Distributed 3D Information Visualization - Towards Integration of the Dynamic 3D Graphics and Web Services

NASA Astrophysics Data System (ADS)

Vucinic, Dean; Deen, Danny; Oanta, Emil; Batarilo, Zvonimir; Lacor, Chris

This paper focuses on visualization and manipulation of graphical content in distributed network environments. The developed graphical middleware and 3D desktop prototypes were specialized for situational awareness. This research was done in the LArge Scale COllaborative decision support Technology (LASCOT) project, which explored and combined software technologies to support human-centred decision support system for crisis management (earthquake, tsunami, flooding, airplane or oil-tanker incidents, chemical, radio-active or other pollutants spreading, etc.). The performed state-of-the-art review did not identify any publicly available large scale distributed application of this kind. Existing proprietary solutions rely on the conventional technologies and 2D representations. Our challenge was to apply the "latest" available technologies, such Java3D, X3D and SOAP, compatible with average computer graphics hardware. The selected technologies are integrated and we demonstrate: the flow of data, which originates from heterogeneous data sources; interoperability across different operating systems and 3D visual representations to enhance the end-users interactions.

Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints

PubMed Central

Diament, Alon; Tuller, Tamir

2015-01-01

The study of the 3D architecture of chromosomes has been advancing rapidly in recent years. While a number of methods for 3D reconstruction of genomic models based on Hi-C data were proposed, most of the analyses in the field have been performed on different 3D representation forms (such as graphs). Here, we reproduce most of the previous results on the 3D genomic organization of the eukaryote Saccharomyces cerevisiae using analysis of 3D reconstructions. We show that many of these results can be reproduced in sparse reconstructions, generated from a small fraction of the experimental data (5% of the data), and study the properties of such models. Finally, we propose for the first time a novel approach for improving the accuracy of 3D reconstructions by introducing additional predicted physical interactions to the model, based on orthologous interactions in an evolutionary-related organism and based on predicted functional interactions between genes. We demonstrate that this approach indeed leads to the reconstruction of improved models. PMID:26000633

Targeting MUC1 mediated tumor stromal metabolic interaction in Triple negative Breast Cancer

DTIC Science & Technology

2016-11-01

biosynthesis, D- Glutamine and D-glutamate metabolism, Nicotinate and nicotinamide metabolism, and Nitrogen metabolism were amongst the redundant...pathways identified in MDA- MB-468 (Fig 3). Nitrogen metabolism and D- Glutamine and D-glutamate metabolism pathways were filtered out as potential...Figure 4. MUC1 alters TNBC metabolism. Representation of (A) D- Glutamine and D- glutamate metabolism and (B

Targeting MUC1-Mediated Tumor-Stromal Metabolic Interaction in Triple-Negative Breast Cancer

DTIC Science & Technology

2016-11-01

biosynthesis, D- Glutamine and D-glutamate metabolism, Nicotinate and nicotinamide metabolism, and Nitrogen metabolism were amongst the redundant...pathways identified in MDA- MB-468 (Fig 3). Nitrogen metabolism and D- Glutamine and D-glutamate metabolism pathways were filtered out as potential...Figure 4. MUC1 alters TNBC metabolism. Representation of (A) D- Glutamine and D- glutamate metabolism and (B

Interactive 2D to 3D stereoscopic image synthesis

NASA Astrophysics Data System (ADS)

Feldman, Mark H.; Lipton, Lenny

2005-03-01

Advances in stereoscopic display technologies, graphic card devices, and digital imaging algorithms have opened up new possibilities in synthesizing stereoscopic images. The power of today"s DirectX/OpenGL optimized graphics cards together with adapting new and creative imaging tools found in software products such as Adobe Photoshop, provide a powerful environment for converting planar drawings and photographs into stereoscopic images. The basis for such a creative process is the focus of this paper. This article presents a novel technique, which uses advanced imaging features and custom Windows-based software that utilizes the Direct X 9 API to provide the user with an interactive stereo image synthesizer. By creating an accurate and interactive world scene with moveable and flexible depth map altered textured surfaces, perspective stereoscopic cameras with both visible frustums and zero parallax planes, a user can precisely model a virtual three-dimensional representation of a real-world scene. Current versions of Adobe Photoshop provide a creative user with a rich assortment of tools needed to highlight elements of a 2D image, simulate hidden areas, and creatively shape them for a 3D scene representation. The technique described has been implemented as a Photoshop plug-in and thus allows for a seamless transition of these 2D image elements into 3D surfaces, which are subsequently rendered to create stereoscopic views.

Interaction Design and Usability of Learning Spaces in 3D Multi-user Virtual Worlds

NASA Astrophysics Data System (ADS)

Minocha, Shailey; Reeves, Ahmad John

Three-dimensional virtual worlds are multimedia, simulated environments, often managed over the Web, which users can 'inhabit' and interact via their own graphical, self-representations known as 'avatars'. 3D virtual worlds are being used in many applications: education/training, gaming, social networking, marketing and commerce. Second Life is the most widely used 3D virtual world in education. However, problems associated with usability, navigation and way finding in 3D virtual worlds may impact on student learning and engagement. Based on empirical investigations of learning spaces in Second Life, this paper presents design guidelines to improve the usability and ease of navigation in 3D spaces. Methods of data collection include semi-structured interviews with Second Life students, educators and designers. The findings have revealed that design principles from the fields of urban planning, Human- Computer Interaction, Web usability, geography and psychology can influence the design of spaces in 3D multi-user virtual environments.

A pseudo-haptic knot diagram interface

NASA Astrophysics Data System (ADS)

Zhang, Hui; Weng, Jianguang; Hanson, Andrew J.

2011-01-01

To make progress in understanding knot theory, we will need to interact with the projected representations of mathematical knots which are of course continuous in 3D but significantly interrupted in the projective images. One way to achieve such a goal would be to design an interactive system that allows us to sketch 2D knot diagrams by taking advantage of a collision-sensing controller and explore their underlying smooth structures through a continuous motion. Recent advances of interaction techniques have been made that allow progress to be made in this direction. Pseudo-haptics that simulates haptic effects using pure visual feedback can be used to develop such an interactive system. This paper outlines one such pseudo-haptic knot diagram interface. Our interface derives from the familiar pencil-and-paper process of drawing 2D knot diagrams and provides haptic-like sensations to facilitate the creation and exploration of knot diagrams. A centerpiece of the interaction model simulates a "physically" reactive mouse cursor, which is exploited to resolve the apparent conflict between the continuous structure of the actual smooth knot and the visual discontinuities in the knot diagram representation. Another value in exploiting pseudo-haptics is that an acceleration (or deceleration) of the mouse cursor (or surface locator) can be used to indicate the slope of the curve (or surface) of whom the projective image is being explored. By exploiting these additional visual cues, we proceed to a full-featured extension to a pseudo-haptic 4D visualization system that simulates the continuous navigation on 4D objects and allows us to sense the bumps and holes in the fourth dimension. Preliminary tests of the software show that main features of the interface overcome some expected perceptual limitations in our interaction with 2D knot diagrams of 3D knots and 3D projective images of 4D mathematical objects.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Curtis L.; Prescott, Steven; Coleman, Justin

This report describes the current progress and status related to the Industry Application #2 focusing on External Hazards. For this industry application within the Light Water Reactor Sustainability (LWRS) Program Risk-Informed Safety Margin Characterization (RISMC) R&D Pathway, we will create the Risk-Informed Margin Management (RIMM) approach to represent meaningful (i.e., realistic facility representation) event scenarios and consequences by using an advanced 3D facility representation that will evaluate external hazards such as flooding and earthquakes in order to identify, model and analyze the appropriate physics that needs to be included to determine plant vulnerabilities related to external events; manage the communicationmore » and interactions between different physics modeling and analysis technologies; and develop the computational infrastructure through tools related to plant representation, scenario depiction, and physics prediction. One of the unique aspects of the RISMC approach is how it couples probabilistic approaches (the scenario) with mechanistic phenomena representation (the physics) through simulation. This simulation-based modeling allows decision makers to focus on a variety of safety, performance, or economic metrics. In this report, we describe the evaluation of various physics toolkits related to flooding representation. Ultimately, we will be coupling the flooding representation with other events such as earthquakes in order to provide coupled physics analysis for scenarios where interactions exist.« less

Graphics to H.264 video encoding for 3D scene representation and interaction on mobile devices using region of interest

NASA Astrophysics Data System (ADS)

Le, Minh Tuan; Nguyen, Congdu; Yoon, Dae-Il; Jung, Eun Ku; Jia, Jie; Kim, Hae-Kwang

2007-12-01

In this paper, we propose a method of 3D graphics to video encoding and streaming that are embedded into a remote interactive 3D visualization system for rapidly representing a 3D scene on mobile devices without having to download it from the server. In particular, a 3D graphics to video framework is presented that increases the visual quality of regions of interest (ROI) of the video by performing more bit allocation to ROI during H.264 video encoding. The ROI are identified by projection 3D objects to a 2D plane during rasterization. The system offers users to navigate the 3D scene and interact with objects of interests for querying their descriptions. We developed an adaptive media streaming server that can provide an adaptive video stream in term of object-based quality to the client according to the user's preferences and the variation of network bandwidth. Results show that by doing ROI mode selection, PSNR of test sample slightly change while visual quality of objects increases evidently.

Virtual Environment Training on Mobile Devices

DTIC Science & Technology

2013-09-01

NONFUNCTIONAL REQUIREMENTS .............................................. 41 G. PRODUCT FEATURES...52 E. SOFTWARE PRODUCTION .............................................................. 52 F. LIMITATIONS...on Android and iOS tablets. G. PRODUCT FEATURES 1. The final product shall include interactive 3D graphics with simulated representation of actual

Towards a 3d Based Platform for Cultural Heritage Site Survey and Virtual Exploration

NASA Astrophysics Data System (ADS)

Seinturier, J.; Riedinger, C.; Mahiddine, A.; Peloso, D.; Boï, J.-M.; Merad, D.; Drap, P.

2013-07-01

This paper present a 3D platform that enables to make both cultural heritage site survey and its virtual exploration. It provides a single and easy way to use framework for merging multi scaled 3D measurements based on photogrammetry, documentation produced by experts and the knowledge of involved domains leaving the experts able to extract and choose the relevant information to produce the final survey. Taking into account the interpretation of the real world during the process of archaeological surveys is in fact the main goal of a survey. New advances in photogrammetry and the capability to produce dense 3D point clouds do not solve the problem of surveys. New opportunities for 3D representation are now available and we must to use them and find new ways to link geometry and knowledge. The new platform is able to efficiently manage and process large 3D data (points set, meshes) thanks to the implementation of space partition methods coming from the state of the art such as octrees and kd-trees and thus can interact with dense point clouds (thousands to millions of points) in real time. The semantisation of raw 3D data relies on geometric algorithms such as geodetic path computation, surface extraction from dense points cloud and geometrical primitive optimization. The platform provide an interface that enables expert to describe geometric representations of interesting objects like ashlar blocs, stratigraphic units or generic items (contour, lines, … ) directly onto the 3D representation of the site and without explicit links to underlying algorithms. The platform provide two ways for describing geometric representation. If oriented photographs are available, the expert can draw geometry on a photograph and the system computes its 3D representation by projection on the underlying mesh or the points cloud. If photographs are not available or if the expert wants to only use the 3D representation then he can simply draw objects shape on it. When 3D representations of objects of a surveyed site are extracted from the mesh, the link with domain related documentation is done by means of a set of forms designed by experts. Information from these forms are linked with geometry such that documentation can be attached to the viewed objects. Additional semantisation methods related to specific domains have been added to the platform. Beyond realistic rendering of surveyed site, the platform embeds non photorealistic rendering (NPR) algorithms. These algorithms enable to dynamically illustrate objects of interest that are related to knowledge with specific styles. The whole platform is implemented with a Java framework and relies on an actual and effective 3D engine that make available latest rendering methods. We illustrate this work on various photogrammetric survey, in medieval archaeology with the Shawbak castle in Jordan and in underwater archaeology on different marine sites.

The Visual Representation of 3D Object Orientation in Parietal Cortex

PubMed Central

Cowan, Noah J.; Angelaki, Dora E.

2013-01-01

An accurate representation of three-dimensional (3D) object orientation is essential for interacting with the environment. Where and how the brain visually encodes 3D object orientation remains unknown, but prior studies suggest the caudal intraparietal area (CIP) may be involved. Here, we develop rigorous analytical methods for quantifying 3D orientation tuning curves, and use these tools to the study the neural coding of surface orientation. Specifically, we show that single neurons in area CIP of the rhesus macaque jointly encode the slant and tilt of a planar surface, and that across the population, the distribution of preferred slant-tilts is not statistically different from uniform. This suggests that all slant-tilt combinations are equally represented in area CIP. Furthermore, some CIP neurons are found to also represent the third rotational degree of freedom that determines the orientation of the image pattern on the planar surface. Together, the present results suggest that CIP is a critical neural locus for the encoding of all three rotational degrees of freedom specifying an object's 3D spatial orientation. PMID:24305830

A real-time 3D end-to-end augmented reality system (and its representation transformations)

NASA Astrophysics Data System (ADS)

Tytgat, Donny; Aerts, Maarten; De Busser, Jeroen; Lievens, Sammy; Rondao Alface, Patrice; Macq, Jean-Francois

2016-09-01

The new generation of HMDs coming to the market is expected to enable many new applications that allow free viewpoint experiences with captured video objects. Current applications usually rely on 3D content that is manually created or captured in an offline manner. In contrast, this paper focuses on augmented reality applications that use live captured 3D objects while maintaining free viewpoint interaction. We present a system that allows live dynamic 3D objects (e.g. a person who is talking) to be captured in real-time. Real-time performance is achieved by traversing a number of representation formats and exploiting their specific benefits. For instance, depth images are maintained for fast neighborhood retrieval and occlusion determination, while implicit surfaces are used to facilitate multi-source aggregation for both geometry and texture. The result is a 3D reconstruction system that outputs multi-textured triangle meshes at real-time rates. An end-to-end system is presented that captures and reconstructs live 3D data and allows for this data to be used on a networked (AR) device. For allocating the different functional blocks onto the available physical devices, a number of alternatives are proposed considering the available computational power and bandwidth for each of the components. As we will show, the representation format can play an important role in this functional allocation and allows for a flexible system that can support a highly heterogeneous infrastructure.

Binocular fusion and invariant category learning due to predictive remapping during scanning of a depthful scene with eye movements

PubMed Central

Grossberg, Stephen; Srinivasan, Karthik; Yazdanbakhsh, Arash

2015-01-01

How does the brain maintain stable fusion of 3D scenes when the eyes move? Every eye movement causes each retinal position to process a different set of scenic features, and thus the brain needs to binocularly fuse new combinations of features at each position after an eye movement. Despite these breaks in retinotopic fusion due to each movement, previously fused representations of a scene in depth often appear stable. The 3D ARTSCAN neural model proposes how the brain does this by unifying concepts about how multiple cortical areas in the What and Where cortical streams interact to coordinate processes of 3D boundary and surface perception, spatial attention, invariant object category learning, predictive remapping, eye movement control, and learned coordinate transformations. The model explains data from single neuron and psychophysical studies of covert visual attention shifts prior to eye movements. The model further clarifies how perceptual, attentional, and cognitive interactions among multiple brain regions (LGN, V1, V2, V3A, V4, MT, MST, PPC, LIP, ITp, ITa, SC) may accomplish predictive remapping as part of the process whereby view-invariant object categories are learned. These results build upon earlier neural models of 3D vision and figure-ground separation and the learning of invariant object categories as the eyes freely scan a scene. A key process concerns how an object's surface representation generates a form-fitting distribution of spatial attention, or attentional shroud, in parietal cortex that helps maintain the stability of multiple perceptual and cognitive processes. Predictive eye movement signals maintain the stability of the shroud, as well as of binocularly fused perceptual boundaries and surface representations. PMID:25642198

Binocular fusion and invariant category learning due to predictive remapping during scanning of a depthful scene with eye movements.

PubMed

Grossberg, Stephen; Srinivasan, Karthik; Yazdanbakhsh, Arash

2014-01-01

How does the brain maintain stable fusion of 3D scenes when the eyes move? Every eye movement causes each retinal position to process a different set of scenic features, and thus the brain needs to binocularly fuse new combinations of features at each position after an eye movement. Despite these breaks in retinotopic fusion due to each movement, previously fused representations of a scene in depth often appear stable. The 3D ARTSCAN neural model proposes how the brain does this by unifying concepts about how multiple cortical areas in the What and Where cortical streams interact to coordinate processes of 3D boundary and surface perception, spatial attention, invariant object category learning, predictive remapping, eye movement control, and learned coordinate transformations. The model explains data from single neuron and psychophysical studies of covert visual attention shifts prior to eye movements. The model further clarifies how perceptual, attentional, and cognitive interactions among multiple brain regions (LGN, V1, V2, V3A, V4, MT, MST, PPC, LIP, ITp, ITa, SC) may accomplish predictive remapping as part of the process whereby view-invariant object categories are learned. These results build upon earlier neural models of 3D vision and figure-ground separation and the learning of invariant object categories as the eyes freely scan a scene. A key process concerns how an object's surface representation generates a form-fitting distribution of spatial attention, or attentional shroud, in parietal cortex that helps maintain the stability of multiple perceptual and cognitive processes. Predictive eye movement signals maintain the stability of the shroud, as well as of binocularly fused perceptual boundaries and surface representations.

Eye Tracking to Explore the Impacts of Photorealistic 3d Representations in Pedstrian Navigation Performance

NASA Astrophysics Data System (ADS)

Dong, Weihua; Liao, Hua

2016-06-01

Despite the now-ubiquitous two-dimensional (2D) maps, photorealistic three-dimensional (3D) representations of cities (e.g., Google Earth) have gained much attention by scientists and public users as another option. However, there is no consistent evidence on the influences of 3D photorealism on pedestrian navigation. Whether 3D photorealism can communicate cartographic information for navigation with higher effectiveness and efficiency and lower cognitive workload compared to the traditional symbolic 2D maps remains unknown. This study aims to explore whether the photorealistic 3D representation can facilitate processes of map reading and navigation in digital environments using a lab-based eye tracking approach. Here we show the differences of symbolic 2D maps versus photorealistic 3D representations depending on users' eye-movement and navigation behaviour data. We found that the participants using the 3D representation were less effective, less efficient and were required higher cognitive workload than using the 2D map for map reading. However, participants using the 3D representation performed more efficiently in self-localization and orientation at the complex decision points. The empirical results can be helpful to improve the usability of pedestrian navigation maps in future designs.

Representation and visualization of variability in a 3D anatomical atlas using the kidney as an example

NASA Astrophysics Data System (ADS)

Hacker, Silke; Handels, Heinz

2006-03-01

Computer-based 3D atlases allow an interactive exploration of the human body. However, in most cases such 3D atlases are derived from one single individual, and therefore do not regard the variability of anatomical structures concerning their shape and size. Since the geometric variability across humans plays an important role in many medical applications, our goal is to develop a framework of an anatomical atlas for representation and visualization of the variability of selected anatomical structures. The basis of the project presented is the VOXEL-MAN atlas of inner organs that was created from the Visible Human data set. For modeling anatomical shapes and their variability we utilize "m-reps" which allow a compact representation of anatomical objects on the basis of their skeletons. As an example we used a statistical model of the kidney that is based on 48 different variants. With the integration of a shape description into the VOXEL-MAN atlas it is now possible to query and visualize different shape variations of an organ, e.g. by specifying a person's age or gender. In addition to the representation of individual shape variants, the average shape of a population can be displayed. Besides a surface representation, a volume-based representation of the kidney's shape variants is also possible. It results from the deformation of the reference kidney of the volume-based model using the m-rep shape description. In this way a realistic visualization of the shape variants becomes possible, as well as the visualization of the organ's internal structures.

Interactive Exploration of Big Scientific Data: New Representations and Techniques.

PubMed

Hjelmervik, Jon M; Barrowclough, Oliver J D

2016-01-01

Although splines have been in popular use in CAD for more than half a century, spline research is still an active field, driven by the challenges we are facing today within isogeometric analysis and big data. Splines are likely to play a vital future role in enabling effective big data exploration techniques in 3D, 4D, and beyond.

Differential patterns of 2D location versus depth decoding along the visual hierarchy.

PubMed

Finlayson, Nonie J; Zhang, Xiaoli; Golomb, Julie D

2017-02-15

Visual information is initially represented as 2D images on the retina, but our brains are able to transform this input to perceive our rich 3D environment. While many studies have explored 2D spatial representations or depth perception in isolation, it remains unknown if or how these processes interact in human visual cortex. Here we used functional MRI and multi-voxel pattern analysis to investigate the relationship between 2D location and position-in-depth information. We stimulated different 3D locations in a blocked design: each location was defined by horizontal, vertical, and depth position. Participants remained fixated at the center of the screen while passively viewing the peripheral stimuli with red/green anaglyph glasses. Our results revealed a widespread, systematic transition throughout visual cortex. As expected, 2D location information (horizontal and vertical) could be strongly decoded in early visual areas, with reduced decoding higher along the visual hierarchy, consistent with known changes in receptive field sizes. Critically, we found that the decoding of position-in-depth information tracked inversely with the 2D location pattern, with the magnitude of depth decoding gradually increasing from intermediate to higher visual and category regions. Representations of 2D location information became increasingly location-tolerant in later areas, where depth information was also tolerant to changes in 2D location. We propose that spatial representations gradually transition from 2D-dominant to balanced 3D (2D and depth) along the visual hierarchy. Copyright © 2016 Elsevier Inc. All rights reserved.

Cortical Dynamics of Figure-Ground Separation in Response to 2D Pictures and 3D Scenes: How V2 Combines Border Ownership, Stereoscopic Cues, and Gestalt Grouping Rules

PubMed Central

Grossberg, Stephen

2016-01-01

The FACADE model, and its laminar cortical realization and extension in the 3D LAMINART model, have explained, simulated, and predicted many perceptual and neurobiological data about how the visual cortex carries out 3D vision and figure-ground perception, and how these cortical mechanisms enable 2D pictures to generate 3D percepts of occluding and occluded objects. In particular, these models have proposed how border ownership occurs, but have not yet explicitly explained the correlation between multiple properties of border ownership neurons in cortical area V2 that were reported in a remarkable series of neurophysiological experiments by von der Heydt and his colleagues; namely, border ownership, contrast preference, binocular stereoscopic information, selectivity for side-of-figure, Gestalt rules, and strength of attentional modulation, as well as the time course during which such properties arise. This article shows how, by combining 3D LAMINART properties that were discovered in two parallel streams of research, a unified explanation of these properties emerges. This explanation proposes, moreover, how these properties contribute to the generation of consciously seen 3D surfaces. The first research stream models how processes like 3D boundary grouping and surface filling-in interact in multiple stages within and between the V1 interblob—V2 interstripe—V4 cortical stream and the V1 blob—V2 thin stripe—V4 cortical stream, respectively. Of particular importance for understanding figure-ground separation is how these cortical interactions convert computationally complementary boundary and surface mechanisms into a consistent conscious percept, including the critical use of surface contour feedback signals from surface representations in V2 thin stripes to boundary representations in V2 interstripes. Remarkably, key figure-ground properties emerge from these feedback interactions. The second research stream shows how cells that compute absolute disparity in cortical area V1 are transformed into cells that compute relative disparity in cortical area V2. Relative disparity is a more invariant measure of an object's depth and 3D shape, and is sensitive to figure-ground properties. PMID:26858665

Cortical Dynamics of Figure-Ground Separation in Response to 2D Pictures and 3D Scenes: How V2 Combines Border Ownership, Stereoscopic Cues, and Gestalt Grouping Rules.

PubMed

Grossberg, Stephen

2015-01-01

The FACADE model, and its laminar cortical realization and extension in the 3D LAMINART model, have explained, simulated, and predicted many perceptual and neurobiological data about how the visual cortex carries out 3D vision and figure-ground perception, and how these cortical mechanisms enable 2D pictures to generate 3D percepts of occluding and occluded objects. In particular, these models have proposed how border ownership occurs, but have not yet explicitly explained the correlation between multiple properties of border ownership neurons in cortical area V2 that were reported in a remarkable series of neurophysiological experiments by von der Heydt and his colleagues; namely, border ownership, contrast preference, binocular stereoscopic information, selectivity for side-of-figure, Gestalt rules, and strength of attentional modulation, as well as the time course during which such properties arise. This article shows how, by combining 3D LAMINART properties that were discovered in two parallel streams of research, a unified explanation of these properties emerges. This explanation proposes, moreover, how these properties contribute to the generation of consciously seen 3D surfaces. The first research stream models how processes like 3D boundary grouping and surface filling-in interact in multiple stages within and between the V1 interblob-V2 interstripe-V4 cortical stream and the V1 blob-V2 thin stripe-V4 cortical stream, respectively. Of particular importance for understanding figure-ground separation is how these cortical interactions convert computationally complementary boundary and surface mechanisms into a consistent conscious percept, including the critical use of surface contour feedback signals from surface representations in V2 thin stripes to boundary representations in V2 interstripes. Remarkably, key figure-ground properties emerge from these feedback interactions. The second research stream shows how cells that compute absolute disparity in cortical area V1 are transformed into cells that compute relative disparity in cortical area V2. Relative disparity is a more invariant measure of an object's depth and 3D shape, and is sensitive to figure-ground properties.

Higher Dimensional Spacetimes for Visualizing and Modeling Subluminal, Luminal and Superluminal Flight

DOE Office of Scientific and Technical Information (OSTI.GOV)

Froning, H. David; Meholic, Gregory V.

2010-01-28

This paper briefly explores higher dimensional spacetimes that extend Meholic's visualizable, fluidic views of: subluminal-luminal-superluminal flight; gravity, inertia, light quanta, and electromagnetism from 2-D to 3-D representations. Although 3-D representations have the potential to better model features of Meholic's most fundamental entities (Transluminal Energy Quantum) and of the zero-point quantum vacuum that pervades all space, the more complex 3-D representations loose some of the clarity of Meholic's 2-D representations of subluminal and superlumimal realms. So, much new work would be needed to replace Meholic's 2-D views of reality with 3-D ones.

DHM simulation in virtual environments: a case-study on control room design.

PubMed

Zamberlan, M; Santos, V; Streit, P; Oliveira, J; Cury, R; Negri, T; Pastura, F; Guimarães, C; Cid, G

2012-01-01

This paper will present the workflow developed for the application of serious games in the design of complex cooperative work settings. The project was based on ergonomic studies and development of a control room among participative design process. Our main concerns were the 3D human virtual representation acquired from 3D scanning, human interaction, workspace layout and equipment designed considering ergonomics standards. Using Unity3D platform to design the virtual environment, the virtual human model can be controlled by users on dynamic scenario in order to evaluate the new work settings and simulate work activities. The results obtained showed that this virtual technology can drastically change the design process by improving the level of interaction between final users and, managers and human factors team.

Three-dimensional reconstruction of Roman coins from photometric image sets

NASA Astrophysics Data System (ADS)

MacDonald, Lindsay; Moitinho de Almeida, Vera; Hess, Mona

2017-01-01

A method is presented for increasing the spatial resolution of the three-dimensional (3-D) digital representation of coins by combining fine photometric detail derived from a set of photographic images with accurate geometric data from a 3-D laser scanner. 3-D reconstructions were made of the obverse and reverse sides of two ancient Roman denarii by processing sets of images captured under directional lighting in an illumination dome. Surface normal vectors were calculated by a "bounded regression" technique, excluding both shadow and specular components of reflection from the metallic surface. Because of the known difficulty in achieving geometric accuracy when integrating photometric normals to produce a digital elevation model, the low spatial frequencies were replaced by those derived from the point cloud produced by a 3-D laser scanner. The two datasets were scaled and registered by matching the outlines and correlating the surface gradients. The final result was a realistic rendering of the coins at a spatial resolution of 75 pixels/mm (13-μm spacing), in which the fine detail modulated the underlying geometric form of the surface relief. The method opens the way to obtain high quality 3-D representations of coins in collections to enable interactive online viewing.

Detailed 3D representations for object recognition and modeling.

PubMed

Zia, M Zeeshan; Stark, Michael; Schiele, Bernt; Schindler, Konrad

2013-11-01

Geometric 3D reasoning at the level of objects has received renewed attention recently in the context of visual scene understanding. The level of geometric detail, however, is typically limited to qualitative representations or coarse boxes. This is linked to the fact that today's object class detectors are tuned toward robust 2D matching rather than accurate 3D geometry, encouraged by bounding-box-based benchmarks such as Pascal VOC. In this paper, we revisit ideas from the early days of computer vision, namely, detailed, 3D geometric object class representations for recognition. These representations can recover geometrically far more accurate object hypotheses than just bounding boxes, including continuous estimates of object pose and 3D wireframes with relative 3D positions of object parts. In combination with robust techniques for shape description and inference, we outperform state-of-the-art results in monocular 3D pose estimation. In a series of experiments, we analyze our approach in detail and demonstrate novel applications enabled by such an object class representation, such as fine-grained categorization of cars and bicycles, according to their 3D geometry, and ultrawide baseline matching.

Interactive distributed hardware-accelerated LOD-sprite terrain rendering with stable frame rates

NASA Astrophysics Data System (ADS)

Swan, J. E., II; Arango, Jesus; Nakshatrala, Bala K.

2002-03-01

A stable frame rate is important for interactive rendering systems. Image-based modeling and rendering (IBMR) techniques, which model parts of the scene with image sprites, are a promising technique for interactive systems because they allow the sprite to be manipulated instead of the underlying scene geometry. However, with IBMR techniques a frequent problem is an unstable frame rate, because generating an image sprite (with 3D rendering) is time-consuming relative to manipulating the sprite (with 2D image resampling). This paper describes one solution to this problem, by distributing an IBMR technique into a collection of cooperating threads and executable programs across two computers. The particular IBMR technique distributed here is the LOD-Sprite algorithm. This technique uses a multiple level-of-detail (LOD) scene representation. It first renders a keyframe from a high-LOD representation, and then caches the frame as an image sprite. It renders subsequent spriteframes by texture-mapping the cached image sprite into a lower-LOD representation. We describe a distributed architecture and implementation of LOD-Sprite, in the context of terrain rendering, which takes advantage of graphics hardware. We present timing results which indicate we have achieved a stable frame rate. In addition to LOD-Sprite, our distribution method holds promise for other IBMR techniques.

Systems and Methods for Data Visualization Using Three-Dimensional Displays

NASA Technical Reports Server (NTRS)

Davidoff, Scott (Inventor); Djorgovski, Stanislav G. (Inventor); Estrada, Vicente (Inventor); Donalek, Ciro (Inventor)

2017-01-01

Data visualization systems and methods for generating 3D visualizations of a multidimensional data space are described. In one embodiment a 3D data visualization application directs a processing system to: load a set of multidimensional data points into a visualization table; create representations of a set of 3D objects corresponding to the set of data points; receive mappings of data dimensions to visualization attributes; determine the visualization attributes of the set of 3D objects based upon the selected mappings of data dimensions to 3D object attributes; update a visibility dimension in the visualization table for each of the plurality of 3D object to reflect the visibility of each 3D object based upon the selected mappings of data dimensions to visualization attributes; and interactively render 3D data visualizations of the 3D objects within the virtual space from viewpoints determined based upon received user input.

Sparse PDF Volumes for Consistent Multi-Resolution Volume Rendering.

PubMed

Sicat, Ronell; Krüger, Jens; Möller, Torsten; Hadwiger, Markus

2014-12-01

This paper presents a new multi-resolution volume representation called sparse pdf volumes, which enables consistent multi-resolution volume rendering based on probability density functions (pdfs) of voxel neighborhoods. These pdfs are defined in the 4D domain jointly comprising the 3D volume and its 1D intensity range. Crucially, the computation of sparse pdf volumes exploits data coherence in 4D, resulting in a sparse representation with surprisingly low storage requirements. At run time, we dynamically apply transfer functions to the pdfs using simple and fast convolutions. Whereas standard low-pass filtering and down-sampling incur visible differences between resolution levels, the use of pdfs facilitates consistent results independent of the resolution level used. We describe the efficient out-of-core computation of large-scale sparse pdf volumes, using a novel iterative simplification procedure of a mixture of 4D Gaussians. Finally, our data structure is optimized to facilitate interactive multi-resolution volume rendering on GPUs.

Do Haptic Representations Help Complex Molecular Learning?

ERIC Educational Resources Information Center

Bivall, Petter; Ainsworth, Shaaron; Tibell, Lena A. E.

2011-01-01

This study explored whether adding a haptic interface (that provides users with somatosensory information about virtual objects by force and tactile feedback) to a three-dimensional (3D) chemical model enhanced students' understanding of complex molecular interactions. Two modes of the model were compared in a between-groups pre- and posttest…

How the venetian blind percept emerges from the laminar cortical dynamics of 3D vision

PubMed Central

Cao, Yongqiang; Grossberg, Stephen

2014-01-01

The 3D LAMINART model of 3D vision and figure-ground perception is used to explain and simulate a key example of the Venetian blind effect and to show how it is related to other well-known perceptual phenomena such as Panum's limiting case. The model proposes how lateral geniculate nucleus (LGN) and hierarchically organized laminar circuits in cortical areas V1, V2, and V4 interact to control processes of 3D boundary formation and surface filling-in that simulate many properties of 3D vision percepts, notably consciously seen surface percepts, which are predicted to arise when filled-in surface representations are integrated into surface-shroud resonances between visual and parietal cortex. Interactions between layers 4, 3B, and 2/3 in V1 and V2 carry out stereopsis and 3D boundary formation. Both binocular and monocular information combine to form 3D boundary and surface representations. Surface contour surface-to-boundary feedback from V2 thin stripes to V2 pale stripes combines computationally complementary boundary and surface formation properties, leading to a single consistent percept, while also eliminating redundant 3D boundaries, and triggering figure-ground perception. False binocular boundary matches are eliminated by Gestalt grouping properties during boundary formation. In particular, a disparity filter, which helps to solve the Correspondence Problem by eliminating false matches, is predicted to be realized as part of the boundary grouping process in layer 2/3 of cortical area V2. The model has been used to simulate the consciously seen 3D surface percepts in 18 psychophysical experiments. These percepts include the Venetian blind effect, Panum's limiting case, contrast variations of dichoptic masking and the correspondence problem, the effect of interocular contrast differences on stereoacuity, stereopsis with polarity-reversed stereograms, da Vinci stereopsis, and perceptual closure. These model mechanisms have also simulated properties of 3D neon color spreading, binocular rivalry, 3D Necker cube, and many examples of 3D figure-ground separation. PMID:25309467

How the venetian blind percept emerges from the laminar cortical dynamics of 3D vision.

PubMed

Cao, Yongqiang; Grossberg, Stephen

2014-01-01

The 3D LAMINART model of 3D vision and figure-ground perception is used to explain and simulate a key example of the Venetian blind effect and to show how it is related to other well-known perceptual phenomena such as Panum's limiting case. The model proposes how lateral geniculate nucleus (LGN) and hierarchically organized laminar circuits in cortical areas V1, V2, and V4 interact to control processes of 3D boundary formation and surface filling-in that simulate many properties of 3D vision percepts, notably consciously seen surface percepts, which are predicted to arise when filled-in surface representations are integrated into surface-shroud resonances between visual and parietal cortex. Interactions between layers 4, 3B, and 2/3 in V1 and V2 carry out stereopsis and 3D boundary formation. Both binocular and monocular information combine to form 3D boundary and surface representations. Surface contour surface-to-boundary feedback from V2 thin stripes to V2 pale stripes combines computationally complementary boundary and surface formation properties, leading to a single consistent percept, while also eliminating redundant 3D boundaries, and triggering figure-ground perception. False binocular boundary matches are eliminated by Gestalt grouping properties during boundary formation. In particular, a disparity filter, which helps to solve the Correspondence Problem by eliminating false matches, is predicted to be realized as part of the boundary grouping process in layer 2/3 of cortical area V2. The model has been used to simulate the consciously seen 3D surface percepts in 18 psychophysical experiments. These percepts include the Venetian blind effect, Panum's limiting case, contrast variations of dichoptic masking and the correspondence problem, the effect of interocular contrast differences on stereoacuity, stereopsis with polarity-reversed stereograms, da Vinci stereopsis, and perceptual closure. These model mechanisms have also simulated properties of 3D neon color spreading, binocular rivalry, 3D Necker cube, and many examples of 3D figure-ground separation.

Point clouds in BIM

NASA Astrophysics Data System (ADS)

Antova, Gergana; Kunchev, Ivan; Mickrenska-Cherneva, Christina

2016-10-01

The representation of physical buildings in Building Information Models (BIM) has been a subject of research since four decades in the fields of Construction Informatics and GeoInformatics. The early digital representations of buildings mainly appeared as 3D drawings constructed by CAD software, and the 3D representation of the buildings was only geometric, while semantics and topology were out of modelling focus. On the other hand, less detailed building representations, with often focus on ‘outside’ representations were also found in form of 2D /2,5D GeoInformation models. Point clouds from 3D laser scanning data give a full and exact representation of the building geometry. The article presents different aspects and the benefits of using point clouds in BIM in the different stages of a lifecycle of a building.

Getting a grip on reality: Grasping movements directed to real objects and images rely on dissociable neural representations.

PubMed

Freud, Erez; Macdonald, Scott N; Chen, Juan; Quinlan, Derek J; Goodale, Melvyn A; Culham, Jody C

2018-01-01

In the current era of touchscreen technology, humans commonly execute visually guided actions directed to two-dimensional (2D) images of objects. Although real, three-dimensional (3D), objects and images of the same objects share high degree of visual similarity, they differ fundamentally in the actions that can be performed on them. Indeed, previous behavioral studies have suggested that simulated grasping of images relies on different representations than actual grasping of real 3D objects. Yet the neural underpinnings of this phenomena have not been investigated. Here we used functional magnetic resonance imaging (fMRI) to investigate how brain activation patterns differed for grasping and reaching actions directed toward real 3D objects compared to images. Multivoxel Pattern Analysis (MVPA) revealed that the left anterior intraparietal sulcus (aIPS), a key region for visually guided grasping, discriminates between both the format in which objects were presented (real/image) and the motor task performed on them (grasping/reaching). Interestingly, during action planning, the representations of real 3D objects versus images differed more for grasping movements than reaching movements, likely because grasping real 3D objects involves fine-grained planning and anticipation of the consequences of a real interaction. Importantly, this dissociation was evident in the planning phase, before movement initiation, and was not found in any other regions, including motor and somatosensory cortices. This suggests that the dissociable representations in the left aIPS were not based on haptic, motor or proprioceptive feedback. Together, these findings provide novel evidence that actions, particularly grasping, are affected by the realness of the target objects during planning, perhaps because real targets require a more elaborate forward model based on visual cues to predict the consequences of real manipulation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Multilayered nonuniform sampling for three-dimensional scene representation

NASA Astrophysics Data System (ADS)

Lin, Huei-Yung; Xiao, Yu-Hua; Chen, Bo-Ren

2015-09-01

The representation of a three-dimensional (3-D) scene is essential in multiview imaging technologies. We present a unified geometry and texture representation based on global resampling of the scene. A layered data map representation with a distance-dependent nonuniform sampling strategy is proposed. It is capable of increasing the details of the 3-D structure locally and is compact in size. The 3-D point cloud obtained from the multilayered data map is used for view rendering. For any given viewpoint, image synthesis with different levels of detail is carried out using the quadtree-based nonuniformly sampled 3-D data points. Experimental results are presented using the 3-D models of reconstructed real objects.

Using optically scanned 3D data in the restoration of Michelangelo's David

NASA Astrophysics Data System (ADS)

Scopigno, Roberto; Cignoni, Paolo; Callieri, Marco; Ganovelli, Fabio; Impoco, G.; Pingi, P.; Ponchio, F.

2003-10-01

Modern 3D scanning technologies allow to reconstruct 3D digital representations of Cultural Heritage artifacts in a semi-automatic way, characterized by very high accuracy and wealth of details. The availability of an accurate digital representation opens several possibilities of utilization to experts (restorers, archivists, museum curators), or to ordinary people (students, museum visitors). 3D scanned data are commonly used for the production of animations, interactive visualizations, or virtual reality applications. A much more exciting opportunity is to use these data in the restoration of Cultural Heritage artworks. The integration between 3D graphic and restoration represents an open research field where many new supporting tools are required; the David restoration project has given several starting points and guidelines to the definition and development of innovative solutions. Digital 3D models can be used in two different but not subsidiary modes: as an instrument for the execution of specific investigations and as a supporting media for the archival and integration of all the restoration-related information, gathered with the different studies and analysis performed on the artwork. In this paper we present some recent work done in the framework of the Michelangelo's David restoration project. A 3D model of the David was reconstructed by the Digital Michelangelo Project, using laser-based 3D scanning technology. We have developed some tools to make those data accessible and useful in the restoration. Preliminary results are reported here together with some directions for further research.

Wireless physiological monitoring and ocular tracking: 3D calibration in a fully-immersive virtual health care environment.

PubMed

Zhang, Lelin; Chi, Yu Mike; Edelstein, Eve; Schulze, Jurgen; Gramann, Klaus; Velasquez, Alvaro; Cauwenberghs, Gert; Macagno, Eduardo

2010-01-01

Wireless physiological/neurological monitoring in virtual reality (VR) offers a unique opportunity for unobtrusively quantifying human responses to precisely controlled and readily modulated VR representations of health care environments. Here we present such a wireless, light-weight head-mounted system for measuring electrooculogram (EOG) and electroencephalogram (EEG) activity in human subjects interacting with and navigating in the Calit2 StarCAVE, a five-sided immersive 3-D visualization VR environment. The system can be easily expanded to include other measurements, such as cardiac activity and galvanic skin responses. We demonstrate the capacity of the system to track focus of gaze in 3-D and report a novel calibration procedure for estimating eye movements from responses to the presentation of a set of dynamic visual cues in the StarCAVE. We discuss cyber and clinical applications that include a 3-D cursor for visual navigation in VR interactive environments, and the monitoring of neurological and ocular dysfunction in vision/attention disorders.

Starting research in interaction design with visuals for low-functioning children in the autistic spectrum: a protocol.

PubMed

Parés, Narcís; Carreras, Anna; Durany, Jaume; Ferrer, Jaume; Freixa, Pere; Gómez, David; Kruglanski, Orit; Parés, Roc; Ribas, J Ignasi; Soler, Miquel; Sanjurjo, Alex

2006-04-01

On starting to think about interaction design for low-functioning persons in the autistic spectrum (PAS), especially children, one finds a number of questions that are difficult to answer: Can we typify the PAS user? Can we engage the user in interactive communication without generating frustrating or obsessive situations? What sort of visual stimuli can we provide? Will they prefer representational or abstract visual stimuli? Will they understand three-dimensional (3D) graphic representation? What sort of interfaces will they accept? Can we set ambitious goals such as education or therapy? Unfortunately, most of these questions have no answer yet. Hence, we decided to set an apparently simple goal: to design a "fun application," with no intention to reach the level of education or therapy. The goal was to be attained by giving the users a sense of agency--by providing first a sense of control in the interaction dialogue. Our approach to visual stimuli design has been based on the use of geometric, abstract, two-dimensional (2D), real-time computer graphics in a full-body, non-invasive, interactive space. The results obtained within the European-funded project MultiSensory Environment Design for an Interface between Autistic and Typical Expressiveness (MEDIATE) have been extremely encouraging.

Learning from graphically integrated 2D and 3D representations improves retention of neuroanatomy

NASA Astrophysics Data System (ADS)

Naaz, Farah

Visualizations in the form of computer-based learning environments are highly encouraged in science education, especially for teaching spatial material. Some spatial material, such as sectional neuroanatomy, is very challenging to learn. It involves learning the two dimensional (2D) representations that are sampled from the three dimensional (3D) object. In this study, a computer-based learning environment was used to explore the hypothesis that learning sectional neuroanatomy from a graphically integrated 2D and 3D representation will lead to better learning outcomes than learning from a sequential presentation. The integrated representation explicitly demonstrates the 2D-3D transformation and should lead to effective learning. This study was conducted using a computer graphical model of the human brain. There were two learning groups: Whole then Sections, and Integrated 2D3D. Both groups learned whole anatomy (3D neuroanatomy) before learning sectional anatomy (2D neuroanatomy). The Whole then Sections group then learned sectional anatomy using 2D representations only. The Integrated 2D3D group learned sectional anatomy from a graphically integrated 3D and 2D model. A set of tests for generalization of knowledge to interpreting biomedical images was conducted immediately after learning was completed. The order of presentation of the tests of generalization of knowledge was counterbalanced across participants to explore a secondary hypothesis of the study: preparation for future learning. If the computer-based instruction programs used in this study are effective tools for teaching anatomy, the participants should continue learning neuroanatomy with exposure to new representations. A test of long-term retention of sectional anatomy was conducted 4-8 weeks after learning was completed. The Integrated 2D3D group was better than the Whole then Sections group in retaining knowledge of difficult instances of sectional anatomy after the retention interval. The benefit of learning from an integrated 2D3D representation suggests that there are some spatial transformations which are better retained if they are learned through an explicit demonstration. Participants also showed evidence of continued learning on the tests of generalization with the help of cues and practice, even without feedback. This finding suggests that the computer-based learning programs used in this study were good tools for instruction of neuroanatomy.

Profile of biology prospective teachers’ representation on plant anatomy learning

NASA Astrophysics Data System (ADS)

Ermayanti; Susanti, R.; Anwar, Y.

2018-04-01

This study aims to obtaining students’ representation ability in understanding the structure and function of plant tissues in plant anatomy course. Thirty students of The Biology Education Department of Sriwijaya University were involved in this study. Data on representation ability were collected using test and observation. The instruments had been validated by expert judgment. Test scores were used to represent students’ ability in 4 categories: 2D-image, 3D-image, spatial, and verbal representations. The results show that students’ representation ability is still low: 2D-image (40.0), 3D-image (25.0), spatial (20.0), and verbal representation (45.0). Based on the results of this study, it is suggested that instructional strategies be developed for plant anatomy course.

An interactive tool for gamut masking

NASA Astrophysics Data System (ADS)

Song, Ying; Lau, Cheryl; Süsstrunk, Sabine

2014-02-01

Artists often want to change the colors of an image to achieve a particular aesthetic goal. For example, they might limit colors to a warm or cool color scheme to create an image with a certain mood or feeling. Gamut masking is a technique that artists use to limit the set of colors they can paint with. They draw a mask over a color wheel and only use the hues within the mask. However, creating the color palette from the mask and applying the colors to the image requires skill. We propose an interactive tool for gamut masking that allows amateur artists to create an image with a desired mood or feeling. Our system extracts a 3D color gamut from the 2D user-drawn mask and maps the image to this gamut. The user can draw a different gamut mask or locally refine the image colors. Our voxel grid gamut representation allows us to represent gamuts of any shape, and our cluster-based image representation allows the user to change colors locally.

Building interactive virtual environments for simulated training in medicine using VRML and Java/JavaScript.

PubMed

Korocsec, D; Holobar, A; Divjak, M; Zazula, D

2005-12-01

Medicine is a difficult thing to learn. Experimenting with real patients should not be the only option; simulation deserves a special attention here. Virtual Reality Modelling Language (VRML) as a tool for building virtual objects and scenes has a good record of educational applications in medicine, especially for static and animated visualisations of body parts and organs. However, to create computer simulations resembling situations in real environments the required level of interactivity and dynamics is difficult to achieve. In the present paper we describe some approaches and techniques which we used to push the limits of the current VRML technology further toward dynamic 3D representation of virtual environments (VEs). Our demonstration is based on the implementation of a virtual baby model, whose vital signs can be controlled from an external Java application. The main contributions of this work are: (a) outline and evaluation of the three-level VRML/Java implementation of the dynamic virtual environment, (b) proposal for a modified VRML Timesensor node, which greatly improves the overall control of system performance, and (c) architecture of the prototype distributed virtual environment for training in neonatal resuscitation comprising the interactive virtual newborn, active bedside monitor for vital signs and full 3D representation of the surgery room.

48 CFR 252.203-7005 - Representation Relating to Compensation of Former DoD Officials.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 48 Federal Acquisition Regulations System 3 2012-10-01 2012-10-01 false Representation Relating to... AND CONTRACT CLAUSES Text of Provisions And Clauses 252.203-7005 Representation Relating to...: Representation Relating to Compensation of Former DoD Officials (NOV 2011) (a) Definition. Covered DoD official...

48 CFR 252.203-7005 - Representation Relating to Compensation of Former DoD Officials.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 48 Federal Acquisition Regulations System 3 2014-10-01 2014-10-01 false Representation Relating to... AND CONTRACT CLAUSES Text of Provisions And Clauses 252.203-7005 Representation Relating to...: Representation Relating to Compensation of Former DoD Officials (NOV 2011) (a) Definition. Covered DoD official...

48 CFR 252.203-7005 - Representation Relating to Compensation of Former DoD Officials.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 48 Federal Acquisition Regulations System 3 2013-10-01 2013-10-01 false Representation Relating to... AND CONTRACT CLAUSES Text of Provisions And Clauses 252.203-7005 Representation Relating to...: Representation Relating to Compensation of Former DoD Officials (NOV 2011) (a) Definition. Covered DoD official...

Sparse PDF Volumes for Consistent Multi-Resolution Volume Rendering

PubMed Central

Sicat, Ronell; Krüger, Jens; Möller, Torsten; Hadwiger, Markus

2015-01-01

This paper presents a new multi-resolution volume representation called sparse pdf volumes, which enables consistent multi-resolution volume rendering based on probability density functions (pdfs) of voxel neighborhoods. These pdfs are defined in the 4D domain jointly comprising the 3D volume and its 1D intensity range. Crucially, the computation of sparse pdf volumes exploits data coherence in 4D, resulting in a sparse representation with surprisingly low storage requirements. At run time, we dynamically apply transfer functions to the pdfs using simple and fast convolutions. Whereas standard low-pass filtering and down-sampling incur visible differences between resolution levels, the use of pdfs facilitates consistent results independent of the resolution level used. We describe the efficient out-of-core computation of large-scale sparse pdf volumes, using a novel iterative simplification procedure of a mixture of 4D Gaussians. Finally, our data structure is optimized to facilitate interactive multi-resolution volume rendering on GPUs. PMID:26146475

Comparing the Microsoft Kinect to a traditional mouse for adjusting the viewed tissue densities of three-dimensional anatomical structures

NASA Astrophysics Data System (ADS)

Juhnke, Bethany; Berron, Monica; Philip, Adriana; Williams, Jordan; Holub, Joseph; Winer, Eliot

2013-03-01

Advancements in medical image visualization in recent years have enabled three-dimensional (3D) medical images to be volume-rendered from magnetic resonance imaging (MRI) and computed tomography (CT) scans. Medical data is crucial for patient diagnosis and medical education, and analyzing these three-dimensional models rather than two-dimensional (2D) slices would enable more efficient analysis by surgeons and physicians, especially non-radiologists. An interaction device that is intuitive, robust, and easily learned is necessary to integrate 3D modeling software into the medical community. The keyboard and mouse configuration does not readily manipulate 3D models because these traditional interface devices function within two degrees of freedom, not the six degrees of freedom presented in three dimensions. Using a familiar, commercial-off-the-shelf (COTS) device for interaction would minimize training time and enable maximum usability with 3D medical images. Multiple techniques are available to manipulate 3D medical images and provide doctors more innovative ways of visualizing patient data. One such example is windowing. Windowing is used to adjust the viewed tissue density of digital medical data. A software platform available at the Virtual Reality Applications Center (VRAC), named Isis, was used to visualize and interact with the 3D representations of medical data. In this paper, we present the methodology and results of a user study that examined the usability of windowing 3D medical imaging using a Kinect™ device compared to a traditional mouse.

DHM and serious games: a case-study oil and gas laboratories.

PubMed

Santos, V; Zamberlan, M; Streit, P; Oliveira, J; Guimarães, C; Pastura, F; Cid, G

2012-01-01

The aim in this paper is to present a research on the application of serious games for the design of laboratories in the oil and gas industries. The focus is in human virtual representation acquired from 3D scanning, human interaction, workspace layout and equipment designed considering ergonomics standards. The laboratory studies were simulated in Unity3D platform, which allows the users to control the DHM1 on the dynamic virtual scenario, in order to simulate work activities. This methodology can change the design process by improving the level of interaction between final users, managers and human factor teams. That helps to better visualize future work settings and improve the level of participation between all stakeholders.

My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development.

PubMed

Rabattu, Pierre-Yves; Massé, Benoit; Ulliana, Federico; Rousset, Marie-Christine; Rohmer, Damien; Léon, Jean-Claude; Palombi, Olivier

2015-01-01

Embryology is a complex morphologic discipline involving a set of entangled mechanisms, sometime difficult to understand and to visualize. Recent computer based techniques ranging from geometrical to physically based modeling are used to assist the visualization and the simulation of virtual humans for numerous domains such as surgical simulation and learning. On the other side, the ontology-based approach applied to knowledge representation is more and more successfully adopted in the life-science domains to formalize biological entities and phenomena, thanks to a declarative approach for expressing and reasoning over symbolic information. 3D models and ontologies are two complementary ways to describe biological entities that remain largely separated. Indeed, while many ontologies providing a unified formalization of anatomy and embryology exist, they remain only descriptive and make the access to anatomical content of complex 3D embryology models and simulations difficult. In this work, we present a novel ontology describing the development of the human embryology deforming 3D models. Beyond describing how organs and structures are composed, our ontology integrates a procedural description of their 3D representations, temporal deformation and relations with respect to their developments. We also created inferences rules to express complex connections between entities. It results in a unified description of both the knowledge of the organs deformation and their 3D representations enabling to visualize dynamically the embryo deformation during the Carnegie stages. Through a simplified ontology, containing representative entities which are linked to spatial position and temporal process information, we illustrate the added-value of such a declarative approach for interactive simulation and visualization of 3D embryos. Combining ontologies and 3D models enables a declarative description of different embryological models that capture the complexity of human developmental anatomy. Visualizing embryos with 3D geometric models and their animated deformations perhaps paves the way towards some kind of hypothesis-driven application. These can also be used to assist the learning process of this complex knowledge. http://www.mycorporisfabrica.org/.

Complex Visual Data Analysis, Uncertainty, and Representation

DTIC Science & Technology

2007-01-01

McNeill, D. (1992). Hand and mind: What gestures reveal about thought. Chicago, IL, USA: University of Chicago Press. Neisser , U . (1976). Cognition and...and Uncertainty 5 representations than on other external representations, and cognitive science talks about this interaction as affordances ( Neisser ...the human body fit into the structure of the external environment to explain human cognition and performance (Gibson, 1979; Neisser

A single-sided representation for the homogeneous Green's function of a unified scalar wave equation.

PubMed

Wapenaar, Kees

2017-06-01

A unified scalar wave equation is formulated, which covers three-dimensional (3D) acoustic waves, 2D horizontally-polarised shear waves, 2D transverse-electric EM waves, 2D transverse-magnetic EM waves, 3D quantum-mechanical waves and 2D flexural waves. The homogeneous Green's function of this wave equation is a combination of the causal Green's function and its time-reversal, such that their singularities at the source position cancel each other. A classical representation expresses this homogeneous Green's function as a closed boundary integral. This representation finds applications in holographic imaging, time-reversed wave propagation and Green's function retrieval by cross correlation. The main drawback of the classical representation in those applications is that it requires access to a closed boundary around the medium of interest, whereas in many practical situations the medium can be accessed from one side only. Therefore, a single-sided representation is derived for the homogeneous Green's function of the unified scalar wave equation. Like the classical representation, this single-sided representation fully accounts for multiple scattering. The single-sided representation has the same applications as the classical representation, but unlike the classical representation it is applicable in situations where the medium of interest is accessible from one side only.

Evaluating the Effectiveness of Organic Chemistry Textbooks in Promoting Representational Fluency and Understanding of 2D-3D Diagrammatic Relationships

ERIC Educational Resources Information Center

Kumi, Bryna C.; Olimpo, Jeffrey T.; Bartlett, Felicia; Dixon, Bonnie L.

2013-01-01

The use of two-dimensional (2D) representations to communicate and reason about micromolecular phenomena is common practice in chemistry. While experts are adept at using such representations, research suggests that novices often exhibit great difficulty in understanding, manipulating, and translating between various representational forms. When…

Somatosensory cortical plasticity in carpal tunnel syndrome--a cross-sectional fMRI evaluation.

PubMed

Napadow, Vitaly; Kettner, Norman; Ryan, Angela; Kwong, Kenneth K; Audette, Joseph; Hui, Kathleen K S

2006-06-01

Carpal tunnel syndrome (CTS) is a common entrapment neuropathy of the median nerve characterized by paresthesias and pain in the first, second, and third digits. We hypothesize that aberrant afferent input in CTS will lead to cortical plasticity. Functional MRI (fMRI) and neurophysiological testing were performed on CTS patients and healthy adults. Median nerve innervated digit 2 (D2), and digit 3 (D3) and ulnar nerve innervated digit 5 (D5) were stimulated during fMRI. Surface-based and ROI-based analyses consistently demonstrated more extensive and stronger contralateral sensorimotor cortical representations of D2 and D3 for CTS patients as compared to healthy adults (P < 0.05). Differences were less profound for D5. Moreover, D3 fMRI activation in both the contralateral SI and motor cortex correlated positively with the D3 sensory conduction latency. Analysis of somatotopy suggested that contralateral SI representations for D2 and D3 were less separated for CTS patients (3.8 +/- 1.0 mm) than for healthy adults (7.5 +/- 1.2 mm). Furthermore, the D3/D2 separation distance correlated negatively with D2 sensory conduction latency-the greater the latency, the closer the D2/D3 cortical representations (r = -0.79, P < 0.05). Coupled with a greater extent of SI representation for these CTS affected digits, the closer cortical representations can be interpreted as a blurred somatotopic arrangement for CTS affected digits. These findings provide further evidence that CTS is not manifest in the periphery alone. Our results are consistent with Hebbian plasticity mechanisms, as our cohort of CTS patients had predominant paresthesias, which produce more temporally coherent afferent signaling from affected digits.

Data Fusion and Visualization with the OpenEarth Framework (OEF)

NASA Astrophysics Data System (ADS)

Nadeau, D. R.; Baru, C.; Fouch, M. J.; Crosby, C. J.

2010-12-01

Data fusion is an increasingly important problem to solve as we strive to integrate data from multiple sources and build better models of the complex processes operating at the Earth’s surface and its interior. These data are often large, multi-dimensional, and subject to differing conventions for file formats, data structures, coordinate spaces, units of measure, and metadata organization. When visualized, these data require differing, and often conflicting, conventions for visual representations, dimensionality, icons, color schemes, labeling, and interaction. These issues make the visualization of fused Earth science data particularly difficult. The OpenEarth Framework (OEF) is an open-source data fusion and visualization suite of software being developed at the Supercomputer Center at the University of California, San Diego. Funded by the NSF, the project is leveraging virtual globe technology from NASA’s WorldWind to create interactive 3D visualization tools that combine layered data from a variety of sources to create a holistic view of features at, above, and beneath the Earth’s surface. The OEF architecture is cross-platform, multi-threaded, modular, and based upon Java. The OEF’s modular approach yields a collection of compatible mix-and-match components for assembling custom applications. Available modules support file format handling, web service communications, data management, data filtering, user interaction, and 3D visualization. File parsers handle a variety of formal and de facto standard file formats. Each one imports data into a general-purpose data representation that supports multidimensional grids, topography, points, lines, polygons, images, and more. From there these data then may be manipulated, merged, filtered, reprojected, and visualized. Visualization features support conventional and new visualization techniques for looking at topography, tomography, maps, and feature geometry. 3D grid data such as seismic tomography may be sliced by multiple oriented cutting planes and isosurfaced to create 3D skins that trace feature boundaries within the data. Topography may be overlaid with satellite imagery along with data such as gravity and magnetics measurements. Multiple data sets may be visualized simultaneously using overlapping layers and a common 3D+time coordinate space. Data management within the OEF handles and hides the quirks of differing file formats, web protocols, storage structures, coordinate spaces, and metadata representations. Derived data are computed automatically to support interaction and visualization while the original data is left unchanged in its original form. Data is cached for better memory and network efficiency, and all visualization is accelerated by 3D graphics hardware found on today’s computers. The OpenEarth Framework project is currently prototyping the software for use in the visualization, and integration of continental scale geophysical data being produced by EarthScope-related research in the Western US. The OEF is providing researchers with new ways to display and interrogate their data and is anticipated to be a valuable tool for future EarthScope-related research.

Canine neuroanatomy: Development of a 3D reconstruction and interactive application for undergraduate veterinary education

PubMed Central

Raffan, Hazel; Guevar, Julien; Poyade, Matthieu; Rea, Paul M.

2017-01-01

Current methods used to communicate and present the complex arrangement of vasculature related to the brain and spinal cord is limited in undergraduate veterinary neuroanatomy training. Traditionally it is taught with 2-dimensional (2D) diagrams, photographs and medical imaging scans which show a fixed viewpoint. 2D representations of 3-dimensional (3D) objects however lead to loss of spatial information, which can present problems when translating this to the patient. Computer-assisted learning packages with interactive 3D anatomical models have become established in medical training, yet equivalent resources are scarce in veterinary education. For this reason, we set out to develop a workflow methodology creating an interactive model depicting the vasculature of the canine brain that could be used in undergraduate education. Using MR images of a dog and several commonly available software programs, we set out to show how combining image editing, segmentation and surface generation, 3D modeling and texturing can result in the creation of a fully interactive application for veterinary training. In addition to clearly identifying a workflow methodology for the creation of this dataset, we have also demonstrated how an interactive tutorial and self-assessment tool can be incorporated into this. In conclusion, we present a workflow which has been successful in developing a 3D reconstruction of the canine brain and associated vasculature through segmentation, surface generation and post-processing of readily available medical imaging data. The reconstructed model was implemented into an interactive application for veterinary education that has been designed to target the problems associated with learning neuroanatomy, primarily the inability to visualise complex spatial arrangements from 2D resources. The lack of similar resources in this field suggests this workflow is original within a veterinary context. There is great potential to explore this method, and introduce a new dimension into veterinary education and training. PMID:28192461

Canine neuroanatomy: Development of a 3D reconstruction and interactive application for undergraduate veterinary education.

PubMed

Raffan, Hazel; Guevar, Julien; Poyade, Matthieu; Rea, Paul M

2017-01-01

Current methods used to communicate and present the complex arrangement of vasculature related to the brain and spinal cord is limited in undergraduate veterinary neuroanatomy training. Traditionally it is taught with 2-dimensional (2D) diagrams, photographs and medical imaging scans which show a fixed viewpoint. 2D representations of 3-dimensional (3D) objects however lead to loss of spatial information, which can present problems when translating this to the patient. Computer-assisted learning packages with interactive 3D anatomical models have become established in medical training, yet equivalent resources are scarce in veterinary education. For this reason, we set out to develop a workflow methodology creating an interactive model depicting the vasculature of the canine brain that could be used in undergraduate education. Using MR images of a dog and several commonly available software programs, we set out to show how combining image editing, segmentation and surface generation, 3D modeling and texturing can result in the creation of a fully interactive application for veterinary training. In addition to clearly identifying a workflow methodology for the creation of this dataset, we have also demonstrated how an interactive tutorial and self-assessment tool can be incorporated into this. In conclusion, we present a workflow which has been successful in developing a 3D reconstruction of the canine brain and associated vasculature through segmentation, surface generation and post-processing of readily available medical imaging data. The reconstructed model was implemented into an interactive application for veterinary education that has been designed to target the problems associated with learning neuroanatomy, primarily the inability to visualise complex spatial arrangements from 2D resources. The lack of similar resources in this field suggests this workflow is original within a veterinary context. There is great potential to explore this method, and introduce a new dimension into veterinary education and training.

Identifying different mechanisms in the control of a nitrogen-vacancy center system

NASA Astrophysics Data System (ADS)

Li, Shouzhi; Yang, Ling; Cao, Dewen; Wang, Yaoxiong; Shuang, Feng; Gao, Fang

2017-10-01

The nitrogen-vacancy (NV) center system has shown great potential in quantum computing due to its long decoherence time at room temperature by encoding the qubit in dressed states [28]. The corresponding control mechanisms, which is expressed by the pathways linking the initial and target states, can be naturally investigated with the Hamiltonian-encoding and observable-decoding (HE-OD) method in the interaction adiabatic representation. This is proved by the fact that the mechanisms change slightly with different detunings, magnetic and driving field intensities, and the dominant pathway is always | g 〉 → | d 〉 → | g 〉 , with | g 〉 and | d 〉 as the first two lowest dressed states. Cases are different in the diabatic representation. The orders of dominant pathways increase the driving field intensities. Tendencies of quantum pathway amplitudes with driving fields, magnetic fields and detunings change at different conditions, which can be analyzed from the Dyson series. HE-OD analysis show that the two states | g 〉 and | d 〉 in the interaction adiabatic representation are preferable to be employed as a qubit than the state pair |0〉 and | - 1 〉 in the diabatic representation under the current Hamiltonian and parameters.

Reconstructing spatial organizations of chromosomes through manifold learning

PubMed Central

Deng, Wenxuan; Hu, Hailin; Ma, Rui; Zhang, Sai; Yang, Jinglin; Peng, Jian; Kaplan, Tommy; Zeng, Jianyang

2018-01-01

Abstract Decoding the spatial organizations of chromosomes has crucial implications for studying eukaryotic gene regulation. Recently, chromosomal conformation capture based technologies, such as Hi-C, have been widely used to uncover the interaction frequencies of genomic loci in a high-throughput and genome-wide manner and provide new insights into the folding of three-dimensional (3D) genome structure. In this paper, we develop a novel manifold learning based framework, called GEM (Genomic organization reconstructor based on conformational Energy and Manifold learning), to reconstruct the three-dimensional organizations of chromosomes by integrating Hi-C data with biophysical feasibility. Unlike previous methods, which explicitly assume specific relationships between Hi-C interaction frequencies and spatial distances, our model directly embeds the neighboring affinities from Hi-C space into 3D Euclidean space. Extensive validations demonstrated that GEM not only greatly outperformed other state-of-art modeling methods but also provided a physically and physiologically valid 3D representations of the organizations of chromosomes. Furthermore, we for the first time apply the modeled chromatin structures to recover long-range genomic interactions missing from original Hi-C data. PMID:29408992

Reconstructing spatial organizations of chromosomes through manifold learning.

PubMed

Zhu, Guangxiang; Deng, Wenxuan; Hu, Hailin; Ma, Rui; Zhang, Sai; Yang, Jinglin; Peng, Jian; Kaplan, Tommy; Zeng, Jianyang

2018-05-04

Decoding the spatial organizations of chromosomes has crucial implications for studying eukaryotic gene regulation. Recently, chromosomal conformation capture based technologies, such as Hi-C, have been widely used to uncover the interaction frequencies of genomic loci in a high-throughput and genome-wide manner and provide new insights into the folding of three-dimensional (3D) genome structure. In this paper, we develop a novel manifold learning based framework, called GEM (Genomic organization reconstructor based on conformational Energy and Manifold learning), to reconstruct the three-dimensional organizations of chromosomes by integrating Hi-C data with biophysical feasibility. Unlike previous methods, which explicitly assume specific relationships between Hi-C interaction frequencies and spatial distances, our model directly embeds the neighboring affinities from Hi-C space into 3D Euclidean space. Extensive validations demonstrated that GEM not only greatly outperformed other state-of-art modeling methods but also provided a physically and physiologically valid 3D representations of the organizations of chromosomes. Furthermore, we for the first time apply the modeled chromatin structures to recover long-range genomic interactions missing from original Hi-C data.

Advanced Visualization of Experimental Data in Real Time Using LiveView3D

NASA Technical Reports Server (NTRS)

Schwartz, Richard J.; Fleming, Gary A.

2006-01-01

LiveView3D is a software application that imports and displays a variety of wind tunnel derived data in an interactive virtual environment in real time. LiveView3D combines the use of streaming video fed into a three-dimensional virtual representation of the test configuration with networked communications to the test facility Data Acquisition System (DAS). This unified approach to real time data visualization provides a unique opportunity to comprehend very large sets of diverse forms of data in a real time situation, as well as in post-test analysis. This paper describes how LiveView3D has been implemented to visualize diverse forms of aerodynamic data gathered during wind tunnel experiments, most notably at the NASA Langley Research Center Unitary Plan Wind Tunnel (UPWT). Planned future developments of the LiveView3D system are also addressed.

The OpenEarth Framework (OEF) for the 3D Visualization of Integrated Earth Science Data

NASA Astrophysics Data System (ADS)

Nadeau, David; Moreland, John; Baru, Chaitan; Crosby, Chris

2010-05-01

Data integration is increasingly important as we strive to combine data from disparate sources and assemble better models of the complex processes operating at the Earth's surface and within its interior. These data are often large, multi-dimensional, and subject to differing conventions for data structures, file formats, coordinate spaces, and units of measure. When visualized, these data require differing, and sometimes conflicting, conventions for visual representations, dimensionality, symbology, and interaction. All of this makes the visualization of integrated Earth science data particularly difficult. The OpenEarth Framework (OEF) is an open-source data integration and visualization suite of applications and libraries being developed by the GEON project at the University of California, San Diego, USA. Funded by the NSF, the project is leveraging virtual globe technology from NASA's WorldWind to create interactive 3D visualization tools that combine and layer data from a wide variety of sources to create a holistic view of features at, above, and beneath the Earth's surface. The OEF architecture is open, cross-platform, modular, and based upon Java. The OEF's modular approach to software architecture yields an array of mix-and-match software components for assembling custom applications. Available modules support file format handling, web service communications, data management, user interaction, and 3D visualization. File parsers handle a variety of formal and de facto standard file formats used in the field. Each one imports data into a general-purpose common data model supporting multidimensional regular and irregular grids, topography, feature geometry, and more. Data within these data models may be manipulated, combined, reprojected, and visualized. The OEF's visualization features support a variety of conventional and new visualization techniques for looking at topography, tomography, point clouds, imagery, maps, and feature geometry. 3D data such as seismic tomography may be sliced by multiple oriented cutting planes and isosurfaced to create 3D skins that trace feature boundaries within the data. Topography may be overlaid with satellite imagery, maps, and data such as gravity and magnetics measurements. Multiple data sets may be visualized simultaneously using overlapping layers within a common 3D coordinate space. Data management within the OEF handles and hides the inevitable quirks of differing file formats, web protocols, storage structures, coordinate spaces, and metadata representations. Heuristics are used to extract necessary metadata used to guide data and visual operations. Derived data representations are computed to better support fluid interaction and visualization while the original data is left unchanged in its original form. Data is cached for better memory and network efficiency, and all visualization makes use of 3D graphics hardware support found on today's computers. The OpenEarth Framework project is currently prototyping the software for use in the visualization, and integration of continental scale geophysical data being produced by EarthScope-related research in the Western US. The OEF is providing researchers with new ways to display and interrogate their data and is anticipated to be a valuable tool for future EarthScope-related research.

Three-dimensional representations of complex carbohydrates and polysaccharides--SweetUnityMol: a video game-based computer graphic software.

PubMed

Pérez, Serge; Tubiana, Thibault; Imberty, Anne; Baaden, Marc

2015-05-01

A molecular visualization program tailored to deal with the range of 3D structures of complex carbohydrates and polysaccharides, either alone or in their interactions with other biomacromolecules, has been developed using advanced technologies elaborated by the video games industry. All the specific structural features displayed by the simplest to the most complex carbohydrate molecules have been considered and can be depicted. This concerns the monosaccharide identification and classification, conformations, location in single or multiple branched chains, depiction of secondary structural elements and the essential constituting elements in very complex structures. Particular attention was given to cope with the accepted nomenclature and pictorial representation used in glycoscience. This achievement provides a continuum between the most popular ways to depict the primary structures of complex carbohydrates to visualizing their 3D structures while giving the users many options to select the most appropriate modes of representations including new features such as those provided by the use of textures to depict some molecular properties. These developments are incorporated in a stand-alone viewer capable of displaying molecular structures, biomacromolecule surfaces and complex interactions of biomacromolecules, with powerful, artistic and illustrative rendering methods. They result in an open source software compatible with multiple platforms, i.e., Windows, MacOS and Linux operating systems, web pages, and producing publication-quality figures. The algorithms and visualization enhancements are demonstrated using a variety of carbohydrate molecules, from glycan determinants to glycoproteins and complex protein-carbohydrate interactions, as well as very complex mega-oligosaccharides and bacterial polysaccharides and multi-stranded polysaccharide architectures. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

3D finite element models of shoulder muscles for computing lines of actions and moment arms.

PubMed

Webb, Joshua D; Blemker, Silvia S; Delp, Scott L

2014-01-01

Accurate representation of musculoskeletal geometry is needed to characterise the function of shoulder muscles. Previous models of shoulder muscles have represented muscle geometry as a collection of line segments, making it difficult to account for the large attachment areas, muscle-muscle interactions and complex muscle fibre trajectories typical of shoulder muscles. To better represent shoulder muscle geometry, we developed 3D finite element models of the deltoid and rotator cuff muscles and used the models to examine muscle function. Muscle fibre paths within the muscles were approximated, and moment arms were calculated for two motions: thoracohumeral abduction and internal/external rotation. We found that muscle fibre moment arms varied substantially across each muscle. For example, supraspinatus is considered a weak external rotator, but the 3D model of supraspinatus showed that the anterior fibres provide substantial internal rotation while the posterior fibres act as external rotators. Including the effects of large attachment regions and 3D mechanical interactions of muscle fibres constrains muscle motion, generates more realistic muscle paths and allows deeper analysis of shoulder muscle function.

LSSGalPy: Interactive Visualization of the Large-scale Environment Around Galaxies

NASA Astrophysics Data System (ADS)

Argudo-Fernández, M.; Duarte Puertas, S.; Ruiz, J. E.; Sabater, J.; Verley, S.; Bergond, G.

2017-05-01

New tools are needed to handle the growth of data in astrophysics delivered by recent and upcoming surveys. We aim to build open-source, light, flexible, and interactive software designed to visualize extensive three-dimensional (3D) tabular data. Entirely written in the Python language, we have developed interactive tools to browse and visualize the positions of galaxies in the universe and their positions with respect to its large-scale structures (LSS). Motivated by a previous study, we created two codes using Mollweide projection and wedge diagram visualizations, where survey galaxies can be overplotted on the LSS of the universe. These are interactive representations where the visualizations can be controlled by widgets. We have released these open-source codes that have been designed to be easily re-used and customized by the scientific community to fulfill their needs. The codes are adaptable to other kinds of 3D tabular data and are robust enough to handle several millions of objects. .

Field-based Information Technology in Geology Education: GeoPads

NASA Astrophysics Data System (ADS)

Knoop, P. A.; van der Pluijm, B.

2004-12-01

During the past two summers, we have successfully incorporated a field-based information technology component into our senior-level, field geology course (GS-440) at the University of Michigan's Camp Davis Geology Field Station, near Jackson, WY. Using GeoPads -- rugged TabletPCs equipped with electronic notebook software, GIS, GPS, and wireless networking -- we have significantly enhanced our field mapping exercises and field trips. While fully retaining the traditional approaches and advantages of field instruction, GeoPads offer important benefits in the development of students' spatial reasoning skills. GeoPads enable students to record observations and directly create geologic maps in the field, using a combination of an electronic field notebook (Microsoft OneNote) tightly integrated with pen-enabled GIS software (ArcGIS-ArcMap). Specifically, this arrangement permits students to analyze and manipulate their data in multiple contexts and representations -- while still in the field -- using both traditional 2-D map views, as well as richer 3-D contexts. Such enhancements provide students with powerful exploratory tools that aid the development of spatial reasoning skills, allowing more intuitive interactions with 2-D representations of our 3-D world. Additionally, field-based GIS mapping enables better error-detection, through immediate interaction with current observations in the context of both supporting data (e.g., topographic maps, aerial photos, magnetic surveys) and students' ongoing observations. The overall field-based IT approach also provides students with experience using tools that are increasingly relevant to their future academic or professional careers.

Fast algorithm for the rendering of three-dimensional surfaces

NASA Astrophysics Data System (ADS)

Pritt, Mark D.

1994-02-01

It is often desirable to draw a detailed and realistic representation of surface data on a computer graphics display. One such representation is a 3D shaded surface. Conventional techniques for rendering shaded surfaces are slow, however, and require substantial computational power. Furthermore, many techniques suffer from aliasing effects, which appear as jagged lines and edges. This paper describes an algorithm for the fast rendering of shaded surfaces without aliasing effects. It is much faster than conventional ray tracing and polygon-based rendering techniques and is suitable for interactive use. On an IBM RISC System/6000TM workstation it renders a 1000 X 1000 surface in about 7 seconds.

SPV: a JavaScript Signaling Pathway Visualizer.

PubMed

Calderone, Alberto; Cesareni, Gianni

2018-03-24

The visualization of molecular interactions annotated in web resources is useful to offer to users such information in a clear intuitive layout. These interactions are frequently represented as binary interactions that are laid out in free space where, different entities, cellular compartments and interaction types are hardly distinguishable. SPV (Signaling Pathway Visualizer) is a free open source JavaScript library which offers a series of pre-defined elements, compartments and interaction types meant to facilitate the representation of signaling pathways consisting of causal interactions without neglecting simple protein-protein interaction networks. freely available under Apache version 2 license; Source code: https://github.com/Sinnefa/SPV_Signaling_Pathway_Visualizer_v1.0. Language: JavaScript; Web technology: Scalable Vector Graphics; Libraries: D3.js. sinnefa@gmail.com.

Interpreting three-dimensional structures from two-dimensional images: a web-based interactive 3D teaching model of surgical liver anatomy

PubMed Central

Crossingham, Jodi L; Jenkinson, Jodie; Woolridge, Nick; Gallinger, Steven; Tait, Gordon A; Moulton, Carol-Anne E

2009-01-01

Background: Given the increasing number of indications for liver surgery and the growing complexity of operations, many trainees in surgical, imaging and related subspecialties require a good working knowledge of the complex intrahepatic anatomy. Computed tomography (CT), the most commonly used liver imaging modality, enhances our understanding of liver anatomy, but comprises a two-dimensional (2D) representation of a complex 3D organ. It is challenging for trainees to acquire the necessary skills for converting these 2D images into 3D mental reconstructions because learning opportunities are limited and internal hepatic anatomy is complicated, asymmetrical and variable. We have created a website that uses interactive 3D models of the liver to assist trainees in understanding the complex spatial anatomy of the liver and to help them create a 3D mental interpretation of this anatomy when viewing CT scans. Methods: Computed tomography scans were imported into DICOM imaging software (OsiriX™) to obtain 3D surface renderings of the liver and its internal structures. Using these 3D renderings as a reference, 3D models of the liver surface and the intrahepatic structures, portal veins, hepatic veins, hepatic arteries and the biliary system were created using 3D modelling software (Cinema 4D™). Results: Using current best practices for creating multimedia tools, a unique, freely available, online learning resource has been developed, entitled Visual Interactive Resource for Teaching, Understanding And Learning Liver Anatomy (VIRTUAL Liver) (http://pie.med.utoronto.ca/VLiver). This website uses interactive 3D models to provide trainees with a constructive resource for learning common liver anatomy and liver segmentation, and facilitates the development of the skills required to mentally reconstruct a 3D version of this anatomy from 2D CT scans. Discussion: Although the intended audience for VIRTUAL Liver consists of residents in various medical and surgical specialties, the website will also be useful for other health care professionals (i.e. radiologists, nurses, hepatologists, radiation oncologists, family doctors) and educators because it provides a comprehensive resource for teaching liver anatomy. PMID:19816618

FastScript3D - A Companion to Java 3D

NASA Technical Reports Server (NTRS)

Koenig, Patti

2005-01-01

FastScript3D is a computer program, written in the Java 3D(TM) programming language, that establishes an alternative language that helps users who lack expertise in Java 3D to use Java 3D for constructing three-dimensional (3D)-appearing graphics. The FastScript3D language provides a set of simple, intuitive, one-line text-string commands for creating, controlling, and animating 3D models. The first word in a string is the name of a command; the rest of the string contains the data arguments for the command. The commands can also be used as an aid to learning Java 3D. Developers can extend the language by adding custom text-string commands. The commands can define new 3D objects or load representations of 3D objects from files in formats compatible with such other software systems as X3D. The text strings can be easily integrated into other languages. FastScript3D facilitates communication between scripting languages [which enable programming of hyper-text markup language (HTML) documents to interact with users] and Java 3D. The FastScript3D language can be extended and customized on both the scripting side and the Java 3D side.

First order augmentation to tensor voting for boundary inference and multiscale analysis in 3D.

PubMed

Tong, Wai-Shun; Tang, Chi-Keung; Mordohai, Philippos; Medioni, Gérard

2004-05-01

Most computer vision applications require the reliable detection of boundaries. In the presence of outliers, missing data, orientation discontinuities, and occlusion, this problem is particularly challenging. We propose to address it by complementing the tensor voting framework, which was limited to second order properties, with first order representation and voting. First order voting fields and a mechanism to vote for 3D surface and volume boundaries and curve endpoints in 3D are defined. Boundary inference is also useful for a second difficult problem in grouping, namely, automatic scale selection. We propose an algorithm that automatically infers the smallest scale that can preserve the finest details. Our algorithm then proceeds with progressively larger scales to ensure continuity where it has not been achieved. Therefore, the proposed approach does not oversmooth features or delay the handling of boundaries and discontinuities until model misfit occurs. The interaction of smooth features, boundaries, and outliers is accommodated by the unified representation, making possible the perceptual organization of data in curves, surfaces, volumes, and their boundaries simultaneously. We present results on a variety of data sets to show the efficacy of the improved formalism.

Advanced 3-dimensional planning in neurosurgery.

PubMed

Ferroli, Paolo; Tringali, Giovanni; Acerbi, Francesco; Schiariti, Marco; Broggi, Morgan; Aquino, Domenico; Broggi, Giovanni

2013-01-01

During the past decades, medical applications of virtual reality technology have been developing rapidly, ranging from a research curiosity to a commercially and clinically important area of medical informatics and technology. With the aid of new technologies, the user is able to process large amounts of data sets to create accurate and almost realistic reconstructions of anatomic structures and related pathologies. As a result, a 3-diensional (3-D) representation is obtained, and surgeons can explore the brain for planning or training. Further improvement such as a feedback system increases the interaction between users and models by creating a virtual environment. Its use for advanced 3-D planning in neurosurgery is described. Different systems of medical image volume rendering have been used and analyzed for advanced 3-D planning: 1 is a commercial "ready-to-go" system (Dextroscope, Bracco, Volume Interaction, Singapore), whereas the others are open-source-based software (3-D Slicer, FSL, and FreesSurfer). Different neurosurgeons at our institution experienced how advanced 3-D planning before surgery allowed them to facilitate and increase their understanding of the complex anatomic and pathological relationships of the lesion. They all agreed that the preoperative experience of virtually planning the approach was helpful during the operative procedure. Virtual reality for advanced 3-D planning in neurosurgery has achieved considerable realism as a result of the available processing power of modern computers. Although it has been found useful to facilitate the understanding of complex anatomic relationships, further effort is needed to increase the quality of the interaction between the user and the model.

Interactive Volume Exploration of Petascale Microscopy Data Streams Using a Visualization-Driven Virtual Memory Approach.

PubMed

Hadwiger, M; Beyer, J; Jeong, Won-Ki; Pfister, H

2012-12-01

This paper presents the first volume visualization system that scales to petascale volumes imaged as a continuous stream of high-resolution electron microscopy images. Our architecture scales to dense, anisotropic petascale volumes because it: (1) decouples construction of the 3D multi-resolution representation required for visualization from data acquisition, and (2) decouples sample access time during ray-casting from the size of the multi-resolution hierarchy. Our system is designed around a scalable multi-resolution virtual memory architecture that handles missing data naturally, does not pre-compute any 3D multi-resolution representation such as an octree, and can accept a constant stream of 2D image tiles from the microscopes. A novelty of our system design is that it is visualization-driven: we restrict most computations to the visible volume data. Leveraging the virtual memory architecture, missing data are detected during volume ray-casting as cache misses, which are propagated backwards for on-demand out-of-core processing. 3D blocks of volume data are only constructed from 2D microscope image tiles when they have actually been accessed during ray-casting. We extensively evaluate our system design choices with respect to scalability and performance, compare to previous best-of-breed systems, and illustrate the effectiveness of our system for real microscopy data from neuroscience.

Three 3D graphical representations of DNA primary sequences based on the classifications of DNA bases and their applications.

PubMed

Xie, Guosen; Mo, Zhongxi

2011-01-21

In this article, we introduce three 3D graphical representations of DNA primary sequences, which we call RY-curve, MK-curve and SW-curve, based on three classifications of the DNA bases. The advantages of our representations are that (i) these 3D curves are strictly non-degenerate and there is no loss of information when transferring a DNA sequence to its mathematical representation and (ii) the coordinates of every node on these 3D curves have clear biological implication. Two applications of these 3D curves are presented: (a) a simple formula is derived to calculate the content of the four bases (A, G, C and T) from the coordinates of nodes on the curves; and (b) a 12-component characteristic vector is constructed to compare similarity among DNA sequences from different species based on the geometrical centers of the 3D curves. As examples, we examine similarity among the coding sequences of the first exon of beta-globin gene from eleven species and validate similarity of cDNA sequences of beta-globin gene from eight species. Copyright © 2010 Elsevier Ltd. All rights reserved.

Towards a more efficient and robust representation of subsurface hydrological processes in Earth System Models

NASA Astrophysics Data System (ADS)

Rosolem, R.; Rahman, M.; Kollet, S. J.; Wagener, T.

2017-12-01

Understanding the impacts of land cover and climate changes on terrestrial hydrometeorology is important across a range of spatial and temporal scales. Earth System Models (ESMs) provide a robust platform for evaluating these impacts. However, current ESMs lack the representation of key hydrological processes (e.g., preferential water flow, and direct interactions with aquifers) in general. The typical "free drainage" conceptualization of land models can misrepresent the magnitude of those interactions, consequently affecting the exchange of energy and water at the surface as well as estimates of groundwater recharge. Recent studies show the benefits of explicitly simulating the interactions between subsurface and surface processes in similar models. However, such parameterizations are often computationally demanding resulting in limited application for large/global-scale studies. Here, we take a different approach in developing a novel parameterization for groundwater dynamics. Instead of directly adding another complex process to an established land model, we examine a set of comprehensive experimental scenarios using a very robust and establish three-dimensional hydrological model to develop a simpler parameterization that represents the aquifer to land surface interactions. The main goal of our developed parameterization is to simultaneously maximize the computational gain (i.e., "efficiency") while minimizing simulation errors in comparison to the full 3D model (i.e., "robustness") to allow for easy implementation in ESMs globally. Our study focuses primarily on understanding both the dynamics for groundwater recharge and discharge, respectively. Preliminary results show that our proposed approach significantly reduced the computational demand while model deviations from the full 3D model are considered to be small for these processes.

Geoinformation techniques for the 3D visualisation of historic buildings and representation of a building's pathology

NASA Astrophysics Data System (ADS)

Tsilimantou, Elisavet; Delegou, Ekaterini; Ioannidis, Charalabos; Moropoulou, Antonia

2016-08-01

In this paper, the documentation of an historic building registered as Cultural Heritage asset is presented. The aim of the survey is to create a 3D geometric representation of a historic building and in accordance with multidisciplinary study extract useful information regarding the extent of degradation, constructions' durability etc. For the implementation of the survey, a combination of different types of acquisition technologies is used. The project focuses on the study of Villa Klonaridi, in Athens, Greece. For the complete documentation of the building, conventional topography, photogrammetric and laser scanning techniques is combined. Close range photogrammetric techniques are used for the acquisition of the façades and architectural details. One of the main objectives is the development of an accurate 3D model, where the photorealistic representation of the building is achieved, along with the decay pathology, historical phases and architectural components. In order to achieve a suitable graphical representation for the study of the material and decay patterns beyond the 2D representation, 3D modelling and additional information modelling is performed for comparative analysis. The study provides various conclusions regarding the scale of deterioration obtained by the 2D and 3D analysis respectively. Considering the variation in material and decay patterns, comparative results are obtained regarding the degradation of the building. Overall, the paper describes a process performed on a Historic Building, where the 3D digital acquisition of the monuments' structure is realized with the combination of close range surveying and laser scanning methods.

Fast protein tertiary structure retrieval based on global surface shape similarity.

PubMed

Sael, Lee; Li, Bin; La, David; Fang, Yi; Ramani, Karthik; Rustamov, Raif; Kihara, Daisuke

2008-09-01

Characterization and identification of similar tertiary structure of proteins provides rich information for investigating function and evolution. The importance of structure similarity searches is increasing as structure databases continue to expand, partly due to the structural genomics projects. A crucial drawback of conventional protein structure comparison methods, which compare structures by their main-chain orientation or the spatial arrangement of secondary structure, is that a database search is too slow to be done in real-time. Here we introduce a global surface shape representation by three-dimensional (3D) Zernike descriptors, which represent a protein structure compactly as a series expansion of 3D functions. With this simplified representation, the search speed against a few thousand structures takes less than a minute. To investigate the agreement between surface representation defined by 3D Zernike descriptor and conventional main-chain based representation, a benchmark was performed against a protein classification generated by the combinatorial extension algorithm. Despite the different representation, 3D Zernike descriptor retrieved proteins of the same conformation defined by combinatorial extension in 89.6% of the cases within the top five closest structures. The real-time protein structure search by 3D Zernike descriptor will open up new possibility of large-scale global and local protein surface shape comparison. 2008 Wiley-Liss, Inc.

High-resolution FTIR spectroscopy of the Coriolis interacting nu3 and nu9 fundamentals of methylene fluoride-d2

NASA Astrophysics Data System (ADS)

Goh, K. L.; Tan, T. L.; Ong, P. P.; Chaw, K. H.; Teo, H. H.

The Fourier transform infrared spectrum of the υ3 and υ9 bands of methylene fluoride-d2 (CD2F2) has been recorded with an unapodized resolution of 0.0024cm-1 in the frequency range 970-1080cm-1. These two bands with band centres approximately 26 cm-1 apart were mutually coupled by Coriolis interactions. By fitting a total of 1639 infrared transitions of both υ3 and υ9 with a standard deviation of 0.00084cm-1 S/S using a Watson's A-reduced Hamiltonian in the Ir representation with the inclusion of a first order c-type Coriolis resonance term, two sets of rovibrational constants for υ3 = 1 and υ9 = 1 states were derived. The υ3 band is B-type while the υ9 band is A-type with band centres at 1030.1573 ± 0.0003 and 1003.7435 ± 0.0001cm-1, respectively.

WWW creates new interactive 3D graphics and collaborative environments for medical research and education.

PubMed

Samothrakis, S; Arvanitis, T N; Plataniotis, A; McNeill, M D; Lister, P F

1997-11-01

Virtual Reality Modelling Language (VRML) is the start of a new era for medicine and the World Wide Web (WWW). Scientists can use VRML across the Internet to explore new three-dimensional (3D) worlds, share concepts and collaborate together in a virtual environment. VRML enables the generation of virtual environments through the use of geometric, spatial and colour data structures to represent 3D objects and scenes. In medicine, researchers often want to interact with scientific data, which in several instances may also be dynamic (e.g. MRI data). This data is often very large and is difficult to visualise. A 3D graphical representation can make the information contained in such large data sets more understandable and easier to interpret. Fast networks and satellites can reliably transfer large data sets from computer to computer. This has led to the adoption of remote tale-working in many applications including medical applications. Radiology experts, for example, can view and inspect in near real-time a 3D data set acquired from a patient who is in another part of the world. Such technology is destined to improve the quality of life for many people. This paper introduces VRML (including some technical details) and discusses the advantages of VRML in application developing.

On the representation of many-body interactions in water

DOE PAGES

Medders, Gregory R.; Gotz, Andreas W.; Morales, Miguel A.; ...

2015-09-09

Our recent work has shown that the many-body expansion of the interactionenergy can be used to develop analytical representations of global potential energy surfaces (PESs) for water. In this study, the role of short- and long-range interactions at different orders is investigated by analyzing water potentials that treat the leading terms of the many-body expansion through implicit (i.e., TTM3-F and TTM4-F PESs) and explicit (i.e., WHBB and MB-pol PESs) representations. Moreover, it is found that explicit short-range representations of 2-body and 3-body interactions along with a physically correct incorporation of short- and long-range contributions are necessary for an accurate representationmore » of the waterinteractions from the gas to the condensed phase. Likewise, a complete many-body representation of the dipole moment surface is found to be crucial to reproducing the correct intensities of the infrared spectrum of liquid water.« less

Optimal graph search segmentation using arc-weighted graph for simultaneous surface detection of bladder and prostate.

PubMed

Song, Qi; Wu, Xiaodong; Liu, Yunlong; Smith, Mark; Buatti, John; Sonka, Milan

2009-01-01

We present a novel method for globally optimal surface segmentation of multiple mutually interacting objects, incorporating both edge and shape knowledge in a 3-D graph-theoretic approach. Hard surface interacting constraints are enforced in the interacting regions, preserving the geometric relationship of those partially interacting surfaces. The soft smoothness a priori shape compliance is introduced into the energy functional to provide shape guidance. The globally optimal surfaces can be simultaneously achieved by solving a maximum flow problem based on an arc-weighted graph representation. Representing the segmentation problem in an arc-weighted graph, one can incorporate a wider spectrum of constraints into the formulation, thus increasing segmentation accuracy and robustness in volumetric image data. To the best of our knowledge, our method is the first attempt to introduce the arc-weighted graph representation into the graph-searching approach for simultaneous segmentation of multiple partially interacting objects, which admits a globally optimal solution in a low-order polynomial time. Our new approach was applied to the simultaneous surface detection of bladder and prostate. The result was quite encouraging in spite of the low saliency of the bladder and prostate in CT images.

3D chromosome rendering from Hi-C data using virtual reality

NASA Astrophysics Data System (ADS)

Zhu, Yixin; Selvaraj, Siddarth; Weber, Philip; Fang, Jennifer; Schulze, Jürgen P.; Ren, Bing

2015-01-01

Most genome browsers display DNA linearly, using single-dimensional depictions that are useful to examine certain epigenetic mechanisms such as DNA methylation. However, these representations are insufficient to visualize intrachromosomal interactions and relationships between distal genome features. Relationships between DNA regions may be difficult to decipher or missed entirely if those regions are distant in one dimension but could be spatially proximal when mapped to three-dimensional space. For example, the visualization of enhancers folding over genes is only fully expressed in three-dimensional space. Thus, to accurately understand DNA behavior during gene expression, a means to model chromosomes is essential. Using coordinates generated from Hi-C interaction frequency data, we have created interactive 3D models of whole chromosome structures and its respective domains. We have also rendered information on genomic features such as genes, CTCF binding sites, and enhancers. The goal of this article is to present the procedure, findings, and conclusions of our models and renderings.

Multi-view and 3D deformable part models.

PubMed

Pepik, Bojan; Stark, Michael; Gehler, Peter; Schiele, Bernt

2015-11-01

As objects are inherently 3D, they have been modeled in 3D in the early days of computer vision. Due to the ambiguities arising from mapping 2D features to 3D models, 3D object representations have been neglected and 2D feature-based models are the predominant paradigm in object detection nowadays. While such models have achieved outstanding bounding box detection performance, they come with limited expressiveness, as they are clearly limited in their capability of reasoning about 3D shape or viewpoints. In this work, we bring the worlds of 3D and 2D object representations closer, by building an object detector which leverages the expressive power of 3D object representations while at the same time can be robustly matched to image evidence. To that end, we gradually extend the successful deformable part model [1] to include viewpoint information and part-level 3D geometry information, resulting in several different models with different level of expressiveness. We end up with a 3D object model, consisting of multiple object parts represented in 3D and a continuous appearance model. We experimentally verify that our models, while providing richer object hypotheses than the 2D object models, provide consistently better joint object localization and viewpoint estimation than the state-of-the-art multi-view and 3D object detectors on various benchmarks (KITTI [2] , 3D object classes [3] , Pascal3D+ [4] , Pascal VOC 2007 [5] , EPFL multi-view cars[6] ).

Chemotaxis of C. elegans in 3D media: a model for navigation of undulatory microswimmers

NASA Astrophysics Data System (ADS)

Patel, Amar; Bilbao, Alejandro; Rahman, Mizanur; Vanapalli, Siva; Blawzdziewicz, Jerzy

2017-11-01

While the natural environment of C. elegans consists of complex 3D media (e.g., decomposing organic matter and water), most studies of chemotactic behavior of this nematode are limited to 2D. We present a 3D chemotaxis model that combines a realistic geometrical representation of body movements associated with 3D maneuvers, an analysis of mechanical interactions of the nematode body with the surrounding medium to determine nematode trajectories, and a simple memory-function description of chemosensory apparatus that controls the frequency, magnitude, and timing of turning maneuvers. We show that two main chemotaxis strategies of C. elegans moving in 2D, i.e., the biased random walk and gradual turn, are effective also in 3D, provided that 2D turns are supplemented by the roll maneuvers that enable 3D reorientation. Optimal choices of chemosensing and gait-control parameters are discussed; we show that the nematode can maintain efficient chemotaxis in burrowing and swimming by adjusting the undulation frequency alone, without changing the chemotactic component of the body control. Understanding how C. elegans efficiently navigates in 3D media may help in developing self-navigating artificial microswimmers. Supported by NSF Grant No. CBET 1603627.

Acquisition and Neural Network Prediction of 3D Deformable Object Shape Using a Kinect and a Force-Torque Sensor.

PubMed

Tawbe, Bilal; Cretu, Ana-Maria

2017-05-11

The realistic representation of deformations is still an active area of research, especially for deformable objects whose behavior cannot be simply described in terms of elasticity parameters. This paper proposes a data-driven neural-network-based approach for capturing implicitly and predicting the deformations of an object subject to external forces. Visual data, in the form of 3D point clouds gathered by a Kinect sensor, is collected over an object while forces are exerted by means of the probing tip of a force-torque sensor. A novel approach based on neural gas fitting is proposed to describe the particularities of a deformation over the selectively simplified 3D surface of the object, without requiring knowledge of the object material. An alignment procedure, a distance-based clustering, and inspiration from stratified sampling support this process. The resulting representation is denser in the region of the deformation (an average of 96.6% perceptual similarity with the collected data in the deformed area), while still preserving the object's overall shape (86% similarity over the entire surface) and only using on average of 40% of the number of vertices in the mesh. A series of feedforward neural networks is then trained to predict the mapping between the force parameters characterizing the interaction with the object and the change in the object shape, as captured by the fitted neural gas nodes. This series of networks allows for the prediction of the deformation of an object when subject to unknown interactions.

Services Oriented Smart City Platform Based On 3d City Model Visualization

NASA Astrophysics Data System (ADS)

Prandi, F.; Soave, M.; Devigili, F.; Andreolli, M.; De Amicis, R.

2014-04-01

The rapid technological evolution, which is characterizing all the disciplines involved within the wide concept of smart cities, is becoming a key factor to trigger true user-driven innovation. However to fully develop the Smart City concept to a wide geographical target, it is required an infrastructure that allows the integration of heterogeneous geographical information and sensor networks into a common technological ground. In this context 3D city models will play an increasingly important role in our daily lives and become an essential part of the modern city information infrastructure (Spatial Data Infrastructure). The work presented in this paper describes an innovative Services Oriented Architecture software platform aimed at providing smartcities services on top of 3D urban models. 3D city models are the basis of many applications and can became the platform for integrating city information within the Smart-Cites context. In particular the paper will investigate how the efficient visualisation of 3D city models using different levels of detail (LODs) is one of the pivotal technological challenge to support Smart-Cities applications. The goal is to provide to the final user realistic and abstract 3D representations of the urban environment and the possibility to interact with a massive amounts of semantic information contained into the geospatial 3D city model. The proposed solution, using OCG standards and a custom service to provide 3D city models, lets the users to consume the services and interact with the 3D model via Web in a more effective way.

3-D World Modeling For An Autonomous Robot

NASA Astrophysics Data System (ADS)

Goldstein, M.; Pin, F. G.; Weisbin, C. R.

1987-01-01

This paper presents a methodology for a concise representation of the 3-D world model for a mobile robot, using range data. The process starts with the segmentation of the scene into "objects" that are given a unique label, based on principles of range continuity. Then the external surface of each object is partitioned into homogeneous surface patches. Contours of surface patches in 3-D space are identified by estimating the normal and curvature associated with each pixel. The resulting surface patches are then classified as planar, convex or concave. Since the world model uses a volumetric representation for the 3-D environment, planar surfaces are represented by thin volumetric polyhedra. Spherical and cylindrical surfaces are extracted and represented by appropriate volumetric primitives. All other surfaces are represented using the boolean union of spherical volumes (as described in a separate paper by the same authors). The result is a general, concise representation of the external 3-D world, which allows for efficient and robust 3-D object recognition.

Graphics and Flow Visualization of Computer Generated Flow Fields

NASA Technical Reports Server (NTRS)

Kathong, M.; Tiwari, S. N.

1987-01-01

Flow field variables are visualized using color representations described on surfaces that are interpolated from computational grids and transformed to digital images. Techniques for displaying two and three dimensional flow field solutions are addressed. The transformations and the use of an interactive graphics program for CFD flow field solutions, called PLOT3D, which runs on the color graphics IRIS workstation are described. An overview of the IRIS workstation is also described.

3D visualization and stereographic techniques for medical research and education.

PubMed

Rydmark, M; Kling-Petersen, T; Pascher, R; Philip, F

2001-01-01

While computers have been able to work with true 3D models for a long time, the same does not apply to the users in common. Over the years, a number of 3D visualization techniques have been developed to enable a scientist or a student, to see not only a flat representation of an object, but also an approximation of its Z-axis. In addition to the traditional flat image representation of a 3D object, at least four established methodologies exist: Stereo pairs. Using image analysis tools or 3D software, a set of images can be made, each representing the left and the right eye view of an object. Placed next to each other and viewed through a separator, the three dimensionality of an object can be perceived. While this is usually done on still images, tests at Mednet have shown this to work with interactively animated models as well. However, this technique requires some training and experience. Pseudo3D, such as VRML or QuickTime VR, where the interactive manipulation of a 3D model lets the user achieve a sense of the model's true proportions. While this technique works reasonably well, it is not a "true" stereographic visualization technique. Red/Green separation, i.e. "the traditional 3D image" where a red and a green representation of a model is superimposed at an angle corresponding to the viewing angle of the eyes and by using a similar set of eyeglasses, a person can create a mental 3D image. The end result does produce a sense of 3D but the effect is difficult to maintain. Alternating left/right eye systems. These systems (typified by the StereoGraphics CrystalEyes system) let the computer display a "left eye" image followed by a "right eye" image while simultaneously triggering the eyepiece to alternatively make one eye "blind". When run at 60 Hz or higher, the brain will fuse the left/right images together and the user will effectively see a 3D object. Depending on configurations, the alternating systems run at between 50 and 60 Hz, thereby creating a flickering effect, which is strenuous for prolonged use. However, all of the above have one or more drawbacks such as high costs, poor quality and localized use. A fifth system, recently released by Barco Systems, modifies the CrystalEyes system by projecting two superimposed images, using polarized light, with the wave plane of the left image at right angle to that of the right image. By using polarized glasses, each eye will see the appropriate image and true stereographic vision is achieved. While the system requires very expensive hardware, it solves some of the more important problems mentioned above, such as the capacity to use higher frame rates and the ability to display images to a large audience. Mednet has instigated a research project which uses reconstructed models from the central nervous system (human brain and basal ganglia, cortex, dendrites and dendritic spines) and peripheral nervous system (nodes of Ranvier and axoplasmic areas). The aim is to modify the models to fit the different visualization techniques mentioned above and compare a group of users perceived degree of 3D for each technique.

Visual Representations of DNA Replication: Middle Grades Students' Perceptions and Interpretations

NASA Astrophysics Data System (ADS)

Patrick, Michelle D.; Carter, Glenda; Wiebe, Eric N.

2005-09-01

Visual representations play a critical role in the communication of science concepts for scientists and students alike. However, recent research suggests that novice students experience difficulty extracting relevant information from representations. This study examined students' interpretations of visual representations of DNA replication. Each of the four steps of DNA replication included in the instructional presentation was represented as a text slide, a simple 2D graphic, and a rich 3D graphic. Participants were middle grade girls ( n = 21) attending a summer math and science program. Students' eye movements were measured as they viewed the representations. Participants were interviewed following instruction to assess their perceived salient features. Eye tracking fixation counts indicated that the same features (look zones) in the corresponding 2D and 3D graphics had different salience. The interviews revealed that students used different characteristics such as color, shape, and complexity to make sense of the graphics. The results of this study have implications for the design of instructional representations. Since many students have difficulty distinguishing between relevant and irrelevant information, cueing and directing student attention through the instructional representation could allow cognitive resources to be directed to the most relevant material.

3D Geovisualization & Stylization to Manage Comprehensive and Participative Local Urban Plans

NASA Astrophysics Data System (ADS)

Brasebin, M.; Christophe, S.; Jacquinod, F.; Vinesse, A.; Mahon, H.

2016-10-01

3D geo-visualization is more and more used and appreciated to support public participation, and is generally used to present predesigned planned projects. Nevertheless, other participatory processes may benefit from such technology such as the elaboration of urban planning documents. In this article, we present one of the objectives of the PLU++ project: the design of a 3D geo-visualization system that eases the participation concerning local urban plans. Through a pluridisciplinary approach, it aims at covering the different aspects of such a system: the simulation of built configurations to represent regulation information, the efficient stylization of these objects to make people understand their meanings and the interaction between 3D simulation and stylization. The system aims at being adaptive according to the participation context and to the dynamic of the participation. It will offer the possibility to modify simulation results and the rendering styles of the 3D representations to support participation. The proposed 3D rendering styles will be used in a set of practical experiments in order to test and validate some hypothesis from past researches of the project members about 3D simulation, 3D semiotics and knowledge about uses.

Isoantigens of the H-2 and Tla loci of the mouse: interactions affecting their representation on thymocytes.

PubMed

Boyse, E A; Stockert, E; Old, L J

1968-07-01

H-2 and TL isoantigens of the mouse are specified by the closely linked genetic loci H-2 and Tla. A. study of their representation on thymocytes was performed in order to reveal any interactions between the determinant genes or their products affecting the synthesis or disposition of these components of the thymocyte surface. The method employed was quantitative absorption of cytotoxic antibody by viable thymocytes. The phenotypic expression of TL antigens was found to reduce the demonstrable amount of certain H-2 antigens to as little as 34% of the quantity demonstrable on TL- thymocytes. A reduction was observed in all three H-2 types tested, (H-2(b), H-2(a), and H-2(k)). As antigenic modulation (change of TL phenotype from TL+ to TL-, produced by TL antibody) is known to entail a compensatory increase in H-2(D) antigen, it is concluded that the TL phenotype, rather than the Tla genotype, influences the surface representation of H-2 antigens. The two known TL+ phenotypes of thymocytes (TL.2 and TL.1,2,3) depress H-2 equally. The H-2 specificities affected are those determined by the D end of the E-2 locus, which is adjacent to Tla; antigens of the K end, which is distal to Tla, are not depressed. The reduction of demonstrable H-2 antigen on the thymocytes of TL+ x TL- progeny is half that of thymocytes of TL+ x TL+ progeny and the reduction affects equally the products of both H-2 alleles (cis and trans in relation to Tla), indicating that the mechanism of H-2 reduction by TL is extrachromosomal. Whether it involves diminished synthesis of H-2 or steric masking by TL at the cell membrane is unknown, but in either case the reciprocal relation of TL and H-2(D) antigens implies that they probably occupy adjacent positions on thymocytes and that the gene order, H-2(K): H-2(D):Tla is reflected in cell surface structure. Extrachromosomal interaction, apparently involving control of synthesis, occurs also within the TL system of antigens. Thymocytes of TL.2 x TL.1,2,3 progeny express the full homozygous quantity of antigens TL.1 and TL.3 (but not of TL.2), in contrast to the half-quantity present in thymocytes of TL- x TL.1,2,3 progeny. Another example of interaction is implicit in the finding that thymocytes of TL-1,2,3 x TL.1,2,3 progeny have more TL.2 antigen than thymocytes of TL.2 x TL.2 progeny, but in this instance there is nothing to indicate whether the mechanism is chromosomal or extrachromosomal. Thus the quantitative surface representation of at least some H-2 and TL antigens is influenced by the cellular complement of H-2:Tla genes as a whole. Comparison of H-2 heterozygous thymocytes with H-2 homozygous thymocytes in quantitative absorption tests shows (a) more than the expected 50% of each parental-type H-2 antigen on heterozygous cells, and (b) a greater suppression of H-2 by TL in H-2 heterozygotes in comparison with H-2 homozygotes. Both results may be explained on the basis of differences in the density of H-2 antigenic sites and consequent differences in the efficiency of absorption of H-2 antibody. These considerations may be useful in other contexts, e.g. in estimating the representation of Rh antigens on the red cells of human subjects homozygous and heterozygous for Rh components.

3D Printing of Biomolecular Models for Research and Pedagogy

PubMed Central

Da Veiga Beltrame, Eduardo; Tyrwhitt-Drake, James; Roy, Ian; Shalaby, Raed; Suckale, Jakob; Pomeranz Krummel, Daniel

2017-01-01

The construction of physical three-dimensional (3D) models of biomolecules can uniquely contribute to the study of the structure-function relationship. 3D structures are most often perceived using the two-dimensional and exclusively visual medium of the computer screen. Converting digital 3D molecular data into real objects enables information to be perceived through an expanded range of human senses, including direct stereoscopic vision, touch, and interaction. Such tangible models facilitate new insights, enable hypothesis testing, and serve as psychological or sensory anchors for conceptual information about the functions of biomolecules. Recent advances in consumer 3D printing technology enable, for the first time, the cost-effective fabrication of high-quality and scientifically accurate models of biomolecules in a variety of molecular representations. However, the optimization of the virtual model and its printing parameters is difficult and time consuming without detailed guidance. Here, we provide a guide on the digital design and physical fabrication of biomolecule models for research and pedagogy using open source or low-cost software and low-cost 3D printers that use fused filament fabrication technology. PMID:28362403

Inferring segmented dense motion layers using 5D tensor voting.

PubMed

Min, Changki; Medioni, Gérard

2008-09-01

We present a novel local spatiotemporal approach to produce motion segmentation and dense temporal trajectories from an image sequence. A common representation of image sequences is a 3D spatiotemporal volume, (x,y,t), and its corresponding mathematical formalism is the fiber bundle. However, directly enforcing the spatiotemporal smoothness constraint is difficult in the fiber bundle representation. Thus, we convert the representation into a new 5D space (x,y,t,vx,vy) with an additional velocity domain, where each moving object produces a separate 3D smooth layer. The smoothness constraint is now enforced by extracting 3D layers using the tensor voting framework in a single step that solves both correspondence and segmentation simultaneously. Motion segmentation is achieved by identifying those layers, and the dense temporal trajectories are obtained by converting the layers back into the fiber bundle representation. We proceed to address three applications (tracking, mosaic, and 3D reconstruction) that are hard to solve from the video stream directly because of the segmentation and dense matching steps, but become straightforward with our framework. The approach does not make restrictive assumptions about the observed scene or camera motion and is therefore generally applicable. We present results on a number of data sets.

Stereopsis and 3D surface perception by spiking neurons in laminar cortical circuits: a method for converting neural rate models into spiking models.

PubMed

Cao, Yongqiang; Grossberg, Stephen

2012-02-01

A laminar cortical model of stereopsis and 3D surface perception is developed and simulated. The model shows how spiking neurons that interact in hierarchically organized laminar circuits of the visual cortex can generate analog properties of 3D visual percepts. The model describes how monocular and binocular oriented filtering interact with later stages of 3D boundary formation and surface filling-in in the LGN and cortical areas V1, V2, and V4. It proposes how interactions between layers 4, 3B, and 2/3 in V1 and V2 contribute to stereopsis, and how binocular and monocular information combine to form 3D boundary and surface representations. The model suggests how surface-to-boundary feedback from V2 thin stripes to pale stripes helps to explain how computationally complementary boundary and surface formation properties lead to a single consistent percept, eliminate redundant 3D boundaries, and trigger figure-ground perception. The model also shows how false binocular boundary matches may be eliminated by Gestalt grouping properties. In particular, the disparity filter, which helps to solve the correspondence problem by eliminating false matches, is realized using inhibitory interneurons as part of the perceptual grouping process by horizontal connections in layer 2/3 of cortical area V2. The 3D sLAMINART model simulates 3D surface percepts that are consciously seen in 18 psychophysical experiments. These percepts include contrast variations of dichoptic masking and the correspondence problem, the effect of interocular contrast differences on stereoacuity, Panum's limiting case, the Venetian blind illusion, stereopsis with polarity-reversed stereograms, da Vinci stereopsis, and perceptual closure. The model hereby illustrates a general method of unlumping rate-based models that use the membrane equations of neurophysiology into models that use spiking neurons, and which may be embodied in VLSI chips that use spiking neurons to minimize heat production. Copyright © 2011 Elsevier Ltd. All rights reserved.

An open source workflow for 3D printouts of scientific data volumes

NASA Astrophysics Data System (ADS)

Loewe, P.; Klump, J. F.; Wickert, J.; Ludwig, M.; Frigeri, A.

2013-12-01

As the amount of scientific data continues to grow, researchers need new tools to help them visualize complex data. Immersive data-visualisations are helpful, yet fail to provide tactile feedback and sensory feedback on spatial orientation, as provided from tangible objects. The gap in sensory feedback from virtual objects leads to the development of tangible representations of geospatial information to solve real world problems. Examples are animated globes [1], interactive environments like tangible GIS [2], and on demand 3D prints. The production of a tangible representation of a scientific data set is one step in a line of scientific thinking, leading from the physical world into scientific reasoning and back: The process starts with a physical observation, or from a data stream generated by an environmental sensor. This data stream is turned into a geo-referenced data set. This data is turned into a volume representation which is converted into command sequences for the printing device, leading to the creation of a 3D printout. As a last, but crucial step, this new object has to be documented and linked to the associated metadata, and curated in long term repositories to preserve its scientific meaning and context. The workflow to produce tangible 3D data-prints from science data at the German Research Centre for Geosciences (GFZ) was implemented as a software based on the Free and Open Source Geoinformatics tools GRASS GIS and Paraview. The workflow was successfully validated in various application scenarios at GFZ using a RapMan printer to create 3D specimens of elevation models, geological underground models, ice penetrating radar soundings for planetology, and space time stacks for Tsunami model quality assessment. While these first pilot applications have demonstrated the feasibility of the overall approach [3], current research focuses on the provision of the workflow as Software as a Service (SAAS), thematic generalisation of information content and long term curation. [1] http://www.arcscience.com/systemDetails/omniTechnology.html [2] http://video.esri.com/watch/53/landscape-design-with-tangible-gis [3] Löwe et al. (2013), Geophysical Research Abstracts, Vol. 15, EGU2013-1544-1.

Improving Low-dose Cardiac CT Images based on 3D Sparse Representation

NASA Astrophysics Data System (ADS)

Shi, Luyao; Hu, Yining; Chen, Yang; Yin, Xindao; Shu, Huazhong; Luo, Limin; Coatrieux, Jean-Louis

2016-03-01

Cardiac computed tomography (CCT) is a reliable and accurate tool for diagnosis of coronary artery diseases and is also frequently used in surgery guidance. Low-dose scans should be considered in order to alleviate the harm to patients caused by X-ray radiation. However, low dose CT (LDCT) images tend to be degraded by quantum noise and streak artifacts. In order to improve the cardiac LDCT image quality, a 3D sparse representation-based processing (3D SR) is proposed by exploiting the sparsity and regularity of 3D anatomical features in CCT. The proposed method was evaluated by a clinical study of 14 patients. The performance of the proposed method was compared to the 2D spares representation-based processing (2D SR) and the state-of-the-art noise reduction algorithm BM4D. The visual assessment, quantitative assessment and qualitative assessment results show that the proposed approach can lead to effective noise/artifact suppression and detail preservation. Compared to the other two tested methods, 3D SR method can obtain results with image quality most close to the reference standard dose CT (SDCT) images.

Matter in transition

DOE PAGES

Anderson, Lara B.; Gray, James; Raghuram, Nikhil; ...

2016-04-13

In this study, we explore a novel type of transition in certain 6D and 4D quantum field theories, in which the matter content of the theory changes while the gauge group and other parts of the spectrum remain invariant. Such transitions can occur, for example, for SU(6) and SU(7) gauge groups, where matter fields in a three-index antisymmetric representation and the fundamental representation are exchanged in the transition for matter in the two-index antisymmetric representation. These matter transitions are realized by passing through superconformal theories at the transition point. We explore these transitions in dual F-theory and heterotic descriptions, wheremore » a number of novel features arise. For example, in the heterotic description the relevant 6D SU(7) theories are described by bundles on K3 surfaces where the geometry of the K3 is constrained in addition to the bundle structure. On the F-theory side, non-standard representations such as the three-index antisymmetric representation of SU(N) require Weierstrass models that cannot be realized from the standard SU(N) Tate form. We also briefly describe some other situations, with groups such as Sp(3), SO(12), and SU(3), where analogous matter transitions can occur between different representations. For SU(3), in particular, we find a matter transition between adjoint matter and matter in the symmetric representation, giving an explicit Weierstrass model for the F-theory description of the symmetric representation that complements another recent analogous construction.« less

Solutions of the Quantum Yang-Baxter Equations Associated with (1-3/2)-D Representations of SU(sub q) (2)

NASA Technical Reports Server (NTRS)

Yijun, Huang; Guochen, Yu; Hong, Sun

1996-01-01

The solutions of the spectral independent QYBE associated with (1-3/2)-D representations of SU(sub q) (2) are derived, based on the weight conservation and extended Kauffman diagrammatic technique. It is found that there are nonstandard solutions.

Plot Scale Factor Models for Standard Orthographic Views

ERIC Educational Resources Information Center

Osakue, Edward E.

2007-01-01

Geometric modeling provides graphic representations of real or abstract objects. Realistic representation requires three dimensional (3D) attributes since natural objects have three principal dimensions. CAD software gives the user the ability to construct realistic 3D models of objects, but often prints of these models must be generated on two…

Refinement of Representation Theorems for Context-Free Languages

NASA Astrophysics Data System (ADS)

Fujioka, Kaoru

In this paper, we obtain some refinement of representation theorems for context-free languages by using Dyck languages, insertion systems, strictly locally testable languages, and morphisms. For instance, we improved the Chomsky-Schützenberger representation theorem and show that each context-free language L can be represented in the form L = h (D ∩ R), where D is a Dyck language, R is a strictly 3-testable language, and h is a morphism. A similar representation for context-free languages can be obtained, using insertion systems of weight (3, 0) and strictly 4-testable languages.

Review of Zero-D and 1-D Models of Blood Flow in the Cardiovascular System

PubMed Central

2011-01-01

Background Zero-dimensional (lumped parameter) and one dimensional models, based on simplified representations of the components of the cardiovascular system, can contribute strongly to our understanding of circulatory physiology. Zero-D models provide a concise way to evaluate the haemodynamic interactions among the cardiovascular organs, whilst one-D (distributed parameter) models add the facility to represent efficiently the effects of pulse wave transmission in the arterial network at greatly reduced computational expense compared to higher dimensional computational fluid dynamics studies. There is extensive literature on both types of models. Method and Results The purpose of this review article is to summarise published 0D and 1D models of the cardiovascular system, to explore their limitations and range of application, and to provide an indication of the physiological phenomena that can be included in these representations. The review on 0D models collects together in one place a description of the range of models that have been used to describe the various characteristics of cardiovascular response, together with the factors that influence it. Such models generally feature the major components of the system, such as the heart, the heart valves and the vasculature. The models are categorised in terms of the features of the system that they are able to represent, their complexity and range of application: representations of effects including pressure-dependent vessel properties, interaction between the heart chambers, neuro-regulation and auto-regulation are explored. The examination on 1D models covers various methods for the assembly, discretisation and solution of the governing equations, in conjunction with a report of the definition and treatment of boundary conditions. Increasingly, 0D and 1D models are used in multi-scale models, in which their primary role is to provide boundary conditions for sophisticate, and often patient-specific, 2D and 3D models, and this application is also addressed. As an example of 0D cardiovascular modelling, a small selection of simple models have been represented in the CellML mark-up language and uploaded to the CellML model repository http://models.cellml.org/. They are freely available to the research and education communities. Conclusion Each published cardiovascular model has merit for particular applications. This review categorises 0D and 1D models, highlights their advantages and disadvantages, and thus provides guidance on the selection of models to assist various cardiovascular modelling studies. It also identifies directions for further development, as well as current challenges in the wider use of these models including service to represent boundary conditions for local 3D models and translation to clinical application. PMID:21521508

Seeing music: The perception of melodic 'ups and downs' modulates the spatial processing of visual stimuli.

PubMed

Romero-Rivas, Carlos; Vera-Constán, Fátima; Rodríguez-Cuadrado, Sara; Puigcerver, Laura; Fernández-Prieto, Irune; Navarra, Jordi

2018-05-10

Musical melodies have "peaks" and "valleys". Although the vertical component of pitch and music is well-known, the mechanisms underlying its mental representation still remain elusive. We show evidence regarding the importance of previous experience with melodies for crossmodal interactions to emerge. The impact of these crossmodal interactions on other perceptual and attentional processes was also studied. Melodies including two tones with different frequency (e.g., E4 and D3) were repeatedly presented during the study. These melodies could either generate strong predictions (e.g., E4-D3-E4-D3-E4-[D3]) or not (e.g., E4-D3-E4-E4-D3-[?]). After the presentation of each melody, the participants had to judge the colour of a visual stimulus that appeared in a position that was, according to the traditional vertical connotations of pitch, either congruent (e.g., high-low-high-low-[up]), incongruent (high-low-high-low-[down]) or unpredicted with respect to the melody. Behavioural and electroencephalographic responses to the visual stimuli were obtained. Congruent visual stimuli elicited faster responses at the end of the experiment than at the beginning. Additionally, incongruent visual stimuli that broke the spatial prediction generated by the melody elicited larger P3b amplitudes (reflecting 'surprise' responses). Our results suggest that the passive (but repeated) exposure to melodies elicits spatial predictions that modulate the processing of other sensory events. Copyright © 2018 Elsevier Ltd. All rights reserved.

Development of visual 3D virtual environment for control software

NASA Technical Reports Server (NTRS)

Hirose, Michitaka; Myoi, Takeshi; Amari, Haruo; Inamura, Kohei; Stark, Lawrence

1991-01-01

Virtual environments for software visualization may enable complex programs to be created and maintained. A typical application might be for control of regional electric power systems. As these encompass broader computer networks than ever, construction of such systems becomes very difficult. Conventional text-oriented environments are useful in programming individual processors. However, they are obviously insufficient to program a large and complicated system, that includes large numbers of computers connected to each other; such programming is called 'programming in the large.' As a solution for this problem, the authors are developing a graphic programming environment wherein one can visualize complicated software in virtual 3D world. One of the major features of the environment is the 3D representation of concurrent process. 3D representation is used to supply both network-wide interprocess programming capability (capability for 'programming in the large') and real-time programming capability. The authors' idea is to fuse both the block diagram (which is useful to check relationship among large number of processes or processors) and the time chart (which is useful to check precise timing for synchronization) into a single 3D space. The 3D representation gives us a capability for direct and intuitive planning or understanding of complicated relationship among many concurrent processes. To realize the 3D representation, a technology to enable easy handling of virtual 3D object is a definite necessity. Using a stereo display system and a gesture input device (VPL DataGlove), our prototype of the virtual workstation has been implemented. The workstation can supply the 'sensation' of the virtual 3D space to a programmer. Software for the 3D programming environment is implemented on the workstation. According to preliminary assessments, a 50 percent reduction of programming effort is achieved by using the virtual 3D environment. The authors expect that the 3D environment has considerable potential in the field of software engineering.

Interrogation of patient data delivered to the operating theatre during hepato-pancreatic surgery using high-performance computing.

PubMed

John, Nigel W; McCloy, Rory F; Herrman, Simone

2004-01-01

The Op3D visualization system allows, for the first time, a surgeon in the operating theatre to interrogate patient-specific medical data sets rendered in three dimensions using high-performance computing. The hypothesis of this research is that the success rate of hepato-pancreatic surgical resections can be improved by replacing the light box with an interactive 3D representation of the medical data in the operating theatre. A laptop serves as the client computer and an easy-to-use interface has been developed for the surgeon to interact with and interrogate the patient data. To date, 16 patients have had 3D reconstructions of their DICOM data sets, including preoperative interrogation and planning of surgery. Interrogation of the 3D images live in theatre and comparison with the surgeons' operative findings (including intraoperative ultrasound) led to the operation being abandoned in 25% of cases, adoption of an alternative surgical approach in 25% of cases, and helpful image guidance for successful resection in 50% of cases. The clinical value of the latest generation of scanners and digital imaging techniques cannot be realized unless appropriate dissemination of the images takes place. This project has succeeded in translating the image technology into a user-friendly form and delivers 3D reconstructions of patient-specific data to the "sharp end"-the surgeon undertaking the tumor resection in theatre, in a manner that allows interaction and interpretation. More time interrogating the 3D data sets preoperatively would help reduce the incidence of abandoned operations-this is part of the surgeons' learning curve. We have developed one of the first practical applications to benefit from remote visualization, and certainly the first medical visualization application of this kind.

Interdisciplinary Data Fusion for Diachronic 3d Reconstruction of Historic Sites

NASA Astrophysics Data System (ADS)

Micoli, L. L.; Gonizzi Barsanti, S.; Guidi, G.

2017-02-01

In recent decades, 3D reconstruction has progressively become a tool to show archaeological and architectural monuments in their current state, presumed past aspect and to predict their future evolution. The 3D representations trough time can be useful in order to study and preserve the memory of Cultural Heritage and to plan maintenance and promotion of the historical sites. This paper represent a case study, at architectonic and urbanistic scale, based on methodological approach for CH time-varying representations proposed by JPI-CH European Project called Cultural Heritage Through Time (CHT2). The work is focused on the area of Milan Roman circus, relatively to which was conducted both a thorough philological research based on several sources and a 3D survey campaign of still accessible remains, aiming at obtaining the monumental representation of the area in 3 different ages.

A two-level generative model for cloth representation and shape from shading.

PubMed

Han, Feng; Zhu, Song-Chun

2007-07-01

In this paper, we present a two-level generative model for representing the images and surface depth maps of drapery and clothes. The upper level consists of a number of folds which will generate the high contrast (ridge) areas with a dictionary of shading primitives (for 2D images) and fold primitives (for 3D depth maps). These primitives are represented in parametric forms and are learned in a supervised learning phase using 3D surfaces of clothes acquired through photometric stereo. The lower level consists of the remaining flat areas which fill between the folds with a smoothness prior (Markov random field). We show that the classical ill-posed problem-shape from shading (SFS) can be much improved by this two-level model for its reduced dimensionality and incorporation of middle-level visual knowledge, i.e., the dictionary of primitives. Given an input image, we first infer the folds and compute a sketch graph using a sketch pursuit algorithm as in the primal sketch [10], [11]. The 3D folds are estimated by parameter fitting using the fold dictionary and they form the "skeleton" of the drapery/cloth surfaces. Then, the lower level is computed by conventional SFS method using the fold areas as boundary conditions. The two levels interact at the final stage by optimizing a joint Bayesian posterior probability on the depth map. We show a number of experiments which demonstrate more robust results in comparison with state-of-the-art work. In a broader scope, our representation can be viewed as a two-level inhomogeneous MRF model which is applicable to general shape-from-X problems. Our study is an attempt to revisit Marr's idea [23] of computing the 2(1/2)D sketch from primal sketch. In a companion paper [2], we study shape from stereo based on a similar two-level generative sketch representation.

Separating the Representation from the Science: Training Students in Comprehending 3D Diagrams

NASA Astrophysics Data System (ADS)

Bemis, K. G.; Silver, D.; Chiang, J.; Halpern, D.; Oh, K.; Tremaine, M.

2011-12-01

Studies of students taking first year geology and earth science courses at universities find that a remarkable number of them are confused by the three-dimensional representations used to explain the science [1]. Comprehension of these 3D representations has been found to be related to an individual's spatial ability [2]. A variety of interactive programs and animations have been created to help explain the diagrams to beginning students [3, 4]. This work has demonstrated comprehension improvement and removed a gender gap between male (high spatial) and female (low spatial) students [5]. However, not much research has examined what makes the 3D diagrams so hard to understand or attempted to build a theory for creating training designed to remove these difficulties. Our work has separated the science labeling and comprehension of the diagrams from the visualizations to examine how individuals mentally see the visualizations alone. In particular, we asked subjects to create a cross-sectional drawing of the internal structure of various 3D diagrams. We found that viewing planes (the coordinate system the designer applies to the diagram), cutting planes (the planes formed by the requested cross sections) and visual property planes (the planes formed by the prominent features of the diagram, e.g., a layer at an angle of 30 degrees to the top surface of the diagram) that deviated from a Cartesian coordinate system imposed by the viewer caused significant problems for subjects, in part because these deviations forced them to mentally re-orient their viewing perspective. Problems with deviations in all three types of plane were significantly harder than those deviating on one or two planes. Our results suggest training that does not focus on showing how the components of various 3D geologic formations are put together but rather training that guides students in re-orienting themselves to deviations that differ from their right-angle view of the world, e.g., by showing how a particular 3D visualization evolves from their Cartesian representation of the world. 1. Y. Kali and N. Orion, Spatial abilities of high-school students in the perception of geologic structures, Journal of Research in Science Teaching, 33, 4, 369-391, 1996. 2. A. Black, Spatial ability and earth science conceptual understanding, Journal of Geoscience Education, 53, 402-414, 2005 3. S. A. Sorby and B. J. Baartmans, The development and assessment of a course for enhancing the 3-D spatial visualization skills of first-year engineering students, Journal of Engineering Education Washington, 89, 301-308, 2000. 4. Y. Kali, N. Orion and E. Mazor, Software for assisting high-school students in the spatial perception of geological structures, Journal of Geoscience Education,45, 10-20, 1997. 5. D. Ben-Chaim. G. Lappan, and R. T. Houang, The effect of instruction on spatial visualization skills of middle school boys and girls, American Educational Research Journal, 25, 1, 51-71, 1988.

Forest representation of vessels in cone-beam computed tomographic angiography.

PubMed

Chen, Zikuan; Ning, Ruola

2005-01-01

Cone-beam computed tomographic angiography (CBCTA) provides a fast three-dimensional (3D) vascular imaging modality, aiming at digitally representing the spatial vascular structure in an angiographic volume. Due to the finite coverage of cone-beam scan, as well as the volume cropping in volumetric image processing, an angiographic volume may fail to contain a whole vascular tree, but rather consist of a multitude of vessel segments or subtrees. As such, it is convenient to represent multitudinal components by a forest. The vessel tracking issue then becomes component characterization/identification in the forest. The forest representation brings several conveniences for vessel tracking: (1) to sort and count the vessels in an angiographic volume, for example, according to spatial occupancy and skeleton pathlength; (2) to single out a vessel and perform in situ 3D measurement and 3D visualization in the support space; (3) to delineate individual vessels from the original angiographic volume; and (4) to cull the forest by getting rid of non-vessels and small vessels. A 3D skeletonization is used to generate component skeletons. For tree construction from skeletons, we suggest a pathlength-based procedure, which lifts the restrictions of unit-width skeleton and root determination. We experimentally demonstrate the forest representation of a dog's carotid arteries in a CBCTA system. In principle, the forest representation is useful for managing vessels in both 2D angiographic images and 3D angiographic volumes.

Visualizing 3D data obtained from microscopy on the Internet.

PubMed

Pittet, J J; Henn, C; Engel, A; Heymann, J B

1999-01-01

The Internet is a powerful communication medium increasingly exploited by business and science alike, especially in structural biology and bioinformatics. The traditional presentation of static two-dimensional images of real-world objects on the limited medium of paper can now be shown interactively in three dimensions. Many facets of this new capability have already been developed, particularly in the form of VRML (virtual reality modeling language), but there is a need to extend this capability for visualizing scientific data. Here we introduce a real-time isosurfacing node for VRML, based on the marching cube approach, allowing interactive isosurfacing. A second node does three-dimensional (3D) texture-based volume-rendering for a variety of representations. The use of computers in the microscopic and structural biosciences is extensive, and many scientific file formats exist. To overcome the problem of accessing such data from VRML and other tools, we implemented extensions to SGI's IFL (image format library). IFL is a file format abstraction layer defining communication between a program and a data file. These technologies are developed in support of the BioImage project, aiming to establish a database prototype for multidimensional microscopic data with the ability to view the data within a 3D interactive environment. Copyright 1999 Academic Press.

Size-Sensitive Perceptual Representations Underlie Visual and Haptic Object Recognition

PubMed Central

Craddock, Matt; Lawson, Rebecca

2009-01-01

A variety of similarities between visual and haptic object recognition suggests that the two modalities may share common representations. However, it is unclear whether such common representations preserve low-level perceptual features or whether transfer between vision and haptics is mediated by high-level, abstract representations. Two experiments used a sequential shape-matching task to examine the effects of size changes on unimodal and crossmodal visual and haptic object recognition. Participants felt or saw 3D plastic models of familiar objects. The two objects presented on a trial were either the same size or different sizes and were the same shape or different but similar shapes. Participants were told to ignore size changes and to match on shape alone. In Experiment 1, size changes on same-shape trials impaired performance similarly for both visual-to-visual and haptic-to-haptic shape matching. In Experiment 2, size changes impaired performance on both visual-to-haptic and haptic-to-visual shape matching and there was no interaction between the cost of size changes and direction of transfer. Together the unimodal and crossmodal matching results suggest that the same, size-specific perceptual representations underlie both visual and haptic object recognition, and indicate that crossmodal memory for objects must be at least partly based on common perceptual representations. PMID:19956685

Understanding Human Perception of Building Categories in Virtual 3d Cities - a User Study

NASA Astrophysics Data System (ADS)

Tutzauer, P.; Becker, S.; Niese, T.; Deussen, O.; Fritsch, D.

2016-06-01

Virtual 3D cities are becoming increasingly important as a means of visually communicating diverse urban-related information. To get a deeper understanding of a human's cognitive experience of virtual 3D cities, this paper presents a user study on the human ability to perceive building categories (e.g. residential home, office building, building with shops etc.) from geometric 3D building representations. The study reveals various dependencies between geometric properties of the 3D representations and the perceptibility of the building categories. Knowledge about which geometries are relevant, helpful or obstructive for perceiving a specific building category is derived. The importance and usability of such knowledge is demonstrated based on a perception-guided 3D building abstraction process.

An upwind method for the solution of the 3D Euler and Navier-Stokes equations on adaptively refined meshes

NASA Astrophysics Data System (ADS)

Aftosmis, Michael J.

1992-10-01

A new node based upwind scheme for the solution of the 3D Navier-Stokes equations on adaptively refined meshes is presented. The method uses a second-order upwind TVD scheme to integrate the convective terms, and discretizes the viscous terms with a new compact central difference technique. Grid adaptation is achieved through directional division of hexahedral cells in response to evolving features as the solution converges. The method is advanced in time with a multistage Runge-Kutta time stepping scheme. Two- and three-dimensional examples establish the accuracy of the inviscid and viscous discretization. These investigations highlight the ability of the method to produce crisp shocks, while accurately and economically resolving viscous layers. The representation of these and other structures is shown to be comparable to that obtained by structured methods. Further 3D examples demonstrate the ability of the adaptive algorithm to effectively locate and resolve multiple scale features in complex 3D flows with many interacting, viscous, and inviscid structures.

Immersive Visual Analytics for Transformative Neutron Scattering Science

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steed, Chad A; Daniel, Jamison R; Drouhard, Margaret

The ORNL Spallation Neutron Source (SNS) provides the most intense pulsed neutron beams in the world for scientific research and development across a broad range of disciplines. SNS experiments produce large volumes of complex data that are analyzed by scientists with varying degrees of experience using 3D visualization and analysis systems. However, it is notoriously difficult to achieve proficiency with 3D visualizations. Because 3D representations are key to understanding the neutron scattering data, scientists are unable to analyze their data in a timely fashion resulting in inefficient use of the limited and expensive SNS beam time. We believe a moremore » intuitive interface for exploring neutron scattering data can be created by combining immersive virtual reality technology with high performance data analytics and human interaction. In this paper, we present our initial investigations of immersive visualization concepts as well as our vision for an immersive visual analytics framework that could lower the barriers to 3D exploratory data analysis of neutron scattering data at the SNS.« less

Group-sparse representation with dictionary learning for medical image denoising and fusion.

PubMed

Li, Shutao; Yin, Haitao; Fang, Leyuan

2012-12-01

Recently, sparse representation has attracted a lot of interest in various areas. However, the standard sparse representation does not consider the intrinsic structure, i.e., the nonzero elements occur in clusters, called group sparsity. Furthermore, there is no dictionary learning method for group sparse representation considering the geometrical structure of space spanned by atoms. In this paper, we propose a novel dictionary learning method, called Dictionary Learning with Group Sparsity and Graph Regularization (DL-GSGR). First, the geometrical structure of atoms is modeled as the graph regularization. Then, combining group sparsity and graph regularization, the DL-GSGR is presented, which is solved by alternating the group sparse coding and dictionary updating. In this way, the group coherence of learned dictionary can be enforced small enough such that any signal can be group sparse coded effectively. Finally, group sparse representation with DL-GSGR is applied to 3-D medical image denoising and image fusion. Specifically, in 3-D medical image denoising, a 3-D processing mechanism (using the similarity among nearby slices) and temporal regularization (to perverse the correlations across nearby slices) are exploited. The experimental results on 3-D image denoising and image fusion demonstrate the superiority of our proposed denoising and fusion approaches.

Profile of students' comprehension of 3D molecule representation and its interconversion on chirality

NASA Astrophysics Data System (ADS)

Setyarini, M.; Liliasari, Kadarohman, Asep; Martoprawiro, Muhamad A.

2016-02-01

This study aims at describing (1) students' level comprehension; (2) factors causing difficulties to 3D comprehend molecule representation and its interconversion on chirality. Data was collected using multiple-choice test consisting of eight questions. The participants were required to give answers along with their reasoning. The test was developed based on the indicators of concept comprehension. The study was conducted to 161 college students enrolled in stereochemistry topic in the odd semester (2014/2015) from two LPTK (teacher training institutes) in Bandar Lampung and Gorontalo, and one public university in Bandung. The result indicates that college students' level of comprehension towards 3D molecule representations and its inter-conversion was 5% on high level, 22 % on the moderate level, and 73 % on the low level. The dominant factors identified as the cause of difficulties to comprehend 3D molecule representation and its interconversion were (i) the lack of spatial awareness, (ii) violation of absolute configuration determination rules, (iii) imprecise placement of observers, (iv) the lack of rotation operation, and (v) the lack of understanding of correlation between the representations. This study recommends that learning show more rigorous spatial awareness training tasks accompanied using dynamic visualization media of molecules associated. Also students learned using static molecular models can help them overcome their difficulties encountered.

Ray-based approach to integrated 3D visual communication

NASA Astrophysics Data System (ADS)

Naemura, Takeshi; Harashima, Hiroshi

2001-02-01

For a high sense of reality in the next-generation communications, it is very important to realize three-dimensional (3D) spatial media, instead of existing 2D image media. In order to comprehensively deal with a variety of 3D visual data formats, the authors first introduce the concept of "Integrated 3D Visual Communication," which reflects the necessity of developing a neutral representation method independent of input/output systems. Then, the following discussions are concentrated on the ray-based approach to this concept, in which any visual sensation is considered to be derived from a set of light rays. This approach is a simple and straightforward to the problem of how to represent 3D space, which is an issue shared by various fields including 3D image communications, computer graphics, and virtual reality. This paper mainly presents the several developments in this approach, including some efficient methods of representing ray data, a real-time video-based rendering system, an interactive rendering system based on the integral photography, a concept of virtual object surface for the compression of tremendous amount of data, and a light ray capturing system using a telecentric lens. Experimental results demonstrate the effectiveness of the proposed techniques.

Structure-based Understanding of Binding Affinity and Mode ...

EPA Pesticide Factsheets

The flexible hydrophobic ligand binding pocket (LBP) of estrogen receptor α (ERα) allows the binding of a wide variety of endocrine disruptors. Upon ligand binding, the LBP reshapes around the contours of the ligand and stabilizes the complex by complementary hydrophobic interactions and specific hydrogen bonds with the ligand. Here we present a framework for quantitative analysis of the steric and electronic features of the human ERα-ligand complex using three dimensional (3D) protein-ligand interaction description combined with 3D-QSAR approach. An empirical hydrophobicity density field is applied to account for hydrophobic contacts of ligand within the LBP. The obtained 3D-QSAR model revealed that hydrophobic contacts primarily determine binding affinity and govern binding mode with hydrogen bonds. Several residues of the LBP appear to be quite flexible and adopt a spectrum of conformations in various ERα-ligand complexes, in particular His524. The 3D-QSAR was combined with molecular docking based on three receptor conformations to accommodate receptor flexibility. The model indicates that the dynamic character of the LBP allows accommodation and stable binding of structurally diverse ligands, and proper representation of the protein flexibility is critical for reasonable description of binding of the ligands. Our results provide a quantitative and mechanistic understanding of binding affinity and mode of ERα agonists and antagonists that may be applicab

Perceptualization of geometry using intelligent haptic and visual sensing

NASA Astrophysics Data System (ADS)

Weng, Jianguang; Zhang, Hui

2013-01-01

We present a set of paradigms for investigating geometric structures using haptic and visual sensing. Our principal test cases include smoothly embedded geometry shapes such as knotted curves embedded in 3D and knotted surfaces in 4D, that contain massive intersections when projected to one lower dimension. One can exploit a touch-responsive 3D interactive probe to haptically override this conflicting evidence in the rendered images, by forcing continuity in the haptic representation to emphasize the true topology. In our work, we exploited a predictive haptic guidance, a "computer-simulated hand" with supplementary force suggestion, to support intelligent exploration of geometry shapes that will smooth and maximize the probability of recognition. The cognitive load can be reduced further when enabling an attention-driven visual sensing during the haptic exploration. Our methods combine to reveal the full richness of the haptic exploration of geometric structures, and to overcome the limitations of traditional 4D visualization.

Biologically Inspired Model for Inference of 3D Shape from Texture

PubMed Central

Gomez, Olman; Neumann, Heiko

2016-01-01

A biologically inspired model architecture for inferring 3D shape from texture is proposed. The model is hierarchically organized into modules roughly corresponding to visual cortical areas in the ventral stream. Initial orientation selective filtering decomposes the input into low-level orientation and spatial frequency representations. Grouping of spatially anisotropic orientation responses builds sketch-like representations of surface shape. Gradients in orientation fields and subsequent integration infers local surface geometry and globally consistent 3D depth. From the distributions in orientation responses summed in frequency, an estimate of the tilt and slant of the local surface can be obtained. The model suggests how 3D shape can be inferred from texture patterns and their image appearance in a hierarchically organized processing cascade along the cortical ventral stream. The proposed model integrates oriented texture gradient information that is encoded in distributed maps of orientation-frequency representations. The texture energy gradient information is defined by changes in the grouped summed normalized orientation-frequency response activity extracted from the textured object image. This activity is integrated by directed fields to generate a 3D shape representation of a complex object with depth ordering proportional to the fields output, with higher activity denoting larger distance in relative depth away from the viewer. PMID:27649387

Improving Low-dose Cardiac CT Images based on 3D Sparse Representation

PubMed Central

Shi, Luyao; Hu, Yining; Chen, Yang; Yin, Xindao; Shu, Huazhong; Luo, Limin; Coatrieux, Jean-Louis

2016-01-01

Cardiac computed tomography (CCT) is a reliable and accurate tool for diagnosis of coronary artery diseases and is also frequently used in surgery guidance. Low-dose scans should be considered in order to alleviate the harm to patients caused by X-ray radiation. However, low dose CT (LDCT) images tend to be degraded by quantum noise and streak artifacts. In order to improve the cardiac LDCT image quality, a 3D sparse representation-based processing (3D SR) is proposed by exploiting the sparsity and regularity of 3D anatomical features in CCT. The proposed method was evaluated by a clinical study of 14 patients. The performance of the proposed method was compared to the 2D spares representation-based processing (2D SR) and the state-of-the-art noise reduction algorithm BM4D. The visual assessment, quantitative assessment and qualitative assessment results show that the proposed approach can lead to effective noise/artifact suppression and detail preservation. Compared to the other two tested methods, 3D SR method can obtain results with image quality most close to the reference standard dose CT (SDCT) images. PMID:26980176

Surveying Medieval Archaeology: a New Form for Harris Paradigm Linking Photogrammetry and Temporal Relations

NASA Astrophysics Data System (ADS)

Drap, P.; Papini, O.; Pruno, E.; Nucciotti, M.; Vannini, G.

2017-02-01

The paper presents some reflexions concerning an interdisciplinary project between Medieval Archaeologists from the University of Florence (Italy) and ICT researchers from CNRS LSIS of Marseille (France), aiming towards a connection between 3D spatial representation and archaeological knowledge. It is well known that Laser Scanner, Photogrammetry and Computer Vision are very attractive tools for archaeologists, although the integration of representation of space and representation of archaeological time has not yet found a methodological standard of reference. We try to develop an integrated system for archaeological 3D survey and all other types of archaeological data and knowledge through integrating observable (material) and non-graphic (interpretive) data. Survey plays a central role, since it is both a metric representation of the archaeological site and, to a wider extent, an interpretation of it (being also a common basis for communication between the 2 teams). More specifically 3D survey is crucial, allowing archaeologists to connect actual spatial assets to the stratigraphic formation processes (i.e. to the archaeological time) and to translate spatial observations into historical interpretation of the site. We propose a common formalism for describing photogrammetrical survey and archaeological knowledge stemming from ontologies: Indeed, ontologies are fully used to model and store 3D data and archaeological knowledge. Xe equip this formalism with a qualitative representation of time. Stratigraphic analyses (both of excavated deposits and of upstanding structures) are closely related to E. C. Harris theory of "Stratigraphic Unit" ("US" from now on). Every US is connected to the others by geometric, topological and, eventually, temporal links, and are recorded by the 3D photogrammetric survey. However, the limitations of the Harris Matrix approach lead to use another representation formalism for stratigraphic relationships, namely Qualitative Constraints Networks (QCN) successfully used in the domain of knowledge representation and reasoning in artificial intelligence for representing temporal relations.

Real-Time Simulation

NASA Technical Reports Server (NTRS)

1997-01-01

Coryphaeus Software, founded in 1989 by former NASA electronic engineer Steve Lakowske, creates real-time 3D software. Designer's Workbench, the company flagship product, is a modeling and simulation tool for the development of both static and dynamic 3D databases. Other products soon followed. Activation, specifically designed for game developers, allows developers to play and test the 3D games before they commit to a target platform. Game publishers can shorten development time and prove the "playability" of the title, maximizing their chances of introducing a smash hit. Another product, EasyT, lets users create massive, realistic representation of Earth terrains that can be viewed and traversed in real time. Finally, EasyScene software control the actions among interactive objects within a virtual world. Coryphaeus products are used on Silican Graphics workstation and supercomputers to simulate real-world performance in synthetic environments. Customers include aerospace, aviation, architectural and engineering firms, game developers, and the entertainment industry.

A high-level 3D visualization API for Java and ImageJ.

PubMed

Schmid, Benjamin; Schindelin, Johannes; Cardona, Albert; Longair, Mark; Heisenberg, Martin

2010-05-21

Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de.

Intumescent Reaction Mechanisms: An Analytic Model.

DTIC Science & Technology

1983-05-01

or amide (such as urea , melamine , dicyan- diamide, urea formaldehyde , etc.) is the release of nonflammable gases (CO2, E . etc.) that physically...mo)/dT Versus I/T (Polysulfide) 34 5-3 Fourier Series Representation of TGA Data for Polysulfide, DIP-30, EPON Resin , and Borax 40 5-4 Fourier Series...Representation of TGA Data for Part A, Part B, and Part A+B 41 5-S Fourier Series Representation of d(m/m )/dT for Polysul- fide, DIP-30, EPOI Resin

Increasing situation awareness of the CBRNE robot operators

NASA Astrophysics Data System (ADS)

Jasiobedzki, Piotr; Ng, Ho-Kong; Bondy, Michel; McDiarmid, Carl H.

2010-04-01

Situational awareness of CBRN robot operators is quite limited, as they rely on images and measurements from on-board detectors. This paper describes a novel framework that enables a uniform and intuitive access to live and recent data via 2D and 3D representations of visited sites. These representations are created automatically and augmented with images, models and CBRNE measurements. This framework has been developed for CBRNE Crime Scene Modeler (C2SM), a mobile CBRNE mapping system. The system creates representations (2D floor plans and 3D photorealistic models) of the visited sites, which are then automatically augmented with CBRNE detector measurements. The data stored in a database is accessed using a variety of user interfaces providing different perspectives and increasing operators' situational awareness.

A multimodal biometric authentication system based on 2D and 3D palmprint features

NASA Astrophysics Data System (ADS)

Aggithaya, Vivek K.; Zhang, David; Luo, Nan

2008-03-01

This paper presents a new personal authentication system that simultaneously exploits 2D and 3D palmprint features. Here, we aim to improve the accuracy and robustness of existing palmprint authentication systems using 3D palmprint features. The proposed system uses an active stereo technique, structured light, to capture 3D image or range data of the palm and a registered intensity image simultaneously. The surface curvature based method is employed to extract features from 3D palmprint and Gabor feature based competitive coding scheme is used for 2D representation. We individually analyze these representations and attempt to combine them with score level fusion technique. Our experiments on a database of 108 subjects achieve significant improvement in performance (Equal Error Rate) with the integration of 3D features as compared to the case when 2D palmprint features alone are employed.

A 2.5-D Representation of the Human Hand

ERIC Educational Resources Information Center

Longo, Matthew R.; Haggard, Patrick

2012-01-01

Primary somatosensory maps in the brain represent the body as a discontinuous, fragmented set of two-dimensional (2-D) skin regions. We nevertheless experience our body as a coherent three-dimensional (3-D) volumetric object. The links between these different aspects of body representation, however, remain poorly understood. Perceiving the body's…

Model Manipulation and Learning: Fostering Representational Competence with Virtual and Concrete Models

ERIC Educational Resources Information Center

Stull, Andrew T.; Hegarty, Mary

2016-01-01

This study investigated the development of representational competence among organic chemistry students by using 3D (concrete and virtual) models as aids for teaching students to translate between multiple 2D diagrams. In 2 experiments, students translated between different diagrams of molecules and received verbal feedback in 1 of the following 3…

Multiview 3D sensing and analysis for high quality point cloud reconstruction

NASA Astrophysics Data System (ADS)

Satnik, Andrej; Izquierdo, Ebroul; Orjesek, Richard

2018-04-01

Multiview 3D reconstruction techniques enable digital reconstruction of 3D objects from the real world by fusing different viewpoints of the same object into a single 3D representation. This process is by no means trivial and the acquisition of high quality point cloud representations of dynamic 3D objects is still an open problem. In this paper, an approach for high fidelity 3D point cloud generation using low cost 3D sensing hardware is presented. The proposed approach runs in an efficient low-cost hardware setting based on several Kinect v2 scanners connected to a single PC. It performs autocalibration and runs in real-time exploiting an efficient composition of several filtering methods including Radius Outlier Removal (ROR), Weighted Median filter (WM) and Weighted Inter-Frame Average filtering (WIFA). The performance of the proposed method has been demonstrated through efficient acquisition of dense 3D point clouds of moving objects.

Energy-consistent small-core pseudopotentials for 3d-transition metals adapted to quantum Monte Carlo calculations.

PubMed

Burkatzki, M; Filippi, Claudia; Dolg, M

2008-10-28

We extend our recently published set of energy-consistent scalar-relativistic Hartree-Fock pseudopotentials by the 3d-transition metal elements, scandium through zinc. The pseudopotentials do not exhibit a singularity at the nucleus and are therefore suitable for quantum Monte Carlo (QMC) calculations. The pseudopotentials and the accompanying basis sets (VnZ with n=T,Q) are given in standard Gaussian representation and their parameter sets are presented. Coupled cluster, configuration interaction, and QMC studies are carried out for the scandium and titanium atoms and their oxides, demonstrating the good performance of the pseudopotentials. Even though the choice of pseudopotential form is motivated by QMC, these pseudopotentials can also be employed in other quantum chemical approaches.

A web-based instruction module for interpretation of craniofacial cone beam CT anatomy.

PubMed

Hassan, B A; Jacobs, R; Scarfe, W C; Al-Rawi, W T

2007-09-01

To develop a web-based module for learner instruction in the interpretation and recognition of osseous anatomy on craniofacial cone-beam CT (CBCT) images. Volumetric datasets from three CBCT systems were acquired (i-CAT, NewTom 3G and AccuiTomo FPD) for various subjects using equipment-specific scanning protocols. The datasets were processed using multiple software to provide two-dimensional (2D) multiplanar reformatted (MPR) images (e.g. sagittal, coronal and axial) and three-dimensional (3D) visual representations (e.g. maximum intensity projection, minimum intensity projection, ray sum, surface and volume rendering). Distinct didactic modules which illustrate the principles of CBCT systems, guided navigation of the volumetric dataset, and anatomic correlation of 3D models and 2D MPR graphics were developed using a hybrid combination of web authoring and image analysis techniques. Interactive web multimedia instruction was facilitated by the use of dynamic highlighting and labelling, and rendered video illustrations, supplemented with didactic textual material. HTML coding and Java scripting were heavily implemented for the blending of the educational modules. An interactive, multimedia educational tool for visualizing the morphology and interrelationships of osseous craniofacial anatomy, as depicted on CBCT MPR and 3D images, was designed and implemented. The present design of a web-based instruction module may assist radiologists and clinicians in learning how to recognize and interpret the craniofacial anatomy of CBCT based images more efficiently.

A novel approach for introducing cloud spatial structure into cloud radiative transfer parameterizations

NASA Astrophysics Data System (ADS)

Huang, Dong; Liu, Yangang

2014-12-01

Subgrid-scale variability is one of the main reasons why parameterizations are needed in large-scale models. Although some parameterizations started to address the issue of subgrid variability by introducing a subgrid probability distribution function for relevant quantities, the spatial structure has been typically ignored and thus the subgrid-scale interactions cannot be accounted for physically. Here we present a new statistical-physics-like approach whereby the spatial autocorrelation function can be used to physically capture the net effects of subgrid cloud interaction with radiation. The new approach is able to faithfully reproduce the Monte Carlo 3D simulation results with several orders less computational cost, allowing for more realistic representation of cloud radiation interactions in large-scale models.

Issues in Interaction Language Specification and Representation.

DTIC Science & Technology

1983-11-01

of Dialogues for Human-Computer Interfaces," to be submitted for publication (1983). IHEINL75] Heindel, L. and J. Roberto . "LANG-PAK: An Interactive...22043 Bolling Air Force Base Washington, D.C. 20332 Dr. Paul E. Lehner PAR Technology Corp. AFHRL/LRS TDC P.O. Box 2005 Attn: Susan Ewing Reston, VA 22090

Computer Graphics Special Issue on 1992 Symposium on Interactive 3D graphics Held in Cambridge, Massachusetts on 29 March-1 April 1992

DTIC Science & Technology

1992-01-01

it * five representations of a desk: 1) a highly detailed desk with ,m ~ ~ ~ ~ Dlla L.._ ’ ,,,e ".. l, faces subdivided along gradients of radiosity , 2...created by our implementation, including timings and polygon using radiosity approaches [9, 61, by summing the counts. contributions of an approximating...and Winget, J. Improving Radiosity Solutions Through the Use of Analytically Determined Form-Factors. Proc. SIGGRAPH 󈨝 Plate 4, illuminated by both

Interactive Multiple-Representation Editing of Physically-based 3D Animation

DTIC Science & Technology

1994-05-29

view similar to that of FrameMaker [46], but with a stronger model of structured editing, and a language window, which displays a formal description of...used. This is partly a result of the power of a good direct manipulation editor { most users of good editors like FrameMaker don’t seem to miss having a...re nement. In SIG- GRAPH, pages 205{212, August 1988. [46] Frame Technology Inc. Using FrameMaker , 1990. [47] Bjorn N. Freeman-Benson and John Maloney

Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking.

PubMed

Kihara, Daisuke; Sael, Lee; Chikhi, Rayan; Esquivel-Rodriguez, Juan

2011-09-01

The tertiary structures of proteins have been solved in an increasing pace in recent years. To capitalize the enormous efforts paid for accumulating the structure data, efficient and effective computational methods need to be developed for comparing, searching, and investigating interactions of protein structures. We introduce the 3D Zernike descriptor (3DZD), an emerging technique to describe molecular surfaces. The 3DZD is a series expansion of mathematical three-dimensional function, and thus a tertiary structure is represented compactly by a vector of coefficients of terms in the series. A strong advantage of the 3DZD is that it is invariant to rotation of target object to be represented. These two characteristics of the 3DZD allow rapid comparison of surface shapes, which is sufficient for real-time structure database screening. In this article, we review various applications of the 3DZD, which have been recently proposed.

Manifestation of a strong quadrupole interaction and peculiarities in the SERS and SEHRS spectra of 4,4'-bipyridine

NASA Astrophysics Data System (ADS)

Golovin, A. V.; Polubotko, A. M.

2017-07-01

The paper analyzes Surface Enhanced Raman Scattering (SERS) and Surface Enhanced Hyper Raman Scattering (SEHRS) spectra of 4,4'-bypiridine molecule for two possible geometries, which are described by D 2 and D 2 h symmetry groups. It is pointed out on appearance of sufficiently strong lines, caused by vibrations with the unit irreducible representation for both possible configurations. Appearance of these lines in the SEHRS spectrum points out the existence of a strong quadrupole light-molecule interaction. In addition one observes the lines, caused by vibrations both with the unit irreducible representations A or A g and the irreducible representation B 1 or B 1 u . The last ones describe transformational properties of the d z component of the dipole moment, which is perpendicular to the surface. This property of the spectrum is caused by peculiarity of the geometry of the molecule, which consists of two benzene rings, which are weakly connected with each other. The linear combinations of the vibrations of the rings create two nearly degenerated symmetric and anti symmetrical states, which cannot be identified in the experimental spectra. The result is in a full agreement with the dipole-quadrupole theory of SERS and SEHRS.

Three-dimensional capture, representation, and manipulation of Cuneiform tablets

NASA Astrophysics Data System (ADS)

Woolley, Sandra I.; Flowers, Nicholas J.; Arvanitis, Theodoros N.; Livingstone, Alasdair; Davis, Tom R.; Ellison, John

2001-04-01

This paper presents the digital imaging results of a collaborative research project working toward the generation of an on-line interactive digital image database of signs from ancient cuneiform tablets. An important aim of this project is the application of forensic analysis to the cuneiform symbols to identify scribal hands. Cuneiform tablets are amongst the earliest records of written communication, and could be considered as one of the original information technologies; an accessible, portable and robust medium for communication across distance and time. The earliest examples are up to 5,000 years old, and the writing technique remained in use for some 3,000 years. Unfortunately, only a small fraction of these tablets can be made available for display in museums and much important academic work has yet to be performed on the very large numbers of tablets to which there is necessarily restricted access. Our paper will describe the challenges encountered in the 2D image capture of a sample set of tablets held in the British Museum, explaining the motivation for attempting 3D imaging and the results of initial experiments scanning the smaller, more densely inscribed cuneiform tablets. We will also discuss the tractability of 3D digital capture, representation and manipulation, and investigate the requirements for scaleable data compression and transmission methods. Additional information can be found on the project website: www.cuneiform.net

Efficient LBM visual simulation on face-centered cubic lattices.

PubMed

Petkov, Kaloian; Qiu, Feng; Fan, Zhe; Kaufman, Arie E; Mueller, Klaus

2009-01-01

The Lattice Boltzmann method (LBM) for visual simulation of fluid flow generally employs cubic Cartesian (CC) lattices such as the D3Q13 and D3Q19 lattices for the particle transport. However, the CC lattices lead to suboptimal representation of the simulation space. We introduce the face-centered cubic (FCC) lattice, fD3Q13, for LBM simulations. Compared to the CC lattices, the fD3Q13 lattice creates a more isotropic sampling of the simulation domain and its single lattice speed (i.e., link length) simplifies the computations and data storage. Furthermore, the fD3Q13 lattice can be decomposed into two independent interleaved lattices, one of which can be discarded, which doubles the simulation speed. The resulting LBM simulation can be efficiently mapped to the GPU, further increasing the computational performance. We show the numerical advantages of the FCC lattice on channeled flow in 2D and the flow-past-a-sphere benchmark in 3D. In both cases, the comparison is against the corresponding CC lattices using the analytical solutions for the systems as well as velocity field visualizations. We also demonstrate the performance advantages of the fD3Q13 lattice for interactive simulation and rendering of hot smoke in an urban environment using thermal LBM.

ISOANTIGENS OF THE H-2 AND Tla LOCI OF THE MOUSE

PubMed Central

Boyse, Edward A.; Stockert, Elisabeth; Old, Lloyd J.

1968-01-01

H-2 and TL isoantigens of the mouse are specified by the closely linked genetic loci H-2 and Tla. A. study of their representation on thymocytes was performed in order to reveal any interactions between the determinant genes or their products affecting the synthesis or disposition of these components of the thymocyte surface. The method employed was quantitative absorption of cytotoxic antibody by viable thymocytes. The phenotypic expression of TL antigens was found to reduce the demonstrable amount of certain H-2 antigens to as little as 34% of the quantity demonstrable on TL- thymocytes. A reduction was observed in all three H-2 types tested, (H-2b, H-2a, and H-2k). As antigenic modulation (change of TL phenotype from TL+ to TL-, produced by TL antibody) is known to entail a compensatory increase in H-2(D) antigen, it is concluded that the TL phenotype, rather than the Tla genotype, influences the surface representation of H-2 antigens. The two known TL+ phenotypes of thymocytes (TL.2 and TL.1,2,3) depress H-2 equally. The H-2 specificities affected are those determined by the D end of the E-2 locus, which is adjacent to Tla; antigens of the K end, which is distal to Tla, are not depressed. The reduction of demonstrable H-2 antigen on the thymocytes of TL+ x TL- progeny is half that of thymocytes of TL+ x TL+ progeny and the reduction affects equally the products of both H-2 alleles (cis and trans in relation to Tla), indicating that the mechanism of H-2 reduction by TL is extrachromosomal. Whether it involves diminished synthesis of H-2 or steric masking by TL at the cell membrane is unknown, but in either case the reciprocal relation of TL and H-2(D) antigens implies that they probably occupy adjacent positions on thymocytes and that the gene order, H-2(K): H-2(D):Tla is reflected in cell surface structure. Extrachromosomal interaction, apparently involving control of synthesis, occurs also within the TL system of antigens. Thymocytes of TL.2 x TL.1,2,3 progeny express the full homozygous quantity of antigens TL.1 and TL.3 (but not of TL.2), in contrast to the half-quantity present in thymocytes of TL- x TL.1,2,3 progeny. Another example of interaction is implicit in the finding that thymocytes of TL-1,2,3 x TL.1,2,3 progeny have more TL.2 antigen than thymocytes of TL.2 x TL.2 progeny, but in this instance there is nothing to indicate whether the mechanism is chromosomal or extrachromosomal. Thus the quantitative surface representation of at least some H-2 and TL antigens is influenced by the cellular complement of H-2:Tla genes as a whole. Comparison of H-2 heterozygous thymocytes with H-2 homozygous thymocytes in quantitative absorption tests shows (a) more than the expected 50% of each parental-type H-2 antigen on heterozygous cells, and (b) a greater suppression of H-2 by TL in H-2 heterozygotes in comparison with H-2 homozygotes. Both results may be explained on the basis of differences in the density of H-2 antigenic sites and consequent differences in the efficiency of absorption of H-2 antibody. These considerations may be useful in other contexts, e.g. in estimating the representation of Rh antigens on the red cells of human subjects homozygous and heterozygous for Rh components. PMID:5662018

PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides.

PubMed

Sarkar, Anita; Pérez, Serge

2012-11-14

Polysaccharides are ubiquitously present in the living world. Their structural versatility makes them important and interesting components in numerous biological and technological processes ranging from structural stabilization to a variety of immunologically important molecular recognition events. The knowledge of polysaccharide three-dimensional (3D) structure is important in studying carbohydrate-mediated host-pathogen interactions, interactions with other bio-macromolecules, drug design and vaccine development as well as material science applications or production of bio-ethanol. PolySac3DB is an annotated database that contains the 3D structural information of 157 polysaccharide entries that have been collected from an extensive screening of scientific literature. They have been systematically organized using standard names in the field of carbohydrate research into 18 categories representing polysaccharide families. Structure-related information includes the saccharides making up the repeat unit(s) and their glycosidic linkages, the expanded 3D representation of the repeat unit, unit cell dimensions and space group, helix type, diffraction diagram(s) (when applicable), experimental and/or simulation methods used for structure description, link to the abstract of the publication, reference and the atomic coordinate files for visualization and download. The database is accompanied by a user-friendly graphical user interface (GUI). It features interactive displays of polysaccharide structures and customized search options for beginners and experts, respectively. The site also serves as an information portal for polysaccharide structure determination techniques. The web-interface also references external links where other carbohydrate-related resources are available. PolySac3DB is established to maintain information on the detailed 3D structures of polysaccharides. All the data and features are available via the web-interface utilizing the search engine and can be accessed at http://polysac3db.cermav.cnrs.fr.

3D Printed Potential and Free Energy Surfaces for Teaching Fundamental Concepts in Physical Chemistry

ERIC Educational Resources Information Center

Kaliakin, Danil S.; Zaari, Ryan R.; Varganov, Sergey A.

2015-01-01

Teaching fundamental physical chemistry concepts such as the potential energy surface, transition state, and reaction path is a challenging task. The traditionally used oversimplified 2D representation of potential and free energy surfaces makes this task even more difficult and often confuses students. We show how this 2D representation can be…

To What Degree Does Handling Concrete Molecular Models Promote the Ability to Translate and Coordinate between 2D and 3D Molecular Structure Representations? A Case Study with Algerian Students

ERIC Educational Resources Information Center

Mohamed-Salah, Boukhechem; Alain, Dumon

2016-01-01

This study aims to assess whether the handling of concrete ball-and-stick molecular models promotes translation between diagrammatic representations and a concrete model (or vice versa) and the coordination of the different types of structural representations of a given molecular structure. Forty-one Algerian undergraduate students were requested…

Automated segmentation and geometrical modeling of the tricuspid aortic valve in 3D echocardiographic images.

PubMed

Pouch, Alison M; Wang, Hongzhi; Takabe, Manabu; Jackson, Benjamin M; Sehgal, Chandra M; Gorman, Joseph H; Gorman, Robert C; Yushkevich, Paul A

2013-01-01

The aortic valve has been described with variable anatomical definitions, and the consistency of 2D manual measurement of valve dimensions in medical image data has been questionable. Given the importance of image-based morphological assessment in the diagnosis and surgical treatment of aortic valve disease, there is considerable need to develop a standardized framework for 3D valve segmentation and shape representation. Towards this goal, this work integrates template-based medial modeling and multi-atlas label fusion techniques to automatically delineate and quantitatively describe aortic leaflet geometry in 3D echocardiographic (3DE) images, a challenging task that has been explored only to a limited extent. The method makes use of expert knowledge of aortic leaflet image appearance, generates segmentations with consistent topology, and establishes a shape-based coordinate system on the aortic leaflets that enables standardized automated measurements. In this study, the algorithm is evaluated on 11 3DE images of normal human aortic leaflets acquired at mid systole. The clinical relevance of the method is its ability to capture leaflet geometry in 3DE image data with minimal user interaction while producing consistent measurements of 3D aortic leaflet geometry.

Nematic and chiral superconductivity induced by odd-parity fluctuations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Fengcheng; Martin, Ivar

Recent experiments indicate that superconductivity in Bi 2Se 3 intercalated with Cu, Nb, or Sr is nematic with rotational symmetry breaking. Motivated by this observation, we present a model study of nematic and chiral superconductivity induced by odd-parity fluctuations. Additionally, we show that odd-parity fluctuations in the two-component E u representation of D 3d crystal point group can generate attractive interaction in both the even-parity s-wave and odd-parity E-u pairing channels, but repulsive interaction in other odd-parity pairing channels. Coulomb repulsion can suppress s-wave pairing relative to E u pairing, and thus the latter can have a higher critical temperature.more » E u pairing has two distinct phases: a nematic phase and a chiral phase, both of which can be realized in our model. Finally, when s-wave and E u pairings have similar instability temperature, we find an intermediate phase in which both types of pairing coexist.« less

Nematic and chiral superconductivity induced by odd-parity fluctuations

DOE PAGES

Wu, Fengcheng; Martin, Ivar

2017-10-09

Recent experiments indicate that superconductivity in Bi 2Se 3 intercalated with Cu, Nb, or Sr is nematic with rotational symmetry breaking. Motivated by this observation, we present a model study of nematic and chiral superconductivity induced by odd-parity fluctuations. Additionally, we show that odd-parity fluctuations in the two-component E u representation of D 3d crystal point group can generate attractive interaction in both the even-parity s-wave and odd-parity E-u pairing channels, but repulsive interaction in other odd-parity pairing channels. Coulomb repulsion can suppress s-wave pairing relative to E u pairing, and thus the latter can have a higher critical temperature.more » E u pairing has two distinct phases: a nematic phase and a chiral phase, both of which can be realized in our model. Finally, when s-wave and E u pairings have similar instability temperature, we find an intermediate phase in which both types of pairing coexist.« less

Use of 3D techniques for virtual production

NASA Astrophysics Data System (ADS)

Grau, Oliver; Price, Marc C.; Thomas, Graham A.

2000-12-01

Virtual production for broadcast is currently mainly used in the form of virtual studios, where the resulting media is a sequence of 2D images. With the steady increase of 3D computing power in home PCs and the technical progress in 3D display technology, the content industry is looking for new kinds of program material, which makes use of 3D technology. The applications range form analysis of sport scenes, 3DTV, up to the creation of fully immersive content. In a virtual studio a camera films one or more actors in a controlled environment. The pictures of the actors can be segmented very accurately in real time using chroma keying techniques. The isolated silhouette can be integrated into a new synthetic virtual environment using a studio mixer. The resulting shape description of the actors is 2D so far. For the realization of more sophisticated optical interactions of the actors with the virtual environment, such as occlusions and shadows, an object-based 3D description of scenes is needed. However, the requirements of shape accuracy, and the kind of representation, differ in accordance with the application. This contribution gives an overview of requirements and approaches for the generation of an object-based 3D description in various applications studied by the BBC R and D department. An enhanced Virtual Studio for 3D programs is proposed that covers a range of applications for virtual production.

3D Data Acquisition Platform for Human Activity Understanding

DTIC Science & Technology

2016-03-02

address fundamental research problems of representation and invariant description of3D data, human motion modeling and applications of human activity analysis, and computational optimization of large-scale 3D data.

3D Data Acquisition Platform for Human Activity Understanding

DTIC Science & Technology

2016-03-02

address fundamental research problems of representation and invariant description of 3D data, human motion modeling and applications of human activity analysis, and computational optimization of large-scale 3D data.

Extra dimensions: 3d and time in pdf documentation

NASA Astrophysics Data System (ADS)

Graf, N. A.

2008-07-01

High energy physics is replete with multi-dimensional information which is often poorly represented by the two dimensions of presentation slides and print media. Past efforts to disseminate such information to a wider audience have failed for a number of reasons, including a lack of standards which are easy to implement and have broad support. Adobe's Portable Document Format (PDF) has in recent years become the de facto standard for secure, dependable electronic information exchange. It has done so by creating an open format, providing support for multiple platforms and being reliable and extensible. By providing support for the ECMA standard Universal 3D (U3D) file format in its free Adobe Reader software, Adobe has made it easy to distribute and interact with 3D content. By providing support for scripting and animation, temporal data can also be easily distributed to a wide audience. In this talk, we present examples of HEP applications which take advantage of this functionality. We demonstrate how 3D detector elements can be documented, using either CAD drawings or other sources such as GEANT visualizations as input. Using this technique, higher dimensional data, such as LEGO plots or time-dependent information can be included in PDF files. In principle, a complete event display, with full interactivity, can be incorporated into a PDF file. This would allow the end user not only to customize the view and representation of the data, but to access the underlying data itself.

Extra Dimensions: 3D and Time in PDF Documentation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graf, Norman A.; /SLAC

2011-11-10

High energy physics is replete with multi-dimensional information which is often poorly represented by the two dimensions of presentation slides and print media. Past efforts to disseminate such information to a wider audience have failed for a number of reasons, including a lack of standards which are easy to implement and have broad support. Adobe's Portable Document Format (PDF) has in recent years become the de facto standard for secure, dependable electronic information exchange. It has done so by creating an open format, providing support for multiple platforms and being reliable and extensible. By providing support for the ECMA standardmore » Universal 3D (U3D) file format in its free Adobe Reader software, Adobe has made it easy to distribute and interact with 3D content. By providing support for scripting and animation, temporal data can also be easily distributed to a wide audience. In this talk, we present examples of HEP applications which take advantage of this functionality. We demonstrate how 3D detector elements can be documented, using either CAD drawings or other sources such as GEANT visualizations as input. Using this technique, higher dimensional data, such as LEGO plots or time-dependent information can be included in PDF files. In principle, a complete event display, with full interactivity, can be incorporated into a PDF file. This would allow the end user not only to customize the view and representation of the data, but to access the underlying data itself.« less

3D-Holoscopic Imaging: A New Dimension to Enhance Imaging in Minimally Invasive Therapy in Urologic Oncology

PubMed Central

Aggoun, Amar; Swash, Mohammad; Grange, Philippe C.R.; Challacombe, Benjamin; Dasgupta, Prokar

2013-01-01

Abstract Background and Purpose Existing imaging modalities of urologic pathology are limited by three-dimensional (3D) representation on a two-dimensional screen. We present 3D-holoscopic imaging as a novel method of representing Digital Imaging and Communications in Medicine data images taken from CT and MRI to produce 3D-holographic representations of anatomy without special eyewear in natural light. 3D-holoscopic technology produces images that are true optical models. This technology is based on physical principles with duplication of light fields. The 3D content is captured in real time with the content viewed by multiple viewers independently of their position, without 3D eyewear. Methods We display 3D-holoscopic anatomy relevant to minimally invasive urologic surgery without the need for 3D eyewear. Results The results have demonstrated that medical 3D-holoscopic content can be displayed on commercially available multiview auto-stereoscopic display. Conclusion The next step is validation studies comparing 3D-Holoscopic imaging with conventional imaging. PMID:23216303

Analysis of students’ spatial thinking in geometry: 3D object into 2D representation

NASA Astrophysics Data System (ADS)

Fiantika, F. R.; Maknun, C. L.; Budayasa, I. K.; Lukito, A.

2018-05-01

The aim of this study is to find out the spatial thinking process of students in transforming 3-dimensional (3D) object to 2-dimensional (2D) representation. Spatial thinking is helpful in using maps, planning routes, designing floor plans, and creating art. The student can engage geometric ideas by using concrete models and drawing. Spatial thinking in this study is identified through geometrical problems of transforming a 3-dimensional object into a 2-dimensional object image. The problem was resolved by the subject and analyzed by reference to predetermined spatial thinking indicators. Two representative subjects of elementary school were chosen based on mathematical ability and visual learning style. Explorative description through qualitative approach was used in this study. The result of this study are: 1) there are different representations of spatial thinking between a boy and a girl object, 2) the subjects has their own way to invent the fastest way to draw cube net.

A laminar cortical model of stereopsis and 3D surface perception: closure and da Vinci stereopsis.

PubMed

Cao, Yongqiang; Grossberg, Stephen

2005-01-01

A laminar cortical model of stereopsis and 3D surface perception is developed and simulated. The model describes how monocular and binocular oriented filtering interact with later stages of 3D boundary formation and surface filling-in in the LGN and cortical areas V1, V2, and V4. It proposes how interactions between layers 4, 3B, and 2/3 in V1 and V2 contribute to stereopsis, and how binocular and monocular information combine to form 3D boundary and surface representations. The model includes two main new developments: (1) It clarifies how surface-to-boundary feedback from V2 thin stripes to pale stripes helps to explain data about stereopsis. This feedback has previously been used to explain data about 3D figure-ground perception. (2) It proposes that the binocular false match problem is subsumed under the Gestalt grouping problem. In particular, the disparity filter, which helps to solve the correspondence problem by eliminating false matches, is realized using inhibitory interneurons as part of the perceptual grouping process by horizontal connections in layer 2/3 of cortical area V2. The enhanced model explains all the psychophysical data previously simulated by Grossberg and Howe (2003), such as contrast variations of dichoptic masking and the correspondence problem, the effect of interocular contrast differences on stereoacuity, Panum's limiting case, the Venetian blind illusion, stereopsis with polarity-reversed stereograms, and da Vinci stereopsis. It also explains psychophysical data about perceptual closure and variations of da Vinci stereopsis that previous models cannot yet explain.

Generating Cognitive Dissonance in Student Interviews through Multiple Representations

ERIC Educational Resources Information Center

Linenberger, Kimberly J.; Bretz, Stacey Lowery

2012-01-01

This study explores what students understand about enzyme-substrate interactions, using multiple representations of the phenomenon. In this paper we describe our use of the 3 Phase-Single Interview Technique with multiple representations to generate cognitive dissonance within students in order to uncover misconceptions of enzyme-substrate…

D Digitization and Mapping of Heritage Monuments and Comparison with Historical Drawings

NASA Astrophysics Data System (ADS)

Fiorillo, F.; Remondino, F.; Barba, S.; Santoriello, A.; De Vita, C. B.; Casellato, A.

2013-07-01

The paper presents the integration of different 3D recording techniques and instruments to survey the archaeological area of Paestum (Italy). Paestum was included in the UNESCO World Heritage list since 1998, and still preserves the ruins of Greek and Roman times. Photogrammetry and terrestrial laser scanning (TLS) acquisitions were integrated in order to exploit the advantages of the 3D surveying techniques and produce digital models, orthoimages, maps and other geometric representations useful for archaeological, architectural and cultural touristic purposes. The obtained 3D results are then compared to historical representations to show the high quality of such ancient manual drawings.

Three-dimensional Talairach-Tournoux brain atlas

NASA Astrophysics Data System (ADS)

Fang, Anthony; Nowinski, Wieslaw L.; Nguyen, Bonnie T.; Bryan, R. Nick

1995-04-01

The Talairach-Tournoux Stereotaxic Atlas of the human brain is a frequently consulted resource in stereotaxic neurosurgery and computer-based neuroradiology. Its primary application lies in the 2-D analysis and interpretation of neurological images. However, for the purpose of the analysis and visualization of shapes and forms, accurate mensuration of volumes, or 3-D models matching, a 3-D representation of the atlas is essential. This paper proposes and describes, along with its difficulties, a 3-D geometric extension of the atlas. We introduce a `zero-potential' surface smoothing technique, along with a space-dependent convolution kernel and space-dependent normalization. The mesh-based atlas structures are hierarchically organized, and anatomically conform to the original atlas. Structures and their constituents can be independently selected and manipulated in real-time within an integrated system. The extended atlas may be navigated by itself, or interactively registered with patient data with the proportional grid system (piecewise linear) transformation. Visualization of the geometric atlas along with patient data gives a remarkable visual `feel' of the biological structures, not usually perceivable to the untrained eyes in conventional 2-D atlas to image analysis.

3D Reasoning from Blocks to Stability.

PubMed

Zhaoyin Jia; Gallagher, Andrew C; Saxena, Ashutosh; Chen, Tsuhan

2015-05-01

Objects occupy physical space and obey physical laws. To truly understand a scene, we must reason about the space that objects in it occupy, and how each objects is supported stably by each other. In other words, we seek to understand which objects would, if moved, cause other objects to fall. This 3D volumetric reasoning is important for many scene understanding tasks, ranging from segmentation of objects to perception of a rich 3D, physically well-founded, interpretations of the scene. In this paper, we propose a new algorithm to parse a single RGB-D image with 3D block units while jointly reasoning about the segments, volumes, supporting relationships, and object stability. Our algorithm is based on the intuition that a good 3D representation of the scene is one that fits the depth data well, and is a stable, self-supporting arrangement of objects (i.e., one that does not topple). We design an energy function for representing the quality of the block representation based on these properties. Our algorithm fits 3D blocks to the depth values corresponding to image segments, and iteratively optimizes the energy function. Our proposed algorithm is the first to consider stability of objects in complex arrangements for reasoning about the underlying structure of the scene. Experimental results show that our stability-reasoning framework improves RGB-D segmentation and scene volumetric representation.

Knowledge-Based, Interactive, Custom Anatomical Scene Creation for Medical Education: The Biolucida System

PubMed Central

Warren, Wayne; Brinkley, James F.

2005-01-01

Few biomedical subjects of study are as resource-intensive to teach as gross anatomy. Medical education stands to benefit greatly from applications which deliver virtual representations of human anatomical structures. While many applications have been created to achieve this goal, their utility to the student is limited because of a lack of interactivity or customizability by expert authors. Here we describe the first version of the Biolucida system, which allows an expert anatomist author to create knowledge-based, customized, and fully interactive scenes and lessons for students of human macroscopic anatomy. Implemented in Java and VRML, Biolucida allows the sharing of these instructional 3D environments over the internet. The system simplifies the process of authoring immersive content while preserving its flexibility and expressivity. PMID:16779148

A novel approach for introducing cloud spatial structure into cloud radiative transfer parameterizations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Dong; Liu, Yangang

2014-12-18

Subgrid-scale variability is one of the main reasons why parameterizations are needed in large-scale models. Although some parameterizations started to address the issue of subgrid variability by introducing a subgrid probability distribution function for relevant quantities, the spatial structure has been typically ignored and thus the subgrid-scale interactions cannot be accounted for physically. Here we present a new statistical-physics-like approach whereby the spatial autocorrelation function can be used to physically capture the net effects of subgrid cloud interaction with radiation. The new approach is able to faithfully reproduce the Monte Carlo 3D simulation results with several orders less computational cost,more » allowing for more realistic representation of cloud radiation interactions in large-scale models.« less

Knowledge-based, interactive, custom anatomical scene creation for medical education: the Biolucida system.

PubMed

Warren, Wayne; Brinkley, James F

2005-01-01

Few biomedical subjects of study are as resource-intensive to teach as gross anatomy. Medical education stands to benefit greatly from applications which deliver virtual representations of human anatomical structures. While many applications have been created to achieve this goal, their utility to the student is limited because of a lack of interactivity or customizability by expert authors. Here we describe the first version of the Biolucida system, which allows an expert anatomist author to create knowledge-based, customized, and fully interactive scenes and lessons for students of human macroscopic anatomy. Implemented in Java and VRML, Biolucida allows the sharing of these instructional 3D environments over the internet. The system simplifies the process of authoring immersive content while preserving its flexibility and expressivity.

Three-dimensional visual feature representation in the primary visual cortex

PubMed Central

Tanaka, Shigeru; Moon, Chan-Hong; Fukuda, Mitsuhiro; Kim, Seong-Gi

2011-01-01

In the cat primary visual cortex, it is accepted that neurons optimally responding to similar stimulus orientations are clustered in a column extending from the superficial to deep layers. The cerebral cortex is, however, folded inside a skull, which makes gyri and fundi. The primary visual area of cats, area 17, is located on the fold of the cortex called the lateral gyrus. These facts raise the question of how to reconcile the tangential arrangement of the orientation columns with the curvature of the gyrus. In the present study, we show a possible configuration of feature representation in the visual cortex using a three-dimensional (3D) self-organization model. We took into account preferred orientation, preferred direction, ocular dominance and retinotopy, assuming isotropic interaction. We performed computer simulation only in the middle layer at the beginning and expanded the range of simulation gradually to other layers, which was found to be a unique method in the present model for obtaining orientation columns spanning all the layers in the flat cortex. Vertical columns of preferred orientations were found in the flat parts of the model cortex. On the other hand, in the curved parts, preferred orientations were represented in wedge-like columns rather than straight columns, and preferred directions were frequently reversed in the deeper layers. Singularities associated with orientation representation appeared as warped lines in the 3D model cortex. Direction reversal appeared on the sheets that were delimited by orientation-singularity lines. These structures emerged from the balance between periodic arrangements of preferred orientations and vertical alignment of same orientations. Our theoretical predictions about orientation representation were confirmed by multi-slice, high-resolution functional MRI in the cat visual cortex. We obtained a close agreement between theoretical predictions and experimental observations. The present study throws a doubt about the conventional columnar view of orientation representation, although more experimental data are needed. PMID:21724370

Three-dimensional visual feature representation in the primary visual cortex.

PubMed

Tanaka, Shigeru; Moon, Chan-Hong; Fukuda, Mitsuhiro; Kim, Seong-Gi

2011-12-01

In the cat primary visual cortex, it is accepted that neurons optimally responding to similar stimulus orientations are clustered in a column extending from the superficial to deep layers. The cerebral cortex is, however, folded inside a skull, which makes gyri and fundi. The primary visual area of cats, area 17, is located on the fold of the cortex called the lateral gyrus. These facts raise the question of how to reconcile the tangential arrangement of the orientation columns with the curvature of the gyrus. In the present study, we show a possible configuration of feature representation in the visual cortex using a three-dimensional (3D) self-organization model. We took into account preferred orientation, preferred direction, ocular dominance and retinotopy, assuming isotropic interaction. We performed computer simulation only in the middle layer at the beginning and expanded the range of simulation gradually to other layers, which was found to be a unique method in the present model for obtaining orientation columns spanning all the layers in the flat cortex. Vertical columns of preferred orientations were found in the flat parts of the model cortex. On the other hand, in the curved parts, preferred orientations were represented in wedge-like columns rather than straight columns, and preferred directions were frequently reversed in the deeper layers. Singularities associated with orientation representation appeared as warped lines in the 3D model cortex. Direction reversal appeared on the sheets that were delimited by orientation-singularity lines. These structures emerged from the balance between periodic arrangements of preferred orientations and vertical alignment of the same orientations. Our theoretical predictions about orientation representation were confirmed by multi-slice, high-resolution functional MRI in the cat visual cortex. We obtained a close agreement between theoretical predictions and experimental observations. The present study throws a doubt about the conventional columnar view of orientation representation, although more experimental data are needed. Copyright © 2011 Elsevier Ltd. All rights reserved.

3D shape representation with spatial probabilistic distribution of intrinsic shape keypoints

NASA Astrophysics Data System (ADS)

Ghorpade, Vijaya K.; Checchin, Paul; Malaterre, Laurent; Trassoudaine, Laurent

2017-12-01

The accelerated advancement in modeling, digitizing, and visualizing techniques for 3D shapes has led to an increasing amount of 3D models creation and usage, thanks to the 3D sensors which are readily available and easy to utilize. As a result, determining the similarity between 3D shapes has become consequential and is a fundamental task in shape-based recognition, retrieval, clustering, and classification. Several decades of research in Content-Based Information Retrieval (CBIR) has resulted in diverse techniques for 2D and 3D shape or object classification/retrieval and many benchmark data sets. In this article, a novel technique for 3D shape representation and object classification has been proposed based on analyses of spatial, geometric distributions of 3D keypoints. These distributions capture the intrinsic geometric structure of 3D objects. The result of the approach is a probability distribution function (PDF) produced from spatial disposition of 3D keypoints, keypoints which are stable on object surface and invariant to pose changes. Each class/instance of an object can be uniquely represented by a PDF. This shape representation is robust yet with a simple idea, easy to implement but fast enough to compute. Both Euclidean and topological space on object's surface are considered to build the PDFs. Topology-based geodesic distances between keypoints exploit the non-planar surface properties of the object. The performance of the novel shape signature is tested with object classification accuracy. The classification efficacy of the new shape analysis method is evaluated on a new dataset acquired with a Time-of-Flight camera, and also, a comparative evaluation on a standard benchmark dataset with state-of-the-art methods is performed. Experimental results demonstrate superior classification performance of the new approach on RGB-D dataset and depth data.

D Virtual CH Interactive Information Systems for a Smart Web Browsing Experience for Desktop Pcs and Mobile Devices

NASA Astrophysics Data System (ADS)

Scianna, A.; La Guardia, M.

2018-05-01

Recently, the diffusion of knowledge on Cultural Heritage (CH) has become an element of primary importance for its valorization. At the same time, the diffusion of surveys based on UAV Unmanned Aerial Vehicles (UAV) technologies and new methods of photogrammetric reconstruction have opened new possibilities for 3D CH representation. Furthermore the recent development of faster and more stable internet connections leads people to increase the use of mobile devices. In the light of all this, the importance of the development of Virtual Reality (VR) environments applied to CH is strategic for the diffusion of knowledge in a smart solution. In particular, the present work shows how, starting from a basic survey and the further photogrammetric reconstruction of a cultural good, is possible to built a 3D CH interactive information system useful for desktop and mobile devices. For this experimentation the Arab-Norman church of the Trinity of Delia (in Castelvetrano-Sicily-Italy) has been adopted as case study. The survey operations have been carried out considering different rapid methods of acquisition (UAV camera, SLR camera and smartphone camera). The web platform to publish the 3D information has been built using HTML5 markup language and WebGL JavaScript libraries (Three.js libraries). This work presents the construction of a 3D navigation system for a web-browsing of a virtual CH environment, with the integration of first person controls and 3D popup links. This contribution adds a further step to enrich the possibilities of open-source technologies applied to the world of CH valorization on web.

Development of the Bonding Representations Inventory to Identify Student Misconceptions about Covalent and Ionic Bonding Representations

ERIC Educational Resources Information Center

Luxford, Cynthia J.; Bretz, Stacey Lowery

2014-01-01

Teachers use multiple representations to communicate the concepts of bonding, including Lewis structures, formulas, space-filling models, and 3D manipulatives. As students learn to interpret these multiple representations, they may develop misconceptions that can create problems in further learning of chemistry. Interviews were conducted with 28…

Bite mark documentation and analysis: the forensic 3D/CAD supported photogrammetry approach.

PubMed

Thali, M J; Braun, M; Markwalder, Th H; Brueschweiler, W; Zollinger, U; Malik, Naseem J; Yen, K; Dirnhofer, R

2003-08-12

Bite mark identification is based on the individuality of a dentition, which is used to match a bite mark to a suspected perpetrator. This matching is based on a tooth-by-tooth and arch-to-arch comparison utilising parameters of size, shape and alignment. The most common method used to analyse bite mark are carried out in 2D space. That means that the 3D information is preserved only two dimensionally with distortions. This paper presents a new 3D documentation, analysis and visualisation approach based on forensic 3D/CAD supported photogrammetry (FPHG) and the use of a 3D surface scanner. Our photogrammetric approach and the used visualisation method is, to the best to our knowledge, the first 3D approach for bite mark analysis in an actual case. The documentation has no distortion artifacts as can be found with standard photography. All the data are documented with a metric 3D measurement, orientation and subsequent analysis in 3D space. Beside the metrical analysis between bite mark and cast, it is possible using our method to utilise the topographical 3D feature of each individual tooth. This means that the 3D features of the biting surfaces and edges of each teeth are respected which is--as shown in our case--very important especially in the front teeth which have the first contact to the skin. Based upon the 3D detailed representation of the cast with the 3D topographic characteristics of the teeth, the interaction with the 3D documented skin can be visualised and analysed on the computer screen.

Building generic anatomical models using virtual model cutting and iterative registration.

PubMed

Xiao, Mei; Soh, Jung; Meruvia-Pastor, Oscar; Schmidt, Eric; Hallgrímsson, Benedikt; Sensen, Christoph W

2010-02-08

Using 3D generic models to statistically analyze trends in biological structure changes is an important tool in morphometrics research. Therefore, 3D generic models built for a range of populations are in high demand. However, due to the complexity of biological structures and the limited views of them that medical images can offer, it is still an exceptionally difficult task to quickly and accurately create 3D generic models (a model is a 3D graphical representation of a biological structure) based on medical image stacks (a stack is an ordered collection of 2D images). We show that the creation of a generic model that captures spatial information exploitable in statistical analyses is facilitated by coupling our generalized segmentation method to existing automatic image registration algorithms. The method of creating generic 3D models consists of the following processing steps: (i) scanning subjects to obtain image stacks; (ii) creating individual 3D models from the stacks; (iii) interactively extracting sub-volume by cutting each model to generate the sub-model of interest; (iv) creating image stacks that contain only the information pertaining to the sub-models; (v) iteratively registering the corresponding new 2D image stacks; (vi) averaging the newly created sub-models based on intensity to produce the generic model from all the individual sub-models. After several registration procedures are applied to the image stacks, we can create averaged image stacks with sharp boundaries. The averaged 3D model created from those image stacks is very close to the average representation of the population. The image registration time varies depending on the image size and the desired accuracy of the registration. Both volumetric data and surface model for the generic 3D model are created at the final step. Our method is very flexible and easy to use such that anyone can use image stacks to create models and retrieve a sub-region from it at their ease. Java-based implementation allows our method to be used on various visualization systems including personal computers, workstations, computers equipped with stereo displays, and even virtual reality rooms such as the CAVE Automated Virtual Environment. The technique allows biologists to build generic 3D models of their interest quickly and accurately.

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.

PubMed

Boniecki, Michal J; Lach, Grzegorz; Dawson, Wayne K; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M; Bujnicki, Janusz M

2016-04-20

RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Geo3DML: A standard-based exchange format for 3D geological models

NASA Astrophysics Data System (ADS)

Wang, Zhangang; Qu, Honggang; Wu, Zixing; Wang, Xianghong

2018-01-01

A geological model (geomodel) in three-dimensional (3D) space is a digital representation of the Earth's subsurface, recognized by geologists and stored in resultant geological data (geodata). The increasing demand for data management and interoperable applications of geomodelscan be addressed by developing standard-based exchange formats for the representation of not only a single geological object, but also holistic geomodels. However, current standards such as GeoSciML cannot incorporate all the geomodel-related information. This paper presents Geo3DML for the exchange of 3D geomodels based on the existing Open Geospatial Consortium (OGC) standards. Geo3DML is based on a unified and formal representation of structural models, attribute models and hierarchical structures of interpreted resultant geodata in different dimensional views, including drills, cross-sections/geomaps and 3D models, which is compatible with the conceptual model of GeoSciML. Geo3DML aims to encode all geomodel-related information integrally in one framework, including the semantic and geometric information of geoobjects and their relationships, as well as visual information. At present, Geo3DML and some supporting tools have been released as a data-exchange standard by the China Geological Survey (CGS).

Smart-Geology for the World's largest fossil oyster reef

NASA Astrophysics Data System (ADS)

Dorninger, Peter; Nothegger, Clemens; Djuricic, Ana; Rasztovits, Sascha; Harzhauser, Mathias

2014-05-01

The geo-edutainment park "Fossilienwelt Weinviertel" at Stetten in Lower Austria exposes the world's largest fossil oyster biostrome. In the past decade, significant progress has been made in 3D digitizing sensor technology. To cope with the high amount of data, processing methods have been automated to a high degree. Consequently, we formulated the hypothesis that appropriate application of state-of-the-art 3D digitizing, data processing, and visualization technologies allows for a significant automation in paleontological prospection, making an evaluation of huge areas commercially feasible in both time and costs. We call the necessary processing steps "Smart Geology", being characterized by automation and large volumes of data. The Smart Geology project (FWF P 25883-N29) investigates three topics, 3D digitizing, automated geological and paleontological analysis and interpretation and finally investigating the applicability of smart devices for on-site accessibility of project data in order to support the two scientific hypotheses concerning the emerging process of the shell bed, i.e. was it formed by a tsunami or a major storm, and does it preserve pre- and post-event features. This contribution concentrates on the innovative and sophisticated 3D documentation and visualization processes being applied to virtualise approximately 15.000 fossil oysters at the approximately 25 by 17 m accessible shell bad. We decided to use a Terrestrial Laserscanner (TLS) for the determination of the geometrical 3D structures. The TLS achieves about 2 mm single point measurement accuracy. The scanning campaign provides a "raw" point cloud of approximately 1 bio. points at the respective area. Due to the scanning configuration used, the occurrence of occluded ares is minimized hence the full 3D structure of this unique site can be modelled. In addition, approximately 300 photos were taken with a nominal resolution of 0.6 mm per pixel. Sophisticated artificial lightning (close to studio conditions) is used in order to minimize the occurrence of shadows. The resulting datasets can be characterized as follows: A virtual 3D representation with a nominal resolution of 1 mm, a local accuracy of 1 mm (after noise minimization), a global accuracy of < 3 mm with respect to a network of reference points and integrated colour information with a resolution of 0.6 mm per pixel. In order to support both interactive and automated geological and palaeontologcial research questions of the entire site in an economically feasible manner, various data reduction and representation methods were evaluated. Within this contribution we will present and discuss results of 2D image representations, 3D documentation models, and combinations, i.e. textured models. Effects of data reduction (i.e. to make them more convenient for the analysis of large areas) and data acquisition configuration (e.g. the necessity for high-resolution data acquisition) as well as the applicability of the data for advanced visualization purposes (e.g. 3D real-time rendering; foundation for augmented- reality based applications) will be discussed.

Visual shape perception as Bayesian inference of 3D object-centered shape representations.

PubMed

Erdogan, Goker; Jacobs, Robert A

2017-11-01

Despite decades of research, little is known about how people visually perceive object shape. We hypothesize that a promising approach to shape perception is provided by a "visual perception as Bayesian inference" framework which augments an emphasis on visual representation with an emphasis on the idea that shape perception is a form of statistical inference. Our hypothesis claims that shape perception of unfamiliar objects can be characterized as statistical inference of 3D shape in an object-centered coordinate system. We describe a computational model based on our theoretical framework, and provide evidence for the model along two lines. First, we show that, counterintuitively, the model accounts for viewpoint-dependency of object recognition, traditionally regarded as evidence against people's use of 3D object-centered shape representations. Second, we report the results of an experiment using a shape similarity task, and present an extensive evaluation of existing models' abilities to account for the experimental data. We find that our shape inference model captures subjects' behaviors better than competing models. Taken as a whole, our experimental and computational results illustrate the promise of our approach and suggest that people's shape representations of unfamiliar objects are probabilistic, 3D, and object-centered. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

The effects of 3D interactive animated graphics on student learning and attitudes in computer-based instruction

NASA Astrophysics Data System (ADS)

Moon, Hye Sun

Visuals are most extensively used as instructional tools in education to present spatially-based information. Recent computer technology allows the generation of 3D animated visuals to extend the presentation in computer-based instruction. Animated visuals in 3D representation not only possess motivational value that promotes positive attitudes toward instruction but also facilitate learning when the subject matter requires dynamic motion and 3D visual cue. In this study, three questions are explored: (1) how 3D graphics affects student learning and attitude, in comparison with 2D graphics; (2) how animated graphics affects student learning and attitude, in comparison with static graphics; and (3) whether the use of 3D graphics, when they are supported by interactive animation, is the most effective visual cues to improve learning and to develop positive attitudes. A total of 145 eighth-grade students participated in a 2 x 2 factorial design study. The subjects were randomly assigned to one of four computer-based instructions: 2D static; 2D animated; 3D static; and 3D animated. The results indicated that: (1) Students in the 3D graphic condition exhibited more positive attitudes toward instruction than those in the 2D graphic condition. No group differences were found between the posttest score of 3D graphic condition and that of 2D graphic condition. However, students in the 3D graphic condition took less time for information retrieval on posttest than those in the 2D graphic condition. (2) Students in the animated graphic condition exhibited slightly more positive attitudes toward instruction than those in the static graphic condition. No group differences were found between the posttest score of animated graphic condition and that of static graphic condition. However, students in the animated graphic condition took less time for information retrieval on posttest than those in the static graphic condition. (3) Students in the 3D animated graphic condition exhibited more positive attitudes toward instruction than those in other treatment conditions (2D static, 2D animated, and 3D static conditions). No group differences were found in the posttest scores among four treatment conditions. However, students in the 3D animated condition took less time for information retrieval on posttest than those in other treatment conditions.

Eye Detection and Tracking for Intelligent Human Computer Interaction

DTIC Science & Technology

2006-02-01

Meer and I. Weiss, “Smoothed Differentiation Filters for Images”, Journal of Visual Communication and Image Representation, 3(1):58-72, 1992. [13...25] P. Meer and I. Weiss. “Smoothed differentiation filters for images”. Journal of Visual Communication and Image Representation, 3(1), 1992

Inscriptions Becoming Representations in Representational Practices

ERIC Educational Resources Information Center

Medina, Richard; Suthers, Daniel

2013-01-01

We analyze the interaction of 3 students working on mathematics problems over several days in a virtual math team. Our analysis traces out how successful collaboration in a later session is contingent upon the work of prior sessions and shows how the development of representational practices is an important aspect of these participants' problem…

Predicting phase behavior of mixtures of reservoir fluids with carbon dioxide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grigg, R.B.; Lingane, P.J.

1983-10-01

The use of an equation of state to predict phase behavior during carbon dioxide flooding is well established. There is consensus that the characterization of the C fraction, the grouping of this fraction into ''pseudo components'', and the selection of interaction parameters are the most important variables. However, the literature is vague as to how to best select the pseudo components, especially when aiming for a few-component representation as for a field scale compositional simulation. Single-contact phase behavior is presented for mixtures of Ford Geraldine (Delaware), Maljamar (Grayburg), West Sussex (Shannon), and Reservoir D reservoir fluids, and of a syntheticmore » oil C/C/C, with carbon dioxide. One can reproduce the phase behavior of these mixtures using 3-5 pseudo components and common interaction parameters. The critical properties of the pseudo components are calculated from detailed oil characterizations. Because the parameters are not further adjusted, this approach reduces the empiricism in fitting phase data and may result in a more accurate representation of the system as the composition of the oil changes during the approach to miscibility.« less

Interactive Scene Analysis Module - A sensor-database fusion system for telerobotic environments

NASA Technical Reports Server (NTRS)

Cooper, Eric G.; Vazquez, Sixto L.; Goode, Plesent W.

1992-01-01

Accomplishing a task with telerobotics typically involves a combination of operator control/supervision and a 'script' of preprogrammed commands. These commands usually assume that the location of various objects in the task space conform to some internal representation (database) of that task space. The ability to quickly and accurately verify the task environment against the internal database would improve the robustness of these preprogrammed commands. In addition, the on-line initialization and maintenance of a task space database is difficult for operators using Cartesian coordinates alone. This paper describes the Interactive Scene' Analysis Module (ISAM) developed to provide taskspace database initialization and verification utilizing 3-D graphic overlay modelling, video imaging, and laser radar based range imaging. Through the fusion of taskspace database information and image sensor data, a verifiable taskspace model is generated providing location and orientation data for objects in a task space. This paper also describes applications of the ISAM in the Intelligent Systems Research Laboratory (ISRL) at NASA Langley Research Center, and discusses its performance relative to representation accuracy and operator interface efficiency.

Interactive Classification Technology

NASA Technical Reports Server (NTRS)

deBessonet, Cary

2000-01-01

The investigators upgraded a knowledge representation language called SL (Symbolic Language) and an automated reasoning system called SMS (Symbolic Manipulation System) to enable the more effective use of the technologies in automated reasoning and interactive classification systems. The overall goals of the project were: 1) the enhancement of the representation language SL to accommodate a wider range of meaning; 2) the development of a default inference scheme to operate over SL notation as it is encoded; and 3) the development of an interpreter for SL that would handle representations of some basic cognitive acts and perspectives.

CEREBRA: a 3-D visualization tool for brain network extracted from fMRI data.

PubMed

Nasir, Baris; Yarman Vural, Fatos T

2016-08-01

In this paper, we introduce a new tool, CEREBRA, to visualize the 3D network of human brain, extracted from the fMRI data. The tool aims to analyze the brain connectivity by representing the selected voxels as the nodes of the network. The edge weights among the voxels are estimated by considering the relationships among the voxel time series. The tool enables the researchers to observe the active brain regions and the interactions among them by using graph theoretic measures, such as, the edge weight and node degree distributions. CEREBRA provides an interactive interface with basic display and editing options for the researchers to study their hypotheses about the connectivity of the brain network. CEREBRA interactively simplifies the network by selecting the active voxels and the most correlated edge weights. The researchers may remove the voxels and edges by using local and global thresholds selected on the window. The built-in graph reduction algorithms are then eliminate the irrelevant regions, voxels and edges and display various properties of the network. The toolbox is capable of space-time representation of the voxel time series and estimated arc weights by using the animated heat maps.

3D acquisition and modeling for flint artefacts analysis

NASA Astrophysics Data System (ADS)

Loriot, B.; Fougerolle, Y.; Sestier, C.; Seulin, R.

2007-07-01

In this paper, we are interested in accurate acquisition and modeling of flint artefacts. Archaeologists needs accurate geometry measurements to refine their understanding of the flint artefacts manufacturing process. Current techniques require several operations. First, a copy of a flint artefact is reproduced. The copy is then sliced. A picture is taken for each slice. Eventually, geometric information is manually determined from the pictures. Such a technique is very time consuming, and the processing applied to the original, as well as the reproduced object, induces several measurement errors (prototyping approximations, slicing, image acquisition, and measurement). By using 3D scanners, we significantly reduce the number of operations related to data acquisition and completely suppress the prototyping step to obtain an accurate 3D model. The 3D models are segmented into sliced parts that are then analyzed. Each slice is then automatically fitted by mathematical representation. Such a representation offers several interesting properties: geometric features can be characterized (e.g. shapes, curvature, sharp edges, etc), and a shape of the original piece of stone can be extrapolated. The contributions of this paper are an acquisition technique using 3D scanners that strongly reduces human intervention, acquisition time and measurement errors, and the representation of flint artefacts as mathematical 2D sections that enable accurate analysis.

Transforming GIS data into functional road models for large-scale traffic simulation.

PubMed

Wilkie, David; Sewall, Jason; Lin, Ming C

2012-06-01

There exists a vast amount of geographic information system (GIS) data that model road networks around the world as polylines with attributes. In this form, the data are insufficient for applications such as simulation and 3D visualization-tools which will grow in power and demand as sensor data become more pervasive and as governments try to optimize their existing physical infrastructure. In this paper, we propose an efficient method for enhancing a road map from a GIS database to create a geometrically and topologically consistent 3D model to be used in real-time traffic simulation, interactive visualization of virtual worlds, and autonomous vehicle navigation. The resulting representation provides important road features for traffic simulations, including ramps, highways, overpasses, legal merge zones, and intersections with arbitrary states, and it is independent of the simulation methodologies. We test the 3D models of road networks generated by our algorithm on real-time traffic simulation using both macroscopic and microscopic techniques.

Metaphores et representations du cerveau plurilingue: conceptions naives ou construction du savior? Exemples dans le contexte d'enseignement andorran (Metaphors and Representations of the Multilingual Brain: Naive Conceptions or Knowledge Construction? Examples in the Context of Andorran Education).

ERIC Educational Resources Information Center

Larruy, Martine Marquillo

2000-01-01

This article concentrates on the use of metaphors characterizing a multilingual brain in a corpus of oral interactions drawn from the Andorran part of an international research study. First, the situation and the status of metaphors in fields connected to the elaboration of knowledge is questioned. Next, the most important metaphors associated to…

Core geometry in perspective

PubMed Central

Dillon, Moira R.; Spelke, Elizabeth S.

2015-01-01

Research on animals, infants, children, and adults provides evidence that distinct cognitive systems underlie navigation and object recognition. Here we examine whether and how these systems interact when children interpret 2D edge-based perspectival line drawings of scenes and objects. Such drawings serve as symbols early in development, and they preserve scene and object geometry from canonical points of view. Young children show limits when using geometry both in non-symbolic tasks and in symbolic map tasks that present 3D contexts from unusual, unfamiliar points of view. When presented with the familiar viewpoints in perspectival line drawings, however, do children engage more integrated geometric representations? In three experiments, children successfully interpreted line drawings with respect to their depicted scene or object. Nevertheless, children recruited distinct processes when navigating based on the information in these drawings, and these processes depended on the context in which the drawings were presented. These results suggest that children are flexible but limited in using geometric information to form integrated representations of scenes and objects, even when interpreting spatial symbols that are highly familiar and faithful renditions of the visual world. PMID:25441089

MATERNAL REPRESENTATIONS AND INFANT ATTACHMENT: AN EXAMINATION OF THE PROTOTYPE HYPOTHESIS.

PubMed

Madigan, Sheri; Hawkins, Erinn; Plamondon, Andre; Moran, Greg; Benoit, Diane

2015-01-01

The prototype hypothesis suggests that attachment representations derived in infancy continue to influence subsequent relationships over the life span, including those formed with one's own children. In the current study, we test the prototype hypothesis by exploring (a) whether child-specific representations following actual experience in interaction with a specific child impacts caregiver-child attachment over and above the prenatal forecast of that representation and (b) whether maternal attachment representations exert their influence on infant attachment via the more child-specific representation of that relationship. In a longitudinal study of 84 mother-infant dyads, mothers' representations of their attachment history were obtained prenatally with the Adult Attachment Interview (AAI; M. Main, R. Goldwyn, & E. Hesse, 2002), representations of relationship with a specific child were assessed with the Working Model of the Child Interview (WMCI; C.H. Zeanah, D. Benoit, & L. Barton, 1986), collected both prenatally and again at infant age 11 months, and infant attachment was assessed in the Strange Situation Procedure (M.D.S. Ainsworth, M.C. Blehar, E. Walters, & S. Wall, 1978) when infants were 11 months of age. Consistent with the prototype hypothesis, considerable correspondence was found between mothers' AAI and WMCI classifications. A mediation analysis showed that WMCI fully accounted for the association between AAI and infant attachment. Postnatal WMCI measured at 11 months' postpartum did not add to the prediction of infant attachment, over and above that explained by the prenatal WMCI. Implications for these findings are discussed. © 2015 Michigan Association for Infant Mental Health.

Neural dynamics of 3-D surface perception: figure-ground separation and lightness perception.

PubMed

Kelly, F; Grossberg, S

2000-11-01

This article develops the FACADE theory of three-dimensional (3-D) vision to simulate data concerning how two-dimensional pictures give rise to 3-D percepts of occluded and occluding surfaces. The theory suggests how geometrical and contrastive properties of an image can either cooperate or compete when forming the boundary and surface representations that subserve conscious visual percepts. Spatially long-range cooperation and short-range competition work together to separate boundaries of occluding figures from their occluded neighbors, thereby providing sensitivity to T-junctions without the need to assume that T-junction "detectors" exist. Both boundary and surface representations of occluded objects may be amodally completed, whereas the surface representations of unoccluded objects become visible through modal processes. Computer simulations include Bregman-Kanizsa figure-ground separation, Kanizsa stratification, and various lightness percepts, including the Münker-White, Benary cross, and checkerboard percepts.

Overview of EVE - the event visualization environment of ROOT

NASA Astrophysics Data System (ADS)

Tadel, Matevž

2010-04-01

EVE is a high-level visualization library using ROOT's data-processing, GUI and OpenGL interfaces. It is designed as a framework for object management offering hierarchical data organization, object interaction and visualization via GUI and OpenGL representations. Automatic creation of 2D projected views is also supported. On the other hand, it can serve as an event visualization toolkit satisfying most HEP requirements: visualization of geometry, simulated and reconstructed data such as hits, clusters, tracks and calorimeter information. Special classes are available for visualization of raw-data. Object-interaction layer allows for easy selection and highlighting of objects and their derived representations (projections) across several views (3D, Rho-Z, R-Phi). Object-specific tooltips are provided in both GUI and GL views. The visual-configuration layer of EVE is built around a data-base of template objects that can be applied to specific instances of visualization objects to ensure consistent object presentation. The data-base can be retrieved from a file, edited during the framework operation and stored to file. EVE prototype was developed within the ALICE collaboration and has been included into ROOT in December 2007. Since then all EVE components have reached maturity. EVE is used as the base of AliEve visualization framework in ALICE, Firework physics-oriented event-display in CMS, and as the visualization engine of FairRoot in FAIR.

Implementation multi representation and oral communication skills in Department of Physics Education on Elementary Physics II

NASA Astrophysics Data System (ADS)

Kusumawati, Intan; Marwoto, Putut; Linuwih, Suharto

2015-09-01

The ability of multi representation has been widely studied, but there has been no implementation through a model of learning. This study aimed to determine the ability of the students multi representation, relationships multi representation capabilities and oral communication skills, as well as the application of the relations between the two capabilities through learning model Presentatif Based on Multi representation (PBM) in solving optical geometric (Elementary Physics II). A concurrent mixed methods research methods with qualitative-quantitative weights. Means of collecting data in the form of the pre-test and post-test with essay form, observation sheets oral communication skills, and assessment of learning by observation sheet PBM-learning models all have a high degree of respectively validity category is 3.91; 4.22; 4.13; 3.88. Test reliability with Alpha Cronbach technique, reliability coefficient of 0.494. The students are department of Physics Education Unnes as a research subject. Sequence multi representation tendency of students from high to low in sequence, representation of M, D, G, V; whereas the order of accuracy, the group representation V, D, G, M. Relationship multi representation ability and oral communication skills, comparable/proportional. Implementation conjunction generate grounded theory. This study should be applied to the physics of matter, or any other university for comparison.

Creating 3D visualizations of MRI data: A brief guide.

PubMed

Madan, Christopher R

2015-01-01

While magnetic resonance imaging (MRI) data is itself 3D, it is often difficult to adequately present the results papers and slides in 3D. As a result, findings of MRI studies are often presented in 2D instead. A solution is to create figures that include perspective and can convey 3D information; such figures can sometimes be produced by standard functional magnetic resonance imaging (fMRI) analysis packages and related specialty programs. However, many options cannot provide functionality such as visualizing activation clusters that are both cortical and subcortical (i.e., a 3D glass brain), the production of several statistical maps with an identical perspective in the 3D rendering, or animated renderings. Here I detail an approach for creating 3D visualizations of MRI data that satisfies all of these criteria. Though a 3D 'glass brain' rendering can sometimes be difficult to interpret, they are useful in showing a more overall representation of the results, whereas the traditional slices show a more local view. Combined, presenting both 2D and 3D representations of MR images can provide a more comprehensive view of the study's findings.

Creating 3D visualizations of MRI data: A brief guide

PubMed Central

Madan, Christopher R.

2015-01-01

While magnetic resonance imaging (MRI) data is itself 3D, it is often difficult to adequately present the results papers and slides in 3D. As a result, findings of MRI studies are often presented in 2D instead. A solution is to create figures that include perspective and can convey 3D information; such figures can sometimes be produced by standard functional magnetic resonance imaging (fMRI) analysis packages and related specialty programs. However, many options cannot provide functionality such as visualizing activation clusters that are both cortical and subcortical (i.e., a 3D glass brain), the production of several statistical maps with an identical perspective in the 3D rendering, or animated renderings. Here I detail an approach for creating 3D visualizations of MRI data that satisfies all of these criteria. Though a 3D ‘glass brain’ rendering can sometimes be difficult to interpret, they are useful in showing a more overall representation of the results, whereas the traditional slices show a more local view. Combined, presenting both 2D and 3D representations of MR images can provide a more comprehensive view of the study’s findings. PMID:26594340

On the elimination of the electronic structure bottleneck in on the fly nonadiabatic dynamics for small to moderate sized (10-15 atom) molecules using fit diabatic representations based solely on ab initio electronic structure data: The photodissociation of phenol

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Xiaolei, E-mail: virtualzx@gmail.com; Yarkony, David R., E-mail: yarkony@jhu.edu

2016-01-14

In this work, we demonstrate that for moderate sized systems, here a system with 13 atoms, global coupled potential energy surfaces defined for several electronic states over a wide energy range and for distinct regions of nuclear coordinate space characterized by distinct electron configurations, can be constructed with precise energetics and an excellent description of non-adiabatic interactions in all regions. This is accomplished using a recently reported algorithm for constructing quasi-diabatic representations, H{sup d}, of adiabatic electronic states coupled by conical intersections. In this work, the algorithm is used to construct an H{sup d} to describe the photodissociation of phenolmore » from its first and second excited electronic states. The representation treats all 33 internal degrees of freedom in an even handed manner. The ab initio adiabatic electronic structure data used to construct the fit are obtained exclusively from multireference configuration interaction with single and double excitation wave functions comprised of 88 × 10{sup 6} configuration state functions, at geometries determined by quasi-classical trajectories. Since the algorithm uses energy gradients and derivative couplings in addition to electronic energies to construct H{sup d}, data at only 7379 nuclear configurations are required to construct a representation, which describes all nuclear configurations involved in H atom photodissociation to produce the phenoxyl radical in its ground or first excited electronic state, with a mean unsigned energy error of 202.9 cm{sup −1} for electronic energies <60 000 cm{sup −1}.« less

Surveying, Modeling and 3d Representation of a wreck for Diving Purposes: Cargo Ship "vera"

NASA Astrophysics Data System (ADS)

Ktistis, A.; Tokmakidis, P.; Papadimitriou, K.

2017-02-01

This paper presents the results from an underwater recording of the stern part of a contemporary cargo-ship wreck. The aim of this survey was to create 3D representations of this wreck mainly for recreational diving purposes. The key points of this paper are: a) the implementation of the underwater recording at a diving site; b) the reconstruction of a 3d model from data that have been captured by recreational divers; and c) the development of a set of products to be used by the general public for the ex situ presentation or for the in situ navigation. The idea behind this project is to define a simple and low cost procedure for the surveying, modeling and 3D representation of a diving site. The perspective of our team is to repeat the proposed methodology for the documentation and the promotion of other diving sites with cultural features, as well as to train recreational divers in underwater surveying procedures towards public awareness and community engagement in the maritime heritage.

Rhorix: An interface between quantum chemical topology and the 3D graphics program blender

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mills, Matthew J. L.; Sale, Kenneth L.; Simmons, Blake A.

Journal of Computational Chemistry Published by Wiley Periodicals, Inc. Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter-free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition ofmore » mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add-On” named Rhorix for the state-of-the-art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. Finally, a number of examples are discussed..« less

Rhorix: An interface between quantum chemical topology and the 3D graphics program blender

PubMed Central

Sale, Kenneth L.; Simmons, Blake A.; Popelier, Paul L. A.

2017-01-01

Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter‐free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition of mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add‐On” named Rhorix for the state‐of‐the‐art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. A number of examples are discussed. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:28857244

Face recognition from unconstrained three-dimensional face images using multitask sparse representation

NASA Astrophysics Data System (ADS)

Bentaieb, Samia; Ouamri, Abdelaziz; Nait-Ali, Amine; Keche, Mokhtar

2018-01-01

We propose and evaluate a three-dimensional (3D) face recognition approach that applies the speeded up robust feature (SURF) algorithm to the depth representation of shape index map, under real-world conditions, using only a single gallery sample for each subject. First, the 3D scans are preprocessed, then SURF is applied on the shape index map to find interest points and their descriptors. Each 3D face scan is represented by keypoints descriptors, and a large dictionary is built from all the gallery descriptors. At the recognition step, descriptors of a probe face scan are sparsely represented by the dictionary. A multitask sparse representation classification is used to determine the identity of each probe face. The feasibility of the approach that uses the SURF algorithm on the shape index map for face identification/authentication is checked through an experimental investigation conducted on Bosphorus, University of Milano Bicocca, and CASIA 3D datasets. It achieves an overall rank one recognition rate of 97.75%, 80.85%, and 95.12%, respectively, on these datasets.

Rhorix: An interface between quantum chemical topology and the 3D graphics program blender

DOE PAGES

Mills, Matthew J. L.; Sale, Kenneth L.; Simmons, Blake A.; ...

2017-08-31

Journal of Computational Chemistry Published by Wiley Periodicals, Inc. Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter-free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition ofmore » mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add-On” named Rhorix for the state-of-the-art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. Finally, a number of examples are discussed..« less

Spontaneous breaking of scale invariance in a D = 3 U(N ) model with Chern-Simons gauge fields

DOE PAGES

Bardeen, William A.; Moshe, Moshe

2014-06-18

We study spontaneous breaking of scale invariance in the large N limit of three dimensional U(N ) κ Chern-Simons theories coupled to a scalar field in the fundamental representation. When a λ 6 ( Ø † · Ø) 3 self interaction term is added to the action we find a massive phase at a certain critical value for a combination of the λ(6) and ’t Hooft’s λ = N/κ couplings. This model attracted recent attention since at finite κ it contains a singlet sector which is conjectured to be dual to Vasiliev’s higher spin gravity on AdS 4. Our papermore » concentrates on the massive phase of the 3d boundary theory. We discuss the advantage of introducing masses in the boundary theory through spontaneous breaking of scale invariance.« less

The Effect of Using a Visual Representation Tool in a Teaching-Learning Sequence for Teaching Newton's Third Law

ERIC Educational Resources Information Center

Savinainen, Antti; Mäkynen, Asko; Nieminen, Pasi; Viiri, Jouni

2017-01-01

This paper presents a research-based teaching-learning sequence (TLS) that focuses on the notion of interaction in teaching Newton's third law (N3 law) which is, as earlier studies have shown, a challenging topic for students to learn. The TLS made systematic use of a visual representation tool--an interaction diagram (ID)--highlighting…

Study on Information Management for the Conservation of Traditional Chinese Architectural Heritage - 3d Modelling and Metadata Representation

NASA Astrophysics Data System (ADS)

Yen, Y. N.; Weng, K. H.; Huang, H. Y.

2013-07-01

After over 30 years of practise and development, Taiwan's architectural conservation field is moving rapidly into digitalization and its applications. Compared to modern buildings, traditional Chinese architecture has considerably more complex elements and forms. To document and digitize these unique heritages in their conservation lifecycle is a new and important issue. This article takes the caisson ceiling of the Taipei Confucius Temple, octagonal with 333 elements in 8 types, as a case study for digitization practise. The application of metadata representation and 3D modelling are the two key issues to discuss. Both Revit and SketchUp were appliedin this research to compare its effectiveness to metadata representation. Due to limitation of the Revit database, the final 3D models wasbuilt with SketchUp. The research found that, firstly, cultural heritage databasesmustconvey that while many elements are similar in appearance, they are unique in value; although 3D simulations help the general understanding of architectural heritage, software such as Revit and SketchUp, at this stage, could onlybe used tomodel basic visual representations, and is ineffective indocumenting additional critical data ofindividually unique elements. Secondly, when establishing conservation lifecycle information for application in management systems, a full and detailed presentation of the metadata must also be implemented; the existing applications of BIM in managing conservation lifecycles are still insufficient. Results of the research recommends SketchUp as a tool for present modelling needs, and BIM for sharing data between users, but the implementation of metadata representation is of the utmost importance.

A kinematic model for 3-D head-free gaze-shifts

PubMed Central

Daemi, Mehdi; Crawford, J. Douglas

2015-01-01

Rotations of the line of sight are mainly implemented by coordinated motion of the eyes and head. Here, we propose a model for the kinematics of three-dimensional (3-D) head-unrestrained gaze-shifts. The model was designed to account for major principles in the known behavior, such as gaze accuracy, spatiotemporal coordination of saccades with vestibulo-ocular reflex (VOR), relative eye and head contributions, the non-commutativity of rotations, and Listing's and Fick constraints for the eyes and head, respectively. The internal design of the model was inspired by known and hypothesized elements of gaze control physiology. Inputs included retinocentric location of the visual target and internal representations of initial 3-D eye and head orientation, whereas outputs were 3-D displacements of eye relative to the head and head relative to shoulder. Internal transformations decomposed the 2-D gaze command into 3-D eye and head commands with the use of three coordinated circuits: (1) a saccade generator, (2) a head rotation generator, (3) a VOR predictor. Simulations illustrate that the model can implement: (1) the correct 3-D reference frame transformations to generate accurate gaze shifts (despite variability in other parameters), (2) the experimentally verified constraints on static eye and head orientations during fixation, and (3) the experimentally observed 3-D trajectories of eye and head motion during gaze-shifts. We then use this model to simulate how 2-D eye-head coordination strategies interact with 3-D constraints to influence 3-D orientations of the eye-in-space, and the implications of this for spatial vision. PMID:26113816

Visual Representations of Texture

DTIC Science & Technology

1988-12-15

mm 󈧏 I I I In o,. ITY CkASISIFICATION OF THIS G , - - -REPORT DOCUMENTATION PAGE la. REPORT SECURITY CLASSIFICATION b . RESTRICTIVE MARKINGS ,ij...experiments investigating the interaction of size and contrast in texture segregation,( b ) compared our experimental results with the calculated outputs of a M...investigating the interaction of size and contrast in texture segregation, ( b ) compared our experimental results with the calculated outputs of a 2D

Using "Slowmation" to Enable Preservice Primary Teachers to Create Multimodal Representations of Science Concepts

ERIC Educational Resources Information Center

Hoban, Garry; Nielsen, Wendy

2012-01-01

Research has identified the value of students constructing their own representations of science concepts using modes such as writing, diagrams, 2-D and 3-D models, images or speech to communicate meaning. "Slowmation" (abbreviated from "Slow Animation") is a simplified way for students, such as preservice teachers, to make a narrated animation…

Quantum-mechanical approach to predissociation of water dimers in the vibrational adiabatic representation: Importance of channel interactions.

PubMed

Mineo, H; Niu, Y L; Kuo, J L; Lin, S H; Fujimura, Y

2015-08-28

The results of application of the quantum-mechanical adiabatic theory to vibrational predissociation (VPD) of water dimers, (H2O)2 and (D2O)2, are presented. We consider the VPD processes including the totally symmetric OH mode of the dimer and the bending mode of the fragment. The VPD in the adiabatic representation is induced by breakdown of the vibrational adiabatic approximation, and two types of nonadiabatic coupling matrix elements are involved: one provides the VPD induced by the low-frequency dissociation mode and the other provides the VPD through channel interactions induced by the low-frequency modes. The VPD rate constants were calculated using the Fermi golden rule expression. A closed form for the nonadiabatic transition matrix element between the discrete and continuum states was derived in the Morse potential model. All of the parameters used were obtained from the potential surfaces of the water dimers, which were calculated by the density functional theory procedures. The VPD rate constants for the two processes were calculated in the non-Condon scheme beyond the so-called Condon approximation. The channel interactions in and between the initial and final states were taken into account, and those are found to increase the VPD rates by 3(1) orders of magnitude for the VPD processes in (H2O)2 ((D2O)2). The fraction of the bending-excited donor fragments is larger than that of the bending-excited acceptor fragments. The results obtained by quantum-mechanical approach are compared with both experimental and quasi-classical trajectory calculation results.

Planning 3-D collision-free paths using spheres

NASA Technical Reports Server (NTRS)

Bonner, Susan; Kelley, Robert B.

1989-01-01

A scheme for the representation of objects, the Successive Spherical Approximation (SSA), facilitates the rapid planning of collision-free paths in a 3-D, dynamic environment. The hierarchical nature of the SSA allows collision-free paths to be determined efficiently while still providing for the exact representation of dynamic objects. The concept of a freespace cell is introduced to allow human 3-D conceptual knowledge to be used in facilitating satisfying choices for paths. Collisions can be detected at a rate better than 1 second per environment object per path. This speed enables the path planning process to apply a hierarchy of rules to create a heuristically satisfying collision-free path.

Towards a Normalised 3D Geovisualisation: The Viewpoint Management

NASA Astrophysics Data System (ADS)

Neuville, R.; Poux, F.; Hallot, P.; Billen, R.

2016-10-01

This paper deals with the viewpoint management in 3D environments considering an allocentric environment. The recent advances in computer sciences and the growing number of affordable remote sensors lead to impressive improvements in the 3D visualisation. Despite some research relating to the analysis of visual variables used in 3D environments, we notice that it lacks a real standardisation of 3D representation rules. In this paper we study the "viewpoint" as being the first considered parameter for a normalised visualisation of 3D data. Unlike in a 2D environment, the viewing direction is not only fixed in a top down direction in 3D. A non-optimal camera location means a poor 3D representation in terms of relayed information. Based on this statement we propose a model based on the analysis of the computational display pixels that determines a viewpoint maximising the relayed information according to one kind of query. We developed an OpenGL prototype working on screen pixels that allows to determine the optimal camera location based on a screen pixels colour algorithm. The viewpoint management constitutes a first step towards a normalised 3D geovisualisation.

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels.

PubMed

Berka, Karel; Hanák, Ondrej; Sehnal, David; Banás, Pavel; Navrátilová, Veronika; Jaiswal, Deepti; Ionescu, Crina-Maria; Svobodová Vareková, Radka; Koca, Jaroslav; Otyepka, Michal

2012-07-01

Biomolecular channels play important roles in many biological systems, e.g. enzymes, ribosomes and ion channels. This article introduces a web-based interactive MOLEonline 2.0 application for the analysis of access/egress paths to interior molecular voids. MOLEonline 2.0 enables platform-independent, easy-to-use and interactive analyses of (bio)macromolecular channels, tunnels and pores. Results are presented in a clear manner, making their interpretation easy. For each channel, MOLEonline displays a 3D graphical representation of the channel, its profile accompanied by a list of lining residues and also its basic physicochemical properties. The users can tune advanced parameters when performing a channel search to direct the search according to their needs. The MOLEonline 2.0 application is freely available via the Internet at http://ncbr.muni.cz/mole or http://mole.upol.cz.

Computer display and manipulation of biological molecules

NASA Technical Reports Server (NTRS)

Coeckelenbergh, Y.; Macelroy, R. D.; Hart, J.; Rein, R.

1978-01-01

This paper describes a computer model that was designed to investigate the conformation of molecules, macromolecules and subsequent complexes. Utilizing an advanced 3-D dynamic computer display system, the model is sufficiently versatile to accommodate a large variety of molecular input and to generate data for multiple purposes such as visual representation of conformational changes, and calculation of conformation and interaction energy. Molecules can be built on the basis of several levels of information. These include the specification of atomic coordinates and connectivities and the grouping of building blocks and duplicated substructures using symmetry rules found in crystals and polymers such as proteins and nucleic acids. Called AIMS (Ames Interactive Molecular modeling System), the model is now being used to study pre-biotic molecular evolution toward life.

4D Hyperspherical Harmonic (HyperSPHARM) Representation of Multiple Disconnected Brain Subcortical Structures

PubMed Central

Hosseinbor, A. Pasha; Chung, Moo K.; Schaefer, Stacey M.; van Reekum, Carien M.; Peschke-Schmitz, Lara; Sutterer, Matt; Alexander, Andrew L.; Davidson, Richard J.

2014-01-01

We present a novel surface parameterization technique using hyperspherical harmonics (HSH) in representing compact, multiple, disconnected brain subcortical structures as a single analytic function. The proposed hyperspherical harmonic representation (HyperSPHARM) has many advantages over the widely used spherical harmonic (SPHARM) parameterization technique. SPHARM requires flattening 3D surfaces to 3D sphere which can be time consuming for large surface meshes, and can’t represent multiple disconnected objects with single parameterization. On the other hand, HyperSPHARM treats 3D object, via simple stereographic projection, as a surface of 4D hypersphere with extremely large radius, hence avoiding the computationally demanding flattening process. HyperSPHARM is shown to achieve a better reconstruction with only 5 basis compared to SPHARM that requires more than 441. PMID:24505716

Microscopic transport model animation visualisation on KML base

NASA Astrophysics Data System (ADS)

Yatskiv, I.; Savrasovs, M.

2012-10-01

By reading classical literature devoted to the simulation theory it could be found that one of the greatest possibilities of simulation is the ability to present processes inside the system by animation. This gives to the simulation model additional value during presentation of simulation results for the public and authorities who are not familiar enough with simulation. That is why most of universal and specialised simulation tools have the ability to construct 2D and 3D representation of the model. Usually the development of such representation could take much time and there must be put a lot forces into creating an adequate 3D representation of the model. For long years such well-known microscopic traffic flow simulation software tools as VISSIM, AIMSUN and PARAMICS have had a possibility to produce 2D and 3D animation. But creation of realistic 3D model of the place where traffic flows are simulated, even in these professional software tools it is a hard and time consuming action. The goal of this paper is to describe the concepts of use the existing on-line geographical information systems for visualisation of animation produced by simulation software. For demonstration purposes the following technologies and tools have been used: PTV VISION VISSIM, KML and Google Earth.

High-quality and interactive animations of 3D time-varying vector fields.

PubMed

Helgeland, Anders; Elboth, Thomas

2006-01-01

In this paper, we present an interactive texture-based method for visualizing three-dimensional unsteady vector fields. The visualization method uses a sparse and global representation of the flow, such that it does not suffer from the same perceptual issues as is the case for visualizing dense representations. The animation is made by injecting a collection of particles evenly distributed throughout the physical domain. These particles are then tracked along their path lines. At each time step, these particles are used as seed points to generate field lines using any vector field such as the velocity field or vorticity field. In this way, the animation shows the advection of particles while each frame in the animation shows the instantaneous vector field. In order to maintain a coherent particle density and to avoid clustering as time passes, we have developed a novel particle advection strategy which produces approximately evenly-spaced field lines at each time step. To improve rendering performance, we decouple the rendering stage from the preceding stages of the visualization method. This allows interactive exploration of multiple fields simultaneously, which sets the stage for a more complete analysis of the flow field. The final display is rendered using texture-based direct volume rendering.

Structure-based barcoding of proteins.

PubMed

Metri, Rahul; Jerath, Gaurav; Kailas, Govind; Gacche, Nitin; Pal, Adityabarna; Ramakrishnan, Vibin

2014-01-01

A reduced representation in the format of a barcode has been developed to provide an overview of the topological nature of a given protein structure from 3D coordinate file. The molecular structure of a protein coordinate file from Protein Data Bank is first expressed in terms of an alpha-numero code and further converted to a barcode image. The barcode representation can be used to compare and contrast different proteins based on their structure. The utility of this method has been exemplified by comparing structural barcodes of proteins that belong to same fold family, and across different folds. In addition to this, we have attempted to provide an illustration to (i) the structural changes often seen in a given protein molecule upon interaction with ligands and (ii) Modifications in overall topology of a given protein during evolution. The program is fully downloadable from the website http://www.iitg.ac.in/probar/. © 2013 The Protein Society.

The Impact of Air-Sea Interactions on the Representation of Tropical Precipitation Extremes

NASA Astrophysics Data System (ADS)

Hirons, L. C.; Klingaman, N. P.; Woolnough, S. J.

2018-02-01

The impacts of air-sea interactions on the representation of tropical precipitation extremes are investigated using an atmosphere-ocean-mixed-layer coupled model. The coupled model is compared to two atmosphere-only simulations driven by the coupled-model sea-surface temperatures (SSTs): one with 31 day running means (31 d), the other with a repeating mean annual cycle. This allows separation of the effects of interannual SST variability from those of coupled feedbacks on shorter timescales. Crucially, all simulations have a consistent mean state with very small SST biases against present-day climatology. 31d overestimates the frequency, intensity, and persistence of extreme tropical precipitation relative to the coupled model, likely due to excessive SST-forced precipitation variability. This implies that atmosphere-only attribution and time-slice experiments may overestimate the strength and duration of precipitation extremes. In the coupled model, air-sea feedbacks damp extreme precipitation, through negative local thermodynamic feedbacks between convection, surface fluxes, and SST.

Volumetric 3D display using a DLP projection engine

NASA Astrophysics Data System (ADS)

Geng, Jason

2012-03-01

In this article, we describe a volumetric 3D display system based on the high speed DLPTM (Digital Light Processing) projection engine. Existing two-dimensional (2D) flat screen displays often lead to ambiguity and confusion in high-dimensional data/graphics presentation due to lack of true depth cues. Even with the help of powerful 3D rendering software, three-dimensional (3D) objects displayed on a 2D flat screen may still fail to provide spatial relationship or depth information correctly and effectively. Essentially, 2D displays have to rely upon capability of human brain to piece together a 3D representation from 2D images. Despite the impressive mental capability of human visual system, its visual perception is not reliable if certain depth cues are missing. In contrast, volumetric 3D display technologies to be discussed in this article are capable of displaying 3D volumetric images in true 3D space. Each "voxel" on a 3D image (analogous to a pixel in 2D image) locates physically at the spatial position where it is supposed to be, and emits light from that position toward omni-directions to form a real 3D image in 3D space. Such a volumetric 3D display provides both physiological depth cues and psychological depth cues to human visual system to truthfully perceive 3D objects. It yields a realistic spatial representation of 3D objects and simplifies our understanding to the complexity of 3D objects and spatial relationship among them.

A Representation for Visual Information.

DTIC Science & Technology

1981-11-01

receive 3-D information. Tlhe representation described here is well suited for the analysis of stereo pairs. It is also well suited for the...cylinder representation [Agin and Binford 731, [Nevadia and Binford 741 and de Medial Axis Transfonm [Blum 67] as examples of representations that have...negative minimum are de points at which that filter most strongly resembles the input signal. If the inner- product at that point is also larger than inner

Thalamocortical dynamics of the McCollough effect: boundary-surface alignment through perceptual learning.

PubMed

Grossberg, Stephen; Hwang, Seungwoo; Mingolla, Ennio

2002-05-01

This article further develops the FACADE neural model of 3-D vision and figure-ground perception to quantitatively explain properties of the McCollough effect (ME). The model proposes that many ME data result from visual system mechanisms whose primary function is to adaptively align, through learning, boundary and surface representations that are positionally shifted due to the process of binocular fusion. For example, binocular boundary representations are shifted by binocular fusion relative to monocular surface representations, yet the boundaries must become positionally aligned with the surfaces to control binocular surface capture and filling-in. The model also includes perceptual reset mechanisms that use habituative transmitters in opponent processing circuits. Thus the model shows how ME data may arise from a combination of mechanisms that have a clear functional role in biological vision. Simulation results with a single set of parameters quantitatively fit data from 13 experiments that probe the nature of achromatic/chromatic and monocular/binocular interactions during induction of the ME. The model proposes how perceptual learning, opponent processing, and habituation at both monocular and binocular surface representations are involved, including early thalamocortical sites. In particular, it explains the anomalous ME utilizing these multiple processing sites. Alternative models of the ME are also summarized and compared with the present model.

Use of molecular modeling to determine the interaction and competition of gases within coal for carbon dioxide sequestration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jeffrey D. Evanseck; Jeffry D. Madura; Jonathan P. Mathews

2006-04-21

Molecular modeling was employed to both visualize and probe our understanding of carbon dioxide sequestration within a bituminous coal. A large-scale (>20,000 atoms) 3D molecular representation of Pocahontas No. 3 coal was generated. This model was constructed based on a the review data of Stock and Muntean, oxidation and decarboxylation data for aromatic clustersize frequency of Stock and Obeng, and the combination of Laser Desorption Mass Spectrometry data with HRTEM, enabled the inclusion of a molecular weight distribution. The model contains 21,931 atoms, with a molecular mass of 174,873 amu, and an average molecular weight of 714 amu, with 201more » structural components. The structure was evaluated based on several characteristics to ensure a reasonable constitution (chemical and physical representation). The helium density of Pocahontas No. 3 coal is 1.34 g/cm{sup 3} (dmmf) and the model was 1.27 g/cm{sup 3}. The structure is microporous, with a pore volume comprising 34% of the volume as expected for a coal of this rank. The representation was used to visualize CO{sub 2}, and CH{sub 4} capacity, and the role of moisture in swelling and CO{sub 2}, and CH{sub 4} capacity reduction. Inclusion of 0.68% moisture by mass (ash-free) enabled the model to swell by 1.2% (volume). Inclusion of CO{sub 2} enabled volumetric swelling of 4%.« less

PL-PatchSurfer: a novel molecular local surface-based method for exploring protein-ligand interactions.

PubMed

Hu, Bingjie; Zhu, Xiaolei; Monroe, Lyman; Bures, Mark G; Kihara, Daisuke

2014-08-27

Structure-based computational methods have been widely used in exploring protein-ligand interactions, including predicting the binding ligands of a given protein based on their structural complementarity. Compared to other protein and ligand representations, the advantages of a surface representation include reduced sensitivity to subtle changes in the pocket and ligand conformation and fast search speed. Here we developed a novel method named PL-PatchSurfer (Protein-Ligand PatchSurfer). PL-PatchSurfer represents the protein binding pocket and the ligand molecular surface as a combination of segmented surface patches. Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD). We first tested PL-PatchSurfer on binding ligand prediction and found it outperformed the pocket-similarity based ligand prediction program. We then optimized the search algorithm of PL-PatchSurfer using the PDBbind dataset. Finally, we explored the utility of applying PL-PatchSurfer to a larger and more diverse dataset and showed that PL-PatchSurfer was able to provide a high early enrichment for most of the targets. To the best of our knowledge, PL-PatchSurfer is the first surface patch-based method that treats ligand complementarity at protein binding sites. We believe that using a surface patch approach to better understand protein-ligand interactions has the potential to significantly enhance the design of new ligands for a wide array of drug-targets.

PL-PatchSurfer: A Novel Molecular Local Surface-Based Method for Exploring Protein-Ligand Interactions

PubMed Central

Hu, Bingjie; Zhu, Xiaolei; Monroe, Lyman; Bures, Mark G.; Kihara, Daisuke

2014-01-01

Structure-based computational methods have been widely used in exploring protein-ligand interactions, including predicting the binding ligands of a given protein based on their structural complementarity. Compared to other protein and ligand representations, the advantages of a surface representation include reduced sensitivity to subtle changes in the pocket and ligand conformation and fast search speed. Here we developed a novel method named PL-PatchSurfer (Protein-Ligand PatchSurfer). PL-PatchSurfer represents the protein binding pocket and the ligand molecular surface as a combination of segmented surface patches. Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD). We first tested PL-PatchSurfer on binding ligand prediction and found it outperformed the pocket-similarity based ligand prediction program. We then optimized the search algorithm of PL-PatchSurfer using the PDBbind dataset. Finally, we explored the utility of applying PL-PatchSurfer to a larger and more diverse dataset and showed that PL-PatchSurfer was able to provide a high early enrichment for most of the targets. To the best of our knowledge, PL-PatchSurfer is the first surface patch-based method that treats ligand complementarity at protein binding sites. We believe that using a surface patch approach to better understand protein-ligand interactions has the potential to significantly enhance the design of new ligands for a wide array of drug-targets. PMID:25167137

New approaches to high-resolution mapping of marine vertical structures.

PubMed

Robert, Katleen; Huvenne, Veerle A I; Georgiopoulou, Aggeliki; Jones, Daniel O B; Marsh, Leigh; D O Carter, Gareth; Chaumillon, Leo

2017-08-21

Vertical walls in marine environments can harbour high biodiversity and provide natural protection from bottom-trawling activities. However, traditional mapping techniques are usually restricted to down-looking approaches which cannot adequately replicate their 3D structure. We combined sideways-looking multibeam echosounder (MBES) data from an AUV, forward-looking MBES data from ROVs and ROV-acquired videos to examine walls from Rockall Bank and Whittard Canyon, Northeast Atlantic. High-resolution 3D point clouds were extracted from each sonar dataset and structure from motion photogrammetry (SfM) was applied to recreate 3D representations of video transects along the walls. With these reconstructions, it was possible to interact with extensive sections of video footage and precisely position individuals. Terrain variables were derived on scales comparable to those experienced by megabenthic individuals. These were used to show differences in environmental conditions between observed and background locations as well as explain spatial patterns in ecological characteristics. In addition, since the SfM 3D reconstructions retained colours, they were employed to separate and quantify live coral colonies versus dead framework. The combination of these new technologies allows us, for the first time, to map the physical 3D structure of previously inaccessible habitats and demonstrates the complexity and importance of vertical structures.

IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data

PubMed Central

Kaas, Quentin; Ruiz, Manuel; Lefranc, Marie-Paule

2004-01-01

IMGT/3Dstructure-DB and IMGT/Structural-Query are a novel 3D structure database and a new tool for immunological proteins. They are part of IMGT, the international ImMunoGenetics information system®, a high-quality integrated knowledge resource specializing in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) and related proteins of the immune system (RPI) of human and other vertebrate species, which consists of databases, Web resources and interactive on-line tools. IMGT/3Dstructure-DB data are described according to the IMGT Scientific chart rules based on the IMGT-ONTOLOGY concepts. IMGT/3Dstructure-DB provides IMGT gene and allele identification of IG, TR and MHC proteins with known 3D structures, domain delimitations, amino acid positions according to the IMGT unique numbering and renumbered coordinate flat files. Moreover IMGT/3Dstructure-DB provides 2D graphical representations (or Collier de Perles) and results of contact analysis. The IMGT/StructuralQuery tool allows search of this database based on specific structural characteristics. IMGT/3Dstructure-DB and IMGT/StructuralQuery are freely available at http://imgt.cines.fr. PMID:14681396

Excitation basis for (3+1)d topological phases

NASA Astrophysics Data System (ADS)

Delcamp, Clement

2017-12-01

We consider an exactly solvable model in 3+1 dimensions, based on a finite group, which is a natural generalization of Kitaev's quantum double model. The corresponding lattice Hamiltonian yields excitations located at torus-boundaries. By cutting open the three-torus, we obtain a manifold bounded by two tori which supports states satisfying a higher-dimensional version of Ocneanu's tube algebra. This defines an algebraic structure extending the Drinfel'd double. Its irreducible representations, labeled by two fluxes and one charge, characterize the torus-excitations. The tensor product of such representations is introduced in order to construct a basis for (3+1)d gauge models which relies upon the fusion of the defect excitations. This basis is defined on manifolds of the form Σ × S_1 , with Σ a two-dimensional Riemann surface. As such, our construction is closely related to dimensional reduction from (3+1)d to (2+1)d topological orders.

Implementation multi representation and oral communication skills in Department of Physics Education on Elementary Physics II

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kusumawati, Intan, E-mail: intankusumawati10@gmail.com; Marwoto, Putut, E-mail: pmarwoto@yahoo.com; Linuwih, Suharto, E-mail: suhartolinuwih@gmail.com

The ability of multi representation has been widely studied, but there has been no implementation through a model of learning. This study aimed to determine the ability of the students multi representation, relationships multi representation capabilities and oral communication skills, as well as the application of the relations between the two capabilities through learning model Presentatif Based on Multi representation (PBM) in solving optical geometric (Elementary Physics II). A concurrent mixed methods research methods with qualitative–quantitative weights. Means of collecting data in the form of the pre-test and post-test with essay form, observation sheets oral communication skills, and assessment ofmore » learning by observation sheet PBM–learning models all have a high degree of respectively validity category is 3.91; 4.22; 4.13; 3.88. Test reliability with Alpha Cronbach technique, reliability coefficient of 0.494. The students are department of Physics Education Unnes as a research subject. Sequence multi representation tendency of students from high to low in sequence, representation of M, D, G, V; whereas the order of accuracy, the group representation V, D, G, M. Relationship multi representation ability and oral communication skills, comparable/proportional. Implementation conjunction generate grounded theory. This study should be applied to the physics of matter, or any other university for comparison.« less

Optimal management of reconfigurable manufacturing system modeling with Petri nets developed three-dimensional - RPD3D

NASA Astrophysics Data System (ADS)

Teodor, F.; Marinescu, V.; Epureanu, A.

2016-11-01

Modeling of reconfigurable manufacturing systems would have done using existing Petri net types, but the complexity and dynamics of the new manufacturing system, mainly data reconfiguration feature, required looking for a more compact representation with many variables that to model as accurately not only the normal operation of the production system but can capture and model and reconfiguration process. Thus, it was necessary to create a new class of Petri nets, called RPD3D (Developed Petri nets with three dimensional) showing the name of both lineage (new class derived from Petri nets developed, created in 2000 by Prof. Dr. Ing Vasile Marinescu in his doctoral thesis) [1], but the most important of the new features defining (transformation from one 2D model into a 3D model).The idea was to introduce the classical model of a Petri third dimension to be able to overlay multiple levels (layers) formed in 2D or 3D Petri nets that interact with each other (receiving or giving commands to enable or disable the various modules together simulating the operation of reconfigurable manufacturing systems). The aim is to present a new type of Petri nets called RPD3D - Developed Petri three-dimensional model used for optimal control and simulation of reconfigurable manufacturing systems manufacture of products such systems.

Positive Interactions and Avoidant and Anxious Representations in Relationships with Parents, Friends, and Romantic Partners

PubMed Central

Furman, Wyndol; Stephenson, J. Claire; Rhoades, Galena K.

2013-01-01

We examined associations between positive interactions and avoidant and anxious representations in relationships with parents, friends, and romantic partners. Two hundred adolescents completed questionnaires, observations, and attachment interviews. From a between-person perspective, those adolescents with more positive interactions overall had less avoidant representations. Within persons, more positive interactions were relative to one’s own average level in relationships, the less avoidant representations were for that type of relationship. Adolescents were less anxious about a particular type of relationship if they have positive interactions in their other types of relationships. Finally, representations were primarily predicted by interactions in the same type of relationship; interactions in other relationships contributed little. The findings underscore the importance of examining representations of particular types of relationships. PMID:26346530

Interactive Effects of Cognitive Representations of Formidability and Technology on Aggression

DTIC Science & Technology

2014-09-08

defensive technologies; their fighting skill ; the number and proximity of their allies; the quality of their leadership; their degree of unit...since the last review) 1. Gneezy, A. and Fessler, D.M.T. (2011) Conflict, sticks, and carrots: War increases prosocial punishments and rewards

Interactive X-ray and proton therapy training and simulation.

PubMed

Hamza-Lup, Felix G; Farrar, Shane; Leon, Erik

2015-10-01

External beam X-ray therapy (XRT) and proton therapy (PT) are effective and widely accepted forms of treatment for many types of cancer. However, the procedures require extensive computerized planning. Current planning systems for both XRT and PT have insufficient visual aid to combine real patient data with the treatment device geometry to account for unforeseen collisions among system components and the patient. The 3D surface representation (S-rep) is a widely used scheme to create 3D models of physical objects. 3D S-reps have been successfully used in CAD/CAM and, in conjunction with texture mapping, in the modern gaming industry to customize avatars and improve the gaming realism and sense of presence. We are proposing a cost-effective method to extract patient-specific S-reps in real time and combine them with the treatment system geometry to provide a comprehensive simulation of the XRT/PT treatment room. The X3D standard is used to implement and deploy the simulator on the web, enabling its use not only for remote specialists' collaboration, simulation, and training, but also for patient education. An objective assessment of the accuracy of the S-reps obtained proves the potential of the simulator for clinical use.

Importance of conduction electron correlation in a Kondo lattice, Ce₂CoSi₃.

PubMed

Patil, Swapnil; Pandey, Sudhir K; Medicherla, V R R; Singh, R S; Bindu, R; Sampathkumaran, E V; Maiti, Kalobaran

2010-06-30

Kondo systems are usually described by the interaction of the correlation induced local moments with the highly itinerant conduction electrons. Here, we study the role of electron correlations among conduction electrons in the electronic structure of a Kondo lattice compound, Ce₂CoSi₃, using high resolution photoemission spectroscopy and ab initio band structure calculations, where Co 3d electrons contribute in the conduction band. High energy resolution employed in the measurements helped to reveal the signatures of Ce 4f states derived Kondo resonance features at the Fermi level and the dominance of Co 3d contributions at higher binding energies in the conduction band. The lineshape of the experimental Co 3d band is found to be significantly different from that obtained from the band structure calculations within the local density approximations, LDA. Consideration of electron-electron Coulomb repulsion, U, among Co 3d electrons within the LDA + U method leads to a better representation of experimental results. The signature of an electron correlation induced satellite feature is also observed in the Co 2p core level spectrum. These results clearly demonstrate the importance of the electron correlation among conduction electrons in deriving the microscopic description of such Kondo systems.

Enabling Real-Time Volume Rendering of Functional Magnetic Resonance Imaging on an iOS Device.

PubMed

Holub, Joseph; Winer, Eliot

2017-12-01

Powerful non-invasive imaging technologies like computed tomography (CT), ultrasound, and magnetic resonance imaging (MRI) are used daily by medical professionals to diagnose and treat patients. While 2D slice viewers have long been the standard, many tools allowing 3D representations of digital medical data are now available. The newest imaging advancement, functional MRI (fMRI) technology, has changed medical imaging from viewing static to dynamic physiology (4D) over time, particularly to study brain activity. Add this to the rapid adoption of mobile devices for everyday work and the need to visualize fMRI data on tablets or smartphones arises. However, there are few mobile tools available to visualize 3D MRI data, let alone 4D fMRI data. Building volume rendering tools on mobile devices to visualize 3D and 4D medical data is challenging given the limited computational power of the devices. This paper describes research that explored the feasibility of performing real-time 3D and 4D volume raycasting on a tablet device. The prototype application was tested on a 9.7" iPad Pro using two different fMRI datasets of brain activity. The results show that mobile raycasting is able to achieve between 20 and 40 frames per second for traditional 3D datasets, depending on the sampling interval, and up to 9 frames per second for 4D data. While the prototype application did not always achieve true real-time interaction, these results clearly demonstrated that visualizing 3D and 4D digital medical data is feasible with a properly constructed software framework.

Multi-Fidelity Uncertainty Propagation for Cardiovascular Modeling

NASA Astrophysics Data System (ADS)

Fleeter, Casey; Geraci, Gianluca; Schiavazzi, Daniele; Kahn, Andrew; Marsden, Alison

2017-11-01

Hemodynamic models are successfully employed in the diagnosis and treatment of cardiovascular disease with increasing frequency. However, their widespread adoption is hindered by our inability to account for uncertainty stemming from multiple sources, including boundary conditions, vessel material properties, and model geometry. In this study, we propose a stochastic framework which leverages three cardiovascular model fidelities: 3D, 1D and 0D models. 3D models are generated from patient-specific medical imaging (CT and MRI) of aortic and coronary anatomies using the SimVascular open-source platform, with fluid structure interaction simulations and Windkessel boundary conditions. 1D models consist of a simplified geometry automatically extracted from the 3D model, while 0D models are obtained from equivalent circuit representations of blood flow in deformable vessels. Multi-level and multi-fidelity estimators from Sandia's open-source DAKOTA toolkit are leveraged to reduce the variance in our estimated output quantities of interest while maintaining a reasonable computational cost. The performance of these estimators in terms of computational cost reductions is investigated for a variety of output quantities of interest, including global and local hemodynamic indicators. Sandia National Labs is a multimission laboratory managed and operated by NTESS, LLC, for the U.S. DOE under contract DE-NA0003525. Funding for this project provided by NIH-NIBIB R01 EB018302.

The Modeling of Virtual Environment Distance Education

NASA Astrophysics Data System (ADS)

Xueqin, Chang

This research presented a virtual environment that integrates in a virtual mockup services available in a university campus for students and teachers communication in different actual locations. Advantages of this system include: the remote access to a variety of services and educational tools, the representation of real structures and landscapes in an interactive 3D model that favors localization of services and preserves the administrative organization of the university. For that, the system was implemented a control access for users and an interface to allow the use of previous educational equipments and resources not designed for distance education mode.

3D Model Generation From the Engineering Drawing

NASA Astrophysics Data System (ADS)

Vaský, Jozef; Eliáš, Michal; Bezák, Pavol; Červeňanská, Zuzana; Izakovič, Ladislav

2010-01-01

The contribution deals with the transformation of engineering drawings in a paper form into a 3D computer representation. A 3D computer model can be further processed in CAD/CAM system, it can be modified, archived, and a technical drawing can be then generated from it as well. The transformation process from paper form to the data one is a complex and difficult one, particularly owing to the different types of drawings, forms of displayed objects and encountered errors and deviations from technical standards. The algorithm for 3D model generating from an orthogonal vector input representing a simplified technical drawing of the rotational part is described in this contribution. The algorithm was experimentally implemented as ObjectARX application in the AutoCAD system and the test sample as the representation of the rotational part was used for verificaton.

DspaceOgreTerrain 3D Terrain Visualization Tool

NASA Technical Reports Server (NTRS)

Myint, Steven; Jain, Abhinandan; Pomerantz, Marc I.

2012-01-01

DspaceOgreTerrain is an extension to the DspaceOgre 3D visualization tool that supports real-time visualization of various terrain types, including digital elevation maps, planets, and meshes. DspaceOgreTerrain supports creating 3D representations of terrains and placing them in a scene graph. The 3D representations allow for a continuous level of detail, GPU-based rendering, and overlaying graphics like wheel tracks and shadows. It supports reading data from the SimScape terrain- modeling library. DspaceOgreTerrain solves the problem of displaying the results of simulations that involve very large terrains. In the past, it has been used to visualize simulations of vehicle traverses on Lunar and Martian terrains. These terrains were made up of billions of vertices and would not have been renderable in real-time without using a continuous level of detail rendering technique.

Model Package Report: Central Plateau Vadose Zone Geoframework Version 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Springer, Sarah D.

The purpose of the Central Plateau Vadose Zone (CPVZ) Geoframework model (GFM) is to provide a reasonable, consistent, and defensible three-dimensional (3D) representation of the vadose zone beneath the Central Plateau at the Hanford Site to support the Composite Analysis (CA) vadose zone contaminant fate and transport models. The GFM is a 3D representation of the subsurface geologic structure. From this 3D geologic model, exported results in the form of point, surface, and/or volumes are used as inputs to populate and assemble the various numerical model architectures, providing a 3D-layered grid that is consistent with the GFM. The objective ofmore » this report is to define the process used to produce a hydrostratigraphic model for the vadose zone beneath the Hanford Site Central Plateau and the corresponding CA domain.« less

Ophthalmologic diagnostic tool using MR images for biomechanically-based muscle volume deformation

NASA Astrophysics Data System (ADS)

Buchberger, Michael; Kaltofen, Thomas

2003-05-01

We would like to give a work-in-progress report on our ophthalmologic diagnostic software system which performs biomechanically-based muscle volume deformations using MR images. For reconstructing a three-dimensional representation of an extraocular eye muscle, a sufficient amount of high resolution MR images is used, each representing a slice of the muscle. In addition, threshold values are given, which restrict the amount of data used from the MR images. The Marching Cube algorithm is applied to the polygons, resulting in a 3D representation of the muscle, which can efficiently be rendered. A transformation to a dynamic, deformable model is applied by calculating the center of gravity of each muscle slice, approximating the muscle path and subsequently adding Hermite splines through the centers of gravity of all slices. Then, a radius function is defined for each slice, completing the transformation of the static 3D polygon model. Finally, this paper describes future extensions to our system. One of these extensions is the support for additional calculations and measurements within the reconstructed 3D muscle representation. Globe translation, localization of muscle pulleys by analyzing the 3D reconstruction in two different gaze positions and other diagnostic measurements will be available.

Computational representation of the aponeuroses as NURBS surfaces in 3D musculoskeletal models.

PubMed

Wu, Florence T H; Ng-Thow-Hing, Victor; Singh, Karan; Agur, Anne M; McKee, Nancy H

2007-11-01

Computational musculoskeletal (MSK) models - 3D graphics-based models that accurately simulate the anatomical architecture and/or the biomechanical behaviour of organ systems consisting of skeletal muscles, tendons, ligaments, cartilage and bones - are valued biomedical tools, with applications ranging from pathological diagnosis to surgical planning. However, current MSK models are often limited by their oversimplifications in anatomical geometries, sometimes lacking discrete representations of connective tissue components entirely, which ultimately affect their accuracy in biomechanical simulation. In particular, the aponeuroses - the flattened fibrous connective sheets connecting muscle fibres to tendons - have never been geometrically modeled. The initiative was thus to extend Anatomy3D - a previously developed software bundle for reconstructing muscle fibre architecture - to incorporate aponeurosis-modeling capacity. Two different algorithms for aponeurosis reconstruction were written in the MEL scripting language of the animation software Maya 6.0, using its NURBS (non-uniform rational B-splines) modeling functionality for aponeurosis surface representation. Both algorithms were validated qualitatively against anatomical and functional criteria.

3D Visualization Development of SIUE Campus

NASA Astrophysics Data System (ADS)

Nellutla, Shravya

Geographic Information Systems (GIS) has progressed from the traditional map-making to the modern technology where the information can be created, edited, managed and analyzed. Like any other models, maps are simplified representations of real world. Hence visualization plays an essential role in the applications of GIS. The use of sophisticated visualization tools and methods, especially three dimensional (3D) modeling, has been rising considerably due to the advancement of technology. There are currently many off-the-shelf technologies available in the market to build 3D GIS models. One of the objectives of this research was to examine the available ArcGIS and its extensions for 3D modeling and visualization and use them to depict a real world scenario. Furthermore, with the advent of the web, a platform for accessing and sharing spatial information on the Internet, it is possible to generate interactive online maps. Integrating Internet capacity with GIS functionality redefines the process of sharing and processing the spatial information. Enabling a 3D map online requires off-the-shelf GIS software, 3D model builders, web server, web applications and client server technologies. Such environments are either complicated or expensive because of the amount of hardware and software involved. Therefore, the second objective of this research was to investigate and develop simpler yet cost-effective 3D modeling approach that uses available ArcGIS suite products and the free 3D computer graphics software for designing 3D world scenes. Both ArcGIS Explorer and ArcGIS Online will be used to demonstrate the way of sharing and distributing 3D geographic information on the Internet. A case study of the development of 3D campus for the Southern Illinois University Edwardsville is demonstrated.

Learning dictionaries of sparse codes of 3D movements of body joints for real-time human activity understanding.

PubMed

Qi, Jin; Yang, Zhiyong

2014-01-01

Real-time human activity recognition is essential for human-robot interactions for assisted healthy independent living. Most previous work in this area is performed on traditional two-dimensional (2D) videos and both global and local methods have been used. Since 2D videos are sensitive to changes of lighting condition, view angle, and scale, researchers begun to explore applications of 3D information in human activity understanding in recently years. Unfortunately, features that work well on 2D videos usually don't perform well on 3D videos and there is no consensus on what 3D features should be used. Here we propose a model of human activity recognition based on 3D movements of body joints. Our method has three steps, learning dictionaries of sparse codes of 3D movements of joints, sparse coding, and classification. In the first step, space-time volumes of 3D movements of body joints are obtained via dense sampling and independent component analysis is then performed to construct a dictionary of sparse codes for each activity. In the second step, the space-time volumes are projected to the dictionaries and a set of sparse histograms of the projection coefficients are constructed as feature representations of the activities. Finally, the sparse histograms are used as inputs to a support vector machine to recognize human activities. We tested this model on three databases of human activities and found that it outperforms the state-of-the-art algorithms. Thus, this model can be used for real-time human activity recognition in many applications.

Selective 4D modelling framework for spatial-temporal land information management system

NASA Astrophysics Data System (ADS)

Doulamis, Anastasios; Soile, Sofia; Doulamis, Nikolaos; Chrisouli, Christina; Grammalidis, Nikos; Dimitropoulos, Kosmas; Manesis, Charalambos; Potsiou, Chryssy; Ioannidis, Charalabos

2015-06-01

This paper introduces a predictive (selective) 4D modelling framework where only the spatial 3D differences are modelled at the forthcoming time instances, while regions of no significant spatial-temporal alterations remain intact. To accomplish this, initially spatial-temporal analysis is applied between 3D digital models captured at different time instances. So, the creation of dynamic change history maps is made. Change history maps indicate spatial probabilities of regions needed further 3D modelling at forthcoming instances. Thus, change history maps are good examples for a predictive assessment, that is, to localize surfaces within the objects where a high accuracy reconstruction process needs to be activated at the forthcoming time instances. The proposed 4D Land Information Management System (LIMS) is implemented using open interoperable standards based on the CityGML framework. CityGML allows the description of the semantic metadata information and the rights of the land resources. Visualization aspects are also supported to allow easy manipulation, interaction and representation of the 4D LIMS digital parcels and the respective semantic information. The open source 3DCityDB incorporating a PostgreSQL geo-database is used to manage and manipulate 3D data and their semantics. An application is made to detect the change through time of a 3D block of plots in an urban area of Athens, Greece. Starting with an accurate 3D model of the buildings in 1983, a change history map is created using automated dense image matching on aerial photos of 2010. For both time instances meshes are created and through their comparison the changes are detected.

Glomerular and Mitral-Granule Cell Microcircuits Coordinate Temporal and Spatial Information Processing in the Olfactory Bulb.

PubMed

Cavarretta, Francesco; Marasco, Addolorata; Hines, Michael L; Shepherd, Gordon M; Migliore, Michele

2016-01-01

The olfactory bulb processes inputs from olfactory receptor neurons (ORNs) through two levels: the glomerular layer at the site of input, and the granule cell level at the site of output to the olfactory cortex. The sequence of action of these two levels has not yet been examined. We analyze this issue using a novel computational framework that is scaled up, in three-dimensions (3D), with realistic representations of the interactions between layers, activated by simulated natural odors, and constrained by experimental and theoretical analyses. We suggest that the postulated functions of glomerular circuits have as their primary role transforming a complex and disorganized input into a contrast-enhanced and normalized representation, but cannot provide for synchronization of the distributed glomerular outputs. By contrast, at the granule cell layer, the dendrodendritic interactions mediate temporal decorrelation, which we show is dependent on the preceding contrast enhancement by the glomerular layer. The results provide the first insights into the successive operations in the olfactory bulb, and demonstrate the significance of the modular organization around glomeruli. This layered organization is especially important for natural odor inputs, because they activate many overlapping glomeruli.

Implementation of a graphical user interface for the virtual multifrequency spectrometer: The VMS-Draw tool.

PubMed

Licari, Daniele; Baiardi, Alberto; Biczysko, Malgorzata; Egidi, Franco; Latouche, Camille; Barone, Vincenzo

2015-02-15

This article presents the setup and implementation of a graphical user interface (VMS-Draw) for a virtual multifrequency spectrometer. Special attention is paid to ease of use, generality and robustness for a panel of spectroscopic techniques and quantum mechanical approaches. Depending on the kind of data to be analyzed, VMS-Draw produces different types of graphical representations, including two-dimensional or three-dimesional (3D) plots, bar charts, or heat maps. Among other integrated features, one may quote the convolution of stick spectra to obtain realistic line-shapes. It is also possible to analyze and visualize, together with the structure, the molecular orbitals and/or the vibrational motions of molecular systems thanks to 3D interactive tools. On these grounds, VMS-Draw could represent a useful additional tool for spectroscopic studies integrating measurements and computer simulations. Copyright © 2014 Wiley Periodicals, Inc.

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

NASA Technical Reports Server (NTRS)

Gomez, Julian E.; Keller, Paul J.

2003-01-01

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.

Disconnection of the Perirhinal and Postrhinal Cortices Impairs Recognition of Objects in Context But Not Contextual Fear Conditioning

PubMed Central

2017-01-01

The perirhinal cortex (PER) is known to process object information, whereas the rodent postrhinal cortex (POR), homolog to the parahippocampal cortex in primates, is thought to process spatial information. A number of studies, however, provide evidence that both areas are involved in processing contextual information. In this study, we tested the hypothesis that the rat POR relies on object information received from the PER to form complex representations of context. Using three fear-conditioning (FC) paradigms (signaled, unsignaled, and renewal) and two context-guided object recognition tasks (with 3D and 2D objects), we examined the effects of crossed excitotoxic lesions to the POR and the contralateral PER. Performance of rats with crossed lesions was compared with that of rats with ipsilateral POR plus PER lesions and sham-operated rats. We found that rats with contralateral PER–POR lesions were impaired in object–context recognition but not in contextual FC. Therefore, interaction between the POR and PER is necessary for context-guided exploratory behavior but not for associating fear with context. Our results provide evidence for the hypothesis that the POR relies on object and pattern information from the PER to encode representations of context. The association of fear with a context, however, may be supported by alternate cortical and/or subcortical pathways when PER–POR interaction is not available. Our results suggest that contextual FC may represent a special case of context-guided behavior. SIGNIFICANCE STATEMENT Representations of context are important for perception, memory, decision making, and other cognitive processes. Moreover, there is extensive evidence that the use of contextual representations to guide appropriate behavior is disrupted in neuropsychiatric and neurological disorders including developmental disorders, schizophrenia, affective disorders, and Alzheimer's disease. Many of these disorders are accompanied by changes in parahippocampal and hippocampal structures. Understanding how context is represented in the brain and how parahippocampal structures are involved will enhance our understanding and treatment of the cognitive and behavioral symptoms associated with neurological disorders and neuropsychiatric disease. PMID:28411272

Disconnection of the Perirhinal and Postrhinal Cortices Impairs Recognition of Objects in Context But Not Contextual Fear Conditioning.

PubMed

Heimer-McGinn, Victoria R; Poeta, Devon L; Aghi, Krishan; Udawatta, Methma; Burwell, Rebecca D

2017-05-03

The perirhinal cortex (PER) is known to process object information, whereas the rodent postrhinal cortex (POR), homolog to the parahippocampal cortex in primates, is thought to process spatial information. A number of studies, however, provide evidence that both areas are involved in processing contextual information. In this study, we tested the hypothesis that the rat POR relies on object information received from the PER to form complex representations of context. Using three fear-conditioning (FC) paradigms (signaled, unsignaled, and renewal) and two context-guided object recognition tasks (with 3D and 2D objects), we examined the effects of crossed excitotoxic lesions to the POR and the contralateral PER. Performance of rats with crossed lesions was compared with that of rats with ipsilateral POR plus PER lesions and sham-operated rats. We found that rats with contralateral PER-POR lesions were impaired in object-context recognition but not in contextual FC. Therefore, interaction between the POR and PER is necessary for context-guided exploratory behavior but not for associating fear with context. Our results provide evidence for the hypothesis that the POR relies on object and pattern information from the PER to encode representations of context. The association of fear with a context, however, may be supported by alternate cortical and/or subcortical pathways when PER-POR interaction is not available. Our results suggest that contextual FC may represent a special case of context-guided behavior. SIGNIFICANCE STATEMENT Representations of context are important for perception, memory, decision making, and other cognitive processes. Moreover, there is extensive evidence that the use of contextual representations to guide appropriate behavior is disrupted in neuropsychiatric and neurological disorders including developmental disorders, schizophrenia, affective disorders, and Alzheimer's disease. Many of these disorders are accompanied by changes in parahippocampal and hippocampal structures. Understanding how context is represented in the brain and how parahippocampal structures are involved will enhance our understanding and treatment of the cognitive and behavioral symptoms associated with neurological disorders and neuropsychiatric disease. Copyright © 2017 the authors 0270-6474/17/374819-11$15.00/0.

SITEHOUND-web: a server for ligand binding site identification in protein structures.

PubMed

Hernandez, Marylens; Ghersi, Dario; Sanchez, Roberto

2009-07-01

SITEHOUND-web (http://sitehound.sanchezlab.org) is a binding-site identification server powered by the SITEHOUND program. Given a protein structure in PDB format SITEHOUND-web will identify regions of the protein characterized by favorable interactions with a probe molecule. These regions correspond to putative ligand binding sites. Depending on the probe used in the calculation, sites with preference for different ligands will be identified. Currently, a carbon probe for identification of binding sites for drug-like molecules, and a phosphate probe for phosphorylated ligands (ATP, phoshopeptides, etc.) have been implemented. SITEHOUND-web will display the results in HTML pages including an interactive 3D representation of the protein structure and the putative sites using the Jmol java applet. Various downloadable data files are also provided for offline data analysis.

A topological multilayer model of the human body.

PubMed

Barbeito, Antonio; Painho, Marco; Cabral, Pedro; O'Neill, João

2015-11-04

Geographical information systems deal with spatial databases in which topological models are described with alphanumeric information. Its graphical interfaces implement the multilayer concept and provide powerful interaction tools. In this study, we apply these concepts to the human body creating a representation that would allow an interactive, precise, and detailed anatomical study. A vector surface component of the human body is built using a three-dimensional (3-D) reconstruction methodology. This multilayer concept is implemented by associating raster components with the corresponding vector surfaces, which include neighbourhood topology enabling spatial analysis. A root mean square error of 0.18 mm validated the three-dimensional reconstruction technique of internal anatomical structures. The expansion of the identification and the development of a neighbourhood analysis function are the new tools provided in this model.

From GCode to STL: Reconstruct Models from 3D Printing as a Service

NASA Astrophysics Data System (ADS)

Baumann, Felix W.; Schuermann, Martin; Odefey, Ulrich; Pfeil, Markus

2017-12-01

The authors present a method to reverse engineer 3D printer specific machine instructions (GCode) to a point cloud representation and then a STL (Stereolithography) file format. GCode is a machine code that is used for 3D printing among other applications, such as CNC routers. Such code files contain instructions for the 3D printer to move and control its actuator, in case of Fused Deposition Modeling (FDM), the printhead that extrudes semi-molten plastics. The reverse engineering method presented here is based on the digital simulation of the extrusion process of FDM type 3D printing. The reconstructed models and pointclouds do not accommodate for hollow structures, such as holes or cavities. The implementation is performed in Python and relies on open source software and libraries, such as Matplotlib and OpenCV. The reconstruction is performed on the model’s extrusion boundary and considers mechanical imprecision. The complete reconstruction mechanism is available as a RESTful (Representational State Transfer) Web service.

3D Data Acquisition Platform for Human Activity Understanding

DTIC Science & Technology

2016-03-02

3D data. The support for the acquisition of such research instrumentation have significantly facilitated our current and future research and educate ...SECURITY CLASSIFICATION OF: In this project, we incorporated motion capture devices, 3D vision sensors, and EMG sensors to cross validate...multimodality data acquisition, and address fundamental research problems of representation and invariant description of 3D data, human motion modeling and

A new model for simulating 3-d crystal growth and its application to the study of antifreeze proteins.

PubMed

Wathen, Brent; Kuiper, Michael; Walker, Virginia; Jia, Zongchao

2003-01-22

A novel computational technique for modeling crystal formation has been developed that combines three-dimensional (3-D) molecular representation and detailed energetics calculations of molecular mechanics techniques with the less-sophisticated probabilistic approach used by statistical techniques to study systems containing millions of molecules undergoing billions of interactions. Because our model incorporates both the structure of and the interaction energies between participating molecules, it enables the 3-D shape and surface properties of these molecules to directly affect crystal formation. This increase in model complexity has been achieved while simultaneously increasing the number of molecules in simulations by several orders of magnitude over previous statistical models. We have applied this technique to study the inhibitory effects of antifreeze proteins (AFPs) on ice-crystal formation. Modeling involving both fish and insect AFPs has produced results consistent with experimental observations, including the replication of ice-etching patterns, ice-growth inhibition, and specific AFP-induced ice morphologies. Our work suggests that the degree of AFP activity results more from AFP ice-binding orientation than from AFP ice-binding strength. This technique could readily be adapted to study other crystal and crystal inhibitor systems, or to study other noncrystal systems that exhibit regularity in the structuring of their component molecules, such as those associated with the new nanotechnologies.

Controlled implant/soft tissue interaction by nanoscale surface modifications of 3D porous titanium implants.

PubMed

Rieger, Elisabeth; Dupret-Bories, Agnès; Salou, Laetitia; Metz-Boutigue, Marie-Helene; Layrolle, Pierre; Debry, Christian; Lavalle, Philippe; Vrana, Nihal Engin

2015-06-07

Porous titanium implants are widely employed in the orthopaedics field to ensure good bone fixation. Recently, the use of porous titanium implants has also been investigated in artificial larynx development in a clinical setting. Such uses necessitate a better understanding of the interaction of soft tissues with porous titanium structures. Moreover, surface treatments of titanium have been generally evaluated in planar structures, while the porous titanium implants have complex 3 dimensional (3D) architectures. In this study, the determining factors for soft tissue integration of 3D porous titanium implants were investigated as a function of surface treatments via quantification of the interaction of serum proteins and cells with single titanium microbeads (300-500 μm in diameter). Samples were either acid etched or nanostructured by anodization. When the samples are used in 3D configuration (porous titanium discs of 2 mm thickness) in vivo (in subcutis of rats for 2 weeks), a better integration was observed for both anodized and acid etched samples compared to the non-treated implants. If the implants were also pre-treated with rat serum before implantation, the integration was further facilitated. In order to understand the underlying reasons for this effect, human fibroblast cell culture tests under several conditions (directly on beads, beads in suspension, beads encapsulated in gelatin hydrogels) were conducted to mimic the different interactions of cells with Ti implants in vivo. Physical characterization showed that surface treatments increased hydrophilicity, protein adsorption and roughness. Surface treatments also resulted in improved adsorption of serum albumin which in turn facilitated the adsorption of other proteins such as apolipoprotein as quantified by protein sequencing. The cellular response to the beads showed considerable difference with respect to the cell culture configuration. When the titanium microbeads were entrapped in cell-laden gelatin hydrogels, significantly more cells migrated towards the acid etched beads. In conclusion, the nanoscale surface treatment of 3D porous titanium structures can modulate in vivo integration by the accumulative effect of the surface treatment on several physical factors such as protein adsorption, surface hydrophilicity and surface roughness. The improved protein adsorption capacity of the treated implants can be further exploited by a pre-treatment with autologous serum to render the implant surface more bioactive. Titanium microbeads are a good model system to observe these effects in a 3D microenvironment and provide a better representation of cellular responses in 3D.

Transfer of learning between 2D and 3D sources during infancy: Informing theory and practice

PubMed Central

Barr, Rachel

2010-01-01

The ability to transfer learning across contexts is an adaptive skill that develops rapidly during early childhood. Learning from television is a specific instance of transfer of learning between a 2-Dimensional (2D) representation and a 3-Dimensional (3D) object. Understanding the conditions under which young children might accomplish this particular kind of transfer is important because by 2 years of age 90% of US children are viewing television on a daily basis. Recent research shows that children can imitate actions presented on television using the corresponding real-world objects, but this same research also shows that children learn less from television than they do from live demonstrations until they are at least 3 years old; termed the video deficit effect. At present, there is no coherent theory to account for the video deficit effect; how learning is disrupted by this change in context is poorly understood. The aims of the present review are (1) to review the conditions under which children transfer learning between 2D images and 3D objects during early childhood, and (2) to integrate developmental theories of memory processing into the transfer of learning from media literature using Hayne’s (2004) developmental representational flexibility account. The review will conclude that studies on the transfer of learning between 2D and 3D sources have important theoretical implications for general developmental theories of cognitive development, and in particular the development of a flexible representational system, as well as policy implications for early education regarding the potential use and limitations of media as effective teaching tools during early childhood. PMID:20563302

Multi-Dimensional Simulation of LWR Fuel Behavior in the BISON Fuel Performance Code

NASA Astrophysics Data System (ADS)

Williamson, R. L.; Capps, N. A.; Liu, W.; Rashid, Y. R.; Wirth, B. D.

2016-11-01

Nuclear fuel operates in an extreme environment that induces complex multiphysics phenomena occurring over distances ranging from inter-atomic spacing to meters, and times scales ranging from microseconds to years. To simulate this behavior requires a wide variety of material models that are often complex and nonlinear. The recently developed BISON code represents a powerful fuel performance simulation tool based on its material and physical behavior capabilities, finite-element versatility of spatial representation, and use of parallel computing. The code can operate in full three dimensional (3D) mode, as well as in reduced two dimensional (2D) modes, e.g., axisymmetric radial-axial ( R- Z) or plane radial-circumferential ( R- θ), to suit the application and to allow treatment of global and local effects. A BISON case study was used to illustrate analysis of Pellet Clad Mechanical Interaction failures from manufacturing defects using combined 2D and 3D analyses. The analysis involved commercial fuel rods and demonstrated successful computation of metrics of interest to fuel failures, including cladding peak hoop stress and strain energy density. In comparison with a failure threshold derived from power ramp tests, results corroborate industry analyses of the root cause of the pellet-clad interaction failures and illustrate the importance of modeling 3D local effects around fuel pellet defects, which can produce complex effects including cold spots in the cladding, stress concentrations, and hot spots in the fuel that can lead to enhanced cladding degradation such as hydriding, oxidation, CRUD formation, and stress corrosion cracking.

Multi-Dimensional Simulation of LWR Fuel Behavior in the BISON Fuel Performance Code

DOE PAGES

Williamson, R. L.; Capps, N. A.; Liu, W.; ...

2016-09-27

Nuclear fuel operates in an extreme environment that induces complex multiphysics phenomena occurring over distances ranging from inter-atomic spacing to meters, and times scales ranging from microseconds to years. To simulate this behavior requires a wide variety of material models that are often complex and nonlinear. The recently developed BISON code represents a powerful fuel performance simulation tool based on its material and physical behavior capabilities, finite-element versatility of spatial representation, and use of parallel computing. The code can operate in full three dimensional (3D) mode, as well as in reduced two dimensional (2D) modes, e.g., axisymmetric radial-axial (R-Z) ormore » plane radial-circumferential (R-θ), to suit the application and to allow treatment of global and local effects. A BISON case study was used in this paper to illustrate analysis of Pellet Clad Mechanical Interaction failures from manufacturing defects using combined 2D and 3D analyses. The analysis involved commercial fuel rods and demonstrated successful computation of metrics of interest to fuel failures, including cladding peak hoop stress and strain energy density. Finally, in comparison with a failure threshold derived from power ramp tests, results corroborate industry analyses of the root cause of the pellet-clad interaction failures and illustrate the importance of modeling 3D local effects around fuel pellet defects, which can produce complex effects including cold spots in the cladding, stress concentrations, and hot spots in the fuel that can lead to enhanced cladding degradation such as hydriding, oxidation, CRUD formation, and stress corrosion cracking.« less

A Prototype Digital Library for 3D Collections: Tools To Capture, Model, Analyze, and Query Complex 3D Data.

ERIC Educational Resources Information Center

Rowe, Jeremy; Razdan, Anshuman

The Partnership for Research in Spatial Modeling (PRISM) project at Arizona State University (ASU) developed modeling and analytic tools to respond to the limitations of two-dimensional (2D) data representations perceived by affiliated discipline scientists, and to take advantage of the enhanced capabilities of three-dimensional (3D) data that…

2D and 3D graphical representation of the propagation of electromagnetic waves at the interface with a material with general effective complex permittivity and permeability

NASA Astrophysics Data System (ADS)

Diaz, A.; Ramos, J. G.; Friedman, J. S.

2017-09-01

We developed a web-based instructional and research tool that demonstrates the behavior of electromagnetic waves as they propagate through a homogenous medium and through an interface where the second medium can be characterized by an effective complex permittivity and permeability. Either p- or s-polarization wave components can be chosen and the graphical interface includes 2D wave and 3D component representations. The program enables the study of continuity of electromagnetic components, critical angle, Brewster angle, absorption and amplification, behavior of light in sub-unity and negative-index materials, Poynting vector and phase velocity behavior, and positive and negative Goos- Hänchen shifts.

The construction of tridimensional representation of body and external reality in man. The greatest achievement of evolution to date implications for virtual reality.

PubMed

Woodbury, M A; Woodbury, M F

1998-01-01

Our 3-D Body Representation constructed during development by our Central Nervous System under the direction of our DNA, consists of a holographic representation arising from sensory input in the cerebellum and projected extraneurally in the brain ventricular fluid which has the chemical structure of liquid crystal. The structure of 3-D holographic Body Representation is then extrapolated by such cognitive instruments as boundarization, geometrization and gestalt organization upon the external environment which is perceived consequently as three dimensional. When the Body Representation collapses as in psychotic panic states. patients become terrified as they suddenly lose the perception of themselves and the world around them as three dimensional, solid in a reliably solid environment but feel suddenly that they are no longer a person but a disorganized blob. In our clinical practice we found serendipitously that the structure of three dimensionality can be restored even without medication by techniques involving stimulation of the body sensory system in the presence of a benevolent psychotherapist. Implications for Virtual Reality will be discussed.

Interactions between visual working memory representations.

PubMed

Bae, Gi-Yeul; Luck, Steven J

2017-11-01

We investigated whether the representations of different objects are maintained independently in working memory or interact with each other. Observers were shown two sequentially presented orientations and required to reproduce each orientation after a delay. The sequential presentation minimized perceptual interactions so that we could isolate interactions between memory representations per se. We found that similar orientations were repelled from each other whereas dissimilar orientations were attracted to each other. In addition, when one of the items was given greater attentional priority by means of a cue, the representation of the high-priority item was not influenced very much by the orientation of the low-priority item, but the representation of the low-priority item was strongly influenced by the orientation of the high-priority item. This indicates that attention modulates the interactions between working memory representations. In addition, errors in the reported orientations of the two objects were positively correlated under some conditions, suggesting that representations of distinct objects may become grouped together in memory. Together, these results demonstrate that working-memory representations are not independent but instead interact with each other in a manner that depends on attentional priority.

True-3D Accentuating of Grids and Streets in Urban Topographic Maps Enhances Human Object Location Memory

PubMed Central

Edler, Dennis; Bestgen, Anne-Kathrin; Kuchinke, Lars; Dickmann, Frank

2015-01-01

Cognitive representations of learned map information are subject to systematic distortion errors. Map elements that divide a map surface into regions, such as content-related linear symbols (e.g. streets, rivers, railway systems) or additional artificial layers (coordinate grids), provide an orientation pattern that can help users to reduce distortions in their mental representations. In recent years, the television industry has started to establish True-3D (autostereoscopic) displays as mass media. These modern displays make it possible to watch dynamic and static images including depth illusions without additional devices, such as 3D glasses. In these images, visual details can be distributed over different positions along the depth axis. Some empirical studies of vision research provided first evidence that 3D stereoscopic content attracts higher attention and is processed faster. So far, the impact of True-3D accentuating has not yet been explored concerning spatial memory tasks and cartography. This paper reports the results of two empirical studies that focus on investigations whether True-3D accentuating of artificial, regular overlaying line features (i.e. grids) and content-related, irregular line features (i.e. highways and main streets) in official urban topographic maps (scale 1/10,000) further improves human object location memory performance. The memory performance is measured as both the percentage of correctly recalled object locations (hit rate) and the mean distances of correctly recalled objects (spatial accuracy). It is shown that the True-3D accentuating of grids (depth offset: 5 cm) significantly enhances the spatial accuracy of recalled map object locations, whereas the True-3D emphasis of streets significantly improves the hit rate of recalled map object locations. These results show the potential of True-3D displays for an improvement of the cognitive representation of learned cartographic information. PMID:25679208

3D radiation belt diffusion model results using new empirical models of whistler chorus and hiss

NASA Astrophysics Data System (ADS)

Cunningham, G.; Chen, Y.; Henderson, M. G.; Reeves, G. D.; Tu, W.

2012-12-01

3D diffusion codes model the energization, radial transport, and pitch angle scattering due to wave-particle interactions. Diffusion codes are powerful but are limited by the lack of knowledge of the spatial & temporal distribution of waves that drive the interactions for a specific event. We present results from the 3D DREAM model using diffusion coefficients driven by new, activity-dependent, statistical models of chorus and hiss waves. Most 3D codes parameterize the diffusion coefficients or wave amplitudes as functions of magnetic activity indices like Kp, AE, or Dst. These functional representations produce the average value of the wave intensities for a given level of magnetic activity; however, the variability of the wave population at a given activity level is lost with such a representation. Our 3D code makes use of the full sample distributions contained in a set of empirical wave databases (one database for each wave type, including plasmaspheric hiss, lower and upper hand chorus) that were recently produced by our team using CRRES and THEMIS observations. The wave databases store the full probability distribution of observed wave intensity binned by AE, MLT, MLAT and L*. In this presentation, we show results that make use of the wave intensity sample probability distributions for lower-band and upper-band chorus by sampling the distributions stochastically during a representative CRRES-era storm. The sampling of the wave intensity probability distributions produces a collection of possible evolutions of the phase space density, which quantifies the uncertainty in the model predictions caused by the uncertainty of the chorus wave amplitudes for a specific event. A significant issue is the determination of an appropriate model for the spatio-temporal correlations of the wave intensities, since the diffusion coefficients are computed as spatio-temporal averages of the waves over MLT, MLAT and L*. The spatiotemporal correlations cannot be inferred from the wave databases. In this study we use a temporal correlation of ~1 hour for the sampled wave intensities that is informed by the observed autocorrelation in the AE index, a spatial correlation length of ~100 km in the two directions perpendicular to the magnetic field, and a spatial correlation length of 5000 km in the direction parallel to the magnetic field, according to the work of Santolik et al (2003), who used multi-spacecraft measurements from Cluster to quantify the correlation length scales for equatorial chorus . We find that, despite the small correlation length scale for chorus, there remains significant variability in the model outcomes driven by variability in the chorus wave intensities.

GREEN: A program package for docking studies in rational drug design

NASA Astrophysics Data System (ADS)

Tomioka, Nobuo; Itai, Akiko

1994-08-01

A program package, GREEN, has been developed that enables docking studies between ligand molecules and a protein molecule. Based on the structure of the protein molecule, the physical and chemical environment of the ligand-binding site is expressed as three-dimensional grid-point data. The grid-point data are used for the real-time evaluation of the protein-ligand interaction energy, as well as for the graphical representation of the binding-site environment. The interactive docking operation is facilitated by various built-in functions, such as energy minimization, energy contribution analysis and logging of the manipulation trajectory. Interactive modeling functions are incorporated for designing new ligand molecules while considering the binding-site environment and the protein-ligand interaction. As an example of the application of GREEN, a docking study is presented on the complex between trypsin and a synthetic trypsin inhibitor. The program package will be useful for rational drug design, based on the 3D structure of the target protein.

Cosmic sculpture: a new way to visualise the cosmic microwave background

NASA Astrophysics Data System (ADS)

Clements, D. L.; Sato, S.; Portela Fonseca, A.

2017-01-01

3D printing presents an attractive alternative to visual representation of physical datasets such as astronomical images that can be used for research, outreach or teaching purposes, and is especially relevant to people with a visual disability. We here report the use of 3D printing technology to produce a representation of the all-sky cosmic microwave background (CMB) intensity anisotropy maps produced by the Planck mission. The success of this work in representing key features of the CMB is discussed as is the potential of this approach for representing other astrophysical data sets. 3D printing such datasets represents a highly complementary approach to the usual 2D projections used in teaching and outreach work, and can also form the basis of undergraduate projects. The CAD files used to produce the models discussed in this paper are made available.

Systematic Parameterization, Storage, and Representation of Volumetric DICOM Data.

PubMed

Fischer, Felix; Selver, M Alper; Gezer, Sinem; Dicle, Oğuz; Hillen, Walter

Tomographic medical imaging systems produce hundreds to thousands of slices, enabling three-dimensional (3D) analysis. Radiologists process these images through various tools and techniques in order to generate 3D renderings for various applications, such as surgical planning, medical education, and volumetric measurements. To save and store these visualizations, current systems use snapshots or video exporting, which prevents further optimizations and requires the storage of significant additional data. The Grayscale Softcopy Presentation State extension of the Digital Imaging and Communications in Medicine (DICOM) standard resolves this issue for two-dimensional (2D) data by introducing an extensive set of parameters, namely 2D Presentation States (2DPR), that describe how an image should be displayed. 2DPR allows storing these parameters instead of storing parameter applied images, which cause unnecessary duplication of the image data. Since there is currently no corresponding extension for 3D data, in this study, a DICOM-compliant object called 3D presentation states (3DPR) is proposed for the parameterization and storage of 3D medical volumes. To accomplish this, the 3D medical visualization process is divided into four tasks, namely pre-processing, segmentation, post-processing, and rendering. The important parameters of each task are determined. Special focus is given to the compression of segmented data, parameterization of the rendering process, and DICOM-compliant implementation of the 3DPR object. The use of 3DPR was tested in a radiology department on three clinical cases, which require multiple segmentations and visualizations during the workflow of radiologists. The results show that 3DPR can effectively simplify the workload of physicians by directly regenerating 3D renderings without repeating intermediate tasks, increase efficiency by preserving all user interactions, and provide efficient storage as well as transfer of visualized data.

Global SO(3) x SO(3) x U(1) symmetry of the Hubbard model on bipartite lattices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carmelo, J.M.P., E-mail: carmelo@fisica.uminho.p; Ostlund, Stellan; Sampaio, M.J.

2010-08-15

In this paper the global symmetry of the Hubbard model on a bipartite lattice is found to be larger than SO(4). The model is one of the most studied many-particle quantum problems, yet except in one dimension it has no exact solution, so that there remain many open questions about its properties. Symmetry plays an important role in physics and often can be used to extract useful information on unsolved non-perturbative quantum problems. Specifically, here it is found that for on-site interaction U {ne} 0 the local SU(2) x SU(2) x U(1) gauge symmetry of the Hubbard model on amore » bipartite lattice with N{sub a}{sup D} sites and vanishing transfer integral t = 0 can be lifted to a global [SU(2) x SU(2) x U(1)]/Z{sub 2}{sup 2} = SO(3) x SO(3) x U(1) symmetry in the presence of the kinetic-energy hopping term of the Hamiltonian with t > 0. (Examples of a bipartite lattice are the D-dimensional cubic lattices of lattice constant a and edge length L = N{sub a}a for which D = 1, 2, 3,... in the number N{sub a}{sup D} of sites.) The generator of the new found hidden independent charge global U(1) symmetry, which is not related to the ordinary U(1) gauge subgroup of electromagnetism, is one half the rotated-electron number of singly occupied sites operator. Although addition of chemical-potential and magnetic-field operator terms to the model Hamiltonian lowers its symmetry, such terms commute with it. Therefore, its 4{sup N}{sub a}{sup D} energy eigenstates refer to representations of the new found global [SU(2) x SU(2) x U(1)]/Z{sub 2}{sup 2} = SO(3) x SO(3) x U(1) symmetry. Consistently, we find that for the Hubbard model on a bipartite lattice the number of independent representations of the group SO(3) x SO(3) x U(1) equals the Hilbert-space dimension 4{sup N}{sub a}{sup D}. It is confirmed elsewhere that the new found symmetry has important physical consequences.« less

a Range Based Method for Complex Facade Modeling

NASA Astrophysics Data System (ADS)

Adami, A.; Fregonese, L.; Taffurelli, L.

2011-09-01

3d modelling of Architectural Heritage does not follow a very well-defined way, but it goes through different algorithms and digital form according to the shape complexity of the object, to the main goal of the representation and to the starting data. Even if the process starts from the same data, such as a pointcloud acquired by laser scanner, there are different possibilities to realize a digital model. In particular we can choose between two different attitudes: the mesh and the solid model. In the first case the complexity of architecture is represented by a dense net of triangular surfaces which approximates the real surface of the object. In the other -opposite- case the 3d digital model can be realized by the use of simple geometrical shapes, by the use of sweeping algorithm and the Boolean operations. Obviously these two models are not the same and each one is characterized by some peculiarities concerning the way of modelling (the choice of a particular triangulation algorithm or the quasi-automatic modelling by known shapes) and the final results (a more detailed and complex mesh versus an approximate and more simple solid model). Usually the expected final representation and the possibility of publishing lead to one way or the other. In this paper we want to suggest a semiautomatic process to build 3d digital models of the facades of complex architecture to be used for example in city models or in other large scale representations. This way of modelling guarantees also to obtain small files to be published on the web or to be transmitted. The modelling procedure starts from laser scanner data which can be processed in the well known way. Usually more than one scan is necessary to describe a complex architecture and to avoid some shadows on the facades. These have to be registered in a single reference system by the use of targets which are surveyed by topography and then to be filtered in order to obtain a well controlled and homogeneous point cloud of the complex architecture. From the point cloud we can extract a false colour map depending on the distance of each point from the average plane. In this way we can represent each point of the facades by a height map in grayscale. In this operation it is important to define the scale of the final result in order to set the correct pixel size in the map. The following step is concerning the use of a modifier which is well-known in computer graphics. In fact the modifier Displacement allows to simulate on a planar surface the original roughness of the object according to a grayscale map. The value of gray is read by the modifier as the distance from the reference plane and it represents the displacement of the corresponding element of the virtual plane. Similar to the bump map, the displacement modifier does not only simulate the effect, but it really deforms the planar surface. In this way the 3d model can be use not only in a static representation, but also in dynamic animation or interactive application. The setting of the plane to be deformed is the most important step in this process. In 3d Max the planar surface has to be characterized by the real dimension of the façade and also by a correct number of quadrangular faces which are the smallest part of the whole surface. In this way we can consider the modified surface as a 3d raster representation where each quadrangular face (corresponding to traditional pixel) is displaced according the value of gray (= distance from the plane). This method can be applied in different context, above all when the object to be represented can be considered as a 2,5 dimension such as facades of architecture in city model or large scale representation. But also it can be used to represent particular effect such as deformation of walls in a complete 3d way.

Intuitive representation of surface properties of biomolecules using BioBlender.

PubMed

Andrei, Raluca Mihaela; Callieri, Marco; Zini, Maria Francesca; Loni, Tiziana; Maraziti, Giuseppe; Pan, Mike Chen; Zoppè, Monica

2012-03-28

In living cells, proteins are in continuous motion and interaction with the surrounding medium and/or other proteins and ligands. These interactions are mediated by protein features such as electrostatic and lipophilic potentials. The availability of protein structures enables the study of their surfaces and surface characteristics, based on atomic contribution. Traditionally, these properties are calculated by physico-chemical programs and visualized as range of colors that vary according to the tool used and imposes the necessity of a legend to decrypt it. The use of color to encode both characteristics makes the simultaneous visualization almost impossible, requiring these features to be visualized in different images. In this work, we describe a novel and intuitive code for the simultaneous visualization of these properties. Recent advances in 3D animation and rendering software have not yet been exploited for the representation of biomolecules in an intuitive, animated form. For our purpose we use Blender, an open-source, free, cross-platform application used professionally for 3D work. On the basis Blender, we developed BioBlender, dedicated to biological work: elaboration of protein motion with simultaneous visualization of their chemical and physical features. Electrostatic and lipophilic potentials are calculated using physico-chemical software and scripts, organized and accessed through BioBlender interface. A new visual code is introduced for molecular lipophilic potential: a range of optical features going from smooth-shiny for hydrophobic regions to rough-dull for hydrophilic ones. Electrostatic potential is represented as animated line particles that flow along field lines, proportional to the total charge of the protein. Our system permits visualization of molecular features and, in the case of moving proteins, their continuous perception, calculated for each conformation during motion. Using real world tactile/sight feelings, the nanoscale world of proteins becomes more understandable, familiar to our everyday life, making it easier to introduce "un-seen" phenomena (concepts) such as hydropathy or charges. Moreover, this representation contributes to gain insight into molecular functions by drawing viewer's attention to the most active regions of the protein. The program, available for Windows, Linux and MacOS, can be downloaded freely from the dedicated website http://www.bioblender.eu.

Intuitive representation of surface properties of biomolecules using BioBlender

PubMed Central

2012-01-01

Background In living cells, proteins are in continuous motion and interaction with the surrounding medium and/or other proteins and ligands. These interactions are mediated by protein features such as electrostatic and lipophilic potentials. The availability of protein structures enables the study of their surfaces and surface characteristics, based on atomic contribution. Traditionally, these properties are calculated by physico-chemical programs and visualized as range of colors that vary according to the tool used and imposes the necessity of a legend to decrypt it. The use of color to encode both characteristics makes the simultaneous visualization almost impossible, requiring these features to be visualized in different images. In this work, we describe a novel and intuitive code for the simultaneous visualization of these properties. Methods Recent advances in 3D animation and rendering software have not yet been exploited for the representation of biomolecules in an intuitive, animated form. For our purpose we use Blender, an open-source, free, cross-platform application used professionally for 3D work. On the basis Blender, we developed BioBlender, dedicated to biological work: elaboration of protein motion with simultaneous visualization of their chemical and physical features. Electrostatic and lipophilic potentials are calculated using physico-chemical software and scripts, organized and accessed through BioBlender interface. Results A new visual code is introduced for molecular lipophilic potential: a range of optical features going from smooth-shiny for hydrophobic regions to rough-dull for hydrophilic ones. Electrostatic potential is represented as animated line particles that flow along field lines, proportional to the total charge of the protein. Conclusions Our system permits visualization of molecular features and, in the case of moving proteins, their continuous perception, calculated for each conformation during motion. Using real world tactile/sight feelings, the nanoscale world of proteins becomes more understandable, familiar to our everyday life, making it easier to introduce "un-seen" phenomena (concepts) such as hydropathy or charges. Moreover, this representation contributes to gain insight into molecular functions by drawing viewer's attention to the most active regions of the protein. The program, available for Windows, Linux and MacOS, can be downloaded freely from the dedicated website http://www.bioblender.eu PMID:22536962

Efficient local representations for three-dimensional palmprint recognition

NASA Astrophysics Data System (ADS)

Yang, Bing; Wang, Xiaohua; Yao, Jinliang; Yang, Xin; Zhu, Wenhua

2013-10-01

Palmprints have been broadly used for personal authentication because they are highly accurate and incur low cost. Most previous works have focused on two-dimensional (2-D) palmprint recognition in the past decade. Unfortunately, 2-D palmprint recognition systems lose the shape information when capturing palmprint images. Moreover, such 2-D palmprint images can be easily forged or affected by noise. Hence, three-dimensional (3-D) palmprint recognition has been regarded as a promising way to further improve the performance of palmprint recognition systems. We have developed a simple, but efficient method for 3-D palmprint recognition by using local features. We first utilize shape index representation to describe the geometry of local regions in 3-D palmprint data. Then, we extract local binary pattern and Gabor wavelet features from the shape index image. The two types of complementary features are finally fused at a score level for further improvements. The experimental results on the Hong Kong Polytechnic 3-D palmprint database, which contains 8000 samples from 400 palms, illustrate the effectiveness of the proposed method.

Integration of a 3D perspective view in the navigation display: featuring pilot's mental model

NASA Astrophysics Data System (ADS)

Ebrecht, L.; Schmerwitz, S.

2015-05-01

Synthetic vision systems (SVS) appear as spreading technology in the avionic domain. Several studies prove enhanced situational awareness when using synthetic vision. Since the introduction of synthetic vision a steady change and evolution started concerning the primary flight display (PFD) and the navigation display (ND). The main improvements of the ND comprise the representation of colored ground proximity warning systems (EGPWS), weather radar, and TCAS information. Synthetic vision seems to offer high potential to further enhance cockpit display systems. Especially, concerning the current trend having a 3D perspective view in a SVS-PFD while leaving the navigational content as well as methods of interaction unchanged the question arouses if and how the gap between both displays might evolve to a serious problem. This issue becomes important in relation to the transition and combination of strategic and tactical flight guidance. Hence, pros and cons of 2D and 3D views generally as well as the gap between the egocentric perspective 3D view of the PFD and the exocentric 2D top and side view of the ND will be discussed. Further a concept for the integration of a 3D perspective view, i.e., bird's eye view, in synthetic vision ND will be presented. The combination of 2D and 3D views in the ND enables a better correlation of the ND and the PFD. Additionally, this supports the building of pilot's mental model. The authors believe it will improve the situational and spatial awareness. It might prove to further raise the safety margin when operating in mountainous areas.

A novel physical eco-hydrological model concept for preferential flow based on experimental applications.

NASA Astrophysics Data System (ADS)

Jackisch, Conrad; van Schaik, Loes; Graeff, Thomas; Zehe, Erwin

2014-05-01

Preferential flow through macropores often determines hydrological characteristics - especially regarding runoff generation and fast transport of solutes. Macropore settings may yet be very different in nature and dynamics, depending on their origin. While biogenic structures follow activity cycles (e.g. earth worms) and population conditions (e.g. roots), pedogenic and geogenic structures may depend on water stress (e.g. cracks) or large events (e.g. flushed voids between skeleton and soil pipes) or simply persist (e.g. bedrock interface). On the one hand, such dynamic site characteristics can be observed in seasonal changes in its reaction to precipitation. On the other hand, sprinkling experiments accompanied by tracers or time-lapse 3D Ground-Penetrating-Radar are suitable tools to determine infiltration patterns and macropore configuration. However, model representation of the macropore-matrix system is still problematic, because models either rely on effective parameters (assuming well-mixed state) or on explicit advection strongly simplifying or neglecting interaction with the diffusive flow domain. Motivated by the dynamic nature of macropores, we present a novel model approach for interacting diffusive and advective water, solutes and energy transport in structured soils. It solely relies on scale- and process-aware observables. A representative set of macropores (data from sprinkling experiments) determines the process model scale through 1D advective domains. These are connected to a 2D matrix domain which is defined by pedo-physical retention properties. Water is represented as particles. Diffusive flow is governed by a 2D random walk of these particles while advection may take place in the macropore domain. Macropore-matrix interaction is computed as dissipation of the advective momentum of a particle by its experienced drag from the matrix domain. Through a representation of matrix and macropores as connected diffusive and advective domains for water transport we open up double domain concepts linking porescale physics to preferential macroscale fingerprints without effective parameterisation or mixing assumptions. Moreover, solute transport, energy balance aspects and lateral heterogeneity in soil moisture distribution are intrinsically captured. In addition, macropore and matrix domain settings may change over time based on physical and stochastic observations. The representativity concept allows scaleability from plotscale to the lower mesoscale.

Sparse representation-based volumetric super-resolution algorithm for 3D CT images of reservoir rocks

NASA Astrophysics Data System (ADS)

Li, Zhengji; Teng, Qizhi; He, Xiaohai; Yue, Guihua; Wang, Zhengyong

2017-09-01

The parameter evaluation of reservoir rocks can help us to identify components and calculate the permeability and other parameters, and it plays an important role in the petroleum industry. Until now, computed tomography (CT) has remained an irreplaceable way to acquire the microstructure of reservoir rocks. During the evaluation and analysis, large samples and high-resolution images are required in order to obtain accurate results. Owing to the inherent limitations of CT, however, a large field of view results in low-resolution images, and high-resolution images entail a smaller field of view. Our method is a promising solution to these data collection limitations. In this study, a framework for sparse representation-based 3D volumetric super-resolution is proposed to enhance the resolution of 3D voxel images of reservoirs scanned with CT. A single reservoir structure and its downgraded model are divided into a large number of 3D cubes of voxel pairs and these cube pairs are used to calculate two overcomplete dictionaries and the sparse-representation coefficients in order to estimate the high frequency component. Future more, to better result, a new feature extract method with combine BM4D together with Laplacian filter are introduced. In addition, we conducted a visual evaluation of the method, and used the PSNR and FSIM to evaluate it qualitatively.

Dynamic representation of 3D auditory space in the midbrain of the free-flying echolocating bat

PubMed Central

2018-01-01

Essential to spatial orientation in the natural environment is a dynamic representation of direction and distance to objects. Despite the importance of 3D spatial localization to parse objects in the environment and to guide movement, most neurophysiological investigations of sensory mapping have been limited to studies of restrained subjects, tested with 2D, artificial stimuli. Here, we show for the first time that sensory neurons in the midbrain superior colliculus (SC) of the free-flying echolocating bat encode 3D egocentric space, and that the bat’s inspection of objects in the physical environment sharpens tuning of single neurons, and shifts peak responses to represent closer distances. These findings emerged from wireless neural recordings in free-flying bats, in combination with an echo model that computes the animal’s instantaneous stimulus space. Our research reveals dynamic 3D space coding in a freely moving mammal engaged in a real-world navigation task. PMID:29633711

3D face recognition based on multiple keypoint descriptors and sparse representation.

PubMed

Zhang, Lin; Ding, Zhixuan; Li, Hongyu; Shen, Ying; Lu, Jianwei

2014-01-01

Recent years have witnessed a growing interest in developing methods for 3D face recognition. However, 3D scans often suffer from the problems of missing parts, large facial expressions, and occlusions. To be useful in real-world applications, a 3D face recognition approach should be able to handle these challenges. In this paper, we propose a novel general approach to deal with the 3D face recognition problem by making use of multiple keypoint descriptors (MKD) and the sparse representation-based classification (SRC). We call the proposed method 3DMKDSRC for short. Specifically, with 3DMKDSRC, each 3D face scan is represented as a set of descriptor vectors extracted from keypoints by meshSIFT. Descriptor vectors of gallery samples form the gallery dictionary. Given a probe 3D face scan, its descriptors are extracted at first and then its identity can be determined by using a multitask SRC. The proposed 3DMKDSRC approach does not require the pre-alignment between two face scans and is quite robust to the problems of missing data, occlusions and expressions. Its superiority over the other leading 3D face recognition schemes has been corroborated by extensive experiments conducted on three benchmark databases, Bosphorus, GavabDB, and FRGC2.0. The Matlab source code for 3DMKDSRC and the related evaluation results are publicly available at http://sse.tongji.edu.cn/linzhang/3dmkdsrcface/3dmkdsrc.htm.

Advancing the Theory of Nuclear Reactions with Rare Isotopes: From the Laboratory to the Cosmos

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elster, Charlotte

2015-06-01

The mission of the TORUS Topical Collaboration is to develop new methods that will advance nuclear reaction theory for unstable isotopes by using three-body techniques to improve direct-reaction calculations, and, by using a new partial-fusion theory, to integrate descriptions of direct and compound-nucleus reactions. Ohio University concentrates its efforts on the first part of the mission. Since direct measurements are often not feasible, indirect methods, e.g. (d,p) reactions, should be used. Those (d,p) reactions may be viewed as three-body reactions and described with Faddeev techniques. Faddeev equations in momentum space have a long tradition of utilizing separable interactions in ordermore » to arrive at sets of coupled integral equations in one variable. While there exist several separable representations for the nucleon-nucleon interaction, the optical potential between a neutron (proton) and a nucleus is not readily available in separable form. For this reason we first embarked in introducing a separable representation for complex phenomenological optical potentials of Woods-Saxon type.« less

Beyond Point Clouds and Virtual Reality. Innovative Methods and Technologies for the Protection and Promotion of Cultural Heritage

NASA Astrophysics Data System (ADS)

Canevese, E. P.; De Gottardo, T.

2017-05-01

The morphometric and photogrammetric knowledge, combined with the historical research, are the indispensable prerequisites for the protection and enhancement of historical, architectural and cultural heritage. Nowadays the use of BIM (Building Information Modeling) as a supporting tool for restoration and conservation purposes is becoming more and more popular. However this tool is not fully adequate in this context because of its simplified representation of three-dimensional models, resulting from solid modelling techniques (mostly used in virtual reality) causing the loss of important morphometric information. One solution to this problem is imagining new advanced tools and methods that enable the building of effective and efficient three-dimensional representations backing the correct geometric analysis of the built model. Twenty-year of interdisciplinary research activities implemented by Virtualgeo focused on developing new methods and tools for 3D modeling that go beyond the simplified digital-virtual reconstruction used in standard solid modeling. Methods and tools allowing the creation of informative and true to life three-dimensional representations, that can be further used by various academics or industry professionals to carry out diverse analysis, research and design activities. Virtualgeo applied research activities, in line with the European Commission 2013's directives of Reflective 7 - Horizon 2020 Project, gave birth to GeomaticsCube Ecosystem, an ecosystem resulting from different technologies based on experiences garnered from various fields, metrology in particular, a discipline used in the automotive and aviation industry, and in general mechanical engineering. The implementation of the metrological functionality is only possible if the 3D model is created with special modeling techniques, based on surface modeling that allow, as opposed to solid modeling, a 3D representation of the manufact that is true to life. The advantages offered by metrological analysis are varied and important because they permit a precise and detailed overview of the 3D model's characteristics, and especially the over time monitoring of the model itself, these informations are impossible to obtain from a three-dimensional representation produced with solid modelling techniques. The applied research activities are also focused on the possibility of obtaining a photogrammetric and informative 3D model., Two distinct applications have been developed for this purpose, the first allows the classification of each individual element and the association of its material characteristics during the 3D modelling phase, whilst the second allows segmentations of the photogrammetric 3D model in its diverse aspects (materic, related to decay, chronological) with the possibility to make use and to populate the database, associated with the 3D model, with all types of multimedia contents.

Development of a global aerosol model using a two-dimensional sectional method: 1. Model design

NASA Astrophysics Data System (ADS)

Matsui, H.

2017-08-01

This study develops an aerosol module, the Aerosol Two-dimensional bin module for foRmation and Aging Simulation version 2 (ATRAS2), and implements the module into a global climate model, Community Atmosphere Model. The ATRAS2 module uses a two-dimensional (2-D) sectional representation with 12 size bins for particles from 1 nm to 10 μm in dry diameter and 8 black carbon (BC) mixing state bins. The module can explicitly calculate the enhancement of absorption and cloud condensation nuclei activity of BC-containing particles by aging processes. The ATRAS2 module is an extension of a 2-D sectional aerosol module ATRAS used in our previous studies within a framework of a regional three-dimensional model. Compared with ATRAS, the computational cost of the aerosol module is reduced by more than a factor of 10 by simplifying the treatment of aerosol processes and 2-D sectional representation, while maintaining good accuracy of aerosol parameters in the simulations. Aerosol processes are simplified for condensation of sulfate, ammonium, and nitrate, organic aerosol formation, coagulation, and new particle formation processes, and box model simulations show that these simplifications do not substantially change the predicted aerosol number and mass concentrations and their mixing states. The 2-D sectional representation is simplified (the number of advected species is reduced) primarily by the treatment of chemical compositions using two interactive bin representations. The simplifications do not change the accuracy of global aerosol simulations. In part 2, comparisons with measurements and the results focused on aerosol processes such as BC aging processes are shown.

SimRNAweb: a web server for RNA 3D structure modeling with optional restraints.

PubMed

Magnus, Marcin; Boniecki, Michał J; Dawson, Wayne; Bujnicki, Janusz M

2016-07-08

RNA function in many biological processes depends on the formation of three-dimensional (3D) structures. However, RNA structure is difficult to determine experimentally, which has prompted the development of predictive computational methods. Here, we introduce a user-friendly online interface for modeling RNA 3D structures using SimRNA, a method that uses a coarse-grained representation of RNA molecules, utilizes the Monte Carlo method to sample the conformational space, and relies on a statistical potential to describe the interactions in the folding process. SimRNAweb makes SimRNA accessible to users who do not normally use high performance computational facilities or are unfamiliar with using the command line tools. The simplest input consists of an RNA sequence to fold RNA de novo. Alternatively, a user can provide a 3D structure in the PDB format, for instance a preliminary model built with some other technique, to jump-start the modeling close to the expected final outcome. The user can optionally provide secondary structure and distance restraints, and can freeze a part of the starting 3D structure. SimRNAweb can be used to model single RNA sequences and RNA-RNA complexes (up to 52 chains). The webserver is available at http://genesilico.pl/SimRNAweb. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Allosteric pathway identification through network analysis: from molecular dynamics simulations to interactive 2D and 3D graphs.

PubMed

Allain, Ariane; Chauvot de Beauchêne, Isaure; Langenfeld, Florent; Guarracino, Yann; Laine, Elodie; Tchertanov, Luba

2014-01-01

Allostery is a universal phenomenon that couples the information induced by a local perturbation (effector) in a protein to spatially distant regulated sites. Such an event can be described in terms of a large scale transmission of information (communication) through a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. To elaborate a rational description of allosteric coupling, we propose an original approach - MOdular NETwork Analysis (MONETA) - based on the analysis of inter-residue dynamical correlations to localize the propagation of both structural and dynamical effects of a perturbation throughout a protein structure. MONETA uses inter-residue cross-correlations and commute times computed from molecular dynamics simulations and a topological description of a protein to build a modular network representation composed of clusters of residues (dynamic segments) linked together by chains of residues (communication pathways). MONETA provides a brand new direct and simple visualization of protein allosteric communication. A GEPHI module implemented in the MONETA package allows the generation of 2D graphs of the communication network. An interactive PyMOL plugin permits drawing of the communication pathways between chosen protein fragments or residues on a 3D representation. MONETA is a powerful tool for on-the-fly display of communication networks in proteins. We applied MONETA for the analysis of communication pathways (i) between the main regulatory fragments of receptors tyrosine kinases (RTKs), KIT and CSF-1R, in the native and mutated states and (ii) in proteins STAT5 (STAT5a and STAT5b) in the phosphorylated and the unphosphorylated forms. The description of the physical support for allosteric coupling by MONETA allowed a comparison of the mechanisms of (a) constitutive activation induced by equivalent mutations in two RTKs and (b) allosteric regulation in the activated and non-activated STAT5 proteins. Our theoretical prediction based on results obtained with MONETA was validated for KIT by in vitro experiments. MONETA is a versatile analytical and visualization tool entirely devoted to the understanding of the functioning/malfunctioning of allosteric regulation in proteins - a crucial basis to guide the discovery of next-generation allosteric drugs.

3D tomography of cells in micro-channels

NASA Astrophysics Data System (ADS)

Quint, S.; Christ, A. F.; Guckenberger, A.; Himbert, S.; Kaestner, L.; Gekle, S.; Wagner, C.

2017-09-01

We combine confocal imaging, microfluidics, and image analysis to record 3D-images of cells in flow. This enables us to recover the full 3D representation of several hundred living cells per minute. Whereas 3D confocal imaging has thus far been limited to steady specimens, we overcome this restriction and present a method to access the 3D shape of moving objects. The key of our principle is a tilted arrangement of the micro-channel with respect to the focal plane of the microscope. This forces cells to traverse the focal plane in an inclined manner. As a consequence, individual layers of passing cells are recorded, which can then be assembled to obtain the volumetric representation. The full 3D information allows for a detailed comparison with theoretical and numerical predictions unfeasible with, e.g., 2D imaging. Our technique is exemplified by studying flowing red blood cells in a micro-channel reflecting the conditions prevailing in the microvasculature. We observe two very different types of shapes: "croissants" and "slippers." Additionally, we perform 3D numerical simulations of our experiment to confirm the observations. Since 3D confocal imaging of cells in flow has not yet been realized, we see high potential in the field of flow cytometry where cell classification thus far mostly relies on 1D scattering and fluorescence signals.

Telerobotic Haptic Exploration in Art Galleries and Museums for Individuals with Visual Impairments.

PubMed

Park, Chung Hyuk; Ryu, Eun-Seok; Howard, Ayanna M

2015-01-01

This paper presents a haptic telepresence system that enables visually impaired users to explore locations with rich visual observation such as art galleries and museums by using a telepresence robot, a RGB-D sensor (color and depth camera), and a haptic interface. The recent improvement on RGB-D sensors has enabled real-time access to 3D spatial information in the form of point clouds. However, the real-time representation of this data in the form of tangible haptic experience has not been challenged enough, especially in the case of telepresence for individuals with visual impairments. Thus, the proposed system addresses the real-time haptic exploration of remote 3D information through video encoding and real-time 3D haptic rendering of the remote real-world environment. This paper investigates two scenarios in haptic telepresence, i.e., mobile navigation and object exploration in a remote environment. Participants with and without visual impairments participated in our experiments based on the two scenarios, and the system performance was validated. In conclusion, the proposed framework provides a new methodology of haptic telepresence for individuals with visual impairments by providing an enhanced interactive experience where they can remotely access public places (art galleries and museums) with the aid of haptic modality and robotic telepresence.

Semiclassical initial value representation for the quantum propagator in the Heisenberg interaction representation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petersen, Jakob; Pollak, Eli, E-mail: eli.pollak@weizmann.ac.il

2015-12-14

One of the challenges facing on-the-fly ab initio semiclassical time evolution is the large expense needed to converge the computation. In this paper, we suggest that a significant saving in computational effort may be achieved by employing a semiclassical initial value representation (SCIVR) of the quantum propagator based on the Heisenberg interaction representation. We formulate and test numerically a modification and simplification of the previous semiclassical interaction representation of Shao and Makri [J. Chem. Phys. 113, 3681 (2000)]. The formulation is based on the wavefunction form of the semiclassical propagation instead of the operator form, and so is simpler andmore » cheaper to implement. The semiclassical interaction representation has the advantage that the phase and prefactor vary relatively slowly as compared to the “standard” SCIVR methods. This improves its convergence properties significantly. Using a one-dimensional model system, the approximation is compared with Herman-Kluk’s frozen Gaussian and Heller’s thawed Gaussian approximations. The convergence properties of the interaction representation approach are shown to be favorable and indicate that the interaction representation is a viable way of incorporating on-the-fly force field information within a semiclassical framework.« less

A Study of Multi-Representation of Geometry Problem Solving with Virtual Manipulatives and Whiteboard System

ERIC Educational Resources Information Center

Hwang, Wu-Yuin; Su, Jia-Han; Huang, Yueh-Min; Dong, Jian-Jie

2009-01-01

In this paper, the development of an innovative Virtual Manipulatives and Whiteboard (VMW) system is described. The VMW system allowed users to manipulate virtual objects in 3D space and find clues to solve geometry problems. To assist with multi-representation transformation, translucent multimedia whiteboards were used to provide a virtual 3D…

Computational Flow Modeling of Hydrodynamics in Multiphase Trickle-Bed Reactors

NASA Astrophysics Data System (ADS)

Lopes, Rodrigo J. G.; Quinta-Ferreira, Rosa M.

2008-05-01

This study aims to incorporate most recent multiphase models in order to investigate the hydrodynamic behavior of a TBR in terms of pressure drop and liquid holdup. Taking into account transport phenomena such as mass and heat transfer, an Eulerian k-fluid model was developed resulting from the volume averaging of the continuity and momentum equations and solved for a 3D representation of the catalytic bed. Computational fluid dynamics (CFD) model predicts hydrodynamic parameters quite well if good closures for fluid/fluid and fluid/particle interactions are incorporated in the multiphase model. Moreover, catalytic performance is investigated with the catalytic wet oxidation of a phenolic pollutant.

SA-Search: a web tool for protein structure mining based on a Structural Alphabet

PubMed Central

Guyon, Frédéric; Camproux, Anne-Claude; Hochez, Joëlle; Tufféry, Pierre

2004-01-01

SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of fast 3D similarity searches such as the extraction of exact words using a suffix tree approach, and the search for fuzzy words viewed as a simple 1D sequence alignment problem. SA-Search is available at http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search. PMID:15215446

SA-Search: a web tool for protein structure mining based on a Structural Alphabet.

PubMed

Guyon, Frédéric; Camproux, Anne-Claude; Hochez, Joëlle; Tufféry, Pierre

2004-07-01

SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of fast 3D similarity searches such as the extraction of exact words using a suffix tree approach, and the search for fuzzy words viewed as a simple 1D sequence alignment problem. SA-Search is available at http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search.

Representation of the quantum Fourier transform on multilevel basic elements by a sequence of selective rotation operators

NASA Astrophysics Data System (ADS)

Ermilov, A. S.; Zobov, V. E.

2007-12-01

To experimentally realize quantum computations on d-level basic elements (qudits) at d > 2, it is necessary to develop schemes for the technical realization of elementary logical operators. We have found sequences of selective rotation operators that represent the operators of the quantum Fourier transform (Walsh-Hadamard matrices) for d = 3-10. For the prime numbers 3, 5, and 7, the well-known method of linear algebra is applied, whereas, for the factorable numbers 6, 9, and 10, the representation of virtual spins is used (which we previously applied for d = 4, 8). Selective rotations can be realized, for example, by means of pulses of an RF magnetic field for systems of quadrupole nuclei or laser pulses for atoms and ions in traps.

Generation of large scale urban environments to support advanced sensor and seeker simulation

NASA Astrophysics Data System (ADS)

Giuliani, Joseph; Hershey, Daniel; McKeown, David, Jr.; Willis, Carla; Van, Tan

2009-05-01

One of the key aspects for the design of a next generation weapon system is the need to operate in cluttered and complex urban environments. Simulation systems rely on accurate representation of these environments and require automated software tools to construct the underlying 3D geometry and associated spectral and material properties that are then formatted for various objective seeker simulation systems. Under an Air Force Small Business Innovative Research (SBIR) contract, we have developed an automated process to generate 3D urban environments with user defined properties. These environments can be composed from a wide variety of source materials, including vector source data, pre-existing 3D models, and digital elevation models, and rapidly organized into a geo-specific visual simulation database. This intermediate representation can be easily inspected in the visible spectrum for content and organization and interactively queried for accuracy. Once the database contains the required contents, it can then be exported into specific synthetic scene generation runtime formats, preserving the relationship between geometry and material properties. To date an exporter for the Irma simulation system developed and maintained by AFRL/Eglin has been created and a second exporter to Real Time Composite Hardbody and Missile Plume (CHAMP) simulation system for real-time use is currently being developed. This process supports significantly more complex target environments than previous approaches to database generation. In this paper we describe the capabilities for content creation for advanced seeker processing algorithms simulation and sensor stimulation, including the overall database compilation process and sample databases produced and exported for the Irma runtime system. We also discuss the addition of object dynamics and viewer dynamics within the visual simulation into the Irma runtime environment.

Translating between Representations in a Social Context: A Study of Undergraduate Science Students' Representational Fluency

ERIC Educational Resources Information Center

Nichols, Kim; Ranasinghe, Muditha; Hanan, Jim

2013-01-01

Interacting with and translating across multiple representations is an essential characteristic of expertise and representational fluency. In this study, we explored the effect of interacting with and translating between representations in a computer simulation or in a paper-based assignment on scientific accuracy of undergraduate science…

Frequency Representation: Visualization and Clustering of Acoustic Data Using Self-Organizing Maps.

PubMed

Guo, Xinhua; Sun, Song; Yu, Xiantao; Wang, Pan; Nakamura, Kentaro

2017-11-01

Extraction and display of frequency information in three-dimensional (3D) acoustic data are important steps to analyze object characteristics, because the characteristics, such as profiles, sizes, surface structures, and material properties, may show frequency dependence. In this study, frequency representation (FR) based on phase information in multispectral acoustic imaging (MSAI) is proposed to overcome the limit of intensity or amplitude information in image display. Experiments are performed on 3D acoustic data collected from a rigid surface engraved with five different letters. The results show that the proposed FR technique can not only identify the depth of the five letters by the colors representing frequency characteristics but also demonstrate the 3D image of the five letters, providing more detailed characteristics that are unavailable by conventional acoustic imaging.

Approaches to integrating indicators into 3D landscape visualisations and their benefits for participative planning situations.

PubMed

Wissen, Ulrike; Schroth, Olaf; Lange, Eckart; Schmid, Willy A

2008-11-01

In discussing issues of landscape change, the complex relationships in the landscape have to be assessed. In participative planning processes, 3D visualisations have a high potential as an aid in understanding and communicating characteristics of landscape conditions by integrating visual and non-visual landscape information. Unclear is, which design and how much interactivity is required for an indicator visualisation that would suit stakeholders best in workshop situations. This paper describes the preparation and application of three different types of integrated 3D visualisations in workshops conducted in the Entlebuch UNESCO Biosphere Reserve (CH). The results reveal that simple representations of a complex issue created by draping thematic maps on the 3D model can make problematic developments visible at a glance; that diagrams linked to the spatial context can help draw attention to problematic relationships not considered beforehand; and that the size of species as indicators of conditions of the landscape's production and biotope function seems to provide a common language for stakeholders with different perspectives. Overall, the of the indicators the functions required to assist in information processing. Further research should focus on testing the effectiveness of the integrated visualisation tools in participative processes for the general public.

Method and apparatus for modeling interactions

DOEpatents

Xavier, Patrick G.

2000-08-08

A method and apparatus for modeling interactions between bodies. The method comprises representing two bodies undergoing translations and rotations by two hierarchical swept volume representations. Interactions such as nearest approach and collision can be modeled based on the swept body representations. The present invention can serve as a practical tool in motion planning, CAD systems, simulation systems, safety analysis, and applications that require modeling time-based interactions. A body can be represented in the present invention by a union of convex polygons and convex polyhedra. As used generally herein, polyhedron includes polygon, and polyhedra includes polygons. The body undergoing translation can be represented by a swept body representation, where the swept body representation comprises a hierarchical bounding volume representation whose leaves each contain a representation of the region swept by a section of the body during the translation, and where the union of the regions is a superset of the region swept by the surface of the body during translation. Interactions between two bodies thus represented can be modeled by modeling interactions between the convex hulls of the finite sets of discrete points in the swept body representations.

Fluid-Structure Interaction Simulation of Prosthetic Aortic Valves: Comparison between Immersed Boundary and Arbitrary Lagrangian-Eulerian Techniques for the Mesh Representation

PubMed Central

Iannaccone, Francesco; Degroote, Joris; Vierendeels, Jan; Segers, Patrick

2016-01-01

In recent years the role of FSI (fluid-structure interaction) simulations in the analysis of the fluid-mechanics of heart valves is becoming more and more important, being able to capture the interaction between the blood and both the surrounding biological tissues and the valve itself. When setting up an FSI simulation, several choices have to be made to select the most suitable approach for the case of interest: in particular, to simulate flexible leaflet cardiac valves, the type of discretization of the fluid domain is crucial, which can be described with an ALE (Arbitrary Lagrangian-Eulerian) or an Eulerian formulation. The majority of the reported 3D heart valve FSI simulations are performed with the Eulerian formulation, allowing for large deformations of the domains without compromising the quality of the fluid grid. Nevertheless, it is known that the ALE-FSI approach guarantees more accurate results at the interface between the solid and the fluid. The goal of this paper is to describe the same aortic valve model in the two cases, comparing the performances of an ALE-based FSI solution and an Eulerian-based FSI approach. After a first simplified 2D case, the aortic geometry was considered in a full 3D set-up. The model was kept as similar as possible in the two settings, to better compare the simulations’ outcomes. Although for the 2D case the differences were unsubstantial, in our experience the performance of a full 3D ALE-FSI simulation was significantly limited by the technical problems and requirements inherent to the ALE formulation, mainly related to the mesh motion and deformation of the fluid domain. As a secondary outcome of this work, it is important to point out that the choice of the solver also influenced the reliability of the final results. PMID:27128798

Advanced Pellet-Cladding Interaction Modeling using the US DOE CASL Fuel Performance Code: Peregrine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Montgomery, Robert O.; Capps, Nathan A.; Sunderland, Dion J.

The US DOE’s Consortium for Advanced Simulation of LWRs (CASL) program has undertaken an effort to enhance and develop modeling and simulation tools for a virtual reactor application, including high fidelity neutronics, fluid flow/thermal hydraulics, and fuel and material behavior. The fuel performance analysis efforts aim to provide 3-dimensional capabilities for single and multiple rods to assess safety margins and the impact of plant operation and fuel rod design on the fuel thermo-mechanical-chemical behavior, including Pellet-Cladding Interaction (PCI) failures and CRUD-Induced Localized Corrosion (CILC) failures in PWRs. [1-3] The CASL fuel performance code, Peregrine, is an engineering scale code thatmore » is built upon the MOOSE/ELK/FOX computational FEM framework, which is also common to the fuel modeling framework, BISON [4,5]. Peregrine uses both 2-D and 3-D geometric fuel rod representations and contains a materials properties and fuel behavior model library for the UO2 and Zircaloy system common to PWR fuel derived from both open literature sources and the FALCON code [6]. The primary purpose of Peregrine is to accurately calculate the thermal, mechanical, and chemical processes active throughout a single fuel rod during operation in a reactor, for both steady state and off-normal conditions.« less

Advanced Pellet Cladding Interaction Modeling Using the US DOE CASL Fuel Performance Code: Peregrine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jason Hales; Various

The US DOE’s Consortium for Advanced Simulation of LWRs (CASL) program has undertaken an effort to enhance and develop modeling and simulation tools for a virtual reactor application, including high fidelity neutronics, fluid flow/thermal hydraulics, and fuel and material behavior. The fuel performance analysis efforts aim to provide 3-dimensional capabilities for single and multiple rods to assess safety margins and the impact of plant operation and fuel rod design on the fuel thermomechanical- chemical behavior, including Pellet-Cladding Interaction (PCI) failures and CRUD-Induced Localized Corrosion (CILC) failures in PWRs. [1-3] The CASL fuel performance code, Peregrine, is an engineering scale codemore » that is built upon the MOOSE/ELK/FOX computational FEM framework, which is also common to the fuel modeling framework, BISON [4,5]. Peregrine uses both 2-D and 3-D geometric fuel rod representations and contains a materials properties and fuel behavior model library for the UO2 and Zircaloy system common to PWR fuel derived from both open literature sources and the FALCON code [6]. The primary purpose of Peregrine is to accurately calculate the thermal, mechanical, and chemical processes active throughout a single fuel rod during operation in a reactor, for both steady state and off-normal conditions.« less

Active-Vision Control Systems for Complex Adversarial 3-D Environments

DTIC Science & Technology

2009-03-01

Control Systems MURI Final Report 36 51. D. Nain, S. Haker , A. Bobick, A. Tannenbaum, "Multiscale 3D shape representation and segmentation using...Conference, August 2008. 99. L. Zhu, Y. Yang, S. Haker , and A. Tannenbaum, "An image morphing technique based on optimal mass preserving mapping," IEEE

The tensor hierarchy algebra

DOE Office of Scientific and Technical Information (OSTI.GOV)

Palmkvist, Jakob, E-mail: palmkvist@ihes.fr

We introduce an infinite-dimensional Lie superalgebra which is an extension of the U-duality Lie algebra of maximal supergravity in D dimensions, for 3 ⩽ D ⩽ 7. The level decomposition with respect to the U-duality Lie algebra gives exactly the tensor hierarchy of representations that arises in gauge deformations of the theory described by an embedding tensor, for all positive levels p. We prove that these representations are always contained in those coming from the associated Borcherds-Kac-Moody superalgebra, and we explain why some of the latter representations are not included in the tensor hierarchy. The most remarkable feature of ourmore » Lie superalgebra is that it does not admit a triangular decomposition like a (Borcherds-)Kac-Moody (super)algebra. Instead the Hodge duality relations between level p and D − 2 − p extend to negative p, relating the representations at the first two negative levels to the supersymmetry and closure constraints of the embedding tensor.« less

Using 3D modeling techniques to enhance teaching of difficult anatomical concepts

PubMed Central

Pujol, Sonia; Baldwin, Michael; Nassiri, Joshua; Kikinis, Ron; Shaffer, Kitt

2016-01-01

Rationale and Objectives Anatomy is an essential component of medical education as it is critical for the accurate diagnosis in organs and human systems. The mental representation of the shape and organization of different anatomical structures is a crucial step in the learning process. The purpose of this pilot study is to demonstrate the feasibility and benefits of developing innovative teaching modules for anatomy education of first-year medical students based on 3D reconstructions from actual patient data. Materials and Methods A total of 196 models of anatomical structures from 16 anonymized CT datasets were generated using the 3D Slicer open-source software platform. The models focused on three anatomical areas: the mediastinum, the upper abdomen and the pelvis. Online optional quizzes were offered to first-year medical students to assess their comprehension in the areas of interest. Specific tasks were designed for students to complete using the 3D models. Results Scores of the quizzes confirmed a lack of understanding of 3D spatial relationships of anatomical structures despite standard instruction including dissection. Written task material and qualitative review by students suggested that interaction with 3D models led to a better understanding of the shape and spatial relationships among structures, and helped illustrate anatomical variations from one body to another. Conclusion The study demonstrates the feasibility of one possible approach to the generation of 3D models of the anatomy from actual patient data. The educational materials developed have the potential to supplement the teaching of complex anatomical regions and help demonstrate the anatomic variation among patients. PMID:26897601

Bringing 3D Printing to Geophysical Science Education

NASA Astrophysics Data System (ADS)

Boghosian, A.; Turrin, M.; Porter, D. F.

2014-12-01

3D printing technology has been embraced by many technical fields, and is rapidly making its way into peoples' homes and schools. While there is a growing educational and hobbyist community engaged in the STEM focused technical and intellectual challenges associated with 3D printing, there is unrealized potential for the earth science community to use 3D printing to communicate scientific research to the public. Moreover, 3D printing offers scientists the opportunity to connect students and the public with novel visualizations of real data. As opposed to introducing terrestrial measurements through the use of colormaps and gradients, scientists can represent 3D concepts with 3D models, offering a more intuitive education tool. Furthermore, the tactile aspect of models make geophysical concepts accessible to a wide range of learning styles like kinesthetic or tactile, and learners including both visually impaired and color-blind students.We present a workflow whereby scientists, students, and the general public will be able to 3D print their own versions of geophysical datasets, even adding time through layering to include a 4th dimension, for a "4D" print. This will enable scientists with unique and expert insights into the data to easily create the tools they need to communicate their research. It will allow educators to quickly produce teaching aids for their students. Most importantly, it will enable the students themselves to translate the 2D representation of geophysical data into a 3D representation of that same data, reinforcing spatial reasoning.

Deformed twistors and higher spin conformal (super-)algebras in four dimensions

DOE PAGES

Govil, Karan; Gunaydin, Murat

2015-03-05

Massless conformal scalar field in d = 4 corresponds to the minimal unitary representation (minrep) of the conformal group SU(2, 2) which admits a one-parameter family of deformations that describe massless fields of arbitrary helicity. The minrep and its deformations were obtained by quantization of the nonlinear realization of SU(2, 2) as a quasiconformal group in arXiv:0908.3624. We show that the generators of SU(2,2) for these unitary irreducible representations can be written as bilinears of deformed twistorial oscillators which transform nonlinearly under the Lorentz group and apply them to define and study higher spin algebras and superalgebras in AdS 5.more » The higher spin (HS) algebra of Fradkin-Vasiliev type in AdS 5 is simply the enveloping algebra of SU(2, 2) quotiented by a two-sided ideal (Joseph ideal) which annihilates the minrep. We show that the Joseph ideal vanishes identically for the quasiconformal realization of the minrep and its enveloping algebra leads directly to the HS algebra in AdS 5. Furthermore, the enveloping algebras of the deformations of the minrep define a one parameter family of HS algebras in AdS 5 for which certain 4d covariant deformations of the Joseph ideal vanish identically. These results extend to superconformal algebras SU(2, 2|N) and we find a one parameter family of HS superalgebras as enveloping algebras of the minimal unitary supermultiplet and its deformations. Our results suggest the existence of a family of (supersymmetric) HS theories in AdS 5 which are dual to free (super)conformal field theories (CFTs) or to interacting but integrable (supersymmetric) CFTs in 4d. We also discuss the corresponding picture in HS algebras in AdS 4 where the corresponding 3d conformal group Sp(4,R) admits only two massless representations (minreps), namely the scalar and spinor singletons.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Govil, Karan; Gunaydin, Murat

Massless conformal scalar field in d = 4 corresponds to the minimal unitary representation (minrep) of the conformal group SU(2, 2) which admits a one-parameter family of deformations that describe massless fields of arbitrary helicity. The minrep and its deformations were obtained by quantization of the nonlinear realization of SU(2, 2) as a quasiconformal group in arXiv:0908.3624. We show that the generators of SU(2,2) for these unitary irreducible representations can be written as bilinears of deformed twistorial oscillators which transform nonlinearly under the Lorentz group and apply them to define and study higher spin algebras and superalgebras in AdS 5.more » The higher spin (HS) algebra of Fradkin-Vasiliev type in AdS 5 is simply the enveloping algebra of SU(2, 2) quotiented by a two-sided ideal (Joseph ideal) which annihilates the minrep. We show that the Joseph ideal vanishes identically for the quasiconformal realization of the minrep and its enveloping algebra leads directly to the HS algebra in AdS 5. Furthermore, the enveloping algebras of the deformations of the minrep define a one parameter family of HS algebras in AdS 5 for which certain 4d covariant deformations of the Joseph ideal vanish identically. These results extend to superconformal algebras SU(2, 2|N) and we find a one parameter family of HS superalgebras as enveloping algebras of the minimal unitary supermultiplet and its deformations. Our results suggest the existence of a family of (supersymmetric) HS theories in AdS 5 which are dual to free (super)conformal field theories (CFTs) or to interacting but integrable (supersymmetric) CFTs in 4d. We also discuss the corresponding picture in HS algebras in AdS 4 where the corresponding 3d conformal group Sp(4,R) admits only two massless representations (minreps), namely the scalar and spinor singletons.« less

Topology reconstruction for B-Rep modeling from 3D mesh in reverse engineering applications

NASA Astrophysics Data System (ADS)

Bénière, Roseline; Subsol, Gérard; Gesquière, Gilles; Le Breton, François; Puech, William

2012-03-01

Nowadays, most of the manufactured objects are designed using CAD (Computer-Aided Design) software. Nevertheless, for visualization, data exchange or manufacturing applications, the geometric model has to be discretized into a 3D mesh composed of a finite number of vertices and edges. But, in some cases, the initial model may be lost or unavailable. In other cases, the 3D discrete representation may be modified, for example after a numerical simulation, and does not correspond anymore to the initial model. A reverse engineering method is then required to reconstruct a 3D continuous representation from the discrete one. In previous work, we have presented a new approach for 3D geometric primitive extraction. In this paper, to complete our automatic and comprehensive reverse engineering process, we propose a method to construct the topology of the retrieved object. To reconstruct a B-Rep model, a new formalism is now introduced to define the adjacency relations. Then a new process is used to construct the boundaries of the object. The whole process is tested on 3D industrial meshes and bring a solution to recover B-Rep models.

Transfer of Learning between 2D and 3D Sources during Infancy: Informing Theory and Practice

ERIC Educational Resources Information Center

Barr, Rachel

2010-01-01

The ability to transfer learning across contexts is an adaptive skill that develops rapidly during early childhood. Learning from television is a specific instance of transfer of learning between a two-dimensional (2D) representation and a three-dimensional (3D) object. Understanding the conditions under which young children might accomplish this…

Entanglement of heavy quark impurities and generalized gravitational entropy

NASA Astrophysics Data System (ADS)

Kumar, S. Prem; Silvani, Dorian

2018-01-01

We calculate the contribution from non-conformal heavy quark sources to the entanglement entropy (EE) of a spherical region in N=4 SUSY Yang-Mills theory. We apply the generalized gravitational entropy method to non-conformal probe D-brane embeddings in AdS5×S5, dual to pointlike impurities exhibiting flows between quarks in large-rank tensor representations and the fundamental representation. For the D5-brane embedding which describes the screening of fundamental quarks in the UV to the antisymmetric tensor representation in the IR, the EE excess decreases non-monotonically towards its IR asymptotic value, tracking the qualitative behaviour of the one-point function of static fields sourced by the impurity. We also examine two classes of D3-brane embeddings, one which connects a symmetric representation source in the UV to fundamental quarks in the IR, and a second category which yields the symmetric representation source on the Coulomb branch. The EE excess for the former increases from the UV to the IR, whilst decreasing and becoming negative for the latter. In all cases, the probe free energy on hyperbolic space with β = 2 π increases monotonically towards the IR, supporting its interpretation as a relative entropy. We identify universal corrections, depending logarithmically on the VEV, for the symmetric representation on the Coulomb branch.

Real object-based 360-degree integral-floating display using multiple depth camera

NASA Astrophysics Data System (ADS)

Erdenebat, Munkh-Uchral; Dashdavaa, Erkhembaatar; Kwon, Ki-Chul; Wu, Hui-Ying; Yoo, Kwan-Hee; Kim, Young-Seok; Kim, Nam

2015-03-01

A novel 360-degree integral-floating display based on the real object is proposed. The general procedure of the display system is similar with conventional 360-degree integral-floating displays. Unlike previously presented 360-degree displays, the proposed system displays the 3D image generated from the real object in 360-degree viewing zone. In order to display real object in 360-degree viewing zone, multiple depth camera have been utilized to acquire the depth information around the object. Then, the 3D point cloud representations of the real object are reconstructed according to the acquired depth information. By using a special point cloud registration method, the multiple virtual 3D point cloud representations captured by each depth camera are combined as single synthetic 3D point cloud model, and the elemental image arrays are generated for the newly synthesized 3D point cloud model from the given anamorphic optic system's angular step. The theory has been verified experimentally, and it shows that the proposed 360-degree integral-floating display can be an excellent way to display real object in the 360-degree viewing zone.

The interplay of representations and patterns of classroom discourse in science teaching sequences

NASA Astrophysics Data System (ADS)

Tang, Kok-Sing

2016-09-01

The purpose of this study is to examines the relationship between the communicative approach of classroom talk and the modes of representations used by science teachers. Based on video data from two physics classrooms in Singapore, a recurring pattern in the relationship was observed as the teaching sequence of a lesson unfolded. It was found that as the mode of representation shifted from enactive (action based) to iconic (image based) to symbolic (language based), there was a concurrent and coordinated shift in the classroom communicative approach from interactive-dialogic to interactive-authoritative to non-interactive-authoritative. Specifically, the shift from enactive to iconic to symbolic representations occurred mainly within the interactive-dialogic approach while the shift towards the interactive-authoritative and non-interactive-authoritative approaches occurred when symbolic modes of representation were used. This concurrent and coordinated shift has implications on how we conceive the use of representations in conjunction with the co-occurring classroom discourse, both theoretically and pedagogically.

3D surface parameterization using manifold learning for medial shape representation

NASA Astrophysics Data System (ADS)

Ward, Aaron D.; Hamarneh, Ghassan

2007-03-01

The choice of 3D shape representation for anatomical structures determines the effectiveness with which segmentation, visualization, deformation, and shape statistics are performed. Medial axis-based shape representations have attracted considerable attention due to their inherent ability to encode information about the natural geometry of parts of the anatomy. In this paper, we propose a novel approach, based on nonlinear manifold learning, to the parameterization of medial sheets and object surfaces based on the results of skeletonization. For each single-sheet figure in an anatomical structure, we skeletonize the figure, and classify its surface points according to whether they lie on the upper or lower surface, based on their relationship to the skeleton points. We then perform nonlinear dimensionality reduction on the skeleton, upper, and lower surface points, to find the intrinsic 2D coordinate system of each. We then center a planar mesh over each of the low-dimensional representations of the points, and map the meshes back to 3D using the mappings obtained by manifold learning. Correspondence between mesh vertices, established in their intrinsic 2D coordinate spaces, is used in order to compute the thickness vectors emanating from the medial sheet. We show results of our algorithm on real brain and musculoskeletal structures extracted from MRI, as well as an artificial multi-sheet example. The main advantages to this method are its relative simplicity and noniterative nature, and its ability to correctly compute nonintersecting thickness vectors for a medial sheet regardless of both the amount of coincident bending and thickness in the object, and of the incidence of local concavities and convexities in the object's surface.

Measurable realistic image-based 3D mapping

NASA Astrophysics Data System (ADS)

Liu, W.; Wang, J.; Wang, J. J.; Ding, W.; Almagbile, A.

2011-12-01

Maps with 3D visual models are becoming a remarkable feature of 3D map services. High-resolution image data is obtained for the construction of 3D visualized models.The3D map not only provides the capabilities of 3D measurements and knowledge mining, but also provides the virtual experienceof places of interest, such as demonstrated in the Google Earth. Applications of 3D maps are expanding into the areas of architecture, property management, and urban environment monitoring. However, the reconstruction of high quality 3D models is time consuming, and requires robust hardware and powerful software to handle the enormous amount of data. This is especially for automatic implementation of 3D models and the representation of complicated surfacesthat still need improvements with in the visualisation techniques. The shortcoming of 3D model-based maps is the limitation of detailed coverage since a user can only view and measure objects that are already modelled in the virtual environment. This paper proposes and demonstrates a 3D map concept that is realistic and image-based, that enables geometric measurements and geo-location services. Additionally, image-based 3D maps provide more detailed information of the real world than 3D model-based maps. The image-based 3D maps use geo-referenced stereo images or panoramic images. The geometric relationships between objects in the images can be resolved from the geometric model of stereo images. The panoramic function makes 3D maps more interactive with users but also creates an interesting immersive circumstance. Actually, unmeasurable image-based 3D maps already exist, such as Google street view, but only provide virtual experiences in terms of photos. The topographic and terrain attributes, such as shapes and heights though are omitted. This paper also discusses the potential for using a low cost land Mobile Mapping System (MMS) to implement realistic image 3D mapping, and evaluates the positioning accuracy that a measureable realistic image-based (MRI) system can produce. The major contribution here is the implementation of measurable images on 3D maps to obtain various measurements from real scenes.

Improved protein surface comparison and application to low-resolution protein structure data.

PubMed

Sael, Lee; Kihara, Daisuke

2010-12-14

Recent advancements of experimental techniques for determining protein tertiary structures raise significant challenges for protein bioinformatics. With the number of known structures of unknown function expanding at a rapid pace, an urgent task is to provide reliable clues to their biological function on a large scale. Conventional approaches for structure comparison are not suitable for a real-time database search due to their slow speed. Moreover, a new challenge has arisen from recent techniques such as electron microscopy (EM), which provide low-resolution structure data. Previously, we have introduced a method for protein surface shape representation using the 3D Zernike descriptors (3DZDs). The 3DZD enables fast structure database searches, taking advantage of its rotation invariance and compact representation. The search results of protein surface represented with the 3DZD has showngood agreement with the existing structure classifications, but some discrepancies were also observed. The three new surface representations of backbone atoms, originally devised all-atom-surface representation, and the combination of all-atom surface with the backbone representation are examined. All representations are encoded with the 3DZD. Also, we have investigated the applicability of the 3DZD for searching protein EM density maps of varying resolutions. The surface representations are evaluated on structure retrieval using two existing classifications, SCOP and the CE-based classification. Overall, the 3DZDs representing backbone atoms show better retrieval performance than the original all-atom surface representation. The performance further improved when the two representations are combined. Moreover, we observed that the 3DZD is also powerful in comparing low-resolution structures obtained by electron microscopy.

Baryon-baryon interactions and spin-flavor symmetry from lattice quantum chromodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wagman, Michael L.; Winter, Frank; Chang, Emmanuel

Lattice quantum chromodynamics is used to constrain the interactions of two octet baryons at the SU(3) flavor-symmetric point, with quark masses that are heavier than those in nature (equal to that of the physical strange quark mass and corresponding to a pion mass ofmore » $$\\approx 806~\\tt{MeV}$$). Specifically, the S-wave scattering phase shifts of two-baryon systems at low energies are obtained with the application of L\\"uscher's formalism, mapping the energy eigenvalues of two interacting baryons in a finite volume to the two-particle scattering amplitudes below the relevant inelastic thresholds. The values of the leading-order low-energy scattering parameters in the irreducible representations of SU(3) are consistent with an approximate SU(6) spin-flavor symmetry in the nuclear and hypernuclear forces that is predicted in the large-$$N_c$$ limit of QCD. The two distinct SU(6)-invariant interactions between two baryons are constrained at this value of the quark masses, and their values indicate an approximate accidental SU(16) symmetry. The SU(3) irreducible representations containing the $$NN~({^1}S_0)$$, $$NN~({^3}S_1)$$ and $$\\frac{1}{\\sqrt{2}}(\\Xi^0n+\\Xi^-p)~({^3}S_1)$$ channels unambiguously exhibit a single bound state, while the irreducible representation containing the $$\\Sigma^+ p~({^3}S_1)$$ channel exhibits a state that is consistent with either a bound state or a scattering state close to threshold. These results are in agreement with the previous conclusions of the NPLQCD collaboration regarding the existence of two-nucleon bound states at this value of the quark masses.« less

Baryon-baryon interactions and spin-flavor symmetry from lattice quantum chromodynamics

DOE PAGES

Wagman, Michael L.; Winter, Frank; Chang, Emmanuel; ...

2017-12-28

Lattice quantum chromodynamics is used to constrain the interactions of two octet baryons at the SU(3) flavor-symmetric point, with quark masses that are heavier than those in nature (equal to that of the physical strange quark mass and corresponding to a pion mass ofmore » $$\\approx 806~\\tt{MeV}$$). Specifically, the S-wave scattering phase shifts of two-baryon systems at low energies are obtained with the application of L\\"uscher's formalism, mapping the energy eigenvalues of two interacting baryons in a finite volume to the two-particle scattering amplitudes below the relevant inelastic thresholds. The values of the leading-order low-energy scattering parameters in the irreducible representations of SU(3) are consistent with an approximate SU(6) spin-flavor symmetry in the nuclear and hypernuclear forces that is predicted in the large-$$N_c$$ limit of QCD. The two distinct SU(6)-invariant interactions between two baryons are constrained at this value of the quark masses, and their values indicate an approximate accidental SU(16) symmetry. The SU(3) irreducible representations containing the $$NN~({^1}S_0)$$, $$NN~({^3}S_1)$$ and $$\\frac{1}{\\sqrt{2}}(\\Xi^0n+\\Xi^-p)~({^3}S_1)$$ channels unambiguously exhibit a single bound state, while the irreducible representation containing the $$\\Sigma^+ p~({^3}S_1)$$ channel exhibits a state that is consistent with either a bound state or a scattering state close to threshold. These results are in agreement with the previous conclusions of the NPLQCD collaboration regarding the existence of two-nucleon bound states at this value of the quark masses.« less

Optimization of spine surgery planning with 3D image templating tools

NASA Astrophysics Data System (ADS)

Augustine, Kurt E.; Huddleston, Paul M.; Holmes, David R., III; Shridharani, Shyam M.; Robb, Richard A.

2008-03-01

The current standard of care for patients with spinal disorders involves a thorough clinical history, physical exam, and imaging studies. Simple radiographs provide a valuable assessment but prove inadequate for surgery planning because of the complex 3-dimensional anatomy of the spinal column and the close proximity of the neural elements, large blood vessels, and viscera. Currently, clinicians still use primitive techniques such as paper cutouts, pencils, and markers in an attempt to analyze and plan surgical procedures. 3D imaging studies are routinely ordered prior to spine surgeries but are currently limited to generating simple, linear and angular measurements from 2D views orthogonal to the central axis of the patient. Complex spinal corrections require more accurate and precise calculation of 3D parameters such as oblique lengths, angles, levers, and pivot points within individual vertebra. We have developed a clinician friendly spine surgery planning tool which incorporates rapid oblique reformatting of each individual vertebra, followed by interactive templating for 3D placement of implants. The template placement is guided by the simultaneous representation of multiple 2D section views from reformatted orthogonal views and a 3D rendering of individual or multiple vertebrae enabling superimposition of virtual implants. These tools run efficiently on desktop PCs typically found in clinician offices or workrooms. A preliminary study conducted with Mayo Clinic spine surgeons using several actual cases suggests significantly improved accuracy of pre-operative measurements and implant localization, which is expected to increase spinal procedure efficiency and safety, and reduce time and cost of the operation.

3D Face Recognition Based on Multiple Keypoint Descriptors and Sparse Representation

PubMed Central

Zhang, Lin; Ding, Zhixuan; Li, Hongyu; Shen, Ying; Lu, Jianwei

2014-01-01

Recent years have witnessed a growing interest in developing methods for 3D face recognition. However, 3D scans often suffer from the problems of missing parts, large facial expressions, and occlusions. To be useful in real-world applications, a 3D face recognition approach should be able to handle these challenges. In this paper, we propose a novel general approach to deal with the 3D face recognition problem by making use of multiple keypoint descriptors (MKD) and the sparse representation-based classification (SRC). We call the proposed method 3DMKDSRC for short. Specifically, with 3DMKDSRC, each 3D face scan is represented as a set of descriptor vectors extracted from keypoints by meshSIFT. Descriptor vectors of gallery samples form the gallery dictionary. Given a probe 3D face scan, its descriptors are extracted at first and then its identity can be determined by using a multitask SRC. The proposed 3DMKDSRC approach does not require the pre-alignment between two face scans and is quite robust to the problems of missing data, occlusions and expressions. Its superiority over the other leading 3D face recognition schemes has been corroborated by extensive experiments conducted on three benchmark databases, Bosphorus, GavabDB, and FRGC2.0. The Matlab source code for 3DMKDSRC and the related evaluation results are publicly available at http://sse.tongji.edu.cn/linzhang/3dmkdsrcface/3dmkdsrc.htm. PMID:24940876

STRUCTURAL SCALE LIFE PREDICTION OF AERO STRUCTURES EXPERIENCING COMBINED EXTREME ENVIRONMENTS

DTIC Science & Technology

2017-07-01

representation is converted into a tetrahedral FE mesh using the software DREAM .3D. Due to a special voxel-identification scheme the FE mesh includes...research team met with DREAM .3D developers at AFRL (Drs. Mike Groeber and Sean Donegan) to discuss possible solutions. Together, the group proposed the...development of a DREAM .3D extension that can leverage the topological data structure within DREAM .3D instead of relying on an image-based

Interactive Mapping on Virtual Terrain Models Using RIMS (Real-time, Interactive Mapping System)

NASA Astrophysics Data System (ADS)

Bernardin, T.; Cowgill, E.; Gold, R. D.; Hamann, B.; Kreylos, O.; Schmitt, A.

2006-12-01

Recent and ongoing space missions are yielding new multispectral data for the surfaces of Earth and other planets at unprecedented rates and spatial resolution. With their high spatial resolution and widespread coverage, these data have opened new frontiers in observational Earth and planetary science. But they have also precipitated an acute need for new analytical techniques. To address this problem, we have developed RIMS, a Real-time, Interactive Mapping System that allows scientists to visualize, interact with, and map directly on, three-dimensional (3D) displays of georeferenced texture data, such as multispectral satellite imagery, that is draped over a surface representation derived from digital elevation data. The system uses a quadtree-based multiresolution method to render in real time high-resolution (3 to 10 m/pixel) data over large (800 km by 800 km) spatial areas. It allows users to map inside this interactive environment by generating georeferenced and attributed vector-based elements that are draped over the topography. We explain the technique using 15 m ASTER stereo-data from Iraq, P.R. China, and other remote locations because our particular motivation is to develop a technique that permits the detailed (10 m to 1000 m) neotectonic mapping over large (100 km to 1000 km long) active fault systems that is needed to better understand active continental deformation on Earth. RIMS also includes a virtual geologic compass that allows users to fit a plane to geologic surfaces and thereby measure their orientations. It also includes tools that allow 3D surface reconstruction of deformed and partially eroded surfaces such as folded bedding planes. These georeferenced map and measurement data can be exported to, or imported from, a standard GIS (geographic information systems) file format. Our interactive, 3D visualization and analysis system is designed for those who study planetary surfaces, including neotectonic geologists, geomorphologists, marine geophysicists, and planetary scientists. The strength of our system is that it combines interactive rendering with interactive mapping and measurement of features observed in topographic and texture data. Comparison with commercially available software indicates that our system improves mapping accuracy and efficiency. More importantly, it enables Earth scientists to rapidly achieve a deeper level of understanding of remotely sensed data, as observations can be made that are not possible with existing systems.

Virtual reality in the operating room of the future.

PubMed

Müller, W; Grosskopf, S; Hildebrand, A; Malkewitz, R; Ziegler, R

1997-01-01

In cooperation with the Max-Delbrück-Centrum/Robert-Rössle-Klinik (MDC/RRK) in Berlin, the Fraunhofer Institute for Computer Graphics is currently designing and developing a scenario for the operating room of the future. The goal of this project is to integrate new analysis, visualization and interaction tools in order to optimize and refine tumor diagnostics and therapy in combination with laser technology and remote stereoscopic video transfer. Hence, a human 3-D reference model is reconstructed using CT, MR, and anatomical cryosection images from the National Library of Medicine's Visible Human Project. Applying segmentation algorithms and surface-polygonization methods a 3-D representation is obtained. In addition, a "fly-through" the virtual patient is realized using 3-D input devices (data glove, tracking system, 6-DOF mouse). In this way, the surgeon can experience really new perspectives of the human anatomy. Moreover, using a virtual cutting plane any cut of the CT volume can be interactively placed and visualized in realtime. In conclusion, this project delivers visions for the application of effective visualization and VR systems. Commonly known as Virtual Prototyping and applied by the automotive industry long ago, this project shows, that the use of VR techniques can also prototype an operating room. After evaluating design and functionality of the virtual operating room, MDC plans to build real ORs in the near future. The use of VR techniques provides a more natural interface for the surgeon in the OR (e.g., controlling interactions by voice input). Besides preoperative planning future work will focus on supporting the surgeon in performing surgical interventions. An optimal synthesis of real and synthetic data, and the inclusion of visual, aural, and tactile senses in virtual environments can meet these requirements. This Augmented Reality could represent the environment for the surgeons of tomorrow.

a Procedural Solution to Model Roman Masonry Structures

NASA Astrophysics Data System (ADS)

Cappellini, V.; Saleri, R.; Stefani, C.; Nony, N.; De Luca, L.

2013-07-01

The paper will describe a new approach based on the development of a procedural modelling methodology for archaeological data representation. This is a custom-designed solution based on the recognition of the rules belonging to the construction methods used in roman times. We have conceived a tool for 3D reconstruction of masonry structures starting from photogrammetric surveying. Our protocol considers different steps. Firstly we have focused on the classification of opus based on the basic interconnections that can lead to a descriptive system used for their unequivocal identification and design. Secondly, we have chosen an automatic, accurate, flexible and open-source photogrammetric pipeline named Pastis Apero Micmac - PAM, developed by IGN (Paris). We have employed it to generate ortho-images from non-oriented images, using a user-friendly interface implemented by CNRS Marseille (France). Thirdly, the masonry elements are created in parametric and interactive way, and finally they are adapted to the photogrammetric data. The presented application, currently under construction, is developed with an open source programming language called Processing, useful for visual, animated or static, 2D or 3D, interactive creations. Using this computer language, a Java environment has been developed. Therefore, even if the procedural modelling reveals an accuracy level inferior to the one obtained by manual modelling (brick by brick), this method can be useful when taking into account the static evaluation on buildings (requiring quantitative aspects) and metric measures for restoration purposes.

Super Normal Vector for Human Activity Recognition with Depth Cameras.

PubMed

Yang, Xiaodong; Tian, YingLi

2017-05-01

The advent of cost-effectiveness and easy-operation depth cameras has facilitated a variety of visual recognition tasks including human activity recognition. This paper presents a novel framework for recognizing human activities from video sequences captured by depth cameras. We extend the surface normal to polynormal by assembling local neighboring hypersurface normals from a depth sequence to jointly characterize local motion and shape information. We then propose a general scheme of super normal vector (SNV) to aggregate the low-level polynormals into a discriminative representation, which can be viewed as a simplified version of the Fisher kernel representation. In order to globally capture the spatial layout and temporal order, an adaptive spatio-temporal pyramid is introduced to subdivide a depth video into a set of space-time cells. In the extensive experiments, the proposed approach achieves superior performance to the state-of-the-art methods on the four public benchmark datasets, i.e., MSRAction3D, MSRDailyActivity3D, MSRGesture3D, and MSRActionPairs3D.

Detection and 3D representation of pulmonary air bubbles in HRCT volumes

NASA Astrophysics Data System (ADS)

Silva, Jose S.; Silva, Augusto F.; Santos, Beatriz S.; Madeira, Joaquim

2003-05-01

Bubble emphysema is a disease characterized by the presence of air bubbles within the lungs. With the purpose of identifying pulmonary air bubbles, two alternative methods were developed, using High Resolution Computer Tomography (HRCT) exams. The search volume is confined to the pulmonary volume through a previously developed pulmonary contour detection algorithm. The first detection method follows a slice by slice approach and uses selection criteria based on the Hounsfield levels, dimensions, shape and localization of the bubbles. Candidate regions that do not exhibit axial coherence along at least two sections are excluded. Intermediate sections are interpolated for a more realistic representation of lungs and bubbles. The second detection method, after the pulmonary volume delimitation, follows a fully 3D approach. A global threshold is applied to the entire lung volume returning candidate regions. 3D morphologic operators are used to remove spurious structures and to circumscribe the bubbles. Bubble representation is accomplished by two alternative methods. The first generates bubble surfaces based on the voxel volumes previously detected; the second method assumes that bubbles are approximately spherical. In order to obtain better 3D representations, fits super-quadrics to bubble volume. The fitting process is based on non-linear least squares optimization method, where a super-quadric is adapted to a regular grid of points defined on each bubble. All methods were applied to real and semi-synthetical data where artificial and randomly deformed bubbles were embedded in the interior of healthy lungs. Quantitative results regarding bubble geometric features are either similar to a priori known values used in simulation tests, or indicate clinically acceptable dimensions and locations when dealing with real data.

Numerical Optimization Strategy for Determining 3D Flow Fields in Microfluidics

NASA Astrophysics Data System (ADS)

Eden, Alex; Sigurdson, Marin; Mezic, Igor; Meinhart, Carl

2015-11-01

We present a hybrid experimental-numerical method for generating 3D flow fields from 2D PIV experimental data. An optimization algorithm is applied to a theory-based simulation of an alternating current electrothermal (ACET) micromixer in conjunction with 2D PIV data to generate an improved representation of 3D steady state flow conditions. These results can be used to investigate mixing phenomena. Experimental conditions were simulated using COMSOL Multiphysics to solve the temperature and velocity fields, as well as the quasi-static electric fields. The governing equations were based on a theoretical model for ac electrothermal flows. A Nelder-Mead optimization algorithm was used to achieve a better fit by minimizing the error between 2D PIV experimental velocity data and numerical simulation results at the measurement plane. By applying this hybrid method, the normalized RMS velocity error between the simulation and experimental results was reduced by more than an order of magnitude. The optimization algorithm altered 3D fluid circulation patterns considerably, providing a more accurate representation of the 3D experimental flow field. This method can be generalized to a wide variety of flow problems. This research was supported by the Institute for Collaborative Biotechnologies through grant W911NF-09-0001 from the U.S. Army Research Office.

Relations between maternal attachment representations and the quality of mother-infant interaction in preterm and full-term infants.

PubMed

Korja, Riikka; Ahlqvist-Björkroth, Sari; Savonlahti, Elina; Stolt, Suvi; Haataja, Leena; Lapinleimu, Helena; Piha, Jorma; Lehtonen, Liisa

2010-06-01

The aim of the study was to assess the relationship between maternal representations and the quality of mother-infant interaction in a group of preterm and full-term infants. The study groups consisted of 38 mothers and their preterm infants (

NeuroMap: A Spline-Based Interactive Open-Source Software for Spatiotemporal Mapping of 2D and 3D MEA Data

PubMed Central

Abdoun, Oussama; Joucla, Sébastien; Mazzocco, Claire; Yvert, Blaise

2010-01-01

A major characteristic of neural networks is the complexity of their organization at various spatial scales, from microscopic local circuits to macroscopic brain-scale areas. Understanding how neural information is processed thus entails the ability to study them at multiple scales simultaneously. This is made possible using microelectrodes array (MEA) technology. Indeed, high-density MEAs provide large-scale coverage (several square millimeters) of whole neural structures combined with microscopic resolution (about 50 μm) of unit activity. Yet, current options for spatiotemporal representation of MEA-collected data remain limited. Here we present NeuroMap, a new interactive Matlab-based software for spatiotemporal mapping of MEA data. NeuroMap uses thin plate spline interpolation, which provides several assets with respect to conventional mapping methods used currently. First, any MEA design can be considered, including 2D or 3D, regular or irregular, arrangements of electrodes. Second, spline interpolation allows the estimation of activity across the tissue with local extrema not necessarily at recording sites. Finally, this interpolation approach provides a straightforward analytical estimation of the spatial Laplacian for better current sources localization. In this software, coregistration of 2D MEA data on the anatomy of the neural tissue is made possible by fine matching of anatomical data with electrode positions using rigid-deformation-based correction of anatomical pictures. Overall, NeuroMap provides substantial material for detailed spatiotemporal analysis of MEA data. The package is distributed under GNU General Public License and available at http://sites.google.com/site/neuromapsoftware. PMID:21344013

NeuroMap: A Spline-Based Interactive Open-Source Software for Spatiotemporal Mapping of 2D and 3D MEA Data.

PubMed

Abdoun, Oussama; Joucla, Sébastien; Mazzocco, Claire; Yvert, Blaise

2011-01-01

A major characteristic of neural networks is the complexity of their organization at various spatial scales, from microscopic local circuits to macroscopic brain-scale areas. Understanding how neural information is processed thus entails the ability to study them at multiple scales simultaneously. This is made possible using microelectrodes array (MEA) technology. Indeed, high-density MEAs provide large-scale coverage (several square millimeters) of whole neural structures combined with microscopic resolution (about 50 μm) of unit activity. Yet, current options for spatiotemporal representation of MEA-collected data remain limited. Here we present NeuroMap, a new interactive Matlab-based software for spatiotemporal mapping of MEA data. NeuroMap uses thin plate spline interpolation, which provides several assets with respect to conventional mapping methods used currently. First, any MEA design can be considered, including 2D or 3D, regular or irregular, arrangements of electrodes. Second, spline interpolation allows the estimation of activity across the tissue with local extrema not necessarily at recording sites. Finally, this interpolation approach provides a straightforward analytical estimation of the spatial Laplacian for better current sources localization. In this software, coregistration of 2D MEA data on the anatomy of the neural tissue is made possible by fine matching of anatomical data with electrode positions using rigid-deformation-based correction of anatomical pictures. Overall, NeuroMap provides substantial material for detailed spatiotemporal analysis of MEA data. The package is distributed under GNU General Public License and available at http://sites.google.com/site/neuromapsoftware.

MicroEcos: Micro-Scale Explorations of Large-Scale Late Pleistocene Ecosystems

NASA Astrophysics Data System (ADS)

Gellis, B. S.

2017-12-01

Pollen data can inform the reconstruction of early-floral environments by providing data for artistic representations of what early-terrestrial ecosystems looked like, and how existing terrestrial landscapes have evolved. For example, what did the Bighorn Basin look like when large ice sheets covered modern Canada, the Yellowstone Plateau had an ice cap, and the Bighorn Mountains were mantled with alpine glaciers? MicroEcos is an immersive, multimedia project that aims to strengthen human-nature connections through the understanding and appreciation of biological ecosystems. Collected pollen data elucidates flora that are visible in the fossil record - associated with the Late-Pleistocene - and have been illustrated and described in botanical literature. It aims to make scientific data accessible and interesting to all audiences through a series of interactive-digital sculptures, large-scale photography and field-based videography. While this project is driven by scientific data, it is rooted in deeply artistic and outreach-based practices, which include broad artistic practices, e.g.: digital design, illustration, photography, video and sound design. Using 3D modeling and printing technology MicroEcos centers around a series of 3D-printed models of the Last Canyon rock shelter on the Wyoming and Montana border, Little Windy Hill pond site in Wyoming's Medicine Bow National Forest, and Natural Trap Cave site in Wyoming's Big Horn Basin. These digital, interactive-3D sculpture provide audiences with glimpses of three-dimensional Late-Pleistocene environments, and helps create dialogue of how grass, sagebrush, and spruce based ecosystems form. To help audiences better contextualize how MicroEcos bridges notions of time, space, and place, modern photography and videography of the Last Canyon, Little Windy Hill and Natural Trap Cave sites surround these 3D-digital reconstructions.

An Unified Multiscale Framework for Planar, Surface, and Curve Skeletonization.

PubMed

Jalba, Andrei C; Sobiecki, Andre; Telea, Alexandru C

2016-01-01

Computing skeletons of 2D shapes, and medial surface and curve skeletons of 3D shapes, is a challenging task. In particular, there is no unified framework that detects all types of skeletons using a single model, and also produces a multiscale representation which allows to progressively simplify, or regularize, all skeleton types. In this paper, we present such a framework. We model skeleton detection and regularization by a conservative mass transport process from a shape's boundary to its surface skeleton, next to its curve skeleton, and finally to the shape center. The resulting density field can be thresholded to obtain a multiscale representation of progressively simplified surface, or curve, skeletons. We detail a numerical implementation of our framework which is demonstrably stable and has high computational efficiency. We demonstrate our framework on several complex 2D and 3D shapes.

A SPECT system simulator built on the SolidWorks TM 3D-Design package.

PubMed

Li, Xin; Furenlid, Lars R

2014-08-17

We have developed a GPU-accelerated SPECT system simulator that integrates into instrument-design workflow [1]. This simulator includes a gamma-ray tracing module that can rapidly propagate gamma-ray photons through arbitrary apertures modeled by SolidWorks TM -created stereolithography (.STL) representations with a full complement of physics cross sections [2, 3]. This software also contains a scintillation detector simulation module that can model a scintillation detector with arbitrary scintillation crystal shape and light-sensor arrangement. The gamma-ray tracing module enables us to efficiently model aperture and detector crystals in SolidWorks TM and save them as STL file format, then load the STL-format model into this module to generate list-mode results of interacted gamma-ray photon information (interaction positions and energies) inside the detector crystals. The Monte-Carlo scintillation detector simulation module enables us to simulate how scintillation photons get reflected, refracted and absorbed inside a scintillation detector, which contributes to more accurate simulation of a SPECT system.

A SPECT system simulator built on the SolidWorksTM 3D design package

NASA Astrophysics Data System (ADS)

Li, Xin; Furenlid, Lars R.

2014-09-01

We have developed a GPU-accelerated SPECT system simulator that integrates into instrument-design work flow [1]. This simulator includes a gamma-ray tracing module that can rapidly propagate gamma-ray photons through arbitrary apertures modeled by SolidWorksTM-created stereolithography (.STL) representations with a full com- plement of physics cross sections [2, 3]. This software also contains a scintillation detector simulation module that can model a scintillation detector with arbitrary scintillation crystal shape and light-sensor arrangement. The gamma-ray tracing module enables us to efficiently model aperture and detector crystals in SolidWorksTM and save them as STL file format, then load the STL-format model into this module to generate list-mode results of interacted gamma-ray photon information (interaction positions and energies) inside the detector crystals. The Monte-Carlo scintillation detector simulation module enables us to simulate how scintillation photons get reflected, refracted and absorbed inside a scintillation detector, which contributes to more accurate simulation of a SPECT system.

Three-dimensional visualisation improves understanding of surgical liver anatomy.

PubMed

Beermann, Judith; Tetzlaff, Ralf; Bruckner, Thomas; Schöebinger, Max; Müller-Stich, Beat P; Gutt, Carsten N; Meinzer, Hans-Peter; Kadmon, Martina; Fischer, Lars

2010-09-01

Three-dimensional (3-D) representation is thought to improve understanding of complex spatial interactions and is being used more frequently in diagnostic and therapeutic procedures. It has been suggested that males benefit more than females from 3-D presentations. There have been few randomised trials to confirm these issues. We carried out a randomised trial, based on the identification of complex surgical liver anatomy, to evaluate whether 3-D presentation has a beneficial impact and if gender differences were evident. A computer-based teaching module (TM) was developed to test whether two-dimensional (2-D) computed tomography (CT) images or 3-D presentations result in better understanding of liver anatomy. Following a PowerPoint lecture, students were randomly selected to participate in computer-based testing which used either 2-D images presented as consecutive transversal slices, or one of two 3-D variations. In one of these the vessel tree of portal and hepatic veins was shown in one colour (3-D) and in the other the two vessel systems were coloured differently (3-Dc). Participants were asked to answer 11 medical questions concerning surgical anatomy and four questions on their subjective assessment of the TM. Of the 160 Year 4 and 5 medical students (56.8% female) who participated in this prospective randomised trial, students exposed to 3-D presentation performed significantly better than those exposed to 2-D images (p < 0.001). Comparison of the number of correct answers revealed no significant differences between the 3-D and 3-Dc modalities p > 0.1). Male students gave significantly more correct answers in the 3-D and 3-Dc modalities than female students (p < 0.03). The gender difference observed in both 3-D modalities was not evident in the 2-D group (p = 0.21). This study showed that 3-D imaging significantly improved the identification of complex surgical liver anatomy. Male students benefited significantly more than female students from 3-D presentations. Use of colour in 3-D presentation did not improve student performance.

Method of transition from 3D model to its ontological representation in aircraft design process

NASA Astrophysics Data System (ADS)

Govorkov, A. S.; Zhilyaev, A. S.; Fokin, I. V.

2018-05-01

This paper proposes the method of transition from a 3D model to its ontological representation and describes its usage in the aircraft design process. The problems of design for manufacturability and design automation are also discussed. The introduced method is to aim to ease the process of data exchange between important aircraft design phases, namely engineering and design control. The method is also intended to increase design speed and 3D model customizability. This requires careful selection of the complex systems (CAD / CAM / CAE / PDM), providing the basis for the integration of design and technological preparation of production and more fully take into account the characteristics of products and processes for their manufacture. It is important to solve this problem, as investment in the automation define the company's competitiveness in the years ahead.

The use of virtual reality to reimagine two-dimensional representations of three-dimensional spaces

NASA Astrophysics Data System (ADS)

Fath, Elaine

2015-03-01

A familiar realm in the world of two-dimensional art is the craft of taking a flat canvas and creating, through color, size, and perspective, the illusion of a three-dimensional space. Using well-explored tricks of logic and sight, impossible landscapes such as those by surrealists de Chirico or Salvador Dalí seem to be windows into new and incredible spaces which appear to be simultaneously feasible and utterly nonsensical. As real-time 3D imaging becomes increasingly prevalent as an artistic medium, this process takes on an additional layer of depth: no longer is two-dimensional space restricted to strategies of light, color, line and geometry to create the impression of a three-dimensional space. A digital interactive environment is a space laid out in three dimensions, allowing the user to explore impossible environments in a way that feels very real. In this project, surrealist two-dimensional art was researched and reimagined: what would stepping into a de Chirico or a Magritte look and feel like, if the depth and distance created by light and geometry were not simply single-perspective illusions, but fully formed and explorable spaces? 3D environment-building software is allowing us to step into these impossible spaces in ways that 2D representations leave us yearning for. This art project explores what we gain--and what gets left behind--when these impossible spaces become doors, rather than windows. Using sketching, Maya 3D rendering software, and the Unity Engine, surrealist art was reimagined as a fully navigable real-time digital environment. The surrealist movement and its key artists were researched for their use of color, geometry, texture, and space and how these elements contributed to their work as a whole, which often conveys feelings of unexpectedness or uneasiness. The end goal was to preserve these feelings while allowing the viewer to actively engage with the space.

Optimize scientific communication skills on work and energy concept with implementation of interactive conceptual instruction and multi representation approach

NASA Astrophysics Data System (ADS)

Patriot, E. A.; Suhandi, A.; Chandra, D. T.

2018-05-01

The ultimate goal of learning in the curriculum 2013 is that learning must improve and balance between soft skills and hard skills of learners. In addition to the knowledge aspect, one of the other skills to be trained in the learning process using a scientific approach is communication skills. This study aims to get an overview of the implementation of interactive conceptual instruction with multi representation to optimize the achievement of students’ scientific communication skills on work and energy concept. The scientific communication skills contains the sub-skills were searching the information, scientific writing, group discussion and knowledge presentation. This study was descriptive research with observation method. Subjects in this study were 35 students of class X in Senior High School at Sumedang. The results indicate an achievement of optimal scientific communication skills. The greatest achievement of KKI based on observation is at fourth meeting of KKI-3, which is a sub-skill of resume writing of 89%. Allmost students responded positively to the implication of interactive conceptual instruction with multi representation approach. It can be concluded that the implication of interactive conceptual instruction with multi representation approach can optimize the achievement of students’ scientific communication skill on work and energy concept.

A polygon soup representation for free viewpoint video

NASA Astrophysics Data System (ADS)

Colleu, T.; Pateux, S.; Morin, L.; Labit, C.

2010-02-01

This paper presents a polygon soup representation for multiview data. Starting from a sequence of multi-view video plus depth (MVD) data, the proposed representation takes into account, in a unified manner, different issues such as compactness, compression, and intermediate view synthesis. The representation is built in two steps. First, a set of 3D quads is extracted using a quadtree decomposition of the depth maps. Second, a selective elimination of the quads is performed in order to reduce inter-view redundancies and thus provide a compact representation. Moreover, the proposed methodology for extracting the representation allows to reduce ghosting artifacts. Finally, an adapted compression technique is proposed that limits coding artifacts. The results presented on two real sequences show that the proposed representation provides a good trade-off between rendering quality and data compactness.

Lagrangian transport near perturbed periodic lines in three-dimensional unsteady flows

NASA Astrophysics Data System (ADS)

Speetjens, Michel

2015-11-01

Periodic lines formed by continuous strings of periodic points are key organizing entities in the Lagrangian flow topology of certain three-dimensional (3D) time-periodic flows. Such lines generically consist of elliptic and/or hyperbolic points and thus give rise to 3D flow topologies made up of families of concentric closed trajectories embedded in chaotic regions. Weak perturbation destroys the periodic lines and causes said trajectories to coalesce into families of concentric tubes. However, emergence of isolated periodic points near the disintegrating periodic lines and/or partitioning of the original lines into elliptic and hyperbolic segments interrupt the tube formation. This yields incomplete tubes that interact with the (chaotic) environment through their open ends, resulting in intricate and essentially 3D flow topologies These phenomena have been observed in various realistic flows yet the underlying mechanisms are to date only partially understood. This study deepens insight into the (perturbed) Lagrangian dynamics of these flows by way of a linearized representation of the equations of motion near the periodic lines. Predictions on the basis of this investigation are in full (qualitative) agreement with observed behavior in the actual flows

Sensitivity Analysis and Parameter Estimation for a Reactive Transport Model of Uranium Bioremediation

NASA Astrophysics Data System (ADS)

Meyer, P. D.; Yabusaki, S.; Curtis, G. P.; Ye, M.; Fang, Y.

2011-12-01

A three-dimensional, variably-saturated flow and multicomponent biogeochemical reactive transport model of uranium bioremediation was used to generate synthetic data . The 3-D model was based on a field experiment at the U.S. Dept. of Energy Rifle Integrated Field Research Challenge site that used acetate biostimulation of indigenous metal reducing bacteria to catalyze the conversion of aqueous uranium in the +6 oxidation state to immobile solid-associated uranium in the +4 oxidation state. A key assumption in past modeling studies at this site was that a comprehensive reaction network could be developed largely through one-dimensional modeling. Sensitivity analyses and parameter estimation were completed for a 1-D reactive transport model abstracted from the 3-D model to test this assumption, to identify parameters with the greatest potential to contribute to model predictive uncertainty, and to evaluate model structure and data limitations. Results showed that sensitivities of key biogeochemical concentrations varied in space and time, that model nonlinearities and/or parameter interactions have a significant impact on calculated sensitivities, and that the complexity of the model's representation of processes affecting Fe(II) in the system may make it difficult to correctly attribute observed Fe(II) behavior to modeled processes. Non-uniformity of the 3-D simulated groundwater flux and averaging of the 3-D synthetic data for use as calibration targets in the 1-D modeling resulted in systematic errors in the 1-D model parameter estimates and outputs. This occurred despite using the same reaction network for 1-D modeling as used in the data-generating 3-D model. Predictive uncertainty of the 1-D model appeared to be significantly underestimated by linear parameter uncertainty estimates.

Virtual Representations in 3D Learning Environments

ERIC Educational Resources Information Center

Shonfeld, Miri; Kritz, Miki

2013-01-01

This research explores the extent to which virtual worlds can serve as online collaborative learning environments for students by increasing social presence and engagement. 3D environments enable learning, which simulates face-to-face encounters while retaining the advantages of online learning. Students in Education departments created avatars…

Computer Series, 37: Bits and Pieces, 14.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1983-01-01

Thirteen computer/calculator programs (available from authors) are described. These include: representation of molecules as 3-D models; animated 3-D graphical display of line drawings of molecules; principles of Fourier-transform nuclear magnetic resonance; tutorial program for pH calculation; balancing chemical reactions using a hand-held…

Cognitive/emotional models for human behavior representation in 3D avatar simulations

NASA Astrophysics Data System (ADS)

Peterson, James K.

2004-08-01

Simplified models of human cognition and emotional response are presented which are based on models of auditory/ visual polymodal fusion. At the core of these models is a computational model of Area 37 of the temporal cortex which is based on new isocortex models presented recently by Grossberg. These models are trained using carefully chosen auditory (musical sequences), visual (paintings) and higher level abstract (meta level) data obtained from studies of how optimization strategies are chosen in response to outside managerial inputs. The software modules developed are then used as inputs to character generation codes in standard 3D virtual world simulations. The auditory and visual training data also enable the development of simple music and painting composition generators which significantly enhance one's ability to validate the cognitive model. The cognitive models are handled as interacting software agents implemented as CORBA objects to allow the use of multiple language coding choices (C++, Java, Python etc) and efficient use of legacy code.

Observations and laboratory simulations of tornadoes in complex topographical regions

NASA Astrophysics Data System (ADS)

Karstens, Christopher Daniel

Aerial photos taken along the damage paths of the Joplin, MO, and Tuscaloosa-Birmingham, AL, tornadoes of 2011 captured and preserved several unique patterns of damage. In particular, a few distinct tree-fall patterns were noted along the Tuscaloosa-Birmingham tornado track that appeared highly influenced by the underlying topography. One such region was the focus of a damage survey and motivated laboratory vortex simulations with a 3-D foam representation of the underlying topography, in addition to simulations performed with idealized 2D topographic features, using Iowa State University's tornado simulator. The purpose of this dissertation is to explore various aspects related to the interaction of a tornado or a tornado-like vortex with its underlying topography. Three topics are examined: 1) Analysis of tornado-induced tree-fall using aerial photography from the Joplin, MO, and Tuscaloosa-Birmingham, AL, tornadoes of 2011, 2) Laboratory investigation of topographical influences on a simulated tornado-like vortex, and 3) On the use of non-standard EF-scale damage indicators to categorize tornadoes.

Data representation for joint kinematics simulation of the lower limb within an educational context.

PubMed

Van Sint Jan, Serge; Hilal, Isam; Salvia, Patrick; Sholukha, Victor; Poulet, Pascal; Kirokoya, Ibrahim; Rooze, Marcel

2003-04-01

Three-dimensional (3D) visualization is becoming increasingly frequent in both qualitative and quantitative biomechanical studies of anatomical structures involving multiple data sources (e.g. morphological data and kinematics data). For many years, this kind of experiment was limited to the use of bi-dimensional images due to a lack of accurate 3D data. However, recent progress in medical imaging and computer graphics has forged new perspectives. Indeed, new techniques allow the development of an interactive interface for the simulation of human motions combining data from both medical imaging (i.e., morphology) and biomechanical studies (i.e., kinematics). Fields of application include medical education, biomechanical research and clinical research. This paper presents an experimental protocol for the development of anatomically realistic joint simulation within a pedagogical context. Results are shown for the lower limb. Extension to other joints is straightforward. This work is part of the Virtual Animation of the Kinematics of the Human project (VAKHUM) (http://www.ulb.ac.be/project/vakhum).

Possible extinction of Berezinskii-Kosterlitz-Thouless transition by diagonal interactions in the checkerboard lattice

NASA Astrophysics Data System (ADS)

Lopes, R. J. C.; Moura, A. R.

2018-06-01

We study the thermodynamics of the classical anisotropic antiferromagnetic Heisenberg model in a checkerboard lattice. The checkerboard lattice is distinguished from the antiferromagnetic square lattice (with coupling constant J) by the presence of a diagonal crossing (coupling constant J‧) in half of the sites. This lattice model is the direct analog of the three-dimensional pyrochlore lattice on a two-dimensional surface. Besides, we considered a single-ion anisotropy D that breaks the O (3) symmetry and contributes to planar spin fields. Since the model is two-dimensional endowed with an O (2) symmetry, a Berezinskii-Kosterlitz-Thouless (BKT) transition is expected to take place. We also investigated the BKT temperature as a function of the coupling constants J‧ and D. The problem is developed through a continuous representation given by the O (3) Nonlinear Sigma Model (NLSM). Computer simulations were also carried out, and the results were in accordance with the analytical model.

Improved performance in CAPRI round 37 using LZerD docking and template-based modeling with combined scoring functions.

PubMed

Peterson, Lenna X; Shin, Woong-Hee; Kim, Hyungrae; Kihara, Daisuke

2018-03-01

We report our group's performance for protein-protein complex structure prediction and scoring in Round 37 of the Critical Assessment of PRediction of Interactions (CAPRI), an objective assessment of protein-protein complex modeling. We demonstrated noticeable improvement in both prediction and scoring compared to previous rounds of CAPRI, with our human predictor group near the top of the rankings and our server scorer group at the top. This is the first time in CAPRI that a server has been the top scorer group. To predict protein-protein complex structures, we used both multi-chain template-based modeling (TBM) and our protein-protein docking program, LZerD. LZerD represents protein surfaces using 3D Zernike descriptors (3DZD), which are based on a mathematical series expansion of a 3D function. Because 3DZD are a soft representation of the protein surface, LZerD is tolerant to small conformational changes, making it well suited to docking unbound and TBM structures. The key to our improved performance in CAPRI Round 37 was to combine multi-chain TBM and docking. As opposed to our previous strategy of performing docking for all target complexes, we used TBM when multi-chain templates were available and docking otherwise. We also describe the combination of multiple scoring functions used by our server scorer group, which achieved the top rank for the scorer phase. © 2017 Wiley Periodicals, Inc.

Improved protein surface comparison and application to low-resolution protein structure data

PubMed Central

2010-01-01

Background Recent advancements of experimental techniques for determining protein tertiary structures raise significant challenges for protein bioinformatics. With the number of known structures of unknown function expanding at a rapid pace, an urgent task is to provide reliable clues to their biological function on a large scale. Conventional approaches for structure comparison are not suitable for a real-time database search due to their slow speed. Moreover, a new challenge has arisen from recent techniques such as electron microscopy (EM), which provide low-resolution structure data. Previously, we have introduced a method for protein surface shape representation using the 3D Zernike descriptors (3DZDs). The 3DZD enables fast structure database searches, taking advantage of its rotation invariance and compact representation. The search results of protein surface represented with the 3DZD has showngood agreement with the existing structure classifications, but some discrepancies were also observed. Results The three new surface representations of backbone atoms, originally devised all-atom-surface representation, and the combination of all-atom surface with the backbone representation are examined. All representations are encoded with the 3DZD. Also, we have investigated the applicability of the 3DZD for searching protein EM density maps of varying resolutions. The surface representations are evaluated on structure retrieval using two existing classifications, SCOP and the CE-based classification. Conclusions Overall, the 3DZDs representing backbone atoms show better retrieval performance than the original all-atom surface representation. The performance further improved when the two representations are combined. Moreover, we observed that the 3DZD is also powerful in comparing low-resolution structures obtained by electron microscopy. PMID:21172052

Map-Reading Skill Development with 3D Technologies

ERIC Educational Resources Information Center

Carbonell Carrera, Carlos; Avarvarei, Bogdan Vlad; Chelariu, Elena Liliana; Draghia, Lucia; Avarvarei, Simona Catrinel

2017-01-01

Landforms often are represented on maps using abstract cartographic techniques that the reader must interpret for successful three-dimensional terrain visualization. New technologies in 3D landscape representation, both digital and tangible, offer the opportunity to visualize terrain in new ways. The results of a university student workshop, in…

Evaluation of Holographic Technology in Close Air Support Mission Planning and Execution

DTIC Science & Technology

2008-03-18

Figures Figure 1: 2D representation of 3D hologram of Baghdad area using 1-meter resolution LIDAR data...Alias Maya Software................................................................................................. 11 Figure 3: Suburban...and light detection and ranging ( LIDAR ) sensors for several geographic areas was performed in parallel with formulation of the approach

Demonstration of a 3D vision algorithm for space applications

NASA Technical Reports Server (NTRS)

Defigueiredo, Rui J. P. (Editor)

1987-01-01

This paper reports an extension of the MIAG algorithm for recognition and motion parameter determination of general 3-D polyhedral objects based on model matching techniques and using movement invariants as features of object representation. Results of tests conducted on the algorithm under conditions simulating space conditions are presented.

iview: an interactive WebGL visualizer for protein-ligand complex.

PubMed

Li, Hongjian; Leung, Kwong-Sak; Nakane, Takanori; Wong, Man-Hon

2014-02-25

Visualization of protein-ligand complex plays an important role in elaborating protein-ligand interactions and aiding novel drug design. Most existing web visualizers either rely on slow software rendering, or lack virtual reality support. The vital feature of macromolecular surface construction is also unavailable. We have developed iview, an easy-to-use interactive WebGL visualizer of protein-ligand complex. It exploits hardware acceleration rather than software rendering. It features three special effects in virtual reality settings, namely anaglyph, parallax barrier and oculus rift, resulting in visually appealing identification of intermolecular interactions. It supports four surface representations including Van der Waals surface, solvent excluded surface, solvent accessible surface and molecular surface. Moreover, based on the feature-rich version of iview, we have also developed a neat and tailor-made version specifically for our istar web platform for protein-ligand docking purpose. This demonstrates the excellent portability of iview. Using innovative 3D techniques, we provide a user friendly visualizer that is not intended to compete with professional visualizers, but to enable easy accessibility and platform independence.

3D shape recovery from image focus using Gabor features

NASA Astrophysics Data System (ADS)

Mahmood, Fahad; Mahmood, Jawad; Zeb, Ayesha; Iqbal, Javaid

2018-04-01

Recovering an accurate and precise depth map from a set of acquired 2-D image dataset of the target object each having different focus information is an ultimate goal of 3-D shape recovery. Focus measure algorithm plays an important role in this architecture as it converts the corresponding color value information into focus information which will be then utilized for recovering depth map. This article introduces Gabor features as focus measure approach for recovering depth map from a set of 2-D images. Frequency and orientation representation of Gabor filter features is similar to human visual system and normally applied for texture representation. Due to its little computational complexity, sharp focus measure curve, robust to random noise sources and accuracy, it is considered as superior alternative to most of recently proposed 3-D shape recovery approaches. This algorithm is deeply investigated on real image sequences and synthetic image dataset. The efficiency of the proposed scheme is also compared with the state of art 3-D shape recovery approaches. Finally, by means of two global statistical measures, root mean square error and correlation, we claim that this approach, in spite of simplicity, generates accurate results.

Predicting phase behavior of mixtures of reservoir fluids with carbon dioxide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grigg, R.B.; Lingane, P.J.

1983-01-01

The use of an equation of state to predict phase behavior during carbon dioxide flooding is well established. The characterization of the C/sub 7/ fraction and the selection of interaction parameters are the most important variables. Single-contact phase behavior is presented for mixtures of Ford Geraldine (Delaware), Maljamar (Grayburg), West Sussex (Shannon), and Reservoir D reservoir fluids, and of a synthetic oil with carbon dioxide. The phase behavior of these mixtures can be reproduced using 3 to 5 pseudo components and common interaction parameters. The critical properties of the pseudo components are calculated from detailed oil characterizations. Because the parametersmore » are not further adjusted, this approach reduces the empiricism in fitting phase data and may result in a more accurate representation of the system as the composition of the oil changes during the approach to miscibility. 21 references.« less

5D Modelling: An Efficient Approach for Creating Spatiotemporal Predictive 3D Maps of Large-Scale Cultural Resources

NASA Astrophysics Data System (ADS)

Doulamis, A.; Doulamis, N.; Ioannidis, C.; Chrysouli, C.; Grammalidis, N.; Dimitropoulos, K.; Potsiou, C.; Stathopoulou, E.-K.; Ioannides, M.

2015-08-01

Outdoor large-scale cultural sites are mostly sensitive to environmental, natural and human made factors, implying an imminent need for a spatio-temporal assessment to identify regions of potential cultural interest (material degradation, structuring, conservation). On the other hand, in Cultural Heritage research quite different actors are involved (archaeologists, curators, conservators, simple users) each of diverse needs. All these statements advocate that a 5D modelling (3D geometry plus time plus levels of details) is ideally required for preservation and assessment of outdoor large scale cultural sites, which is currently implemented as a simple aggregation of 3D digital models at different time and levels of details. The main bottleneck of such an approach is its complexity, making 5D modelling impossible to be validated in real life conditions. In this paper, a cost effective and affordable framework for 5D modelling is proposed based on a spatial-temporal dependent aggregation of 3D digital models, by incorporating a predictive assessment procedure to indicate which regions (surfaces) of an object should be reconstructed at higher levels of details at next time instances and which at lower ones. In this way, dynamic change history maps are created, indicating spatial probabilities of regions needed further 3D modelling at forthcoming instances. Using these maps, predictive assessment can be made, that is, to localize surfaces within the objects where a high accuracy reconstruction process needs to be activated at the forthcoming time instances. The proposed 5D Digital Cultural Heritage Model (5D-DCHM) is implemented using open interoperable standards based on the CityGML framework, which also allows the description of additional semantic metadata information. Visualization aspects are also supported to allow easy manipulation, interaction and representation of the 5D-DCHM geometry and the respective semantic information. The open source 3DCityDB incorporating a PostgreSQL geo-database is used to manage and manipulate 3D data and their semantics.

Grid-based lattice summation of electrostatic potentials by assembled rank-structured tensor approximation

NASA Astrophysics Data System (ADS)

Khoromskaia, Venera; Khoromskij, Boris N.

2014-12-01

Our recent method for low-rank tensor representation of sums of the arbitrarily positioned electrostatic potentials discretized on a 3D Cartesian grid reduces the 3D tensor summation to operations involving only 1D vectors however retaining the linear complexity scaling in the number of potentials. Here, we introduce and study a novel tensor approach for fast and accurate assembled summation of a large number of lattice-allocated potentials represented on 3D N × N × N grid with the computational requirements only weakly dependent on the number of summed potentials. It is based on the assembled low-rank canonical tensor representations of the collected potentials using pointwise sums of shifted canonical vectors representing the single generating function, say the Newton kernel. For a sum of electrostatic potentials over L × L × L lattice embedded in a box the required storage scales linearly in the 1D grid-size, O(N) , while the numerical cost is estimated by O(NL) . For periodic boundary conditions, the storage demand remains proportional to the 1D grid-size of a unit cell, n = N / L, while the numerical cost reduces to O(N) , that outperforms the FFT-based Ewald-type summation algorithms of complexity O(N3 log N) . The complexity in the grid parameter N can be reduced even to the logarithmic scale O(log N) by using data-sparse representation of canonical N-vectors via the quantics tensor approximation. For justification, we prove an upper bound on the quantics ranks for the canonical vectors in the overall lattice sum. The presented approach is beneficial in applications which require further functional calculus with the lattice potential, say, scalar product with a function, integration or differentiation, which can be performed easily in tensor arithmetics on large 3D grids with 1D cost. Numerical tests illustrate the performance of the tensor summation method and confirm the estimated bounds on the tensor ranks.

Microstructure representations for sound absorbing fibrous media: 3D and 2D multiscale modelling and experiments

NASA Astrophysics Data System (ADS)

Zieliński, Tomasz G.

2017-11-01

The paper proposes and investigates computationally-efficient microstructure representations for sound absorbing fibrous media. Three-dimensional volume elements involving non-trivial periodic arrangements of straight fibres are examined as well as simple two-dimensional cells. It has been found that a simple 2D quasi-representative cell can provide similar predictions as a volume element which is in general much more geometrically accurate for typical fibrous materials. The multiscale modelling allowed to determine the effective speeds and damping of acoustic waves propagating in such media, which brings up a discussion on the correlation between the speed, penetration range and attenuation of sound waves. Original experiments on manufactured copper-wire samples are presented and the microstructure-based calculations of acoustic absorption are compared with the corresponding experimental results. In fact, the comparison suggested the microstructure modifications leading to representations with non-uniformly distributed fibres.

On Complex Networks Representation and Computation of Hydrologycal Quantities

NASA Astrophysics Data System (ADS)

Serafin, F.; Bancheri, M.; David, O.; Rigon, R.

2017-12-01

Water is our blue gold. Despite results of discovery-based science keep warning public opinion about the looming worldwide water crisis, water is still treated as a not worth taking resource. Could a different multi-scale perspective affect environmental decision-making more deeply? Can also a further pairing to a new graphical representation of processes interaction sway decision-making more effectively and public opinion consequently?This abstract introduces a complex networks driven way to represent catchments eco-hydrology and related flexible informatics to manage it. The representation is built upon mathematical category. A category is an algebraic structure that comprises "objects" linked by "arrows". It is an evolution of Petri Nets said Time Continuous Petri Nets (TCPN). It aims to display (water) budgets processes and catchment interactions using explicative and self-contained symbolism. The result improves readability of physical processes compared to current descriptions. The IT perspective hinges on the Object Modeling System (OMS) v3. The latter is a non-invasive flexible environmental modeling framework designed to support component-based model development. The implementation of a Directed Acyclic Graph (DAG) data structure, named Net3, has recently enhanced its flexibility. Net3 represents interacting systems as complex networks: vertices match up with any sort of time evolving quantity; edges correspond to their data (fluxes) interchange. It currently hosts JGrass-NewAge components, and those implementing travel time analysis of fluxes. Further bio-physical or management oriented components can be easily added.This talk introduces both graphical representation and related informatics exercising actual applications and examples.

A novel structured dictionary for fast processing of 3D medical images, with application to computed tomography restoration and denoising

NASA Astrophysics Data System (ADS)

Karimi, Davood; Ward, Rabab K.

2016-03-01

Sparse representation of signals in learned overcomplete dictionaries has proven to be a powerful tool with applications in denoising, restoration, compression, reconstruction, and more. Recent research has shown that learned overcomplete dictionaries can lead to better results than analytical dictionaries such as wavelets in almost all image processing applications. However, a major disadvantage of these dictionaries is that their learning and usage is very computationally intensive. In particular, finding the sparse representation of a signal in these dictionaries requires solving an optimization problem that leads to very long computational times, especially in 3D image processing. Moreover, the sparse representation found by greedy algorithms is usually sub-optimal. In this paper, we propose a novel two-level dictionary structure that improves the performance and the speed of standard greedy sparse coding methods. The first (i.e., the top) level in our dictionary is a fixed orthonormal basis, whereas the second level includes the atoms that are learned from the training data. We explain how such a dictionary can be learned from the training data and how the sparse representation of a new signal in this dictionary can be computed. As an application, we use the proposed dictionary structure for removing the noise and artifacts in 3D computed tomography (CT) images. Our experiments with real CT images show that the proposed method achieves results that are comparable with standard dictionary-based methods while substantially reducing the computational time.

A Parallel Product-Convolution approach for representing the depth varying Point Spread Functions in 3D widefield microscopy based on principal component analysis.

PubMed

Arigovindan, Muthuvel; Shaevitz, Joshua; McGowan, John; Sedat, John W; Agard, David A

2010-03-29

We address the problem of computational representation of image formation in 3D widefield fluorescence microscopy with depth varying spherical aberrations. We first represent 3D depth-dependent point spread functions (PSFs) as a weighted sum of basis functions that are obtained by principal component analysis (PCA) of experimental data. This representation is then used to derive an approximating structure that compactly expresses the depth variant response as a sum of few depth invariant convolutions pre-multiplied by a set of 1D depth functions, where the convolving functions are the PCA-derived basis functions. The model offers an efficient and convenient trade-off between complexity and accuracy. For a given number of approximating PSFs, the proposed method results in a much better accuracy than the strata based approximation scheme that is currently used in the literature. In addition to yielding better accuracy, the proposed methods automatically eliminate the noise in the measured PSFs.

A study of modelling simplifications in ground vibration predictions for railway traffic at grade

NASA Astrophysics Data System (ADS)

Germonpré, M.; Degrande, G.; Lombaert, G.

2017-10-01

Accurate computational models are required to predict ground-borne vibration due to railway traffic. Such models generally require a substantial computational effort. Therefore, much research has focused on developing computationally efficient methods, by either exploiting the regularity of the problem geometry in the direction along the track or assuming a simplified track structure. This paper investigates the modelling errors caused by commonly made simplifications of the track geometry. A case study is presented investigating a ballasted track in an excavation. The soil underneath the ballast is stiffened by a lime treatment. First, periodic track models with different cross sections are analyzed, revealing that a prediction of the rail receptance only requires an accurate representation of the soil layering directly underneath the ballast. A much more detailed representation of the cross sectional geometry is required, however, to calculate vibration transfer from track to free field. Second, simplifications in the longitudinal track direction are investigated by comparing 2.5D and periodic track models. This comparison shows that the 2.5D model slightly overestimates the track stiffness, while the transfer functions between track and free field are well predicted. Using a 2.5D model to predict the response during a train passage leads to an overestimation of both train-track interaction forces and free field vibrations. A combined periodic/2.5D approach is therefore proposed in this paper. First, the dynamic axle loads are computed by solving the train-track interaction problem with a periodic model. Next, the vibration transfer to the free field is computed with a 2.5D model. This combined periodic/2.5D approach only introduces small modelling errors compared to an approach in which a periodic model is used in both steps, while significantly reducing the computational cost.

Accelerated computer generated holography using sparse bases in the STFT domain.

PubMed

Blinder, David; Schelkens, Peter

2018-01-22

Computer-generated holography at high resolutions is a computationally intensive task. Efficient algorithms are needed to generate holograms at acceptable speeds, especially for real-time and interactive applications such as holographic displays. We propose a novel technique to generate holograms using a sparse basis representation in the short-time Fourier space combined with a wavefront-recording plane placed in the middle of the 3D object. By computing the point spread functions in the transform domain, we update only a small subset of the precomputed largest-magnitude coefficients to significantly accelerate the algorithm over conventional look-up table methods. We implement the algorithm on a GPU, and report a speedup factor of over 30. We show that this transform is superior over wavelet-based approaches, and show quantitative and qualitative improvements over the state-of-the-art WASABI method; we report accuracy gains of 2dB PSNR, as well improved view preservation.

"Interactive Classification Technology"

NASA Technical Reports Server (NTRS)

deBessonet, Cary

1999-01-01

The investigators are upgrading a knowledge representation language called SL (Symbolic Language) and an automated reasoning system called SMS (Symbolic Manipulation System) to enable the technologies to be used in automated reasoning and interactive classification systems. The overall goals of the project are: a) the enhancement of the representation language SL to accommodate multiple perspectives and a wider range of meaning; b) the development of a sufficient set of operators to enable the interpreter of SL to handle representations of basic cognitive acts; and c) the development of a default inference scheme to operate over SL notation as it is encoded. As to particular goals the first-year work plan focused on inferencing and.representation issues, including: 1) the development of higher level cognitive/ classification functions and conceptual models for use in inferencing and decision making; 2) the specification of a more detailed scheme of defaults and the enrichment of SL notation to accommodate the scheme; and 3) the adoption of additional perspectives for inferencing.

The chemistry side of AOP: implications for toxicity ...

EPA Pesticide Factsheets

An adverse outcome pathway (AOP) is a structured representation of the biological events that lead to adverse impacts following a molecular initiating event caused by chemical interaction with a macromolecule. AOPs have been proposed to facilitate toxicity extrapolation across species through understanding of species similarity in the sequence of molecular, cellular, organ and organismal level responses. However, AOPs are non-specific regarding the identity of the chemical initiators, and the range of structures for which an AOP is considered applicable has generally been poorly defined. Applicability domain has been widely understood in the field of QSAR as the response and chemical structure space in which the model makes predictions with a given reliability, and has been traditionally applied to define the similarity of query molecules within the training set. Three dimensional (3D) receptor modeling offers an approach to better define the applicability domain for selected AOPs through determination of the chemical space of the molecular initiating event. Universal 3D-QSAR models were developed for acetylcholinesterase inhibitors and estrogen receptor agonists and antagonists using a combination of fingerprint, molecular docking and structure-based pharmacophore approaches. The models were based on the critical molecular interactions within each receptor ligand binding domain, and included the key amino acid residues responsible for high binding affinity. T

Tensor Target Spin Asymmetries in Coherent π 0-Photoproduction on the Deuteron Including Intermediate η N N Interaction Within a Three-Body Approach

NASA Astrophysics Data System (ADS)

Darwish, Eed M.; Abou-Elsebaa, Hoda M.; Hassaneen, Khaled S. A.

2018-04-01

Motivated by the recent measurements from the VEPP-3 electron storage ring, we investigate the tensor target polarization asymmetries T 2 M ( M = 0, 1, 2) in the reaction γ d → π 0 d with a particular interest in the effect of the intermediate η N N three-body approach. This approach is based on realistic separable representations of the driving two-body interaction in the π N, η N, and NN subsystems. It is shown that the influence of rescattering effects in the intermediate state on the tensor target spin asymmetries is sizable at extreme backward pion angles. At forward angles, the contribution from the pure impulse approximation is dominated and the spin asymmetries show very little influence of rescattering effects. The sensitivity of results to the elementary pion photoproduction operator and to the NN potential model adopted for the deuteron wave function is investigated, and considerable dependences are found. The predicted spin asymmetries are also compared with available experimental data, and a satisfactory agreement with the recent data from VEPP-3 is obtained at photon energies below 400 MeV. At higher energies, the calculated spin asymmetries slightly underestimate the data.

N=2 Minimal Conformal Field Theories and Matrix Bifactorisations of x d

NASA Astrophysics Data System (ADS)

Davydov, Alexei; Camacho, Ana Ros; Runkel, Ingo

2018-01-01

We establish an action of the representations of N = 2-superconformal symmetry on the category of matrix factorisations of the potentials x d and x d - y d , for d odd. More precisely we prove a tensor equivalence between (a) the category of Neveu-Schwarz-type representations of the N = 2 minimal super vertex operator algebra at central charge 3-6/d, and (b) a full subcategory of graded matrix factorisations of the potential x d - y d . The subcategory in (b) is given by permutation-type matrix factorisations with consecutive index sets. The physical motivation for this result is the Landau-Ginzburg/conformal field theory correspondence, where it amounts to the equivalence of a subset of defects on both sides of the correspondence. Our work builds on results by Brunner and Roggenkamp [BR], where an isomorphism of fusion rules was established.

Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol.

PubMed

Lounnas, Valère; Wedler, Henry B; Newman, Timothy; Schaftenaar, Gijs; Harrison, Jason G; Nepomuceno, Gabriella; Pemberton, Ryan; Tantillo, Dean J; Vriend, Gert

2014-11-01

In molecular sciences, articles tend to revolve around 2D representations of 3D molecules, and sighted scientists often resort to 3D virtual reality software to study these molecules in detail. Blind and visually impaired (BVI) molecular scientists have access to a series of audio devices that can help them read the text in articles and work with computers. Reading articles published in this journal, though, is nearly impossible for them because they need to generate mental 3D images of molecules, but the article-reading software cannot do that for them. We have previously designed AsteriX, a web server that fully automatically decomposes articles, detects 2D plots of low molecular weight molecules, removes meta data and annotations from these plots, and converts them into 3D atomic coordinates. AsteriX-BVI goes one step further and converts the 3D representation into a 3D printable, haptic-enhanced format that includes Braille annotations. These Braille-annotated physical 3D models allow BVI scientists to generate a complete mental model of the molecule. AsteriX-BVI uses Molden to convert the meta data of quantum chemistry experiments into BVI friendly formats so that the entire line of scientific information that sighted people take for granted-from published articles, via printed results of computational chemistry experiments, to 3D models-is now available to BVI scientists too. The possibilities offered by AsteriX-BVI are illustrated by a project on the isomerization of a sterol, executed by the blind co-author of this article (HBW).

Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol

NASA Astrophysics Data System (ADS)

Lounnas, Valère; Wedler, Henry B.; Newman, Timothy; Schaftenaar, Gijs; Harrison, Jason G.; Nepomuceno, Gabriella; Pemberton, Ryan; Tantillo, Dean J.; Vriend, Gert

2014-11-01

In molecular sciences, articles tend to revolve around 2D representations of 3D molecules, and sighted scientists often resort to 3D virtual reality software to study these molecules in detail. Blind and visually impaired (BVI) molecular scientists have access to a series of audio devices that can help them read the text in articles and work with computers. Reading articles published in this journal, though, is nearly impossible for them because they need to generate mental 3D images of molecules, but the article-reading software cannot do that for them. We have previously designed AsteriX, a web server that fully automatically decomposes articles, detects 2D plots of low molecular weight molecules, removes meta data and annotations from these plots, and converts them into 3D atomic coordinates. AsteriX-BVI goes one step further and converts the 3D representation into a 3D printable, haptic-enhanced format that includes Braille annotations. These Braille-annotated physical 3D models allow BVI scientists to generate a complete mental model of the molecule. AsteriX-BVI uses Molden to convert the meta data of quantum chemistry experiments into BVI friendly formats so that the entire line of scientific information that sighted people take for granted—from published articles, via printed results of computational chemistry experiments, to 3D models—is now available to BVI scientists too. The possibilities offered by AsteriX-BVI are illustrated by a project on the isomerization of a sterol, executed by the blind co-author of this article (HBW).

Going Virtual… or Not: Development and Testing of a 3D Virtual Astronomy Environment

NASA Astrophysics Data System (ADS)

Ruzhitskaya, L.; Speck, A.; Ding, N.; Baldridge, S.; Witzig, S.; Laffey, J.

2013-04-01

We present our preliminary results of a pilot study of students' knowledge transfer of an astronomy concept into a new environment. We also share our discoveries on what aspects of a 3D environment students consider being motivational and discouraging for their learning. This study was conducted among 64 non-science major students enrolled in an astronomy laboratory course. During the course, students learned the concept and applications of Kepler's laws using a 2D interactive environment. Later in the semester, the students were placed in a 3D environment in which they were asked to conduct observations and to answers a set of questions pertaining to the Kepler's laws of planetary motion. In this study, we were interested in observing scrutinizing and assessing students' behavior: from choices that they made while creating their avatars (virtual representations) to tools they choose to use, to their navigational patterns, to their levels of discourse in the environment. These helped us to identify what features of the 3D environment our participants found to be helpful and interesting and what tools created unnecessary clutter and distraction. The students' social behavior patterns in the virtual environment together with their answers to the questions helped us to determine how well they understood Kepler's laws, how well they could transfer the concepts to a new situation, and at what point a motivational tool such as a 3D environment becomes a disruption to the constructive learning. Our founding confirmed that students construct deeper knowledge of a concept when they are fully immersed in the environment.

Human and Server Docking Prediction for CAPRI Round 30–35 Using LZerD with Combined Scoring Functions

PubMed Central

Peterson, Lenna X.; Kim, Hyungrae; Esquivel-Rodriguez, Juan; Roy, Amitava; Han, Xusi; Shin, Woong-Hee; Zhang, Jian; Terashi, Genki; Lee, Matt; Kihara, Daisuke

2016-01-01

We report the performance of protein-protein docking predictions by our group for recent rounds of the Critical Assessment of Prediction of Interactions (CAPRI), a community-wide assessment of state-of-the-art docking methods. Our prediction procedure uses a protein-protein docking program named LZerD developed in our group. LZerD represents a protein surface with 3D Zernike descriptors (3DZD), which are based on a mathematical series expansion of a 3D function. The appropriate soft representation of protein surface with 3DZD makes the method more tolerant to conformational change of proteins upon docking, which adds an advantage for unbound docking. Docking was guided by interface residue prediction performed with BindML and cons-PPISP as well as literature information when available. The generated docking models were ranked by a combination of scoring functions, including PRESCO, which evaluates the native-likeness of residues’ spatial environments in structure models. First, we discuss the overall performance of our group in the CAPRI prediction rounds and investigate the reasons for unsuccessful cases. Then, we examine the performance of several knowledge-based scoring functions and their combinations for ranking docking models. It was found that the quality of a pool of docking models generated by LZerD, i.e. whether or not the pool includes near-native models, can be predicted by the correlation of multiple scores. Although the current analysis used docking models generated by LZerD, findings on scoring functions are expected to be universally applicable to other docking methods. PMID:27654025

Anatomical Evidence for Classical and Extra-classical Receptive Field Completion Across the Discontinuous Horizontal Meridian Representation of Primate Area V2

PubMed Central

Jeffs, Janelle; Ichida, Jennifer M.; Federer, Frederick

2009-01-01

In primates, a split of the horizontal meridian (HM) representation at the V2 rostral border divides this area into dorsal (V2d) and ventral (V2v) halves (representing lower and upper visual quadrants, respectively), causing retinotopically neighboring loci across the HM to be distant within V2. How is perceptual continuity maintained across this discontinuous HM representation? Injections of neuroanatomical tracers in marmoset V2d demonstrated that cells near the V2d rostral border can maintain retinotopic continuity within their classical and extra-classical receptive field (RF), by making both local and long-range intra- and interareal connections with ventral cortex representing the upper visual quadrant. V2d neurons located <0.9–1.3 mm from the V2d rostral border, whose RFs presumably do not cross the HM, make nonretinotopic horizontal connections with V2v neurons in the supra- and infragranular layers. V2d neurons located <0.6–0.9 mm from the border, whose RFs presumably cross the HM, in addition make retinotopic local connections with V2v neurons in layer 4. V2d neurons also make interareal connections with upper visual field regions of extrastriate cortex, but not of MT or MTc outside the foveal representation. Labeled connections in ventral cortex appear to represent the “missing” portion of the connectional fields in V2d across the HM. We conclude that connections between dorsal and ventral cortex can create visual field continuity within a second-order discontinuous visual topography. PMID:18755777

Generation, recognition, and consistent fusion of partial boundary representations from range images

NASA Astrophysics Data System (ADS)

Kohlhepp, Peter; Hanczak, Andrzej M.; Li, Gang

1994-10-01

This paper presents SOMBRERO, a new system for recognizing and locating 3D, rigid, non- moving objects from range data. The objects may be polyhedral or curved, partially occluding, touching or lying flush with each other. For data collection, we employ 2D time- of-flight laser scanners mounted to a moving gantry robot. By combining sensor and robot coordinates, we obtain 3D cartesian coordinates. Boundary representations (Brep's) provide view independent geometry models that are both efficiently recognizable and derivable automatically from sensor data. SOMBRERO's methods for generating, matching and fusing Brep's are highly synergetic. A split-and-merge segmentation algorithm with dynamic triangular builds a partial (21/2D) Brep from scattered data. The recognition module matches this scene description with a model database and outputs recognized objects, their positions and orientations, and possibly surfaces corresponding to unknown objects. We present preliminary results in scene segmentation and recognition. Partial Brep's corresponding to different range sensors or viewpoints can be merged into a consistent, complete and irredundant 3D object or scene model. This fusion algorithm itself uses the recognition and segmentation methods.

The new generation of OpenGL support in ROOT

NASA Astrophysics Data System (ADS)

Tadel, M.

2008-07-01

OpenGL has been promoted to become the main 3D rendering engine of the ROOT framework. This required a major re-modularization of OpenGL support on all levels, from basic window-system specific interface to medium-level object-representation and top-level scene management. This new architecture allows seamless integration of external scene-graph libraries into the ROOT OpenGL viewer as well as inclusion of ROOT 3D scenes into external GUI and OpenGL-based 3D-rendering frameworks. Scene representation was removed from inside of the viewer, allowing scene-data to be shared among several viewers and providing for a natural implementation of multi-view canvas layouts. The object-graph traversal infrastructure allows free mixing of 3D and 2D-pad graphics and makes implementation of ROOT canvas in pure OpenGL possible. Scene-elements representing ROOT objects trigger automatic instantiation of user-provided rendering-objects based on the dictionary information and class-naming convention. Additionally, a finer, per-object control over scene-updates is available to the user, allowing overhead-free maintenance of dynamic 3D scenes and creation of complex real-time animations. User-input handling was modularized as well, making it easy to support application-specific scene navigation, selection handling and tool management.

Object Interpolation in Three Dimensions

ERIC Educational Resources Information Center

Kellman, Philip J.; Garrigan, Patrick; Shipley, Thomas F.

2005-01-01

Perception of objects in ordinary scenes requires interpolation processes connecting visible areas across spatial gaps. Most research has focused on 2-D displays, and models have been based on 2-D, orientation-sensitive units. The authors present a view of interpolation processes as intrinsically 3-D and producing representations of contours and…

3D Human Motion Editing and Synthesis: A Survey

PubMed Central

Wang, Xin; Chen, Qiudi; Wang, Wanliang

2014-01-01

The ways to compute the kinematics and dynamic quantities of human bodies in motion have been studied in many biomedical papers. This paper presents a comprehensive survey of 3D human motion editing and synthesis techniques. Firstly, four types of methods for 3D human motion synthesis are introduced and compared. Secondly, motion capture data representation, motion editing, and motion synthesis are reviewed successively. Finally, future research directions are suggested. PMID:25045395

The Interaction between Semantic Representation and Episodic Memory.

PubMed

Fang, Jing; Rüther, Naima; Bellebaum, Christian; Wiskott, Laurenz; Cheng, Sen

2018-02-01

The experimental evidence on the interrelation between episodic memory and semantic memory is inconclusive. Are they independent systems, different aspects of a single system, or separate but strongly interacting systems? Here, we propose a computational role for the interaction between the semantic and episodic systems that might help resolve this debate. We hypothesize that episodic memories are represented as sequences of activation patterns. These patterns are the output of a semantic representational network that compresses the high-dimensional sensory input. We show quantitatively that the accuracy of episodic memory crucially depends on the quality of the semantic representation. We compare two types of semantic representations: appropriate representations, which means that the representation is used to store input sequences that are of the same type as those that it was trained on, and inappropriate representations, which means that stored inputs differ from the training data. Retrieval accuracy is higher for appropriate representations because the encoded sequences are less divergent than those encoded with inappropriate representations. Consistent with our model prediction, we found that human subjects remember some aspects of episodes significantly more accurately if they had previously been familiarized with the objects occurring in the episode, as compared to episodes involving unfamiliar objects. We thus conclude that the interaction with the semantic system plays an important role for episodic memory.

Higher Rank ABJM Wilson Loops from Matrix Models

NASA Astrophysics Data System (ADS)

Cookmeyer, Jonathan; Liu, James; Zayas, Leopoldo

2017-01-01

We compute the expectation values of 1/6 supersymmetric Wilson Loops in ABJM theory in higher rank representations. Using standard matrix model techniques, we calculate the expectation value in the rank m fully symmetric and fully antisymmetric representation where m is scaled with N. To leading order, we find agreement with the classical action of D6 and D2 branes in AdS4 ×CP3 respectively. Further, we compute the first subleading order term, which, on the AdS side, makes a prediction for the one-loop effective action of the corresponding D6 and D2 branes. Supported by the National Science Foundation under Grant No. PHY 1559988 and the US Department of Energy under Grant No. DE-SC0007859.

Research on application of LADAR in ground vehicle recognition

NASA Astrophysics Data System (ADS)

Lan, Jinhui; Shen, Zhuoxun

2009-11-01

For the requirement of many practical applications in the field of military, the research of 3D target recognition is active. The representation that captures the salient attributes of a 3D target independent of the viewing angle will be especially useful to the automatic 3D target recognition system. This paper presents a new approach of image generation based on Laser Detection and Ranging (LADAR) data. Range image of target is obtained by transformation of point cloud. In order to extract features of different ground vehicle targets and to recognize targets, zernike moment properties of typical ground vehicle targets are researched in this paper. A technique of support vector machine is applied to the classification and recognition of target. The new method of image generation and feature representation has been applied to the outdoor experiments. Through outdoor experiments, it can be proven that the method of image generation is stability, the moments are effective to be used as features for recognition, and the LADAR can be applied to the field of 3D target recognition.

A model for process representation and synthesis. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Thomas, R. H.

1971-01-01

The problem of representing groups of loosely connected processes is investigated, and a model for process representation useful for synthesizing complex patterns of process behavior is developed. There are three parts, the first part isolates the concepts which form the basis for the process representation model by focusing on questions such as: What is a process; What is an event; Should one process be able to restrict the capabilities of another? The second part develops a model for process representation which captures the concepts and intuitions developed in the first part. The model presented is able to describe both the internal structure of individual processes and the interface structure between interacting processes. Much of the model's descriptive power derives from its use of the notion of process state as a vehicle for relating the internal and external aspects of process behavior. The third part demonstrates by example that the model for process representation is a useful one for synthesizing process behavior patterns. In it the model is used to define a variety of interesting process behavior patterns. The dissertation closes by suggesting how the model could be used as a semantic base for a very potent language extension facility.

Multi-energy method of digital radiography for imaging of biological objects

NASA Astrophysics Data System (ADS)

Ryzhikov, V. D.; Naydenov, S. V.; Opolonin, O. D.; Volkov, V. G.; Smith, C. F.

2016-03-01

This work has been dedicated to the search for a new possibility to use multi-energy digital radiography (MER) for medical applications. Our work has included both theoretical and experimental investigations of 2-energy (2E) and 3- energy (3D) radiography for imaging the structure of biological objects. Using special simulation methods and digital analysis based on the X-ray interaction energy dependence for each element of importance to medical applications in the X-ray range of energy up to 150 keV, we have implemented a quasi-linear approximation for the energy dependence of the X-ray linear mass absorption coefficient μm (E) that permits us to determine the intrinsic structure of the biological objects. Our measurements utilize multiple X-ray tube voltages (50, 100, and 150 kV) with Al and Cu filters of different thicknesses to achieve 3-energy X-ray examination of objects. By doing so, we are able to achieve significantly improved imaging quality of the structure of the subject biological objects. To reconstruct and visualize the final images, we use both two-dimensional (2D) and three-dimensional (3D) palettes of identification. The result is a 2E and/or 3E representation of the object with color coding of each pixel according to the data outputs. Following the experimental measurements and post-processing, we produce a 3D image of the biological object - in the case of our trials, fragments or parts of chicken and turkey.

Characterizing Interaction with Visual Mathematical Representations

ERIC Educational Resources Information Center

Sedig, Kamran; Sumner, Mark

2006-01-01

This paper presents a characterization of computer-based interactions by which learners can explore and investigate visual mathematical representations (VMRs). VMRs (e.g., geometric structures, graphs, and diagrams) refer to graphical representations that visually encode properties and relationships of mathematical structures and concepts.…

New solutions for climate network visualization

NASA Astrophysics Data System (ADS)

Nocke, Thomas; Buschmann, Stefan; Donges, Jonathan F.; Marwan, Norbert

2016-04-01

An increasing amount of climate and climate impact research methods deals with geo-referenced networks, including energy, trade, supply-chain, disease dissemination and climatic tele-connection networks. At the same time, the size and complexity of these networks increases, resulting in networks of more than hundred thousand or even millions of edges, which are often temporally evolving, have additional data at nodes and edges, and can consist of multiple layers even in real 3D. This gives challenges to both the static representation and the interactive exploration of these networks, first of all avoiding edge clutter ("edge spagetti") and allowing interactivity even for unfiltered networks. Within this presentation, we illustrate potential solutions to these challenges. Therefore, we give a glimpse on a questionnaire performed with climate and complex system scientists with respect to their network visualization requirements, and on a review of available state-of-the-art visualization techniques and tools for this purpose (see as well Nocke et al., 2015). In the main part, we present alternative visualization solutions for several use cases (global, regional, and multi-layered climate networks) including alternative geographic projections, edge bundling, and 3-D network support (based on CGV and GTX tools), and implementation details to reach interactive frame rates. References: Nocke, T., S. Buschmann, J. F. Donges, N. Marwan, H.-J. Schulz, and C. Tominski: Review: Visual analytics of climate networks, Nonlinear Processes in Geophysics, 22, 545-570, doi:10.5194/npg-22-545-2015, 2015

Modeling the effects of vegetation heterogeneity on wildland fire behavior

NASA Astrophysics Data System (ADS)

Atchley, A. L.; Linn, R.; Sieg, C.; Middleton, R. S.

2017-12-01

Vegetation structure and densities are known to drive fire-spread rate and burn severity. Many fire-spread models incorporate an average, homogenous fuel density in the model domain to drive fire behavior. However, vegetation communities are rarely homogenous and instead present significant heterogeneous structure and fuel densities in the fires path. This results in observed patches of varied burn severities and mosaics of disturbed conditions that affect ecological recovery and hydrologic response. Consequently, to understand the interactions of fire and ecosystem functions, representations of spatially heterogeneous conditions need to be incorporated into fire models. Mechanistic models of fire disturbance offer insight into how fuel load characterization and distribution result in varied fire behavior. Here we use a physically-based 3D combustion model—FIRETEC—that solves conservation of mass, momentum, energy, and chemical species to compare fire behavior on homogenous representations to a heterogeneous vegetation distribution. Results demonstrate the impact vegetation heterogeneity has on the spread rate, intensity, and extent of simulated wildfires thus providing valuable insight in predicted wildland fire evolution and enhanced ability to estimate wildland fire inputs into regional and global climate models.

Single- or multi-flavor Kondo effect in graphene

NASA Astrophysics Data System (ADS)

Zhu, Zhen-Gang; Ding, Kai-He; Berakdar, Jamal

2010-06-01

Based on the tight-binding formalism, we investigate the Anderson and the Kondo model for an adatom magnetic impurity above graphene. Different impurity positions are analyzed. Employing a partial-wave representation we study the nature of the coupling between the impurity and the conducting electrons. The components from the two Dirac points are mixed while interacting with the impurity. Two configurations are considered explicitly: the adatom is above one atom (ADA), the other case is the adatom above the center the honeycomb (ADC). For ADA the impurity is coupled with one flavor for both A and B sublattice and both Dirac points. For ADC the impurity couples with multi-flavor states for a spinor state of the impurity. We show, explicitly for a 3d magnetic atom, dz2, (dxz,dyz), and (dx2- y2,dxy) couple respectively with the Γ1, Γ5(E1), and Γ6(E2) representations (reps) of C6v group in ADC case. The bases for these reps of graphene are also derived explicitly. For ADA we calculate the Kondo temperature.

Dependency-based Siamese long short-term memory network for learning sentence representations

PubMed Central

Zhu, Wenhao; Ni, Jianyue; Wei, Baogang; Lu, Zhiguo

2018-01-01

Textual representations play an important role in the field of natural language processing (NLP). The efficiency of NLP tasks, such as text comprehension and information extraction, can be significantly improved with proper textual representations. As neural networks are gradually applied to learn the representation of words and phrases, fairly efficient models of learning short text representations have been developed, such as the continuous bag of words (CBOW) and skip-gram models, and they have been extensively employed in a variety of NLP tasks. Because of the complex structure generated by the longer text lengths, such as sentences, algorithms appropriate for learning short textual representations are not applicable for learning long textual representations. One method of learning long textual representations is the Long Short-Term Memory (LSTM) network, which is suitable for processing sequences. However, the standard LSTM does not adequately address the primary sentence structure (subject, predicate and object), which is an important factor for producing appropriate sentence representations. To resolve this issue, this paper proposes the dependency-based LSTM model (D-LSTM). The D-LSTM divides a sentence representation into two parts: a basic component and a supporting component. The D-LSTM uses a pre-trained dependency parser to obtain the primary sentence information and generate supporting components, and it also uses a standard LSTM model to generate the basic sentence components. A weight factor that can adjust the ratio of the basic and supporting components in a sentence is introduced to generate the sentence representation. Compared with the representation learned by the standard LSTM, the sentence representation learned by the D-LSTM contains a greater amount of useful information. The experimental results show that the D-LSTM is superior to the standard LSTM for sentences involving compositional knowledge (SICK) data. PMID:29513748

Deducing 2D crystal structure at the liquid/solid interface with atomic resolution: a combined STM and SFG study.

PubMed

McClelland, Arthur A; Ahn, Seokhoon; Matzger, Adam J; Chen, Zhan

2009-11-17

Sum frequency generation vibrational spectroscopy (SFG) has been applied to study two-dimensional (2D) crystals formed by an isophthalic acid diester on the surface of highly oriented pyrolytic graphite, providing complementary measurements to scanning tunneling microscopy (STM) and computational modeling. SFG results indicate that both aromatic and C=O groups in the 2D crystal tilt from the surface. This study demonstrates that a combination of SFG and STM techniques can be used to gain a more complete picture of 2D crystal structure, and it is necessary to consider solvent-2D crystal interactions and dynamics in the computer models to achieve an accurate representation of interfacial structure.

From experimental imaging techniques to virtual embryology.

PubMed

Weninger, Wolfgang J; Tassy, Olivier; Darras, Sébastien; Geyer, Stefan H; Thieffry, Denis

2004-01-01

Modern embryology increasingly relies on descriptive and functional three dimensional (3D) and four dimensional (4D) analysis of physically, optically, or virtually sectioned specimens. To cope with the technical requirements, new methods for high detailed in vivo imaging, as well as the generation of high resolution digital volume data sets for the accurate visualisation of transgene activity and gene product presence, in the context of embryo morphology, were recently developed and are under construction. These methods profoundly change the scientific applicability, appearance and style of modern embryo representations. In this paper, we present an overview of the emerging techniques to create, visualise and administrate embryo representations (databases, digital data sets, 3-4D embryo reconstructions, models, etc.), and discuss the implications of these new methods on the work of modern embryologists, including, research, teaching, the selection of specific model organisms, and potential collaborators.

Crack Detection with Lamb Wave Wavenumber Analysis

NASA Technical Reports Server (NTRS)

Tian, Zhenhua; Leckey, Cara; Rogge, Matt; Yu, Lingyu

2013-01-01

In this work, we present our study of Lamb wave crack detection using wavenumber analysis. The aim is to demonstrate the application of wavenumber analysis to 3D Lamb wave data to enable damage detection. The 3D wavefields (including vx, vy and vz components) in time-space domain contain a wealth of information regarding the propagating waves in a damaged plate. For crack detection, three wavenumber analysis techniques are used: (i) two dimensional Fourier transform (2D-FT) which can transform the time-space wavefield into frequency-wavenumber representation while losing the spatial information; (ii) short space 2D-FT which can obtain the frequency-wavenumber spectra at various spatial locations, resulting in a space-frequency-wavenumber representation; (iii) local wavenumber analysis which can provide the distribution of the effective wavenumbers at different locations. All of these concepts are demonstrated through a numerical simulation example of an aluminum plate with a crack. The 3D elastodynamic finite integration technique (EFIT) was used to obtain the 3D wavefields, of which the vz (out-of-plane) wave component is compared with the experimental measurement obtained from a scanning laser Doppler vibrometer (SLDV) for verification purposes. The experimental and simulated results are found to be in close agreement. The application of wavenumber analysis on 3D EFIT simulation data shows the effectiveness of the analysis for crack detection. Keywords: : Lamb wave, crack detection, wavenumber analysis, EFIT modeling

Spacecraft-plasma interaction codes: NASCAP/GEO, NASCAP/LEO, POLAR, DynaPAC, and EPSAT

NASA Technical Reports Server (NTRS)

Mandell, M. J.; Jongeward, G. A.; Cooke, D. L.

1992-01-01

Development of a computer code to simulate interactions between the surfaces of a geometrically complex spacecraft and the space plasma environment involves: (1) defining the relevant physical phenomena and formulating them in appropriate levels of approximation; (2) defining a representation for the 3-D space external to the spacecraft and a means for defining the spacecraft surface geometry and embedding it in the surrounding space; (3) packaging the code so that it is easy and practical to use, interpret, and present the results; and (4) validating the code by continual comparison with theoretical models, ground test data, and spaceflight experiments. The physical content, geometrical capabilities, and application of five S-CUBED developed spacecraft plasma interaction codes are discussed. The NASA Charging Analyzer Program/geosynchronous earth orbit (NASCAP/GEO) is used to illustrate the role of electrostatic barrier formation in daylight spacecraft charging. NASCAP/low Earth orbit (LEO) applications to the CHARGE-2 and Space Power Experiment Aboard Rockets (SPEAR)-1 rocket payloads are shown. DynaPAC application to the SPEAR-2 rocket payloads is described. Environment Power System Analysis Tool (EPSAT) is illustrated by application to Tethered Satellite System 1 (TSS-1), SPEAR-3, and Sundance. A detailed description and application of the Potentials of Large Objects in the Auroral Region (POLAR) Code are presented.

Collisions of O+ with He at low energies

NASA Astrophysics Data System (ADS)

Joseph, Dwayne C.; Saha, B. C.; Zhao, L. B.

2009-05-01

We have investigated the following charge transfer processO^+( ^4S^0, ^2D^0, ^2P^0)+He->O( ^3P)+He^+-δE using the full quantum [1] and semi-classical molecular [2]orbital close-coupling (MOCC) approximations. The quantum MOCC equations are solved numerically in the adiabatic representation [3]. Using MRD-CI package [4] the ab initio configuration interaction calculation is carried out for potential energies. Details of our findings will be reported in the conference. [1] B. H. Bransden and M. R. C. McDowell, ``Charge Exchange and the Theory of Ion-Atom Collisions'', Clarendon Press, Oxford, 1992. [2] M. Kimura and N. F. Lane, At. Mol. Opt. Phys 26, 79 (1990). [3] J. P. Braga and J. C. Belchoir, J. Comput. Chem 17, 1559 (1996). [4] R. J. Buenker, ``Current Aspects of Quantum Chemistry 1981, Vol 21, edited by R. Carbo (Elsevier, Amsterdam), p 17.

Unitary Transformations in 3 D Vector Representation of Qutrit States

DTIC Science & Technology

2018-03-12

Representation of Qutrit States Vinod K Mishra Computational and Information Sciences Directorate, ARL Approved for public... information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and...maintaining the data needed, and completing and reviewing the collection information . Send comments regarding this burden estimate or any other aspect

The partition dimension of cycle books graph

NASA Astrophysics Data System (ADS)

Santoso, Jaya; Darmaji

2018-03-01

Let G be a nontrivial and connected graph with vertex set V(G), edge set E(G) and S ⊆ V(G) with v ∈ V(G), the distance between v and S is d(v,S) = min{d(v,x)|x ∈ S}. For an ordered partition ∏ = {S 1, S 2, S 3,…, Sk } of V(G), the representation of v with respect to ∏ is defined by r(v|∏) = (d(v, S 1), d(v, S 2),…, d(v, Sk )). The partition ∏ is called a resolving partition of G if all representations of vertices are distinct. The partition dimension pd(G) is the smallest integer k such that G has a resolving partition set with k members. In this research, we will determine the partition dimension of Cycle Books {B}{Cr,m}. Cycle books graph {B}{Cr,m} is a graph consisting of m copies cycle Cr with the common path P 2. It is shown that the partition dimension of cycle books graph, pd({B}{C3,m}) is 3 for m = 2, 3, and m for m ≥ 4. pd({B}{C4,m}) is 3 + 2k for m = 3k + 2, 4 + 2(k ‑ 1) for m = 3k + 1, and 3 + 2(k ‑ 1) for m = 3k. pd({B}{C5,m}) is m + 1.

Modeling late rectal toxicities based on a parameterized representation of the 3D dose distribution

NASA Astrophysics Data System (ADS)

Buettner, Florian; Gulliford, Sarah L.; Webb, Steve; Partridge, Mike

2011-04-01

Many models exist for predicting toxicities based on dose-volume histograms (DVHs) or dose-surface histograms (DSHs). This approach has several drawbacks as firstly the reduction of the dose distribution to a histogram results in the loss of spatial information and secondly the bins of the histograms are highly correlated with each other. Furthermore, some of the complex nonlinear models proposed in the past lack a direct physical interpretation and the ability to predict probabilities rather than binary outcomes. We propose a parameterized representation of the 3D distribution of the dose to the rectal wall which explicitly includes geometrical information in the form of the eccentricity of the dose distribution as well as its lateral and longitudinal extent. We use a nonlinear kernel-based probabilistic model to predict late rectal toxicity based on the parameterized dose distribution and assessed its predictive power using data from the MRC RT01 trial (ISCTRN 47772397). The endpoints under consideration were rectal bleeding, loose stools, and a global toxicity score. We extract simple rules identifying 3D dose patterns related to a specifically low risk of complication. Normal tissue complication probability (NTCP) models based on parameterized representations of geometrical and volumetric measures resulted in areas under the curve (AUCs) of 0.66, 0.63 and 0.67 for predicting rectal bleeding, loose stools and global toxicity, respectively. In comparison, NTCP models based on standard DVHs performed worse and resulted in AUCs of 0.59 for all three endpoints. In conclusion, we have presented low-dimensional, interpretable and nonlinear NTCP models based on the parameterized representation of the dose to the rectal wall. These models had a higher predictive power than models based on standard DVHs and their low dimensionality allowed for the identification of 3D dose patterns related to a low risk of complication.

Customised 3D Printing: An Innovative Training Tool for the Next Generation of Orbital Surgeons.

PubMed

Scawn, Richard L; Foster, Alex; Lee, Bradford W; Kikkawa, Don O; Korn, Bobby S

2015-01-01

Additive manufacturing or 3D printing is the process by which three dimensional data fields are translated into real-life physical representations. 3D printers create physical printouts using heated plastics in a layered fashion resulting in a three-dimensional object. We present a technique for creating customised, inexpensive 3D orbit models for use in orbital surgical training using 3D printing technology. These models allow trainee surgeons to perform 'wet-lab' orbital decompressions and simulate upcoming surgeries on orbital models that replicate a patient's bony anatomy. We believe this represents an innovative training tool for the next generation of orbital surgeons.

3D geospatial visualizations: Animation and motion effects on spatial objects

NASA Astrophysics Data System (ADS)

Evangelidis, Konstantinos; Papadopoulos, Theofilos; Papatheodorou, Konstantinos; Mastorokostas, Paris; Hilas, Constantinos

2018-02-01

Digital Elevation Models (DEMs), in combination with high quality raster graphics provide realistic three-dimensional (3D) representations of the globe (virtual globe) and amazing navigation experience over the terrain through earth browsers. In addition, the adoption of interoperable geospatial mark-up languages (e.g. KML) and open programming libraries (Javascript) makes it also possible to create 3D spatial objects and convey on them the sensation of any type of texture by utilizing open 3D representation models (e.g. Collada). One step beyond, by employing WebGL frameworks (e.g. Cesium.js, three.js) animation and motion effects are attributed on 3D models. However, major GIS-based functionalities in combination with all the above mentioned visualization capabilities such as for example animation effects on selected areas of the terrain texture (e.g. sea waves) as well as motion effects on 3D objects moving in dynamically defined georeferenced terrain paths (e.g. the motion of an animal over a hill, or of a big fish in an ocean etc.) are not widely supported at least by open geospatial applications or development frameworks. Towards this we developed and made available to the research community, an open geospatial software application prototype that provides high level capabilities for dynamically creating user defined virtual geospatial worlds populated by selected animated and moving 3D models on user specified locations, paths and areas. At the same time, the generated code may enhance existing open visualization frameworks and programming libraries dealing with 3D simulations, with the geospatial aspect of a virtual world.

Computer aided three-dimensional reconstruction and modeling of the pelvis, by using plastinated cross sections, as a powerful tool for morphological investigations.

PubMed

Sora, Mircea-Constantin; Jilavu, Radu; Matusz, Petru

2012-10-01

The aim of this study was to describe a method of developing a computerized model of the human female pelvis using plastinated slices. Computerized reconstruction of anatomical structures is becoming very useful for developing anatomical teaching, research modules and animations. Although databases consisting of serial sections derived from frozen cadaver material exist, plastination represents an alternative method for developing anatomical data useful for computerized reconstruction. A slice anatomy study, using plastinated transparent pelvis cross sections, was performed to obtain a 3D reconstruction. One female human pelvis used for this study, first plastinated as a block, then sliced into thin slices and in the end subjected to 3D computerized reconstruction using WinSURF modeling system (SURFdriver Software). To facilitate the understanding of the complex pelvic floor anatomy on sectional images obtained through MR imaging, and to make the representation more vivid, a female pelvis computer-aided 3D model was created. Qualitative observations revealed that the morphological features of the model were consistent with those displayed by typical cadaveric specimens. The quality of the reconstructed images appeared distinct, especially the spatial positions and complicated relationships of contiguous structures of the female pelvis. All reconstructed structures can be displayed in groups or as a whole and interactively rotated in 3D space. The utilization of plastinates for generating tissue sections is useful for 3D computerized modeling. The 3D model of the female pelvis presented in this paper provides a stereoscopic view to study the adjacent relationship and arrangement of respective pelvis sections. A better understanding of the pelvic floor anatomy is relevant to gynaecologists, radiologists, surgeons, urologists, physical therapists and all professionals who take care of women with pelvic floor dysfunction.

Yield Scaling of Frequency Domain Moment Tensors from Contained Chemical Explosions Detonated in Granite

NASA Astrophysics Data System (ADS)

MacPhail, M. D.; Stump, B. W.; Zhou, R.

2017-12-01

The Source Phenomenology Experiment (SPE - Arizona) was a series of nine, contained and partially contained chemical explosions within the porphyry granite at the Morenci Copper mine in Arizona. Its purpose was to detonate, record and analyze seismic waveforms from these single-fired explosions. Ground motion data from the SPE is analyzed in this study to assess the uniqueness of the time domain moment tensor source representation and its ability to quantify containment and yield scaling. Green's functions were computed for each of the explosions based on a 1D velocity model developed for the SPE. The Green's functions for the sixteen, near-source stations focused on observations from 37 to 680 m. This study analyzes the three deepest, fully contained explosions with a depth of burial of 30 m and yields of 0.77e-3, 3.08e-3 and 6.17e-3 kt. Inversions are conducted within the frequency domain and moment tensors are decomposed into deviatoric and isotropic components to evaluate the effects of containment and yield on the resulting source representation. Isotropic moments are compared to those for other contained explosions as reported by Denny and Johnson, 1991, and are in good agreement with their scaling results. The explosions in this study have isotropic moments of 1.2e12, 3.1e12 and 6.1e13 n*m. Isotropic and Mzz moment tensor spectra are compared to Mueller-Murphy, Denny-Johnson and revised Heard-Ackerman (HA) models and suggest that the larger explosions fit the HA model better. Secondary source effects resulting from free surface interactions including the effects of spallation contribute to the resulting moment tensors which include a CLVD component. Hudson diagrams, using frequency domain moment tensor data, are computed as a tool to assess how these containment scenarios affect the source representation. Our analysis suggests that, within our band of interest (2-20 Hz), as the frequency increases, the source representation becomes more explosion like, peaking at around 20 Hz. These results guide additional analysis of the observational data and the practical resolution of physical phenomenology accompanying underground explosions.

Tangible Models and Haptic Representations Aid Learning of Molecular Biology Concepts

ERIC Educational Resources Information Center

Johannes, Kristen; Powers, Jacklyn; Couper, Lisa; Silberglitt, Matt; Davenport, Jodi

2016-01-01

Can novel 3D models help students develop a deeper understanding of core concepts in molecular biology? We adapted 3D molecular models, developed by scientists, for use in high school science classrooms. The models accurately represent the structural and functional properties of complex DNA and Virus molecules, and provide visual and haptic…

Space-Time Error Representation and Estimation in Navier-Stokes Calculations

NASA Technical Reports Server (NTRS)

Barth, Timothy J.

2006-01-01

The mathematical framework for a-posteriori error estimation of functionals elucidated by Eriksson et al. [7] and Becker and Rannacher [3] is revisited in a space-time context. Using these theories, a hierarchy of exact and approximate error representation formulas are presented for use in error estimation and mesh adaptivity. Numerical space-time results for simple model problems as well as compressible Navier-Stokes flow at Re = 300 over a 2D circular cylinder are then presented to demonstrate elements of the error representation theory for time-dependent problems.

IMRT vs. 3D Noncoplanar Treatment Plans for Maxillary Sinus Tumors: A New Tool for Quantitative Evaluation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Levin, Daphne; Menhel, Janna; Alezra, Dror

2008-01-01

We compared 9-field, equispaced intensity modulated radiation therapy (IMRT), 4- to 5-field, directionally optimized IMRT, and 3-dimensional (3D) noncoplanar planning approaches for tumors of the maxillary sinus. Ten patients were planned retrospectively to compare the different treatment techniques. Prescription doses were 60 to 70 Gy. Critical structures contoured included optic nerves and chiasm, lacrimal glands, lenses, and retinas. As an aid for plan assessment, we introduced a new tool: Critical Organ Scoring Index (COSI), which allows quantitative evaluation of the tradeoffs between target coverage and critical organ sparing. This index was compared with other, commonly used conformity indices. For amore » reliable assessment of both tumor coverage and dose to critical organs in the different planning techniques, we introduced a 2D, graphical representation of COSI vs. conformity index (CI). Dose-volume histograms and mean, maximum, and minimum organ doses were also compared. IMRT plans delivered lower doses to ipsilateral structures, but were unable to spare them. 3D plans delivered less dose to contralateral structures, and were more homogeneous, as well. Both IMRT approaches gave similar results. In cases where choice of optimal plan was difficult, the novel 2D COSI-CI representation gave an accurate picture of the tradeoffs between target coverage and organ sparing, even in cases where other conformity indices failed. Due to their unique anatomy, maxillary sinus tumors may benefit more from a noncoplanar approach than from IMRT. The new graphical representation proposed is a quick, visual, reliable tool, which may facilitate the physician's choice of best treatment plan for a given patient.« less

Interactivity of Visual Mathematical Representations: Factors Affecting Learning and Cognitive Processes

ERIC Educational Resources Information Center

Sedig, Kamran; Liang, Hai-Ning

2006-01-01

Computer-based mathematical cognitive tools (MCTs) are a category of external aids intended to support and enhance learning and cognitive processes of learners. MCTs often contain interactive visual mathematical representations (VMRs), where VMRs are graphical representations that encode properties and relationships of mathematical concepts. In…

Thermal and log-normal distributions of plasma in laser driven Coulomb explosions of deuterium clusters

NASA Astrophysics Data System (ADS)

Barbarino, M.; Warrens, M.; Bonasera, A.; Lattuada, D.; Bang, W.; Quevedo, H. J.; Consoli, F.; de Angelis, R.; Andreoli, P.; Kimura, S.; Dyer, G.; Bernstein, A. C.; Hagel, K.; Barbui, M.; Schmidt, K.; Gaul, E.; Donovan, M. E.; Natowitz, J. B.; Ditmire, T.

2016-08-01

In this work, we explore the possibility that the motion of the deuterium ions emitted from Coulomb cluster explosions is highly disordered enough to resemble thermalization. We analyze the process of nuclear fusion reactions driven by laser-cluster interactions in experiments conducted at the Texas Petawatt laser facility using a mixture of D2+3He and CD4+3He cluster targets. When clusters explode by Coulomb repulsion, the emission of the energetic ions is “nearly” isotropic. In the framework of cluster Coulomb explosions, we analyze the energy distributions of the ions using a Maxwell-Boltzmann (MB) distribution, a shifted MB distribution (sMB), and the energy distribution derived from a log-normal (LN) size distribution of clusters. We show that the first two distributions reproduce well the experimentally measured ion energy distributions and the number of fusions from d-d and d-3He reactions. The LN distribution is a good representation of the ion kinetic energy distribution well up to high momenta where the noise becomes dominant, but overestimates both the neutron and the proton yields. If the parameters of the LN distributions are chosen to reproduce the fusion yields correctly, the experimentally measured high energy ion spectrum is not well represented. We conclude that the ion kinetic energy distribution is highly disordered and practically not distinguishable from a thermalized one.

Use of stereo vision and 24-bit false-color imagery to enhance visualization of multimodal confocal images

NASA Astrophysics Data System (ADS)

Beltrame, Francesco; Diaspro, Alberto; Fato, Marco; Martin, I.; Ramoino, Paola; Sobel, Irwin E.

1995-03-01

Confocal microscopy systems can be linked to 3D data oriented devices for the interactive navigation of the operator through a 3D object space. Sometimes, such environments are named `virtual reality' or `augmented reality' systems. We consider optical confocal laser scanning microscopy images, in fluorescence with various excitations and emissions, and versus time The aim of our study has been the quantitative spatial analysis of confocal data using the false-color composition technique. Starting from three 2D confocal fluorescent images at the same slice location in a given biological specimen, a new single image representation of all three parameters has been generated by the false-color technique on a HP 9000/735 workstation, connected to the confocal microscope. The color composite result of the mapping of the three parameters is displayed using a resolution of 24 bits per pixel. The operator may independently vary the mix of each of the three components in the false-color composite via three (R, G, B) mixing sliders. Furthermore, by using the pixel data in the three fluorescent component images, a 3D space containing the density distribution of these three parameters has been constructed. The histogram has been displayed in stereo: it can be used for clustering purposes from the operator, through an original thresholding algorithm.

Benchmarking of HPCC: A novel 3D molecular representation combining shape and pharmacophoric descriptors for efficient molecular similarity assessments.

PubMed

Karaboga, Arnaud S; Petronin, Florent; Marchetti, Gino; Souchet, Michel; Maigret, Bernard

2013-04-01

Since 3D molecular shape is an important determinant of biological activity, designing accurate 3D molecular representations is still of high interest. Several chemoinformatic approaches have been developed to try to describe accurate molecular shapes. Here, we present a novel 3D molecular description, namely harmonic pharma chemistry coefficient (HPCC), combining a ligand-centric pharmacophoric description projected onto a spherical harmonic based shape of a ligand. The performance of HPCC was evaluated by comparison to the standard ROCS software in a ligand-based virtual screening (VS) approach using the publicly available directory of useful decoys (DUD) data set comprising over 100,000 compounds distributed across 40 protein targets. Our results were analyzed using commonly reported statistics such as the area under the curve (AUC) and normalized sum of logarithms of ranks (NSLR) metrics. Overall, our HPCC 3D method is globally as efficient as the state-of-the-art ROCS software in terms of enrichment and slightly better for more than half of the DUD targets. Since it is largely admitted that VS results depend strongly on the nature of the protein families, we believe that the present HPCC solution is of interest over the current ligand-based VS methods. Copyright © 2013 Elsevier Inc. All rights reserved.

Hippocampus, Retrosplenial and Parahippocampal Cortices Encode Multicompartment 3D Space in a Hierarchical Manner.

PubMed

Kim, Misun; Maguire, Eleanor A

2018-05-01

Humans commonly operate within 3D environments such as multifloor buildings and yet there is a surprising dearth of studies that have examined how these spaces are represented in the brain. Here, we had participants learn the locations of paintings within a virtual multilevel gallery building and then used behavioral tests and fMRI repetition suppression analyses to investigate how this 3D multicompartment space was represented, and whether there was a bias in encoding vertical and horizontal information. We found faster response times for within-room egocentric spatial judgments and behavioral priming effects of visiting the same room, providing evidence for a compartmentalized representation of space. At the neural level, we observed a hierarchical encoding of 3D spatial information, with left anterior hippocampus representing local information within a room, while retrosplenial cortex, parahippocampal cortex, and posterior hippocampus represented room information within the wider building. Of note, both our behavioral and neural findings showed that vertical and horizontal location information was similarly encoded, suggesting an isotropic representation of 3D space even in the context of a multicompartment environment. These findings provide much-needed information about how the human brain supports spatial memory and navigation in buildings with numerous levels and rooms.

Real-Time Ligand Binding Pocket Database Search Using Local Surface Descriptors

PubMed Central

Chikhi, Rayan; Sael, Lee; Kihara, Daisuke

2010-01-01

Due to the increasing number of structures of unknown function accumulated by ongoing structural genomics projects, there is an urgent need for computational methods for characterizing protein tertiary structures. As functions of many of these proteins are not easily predicted by conventional sequence database searches, a legitimate strategy is to utilize structure information in function characterization. Of a particular interest is prediction of ligand binding to a protein, as ligand molecule recognition is a major part of molecular function of proteins. Predicting whether a ligand molecule binds a protein is a complex problem due to the physical nature of protein-ligand interactions and the flexibility of both binding sites and ligand molecules. However, geometric and physicochemical complementarity is observed between the ligand and its binding site in many cases. Therefore, ligand molecules which bind to a local surface site in a protein can be predicted by finding similar local pockets of known binding ligands in the structure database. Here, we present two representations of ligand binding pockets and utilize them for ligand binding prediction by pocket shape comparison. These representations are based on mapping of surface properties of binding pockets, which are compactly described either by the two dimensional pseudo-Zernike moments or the 3D Zernike descriptors. These compact representations allow a fast real-time pocket searching against a database. Thorough benchmark study employing two different datasets show that our representations are competitive with the other existing methods. Limitations and potentials of the shape-based methods as well as possible improvements are discussed. PMID:20455259

Display And Analysis Of Tomographic Volumetric Images Utilizing A Vari-Focal Mirror

NASA Astrophysics Data System (ADS)

Harris, L. D.; Camp, J. J.

1984-10-01

A system for the three-dimensional (3-D) display and analysis of stacks of tomographic images is described. The device utilizes the principle of a variable focal (vari-focal) length optical element in the form of an aluminized membrane stretched over a loudspeaker to generate a virtual 3-D image which is a visible representation of a 3-D array of image elements (voxels). The system displays 500,000 voxels per mirror cycle in a 3-D raster which appears continuous and demonstrates no distracting artifacts. The display is bright enough so that portions of the image can be dimmed without compromising the number of shades of gray. For x-ray CT, a displayed volume image looks like a 3-D radiograph which appears to be in the space directly behind the mirror. The viewer sees new views by moving his/her head from side to side or up and down. The system facilitates a variety of operator interactive functions which allow the user to point at objects within the image, control the orientation and location of brightened oblique planes within the volume, numerically dissect away selected image regions, and control intensity window levels. Photographs of example volume images displayed on the system illustrate, to the degree possible in a flat picture, the nature of displayed images and the capabilities of the system. Preliminary application of the display device to the analysis of volume reconstructions obtained from the Dynamic Spatial Reconstructor indicates significant utility of the system in selecting oblique sections and gaining an appreciation of the shape and dimensions of complex organ systems.

Combinatorial Drug Testing in 3D Microtumors Derived from GBM Patient-Derived Xenografts Reveals Cytotoxic Synergy in Pharmacokinomics-informed Pathway Interactions.

PubMed

Gilbert, Ashley N; Anderson, Joshua C; Duarte, Christine W; Shevin, Rachael S; Langford, Catherine P; Singh, Raj; Gillespie, G Yancey; Willey, Christopher D

2018-05-30

Glioblastoma multiforme (GBM), the most common form of primary malignant brain cancer in adults, is a devastating disease for which effective treatment has remained elusive for over 75 years. One reason for the minimal progress during this time is the lack of accurate preclinical models to represent the patient's tumor's in vivo environment, causing a disconnect in drug therapy effectiveness between the laboratory and clinic. While patient-derived xenografts (PDX's or xenolines) are excellent human tumor representations, they are not amenable to high throughput testing. Therefore, we developed a miniaturized xenoline system (microtumors) for drug testing. Nineteen GBM xenolines were profiled for global kinase (kinomic) activity revealing actionable kinase targets associated with intracranial tumor growth rate. Kinase inhibitors for these targets (WP1066, selumetinib, crizotinib, and cediranib) were selected for single and combination therapy using a fully human-derived three-dimensional (3D) microtumor model of GBM xenoline cells embedded in HuBiogel for subsequent molecular and phenotype assays. GBM microtumors closely resembled orthotopically-implanted tumors based on immunohistochemical analysis and displayed kinomic and morphological diversity. Drug response testing could be reproducibly performed in a 96-well format identifying several synergistic combinations. Our findings indicate that 3D microtumors can provide a suitable high-throughput model for combination drug testing.

The Attachment Doll Play Assessment: Predictive Validity with Concurrent Mother-Child Interaction and Maternal Caregiving Representations

PubMed Central

George, Carol; Solomon, Judith

2016-01-01

Attachment is central to the development of children’s regulatory processes. It has been associated with developmental and psychiatric health across the life span, especially emotional and behavioral regulation of negative affect when stressed (Schore, 2001; Schore and Schore, 2008). Assessment of attachment patterns provides a critical frame for understanding emerging developmental competencies and formulating treatment and intervention. Play-based attachment assessments provide access to representational models of attachment, which are regarded in attachment theory as the central organizing mechanisms associated with stability or change (Bowlby, 1969/1982; Bretherton and Munholland, 2008). The Attachment Doll Play Assessment (ADPA, George and Solomon, 1990–2016; Solomon et al., 1995) is a prominent established representational attachment measure for children aged early latency through childhood. This study examines the predictive validity of the ADPA to caregiving accessibility and responsiveness assessed from mother-child interaction and maternal representation. Sixty nine mothers and their 5–7-year-old children participated in this study. Mother-child interaction was observed during a pre-separation dyadic interaction task. Caregiving representations were rated from the Caregiving Interview (George and Solomon, 1988/1993/2005/2007). Child security with mother was associated with positive dyadic interaction and flexibly integrated maternal caregiving representations. Child controlling/disorganized attachments were significantly associated with problematic dyadic interaction and dysregulated-helpless maternal caregiving representations. The clinical implications and the use of the ADPA in clinical and educational settings are discussed. PMID:27803683

The Attachment Doll Play Assessment: Predictive Validity with Concurrent Mother-Child Interaction and Maternal Caregiving Representations.

PubMed

George, Carol; Solomon, Judith

2016-01-01

Attachment is central to the development of children's regulatory processes. It has been associated with developmental and psychiatric health across the life span, especially emotional and behavioral regulation of negative affect when stressed (Schore, 2001; Schore and Schore, 2008). Assessment of attachment patterns provides a critical frame for understanding emerging developmental competencies and formulating treatment and intervention. Play-based attachment assessments provide access to representational models of attachment, which are regarded in attachment theory as the central organizing mechanisms associated with stability or change (Bowlby, 1969/1982; Bretherton and Munholland, 2008). The Attachment Doll Play Assessment (ADPA, George and Solomon, 1990-2016; Solomon et al., 1995) is a prominent established representational attachment measure for children aged early latency through childhood. This study examines the predictive validity of the ADPA to caregiving accessibility and responsiveness assessed from mother-child interaction and maternal representation. Sixty nine mothers and their 5-7-year-old children participated in this study. Mother-child interaction was observed during a pre-separation dyadic interaction task. Caregiving representations were rated from the Caregiving Interview (George and Solomon, 1988/1993/2005/2007). Child security with mother was associated with positive dyadic interaction and flexibly integrated maternal caregiving representations. Child controlling/disorganized attachments were significantly associated with problematic dyadic interaction and dysregulated-helpless maternal caregiving representations. The clinical implications and the use of the ADPA in clinical and educational settings are discussed.

Real-time 3D visualization of volumetric video motion sensor data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carlson, J.; Stansfield, S.; Shawver, D.

1996-11-01

This paper addresses the problem of improving detection, assessment, and response capabilities of security systems. Our approach combines two state-of-the-art technologies: volumetric video motion detection (VVMD) and virtual reality (VR). This work capitalizes on the ability of VVMD technology to provide three-dimensional (3D) information about the position, shape, and size of intruders within a protected volume. The 3D information is obtained by fusing motion detection data from multiple video sensors. The second component involves the application of VR technology to display information relating to the sensors and the sensor environment. VR technology enables an operator, or security guard, to bemore » immersed in a 3D graphical representation of the remote site. VVMD data is transmitted from the remote site via ordinary telephone lines. There are several benefits to displaying VVMD information in this way. Because the VVMD system provides 3D information and because the sensor environment is a physical 3D space, it seems natural to display this information in 3D. Also, the 3D graphical representation depicts essential details within and around the protected volume in a natural way for human perception. Sensor information can also be more easily interpreted when the operator can `move` through the virtual environment and explore the relationships between the sensor data, objects and other visual cues present in the virtual environment. By exploiting the powerful ability of humans to understand and interpret 3D information, we expect to improve the means for visualizing and interpreting sensor information, allow a human operator to assess a potential threat more quickly and accurately, and enable a more effective response. This paper will detail both the VVMD and VR technologies and will discuss a prototype system based upon their integration.« less

The origins of intra- and inter-molecular vibrational couplings: A case study of H{sub 2}O-Ar on full and reduced-dimensional potential energy surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hou, Dan; Ma, Yong-Tao; Zhang, Xiao-Long

2016-01-07

The origin and strength of intra- and inter-molecular vibrational coupling is difficult to probe by direct experimental observations. However, explicitly including or not including some specific intramolecular vibrational modes to study intermolecular interaction provides a precise theoretical way to examine the effects of anharmonic coupling between modes. In this work, a full-dimension intra- and inter-molecular ab initio potential energy surface (PES) for H{sub 2}O–Ar, which explicitly incorporates interdependence on the intramolecular (Q{sub 1},  Q{sub 2},  Q{sub 3}) normal-mode coordinates of the H{sub 2}O monomer, has been calculated. In addition, four analytic vibrational-quantum-state-specific PESs are obtained by least-squares fitting vibrationally averagedmore » interaction energies for the (v{sub 1},  v{sub 2},  v{sub 3}) =  (0,  0,  0), (0,  0,  1), (1,  0,  0), (0,  1,  0) states of H{sub 2}O to the three-dimensional Morse/long-range potential function. Each vibrationally averaged PES fitted to 442 points has root-mean-square (rms) deviation smaller than 0.15 cm{sup −1}, and required only 58 parameters. With the 3D PESs of H{sub 2}O–Ar dimer system, we employed the combined radial discrete variable representation/angular finite basis representation method and Lanczos algorithm to calculate rovibrational energy levels. This showed that the resulting vibrationally averaged PESs provide good representations of the experimental infrared data, with rms discrepancies smaller than 0.02 cm{sup −1} for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H{sub 2}O in H{sub 2}O–Ar complex are predicted for the first time and are found to be in good agreement with the (extrapolated) experimental values. Upon introduction of additional intramolecular degrees of freedom into the intermolecular potential energy surface, there is clear spectroscopic evidence of intra- and intermolecular vibrational couplings.« less

Longitudinal associations between maternal disrupted representations, maternal interactive behavior and infant attachment: a comparison between full-term and preterm dyads.

PubMed

Hall, R A S; Hoffenkamp, H N; Tooten, A; Braeken, J; Vingerhoets, A J J M; van Bakel, H J A

2015-04-01

This prospective study examined whether or not a mother's representations of her infant were more often disrupted after premature childbirth. Furthermore, the study examined if different components of maternal interactive behavior mediated the relation between maternal disrupted representations and infant attachment. The participants were mothers of full-term (n = 75), moderately preterm (n = 68) and very preterm infants (n = 67). Maternal representations were assessed by the Working Model of the Child Interview at 6 months post-partum. Maternal interactive behavior was evaluated at 6 and 24 months post-partum, using the National Institute of Child Health and Human Development Early Care Research Network mother-infant observation scales. Infant attachment was observed at 24 months post-partum and was coded by the Attachment Q-Set. The results reveal that a premature childbirth does not necessarily generate disrupted maternal representations of the infant. Furthermore, maternal interactive behavior appears to be an important mechanism through which maternal representations influence the development of infant attachment in full-term and preterm infants. Early assessment of maternal representations can identify mother-infant dyads at risk, in full-term and preterm samples.

Density-functional formulation of the generalized pseudopotential theory. III. Transition-metal interatomic potentials

NASA Astrophysics Data System (ADS)

Moriarty, John A.

1988-08-01

The first-principles, density-functional version of the generalized pseudopotential theory (GPT) developed in papers I and II of this series [Phys. Rev. B 16, 2537 (1977); 26, 1754 (1982)] for empty- and filled-d-band metals is here extended to pure transition metals with partially filled d bands. The present focus is on a rigorous, real-space expansion of the bulk total energy in terms of widely transferable, structure-independent interatomic potentials, including both central-force pair interactions and angular-force triplet and quadruplet interactions. To accomplish this expansion, a specialized set of starting equations is derived from the basic local-density formalism for a pure metal, including refined expansions for the exchange-correlation terms and a simplified yet accurate representation of the cohesive energy. The parent pseudo-Green's-function formalism of the GPT is then used to develop these equations in a plane-wave, localized-d-state basis. In this basis, the cohesive energy divides quite naturally into a large volume component and a smaller structural component. The volume component,which includes all one-ion intra-atomic energy contributions, already gives a good description of the cohesion in lowest order. The structural component is expanded in terms of weak interatomic matrix elements and gives rise to a multi-ion series which establishes the interatomic potentials. Special attention is focused on the dominant d-electron contributions to this series and complete formal results for the two-ion, three-ion, and four-ion d-state potentials (vd2, vd3, and vd4) are derived. In addition, a simplified model is used to demonstrate that while vd3 can be of comparable importance to vd2, vd4 is inherently small and the series is rapidly convergent beyond three-ion interactions. Analytic model forms are also derived for vd2 and vd3 in the case of canonical d bands. In this limit, vd2 is purely attractive and varies with interatomic distance as r-10, while vd3 is weak and attractive for almost empty or filled d bands and maximum in strength and repulsive for half-filled d bands. Full first-principles expressions are then developed for the total two-ion and three-ion potentials and implemented for all 20 3d and 4d transition metals. The first-principles potentials qualitatively display all of the trends predicted by the model results, but they also reflect additional effects, including long-range hybridization tails which must be suitably screened in real-space calculations. Finally, illustrative application of the first-principles potentials is made to the calculation of the [100] phonon spectrum for V and Cr, where the importance of three-ion angular forces is explicitly demonstrated.

3DView: Space physics data visualizer

NASA Astrophysics Data System (ADS)

Génot, V.; Beigbeder, L.; Popescu, D.; Dufourg, N.; Gangloff, M.; Bouchemit, M.; Caussarieu, S.; Toniutti, J.-P.; Durand, J.; Modolo, R.; André, N.; Cecconi, B.; Jacquey, C.; Pitout, F.; Rouillard, A.; Pinto, R.; Erard, S.; Jourdane, N.; Leclercq, L.; Hess, S.; Khodachenko, M.; Al-Ubaidi, T.; Scherf, M.; Budnik, E.

2018-04-01

3DView creates visualizations of space physics data in their original 3D context. Time series, vectors, dynamic spectra, celestial body maps, magnetic field or flow lines, and 2D cuts in simulation cubes are among the variety of data representation enabled by 3DView. It offers direct connections to several large databases and uses VO standards; it also allows the user to upload data. 3DView's versatility covers a wide range of space physics contexts.

Thalamic amplification of cortical connectivity sustains attentional control

PubMed Central

Schmitt, L. Ian; Wimmer, Ralf D.; Nakajima, Miho; Happ, Michael; Mofakham, Sima; Halassa, Michael M.

2017-01-01

While interactions between the thalamus and cortex are critical for cognitive function1–3, the exact contribution of the thalamus to these interactions is often unclear. Recent studies have shown diverse connectivity patterns across the thalamus 4,5, but whether this diversity translates to thalamic functions beyond relaying information to or between cortical regions6 is unknown. Here, by investigating prefrontal cortical (PFC) representation of two rules used to guide attention, we find that the mediodorsal thalamus (MD) sustains these representations without relaying categorical information. Specifically, MD input amplifies local PFC connectivity, enabling rule-specific neural sequences to emerge and thereby maintain rule representations. Consistent with this notion, broadly enhancing PFC excitability diminishes rule specificity and behavioral performance, while enhancing MD excitability improves both. Overall, our results define a previously unknown principle in neuroscience; thalamic control of functional cortical connectivity. This function indicates that the thalamus plays much more central roles in cognition than previously thought. PMID:28467827

GATOR: Requirements capturing of telephony features

NASA Technical Reports Server (NTRS)

Dankel, Douglas D., II; Walker, Wayne; Schmalz, Mark

1992-01-01

We are developing a natural language-based, requirements gathering system called GATOR (for the GATherer Of Requirements). GATOR assists in the development of more accurate and complete specifications of new telephony features. GATOR interacts with a feature designer who describes a new feature, set of features, or capability to be implemented. The system aids this individual in the specification process by asking for clarifications when potential ambiguities are present, by identifying potential conflicts with other existing features, and by presenting its understanding of the feature to the designer. Through user interaction with a model of the existing telephony feature set, GATOR constructs a formal representation of the new, 'to be implemented' feature. Ultimately GATOR will produce a requirements document and will maintain an internal representation of this feature to aid in future design and specification. This paper consists of three sections that describe (1) the structure of GATOR, (2) POND, GATOR's internal knowledge representation language, and (3) current research issues.

C2 Approaches: Looking for the Sweet Spot

DTIC Science & Technology

2013-06-01

more information) IMAGE (see Lizotte et al., 2008; Lizotte, Bernier, Mokhtari , & Boivin, 2013) was developed as a suite of generic representation...439–446). Fukuoka, Japan. Lizotte, M., Bernier, F., Mokhtari , M., & Boivin, E. (2013). IMAGE Final Report: An Interactive Computer-aided Cognition...Capability for C4ISR Complexity Discovery (No. TR 2013-397). Québec, Canada: Defence R&D Canada - Valcartier. Lizotte, M., Bernier, F., Mokhtari , M

Resonance dynamics of DCO (X ˜ '2A ) simulated with the dynamically pruned discrete variable representation (DP-DVR)

NASA Astrophysics Data System (ADS)

Larsson, Henrik R.; Riedel, Jens; Wei, Jie; Temps, Friedrich; Hartke, Bernd

2018-05-01

Selected resonance states of the deuterated formyl radical in the electronic ground state X ˜ '2A are computed using our recently introduced dynamically pruned discrete variable representation [H. R. Larsson, B. Hartke, and D. J. Tannor, J. Chem. Phys. 145, 204108 (2016)]. Their decay and asymptotic distributions are analyzed and, for selected resonances, compared to experimental results obtained by a combination of stimulated emission pumping and velocity-map imaging of the product D atoms. The theoretical results show good agreement with the experimental kinetic energy distributions. The intramolecular vibrational energy redistribution is analyzed and compared with previous results from an effective polyad Hamiltonian. Specifically, we analyzed the part of the wavefunction that remains in the interaction region during the decay. The results from the polyad Hamiltonian could mainly be confirmed. The C=O stretch quantum number is typically conserved, while the D—C=O bend quantum number decreases. Differences are due to strong anharmonic coupling such that all resonances have major contributions from several zero-order states. For some of the resonances, the coupling is so strong that no further zero-order states appear during the dynamics in the interaction region, even after propagating for 300 ps.

Interactions as intertwiners in 4D QFT

NASA Astrophysics Data System (ADS)

de Mello Koch, Robert; Ramgoolam, Sanjaye

2016-03-01

In a recent paper we showed that the correlators of free scalar field theory in four dimensions can be constructed from a two dimensional topological field theory based on so(4 , 2) equivariant maps (intertwiners). The free field result, along with recent results of Frenkel and Libine on equivariance properties of Feynman integrals, are developed further in this paper. We show that the coefficient of the log term in the 1-loop 4-point conformal integral is a projector in the tensor product of so(4 , 2) representations. We also show that the 1-loop 4-point integral can be written as a sum of four terms, each associated with the quantum equation of motion for one of the four external legs. The quantum equation of motion is shown to be related to equivariant maps involving indecomposable representations of so(4 , 2), a phenomenon which illuminates multiplet recombination. The harmonic expansion method for Feynman integrals is a powerful tool for arriving at these results. The generalization to other interactions and higher loops is discussed.

Bimanual Interaction with Interscopic Multi-Touch Surfaces

NASA Astrophysics Data System (ADS)

Schöning, Johannes; Steinicke, Frank; Krüger, Antonio; Hinrichs, Klaus; Valkov, Dimitar

Multi-touch interaction has received considerable attention in the last few years, in particular for natural two-dimensional (2D) interaction. However, many application areas deal with three-dimensional (3D) data and require intuitive 3D interaction techniques therefore. Indeed, virtual reality (VR) systems provide sophisticated 3D user interface, but then lack efficient 2D interaction, and are therefore rarely adopted by ordinary users or even by experts. Since multi-touch interfaces represent a good trade-off between intuitive, constrained interaction on a touch surface providing tangible feedback, and unrestricted natural interaction without any instrumentation, they have the potential to form the foundation of the next generation user interface for 2D as well as 3D interaction. In particular, stereoscopic display of 3D data provides an additional depth cue, but until now the challenges and limitations for multi-touch interaction in this context have not been considered. In this paper we present new multi-touch paradigms and interactions that combine both traditional 2D interaction and novel 3D interaction on a touch surface to form a new class of multi-touch systems, which we refer to as interscopic multi-touch surfaces (iMUTS). We discuss iMUTS-based user interfaces that support interaction with 2D content displayed in monoscopic mode and 3D content usually displayed stereoscopically. In order to underline the potential of the proposed iMUTS setup, we have developed and evaluated two example interaction metaphors for different domains. First, we present intuitive navigation techniques for virtual 3D city models, and then we describe a natural metaphor for deforming volumetric datasets in a medical context.

Biochemistry students' ideas about shape and charge in enzyme-substrate interactions.

PubMed

Linenberger, Kimberly J; Bretz, Stacey Lowery

2014-01-01

Biochemistry is a visual discipline that requires students to develop an understanding of numerous representations. However, there is very little known about what students actually understand about the representations that are used to communicate ideas in biochemistry. This study investigated biochemistry students' understanding of multiple representations of enzyme-substrate interactions through both student interviews (N = 25) and responses by a national sample (N = 707) to the Enzyme-Substrate Interactions Concept Inventory. This manuscript reports the findings regarding one category of misconceptions measured by the concept inventory, namely, students' understandings of shape and charge in the context of enzyme-substrate interactions. Students interpret molecular representations depicting such interactions by determining the complementarity between enzyme and substrate by focusing upon charge and hydrogen bonding, but with a disregard for stereochemistry. Copyright © 2014 by The International Union of Biochemistry and Molecular Biology.

The Representation of Cultural Heritage from Traditional Drawing to 3d Survey: the Case Study of Casamary's Abbey

NASA Astrophysics Data System (ADS)

Canciani, M.; Saccone, M.

2016-06-01

In 3D survey the aspects most discussed in the scientific community are those related to the acquisition of data from integrated survey (laser scanner, photogrammetric, topographic and traditional direct), rather than those relating to the interpretation of the data. Yet in the methods of traditional representation, the data interpretation, such as that of the philological reconstruction, constitutes the most important aspect. It is therefore essential in modern systems of survey and representation, filter the information acquired. In the system, based on the integrated survey that we have adopted, the 3D object, characterized by a cloud of georeferenced points, defined but their color values, defines the core of the elaboration. It allows to carry out targeted analysis, using section planes as a tool of selection and filtering data, comparable with those of traditional drawings. In the case study of the Abbey of Casamari (Veroli), one of the most important Cistercian Settlement in Italy, the survey made for an Agreement with the Ministry of Cultural Heritage and Activities and Tourism (MiBACT) and University of RomaTre, within the project "Accessment of the sismic safety of the state museum", the reference 3D model, consisting of the superposition and geo-references data from various surveys, is the tool with which yo develop representative models comparable to traditional ones. It provides the necessary spatial environment for drawing up plans and sections with a definition such as to develop thematic analysis related to phases of construction, state of deterioration and structural features.

Social representations of climate change in Swedish lay focus groups: local or distant, gradual or catastrophic?

PubMed

Wibeck, Victoria

2014-02-01

This paper explores social representations of climate change, investigating how climate change is discussed by Swedish laypeople interacting in focus group interviews. The analysis focuses on prototypical examples and metaphors, which were key devices for objectifying climate change representations. The paper analyzes how the interaction of focus group participants with other speakers, ideas, arguments, and broader social representations shaped their representations of climate change. Climate change was understood as a global but distant issue with severe consequences. There was a dynamic tension between representations of climate change as a gradual vs. unpredictable process. Implications for climate change communication are discussed.

Feature point based 3D tracking of multiple fish from multi-view images

PubMed Central

Qian, Zhi-Ming

2017-01-01

A feature point based method is proposed for tracking multiple fish in 3D space. First, a simplified representation of the object is realized through construction of two feature point models based on its appearance characteristics. After feature points are classified into occluded and non-occluded types, matching and association are performed, respectively. Finally, the object's motion trajectory in 3D space is obtained through integrating multi-view tracking results. Experimental results show that the proposed method can simultaneously track 3D motion trajectories for up to 10 fish accurately and robustly. PMID:28665966

Feature point based 3D tracking of multiple fish from multi-view images.

PubMed

Qian, Zhi-Ming; Chen, Yan Qiu

2017-01-01

A feature point based method is proposed for tracking multiple fish in 3D space. First, a simplified representation of the object is realized through construction of two feature point models based on its appearance characteristics. After feature points are classified into occluded and non-occluded types, matching and association are performed, respectively. Finally, the object's motion trajectory in 3D space is obtained through integrating multi-view tracking results. Experimental results show that the proposed method can simultaneously track 3D motion trajectories for up to 10 fish accurately and robustly.

General tensor discriminant analysis and gabor features for gait recognition.

PubMed

Tao, Dacheng; Li, Xuelong; Wu, Xindong; Maybank, Stephen J

2007-10-01

The traditional image representations are not suited to conventional classification methods, such as the linear discriminant analysis (LDA), because of the under sample problem (USP): the dimensionality of the feature space is much higher than the number of training samples. Motivated by the successes of the two dimensional LDA (2DLDA) for face recognition, we develop a general tensor discriminant analysis (GTDA) as a preprocessing step for LDA. The benefits of GTDA compared with existing preprocessing methods, e.g., principal component analysis (PCA) and 2DLDA, include 1) the USP is reduced in subsequent classification by, for example, LDA; 2) the discriminative information in the training tensors is preserved; and 3) GTDA provides stable recognition rates because the alternating projection optimization algorithm to obtain a solution of GTDA converges, while that of 2DLDA does not. We use human gait recognition to validate the proposed GTDA. The averaged gait images are utilized for gait representation. Given the popularity of Gabor function based image decompositions for image understanding and object recognition, we develop three different Gabor function based image representations: 1) the GaborD representation is the sum of Gabor filter responses over directions, 2) GaborS is the sum of Gabor filter responses over scales, and 3) GaborSD is the sum of Gabor filter responses over scales and directions. The GaborD, GaborS and GaborSD representations are applied to the problem of recognizing people from their averaged gait images.A large number of experiments were carried out to evaluate the effectiveness (recognition rate) of gait recognition based on first obtaining a Gabor, GaborD, GaborS or GaborSD image representation, then using GDTA to extract features and finally using LDA for classification. The proposed methods achieved good performance for gait recognition based on image sequences from the USF HumanID Database. Experimental comparisons are made with nine state of the art classification methods in gait recognition.

Surface similarity-based molecular query-retrieval

PubMed Central

Singh, Rahul

2007-01-01

Background Discerning the similarity between molecules is a challenging problem in drug discovery as well as in molecular biology. The importance of this problem is due to the fact that the biochemical characteristics of a molecule are closely related to its structure. Therefore molecular similarity is a key notion in investigations targeting exploration of molecular structural space, query-retrieval in molecular databases, and structure-activity modelling. Determining molecular similarity is related to the choice of molecular representation. Currently, representations with high descriptive power and physical relevance like 3D surface-based descriptors are available. Information from such representations is both surface-based and volumetric. However, most techniques for determining molecular similarity tend to focus on idealized 2D graph-based descriptors due to the complexity that accompanies reasoning with more elaborate representations. Results This paper addresses the problem of determining similarity when molecules are described using complex surface-based representations. It proposes an intrinsic, spherical representation that systematically maps points on a molecular surface to points on a standard coordinate system (a sphere). Molecular surface properties such as shape, field strengths, and effects due to field super-positioningcan then be captured as distributions on the surface of the sphere. Surface-based molecular similarity is subsequently determined by computing the similarity of the surface-property distributions using a novel formulation of histogram-intersection. The similarity formulation is not only sensitive to the 3D distribution of the surface properties, but is also highly efficient to compute. Conclusion The proposed method obviates the computationally expensive step of molecular pose-optimisation, can incorporate conformational variations, and facilitates highly efficient determination of similarity by directly comparing molecular surfaces and surface-based properties. Retrieval performance, applications in structure-activity modeling of complex biological properties, and comparisons with existing research and commercial methods demonstrate the validity and effectiveness of the approach. PMID:17634096

3D visualization of solar wind ion data from the Chang'E-1 exploration

NASA Astrophysics Data System (ADS)

Zhang, Tian; Sun, Yankui; Tang, Zesheng

2011-10-01

Chang'E-1 (abbreviation CE-1), China's first Moon-orbiting spacecraft launched in 2007, carried equipment called the Solar Wind Ion Detector (abbreviation SWID), which sent back tens of gigabytes of solar wind ion differential number flux data. These data are essential for furthering our understanding of the cislunar space environment. However, to fully comprehend and analyze these data presents considerable difficulties, not only because of their huge size (57 GB), but also because of their complexity. Therefore, a new 3D visualization method is developed to give a more intuitive representation than traditional 1D and 2D visualizations, and in particular to offer a better indication of the direction of the incident ion differential number flux and the relative spatial position of CE-1 with respect to the Sun, the Earth, and the Moon. First, a coordinate system named Selenocentric Solar Ecliptic (SSE) which is more suitable for our goal is chosen, and solar wind ion differential number flux vectors in SSE are calculated from Geocentric Solar Ecliptic System (GSE) and Moon Center Coordinate (MCC) coordinates of the spacecraft, and then the ion differential number flux distribution in SSE is visualized in 3D space. This visualization method is integrated into an interactive visualization analysis software tool named vtSWIDs, developed in MATLAB, which enables researchers to browse through numerous records and manipulate the visualization results in real time. The tool also provides some useful statistical analysis functions, and can be easily expanded.

Somatosensory cortical plasticity in carpal tunnel syndrome treated by acupuncture.

PubMed

Napadow, Vitaly; Liu, Jing; Li, Ming; Kettner, Norman; Ryan, Angela; Kwong, Kenneth K; Hui, Kathleen K S; Audette, Joseph F

2007-03-01

Carpal tunnel syndrome (CTS) is a common entrapment neuropathy of the median nerve characterized by paresthesias and pain in the first through fourth digits. We hypothesize that aberrant afferent input from CTS will lead to maladaptive cortical plasticity, which may be corrected by appropriate therapy. Functional MRI (fMRI) scanning and clinical testing was performed on CTS patients at baseline and after 5 weeks of acupuncture treatment. As a control, healthy adults were also tested 5 weeks apart. During fMRI, sensory stimulation was performed for median nerve innervated digit 2 (D2) and digit 3 (D3), and ulnar nerve innervated digit 5 (D5). Surface-based and region of interest (ROI)-based analyses demonstrated that while the extent of fMRI activity in contralateral Brodmann Area 1 (BA 1) and BA 4 was increased in CTS compared to healthy adults, after acupuncture there was a significant decrease in contralateral BA 1 (P < 0.005) and BA 4 (P < 0.05) activity during D3 sensory stimulation. Healthy adults demonstrated no significant test-retest differences for any digit tested. While D3/D2 separation was contracted or blurred in CTS patients compared to healthy adults, the D2 SI representation shifted laterally after acupuncture treatment, leading to increased D3/D2 separation. Increasing D3/D2 separation correlated with decreasing paresthesias in CTS patients (P < 0.05). As CTS-induced paresthesias constitute diffuse, synchronized, multidigit symptomatology, our results for maladaptive change and correction are consistent with Hebbian plasticity mechanisms. Acupuncture, a somatosensory conditioning stimulus, shows promise in inducing beneficial cortical plasticity manifested by more focused digital representations. (c) 2006 Wiley-Liss, Inc.

Comparison of a vertically-averaged and a vertically-resolved model for hyporheic flow beneath a pool-riffle bedform

NASA Astrophysics Data System (ADS)

Ibrahim, Ahmad; Steffler, Peter; She, Yuntong

2018-02-01

The interaction between surface water and groundwater through the hyporheic zone is recognized to be important as it impacts the water quantity and quality in both flow systems. Three-dimensional (3D) modeling is the most complete representation of a real-world hyporheic zone. However, 3D modeling requires extreme computational power and efforts; the sophistication is often significantly compromised by not being able to obtain the required input data accurately. Simplifications are therefore often needed. The objective of this study was to assess the accuracy of the vertically-averaged approximation compared to a more complete vertically-resolved model of the hyporheic zone. The groundwater flow was modeled by either a simple one-dimensional (1D) Dupuit approach or a two-dimensional (2D) horizontal/vertical model in boundary fitted coordinates, with the latter considered as a reference model. Both groundwater models were coupled with a 1D surface water model via the surface water depth. Applying the two models to an idealized pool-riffle sequence showed that the 1D Dupuit approximation gave comparable results in determining the characteristics of the hyporheic zone to the reference model when the stratum thickness is not very large compared to the surface water depth. Conditions under which the 1D model can provide reliable estimate of the seepage discharge, upwelling/downwelling discharges and locations, the hyporheic flow, and the residence time were determined.

The Use of Digitized Images in Developing Software for Young Children.

ERIC Educational Resources Information Center

Wright, June L.

1992-01-01

Parents and children interacted with computer-based representations of a park, one with animated picture graphics and one with digitized full motion video. Children who interacted with the digitized representation replayed the program more and showed a stronger cognitive focus on the representation than did the other children. (LB)

3D hierarchical spatial representation and memory of multimodal sensory data

NASA Astrophysics Data System (ADS)

Khosla, Deepak; Dow, Paul A.; Huber, David J.

2009-04-01

This paper describes an efficient method and system for representing, processing and understanding multi-modal sensory data. More specifically, it describes a computational method and system for how to process and remember multiple locations in multimodal sensory space (e.g., visual, auditory, somatosensory, etc.). The multimodal representation and memory is based on a biologically-inspired hierarchy of spatial representations implemented with novel analogues of real representations used in the human brain. The novelty of the work is in the computationally efficient and robust spatial representation of 3D locations in multimodal sensory space as well as an associated working memory for storage and recall of these representations at the desired level for goal-oriented action. We describe (1) A simple and efficient method for human-like hierarchical spatial representations of sensory data and how to associate, integrate and convert between these representations (head-centered coordinate system, body-centered coordinate, etc.); (2) a robust method for training and learning a mapping of points in multimodal sensory space (e.g., camera-visible object positions, location of auditory sources, etc.) to the above hierarchical spatial representations; and (3) a specification and implementation of a hierarchical spatial working memory based on the above for storage and recall at the desired level for goal-oriented action(s). This work is most useful for any machine or human-machine application that requires processing of multimodal sensory inputs, making sense of it from a spatial perspective (e.g., where is the sensory information coming from with respect to the machine and its parts) and then taking some goal-oriented action based on this spatial understanding. A multi-level spatial representation hierarchy means that heterogeneous sensory inputs (e.g., visual, auditory, somatosensory, etc.) can map onto the hierarchy at different levels. When controlling various machine/robot degrees of freedom, the desired movements and action can be computed from these different levels in the hierarchy. The most basic embodiment of this machine could be a pan-tilt camera system, an array of microphones, a machine with arm/hand like structure or/and a robot with some or all of the above capabilities. We describe the approach, system and present preliminary results on a real-robotic platform.

2D biological representations with reduced speckle obtained from two perpendicular ultrasonic arrays.

PubMed

Rodriguez-Hernandez, Miguel A; Gomez-Sacristan, Angel; Sempere-Payá, Víctor M

2016-04-29

Ultrasound diagnosis is a widely used medical tool. Among the various ultrasound techniques, ultrasonic imaging is particularly relevant. This paper presents an improvement to a two-dimensional (2D) ultrasonic system using measurements taken from perpendicular planes, where digital signal processing techniques are used to combine one-dimensional (1D) A-scans were acquired by individual transducers in arrays located in perpendicular planes. An algorithm used to combine measurements is improved based on the wavelet transform, which includes a denoising step during the 2D representation generation process. The inclusion of this new denoising stage generates higher quality 2D representations with a reduced level of speckling. The paper includes different 2D representations obtained from noisy A-scans and compares the improvements obtained by including the denoising stage.

Human and server docking prediction for CAPRI round 30-35 using LZerD with combined scoring functions.

PubMed

Peterson, Lenna X; Kim, Hyungrae; Esquivel-Rodriguez, Juan; Roy, Amitava; Han, Xusi; Shin, Woong-Hee; Zhang, Jian; Terashi, Genki; Lee, Matt; Kihara, Daisuke

2017-03-01

We report the performance of protein-protein docking predictions by our group for recent rounds of the Critical Assessment of Prediction of Interactions (CAPRI), a community-wide assessment of state-of-the-art docking methods. Our prediction procedure uses a protein-protein docking program named LZerD developed in our group. LZerD represents a protein surface with 3D Zernike descriptors (3DZD), which are based on a mathematical series expansion of a 3D function. The appropriate soft representation of protein surface with 3DZD makes the method more tolerant to conformational change of proteins upon docking, which adds an advantage for unbound docking. Docking was guided by interface residue prediction performed with BindML and cons-PPISP as well as literature information when available. The generated docking models were ranked by a combination of scoring functions, including PRESCO, which evaluates the native-likeness of residues' spatial environments in structure models. First, we discuss the overall performance of our group in the CAPRI prediction rounds and investigate the reasons for unsuccessful cases. Then, we examine the performance of several knowledge-based scoring functions and their combinations for ranking docking models. It was found that the quality of a pool of docking models generated by LZerD, that is whether or not the pool includes near-native models, can be predicted by the correlation of multiple scores. Although the current analysis used docking models generated by LZerD, findings on scoring functions are expected to be universally applicable to other docking methods. Proteins 2017; 85:513-527. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

A highly accurate boundary integral equation method for surfactant-laden drops in 3D

NASA Astrophysics Data System (ADS)

Sorgentone, Chiara; Tornberg, Anna-Karin

2018-05-01

The presence of surfactants alters the dynamics of viscous drops immersed in an ambient viscous fluid. This is specifically true at small scales, such as in applications of droplet based microfluidics, where the interface dynamics become of increased importance. At such small scales, viscous forces dominate and inertial effects are often negligible. Considering Stokes flow, a numerical method based on a boundary integral formulation is presented for simulating 3D drops covered by an insoluble surfactant. The method is able to simulate drops with different viscosities and close interactions, automatically controlling the time step size and maintaining high accuracy also when substantial drop deformation appears. To achieve this, the drop surfaces as well as the surfactant concentration on each surface are represented by spherical harmonics expansions. A novel reparameterization method is introduced to ensure a high-quality representation of the drops also under deformation, specialized quadrature methods for singular and nearly singular integrals that appear in the formulation are evoked and the adaptive time stepping scheme for the coupled drop and surfactant evolution is designed with a preconditioned implicit treatment of the surfactant diffusion.

Titan's Ionic Species: Theoretical Treatment of N2H+ and Related Ions

NASA Astrophysics Data System (ADS)

Brites, V.; Hochlaf, M.

2009-06-01

We use different ab initio methods to compute the three-dimensional potential energy surface (3D-PES) of the ground state of N2H+. This includes the standard coupled cluster, the complete active space self-consistent field, the internally contacted multi reference configuration interaction, and the newly developed CCSD(T)-F12 methods. For the description of H and N atoms, several basis sets are tested. Then, we incorporate the 3D-PES analytical representations into variational calculations of the rovibrational spectrum of N2H+(X˜1Σ+) up to 7200 cm-1 above the zero point vibrational energy. Our data show that the CCSD(T)-F12/aug-cc-pVTZ approach represents a compromise for good description of the PES and computation cost. This technique is recommended for full dimensional PES generation of atmospheric and astrophysical relevant polyatomic systems. We applied this method to derive the rovibrational spectra of N2H+(X˜1Σ+) and of N2H++(X˜2Σ+). Finally, we discuss the existence of the N2H++(X˜2Σ+) in Titan's atmosphere.

Teaching with AR as a Tool for Relief Visualization: Usability and Motivation Study

ERIC Educational Resources Information Center

Carrera, Carlos Carbonell; Perez, Jose Luis Saorin; Cantero, Jorge de la Torre

2018-01-01

In the field of geographical and environmental education, maps and geo-referenced information are frequently used, in which the earth's surfaces are represented in a two-dimensional (2D) way. Students have difficulty interpreting the relief representation and switching between 2D and 3D scenarios. Digital terrain modelling is added to the…

Generative Representations for Computer-Automated Evolutionary Design

NASA Technical Reports Server (NTRS)

Hornby, Gregory S.

2006-01-01

With the increasing computational power of computers, software design systems are progressing from being tools for architects and designers to express their ideas to tools capable of creating designs under human guidance. One of the main limitations for these computer-automated design systems is the representation with which they encode designs. If the representation cannot encode a certain design, then the design system cannot produce it. To be able to produce new types of designs, and not just optimize pre-defined parameterizations, evolutionary design systems must use generative representations. Generative representations are assembly procedures, or algorithms, for constructing a design thereby allowing for truly novel design solutions to be encoded. In addition, by enabling modularity, regularity and hierarchy, the level of sophistication that can be evolved is increased. We demonstrate the advantages of generative representations on two different design domains: the evolution of spacecraft antennas and the evolution of 3D objects.

Review of Quantum Electromagnetic States

DTIC Science & Technology

1999-10-01

product space. 227 The wave functions used in the Jaynes - Cummings ’ model reside in a direct product space Va ɠ> Vf where Va and Vf are the Hubert...Dependent Probability 215 5.1.3 The Relaxation Term 217 5.2 Jaynes - Cummings ’ Model for Matter-Field Interactions 218 5.2.1 The Atomic Hamiltonian 218...5.3 The Interaction Representation for the Jaynes - Cummings ’ Model 224 5.3.1 Atomic Creation and Annihilation Operators 224 5.3.2 The Boson Creation

Photoionization of Co+ and electron-impact excitation of Co2 + using the Dirac R-matrix method

NASA Astrophysics Data System (ADS)

Tyndall, N. B.; Ramsbottom, C. A.; Ballance, C. P.; Hibbert, A.

2016-11-01

Modelling of massive stars and supernovae (SNe) plays a crucial role in understanding galaxies. From this modelling we can derive fundamental constraints on stellar evolution, mass-loss processes, mixing, and the products of nucleosynthesis. Proper account must be taken of all important processes that populate and depopulate the levels (collisional excitation, de-excitation, ionization, recombination, photoionization, bound-bound processes). For the analysis of Type Ia SNe and core collapse SNe (Types Ib, Ic and II) Fe group elements are particularly important. Unfortunately little data is currently available and most noticeably absent are the photoionization cross-sections for the Fe-peaks which have high abundances in SNe. Important interactions for both photoionization and electron-impact excitation are calculated using the relativistic Dirac atomic R-matrix codes (DARC) for low-ionization stages of Cobalt. All results are calculated up to photon energies of 45 eV and electron energies up to 20 eV. The wavefunction representation of Co III has been generated using GRASP0 by including the dominant 3d7, 3d6[4s, 4p], 3p43d9 and 3p63d9 configurations, resulting in 292 fine structure levels. Electron-impact collision strengths and Maxwellian averaged effective collision strengths across a wide range of astrophysically relevant temperatures are computed for Co III. In addition, statistically weighted level-resolved ground and metastable photoionization cross-sections are presented for Co II and compared directly with existing work.

Homology modeling a fast tool for drug discovery: current perspectives.

PubMed

Vyas, V K; Ukawala, R D; Ghate, M; Chintha, C

2012-01-01

Major goal of structural biology involve formation of protein-ligand complexes; in which the protein molecules act energetically in the course of binding. Therefore, perceptive of protein-ligand interaction will be very important for structure based drug design. Lack of knowledge of 3D structures has hindered efforts to understand the binding specificities of ligands with protein. With increasing in modeling software and the growing number of known protein structures, homology modeling is rapidly becoming the method of choice for obtaining 3D coordinates of proteins. Homology modeling is a representation of the similarity of environmental residues at topologically corresponding positions in the reference proteins. In the absence of experimental data, model building on the basis of a known 3D structure of a homologous protein is at present the only reliable method to obtain the structural information. Knowledge of the 3D structures of proteins provides invaluable insights into the molecular basis of their functions. The recent advances in homology modeling, particularly in detecting and aligning sequences with template structures, distant homologues, modeling of loops and side chains as well as detecting errors in a model contributed to consistent prediction of protein structure, which was not possible even several years ago. This review focused on the features and a role of homology modeling in predicting protein structure and described current developments in this field with victorious applications at the different stages of the drug design and discovery.

Homology Modeling a Fast Tool for Drug Discovery: Current Perspectives

PubMed Central

Vyas, V. K.; Ukawala, R. D.; Ghate, M.; Chintha, C.

2012-01-01

Major goal of structural biology involve formation of protein-ligand complexes; in which the protein molecules act energetically in the course of binding. Therefore, perceptive of protein-ligand interaction will be very important for structure based drug design. Lack of knowledge of 3D structures has hindered efforts to understand the binding specificities of ligands with protein. With increasing in modeling software and the growing number of known protein structures, homology modeling is rapidly becoming the method of choice for obtaining 3D coordinates of proteins. Homology modeling is a representation of the similarity of environmental residues at topologically corresponding positions in the reference proteins. In the absence of experimental data, model building on the basis of a known 3D structure of a homologous protein is at present the only reliable method to obtain the structural information. Knowledge of the 3D structures of proteins provides invaluable insights into the molecular basis of their functions. The recent advances in homology modeling, particularly in detecting and aligning sequences with template structures, distant homologues, modeling of loops and side chains as well as detecting errors in a model contributed to consistent prediction of protein structure, which was not possible even several years ago. This review focused on the features and a role of homology modeling in predicting protein structure and described current developments in this field with victorious applications at the different stages of the drug design and discovery. PMID:23204616

Non-Abelian string and particle braiding in topological order: Modular SL (3 ,Z ) representation and (3 +1 ) -dimensional twisted gauge theory

NASA Astrophysics Data System (ADS)

Wang, Juven C.; Wen, Xiao-Gang

2015-01-01

String and particle braiding statistics are examined in a class of topological orders described by discrete gauge theories with a gauge group G and a 4-cocycle twist ω4 of G 's cohomology group H4(G ,R /Z ) in three-dimensional space and one-dimensional time (3 +1 D ) . We establish the topological spin and the spin-statistics relation for the closed strings and their multistring braiding statistics. The 3 +1 D twisted gauge theory can be characterized by a representation of a modular transformation group, SL (3 ,Z ) . We express the SL (3 ,Z ) generators Sx y z and Tx y in terms of the gauge group G and the 4-cocycle ω4. As we compactify one of the spatial directions z into a compact circle with a gauge flux b inserted, we can use the generators Sx y and Tx y of an SL (2 ,Z ) subgroup to study the dimensional reduction of the 3D topological order C3 D to a direct sum of degenerate states of 2D topological orders Cb2 D in different flux b sectors: C3 D=⊕bCb2 D . The 2D topological orders Cb2 D are described by 2D gauge theories of the group G twisted by the 3-cocycle ω3 (b ), dimensionally reduced from the 4-cocycle ω4. We show that the SL (2 ,Z ) generators, Sx y and Tx y, fully encode a particular type of three-string braiding statistics with a pattern that is the connected sum of two Hopf links. With certain 4-cocycle twists, we discover that, by threading a third string through two-string unlink into a three-string Hopf-link configuration, Abelian two-string braiding statistics is promoted to non-Abelian three-string braiding statistics.

Constructing Molecular Models with Low-Cost Toy Beads

ERIC Educational Resources Information Center

Ng, Pun-hon; Wong, Siu-ling; Mak, Se-yuen

2012-01-01

In teaching the science of the nano world, ball-and-stick molecular models are frequently used as 3D representations of molecules. Unlike a chemical formula, a molecular model allows us to visualise the 3D shape of the molecule and the relative positions of its atoms, the bonds between atoms and why a pair of mirror isomers with the same atoms,…

Recognition Of Complex Three Dimensional Objects Using Three Dimensional Moment Invariants

NASA Astrophysics Data System (ADS)

Sadjadi, Firooz A.

1985-01-01

A technique for the recognition of complex three dimensional objects is presented. The complex 3-D objects are represented in terms of their 3-D moment invariants, algebraic expressions that remain invariant independent of the 3-D objects' orientations and locations in the field of view. The technique of 3-D moment invariants has been used successfully for simple 3-D object recognition in the past. In this work we have extended this method for the representation of more complex objects. Two complex objects are represented digitally; their 3-D moment invariants have been calculated, and then the invariancy of these 3-D invariant moment expressions is verified by changing the orientation and the location of the objects in the field of view. The results of this study have significant impact on 3-D robotic vision, 3-D target recognition, scene analysis and artificial intelligence.

Covariant spinor representation of iosp(d,2/2) and quantization of the spinning relativistic particle

NASA Astrophysics Data System (ADS)

Jarvis, P. D.; Corney, S. P.; Tsohantjis, I.

1999-12-01

A covariant spinor representation of iosp(d,2/2) is constructed for the quantization of the spinning relativistic particle. It is found that, with appropriately defined wavefunctions, this representation can be identified with the state space arising from the canonical extended BFV-BRST quantization of the spinning particle with admissible gauge fixing conditions after a contraction procedure. For this model, the cohomological determination of physical states can thus be obtained purely from the representation theory of the iosp(d,2/2) algebra.

The hologram as a space of illusion

NASA Astrophysics Data System (ADS)

Oliveira, Rosa M.

2013-03-01

One of the most interesting aspects of art holography is the study of 3D holographic image. Over the centuries, artists have chased the best way to represent the third dimension as similar to reality as possible. Several steps have been given in this direction, first using perspective, then photography, and later with movies, but all of these representations of reality wouldn't reach the complete objective. The realism of a 3D representation on a 2D support (paper, canvas, celluloid) is completely overcome by holography. In spite of the fact that the holographic plate or film is also a 2D support, the holographic image is a recording of all the information of the object contained in light. Our perception doesn't need to translate the object as real. It is real. Though immaterial, the holographic image is real because it exists in light. The same parallax, the same shape. The representation is no more an imitation of reality but a replacement of the real object or scene. The space where it exists is a space of illusion and multiple objects can occupy the same place in the hologram, depending on the viewer's time and place. This introduces the fourth dimension in the hologram: time, as well as the apparent conflict between the presence and the absence of images, which is just possible in holography.

Geometry of the generalized Bloch sphere for qutrits

NASA Astrophysics Data System (ADS)

Goyal, Sandeep K.; Neethi Simon, B.; Singh, Rajeev; Simon, Sudhavathani

2016-04-01

The geometry of the generalized Bloch sphere Ω3, the state space of a qutrit, is studied. Closed form expressions for Ω3, its boundary ∂Ω3, and the set of extremals {{{Ω }}}3{{ext}} are obtained by use of an elementary observation. These expressions and analytic methods are used to classify the 28 two-sections and the 56 three-sections of Ω3 into unitary equivalence classes, completing the works of earlier authors. It is shown, in particular, that there are families of two-sections and of three-sections which are equivalent geometrically but not unitarily, a feature that does not appear to have been appreciated earlier. A family of three-sections of obese-tetrahedral shape whose symmetry corresponds to the 24-element tetrahedral point group T d is examined in detail. This symmetry is traced to the natural reduction of the adjoint representation of SU(3), the symmetry underlying Ω3, into direct sum of the two-dimensional and the two (inequivalent) three-dimensional irreducible representations of T d .

Protein-protein docking using region-based 3D Zernike descriptors

PubMed Central

2009-01-01

Background Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understanding the interaction mechanism. However, experimental techniques to solve the structure of the complex are often found to be difficult. To this end, computational protein-protein docking approaches can provide a useful alternative to address this issue. Prediction of docking conformations relies on methods that effectively capture shape features of the participating proteins while giving due consideration to conformational changes that may occur. Results We present a novel protein docking algorithm based on the use of 3D Zernike descriptors as regional features of molecular shape. The key motivation of using these descriptors is their invariance to transformation, in addition to a compact representation of local surface shape characteristics. Docking decoys are generated using geometric hashing, which are then ranked by a scoring function that incorporates a buried surface area and a novel geometric complementarity term based on normals associated with the 3D Zernike shape description. Our docking algorithm was tested on both bound and unbound cases in the ZDOCK benchmark 2.0 dataset. In 74% of the bound docking predictions, our method was able to find a near-native solution (interface C-αRMSD ≤ 2.5 Å) within the top 1000 ranks. For unbound docking, among the 60 complexes for which our algorithm returned at least one hit, 60% of the cases were ranked within the top 2000. Comparison with existing shape-based docking algorithms shows that our method has a better performance than the others in unbound docking while remaining competitive for bound docking cases. Conclusion We show for the first time that the 3D Zernike descriptors are adept in capturing shape complementarity at the protein-protein interface and useful for protein docking prediction. Rigorous benchmark studies show that our docking approach has a superior performance compared to existing methods. PMID:20003235

Protein-protein docking using region-based 3D Zernike descriptors.

PubMed

Venkatraman, Vishwesh; Yang, Yifeng D; Sael, Lee; Kihara, Daisuke

2009-12-09

Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understanding the interaction mechanism. However, experimental techniques to solve the structure of the complex are often found to be difficult. To this end, computational protein-protein docking approaches can provide a useful alternative to address this issue. Prediction of docking conformations relies on methods that effectively capture shape features of the participating proteins while giving due consideration to conformational changes that may occur. We present a novel protein docking algorithm based on the use of 3D Zernike descriptors as regional features of molecular shape. The key motivation of using these descriptors is their invariance to transformation, in addition to a compact representation of local surface shape characteristics. Docking decoys are generated using geometric hashing, which are then ranked by a scoring function that incorporates a buried surface area and a novel geometric complementarity term based on normals associated with the 3D Zernike shape description. Our docking algorithm was tested on both bound and unbound cases in the ZDOCK benchmark 2.0 dataset. In 74% of the bound docking predictions, our method was able to find a near-native solution (interface C-alphaRMSD < or = 2.5 A) within the top 1000 ranks. For unbound docking, among the 60 complexes for which our algorithm returned at least one hit, 60% of the cases were ranked within the top 2000. Comparison with existing shape-based docking algorithms shows that our method has a better performance than the others in unbound docking while remaining competitive for bound docking cases. We show for the first time that the 3D Zernike descriptors are adept in capturing shape complementarity at the protein-protein interface and useful for protein docking prediction. Rigorous benchmark studies show that our docking approach has a superior performance compared to existing methods.

An activity canyon characterization of the pharmacological topography.

PubMed

Kulkarni, Varsha S; Wild, David J

2016-01-01

Highly chemically similar drugs usually possess similar biological activities, but sometimes, small changes in chemistry can result in a large difference in biological effects. Chemically similar drug pairs that show extreme deviations in activity represent distinctive drug interactions having important implications. These associations between chemical and biological similarity are studied as discontinuities in activity landscapes. Particularly, activity cliffs are quantified by the drop in similar activity of chemically similar drugs. In this paper, we construct a landscape using a large drug-target network and consider the rises in similarity and variation in activity along the chemical space. Detailed analysis of structure and activity gives a rigorous quantification of distinctive pairs and the probability of their occurrence. We analyze pairwise similarity (s) and variation (d) in activity of drugs on proteins. Interactions between drugs are quantified by considering pairwise s and d weights jointly with corresponding chemical similarity (c) weights. Similarity and variation in activity are measured as the number of common and uncommon targets of two drugs respectively. Distinctive interactions occur between drugs having high c and above (below) average d (s). Computation of predicted probability of distinctiveness employs joint probability of c, s and of c, d assuming independence of structure and activity. Predictions conform with the observations at different levels of distinctiveness. Results are validated on the data used and another drug ensemble. In the landscape, while s and d decrease as c increases, d maintains value more than s. c ∈ [0.3, 0.64] is the transitional region where rises in d are significantly greater than drops in s. It is fascinating that distinctive interactions filtered with high d and low s are different in nature. It is crucial that high c interactions are more probable of having above average d than s. Identification of distinctive interactions is better with high d than low s. These interactions belong to diverse classes. d is greatest between drugs and analogs prepared for treatment of same class of ailments but with different therapeutic specifications. In contrast, analogs having low s would treat ailments from distinct classes. Intermittent spikes in d along the axis of c represent canyons in the activity landscape. This new representation accounts for distinctiveness through relative rises in s and d. It provides a mathematical basis for predicting the probability of occurrence of distinctiveness. It identifies the drug pairs at varying levels of distinctiveness and non-distinctiveness. The predicted probability formula is validated even if data approximately satisfy the conditions of its construction. Also, the postulated independence of structure and activity is of little significance to the overall assessment. The difference in distinctive interactions obtained by s and d highlights the importance of studying both of them, and reveals how the choice of measurement can affect the interpretation. The methods in this paper can be used to interpret whether or not drug interactions are distinctive and the probability of their occurrence. Practitioners and researchers can rely on this identification for quantitative modeling and assessment.

On the partition dimension of comb product of path and complete graph

NASA Astrophysics Data System (ADS)

Darmaji, Alfarisi, Ridho

2017-08-01

For a vertex v of a connected graph G(V, E) with vertex set V(G), edge set E(G) and S ⊆ V(G). Given an ordered partition Π = {S1, S2, S3, …, Sk} of the vertex set V of G, the representation of a vertex v ∈ V with respect to Π is the vector r(v|Π) = (d(v, S1), d(v, S2), …, d(v, Sk)), where d(v, Sk) represents the distance between the vertex v and the set Sk and d(v, Sk) = min{d(v, x)|x ∈ Sk}. A partition Π of V(G) is a resolving partition if different vertices of G have distinct representations, i.e., for every pair of vertices u, v ∈ V(G), r(u|Π) ≠ r(v|Π). The minimum k of Π resolving partition is a partition dimension of G, denoted by pd(G). Finding the partition dimension of G is classified to be a NP-Hard problem. In this paper, we will show that the partition dimension of comb product of path and complete graph. The results show that comb product of complete grapph Km and path Pn namely p d (Km⊳Pn)=m where m ≥ 3 and n ≥ 2 and p d (Pn⊳Km)=m where m ≥ 3, n ≥ 2 and m ≥ n.

Multi-Source 3d Models Supporting Ultrasonic Test to Investigate AN Egyptian Sculpture of the Archaeological Museum in Bologna

NASA Astrophysics Data System (ADS)

Di Pietra, V.; Donadio, E.; Picchi, D.; Sambuelli, L.; Spanò, A.

2017-02-01

The paper presents the workflow and the results of an ultrasonic 3D investigation and a 3D survey application aimed at the assessment of the internal integrity of an ancient sculpture. The work aimed at highlighting the ability of methods devoted to the 3D geometry acquisition of small objects when applied to diagnosis performed by geophysical investigation. In particular, two methods widely applied for small objects modelling are considered and compared, the digital Photogrammetry with the Structure from Motion (SFM) technique and hand-held 3D scanners. The study concludes with the aim to enhance the final graphical representation of the tomographic results and to subject the obtained results to a quantitative analysis. The survey is applied to the Egyptian naophorous statue of Amenmes and Reshpu, which dates to the reign of Ramses II (1279-1213 BC) or later and is now preserved in the Civic Archaeological Museum in Bologna. In order to evaluate the internal persistency of fractures and visible damages, a 3D Ultrasonic Tomographic Imaging (UTI) test has been performed and a multi-sensor survey (image and range based) was conducted, in order to evaluate the locations of the source and receiver points as accurate as possible The presented test allowed to evaluate the material characteristics, its porosity and degradation state, which particularly affect the lower part of the statue. More in general, the project demonstrated how solution coming from the field of 3D modelling of Cultural Heritage allow the application of 3D ultrasonic tomography also on objects with complex shapes, in addition to the improved representation of the obtained results.

Large-scale 3D inversion of marine controlled source electromagnetic data using the integral equation method

NASA Astrophysics Data System (ADS)

Zhdanov, M. S.; Cuma, M.; Black, N.; Wilson, G. A.

2009-12-01

The marine controlled source electromagnetic (MCSEM) method has become widely used in offshore oil and gas exploration. Interpretation of MCSEM data is still a very challenging problem, especially if one would like to take into account the realistic 3D structure of the subsurface. The inversion of MCSEM data is complicated by the fact that the EM response of a hydrocarbon-bearing reservoir is very weak in comparison with the background EM fields generated by an electric dipole transmitter in complex geoelectrical structures formed by a conductive sea-water layer and the terranes beneath it. In this paper, we present a review of the recent developments in the area of large-scale 3D EM forward modeling and inversion. Our approach is based on using a new integral form of Maxwell’s equations allowing for an inhomogeneous background conductivity, which results in a numerically effective integral representation for 3D EM field. This representation provides an efficient tool for the solution of 3D EM inverse problems. To obtain a robust inverse model of the conductivity distribution, we apply regularization based on a focusing stabilizing functional which allows for the recovery of models with both smooth and sharp geoelectrical boundaries. The method is implemented in a fully parallel computer code, which makes it possible to run large-scale 3D inversions on grids with millions of inversion cells. This new technique can be effectively used for active EM detection and monitoring of the subsurface targets.

Interaction and Representational Integration: Evidence from Speech Errors

ERIC Educational Resources Information Center

Goldrick, Matthew; Baker, H. Ross; Murphy, Amanda; Baese-Berk, Melissa

2011-01-01

We examine the mechanisms that support interaction between lexical, phonological and phonetic processes during language production. Studies of the phonetics of speech errors have provided evidence that partially activated lexical and phonological representations influence phonetic processing. We examine how these interactive effects are modulated…

A novel representation for planning 3-D collision-free paths

NASA Technical Reports Server (NTRS)

Bonner, Susan; Kelley, Robert B.

1990-01-01

A new scheme for the representation of objects, the successive spherical approximation (SSA), facilitates the rapid planning of collision-free paths in a dynamic three-dimensional environment. The hierarchical nature of the SSA allows collisions to be determined efficiently while still providing an exact representation of objects. The rapidity with which collisions can be detected, less than 1 sec per environment object per path, makes it possible to use a generate-and-test path-planning strategy driven by human conceptual knowledge to determine collision-free paths in a matter of seconds on a Sun 3/180 computer. A hierarchy of rules, based on the concept of a free space cell, is used to find heuristically satisfying collision-free paths in a structured environment.

Simulation of the Indian Summer Monsoon Using Comprehensive Atmosphere-land Interactions, in the Absence of Two-way Air-sea Interactions

NASA Technical Reports Server (NTRS)

Lim, Young-Kwon; Shin, D. W.; Cocke, Steven; Kang, Sung-Dae; Kim, Hae-Dong

2011-01-01

Community Land Model version 2 (CLM2) as a comprehensive land surface model and a simple land surface model (SLM) were coupled to an atmospheric climate model to investigate the role of land surface processes in the development and the persistence of the South Asian summer monsoon. Two-way air-sea interactions were not considered in order to identify the reproducibility of the monsoon evolution by the comprehensive land model, which includes more realistic vertical soil moisture structures, vegetation and 2-way atmosphere-land interactions at hourly intervals. In the monsoon development phase (May and June). comprehensive land-surface treatment improves the representation of atmospheric circulations and the resulting convergence/divergence through the improvements in differential heating patterns and surface energy fluxes. Coupling with CLM2 also improves the timing and spatial distribution of rainfall maxima, reducing the seasonal rainfall overestimation by approx.60 % (1.8 mm/d for SLM, 0.7 mm/dI for CLM2). As for the interannual variation of the simulated rainfall, correlation coefficients of the Indian seasonal rainfall with observation increased from 0.21 (SLM) to 0.45 (CLM2). However, in the mature monsoon phase (July to September), coupling with the CLM2 does not exhibit a clear improvement. In contrast to the development phase, latent heat flux is underestimated and sensible heat flux and surface temperature over India are markedly overestimated. In addition, the moisture fluxes do not correlate well with lower-level atmospheric convergence, yielding correlation coefficients and root mean square errors worse than those produced by coupling with the SLM. A more realistic representation of the surface temperature and energy fluxes is needed to achieve an improved simulation for the mature monsoon period.

Video-Game-Like Engine for Depicting Spacecraft Trajectories

NASA Technical Reports Server (NTRS)

Upchurch, Paul R.

2009-01-01

GoView is a video-game-like software engine, written in the C and C++ computing languages, that enables real-time, three-dimensional (3D)-appearing visual representation of spacecraft and trajectories (1) from any perspective; (2) at any spatial scale from spacecraft to Solar-system dimensions; (3) in user-selectable time scales; (4) in the past, present, and/or future; (5) with varying speeds; and (6) forward or backward in time. GoView constructs an interactive 3D world by use of spacecraft-mission data from pre-existing engineering software tools. GoView can also be used to produce distributable application programs for depicting NASA orbital missions on personal computers running the Windows XP, Mac OsX, and Linux operating systems. GoView enables seamless rendering of Cartesian coordinate spaces with programmable graphics hardware, whereas prior programs for depicting spacecraft trajectories variously require non-Cartesian coordinates and/or are not compatible with programmable hardware. GoView incorporates an algorithm for nonlinear interpolation between arbitrary reference frames, whereas the prior programs are restricted to special classes of inertial and non-inertial reference frames. Finally, whereas the prior programs present complex user interfaces requiring hours of training, the GoView interface provides guidance, enabling use without any training.

Decision Support Tool for Deep Energy Efficiency Retrofits in DoD Installations

DTIC Science & Technology

2014-01-01

representations (HDMR). Chemical Engineering Science, 57, 4445–4460. 2. Sobol ’, I., 2001. Global sensitivity indices for nonlinear mathematical...models and their Monte Carlo estimates. Mathematics and computers in simulation, 55, 271–280. 3. Sobol , I. and Kucherenko, S., 2009. Derivative based...representations (HDMR). Chemical Engineering Science, 57, 4445–4460. 16. Sobol ’, I., 2001. Global sensitivity indices for nonlinear mathematical models and

Experimental phase-space-based optical amplification of scar modes.

PubMed

Michel, C; Tascu, S; Doya, V; Aschiéri, P; Blanc, W; Legrand, O; Mortessagne, F

2012-04-01

Wave billiards which are chaotic in the geometrical limit are known to support nongeneric spatially localized modes called scar modes. The interaction of the scar modes with gain has been recently investigated in optics in microcavity lasers and vertical-cavity surface-emitting lasers. Exploiting the localization properties of scar modes in their wave-analogous phase-space representation, we report experimental results of scar mode selection by gain in a doped D-shaped optical fiber.

Dynamic neural architecture for social knowledge retrieval

PubMed Central

Wang, Yin; Collins, Jessica A.; Koski, Jessica; Nugiel, Tehila; Metoki, Athanasia; Olson, Ingrid R.

2017-01-01

Social behavior is often shaped by the rich storehouse of biographical information that we hold for other people. In our daily life, we rapidly and flexibly retrieve a host of biographical details about individuals in our social network, which often guide our decisions as we navigate complex social interactions. Even abstract traits associated with an individual, such as their political affiliation, can cue a rich cascade of person-specific knowledge. Here, we asked whether the anterior temporal lobe (ATL) serves as a hub for a distributed neural circuit that represents person knowledge. Fifty participants across two studies learned biographical information about fictitious people in a 2-d training paradigm. On day 3, they retrieved this biographical information while undergoing an fMRI scan. A series of multivariate and connectivity analyses suggest that the ATL stores abstract person identity representations. Moreover, this region coordinates interactions with a distributed network to support the flexible retrieval of person attributes. Together, our results suggest that the ATL is a central hub for representing and retrieving person knowledge. PMID:28289200

vmdICE: a plug-in for rapid evaluation of molecular dynamics simulations using VMD.

PubMed

Knapp, Bernhard; Lederer, Nadja; Omasits, Ulrich; Schreiner, Wolfgang

2010-12-01

Molecular dynamics (MD) is a powerful in silico method to investigate the interactions between biomolecules. It solves Newton's equations of motion for atoms over a specified period of time and yields a trajectory file, containing the different spatial arrangements of atoms during the simulation. The movements and energies of each single atom are recorded. For evaluating of these simulation trajectories with regard to biomedical implications, several methods are available. Three well-known ones are the root mean square deviation (RMSD), the root mean square fluctuation (RMSF) and solvent accessible surface area (SASA). Herein, we present a novel plug-in for the software "visual molecular dynamics" (VMD) that allows an interactive 3D representation of RMSD, RMSF, and SASA, directly on the molecule. On the one hand, our plug-in is easy to handle for inexperienced users, and on the other hand, it provides a fast and flexible graphical impression of the spatial dynamics of a system for experts in the field. © 2010 Wiley Periodicals, Inc.

Agent-based model of diffusion of N-acyl homoserine lactones in a multicellular environment of Pseudomonas aeruginosa and Candida albicans.

PubMed

Pérez-Rodríguez, Gael; Dias, Sónia; Pérez-Pérez, Martín; Fdez-Riverola, Florentino; Azevedo, Nuno F; Lourenço, Anália

2018-03-08

Experimental incapacity to track microbe-microbe interactions in structures like biofilms, and the complexity inherent to the mathematical modelling of those interactions, raises the need for feasible, alternative modelling approaches. This work proposes an agent-based representation of the diffusion of N-acyl homoserine lactones (AHL) in a multicellular environment formed by Pseudomonas aeruginosa and Candida albicans. Depending on the spatial location, C. albicans cells were variably exposed to AHLs, an observation that might help explain why phenotypic switching of individual cells in biofilms occurred at different time points. The simulation and algebraic results were similar for simpler scenarios, although some statistical differences could be observed (p < 0.05). The model was also successfully applied to a more complex scenario representing a small multicellular environment containing C. albicans and P. aeruginosa cells encased in a 3-D matrix. Further development of this model may help create a predictive tool to depict biofilm heterogeneity at the single-cell level.

Dynamic neural architecture for social knowledge retrieval.

PubMed

Wang, Yin; Collins, Jessica A; Koski, Jessica; Nugiel, Tehila; Metoki, Athanasia; Olson, Ingrid R

2017-04-18

Social behavior is often shaped by the rich storehouse of biographical information that we hold for other people. In our daily life, we rapidly and flexibly retrieve a host of biographical details about individuals in our social network, which often guide our decisions as we navigate complex social interactions. Even abstract traits associated with an individual, such as their political affiliation, can cue a rich cascade of person-specific knowledge. Here, we asked whether the anterior temporal lobe (ATL) serves as a hub for a distributed neural circuit that represents person knowledge. Fifty participants across two studies learned biographical information about fictitious people in a 2-d training paradigm. On day 3, they retrieved this biographical information while undergoing an fMRI scan. A series of multivariate and connectivity analyses suggest that the ATL stores abstract person identity representations. Moreover, this region coordinates interactions with a distributed network to support the flexible retrieval of person attributes. Together, our results suggest that the ATL is a central hub for representing and retrieving person knowledge.

Multi-purpose presentation techniques for geoscientific data in various media

NASA Astrophysics Data System (ADS)

Rink, Karsten; Bilke, Lars

2014-05-01

The intuitive presentation of the progression of complex geoscientific phenomena is often an underrated part of the modelling- and simulation workflow. Compiling such a presentation allows to easily communicate progress in joint research projects between participants with different backgrounds. Also, adequate 3D visualisations are usually easier to understand when presenting research results to stakeholders as well as the general public and critical information is conveyed in a more comprehensible manner. We established a workflow that is based on integration and preprocessing of multiple geoscientific data sets in a suitable framework such as the OpenGeoSys Data Explorer or ParaView. After choosing an adequate visual representation of the data in these frameworks, custom-made interfaces are employed to export the data to presentation frameworks. For instance, using the Unity 3D Engine allows to implement interaction techniques such as adding camera paths, concentrating on specific subsets of the data or scene, blending multiple data sets, etc. While a general sequence of the presentation can be predefined, interactive navigation is still possible and allows to focus on particular interests of the audience. Established interfaces and frameworks allow to display existing presentations in multiple ways, including virtual reality environments, novel hardware such as head-mounted displays like the Occulus Rift, or even websites presenting 3D content. Furthermore, the content can be redistributed as an executable for use on arbitrary machines. This versatility enables the use of prepared presentations for a multitude of occasions including exchange of intermediary result to partners in cooperate projects, reports at conferences, the defense of research projects, or use in training courses or for tutorials.

Ray Casting of Large Multi-Resolution Volume Datasets

NASA Astrophysics Data System (ADS)

Lux, C.; Fröhlich, B.

2009-04-01

High quality volume visualization through ray casting on graphics processing units (GPU) has become an important approach for many application domains. We present a GPU-based, multi-resolution ray casting technique for the interactive visualization of massive volume data sets commonly found in the oil and gas industry. Large volume data sets are represented as a multi-resolution hierarchy based on an octree data structure. The original volume data is decomposed into small bricks of a fixed size acting as the leaf nodes of the octree. These nodes are the highest resolution of the volume. Coarser resolutions are represented through inner nodes of the hierarchy which are generated by down sampling eight neighboring nodes on a finer level. Due to limited memory resources of current desktop workstations and graphics hardware only a limited working set of bricks can be locally maintained for a frame to be displayed. This working set is chosen to represent the whole volume at different local resolution levels depending on the current viewer position, transfer function and distinct areas of interest. During runtime the working set of bricks is maintained in CPU- and GPU memory and is adaptively updated by asynchronously fetching data from external sources like hard drives or a network. The CPU memory hereby acts as a secondary level cache for these sources from which the GPU representation is updated. Our volume ray casting algorithm is based on a 3D texture-atlas in GPU memory. This texture-atlas contains the complete working set of bricks of the current multi-resolution representation of the volume. This enables the volume ray casting algorithm to access the whole working set of bricks through only a single 3D texture. For traversing rays through the volume, information about the locations and resolution levels of visited bricks are required for correct compositing computations. We encode this information into a small 3D index texture which represents the current octree subdivision on its finest level and spatially organizes the bricked data. This approach allows us to render a bricked multi-resolution volume data set utilizing only a single rendering pass with no loss of compositing precision. In contrast most state-of-the art volume rendering systems handle the bricked data as individual 3D textures, which are rendered one at a time while the results are composited into a lower precision frame buffer. Furthermore, our method enables us to integrate advanced volume rendering techniques like empty-space skipping, adaptive sampling and preintegrated transfer functions in a very straightforward manner with virtually no extra costs. Our interactive volume ray tracing implementation allows high quality visualizations of massive volume data sets of tens of Gigabytes in size on standard desktop workstations.

The solvent at antigen-binding site regulated C3d-CR2 interactions through the C-terminal tail of C3d at different ion strengths: insights from molecular dynamics simulation.

PubMed

Zhang, Yan; Guo, Jingjing; Li, Lanlan; Liu, Xuewei; Yao, Xiaojun; Liu, Huanxiang

2016-10-01

The interactions of complement receptor 2 (CR2) and the degradation fragment C3d of complement component C3 play important links between the innate and adaptive immune systems. Due to the importance of C3d-CR2 interaction in the design of vaccines and inhibitors, a number of studies have been performed to investigate C3d-CR2 interaction. Many studies have indicated C3d-CR2 interactions are ionic strength-dependent. To investigate the molecular mechanism of C3d-CR2 interaction and the origin of effects of ionic strength, molecular dynamics simulations for C3d-CR2 complex together with the energetic and structural analysis were performed. Our results revealed the increased interactions between charged protein and ions weaken C3d-CR2 association, as ionic strengths increase. Moreover, ion strengths have similar effects on antigen-binding site and CR2 binding site. Meanwhile, Ala17 and Gln20 will transform between the activated and non-activated states mediated by His133 and Glu135 at different ion strengths. Our results reveal the origins of the effects of ionic strengths on C3d-CR2 interactions are due to the changes of water, ion occupancies and distributions. This study uncovers the origin of the effect of ionic strength on C3d-CR2 interaction and deepens the understanding of the molecular mechanism of their interaction, which is valuable for the design of vaccines and small molecule inhibitors. Copyright © 2016 Elsevier B.V. All rights reserved.

Automated objective characterization of visual field defects in 3D

NASA Technical Reports Server (NTRS)

Fink, Wolfgang (Inventor)

2006-01-01

A method and apparatus for electronically performing a visual field test for a patient. A visual field test pattern is displayed to the patient on an electronic display device and the patient's responses to the visual field test pattern are recorded. A visual field representation is generated from the patient's responses. The visual field representation is then used as an input into a variety of automated diagnostic processes. In one process, the visual field representation is used to generate a statistical description of the rapidity of change of a patient's visual field at the boundary of a visual field defect. In another process, the area of a visual field defect is calculated using the visual field representation. In another process, the visual field representation is used to generate a statistical description of the volume of a patient's visual field defect.

MOTHERS' AND FATHERS' PRENATAL REPRESENTATIONS IN RELATION TO MARITAL DISTRESS AND DEPRESSIVE SYMPTOMS.

PubMed

Ahlqvist-Björkroth, Sari; Korja, Riikka; Junttila, Niina; Savonlahti, Elina; Pajulo, Marjukka; Räihä, Hannele; Aromaa, Minna

2016-07-01

Marital distress, parental depression, and weak quality of parental representations are all known risk factors for parent-child relationships. However, the relation between marital distress, depressive symptoms, and parents' prenatal representation is uncertain, especially regarding fathers. The present study aimed to explore how mothers' and fathers' prenatal experience of marital distress and depressive symptoms affects the organization of their prenatal representations in late pregnancy. Participants were 153 pregnant couples from a Finnish follow-up study called "Steps to the Healthy Development and Well-being of Children" (H. Lagström et al., ). Marital distress (Revised Dyadic Adjustment Scale; D.M. Busby, C. Christensen, D. Crane, & J. Larson, 1995) and depressive symptoms (Edinburgh Postnatal Depression Scale) were assessed at 20 gestational weeks, and prenatal representations (Working Model of the Child Interview; D. Benoit, K.C.H. Parker, & C.H. Zeanah, 1997; C.H. Zeanah, D. Benoit, M. Barton, & L. Hirshberg, 1996) were assessed between 29 and 32 gestational weeks. The mothers' risks of distorted representations increased significantly when they had at least minor depressive symptoms. Marital distress was associated with the fathers' prenatal representations, although the association was weak; fathers within the marital distress group had less balanced representations. Coexisting marital distress and depressive symptoms were only associated with the mothers' representations; lack of marital distress and depressive symptoms increased the likelihood for mothers to have balanced representations. The results imply that marital distress and depressive symptoms are differently related to the organizations of mothers' and fathers' prenatal representations. © 2016 Michigan Association for Infant Mental Health.

Data-Driven Neural Network Model for Robust Reconstruction of Automobile Casting

NASA Astrophysics Data System (ADS)

Lin, Jinhua; Wang, Yanjie; Li, Xin; Wang, Lu

2017-09-01

In computer vision system, it is a challenging task to robustly reconstruct complex 3D geometries of automobile castings. However, 3D scanning data is usually interfered by noises, the scanning resolution is low, these effects normally lead to incomplete matching and drift phenomenon. In order to solve these problems, a data-driven local geometric learning model is proposed to achieve robust reconstruction of automobile casting. In order to relieve the interference of sensor noise and to be compatible with incomplete scanning data, a 3D convolution neural network is established to match the local geometric features of automobile casting. The proposed neural network combines the geometric feature representation with the correlation metric function to robustly match the local correspondence. We use the truncated distance field(TDF) around the key point to represent the 3D surface of casting geometry, so that the model can be directly embedded into the 3D space to learn the geometric feature representation; Finally, the training labels is automatically generated for depth learning based on the existing RGB-D reconstruction algorithm, which accesses to the same global key matching descriptor. The experimental results show that the matching accuracy of our network is 92.2% for automobile castings, the closed loop rate is about 74.0% when the matching tolerance threshold τ is 0.2. The matching descriptors performed well and retained 81.6% matching accuracy at 95% closed loop. For the sparse geometric castings with initial matching failure, the 3D matching object can be reconstructed robustly by training the key descriptors. Our method performs 3D reconstruction robustly for complex automobile castings.

Analysis of structural correlations in a model binary 3D liquid through the eigenvalues and eigenvectors of the atomic stress tensors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Levashov, V. A.

2016-03-07

It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids’ structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of the stress tensors or the representation based on spherical harmonics. In this paper we address structural correlations in a 3D model binary liquid using the eigenvalues and eigenvectorsmore » of the atomic stress tensors. This approach allows to interpret correlations relevant to the Green-Kubo expression for viscosity in a simple geometric way. On decrease of temperature the changes in the relevant stress correlation function between different atoms are significantly more pronounced than the changes in the pair density function. We demonstrate that this behaviour originates from the orientational correlations between the eigenvectors of the atomic stress tensors. We also found correlations between the eigenvalues of the same atomic stress tensor. For the studied system, with purely repulsive interactions between the particles, the eigenvalues of every atomic stress tensor are positive and they can be ordered: λ{sub 1} ≥ λ{sub 2} ≥ λ{sub 3} ≥ 0. We found that, for the particles of a given type, the probability distributions of the ratios (λ{sub 2}/λ{sub 1}) and (λ{sub 3}/λ{sub 2}) are essentially identical to each other in the liquids state. We also found that λ{sub 2} tends to be equal to the geometric average of λ{sub 1} and λ{sub 3}. In our view, correlations between the eigenvalues may represent “the Poisson ratio effect” at the atomic scale.« less

Analysis of structural correlations in a model binary 3D liquid through the eigenvalues and eigenvectors of the atomic stress tensors.

PubMed

Levashov, V A

2016-03-07

It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids' structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of the stress tensors or the representation based on spherical harmonics. In this paper we address structural correlations in a 3D model binary liquid using the eigenvalues and eigenvectors of the atomic stress tensors. This approach allows to interpret correlations relevant to the Green-Kubo expression for viscosity in a simple geometric way. On decrease of temperature the changes in the relevant stress correlation function between different atoms are significantly more pronounced than the changes in the pair density function. We demonstrate that this behaviour originates from the orientational correlations between the eigenvectors of the atomic stress tensors. We also found correlations between the eigenvalues of the same atomic stress tensor. For the studied system, with purely repulsive interactions between the particles, the eigenvalues of every atomic stress tensor are positive and they can be ordered: λ1 ≥ λ2 ≥ λ3 ≥ 0. We found that, for the particles of a given type, the probability distributions of the ratios (λ2/λ1) and (λ3/λ2) are essentially identical to each other in the liquids state. We also found that λ2 tends to be equal to the geometric average of λ1 and λ3. In our view, correlations between the eigenvalues may represent "the Poisson ratio effect" at the atomic scale.

Deep linear autoencoder and patch clustering-based unified one-dimensional coding of image and video

NASA Astrophysics Data System (ADS)

Li, Honggui

2017-09-01

This paper proposes a unified one-dimensional (1-D) coding framework of image and video, which depends on deep learning neural network and image patch clustering. First, an improved K-means clustering algorithm for image patches is employed to obtain the compact inputs of deep artificial neural network. Second, for the purpose of best reconstructing original image patches, deep linear autoencoder (DLA), a linear version of the classical deep nonlinear autoencoder, is introduced to achieve the 1-D representation of image blocks. Under the circumstances of 1-D representation, DLA is capable of attaining zero reconstruction error, which is impossible for the classical nonlinear dimensionality reduction methods. Third, a unified 1-D coding infrastructure for image, intraframe, interframe, multiview video, three-dimensional (3-D) video, and multiview 3-D video is built by incorporating different categories of videos into the inputs of patch clustering algorithm. Finally, it is shown in the results of simulation experiments that the proposed methods can simultaneously gain higher compression ratio and peak signal-to-noise ratio than those of the state-of-the-art methods in the situation of low bitrate transmission.

Main Features of a 3d GIS for a Monumental Complex with AN Historical-Cultural Relevance

NASA Astrophysics Data System (ADS)

Scianna, A.; La Guardia, M.

2017-05-01

The last achievements of technologies in geomatics especially in survey and restitution of 3D models (UAV/drones and laser scanner technologies) generated new procedures and higher standards of quality in representation of archaeological sites. Together with Geomatics, the recent development of Information and Communication Technologies (ICT) strongly contribute to document and the Cultural Heritage (CH). The representation and documentation of CH using these new technologies has became necessary in order to satisfy different needs: - for restorers in order to acquire a deep knowledge of the cultural good and to define possible strategies of restoration; - for the conservation of information, allowing to preserve the 3D geometry of the monumental complex with the integration of descriptions about architectural elements; - for touristic aims, giving the opportunity of sharing CH information on web, allowing users to visit and explore, in a virtual way, monumental complexes, acquiring information details about architectural elements or the history of monumental complex. Looking through these new scenarios, the development of a 3D Geographic Information System (GIS) applied to a cultural good could be, today, an added value of fundamental importance for full description and data management of monumental complexes. In this work, the main features necessary for the correct construction of a 3D GIS of a monumental complex will be analyzed, with a particular focus on the possibilities for creating a standardized procedure to follow.

Quantifying the added value of convection-permitting climate simulations in complex terrain: a systematic evaluation of WRF over the Himalayas

NASA Astrophysics Data System (ADS)

Karki, Ramchandra; Hasson, Shabeh ul; Gerlitz, Lars; Schickhoff, Udo; Scholten, Thomas; Böhner, Jürgen

2017-07-01

Mesoscale dynamical refinements of global climate models or atmospheric reanalysis have shown their potential to resolve intricate atmospheric processes, their land surface interactions, and subsequently, realistic distribution of climatic fields in complex terrains. Given that such potential is yet to be explored within the central Himalayan region of Nepal, we investigate the skill of the Weather Research and Forecasting (WRF) model with different spatial resolutions in reproducing the spatial, seasonal, and diurnal characteristics of the near-surface air temperature and precipitation as well as the spatial shifts in the diurnal monsoonal precipitation peak over the Khumbu (Everest), Rolwaling, and adjacent southern areas. Therefore, the ERA-Interim (0.75°) reanalysis has been dynamically refined to 25, 5, and 1 km (D1, D2, and D3) for one complete hydrological year (October 2014-September 2015), using the one-way nested WRF model run with mild nudging and parameterized convection for the outer but explicitly resolved convection for the inner domains. Our results suggest that D3 realistically reproduces the monsoonal precipitation, as compared to its underestimation by D1 but overestimation by D2. All three resolutions, however, overestimate precipitation from the westerly disturbances, owing to simulating anomalously higher intensity of few intermittent events. Temperatures are generally reproduced well by all resolutions; however, winter and pre-monsoon seasons feature a high cold bias for high elevations while lower elevations show a simultaneous warm bias. Unlike higher resolutions, D1 fails to realistically reproduce the regional-scale nocturnal monsoonal peak precipitation observed in the Himalayan foothills and its diurnal shift towards high elevations, whereas D2 resolves these characteristics but exhibits a limited skill in reproducing such a peak on the river valley scale due to the limited representation of the narrow valleys at 5 km resolution. Nonetheless, featuring a substantial skill over D1 and D2, D3 simulates almost realistic shapes of the seasonal and diurnal precipitation and the peak timings even on valley scales. These findings clearly suggest an added value of the convective-scale resolutions in realistically resolving the topoclimates over the central Himalayas, which in turn allows simulating their interactions with the synoptic-scale weather systems prevailing over high Asia.

Exploring the Role of Physics Representations: An Illustrative Example from Students Sharing Knowledge about Refraction

ERIC Educational Resources Information Center

Fredlund, Tobias; Airey, John; Linder, Cedric

2012-01-01

Research has shown that interactive engagement enhances student learning outcomes. A growing body of research suggests that the representations we use in physics are important in such learning environments. In this paper we draw on a number of sources in the literature to explore the role of representations in interactive engagement in physics. In…

Development and Optimization of Viable Human Platforms through 3D Printing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parker, Paul R.; Moya, Monica L.; Wheeler, Elizabeth K.

2015-08-21

3D printing technology offers a unique method for creating cell cultures in a manner far more conducive to accurate representation of human tissues and systems. Here we print cellular structures capable of forming vascular networks and exhibiting qualities of natural tissues and human systems. This allows for cheaper and readily available sources for further study of biological and pharmaceutical agents.

Event Display for the Visualization of CMS Events

NASA Astrophysics Data System (ADS)

Bauerdick, L. A. T.; Eulisse, G.; Jones, C. D.; Kovalskyi, D.; McCauley, T.; Mrak Tadel, A.; Muelmenstaedt, J.; Osborne, I.; Tadel, M.; Tu, Y.; Yagil, A.

2011-12-01

During the last year the CMS experiment engaged in consolidation of its existing event display programs. The core of the new system is based on the Fireworks event display program which was by-design directly integrated with the CMS Event Data Model (EDM) and the light version of the software framework (FWLite). The Event Visualization Environment (EVE) of the ROOT framework is used to manage a consistent set of 3D and 2D views, selection, user-feedback and user-interaction with the graphics windows; several EVE components were developed by CMS in collaboration with the ROOT project. In event display operation simple plugins are registered into the system to perform conversion from EDM collections into their visual representations which are then managed by the application. Full event navigation and filtering as well as collection-level filtering is supported. The same data-extraction principle can also be applied when Fireworks will eventually operate as a service within the full software framework.

Supervoxels for graph cuts-based deformable image registration using guided image filtering

NASA Astrophysics Data System (ADS)

Szmul, Adam; Papież, Bartłomiej W.; Hallack, Andre; Grau, Vicente; Schnabel, Julia A.

2017-11-01

We propose combining a supervoxel-based image representation with the concept of graph cuts as an efficient optimization technique for three-dimensional (3-D) deformable image registration. Due to the pixels/voxels-wise graph construction, the use of graph cuts in this context has been mainly limited to two-dimensional (2-D) applications. However, our work overcomes some of the previous limitations by posing the problem on a graph created by adjacent supervoxels, where the number of nodes in the graph is reduced from the number of voxels to the number of supervoxels. We demonstrate how a supervoxel image representation combined with graph cuts-based optimization can be applied to 3-D data. We further show that the application of a relaxed graph representation of the image, followed by guided image filtering over the estimated deformation field, allows us to model "sliding motion." Applying this method to lung image registration results in highly accurate image registration and anatomically plausible estimations of the deformations. Evaluation of our method on a publicly available computed tomography lung image dataset leads to the observation that our approach compares very favorably with state of the art methods in continuous and discrete image registration, achieving target registration error of 1.16 mm on average per landmark.

Supervoxels for Graph Cuts-Based Deformable Image Registration Using Guided Image Filtering.

PubMed

Szmul, Adam; Papież, Bartłomiej W; Hallack, Andre; Grau, Vicente; Schnabel, Julia A

2017-10-04

In this work we propose to combine a supervoxel-based image representation with the concept of graph cuts as an efficient optimization technique for 3D deformable image registration. Due to the pixels/voxels-wise graph construction, the use of graph cuts in this context has been mainly limited to 2D applications. However, our work overcomes some of the previous limitations by posing the problem on a graph created by adjacent supervoxels, where the number of nodes in the graph is reduced from the number of voxels to the number of supervoxels. We demonstrate how a supervoxel image representation, combined with graph cuts-based optimization can be applied to 3D data. We further show that the application of a relaxed graph representation of the image, followed by guided image filtering over the estimated deformation field, allows us to model 'sliding motion'. Applying this method to lung image registration, results in highly accurate image registration and anatomically plausible estimations of the deformations. Evaluation of our method on a publicly available Computed Tomography lung image dataset (www.dir-lab.com) leads to the observation that our new approach compares very favorably with state-of-the-art in continuous and discrete image registration methods achieving Target Registration Error of 1.16mm on average per landmark.

Kinematic decomposition and classification of octopus arm movements.

PubMed

Zelman, Ido; Titon, Myriam; Yekutieli, Yoram; Hanassy, Shlomi; Hochner, Binyamin; Flash, Tamar

2013-01-01

The octopus arm is a muscular hydrostat and due to its deformable and highly flexible structure it is capable of a rich repertoire of motor behaviors. Its motor control system uses planning principles and control strategies unique to muscular hydrostats. We previously reconstructed a data set of octopus arm movements from records of natural movements using a sequence of 3D curves describing the virtual backbone of arm configurations. Here we describe a novel representation of octopus arm movements in which a movement is characterized by a pair of surfaces that represent the curvature and torsion values of points along the arm as a function of time. This representation allowed us to explore whether the movements are built up of elementary kinematic units by decomposing each surface into a weighted combination of 2D Gaussian functions. The resulting Gaussian functions can be considered as motion primitives at the kinematic level of octopus arm movements. These can be used to examine underlying principles of movement generation. Here we used combination of such kinematic primitives to decompose different octopus arm movements and characterize several movement prototypes according to their composition. The representation and methodology can be applied to the movement of any organ which can be modeled by means of a continuous 3D curve.

Kinematic decomposition and classification of octopus arm movements

PubMed Central

Zelman, Ido; Titon, Myriam; Yekutieli, Yoram; Hanassy, Shlomi; Hochner, Binyamin; Flash, Tamar

2013-01-01

The octopus arm is a muscular hydrostat and due to its deformable and highly flexible structure it is capable of a rich repertoire of motor behaviors. Its motor control system uses planning principles and control strategies unique to muscular hydrostats. We previously reconstructed a data set of octopus arm movements from records of natural movements using a sequence of 3D curves describing the virtual backbone of arm configurations. Here we describe a novel representation of octopus arm movements in which a movement is characterized by a pair of surfaces that represent the curvature and torsion values of points along the arm as a function of time. This representation allowed us to explore whether the movements are built up of elementary kinematic units by decomposing each surface into a weighted combination of 2D Gaussian functions. The resulting Gaussian functions can be considered as motion primitives at the kinematic level of octopus arm movements. These can be used to examine underlying principles of movement generation. Here we used combination of such kinematic primitives to decompose different octopus arm movements and characterize several movement prototypes according to their composition. The representation and methodology can be applied to the movement of any organ which can be modeled by means of a continuous 3D curve. PMID:23745113

Supervoxels for Graph Cuts-Based Deformable Image Registration Using Guided Image Filtering

PubMed Central

Szmul, Adam; Papież, Bartłomiej W.; Hallack, Andre; Grau, Vicente; Schnabel, Julia A.

2017-01-01

In this work we propose to combine a supervoxel-based image representation with the concept of graph cuts as an efficient optimization technique for 3D deformable image registration. Due to the pixels/voxels-wise graph construction, the use of graph cuts in this context has been mainly limited to 2D applications. However, our work overcomes some of the previous limitations by posing the problem on a graph created by adjacent supervoxels, where the number of nodes in the graph is reduced from the number of voxels to the number of supervoxels. We demonstrate how a supervoxel image representation, combined with graph cuts-based optimization can be applied to 3D data. We further show that the application of a relaxed graph representation of the image, followed by guided image filtering over the estimated deformation field, allows us to model ‘sliding motion’. Applying this method to lung image registration, results in highly accurate image registration and anatomically plausible estimations of the deformations. Evaluation of our method on a publicly available Computed Tomography lung image dataset (www.dir-lab.com) leads to the observation that our new approach compares very favorably with state-of-the-art in continuous and discrete image registration methods achieving Target Registration Error of 1.16mm on average per landmark. PMID:29225433

Synthesis multi-projector content for multi-projector three dimension display using a layered representation

NASA Astrophysics Data System (ADS)

Qin, Chen; Ren, Bin; Guo, Longfei; Dou, Wenhua

2014-11-01

Multi-projector three dimension display is a promising multi-view glass-free three dimension (3D) display technology, can produce full colour high definition 3D images on its screen. One key problem of multi-projector 3D display is how to acquire the source images of projector array while avoiding pseudoscopic problem. This paper analysis the displaying characteristics of multi-projector 3D display first and then propose a projector content synthetic method using tetrahedral transform. A 3D video format that based on stereo image pair and associated disparity map is presented, it is well suit for any type of multi-projector 3D display and has advantage in saving storage usage. Experiment results show that our method solved the pseudoscopic problem.

Covariant scalar representation of ? and quantization of the scalar relativistic particle

NASA Astrophysics Data System (ADS)

Jarvis, P. D.; Tsohantjis, I.

1996-03-01

A covariant scalar representation of iosp(d,2/2) is constructed and analysed in comparison with existing BFV-BRST methods for the quantization of the scalar relativistic particle. It is found that, with appropriately defined wavefunctions, this iosp(d,2/2) produced representation can be identified with the state space arising from the canonical BFV-BRST quantization of the modular-invariant, unoriented scalar particle (or antiparticle) with admissible gauge-fixing conditions. For this model, the cohomological determination of physical states can thus be obtained purely from the representation theory of the iosp(d,2/2) algebra.

Dynamical density delay maps: simple, new method for visualising the behaviour of complex systems

PubMed Central

2014-01-01

Background Physiologic signals, such as cardiac interbeat intervals, exhibit complex fluctuations. However, capturing important dynamical properties, including nonstationarities may not be feasible from conventional time series graphical representations. Methods We introduce a simple-to-implement visualisation method, termed dynamical density delay mapping (“D3-Map” technique) that provides an animated representation of a system’s dynamics. The method is based on a generalization of conventional two-dimensional (2D) Poincaré plots, which are scatter plots where each data point, x(n), in a time series is plotted against the adjacent one, x(n + 1). First, we divide the original time series, x(n) (n = 1,…, N), into a sequence of segments (windows). Next, for each segment, a three-dimensional (3D) Poincaré surface plot of x(n), x(n + 1), h[x(n),x(n + 1)] is generated, in which the third dimension, h, represents the relative frequency of occurrence of each (x(n),x(n + 1)) point. This 3D Poincaré surface is then chromatised by mapping the relative frequency h values onto a colour scheme. We also generate a colourised 2D contour plot from each time series segment using the same colourmap scheme as for the 3D Poincaré surface. Finally, the original time series graph, the colourised 3D Poincaré surface plot, and its projection as a colourised 2D contour map for each segment, are animated to create the full “D3-Map.” Results We first exemplify the D3-Map method using the cardiac interbeat interval time series from a healthy subject during sleeping hours. The animations uncover complex dynamical changes, such as transitions between states, and the relative amount of time the system spends in each state. We also illustrate the utility of the method in detecting hidden temporal patterns in the heart rate dynamics of a patient with atrial fibrillation. The videos, as well as the source code, are made publicly available. Conclusions Animations based on density delay maps provide a new way of visualising dynamical properties of complex systems not apparent in time series graphs or standard Poincaré plot representations. Trainees in a variety of fields may find the animations useful as illustrations of fundamental but challenging concepts, such as nonstationarity and multistability. For investigators, the method may facilitate data exploration. PMID:24438439

Modeling of Multiphase Flow through Thin Porous Layers: Application to a Polymer Electrolyte Fuel Cell (PEFC)

NASA Astrophysics Data System (ADS)

Qin, C.; Hassanizadeh, S.

2013-12-01

Multiphase flow and species transport though thin porous layers are encountered in a number of industrial applications, such as fuel cells, filters, and hygiene products. Based on some macroscale models like the Darcy's law, to date, the modeling of flow and transport through such thin layers has been mostly performed in 3D discretized domains with many computational cells. But, there are a number of problems with this approach. First, a proper representative elementary volume (REV) is not defined. Second, one needs to discretize a thin porous medium into computational cells whose size may be comparable to the pore sizes. This suggests that the traditional models are not applicable to such thin domains. Third, the interfacial conditions between neighboring layers are usually not well defined. Last, 3D modeling of a number of interacting thin porous layers often requires heavy computational efforts. So, to eliminate the drawbacks mentioned above, we propose a new approach to modeling multilayers of thin porous media as 2D interacting continua (see Fig. 1). Macroscale 2D governing equations are formulated in terms of thickness-averaged material properties. Also, the exchange of thermodynamic properties between neighboring layers is described by thickness-averaged quantities. In Comparison to previous macroscale models, our model has the distinctive advantages of: (1) it is rigorous thermodynamics-based model; (2) it is formulated in terms of thickness-averaged material properties which are easily measureable; and (3) it reduces 3D modeling to 2D leading to a very significant reduction of computation efforts. As an application, we employ the new approach in the study of liquid water flooding in the cathode of a polymer electrolyte fuel cell (PEFC). To highlight the advantages of the present model, we compare the results of water distribution with those obtained from the traditional 3D Darcy-based modeling. Finally, it is worth noting that, for specific case studies, a number of material properties in the model need to be determined experimentally, such as mass and heat exchange coefficients between neighboring layers. Fig. 1: Schematic representation of three thin porous layers, which may exchange mass, momentum, and energy. Also, a typical averaging domain (REV) is shown. Note that the layer thickness and thus the REV height can be spatially variable. Also, in reality, the layers are tightly stacked and there is no gap between them.

The 3D Elevation Program: summary for Alaska

USGS Publications Warehouse

Carswell, William J.

2013-01-01

Coordination by SDMI and AMEC avoids duplication of effort and ensures a unified approach to consistent, statewide data acquisition; the enhancement of existing data; and support for emerging applications. The 3D Elevation Program (3DEP) initiative, managed by the U.S. Geological Survey (USGS), responds to the growing need for high-quality topographic data and a wide range of other three-dimensional representations of the Nation’s natural and constructed features.

Geometrical interpretation for the outer SU(3) outer multiplicity label

NASA Technical Reports Server (NTRS)

Draayer, Jerry P.; Troltenier, D.

1995-01-01

A geometrical interpretation for the outer multiplicity rho that occurs in a reduction of the product of two SU(3) representations, (lambda(sub pi), mu(sub pi)) x (lambda(sub nu), mu(sub nu)) approaches sigma(sub rho)(lambda, mu)(sub rho), is introduced. This coupling of proton (pi) and neutron (nu) representations arises, for example, in both boson and fermion descriptions of heavy deformed nuclei. Attributing a geometry to the coupling raises the possibility of introducing a simple interaction that provides a physically meaningful way for distinguishing multiple occurrences of (lambda, mu) values that can arise in such products.

D Modelling of a Historical Building Using Close-Range Photogrammetry and Remotely Piloted Aircraft System (rpas)

NASA Astrophysics Data System (ADS)

Lo Brutto, M.; Ebolese, D.; Dardanelli, G.

2018-05-01

The photogrammetric survey of architectural Cultural Heritage is a very useful and standard process in order to obtain accurate 3D data for the documentation and visualization of historical buildings. In particular, the integration of terrestrial close-range photogrammetry and Remotely Piloted Aircraft Systems (RPASs) photogrammetry allows to create accurate and reliable 3D models of buildings and to monitor their state of conservation. The use of RPASs has indeed become more popular in Cultural Heritage survey to measure and detect areas that cannot normally be covered using terrestrial photogrammetry or terrestrial laser scanner. The paper presents the results of a photogrammetric survey executed to document the monumental complex of Villa Lampedusa ai Colli in Palermo (Italy), one of the most important historical buildings of the town. An integrated survey by close-range photogrammetry and RPAS photogrammetry was planned and carried out to reconstruct the 3D digital model of the monumental complex. Different images configurations (terrestrial, aerial nadiral, aerial parallel and oblique to the façades) have been acquired; data have been processed to verify the accuracy of the photogrammetric survey as regards the camera calibration parameters and the number of Ground Control Points (GCPs) measured on building façades. A very detailed 3D digital model and high-resolution ortho-images of the façades were obtained in order to carry out further analysis for historical studies, conservation and restoration project. The final 3D model of Villa Lampedusa ai Colli has been compared with a laser scanner 3D model to evaluate the quality of the photogrammetric approach. Beyond a purely metric assessment, 3D textured model has employed to generate 2D representations, useful for documentation purpose and to highlight the most significant damaged areas. 3D digital models and 2D representations can effectively contribute to monitor the state of conservation of historical buildings and become a very useful support for preliminary restoration works.