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At least 1,765 records · Page 98

A dynamically bi-orthogonal method for time-dependent stochastic partial differential equations I: Derivation and algorithms

We propose a dynamically bi-orthogonal method (DyBO) to solve time dependent stochastic partial differential equations (SPDEs). The objective of our method is to exploit some intrinsic sparse structure in the stochastic solution by constructing the sparsest representation of the stochastic solution via a bi-orthogonal basis. It is well-known that the Karhunen–Loeve expansion (KLE) minimizes the total mean squared error and gives the sparsest representation of stochastic solutions. However, the computation of the KL expansion could be quite expensive since we need to form a covariance matrix and solve a large-scale eigenvalue problem. The main contribution of this paper is that we derive an equivalent system that governs the evolution of the spatial and stochastic basis in the KL expansion. Unlike other reduced model methods, our method constructs the reduced basis on-the-fly without the need to form the covariance matrix or to compute its eigendecomposition. In the first part of our paper, we introduce the derivation of the dynamically bi-orthogonal formulation for SPDEs, discuss several theoretical issues, such as the dynamic bi-orthogonality preservation and some preliminary error analysis of the DyBO method. We also give some numerical implementation details of the DyBO methods, including the representation of stochastic basis and techniques to deal with eigenvalue crossing. In the second part of our paper [11], we will present an adaptive strategy to dynamically remove or add modes, perform a detailed complexity analysis, and discuss various generalizations of this approach. An extensive range of numerical experiments will be provided in both parts to demonstrate the effectiveness of the DyBO method.

97 MATHEMATICS AND COMPUTING↗

Prediction of DIII-D Pedestal Structure From Externally Controllable Parameters

The sharp increase of pressure at the edge of a high confinement mode (H-mode) plasma, the pedestal, strongly impacts overall plasma performance. Predicting the pedestal is a necessity to control and optimize tokamak operations. Here, an experimental data-driven machine learning (ML) approach is presented that predicts the pedestal heights and widths of electron density (n e ) and electron temperature (T e ) profiles as well as the separatrix ne from externally controllable parameters such as the plasma shape, heating method and power, and gas puff rate and integrated gas puff. The OMFIT framework was used with DIII-D data to efficiently, robustly, and automatically build a database of pedestal parameters to train machine learning models. Database creation was enabled by the search engine tool for DIII-D data, TokSearch, which parallelizes data fetching, enabling fast searches through basic signals of thousands of DIII-D shots and selection of relevant time intervals. Principal Component Analysis (PCA) separated the database into three clusters that represent classes of plasma shapes that are regularly used in DIII-D. The most important parameters for setting the pedestal structure were plasma current (I p ), toroidal magnetic field (B Φ ), neutral beam heating power (P NBI ) and shaping quantities. The Deep Jointly Informed Neural Networks (DJINN) algorithm was applied to identify suitable neural network (NN) architectures that appropriately capture the features of the pedestal database. Separate NNs were implemented for each pedestal parameter, and ensembling methods were used to improve the prediction accuracy and allowed estimation of the prediction uncertainty. The pedestal predictions of the test dataset lie within the measurement uncertainties of the pedestal parameters. The NN outperformed simple Linear Regression (LR) analysis, indicating non-linear dependencies in the pedestal structure. The presented achievements illustrate a promising path for future research, using feature extraction to infer experimental trends and thereby improve pedestal models as well as deploying NN for a fast pedestal prediction in DIII-D scenario development.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

All-Electric Nonassociative Learning in Nickel Oxide

Habituation and sensitization represent nonassociative learning mechanisms in both non-neural and neural organisms. They are essential for a range of functions from survival to adaptation in dynamic environments. Design of hardware for neuroinspired computing strives to emulate such features driven by electric bias and can also be incorporated into neural network algorithms. Herein, cellular-like learning in oxygen-deficient NiO x devices is demonstrated. Both habituation learning and sensitization response can be achieved in a single device by simply controlling the magnitude of the electric field. Spontaneous memory relaxations and dynamic redistribution of oxygen vacancies under electric bias enable such learning behavior of NiO x under sequential training. These characteristics in simple device arrays are implemented to learn alphabets as well as demonstrate simulated algorithmic use cases in digit recognition. Transition metal oxides with carefully prepared defect concentrations can be highly sensitive to electronic structure perturbations under moderate electrical stimulus and serve as building blocks for next-generation neuroinspired computing hardware.

36 MATERIALS SCIENCE↗

Uncertainty in inventories for life cycle assessment: State‐of‐the‐art, challenges, and new technologies

Uncertainty is a critical factor that can hinder the quality and potential applications of life cycle assessment (LCA) results. A prominent source of uncertainty stems from the life cycle inventory (LCI) data. Various methodologies exist to estimate the uncertainty associated with LCI data, primarily based on the widely used structured pedigree matrix approach or the computationally intensive Monte Carlo simulation. This perspective review explores how new technologies (e.g., computational algorithms and data collection methods) from data science and related fields can contribute to identifying, quantifying, and reducing uncertainty in LCI modeling. A brief overview of the sources of uncertainty in LCI modeling and how they are addressed in current LCA practice is provided. Additionally, several new technologies are identified, and the potential benefits of their implementation in reducing uncertainties in LCI modeling are discussed. This perspective review concludes by identifying potential areas that require further development for these technologies.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Computation of Effective Radiative Properties of Powders for Selective Laser Sintering Simulations

Selective laser sintering (SLS) is an additive manufacturing technique for rapidly creating parts directly from a computer-aided design (CAD) model by using a laser to fuse successive layers of powder. However, better understanding of the effect of particle-level variations on the overall build quality is needed. In this work, we investigated these effects computationally by considering the role of the particle size distribution and variations in the powder bed depth to mimic the part complexity found in overhangs and protrusions. In addition, the results from these studies can be distilled to obtain better effective material properties such as laser absorptivity and laser extinction coefficient that are needed for continuum models of the process. We implement a Monte Carlo ray-tracing algorithm within the discrete element model in the open-source simulation software MFiX. Random, loose-packed, particle bed structures are generated, and effective absorptivity and extinction coefficients are calculated. Results are compared against previous computational and experimental measurements for free, monodisperse, and deep powder beds, with good agreement being obtained. Correlations along with uncertainties are developed to allow the effective absorptivity and extinction coefficient as a function of various particle and operational parameters to be accurately set in SLS macroscale models.

Moser, Daniel↗

The effect of scanning jitter on geometric phase analysis in STEM images

Geometric phase analysis (GPA) is a useful method to map strain distribution in atomically resolved scanning/transmission electron microscopy (S/TEM) images. Nevertheless, the inevitable periodic jitter of electron probe in STEM along the scanning direction due to the interference of electric power supply, including grounding, can give rise to major artifacts, as evidenced by the appearance of satellite spots surrounding all main peaks in the power spectrum of the images. Here we reveal the origin of the image artifacts related to the probe jitter by mapping the image distortion component εxx using the GPA algorithm. The effect is verified by introducing a periodic displacement field to a STEM image simulated from a perfect crystal structure, and the calculated εxx maps show very good agreement with the experimental observations. Based on the quantitative analysis of the images distortion, we propose and test a feasible strategy to eliminate the effect of probe jitter from STEM images. Successful examples illustrate that the approach can help improve the accuracy in quantification of STEM images.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The System for Classification of Low-Pressure Systems (SyCLoPS): An All-In-One Objective Framework for Large-Scale Data Sets

We propose the first unified objective framework (SyCLoPS) for detecting and classifying all types of low-pressure systems (LPSs) in a given data set. We use the state-of-the-art automated feature tracking software TempestExtremes (TE) to detect and track LPS features globally in ERA5 and compute 16 parameters from commonly found atmospheric variables for classification. A Python classifier is implemented to classify all LPSs at once. The framework assigns 16 different labels (classes) to each LPS data point and designates four different types of high-impact LPS tracks, including tracks of tropical cyclone (TC), monsoonal system, subtropical storm and polar low. The classification process involves disentangling high-altitude and drier LPSs, differentiating tropical and non-tropical LPSs using novel criteria, and optimizing for the detection of the four types of high-impact LPS. A comparison of our labels with those in the International Best Track Archive for Climate Stewardship (IBTrACS) revealed an overall accuracy of 95% in distinguishing between tropical systems, extratropical cyclones, and disturbances. SyCLoPS produces a better TC detection skill compared to the previous algorithms, highlighted by an approximately 6% reduction in the false alarm rate compared to the previous TE algorithm. The vertical cross section composite of the four types of high-impact LPS we detect each shows distinct structural characteristics. Finally, we demonstrate that SyCLoPS is valuable for investigating various aspects of LPSs in climate data, such as the evolution of a single LPS track, patterns of LPS frequencies, and precipitation or wind influence associated with a particular LPS class.

54 ENVIRONMENTAL SCIENCES↗

Genetic algorithms for computational materials discovery accelerated by machine learning

Materials discovery is increasingly being impelled by machine learning methods that rely on pre-existing datasets. Where datasets are lacking, unbiased data generation can be achieved with genetic algorithms. Here a machine learning model is trained on-the-fly as a computationally inexpensive energy predictor before analyzing how to augment convergence in genetic algorithm-based approaches by using the model as a surrogate. This leads to a machine learning accelerated genetic algorithm combining robust qualities of the genetic algorithm with rapid machine learning. The approach is used to search for stable, compositionally variant, geometrically similar nanoparticle alloys to illustrate its capability for accelerated materials discovery, e.g., nanoalloy catalysts. The machine learning accelerated approach, in this case, yields a 50-fold reduction in the number of required energy calculations compared to a traditional “brute force” genetic algorithm. This makes searching through the space of all homotops and compositions of a binary alloy particle in a given structure feasible, using density functional theory calculations.

36 MATERIALS SCIENCE↗

Property space mapping of Pseudomonas aeruginosa permeability to small molecules

Two membrane cell envelopes act as selective permeability barriers in Gram-negative bacteria, protecting cells against antibiotics and other small molecules. Significant efforts are being directed toward understanding how small molecules permeate these barriers. In this study, we developed an approach to analyze the permeation of compounds into Gram-negative bacteria and applied it to Pseudomonas aeruginosa, an important human pathogen notorious for resistance to multiple antibiotics. The approach uses mass spectrometric measurements of accumulation of a library of structurally diverse compounds in four isogenic strains of P. aeruginosa with varied permeability barriers. We further developed a machine learning algorithm that generates a deterministic classification model with minimal synonymity between the descriptors. This model predicted good permeators into P. aeruginosa with an accuracy of 89% and precision above 58%. The good permeators are broadly distributed in the property space and can be mapped to six distinct regions representing diverse chemical scaffolds. We posit that this approach can be used for more detailed mapping of the property space and for rational design of compounds with high Gram-negative permeability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

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↗

Automatic energy calibration algorithm for an RBS setup

This work describes a computer algorithm for automatic extraction of the energy calibration parameters from a Rutherford Back-Scattering Spectroscopy (RBS) spectrum. Parameters like the electronic gain, electronic offset and detection resolution (FWHM) of a RBS setup are usually determined using a standard sample. In our case, the standard sample comprises of a multi-elemental thin film made of a mixture of Ti-Al-Ta that is analyzed at the beginning of each run at defined beam energy. A computer program has been developed to extract automatically the calibration parameters from the spectrum of the standard sample. The code evaluates the first derivative of the energy spectrum, locates the trailing edges of the Al, Ti and Ta peaks and fits a first order polynomial for the energy-channel relation. The detection resolution is determined fitting the convolution of a pre-calculated theoretical spectrum. To test the code, data of two years have been analyzed and the results compared with the manual calculations done previously, obtaining good agreement.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A generalized Ewald decomposition for screened Coulomb interactions

Medium-range interactions occur in a wide range of systems, including charged-particle systems with varying screening lengths. We generalize the Ewald method to charged systems described by interactions involving an arbitrary dielectric response function ϵ(𝐤). We provide an error estimate and optimize the generalization to find the break-even parameters that separate a neighbor list-only algorithm from the particle-particle particle-mesh algorithm. We examine the implications of different choices of the screening length for the computational cost of computing the dynamic structure factor. We then use our new method in molecular dynamics simulations to compute the dynamic structure factor for a model plasma system and examine the wave-dispersion properties of this system.

Dharuman, Gautham↗

High-power test of a C-band linear accelerating structure with an RFSoC-based LLRF system

Normal conducting linear particle accelerators consist of multiple rf stations with accelerating structure cavities. Low-level rf (LLRF) systems are employed to set the phase and amplitude of the field in the accelerating structure and to compensate for the pulse-to-pulse fluctuation of the rf field in the accelerating structures with a feedback loop. The LLRF systems are typically implemented with analog rf mixers, heterodyne-based architectures, and discrete data converters. There are multiple rf signals from each of the rf stations, so the number of rf channels required increases rapidly with multiple rf stations. With a large number of rf channels, the footprint, component cost, and system complexity of the LLRF hardware will increase significantly. To meet the design goals of being compact and affordable for future accelerators, we have designed the next-generation LLRF (NG-LLRF) with a higher integration level based on RFSoC technology. The NG-LLRF system samples rf signals directly and performs rf mixing digitally. Further, the NG-LLRF has been characterized in loopback mode to evaluate the performance of the system and has also been tested with a standing-wave accelerating structure, a prototype for the Cool Copper Collider (C 3 ) with a peak rf power level up to 16.45 MW. The loopback test demonstrated amplitude fluctuation below 0.15% and phase fluctuation below 0.15°, which are considerably better than the requirements of C 3 . The rf signals from the different stages of the accelerating structure at different power levels are measured by the NG-LLRF, which will be critical references for the control algorithm designs. The NG-LLRF also offers flexibility in waveform modulation, so we have used rf pulses with various modulation schemes, which could be useful for controlling some of the rf stations in accelerators. In this paper, the high-power test results at different stages of the test setup will be summarized, analyzed, and discussed.

47 OTHER INSTRUMENTATION↗

Machine learning enables identification of an alternative yeast galactose utilization pathway

How genomic differences contribute to phenotypic differences is a major question in biology. The recently characterized genomes, isolation environments, and qualitative patterns of growth on 122 sources and conditions of 1,154 strains from 1,049 fungal species (nearly all known) in the yeast subphylum Saccharomycotina provide a powerful, yet complex, dataset for addressing this question. We used a random forest algorithm trained on these genomic, metabolic, and environmental data to predict growth on several carbon sources with high accuracy. Known structural genes involved in assimilation of these sources and presence/absence patterns of growth in other sources were important features contributing to prediction accuracy. By further examining growth on galactose, we found that it can be predicted with high accuracy from either genomic (92.2%) or growth data (82.6%) but not from isolation environment data (65.6%). Prediction accuracy was even higher (93.3%) when we combined genomic and growth data. After the GALactose utilization genes, the most important feature for predicting growth on galactose was growth on galactitol, raising the hypothesis that several species in two orders, Serinales and Pichiales (containing the emerging pathogen Candida auris and the genus Ogataea, respectively), have an alternative galactose utilization pathway because they lack the GAL genes. Growth and biochemical assays confirmed that several of these species utilize galactose through an alternative oxidoreductive D-galactose pathway, rather than the canonical GAL pathway. Machine learning approaches are powerful for investigating the evolution of the yeast genotype–phenotype map, and their application will uncover novel biology, even in well-studied traits.

59 BASIC BIOLOGICAL SCIENCES↗

Determination of nuclear PDFs using Markov chain Monte Carlo methods

Global QCD analyses of nuclear parton distribution functions (nPDFs) have traditionally relied on the Hessian method for uncertainty estimation. However, the inherent Gaussian approximation and reliance on local curvature often prove insufficient for nPDF fits, which are frequently characterized by limited data constraints and non-Gaussian likelihoods. In this paper, we present the first nPDF determination based on Markov Chain Monte Carlo (MCMC) techniques, implemented within the nCTEQ framework using an adaptive Metropolis-Hastings algorithm. The MCMC approach enables a direct mapping of the posterior distribution and reveals a highly nontrivial parameter-space structure, including multiple modes and pronounced non-Gaussian behavior, particularly for the valence PDFs. We perform the first single-nucleus global analysis of lead PDFs using exclusively lead data and compare it to a multi-nuclei fit employing a standard analytic A dependence. The inclusion of lighter nuclei reduces quark uncertainties and modifies the shape of the lead PDFs, while leaving the gluon distribution largely unaffected. A complementary Hessian analysis exposes systematic limitations of the Gaussian approximation. Our results demonstrate that MCMC methods provide a more reliable framework for uncertainty quantification in nPDF determinations.

Derakhshanian, N. [Institute of Nuclear Physics Po↗

Cloud Quantum Computing of an Atomic Nucleus

Here, we report a quantum simulation of the deuteron binding energy on quantum processors accessed via cloud servers. We use a Hamiltonian from pionless effective field theory at leading order. We design a low-depth version of the unitary coupled-cluster ansatz, use the variational quantum eigensolver algorithm, and compute the binding energy to within a few percent. Our work is the first step towards scalable nuclear structure computations on a quantum processor via the cloud, and it sheds light on how to map scientific computing applications onto nascent quantum devices.

97 MATHEMATICS AND COMPUTING↗

Hydrogen density mapping in biomolecular crystals through dynamic nuclear polarization

Many fundamental biological processes, including those in photosynthetic reaction centers and enzyme active sites, involve charge and energy transfer, bond cleavage, protonation and hydrogen bonding. Because H atoms play such central roles in these reactions, accurately determining their positions is essential. Yet, conventional X-ray crystallography primarily resolves the heavy atoms in biological structures and provides limited insight into hydrogen, even at atomic resolution. Neutron macromolecular crystallography (NMC) overcomes this limitation by offering exceptional sensitivity to hydrogen and deuterium. Here, we present a theoretical framework for the development of dynamic nuclear polarization NMC (DNP-NMC) techniques, which exploit the alignment of neutron and proton nuclear spins to enhance and tune the hydrogen signal contribution. The DNP-NMC approach advances the resolution of H atoms within biomolecular crystals, whether bound to protein residues or present in solvent. The method establishes key relationships for the coherent structure factor of polarized neutron scattering from hydrogenous matter. It theoretically achieves full accuracy in phase reconstruction and offers a path to improve neutron structure determination, achieving accuracies exceeding ≳80% by incorporating titration states. Using a variant of the hybrid input/output phase-retrieval algorithm, it allows recovery of the hydrogen density with ≳90% phase accuracy. In conclusion, we further discuss sources of experimental uncertainty for the upcoming DNP-enabled, quasi-Laue IMAGINE-X experiment at Oak Ridge National Laboratory's High Flux Isotope Reactor.

dynamic nuclear polarization↗