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At least 901 records · Page 50

Large-Scale Visualization of 3D Unstructured Groundwater Model Using Cave Automated Virtual Environment

The immersive three-dimensional (3D) virtual reality (VR) visualization of groundwater models allows us to deepen our understanding of aquifer systems and provide better solutions to present groundwater-related problems, such as groundwater recharge, water quality, and sustainability. Visualization assists in accurately developing groundwater models and revealing important subsurface features, including faulting, folding, and unconformity. However, assessing model accuracy poses challenges due to the complexity of geology and groundwater systems. This research demonstrates a workflow to visualize and analyze raw 3D unstructured groundwater model data using an immersive Cave Automated Virtual Environment (CAVE). To visualize the unstructured groundwater model data, the raw dataset is converted into interactive CAVE-compatible formats utilizing a set of tools: ParaView, Blender, and Unity. This enables researchers to immerse themselves in the data, identifying influential patterns and relationships. e resulting insights can inform the development of sophisticated machine-learning models for groundwater level prediction. The CAVE’s immersive capabilities allow intuitive exploration from various perspectives, providing a more holistic understanding of the factors affecting groundwater levels. These insights are crucial to improve predictive models. The CAVE results also facilitate collaborative analysis and have potential applications in training and education. is research demonstrates the value of immersive VR tools such as the CAVE for unraveling intricacies within high-dimensional scientific data to drive real-world forecasting and modeling applications.

54 ENVIRONMENTAL SCIENCES↗

Land-use analysis using infrastructure representations and high-resolution flood inundation mapping techniques

In the face of climate change and population growth in coastal regions, land-use analysis efforts are more challenging than ever. Land-use decision-makers in coastal communities are burdened with the difficult choices of where to place new homes versus other assets. While there has been an increased focus on hazard mitigation and disaster resilience in the field of planning, evidence points towards continued development in risk-prone areas including flood zones. Residential development within flood zones specifically continues to be a major issue. To help counter this trend, this study introduces a novel land-use analysis method, coupling topographic flood inundation mapping techniques with digital elevation model (DEM) adaptations. This Topographic Model Scenario Generation workflow can be used by planners early in the land-use decision making process and provides an alternative to high-computational hydraulic models. The analysis also includes the identification of strengths and weaknesses of topographic models' recognition of built infrastructure assets, adding to a limited body of knowledge addressing recommended uses of such models. Levees and canals prove particularly functional in this context while detention ponds less so, likely due to a lack of total water mass accountability. Lastly, we provide a functional demonstration in Southeast Texas to illustrate the workflow's ability to create multiple infrastructure scenarios and visualize their effects across different flood events.

42 ENGINEERING↗

Enhancing ACPF Analysis: Integrating Newton-Raphson Method with Gradient Descent and Computational Graphs

This paper presents a new method for enhancing Alternating Current Power Flow (ACPF) analysis. The method integrates the Newton-Raphson (NR) method with Enhanced-Gradient Descent (GD) and computational graphs. The integration of renewable energy sources in power systems introduces variability and unpredictability, and this method addresses these challenges. It leverages the robustness of NR for accurate approximations and the flexibility of GD for handling variable conditions, all without requiring Jacobian matrix inversion. Furthermore, computational graphs provide a structured and visual framework that simplifies and systematizes the application of these methods. The goal of this fusion is to overcome the limitations of traditional ACPF methods and improve the resilience, adaptability, and efficiency of modern power grid analyses. We validate the effectiveness of our advanced algorithm through comprehensive testing on established IEEE benchmark systems. Furthermore, our findings demonstrate that our approach not only speeds up the convergence process but also ensures consistent performance across diverse system states, representing a significant advancement in power flow computation.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Ultrafast coherent motion and helix rearrangement of homodimeric hemoglobin visualized with femtosecond X-ray solution scattering

Ultrafast motion of molecules, particularly the coherent motion, has been intensively investigated as a key factor guiding the reaction pathways. Recently, X-ray free-electron lasers (XFELs) have been utilized to elucidate the ultrafast motion of molecules. However, the studies on proteins using XFELs have been typically limited to the crystalline phase, and proteins in solution have rarely been investigated. Here we applied femtosecond time-resolved X-ray solution scattering (fs-TRXSS) and a structure refinement method to visualize the ultrafast motion of a protein. We succeeded in revealing detailed ultrafast structural changes of homodimeric hemoglobin involving the coherent motion. In addition to the motion of the protein itself, the time-dependent change of electron density of the hydration shell was tracked. Besides, the analysis on the fs-TRXSS data of myoglobin allows for observing the effect of the oligomeric state on the ultrafast coherent motion.

59 BASIC BIOLOGICAL SCIENCES↗

3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties

Abstract Motivation BISCAP is a state-of-the-art tool for automatically characterizing biofilm images obtained from Optical Coherence Tomography. Limited availability of other software tools is reported in the field. BISCAP’s first version processes 2D images only. Processing 3D images is a problem of greater scientific relevance since it deals with the entire structure of biofilms instead of their 2D slices. Results Building on the image-processing principles and algorithms proposed earlier for 2D images, these were adapted to the 3D case, and a more general implementation of BISCAP was developed. The primary goal concerns the extension of the initial methodology to incorporate the depth axis in 3D images; multiple improvements were also made to boost computational performance. The calculation of structural properties and visual outputs was extended to offer new insights into the 3D structure of biofilms. BISCAP was tested using 3D images of biofilms with different morphologies, consistently delivering accurate characterizations of 3D structures in a few minutes using standard laptop machines. Low user dependency is required for image analysis. Availability and implementation BISCAP is available from https://github.com/diogonarciso/BISCAP. All images used in the tutorials and the validation examples are available from https://web.fe.up.pt/∼fgm/biscap3d.

Narciso, Diogo A. C. (ORCID:0000000227767477)↗

Evaluating and Enhancing Iron Removal via Filterable Iron Precipitates Formation during Coal-Waste Bioleaching

Iron removal via jarosite precipitate formation is a commonly used technique in various hydrometallurgical processes. Excess iron removal often becomes essential to an overall metal recovery circuit. This is particularly important to processes involving iron-bearing minerals. A technique, which involved the use of pyrite to generate acid for leaching, for iron removal is critical to enabling the process. Iron removal using CaO or similar reagents is expensive and often results in lost product. In the present study, various compounds that facilitate jarosite formation, namely Na2SO4, NH4OH, KCl, and KOH, were utilized and their effect in precipitation was observed. Visual Minteq assisted simulations were run in order to evaluate favorable conditions for iron removal. Morphology and elemental composition of precipitates were analyzed using scanning electron microscopy equipped with energy-dispersive X-ray spectroscopy, and the phase purity was identified using X-ray diffraction analysis.

99 GENERAL AND MISCELLANEOUS↗

Evaluating Brightness and Stability of Cathodoluminescence from Colloidal Semiconductor Nanocrystals

Cathodoluminescence offers promise as a technique for correlation of atomic structure with electronic structure at the level of individual nanoparticles or even defects, with the ability to analyze complex nanostructures at length-scales far below those typically available to optical spectroscopy. Unlike other forms of electron microscopy, cathodoluminescence offers direct insights into the electronic structure of the visualized sample. Despite reports more than 10 years ago of individual nanoparticle cathodoluminescence, effective cathodoluminescence collection from colloidal semiconductor materials is relatively rare and remains challenging due to the instability of materials under the conditions of electron beam irradiation. In this work, to clarify the roadblocks for cathodoluminescence analysis of colloidal nanocrystals, we attempt a comprehensive study of the cathodoluminescence properties of semiconductor quantum shells, which have a thin concentric CdSe shell surrounding CdS nanoparticles, then surrounded by a further concentric CdS shell. These same materials were recently demonstrated to show promising scintillation performance in radioluminescence measurements, including high brightness (up to 100 ph/keV) and excellent durability. Comparative quantum yield measurements are designed to assess the brightness of semiconductor nanocrystal films, which show that the quantum shells are much less bright under electron irradiation compared to X-ray photons. Instability of CL emission is assigned to charging effects on the samples—and not thermal effects—through a series of voltage, current, dwell time, and atmospheric pressure experiments.

cathodoluminescence↗

ORNL_AISD_DL-HLgap

This dataset provides supplementary molecular dataset of Deep Learning Workflow for the Inverse Design of Molecules with Specific Optoelectronic Properties. The dataset comprises three main directories such as GDB-9_dataset, Low_HL_Gap_dataset, and High_HL_Gap_dataset which individually has csv files, smiles_txt files, pdb files and xyz files containing information of molecular structures, properties and coordinates generated from deep learning workflow using generative model, surrogate model and DFTB calculation results. GDB-9_dataset contains the molecular data extracted from the original GDB-9 dataset with additional data of DFTB HL gap, surrogate HL gap and molecular property analysis. (the number of atoms, aromaticity and double bond equivalent) Low_HL_Gap_dataset and High_HL_Gap_dataset contains series of dataset for different generations with further split to train and test dataset that were obtained from the iterative workflow described in the manuscript. Additional directory Chemiscope_visualization in Low_HL_Gap_dataset directory contains compressed json files to visualize molecules using chemiscope.org page or application to help readers examine generated molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

In-situ, nanoscale fracture toughness measurements for improved mechanical interfaces

In this project, we demonstrated stable nanoscale fracture in single-crystal silicon using an in-situ wedge-loaded double cantilever beam (DCB) specimen. The fracture toughness KIC was calculated directly from instrumented measurement of force and displacement via finite element analysis with frictional corrections. Measurements on multiple test specimens were used to show K IC = 0.72 ± 0.07 MPa m 1/2 on {111} planes and observe the crack-growth resistance curve in <500 nm increments. The exquisite stability of crack growth, instrumented measurement of material response, and direct visual access to observe nanoscale fracture processes in an ideally brittle material differentiate this approach from prior DCB methods.

36 MATERIALS SCIENCE↗

Connectivity, Centrality, and Bottleneckedness: On Graph Theoretic Methods for Power Systems

This report provides an introduction to selected graph theoretic topics with pertinence to the structural analysis of electric power grid and communication systems. We focus on methodologies for defining, scoring, and identifying connectivity, spectral, and bottleneckeness properties in graphs, as well as vertex and edge importance measures such as centrality. We apply these measures to power systems and communications graph data, discuss and visualize the results, and comment on computational aspects of these methods. We show that graph theoretic methods can provide useful insights into grid and communication network structure, leading to tools and methods that could be used by electric utility engineers to improve key grid and communication network characteristics, such as resilience and scalability.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Geolocated dataset of Chinese overseas development finance

China is now the world's largest source of bilateral development finance and will likely continue to play a prominent role in sovereign lending through its multi-billion-dollar Belt and Road Initiative. This paper introduces major methodological enhancements in tracking this finance: the use of an original application programming interface (API) to gathers news in multiple languages; double verification of every record to ensure every finance commitment has been formalized; and visual geo-location to trace the precise footprint of every project. The resulting dataset enables economic, environmental, and social analyses with high-precision spatial accuracy, as well as spatiotemporal monitoring by project stakeholders and enhanced planning by project managers. It covers the years 2008-2019 to enable analysis before and after the announcement of the Belt and Road Initiative. It includes 862 finance commitments, 669 of which have geographic location, to 94 countries across the world.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

CyclusJS: A Distributed Web-based Fuel Cycle Visual Analytics. Research Performance (Final Report)

The overall aim of the CyclusJS project has been to design novel approaches that support fuel cycle simulations and empower decision-makers and researchers with better tools to compare and contrast results from multiple simulations to understand the landscape of potential outcomes better. In particular, nuclear fuel cycle simulations focus on modeling the nuclear industry and ecosystem at a macroscopic level, and the analysis tools connect such simulations with decision support systems. As a demonstration of the novelty and effectiveness of the proposed approach, we study scenarios for transitioning from one technology, Light Water Reactors (LWR), to a newer Sodium-cooled Fast breeder Reactor (SFR) technology.

60 APPLIED LIFE SCIENCES↗

Design of a graphical user interface for few-shot machine learning classification of electron microscopy data

The recent growth in data generation by modern electron microscopes requires rapid, scalable, and flexible approaches to image segmentation and analysis. Few-shot machine learning, which can richly classify images from a handful of user-provided examples, is a promising route to high-throughput analysis. However, current command-line implementations of such approaches can be slow and unintuitive to use, lacking the real-time feedback necessary to perform effective classification. Here we report on the development of a Python-based graphical user interface that enables end users to easily conduct and visualize the output of few-shot learning models. This interface is portable and can be hosted locally or on the web, providing the opportunity to reproducibly conduct, share, and crowd-source few-shot analyses.

97 MATHEMATICS AND COMPUTING↗

Assessing the Sensitivity of Pourbaix Diagrams to Computational Protocols: Electrochemical Stability of Ni Oxides as a Case Study

Pourbaix diagrams stand as a useful tool in assessing and visualizing materials’ electrochemical stability and are widely used for electrocatalyst design. However, their reliability hinges on the accuracy of the chemical potentials of involved phases, which may bear uncertainties and can be significantly impacted by decision-making steps in the computational protocol. Here, this study introduces a robust sensitivity analysis framework, exemplified through a detailed examination of the computational Pourbaix diagram of Ni, the oxides of which are used as high-activity and cost-friendly catalysts for many electrochemical reactions. Quantities of interest derived from the Pourbaix diagram include the appearance and stability domain of the catalytically active Ni oxide phases along with the onset electrochemical potentials of phase transitions. These metrics can guide the design of operational conditions for Ni oxide electrocatalysts. We find that the employed DFT exchange-correlation functional has the most significant influence on the computed Pourbaix diagram. Uncertainties on crystal structures, along with their related ab initio energetics, are also found to affect the size of the phase stability domain. Higher-order coupling among input parameters is found to play a crucial role in influencing the appearance and distribution of Ni phases in the diagram. Our findings suggest a need to consider variations and uncertainties associated with the computational procedures on predicted Pourbaix diagrams for materials design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology

Metabolic reprogramming in cancer and immune cells occurs to support their increasing energy needs in biological tissues. Here we propose Single Cell Spatially resolved Metabolic (scSpaMet) framework for joint protein-metabolite profiling of single immune and cancer cells in male human tissues by incorporating untargeted spatial metabolomics and targeted multiplexed protein imaging in a single pipeline. We utilized the scSpaMet to profile cell types and spatial metabolomic maps of 19507, 31156, and 8215 single cells in human lung cancer, tonsil, and endometrium tissues, respectively. The scSpaMet analysis revealed cell type-dependent metabolite profiles and local metabolite competition of neighboring single cells in human tissues. Deep learning-based joint embedding revealed unique metabolite states within cell types. Trajectory inference showed metabolic patterns along cell differentiation paths. Here we show scSpaMet’s ability to quantify and visualize the cell-type specific and spatially resolved metabolic-protein mapping as an emerging tool for systems-level understanding of tissue biology.

59 BASIC BIOLOGICAL SCIENCES↗

GenomeDepot v1.0

GenomeDepot is a web-based platform for annotation, management, and comparative analysis of microbial genomic sequences and associated data including ortholog families, protein domains, operons, regulatory interactions, strain taxonomy, and sample metadata. GenomeDepot supports rapid creation of web-sites for user-defined genome collections that include bioinformatic tools for interactive genome browsing, BLAST search, annotation search, comparative genomic neighborhood visualization, and sequence download. Gene function annotations are generated by a customizable annotation pipeline. The pipeline runs annotation tools in Conda environments and can be easily extended with additional user-specified tools.

Kazakov, Alexey [Lawrence Berkeley National Labora↗

Analysis of Electricity Price Differentials for the Utah Office of Energy Development

Operation Gigawatt is a vision for Utah to meet its growing energy needs with a focus on doubling energy generation. One of the greatest challenges to meet this goal will be the transmission and distribution system. Utah seeks analysis to inform discussions on new generation, the likely network congestion based on new power flows, and modeling of the state's energy infrastructure. To support this need, LBNL developed a baseline understanding of recent historical congestion in the existing transmission system based on electricity market prices. The resulting products visualize and provide metrics on congestion within Utah and between Utah and its neighbors during 2015-2023.

24 POWER TRANSMISSION AND DISTRIBUTION↗

T3CO-Go: A web-based dashboard for the Transportation Technology Total Cost of Ownership tool [SWR-25-38]

T3CO-Go is a web-based dashboard with a user interface to modify input assumptions, run the T3CO tool, and visualize results. The dashboard, built using Python, can be run on a local server when installed from PyPI or hosted on the cloud and embedded in a webpage. T3CO-Go allows even non-Python-proficient users to customize their T3CO experience and gain insights from results customized for their analysis purpose. See also, PyPI Package: https://pypi.org/project/t3co-go/

Panneer Selvam, Harish [National Renewable Energy ↗