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At least 253 records · Page 14

RITRACKS: A Software for Simulation of Stochastic Radiation Track Structure, Micro and Nanodosimetry, Radiation Chemistry and DNA Damage for Heavy Ions

The code RITRACKS (Relativistic Ion Tracks) has been developed over the last few years at the NASA Johnson Space Center to simulate the effects of ionizing radiations at the microscopic scale, to understand the effects of space radiation at the biological level. The fundamental part of this code is the stochastic simulation of radiation track structure of heavy ions, an important component of space radiations. The code can calculate many relevant quantities such as the radial dose, voxel dose, and may also be used to calculate the dose in spherical and cylindrical targets of various sizes. Recently, we have incorporated DNA structure and damage simulations at the molecular scale in RITRACKS. The direct effect of radiations is simulated by introducing a slight modification of the existing particle transport algorithms, using the Binary‐Encounter‐Bethe model of ionization cross sections for each molecular orbitals of DNA. The simulation of radiation chemistry is done by a step‐by‐step diffusion‐reaction program based on the Green's functions of the diffusion equation]. This approach is also used to simulate the indirect effect of ionizing radiation on DNA. The software can be installed independently on PC and tablets using the Windows operating system and does not require any coding from the user. It includes a Graphic User Interface (GUI) and a 3D OpenGL visualization interface. The calculations are executed simultaneously (in parallel) on multiple CPUs. The main features of the software will be presented.

Plante, I↗

Interactive automated Bragg peak identification with 3D neutron scattering data

Neutron scattering experiments have undergone significant technological development through large area detectors with concurrent enhancements in neutron transport and electronic functionality. Data collected for neutron events include detector pixel location in 3D, time and associated metadata, such as, sample orientation, neutron wavelength, and environmental conditions. RadiaSoft and Oak Ridge National Laboratory personnel are considering single-crystal diffraction data from the TOPAZ instrument. We are leveraging a new method for rapid, interactive analysis of neutron data using NVIDIA’s IndeX 3D volumetric visualization framework. We have implemented machine learning techniques to automatically identify Bragg peaks and separate them from diffuse backgrounds and analyze the crystalline lattice parameters for further analysis. The implementation of automatic peak identification into IndeX allows scientists to visualize and analyze data in real-time. Our methods include a robust comparison with current analysis techniques which show improvement in a variety of aspects. These improvements will be incorporated into IndeX for visualization to allow scientists an interactive tool for crystal analysis.

Kilpatrick, Matthew↗

Fabrication of FeCrAl cladding for accident tolerant fuel

General Electric (GE) is working with the US Department of Energy (DOE) to develop a high performance nuclear fuel that will have enhanced tolerance to failure under severe accident conditions. The leading FeCrAl alloy candidate for the cladding is APMT, a powder metallurgy alloy developed by Kanthal/Sandvik for high temperature applications. Zirconium alloys have been used for cladding the fuel for over six decades. That is, zirconium alloys can be fabricated as several meters long tubes with an outside diameter of about 10 mm and a wall thickness in the order of 1 mm or less. The GE team is working to demonstrate that APMT can be fabricated as long thin walled tubes for the cladding application. A first production route for 10 x 0.5 mm APMT tubes was established showing that pilgering and drawing are viable processes to fabricate the APMT cladding. The mechanical properties of APMT were evaluated before and after the cold forming. Yield strength, tensile strength and hardness increased and elongation decreased due to cold forming, which was expected. No abnormality has been noted in the microstructures. The 3D image visualization of TIG welded APMT rodlet and the images of welding areas taken at different locations show no welding defects such as distortion, porosity or lack of penetration along/adjacent to the welded areas, confirming overall good welds and no opening or defects across the entire width of the tube thickness. Tests have shown no effect of welding on the hardness or mechanical strength in the area nearing the weld.

36 MATERIALS SCIENCE↗

R and DE Robotic Sensor Intern Team: Remote 3D Mapping Overview

The Department of Energy (DOE) nuclear complex includes many hazardous and challenging environments that must be inspected remotely and routinely for structural integrity evaluation and long-term planning purposes. The H-Canyon Air Exhaust (HCAEX) Tunnel biannual inspection is an example of such an environment. Presently inspections are performed by teleoperated robotic crawlers provide low resolution video feedback to the structural engineers. Advanced sensors such as Lidar and panospheric hi-res cameras have the potential to provide additional valuable data in future inspections. UT-Austin Lidar work in support of an H-Canyon deployment began with the DOE EM sponsored H-Canyon Integrated Research Project. The R and DE Robotic Sensor intern team includes two of the UT-Austin Masters students working on Lidar development to facilitate the pulling of university developed solutions to the field. The goal of this project is to develop a suite of sensors that could be used to gather advanced data in future HCAEX tunnel inspections. Of particular interest is the ability to map the tunnel walls at an accuracy that will allow for the comparison of two scans performed at different time periods to estimate the concrete erosion rate. Additionally, the development of the 3D point cloud in the GPS denied environment is the first step in being able to collect and overlay other 3D data such as radiation mapping. Project specific goals include: - Design and develop 3D mapping sensor suite. Merge Lidar point cloud with high res camera images Incorporate Inertial Measurement Unit (IMU) to assist with positioning. - Develop sensor software and user GUI Sensor data collection and integration software User GUI for reach back system. - Test solution on crawler in tunnel test bed Use crawler base similar to H-Canyon planned crawler Design and build test bed simulating tunnel conditions. To facilitate rapid sensor integration, software coding and user GUI development, the Robot Operating System (ROS) was employed as the development platform. ROS is a set of open source software libraries and tools that assist with the building of robot applications. ROS includes drivers for many sensors, state-of-the-art algorithms, and powerful developer tools. Sensors selected for the summer intern solution included assessment as to whether they possessed ROS drivers and associated sample code. Additionally, the ROS 3D Robot Visualizer (rviz) tool has been employed.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Scaling Building Energy Audits through Machine Learning Methods on Novel Drone Image Data

Building energy audits are time-consuming and labor-intensive. This paper describes a new method using machine learning (ML) techniques on novel data sources (drone images) to improve the identification of building characteristics and retrofit opportunities, and thereby reduce the effort for audits. The new ML method includes: (1) Building footprint extraction using line extraction, polygonization, and polygon-merging, (2) Building envelope extraction using PIX4d modeling software to reconstruct a building 3D model, (3) Visualization tool for viewing images from the 3D model, (4) Window-to-wall ratio (WWR) using state-of-art deep neural network semantic segmentation, (5) Envelope thermal anomaly detection using an unsupervised machine learning clustering algorithm, and (6) Rooftop energy equipment detection based on an object detection algorithm. The testing of this method involved a comparison of additional ML-generated information overlaid on current ‘state-of-practice’ audit and remote assessment baselines using evaluation metrics: labor time and associated cost, marginal benefits of using ML-generated information in workflows for audits and remote assessments, integration potential with existing processes and tools, and replicability/scalability of the method. In two test buildings in California that had comprehensive drawings and meter data available, the ML method effectively generated a building footprint, envelope, rooftop equipment, WWR, and locations of envelope thermal anomalies. Projected target segments of the ML method are sites with minimal drawings and energy data, and underserved sectors such as multistoried housing, disadvantaged communities, and schools for which the ML method can enable identification of building asset characteristics and prioritization of envelope retrofits and decentralized energy equipment retrofits.

Singh, Reshma↗

SU-F-J-72: A Clinical Usable Integrated Contouring Quality Evaluation Software for Radiotherapy

Purpose: To introduce the Auto Contour Evaluation (ACE) software, which is the clinical usable, user friendly, efficient and all-in-one toolbox for automatically identify common contouring errors in radiotherapy treatment planning using supervised machine learning techniques. Methods: ACE is developed with C# using Microsoft .Net framework and Windows Presentation Foundation (WPF) for elegant GUI design and smooth GUI transition animations through the integration of graphics engines and high dots per inch (DPI) settings on modern high resolution monitors. The industrial standard software design pattern, Model-View-ViewModel (MVVM) pattern, is chosen to be the major architecture of ACE for neat coding structure, deep modularization, easy maintainability and seamless communication with other clinical software. ACE consists of 1) a patient data importing module integrated with clinical patient database server, 2) a 2D DICOM image and RT structure simultaneously displaying module, 3) a 3D RT structure visualization module using Visualization Toolkit or VTK library and 4) a contour evaluation module using supervised pattern recognition algorithms to detect contouring errors and display detection results. ACE relies on supervised learning algorithms to handle all image processing and data processing jobs. Implementations of related algorithms are powered by Accord.Net scientific computing library for better efficiency and effectiveness. Results: ACE can take patient’s CT images and RT structures from commercial treatment planning software via direct user input or from patients’ database. All functionalities including 2D and 3D image visualization and RT contours error detection have been demonstrated with real clinical patient cases. Conclusion: ACE implements supervised learning algorithms and combines image processing and graphical visualization modules for RT contours verification. ACE has great potential for automated radiotherapy contouring quality verification. Structured with MVVM pattern, it is highly maintainable and extensible, and support smooth connections with other clinical software tools.

60 APPLIED LIFE SCIENCES↗

Updimensioning strategy derived from synthetic equiaxed grain structures for approximating 3D grain size distributions from 2D visualizations with 1D parameters

We generated synthetic equiaxed grain structures using computer graphics software to explore the relationship between various grain size determination methods and true three-dimensional (3D) grain diameters. Mirroring grain measurement techniques, the synthetic 3D grain structures are imaged as 2D micrographs which are measured to yield 1D grain size parameters. Synthetic grain structures provide data at a mass scale and permit exploration of both polished and fractured surface micrographs, revealing one-to-one correspondence between exposed 2D grain cross-sections and individual 3D grains. Analysis of this correspondence yielded a procedure to approximate 3D equiaxed grain size and volume distributions based on the mode of the 2D fractograph grain size distribution. The 3D approximation procedure is shown to be less susceptible to different imaging conditions that affect small, undiscernible grains compared to the standard planimetric and linear intercept methods, which by design also tend to underestimate the 3D grain diameter. The procedure requires larger sample sizes to lower variance and a deeper analysis which could become more practical with machine learning (ML) models for grain boundary segmentation, which synthetic grain structures can help train. This work lays the foundation for analyzing other grain distributions such as columnar and composite grains in similar depth.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Long non-coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution

Most mosquito-borne flaviviruses, including Zika virus (ZIKV), Dengue virus (DENV), and West Nile virus (WNV), produce long non-coding subgenomic RNAs (sfRNAs) in infected cells that link to pathogenicity and immune evasion. Until now, the structural characterization of these lncRNAs remains limited. Here, we studied the 3D structures of individual and combined subdomains of sfRNAs, and visualized the accessible 3D conformational spaces of complete sfRNAs from DENV2, ZIKV, and WNV by small angle X-ray scattering (SAXS) and computational modeling. The individual xrRNA1s and xrRNA2s adopt similar structures in solution as the crystal structure of ZIKV xrRNA1, and all xrRNA1-2s form compact structures with reduced flexibility. While the DB12 of DENV2 is extended, the DB12s of ZIKV and WNV are compact due to the formation of intertwined double pseudoknots. All 3' stem-loops (3'SLs) share similar rod-like structures. Complete sfRNAs are extended and sample a large conformational space in solution. Our work not only provides structural insight into the function of flavivirus sfRNAs, but also highlights strategies of visualizing other lncRNAs in solution by SAXS and computational methods.

3D structure↗

Sensor Spatial Distortion, Visual Latency, and Update Rate Effects on 3D Tracking in Virtual Environments

Several common defects that we have sought to minimize in immersing virtual environments are: static sensor spatial distortion, visual latency, and low update rates. Human performance within our environments during large amplitude 3D tracking was assessed by objective and subjective methods in the presence and absence of these defects. Results show that 1) removal of our relatively small spatial sensor distortion had minor effects on the tracking activity, 2) an Adapted Cooper-Harper controllability scale proved the most sensitive subjective indicator of the degradation of dynamic fidelity caused by increasing latency and decreasing frame rates, and 3) performance, as measured by normalized RMS tracking error or subjective impressions, was more markedly influenced by changing visual latency than by update rate.

Ellis, S. R.↗

Sci-Vis Framework

SVF is a full featured OpenGL 3d framework that allows for rapid creation of complex visualizations. The SVF framework handles much of the lifecycle and complex tasks required for a 3d visualization. Unlike a game framework SVF was designed to use fewer resources, work well in a windowed environment, and only render when necessary. The scene also takes advantage of multiple threads to free up the UI thread as much as possible. Shapes (actors) in the scene are created by adding or removing functionality (through support objects) during runtime. This allows a highly flexible and dynamic means of creating highly complex actors without the code complexity (it also helps overcome the lack of multiple inheritance in Java.) All classes are highly customizable and there are abstract classes which are intended to be subclassed to allow a developer to create more complex and highly performant actors. There are multiple demos included in the framework to help the developer get started and shows off nearly all of the functionality. Some simple shapes (actors) are already created for you such as text, bordered text, radial text, text area, complex paths, NURBS paths, cube, disk, grid, plane, geometric shapes, and volumetric area. It also comes with various camera types for viewing that can be dragged, zoomed, and rotated. Picking or selecting items in the scene can be accomplished in various ways depending on your needs (raycasting or color picking.) The framework currently has functionality for tooltips, animation, actor pools, color gradients, 2d physics, text, 1d/2d/3d textures, children, blending, clipping planes, view frustum culling, custom shaders, and custom actor states

Arthur Bleeker, PNNL↗

Sci-Vis Framework

SVF is a full featured OpenGL 3d framework that allows for rapid creation of complex visualizations. The SVF framework handles much of the lifecycle and complex tasks required for a 3d visualization. Unlike a game framework SVF was designed to use fewer resources, work well in a windowed environment, and only render when necessary. The scene also takes advantage of multiple threads to free up the UI thread as much as possible. Shapes (actors) in the scene are created by adding or removing functionality (through support objects) during runtime. This allows a highly flexible and dynamic means of creating highly complex actors without the code complexity (it also helps overcome the lack of multiple inheritance in Java.) All classes are highly customizable and there are abstract classes which are intended to be subclassed to allow a developer to create more complex and highly performant actors. There are multiple demos included in the framework to help the developer get started and shows off nearly all of the functionality. Some simple shapes (actors) are already created for you such as text, bordered text, radial text, text area, complex paths, NURBS paths, cube, disk, grid, plane, geometric shapes, and volumetric area. It also comes with various camera types for viewing that can be dragged, zoomed, and rotated. Picking or selecting items in the scene can be accomplished in various ways depending on your needs (raycasting or color picking.) The framework currently has functionality for tooltips, animation, actor pools, color gradients, 2d physics, text, 1d/2d/3d textures, children, blending, clipping planes, view frustum culling, custom shaders, and custom actor states

Arthur Bleeker, PNNL↗

SU-E-J-196: New Visualization Methods for Longitudinal MRI Registrations and Segmentations

Purpose: To develop visualization techniques to facilitate easy assessment of (a) registration and (b) tracking volumetric changes in structures during radiation therapy from MRI. Method: The frequently used method for visualizing registrations between scans is a multi-color overlay technique or deformation vector fields. However, the overlay technique is unintuitive and does not help to appreciate the quality of registration particularly when the registration mismatches are not very large. Similarly, the deformation fields give an indication of extent of deformation but do not help to assess the differences in registration. We present a mirroring and edge-augmented mirroring technique that places the fixed and moving image next to each other and allows the user to quickly assess the small differences in registration. Next, we present a volumetric intersection based 3D model to visualize the changes in diseased lymph node volumes in head and neck cancer. 3D model-based visualization provides more information about the location-specific changes in volume rather than the simplistic one dimensional information obtained from 2D plot of nodal volume changes. Result: We show results comparing our approach with the standard colorbased overlay method for comparing registrations of intra-patient registrations using T2-MRI. Upon comparing the mirroring technique with the color-overlay, one can more easily appreciate the differences in registration. Adding edge-based mirroring seems to further assist in evaluating the registration. Our approach for viewing registrations seems to be more intuitive and easy to use in order to help assess the quality of registration compared to color-based overlays. Similarly, the change volumetric model together with a 2D plot reveals more information including the locations undergoing changes and responding to treatment. Conclusions: Better approaches are necessary for assessing the quality of registrations and changes in diseased structures over time. Our approach presents some novel visualization solutions for registration and segmentation.

60 APPLIED LIFE SCIENCES↗

Versatile compact heater design for in situ nano-tomography by transmission X-ray microscopy

A versatile, compact heater designed at National Synchrotron Light Source-II for in situ X-ray nano-imaging in a full-field transmission X-ray microscope is presented. Heater design for nano-imaging is challenging, combining tight spatial constraints with stringent design requirements for the temperature range and stability. Finite-element modeling and analytical calculations were used to determine the heater design parameters. Performance tests demonstrated reliable and stable performance, including maintaining the exterior casing close to room temperature while the heater is operating at above 1100°C, a homogenous heating zone and small temperature fluctuations. Two scientific experiments are presented to demonstrate the heater capabilities: (i) in situ 3D nano-tomography including a study of metal dealloying in a liquid molten salt extreme environment, and (ii) a study of pore formation in icosahedral quasicrystals. The progression of structural changes in both studies were clearly resolved in 3D, showing that the new heater enables powerful capabilities to directly visualize and quantify 3D morphological evolution of materials under real conditions by X-ray nano-imaging at elevated temperature during synthesis, fabrication and operation processes. This heater design concept can be applied to other applications where a precise, compact heater design is required.

36 MATERIALS SCIENCE↗

EGS Collab: 3D Geophysical Model Around the Sanford Underground Research Facility

This package contains data associated with a proceedings paper (linked below) submitted to the 44th Workshop on Geothermal Reservoir Engineering. The Geophysical Model text file contains density, P- and S-wave seismic speeds on a 3D grid. The file has six columns and provides latitude (degree), longitude (degree), depth (km), P-wave speed (km/s), S-wave speed (km/s), and density (g/cm^3) at each grid point. The Interactive Geophysical Model API file is an interactive visualization of the 3D geophysical model. The visualization allows users to view depth slices and vertical profiles of the model side by side. The depth of the slices and the location of the profile can be changed. Reference: Chai, C., Maceira, M., Santos-Villalobos, H. J., and EGS Collab team, 2019, Subsurface Seismic Structure around the Sanford Underground Research Facility, in PROCEEDINGS, 44th Workshop on Geothermal Reservoir Engineering, edited, Stanford University, Stanford, California.

15 GEOTHERMAL ENERGY↗

The Digital Space Shuttle, 3D Graphics, and Knowledge Management

The Digital Shuttle is a knowledge management project that seeks to define symbiotic relationships between 3D graphics and formal knowledge representations (ontologies). 3D graphics provides geometric and visual content, in 2D and 3D CAD forms, and the capability to display systems knowledge. Because the data is so heterogeneous, and the interrelated data structures are complex, 3D graphics combined with ontologies provides mechanisms for navigating the data and visualizing relationships.

Gomez, Julian E.↗