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At least 91 records · Page 5

Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation

The extensive heterogeneity of biological data poses challenges to analysis and interpretation. Construction of a large-scale mechanistic model of Escherichia coli enabled us to integrate and cross-evaluate a massive, heterogeneous dataset based on measurements reported by various groups over decades. We identified inconsistencies with functional consequences across the data, including that the total output of the ribosomes and RNA polymerases described by data are not sufficient for a cell to reproduce measured doubling times, that measured metabolic parameters are neither fully compatible with each other nor with overall growth, and that essential proteins are absent during the cell cycle—and the cell is robust to this absence. Finally, considering these data as a whole leads to successful predictions of new experimental outcomes, in this case protein half-lives.

59 BASIC BIOLOGICAL SCIENCES↗

Three-dimensional cooperative inversion of airborne magnetic and gravity gradient data using deep-learning techniques

Using multiple geophysical methods has become a prevailing approach in numerous geophysical applications to investigate subsurface structures and parameters. These multimethod-based exploration strategies have the potential to greatly diminish uncertainties and ambiguities encountered during geophysical data analysis and interpretation. One of the applications is the cooperative inversion of airborne magnetic and gravity gradient data for the interpretation of data obtained in mineral, oil and gas, and geothermal explorations. In this paper, a unified cooperative inversion framework is designed by combining the standard separate inversions with a deep neural network (DNN), which serves as the link between different types of data. A well-trained DNN takes the separately inverted susceptibility and density models as the inputs and provides improved models that will be used as the initial models of deterministic inversions. A two-round iteration strategy is adopted to guarantee the reasonability of the recovered models and overall efficiency of the inversion. In addition, this deep-learning (DL)-based framework demonstrates excellent generalization abilities when tested on models that are entirely distinct from the training data sets. The framework can easily incorporate multiphysics without necessitating any structural changes to the network. Synthetic experiments validate that our DL-based method outperforms conventional separate inversions and cross-gradient-based joint inversion in view of the accuracy of the recovered models and inversion efficiency. Successful application to field data further verifies the effectiveness of our DL-based method.

Geochemistry & Geophysics↗

Analysis and Integration of the Hydraulic Fracturing Test Site-2 (HFTS-2) Comprehensive Dataset

Hydraulic Fracturing Test Site-2 (HFTS-2) is a field-based research experiment performed in the Permian (Delaware) Basin. The unique aspect of this program was the acquisition of a unique, comprehensive, diagnostic dataset. Additionally, shorter parent wells drilled three years before the child wells offered clear distinction between the stages influenced by parent-child effects and the stages without any effects. The goal of this study was to analyze and integrate this comprehensive diagnostic dataset to understand the areal and vertical extent of hydraulic fractures (HF). The paper also provides insights on the effects of parent wells’ depletion on child well HF geometry based on various monitoring methods and subsurface models. Areal and vertical coverage for all HFTS-2 wells during stimulation and depletion was estimated based on analysis and interpretation of diagnostics and advanced modeling results. HFTS-2 diagnostics included microseismic (MS), pre- and post-stimulation logs and cores, bottomhole gauges, and fiber optic (FO) data. The diagnostics results (MS, FO, image logs) were integrated and used to calibrate subsurface models. Additional field tests were designed and implemented for depletion monitoring. The tailored program for monitoring depletion included vertical and slant well pressures, interference testing, and a vertical strain depletion trial. Areal Coverage: Conventional MS (and FO MS) were used to compute HF dimensions, which were compared with diagnostics (FO strain, gauge, image logs) observations and calibrated subsurface models. A post-production interference test did not show offset well communication. Vertical Coverage: Vertical coverage during stimulation was monitored using a vertical monitoring well. The stronger mechanical strain signals showed good correlation with MS event intensities, geomechanical properties, and gauge inferences. Vertical depletion was estimated based on vertical/slant well gauges and strain depletion tests. Parent-Child Effects: Diagnostics and calibrated subsurface models show asymmetry in child well fracture geometries for stages that overlap parent wells. Child well image logs serve as a good indicator for parent Downloaded from http://onepetro.org/URTECONF/proceedings-pdf/21URTC/2-21URTC/D021S031R004/2477423/urtec-2021-5241-ms.pdf/1 by Carol Worster on 28 February 2022 URTeC 5241 well HF tracking. Child well MS events had an eastward bias, in line with pre-stimulation image logs, and was confirmed by parent well frac hits. Novel/Additive Information: The dataset presents a unique, over-constrained problem space to compare independent techniques to arrive at HF metrics (i.e., stimulation height and/or half-length), unlike a single source dataset, in which calibration is done using available data to guide predictions. Here, the asymmetry in HF geometry seen in the stages influenced by parent-child effects offers unique insights into well spacing and landing, which are key capital decisions the unconventional resources industry is seeking to optimize.

58 GEOSCIENCES↗

HFTS-2 Completions Design and State-of-the-Art Diagnostics Results

Various completion schemes were tested as part of the Hydraulic Fracture Test Site-2 (HFTS-2) project. The wells were instrumented with permanent fiber optic (FO) cable, and unique near-wellbore and far-field region surveys were acquired to evaluate spatial and temporal hydraulic fracture characteristics. The state-of-the-art diagnostics included substantial monitoring of both the well stimulation and longer-term production performance. The objective was to evaluate and improve stimulation distribution effectiveness (SDE) for different completion designs based on the diagnostics results. A hydraulic fracturing (HF) profile (i.e., proppant/fluid allocation among clusters) was obtained using near-wellbore Distributed Acoustic Sensing (DAS) data acquired during stimulation. Statistical analysis provided a quantitative assessment of SDE for the different completion designs. A novel workflow was developed to assess time-lapse fracture property changes at the cluster and stage levels based on Distributed Strain Sensing (DSS) data acquired during the production phase. These time-lapse fracture property changes were compared with the HF profile. Based on the statistical analysis, Rate Per Cluster (RPC) during proppant slurry placement appears to be a primary completion design variable, rather than the typical Rate Per Perf (RPP). If RPC was not maintained at a certain level, the likelihood of uneven distribution increased dramatically. The stage configurations that created low RPC while maintaining high RPP did not show improved SDE. The strain change results based on DSS data during the production phase indicated near-wellbore fracture property changes (e.g., aperture changes during well shut-in and flow periods) and aligned well with near-wellbore DAS signals acquired during stimulation. More importantly, fracture property changes based on DSS data acquired during two tests over a 7-month period show high consistency and good alignment with the near-wellbore HF profile. This workflow quantitatively evaluates SDE for different completion designs using diagnostic results and could help optimize completion strategy for future development projects. Here, the analysis and interpretation of results demonstrate the technical feasibility of using permanent fiber optic cable for stimulation and production monitoring and indic

58 GEOSCIENCES↗

Pycheron: A Python-Based Seismic Waveform Data Quality Control Software Package

Supplementing an existing high-quality seismic monitoring network with openly available station data could improve coverage and decrease magnitudes of completeness; however, this can present challenges when varying levels of data quality exist. Without discerning the quality of openly available data, using it poses significant data management, analysis, and interpretation issues. Incorporating additional stations without properly identifying and mitigating data quality problems can degrade overall monitoring capability. If openly available stations are to be used routinely, a robust, automated data quality assessment for a wide range of quality control (QC) issues is essential. To meet this need, we developed Pycheron, a Python-based library for QC of seismic waveform data. Pycheron was initially based on the Incorporated Research Institutions for Seismology’s Modular Utility for STAtistical kNowledge Gathering but has been expanded to include more functionality. Pycheron can be implemented at the beginning of a data processing pipeline or can process stand-alone data sets. Its objectives are to (1) identify specific QC issues; (2) automatically assess data quality and instrumentation health; (3) serve as a basic service that all data processing builds on by alerting downstream processing algorithms to any quality degradation; and (4) improve our ability to process orders of magnitudes more data through performance optimizations. This article provides an overview of Pycheron, its features, basic workflow, and an example application using a synthetic QC data set.

58 GEOSCIENCES↗

Fundamental Neutron Physics: Theory and Analysis

The research topic of the project focus on the theoretical study of the possibility to search for manifestations of new physics beyond the Standard model in fundamental neutron physics, with emphasis on fundamental symmetries and "exotic'' interactions. The mail goals concentrate on the search for Time Reversal Invariance Violation (TRIV) in neutron nuclei scattering, and on possible manifestations of new physics in neutron-antineutron oscillations and their interactions with nuclei. Theoretical methods for analysis and interpretations of TRIV parameters in neutron scattering with the possible background interactions, and for unambiguous separation of the effects related to manifestations of new physics have been developed. The obtained results will be applied for the development of experimental programs in fundamental neutron physics at the Spallation Neutron Sources (SNS) in USA, Japan, and Europe.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Materials Dynamics

The Materials Dynamics area of leadership focuses on understanding process-structure-properties-performance (PSPP) relationships for the extreme conditions of dynamic loading. This research encompasses controlled synthesis of materials to meet dynamic performance requirements and entails computational coupling across length and time scales for three-dimensional microstructure modeling. For this leadership area, we define dynamic loading as strain rates ≥ 10 3 /s and often, high pressures. A key grand challenge of this area is to predict and measure the evolution of microstructural phases, defect structures, and electronic structure under dynamic conditions while also measuring local temperature to understand transition states. Solving this challenge will require agile, multi-dimensional data analysis and interpretation capability.

36 MATERIALS SCIENCE↗

TEAMER - Acoustic Particle Velocity Measurements - CRADA 601 (Abstract)

With relatively few deployments of tidal turbines, the extent and effect of underwater sounds generated from these turbines is not well understood. The University of Washington (UW) is deploying a cross-flow turbine system, the Turbine Lander, in the entrance channel to Sequim Bay. The deployment of this system provides an opportunity to understand the noise radiated by the turbine and its sources. There are three hypothesized sound sources associated with operation of the turbine: 1) a continuous tone associated with energized power electronics; 2) sound associated with the generator when the turbine is rotating; and 3) sound associated with the bearing pack that supports the rotor. PNNL is collaborating with UW and Integral Consulting Inc. (Integral) to simultaneously measure sound sources using three different devices. The NoiseSpotter®, an acoustic sensor system designed by Integral, measures acoustic pressure and a three-dimensional particle velocity vector. The NoiseSpotter, along with a commercial-off-the-shelf acoustic particle motion and pressure sensor (M20-105, Geospectrum Technologies Inc.) owned by PNNL will be deployed on the seabed approximately 50-100 m from the Turbine Lander. UW will concurrently deploy Drifting Acoustic Instrumentation SYstems (DAISYs) to characterize acoustic pressure near the Turbine Lander and localize sounds using a Time Delay of Arrival (TDOA) algorithm. Integral, UW, and PNNL will collaborate on data analysis and interpretation, with the intention of jointly authoring an archival paper on the results. The noise generated from the Turbine Lander is not expected to be significant, yet this experiment will help to evaluate the efficacy of combining technologies to characterize noise and provide insights for approaches to consider for future turbine deployments at other locations.

16 TIDAL AND WAVE POWER↗

Elucidating Photoinduced Processes of Photosystem I Via Multidimensional Electronic and Vibrational Spectroscopies

This project was motivated by an overarching goal to elucidate the mechanism of energy and electron transfer that governs the efficient charge separation in photosystem I (PSI) complexes. PSI is a natural light harvesting complex that drives oxygenic photosynthesis in plants, algae, and cyanobacteria. It uses ~300 tightly packed chlorophylls (Chls) to absorb photons, transfer the excitation energy to the reaction center (RC), and generate a charge separated state with near unity quantum efficiency (QE). A better understanding of the mechanism of energy transfer and charge separation in PSI is required for understanding the high QE of natural light harvesting complexes, and it could lead to the further development of artificial photosynthetic systems for solar energy conversion and modification of light harvesting complexes to improve crop yields. We applied two-dimensional optical spectroscopies to different cyanobacterial photosystem I complexes, including PSI complexes that contain Chl f molecules, to map energy transfer pathways and gain insight into the efficient light harvesting of PSI. We used two-dimensional electronic spectroscopies (2DES) to map energy transfer in Chl a and Chl f containing PSI complexes. To investigate the Chl f PSI complexes, we modified our spectrometer to probe the lower energy states associated with Chl f molecules. We interpreted the 2DES spectra through global analysis procedures to generate maps of energy transfer. We also constructed a two-dimensional electronic vibrational (2DEV) spectrometer that will be used to investigate charge transfer transitions and dynamics within PSI complexes. Measurements were performed on model systems to establish general data analysis procedures for interpreting 2D spectra and gain insight into protein cofactor interactions.

14 SOLAR ENERGY↗

Report on the "Symposium on Advancements in Simulating Neutron Scattering Instruments and Experiments"

An international group of researchers gathered for the “Symposium on Advancements in Simulating Neutron Scattering Instruments and Experiments” at Oak Ridge National Laboratory (ORNL) on October 29- 30, 2024. The symposium highlighted state-of-the-art advancements in neutron scattering instrument simulations and the development of digital twins for scattering instruments. This document summarizes the recurring themes from the 19 talks and discussions. A key focus was on the role of neutronics simulations in the design, analysis, and performance optimization of neutron instruments. Presentations featured the most widely used software packages, such as McStas, McVine, Vitess, and MCNP. Another major theme addressed the analysis and interpretation of experimental neutron data, where materials models and simulations play a critical role. Talks on relevant software tools, including NCrystal, OCLimax, and Paradyse, were delivered by their respective developers. During the symposium, both talks and breakout sessions explored strategies to enhance the interplay between neutronics simulations and materials models. A key question emerged: How can we develop a RealTime Explainable Digital Twin of a neutron scattering experiment? Discussions include the idea that the Digital Twin concept has implications for instrument control and testing. Through this symposium, we gained valuable insights into the challenges and requirements for developing a Real-Time Explainable Digital Twin of a neutron scattering experiment. The discussions and presentations paved the way for future innovations in this rapidly advancing field.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in Sorghum

A better understanding of the genetic and metabolic mechanisms that confer stress resistance and tolerance in plants is key to engineering new crops through advanced breeding technologies. This requires a systems biology approach that builds on a genome-wide understanding of the regulation of gene expression, plant metabolism, physiology and growth. In this study, we examine the response to drought stress in Sorghum, as we leverage the tools for transcriptomics and plant metabolic modeling we have implemented at the U.S. Department of Energy Systems Biology Knowledgebase (KBase). KBase enables researchers worldwide to collaborate and advance research by allowing them to upload private or public data into the KBase Narrative Interface, empowering them to analyze this data using a rich, extensible array of computational and data-analytics tools, and allows them to securely share scientific workflows and conclusions. We demonstrate how to use the current RNA-seq tools in KBase, applicable to both plants and microbes, to assemble and quantify long transcripts and identify differentially expressed genes effectively. More specifically, we demonstrate the utility of the platform by identifying key genes that are differentially expressed during drought-stress in Sorghum bicolor, which is an important sustainable production crop plant. We then show how to use KBase tools to predict the membership of genes in metabolic pathways and examine expression data in the context of metabolic subsystems. We demonstrate the power of the platform by making the data analysis and interpretation available to the biologists in the reproducible, re-usable, point-and-click format of a KBase Narrative thus promoting FAIR (Findable, Accessible, Interoperable and Reusable) guiding principles for scientific data management and stewardship.

59 BASIC BIOLOGICAL SCIENCES↗

Perspectives on Citizen Science Data Quality

Information about data quality helps potential data users to determine whether and how data can be used and enables the analysis and interpretation of such data. Providing data quality information improves opportunities for data reuse by increasing the trustworthiness of the data. Recognizing the need for improving the quality of citizen science data, we describe quality assessment and quality control (QA/QC) issues for these data and offer perspectives on aspects of improving or ensuring citizen science data quality and for conducting research on related issues.

54 ENVIRONMENTAL SCIENCES↗

Cliff Retreat Rates Associated with a Low-Level Radioactive Waste Disposal Facility in Los Alamos, New Mexico, USA

We present an analysis and interpretation of potential cliff stability at a low-level waste disposal facility at Los Alamos National Laboratory, New Mexico, using cliff morphologic and fracture characteristics coupled with carbon-14 surface exposure dating. Our study is important as it directly bears on the licensing criteria for low-level radioactive waste sites. We find that future characteristic cliff failures will likely not breach disposal pits and shafts over the 1000-year minimum regulatory period. Further, we find, using a multivariate regression model, that slope angle and cliff face aspect are sub-equal in importance to predict regions of high risk of failure when combined with surface exposure ages and assuming that old exposure ages are most indicative of stability (instability) and therefore can aid decision making in final design implementation.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Enhancing Multi-Step Reservoir Inflow Forecasting: A Time-Variant Encoder–Decoder Approach

Accurate reservoir inflow forecasting is vital for effective water resource management. Reliable forecasts enable operators to optimize storage and release strategies to meet competing sectoral demands—such as water supply, irrigation, and hydropower scheduling—while also mitigating flood and drought risks. To address this need, in this study, we propose a novel time-variant encoder–decoder (ED) model designed specifically to improve multi-step reservoir inflow forecasting, enabling accurate predictions of reservoir inflows up to seven days ahead. Unlike conventional ED-LSTM and recursive ED-LSTM models, which use fixed encoder parameters or recursively propagate predictions, our model incorporates an adaptive encoder structure that dynamically adjusts to evolving conditions at each forecast horizon. Additionally, we introduce the Expected Baseline Integrated Gradients (EB-IGs) method for variable importance analysis, enhancing interpretability of inflow by incorporating multiple baselines to capture a broader range of hydrometeorological conditions. The proposed methods are demonstrated at several diverse reservoirs across the United States. Our results show that they outperform traditional methods, particularly at longer lead times, while also offering insights into the key drivers of inflow forecasting. These advancements contribute to enhanced reservoir management through improved forecasting accuracy and practical decision-making insights under complex hydroclimatic conditions.

58 GEOSCIENCES↗

THEMIS: A Parameter Estimation Framework for the Event Horizon Telescope

The Event Horizon Telescope (EHT) provides the unprecedented ability to directly resolve the structure and dynamics of black hole emission regions on scales smaller than their horizons. This has the potential to critically probe the mechanisms by which black holes accrete and launch outflows, and the structure of supermassive black hole spacetimes. However, accessing this information is a formidable analysis challenge for two reasons. First, the EHT natively produces a variety of data types that encode information about the image structure in nontrivial ways; these are subject to a variety of systematic effects associated with very long baseline interferometry and are supplemented by a wide variety of auxiliary data on the primary EHT targets from decades of other observations. Second, models of the emission regions and their interaction with the black hole are complex, highly uncertain, and computationally expensive to construct. As a result, the scientific utilization of EHT observations requires a flexible, extensible, and powerful analysis framework. We present such a framework, Themis, which defines a set of interfaces between models, data, and sampling algorithms that facilitates future development. We describe the design and currently existing components of Themis, how Themis has been validated thus far, and present additional analyses made possible by Themis that illustrate its capabilities. Importantly, we demonstrate that Themis is able to reproduce prior EHT analyses, extend these, and do so in a computationally efficient manner that can efficiently exploit modern high-performance computing facilities. Themis has already been used extensively in the scientific analysis and interpretation of the first EHT observations of M87.

79 ASTRONOMY AND ASTROPHYSICS↗

Polarimetric Properties of Event Horizon Telescope Targets from ALMA

We present the results from a full polarization study carried out with the Atacama Large Millimeter/submillimeter Array (ALMA) during the first Very Long Baseline Interferometry (VLBI) campaign, which was conducted in 2017 April in the λ3 mm and λ1.3 mm bands, in concert with the Global mm-VLBI Array (GMVA) and the Event Horizon Telescope (EHT), respectively. We determine the polarization and Faraday properties of all VLBI targets, including Sgr A*, M87, and a dozen radio-loud active galactic nuclei (AGNs), in the two bands at several epochs in a time window of 10 days. We detect high linear polarization fractions (2%–15%) and large rotation measures (RM > 10 3.3 –10 5.5 rad m -2 ), confirming the trends of previous AGN studies at millimeter wavelengths. We find that blazars are more strongly polarized than other AGNs in the sample, while exhibiting (on average) order-of-magnitude lower RM values, consistent with the AGN viewing angle unification scheme. For Sgr A* we report a mean RM of (-4.2 ± 0.3) × 10 5 rad m -2 at 1.3 mm, consistent with measurements over the past decade and, for the first time, an RM of (–2.1 ± 0.1) × 10 5 rad m -2 at 3 mm, suggesting that about half of the Faraday rotation at 1.3 mm may occur between the 3 mm photosphere and the 1.3 mm source. We also report the first unambiguous measurement of RM toward the M87 nucleus at millimeter wavelengths, which undergoes significant changes in magnitude and sign reversals on a one year timescale, spanning the range from -1.2 to 0.3 × 10 5 rad m -2 at 3 mm and -4.1 to 1.5 × 10 5 rad m -2 at 1.3 mm. Given this time variability, we argue that, unlike the case of Sgr A*, the RM in M87 does not provide an accurate estimate of the mass accretion rate onto the black hole. We put forward a two-component model, comprised of a variable compact region and a static extended region, that can simultaneously explain the polarimetric properties observed by both the EHT (on horizon scales) and ALMA (which observes the combined emission from both components). These measurements provide critical constraints for the calibration, analysis, and interpretation of simultaneously obtained VLBI data with the EHT and GMVA.

79 ASTRONOMY AND ASTROPHYSICS↗

The effects of storms and a transient sandy veneer on the interannual planform evolution of a low-relief coastal cliff and shore platform at Sargent Beach, Texas, USA

Coastal cliff erosion is alongshore-variable and episodic, with retreat rates that depend upon sediment as either tools of abrasion or protective cover. However, the feedbacks between coastal cliff planform morphology, retreat rate, and sediment cover are poorly quantified. This study investigates Sargent Beach, Texas, USA, at the annual to interannual scale to explore (1) the relationship between temporal and spatial variability in cliff retreat rate, roughness, and sinuosity and (2) the response of retreat rate and roughness to changes in sand and shell hash cover of the underlying mud substrate as well as the impact of major storms using field measurements of sediment cover, erosion, and aerial images to measure shore platform morphology and retreat. A storm event in 2009 increased the planform roughness and sinuosity of the coastal cliff at Sargent Beach. Following the storm, aerial-image-derived shorelines with annual resolution show a decrease in average alongshore erosion rates from 12 to 4 m yr –1 , coincident with a decrease in shoreline roughness and sinuosity (smoothing). Like the previous storm, a storm event in 2017 increased the planform roughness and sinuosity of the cliff. Over shorter timescales, monthly retreat of the sea cliff occurred only when the platform was sparsely covered with sediment cover on the shore platform, indicating that the tools and cover effects can significantly affect short-term erosion rates. The timescale to return to a smooth shoreline following a storm or roughening event, given a steady-state erosion rate, is approximately 24 years, with the long-term rate suggesting a maximum of ~107 years until Sargent Beach breaches, compromising the Gulf Intracoastal Waterway (GIWW) under current conditions and assuming no future storms or intervention. The observed retreat rate varies, both spatially and temporally, with cliff face morphology, demonstrating the importance of multi-scale measurements and analysis for interpretation of coastal processes and patterns of cliff retreat.

58 GEOSCIENCES↗