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At least 559 records · Page 31

Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS

The APBS software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages. APBS has enjoyed widespread adoption throughout the biomedical community and is used in numerous applications involving biomolecular structures. However, visualization of complex biomolecular electrostatic properties can be challenging for two-dimensional graphics systems. Therefore, advanced visualization and manipulation capabilities have been incorporated. In particular, APBS tools have been integrated with the UnityMolX virtual reality platform to provide an immersive experience for preparing biomolecular systems for calculations as well as visualizing and comparing calculated results.

electrostatics, molecular visualization, solvation↗

MISR Instrument Data Visualization

The MISR Interactive eXplorer (MINX) software functions both as a general-purpose tool to visualize Multiangle Imaging SpectroRadiometer (MISR) instrument data, and as a specialized tool to analyze properties of smoke, dust, and volcanic plumes. It includes high-level options to create map views of MISR orbit locations; scrollable, single-camera RGB (red-greenblue) images of MISR level 1B2 (L1B2) radiance data; and animations of the nine MISR camera images that provide a 3D perspective of the scenes that MISR has acquired. NASA Tech Briefs, September 2008 55 The plume height capability provides an accurate estimate of the injection height of plumes that is needed by air quality and climate modelers. MISR provides global high-quality stereo height information, and this program uses that information to perform detailed height retrievals of aerosol plumes. Users can interactively digitize smoke, dust, or volcanic plumes and automatically retrieve heights and winds, and can also archive MISR albedos and aerosol properties, as well as fire power and brightness temperatures associated with smoke plumes derived from Moderate Resolution Imaging Spectroradiometer (MODIS) data. Some of the specialized options in MINX enable the user to do other tasks. Users can display plots of top-of-atmosphere bidirectional reflectance factors (BRFs) versus camera-angle for selected pixels. Images and animations can be saved to disk in various formats. Also, users can apply a geometric registration correction to warp camera images when the standard processing correction is inadequate. It is possible to difference the images of two MISR orbits that share a path (identical ground track), as well as to construct pseudo-color images by assigning different combinations of MISR channels (angle or spectral band) to the RGB display channels. This software is an interactive application written in IDL and compiled into an IDL Virtual Machine (VM) ".sav" file.

Nelson, David↗

Analysis of N-dimensional Klein–Gordon equation for hydrogen molecule in the non-central potential field

We investigate a complete normalized relativistic solutions for N-dimensional Hartmann potential and relativistic effects of non-central potential field for hydrogen molecule within the framework of asymptotic iteration approach. We also discuss in detail the influence of dimensions on the angular probability distribution of hydrogen molecule. N-dimensional bound state wavefunction solutions including angular and radial solutions are expressed in terms of the Jacobi and Laguerre polynomials, respectively. N-dimensional angular wavefunctions of hydrogen molecule were visualized with Matlab software. In hyperspherical coordinates, the recurrence relations between diagonal matrix elements have been derived for N-dimensional Hartmann potential in relativistic theory. We also obtain analytical expressions of diagonal matrix elements and the recurrence formula between off-diagonal matrix elements in N-dimensions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A new synchrotron rapid-scanning X-ray fluorescence (SRS-XRF) imaging station at SSRL beamline 6-2

This paper describes a new large-range rapid-scan X-ray fluorescence (XRF) imaging station at beamline 6-2 at the Stanford Synchrotron Radiation Lightsource at SLAC National Accelerator Laboratory. This station uses a continuous rapid-scan system with a scan range of 1000 × 600 mm and a load capacity of up to 25 kg, capable of 25–100 µm resolution elemental XRF mapping and X-ray absorption spectroscopy (XAS) of a wide range of objects. XRF is measured using a four-element Hitachi Vortex ME4 silicon drift detector coupled to a Quantum Detectors Xspress3 multi-channel analyzer system. A custom system allows the X-ray spot size to be changed quickly and easily via pinholes ranging from 25 to 100 µm, and the use of a poly-capillary or axially symmetric achromatic optic may achieve a <10 µm resolution in the future. The instrument is located at wiggler beamline 6-2 which has an energy range of 2.1–17 keV, creating K emission for elements up to strontium, and L or M emission for all other elements. XAS can also be performed at selected sample positions within the same experiment, allowing for a more detailed chemical characterization of the elements of interest. Furthermore, sparse excitation energy XRF imaging can be performed over a wide range of incident X-ray energies. User friendliness has been emphasized in all stages of the experiment, including versatile sample mounts, He purged chambers for low- Z analyses, and intuitive visualization hardware and software. The station provides analysis capabilities for a wide range of materials and research fields including biological, chemical, environmental and materials science, paleontology, geology and cultural heritage.

47 OTHER INSTRUMENTATION↗

SU-E-T-362: Automatic Catheter Reconstruction of Flap Applicators in HDR Surface Brachytherapy

Purpose: Catheter reconstruction is crucial for the accurate delivery of radiation dose in HDR brachytherapy. The process becomes complicated and time-consuming for large superficial clinical targets with a complex topology. A novel method for the automatic catheter reconstruction of flap applicators is proposed in this study. Methods: We have developed a program package capable of image manipulation, using C++class libraries of The-Visualization-Toolkit(VTK) software system. The workflow for automatic catheter reconstruction is: a)an anchor point is placed in 3D or in the axial view of the first slice at the tip of the first, last and middle points for the curved surface; b)similar points are placed on the last slice of the image set; c)the surface detection algorithm automatically registers the points to the images and applies the surface reconstruction filter; d)then a structured grid surface is generated through the center of the treatment catheters placed at a distance of 5mm from the patient's skin. As a result, a mesh-style plane is generated with the reconstructed catheters placed 10mm apart. To demonstrate automatic catheter reconstruction, we used CT images of patients diagnosed with cutaneous T-cell-lymphoma and imaged with Freiburg-Flap-Applicators (Nucletron™-Elekta, Netherlands). The coordinates for each catheter were generated and compared to the control points selected during the manual reconstruction for 16catheters and 368control point Results: The variation of the catheter tip positions between the automatically and manually reconstructed catheters was 0.17mm(SD=0.23mm). The position difference between the manually selected catheter control points and the corresponding points obtained automatically was 0.17mm in the x-direction (SD=0.23mm), 0.13mm in the y-direction (SD=0.22mm), and 0.14mm in the z-direction (SD=0.24mm). Conclusion: This study shows the feasibility of the automatic catheter reconstruction of flap applicators with a high level of positioning accuracy. Implementation of this technique has potential to decrease the planning time and may improve overall quality in superficial brachytherapy.

60 APPLIED LIFE SCIENCES↗

SU-G-JeP3-10: Update On a Real-Time Treatment Guidance System Using An IR Navigation System for Pleural PDT

Purpose: Photodynamic therapy (PDT) is used in conjunction with surgical debulking of tumorous tissue during treatment for pleural mesothelioma. One of the key components of effective PDT is uniform light distribution. Currently, light is monitored with 8 isotropic light detectors that are placed at specific locations inside the pleural cavity. A tracking system with real-time feedback software can be utilized to improve the uniformity of light in addition to the existing detectors. Methods: An infrared (IR) tracking camera is used to monitor the movement of the light source. The same system determines the pleural geometry of the treatment area. Software upgrades allow visualization of the pleural cavity as a two-dimensional volume. The treatment delivery wand was upgraded for ease of light delivery while incorporating the IR system. Isotropic detector locations are also displayed. Data from the tracking system is used to calculate the light fluence rate delivered. This data is also compared with in vivo data collected via the isotropic detectors. Furthermore, treatment volume information will be used to form light dose volume histograms of the pleural cavity. Results: In a phantom study, the light distribution was improved by using real-time guidance compared to the distribution when using detectors without guidance. With the tracking system, 2D data can be collected regarding light fluence rather than just the 8 discrete locations inside the pleural cavity. Light fluence distribution on the entire cavity can be calculated at every time in the treatment. Conclusion: The IR camera has been used successfully during pleural PDT patient treatment to track the motion of the light source and provide real-time display of 2D light fluence. It is possible to use the feedback system to deliver a more uniform dose of light throughout the pleural cavity.

60 APPLIED LIFE SCIENCES↗

File format for normalizing radiological concentration exposure rate and dose rate data for the effects of radioactive decay and weathering processes

This report specifies the electronic file format that was agreed upon to be used as the file format for normalized radiological data produced by the software tool developed under this TI project. The NA-84 Technology Integration (TI) Program project (SNL17-CM-635, Normalizing Radiological Data for Analysis and Integration into Models) investigators held a teleconference on December 7, 2017 to discuss the tasks to be completed under the TI program project. During this teleconference, the TI project investigators determined that the comma-separated values (CSV) file format is the most suitable file format for the normalized radiological data that will be outputted from the normalizing tool developed under this TI project. The CSV file format was selected because it provides the requisite flexibility to manage different types of radiological data (i.e., activity concentration, exposure rate, dose rate) from other sources [e.g., Radiological Assessment and Monitoring System (RAMS), Aerial Measuring System (AMS), Monitoring and Sampling). The CSV file format also is suitable for the file format of the normalized radiological data because this normalized data can then be ingested by other software [e.g., RAMS, Visual Sampling Plan (VSP)] used by the NA-84’s Consequence Management Program.

97 MATHEMATICS AND COMPUTING↗

Large-Scale Atomistic Simulations: Investigating Free Expansion

The experiment investigates free expansion of a supercritical fluid into a two-phase liquid-vapor coexistence region. A huge molecular dynamics simulation (6 billion Lennard-Jones atoms) was run on 5760 GPUs (33% of LLNL Sierra) using LAMMPS/Kokkos software. This improved visualization workflow and started preliminary simulations of aluminum using SNAP machine learning potential.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Design considerations for a space database

Part of the information used in a real-time simulator is stored in the visual database. This information is processed by an image generator and displayed as a real-time visual image. The database must be constructed in a specific format, and it should efficiently utilize the capacities of the image generator that is was created for. A visual simulation is crucially dependent upon the success with which the database provides visual cues and recognizable scenes. For this reason, more and more attention is being paid to the art and science of creating effective real-time visual databases. Investigated here are the database design considerations required for a space-oriented real-time simulator. Space applications often require unique designs that correspond closely to the particular image-generator hardware and visual-database-management software. Specific examples from the databases constructed for NASA and its Evans and Sutherland CT6 image generator illustrate the various design strategies used in a space-simulation environment. These database design considerations are essential for all who would create a space database.

Moss, Lance M.↗

Data systems and computer science programs: Overview

An external review of the Integrated Technology Plan for the Civil Space Program is presented. The topics are presented in viewgraph form and include the following: onboard memory and storage technology; advanced flight computers; special purpose flight processors; onboard networking and testbeds; information archive, access, and retrieval; visualization; neural networks; software engineering; and flight control and operations.

Smith, Paul H.↗

Introduction to the LaRC central scientific computing complex

The computers and associated equipment that make up the Central Scientific Computing Complex of the Langley Research Center are briefly described. The electronic networks that provide access to the various components of the complex and a number of areas that can be used by Langley and contractors staff for special applications (scientific visualization, image processing, software engineering, and grid generation) are also described. Flight simulation facilities that use the central computers are described. Management of the complex, procedures for its use, and available services and resources are discussed. This document is intended for new users of the complex, for current users who wish to keep appraised of changes, and for visitors who need to understand the role of central scientific computers at Langley.

Shoosmith, John N.↗

Data Understanding Applied to Optimization

The goal of this research is to explore and develop software for supporting visualization and data analysis of search and optimization. Optimization is an ever-present problem in science. The theory of NP-completeness implies that the problems can only be resolved by increasingly smarter problem specific knowledge, possibly for use in some general purpose algorithms. Visualization and data analysis offers an opportunity to accelerate our understanding of key computational bottlenecks in optimization and to automatically tune aspects of the computation for specific problems. We will prototype systems to demonstrate how data understanding can be successfully applied to problems characteristic of NASA's key science optimization tasks, such as central tasks for parallel processing, spacecraft scheduling, and data transmission from a remote satellite.

Buntine, Wray↗

FAST User Guide

The Flow Analysis Software Toolkit, FAST, is a software environment for visualizing data. FAST is a collection of separate programs (modules) that run simultaneously and allow the user to examine the results of numerical and experimental simulations. The user can load data files, perform calculations on the data, visualize the results of these calculations, construct scenes of 3D graphical objects, and plot, animate and record the scenes. Computational Fluid Dynamics (CFD) visualization is the primary intended use of FAST, but FAST can also assist in the analysis of other types of data. FAST combines the capabilities of such programs as PLOT3D, RIP, SURF, and GAS into one environment with modules that share data. Sharing data between modules eliminates the drudgery of transferring data between programs. All the modules in the FAST environment have a consistent, highly interactive graphical user interface. Most commands are entered by pointing and'clicking. The modular construction of FAST makes it flexible and extensible. The environment can be custom configured and new modules can be developed and added as needed. The following modules have been developed for FAST: VIEWER, FILE IO, CALCULATOR, SURFER, TOPOLOGY, PLOTTER, TITLER, TRACER, ARCGRAPH, GQ, SURFERU, SHOTET, and ISOLEVU. A utility is also included to make the inclusion of user defined modules in the FAST environment easy. The VIEWER module is the central control for the FAST environment. From VIEWER, the user can-change object attributes, interactively position objects in three-dimensional space, define and save scenes, create animations, spawn new FAST modules, add additional view windows, and save and execute command scripts. The FAST User Guide uses text and FAST MAPS (graphical representations of the entire user interface) to guide the user through the use of FAST. Chapters include: Maps, Overview, Tips, Getting Started Tutorial, a separate chapter for each module, file formats, and system administration.

Walatka, Pamela P.↗

Downsizing Visualization Platforms: From Crays to Indigos and Beyond

Despite its increasingly negative connotation in other domains, "downsizing" is a positive trend as it applies to the computer hardware necessary to perform scientific visualization. In this talk, we will consider how the visualization of a particular data set, the Digital Terrain Model (DTM) derived from the Viking Orbiter imagery, has been realized in three distinct projects over the past decade. These examples serve to demonstrate how the vast improvements in computational performance both decrease the cost of such visualization efforts, and permit an increasing level of interactivity. We then consider how even today's graphical systems require the visualization designer to make intelligent choices and trade-offs in database rendering. Finally, we discuss how insights from an understanding of human visual perception can guide these design decisions, and suggest new options for visualization hardware and software.

Kaiser, Mary K.↗

Simulation of Rotary-Wing Near-Wake Vortex Structures Using Navier-Stokes CFD Methods

This paper will use high-resolution Navier-Stokes computational fluid dynamics (CFD) simulations to model the near-wake vortex roll-up behind rotor blades. The locations and strengths of the trailing vortices will be determined from newly-developed visualization and analysis software tools applied to the CFD solutions. Computational results for rotor nearwake vortices will be used to study the near-wake vortex roll up for highly-twisted tiltrotor blades. These rotor blades typically have combinations of positive and negative spanwise loading and complex vortex wake interactions. Results of the computational studies will be compared to vortex-lattice wake models that are frequently used in rotorcraft comprehensive codes. Information from these comparisons will be used to improve the rotor wake models in the Tilt-Rotor Acoustic Code (TRAC) portion of NASA's Short Haul Civil Transport program (SHCT). Accurate modeling of the rotor wake is an important part of this program and crucial to the successful design of future civil tiltrotor aircraft. The rotor wake system plays an important role in blade-vortex interaction noise, a major problem for all rotorcraft including tiltrotors.

Kenwright, David↗

Meshing, Visualization, and Computational Environments

There was probably no higher profile application of meshing, visualization, and computational software this past year than that performed in support of the space shuttle's Return to Flight activities. After heavy use of simulation during the accident investigation, these same tools are now helping address safety and operational issues. In turn, these applications are raising the bar for computational tools in terms of simulation fidelity and turnaround time.

Chawner, John R.↗

Improvement in Visual Target Tracking for a Mobile Robot

In an improvement of the visual-target-tracking software used aboard a mobile robot (rover) of the type used to explore the Martian surface, an affine-matching algorithm has been replaced by a combination of a normalized- cross-correlation (NCC) algorithm and a template-image-magnification algorithm. Although neither NCC nor template-image magnification is new, the use of both of them to increase the degree of reliability with which features can be matched is new. In operation, a template image of a target is obtained from a previous rover position, then the magnification of the template image is based on the estimated change in the target distance from the previous rover position to the current rover position (see figure). For this purpose, the target distance at the previous rover position is determined by stereoscopy, while the target distance at the current rover position is calculated from an estimate of the current pose of the rover. The template image is then magnified by an amount corresponding to the estimated target distance to obtain a best template image to match with the image acquired at the current rover position.

Kim, Won↗

Tool for Viewing Faults Under Terrain

Multi Surface Light Table (MSLT) is an interactive software tool that was developed in support of the QuakeSim project, which has created an earthquake- fault database and a set of earthquake- simulation software tools. MSLT visualizes the three-dimensional geometries of faults embedded below the terrain and animates time-varying simulations of stress and slip. The fault segments, represented as rectangular surfaces at dip angles, are organized into collections, that is, faults. An interface built into MSLT queries and retrieves fault definitions from the QuakeSim fault database. MSLT also reads time-varying output from one of the QuakeSim simulation tools, called "Virtual California." Stress intensity is represented by variations in color. Slips are represented by directional indicators on the fault segments. The magnitudes of the slips are represented by the duration of the directional indicators in time. The interactive controls in MSLT provide a virtual track-ball, pan and zoom, translucency adjustment, simulation playback, and simulation movie capture. In addition, geographical information on the fault segments and faults is displayed on text windows. Because of the extensive viewing controls, faults can be seen in relation to one another, and to the terrain. These relations can be realized in simulations. Correlated slips in parallel faults are visible in the playback of Virtual California simulations.

Siegel, Herbert, L.↗