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At least 271 records · Page 15

INVESTIGATION OF ROCK-FLUID INTERACTIONS USING GEOMATERIAL MICROFLUIDICS

Illite and Illite-Smectite clays are reportedly the Caney Shale's most prevalent clay minerals. The swelling and fines migration of clays may occur when water-based fluids contact the clay minerals. This may result in the reduction of pore space and permeability, and wettability alteration. Therefore, we quantified the swelling potentials, fines migration and wettability alteration of Illite and Illite-Smectite clays upon exposure to model brines and a produced water, and a model oil and a crude oil. We measured density, viscosity, pH, TDS, and interfacial tension as they are important in multiphase flow and displacement characteristics. Geomaterial microfluidics is recently being used to study physicochemical interactions of solid-fluid systems. It facilitates visualizing the surface behavior upon exposure to various fluids. This study includes preparation and characterization of Illite-Smectite clay-coated glass capillary tubes. Illite and Illite-Smectite clay-coated geomaterial microfluidic surfaces were prepared to investigate the effects of first contact fluid, brine salinity, and aging on wettability. In this work, advancing and receding contact angles of model brine-air, model oil-air, produced water-air, crude oil-air, model brine-model oil systems, and produced water-crude oil systems have been measured in the untreated, and clay-coated microfluidic channels of 1000 µm width and 50 µm depth. The aging effect was studied by retaining the non-aqueous and aqueous solutions in the corresponding microfluidic channels for approximately 24 h in the case of channels first contacted by aqueous and non-aqueous solutions, respectively. The advancing and receding contact angles of Caney shale-crude oil-produced water systems were also measured. The experimental findings indicate the swelling potential, fines migration, and wettability alteration of Illite and Illite-Smectite clays. The results signify the influence of first contact fluid, brine salinity, and aging on wettability of the untreated and clay-coated microfluidic surfaces. The experiments also demonstrate the wetting nature of the Caney shale samples from reservoir and non-reservoir zones.

02 PETROLEUM↗

Interactive Quantum Chemistry Enabled by Machine Learning, Graphical Processing Units, and Cloud Computing

Modern quantum chemistry algorithms are increasingly able to accurately predict molecular properties that are useful for chemists in research and education. Despite this progress, performing such calculations is currently unattainable to the wider chemistry community, as they often require domain expertise, computer programming skills, and powerful computer hardware. In this review, we outline methods to eliminate these barriers using cutting-edge technologies. We discuss the ingredients needed to create accessible platforms that can compute quantum chemistry properties in real time, including graphical processing units–accelerated quantum chemistry in the cloud, artificial intelligence–driven natural molecule input methods, and extended reality visualization. We end by highlighting a series of exciting applications that assemble these components to create uniquely interactive platforms for computing and visualizing spectra, 3D structures, molecular orbitals, and many other chemical properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular-Scale Insights into the Heterogeneous Interactions between an m -Terphenyl Isocyanide Ligand and Noble Metal Nanoparticles

The structural and chemical properties of metal nanoparticles are often dictated by their interactions with molecular ligand shells. These interactions are highly material-specific and can vary significantly even among elements within the same group or materials with similar crystal structure. In this study, we surveyed the heterogeneous interactions between an m-terphenyl isocyanide ligand and Au and Ag nanoparticles (NPs) at the single-molecule limit. Specifically, we found that the ligation behavior with this molecule differs significantly between that of Au and AgNPs. Surface-enhanced Raman spectroscopy measurements revealed unique enhancement factors for two molecular vibrational modes between two metal surfaces, indicating different ligand binding geometries. Molecular-level characterization using scanning tunneling microscopy allowed us to directly visualize these variations between Ag and Au surfaces, which we assign as two distinct binding mechanisms. This molecular-scale visualization provides clear insights into the different ligand–metal interactions as well as the chemical behavior and spectroscopic characteristics of isocyanide-functionalized NPs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Real-World Cyber Security Demonstration for Networked Electric Drives

In this article, we present the design and implementation of a cyber-physical security testbed for networked electric drive systems, aimed at conducting real-world security demonstrations. To our knowledge, this is one of the first security testbeds for networked electric drives, seamlessly integrating the domains of power electronics and computer science, and cybersecurity. By doing so, the testbed offers a comprehensive platform to explore and understand the intricate and often complex interactions between cyber and physical systems. The core of our testbed consists of four electric machine drives, meticulously configured to emulate small-scale but realistic information technology (IT) and operational technology (OT) networks. This setup both provides a controlled environment for simulating a wide array of cyber-attacks, and mirrors potential real-world attack scenarios with a high degree of fidelity. The testbed serves as an invaluable resource for the study of cyber-physical security, offering a practical and dynamic platform for testing and validating cybersecurity measures in the context of networked electric drive systems. As a concrete example of the testbed's capabilities, we have developed and implemented a Python-based script designed to execute step-stone attacks over a wireless local area network (WLAN). This script leverages a sequence of target IP addresses, simulating a real-world attack vector that could be exploited by adversaries. To counteract such threats, we demonstrate the efficacy of our developed cyber-attack detection algorithms, which are integral to our testbed's security framework. Furthermore, the testbed incorporates a real-time visualization system using InfluxDB and Grafana, providing a dynamic and interactive representation of networked electric drives and their associated security monitoring mechanisms. This visualization component not only enhances the testbed's usability but also offers insightful, real-time data for researchers and practitioners, thereby facilitating a deeper understanding of cyber-physical security dynamics in networked electric drive systems.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Applications of visualization technology in the structural sciences

The structural sciences are undergoing a transformation driven by advancements in visualization technologies that aid researchers in understanding and communicating experimental data from complex molecular systems. New applications of integrative structural biological and biophysical approaches add a wide variety of complementary information from a broad range of scientific disciplines. These approaches extend structural biophysical methodologies to enable research by the incorporation of a variety of data streams and utilization of tools like molecular graphics, virtual reality, and machine learning. To redefine how structural data—particularly from cryo-electron microscopy and x-ray crystallography—are fed forward for scientific exploration and communication, the advances in tools for data visualization and interpretation have been critical. By bringing molecular systems into an interactive three-dimensional space, these novel technologies enhance research workflows, facilitate structure-based drug design, and create engaging educational experiences. Taken together, these visualization innovations are essential tools for advancing the field by making concepts more accessible and compelling.

Eng, Edward T. [New York Structural Biology Center↗

Uncertainty Visualization Challenges in Decision Systems with Ensemble Data & Surrogate Models: Preprint

Uncertainty visualization is a key component in translating important insights from ensemble data into actionable decision-making by visually conveying various aspects of uncertainty within a system. With the recent advent of fast surrogate models for computationally expensive simulations, users can interact with more aspects of data spaces than ever before. However, the integration of ensemble data with surrogate models in a decision-making tool brings up new challenges for uncertainty visualization, namely how to reconcile and communicate the new and different types of uncertainties brought in by surrogates and how to utilize these new data estimates in actionable ways. In this work, we examine these issues as they relate to high-dimensional data visualization, the integration of discrete datasets and the continuous representations of those datasets, and the unique difficulties associated with systems that allow users to iterate between input and output spaces. We assess the role of uncertainty visualization in facilitating intuitive and actionable interaction with ensemble data and surrogate models, and highlight key challenges in this new frontier of computational simulation.

ensemble visualization↗

Transforming Energy Through Computational Excellence: Advanced Scientific Visualization Reveals Energy Insights

The National Renewable Energy Laboratory's world-class researchers and analysts, along with the Insight Center (our state-of-the-art scientific visualization facility) make data immersion a reality, allowing users to step into and explore their data. With the rise of large, diverse, and distributed data sets, scientific visualization is now critical to the process of scientific discovery and to managing and analyzing data and extracting insights. NREL provides visualization capabilities and facilities that are supported by state-of-the-art equipment, leading-edge techniques, and expert staff.

data science↗

BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes

Background: Exploring metagenomic contigs and “binning” them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure. Results: We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena’s usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset. Conclusions: BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena, together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data.

59 BASIC BIOLOGICAL SCIENCES↗

Navigating Uncertainty: Challenges in Visualizing Ensemble Data and Surrogate Models for Decision Systems

Uncertainty visualization plays a critical role in transforming ensemble simulation data into actionable insights by effectively communicating various dimensions of uncertainty within a system. The emergence of artificial intelligence-driven surrogate models trained on multirun ensemble data offers a transformative opportunity to replace computationally intensive simulations with fast estimates, enabling users to explore data spaces with unprecedented depth and interactivity. However, integrating ensemble data and surrogate models into decision-making workflows and tools introduces novel challenges for uncertainty visualization. These include reconciling and clearly communicating the unique uncertainties associated with ensembles and their surrogate model estimates, and leveraging these approximations to inform actionable decisions. This work explores these challenges in the context of high-dimensional data visualization, bridging discrete datasets with their continuous representations and addressing the complexities of systems that support iterative navigation between input and output spaces. We evaluate the role of uncertainty visualization in fostering intuitive, actionable interactions and identify critical hurdles in advancing this frontier of computational simulation.

97 MATHEMATICS AND COMPUTING↗

Quorum-driven microbial consortium for Bioplastic production from agro-waste

Microbial consortia have high relevance in natural environments. Here we present the production of polyhydroxyalkanoates (PHA) from agro-industrial residues by a synthetic interkingdom consortium formed by the saprotrophic fungus Ophiostoma piceae CECT 20146, which encodes a wide range of lignocellulolytic enzymes, and a natural PHA producer, Pseudomonas putida KT2440. Two agro-industrial residues were utilized: Brewer's Spent Grain (BSG) as a carbon/nitrogen source and biofilm scaffold and waste cooking oil (WCO) as a carbon source for PHA synthesis. Through biochemistry, microscopy, and omics analyses, it is shown that P. putida accumulates up to 40.2% of intracellular PHA when the quorum sensing molecule, farnesol (naturally produced by O. piceae) is added, thanks to the increased proliferation of P. putida cells. An interactive Shiny application has also been developed for an easy visualization and comprehension of all the transcriptomics and metabolomics data: https://jgf-bioinformatics.shinyapps.io/Visualization_app/. These results support the increased PHA production of the consortium by an induction of gene phaG, which redirects intermediaries of the fatty acid biosynthesis to PHA precursors, and the repression of the PHA depolymerase phaZ in P. putida. The trophic interaction between microorganisms seems to rely on the citric acid produced by O. piceae and the glycerol liberated from WCO, which can both be consumed by P. putida. Bioreactor scale-up experiments allowed a 3.3-fold increase in the PHA concentration in the consortium (6.7 g·L-1) without pretreatment or sterilization of the substrates, laying the groundwork for the implementation of an industrial consolidated bioprocess (CBP).

Bacteria↗

Visualization for Insight and Data Analysis in Energy Research

This talk explores how advanced visualization technologies are transforming analytical reasoning and knowledge discovery in energy research, drawing on recent work at the National Laboratory of the Rockies' Computational Science Center. Through a series of scientific case studies, we demonstrate how immersive and high-resolution visualization environments enable scientists and engineers to identify previously unseen patterns and features - insights that often remain hidden in traditional desktop-based analysis. By embedding richer information into interactive analytics tools, these approaches support the exploration of complex, multivariate parameter spaces, where interaction itself catalyzes understanding. Beyond capability, we emphasize the critical role of visualization design grounded in perception and cognition, showing how visual encodings directly influence analytical outcomes. Spanning applications from materials science to integrated energy systems, these visualization approaches accelerate innovation and improve decision-making by enabling deeper, more reliable insight into increasingly complex energy data.

97 MATHEMATICS AND COMPUTING↗

A Visual Designer of Layer‐wise Relevance Propagation Models

Abstract Layer‐wise Relevance Propagation (LRP) is an emerging and widely‐used method for interpreting the prediction results of convolutional neural networks (CNN). LRP developers often select and employ different relevance backpropagation rules and parameters, to compute relevance scores on input images. However, there exists no obvious solution to define a “best” LRP model. A satisfied model is highly reliant on pertinent images and designers' goals. We develop a visual model designer, named as VisLRPDesigner, to overcome the challenges in the design and use of LRP models. Various LRP rules are unified into an integrated framework with an intuitive workflow of parameter setup. VisLRPDesigner thus allows users to interactively configure and compare LRP models. It also facilitates relevance‐based visual analysis with two important functions: relevance‐based pixel flipping and neuron ablation. Several use cases illustrate the benefits of VisLRPDesigner. The usability and limitation of the visual designer is evaluated by LRP users.

Huang, Xinyi↗

Ascribe XR v0.1.0

Ascribe XR is an immersive visualization software designed for scientists and engineers working with 3D data sets. Its key features include interactive exploration, multi-user collaboration, and flexible data import capabilities, supporting various formats such as meshes, volumes, and terrain maps. The software utilizes Godot, OpenXR and PC-VR technology to provide an immersive experience. Ascribe XR is used for data analysis, visualization, and collaboration in various fields, enabling users to gain deeper insights into complex data sets. Its advantages over similar technologies include its flexibility, customizability, and ease of use. Ascribe XR's interactive and immersive environment facilitates collaboration and accelerates the discovery process. Compared to traditional 2D visualization tools, Ascribe XR offers a more engaging and intuitive experience, allowing users to explore complex data sets in a more natural and interactive way. Its ability to support multi-user collaboration and flexible data import capabilities make it a versatile tool for various applications. Overall, Ascribe XR provides a unique combination of features, usability, and performance, making it an attractive solution for scientists and engineers working with 3D data sets.

Pandolfi, Ronald [Lawrence Berkeley National Labor↗

Measurement of Deformation Heterogeneity During Shale Swelling Using Digital Image Correlation

Abstract Rock-fluid interactions in shale formations are one of the main sources of wellbore instability issues and inadequate stimulation performance. For better planning of fracturing operations and optimizing production from these reservoirs, it is important to understand the mechanisms behind these interactions. These issues are especially prevalent in clay-rich shales, such as Tuscaloosa Marine Shale, which is the subject of this study. Conventional techniques to quantify these shale-fluid interactions comprise of measuring swelling in powdered rock grains or measurement of deformation in the whole pieces of the core using a linear variable differential transformer and strain gages. However, the contribution from individual laminae to overall deformation cannot be evaluated using these methods. In this study, we developed an experimental setup to evaluate the spatial deformation in shale during interaction with water using digital image correlation (DIC). Deformation of two shale samples, with 34 wt% to 51 wt% clay content, was studied. White paint was used to generate a random speckle pattern on the specimen and then immersed in deionized water. The deformation process was captured using a digital camera and images were analyzed using DIC to quantify the deformation. The implementation of the DIC technique enables the visualization and quantification of spatial deformation in the specimen during interacting with water. The results show the localization of large strains in select laminations. The results provide a better understanding of shale deformation when interacting with water in comparison to traditional measurements that can provide only an average strain value.

Energy & Fuels↗

In‐operando crystallization study of zinc nitrate hexahydrate using zinc oxide nucleators

Abstract Supercooling (∆T Sup ) is one of the crucial problems in utilizing a phase change material (PCM), which has been attempted to overcome using nucleators possessing small lattice disregistry without comprehensive understanding of the nucleation phenomenon. Here, this work studies the interactions between nucleators and PCM via in‐operando direct visualization for the first time, to the best of our knowledge, to better understand the crystallization process during freezing of a PCM using zinc nitrate hexahydrate (ZNH) and a zinc oxide (ZnO) nucleator. According to our in‐operando study, freezing was randomly initiated by only a fraction of the nucleator particles during each thermal cycling. However, previously unresponsive nucleators also suddenly crystalized PCM when the propagating crystal encountered them, improving the crystal initiation and thereby ∆T Sup . Consequently, for equal wt% of ZnO, better nucleation behavior was obtained using uniformly distributed small nucleator particles throughout the PCM, as compared to either large or poorly distributed aggregated nucleators. DSC results using ZnO‐needle as nucleator confirmed a 38% and 33.3% lower ∆T Sup upon employing 5 wt% small (individual) particles (~4 μm on average), as compared to using equal wt% of small (aggregated) particle clusters (~200 μm) and large particles (~46 μm), respectively. Crystallization of ZNH caused additional hair‐like ZnO growth preferentially decorated along lateral faces of the original nucleator particles. The in‐operando studies are valuable tools to correlate inherent crystallization phenomena to the practical thermal energy storage properties of the system.

Chakraborty, Anirban↗

A new database website for nuclear level densities

We introduce a new open-access, web-based database (http://nld.ascsn.net), Current Archive of Nuclear Density of Levels (CANDL), that hosts experimental nuclear level density (NLD) datasets from a variety of techniques and energy ranges. Built using the Dash framework in Python, the database is designed to be interactive and user-friendly, allowing researchers to search, visualize, fit, and export NLD data with minimal effort. This resource includes data extracted from evaporation spectra, Oslo method variants, and other experimental techniques that cover excitation energies beyond the neutron resonance region. The database supports on-the-fly fitting with two widely-used phenomenological models—the Constant Temperature (CT) model and the Back-Shifted Fermi Gas (BSFG) model—selected for their simplicity and computational efficiency. Future versions aim to include additional datasets and model types, as well as easy-to-use interfaces to data science techniques. Here, this platform offers a vital tool for the nuclear physics, astrophysics, medicine, and reactor design communities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Perspectives on Microfluidics for the Study of Asphaltenes in Upstream Hydrocarbon Production: A Minireview

The utilization of microfluidics has generated deep insights into asphaltene precipitation mechanisms and oil–water emulsion stabilization. Agglomeration and precipitation of asphaltenes can cause flow assurance problems during the extraction and transportation of crude oil. Change in temperature, pressure, reservoir conditions, and solvents can change the local environment, leading to asphaltene precipitation. Understanding asphaltene properties and precipitation pathways becomes critical in devising mitigation methods, demulsifiers, and suitable conditions during hydrocarbon processing. Microfluidics has helped in high throughput measurement studies, understanding critical processing conditions, fast demulsifier screening, and the effect of solvent concentration on deposition, generating useful information for utilization at the point of resource extraction facilitating improved resource management. It has become possible to capture the porous, complex nature of reservoir formations and the interaction of chemicals during precipitation through integrated analytics and visualization studies available only through microfluidics. The use of droplet microfluidics, with optical microscopy and high-speed imaging to study the oil–water interface, has resulted in greater understanding of the role of asphaltenes in interfacial properties and emulsion stabilization. Here, this minireview highlights the crucial aspects of microfluidics that have been used to understand physicochemical behavior and dynamics of asphaltene deposition. Some of the unique devices have been presented focusing on the key elements of microfluidics design, fabrication, and analysis, as the insight obtained from microfluidics strongly depends on the device design and the controllability of the experimental parameters. Successful implementation of microfluidics for efficient and controlled experiments, short analysis time scales and rapid screening, and generation of high-quality, reliable data that convey asphaltene deposition issues and interface behavior in emulsions shows the importance of microsystems for advancing knowledge in hydrocarbon production and processing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Decayheatml

This code is designed to predict and analyze the decay heat generated in molten salt reactors (MSRs) using a hybrid approach that combines machine learning and segmented polynomial fitting. The accurate prediction of decay heat is essential for reactor safety and the optimization of spent fuel storage. The code operates through several key components: 1) Data Architecture: It incorporates a modular data architecture that handles various MSR-specific operational parameters such as power density, humidity content, and air ingress. These parameters are sampled using Sobol sequences to ensure comprehensive coverage of operational uncertainties. 2) Machine Learning Framework: The code employs a diverse set of machine learning models, including polynomial regression, decision trees, random forests, gradient boosting, support vector regression, k-nearest neighbors, multi-layer perceptrons, and symbolic regression. These models are trained to predict decay heat over a wide temporal range, from immediate shutdown up to 10,000 years. 3) Region-Optimized Training: The temporal domain is divided into multiple regions, each modeled separately to capture distinct decay heat characteristics across different time scales. This approach significantly improves the accuracy and interpretability of predictions. 4) Segmented Polynomial Interpretation (SPI): The SPI method translates machine learning predictions into piecewise polynomial equations. These equations are physically interpretable and can be directly integrated into existing engineering workflows and safety analyses. 5) Front-End Interfaces: The code includes both a Jupyter notebook interface for research development and a Streamlit web application for operational deployment. These interfaces allow users to interactively explore decay heat predictions, adjust operational parameters, and visualize results in real-time. 6) Applications: The framework supports various applications, including safety system validation and spent fuel container optimization. It enables real-time evaluation of worst-case decay heat scenarios, informing the design of passive safety systems and optimizing container designs for long-term storage. Overall, this code provides a robust, accurate, and user-friendly tool for predicting decay heat in MSRs, enhancing reactor safety, and optimizing spent fuel management.

Retamales, Mauricio Eduardo Tano [Idaho National L↗