic material performance. We used realistic constraints on the VSD and a range of cases were ingested by a physically informed reactive flow model working within a hydrodynamic solver running on high-performance computing resources. The ML algorithm produced a surrogate model that accurately predicted known test points around the parameter space. In addition to the utility of the model and the process used for its development, we noted interesting comparisons between what we, the authors—subject matter experts, would heuristically conclude from the training data and the surrogate model predictions. We detected nuanced details that were missed by the surrogate model; however, these details are not important to an energetic material formulator. We concluded that the algorithm did indeed robustly learn the training data and produce an accurate surrogate model. We further concluded that the surrogate model is a powerful tool to guide the formulator in the absence of subject matter experts and limited-access computing resources.

42 ENGINEERING↗
DOE OSTI2017

Growth of emittance in laser-plasma electron acceleration in guiding structures

We study angular characteristics, such as emittance and fraction of electrons emitted into a prescribed solid angle, for electron bunches that are accelerated in wake fields generated in various guiding structures – capillary waveguides and plasma channels, in which intense laser pulses propagate. The investigation is performed at various injection energies, which simulate input conditions to different cascades of a multistage electron accelerator. It is shown that, in contrast to the limitations issuing from the requirement of trapping and accelerating a substantial part of bunch electrons, the condition of maintaining the low emittance of the bunch, needed for successful transfer of the accelerated bunch to the entry of the next acceleration cascade or other device, imposes much more strict limitations on the accuracy of focusing of laser radiation to the guiding structure. (paper)

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

Learning dynamical systems from data: An introduction to physics-guided deep learning

Modeling complex physical dynamics is a fundamental task in science and engineering. Traditional physics-based models are first-principled, explainable, and sample-efficient. However, they often rely on strong modeling assumptions and expensive numerical integration, requiring significant computational resources and domain expertise. While deep learning (DL) provides efficient alternatives for modeling complex dynamics, they require a large amount of labeled training data. Furthermore, its predictions may disobey the governing physical laws and are difficult to interpret. Physics-guided DL aims to integrate first-principled physical knowledge into data-driven methods. It has the best of both worlds and is well equipped to better solve scientific problems. Recently, this field has gained great progress and has drawn considerable interest across discipline Here, we introduce the framework of physics-guided DL with a special emphasis on learning dynamical systems. We describe the learning pipeline and categorize state-of-the-art methods under this framework. We also offer our perspectives on the open challenges and emerging opportunities.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2012

FAST MAGNETIC RECONNECTION AND PARTICLE ACCELERATION IN RELATIVISTIC LOW-DENSITY ELECTRON-POSITRON PLASMAS WITHOUT GUIDE FIELD

Magnetic reconnection and particle acceleration in relativistic Harris sheets in low-density electron-positron plasmas with no guide field have been studied by means of two-dimensional particle-in-cell simulations. Reconnection rates are of the order of one when the background density in a Harris sheet is of the order of 1% of the density in the current sheet, which is consistent with previous results in the non-relativistic regime. It has been demonstrated that the increase of the Lorentz factors of accelerated particles significantly enhances the collisionless resistivity needed to sustain a large reconnection electric field. It is shown analytically and numerically that the energy spectrum of accelerated particles near the X-line is the product of a power law and an exponential function of energy, {gamma}{sup -1/4}exp (- a{gamma}{sup 1/2}), where {gamma} is the Lorentz factor and a is a constant. However, in the low-density regime, while the most energetic particles are produced near X-lines, many more particles are energized within magnetic islands. Particles are energized in contracting islands by multiple reflection, but the mechanism is different from Fermi acceleration in magnetic islands for magnetized particles in the presence of a guide field. In magnetic islands, strong core fields are generated and plasma beta values are reduced. As a consequence, the fire-hose instability condition is not satisfied in most of the island region, and island contraction and particle acceleration can continue. In island coalescence, reconnection between two islands can accelerate some particles, however, many particles are decelerated and cooled, which is contrary to what has been discussed in the literature on particle acceleration due to reconnection in non-relativistic hydrogen plasmas.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

THREE-DIMENSIONAL MHD MAGNETIC RECONNECTION SIMULATIONS WITH A FINITE GUIDE FIELD: PROPOSAL OF THE SHOCK-EVOKING POSITIVE-FEEDBACK MODEL

Using a three-dimensional (3D) magnetohydrodynamic model, we simulate the magnetic reconnection in a single current sheet. We assume a finite guide field, a random perturbation on the velocity field, and uniform resistivity. Our model enhances the reconnection rate relative to the classical Sweet–Parker model in the same configuration. The efficiency of magnetic energy conversion is increased by interactions between the multiple tearing layers coexisting in the global current sheet. This interaction, which forms a positive-feedback system, arises from coupling of the inflow and outflow regions in different layers across the current sheet. The coupling accelerates the elementary reconnection events, thereby enhancing the global reconnection rate. The reconnection establishes flux tubes along each tearing layer. Slow-mode shocks gradually form along the outer boundaries of these tubes, further accelerating the magnetic energy conversion. Such a positive-feedback system is absent in two-dimensional simulations, 3D reconnection without a guide field, and reconnection under a single perturbation mode. We refer to our model as the “shock-evoking positive-feedback” model.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

The 2026 guided acoustic waves roadmap

Guided elastic waves are a truly cross-disciplinary key enabling technology. For more than five decades, surface acoustic wave (SAW) and bulk acoustic wave devices find widespread applications. Nowadays, different types of guided elastic waves cover the wide spectrum of applications spanning from quantum technologies to the life sciences, from controlling single excitations to macroscopic collective states in condensed matter. Six years after the first 2019 SAW roadmap, we believe it is time to make a step back and take a fresh look at the status of the field and its future challenges. Since the first roadmap in 2019, the spectrum clearly expanded and this new edition presents a current snapshot of the status of this vibrant field and prospects for potential future developments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Ensembles of novelty detection classifiers for structural health monitoring using guided waves

Guided wave structural health monitoring uses sparse sensor networks embedded in sophisticated structures for defect detection and characterization. The biggest challenge of those sensor networks is developing robust techniques for reliable damage detection under changing environmental and operating conditions. To address this challenge, we develop a novelty classifier for damage detection based on one class support vector machines. We identify appropriate features for damage detection and introduce a feature aggregation method which quadratically increases the number of available training observations.We adopt a two-level voting scheme by using an ensemble of classifiers and predictions. Each classifier is trained on a different segment of the guided wave signal, and each classifier makes an ensemble of predictions based on a single observation. Using this approach, the classifier can be trained using a small number of baseline signals. We study the performance using monte-carlo simulations of an analytical model and data from impact damage experiments on a glass fiber composite plate.We also demonstrate the classifier performance using two types of baseline signals: fixed and rolling baseline training set. The former requires prior knowledge of baseline signals from all environmental and operating conditions, while the latter does not and leverages the fact that environmental and operating conditions vary slowly over time and can be modeled as a Gaussian process.

Dib, Gerges (ORCID:0000000255004047)↗
DOE OSTI2012

RANDOM BALLISTIC INTERPRETATION OF NONLINEAR GUIDING CENTER THEORY

Nonlinear guiding center (NLGC) theory has been used to explain the asymptotic perpendicular diffusion coefficient {kappa} of energetic charged particles in a turbulent magnetic field, which can be applied to better understand cosmic ray transport. Here we re-derive NLGC, replacing the assumption of diffusive decorrelation with random ballistic decorrelation (RBD), which yields an explicit formula for {kappa} . We note that scattering processes can cause a reversal of the guiding center motion along the field line, i.e., 'backtracking', leading to partial cancellation of contributions to {kappa}, especially for low-wavenumber components of the magnetic turbulence. We therefore include a heuristic backtracking correction (BC) that can be used in combination with RBD. In comparison with computer simulation results for various cases, NLGC with RBD and BC provides a substantially improved characterization of the perpendicular diffusion coefficient for a fluctuation amplitude less than or equal to the large-scale magnetic field.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

CRISPR-GRIT: Guide RNAs with Integrated Repair Templates Enable Precise Multiplexed Genome Editing in the Diploid Fungal Pathogen Candida albicans

Candida albicans, an opportunistic fungal pathogen, causes severe infections in immunocompromised individuals. Limited classes and overuse of current antifungals have led to the rapid emergence of antifungal resistance. Thus, there is an urgent need to understand fungal pathogen genetics to develop new antifungal strategies. Genetic manipulation of C. albicans is encumbered by its diploid chromosomes requiring editing both alleles to elucidate gene function. Although the recent development of CRISPR-Cas systems has facilitated genome editing in C. albicans, large-scale and multiplexed functional genomic studies are still hindered by the necessity of cotransforming repair templates for homozygous knockouts. Here, we present CRISPR-GRIT (Guide RNAs with Integrated Repair Templates), a repair template-integrated guide RNA design for expedited gene knockouts and multiplexed gene editing in C. albicans. Here, we envision that this method can be used for high-throughput library screens and identification of synthetic lethal pairs in both C. albicans and other diploid organisms with strong homologous recombination machinery.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Pre-screening to guide coronary artery calcium scoring for early identification of high-risk individuals in the general population

Abstract Aims To evaluate the ability of Systematic COronary Risk Estimation 2 (SCORE2) and other pre-screening methods to identify individuals with high coronary artery calcium score (CACS) in the general population. Methods and results Computed tomography-based CACS quantification was performed in 6530 individuals aged 45 years or older from the general population. Various pre-screening methods to guide referral for CACS were evaluated. Miss rates for high CACS (CACS ≥300 and ≥100) were evaluated for various pre-screening methods: moderate (≥5%) and high (≥10%) SCORE2 risk, any traditional coronary artery disease (CAD) risk factor, any Risk Or Benefit IN Screening for CArdiovascular Disease (ROBINSCA) risk factor, and moderately (>3 mg/24 h) increased urine albumin excretion (UAE). Out of 6530 participants, 643 (9.8%) had CACS ≥300 and 1236 (18.9%) had CACS ≥100. For CACS ≥300 and CACS ≥100, miss rate was 32 and 41% for pre-screening by moderate (≥5%) SCORE2 risk and 81 and 87% for high (≥10%) SCORE2 risk, respectively. For CACS ≥300 and CACS ≥100, miss rate was 8 and 11% for pre-screening by at least one CAD risk factor, 24 and 25% for at least one ROBINSCA risk factor, and 67 and 67% for moderately increased UAE, respectively. Conclusion Many individuals with high CACS in the general population are left unidentified when only performing CACS in case of at least moderate (≥5%) SCORE2, which closely resembles current clinical practice. Less stringent pre-screening by presence of at least one CAD risk factor to guide CACS identifies more individuals with high CACS and could improve CAD prevention.

Ties, Daan (ORCID:0000000164729886)↗
DOE OSTI2023

Computer-aided, resistance gene-guided genome mining for proteasome and HMG-CoA reductase inhibitors

Secondary metabolites (SMs) are biologically active small molecules, many of which are medically valuable. Fungal genomes contain vast numbers of SM biosynthetic gene clusters (BGCs) with unknown products, suggesting that huge numbers of valuable SMs remain to be discovered. It is challenging, however, to identify SM BGCs, among the millions present in fungi, that produce useful compounds. One solution is resistance gene-guided genome mining, which takes advantage of the fact that some BGCs contain a gene encoding a resistant version of the protein targeted by the compound produced by the BGC. The bioinformatic signature of such BGCs is that they contain an allele of an essential gene with no SM biosynthetic function, and there is a second allele elsewhere in the genome. We have developed a computer-assisted approach to resistance gene-guided genome mining that allows users to query large databases for BGCs that putatively make compounds that have targets of therapeutic interest. Working with the MycoCosm genome database, we have applied this approach to look for SM BGCs that target the proteasome β6 subunit, the target of the proteasome inhibitor fellutamide B, or HMG-CoA reductase, the target of cholesterol reducing therapeutics such as lovastatin. Our approach proved effective, finding known fellutamide and lovastatin BGCs as well as fellutamide- and lovastatin-related BGCs with variations in the SM genes that suggest they may produce structural variants of fellutamides and lovastatin. Gratifyingly, we also found BGCs that are not closely related to lovastatin BGCs but putatively produce novel HMG-CoA reductase inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences

Abstract RNA-guided nucleases from CRISPR-Cas systems expand opportunities for precise, targeted genome modification. Endogenous CRISPR-Cas systems in many prokaryotes are attractive to circumvent expression, functionality, and unintended activity hurdles posed by heterologous CRISPR-Cas effectors. However, each CRISPR-Cas system recognizes a unique set of protospacer adjacent motifs (PAMs), which requires identification by extensive screening of randomized DNA libraries. This challenge hinders development of endogenous CRISPR-Cas systems, especially those based on multi-protein effectors and in organisms that are slow-growing or have transformation idiosyncrasies. To address this challenge, we present Spacer2PAM, an easy-to-use, easy-to-interpret R package built to predict and guide experimental determination of functional PAM sequences for any CRISPR-Cas system given its corresponding CRISPR array as input. Spacer2PAM can be used in a ‘Quick’ method to generate a single PAM prediction or in a ‘Comprehensive’ method to inform targeted PAM libraries small enough to screen in difficult to transform organisms. We demonstrate Spacer2PAM by predicting PAM sequences for industrially relevant organisms and experimentally identifying seven PAM sequences that mediate interference from the Spacer2PAM-informed PAM library for the type I-B CRISPR-Cas system from Clostridium autoethanogenum. We anticipate that Spacer2PAM will facilitate the use of endogenous CRISPR-Cas systems for industrial biotechnology and synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes

Abstract RNA-guided endonucleases form the crux of diverse biological processes and technologies, including adaptive immunity, transposition, and genome editing. Some of these enzymes are components of insertion sequences (IS) in the IS200/IS605 and IS607 transposon families. Both IS families encode a TnpA transposase and a TnpB nuclease, an RNA-guided enzyme ancestral to CRISPR-Cas12s. In eukaryotes, TnpB homologs occur as two distinct types, Fanzor1s and Fanzor2s. We analyzed the evolutionary relationships between prokaryotic TnpBs and eukaryotic Fanzors, which revealed that both Fanzor1s and Fanzor2s stem from a single lineage of IS607 TnpBs with unusual active site arrangement. The widespread nature of Fanzors implies that the properties of this particular lineage of IS607 TnpBs were particularly suited to adaptation in eukaryotes. Biochemical analysis of an IS607 TnpB and Fanzor1s revealed common strategies employed by TnpBs and Fanzors to co-evolve with their cognate transposases. Collectively, our results provide a new model of sequential evolution from IS607 TnpBs to Fanzor2s, and Fanzor2s to Fanzor1s that details how genes of prokaryotic origin evolve to give rise to new protein families in eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗