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At least 91 records · Page 5

Subcellular Feature-Based Classification of α and β Cells Using Soft X-ray Tomography

The dysfunction of α and β cells in pancreatic islets can lead to diabetes. Many questions remain on the subcellular organization of islet cells during the progression of disease. Existing three-dimensional cellular mapping approaches face challenges such as time-intensive sample sectioning and subjective cellular identification. To address these challenges, we have developed a subcellular feature-based classification approach, which allows us to identify α and β cells and quantify their subcellular structural characteristics using soft X-ray tomography (SXT). We observed significant differences in whole-cell morphological and organelle statistics between the two cell types. Additionally, we characterize subtle biophysical differences between individual insulin and glucagon vesicles by analyzing vesicle size and molecular density distributions, which were not previously possible using other methods. These sub-vesicular parameters enable us to predict cell types systematically using supervised machine learning. We also visualize distinct vesicle and cell subtypes using Uniform Manifold Approximation and Projection (UMAP) embeddings, which provides us with an innovative approach to explore structural heterogeneity in islet cells. This methodology presents an innovative approach for tracking biologically meaningful heterogeneity in cells that can be applied to any cellular system.

3D cell mapping↗

Extending Parsimonious Bayesian Inference

Parsimonious Bayesian inference is a theoretical framework for efficient data assimilation that seeks to balance increased consistency between predictions and training data against corresponding increases in model complexity. Within this framework, over-training is understood as optimization that encodes excessive information within model parameters while only achieving small improvements between predictions and training data. This project aims to develop practical methods of limiting excess model information during optimization. One key observation is that practical heuristics for parsimonious learning in high-dimensions must balance expressivity, i.e. the ability of the model to capture diverse predictions with only a few non-zero parameters, against discoverability, i.e. the ability to train the model with gradient-based optimization and drive parameters to low information states. As such, we developed logical activation functions that are able to adaptively approximate arbitrary truth tables that define Boolean logic operations within a probabilistic framework. These functions have demonstrated the ability to learn exclusive disjunction (XOR) and conditioned disjunction (if [condition] then [result_if_true] else [result_if_false]) within a single layer of a neural network. To efficiently exploit these activation functions to drive parsimonious learning required several other advances within the domain of variational inference. The most efficient form of complexity suppression is structured sparsification, driving most model parameters to zero while achieving the structural coherence among nonzeros needed for bandwidth reduction. Such models are not only far more efficient at suppressing information-theoretic complexity, they also reduce the other forms of complexity (computations, communication, storage, and the number of dependencies needed to evaluate predictions). Aiming to support enhanced sparsification, this project examined new approaches to high-dimensional variational inference that allow us to calibrate and control parameter uncertainty during optimization. By identifying which parameters can sustain sparsifying perturbations with little impact on prediction quality, we can develop better pruning strategies by framing them as approximate Bayesian inference. These advances also open paths to mitigate concerns with deploying advanced learning methods in resource-constrained environments, such as running models on power-limited or communication-limited devices.

97 MATHEMATICS AND COMPUTING↗

Improved energies and local energies with weighted variational Monte Carlo

Neural network parametrizations have increasingly been used to represent the ground and excited states in variational Monte Carlo (VMC) with promising results. However, traditional VMC methods only optimize the wave function in regions of peak probability. The wave function is uncontrolled in the tails of the probability distribution, which can limit the accuracy of the trained wave function. To improve the approximation accuracy in the probability tails, this paper interprets VMC as a gradient flow in the space of wave functions, followed by a projection step. From this perspective, arbitrary probability distributions can be used in the projection step, allowing the user to prioritize accuracy in different regions of state space. Motivated by this theoretical perspective, the paper tests a weighted VMC method on the antiferromagnetic Heisenberg model for a periodic spin chain. Compared to traditional VMC, weighted VMC reduces the error in the ground state energy by a factor of 2, and it reduces the errors in the local energies away from the mode by large factors of 10 2 –10 4 .

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Data assimilation in operator algebras

We develop an algebraic framework for sequential data assimilation of partially observed dynamical systems. In this framework, Bayesian data assimilation is embedded in a nonabelian operator algebra, which provides a representation of observables by multiplication operators and probability densities by density operators (quantum states). In the algebraic approach, the forecast step of data assimilation is represented by a quantum operation induced by the Koopman operator of the dynamical system. Moreover, the analysis step is described by a quantum effect, which generalizes the Bayesian observational update rule. Projecting this formulation to finite-dimensional matrix algebras leads to computational schemes that are i) automatically positivity-preserving and ii) amenable to consistent data-driven approximation using kernel methods for machine learning. Moreover, these methods are natural candidates for implementation on quantum computers. Applications to the Lorenz 96 multiscale system and the El Niño Southern Oscillation in a climate model show promising results in terms of forecast skill and uncertainty quantification.

97 MATHEMATICS AND COMPUTING↗

Hunting for Polluted White Dwarfs and Other Treasures with Gaia XP Spectra and Unsupervised Machine Learning

White dwarfs (WDs) polluted by exoplanetary material provide the unprecedented opportunity to directly observe the interiors of exoplanets. However, spectroscopic surveys are often limited by brightness constraints, and WDs tend to be very faint, making detections of large populations of polluted WDs difficult. In this paper, we aim to increase considerably the number of WDs with multiple metals in their atmospheres. Using 96,134 WDs with Gaia DR3 BP/RP (XP) spectra, we constructed a 2D map using an unsupervised machine-learning technique called Uniform Manifold Approximation and Projection (UMAP) to organize the WDs into identifiable spectral regions. The polluted WDs are among the distinct spectral groups identified in our map. We have shown that this selection method could potentially increase the number of known WDs with five or more metal species in their atmospheres by an order of magnitude. Such systems are essential for characterizing exoplanet diversity and geology.

79 ASTRONOMY AND ASTROPHYSICS↗

EERC Final Topical Report – Findings on Subtask 3.2 – Produced Water Management Through Geologic Homogenization, Conditions, and Reuse

The Energy & Environmental Research Center (EERC) was awarded a contract by the North Dakota Industrial Commission (NDIC) Oil and Gas Research Program (NDIC No. G-051-101) to conduct a study on the recycling of water used in oil and gas operations, also known as produced water, from oil- and gas-producing regions of North Dakota as directed by Section 19 of North Dakota House Bill 1014. This final report provides a compilation of results of the study, which include regulatory, scientific, technological, and feasibility methods and considerations associated with North Dakota produced water management. The report provides a synopsis of this project’s previously submitted produced water assessment report entitled “Produced Water Management and Recycling Options in North Dakota” (Energy & Environmental Research Center, 2020), with updated values provided as appropriate. The report provides the results from the investigation of a novel produced water management strategy, referred to as geologic homogenization, conditioning, and reuse (GHCR), which aims to use a subsurface geologic formation as a natural medium for managing produced water recycling and reuse. Water management is a significant technical and economic challenge for sustainable oil and gas production, and water volumes are intrinsically linked to oil production volumes. North Dakota oil production rose to over 1.5 million barrels (MMbbl)/day in 2019, and despite a downturn in oil price in early 2020, North Dakota oil production has recovered to 1.1 MMbbl/day as of August 2021. Bakken petroleum system development between 2008 and 2020 has resulted in a nearly fourfold increase in produced water volumes to 642 MMbbl/yr in 2020 after peaking at 740 MMbbl/yr in 2019 and a fivefold increase in saltwater disposal (SWD) volumes to 565 MMbbl/yr in 2020 after a peak of 682 MMbbl/yr in 2019. Produced water and SWD volumes are forecasted to double by 2030. SWD is the primary method of produced water management used in North Dakota, with approximately 95% of the SWD volume occurring through subsurface injection into sandstones of the Dakota Group (Dakota). Localized pressurization of the Dakota resulting from SWD and projected increases in produced water volumes could impact the economics of North Dakota oil production. As a result, there is an emerging need to pursue alternative produced water management approaches, including recycling and reuse. While produced water recycling is not yet widespread, commercial operators are making strides in overcoming the technical challenges of using high salinity produced water in completion operations (Marathon Oil, 2020). As water management continues to be a key focal point in companies’ environmental, social, and governance (ESG) initiatives, focus on water management, including recycling, will likely continue to increase. Laboratory column testing, field sample collection, geologic modeling and numerical simulation, and techno-economic analysis all indicate that GHCR could feasibly be implemented as a potential water management option. Laboratory column testing and field sample collection indicate that the Inyan Kara sandstone and native formation fluid are capable of homogenizing with the Bakken produced water to a point where the fluid composition appears to stabilize. Extracting that stabilized fluid could be considered homogeneous and capable of providing individual batches of hydraulic fracturing fluid. Numerical simulation results indicate that extraction of fluids from the Inyan Kara in a GHCR implementation scenario is capable of reducing formation pressure, which would help ease localized pressurization of the Inyan Kara and extend the available capacity for nearby existing SWD wells. Economic analysis indicates that there are scenarios where GHCR implementation can be a competitive or even lower-cost option than a conventional water management approach. Site-specific conditions will dictate the economic potential of GHCR, but potentially attractive sites for GHCR implementation will be those that are located above a pressurized zone of the Inyan Kara, need six or more Bakken infill wells, and face high costs for conventional SWD and/or freshwater. Based on the regulatory review, drilling into the Inyan Kara for SWD and to harness as a source water for industrial use have precedent in North Dakota, and a workable regulatory solution for GHCR seems likely. However, restrictions in the state regarding surface storage and transport of produced fluids may limit some activities, which will affect how GHCR could ultimately be implemented. In summary, this study reveals pursuing GHCR can be a viable approach to water management in North Dakota. The GHCR concept addresses some of the challenges that hinder the more traditional approaches to recycling in the industry. Furthermore, an assessment of the current landscape of water management within the state reveals the ongoing trend of increasing volumes of produced water and SWD. Projections reveal that the volumes of produced water that need to be managed are expected to double over the next decade (Energy & Environmental Research Center, 2020). With the continued development of the Bakken and continuing driving factors related to ESG initiatives, implementing a practice such as GHCR is a feasible approach to adding recycling of produced water to industry within the state. This subtask was cofunded through the EERC–U.S. Department of Energy Joint Program on Research and Development for Fossil Energy-Related Resources Cooperative Agreement No. DE-FE0024233. Nonfederal funding was provided by the North Dakota Industrial Commission Oil and Gas Research Program. References Energy & Environmental Research Center, 2020, Produced water management and recycling options in North Dakota: Final Report for North Dakota Legislative Management Energy Development and Transmission Committee and North Dakota Industrial Commission. Marathon Oil, 2020, Sustainability report: https://cdn.sanity.io/files/ghcnw9z2/website/ 91744eb6ef8fbe59505a911c6b8d2e8dd9a537fa.pdf?dl (accessed November 2021).

02 PETROLEUM↗

Semi-analytical covariance matrices for two-point correlation function for DESI 2024 data

We present an optimized way of producing the fast semi-analytical covariance matrices for the Legendre moments of the two-point correlation function, taking into account survey geometry and mimicking the non-Gaussian effects. We validate the approach on simulated (mock) catalogs for different galaxy types, representative of the Dark Energy Spectroscopic Instrument (DESI) Data Release 1, used in 2024 analyses. We find only a few percent differences between the mock sample covariance matrix and our results, which can be expected given the approximate nature of the mocks, although we do identify discrepancies between the shot-noise properties of the DESI fiber assignment algorithm and the faster approximation (emulator) used in the mocks. Importantly, we find a close agreement (≤ 8% relative differences) in the projected errorbars for distance scale parameters for the baryon acoustic oscillation measurements. This confirms our method as an attractive alternative to simulation-based covariance matrices, especially for non-standard models or galaxy sample selections, making it particularly relevant to the broad current and future analyses of DESI data.

79 ASTRONOMY AND ASTROPHYSICS↗

Exploring Continuous Seismic Data at an Industry Facility Using Unsupervised Machine Learning

Seismic data recorded at industrial sites contain valuable information on anthropogenic activities. With advances in machine learning and computing power, new opportunities have emerged to explore the seismic wavefield in these complex environments. We applied two unsupervised machine learning algorithms to analyze continuous seismic data collected from an industrial facility in Texas, United States. The Uniform Manifold Approximation and Projection for Dimension Reduction algorithm was used to reduce the dimensionality of the data and generate 2D embeddings. Then, the Hierarchical Density-Based Spatial Clustering of Applications with Noise method was employed to automatically group these embeddings into distinct signal clusters. Our analysis of over 1400 hr (around 59 days) of continuous seismic data revealed five and seven signal clusters at two separate stations. At both stations, we identified clusters associated with background noise and vehicle traffic, with the latter’s temporal patterns aligning closely with the facility’s work schedule. Furthermore, the algorithms detected signal clusters from unknown sources and underline the ability of unsupervised machine learning for uncovering previously unrecognized patterns. Our analysis demonstrates the effectiveness of unsupervised approaches in examining continuous seismic data without requiring prior knowledge or pre-existing labels.

58 GEOSCIENCES↗

Spatiotemporal Super-Resolution with Generative Machine Learning for Creating Renewable Energy Resource Data Under Climate Change Scenarios

As we plan for a future with higher penetrations of renewables and increasing electrification, it becomes more important to understand how the electricity grid will operate under a variety of weather events. We must also consider that the weather our future grid will experience will be different and possibly more extreme than the historical weather that we have extensive data for. We can use data from global climate models (GCMs) to help understand how our climate may change over the next several decades, but there is often a significant gap between the low-resolution GCM data and the high-resolution weather data required to study power systems under specific weather events. Therefore, our objective in this work is to develop tools that can bridge this gap by using low-resolution GCM data to create realistic high-resolution weather datasets that can be used to study renewable energy generation and electricity demand. To accomplish this objective, we have developed a set of generative machine learning models that can rapidly downscale GCM daily average output data at an approximate grid resolution of 100km to hourly data at an approximate 4 km grid resolution. The models can be used to create high resolution data from nearly any GCM included in the Coupled Model Intercomparison Project (CMIP) Phase 5 or 6. Our methods include all datasets regularly used to study the integration of wind and solar power plants as well as changes in electricity demand due to heating and cooling loads. These models and datasets enable power systems modelers to study climate change-influenced weather events and their impact on the grid. We have downscaled and validated wind, solar, temperature, and humidity data with very promising results. The generative machine learning methods are computationally efficient and produce data that has similar statistical characteristics to current state-of-the-art historical datasets. We have trained initial generative models and produced an initial dataset collectively referred to as Sup3rCC: Super-Resolved Renewable Energy Resource Data with Climate Change Impacts. The data covers a (mostly) historical period from 2015-2025 and a future period from 2050-2059. We have also taken hypothetical high-electrification load data and scaled the heating and cooling loads with respect to the 2050-2059 high-resolution Sup3rCC meteorology. The results show how future levels of renewable energy generation and electrified load may be impacted by climate change, setting the stage for capacity expansion models to consider a dynamic climate through model years.

climate change↗

Development of the uncertainty quantification toolkit's python interface and surrogate construction tutorial

The uncertainty quantification toolkit (UQTk) is a collection of c++ libraries that assess the confidence of numerical models. Surrogate approximations, often polynomial chaos expansions (PCEs), lessen the computational cost of these assessments. I developed a Python interface in UQTk for regression and Bayesian compressive sensing to add to the existing Galerkin projection method. These methods receive an object containing the polynomial basis information and NumPy arrays of sample points, call c++ methods, and return the PCE coefficients in a NumPy array. To demonstrate these methods, I wrote a tutorial in which I use them to construct surrogates for Genz functions and calculate the resulting error.

97 MATHEMATICS AND COMPUTING↗

CI-MOR Final Report: Analysis and Validation of Critical Infrastructure Models using Model Order Reduction

This report summarizes the research and capabilities developed as part of the project “Analysis and Validation of Critical Infrastructure Models using Model Order Reduction” (CI-MOR) LDRD project. CI-MOR research enables the solution of large, complex optimization models that naturally arise in national security challenges involving critical infrastructures. Specifically, CI-MOR researchers developed methods to (1) rigorously approximate complex, nonlinear optimization formulations, (2) identify alternative near-optimal solutions, (3) accelerate optimization workflows used for complex applications, and (4) rigorously integrate domain knowledge in stochastic-process models. This report provides an overview of the research done in CI-MOR, and we describe application exemplars used to illustrate CI-MOR capabilities. Furthermore, we describe the software developed by CI-MOR that researchers can leverage to analyze new applications.

97 MATHEMATICS AND COMPUTING↗

Wave function methods for canonical ensemble thermal averages in correlated many-fermion systems

We present a wave function representation for the canonical ensemble thermal density matrix by projecting the thermofield double state against the desired number of particles. Furthermore, the resulting canonical thermal state obeys an imaginary-time evolution equation. Starting with the mean-field approximation, where the canonical thermal state becomes an antisymmetrized geminal power (AGP) wave function, we explore two different schemes to add correlation: by number-projecting a correlated grand-canonical thermal state and by adding correlation to the number-projected mean-field state. As benchmark examples, we use number-projected configuration interaction and an AGP-based perturbation theory to study the hydrogen molecule in a minimal basis and the six-site Hubbard model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Density functional based methods for light harvesting molecules

The goal of the proposal was to computationally study the photoinduced charge transfer excited states of organic molecules. The systems of interest are the large organic supramolecules that have potential for photovoltaic applications. The simulation of the charge transfer excited states in large supramolecular assemblies require quantum mechanical methods that can be applied to systems with hundreds of atoms. Through this project we have implemented a perturbative delta-self-consistent field method that can easily describe the charge transfer excited states with regular density functionals without range separation. The cost of the calculations of an excited state is similar to that of the ground state. The method also allows for calculation of the energy gradients of the excited state. The developed method was applied to study a number of different supramolecular systems containing hundreds of atoms with excellent agreement with experiment. The absorption characteristics and the influence of density functional approximations were also examined. These led to several studies on the variety of organic electron donor and acceptor molecules. Apart from these developments through this project we also improved the code capabilities by implementing new meta-GGA functionals. This was a major step since the code is purely density functional and earlier the functional capabilities were limited only to generalized gradient approximations. A total of 23 peer-reviewed publications in top chemical physics journals resulted from this grant.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mapping Thermal Conductivity at the Atomic Scale: A Step toward the Thermal Design of Materials

We describe a spatial decomposition of the thermal conductivity, termed site-projected thermal conductivity, which quantifies the thermal conduction activity at each atomic site—a critical parameter for the thermal design of materials. The method is based on the Green–Kubo formula and the harmonic approximation and requires the force-constant and dynamical matrices, as well as a relaxed structural model. Throughout the study, it uses high quality models previously tested and compared to many experiments. It discusses the method and underlying approximations for amorphous silicon, carries the detailed analysis for amorphous silicon, and then examines an amorphous-crystal silicon interface and representative carbon materials. This study identifies the sites and local structures that reduce heat transport, and quantify these (estimate the spatial range) over which these “thermal defects” are effective. It identifies filamentary structures in the amorphous silicon network which impact heat transport and electronic structure (the Urbach edge) and electronic transport.

36 MATERIALS SCIENCE↗

A hybrid Monte Carlo, discontinuous Galerkin method for linear kinetic transport equations

Here we present a hybrid method for time-dependent particle transport problems that combines Monte Carlo (MC) estimation with deterministic solutions based on discrete ordinates. For spatial discretizations, the MC algorithm computes a piecewise constant solution and the discrete ordinates use bilinear discontinuous finite elements. From the hybridization of the problem, the resulting problem solved by Monte Carlo is scattering free, resulting in a simple, efficient solution procedure. Between time steps, we use a projection approach to “relabel” collided particles as uncollided particles. In conclusion, from a series of standard 2-D Cartesian test problems we observe that our hybrid method has improved accuracy and reduction in computational complexity of approximately an order of magnitude relative to standard discrete ordinates solutions.

97 MATHEMATICS AND COMPUTING↗

DESI mock challenge: Halo and galaxy catalogues with the bias assignment method

We present a novel approach to the construction of mock galaxy catalogues for large-scale structure analysis based on the distribution of dark matter halos obtained with effective bias models at the field level. We aim to produce mock galaxy catalogues capable of generating accurate covariance matrices for a number of cosmological probes that are expected to be measured in current and forthcoming galaxy redshift surveys (e.g. two- and three-point statistics). The construction of the catalogues shown in this paper is part of a mock-comparison project within the Dark Energy Spectroscopic Instrument (DESI) collaboration. We use the bias assignment method ( BAM ) to model the statistics of halo distribution through a learning algorithm using a few detailed N-body simulations, and approximated gravity solvers based on Lagrangian perturbation theory. We introduce cosmic-web-dependent corrections to modelling redshift-space distortions at the N-body level – both in the halo and galaxy distributions –, as well as a multi-scale approach for accurate assignment of halo properties. Using specific models of halo occupation distributions to populate halos, we generate galaxy mocks with the expected number density and central-satellite fraction of emission-line galaxies, which are a key target of the DESI experiment. BAM generates mock catalogues with per cent accuracy in a number of summary statistics, such as the abundance, the two- and three-point statistics of halo distributions, both in real and redshift space. In particular, the mock galaxy catalogues display ~3%-10% accuracy in the multipoles of the power spectrum up to scales of k ~ 0.4 h -1 Mpc. We show that covariance matrices of two- and three-point statistics obtained with BAM display a similar structure to the reference simulation. BAM offers an efficient way to produce mock halo catalogues with accurate two- and three-point statistics and is able to generate a variety of multi-tracer catalogues with precise covariance matrices of several cosmological probes. We discuss future developments of the algorithm towards mock production in DESI and other galaxy-redshift surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

S-OPT: A Points Selection Algorithm for Hyper-Reduction in Reduced Order Models

While projection-based reduced order models can reduce the dimension of full order solutions, the resulting reduced models may still contain terms that scale with the full order dimension. Hyper-reduction techniques are sampling-based methods that further reduce this computational complexity by approximating such terms with a much smaller dimension. The goal of this work is to introduce the points selection algorithm developed by Shin and Xiu as a hyper-reduction method. The selection algorithm was originally proposed as a stochastic collocation method for uncertainty quantification. Since the algorithm aims at maximizing a quantity $\mathcal{S}$ that measures both the column orthogonality and the determinant, we refer to the algorithm as S-OPT. Numerical examples are provided to demonstrate the performance of S-OPT and to compare its performance with a gappy proper orthogonal decomposition (POD) algorithm. Here, we found that using the S-OPT algorithm is shown to predict the full order solutions with higher accuracy than gappy POD especially when the number of sampling points is small, although we note that S-OPT shows slow asymptotic convergence with respect to the number of samples for some applications, e.g., Lagrangian hydrodynamics.

97 MATHEMATICS AND COMPUTING↗

Cosmic Growth Rate as Probe of Dark Matter and Gravity. Final Report

Some 95% of the energy content of the universe lies outside the standard model of particle physics, with approximately 70% arising from physics that accelerates cosmic expansion in opposition to normal gravity and about 25% dark matter that clusters under gravity but does not interact directly with light. This project made significant advances in developing methods to extract information on the former – dark energy or modified gravity – and latter – dark matter through their effects on the expansion history of the universe and the cosmic growth of large scale structures under the influence of gravity and dark energy. These results directly benefit experimental/observational cosmic surveys of large scale structure imaging hundreds of millions of galaxies and mapping spectroscopically the 3D positions of tens of millions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗