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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules

Proteins evolve through the modular rearrangement of elements known as domains. Extant, multidomain proteins are hypothesized to be the result of domain accretion, but there has been limited experimental validation of this idea. Here, we introduce a technique for genetic minimization by iterative size-exclusion and recombination (MISER) for comprehensively making all possible deletions of a protein. Using MISER, we generate a deletion landscape for the CRISPR protein Cas9. We find that the catalytically-dead Streptococcus pyogenes Cas9 can tolerate large single deletions in the REC2, REC3, HNH, and RuvC domains, while still functioning in vitro and in vivo, and that these deletions can be stacked together to engineer minimal, DNA-binding effector proteins. In total, our results demonstrate that extant proteins retain significant modularity from the accretion process and, as genetic size is a major limitation for viral delivery systems, establish a general technique to improve genome editing and gene therapy-based therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Fast and scalable quantum Monte Carlo simulations of electron-phonon models

We introduce methodologies for highly scalable quantum Monte Carlo simulations of electron-phonon models, and report benchmark results for the Holstein model on the square lattice. The determinant quantum Monte Carlo (DQMC) method is a widely used tool for simulating simple electron-phonon models at finite temperatures, but incurs a computational cost that scales cubically with system size. Alternatively, near-linear scaling with system size can be achieved with the hybrid Monte Carlo (HMC) method and an integral representation of the Fermion determinant. Here, we introduce a collection of methodologies that make such simulations even faster. To combat "stiffness" arising from the bosonic action, we review how Fourier acceleration can be combined with time-step splitting. To overcome phonon sampling barriers associated with strongly-bound bipolaron formation, we design global Monte Carlo updates that approximately respect particle-hole symmetry. To accelerate the iterative linear solver, we introduce a preconditioner that becomes exact in the adiabatic limit of infinite atomic mass. Finally, we demonstrate how stochastic measurements can be accelerated using fast Fourier transforms. Here, these methods are all complementary and, combined, may produce multiple orders of magnitude speedup, depending on model details.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Optimizing transmit field inhomogeneity of parallel RF transmit design in 7T MRI using deep learning

Ultrahigh field (UHF) Magnetic Resonance Imaging (MRI) provides a higher signal-to-noise ratio and, thereby, higher spatial resolution. However, UHF MRI introduces challenges such as transmit radiofrequency (RF) field (B+1) inhomogeneities, leading to uneven flip angles and image intensity anomalies. These issues can significantly degrade imaging quality and its medical applications. This study addresses B+1 field homogeneity through a novel deep learning-based strategy. Traditional methods like Magnitude Least Squares (MLS) optimization have been effective but are time-consuming and dependent on the patient’s presence. Recent machine learning approaches, such as RF Shim Prediction by Iteratively Projected Ridge Regression and deep learning frameworks, have shown promise but face limitations like extensive training times and oversimplified architectures. We propose a two-step deep learning strategy. First, we obtain the desired reference RF shimming weights from multi-channel B+1 fields using random-initialized Adaptive Moment Estimation. Then, we employ Residual Networks (ResNets) to train a model that maps B+1 fields to target RF shimming outputs. Our approach does not rely on pre-calculated reference optimizations for the testing process and efficiently learns residual functions. Comparative studies with traditional MLS optimization demonstrate our method’s advantages in terms of speed and accuracy. The proposed strategy achieves a faster and more efficient RF shimming design, significantly improving imaging quality at UHF. This advancement holds potential for broader applications in medical imaging and diagnostics.

Lu, Zhengyi [Vanderbilt University]↗
DOE OSTI2020

mpfit: a robust method for fitting atomic resolution images with multiple Gaussian peaks

The standard technique for sub-pixel estimation of atom positions from atomic resolution scanning transmission electron microscopy images relies on fitting intensity maxima or minima with a two-dimensional Gaussian function. While this is a widespread method of measurement, it can be error prone in images with non-zero aberrations, strong intensity differences between adjacent atoms or in situations where the neighboring atom positions approach the resolution limit of the microscope. Here we demonstrate mpfit, an atom finding algorithm that iteratively calculates a series of overlapping two-dimensional Gaussian functions to fit the experimental dataset and then subsequently uses a subset of the calculated Gaussian functions to perform sub-pixel refinement of atom positions. Based on both simulated and experimental datasets presented in this work, this approach gives lower errors when compared to the commonly used single Gaussian peak fitting approach and demonstrates increased robustness over a wider range of experimental conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

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↗
DOE OSTI2021

Integrating continuous hypermutation with high–throughput screening for optimization of cis,cis –muconic acid production in yeast

Directed evolution is a powerful method to optimize proteins and metabolic reactions towards user-defined goals. It usually involves subjecting genes or pathways to iterative rounds of mutagenesis, selection and amplification. While powerful, systematic searches through large sequence-spaces is a labour-intensive task, and can be further limited by a priori knowledge about the optimal initial search space, and/or limits in terms of screening throughput. Here, we demonstrate an integrated directed evolution workflow for metabolic pathway enzymes that continuously generate enzyme variants using the recently developed orthogonal replication system, OrthoRep and screens for optimal performance in high-throughput using a transcription factor-based biosensor. We demonstrate the strengths of this workflow by evolving a rate-limiting enzymatic reaction of the biosynthetic pathway for cis,cis-muconic acid (CCM), a precursor used for bioplastic and coatings, in Saccharomyces cerevisiae. After two weeks of simply iterating between passaging of cells to generate variant enzymes via OrthoRep and high-throughput sorting of best-performing variants using a transcription factor-based biosensor for CCM, we ultimately identified variant enzymes improving CCM titers > 13-fold compared with reference enzymes. Taken together, the combination of synthetic biology tools as adopted in this study is an efficient approach to debottleneck repetitive workflows associated with directed evolution of metabolic enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Implicit Multirate GARK Methods

This article considers multirate generalized-structure additively partitioned Runge–Kutta methods for solving stiff systems of ordinary differential equations with multiple time scales. These methods treat different partitions of the system with different timesteps for a more targeted and efficient solution compared to monolithic single rate approaches. With implicit methods used across all partitions, methods must find a balance between stability and the cost of solving nonlinear equations for the stages. In order to characterize this important trade-off, we explore multirate coupling strategies, problems for assessing linear stability, and techniques to efficiently implement Newton iterations for stage equations. Unlike much of the existing multirate stability analysis which is limited in scope to particular methods, we present general statements on stability and describe fundamental limitations for certain types of multirate schemes. New implicit multirate methods up to fourth order are derived, and their accuracy and efficiency properties are verified with numerical tests.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Pairing and Pair Breaking by Gauge Fluctuations in Bilayer Composite Fermion Metals

We study interlayer pairing of composite fermions in the total $\nu=1/2+1/2$ quantum Hall bilayer as a possible framework for understanding the experimentally observed transition from a compressible state at large layer spacing to a bilayer quantum Hall state at small layer spacing. We consider a model in which the effective interlayer composite fermion pairing interaction mediated by the Chern-Simons gauge fields in the two layers is singular with both attractive (out-of-phase) and repulsive (in-phase) components diverging at low frequency. If only the more singular attractive interaction is included the pairing gap obtained by solving the gap equation is proportional to the inverse of the layer spacing squared. In the so-called local approximation, we find that when the less singular repulsive interactions are also included the pairing gap still falls off as inverse layer spacing squared, consistent with recent analyses, but is strongly suppressed to a degree that may account for the fact that this predicted inverse square dependence is not observed experimentally. The analytically obtained local approximation solutions are then used as a starting point to numerically iterate the full gap equation to assess the validity of the approximation in this limit.

Deng, Haoyun↗
DOE OSTI2025

Power balance and divertor asymmetries in the Super-X divertors of MAST-U using SOLPS-ITER

Spherical tokamaks (STs) present unique challenges and opportunities in the area of particle and power exhaust, intensified due to their more compact sizes. Substantial efforts are underway in STs to determine the limits in dissipative operational regimes and advanced divertor solutions, including at MAST-U which provides access to the Super-X divertor configuration. Power balance, and upper/lower divertor asymmetries have been studied using SOLPS-ITER simulations of the MAST-U Super-X divertor. A set of simulations with experimentally inferred transport coefficients with E x B and diamagnetic drifts activated, consisting of density and power scans, and high field side vs low field side gas puff locations, have been used for code experimentation to uncover trends beyond the current experimental parameter space. The upper biased asymmetry (U:L > 1) of the ratio of the peaks of the plasma energy flux densities at the outer targets increases with heating power and decreases with gas puff strength, going from symmetric to up to a factor of 15. The upper target electron temperature has been found to be a good ordering quantity for the magnitude of this asymmetry for all heating powers, gas puff strength, and gas puff locations. The lower divertor biased asymmetry (U:L < 1) of the radiation patterns processed through SOLPS-based bolometry synthetic diagnostics is in qualitative agreement with resistive bolometry experimental results, and it is in quantitative agreement with the trend of the total volume radiation within the divertors of SOLPS. However, radiation measurements alone are not sufficient to infer the magnitude of the asymmetry of the peaks of the power loads at the targets.

MAST-U↗
DOE OSTI2024

A note on higher-order and nonlinear limiting approaches for continuously bounds-preserving discontinuous Galerkin methods

In Dzanic (2024), a limiting approach for high-order discontinuous Galerkin schemes was introduced which allowed for imposing constraints on the solution continuously (i.e., everywhere within the element). While exact for linear constraint functionals, this approach only imposed a sufficient (but not the minimum necessary) amount of limiting for nonlinear constraint functionals. This short note shows how this limiting approach can be extended to allow exactness for general nonlinear quasiconcave constraint functionals through a nonlinear limiting procedure, reducing unnecessary numerical dissipation. Finally, some examples are shown for nonlinear pressure and entropy constraints in the compressible gas dynamics equations, where both analytic and iterative approaches are used.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

A new discovery of edge localized modes suppression using ICRH

Here, the high-confinement mode (H-mode) is very important for the fusion performance of ITER and future fusion reactors. The H-mode pedestal is a region featuring strongly reduced turbulence and transport just inside the limiting flux surface with strong plasma gradients, which drive edge localized modes (ELMs) in tokamaks. The ELMs, however, are quasiperiodic relaxations of the pedestal, resulting in a series of hot plasma eruptions similar to magnetospheric substorms, solar and stellar flares, which could potentially damage the ITER divertor plates and first walls. To mitigate and suppress the ELMs in H-mode plasmas, the fusion community has tried to develop effective actuators over the past two decades. Two separate excellent inventions have been awarded to recognize their achievements. The 2018 APS excellence award in Plasma Physics Research was given to Drs. Todd E. Evans, Max E. Fenstermacher, and Richard Alan Moyer for their first experimental demonstration of the stabilization of ELMs in high-confinement diverted discharges by application of very small edge-resonant magnetic perturbations, which led to the adoption of suppression coils in the ITER design. The 2018 Fusion Technology Award from the IEEE’s Nuclear and Plasma Science Society (NPSS) was given to Dr. Larry Baylor for his work designing the fueling, pumping and disruption mitigation system for the US ITER Project and for the implementation of pellet ELM mitigation for ITER.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Real-space solution to the electronic structure problem for nearly a million electrons

We report a Kohn–Sham density functional theory calculation of a system with more than 200 000 atoms and 800 000 electrons using a real-space high-order finite-difference method to investigate the electronic structure of large spherical silicon nanoclusters. Our system of choice was a 20 nm large spherical nanocluster with 202 617 silicon atoms and 13 836 hydrogen atoms used to passivate the dangling surface bonds. To speed up the convergence of the eigenspace, we utilized Chebyshev-filtered subspace iteration, and for sparse matrix–vector multiplications, we used blockwise Hilbert space-filling curves, implemented in the PARSEC code. For this calculation, we also replaced our orthonormalization + Rayleigh–Ritz step with a generalized eigenvalue problem step. We utilized all of the 8192 nodes (458 752 processors) on the Frontera machine at the Texas Advanced Computing Center. We achieved two Chebyshev-filtered subspace iterations, yielding a good approximation of the electronic density of states. Our work pushes the limits on the capabilities of the current electronic structure solvers to nearly 106 electrons and demonstrates the potential of the real-space approach to efficiently parallelize large calculations on modern high-performance computing platforms.

Chemistry↗
DOE OSTI2020

Identification of a network of nonlinear interactions as a mechanism triggering the onset of edge localized modes

Edge localized modes (ELMs) remain a critical issue for the lifetime of in-vessel components of fusion reactors such as ITER. We study ELMs triggered when the pedestal parameters are below the peeling-ballooning limit. These ELMs occur while the pedestal recovers after an ELM crash. We identify a mechanism by which a non-linear perturbation involving many active triads—a network of non-linear interactions – leads to the triggering of these ELMs. Each active triad leads to the non-linear transfer of energy between three waves, such that the network of non-linear interactions lead to a transfer of energy between many waves. The triggering of this non-linear perturbation systematically coincides with a pedestal perturbation induced by the neutral beam injection beams and localized near the magnetic surface of safety factor q = 5. Among the non-linear interactions detected during the ELM by a bi-coherence analysis, the most active triad involves a slow frequency that is qualitatively consistent with a geodesic acoustic mode located at the same location, i.e., near the q = 5 surface.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Quantum Electromagnetic Transients Program

This work devises a quantum electromagnetic transients program (QEMTP) which is the first attempt to tackle the computational challenges in solving EMTP through quantum computing. The main contributions lie in: (1) A quantum-enabled EMTP formulation with Dommel's model encoded in quantum states; 2) An Harrow-Hassidim-Lloyd (HHL)-based QEMTP to solve the discrete-time nodal equations; 3) An iteration-based HHL revision for mitigating temporal errors to achieve high accuracy of QEMTP with limited quantum resources. Case studies verify the correctness and efficacy of QEMTP in simulating both fast and slow dynamics.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2020

Fuel Property-Informed Process Design for the Direct Catalytic Conversion of Cellulosics

The direct catalytic conversion of cellulosics (DC3) with supercritical methanol presents a promising pathway to completely solubilize woody biomass and produce >60% mass yield of C2-C6 oxygenates for light duty vehicle applications. Although the oxygenate composition can be tuned by modifying catalyst and process conditions, limited efforts to date have examined DC3 fuel properties for light duty fuel applications to iteratively inform conversion process design. In this work, we designed and evaluated multi-component surrogate bioblendstocks that represent major DC3 light oxygenates and refined catalyst formulations and distillation parameters to improve the resulting light duty fuel quality. Surrogate design for this novel fuel production pathway was based on a preliminary product slate that was systematically adjusted to determine impacts on fuel properties of interest including heating value, oxidative stability, and heat of vaporization, among others. The resulting predictions and measurements of these surrogates were then used to inform improvement of conversion process, and specifically, reformulation of the catalyst which resulted in production of a higher energy density fuel product primarily comprised of saturated alcohols. Fuel testing outcomes also informed downstream oxygenate separations requirements. This resulted in the production of a promising DC3 light-duty fuel blendstock with >15% greater energy density relative to ethanol, while maintaining high octane number and octane sensitivity.

BIOMASS FUELS↗
DOE OSTI2023

Accurate real space iterative reconstruction (RESIRE) algorithm for tomography

Tomography has made a revolutionary impact on the physical, biological and medical sciences. The mathematical foundation of tomography is to reconstruct a three-dimensional (3D) object from a set of two-dimensional (2D) projections. As the number of projections that can be measured from a sample is usually limited by the tolerable radiation dose and/or the geometric constraint on the tilt range, a main challenge in tomography is to achieve the best possible 3D reconstruction from a limited number of projections with noise. Over the years, a number of tomographic reconstruction methods have been developed including direct inversion, real-space, and Fourier-based iterative algorithms. Here, we report the development of a real-space iterative reconstruction (RESIRE) algorithm for accurate tomographic reconstruction. RESIRE iterates between the update of a reconstructed 3D object and the measured projections using a forward and back projection step. The forward projection step is implemented by the Fourier slice theorem or the Radon transform, and the back projection step by a linear transformation. Our numerical and experimental results demonstrate that RESIRE performs more accurate 3D reconstructions than other existing tomographic algorithms, when there are a limited number of projections with noise. Furthermore, RESIRE can be used to reconstruct the 3D structure of extended objects as demonstrated by the determination of the 3D atomic structure of an amorphous Ta thin film. We expect that RESIRE can be widely employed in the tomography applications in different fields. Finally, to make the method accessible to the general user community, the MATLAB source code of RESIRE and all the simulated and experimental data are available at https://zenodo.org/record/7273314.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Beyond Contrast Transfer: Spectral SNR as a Finite-Dose Metric for STEM Phase Retrieval

The contrast transfer function (CTF) is widely used to evaluate phase retrieval methods in scanning transmission electron microscopy (STEM), including center-of-mass imaging, parallax imaging, direct ptychography, and iterative ptychography. However, the CTF reflects only the maximum usable signal, neglecting the effects of finite electron fluence and the Poisson-limited nature of detection. As a result, it can significantly overestimate practical performance, especially in low-dose regimes. Here, we employ the spectral signal-to-noise ratio (SSNR), as a finite-dose statistical framework to evaluate the recoverable signal as a function of spatial frequency. Using numerical reconstructions of white-noise objects, we show that center-of-mass, parallax, and direct ptychography exhibit dose-independent SSNRs, with close-form analytic expressions. In contrast, iterative ptychography exhibits a surprising dose dependence: at low fluence, its SSNR converges to that of direct ptychography; at high fluence, it saturates at a value consistent with the maximum detective quantum efficiency predicted by recent quantum Fisher information bounds. The results highlight the limitations of CTF-based evaluation and motivate SSNR as a more accurate, finite-dose metric for assessing STEM phase retrieval methods.

STEM phase retrieval↗
DOE OSTI2021

Inter-ELM pedestal evolution and the role of edge fluctuations in the C-Mod and DIII-D tokamaks

Edge localized modes (ELMs) lead to a cyclical behaviour of the H-mode pedestal density, temperature and pressure. Substantial evidence exists associating the ELM crash with violation of ideal MHD stability, via current driven kink/peeling modes and/or pressure gradient driven ballooning modes. Recovery from ELM crashes and buildup to the next ELM crash is an active and critical area of edge physics research for ITER projections. In one set of theories, the pedestal pressure profile in H-mode discharges is predicted to be limited by micro-instabilities. One such micro-instability is the kinetic ballooning mode (KBM), which is hypothesized to provide a ‘soft’ limit that regulates the edge transport, thereby restricting the local pressure gradient. In this picture, e.g. in the EPED model, the pedestal width expands slowly until the ideal MHD stability limit is reached. Experiments were recently performed on the C-Mod and DIII-D devices to search for instabilities correlated with the pedestal evolution between ELMs. The results show correlations between the onset of quasi-coherent fluctuations between type I ELMs and a critical temperature gradient. Linear gyrokinetic calculations have shown that these fluctuations have characteristics similar to those expected for KBMs. These results provide additional data toward validation of the EPED model, increasing confidence in ITER projections.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗