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Building Toward the Future in Chemical and Materials Simulation with Accessible and Intelligently Designed Web Applications

Over the last few decades, significant progress has been made in the development and use of electronic structure and other molecular simulation methods. As these methods become more mature and are able to simulate larger and more complex chemical simulations, the need for improvement in scientific visualization, molecular builders, simplified input to simulation methods, and the development of new approaches and languages to describe simulations, along with workflows to carry them out, becomes more apparent. In this chapter, we describe our recent efforts in developing a prototype open-source computational tool called Arrows that combines NWChem, SQL and NoSQL databases, email, web APIs, and web applications in a way that make molecular and materials modeling accessible to all scientists and engineers. At the same time, because of its simplified input, it provides a framework for expert users to carry out large numbers of calculations and run complex workflows.

TU-A-17A-02: In Memoriam of Ben Galkin: Virtual Tools for Validation of X-Ray Breast Imaging Systems

This symposium will explore simulation methods for the preclinical evaluation of novel 3D and 4D x-ray breast imaging systems – the subject of AAPM taskgroup TG234. Given the complex design of modern imaging systems, simulations offer significant advantages over long and costly clinical studies in terms of reproducibility, reduced radiation exposures, a known reference standard, and the capability for studying patient and disease subpopulations through appropriate choice of simulation parameters. Our focus will be on testing the realism of software anthropomorphic phantoms and virtual clinical trials tools developed for the optimization and validation of breast imaging systems. The symposium will review the stateof- the-science, as well as the advantages and limitations of various approaches to testing realism of phantoms and simulated breast images. Approaches based upon the visual assessment of synthetic breast images by expert observers will be contrasted with approaches based upon comparing statistical properties between synthetic and clinical images. The role of observer models in the assessment of realism will be considered. Finally, an industry perspective will be presented, summarizing the role and importance of virtual tools and simulation methods in product development. The challenges and conditions that must be satisfied in order for computational modeling and simulation to play a significantly increased role in the design and evaluation of novel breast imaging systems will be addressed. Learning Objectives: Review the state-of-the science in testing realism of software anthropomorphic phantoms and virtual clinical trials tools; Compare approaches based upon the visual assessment by expert observers vs. the analysis of statistical properties of synthetic images; Discuss the role of observer models in the assessment of realism; Summarize the industry perspective to virtual methods for breast imaging.

60 APPLIED LIFE SCIENCES↗

Dual-Zone Solar Control Indoor Shade: Demonstration at the Ronald V. Dellums Federal Building and U.S. Courthouse, 1301 Clay Street, Oakland, California and the Lawrence Berkeley National Laboratory Advanced Windows Testbed, Berkeley, California

Standard window shades are used to control sunlight, glare, window heat gains, and daylight. The challenge with conventional shades is that once the shades are lowered to reduce discomfort, daylight is reduced, which, in turn, increases the need for electric lighting. View is also obstructed, reducing the occupants’ connection to the outdoors. The strategy of subdividing the window wall and admitting daylight from above and controlling sunlight and view through the lower aperture can yield significant energy and peak demand savings over conventional shading systems, and improve the daylight quality of the indoor environment. This study evaluated a dual zone solar control (DZSC) shade with an upper, automated, horizontal, venetian blind with concave-up, matte white slats and a lower, manually operated, roller shade made of a transparent, reflective film. The automatic controls were designed to adjust the upper slat angle to maximize daylight to the room interior. The lower shade, when lowered, provided an unobstructed view to the outdoors. For the qualitative analysis, the DZSC shades were installed on windows in the southeast half of one floor in the Ronald V. Dellums Federal Building and U.S. Courthouse or hereafter referred to as the Oakland Federal Building (OFB) in Oakland, California. The position of the DZSC shades were observed and recorded periodically. Surveys were issued to occupants in the private offices and open plan workstations affected by the shades. For the quantitative analysis, the DZSC shades were installed in the south-facing windows of thermally isolated, fully instrumented, test chambers in the Advanced Windows Testbed at the Lawrence Berkeley National Laboratory (LBNL) in Berkeley, California. Measurements of window heat loads, daylight illuminance and environmental conditions related to visual and thermal comfort were collected over a six-month, solstice-to-solstice period. The performance of the DZSC shade was compared to fabric roller shades and venetian blinds since these are the two most common types of shades used in both commercial and Federal buildings. Several DZSC design permutations were evaluated: 1) manual or automated control of the upper louver system (“man” or “auto”) and 2) tinted or silvered reflective film for the lower shade (“Gray-Gray (GG)” or “Gray-Silver (GS)”1). The automated, reflective shade (auto-GS) reduced dimmable fluorescent lighting energy use by 51% and window cooling load by 13-15% compared to a conventional fabric roller shade with dual-pane, spectrally selective, low-e windows during the summer period (winter period was not measured). Qualitative analysis revealed that the auto-GS shade was preferred by 80% of the survey respondents compared to the existing vertical fabric blinds with single-pane, tinted windows in the occupied building. Survey results indicated that visual discomfort was reduced and thermal discomfort was also reduced during warm or hot weather. Occupants expressed greater satisfaction with the unobstructed view. Installation and commissioning of the DZSC shades was fairly straightforward with some minor problems due to inadequate installation instructions and improper wiring. A few occupants expressed dissatisfaction with the automatic controls for the upper louvers due to visual discomfort, erroneous control, and motor noise.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Synergistic foam stabilization and transport improvement in simulated fractures with polyelectrolyte complex nanoparticles: Microscale observation using laser etched glass micromodels

Inaccessibility to direct pore scale observation in hydrocarbon recovery of tight shale formations poses a great challenge to water-energy nexus initiatives and necessitates the use of high throughput technologies to emulate environmentally friendly processes. Herein, we employ a precise glass micromodel fabrication and visualization method to isolate the supercritical CO 2 bubbles surrounded by CO 2 -water lamella prepared in saline produced water stabilized with molecular complexation of zwitterionic surfactants (ZS) and polyelectrolyte complex nanoparticles (PECNP). The Selective Laser Enhanced Etching (SLE) technique was selected for micromodel simulation of high-pressure flow. Two representative designs, (1) fracture/micro-crack network 28 and (2) fracture/matrix were etched on fused silica glass with a laser printing machine and scCO 2 foam was injected to study the foamability, propagation, stability, and fluid loss properties. The highly monodispersed and uniformly distributed array of scCO 2 bubbles were detected in flow of scCO 2 foam in highly saline brine containing ionic complexes of positively charged PECNPs and ZS, whereas foam flow with the lamella containing ZS in fractures offered a noticeably large and polydisperse array of scCO 2 bubbles. scCO 2 bubble motion and deformation were traced, and local description of foam flow was visually examined. The confined array of scCO 2 bubbles stabilized by ZS in microcracks was affected by bubble growth and coalescence, whereas the super-populated array of monodispersed scC O2 bubbles with lamella containing complexes of PECNP and ZS were able to fill the channels with stable configurations within the timeframe of comparative stability measurements. The ability of complex fluid to prevent the formation damage was evaluated through fluid loss visualization in micromodels. Probing scCO 2 foam transport in homogenous porous media revealed smaller volume leak-off for scCO 2 foam containing PECNP-ZS ionic complexes.

04 OIL SHALES AND TAR SANDS↗

Ray-tracing image simulations of transparent objects with complex shape and inhomogeneous refractive index

Optical images of transparent three-dimensional objects can be different from a replica of the object’s cross section in the image plane, due to refraction at the surface or in the body of the object. Simulations of the object’s image are thus needed for the visualization and validation of physical models. We report ray tracing image simulations that achieved high physical fidelity, reproducing optical behaviors and image features not rendered in previous studies. We replicated brightfield microscopy images of drops with complex shapes, and images of pressure and shock waves traveling inside them. For high physical fidelity, the simulations must replicate the spatial and angular distribution of illumination rays, and both the experiment and the simulation must be designed for accurate optical modeling. The simulations are highly sensitive to the properties of the drops and can be used to diagnose and refine fluid dynamics models. The simulated images can also be optimized to extract multiple 3D properties from experimental images. Compared to specialized single-shot 3D imaging methods, this approach has the advantage that it preserves the experimental simplicity, the high resolution, and the visual interpretability characteristic to basic optical imaging. The techniques introduced here are directly applicable to optical microscopy, so they can be used in other fields, such as microfluidics and biology, to expand the type and the accuracy of three-dimensional information that can be extracted from basic optical images.

Cavitation↗

Workspace and Office Design: A Review of the Literature

The Systems Analysis & Decision Support (02150) group completed a review of the research literature on workspace and office design in 2016 for the Asset Management Department (04853). The goal was to characterize results and lessons learned from existing research to understand the effectiveness of current workspaces at Sandia National Laboratories and inform guidance for future workspace design. The study team reviewed 96 documents, published primarily since the year 2000, covering a range of factors associated with workspace design - workspace costs, acoustics, collaboration and privacy, generational preferences, employee health, performance and productivity, organizational retention, and workspace satisfaction. The research literature consistently highlighted the relative deficiencies of open-plan office spaces as compared to traditional private enclosed offices for knowledge workers. While open-plan offices can provide some cost savings, they may not be cost effective in the long term due to future hidden costs incurred by degradations in employee productivity, increased attrition, and increased sickness absences as well as any post-construction modifications needed to resolve emerging workspace issues. The chief deficiencies of open-plan offices include lower levels of employee satisfaction due to reduced visual and auditory privacy, increased interruptions, distractions from irrelevant background speech, less physical space, and more ambient noise. The drawbacks reported in the literature tend to outweigh any benefits associated with potential facilitation of coworker interactions and collaboration. Key suggestions identified in the literature to guide and optimize workspace and office design are provided.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Comparison of three measurement modalities for 3D characterization of manufactured features and process-induced porosity in titanium alloy additively manufactured parts

Nondestructive characterization of internal features and defects within complex components is vital for many industrial applications, particularly with the advent of additive manufacturing (AM) technologies. However, community understanding of the limitations of nondestructive methods such as X-ray Computed Tomography (CT) can be limited in certain industrial sectors as these may be emergent applications. In this paper, we investigate the limits of X-ray CT measurements and compare extracted data with mechanical polishing serial sectioning (MPSS) and confocal laser scanning microscopy (CLSM). The test object is an additively manufactured titanium alloy disk that contains both process-induced porosity and machined features, including focused ion beam milled features designed to probe the resolution limits of X-ray CT. Results show that each of these characterization techniques has advantages and disadvantages. We compare data acquisition times, spatial resolution, geometric measurement accuracy and defect visualization fidelity across these modalities to establish a practical framework.

Additive manufacturing↗

Identification of the Selective Sites for Electrochemical Reduction of CO to C 2+ Products on Copper Nanoparticles by Combining Reactive Force Fields, Density Functional Theory, and Machine Learning

Recent experiments have shown that CO reduction on oxide derived Cu nanoparticles (NP) are highly selective toward C 2+ products. However, understanding of the active sites on such NPs is limited, because the NPs have ~200 000 atoms with more than 10 000 surface sites, far too many for direct quantum mechanical calculations and experimental identifications. We show here how to overcome the computational limitation by combining multiple levels of theoretical computations with machine learning. This approach allows us to map the machine learned CO adsorption energies on the surface of the copper nanoparticle to construct the active site visualization (ASV). Furthermore, we identify the structural criteria for optimizing selective reduction by predicting the reaction energies of the potential determining step, $ΔE_{OCCOH}$, for the C 2+ product. Based on this structural criterion, we design a new periodic copper structure for CO reduction with a theoretical faradaic efficiency of 97%.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Foundation Models for Zero-Shot Segmentation of Scientific Images without AI-Ready Data

Zero-shot and prompt-based models have excelled at visual reasoning tasks by leveraging large-scale natural image corpora, but they often fail on sparse and domain-specific scientific image data. We introduce Zenesis, a no-code interactive computer vision platform designed to reduce data readiness bottlenecks in scientific imaging workflows. Zenesis integrates lightweight multimodal adaptation for zero-shot inference on raw scientific data, human-in-the-loop refinement, and heuristic-based temporal enhancement. We validate our approach on Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) datasets of catalyst-loaded membranes. Zenesis outperforms baselines, achieving an average accuracy of 0.947, Intersection over Union (IoU) of 0.858, and Dice score of 0.923 on amorphous catalyst samples; and 0.987 accuracy, 0.857 IoU, and 0.923 Dice on crystalline samples. These results represent a significant performance gain over conventional methods such as Otsu thresholding and standalone models like the Segment Anything Model (SAM). Zenesis enables effective image segmentation in domains where annotated datasets are limited, offering a scalable solution for scientific discovery.

Mukherjee, Shubhabrata↗

Paracousti v. 2.0.0

Paracousti simulates 3-D acoustic wave propagation in fixed (non-moving) complex media. It solves the linear acoustic equations of motion using the velocity-pressure system of first order linear differential equations on a finite-difference Cartesian grid using Newton’s law of motion and mass continuity equations. It also has the ability to incorporate acoustic attenuation to simulate non-recoverable energy losses via the velocity-memory-pressure system of linear differential equations. We assume stationary, non-heat conducting, adiabatic media (fluid) where the background sound speed and material density are fixed in time. Capabilities include massively parallel design, optimization for high contrast media interfaces, inclusion of arbitrary pressure and force sources defined by the user, inclusion of arbitrary pressure and velocity receivers defined by the user, acoustic wavefield snapshots in time for visualization, and convolutional perfectly matched layers to minimize artificial grid boundary reflections. Paracousti was built upon the foundational framework of TDAAPS (Time-Domain Atmospheric Acoustic Propagation Suite) by Neill Symons, Dave Aldridge, and Leiph Preston.

Preston, Leiph↗

Xi-CAM v1.2.3

Xi-CAM aims to provide a community driven platform for multimodal analysis in synchrotron science. The platform core provides a robust plugin infrastructure for extensibility, allowing continuing development to simply add further functionality. Current modules include tools for characterization with (GI)SAXS, Tomography, and XAS. This will continue to serve as a development base as algorithms for multimodal analysis develop. Seamless remote data access, visualization and analysis are key elements of Xi-CAM, and will become critical to synchrotron data infrastructure as expectations for future data volume and acquisition rates rise with continuously increasing throughputs. The highly interactive design elements of Xi-cam will similarly support a generation of users which depend on immediate data quality feedback during high-throughput or burst acquisition modes.

Pandolfi, Ronald↗

Feasible Actuator Range Modifier (FARM), a Tool Aiding the Solution of Unit Dispatch Problems for Advanced Energy Systems

Integrated energy systems (IESs) seek to minimize power generating costs in future power grids through the coupling of different energy technologies. To accommodate fluctuations in load demand due to the penetration of renewable energy sources, flexible operation capabilities must be fully exploited, and even power plants that are traditionally considered as base-load units need to be operated according to unconventional paradigms. Thermomechanical loads induced by frequent power adjustments can accelerate the wear and tear. If a unit is flexibly operated without respecting limits on materials, the risk of failures of expensive components will eventually increase, nullifying the additional profits ensured by flexible operation. In addition to the bounds on power variations (explicit constraints),the solution of the unit dispatch problem needs to meet the limits on the variation of key process variables, including temperature, pressure and flow rate (implicit constraints).The FARM (Feasible Actuator Range Modifier) module was developed to enable existing optimization algorithms to identify solutions to the unit dispatch problem that are both economically favorable and technologically sustainable. Thanks to the iterative dispatcher–validator scheme, FARM permits addressing all the imposed constraints without excessively increasing the computational costs. In this work, the algorithms constituting the module are described, and the performance was assessed by solving the unit dispatch problem for an IES composed of three units, i.e., balance of plant, gas turbine, and high-temperature steam electrolysis. Finally, the FARM module provides dedicated tools for visualizing the response of the constrained variables of interest during operational transients and a tool aiding the operator at making decisions. These techniques might represent the first step towards the deployment of an ecological interface design (EID) for IES units.

47 OTHER INSTRUMENTATION↗

Sustain

Current building energy simulation technology requires excessive labor, time and expertise to create building energy models, excessive computational time for accurate simulations and difficulties with the interpretation of the results. These deficiencies can be ameliorated using modern graphical user interfaces and algorithms which take advantage of modern computer architectures and display capabilities. To prove this hypothesis, we developed an experimental test bed for building energy simulation. This novel test bed environment offers an easy-to-use interactive graphical interface, provides access to innovative simulation modules that run at accelerated computational speeds, and presents new graphics visualization methods to interpret simulation results. Our system offers the promise of dramatic ease of use in comparison with currently available building energy simulation tools. Its modular structure makes it suitable for early stage building design, as a research platform for the investigation of new simulation methods, and as a tool for teaching concepts of sustainable design. Improvements in the accuracy and execution speed of many of the simulation modules are based on the modification of advanced computer graphics rendering algorithms. Significant performance improvements are demonstrated in several computationally expensive energy simulation modules. The incorporation of these modern graphical techniques should advance the state of the art in the domain of whole building energy analysis and building performance simulation, particularly at the conceptual design stage when decisions have the greatest impact. More importantly, these better simulation tools will enable the transition from prescriptive to performative energy codes, resulting in better, more efficient designs for our future built environment.

Source record↗

Compression-based integral curve data reuse framework for flow visualization

Currently, by default, integral curves are repeatedly re-computed in different flow visualization applications, such as FTLE field computation, source-destination queries, etc., leading to unnecessary resource cost. We present a compression-based data reuse framework for integral curves, to greatly reduce their retrieval cost, especially in a resource-limited environment. In our design, a hierarchical and hybrid compression scheme is proposed to balance three objectives, including high compression ratio, controllable error, and low decompression cost. Specifically, we use and combine digitized curve sparse representation, floating-point data compression, and octree space partitioning to adaptively achieve the objectives. Results have shown that our data reuse framework could acquire tens of times acceleration in the resource-limited environment compared to on-the-fly particle tracing, and keep controllable information loss. Moreover, our method could provide fast integral curve retrieval for more complex data, such as unstructured mesh data.

97 MATHEMATICS AND COMPUTING↗

Coupling SCALE with DAKOTA for Axial Burnup Profiles Assessment in Burnup Credit

This paper presents a computational study that demonstrates the application of the SCALE code system in conjunction with the Design Analysis Kit for Optimization and Terascale Applications (DAKOTA) for the analysis of key factors influencing the evaluation of burnup credit (BUC) in pressurized water reactors (PWRs). The primary objective of this analysis is to characterize the model by utilizing parameterization, uncertainty quantification, and optimization studies. Using this approach, we can comprehensively assess the system and conduct informed predictive studies. This study highlights the effectiveness of the SCALE code system integrated within the DAKOTA framework in terms of efficiency and capability. With the coupling of the burnup code ORIGAMI with the CSAS or TSUNAMI-3D sequence embedded in a DAKOTA analysis, we can characterize the factors that influence the k eff of PWR 17x17 spent nuclear fuel (SNF) in the GBC-32 computational benchmark cask for the assessment of BUC in criticality safety analysis. The coupling methodology used in this study is not exclusive to BUC analysis. However, the choice to apply this methodology to the BUC problem is particularly significant because of the diverse range of aspects it encompasses in nuclear criticality safety analyses. This problem presents a unique opportunity to explore and address multiple facets of such analyses related to BUC and illustrates the capability of the SCALE code system with DAKOTA. This analysis makes use of historical reference data for the axial burnup profile, where the entire space within the bounds is considered. Both SCALE and DAKOTA are currently integrated in the Nuclear Energy Advanced Modeling Simulation (NEAMS) Workbench code system, which has a user-friendly graphical interface that simplifies the setup of simulations and configuration of input parameters as well as the visualization of simulation results.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Netostat: analyzing dynamic flow patterns in high-speed networks

Understanding flow traffic patterns in networks, such as the Internet or service provider networks, is crucial to improving their design and building them robustly. However, as networks grow and become more complex, it is increasingly cumbersome and challenging to study how the many flow patterns, sizes and the continually changing source-destination pairs in the network evolve with time. Here, we present Netostat, a visualization-based network analysis tool that uses visual representation and a mathematics framework to study and capture flow patterns, using graph theoretical methods such as clustering, similarity and difference measures. Netostat generates an interactive graph of all traffic patterns in the network, to isolate key elements that can provide insights for traffic engineering. We present results for U.S. and European research networks, ESnet and GEANT, demonstrating network state changes, to identify major flow trends, potential points of failure, and bottlenecks.

97 MATHEMATICS AND COMPUTING↗

Explaining and predicting human behavior and social dynamics in simulated virtual worlds: reproducibility, generalizability, and robustness of causal discovery methods

Ground Truth program was designed to evaluate social science modeling approaches using simulation test beds with ground truth intentionally and systematically embedded to understand and model complex Human Domain systems and their dynamics Lazer et al. (Science 369:1060–1062, 2020). Our multidisciplinary team of data scientists, statisticians, experts in Artificial Intelligence (AI) and visual analytics had a unique role on the program to investigate accuracy, reproducibility, generalizability, and robustness of the state-of-the-art (SOTA) causal structure learning approaches applied to fully observed and sampled simulated data across virtual worlds. In addition, we analyzed the feasibility of using machine learning models to predict future social behavior with and without causal knowledge explicitly embedded. In this paper, we first present our causal modeling approach to discover the causal structure of four virtual worlds produced by the simulation teams—Urban Life, Financial Governance, Disaster and Geopolitical Conflict. Our approach adapts the state-of-the-art causal discovery (including ensemble models), machine learning, data analytics, and visualization techniques to allow a human-machine team to reverse-engineer the true causal relations from sampled and fully observed data. We next present our reproducibility analysis of two research methods team’s performance using a range of causal discovery models applied to both sampled and fully observed data, and analyze their effectiveness and limitations. We further investigate the generalizability and robustness to sampling of the SOTA causal discovery approaches on additional simulated datasets with known ground truth. Our results reveal the limitations of existing causal modeling approaches when applied to large-scale, noisy, high-dimensional data with unobserved variables and unknown relationships between them. We show that the SOTA causal models explored in our experiments are not designed to take advantage from vasts amounts of data and have difficulty recovering ground truth when latent confounders are present; they do not generalize well across simulation scenarios and are not robust to sampling; they are vulnerable to data and modeling assumptions, and therefore, the results are hard to reproduce. Finally, when we outline lessons learned and provide recommendations to improve models for causal discovery and prediction of human social behavior from observational data, we highlight the importance of learning data to knowledge representations or transformations to improve causal discovery and describe the benefit of causal feature selection for predictive and prescriptive modeling.

97 MATHEMATICS AND COMPUTING↗

Direct Visualization of Li Dendrite Effect on LiCoO 2 Cathode by In Situ TEM

Li dendrites are known to cause deterious, and in many cases catastrophic, effect on the performance of Li rechargeable batteries. However, the mechanistic failure mechanism of cathodes upon in contact with Li metal is far from clear. In this study, using in situ transmission electron microscopy, we directly visualize at an atomic scale the interaction of Li dendrites with well-defined, epitaxial thin films of LiCoO2, the most widely used cathode material. We show that a spontaneous and prompt chemical reaction is trigged once the Li contact is made, leading to expansion and amorphization of the LiCoO2 structure, with Li2O and Co metal being the final reaction products. A topotactic phase transition is identified close to the reaction front, resulting in the formation of CoO as a metastable intermediate. Dynamic structural and chemical imaging in combination with ab inito simulations reveal that a high density of antiphase grain boundaries are formed at the reaction front, which are critical for enabling the short-range topotactic reactions and long-range Li propagation. The fundamental insights are of general importance in mitigating Li dendrites related issues and guiding the design principle for more robust energy materials.

In situ transmission electron microscopy (TEM), Li↗