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At least 163 records · Page 9

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DOE OSTI2023

Vibrational heat-bath configuration interaction with semistochastic perturbation theory using harmonic oscillator or VSCF modals

Vibrational heat-bath configuration interaction (VHCI)—a selected configuration interaction technique for vibrational structure theory—has recently been developed in two independent works [J. H. Fetherolf and T. C. Berkelbach, J. Chem. Phys. 154, 074104 (2021); A. U. Bhatty and K. R. Brorsen, Mol. Phys. 119, e1936250 (2021)], where it was shown to provide accuracy on par with the most accurate vibrational structure methods with a low computational cost. Here, we eliminate the memory bottleneck of the second-order perturbation theory correction using the same (semi)stochastic approach developed previously for electronic structure theory. This allows us to treat, in an unbiased manner, much larger perturbative spaces, which are necessary for high accuracy in large systems. Stochastic errors are easily controlled to be less than 1 cm−1. We also report two other developments: (i) we propose a new heat-bath criterion and an associated exact implicit sorting algorithm for potential energy surfaces expressible as a sum of products of one-dimensional potentials; (ii) we formulate VHCI to use a vibrational self-consistent field (VSCF) reference, as opposed to the harmonic oscillator reference configuration used in previous reports. Our tests are done with quartic and sextic force fields, for which we find that with VSCF, the minor improvements to accuracy are outweighed by the higher computational cost associated the matrix element evaluations. We expect VSCF-based VHCI to be important for more general potential representations, for which the harmonic oscillator basis function integrals are no longer analytic.

Chemistry↗

DOE OSTI2024

Atom-resolved imaging with a silicon tip integrated into an on-chip scanning tunneling microscope

Limited throughput is a shortcoming of the Scanning Tunneling Microscope (STM), particularly when used for atomically precise lithography. To address this issue, we have developed an on-chip STM based on Microelectromechanical-Systems (MEMS) technology. The device reported here has one degree of freedom, replacing the Z axis in a conventional STM. The small footprint of the on-chip STM provides a great opportunity to increase STM throughput by incorporating a number of on-chip STMs in an array to realize parallel STM. The tip methodology adopted for the on-chip STM presented here, which is a batch-fabricated Si tip, makes our design conducive to this goal. In this work, we investigate the capability of this on-chip STM with an integrated Si tip for STM imaging. We integrate the on-chip STM into a commercial ultrahigh-vacuum STM system and perform imaging with atomic resolution on par with conventional STMs but at higher scan speeds due to the higher sensitivity of the MEMS actuator relative to a piezotube. The results attest that it is possible to achieve a parallel and high-throughput STM platform, which is a fully batch-fabricated MEMS STM nanopositioner capable of performing atomic-resolution STM imaging.

Instruments & Instrumentation↗

DOE OSTI2024

Toward ultra-efficient high-fidelity predictions of wind turbine wakes: Augmenting the accuracy of engineering models with machine learning

This study proposes a novel machine learning (ML) methodology for the efficient and cost-effective prediction of high-fidelity three-dimensional velocity fields in the wake of utility-scale turbines. The model consists of an autoencoder convolutional neural network with U-Net skipped connections, fine-tuned using high-fidelity data from large-eddy simulations (LES). The trained model takes the low-fidelity velocity field cost-effectively generated from the analytical engineering wake model as input and produces the high-fidelity velocity fields. The accuracy of the proposed ML model is demonstrated in a utility-scale wind farm for which datasets of wake flow fields were previously generated using LES under various wind speeds, wind directions, and yaw angles. Comparing the ML model results with those of LES, the ML model was shown to reduce the error in the prediction from 20% obtained from the Gauss Curl hybrid (GCH) model to less than 5%. In addition, the ML model captured the non-symmetric wake deflection observed for opposing yaw angles for wake steering cases, demonstrating a greater accuracy than the GCH model. The computational cost of the ML model is on par with that of the analytical wake model while generating numerical outcomes nearly as accurate as those of the high-fidelity LES.

Mechanics↗

DOE OSTI2025

Opportunities in pulsed magnetic fusion energy

Fusion is a potentially transformational energy technology, which promises limitless clean energy. Yet, it requires continued scientific and technological development to realize its potential. The conditions necessary for fusion energy gain in terms of the product of plasma pressure P and confinement time τ have been known for many decades. An underappreciated fact is that pulsed magnetic fusion (PMF) has demonstrated $P_τ$ performance on par with laser-driven inertial confinement fusion and tokamaks despite receiving only a small fraction of investment relative to those concepts. In light of this demonstrated performance, well-established scaling relations, and opportunities for further innovations, here we advocate for PMF as the most attractive path toward commercialization of fusion energy.

Energy technology↗

DOE OSTI2025

Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles

Broad immune responses are needed to mitigate viral evolution and escape. To induce antibodies against conserved receptor-binding domain (RBD) regions of SARS-like betacoronavirus (sarbecovirus) spike proteins that recognize SARS-CoV-2 variants of concern and zoonotic sarbecoviruses, we developed mosaic-8b RBD nanoparticles presenting eight sarbecovirus RBDs arranged randomly on a 60-mer nanoparticle. Mosaic-8b immunizations protected animals from challenges from viruses whose RBDs were matched or mismatched to those on nanoparticles. Here, we describe neutralizing mAbs isolated from mosaic-8b-immunized rabbits, some on par with Pemgarda, the only currently FDA-approved therapeutic mAb. Deep mutational scanning, in vitro selection of spike resistance mutations, and single-particle cryo-electron microscopy structures of spike–antibody complexes demonstrated targeting of conserved RBD epitopes. Rabbit mAbs included critical D-gene segment RBD-recognizing features in common with human anti-RBD mAbs, despite rabbit genomes lacking an equivalent human D-gene segment, thus demonstrating that the immune systems of humans and other mammals can utilize different antibody gene segments to arrive at similar modes of antigen recognition. These results suggest that animal models can be used to elicit anti-RBD mAbs with similar properties to those raised in humans, which can then be humanized for therapeutic use, and that mosaic RBD nanoparticle immunization coupled with multiplexed screening represents an efficient way to generate and select broadly cross-reactive therapeutic pan-sarbecovirus and pan-SARS-CoV-2 variant mAbs.

Science & Technology - Other Topics↗

DOE OSTI2024

Aging heat treatment design for Haynes 282 made by wire-feed additive manufacturing using high-throughput experiments and interpretable machine learning

Wire-feed additive manufacturing (WFAM) produces superalloys with complex thermal cycles and unique microstructures, often requiring optimized heat treatments. To address this challenge, we present a hybrid approach that combines high-throughput experiments, precipitation simulation, and machine learning to design effective aging conditions for the WFAM Haynes 282 superalloy. Our results demonstrate that the γ’ radius is the critical microstructural feature for strengthening Haynes 282 during post-heat treatment compared with the matrix composition and γ’ volume fraction. New aging conditions at 770°C for 50 hours and 730°C for 200 hours were discovered based on the machine learning model and were applied to enhance yield strength, bringing it on par with the wrought counterpart. This approach has significant implications for future AM alloy production, enabling more efficient and effective heat treatment design to achieve desired properties.

CALPHAD↗

DOE OSTI2021

Particle image velocimetry analysis with simultaneous uncertainty quantification using Bayesian neural networks

Particle image velocimetry (PIV) is an effective tool in experimental fluid mechanics for extracting flow fields from images. Recently, convolutional neural networks (CNNs) have been used to perform PIV analysis with accuracy on par with classical methods. Here we extend the use of CNNs to analyze PIV data while providing simultaneous uncertainty quantification on the inferred flow field. The method we apply in this paper is a Bayesian convolutional neural network (BCNN) which learns distributions of the CNN weights through variational Bayes. In order to demonstrate the utility of BCNNs for the PIV task, we compare the performance of three distinct BCNN models with simple architectures. The first network estimates flow velocity from image interrogation regions only. Our second model learns to infer velocity from both the image interrogation regions and interrogation region cross-correlation maps. Finally, our best performing network infers velocities from interrogation region cross-correlation maps only. We find that BCNNs using interrogation region cross-correlation maps as inputs perform better than those using interrogation windows only as inputs and discuss reasons why this may be the case. Additionally, we test the best performing BCNN on a full synthetic test image pair and a real image pair from the 1st International PIV Challenge. We show that ~98% of true particle displacements from the full synthetic image pair can be captured within the BCNN's 95% confidence intervals, and that the BCNN's performance on the real image pair is quantitatively similar to that of algorithms tested in the 1st International PIV Challenge. Finally, we show that BCNNs can be generalized to be used with multi-pass PIV algorithms with a moderate loss in accuracy, which may be overcome by future work on finetuning and training schemes. So to our knowledge, this is the first use of Bayesian neural networks to perform PIV.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Assessment of vertical stability for negative triangularity pilot plants

Abstract Negative triangularity (NT) tokamak configurations may be more susceptible to magneto-hydrodynamic instability, posing challenges for recent reactor designs centered around their favorable properties, such as improved confinement and operation free of edge-localized modes. In this work, we assess the vertical stability of plasmas with NT shaping and develop potential reactor solutions. When coupled with a conformal wall, NT equilibria are confirmed to be less vertically stable than equivalent positive triangularity (PT) configurations. Unlike PT, their vertical stability is degraded at higher poloidal beta. Furthermore, improvements in vertical stability at low aspect ratio do not translate to the NT geometry. NT equilibria are stabilized in PT vacuum vessels due to the increased proximity of the plasma and the wall on the outboard side, but this scenario is found to be undesirable due to reduced vertical gaps which give less spatial margin for control recovery. Instead, we demonstrate that informed positioning of passively conducting plates can lead to improved vertical stability in NT configurations on par with stability metrics expected in PT scenarios. An optimal setup for passive plates in highly elongated NT devices is presented, where plates on the outboard side of the device reduce vertical instability growth rates to 16% of their baseline value. For lower target elongations, integration of passive stabilizers with divertor concepts can lead to significant improvements in vertical stability. Plates on the inboard side of the device are also uniquely enabled in NT geometries, providing opportunity for spatial separation of vertical stability coils and passive stabilizers.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Characterizing the negative triangularity reactor core operating space with integrated modeling

Negative triangularity (NT) has received renewed interest as a fusion reactor regime due to its beneficial power-handling properties, including low scrape-off layer power and a larger divertor wetted area that facilitates simple divertor integration. NT experiments have also demonstrated core performance on par with positive triangularity (PT) high confinement mode (H-mode) without edge-localized modes (ELMs), encouraging further study of an NT reactor core. In this work, we use integrated modeling to scope the operating space around two NT reactor strategies. The first is the high-field, compact fusion pilot plant concept Modular, Adjustable, NT ARC (MANTA) and the second is a low field, high aspect ratio concept based on work by Medvedev et al. By integrating equilibrium, core transport, and edge ballooning instability models, we establish a range of operating points with less than 50 MW scrape-off layer power and fusion power comparable to PT H-mode reactor concepts. Heating and seeded impurities are leveraged to accomplish the same fusion performance and scrape-off layer exhaust power for various pressure edge boundary conditions. Scans over these pressure edge conditions accommodate any current uncertainty of the properties of the NT edge and show that the performance of an NT reactor will be extremely dependent on the edge pressure. The high-field case is found to enable lower scrape-off layer power because it is capable of reaching high fusion powers at a relatively compact size, which allows increased separatrix density without exceeding the Greenwald density limit. Adjustments in NT shaping exhibit small changes in fusion power, with an increase in fusion power density seen at weaker NT. Infinite-n ballooning instability models indicate that an NT reactor core can reach fusion powers comparable to leading PT H-mode reactor concepts while remaining ballooning-stable. Seeded krypton is leveraged to further lower scrape-off layer power since NT does not have a requirement to remain in H-mode while still maintaining high confinement. We contextualize the NT reactor operating space by comparing to popular PT H-mode reactor concepts, and find that NT exhibits competitive ELM-free performance with these concepts for a variety of edge conditions while maintaining relatively low scrape-off layer power.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2026

Application of Portable Parallelization Strategies for GPUs on track reconstruction kernels

Utilizing the computational power of GPUs is one of the key ingredients to meet the computing challenges presented to the next generation of High-Energy Physics (HEP) experiments. Unlike CPUs, developing software for GPUs often involves using architecturespecific programming languages promoted by the GPU vendors and hence limits the platform that the code can run on. Various portability solutions have been developed to achieve portable, performant software across different GPU vendors. Given the rapid evolution of these portability solutions, an early adoption of them in simple HEP testbed applications will help us understand the strengths and weaknesses of respective approaches.We apply several portability solutions, including Alpaka, Kokkos, SYCL and std::execution::par, on kernels for track propagation extracted from the mkFit project. We report on the development experience of the same application with different portability solutions, as well as their performance on GPUs, measured as the throughput of the kernels, from different manufacturers such as NVIDIA, AMD and Intel.

Kwok, Martin [Fermilab] (ORCID:0000000286936146)↗

DOE OSTI2024

Enhancing quantum annealing accuracy through replication-based error mitigation *

Abstract Quantum annealers like those manufactured by D-Wave Systems are designed to find high quality solutions to optimization problems that are typically hard for classical computers. They utilize quantum effects like tunneling to evolve toward low-energy states representing solutions to optimization problems. However, their analog nature and limited control functionalities present challenges to correcting or mitigating hardware errors. As quantum computing advances towards applications, effective error suppression is an important research goal. We propose a new approach called replication based mitigation (RBM) based on parallel quantum annealing (QA). In RBM, physical qubits representing the same logical qubit are dispersed across different copies of the problem embedded in the hardware. This mitigates hardware biases, is compatible with limited qubit connectivity in current annealers, and is well-suited for currently available noisy intermediate-scale quantum annealers. Our experimental analysis shows that RBM provides solution quality on par with previous methods while being more flexible and compatible with a wider range of hardware connectivity patterns. In comparisons against standard QA without error mitigation on larger problem instances that could not be handled by previous methods, RBM consistently gets better energies and ground state probabilities across parameterized problem sets.

Djidjev, Hristo N. (ORCID:0000000192868824)↗

DOE OSTI2023

Identifying strengths and weaknesses of methods for computational network inference from single-cell RNA-seq data

Single-cell RNA-sequencing (scRNA-seq) offers unparalleled insight into the transcriptional programs of different cellular states by measuring the transcriptome of thousands of individual cells. An emerging problem in the analysis of scRNA-seq is the inference of transcriptional gene regulatory networks and a number of methods with different learning frameworks have been developed to address this problem. Here, we present an expanded benchmarking study of eleven recent network inference methods on seven published scRNA-seq datasets in human, mouse, and yeast considering different types of gold standard networks and evaluation metrics. We evaluate methods based on their computing requirements as well as on their ability to recover the network structure. We find that, while most methods have a modest recovery of experimentally derived interactions based on global metrics such as Area Under the Precision Recall curve, methods are able to capture targets of regulators that are relevant to the system under study. Among the top performing methods that use only expression were SCENIC, PIDC, MERLIN or Correlation. Addition of prior biological knowledge and the estimation of transcription factor activities resulted in the best overall performance with the Inferelator and MERLIN methods that use prior knowledge outperforming methods that use expression alone. We found that imputation for network inference did not improve network inference accuracy and could be detrimental. Comparisons of inferred networks for comparable bulk conditions showed that the networks inferred from scRNA-seq datasets are often better or at par with the networks inferred from bulk datasets. Our analysis should be beneficial in selecting methods for network inference. At the same time, this highlights the need for improved methods and better gold standards for regulatory network inference from scRNAseq datasets.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

SPiRaL: a multiresolution global tomography model of seismic wave speeds and radial anisotropy variations in the crust and mantle

SUMMARY SPiRaL is a joint global-scale model of wave speeds (P and S) and anisotropy (vertical transverse isotropy, VTI) variations in the crust and mantle. The model is comprised of >2.1 million nodes with five parameters at each node that capture velocity variations for P- and S-waves travelling at arbitrary directions in transversely isotropic media with a vertical symmetry axis (VTI). The crust (including ice, water, sediments and crystalline layers) is directly incorporated into the model. The default node spacing is approximately 2° in the lower mantle and 1° in the crust and upper mantle. The grid is refined with ∼0.25° minimum node spacing in highly sampled regions of the crust and upper mantle throughout North America and Eurasia. The data considered in the construction of SPiRaL includes millions of body wave traveltimes (crustal, regional and teleseismic phases with multiples) and surface wave (Rayleigh and Love) dispersion. A multiresolution inversion approach is employed to capture long-wavelength heterogeneities commonly depicted in global-scale tomography images as well as more localized details that are typically resolved in more focused regional-scale studies. Our previous work has demonstrated that such global-scale models with regional-scale detail can accurately predict both teleseismic and regional body wave traveltimes, which is necessary for more accurate location of small seismic events that may have limited signal at teleseismic distances. SPiRaL was constructed to predict traveltimes for event location and long-period waveform dispersion for seismic source inversion applications in regions without sufficiently tuned models. SPiRaL may also serve as a starting model for full-waveform inversion (FWI) with the goal of fitting waves with periods 10–50 s over multiple broad regions (thousands of kilometres) and potentially the globe. To gain insight to this possibility, we simulated waveforms for a small set of events using SPiRaL and independent waveform-based models for comparison. For the events tested, the performance of the traveltime-based SPiRaL model is shown to be generally on par with regional 3-D waveform-based models in three regions (western United States, Middle East, Korean Peninsula) suggesting SPiRaL may serve as a starting model for FWI over broad regions.

58 GEOSCIENCES↗

DOE OSTI2022

Image feature extraction and galaxy classification: a novel and efficient approach with automated machine learning

ABSTRACT In this work, we explore the possibility of applying machine learning methods designed for 1D problems to the task of galaxy image classification. The algorithms used for image classification typically rely on multiple costly steps, such as the point spread function deconvolution and the training and application of complex Convolutional Neural Networks of thousands or even millions of parameters. In our approach, we extract features from the galaxy images by analysing the elliptical isophotes in their light distribution and collect the information in a sequence. The sequences obtained with this method present definite features allowing a direct distinction between galaxy types. Then, we train and classify the sequences with machine learning algorithms, designed through the platform Modulos AutoML. As a demonstration of this method, we use the second public release of the Dark Energy Survey (DES DR2). We show that we are able to successfully distinguish between early-type and late-type galaxies, for images with signal-to-noise ratio greater than 300. This yields an accuracy of $86{{\ \rm per\ cent}}$ for the early-type galaxies and $93{{\ \rm per\ cent}}$ for the late-type galaxies, which is on par with most contemporary automated image classification approaches. The data dimensionality reduction of our novel method implies a significant lowering in computational cost of classification. In the perspective of future data sets obtained with e.g. Euclid and the Vera Rubin Observatory, this work represents a path towards using a well-tested and widely used platform from industry in efficiently tackling galaxy classification problems at the peta-byte scale.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Impact of Nutrition on the Gut Microbiota: Implications for Parkinson’s Disease

Abstract Parkinson’s disease (PD) is a multifactorial neurodegenerative disease that is characterized by the degeneration of dopaminergic neurons in the substantia nigra pars compacta and by the anomalous accumulation of α-synuclein aggregates into Lewy bodies and Lewy neurites. Research suggests 2 distinct subtypes of PD: the brain-first subtype if the pathology arises from the brain and then spreads to the peripheral nervous system (PNS) and the body-first subtype, where the pathological process begins in the PNS and then spreads to the central nervous system. This review primarily focuses on the body-first subtype. The influence of the gut microbiota on the development of PD has been the subject of growing interest among researchers. It has been suggested that gut inflammation may be closely associated with pathogenesis in PD, therefore leading to the hypothesis that gut microbiota modulation could play a significant role in this process. Nutrition can influence gut health and alter the risk and progression of PD by altering inflammatory markers. This review provides an overview of recent research that correlates variations in gut microbiota composition between patients with PD and healthy individuals with the impact of certain nutrients and dietary patterns, including the Mediterranean diet, the Western diet, and the ketogenic diet. It explores how these diets influence gut microbiota composition and, consequently, the risk of PD. Last, it examines fecal transplantation and the use of prebiotics, probiotics, or synbiotics as potential therapeutic strategies to balance the gut microbiome, aiming to reduce the risk or delay the progression of PD.

Sobral, Joana (ORCID:0009000334922337)↗

DOE OSTI2020

Modular cell-free expression plasmids to accelerate biological design in cells

Industrial biotechnology aims to produce high-value products from renewable resources. This can be challenging because model microorganisms—organisms that are easy to use like Escherichia coli—often lack the machinery required to utilize desired feedstocks like lignocellulosic biomass or syngas. Non-model organisms, such as Clostridium, are industrially proven and have desirable metabolic features but have several hurdles to mainstream use. Namely, these species grow more slowly than conventional laboratory microbes, and genetic tools for engineering them are far less prevalent. To address these hurdles for accelerating cellular design, cell-free synthetic biology has matured as an approach for characterizing non-model organisms and rapidly testing metabolic pathways in vitro. Unfortunately, cell-free systems can require specialized DNA architectures with minimal regulation that are not compatible with cellular expression. In this work, we develop a modular vector system that allows for T7 expression of desired enzymes for cell-free expression and direct Golden Gate assembly into Clostridium expression vectors. Utilizing the Joint Genome Institute’s DNA Synthesis Community Science Program, we designed and synthesized these plasmids and genes required for our projects allowing us to shuttle DNA easily between our in vitro and in vivo experiments. We next validated that these vectors were sufficient for cell-free expression of functional enzymes, performing on par with the previous state-of-the-art. Lastly, we demonstrated automated six-part DNA assemblies for Clostridium autoethanogenum expression with efficiencies ranging from 68% to 90%. We anticipate this system of plasmids will enable a framework for facile testing of biosynthetic pathways in vitro and in vivo by shortening development cycles.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

From Design to Device: Challenges and Opportunities in Computational Discovery of p -Type Transparent Conductors

A high-performance p -type transparent conductor (TC) does not yet exist but could lead to advances in a wide range of optoelectronic applications and enable new architectures for, e.g., next-generation photovoltaic (PV) devices. High-throughput computational material screenings have been a promising approach to filter databases and identify new p -type TC candidates and some of these predictions have been experimentally validated. However, most of these predicted candidates do not have experimentally achieved properties on par with n -type TCs used in solar cells and therefore have not yet been used in commercial devices. Thus, there is still a significant divide between transforming predictions into results that are actually achievable in the laboratory and an even greater lag in scaling predicted materials into functional devices. In this perspective, we outline some of the major disconnects in this materials discovery process—from scaling computational predictions into synthesizable crystals and thin films in the laboratory to scaling laboratory-grown films into real-world solar devices—and share insights to inform future strategies for TC discovery and design. Published by the American Physical Society 2024

14 SOLAR ENERGY↗

DOE OSTI2023

High Cooperativity Using a Confocal-Cavity–QED Microscope

Cavity quantum electrodynamics (QED) with cooperativity far greater than unity enables high-fidelity quantum sensing and information processing. The high-cooperativity regime is often reached through the use of short single-mode resonators. More complicated multimode resonators, such as the near-confocal optical Fabry-Pérot cavity, can provide intracavity atomic imaging in addition to high cooperativity. This capability has recently proved important for exploring quantum many-body physics in the driven-dissipative setting. In this work, we show that a confocal-cavity–QED microscope can realize cooperativity in excess of 110. This cooperativity is on par with the very best single-mode cavities (which are far shorter) and 21 times greater than single-mode resonators of similar length and mirror radii. The 1.7-µm imaging resolution is naturally identical to the photon-mediated interaction range. We measure these quantities by determining the threshold of cavity superradiance when small optically tweezed BoseEinstein condensates are pumped at various intracavity locations. Transmission measurements of an ex situ cavity corroborate these results. We provide a theoretical description that shows how cooperativity enhancement arises from the dispersive coupling to the atoms of many near-degenerate modes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗