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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

3D Imaging of Microbial Biofilms: Integration of Synchrotron Imaging and an Interactive Visualization Interface

Understanding the interactions of structured communities known as “biofilms” and other complex matrixes is possible through the X-ray micro tomography imaging of the biofilms. Feature detection and image processing for this type of data focuses on efficiently identifying and segmenting biofilms and bacteria in the datasets. The datasets are very large and often require manual interventions due to low contrast between objects and high noise levels. Thus new software is required for the effectual interpretation and analysis of the data. This work specifies the evolution and application of the ability to analyze and visualize high resolution X-ray micro tomography datasets.

Biofilm Viewer↗
DOE OSTI2020

Skeletides: A Modular, Simplified Physical Model of Protein Secondary Structure

Three-dimensional (3D) models are essential for visualization and conceptual understanding of complex architectures such as protein structure. Although there is a plethora of software platforms that allow digital depictions of protein structure at an atomic level in silico, physical models are needed to convey an intuitive understanding of biomolecular architecture. However, it is a challenge to represent all the relevant features of proteins in a single physical model due to their sheer structural complexity. Here, we describe a modular protein model that focuses only on representation of the secondary structure—the underlying structural skeleton. The simplified model consists of amino acid units, which can be linked together to reproduce the two most fundamental structural features of protein secondary structure: the relative positions of the amino acid alpha carbon atoms, and the intra-main chain hydrogen bonding pattern. We use 3D printing and magnets to create a set of three modular amino acid building blocks, which when linked together into a chain, can faithfully represent alpha helices, beta sheets, and turns. These simple to make models can be used to quickly assemble the alpha carbon trace of an entire protein domain, which conveys a tactile experience of the complexity of protein skeletal architecture. These models highlight the modularity of protein structure: where a single structural unit, the amino acid, can be linked together to form a larger, regular secondary structure. These models also have a propensity to spontaneously organize into alpha helices and beta sheets, as demonstrated by their ability to autonomously assemble when placed in a circulating water tank. These models provide a missing educational tool to expand knowledge of protein structure, foster deeper insight into protein folding, and inspire greater interest in biomacromolecular architecture.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Estimation and Visualization of Isosurface Uncertainty from Linear and High-Order Interpolation Methods

Isosurface visualization is fundamental for exploring and analyzing 3D volumetric data. Marching cubes (MC) algorithms with linear interpolation are commonly used for isosurface extraction and visualization. Although linear interpolation is easy to implement, it has limitations when the underlying data is complex and high-order, which is the case for most real-world data. Linear interpolation can output vertices at the wrong location. Its inability to deal with sharp features and features smaller than grid cells can lead to an incorrect isosurface with holes and broken pieces. Despite these limitations, isosurface visualizations typically do not include insight into the spatial location and the magnitude of these errors. We utilize high-order interpolation methods with MC algorithms and interactive visualization to highlight these uncertainties. Our visualization tool helps identify the regions of high interpolation errors. It also allows users to query local areas for details and compare the differences between isosurfaces from different interpolation methods. In addition, we employ high-order methods to identify and reconstruct possible features that linear methods cannot detect. We showcase how our visualization tool helps explore and understand the extracted isosurface errors through synthetic and real-world data.

Ouermi, Timbwaoga↗
DOE OSTI2020

Resolving Triblock Terpolymer Morphologies by Vapor-Phase Infiltration

The spontaneous formation of well-organized three-dimensional (3D) nanostructures from self-assembled block copolymers (BCPs) holds promise for nanofabrication and lithography. The addition of a third block to BCPs provides access to a plethora of 3D geometries, but it remains difficult to resolve the geometry of such “three-color” structures when there is low contrast between the polymeric components at length scales of a few nm. Here, we apply vapor-phase infiltration synthesis to a silicon-containing triblock terpolymer, poly(1,1- dimethyl silacyclobutane-b-styrene-b-lactide) (PDMSB-b-PS-b-PLA or DSL) to distinguish the 3D microdomain morphologies of the two organic blocks, PLA and PS. Selective infiltration of ZnO within the PLA microdomains reveals morphologies consisting of three-color lamellae or lamellae combined with vertically aligned core-shell cylinders, depending on the volume fractions of each block. The infiltration produces ZnO nanoparticles throughout the 260 nm thickness of the DSL film, generating 3D nanocomposites containing ZnO and SiO x . These results provide a strategy for synthesizing multicomponent 3D nanostructures as well as visualizing the phase behavior of multi-block copolymers.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Surface-structure sensitivity of CeO 2 nanocrystals in photocatalysis and enhancing the reactivity with nanogold

Structure–function correlations are a central theme in heterogeneous (photo)catalysis. In this research, using aberration-corrected scanning transmission electron microscopy (STEM), the atomic surface structures of well-defined one-dimensional (1D) CeO 2 nanorods (NRs) and 3D nanocubes (NCs) are directly visualized at subangstrom resolution. CeO 2 NCs predominantly expose the {100} facet, with {110} and {111} as minor cutoff facets at the respective edges and corners. Notably, the outermost surface layer of the {100} facet is nearly O-terminated. Neither surface relaxations nor reconstructions on {100} are observed, indicating unusual polarity compensation, which is primarily mediated by near-surface oxygen vacancies. The surface of CeO 2 NRs is highly stepped, with the enclosed {110} facet exposing Ce cations and O anions on terraces. On the basis of STEM profile-view imaging and electronic structure analysis, the photoreactivity of CeO2 nanocrystals toward aqueous methyl orange degradation under UV is revealed to be surface-structure-sensitive, following the order: {110} >> {100}. The underlying surface-structure sensitivity can be attributed to the variation in low-coordinate surface cerium cations between {110} and {100} facets. To further enhance light absorption, Au nanoparticles (NPs) are deposited on CeO 2 NRs to form Au/CeO 2 plasmonic nanocomposites, which dramatically promotes the photoreactivity that is Au particle size- and excitation light wavelength-dependent. The mechanisms responsible for the enhancement of photocatalytic activity are discussed, highlighting the crucial role of photoexcited charge carrier transfer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Electrostatic Barriers to Nanoparticle Accessibility of a Porous Matrix

Translocation from one cavity to another through a narrow constriction (i.e., a “hole”) represents the fundamental elementary process underlying hindered mass transport of nanoparticles and macromolecules within many natural and synthetic porous materials, including intracellular environments. This process is complex and may be influenced by long-range (e.g., electrostatic) particle–wall interactions, transient adsorption/desorption, surface diffusion, and hydrodynamic effects. In this study, we used a three-dimensional (3D) tracking method to explicitly visualize the process of nanoparticle diffusion within periodic porous nanostructures, where electrostatic interactions were mediated via ionic strength. The effects of electrostatic interactions on nanoparticle transport were surprisingly large. For example, an increase in the Debye length of only a few nanometers (in a material with a hole diameter of ~100 nm) increased the mean cavity escape time 3-fold. A combination of computational and experimental analyses indicated that this hindered cavity escape was due to an electrostatic energy barrier in the region of the hole, which was quantitatively explained using DLVO theory. These findings explicitly demonstrate that the cavity escape process was barrier-limited and dominated by electrostatic effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Ultrafast visualization of incipient plasticity in dynamically compressed matter

Plasticity is ubiquitous and plays a critical role in material deformation and damage; it inherently involves the atomistic length scale and picosecond time scale. A fundamental understanding of the elastic-plastic deformation transition, in particular, incipient plasticity, has been a grand challenge in high-pressure and high-strain-rate environments, impeded largely by experimental limitations on spatial and temporal resolution. Here, we report femtosecond MeV electron diffraction measurements visualizing the three-dimensional (3D) response of single-crystal aluminum to the ultrafast laser-induced compression. We capture lattice transitioning from a purely elastic to a plastically relaxed state within 5 ps, after reaching an elastic limit of ~25 GPa. Our results allow the direct determination of dislocation nucleation and transport that constitute the underlying defect kinetics of incipient plasticity. Large-scale molecular dynamics simulations show good agreement with the experiment and provide an atomic-level description of the dislocation-mediated plasticity.

36 MATERIALS SCIENCE↗
DOE OSTI2024

First look at neutron emission shape characteristics of ignition hotspots at the National Ignition Facility (invited)

The nuclear imaging system has been capturing neutron images of inertial confinement fusion (ICF) driven implosions for over a decade at the National Ignition Facility. This imaging system has evolved from one to three nearly orthogonal lines-of-sight, allowing for the study of three-dimensional shape characteristics of ignition shots. Limited-view tomography algorithms help visualize the burning hotspot in 3D and assess neutron source geometry using Legendre mode parameters. With its neutron, gamma-ray, and x-ray image reconstruction capabilities, NIS has provided critical insight into mechanisms that have limited implosion performance, such as fill tube diameter for ignition-type targets. This comprehensive diagnostic suite opens a window into the shape characteristics of ignition shots and how symmetry affects ICF implosion performance. In more recent ignition shots, neutron yields have visibly increased. Analyzing the shape and size of the reconstructed neutron source has shown an expansion of the burn volume, which is indicative of more efficient alpha heating during the implosion process.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

TU-D-202-03: Gating Is the Best ITV Killer

Respiratory motion has long been recognized as an important factor affecting the precision of radiotherapy. After the introduction of the 4D CT to visualize the respiratory motion in 3D, the internal target volume (ITV) has been widely adopted as simple method to take the motion into account in treatment planning and delivery. The ITV is generated as the union of the CTVs as the patient goes through the respiratory cycle. Many issues have been identified with the ITV. In this session three alternatives for the ITV will be discussed: 1) An alternative motion-inclusive approach with better imaging and smaller margins, called mid-position CT. 2) The tracking approach and 3) The gating approach. The following topics will be addressed by Marcel van Herk (“Is ITV the correct motion encompassing strategy”): Magnitude of respiratory motion, effect of motion on radiotherapy, motion encompassing strategies, and software solutions to assist in motion encompassing strategies. Then Paul Keall (“Make margins simple: Use real-time target tracking”) will discuss tracking with: clinical drivers for tracking, current clinical status of tumor tracking, future tumor tracking technology, and margin margin challenges with and without tracking. Finally Daniel Low will discuss gating (“Gating is the best ITV killer”): why ITV in the first place, requirements for planning, requirements at the machine, benefits and costs. The session will end with a discussion and live demo of motion simulation software to illustrate the issues and explain the relative benefit and appropriate uses for the three methods. Learning Objectives: Explain the 4D imaging and treatment planning process. Summarize the various approaches to deal with respiratory motion during radiotherapy Discuss the tradeoffs involved when choosing one of the three discussed approaches. Explain in which situation each method is the best choice Research is partly funded by Elekta Oncology Systems and the Dutch Cancer Foundation; M. van Herk, Part of the research was funded by Elekta Oncology Systems and the Dutch Cancer Foundation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms

Current methods of root sampling typically only obtain small or incomplete sections of root systems and do not capture their true complexity. To facilitate the visualization and analysis of full-sized plant root systems in 3-dimensions, we developed customized mesocosm growth containers. While highly scalable, the design presented here uses an internal volume of 45 ft 3 (1.27 m 3 ), suitable for large crop and bioenergy grass root systems to grow largely unconstrained. Furthermore, they allow for the excavation and preservation of 3-dimensional root system architecture (RSA), and facilitate the collection of time-resolved subterranean environmental data. Sensor arrays monitoring matric potential, temperature and CO 2 levels are buried in a grid formation at various depths to assess environmental fluxes at regular intervals. Methods of 3D data visualization of fluxes were developed to allow for comparison with root system architectural traits. Following harvest, the recovered root system can be digitally reconstructed in 3D through photogrammetry, which is an inexpensive method requiring only an appropriate studio space and a digital camera. We developed a pipeline to extract features from the 3D point clouds, or from derived skeletons that include point cloud voxel number as a proxy for biomass, total root system length, volume, depth, convex hull volume and solidity as a function of depth. Ground-truthing these features with biomass measurements from manually dissected root systems showed a high correlation. We evaluated switchgrass, maize, and sorghum root systems to highlight the capability for species wide comparisons. We focused on two switchgrass ecotypes, upland (VS16) and lowland (WBC3), in identical environments to demonstrate widely different root system architectures that may be indicative of core differences in their rhizoeconomic foraging strategies. Finally, we imposed a strong physiological water stress and manipulated the growth medium to demonstrate whole root system plasticity in response to environmental stimuli. Hence, these new “3D Root Mesocosms” and accompanying computational analysis provides a new paradigm for study of mature crop systems and the environmental fluxes that shape them.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

3D MRI in Musculoskeletal Imaging: Current and Future Applications

Purpose of Review: This article addresses current clinical applications, recent literature, and potential future applications of 3-dimensional magnetic resonance imaging (3D MRI) for musculoskeletal (MSK) applications. Recent Findings: The main advantage of 3D MRI over standard 2-dimensional MRI is its ability to reduce partial volume averaging artifacts and create multiplanar reconstruction (MPRs) in any plane with any slice thickness from a single high-resolution isotropic acquisition. 3D MRI acquisitions are particularly useful for the evaluation of articular cartilage, which is prone to volume averaging artifacts, and for the assessment of longitudinally coursing structures such as peripheral nerves and tendons, which are better visualized with non-orthogonal MPRs. 3D MRI is also useful for surface and volumetric analysis of bone and cartilage for preoperative and longitudinal assessments. Current research is focused on decreasing acquisition times and automating segmentation through machine learning, thus overcoming some of the current limitations of 3D MRI and providing new applications for this technique. Summary: 3D MRI is widely used in MSK imaging today, and its use is likely to continue to increase in the future, with recent advancements focused on accelerated acquisition techniques and quantitative imaging.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

Framework and algorithms for illustrative visualizations of time-varying flows on unstructured meshes

Photo- and physically realistic techniques are often insufficient for visualization of fluid flow simulations, especially for 3D and time-varying studies. Substantial research effort has been dedicated to the development of non-photorealistic and illustration-inspired visualization techniques for compact and intuitive presentation of such complex datasets. However, a great deal of work has been reproduced in this field, as many research groups have developed specialized visualization software. Additionally, interoperability between illustrative visualization software is limited due to diverse processing and rendering architectures employed in different studies. In this investigation, a framework for illustrative visualization is proposed, and implemented in MarmotViz, a ParaView plug-in, enabling its use on a variety of computing platforms with various data file formats and mesh geometries. Region-of-interest identification and feature-tracking algorithms incorporated into this tool are described. Implementations of multiple illustrative effect algorithms are also presented to demonstrate the use and flexibility of this framework. Here, by providing an integrated framework for illustrative visualization of CFD data, MarmotViz can serve as a valuable asset for the interpretation of simulations of ever-growing scale.

42 ENGINEERING↗
DOE OSTI2015

The dark side of photovoltaic — 3D simulation of glare assessing risk and discomfort

Photovoltaic (PV) systems form an important force in the implementation of renewable energies, but as we all know, the force has always its dark side. Besides efficiency considerations and discussions about architectures of power distribution networks, the increasing numbers of installations of PV systems for implementing renewable energies have secondary effects. PV systems can generate glare due to optical reflections and hence might be a serious concern. On the one hand, glare could affect safety, e.g. regarding traffic. On the other hand, glare is a constant source of discomfort in vicinities of PV systems. Hence, assessment of glare is decisive for the success of renewable energies near municipalities and traffic zones for the success of solar power. Several courts decided on the change of PV systems and even on their de-installation because of glare effects. Thus, location-based assessments are required to limit potential reflections and to avoid risks for public infrastructure or discomfort of residents. The question arises on how to calculate reflections accurately according to the environment's topography. Our approach is founded in a 3D-based simulation methodology to calculate and visualize reflections based on the geometry of the environment of PV systems. This computational model is implemented by an interactive tool for simulation and visualization. Hence, project planners receive flexible assistance for adjusting the parameters of solar panels amid the planning process and in particular before the installation of a PV system. - Highlights: • Solar panels cause glare that impacts neighborhoods and traffic infrastructures. • Glare might cause disability and discomfort. • 3D environment for the calculation of glare • Interactive tool to simulate and visualize reflections • Impact assessment of solar power plant farms.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Emergence of Unstable Focused Flow Induced by Variable‐Density Flows in Vertical Fractures

Abstract Fluids with different densities often coexist in subsurface fractures and lead to variable‐density flows that control subsurface processes such as seawater intrusion, contaminant transport, and geologic carbon sequestration. In nature, fractures have dip angles relative to gravity, and density effects are maximized in vertical fractures. However, most studies on flow and transport through fractures are often limited to horizontal fractures. Here, we study the mixing and transport of variable‐density fluids in vertical fractures by combining three‐dimensional (3D) pore‐scale numerical simulations and visual laboratory experiments. Two miscible fluids with different densities are injected through two inlets at the bottom of a fracture and exit from an outlet at the top of the fracture. Laboratory experiments show the emergence of an unstable focused flow path, which we term a “runlet.” We successfully reproduce the unstable runlet using 3D numerical simulations and elucidate the underlying mechanisms triggering the runlet. Dimensionless number analysis shows that the runlet instability arises due to the Rayleigh‐Taylor instability (RTI), and flow topology analysis is applied to identify 3D vortices that are caused by the RTI. Even under laminar flow regimes, fluid inertia is shown to control the runlet instability by affecting the size and movement of vortices. Finally, we confirm the emergence of a runlet in rough‐walled fractures. Since a runlet dramatically affects fluid distribution, residence time, and mixing, the findings in this study have direct implications for the management of groundwater resources and subsurface applications.

Environmental Sciences & Ecology↗
DOE OSTI2023

PRESSURE-FILM OPEN SOURCE SCANNING AND MAPPING

SF-22-099 Pressure-film Open Source Scanning and Mapping (POSSM) is software that analyses images of pressure-film (scans or photographs). POSSM collects data from that analysis in order to produce a number of visual aides, including pressure maps, histograms, and 3d surface plots. POSSM is designed to be able to analyze an entire folder full of images, exporting numeric data as .csv files and visual graphics as .png files.

Grider, Patrick↗
DOE OSTI2024

An Accelerated Clip Algorithm for Unstructured Meshes: A Batch-Driven Approach

The clip technique is a popular method for visualizing complex structures and phenomena within 3D unstructured meshes. Meshes can be clipped by specifying a scalar isovalue to produce an output unstructured mesh with its external surface as the isovalue. Similar to isocontouring, the clipping process relies on scalar data associated with the mesh points, including scalar data generated by implicit functions such as planes, boxes, and spheres, which facilitates the visualization of results interior to the grid. In this paper, we introduce a novel batch-driven parallel algorithm based on a sequential clip algorithm designed for high-quality results in partial volume extraction. Our algorithm comprises five passes, each progressively processing data to generate the resulting clipped unstructured mesh. The novelty lies in the use of fixed-size batches of points and cells, which enable rapid workload trimming and parallel processing, leading to a significantly improved memory footprint and run-time performance compared to the original version. On a 32-core CPU, the proposed batch-driven parallel algorithm demonstrates a run-time speed-up of up to 32.6x and a memory footprint reduction of up to 4.37x compared to the existing sequential algorithm. The software is currently available under an open-source license in the VTK visualization system.

Tsalikis, Spiros↗
DOE OSTI2015

SU-E-J-214: MR Protocol Development to Visualize Sirius MRI Markers in Prostate Brachytherapy Patients for MR-Based Post-Implant Dosimetry

Purpose: The current CT-based post-implant dosimetry allows precise seed localization but limited anatomical delineation. Switching to MR-based post-implant dosimetry is confounded by imprecise seed localization. One approach is to place positive-contrast markers (Sirius) adjacent to the negative-contrast seeds. This patient study aims to assess the utility of a 3D fast spoiled gradient-recalled echo (FSPGR) sequence to visualize Sirius markers for post-implant dosimetry. Methods: MRI images were acquired in prostate implant patients (n=10) on Day 0 (day-of-implant) and Day 30. The post-implant MR protocol consisted of 3D T2-weighted fast-spin-echo (FSE), T2-weighted 2D-FSE (axial) and T1-weighted 2D-FSE (axial/sagittal/coronal). We incorporated a 3D-FSPGR sequence into the post-implant MR protocol to visualize the Sirius markers. Patients were scanned with different number-of-excitations (6, 8, 10), field-of-view (10cm, 14cm, 18cm), slice thickness (1mm, 0.8mm), flip angle (14 degrees, 20 degrees), bandwidth (122.070 Hz/pixel, 325.508 Hz/pixel, 390.625 Hz/pixel), phase encoding steps (160, 192, 224, 256), frequency-encoding direction (right/left, anterior/posterior), echo-time type (minimum-full, out-of-phase), field strength (1.5T, 3T), contrast (with, without), scanner vendor (Siemens, GE), coil (endorectal-coil only, endorectal-and-torso-coil, torsocoil only), endorectal-coil filling (30cc, 50cc) and endorectal-coil filling type (air, perfluorocarbon [PFC]). For post-implant dosimetric evaluation with greater anatomical detail, 3D-FSE images were fused with 3D-FSPGR images. For comparison with CT-based post-implant dosimetry, CT images were fused with 3D-FSPGR images. Results: The 3D-FSPGR sequence facilitated visualization of markers in patients. Marker visualization helped distinguish signal voids as seeds versus needle tracks for more definitive MR-based post-implant dosimetry. On the CT-MR fused images, the distance between the seed on CT to MR images was 3.2±1.6mm in patients with no endorectal coil, 2.3±0.8mm in patients with 30cc-PFC-filled endorectal-coil and 5.0±1.8mm in patients with 50cc-PFC-filled endorectal-coil. Conclusion: An MR protocol to visualize positive-contrast Sirius markers to assist in the identification of negative-contrast seeds was demonstrated. S Frank is a co-founder of C4 Imaging LLC, the manufacturer of the MRI markers.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Noodles: Cooking Up Collaborative Visualization

NOODLES is a new cross-domain collaborative visualization and analysis capability being developed at NREL. The NOODLES specification is a minimal protocol that can tie different software packages and platforms together. As an example, a simulation code that speaks this protocol could stream iso-surfaces to an immersive VR space and a web browser. Another example is a team (with some members across the country) classifying and discovering features in a statistical data plot, driven from a researcher's existing Python-based workflow. In this talk, we will discuss some background on the problems that this protocol intends to solve, basic principles of the specification, the current state of supporting libraries, and some demonstrations of the protocol in action.

3D↗