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Echo™ User Manual

Echo™ is a MATLAB-based software package designed for robust and scalable analysis of complex data workflows. An alternative to tedious, error-prone conventional processes, Echo is based on three transformative principles for data analysis: self-describing data, name-based indexing, and dynamic resource allocation. The software takes an object-oriented approach to data analysis, intimately connecting measurement data with associated metadata. Echo operations in an analysis workflow automatically track and merge metadata and computation parameters to provide a complete history of the process used to generate final results, while automated figure and report generation tools eliminate the potential to mislabel those results. History reporting and visualization methods provide straightforward auditability of analysis processes. Furthermore, name-based indexing on metadata greatly improves code readability for analyst collaboration and reduces opportunities for errors to occur. Echo efficiently manages large data sets using a framework that seamlessly allocates resources such that only the necessary computations to produce a given result are executed. Echo provides a versatile and extensible framework, allowing advanced users to add their own tools and data classes tailored to their own specific needs. Applying these transformative principles and powerful features, Echo greatly improves analyst efficiency and quality of results in many application areas.

97 MATHEMATICS AND COMPUTING↗

High precision control and deep learning-based corn stand counting algorithms for agricultural robot

This paper presents high precision control and deep learning-based corn stand counting algorithms for a low-cost, ultra-compact 3D printed and autonomous field robot for agricultural operations. Currently, plant traits, such as emergence rate, biomass, vigor, and stand counting, are measured manually. This is highly labor-intensive and prone to errors. The robot, termed TerraSentia, is designed to automate the measurement of plant traits for efficient phenotyping as an alternative to manual measurements. In this paper, we formulate a Nonlinear Moving Horizon Estimator that identifies key terrain parameters using onboard robot sensors and a learning-based Nonlinear Model Predictive Control that ensures high precision path tracking in the presence of unknown wheel-terrain interaction. Moreover, we develop a machine vision algorithm designed to enable an ultra-compact ground robot to count corn stands by driving through the fields autonomously. The algorithm leverages a deep network to detect corn plants in images, and a visual tracking model to re-identify detected objects at different time steps. We collected data from 53 corn plots in various fields for corn plants around 14 days after emergence (stage V3 - V4). The robot predictions have agreed well with the ground truth with C robot =1.02×C human -0.86 and a correlation coefficient R=0.96. The mean relative error given by the algorithm is -3.78%, and the standard deviation is 6.76%. These results indicate a first and significant step towards autonomous robot-based real-time phenotyping using low-cost, ultra-compact ground robots for corn and potentially other crops.

97 MATHEMATICS AND COMPUTING↗

Virtual sensing-enabled digital twin framework for real-time monitoring of nuclear systems leveraging deep neural operators

Abstract Real-time monitoring is a foundation of nuclear digital twin technology, crucial for detecting material degradation and maintaining nuclear system integrity. Traditional physical sensor systems face limitations, particularly in measuring critical parameters in hard-to-reach or harsh environments, often resulting in incomplete data coverage. Machine learning-driven virtual sensors offer a transformative solution by complementing physical sensors in monitoring critical degradation indicators. This paper introduces the use of Deep Operator Networks (DeepONet) to predict key thermal-hydraulic parameters in the hot leg of pressurized water reactor. DeepONet acts as a virtual sensor, mapping operational inputs to spatially distributed system behaviors without requiring frequent retraining. Our results show that DeepONet achieves low mean squared and Relative L2 error, making predictions 1400 times faster than traditional CFD simulations . These characteristics enable DeepONet to function as a real-time virtual sensor, synchronizing with the physical system to track degradation conditions and provide insights within the digital twin framework for nuclear systems.

Hossain, Raisa↗

Coherent manipulation of graph states composed of finite-energy Gottesman-Kitaev-Preskill-encoded qubits

Graph states are a central resource in measurement-based quantum information processing. In the photonic qubit architecture based on Gottesman-Kitaev-Preskill (GKP) encoding, the generation of high-fidelity graph states composed of realistic, finite-energy approximate GKP-encoded qubits thus constitutes a key task. We consider the finite-energy approximation of GKP-qubit states given by a coherent superposition of shifted finite-squeezed vacuum states, where the displacements are Gaussian distributed. We present an exact description of graph states composed of such approximate GKP qubits as a coherent superposition of a Gaussian ensemble of randomly displaced ideal GKP-qubit graph states. Using standard Gaussian dynamics, we track the transformation of the covariance matrix and the mean-displacement vector elements of the Gaussian distribution of the ensemble under tools such as GKP-Steane error-correction and fusion operations that can be used to grow large high-fidelity GKP-qubit graph states. The covariance matrix elements capture the noise in the graph state due to the finite-energy approximation of GKP qubits, while the mean displacements relate to the possible absolute shift errors on the individual qubits arising conditionally from the homodyne measurements that are a part of these tools. Our work thus pins down an exact coherent error model for graph states generated from truly finite-energy GKP qubits, which can shed light on their error-correction properties.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

SU-D-201-05: On the Automatic Recognition of Patient Safety Hazards in a Radiotherapy Setup Using a Novel 3D Camera System and a Deep Learning Framework

Purpose: Patient safety hazards such as a wrong patient/site getting treated can lead to catastrophic results. The purpose of this project is to automatically detect potential patient safety hazards during the radiotherapy setup and alert the therapist before the treatment is initiated. Methods: We employed a set of co-located and co-registered 3D cameras placed inside the treatment room. Each camera provided a point-cloud of fraxels (fragment pixels with 3D depth information). Each of the cameras were calibrated using a custom-built calibration target to provide 3D information with less than 2 mm error in the 500 mm neighborhood around the isocenter. To identify potential patient safety hazards, the treatment room components and the patient’s body needed to be identified and tracked in real-time. For feature recognition purposes, we used a graph-cut based feature recognition with principal component analysis (PCA) based feature-to-object correlation to segment the objects in real-time. Changes in the object’s position were tracked using the CamShift algorithm. The 3D object information was then stored for each classified object (e.g. gantry, couch). A deep learning framework was then used to analyze all the classified objects in both 2D and 3D and was then used to fine-tune a convolutional network for object recognition. The number of network layers were optimized to identify the tracked objects with >95% accuracy. Results: Our systematic analyses showed that, the system was effectively able to recognize wrong patient setups and wrong patient accessories. The combined usage of 2D camera information (color + depth) enabled a topology-preserving approach to verify patient safety hazards in an automatic manner and even in scenarios where the depth information is partially available. Conclusion: By utilizing the 3D cameras inside the treatment room and a deep learning based image classification, potential patient safety hazards can be effectively avoided.

60 APPLIED LIFE SCIENCES↗

Corrections to the General (2,4) and (4,4) FDTD Schemes

The sampling weights associated with two general higher order FDTD schemes were derived by Smith, et al. and published in a IEEE Transactions on Antennas and Propagation article in 2012. Inconsistencies between governing equations and their resulting solutions were discovered within the article. In an effort to track down the root cause of these inconsistencies, the full three-dimensional, higher order FDTD dispersion relation was re-derived using Mathematica TM . During this process, two errors were identi ed in the article. Both errors are highlighted in this document. The corrected sampling weights are also provided. Finally, the original stability limits provided for both schemes are corrected, and presented in a more precise form. It is recommended any future implementations of the two general higher order schemes provided in the Smith, et al. 2012 article should instead use the sampling weights and stability conditions listed in this document.

97 MATHEMATICS AND COMPUTING↗

Uncertainty propagation in full-core Monte Carlo depletion simulations using Serpent

The desire to accurately model the heterogeneity of the nuclear reactor environment combined with the ever more powerful computational resources have made in recent years the use of Monte Carlo method more attractive and feasible (if challenging) even for 3-D full core depletion simulation. However, in this case statistical uncertainty is combined with error propagating through the calculation from previous steps. In an effort to understand this error propagation, a numerical study was undertaken and previously reported modeling depletion of a four fuel assemblies (a 'quad'). This work extends results and analysis on a full nuclear reactor core depletion simulation where isotopics of individual fuel pins is tracked. By changing the code's initial random number seed, the data produced by a series of 19 replica runs was used to investigate the true and apparent variance in k{sub eff} and pin powers. It is hoped that this results can help to identify some common regularities in the behavior of uncertainty in several key parameters, and ultimately develop a predictive model. (authors)

97 MATHEMATICS AND COMPUTING↗

Accuracy and precision of ESI-Orbitrap-IRMS observations of hours to tens of hours via reservoir injection

Here, orbitrap isotope ratio mass spectrometry (Orbitrap-IRMS) has recently been applied to high-precision, natural-abundance isotope ratio measurements of a diverse range of compounds, including amino acids, oxyanions, fatty acids, and metals. These measurements can characterize many isotope ratios simultaneously at high (≈1.0‰) precision. In a successful experiment, observed precision will track the shot-noise limit and be limited by experimental time. Some isotope ratios, for example those involving 17 O in organic compounds or multiply-substituted (‘clumped’) isotopologues, require experimental times of hours to tens of hours to achieve desired precision, while current sample introduction techniques focus on observations on the order of seconds to tens of minutes. In this study, we characterize Orbitrap-IRMS performance for three long duration measurements (individual acquisitions ≥1 h and as long as 24 h) using an automated reservoir injection system coupled to a Q Exactive HF Orbitrap with an electrospray ionization (ESI) source. First, we characterize long-term intra-measurement stability through a 24-h long measurement of acetone. We report the following isotope ratios and precisions (as acquisition errors, errors on the observed ratio within this measurement (σ AE )): 13 C/ 12 C (σ AE = 0.07‰), 17 O/ 16 O (σ AE = 1.1‰), 18 O/ 16 O (σ AE = 0.3‰), and 13 C 13 C/ 12 C (σ AE = 0.65‰). The σ AE of each tracks the shot noise limit throughout and is limited by the challenging conditions (high resolution and low numbers of ions per scan) required for 17 O/ 16 O measurement in the presence of 13 C via Orbitrap. Second, we characterize inter-measurement stability via a sequence of seven 75-min analyses of perchlorate. We observe the following ratios and acquisition errors: 37 Cl/ 35 Cl (σ AE = 0.09‰); 17 O/ 16 O (σ AE = 1.6‰); 18 O/ 16 O (σ AE = 0.7‰), 37 Cl 17 O/ 35 Cl 16 O (σ AE = 2.7‰), and 37 Cl 18 O/ 35 Cl 16 O (σ AE = 1.2‰). However, we find that inter-measurement drift between acquisitions limits our accuracy and precision for standardized measurements (i.e., error on reported δ values) to ≈1‰ for the 37 Cl/ 35 Cl measurement. Hence, the benefits of low σ AE may not be fully realized. Third, we demonstrate accuracy via sample/standard comparisons of a methionine sample with 13 C enrichment of ≈20‰ relative to a known standard. Using a sequence of seven 60-min analyses, we recover the following isotope ratios and standardized precisions (i.e., error on reported δ values, denoted propagated acquisition errors, σ PAE ): 33 S/ 32 S (σ PAE = 1.0‰), 34 S/ 32 S (σ PAE = 0.7‰), 15 N/ 14 N (σ PAE = 2.1‰), 2 H/ 1 H (σ PAE = 3.2‰), 13 C/ 12 C (σ PAE = 0.4‰), 18 O/ 16 O (σ PAE = 1.6‰), & 13 C 13 C/ 12 C (σ PAE = 2.8‰) with confirmation of accurate results for the known 13 C/ 12 C and 13 C 13 C/ 12 C enrichments. Together, our results demonstrate the viability of Orbitrap-IRMS for long duration measurements of diverse sample types via an automated reservoir injection system. Inter-measurement stability remains a challenge; we expect our methods to be most applicable to extended measurements of hard-to-observe properties, such as 17 O in organics and clumped isotopologues.

58 GEOSCIENCES↗

Uncertainty analysis of correlated parameters in automated reaction mechanism generation

Abstract Uncertainty analysis is a useful tool for inspecting and improving detailed kinetic mechanisms because it can identify the greatest sources of model output error. Owing to the very nonlinear relationship between kinetic and thermodynamic parameters and computed concentrations, model predictions can be extremely sensitive to uncertainties in some parameters while uncertainties in other parameters can be irrelevant. Error propagation becomes even more convoluted in automatically generated kinetic models, where input uncertainties are correlated through kinetic rate rules and thermodynamic group values. Local and global uncertainty analyses were implemented and used to analyze error propagation in Reaction Mechanism Generator (RMG), an open‐source software for generating kinetic models. A framework for automatically assigning parameter uncertainties to estimated thermodynamics and kinetics was created, enabling tracking of correlated uncertainties. Local first‐order uncertainty propagation was implemented using sensitivities computed natively within RMG. Global uncertainty analysis was implemented using adaptive Smolyak pseudospectral approximations as implemented in the MIT Uncertainty Quantification Library to efficiently compute and construct polynomial chaos expansions to approximate the dependence of outputs on a subset of uncertain inputs. Cantera was used as a backend for simulating the reactor system in the global analysis. Analyses were performed for a phenyldodecane pyrolysis model. Local and global methods demonstrated similar trends; however, many uncertainties were significantly overestimated by the local analysis. Both local and global analyses show that correlated uncertainties based on kinetic rate rules and thermochemical groups drastically reduce a model's degrees of freedom and have a large impact on the determination of the most influential input parameters. These results highlight the necessity of incorporating uncertainty analysis in the mechanism generation workflow.

Gao, Connie W.↗

Effects of in-situ and reanalysis climate data on estimation of cropland gross primary production using the Vegetation Photosynthesis Model

Satellite-based Production Efficiency Models (PEMs) often require meteorological reanalysis data such as the North America Regional Reanalysis (NARR) by the National Centers for Environmental Prediction (NCEP) as model inputs to simulate Gross Primary Production (GPP) at regional and global scales. This study first evaluated the accuracies of air temperature (TNARR) and downward shortwave radiation (RNARR) of the NARR by comparing with in-situ meteorological measurements at 37 AmeriFlux non-crop eddy flux sites, then used one PEM – the Vegetation Photosynthesis Model (VPM) to simulate 8-day mean GPP (GPPVPM) at seven AmeriFlux crop sites, and investigated the uncertainties in GPPVPM from climate inputs as compared with eddy covariance-based GPP (GPPEC). Results showed that TNARR agreed well with in-situ measurements; RNARR, however, was positively biased. An empirical linear correction was applied to RNARR, and significantly reduced the relative error of RNARR by ~25% for crop site-years. Overall, GPPVPM calculated from the in-situ (GPPVPM(EC)), original (GPPVPM(NARR)) and adjusted NARR (GPPVPM(adjNARR)) climate data tracked the seasonality of GPPEC well, albeit with different degrees of biases. GPPVPM(EC) showed a good match with GPPEC for maize (Zea mays L.), but was slightly underestimated for soybean (Glycine max L.). Replacing the in-situ climate data with the NARR resulted in a significant overestimation of GPPVPM(NARR) (18.4/29.6% for irrigated/rainfed maize and 12.7/12.5% for irrigated/rainfed soybean). GPPVPM(adjNARR) showed a good agreement with GPPVPM(EC) for both crops due to the reduction in the bias of RNARR. The results imply that the bias of RNARR introduced significant uncertainties into the PEM-based GPP estimates, suggesting that more accurate surface radiation datasets are needed to estimate primary production of terrestrial ecosystems at regional and global scales.

AmeriFlux↗

BioWatch SMS Supervisor Guide

The BioWatch Sample Management System is software developed by Los Alamos National Laboratory to support the Department of Homeland Security BioWatch program. Field Operations Supervisors use the software to record, track, and manage data for the BioWatch sample collection process. This includes installing the software, creating and updating databases, assigning user IDs and passwords, editing and customizing reports, correcting data errors, recovering lost data, and troubleshooting. The BioWatch SMS Field Operations Supervisor Guide provides procedures for each task a Field Operations Supervisor performs. The reference information in this guide includes appendices of error messages and solutions, terms used interchangeably, and safety warnings along with a glossary, an index, and a list of suggested reference documents.

99 GENERAL AND MISCELLANEOUS↗

Assessing Historical Variability of South Asian Monsoon Lows and Depressions With an Optimized Tracking Algorithm

Abstract Cyclonic low‐pressure systems (LPS) produce abundant rainfall in South Asia, where they are traditionally categorized as monsoon lows, monsoon depressions, and more intense cyclonic storms. The India Meteorological Department (IMD) has tracked monsoon depressions for over a century, finding a large decline in their number in recent decades, but their methods have changed over time and do not include monsoon lows. This study presents a fast, objective algorithm for identifying monsoon LPS and uses it to assess interannual variability and trends in reanalyses. Variables and thresholds used in the algorithm are selected to best match a subjectively analyzed LPS data set while minimizing disagreement between four reanalyses in a training period. The stream function of 850 hPa horizontal wind is found to be optimal in this sense; it is less noisy than vorticity and represents the complete nondivergent wind, even when flow is not geostrophic. Using this algorithm, LPS statistics are computed for five reanalyses, and none show a detectable trend in monsoon depression counts since 1979. Both the Japanese 55‐year Reanalysis (JRA‐55) and the IMD data set show a step‐like reduction in depression counts when they began using geostationary satellite data, in 1979 and 1982, respectively; the 1958–2018 linear trend in JRA‐55, however, is smaller than in the IMD data set, and its error bar includes 0. There are more LPS in seasons with above‐average monsoon rainfall and in La Niña years, but few other large‐scale modes of interannual variability are found to modulate LPS counts, lifetimes, or track length consistently across reanalyses.

54 ENVIRONMENTAL SCIENCES↗

On the Representation of the Porosity-Pressure Relationship in General Subsurface Flow Codes

The governing equations for subsurface flow codes in a deformable porous media are derived from the balance of fluid mass and Darcy's equation. One class of these codes, which we call general subsurface flow codes (GSFs), allow for more general constitutive relations for material properties such as porosity, permeability and density. Examples of GSFs include PFLOTRAN, FEHM, TOUGH2, STOMP, and some reservoir simulators such as BOAST. Depending on the constitutive relations used in GSFs, an inconsistency arises between the standard groundwater flow equation and the governing equation of GSFs, and we clarify that the reason for this inconsistency is because the Darcy's equation used in the GSFs should account for the velocity of fluid with respect to solid. Due to lack of awareness of this inconsistency, users of the GSFs tend to use a porosity-pressure relationship that comes from the standard groundwater flow equation and assumes that the relative velocity is already accounted for. For the Theis problem, we show that using this traditional relationship in the GSFs leads to significantly large errors. In this work, we propose an alternate porosity-pressure relationship that is consistent with the derivation of the governing equations in the GSFs where the solid velocity is not tracked, and show that, with this relationship, the results are more accurate for the Theis problem. The purpose of this note is to make the users and developers of these GSFs aware of this inconsistency and to advocate that the alternate porosity model derived here should be incorporated in GSFs.

58 GEOSCIENCES↗

Impact of Resonant Magnetic Perturbations on the Toroidal Location of the Runaway Electron Final Loss Strike Point

It is demonstrated that the peak toroidal impact phase of the post-disruption runaway electrons (REs) can be varied shot-to-shot by means of applied static non-axisymmetric (3D) magnetic fields, or resonant magnetic perturbations (RMPs). In the experiments, high-current (500 kA), purged RE plateaus (i.e. low impurity post-disruption plasmas with current carried completely by REs) were terminated on the DIII-D tokamak center post (CP). The global toroidal impact peak of the REs appears to be dominantly set by the toroidal phase of a wall-locked tearing mode, typically (m/n) = (2/1), but sometimes (m/n) = (3/2). In the absence of external RMP, the locked mode reliably locks close to a preferred toroidal phase Φ ≃ 75◦ probably set by intrinsic error fields. With applied RMP, the locked mode and RE impact phase is pushed to a new location. When the tearing mode is (m/n) = (2/1), the phase is well controlled and tracks the applied RMP phase, but in the case of an (m/n) = (3/2) tearing mode, the new phase location is not well controlled. These results could have application in ITER and other fusion power plant (FPP) - sized tokamaks as a method for spreading disruption first wall damage from REs

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Distributed State Estimation Over Time-Varying Graphs: Exploiting the Age-of-Information

Here, we study the problem of designing a distributed observer for an LTI system over a time-varying communication graph. The limited existing work on this topic imposes various restrictions either on the observation model or on the sequence of communication graphs. In contrast, we propose a single-time-scale distributed observer that works under mild assumptions. Specifically, our communication model only requires strong-connectivity to be preserved over non-overlapping, contiguous intervals that are even allowed to grow unbounded over time. We show that under suitable conditions that bound the growth of such intervals, joint observability is sufficient to track the state of any discrete-time LTI system exponentially fast, at any desired rate. We also develop a variant of our algorithm that is provably robust to worst-case adversarial attacks, provided the sequence of graphs is sufficiently connected over time. The key to our approach is the notion of a "freshness-index" that keeps track of the age-of-information being diffused across the network. Such indices enable nodes to reject stale estimates of the state, and, in turn, contribute to stability of the error dynamics.

42 ENGINEERING↗

The Pointing Self-calibration Algorithm for Aperture Synthesis Radio Telescopes

This paper is concerned with algorithms for calibration of direction-dependent effects (DDE) in aperture synthesis radio telescopes (ASRT). After correction of direction-independent effects (DIE) using self-calibration, imaging performance can be limited by the imprecise knowledge of the forward gain of the elements in the array. In general, the forward gain pattern is directionally dependent and varies with time due to a number of reasons. Some factors, such as rotation of the primary beam with Parallactic Angle for Azimuth–Elevation mount antennas are known a priori. Some, such as antenna pointing errors and structural deformation/projection effects for aperture-array elements cannot be measured a priori. Thus, in addition to algorithms to correct for DD effects known a priori, algorithms to solve for DD gains are required for high dynamic range imaging. Here, we discuss a mathematical framework for antenna-based DDE calibration algorithms and show that this framework leads to computationally efficient optimal algorithms that scale well in a parallel computing environment. As an example of an antenna-based DD calibration algorithm, we demonstrate the Pointing SelfCal (PSC) algorithm to solve for the antenna pointing errors. Our analysis show that the sensitivity of modern ASRT is sufficient to solve for antenna pointing errors and other DD effects. We also discuss the use of the PSC algorithm in real-time calibration systems and extensions for antenna Shape SelfCal algorithm for real-time tracking and corrections for pointing offsets and changes in antenna shape.

79 ASTRONOMY AND ASTROPHYSICS↗

DUNE – Simulation Validation of Fermilab Detector Reconstruction

DUNE (Deep Underground Neutrino Experiment) is Fermilab’s flagship international experiment designed to study neutrinos by sending an intense beam from Illinois to detectors located 1,300 kilometers away at the Sanford Underground Research Facility (SURF) in South Dakota. To prepare for such a large-scale experiment, physicists develop detailed simulations to produce mock data sets which are analyzed by the CAFAna framework. During my internship, I developed software using the CAFAna framework to analyze simulated detector data and generated plots to make data trends easier to interpret and identify patterns. My analysis has uncovered inconsistencies in reconstructed neutrino tracks, duplicated reconstructed tracks causing sporadic spikes in the data, and unnatural differences in energy levels between interaction types. These analyses help verify that the improvements to detector simulations do not introduce unintended resolution errors and ensure proper reconstruction performance, supporting DUNE’s goal of making precise neutrino measurements and advancing the Department of Energy’s mission of fundamental scientific discovery.

Vershaw, Andre [Unlisted, US, IL; Fermilab] (ORCID↗