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DOE OSTI2023

Atomic Resolution Cryogenic 4D-STEM Imaging via Robust Distortion Correction

Cryogenic four-dimensional scanning transmission electron microscopy (4D-STEM) imaging is a useful technique for studying quantum materials and their interfaces by simultaneously probing charge, lattice, spin, and chemistry on the atomic scale with the sample held at temperatures ranging from room to cryogenic. However, its applications are currently limited by the instabilities of cryo-stages and electronics. To overcome this challenge, we develop an algorithm to effectively correct the complex distortions present in atomic resolution cryogenic 4D-STEM data sets. This method uses nonrigid registration to identify localized distortions in a 4D-STEM and relate them to an undistorted experimental STEM image, followed by a series of affine transformations for distortion corrections. This method allows a minimum loss of information in both reciprocal and real spaces, enabling the reconstruction of sample information from 4D-STEM data sets. This method is computationally cheap, fast, and applicable for on-the-fly data analysis in future in situ cryogenic 4D-STEM experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Exploratory analysis and performance prediction of big data transfer in High-performance Networks

Big data transfer in large-scale scientific and business applications is increasingly carried out over connections with guaranteed bandwidth provisioned in High-performance Networks (HPNs) via advance bandwidth reservation. Provisioning agents need to carefully schedule data transfer requests, compute network paths, and allocate appropriate bandwidths. Such reserved bandwidths, if not fully utilized, could be simply wasted due to the exclusive access during the approved time window, and cause extra overhead and complexity for resource management. This calls for accurate performance prediction to reserve bandwidths that match actual needs and avoid over-provisioning. We employ machine learning algorithms to predict big data transfer performance based on extensive performance measurements collected in the past several years from data transfer tests using different protocols and toolkits between various end sites on several real-life physical or emulated testbeds. We first analyze the performance patterns in response to a comprehensive list of parameters in end-host systems, network connections, and data transfer applications, which motivate the use of machine learning and also help us identify the effects of latent factors. We then propose threshold- and clustering-based methods to eliminate negative effects of latent factors in data preprocessing and build a robust performance predictor based on customized domain-oriented loss functions. The performance of the proposed methods is verified by extensive experiments using SVR and RFR as well as theoretical analysis of the general performance bound.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Introducing Molecular Hypernetworks for Discovery in Multidimensional Metabolomics Data

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and address challenges of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used in the Global Natural Products Social Molecular Networking platform, are a prominent strategy for exploring and visualizing molecular relationships and improving annotation. MNs are mathematical graphs showing the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated with a single molecular identity. Here, this paper introduces “molecular hypernetworks” (MHNs) as more complex MN models able to natively represent multiway relationships among observations. Compared to MNs, MHNs can more parsimoniously represent the inherent complexity present among groups of observations, initially supporting improved exploratory data analysis and visualization. MHNs also promise to increase confidence in annotation propagation, for both human and analytical processing. We first illustrate MHNs with simple examples, and build them from liquid chromatography- and ion mobility spectrometry-separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Phase retrieval for refraction-enhanced x-ray radiography using a deep neural network

X-ray refraction-enhanced radiography (RER) or phase contrast imaging is widely used to study internal discontinuities within materials. The resulting radiograph captures both the decrease in intensity caused by material absorption along the x-ray path, as well as the phase shift, which is highly sensitive to gradients in density. A significant challenge lies in effectively analyzing the radiographs to decouple the intensity and phase information and accurately ascertain the density profile. Conventional algorithms often yield ambiguous and unrealistic results due to difficulties in including physical constraints and other relevant information. We have developed an algorithm that uses a deep neural network to address these issues and applied it to extract the detailed density profile from an experimental RER. To generalize the applicability of our algorithm, we have developed a technique that quantitatively evaluates the complexity of the phase retrieval process based on the characteristics of the sample and the configuration of the experiment. Accordingly, this evaluation aids in the selection of the neural network architecture for each specific case. Beyond RER, the model has potential applications for other diagnostics where phase retrieval analysis is required.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS1990

A three-dimensional application with the numerical grid generation code: EAGLE (utilizing an externally generated surface)

Program EAGLE (Eglin Arbitrary Geometry Implicit Euler) is a multiblock grid generation and steady-state flow solver system. This system combines a boundary conforming surface generation, a composite block structure grid generation scheme, and a multiblock implicit Euler flow solver algorithm. The three codes are intended to be used sequentially from the definition of the configuration under study to the flow solution about the configuration. EAGLE was specifically designed to aid in the analysis of both freestream and interference flow field configurations. These configurations can be comprised of single or multiple bodies ranging from simple axisymmetric airframes to complex aircraft shapes with external weapons. Each body can be arbitrarily shaped with or without multiple lifting surfaces. Program EAGLE is written to compile and execute efficiently on any CRAY machine with or without Solid State Disk (SSD) devices. Also, the code uses namelist inputs which are supported by all CRAY machines using the FORTRAN Compiler CF177. The use of namelist inputs makes it easier for the user to understand the inputs and to operate Program EAGLE. Recently, the Code was modified to operate on other computers, especially the Sun Spare4 Workstation. Several two-dimensional grid configurations were completely and successfully developed using EAGLE. Currently, EAGLE is being used for three-dimension grid applications.

Houston, Johnny L.↗

NASA NTRS2009

Adaptive Morphological Feature-Based Object Classifier for a Color Imaging System

Utilizing a Compact Color Microscope Imaging System (CCMIS), a unique algorithm has been developed that combines human intelligence along with machine vision techniques to produce an autonomous microscope tool for biomedical, industrial, and space applications. This technique is based on an adaptive, morphological, feature-based mapping function comprising 24 mutually inclusive feature metrics that are used to determine the metrics for complex cell/objects derived from color image analysis. Some of the features include: Area (total numbers of non-background pixels inside and including the perimeter), Bounding Box (smallest rectangle that bounds and object), centerX (x-coordinate of intensity-weighted, center-of-mass of an entire object or multi-object blob), centerY (y-coordinate of intensity-weighted, center-of-mass, of an entire object or multi-object blob), Circumference (a measure of circumference that takes into account whether neighboring pixels are diagonal, which is a longer distance than horizontally or vertically joined pixels), . Elongation (measure of particle elongation given as a number between 0 and 1. If equal to 1, the particle bounding box is square. As the elongation decreases from 1, the particle becomes more elongated), . Ext_vector (extremal vector), . Major Axis (the length of a major axis of a smallest ellipse encompassing an object), . Minor Axis (the length of a minor axis of a smallest ellipse encompassing an object), . Partial (indicates if the particle extends beyond the field of view), . Perimeter Points (points that make up a particle perimeter), . Roundness [(4(pi) x area)/perimeter(squared)) the result is a measure of object roundness, or compactness, given as a value between 0 and 1. The greater the ratio, the rounder the object.], . Thin in center (determines if an object becomes thin in the center, (figure-eight-shaped), . Theta (orientation of the major axis), . Smoothness and color metrics for each component (red, green, blue) the minimum, maximum, average, and standard deviation within the particle are tracked. These metrics can be used for autonomous analysis of color images from a microscope, video camera, or digital, still image. It can also automatically identify tumor morphology of stained images and has been used to detect stained cell phenomena (see figure).

McDowell, Mark↗

NASA NTRS2015

Simulation Apps Bring Us Closer to Mars

My work with mathematical modeling and computer simulations began in earnest in 1987 when I signed on with the National Aeronautics and Space Administration, better known as NASA. At the time I was developing computer simulations to support the design of carbon dioxide (CO2) removal systems for the International Space Station (ISS) life support system. CO2 is a human metabolic waste, produced at a rate of a kilogram per day per crewmember. CO2 must be removed from the crew cabin, as it will quickly become detrimental to crew health. The systems used to remove CO2 are typically based on sorption processes, which include complex interactions of heat transfer, mass transfer, and gas flow through porous media. At this time, there were no commercial options for solving a set of coupled mathematical models such as partial differential equations (PDEs); you either force-fit the physics into a thermal analysis package or wrote your own code, complete with discretization, meshing, and solution algorithms. Unfortunately, coding CO2 removal processes from scratch did not allow an appropriate focus on the challenging yet crucial task of understanding and capturing the underlying physics via appropriate mathematical models. Configuration control was often simply ignored due to tight schedules, resulting in a code that would be quicker for a second party to rewrite than modify. In the early 2000s, I decided to move CO2 removal simulations to a platform with built-in meshing, solvers, and postprocessing capabilities, and that could solve user-defined multiphysics PDEs. The program chosen to meet these needs was COMSOL Multiphysics®. Along with freeing the engineer to focus on the underlying physics, a degree of configuration control was automatically achieved via a consistent user interface, thus allowing COMSOL users to share computer models. My team has developed simulations that are already providing a valuable debugging capability for the ISS CO2 removal system, and will provide guidance in upgrades to that system.

Knox, Jim↗

NASA NTRS2021

A Three-Step Semi Analytical Algorithm (3SAA) for Estimating Inherent Optical Properties Over Oceanic, Coastal, and Inland Waters From Remote Sensing Reflectance

We present a three-step inverse model (3SAA) for estimating the inherent optical properties (IOPs) of surface waters from the remote sensing reflectance spectra, Rrs(). The derived IOPs include the total (a()), phytoplankton (aphy()), and colored detrital matter (acdm()), absorption coefficients, and the total (bb()) and particulate (bbp()) backscattering coefficients. The first step uses an improved neural network approach to estimate the diffuse attenuation coefficient of downwelling irradiance from Rrs. a() and bbp() are then estimated using the LS2 model (Loisel et al., 2018), which does not require spectral assumptions on IOPs and hence can assess a() and bb() at any wavelength at which Rrs() is measured. Then, an inverse optimization algorithm is combined with an optical water class (OWC) approach to assess aphy() and acdm() from anw().The proposed model is evaluated using an in situ dataset collected in open oceanic, coastal, and inland waters. Comparisons with other standard semi-analytical algorithms (QAA and GSM), as well as match-up exercises, have also been performed. The applicability of the algorithm on OLCI observations was assessed through the analysis of global IOPs spatial patterns derived from 3SAA and GSM. The good performance of 3SAA is manifested by median absolute percentage differences (MAPD) of 13%, 23%, 34% and 34% for bbp(443), anw(443), aphy(443) and acdm(443), respectively for oceanic waters. Due to the absence of spectral constraints on IOPs in the inversion of total IOPs, and the adoption of an OWC-based approach, the performance of 3SAA is only slightly degraded in bio-optical complex inland waters.

ocean color↗

NASA NTRS2004

Visual data mining for quantized spatial data

In previous papers we've shown how a well known data compression algorithm called Entropy-constrained Vector Quantization ( can be modified to reduce the size and complexity of very large, satellite data sets. In this paper, we descuss how to visualize and understand the content of such reduced data sets.

cluster analysis↗

DOE OSTI2021

Data-driven optimization of mixed-integer bi-level multi-follower integrated planning and scheduling problems under demand uncertainty

The coordination of interconnected elements across the different layers of the supply chain is essential for all industrial processes and the key to optimal decision-making. Yet, the modeling and optimization of such interdependent systems are still burdensome. Here we address the simultaneous modeling and optimization of medium-term planning and short-term scheduling problems under demand uncertainty using mixed-integer bi-level multi-follower programming and data-driven optimization. Bi-level multi-follower programs model the natural hierarchy between different layers of supply chain management holistically, while scenario analysis and data-driven optimization allow us to retrieve the guaranteed feasible solutions of the integrated formulation under various demand considerations. We address the data-driven optimization of this challenging class of problems using the DOMINO framework, which was initially developed to solve single-leader single-follower bi-level optimization problems to guaranteed feasibility. This framework is extended to solve single-leader multi-follower stochastic formulations and its performance is characterized by well-known single and multi-product process scheduling case studies. Through our data-driven algorithmic approach, we present guaranteed feasible solutions to linear and nonlinear mixed-integer bi-level formulations of simultaneous planning and scheduling problems and further characterize the effects of the scheduling level complexity on the solution performance, which spans over several hundred continuous and binary variables, and thousands of constraints.

42 ENGINEERING↗

DOE OSTI2021

Algorithms and file structures to enhance software workflows for ion mobility mass spectrometry (IM-MS): CRADA 410 (Final Report)

This document is the final report for CRADA 410 (Project No. 72496). The purpose of this project was supporting customizations of algorithms and raw data file structures to enhance software workflows for liquid chromatography (LC), mass spectrometry (MS) and ion mobility mass spectrometry (IM-MS)-based metabolite characterization. PNNL worked with Agilent to evaluate and improve the integration of ion mobility into existing MS data analysis methods of Agilent software tools. The project augmented PNNL’s capabilities to analyze complex omics samples. These capabilities are directly beneficial to DOE and PNNL efforts to characterize and analyze compounds in microbial and plant communities. The project assisted Agilent in further developing improved instrument-software solutions combining ion mobility with mass spectrometry for widespread applications in life sciences and other fields.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1972

Mariner 9 - Image processing and products.

The purpose of this paper is to describe the system for the display, processing, and production of image data products created to support the Mariner 9 Television Experiment. Of necessity, the system was large in order to respond to the needs of a large team of scientists with a broad scope of experimental objectives. The desire to generate processed data products as rapidly as possible to take advantage of adaptive planning during the mission, coupled with the complexities introduced by the nature of the vidicon camera, greatly increased the scale of the ground image processing effort. This paper describes the systems that carried out the processes and delivered the products necessary for real-time and near-real-time analyses. References are made to the computer algorithms used for the different levels of decalibration and analysis.

Levinthal, E. C.↗

DOE OSTI2026

WM26 Paper Multi-Robot Collaboration for Hazardous Environments

Hazardous nuclear and industrial facilities are rarely designed for robots. Work in these domains demand precise manipulation and robust mobility in cluttered, constrained spaces where off-the-shelf platforms struggle and “one-size-fits-all” machines become costly and complex. Idaho National Laboratory (INL) is developing an autonomous, multi-robot inspection system that coordinates task-specific platforms rather than relying on a single omni-tool robot. An electric truck serves as a power and compute hub for a custom manipulator co-developed with Florida International University (FIU), a commercial mini crawler, a pan–tilt–zoom camera, and a Nexxis Argus LiDAR mapping system. Working in concert, these robots generate spatial, radiation, and temperature maps of the pit environments at the Hanford Waste Tank Farms. These systems will capture visual records and environmental telemetry to allow for analysis post inspection. The system architecture uses Robot Operating System 2 (ROS 2) for publish/subscribe integration, NVIDIA Isaac Sim and Unity for simulation and visualization, and algorithms such as NVBlox to fuse data into unified 3D overlays. This robot-agnostic approach reduces operator burden by enabling autonomy across heterogeneous platforms and lets each robot be used where it is strongest. Having autonomous functions means operators don’t have to fully control multiple different components. The ease of use could allow for more widespread adoption of advanced robotics at waste management sites that see continued use. By coordinating simpler, purpose-built mechanisms, the approach lowers design and manufacturing complexity, reduces capital risk in contaminated settings, and improves controllability for complex inspection and manipulation tasks. We present the architecture, early results, and lessons learned from building and deploying this coordinated multi-robot system, with the goal of accelerating safe, cost-effective adoption of advanced robotics at waste-management sites.

42 - ENGINEERING↗

NASA NTRS1983

Texture functions in image analysis: A computationally efficient solution

A computationally efficient means for calculating texture measurements from digital images by use of the co-occurrence technique is presented. The calculation of the statistical descriptors of image texture and a solution that circumvents the need for calculating and storing a co-occurrence matrix are discussed. The results show that existing efficient algorithms for calculating sums, sums of squares, and cross products can be used to compute complex co-occurrence relationships directly from the digital image input.

Cox, S. C.↗

NASA NTRS1984

Validation of a transonic analysis code for use in preliminary design of advanced transport configurations

The WBPPW code has the capability of analyzing flow-field effects about configurations which include wing pylons and engine nacelles or pods in addition to the basic wing/fuselage combination. Using the concept of grid embedding, the code solves the extended small disturbance transonic flow equation for complex flow interactions of the various configuration components. A general description of the code and solution algorithm is included. Results are presented and compared with experiment for various configurations which encompass the code capabilities. These include wing planform and wing contour modifications and variations in nacelle position beneath a high-aspect-ratio wing. Results are analyzed in the light of preliminary design, where the capability to accurately compute flow-field effects resulting from various configuration perturbations is important. The comparisons show that the computational results are sensitive to subtle design modifications and that the code could be used as an effective guide during the design process for transport configurations.

Waggoner, E. G.↗

DOE OSTI2017

Modified GMDH-NN algorithm and its application for global sensitivity analysis

Global sensitivity analysis (GSA) is a very useful tool to evaluate the influence of input variables in the whole distribution range. Sobol' method is the most commonly used among variance-based methods, which are efficient and popular GSA techniques. High dimensional model representation (HDMR) is a popular way to compute Sobol' indices, however, its drawbacks cannot be ignored. We show that modified GMDH-NN algorithm can calculate coefficients of metamodel efficiently, so this paper aims at combining it with HDMR and proposes GMDH-HDMR method. The new method shows higher precision and faster convergent rate. Several numerical and engineering examples are used to confirm its advantages. - Highlights: • The GMDH-NN is improved to construct the explicit polynomial model of optimal complexity by self-organization. • The paper aims at combining improved GMDH-NN with HDMR expansions and using it to compute Sobol' indices directly. • The method can be applied in uniform, normal and exponential distribution by using suitable orthogonal polynomials. • Engineering examples, e.g., electronic circuit models can be solved by the presented method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Data-Driven Learning for the Mori--Zwanzig Formalism: A Generalization of the Koopman Learning Framework

A theoretical framework which unifies the conventional Mori--Zwanzig formalism and the approximate Koopman learning of deterministic dynamical systems from noiseless observation is presented. In this framework, the Mori--Zwanzig formalism, developed in statistical mechanics to tackle the hard problem of construction of reduced-order dynamics for high-dimensional dynamical systems, can be considered as a natural generalization of the Koopman description of the dynamical system. We next show that, similar to the approximate Koopman learning methods, data-driven methods can be developed for the Mori--Zwanzig formalism with Mori's linear projection operator. We have developed two algorithms to extract the key operators, the Markov and the memory kernel, using time series of a reduced set of observables in a dynamical system. We have adopted the Lorenz `96 system as a test problem and solved for the above operators. These operators exhibit complex behaviors, which are unlikely to be captured by traditional modeling approaches in Mori--Zwanzig analysis. The nontrivial generalized fluctuation-dissipation relationship, which relates the memory kernel with the two-time correlation statistics of the orthogonal dynamics, was numerically verified as a validation of the solved operators. Here we present numerical evidence that the generalized Langevin equation, a key construct in the Mori--Zwanzig formalism, is more advantageous in predicting the evolution of the reduced set of observables than the conventional approximate Koopman operators.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Machine-Learning Enabled Evaluation of Probability of Piping Degradation In Secondary Systems of Nuclear Power Plants

The transition to condition-based, risk-informed automated maintenance will contribute to a significant reduction of operations and maintenance costs that account for the majority of nuclear power generation costs. Furthermore, of the operations and maintenance costs in U.S. plants, approximately 80% are labor costs. To address the issue of rising operating costs and economic viability, technologies used to perform online monitoring of piping and other secondary system structural components in commercial nuclear power plants (NPPs) are under evaluation. These online monitoring systems have the potential to identify when a more detailed inspection is needed using real time measurements, rather than at a pre-determined inspection interval thus reducing the maintenance cost. This paper describes distributed high-temperature stable fiber sensors fabricated in optical fibers through a roll-to-roll laser direct writing process using femtosecond lasers. Using phase-sensitive optical time domain reflectometry, distributed acoustic and vibration sensors can be developed and deployed to critical components and systems in NPPs to perform active measurements with spatial resolution down to 0.5-meter throughout the piping systems. Complex acoustic and vibration signatures harnessed by distributed sensors are registered and analyzed by artificial intelligence algorithms for degradation detection and flaw identification. Piping elbows with machined-in flaws were instrumented with fiber sensors. High-spatial-resolution data were used to develop and validate machine learning algorithms, including both linear and nonlinear regression, and classification. Additionally, classification and sensor analysis were also performed for data analysis. The paper concludes with recommendations and future work on applications of machine learning enabled high-resolution fiber sensors for piping degradation monitoring in current or future NPPs.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗